Library - Science topic

Hello everyone, We have done library preparation for Genotyping-by-Sequencing (GBS). The sample source is gDNA from chili leaves. The restriction enzymes are using EcoR1 dan Mse1. We've designed the common adapter that compatible with overhang restriction site and universal adapter for Illumina sequencing. Then we'use DNA/RNA UDI index illumina. In sequencing procees final library from GBS, we pool with final library of amplicon and mRNA. We use PE 150 for sequencing. Unfortunately, we didn't get any reads after sequencing.

Could you give us any recomendation how to optimize the library preparation and sequencing to get the optimal output of sequencing.

Your suggestion is very helpful

I am working on a ddRAD-seq experiment and looking for a detailed protocol, particularly focusing on restriction enzyme selection, library preparation, and adapter selection. I would appreciate if anyone could share an optimized protocol or insights on choosing the best restriction enzymes for different genomes. Additionally, any recommendations on adapter design and ligation efficiency would be helpful.

Has anyone encountered challenges in enzyme compatibility or library preparation steps? Any troubleshooting tips would also be valuable.

I am working on a ddRAD-seq experiment and looking for a detailed protocol, particularly focusing on restriction enzyme selection, library preparation, and adapter selection. I would appreciate if anyone could share an optimized protocol or insights on choosing the best restriction enzymes for different genomes. Additionally, any recommendations on adapter design and ligation efficiency would be helpful.

Has anyone encountered challenges in enzyme compatibility or library preparation steps? Any troubleshooting tips would also be valuable.

its a research topic

My study is about cell metabolomics. I’m currently analyzing MS/MS data using MS-DIAL 5 for untargeted metabolomics, but I’m facing an issue where I don’t get any reference-matched/library-matched compounds (I got some, like 4 or 5, but they're not from metabolites of interest and seem like they're from contaminations). Instead, most of the annotated metabolites are either "suggested" or "w/o MS2" annotations. And some of the metabolites of interest regarding energy metabolism are also annotated with "w/o MS2". From what I understand, you cannot take w/o MS2 results with confidence.

Previously, I have also tried increasing the concentration and extracting more cells for metabolites but still face similar issues. I have also played around with MS-DIAL parameters, but still, I can't get the library matched.

My questions are:

1. Can w/o MS2 annotations be considered confident identifications and be used as results or in publication?

2. Are there specific parameter settings in MS-DIAL that I should check to ensure MS2 spectra are being used correctly for annotation?

3. Could this be the problem with the sample preparation or instruments/methods rather than data analysis?

Any advice on troubleshooting or optimizing settings of either MSDIAL or the instrument would be greatly appreciated!

Thank you!

Hello i have a problem with I have a problem with creating a mathematical model using the Simscape Fluids library. Someone can help me with that ?.

I found an error how do I report it ? The "cover page" you create and attach to an article is the wrong one , it is for a different article.

I have the file attached to show you.

Gail Cathey, M.L.S.

Print Resources / Access Services Librarian

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Hi

I want to export ACM library articles for my SLR. I have this problem. When I do that, it just gives me 1000 records, and I still have 642 records left.

Can anyone suggest how I can export all of the citations?

Kind regards

Can I know step by step how can spectragryph be used to create libraries to identify if specific compounds in my sample are present?

For example if my sample contains many phytochemicals such as Aucubin, Curcumin etc how and can I create a library of already spectra of those specific phytochemicaks and use ro compare with my FT-IR results to check their presence?

Also other than spectragryph are there any other library softwares that can perform this task?

Thanks

I prepped a cDNA library from ovarian cancer cell line RNA (all RIN scores were 9+ on TapeStation 4200) using a KAPA HyperPrep mRNA kit and UDI adapters for Illumina sequencing. When we ran the TapeStation (D1000 HS screen tapes) on the prepped libraries, we saw extra peaks around 230-250bp. On some samples it was a more pronounced peak, but others it was more of a shoulder. We are baffled on what this could be from. We did a QC sequencing run on an illumina nextseq P2 100 cycle and are wondering if our inner distance plot could look like this due to the smaller fragments we see on the tape station? I've had some people suggest the extra peak on the tapestation a bubble peak from over amplification of the library, but bubble peaks would appear larger, not smaller. Our anticipated library size was 200-300bp. For most samples the average size was 350bp, so including the adapter sequences this seems right. We just have no idea what the smaller peak would be that appear in nearly every sample. I've included images of a couple electropherograms and gel images from the tapestation and the inner distance plot. You can see these smaller extra peaks appear as bands on the gel images and how they slightly vary in size from sample to sample.

Hello,

I am new to coding in R and have come up with the following code to perform a nested 2-way ANOVA (with Tukey post-hoc) to be able to account for individual animal variability within each group. I am wondering if someone can confirm this is correct or provide alternative methods? I am assessing the effects of diet and stress on certain cellular outcomes, with n=3-5 animals/group. Thank you!

# Load required packages

library(lme4)

library(emmeans)

library(ggplot2)

# Convert factors

Data_For_R$Diet <- as.factor(Data_For_R$Diet)

Data_For_R$Stress <- as.factor(Data_For_R$Stress)

Data_For_R$Animal <- as.factor(Data_For_R$Animal)

# Nested 2-way ANOVA models

model_aov_stress <- aov(SomaVolume ~ Stress / Animal, data = Data_For_R)

model_aov_diet <- aov(SomaVolume ~ Diet / Animal, data = Data_For_R)

model_aov_combine <- aov(SomaVolume ~ Diet * Stress / Animal, data = Data_For_R)

# Mixed-effects model accounting for animal variability

model_lmer <- lmer(SomaVolume ~ Diet * Stress + (1 | Animal), data = Data_For_R)

# Obtain estimated marginal means for Diet and Stress, considering random effect for Animal

emmeans_result <- emmeans(model_lmer, ~ Diet * Stress)

# Perform pairwise comparisons for the interaction between Diet and Stress, adjusting for animal variability

pairs(emmeans_result, adjust = "tukey")

# Create a new factor to represent the combination of Diet, Stress, and Animal

Data_For_R$Diet_Stress_Animal <- interaction(Data_For_R$Diet, Data_For_R$Stress, Data_For_R$Animal, drop = TRUE)

# Summaries of the models

summary(model_aov_stress)

summary(model_aov_diet)

summary(model_aov_combine)

Greetings from Abuja-Nigeria.I suddenly and rudely discovered my copy of Y.B Usman's seminal publication Manipulation of Religion in Nigeria is missing from my library at a time I most needed the book.Could anyone with a copy to hand help with this?Thanks.

Comsol Multiphysics

We were using the Zinc database for the virtual compound library in our studies, but there have been problems downloading a large number of compounds for a while. Are there different databases that can be used or how can I solve this problem in the Zinc database?

📷

I need to identify the metabolites in the blood. I have done LC-HRMS. since there is no library provided, I am finding difficulties identifying the hits. Any suggestions..?

This call for papers invites the submission of high-quality, unpublished manuscripts that explore the challenges and opportunities faced by banks in a historical context characterized by the energy transition of national economic systems.

Topics of interest include, but are not limited to, the following three areas:

It is considered important to broaden the discussion on whether, and how, ten years after the SSM Regulation, the new Community architecture has contributed significantly to improving the stability of individual banks in several ways, such as: (i) Harmonisation of supervisory practices (Carretta et al., 2015; Scannella, 2015); (ii) Strengthening prudential supervision (Beccalli & Cesarini, 2021); (iii) Improving the stability of the banking system and the market power of European banks (Banfi & Pampurini, 2016; Bikker. J. & Okolelova. I. 2022); (iv) Reduction of systemic and idiosyncratic risk (Beccalli & Poli, 2015; ECB, 2024b); (v) Improved risk disclosure (Altunbaş et al., 2022).

A crucial aspect of the SSM is the sanctioning activities, which has evolved to raise new questions about: (i)The effectiveness of sanctions in improving banking stability (Caiazza et al., 2015) also in consideration of the information about the motivations behind them (Guerello et al., 2019); (ii)The impact of sanctions on stock price (Linder, 2016); (iii) The effectiveness of supervisory action in which there is a comparison between the European and US supervisory sector (Götz & Tröger, 2017); (iv) The restrictiveness of supervisory action in Europe on the basis of the frequency with which sanctions are imposed and their contribution to systemic risk (Korzeb et al., 2024); (v) The contribution of sanctions to the risk of bank default (Murè et al., 2020); (vi) The combination of ESG and sanctions (Murè et al., 2021; Mango et al., 2023); (vii) The impact of sanctions on reputation (Armour et al., 2017); (viii)The impact of sanctions on banks’ performance (Murè, 2014; Murè & Spallone, 2018); (ix) The probability of sanction (Murè et al., 2018); (x) The possible evolutions of the legislation on the adequacy of top management bodies (ECB, 2017; MEF, 2020); (xi) The sanctioning activity of the Bank of Italy in the context of the SSM (Banca d’Italia, 2023).

Compliance to support the strategic process in intermediaries, also in consideration of the possibility of resorting to the outsourcing of corporate functions (Murè & Bittucci, 2020; Murè, 2021; ECB 2024a).

Please find attached more information, including opportunities for publication related to the JFMMI special issue. Other possibilities will be available soon.

***

I am infecting 4T1 with a lentiviral library and need to sort the cells to recover the transduced ones. I am running into problems with these cells clumping even after filtering. I use trypsin with EDTA to get them off the dish, inactivate the trypsin with serum containing media, wash 2x with PBS+4% FBS and then filter. During the sort I end up with many cells being 2 stuck together. This is also a problem during passage. Anyone have any experience with these?

Dear researchers, I am trying to assess specific indirect effects in my model with three moderators. However, AMOS always gives a syntax error and my estimand could not run. When I try it on R studio (with lavaan and psych packages), I could not assign parameters to calculate specific indirect effects. Could you please help me identify problems and solutions for this?

Below is the code in R studio:

library(psych)

library(lavaan)

# I already input my CSV data so now I just describe it

describe(my.data)

A =~ A2+ A3 + A4 + A5 + A7 + A8

MS =~ MS1 + MS2 + MS3 + MS4 + MS6 + MS7+ MS8

M =~ M1 + M2 + M4 + MA8

IM =~ IM1 + IM2 + IM3 + IM4

FLA =~ Listen + Speak + Read + Write

# Regression paths from IV to mediators

M ~ a1*IM

A ~ a2*IM

MS ~ a3*IM

# Regression paths from mediators to DV (FLA)

FLA ~ b1*M + b2*A + b3*MS + c1*IM

#From this moment, I tried to assign parameters to calculate specific indirect effects. However, none of the below functions works!

direct : c1

Error: object 'direct' not found

direct:= c1

Error in `:=`(direct, c1) : could not find function ":="

direct<-c1

Error: object 'c1' not found

direct=c1

Error: object 'c1' not found

Bibliometric analysis is a research method that uses quantitative analysis and statistics to assess and analyze scientific literature. It is often used to evaluate the impact and trends of research within a specific field by examining published articles, citation counts, and other metrics. Commonly used in fields like library and information science, bibliometric analysis helps in understanding research productivity, collaboration patterns, influential authors, and high-impact journals.

I am reading an Endnote library file in Vosviewer; however, it gives me the attached message: Vosviewer cannot read the file. There is no valid (%Authors) and (%keywords) fields.

Can you please help me out this issue?

Best Regards,

Fazli

What will be the criteria for selection of compounds for docking from the LC-MS compound library? Is it abundance or other criteria?

Does anyone know of a free Python library for machine learning that can be used on a personal computer? I am particularly interested in neural network libraries similar to FANN.

Good morning,

I am very new to ATAC-seq and library preparation.

I just did my first trial in Arabidopsis samples and after tagmentation and library prep the bioanalyzer profile doesn't look very promising (see attached).

What I really don't understand is the very concentrated peak around 1000-1500bp (100s) in all samples. Even in the last one (which is genomic, it can be seen).

Any idea of the origin of this band/peak? (I have my theories but I want unbiased answers! xd)

Thanks!

Hi everyone,

While running the certain material available in Eco invent library, I came across the negative water depletion values,

What could be probable reason behind it?

The number of pores in the R.10.4.1 flow cell decreased significantly from +/- 1400 to 291 after nanopore sequencing with only 24 samples multiplexing. I used the SQK-RPB114-24 kit for processing the 24 samples as one library. Would anyone recommend anything about the protocol or to change something about it? Does anyone have about the same experience and what did you do to make it in some way better?

The protocol fro the new NEBNext UltraExpress® RNA Library Prep Kit NEB #E3330S/L closely follows to the previous version NEBNext Ultra II RNA library Prep Kit # E7770 S/L, but random primer step is missing. How 1st strand synthesis works without it? Is random primer added into some mix now?

We use the NEBNext Library Quant Kit for Illumina to determine our Illumina library concentrations. Before taking the library to qPCR, we usually run the library on Bioanalyzer to get an idea of the concentration. Based on Bioanalyzer, we will dilute the library down to 5,000pM for qPCR. Most of the time, qPCR results will show libraries around 5,000pM (maybe 4,000-6000pM). In some cases, the qPCR concentration can be double or even triple the Bioanalyzer concentration. When this happens we QC the library by Qubit. In most cases, the Qubit concentration will be similar to the Bioanalzyer concentration.

This makes it challenging for us to determine which concentration to use for loading the sequencer. If we use the qPCR concentration, the runs will be under-clustered. We are trying to understand why we would get higher concentrations from qPCR. It makes more sense if the qPCR concentrations were lower than Qubit/BA suggesting that the adapter ligation was not very successful.

Why do you think we would get such high qPCR concentrations? One thought is that there may be single stranded DNA in the library which is not detected by Qubit or BA, but qPCR is able to amplify. Curious to know your thoughts.

Thank you,

Karrie

Hi ya'll,

I am here to ask for recommendations on software or platforms I can use to manage a massive database.

I am working on a big museum samples barcoding project. For now, we are going through ~6000 specimen drawers one by one and selecting two to four specimens of each species for the barcoding process. Our database is getting bigger and bigger as we keep doing this.

For each specimen, we have a specimen barcode (including species name, collect year, identifier names, collect locality et al.), the drawer code (which drawer it was selected from), the DNA extraction plate code, the DNA extraction well code (we are using the 96-well plate), PCR plate code, Library pool code, Sequencing run No., Freezer code, freezer rack code (we have four -80 freezers and lots of racks to store DNAs) and a lot of other information.

I right now have 5 people working on this project and I am using the Google spreadsheet to manage and share the progress with all the collaborators. But the sheet is getting bigger and bigger, and there are lots of tabs created. Specifically, it is not easy to figure out the errors, like typos, two specimens were given the same code, and some drawers were samples twice....

I am wondering if there is any specimen tracking system, software, or functions I can use to manage the dataset easier, like linking all the information together while avoiding duplication errors?

Thank you for your time and my best wishes,

Menglin

Is the spectral library in python , helpful for reading SAR images

South Indian Journal of Library and Information Science "Integration of E-Resources and Smart Technologies in Law College Libraries: Enhancing Access and Learning Experiences"

latest trends or topics

Hi All,

I am ordering an overalapping peptide library to study the binding epitope of my antibody. I wonder if there is a formula to calculate the probability of number of epitope hits (e.g. single, double) with different epitope length, peptide length and offset (or peptide overlap). Knowing the probability of double hit would be helpful to determine how many peptides to order (as they are quite expensive!). Thank you for your help.

I am looking for Proteus Library for current transformer SCT-013 . Where can i find it?

...

Hello all,

I am trying to determine the dependence of the energy gap of silicon as a function of temperature. In the literature, it is stated that the decrease in the energy gap of silicon with increasing temperature can be explained by thermal expansion and electron-phonon interaction.

First, I used the thermo_pw library (which uses the QHA approximation) to determine the lattice parameter of silicon as a function of temperature. Then, I ran the following calculations: SCF, NSCF, DOS, band, and finally plotband. I performed these calculations using the lattice parameters of Si corresponding to temperatures in a range from 4K to 800K. For this simulation, I am using PBE pseudopotentials, an ecutwfc of 25 Ry, and a unit cell with 2 atoms.

The problem is that the gap increases with temperature instead of decreasing. I obtained a gap of 0.6187 eV at 4K and 0.6315 eV at 800K.

I also tried calculating the band structure considering electron-phonon coupling using the EPW library, but the gap still increases with temperature.

Has anyone already tried to calculate the silicon gap as a function of temperature? What am I doing wrong?

I received C. elegans nuclei (20 million nuclei) for ATAC-seq and prepared the library based on the Buenrostro 2015 protocol. The final cycle number was determined by 1/3rd maximal qPCR fluorescence and total cycle number used was 14. Could this be due to too high input or have others seen anything similar due to a different reason? We are going to try lowering the input significantly and titrate input amount to find the nucleosome pattern. Any input would be appreciated. Thank you.

How can we can train our model using the data, so that it can identify the disease and recommend possible treatment.(subject to the review of concerned expert). Also, suggestions are welcome on possibility of making the maximum utilization of this proposed model using stream-lit library by making it go public. I have built certain disease prediction model and looking forward to build a multi in one model that accepts multiple type of values for better analysis.

I don't know how to submit my article?, then I inform you that I registered with Ajol

. Thank you in advance for your attention to this submission

The idea of Bayesian Neural network is as primitive as the answer of failing student. You have a neural network model but no matter how hard you train it, there is always a residual error, so what to do? And student tells you, - than replace each scalar in the network by normally distributed random variable and tune expectations and variances to match the data.

Although this concept is failing miserably, we can find large group of scientists who keep pushing it into usage. I can easily provide the proof of these strong statements. The elementary stochastic system, which anyone can reproduce at home is a coin and dice. You pick two random inputs by rolling one die twice, let say they are 3 and 5 and flip the coin. In case of head you roll 3 dice, add outcomes, otherwise 5 dice. The sum of outcomes is your stochastic output. Simple, right? Now make few hundred records and try to obtain bimodal distribution by any of publicly available library designed to support BNN. The result will not be even remotely close to reality. But the solution is simple and know for at least 50 years. It is KNN. For each given input you find several similar records. Each output is considered as expectation of normal distribution, you assign variance from common sense, and you see this beautiful bimodal distribution very close the real. Called KDE, known for decades. Funny?

That is not all. Freely available library Tensorflow is capable to detect gaps in data and return your confidence interval, which becomes larger for sparse data. That is already mocking of the science. All you need to do to identify these gaps is to generate new inputs as evenly distributed points in the field of definition, find the distance to nearest dataset point for each, record it and make a new model, which tells you your training data density. Why to use Tensorflow, when it needs 50 lines of code and can be done by student for an hour.

I tested Tensorflow with coin and dice data. The returned result was compared to true distribution by Kramer von Mises criteria. The accuracy was 15%. KNN gives 85%. I made my own method, which is slight improvement of KNN, and improved it to 90%.

I never believe that scientists promoting BNN is not aware that this technology is fake. My question is what we can do about it? Let say I publish my research, I contact scientists promoting BNN directly, he ignores and keeps promoting his research. We all don't like when doctors prescribe us expensive drugs when regular drugs is a cure and when auto mechanics suggesting to replace parts that can work. Isn't that the same thing?

I will add the links to my published research exposing weakness of BNN for those who interested.

"Today several adjectival phrases have been used to describe English like ‘International Language’, ‘Lingua-Franca’, ‘Language for Globally Connecting’, ‘Library Language’, ‘Official Language’, ‘Administrative Language’, ‘Queen of Languages’, ‘Employment Passport’ and ‘the most Preferred Language’ etc." (Jabir, M. 2019)

Reference:

Jabir, M. (2019). The Use of ICT in Teaching English: A Study of ELT in the Secondary Schools of Kargil District . An M. Phil Dissertation Submitted to Jaipur National University, p. 5.

Dogwood RNA isolations From leaf tissue

used Zymo modified protocol

KAPA mRNA-stranded library prep.

RNA QC looks decent, input of RNA into library is 1.5micrograms

RNA QC looks good

libraries failed

Per Zymo ran RNA elutes through cleanup column and re-ran libraries still all libraries failed.

I have been preparing NGS Library, where the samples input volumes, conditions followed and the PCR Cycles are same but still the concentration obtained was uneven and the fragments size where also differ from sample to sample. What could be the possible reason for this uneven results.

Until the early 2000s, the National Bibliography used to be an important source for the development of library collections, mainly for the acquisition of new items. I would like to know if in your country it remains important for research in your library. Please, could you tell me?

How can contexual bandits (used in Recommendation Systems) be implemented in code via library package ?

Dear all,

I've recently processed some samples for ATAC-seq. My corresponding ATAC-seq library looks different (see picture: Bio-Analyzer) than the expected profile. I was wondering if I can still sequence it or it will be too biased.

Thank you for your help

Best,

Karim

Hello everyone,

I am facing a problem when making a plot in "R". I am generating a ROC curve, but in the graph I have been oberving that my "0.0" scale of of X-axis is far from "0.0" scale of Y-axis. I don't understand where is problem. I want to make the plot where "0.0" will start from the same point. I am giving you the example of what I found from R (Please check figure of R) and also what I want (Like figure drawn by GraphPad)

If anyone please help me to find the solution, I will be highly benefited. I am providing the script that I use.

# Install and load necessary packages

install.packages("pROC")

# install.packages("readxl")

library(pROC)

library(readxl)

# Read data from Excel file (replace with your file path)

data <- read_excel("D:\\Samsun medical center\\ELISA data analysis\\elisadata\\New prism analysis for AUC curve analysis\\Sample data for R.xlsx")

# Extract control and cancer patient data

control <- data$Control

cancer <- data$Cancer

# Combine data and create a grouping variable

data_combined <- c(control, cancer)

group <- factor(c(rep("Control", length(control)), rep("Cancer", length(cancer))))

# Create ROC curve

roc_data <- roc(group, data_combined)

# Plot ROC curve

plot(roc_data, main = "ROC Curve", col = c("blue", "red"), legacy.axes = TRUE,

print.auc = TRUE

xlab = "100% - Specificity", ylab = "Sensitivity", asp = 1) # Set aspect ratio to 1:1

# Calculate AUC with confidence interval

auc_value <- auc(roc_data)

ci_value <- ci.auc(roc_data)

# Extract AUCs for control and cancer groups

auc_control <- roc_data$aucs[group == "Control"]

auc_cancer <- roc_data$aucs[group == "Cancer"]

# Perform Mann-Whitney U test to compare AUCs

p_value <- wilcox.test(auc_control, auc_cancer, alternative = "greater")$p.value

# Display AUC, CI, and p-value on the plot

legend("bottomright",

legend = paste("AUC =", round(auc_value, 2),

"\n95% CI =", round(ci_value[1], 2), "-", round(ci_value[3], 2),

"\np-value =", signif(p_value, 3)),

bty = "n")

# Calculate Youden's Index

youden_index <- roc_data$thresholds[which.max(roc_data$sensitivities + roc_data$specificities - 1)]

cat("Youden's Index Cutoff:", youden_index, "\n")

# Find the index corresponding to Youden's Index

index <- which(roc_data$thresholds == youden_index)

# Extract sensitivity and specificity at Youden's Index

sensitivity_value <- roc_data$sensitivities[index]

specificity_value <- roc_data$specificities[index]

# Convert sensitivity and specificity values to percentages

sensitivity_percentage <- sensitivity_value * 100

specificity_percentage <- specificity_value * 100

# Print sensitivity and specificity values as percentages

cat("Sensitivity at Youden's Index:", sensitivity_percentage, "%\n")

cat("Specificity at Youden's Index:", specificity_percentage, "%\n")

Hi, I am trying to make synthetic phage library. Right now , do people still use Kunkel method or other methods? Since it looks like Kunkel method is an old method. I am looking for more convenient method to build the library.

I researched about this but most of the instructions online is for AutoDock 4. I tried the same steps by adding the needed parameters to AD4_Parameter.dat and AD4.1_bound.dat but I cannot find the .gpf and .dpf files so the changes i made with the parameters were useless. Please help me, what should I do if I cannot find the .gpf and .dpf? Thank you.

Some of my in-text citations references show up with an 'a' at the end (e.g., Smith, 2023a). The author does not have a 2nd publication in my Mendeley library, and I have checked for duplicates. Can someone please advise how to fix this other than to continually manually update the citation?

Thank you!

I'm performing an antibody phage display with a VHH library and I consistently get frameshift mutants (mainly frame +2) after biopanning. I'm using TG-1 cells for amplification of phagemids and VCSM13 as helper phage. Biopannings are performed in target protein-coated immunotubes and PBS-milk is used as blocking agent. I have tried to coat the immunotubes with different protein concentrations (10-100 ug/mL in carbonate coating buffer) with the same results. Also tried the microtiter plate format. When I analyze the original library, all the clones are in the correct frame. I would appreciate any explanation or suggestion. Thanks!

What is scope of the implementing LIS classification and cataloguing in different field ?

Dear ResearchGate Community,

I am currently engaged in a thesis project involving the analysis of essential oils using gas chromatography-mass spectrometry (GC-MS), PerkinElmer, Clarus 690. Specifically, I am examining tea tree (Melaleuca alternifolia) essential oil, which is expected to contain terpinene-4-ol as its main constituent.

My challenge lies in the identification process, particularly when utilizing the NIST library for peak identification. Despite following standard protocols and procedures, I consistently encounter very low probabilities for matches, even for well-known compounds like terpinene-4-ol. These low probabilities persist across all unknown peaks, making it difficult to confidently identify compounds present in the essential oil samples.

Attached to this inquiry are screenshots illustrating the methodology employed, chromatograms, spectrograms, and the peak identification results from the NIST library.

I am reaching out to the community for insights, suggestions, or potential solutions to address this issue. Any advice on improving the accuracy and reliability of peak identification in GC-MS analysis of essential oils would be greatly appreciated.

Thank you for your time and assistance.

Best regards,

Achwek Meftehi

PhD Student Neurosciences and Biochemistry

Faculty of Sciences, Tunis

Can anyone give clear explanation add parameters for it to the parameter library first for auto dock. Because Ni atom is not in the library it seems? Step by step instruction.

Why all the buzz about AI-assisted writing? Think about it—haven’t we already embraced tools like Grammarly and Quillbot and other AI-assisted and Computer Assisted Writing to help us write better(Wang, 2022)? And remember when we switched from digging through library cards to hopping onto research databases? Evidently, each has advantages and disadvantages (Falagas, 2008). Sure, there was a time when many educators were wary about students using computers for writing, worried it might spoil their writing skills (Billings, 1986) or second language acquisition (Lai, 2006; Gündüz, 2005). But look how that turned out: we adapted and learned to see the value in the technology. So, what's the big deal now? AI writing tools are just the next step. Instead of pushing back, why not dive in, learn how it works, and show others how to use it? Let's make the most of what tech can offer and keep up with the times!

Billings, D. M. (1986). Advantages and disadvantages of computer-assisted instruction. Dimensions of Critical Care Nursing, 5(6), 356-362.

Falagas, M. E., Pitsouni, E. I., Malietzis, G. A., & Pappas, G. (2008). Comparison of PubMed, Scopus, web of science, and Google scholar: strengths and weaknesses. The FASEB journal, 22(2), 338-342.

Gündüz, N. (2005). Computer-assisted language learning. Journal of language and linguistic studies, 1(2), 193-214.

Lai, C. C., & Kritsonis, W. A. (2006). The advantages and disadvantages of computer technology in second language acquisition. Online Submission, 3(1).

Wang, Z. (2022). Computer-assisted EFL writing and evaluations based on artificial intelligence: a case from a college reading and writing course. Library Hi Tech, 40(1), 80-97.

When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Se" -- Add parameters for it to the parameter library first!

How do i handle it? Thanks

I have 10 pre-processed studies for which I have prepared ASV tables, Taxa tables, Metadata, and phylogenetic trees. Now I want to merge these studies and create and single or merged phyloseq object to do further downstream processing.

ASV tables, Taxa tables, Metadata - these are the CSV files while tree is in text format.

# Load required libraries

library(phyloseq)

library("ape")

# Function to load metadata files from a folder

load_metadata_files <- function(folder_path) {

metadata_files <- list.files(path = folder_path, pattern = "\\.csv", full.names = TRUE)

metadata_list <- lapply(metadata_files, read.csv, header = TRUE, row.names = NULL)

return(metadata_list)

}

# Function to load ASV files from a folder

load_asv_files <- function(folder_path) {

asv_files <- list.files(path = folder_path, pattern = "\\.csv", full.names = TRUE)

asv_list <- lapply(asv_files, read.csv, header = TRUE, row.names = 1)

return(asv_list)

}

# Function to load taxonomy files from a folder

load_taxonomy_files <- function(folder_path) {

taxonomy_files <- list.files(path = folder_path, pattern = "\\.csv", full.names = TRUE)

taxonomy_list <- lapply(taxonomy_files, read.csv, header = TRUE, row.names = 1)

return(taxonomy_list)

}

# Function to load phylogenetic tree files from a folder

load_tree_files <- function(folder_path) {

tree_files <- list.files(path = folder_path, pattern = "\\.txt", full.names = TRUE)

trees <- lapply(tree_files, read.tree)

return(trees)

}

# Specify folder paths

metadata_folder <- "C:/Users/Saesha Verma/OneDrive/Desktop/Metadata_SB"

asv_folder <- "C:/Users/Saesha Verma/OneDrive/Desktop/ASV_SB"

taxonomy_folder <- "C:/Users/Saesha Verma/OneDrive/Desktop/Taxa_SB"

tree_folder <- "C:/Users/Saesha Verma/OneDrive/Desktop/Tree_SB"

# Load metadata, ASV, and taxonomy files

metadata_list <- load_metadata_files(metadata_folder)

asv_list <- load_asv_files(asv_folder)

taxonomy_list <- load_taxonomy_files(taxonomy_folder)

tree_list <- load_tree_files(tree_folder)

create_phyloseq <- function(asv_list, taxonomy_list, metadata_list, tree_list) {

# Merge ASV tables based on sample IDs

merged_asv <- do.call(rbind, asv_list)

# Combine taxonomy tables into a single tax_table

tax_table <- do.call(rbind, taxonomy_list)

# Combine metadata tables into a single sample_data object

sample_data <- do.call(rbind, metadata_list)

# Merge phylogenetic trees

merged_tree <- lapply(tree_list, function(x) list(phylo(x)))

# Create phyloseq object

ps <- phyloseq(otu_table(merged_asv, taxa_are_rows = TRUE),

tax_table = tax_table,

sample_data = sample_data,

phy_tree = merged_tree)

return(ps)

}

ps <- create_phyloseq(asv_list, taxonomy_list, metadata_list, tree_list)

I am using this code but I encounter error :

ps <- create_phyloseq(asv_list, taxonomy_list, metadata_list, tree_list)

Error in rbind(deparse.level, ...) : numbers of columns of arguments do not match

My endnote library doesn't accept adding more than 10 references! I want to make a library to use for citing while writing, that could exceed 10 references. Any help?

I've been working in the Library Department for the past six years, and I've noticed that only about 10% of students visit the library. I'm wondering if there is anywhere, for example, a set of data that can help me understand how we can increase the number of users for academic libraries.

I'm working on library prep for ITS NGS using Earth Microbiome Protocol and am getting double banding and smearing on my gels. What might be the cause for this? I should be seeing a band around 230 bp.

I am searching for all the possible ways to measure this gap and validate it statistically.

Hi,

I was lucky enough to get my paper in the cover of Deep Sea Rearch Part I: Oceanographic Research Papers in 2022. Now I'm wondering to get a good picture of the cover to frame it. Unfortunately, they did send us the cover with the final design and at the DSR page the quality is very (very) low. They offer download the cover but just the picture without the journal graphic design. To add more sadness and touch your souls, we don't get the journal in our library.... So, if someone have for any chance access to the volume 186 of Deep Sea Research Part I and can send the scan, or a good picture, I would deeply graceful. It was one of my PhD tessis papers and having a cover was a nice thing to keep in my studio.

thanks in advance

Iván

The sentence above are largely rhetorical and perhaps it would be fairer to ask how these attacks are reacted to.

The British Library recently suffered a cyber attack by a criminal gang (I have done work on the Russian involvement with such criminal gangs but other than disruption it is difficult to see what could be obtained by Putin's government) and their personnel's data was dumped on the Dark Web when they refused to pay ransom. The BLs chief executive expressed the view that such people were against everything which libraries represent: openness, empowerment, access to knowledge." Such attacks have been slowly rising. Bostin city library was shut down in a ransomware attack in 2021. Toronto Public Library suffered a massive cyber attack in October. The city responded by declaring that such attacks were directed essentially towards civilised values.

While these attacks are criminal ones, Putin funded many of these criminal cyber groups and eventually they helped construct Russian misinformation and began working directly with Russia.

Are these actions to do with authoritarian states? Traditionally the Romans are suspected of destroying the Alexandrian Library. Generally, information is cut off in religious societies. Information dealing with understanding reality and the senses is attacked.

The bombing of Ukrainian information centres, archives, schools, museums, universities have been noted in the present war as in Gaza. Is the fate of Hypatia to be renewed?

Hypatia

📷

They attacked her in mid exploration Cutting away her golden thoughts As they cut away her flesh, destroying A mind that they couldn’t destroy in Debate, a sparkling old woman Whose thoughts were spun from steel.

The screaming mob desecrated her tiny form Dragging it into the dust, through the rubbish And shit. Tearing off her clothes The Parabalani exposed her to celestial winds crossing The arora, rubbing Spoilt Alexandrian soil into her unexplored vagina. She did not die as a philosopher, calculating and Learning, but, torn apart, the old woman Screamed out for her father, Terrified, in sacrificial pain so much worse Than beheadings and crucifixion. Her modesty, Kept for 60 years, mutilated by a 1000 killers in a single Minute.

Her head bounced in the forum, Her arms thrown to the 4 corners, Her soul stamped into the gutter, As the new religion cried out for tolerance. In a morning thinking became forbidden Books burnt, laughs ignored and fires built for heretics.

Hypatia was a female philosopher in Alexandria in the 4th century who was torn apart by a Christian mob, her skin scraped from her bones.

I need to teach how to conduct research using internet or library sources, therefore I need to develop a successful curriculum for the proposed training on how to conduct research>

I have papers

On May 30, 2023, I gave a lecture on "The Ontology of Computer Games" at the Immanuel Kant Baltic Federal University Research Library.

Here's a link to the full lecture on YouTube: https://www.youtube.com/watch?v=7QEFsrQcJak

The lecture is in Russian.

The questions posed by my lecture are:

What is the reality of computer games?

Do they affect the human mentality?

Do they change moral principles?

Do games encourage violence?

Do games weaken empathy?

I am trying to generate topology file in GROMACS for an enzyme (PDB code =1HBN). But I encountered the following error.

Fatal error:

"The residues in the chain ALA2--ALA549 do not have a consistent type. The

first residue has type 'Protein', while residue MHS257 is of type 'Other'.

Either there is a mistake in your chain, or it includes nonstandard residue

names that have not yet been added to the residuetypes.dat file in the GROMACS

library directory. If there are other molecules such as ligands, they should

not have the same chain ID as the adjacent protein chain since it's a separate

molecule."

Can anyone please kindly help me to solve this.

Hi i have estimated an armax model using python sippy library. The estimation gives me two transfer functions H and G. How can I combine them into a single one to predict model output for new input u(t)or to compute unit step response? I thought to somehow derive state space representation maybe...

I am using Haddock 2.4 to check docking parameters between DNA and ligand . My DNA file contain Na ion and I format it as given in Haddock library but it still gives the error -

"Error in PDB file.Issue when parsing the PDB file at line 308.ATOM/HETATM line does not meet the expected format"

format of ions in my pdb file-

HETATM 307 NA+1 NA1D 101 8.118 -6.766 34.223 0.50 15.72 NA

HETATM 308 NA+1 NA1D 101 8.498 -6.164 34.656 0.50 20.12 NA

I have attached my pdb file of DNA

I have encountered an error to measure the light intensity of my laser source (650nm) (see image attached). The serial plot remains constant even i have changed the intensity of my light source, I have even tried both extremes: dark environment and close to lase source, yet there are no changes to the serial plot. Have anyone enconutered similar problem? How do i solve this error?

Here, the codes were used for the complete setup of photodiode BH1750 and Arduino Nano:

/*

Advanced BH1750 library usage example

This example has some comments about advanced usage features.

Connection:

VCC -> 3V3 or 5V

GND -> GND

SCL -> SCL (A5 on Arduino Uno, Leonardo, etc or 21 on Mega and Due, on esp8266 free selectable)

SDA -> SDA (A4 on Arduino Uno, Leonardo, etc or 20 on Mega and Due, on esp8266 free selectable)

ADD -> (not connected) or GND

ADD pin is used to set sensor I2C address. If it has voltage greater or equal to

0.7VCC voltage (e.g. you've connected it to VCC) the sensor address will be

0x5C. In other case (if ADD voltage less than 0.7 * VCC) the sensor address will

be 0x23 (by default).

*/

#include <Wire.h>

#include <BH1750.h>

/*

BH1750 can be physically configured to use two I2C addresses:

- 0x23 (most common) (if ADD pin had < 0.7VCC voltage)

- 0x5C (if ADD pin had > 0.7VCC voltage)

Library uses 0x23 address as default, but you can define any other address.

If you had troubles with default value - try to change it to 0x5C.

*/

BH1750 lightMeter(0x23);

void setup(){

Serial.begin(9600);

// Initialize the I2C bus (BH1750 library doesn't do this automatically)

Wire.begin();

// On esp8266 you can select SCL and SDA pins using Wire.begin(D4, D3);

/*

BH1750 has six different measurement modes. They are divided in two groups;

continuous and one-time measurements. In continuous mode, sensor continuously

measures lightness value. In one-time mode the sensor makes only one

measurement and then goes into Power Down mode.

Each mode, has three different precisions:

- Low Resolution Mode - (4 lx precision, 16ms measurement time)

- High Resolution Mode - (1 lx precision, 120ms measurement time)

- High Resolution Mode 2 - (0.5 lx precision, 120ms measurement time)

By default, the library uses Continuous High Resolution Mode, but you can

set any other mode, by passing it to BH1750.begin() or BH1750.configure()

functions.

[!] Remember, if you use One-Time mode, your sensor will go to Power Down

mode each time, when it completes a measurement and you've read it.

Full mode list:

BH1750_CONTINUOUS_LOW_RES_MODE

BH1750_CONTINUOUS_HIGH_RES_MODE (default)

BH1750_CONTINUOUS_HIGH_RES_MODE_2

BH1750_ONE_TIME_LOW_RES_MODE

BH1750_ONE_TIME_HIGH_RES_MODE

BH1750_ONE_TIME_HIGH_RES_MODE_2

*/

// begin returns a boolean that can be used to detect setup problems.

if (lightMeter.begin(BH1750::CONTINUOUS_HIGH_RES_MODE)) {

Serial.println(F("BH1750 Advanced begin"));

}

else {

Serial.println(F("Error initialising BH1750"));

}

}

void loop() {

float lux = lightMeter.readLightLevel();

Serial.print("Light: ");

Serial.print(lux);

Serial.println(" lx");

delay(1000);

}

In a metagenomic library profile desired size is 450-550bp,getting unwanted fragments which is causing failure of the library or it is difficult to get the desired data after sequencing.

My analyte standards are highly pure. R match and F match were good (800-900) but probability of match with the coumpound in Nist Library was Low(20-60%). How can i improve it? I am Using 10PPM standards prepared in HPLC grade N-Hexane. I am using Helium as my carrier gas?