Academic Users Research Articles

REFERENCE SERVICES IN PRIVATE UNIVERSITY LIBRARIES OF ASSAM DURING COVID- 19 PANDEMIC: A STUDY

The cause of the present study was to explore the private university libraries of Assam and to determine their library working practices and to investigate the different library practices and strategies that had been applied during the COVID-19 pandemic. The study basically gives special emphasized on utilization of reference services in online and offline modeto the academic user community where the data has been collected through designed questionnaire or in-depth personal interviews. For the study six private university libraries of Assam have been selected and that all the selected private university has been established as per the Assam private university act 2007. During the pandemic all the university libraries were closed for the library users but digital and online library services are being provided by the library professional with different systematic and collective resources. During this Pandemic all the private university library makes an effort via library webpage’s, social media and online tools.

De novo protein design by an energy function based on series expansion in distance and orientation dependence.

Despite many successes, de novo protein design is not yet a solved problem as its success rate remains low. The low success rate is largely because we do not yet have an accurate energy function for describing the solvent-mediated interaction between amino acid residues in a protein chain. Previous studies showed that an energy function based on series expansions with its parameters optimized for side-chain and loop conformations can lead to one of the most accurate methods for side chain (OSCAR) and loop prediction (LEAP). Following the same strategy, we developed an energy function based on series expansions with the parameters optimized in four separate stages (recovering single-residue types without and with orientation dependence, selecting loop decoys and maintaining the composition of amino acids). We tested the energy function for de novo design by using Monte Carlo simulated annealing. The method for protein design (OSCAR-Design) is found to be as accurate as OSCAR and LEAP for side-chain and loop prediction, respectively. In de novo design, it can recover native residue types ranging from 38% to 43% depending on test sets, conserve hydrophobic/hydrophilic residues at ∼75%, and yield the overall similarity in amino acid compositions at more than 90%. These performance measures are all statistically significantly better than several protein design programs compared. Moreover, the largest hydrophobic patch areas in designed proteins are near or smaller than those in native proteins. Thus, an energy function based on series expansion can be made useful for protein design. The Linux executable version is freely available for academic users at http://zhouyq-lab.szbl.ac.cn/resources/.

Understandings the Reading Habit and Reading Attitudes Among Students in Research University Library in Malaysia

Reading is one of the activities known to give a lot of benefits to readers. In the context of university students, reading can improve their academic performance. However, literature indicated that students read-only to pass their examination and not for pleasure and acquiring knowledge. The study reported in this paper investigated the reading habit and reading attitudes among students in the research university library in Malaysia. It is believed that positive reading attitudes towards education materials or non-education materials lead to positive reading experiences, which also lead to higher academic performance. A descriptive study used questionnaires as an instrument of a quantitative method. Convenience sampling was employed and 400 respondents from four research university status libraries were selected. Moderate levels of reading attitude were obtained from the result of the study, in which several variables produced a significant relationship in the reading attitude (education background and favorite activities during leisure time). The findings of this study have shown the behavior of academic library users in terms of reading habits, reading attitudes, and selection of reading materials. Several suggestions such as providing a variety of reading material (sense of humor and humanities, public figures and tv personalities) and reading encouragement activities have been suggested. This study provides useful inputs to the Ministry of Higher Education (MOHE) in constructing effective strategies to cultivate reading habits among reluctant readers in public universities.

Decentralized Finance & Accounting – Implications, Considerations, and Opportunities for Development

The blockchain and cryptoasset sector, since coming to the attention of the mainstream business and financial markets during the bitcoin bull run of 2017, continues to accelerate and evolve rapidly. Decentralized finance (DeFi), a new iteration of what was previously referred to as open finance, has emerged as an innovative use case and service enabled by blockchain technology. As with any innovation or new tool, however, there remains a range of questions and considerations that will have to be addressed prior to wider adoption and utilization. This research attempts to contextualize the development of DeFi, frame it within the blockchain and cryptoasset sector, and explain potential obstacles and challenges to further development. Subsequent to this examination of DeFi trends, challenges, and opportunities, a potential framework for further development and implementation will be presented. Outlined and written in a manner approachable to both practitioners and academic users, this research should be used a springboard for further discussion, analysis, and progress.

The effects of location and layout of offices on perceptual evaluations of users

PurposeThis paper aims to focus on determining the effects of location of closed offices on the front facade, rear facade and side facade plans and the indoor layout (left and right users’ cabinets) on perceptual evaluations of users of physical environmental factors.Design/methodology/approachFor this purpose, the responses of 54 academic users who use the Gazi University Technology Faculty Taskent Building offices were taken with the help of a survey.FindingsAs a result, it was determined that office users on the front and side facades generally perceived more positively the offices’ environmental factors than office users on the back facade. In addition, it was determined that offices with storage cabinets located to the right of users (Type A) were perceived more positively than storage cabinets located to the left of users (Type B). On the other hand, it was determined that users between the ages of 25–45 who used closed offices generally perceived the physical environmental factors of offices more positively than users between the ages of 46 and 65.Originality/valueEspecially the location of the building, the landscaping, the plan of the rooms and the landscape to which they are directed are major design decisions that cannot be controlled by employees. Therefore, it is necessary to know the positive/negative effects that may occur during use before making design decisions.

Online database for brain cancer-implicated genes: exploring the subtype-specific mechanisms of brain cancer

BackgroundBrain cancer is one of the eight most common cancers occurring in people aged 40+ and is the fifth-leading cause of cancer-related deaths for males aged 40–59. Accurate subtype identification is crucial for precise therapeutic treatment, which largely depends on understanding the biological pathways and regulatory mechanisms associated with different brain cancer subtypes. Unfortunately, the subtype-implicated genes that have been identified are scattered in thousands of published studies. So, systematic literature curation and cross-validation could provide a solid base for comparative genetic studies about major subtypes.ResultsHere, we constructed a literature-based brain cancer gene database (BCGene). In the current release, we have a collection of 1421 unique human genes gathered through an extensive manual examination of over 6000 PubMed abstracts. We comprehensively annotated those curated genes to facilitate biological pathway identification, cancer genomic comparison, and differential expression analysis in various anatomical brain regions. By curating cancer subtypes from the literature, our database provides a basis for exploring the common and unique genetic mechanisms among 40 brain cancer subtypes. By further prioritizing the relative importance of those curated genes in the development of brain cancer, we identified 33 top-ranked genes with evidence mentioned only once in the literature, which were significantly associated with survival rates in a combined dataset of 2997 brain cancer cases.ConclusionBCGene provides a useful tool for exploring the genetic mechanisms of and gene priorities in brain cancer. BCGene is freely available to academic users at http://soft.bioinfo-minzhao.org/bcgene/.

Richang: An Affect-Inflected Ethnography of Chinese Livestreams

Abstract I tracked one Chinese livestreaming platform Douyu from its emergence as experimental subsidiary of a Video on Demand platform in 2013 to its status as an ordinary medium of mass entertainment in 2018. This affect-inflected ethnography is written based on participant observation of three channels on Douyu as I exhibit the microcontexts of each channel in chronicles of affective events, long pauses of silence, repetitive and incoherent dialogues, asymmetrical debates, and sporadic moments of emotional meltdown. This ethnographic writing is a contact zone, a provocation, and, by proxy, a dialogue between academic theories (especially from television studies), user practices, and my informants’ own attempts at theorising how and what livestream feels and means for them.

A Mediated Approach to the Virtual Learning Environment (VLE)

This paper examines the Virtual Learning Environment (VLE) in relation to its implication for academic libraries in the 21st century. It sheds light on how technological development has had major impacts in the academic library, with regards to how information is being constructed, transmitted and accessed by library users. In the course of this discourse it was deduced that students constitute a significant percentage of the academic library users. The technological development in the academic sphere has enabled ubiquitous interactions between students and teachers, in which students are enabled to learn and communicate with their teachers from remote locations, thus inducing the notion of VLE. The VLE is regarded as technological-based environment where learners are enabled to access learning outside the classroom. With the aid of VLE students are granted ownership of their learning process, thus ensuring positive learning outcomes. Finally, the Technology Acceptance Model (TAM) was employed to serve as the theoretical basis of this discourse.

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source.

In fragment-based drug discovery, hundreds or often thousands of compounds smaller than ~300 Da are tested against the protein of interest to identify chemical entities that can be developed into potent drug candidates. Since the compounds are small, interactions are weak, and the screening method must therefore be highly sensitive; moreover, structural information tends to be crucial for elaborating these hits into lead-like compounds. Therefore, protein crystallography has always been a gold-standard technique, yet historically too challenging to find widespread use as a primary screen. Initial XChem experiments were demonstrated in 2014 and then trialed with academic and industrial collaborators to validate the process. Since then, a large research effort and significant beamtime have streamlined sample preparation, developed a fragment library with rapid follow-up possibilities, automated and improved the capability of I04-1 beamline for unattended data collection, and implemented new tools for data management, analysis and hit identification. XChem is now a facility for large-scale crystallographic fragment screening, supporting the entire crystals-to-deposition process, and accessible to academic and industrial users worldwide. The peer-reviewed academic user program has been actively developed since 2016, to accommodate projects from as broad a scientific scope as possible, including well-validated as well as exploratory projects. Academic access is allocated through biannual calls for peer-reviewed proposals, and proprietary work is arranged by Diamond's Industrial Liaison group. This workflow has already been routinely applied to over a hundred targets from diverse therapeutic areas, and effectively identifies weak binders (1%-30% hit rate), which both serve as high-quality starting points for compound design and provide extensive structural information on binding sites. The resilience of the process was demonstrated by continued screening of SARS-CoV-2 targets during the COVID-19 pandemic, including a 3-week turn-around for the main protease.

XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties.

Determining the properties of chemical molecules is essential for screening candidates similar to a specific drug. These candidate molecules are further evaluated for their target binding affinities, side effects, target missing probabilities, etc. Conventional machine learning algorithms demonstrated satisfying prediction accuracies of molecular properties. A molecule cannot be directly loaded into a machine learning model, and a set of engineered features needs to be designed and calculated from a molecule. Such hand-crafted features rely heavily on the experiences of the investigating researchers. The concept of graph neural networks (GNNs) was recently introduced to describe the chemical molecules. The features may be automatically and objectively extracted from the molecules through various types of GNNs, e.g., GCN (graph convolution network), GGNN (gated graph neural network), DMPNN (directed message passing neural network), etc. However, the training of a stable GNN model requires a huge number of training samples and a large amount of computing power, compared with the conventional machine learning strategies. This study proposed the integrated framework XGraphBoost to extract the features using a GNN and build an accurate prediction model of molecular properties using the classifier XGBoost. The proposed framework XGraphBoost fully inherits the merits of the GNN-based automatic molecular feature extraction and XGBoost-based accurate prediction performance. Both classification and regression problems were evaluated using the framework XGraphBoost. The experimental results strongly suggest that XGraphBoost may facilitate the efficient and accurate predictions of various molecular properties. The source code is freely available to academic users at https://github.com/chenxiaowei-vincent/XGraphBoost.git.

Library as place: Understanding contradicting user expectations

In the 21st century, academic libraries continue their transition from warehouses of information to laboratories of knowledge creation. This case study examines the disconnect between the assessment by academic library users of what library resources and services are important and their lack of use of those resources and services. Focus group interviews with selected target populations explore differences based on level of study and discipline. The key finding is the importance of the library as place and what resources and services contribute to a library's sense of place.

IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease.

To date, research on inflammatory bowel disease (IBD, encompassing Crohn’s disease and ulcerative colitis), a chronic complex disorder, has generated a large amount of data scattered across published literature (1 06 333) listed in PubMed on 14 October 2020, and no dedicated database currently exists that catalogues information on genes associated with IBD. We aimed to manually curate 289 genes that are experimentally validated to be linked with IBD and its known phenotypes. Furthermore, we have developed an integrated platform providing information about different aspects of these genes by incorporating several resources and an extensive text-mined knowledgebase. The curated IBD database (IBDDB) allows the selective display of collated 34 subject-specific concepts (listed as columns) exportable through a user-friendly IBDDB portal. The information embedded in concepts was acquired via text-mining of PubMed (manually cleaned and curated), accompanied by data-mining from varied resources. The user can also explore different biomedical entities and their co-occurrence with other entities (about one million) from 11 curated dictionaries in the indexed PubMed records. This functionality permits the user to generate and cross-examine a new hypothesis that is otherwise not easy to comprehend by just reading the published abstracts and papers. Users can download required information using various file formats and can display information in the form of networks. To our knowledge, no curated database of IBD-related genes is available so far. IBDDB is free for academic users and can be accessed at https://www.cbrc.kaust.edu.sa/ibd/.

Altmetrics: The awareness and interest

The characteristics of academic users interested in altmetrical infor-mation are defined. The online survey of 302 academic respondents was conduc-ted to reveal the level of awareness and interest of scientific community. The analysis of the responses about altmetrics is supplemented with the data on the respondents' using traditional scientometric information. It was found that with a high degree of interest in traditional scientometric indicators (91.4% of respondents refer to them), altmetrics remained mostly out of the eye of scien-tists. Only 6.6% respondents use altmetrics, while the others are still unfamiliar with altmetrics or do not use them. However, over the half of respondents ex-pressed interest in altmetrics: 11.9% consider the method necessary, and 43% would like to learn more about it. The correlation between academic status and awareness of/or interest in altmetrics was found: applicants and candidates of science and applicants for this degree proved to be more interested in altmetrics information than doctors of science. The correlation between the aware-ness/interest and researcher’s area of studies appeared insignificant. The findings of the study may be used to improve the information support of scientists. The research model can be applied to other groups of library users.

FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening.

To reduce time and cost, virtual ligand screening (VLS) often precedes experimental ligand screening in modern drug discovery. Traditionally, high-resolution structure-based docking approaches rely on experimental structures, while ligand-based approaches need known binders to the target protein and only explore their nearby chemical space. In contrast, our structure-based FINDSITEcomb2.0 approach takes advantage of predicted, low-resolution structures and information from ligands that bind distantly related proteins whose binding sites are similar to the target protein. Using a boosted tree regression machine learning framework, we significantly improved FINDSITEcomb2.0 by integrating ligand fragment scores as encoded by molecular fingerprints with the global ligand similarity scores of FINDSITEcomb2.0. The new approach, FRAGSITE, exploits our observation that ligand fragments, e.g., rings, tend to interact with stereochemically conserved protein subpockets that also occur in evolutionarily unrelated proteins. FRAGSITE was benchmarked on the 102 protein DUD-E set, where any template protein whose sequence identify >30% to the target was excluded. Within the top 100 ranked molecules, FRAGSITE improves VLS precision and recall by 14.3 and 18.5%, respectively, relative to FINDSITEcomb2.0. Moreover, the mean top 1% enrichment factor increases from 25.2 to 30.2. On average, both outperform state-of-the-art deep learning-based methods such as AtomNet. On the more challenging unbiased set LIT-PCBA, FRAGSITE also shows better performance than ligand similarity-based and docking approaches such as two-dimensional ECFP4 and Surflex-Dock v.3066. On a subset of 23 targets from DEKOIS 2.0, FRAGSITE shows much better performance than the boosted tree regression-based, vScreenML scoring function. Experimental testing of FRAGSITE's predictions shows that it has more hits and covers a more diverse region of chemical space than FINDSITEcomb2.0. For the two proteins that were experimentally tested, DHFR, a well-studied protein that catalyzes the conversion of dihydrofolate to tetrahydrofolate, and the kinase ACVR1, FRAGSITE identified new small-molecule nanomolar binders. Interestingly, one new binder of DHFR is a kinase inhibitor predicted to bind in a new subpocket. For ACVR1, FRAGSITE identified new molecules that have diverse scaffolds and estimated nanomolar to micromolar affinities. Thus, FRAGSITE shows significant improvement over prior state-of-the-art ligand virtual screening approaches. A web server is freely available for academic users at http:/sites.gatech.edu/cssb/FRAGSITE.

Reaching academic library users during the COVID-19 pandemic: New and adapted approaches in access services

The COVID-19 pandemic, which hit academic libraries in the United States during the spring semester of 2020, forced librarians and staff to redouble their efforts to reach out to users in light of newly enforced safety measures such as building closures, quarantine periods, enforced social distancing, etc. This article describes three services—one adapted, one newly developed, and one a collaboration across several units on campus—to allow users to continue receiving the assistance and the materials they needed despite the obstacles inherent to the pandemic. Unexpectedly, these changes also helped streamline processes in a post-pandemic academic library environment.

Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition.

Chemical cross-linking coupled to mass spectrometry (XLMS) emerged as a powerful technique for studying protein structures and large-scale protein-protein interactions. Nonetheless, XLMS lacks software tailored toward dealing with multiple conformers; this scenario can lead to high-quality identifications that are mutually exclusive. This limitation hampers the applicability of XLMS in structural experiments of dynamic protein systems, where less abundant conformers of the target protein are expected in the sample. We present QUIN-XL, a software that uses unsupervised clustering to group cross-link identifications by their quantitative profile across multiple samples. QUIN-XL highlights regions of the protein or system presenting changes in its conformation when comparing different biological conditions. We demonstrate our software's usefulness by revisiting the HSP90 protein, comparing three of its different conformers. QUIN-XL's clusters correlate directly to known protein 3D structures of the conformers and therefore validates our software. QUIN-XL and a user tutorial are freely available at http://patternlabforproteomics.org/quinxl for academic users. Supplementary data are available at Bioinformatics online.

Contemporary academic library users in Kenya: their needs and preferences in access and use of information resources

PurposeThe purpose of this study is to assess the influence of generations on information behavior and needs to access and use of library resources and how well academic libraries in Kenya are simultaneously serving both generations. From literature reviewed, a study on the Kenyan scenario on generational behavior and needs was not identified and this study sought to fill that gap.Design/methodology/approachData collected were done through mixed-methods research using observation, structured interviews and questionnaires. The sample included 143 students and faculty within different generations, and three library staffs at The United States International University-Africa’s Library. Quantitative data were analyzed through SPSS and Excel, while qualitative data were analyzed according to the theme of this study. Likert-scale responses were used to measure information behavior of users’ needs and preferences.FindingsFindings showed that the library is serving two distinct generations with different needs: out of a mean score of 5.00 of sample surveyed; digital immigrants need information resources mainly for research at an aggregate 3.93 while digital natives need information resources mainly for examinations at an aggregate 4.01. Both generations need to use technology to access and use information resources at 94% of digital immigrants and an aggregate 81.5% of digital natives surveyed. The library is training both user groups accordingly. This answered the research problem this study sought to assess.Research limitations/implicationsThe generation of users was known only after administering the questionnaires. Consequently, the researcher targeted them using the status of respondents, faculty or student, to maximize sampling for each generation. Undergraduate and master’s students were used to target digital natives, while the faculty was used to target digital immigrants. PhD students were used to target both digital immigrants and digital natives. This study was done only in one location, USIU-Africa’s Library.Originality/valueThis study assessed how different generations within academic libraries in Kenya could be guided to effectively and efficiently adapt to global changes. This study assessed generational influence on needs and preferences in access and use of information resources, and assessed how academic libraries are concurrently and successfully serving variant user needs in Kenya,

Let’s understand the position of academic libraries in views of different users

This paper attempts to understand the position of academic libraries in views of different users include stakeholders, employer and service providers. Academic libraries have gone through computerization and then are practicing use of ICT. While functioning they are tackling variety of issues at a time and thus it has resulted it some confusion and difficult stage. Focusing on these issues few questions were asked to the experienced librarians and then views of different groups are discussed in the paper. Knowing difficult issues recommendations are suggested. There is need to counsel different user groups particularly students group is recommended in the paper. Keywords: Academic libraries, Users, Teaching and non-teaching staff and Library staff etc.

Influence of satisfaction and loyalty on Net Promoter Score (NPS) in academic libraries in Indonesia

PurposeThis study aims to determine the NPS score of state academic libraries users in Indonesia, the relationship between user loyalty and NPS scores and the relationship between user satisfaction with NPS.Design/methodology/approachThe method used in this research is quantitative explanatory method, which surveyed the relationship between satisfaction, loyalty and NPS variables based on the development of previous studies and existing theories. The population in this study were students visiting the state university library in Surabaya, Indonesia, namely Library A, Library B, Library C and Library D. The total number of samples taken was 200 divided equally to each of the universities, with 50 respondents respectively. Data collection was done with a questionnaire.FindingsThe Result shows that NPS value for academic library in Indonesia was 8. (1) The probability value of satisfaction with NPS is 0.18 (greater than 0.01) so H1 is rejected, meaning that satisfaction has no significant effect on NPS, (2) The probability value of satisfaction with loyalty is < 0.01 so that H0 is accepted. This means that satisfaction has a significant effect on loyalty and (3) The probability value of loyalty to NPS is < 0.01 so that H0 is accepted. This indicates that loyalty has a significant effect on NPS.Research limitations/implicationsTo get user satisfaction, libraries need to improve facilities and services in accordance with the characteristics and needs of users, so that user expectations will be met and achieve satisfaction. When user satisfaction has been fulfilled, user loyalty to library products will be formed, so the NPS score will increase which is manifested by users recommending the library to others. This research has limitations, namely that the object of research is only in public higher education centers, so for generalization it is necessary to add research objects such as private college libraries, public libraries or school libraries.Originality/valueResearch on loyalty by using NPS has not been done much especially in Indonesia. This study also examines the relationship between satisfaction and loyalty on NPS scores.

ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis.

The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus-based concentration-independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi-atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy - a PyMOL plugin to run a subset of ATSAS tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.