bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards a structurally resolved human protein interaction network
Authors: Burke David F. , Bryant Patrick , Barrio-Hernandez Inigo , Memon Danish , Pozzati Gabriele , Shenoy Aditi , Zhu Wensi , Dunham Alistair S , Albanese Pascal , Keller Andrew , Scheltema Richard A. , Bruce James E. , Leitner Alexander , Kundrotas Petras , Beltrao Pedro , Elofsson Arne 
Published: November 2021

AbstractAll cellular functions are governed by complex molecular machines that assemble through protein-protein interactions. Their atomic details are critical to the study of their molecular mechanisms but fewer than 5% of hundreds of thousands of human interactions have been structurally characterized. Here, we test the potential and limitations of recent progress in deep-learning methods using AlphaFold2 to predict structures for 65,484 human interactions. We show that higher confidence models are enriched in interactions supported by affinity or structure-based methods and can be orthogonally confirmed by spatial constraints defined by cross-link data. We identify 3,137 high confidence models, of which 1,371 have no homology to a known structure, from which we identify interface residues harbouring disease mutations, suggesting potential mechanisms for pathogenic variants. We find groups of interface phosphorylation sites that show patterns of co-regulation across conditions, suggestive of coordinated tuning of multiple interactions as signalling responses. Finally, we provide examples of how the predicted binary complexes can be used to build larger assemblies. Accurate prediction of protein complexes promises to greatly expand our understanding of the atomic details of human cell biology in health and disease.
Open Access publishing in Medicine: lights and shadows
Authors: Bernabò Nicola , Valbonetti Luca , Ordinelli Alessandra , Ciccarelli Rosa , Barboni Barbara 
Published: November 2021

AbstractThe widespread use of internet has had enormous consequences in changing the way of accessing to scientific literature in all domains of knowledge and, in particular, in medicine. One of the most important related factors is the idea of making research output freely available: the so-called Open Access (OA) option. OA is considered very important in spreading of knowledge, breaking down barriers in benefit of research, and increasing the impact of research outputs within the scientific community.Here, we carried out a comparison between Non-Open Access (NOA) and OA medical Journals in terms of growing rate, geographical distribution, and the impact on scientific community.We collected the bibliometric data on the scientific Journals indexed in Scopus starting from 2001 to 2016 published either as NOA or OA. Then, we analysed the number of Journals, their geolocalization, their impact on the scientific community, and the parameters as SJR, H index, and cites for document (2 years).As a result, we found that while the number of NOA Journals is virtually stable, that of OA is dramatically increasing, with a growing rate higher than 400% in 2016. Then, the majority of OA Journals are published in developing Countries (Brazil, India, South Africa, South Korea, New Zealand, Serbia, and Poland) and their impact within researchers is lower compared to the NOA Journals.In conclusion, our data provide an updated and unprecedented picture of OA adoption in medical field, with its lights and shadows.Article HighlightsWe are seeing in medicine a huge increase in the number of Journals that use OA;This trend is mainly due to the increase in publishing Journals in Countries with emergent economies;The use of OA for Journals in the medical field, did not guarantee a vantage in term of bibliometric parameters.MCS92C99JELI30
Deletion of Abi3/Gngt2 influences age-progressive amyloid β and tau pathologies in distinctive ways
Authors: Ibanez Kristen R , McFarland Karen N , Phillips Jennifer , Allen Mariet , Lessard Christian , Zobel Lillian , De La Cruz Elsa Gonzalez , Shah Shivani , Vo Quan , Wang Xue , Quicksall Zach , Ryu Daniel , Funk Cory , Ertekin-Taner Nilufer , Prokop Stefan , Golde Todd E , Chakrabarty Paramita 
Published: November 2021

AbstractThe S209F variant of Abelson Interactor Protein 3 (ABI3) increases risk for Alzheimer’s disease (AD), but little is known about ABI3 function. RNAscope showed Abi3 is expressed in microglial and non-microglial cells, though its increased expression appears to be driven in plaque-associated microglia. Here, we evaluated Abi3-/- mice and document that both Abi3 and its overlapping gene, Gngt2, are disrupted in these mice. Expression of Abi3 and Gngt2 are tightly correlated, and elevated, in rodent models of AD. RNA-seq of the Abi3-Gngt2-/- mice revealed robust induction of an AD-associated neurodegenerative signature, including upregulation of Trem2, Plcg2 and Tyrobp. In APP mice, loss of Abi3-Gngt2 resulted in a gene dose- and age-dependent reduction in Aβ deposition. Additionally, in Abi3-Gngt2-/- mice, expression of a pro-aggregant form of human tau exacerbated tauopathy and astrocytosis. Further, the AD-associated S209F mutation alters the extent of ABI3 phosphorylation. These data provide an important experimental framework for understanding the role of Abi3-Gngt2 function in AD. Our studies also demonstrate that manipulation of glial function could have opposing effects on amyloid and tau pathology, highlighting the unpredictability of targeting such pathways in AD.
High Throughput Intact Protein Analysis for Drug Discovery Using Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry
Authors: Pu Fan , Ugrin Scott A. , Radosevich Andrew J. , Chang-Yen David , Sawicki James W. , Talaty Nari N. , Elsen Nathaniel L. , Williams Jon D. 
Published: November 2021

AbstractMass spectrometry (MS) is the primary analytical tool used to characterize proteins within the biopharmaceutical industry. Electrospray ionization (ESI) coupled to liquid chromatography (LC) is the current gold standard for intact protein analysis. However, inherent speed limitations of LC/MS prevent analysis of large sample numbers (>1000) in a day. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI-MS), an ambient ionization MS technology, has recently been established as a platform for high throughput small molecule analysis. Here we report the applications of such a system for the analysis of intact proteins commonly performed within the drug discovery process. A wide molecular weight range of proteins 10 – 150 kDa was detected on the system with improved tolerance to salts and buffers compared to ESI. With high concentrations and model proteins, a sample rate up to 22 Hz was obtained. For proteins at low concentrations and in buffers used in commonly employed assays, robust data at a sample rate of 1.5 Hz was achieved, which is ∼ 22x faster than current technologies used for high throughput ESI-MS-based protein assays. In addition, two multiplexed plate-based high throughput sample cleanup methods were coupled to IR-MALDESI-MS to enable analysis of samples containing excessive amounts of salts and buffers without fully compromising productivity. Example experiments, which leverage the speed of the IR-MALDESI-MS system to monitor NISTmAb reduction, protein autophosphorylation and compound binding kinetics in near real-time, are demonstrated.Graphical Abstract
Ubiquitination of stalled ribosomes enables mRNA decay via HBS-1 and NONU-1in vivo
Authors: Monem Parissa C. , Vidyasagar Nitin , Piatt Audrey L. , Sehgal Enisha , Arribere Joshua A. 
Published: November 2021

ABSTRACTAs ribosomes translate the genetic code, they can encounter a variety of obstacles that hinder their progress. If ribosomes stall for prolonged times, cells suffer due to the loss of translating ribosomes and the accumulation of aberrant protein products. Thus to protect cells, stalled ribosomes experience a series of reactions to relieve the stall and degrade the offending mRNA, a process known as No-Go mRNA Decay (NGD). While much of the machinery for NGD is known, the precise ordering of events and factors along this pathway has not been tested. Here, we deployC. elegansto unravel the coordinated events comprising NGD. Utilizing a novel reporter and forward and reverse genetics, we identify the machinery required for NGD. Our subsequent molecular analyses define a functional requirement for ubiquitination on at least two ribosomal proteins (eS10 and uS10), and we show that ribosomes lacking ubiquitination sites on eS10 and uS10 fail to perform NGDin vivo. We show that the nuclease NONU-1 acts after the ubiquitin ligase ZNF-598, and discover a novel requirement for the ribosome rescue factors HBS-1/PELO-1 in mRNA decay via NONU-1. Taken together, our work demonstrates mechanisms by which ribosomes signal to effectors of mRNA repression, and we delineate links between repressive factors working toward a well-defined NGD pathway.AUTHOR SUMMARYRibosomes are large molecular machines entrusted with the essential task of reading mRNAs and building proteins. It is critical that ribosomes proceed with their work undeterred, so as to avoid traffic jams between ribosomes on mRNAs; however, they sometimes experience challenges which make traffic jams unavoidable. In these cases, cells have evolved machinery to clean up stalled ribosomes and remove offending mRNAs. Much of this machinery is now identified, but the relationships between factors has yet to be tested. Here, inC. eleganswe identify the machinery that responds to stalls, and we order factors relative to one another. We find that ribosomes must be tagged by ubiquitin to signal mRNA decay, as ribosomes lacking ubiquitin sites fail to elicit mRNA decay. Furthermore, we find that these ubiquitin signals recruit an enzyme which cuts mRNA, and we present evidence that ribosome rescue factors are required for the mRNA decay reaction as well. Overall, our work provides new connections between factors orchestrating the elimination of problematic mRNAs that stall ribosomes.
Context-dependent inversion of the response in a single sensory neuron type reverses olfactory preference behavior
Authors: Khan Munzareen , Hartmann Anna H. , O’Donnell Michael P. , Piccione Madeline , Chao Pin-Hao , Dwyer Noelle D. , Bargmann Cornelia I. , Sengupta Piali 
Published: November 2021

ABSTRACTThe valence and salience of individual odorants are modulated by an animal’s innate preferences, learned associations, and internal state, as well as by the context of odorant presentation. The mechanisms underlying context-dependent flexibility in odor valence are not fully understood. Here we show that the behavioral response of C. elegans to bacterially-produced medium-chain alcohols switches from attraction to avoidance when presented in the background of a subset of additional attractive chemicals. This context-dependent reversal of odorant preference is driven by cell-autonomous inversion of the response to alcohols in the single AWC olfactory neuron pair. We find that while medium-chain alcohols inhibit the AWC olfactory neurons to drive attraction, these alcohols instead activate AWC to promote avoidance when presented in the background of a second AWC-sensed odorant. We show that these opposing responses are driven via engagement of different odorant-directed signal transduction pathways within AWC. Our results indicate that context-dependent recruitment of alternative intracellular signaling pathways within a single sensory neuron type conveys opposite hedonic valences, thereby providing a robust mechanism for odorant encoding and discrimination at the periphery.
Ciliary Generation of a Peptidergic Sexual Signal
Authors: Luxmi Raj , Mains Richard E. , Eipper Betty A. , King Stephen M. 
Published: November 2021

AbstractPeptidergic intercellular communication occurs throughout the eukaryotes, and regulates a wide range of physiological and behavioral responses. Cilia are sensory and secretory organelles that both receive information from the environment and transmit signals. Cilia derived vesicles (ectosomes), formed by outward budding of the ciliary membrane, carry enzymes and other bioactive products; this process represents an ancient mode of regulated secretion. Our previous study revealed the presence of the peptide amidating enzyme, peptidylglycine α-amidating monooxygenase (PAM), in cilia and its key role in ciliogenesis. Furthermore, PAM and its amidated products are released in ciliary ectosomes from the green alga Chlamydomonas reinhardtii. One amidated product (GATI-amide) serves as a chemotactic modulator for C. reinhardtii gametes, attracting minus gametes while repelling plus gametes. Here we dissect the complex processing pathway that leads to formation of this amidated peptidergic sexual signal specifically on the ectosomes of plus gametes. We also identify a potential prohormone convertase that undergoes domain rearrangement during ectosomal secretion as a substrate for PAM. Analysis of this pathway affords insight into how single-celled organisms lacking dense core vesicles engage in regulated secretion, and provides a paradigm for understanding how amidated peptides that transmit sexual and other signals through cilia are generated.
Evaluation of access to electricity and the socioeconomic effects in rural and urban expanses of Nigeria
Authors: Ogunro Toluwalope , Afolabi Luqman 
Published: November 2021

PurposeRecently, multidimensional aspects of poverty has been increasingly focused on which includes education, economy and health, while access to modern energy such as stable electricity is also one of the possible solution; thus, this article aims to divulge the relation between access to electricity and progression in socioeconomic status in urban and rural areas of Nigeria in an attempt to propose a sustainable framework for access to electricity.Design/methodology/approachDemographic and health survey data are collected using four categories of model of questionnaires. A standard questionnaire was designed to gather information on features of the household's dwelling element and attributes of visitors and usual residents between the 2018 period. Biomarker questionnaire was used to gather biomarker data on men, women and children. Logistic model estimation technique was employed to estimate the socioeconomic factors affecting access to electricity in Nigeria.FindingsThese studies discovered that there are diverse set of factors affecting access to electricity in Nigeria especially in the rural areas. However, respondent residing in rural areas are still largely deprived access to electricity; most importantly, households with no access to electricity are more likely to use self-generating sets as revealed. Additionally, empirical findings indicated that the higher the level of your education and wealth, the higher the likelihood of having access to electricity in Nigeria. These factors included political will to connect the rural areas to the national grid, development of other infrastructures in those deprived areas and others.Practical implicationsThe problem confronting access to electricity in Nigeria has three components. The first is the significance of those deprived access to electricity in the rural areas and the physical resources needed to connect them to the national grid. The second is the political willingness of the government to have equitable distribution of public goods evenly between rural and urban areas especially on electricity access which will go a long way in reducing poverty in Nigeria. The third is lack of robust national development plans and strategy to tackle the problems facing electricity access in Nigeria.Social implicationsAs the rate of socioeconomic status/development increases, access to electricity is anticipated to rise up in Nigeria.Originality/valueThe findings can be used by the policy makers to address problems facing access to electricity in Nigeria.
Key skills and competencies of LIS professionals in the digital library environment: a content analysis of job advertisements
Authors: Yadav Akhilesh K.S. 
Published: November 2021

PurposeThe main purpose of this research study is to identify the essential skills and competencies sought by prospective employers for library and information science (LIS) positions in India. The research study aims to find out various designated positions in job advertisements.Design/methodology/approachThe data were collected from a major weekly job journal “Employment News” in India over five years from 2016 to 2020. The Employment News provides the latest job vacancies of central/state governments, public sector undertakings and autonomous bodies in India. Each issue of Employment News was carefully scanned and searched for job advertisements in the field of LIS. The researcher analyzed various posts on permanent, deputation and short-term contracts to gain insights into the job’s skills.FindingsThe findings highlight that public sector academic and school libraries are the top employers of LIS professionals. One of the most frequent demands of employers is profession-related work experience. Results show that employers place the strongest emphasis on library administration, computer knowledge, technical skills, managerial skills and soft skills. Library management, library supervision and procurement of journals and books are the primary job responsibilities for top-level positions.Research limitations/implicationsThe weekly job journal, Employment News, is the largest source of LIS jobs in publicly funded organizations and institutions in India. It does not cover private educational institutes, industries and corporates. Job-related data were collected solely from this journal for the duration of 2016–2020. Therefore, this research study does not fully represent the LIS job market with regard to private educational institutes and corporate organizations.Practical implicationsThe research findings can help LIS professionals prepare themselves according to market needs and demands. The LIS school should integrate these required skills and competencies into the course curriculum for preparing professionals in the digital age.Originality/valueThe results are benchmarked to guide and evaluate LIS course curricula in India. LIS schools may emphasize soft skills in future curriculum design, which employers frequently seek.
Integrated solid-state wearable sweat sensor system for sodium and potassium ion concentration detection
Authors: Zhang Haowei , Sun Lili , Song Chengli , Liu Ying , Xuan Xueting , Wang Fei , Zhong Jing , Sun Li 
Published: November 2021

Purpose
Design, fabricate and evaluate all-solid-state wearable sensor systems that can monitor ion concentrations in human sweat to provide real time health analysis and disease diagnosis capabilities.

Design/methodology/approach
A human health monitoring system includes disposable customized flexible electrode array and a compact signal transmission-processing electronic unit.

Findings
Patterned rGO (reduced-graphene oxide) layers can replace traditional metal electrodes for the fabrication of free-standing all solid film sensors to provide improved flexibility, sensitivity, selectivity, and stability in ion concentration monitoring. Electrochemical measurements show the open circuit potential of current selective electrodes exhibit near Nernst responses versus Na+ and K+ ion concentration in sweat. These signals show great stability during a typical measurement period of 3 weeks. Sensor performances evaluated through real time measurements on human subjects show strong correlations between subject activity and sweating levels, confirming high degree of robustness, sensitivity, reliability and practicality of current sensor systems.

Originality/value
In improving flexibility, stability and interfacial coherency of chemical sensor arrays, rGO films have been the developed as a high-performance alternative to conventional electrode with significant cost and processing complexity reduction. rGO supported solid state electrode arrays have been found to have linear potential response versus ion concentration, suitable for electrochemical sensing applications. Current sweat sensor system has a high degree of integration, including electrode arrays, signal processing circuits, and data visualization interfaces.
A simulated crime scene footwear impression database for teaching and research purposes
Authors: Lin En‐Tni , DeBat Tabitha , Speir Jacqueline A. 
Published: November 2021

AbstractCommunity‐shared open‐source forensic footwear databases are relatively rare, although it is generally agreed that access to such resources can support a multitude of research and teaching/training goals. The objective of this technical report is to detail the creation of such a dataset that includes both high‐quality exemplars and simulated crime scene impressions. To achieve this goal, a variety of shoe makes, models, sizes, substrates, matrices, lifting methods, and enhancement (chemical/digital) techniques were employed and are fully described. The result is an open‐source dataset available for download, and comprised of 214 high‐quality impressions (87 right outsoles × 2 replicates + 40 left (close non‐mated) outsoles), 138 dust impressions (46 outsoles × 3 replicates), and 73 blood impressions (24 outsoles × 3 replicates = 72 + 1 additional replicate). Of the 138 dust impressions, 117 are provided in a digitally enhanced form (via Adobe® Photoshop and/or Photoshop Camera Raw software), and 120 are provided in an unenhanced form for a total of 237 images. For the blood impressions, all 73 are provided in both unenhanced and chemically enhanced forms for a total of 146 images. Thus, in addition to the outsole scans, a total of 597 simulated crime scene and/or known test impressions are included and fully documented.
Invasion and defense of the basic social unit in a nonhuman primate society leads to sexual differences in the gut microbiome
Authors: XIA Wancai , ZHAO Mei , WANG Dali , WANG Fan , CHEN Hua , LIU Guoqi , ZHU Lifeng , LI Dayong 
Published: November 2021

AbstractMultilevel society is one of the most complex social systems in natural ecosystems and is a typical feature among some primates. Given the potential connection between social behavior and gut microbiome composition, the multilevel social system could affect the primate gut microbiome. Here, based on long‐term observation (e.g. social unit dynamics, transfer, and behavior), we investigated this potential integrating 16S rRNA gene amplicon sequencing and behavior data in Yunnan snub‐nosed monkeys (Rhinopithecus bieti), which possess a multilevel social group based on one male units (OMUs, each unit with several breeding females and their offspring) and all‐male unit (AMU, several bachelor males residing together). We found that the mean unweighted Unifrac distance between adult males from different OMUs was significantly lower than that between adult females from different OMUs (paired Wilcoxon test, P = 0.007). There was no significant difference in the mean unweighted Unifrac distance between females within the same OMU or between females from different OMUs. These findings indicated the potential connection between the defense and invasion of social units and the gut microbiome community in wild Yunnan snub‐nosed monkeys. We speculated that the resident males of OMUs displaying a significantly higher similarity in the gut microbial community than that of adult females in separate OMUs might be associated with the sexual differences in their interactions and from previously having cohabitated together in the AMU. Therefore, this study suggested that multilevel societies might have an effect on the gut microbial community in this wild nonhuman primate species.