bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the fecal microbiome in cats with inflammatory bowel disease or alimentary small cell lymphoma
Authors: Marsilio Sina , Pilla Rachel , Sarawichitr Benjamin , Chow Betty , Hill Steve L. , Ackermann Mark R. , Estep J. Scot , Lidbury Jonathan A. , Steiner Joerg M. , Suchodolski Jan S. 
Published: December 2019

AbstractFeline chronic enteropathy (CE) is a common gastrointestinal disorder in cats and mainly comprises inflammatory bowel disease (IBD) and small cell lymphoma (SCL). Both IBD and SCL in cats share features with chronic enteropathies such as IBD and monomorphic epitheliotropic intestinal T-cell lymphoma in humans. The aim of this study was to characterize the fecal microbiome of 38 healthy cats and 27 cats with CE (13 cats with IBD and 14 cats with SCL). Alpha diversity indices were significantly decreased in cats with CE (OTU p = 0.003, Shannon Index p = 0.008, Phylogenetic Diversity p = 0.019). ANOSIM showed a significant difference in bacterial communities, albeit with a small effect size (P = 0.023, R = 0.073). Univariate analysis and LEfSE showed a lower abundance of facultative anaerobic taxa of the phylaFirmicutes(families Ruminococcaceae andTuricibacteraceae),Actinobacteria(genusBifidobacterium) andBacteroidetes(i.a.Bacteroides plebeius) in cats with CE. The facultative anaerobic taxaEnterobacteriaceaeandStreptococcaceaewere increased in cats with CE. No significant difference between the microbiome of cats with IBD and those with SCL was found. Cats with CE showed patterns of dysbiosis similar to those in found people with IBD.
Towards Rational Computational Engineering of Psychrophilic Enzymes
Authors: Sočan Jaka , Isaksen Geir Villy , Brandsdal Bjørn Olav , Åqvist Johan 
Published: December 2019

AbstractCold-adapted enzymes from psychrophilic species achieve their high catalytic efficiency at low temperature by a different partitioning of the activation free energy into its enthalpic and entropic components, compared to orthologous mesophilic enzymes. Their lower activation enthalpy, partly compensated by an increased entropic penalty, has been suggested to originate from changes in flexibility of the protein surface. Multiple sequence alignments of psychrophilic and mesophilic enzymes also show characteristic motifs located in surface loops of the protein. Here, we use computer simulations to examine the effects of a number of designed surface mutations of psychrophilic and mesophilic elastases on the temperature dependence of the catalyzed peptide cleavage reaction. For each of 14 mutant enzyme variants we report calculations of their thermodynamic activation parameters. The results show that substitution of psychrophilic loop residues into the mesophilic enzyme consistently changes both the activation parameters and loop flexibilities towards the former, and vice versa for opposite substitutions.
Prey size as a critical factor for bird bone taphonomy in Eagle Owl (Bubo bubo) pellets
Authors: Rufà Anna , Laroulandie Véronique 
Published: December 2019

AbstractEach predator hunts and consumes its prey in a particular way. Consequently, the traces left by predators on bones might vary according to the manner in which the prey are processed. For this reason, prey size has been proposed as a key issue that affects the damage inflicted on bones. The Eagle Owl (Bubo bubo) is one of the main potential predators of small prey found in archaeological sites. However, detailed taphonomic research describing bone accumulations produced by this nocturnal raptor is still scarce. The aim of the present work is to describe a modern accumulation of pellets originated by the Eagle Owl from this perspective, with a specific focus on birds. Particular attention is paid to prey size to evaluate the real significance of this variable when assessing bone damage. The results confirm that bone alterations reflect how prey was ingested, as the bones show greater damage with increasing prey size. This finding emphasises the complexity of characterising archaeological accumulations, as the alterations will vary according to prey size. In addition, bone architecture—or other aspects that cannot be controlled—may hinder accurate diagnosis and should be taken into account.
Circulating proteomic signature of early death in heart failure patients with reduced ejection fraction
Authors: Cuvelliez Marie , Vandewalle Vincent , Brunin Maxime , Beseme Olivia , Hulot Audrey , de Groote Pascal , Amouyel Philippe , Bauters Christophe , Marot Guillemette , Pinet Florence 
Published: December 2019

AbstractHeart failure (HF) remains a main cause of mortality worldwide. Risk stratification of patients with systolic chronic HF is critical to identify those who may benefit from advanced HF therapies. The aim of this study is to identify plasmatic proteins that could predict the early death (within 3 years) of HF patients with reduced ejection fraction hospitalized in CHRU de Lille. The subproteome targeted by an aptamer-based technology, the Slow Off-rate Modified Aptamer (SOMA) scan assay of 1310 proteins, was profiled in blood samples from 168 HF patients, and 203 proteins were significantly modulated between patients who died of cardiovascular death and patients who were alive after 3 years of HF evaluation (Wilcoxon test, FDR 5%). A molecular network was built using these 203 proteins, and the resulting network contained 2281 molecules assigned to 34 clusters annotated to biological pathways by Gene Ontology. This network model highlighted extracellular matrix organization as the main mechanism involved in early death in HF patients. In parallel, an adaptive Least Absolute Shrinkage and Selection Operator (LASSO) was performed on these 203 proteins, and six proteins were selected as candidates to predict early death in HF patients: complement C3, cathepsin S and F107B were decreased and MAPK5, MMP1 and MMP7 increased in patients who died of cardiovascular causes compared with patients living 3 years after HF evaluation. This proteomic signature of 6 circulating plasma proteins allows the identification of systolic HF patients with a risk of early death.
Protein components of ribonucleoprotein granules from Drosophila germ cells oligomerize and show distinct spatial organization during germline development
Authors: Vo Hieu D. L. , Wahiduzzaman  , Tindell Samuel J. , Zheng Jimiao , Gao Ming , Arkov Alexey L. 
Published: December 2019

AbstractThe assembly of large RNA-protein granules occurs in germ cells of many animals and these germ granules have provided a paradigm to study structure-functional aspects of similar structures in different cells. Germ granules in Drosophila oocyte’s posterior pole (polar granules) are composed of RNA, in the form of homotypic clusters, and proteins required for germline development. In the granules, Piwi protein Aubergine binds to a scaffold protein Tudor, which contains 11 Tudor domains. Using a super-resolution microscopy, we show that surprisingly, Aubergine and Tudor form distinct clusters within the same polar granules in early Drosophila embryos. These clusters partially overlap and, after germ cells form, they transition into spherical granules with the structural organization unexpected from these interacting proteins: Aubergine shell around the Tudor core. Consistent with the formation of distinct clusters, we show that Aubergine forms homo-oligomers and using all purified Tudor domains, we demonstrate that multiple domains, distributed along the entire Tudor structure, interact with Aubergine. Our data suggest that in polar granules, Aubergine and Tudor are assembled into distinct phases, partially mixed at their “interaction hubs”, and that association of distinct protein clusters may be an evolutionarily conserved mechanism for the assembly of germ granules.
AutoCLEM: An Automated Workflow for Correlative Live-Cell Fluorescence Microscopy and Cryo-Electron Tomography
Authors: Fu Xiaofeng , Ning Jiying , Zhong Zhou , Ambrose Zandrea , Charles Watkins Simon , Zhang Peijun 
Published: December 2019

AbstractCorrelative light and electron microscopy (CLEM) combines the strengths of both light and electron imaging modalities and enables linking of biological spatiotemporal information from live-cell fluorescence light microscopy (fLM) to high-resolution cellular ultra-structures from cryo-electron microscopy and tomography (cryoEM/ET). This has been previously achieved by using fLM signals to localize the regions of interest under cryogenic conditions. The correlation process, however, is often tedious and time-consuming with low throughput and limited accuracy, because multiple correlation steps at different length scales are largely carried out manually. Here, we present an experimental workflow, AutoCLEM, which overcomes the existing limitations and improves the performance and throughput of CLEM methods, and associated software. The AutoCLEM system encompasses a high-speed confocal live-cell imaging module to acquire an automated fLM grid atlas that is linked to the cryoEM grid atlas, followed by cryofLM imaging after freezing. The fLM coordinates of the targeted areas are automatically converted to cryoEM/ET and refined using fluorescent fiducial beads. This AutoCLEM workflow significantly accelerates the correlation efficiency between live-cell fluorescence imaging and cryoEM/ET structural analysis, as demonstrated by visualizing human immunodeficiency virus type 1 (HIV-1) interacting with host cells.
A ligand-based system for receptor-specific delivery of proteins
Authors: Maffei Mariano , Morelli Chiara , Graham Ellie , Patriarca Stefano , Donzelli Laura , Doleschall Balint , de Castro Reis Fernanda , Nocchi Linda , Chadick Cora H. , Reymond Luc , Corrêa Ivan R. , Johnsson Kai , Hackett Jamie A. , Heppenstall Paul A. 
Published: December 2019

AbstractGene delivery using vector or viral-based methods is often limited by technical and safety barriers. A promising alternative that circumvents these shortcomings is the direct delivery of proteins into cells. Here we introduce a non-viral, ligand-mediated protein delivery system capable of selectively targeting primary skin cells in-vivo. Using orthologous self-labelling tags and chemical cross-linkers, we conjugate large proteins to ligands that bind their natural receptors on the surface of keratinocytes. Targeted CRE-mediated recombination was achieved by delivery of ligand cross-linked CRE protein to the skin of transgenic reporter mice, but was absent in mice lacking the ligand’s cell surface receptor. We further show that ligands mediate the intracellular delivery of Cas9 allowing for CRISPR-mediated gene editing in the skin more efficiently than adeno-associated viral gene delivery. Thus, a ligand-based system enables the effective and receptor-specific delivery of large proteins and may be applied to the treatment of skin-related genetic diseases.
Genetically inherited tolerance may unveil trait dominance patterns in an amphibian model
Authors: Fasola E. , Ribeiro R. , Lopes I. 
Published: December 2019

AbstractChemical contamination may cause genetic erosion in natural populations by wiping out the most sensitive genotypes. This is of upmost concern if the loss of genetic variability is irreversible due to contaminant-driven elimination of alleles, which may happen if tolerance is a recessive or incompletely dominant trait – the recessive tolerance inheritance (working-) hypothesis. Accordingly, this work investigated the tolerance inheritance to lethal levels of a metal-rich acid mine drainage (AMD) and to copper sulphate in a population ofPelophylax perezi. Time-to-death for each egg, after being exposed to 60% of a sample of acid mine drainage and to 9 mg/L Cu, was registered, and, for each egg mass, the median lethal time (LT50) and respective quartiles (LT25and LT75) were computed. Results suggested that genetically determined tolerance could be probably driven by incomplete dominance (with possible maternal effect influence), preliminarily supporting the initial hypothesis.
A genome-scale CRISPR/Cas9 knockout screening reveals SH3D21 as a sensitizer for gemcitabine
Authors: Masoudi Mohammad , Seki Motoaki , Yazdanparast Razieh , Yachie Nozomu , Aburatani Hiroyuki 
Published: December 2019

AbstractGemcitabine, 2′,2′-difluoro-2′-deoxycytidine, is used as a pro-drug in treatment of variety of solid tumour cancers including pancreatic cancer. After intake, gemcitabine is transferred to the cells by the membrane nucleoside transporter proteins. Once inside the cells, it is converted to gemcitabine triphosphate followed by incorporation into DNA chains where it causes inhibition of DNA replication and thereby cell cycle arrest and apoptosis. Currently gemcitabine is the standard drug for treatment of pancreatic cancer and despite its widespread use its effect is moderate. In this study, we performed a genome-scale CRISPR/Cas9 knockout screening on pancreatic cancer cell line Panc1 to explore the genes that are important for gemcitabine efficacy. We found SH3D21 as a novel gemcitabine sensitizer implying it may act as a therapeutic target for improvement of gemcitabine efficacy in treatment of pancreatic cancer.
Association betweenFASgene −670 A/G and −1377 G/A polymorphisms and the risk of autoimmune diseases: a meta-analysis
Authors: Yan Hongwei , Hong Yuxiao , Cai Yunfei 
Published: December 2019

AbstractObjectives: FAS plays a critical role in the extrinsic apoptosis pathway in autoimmune diseases. Previous studies investigating the association between FAS gene −670 A/G and −1377 G/A polymorphisms and the risk of autoimmune diseases reported controversial results. We performed the meta-analysis to evaluate the possible association. Methods: Relevant studies were identified by searching the PubMed, Embase, CNKI, and Wanfang databases up to December 2018. Odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were calculated to determine the association. Results: A total of 43 articles including 67 studies (52 studies for FAS −670 A/G and 15 studies for −1377 G/A) were included in the meta-analysis. Our meta-analysis showed that the FAS −670 A/G polymorphism was associated with the risk of autoimmune diseases (GG vs. GA: OR = 1.079, 95% CI = 1.004–1.160, P=0.038), especially in Caucasians (GG vs. GA: OR = 1.12, 95% CI = 1.03–1.23, P=0.012), Asians (G vs. A: OR = 0.89, 95% CI = 0.83–0.96, P=0.002), systemic lupus erythematosus (SLE) (G vs. A: OR = 0.85, 95% CI = 0.77–0.94, P=0.001), multiple sclerosis (MS) (GG+GA vs. AA: OR = 0.83, 95% CI = 0.70–0.99, P=0.043), systemic sclerosis (SSc) (GG vs. GA: OR = 1.20, 95% CI = 1.07–1.36, P=0.003) and Hashimoto’s thyroiditis (HT) (G vs. A: OR = 1.45, 95% CI = 1.10–1.90, P=0.008); the FAS −1377 G/A polymorphism was associated with the risk of autoimmune diseases (A vs. G: OR = 1.11, 95% CI = 1.03–1.20, P=0.008), especially in Asians (A vs. G: OR = 1.15, 95% CI = 1.05–1.25, P=0.002) and high quality studies (A vs. G: OR = 1.14, 95% CI = 1.05–1.24, P=0.002). Conclusion: This meta-analysis demonstrated that the FAS –670A/G and –1377 G/A polymorphisms were associated with the risk of autoimmune diseases.
Individual Differences in Distributional Learning for Speech: What's Ideal for Ideal Observers?
Authors: Theodore Rachel M. , Monto Nicholas R. , Graham Stephen 
Published: December 2019

Purpose
Speech perception is facilitated by listeners' ability to dynamically modify the mapping to speech sounds given systematic variation in speech input. For example, the degree to which listeners show categorical perception of speech input changes as a function of distributional variability in the input, with perception becoming less categorical as the input, becomes more variable. Here, we test the hypothesis that higher level receptive language ability is linked to the ability to adapt to low-level distributional cues in speech input.

Method

Listeners (
n
= 58) completed a distributional learning task consisting of 2 blocks of phonetic categorization for words beginning with /g/ and /k/. In 1 block, the distributions of voice onset time values specifying /g/ and /k/ had narrow variances (i.e., minimal variability). In the other block, the distributions of voice onset times specifying /g/ and /k/ had wider variances (i.e., increased variability). In addition, all listeners completed an assessment battery for receptive language, nonverbal intelligence, and reading fluency.

Results
As predicted by an ideal observer computational framework, the participants in aggregate showed identification responses that were more categorical for consistent compared to inconsistent input, indicative of distributional learning. However, the magnitude of learning across participants showed wide individual variability, which was predicted by receptive language ability but not by nonverbal intelligence or by reading fluency.

Conclusion
The results suggest that individual differences in distributional learning for speech are linked, at least in part, to receptive language ability, reflecting a decreased ability among those with weaker receptive language to capitalize on consistent input distributions.
Enhancement of OTP stream cipher algorithm based on bit separation
Authors: Arisman  , Nasution Mahyuddin K M , Efendi Syahril 
Published: December 2019

Abstract
Along with the increasing development of cryptography and computer science, It is appropriate that we try to prepare and improve the ability of cryptographic algorithms To counteract and prevent threats. Generally This algorithm encrypt the text with combined using key. The original message must be the same length of the key used. Actually in this study, a new method for improve OTP was successfully carried out. first, key will be generated using PRNG algorithm then bits of Plaintext will be separate each into 2 bits then rotating it key using matrix table, further key will be inserted into separated Plaintext and re-separate each it into 1 byte, hereinafter the new Plaintext will be XORed with a rotated key. To produce more advanced cipher.
Improving the Modelling of Robot Bunker With Camera
Authors: Naf`an Emil , Sulaiman Riza , Mohamad Ali Nazlena , Priambodo Bagus , Hazidar Al Hamidy , Kudr Nseaf Asama , Pratama Putra Zico , Theozard Fikri Harry , Handriani Inge 
Published: December 2019

Abstract
This study proposed an improvement on the model of robot bunker with camera. This is designed in order that robot is difficult to steal. The previous model is equipped with a security system. However, the system is not equipped with a camera so that when theft occurs, the action cannot be recorded. This study used 16 rules, because of the addition of variable pixels produced by the camera. The simulation is carried out as many as 30 (thirty) possible conditions of actions taken by the people on the robot with Matlab Fuzzy Toolbox. In the result of the simulations, the test results can change from safe conditions to alert or dangerous conditions. This is caused by changes in the number of pixels. The pixel value increases when someone tries to take a robot from the robot bunker. Thus the proposed model is more sensitive in detecting changes that occur around the robot bunker. Therefore this model can be applied in securing/protecting robot from theft.
Expert System Application for Diagnosing of Bipolar Disorder with Certainty Factor Method Based on Web and Android
Authors: Muhammad A , Hendrik B , Iswara R 
Published: December 2019

Abstract
The purpose of this research is to design and develop software engineering of expert system based on web and android that is capable of diagnosing Bipolar Disorder to get the same level of solution and information with the expert. The expert system application has been developed by using PHP as the web programming language and by using Java with the Web View method as the android programming, and by using MySQL as the databases. This research used analytical method of certainty factor based on the user answers for the questions asked by this expert system. The result showed that the user condition related with bipolar disorder and completed with suggestion of solution medical or treatment and the list of psychiatrist. The conclusion of this research is certainty factor method evidently could give result in the form of early diagnosis and could provide the consistent and effective solutions.
Supplier Selection by Using Analytical Hierarchy Process (AHP) and Techniques for Order Preference Methods with Similarities to Ideal Solutions (TOPSIS)
Authors: Siregar I 
Published: December 2019

Abstract
One company that is engaged in drying coffee beans has problems, the problem is suppliers have not been able to meet the criteria set by the company. Within the last six months, there were coffee bean sacks that the company rejected because of the mismatch of the quality of the coffee beans obtained from suppliers with the standards set by the company so that the selection of suppliers that could meet the criteria of the company was needed. The criteria used by the company are quality, price, quantity, delivery time and response to claims. This study aims to determine the best suppliers based on criteria weights and to rank each alternative supplier. The method used by researchers for this problem is the method of Analytical Hierarchy Process (AHP) and Technique for Order Preference by Similarity to Ideal Solution (TOPSIS). This method is used to determine supplier priorities. Determination of criteria and subcriteria is built based on expert answers using a questionnaire. Assessment of the importance of criteria and alternative weights based on the AHP questionnaire. The results obtained using this method indicate that the supplier who gets the first and deserves priority is PT ABC with the highest preference value of 0.8639.
Application of Theory of Constraints in Bottleneck Work Stations Optimization
Authors: Siregar I 
Published: December 2019

Abstract
Manufacturing industries engaged in making of instant noodles in Medan city have problems in production planning. The process studied is the manufacture of GCGEP, GCST and G-1000GSP products. The constraints faced by the company are the presence of bottlenecks on mixing and cooking work stations due to differences in capacity between the work station and the previous work station, namely the sieving work station and dough forming work station. Bottleneck work stations happens in mixing work stations in January, February, March, May, June, July and August 2014 as well as cooking work stations in January, May and July 2014. This study uses the principle of continuous improvement of Theory of Constraints (TOC) to eliminate constraints on bottleneck work stations and to facilitate the overall production flow. In applying TOC, to optimize the production master schedule and to know the maximum advantage cost, linear programming method is used. After the optimal master schedule results are known, revisions to rough cut capacity planning are carried out and the result shows that the bottleneck work station found has become a non-bottleneck work station.
Expert systems diagnosing of banana pests and diseases use case-based reasoning method with android
Authors: Kurnia Hezy , Ariandi Vicky , Heriyanto  , Elva Yesri 
Published: December 2019

AbstractDesigning a Case-based rasoning (CBR) android application is a method used to build a knowledge-based system. Source of system knowledge is obtained by collecting handling cases by an expert or expert. In this study the author makes or analyzes Banana Plant disease through the symptoms experienced by the Plant so that it can help a person or farmer in diagnosing the types of diseases and pests of banana plants based on their symptoms. The advantage with the application of this method is that farmers do not need to ask symptoms and diseases to an expert. This application is expected to make it easier for farmers to recognize the types of pests and diseases of banana plants and also this application has a clear calculation of the pests and diseases of banana plants. This application can be done offline.