bluuebunny/crossref_metadata_2025_split huggingface dataset:
A scoping review of distributed ledger technology in genomics: thematic analysis and directions for future research
Authors: Beyene Mikael , Toussaint Philipp A , Thiebes Scott , Schlesner Matthias , Brors Benedikt , Sunyaev Ali 
Published: May 2022

Abstract

Objective
Rising interests in distributed ledger technology (DLT) and genomics have sparked various interdisciplinary research streams with a proliferating number of scattered publications investigating the application of DLT in genomics. This review aims to uncover the current state of research on DLT in genomics, in terms of focal research themes and directions for future research.

Materials and Methods
We conducted a scoping review and thematic analysis. To identify the 60 relevant papers, we queried Scopus, Web of Science, PubMed, ACM Digital Library, IEEE Xplore, arXiv, and BiorXiv.

Results
Our analysis resulted in 7 focal themes on DLT in genomics discussed in literature, namely: (1) Data economy and sharing; (2) Data management; (3) Data protection; (4) Data storage; (5) Decentralized data analysis; (6) Proof of useful work; and (7) Ethical, legal, and social implications.

Discussion
Based on the identified themes, we present 7 future research directions: (1) Investigate opportunities for the application of DLT concepts other than Blockchain; (2) Explore people’s attitudes and behaviors regarding the commodification of genetic data through DLT-based genetic data markets; (3) Examine opportunities for joint consent management via DLT; (4) Investigate and evaluate data storage models appropriate for DLT; (5) Research the regulation-compliant use of DLT in healthcare information systems; (6) Investigate alternative consensus mechanisms based on Proof of Useful Work; and (7) Explore DLT-enabled approaches for the protection of genetic data ensuring user privacy.

Conclusion
While research on DLT in genomics is currently growing, there are many unresolved problems. This literature review outlines extant research and provides future directions for researchers and practitioners.
Influence of environmental factors and genetic variation on mitochondrial DNA copy number
Authors: Sanglard Leticia P , Kuehn Larry A , Snelling Warren M , Spangler Matthew L 
Published: May 2022

Abstract
Mitochondrial DNA copy number (mtDNA CN) has been shown to be highly heritable and associated with traits of interest in humans. However, studies are lacking in the literature for livestock species such as beef cattle. In this study, 2,371 individuals from a crossbred beef population comprising the Germplasm Evaluation program from the U.S. Meat Animal Research Center had samples of blood, leucocyte, or semen collected for low-pass sequencing (LPS) that resulted in both nuclear DNA (nuDNA) and mitochondrial DNA (mtDNA) sequence reads. Mitochondrial DNA CN was estimated based on the ratio of mtDNA to nuDNA coverages. Genetic parameters for mtDNA CN were estimated from an animal model based on a genomic relationship matrix (~87K SNP from the nuDNA). Different models were used to test the effects of tissue, sex, age at sample collection, heterosis, and breed composition. Maternal effects, assessed by fitting a maternal additive component and by fitting eleven SNP on the mtDNA, were also obtained. As previously reported, mtDNA haplotypes were used to classify individuals into Taurine haplogroups (T1, T2, T3/T4, and T5). Estimates of heritability when fitting fixed effects in addition to the intercept were moderate, ranging from 0.11 to 0.31 depending on the model. From a model ignoring contemporary group, semen samples had the lowest mtDNA CN, as expected, followed by blood and leucocyte samples (P ≤ 0.001). The effect of sex and the linear and quadratic effects of age were significant (P ≤ 0.02) depending on the model. When significant, females had greater mtDNA CN than males. The effects of heterosis and maternal heterosis were not significant (P ≥ 0.47). The estimates of maternal and mtDNA heritability were near zero (≤0.03). Most of the samples (98%) were classified as haplogroup T3. Variation was observed in the mtDNA within Taurine haplogroups, which enabled the identification of 24 haplotypes. These results suggest that mtDNA CN is under nuclear genetic control and would respond favorably to selection.
Effects of dietary energy density and supplemental rumen undegradable protein on intake, viscera, and carcass composition of lambs recovering from nutritional restriction
Authors: Dougherty Holland C , Evered Mark , Oltjen James W , Hegarty Roger S , Neutze Stephen A , Oddy V Hutton 
Published: May 2022

Abstract
Variation in nutrition is a key determinant of growth, body composition, and the ability of animals to perform to their genetic potential. Depending on the quality of feed available, animals may be able to overcome negative effects of prior nutritional restriction, increasing intake and rates of tissue gain, but full compensation may not occur. A 2 × 3 × 4 factorial serial slaughter study was conducted to examine the effects of prior nutritional restriction, dietary energy density, and supplemental rumen undegradable protein (RUP) on intake, growth, and body composition of lambs. After an initial slaughter (n = 8), 124 4-mo-old Merino cross wethers (28.4 ± 1.8 kg) were assigned to either restricted (LO, 500 g/d) or unrestricted (HI, 1500 g/d) intake of lucerne and oat pellets. After 8 wk, eight lambs/group were slaughtered and tissue weights and chemical composition were measured. Remaining lambs were randomly assigned to a factorial combination of dietary energy density (7.8, 9.2, and 10.7 MJ/kg DM) and supplemental RUP (0, 30, 60, and 90 g/d) and fed ad libitum for a 12- to 13-wk experimental period before slaughter and analysis. By week 3 of the experimental period, lambs fed the same level of energy had similar DMI (g/d) and MEI (MJ/d) (P &gt; 0.05), regardless of prior level of nutrition. Restricted-refed (LO) lambs had higher rates of fat and protein gain than HI lambs (P &lt; 0.05) but had similar visceral masses (P &gt; 0.05). However, LO lambs were lighter and leaner at slaughter, with proportionally larger rumens and livers (P &lt; 0.05). Tissue masses increased with increasing dietary energy density, as did DMI, energy and nitrogen (N) retention (% intake), and rates of protein and fat gain (P &lt; 0.05). The liver increased proportionally with increasing dietary energy density and RUP (P &lt; 0.05), but rumen size decreased relative to the empty body as dietary energy density increased (P &lt; 0.05) and did not respond to RUP (P &gt; 0.05). Fat deposition was greatest in lambs fed 60 g/d supplemental RUP (P &lt; 0.05). However, lambs fed 90 g/d were as lean as lambs that did not receive supplement (P0, P &gt; 0.05), with poorer nitrogen retention and proportionally heavier livers than P0 lambs (P &lt; 0.05). In general, visceral protein was the first tissue to respond to increased intake during refeeding, followed by non-visceral protein and fat, highlighting the influence of differences in tissue response over time on animal performance and body composition.
Reproductive status affects isotopic niches of Miniopterus natalensis in northeastern South Africa
Authors: Pretorius Mariëtte , Broders Hugh , Hall Grant , Keith Mark 
Published: May 2022

Abstract
The Natal long-fingered bat, Miniopterus natalensis, is an insectivorous, regional migrating species that exhibits sex-specific migration patterns. We explored the variability of isotopic niches using δ13C and δ15N ratios in fur from female and male bats in different reproductive states: pregnant, reproductive (but not pregnant at the time of this study), and nonreproductive females; nonscrotal and scrotal males using Bayesian standard ellipse areas and generalized linear models. Reproductive status was an informative predictor for the observed variation of both δ13C and δ15N ratios. Pregnant females displayed the highest mean δ13C and δ15N ratios and were distinct from other reproductive states. Reproductive females exhibited significantly higher δ15N ratios than nonreproductive females or nonscrotal and scrotal males, which may reflect state-dependent foraging and/or higher metabolic stress. Scrotal males displayed the lowest mean δ13C and δ15N ratios. Nonscrotal males exhibited the broadest isotopic niche, whereas reproductive females had the narrowest isotopic niche. Differences in isotopic niche sizes between the different reproductive groups may relate to variable individual feeding behavior and/or geographically different foraging areas/migratory stopover sites at individual and intraspecific levels in M. natalensis. This suggests that group-living, cave-dwelling bats may employ individual foraging specialization to facilitate coexistence in the broader geographic landscape.
Computational flow analysis with boundary layer and contact representation: II. Heart valve flow with leaflet contact
Authors: Terahara Takuya , Kuraishi Takashi , Takizawa Kenji , Tezduyar Tayfun E 
Published: May 2022

Abstract
In this second part of a two-part article, we provide an overview of the heart valve flow analyses conducted with boundary layer and contact representation, made possible with the space–time (ST) computational methods described in the first part. With these ST methods, we are able to represent the boundary layers near moving solid surfaces, including the valve leaflet surfaces, with the accuracy one gets from moving-mesh methods and without the need for leaving a mesh protection gap between the surfaces coming into contact. The challenge of representing the contact between the leaflets without giving up on high-resolution flow representation near the leaflet surfaces has been overcome. The other challenges that have been overcome include the complexities of a near-actual valve geometry, having in the computational model a left ventricle with an anatomically realistic motion and an aorta from CT scans and maintaining the flow stability at the inflow of the ventricle-valve-aorta sequence, where we have a traction boundary condition during part of the cardiac cycle.
A History of the Passive in Pre-modern Aramaic: An Outline
Authors: Kalinin Maksim , Loesov Sergey 
Published: May 2022

Abstract
In Proto-Aramaic, the passive of transitive verbs belonging to all three principal stems—G, D and C—was formed internally. Some verbs of the G- and D-stems also possessed detransitive derivatives. Transitive verbs of the G-, D- and C-stems lost their internal passives early on, and the passives of G- and D-verbs were encoded by their respective t-stems. Against this general Aramaic picture, in Imperial Aramaic the passive forms of the G-stem were in complementary distribution: the passive Past was encoded by the internal passive of the Suffix Conjugation (Gp SC), while the passive non-Past was rendered by the Gt participle and the Gt Prefix Conjugation. Gp SC stopped being used with Imperial Aramaic once it was replaced, as a written language, by vernacular-based literary varieties. The Ct-stem, non-existent in Imperial Aramaic, must have first emerged among spoken varieties of Aramaic in the first half of the first millennium bce, and only within I-w and II-w/y roots. Within the Imperial Aramaic corpus, both the rare Gt SC passive forms and Ct-stem forms reflect the influence of spoken Aramaic varieties in the diglossic situation. In Syriac, the Ct-stem of sound roots is unattested during its golden age. The Ct-forms of sound roots appeared in original Syriac texts only after the Arab conquest, and these also come from spoken Aramaic varieties.
Culturing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) for Diagnosis and Genome Sequencing
Authors: Zeng Zhiqi , Guo Hua , Chen Liping , Lin Zhengshi , Guan Wenda , Wang Yutao , Jiang Haiming , Wu Xiao , Yin Yong , Gao Zelong , Chen Canxiong , Yang Zifeng 
Published: May 2022

Abstract

Objective
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid detection “re-positive” phenomenon is encountered clinically. The accuracy of a viral nucleic acid test is crucial to prevent reintroduction of the virus into the community. This study evaluated the effect of virus culturing on increasing the sensitivity and specificity of real-time polymerase chain reaction (RT-PCR) detection and viral genomic sequencing.

Methods
A series of tenfold dilutions of a SARS-CoV-2 viral stock were conducted and cultured for either 24 or 48 hours. The viral load of cultured samples was determined by RT-PCR. The cultured and non-cultured samples of 1x 50% tissue culture infectious dose (TCID50) were sequenced using metagenomic next-generation sequencing. The depth and coverage of SARS-CoV-2 genome were measured.

Results
The lowest viral load detectable in a sample with RT-PCR was 0.01 TCID50. After a 24-h culture, the viral ORF 1ab and N-gene cycle threshold (CT) values were reduced by 4.4 points and 1 point, respectively. One TCID50 viral load of post 24-h culture revealed the sequence depth reached an average of 752 reads, compared with 0.15 in the nonculture; furthermore, the coverage was 99.99% while 6.42% in the nonculture.

Conclusion
These results indicate that virus culturing can significantly increase the viral load, which can increase the certainty of true-positive detection of the viral nucleic acids, and improve the quality of virus genomic sequencing.
Multi-epoch machine learning 1: Unravelling nature versus nurture for galaxy formation
Authors: McGibbon Robert J , Khochfar Sadegh 
Published: May 2022

Abstract
We present a novel machine learning method for predicting the baryonic properties of dark matter only subhalos from N-body simulations. Our model is built using the extremely randomized tree (ERT) algorithm and takes subhalo properties over a wide range of redshifts as its input features. We train our model using the IllustrisTNG simulations to predict blackhole mass, gas mass, magnitudes, star formation rate, stellar mass, and metallicity. We compare the results of our method with a baseline model from previous works, and against a model that only considers the mass history of the subhalo. We find that our new model significantly outperforms both of the other models. We then investigate the predictive power of each input by looking at feature importance scores from the ERT algorithm. We produce feature importance plots for each baryonic property, and find that they differ significantly. We identify low redshifts as being most important for predicting star formation rate and gas mass, with high redshifts being most important for predicting stellar mass and metallicity, and consider what this implies for nature versus nurture. We find that the physical properties of galaxies investigated in this study are all driven by nurture and not nature. The only property showing a somewhat stronger impact of nature is the present-day star formation rate of galaxies. Finally we verify that the feature importance plots are discovering physical patterns, and that the trends shown are not an artefact of the ERT algorithm.
Real-Time and Remote MCMC Trace Inspection with Beastiary
Authors: Wirth Wytamma , Duchene Sebastian 
Published: May 2022

Abstract
Bayesian phylogenetics has gained substantial popularity in the last decade, with most implementations relying on Markov chain Monte Carlo (MCMC). The computational demands of MCMC mean that remote servers are increasingly used. We present Beastiary, a package for real-time and remote inspection of log files generated by MCMC analyses. Beastiary is an easily deployed web-app that can be used to summarize and visualize the output of many popular software packages including BEAST, BEAST2, RevBayes, and MrBayes via a web browser. We describe the design and implementation of Beastiary and some typical use-cases, with a focus on real-time remote monitoring.
DDGun: an untrained predictor of protein stability changes upon amino acid variants
Authors: Montanucci Ludovica , Capriotti Emidio , Birolo Giovanni , Benevenuta Silvia , Pancotti Corrado , Lal Dennis , Fariselli Piero 
Published: May 2022

Abstract
Estimating the functional effect of single amino acid variants in proteins is fundamental for predicting the change in the thermodynamic stability, measured as the difference in the Gibbs free energy of unfolding, between the wild-type and the variant protein (ΔΔG). Here, we present the web-server of the DDGun method, which was previously developed for the ΔΔG prediction upon amino acid variants. DDGun is an untrained method based on basic features derived from evolutionary information. It is antisymmetric, as it predicts opposite ΔΔG values for direct (A → B) and reverse (B → A) single and multiple site variants. DDGun is available in two versions, one based on only sequence information and the other one based on sequence and structure information. Despite being untrained, DDGun reaches prediction performances comparable to those of trained methods. Here we make DDGun available as a web server. For the web server version, we updated the protein sequence database used for the computation of the evolutionary features, and we compiled two new data sets of protein variants to do a blind test of its performances. On these blind data sets of single and multiple site variants, DDGun confirms its prediction performance, reaching an average correlation coefficient between experimental and predicted ΔΔG of 0.45 and 0.49 for the sequence-based and structure-based versions, respectively. Besides being used for the prediction of ΔΔG, we suggest that DDGun should be adopted as a benchmark method to assess the predictive capabilities of newly developed methods. Releasing DDGun as a web-server, stand-alone program and docker image will facilitate the necessary process of method comparison to improve ΔΔG prediction.
Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq
Authors: Ghaddar Bassel , De Subhajyoti 
Published: May 2022

Abstract
Cell-cell interactions are the fundamental building blocks of tissue organization and multicellular life. We developed Neighbor-seq, a method to identify and annotate the architecture of direct cell–cell interactions and relevant ligand–receptor signaling from the undissociated cell fractions in massively parallel single cell sequencing data. Neighbor-seq accurately identifies microanatomical features of diverse tissue types such as the small intestinal epithelium, terminal respiratory tract, and splenic white pulp. It also captures the differing topologies of cancer-immune-stromal cell communications in pancreatic and skin tumors, which are consistent with the patterns observed in spatial transcriptomic data. Neighbor-seq is fast and scalable. It draws inferences from routine single-cell data and does not require prior knowledge about sample cell-types or multiplets. Neighbor-seq provides a framework to study the organ-level cellular interactome in health and disease, bridging the gap between single-cell and spatial transcriptomics.
CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting
Authors: Liu Yang , Yang Xiaocong , Gan Jianhong , Chen Shuang , Xiao Zhi-Xiong , Cao Yang 
Published: May 2022

AbstractProtein-ligand blind docking is a powerful method for exploring the binding sites of receptors and the corresponding binding poses of ligands. It has seen wide applications in pharmaceutical and biological researches. Previously, we proposed a blind docking server, CB-Dock, which has been under heavy use (over 200 submissions per day) by researchers worldwide since 2019. Here, we substantially improved the docking method by combining CB-Dock with our template-based docking engine to enhance the accuracy in binding site identification and binding pose prediction. In the benchmark tests, it yielded the success rate of ∼85% for binding pose prediction (RMSD &lt; 2.0 Å), which outperformed original CB-Dock and most popular blind docking tools. This updated docking server, named CB-Dock2, reconfigured the input and output web interfaces, together with a highly automatic docking pipeline, making it a particularly efficient and easy-to-use tool for the bioinformatics and cheminformatics communities. The web server is freely available at https://cadd.labshare.cn/cb-dock2/.
MO006: Identifying the Main Predictors of Urine Output in Autosomal Dominant Polycystic Kidney Disease (ADPKD) Patients taking Tolvaptan
Authors: Borrego-Utiel Francisco-Jose , Isabel Morales García Ana , Polo Moyano Aurora , Roca Oporto Francisco , Merino Garcia Enoc , Jose Esteban de la Rosa Rafael 
Published: May 2022

Abstract

BACKGROUND AND AIMS
Tolvaptan (TVP) blocks vasopressin V2 receptors causing severe polyuria. Few works have analyzed factors associated with urine output in autosomal dominant polycystic kidney disease (ADPKD) patients taking TVP.

METHOD
We selected 24 h urine samples from ADPKD patients treated with TVP. Urine osmolality/creatinine ratio was used as estimator of urine daily osmolar load.

RESULTS
We included 122 urine samples from 54 patients. After TVP, urine output doubled with a parallel reduction in solutes in urine with parallel reduction in urine solute concentration. However, when they were expressed as urine solute/creatinine ratios, no significant changes were observed. Daily osmolar load and osmolality/creatinine ratio did not change significantly.
Before TVP, urine output was positively correlated with body weight and urine osmolality/creatinine ratio and negatively with estimated glomerular filtration rate (eGFR), urine morning osmolality and 24 h urine calculated osmolality. After TVP, urine output was positively correlated with body weight, eGFR and negatively with age. There was a poor correlation with urine calculated osmolality.
We built a predictor model using general linear modeling, and we found that urine output was related to lower age, higher body weight, higher eGFR and greater doses of TVP. When body weight was removed, urine output was also related to male sex and higher daily osmolar excretion.

CONCLUSION
Patients taking TVP will undergo an increase about twice in urine production from baseline. Greater doses of TVP cause a progressive increase in urine output independent of renal function. GFR and specially age and body weight are the most important predictors of future urine output in patients taking TVP.