bluuebunny/crossref_metadata_2025_split huggingface dataset:
NIBNA: a network-based node importance approach for identifying breast cancer drivers
Authors: Chaudhary Mandar S. , Pham Vu V.H. , Le Thuc D. 
Published: February 2021

Abstract

Motivation
Identifying meaningful cancer driver genes in a cohort of tumors is a challenging task in cancer genomics. Although existing studies have identified known cancer drivers, most of them focus on detecting coding drivers with mutations. It is acknowledged that non-coding drivers can regulate driver mutations to promote cancer growth. In this work, we propose a novel node importance-based network analysis (NIBNA) framework to detect coding and non-coding cancer drivers. We hypothesize that cancer drivers are crucial to the formation of community structures in cancer network, and removing them from the network greatly perturbs the network structure thereby critically affecting the functioning of the network. NIBNA detects cancer drivers using a three-step process: first, a condition-specific network is built by incorporating gene expression data and gene networks; second, the community structures in the network are estimated; and third, a centrality-based metric is applied to compute node importance.

Results
We apply NIBNA to the BRCA dataset, and it outperforms existing state-of-art methods in detecting coding cancer drivers. NIBNA also predicts 265 miRNA drivers, and majority of these drivers have been validated in literature. Further we apply NIBNA to detect cancer subtype-specific drivers, and several predicted drivers have been validated to be associated with cancer subtypes. Lastly, we evaluate NIBNA’s performance in detecting epithelial–mesenchymal transition drivers, and we confirmed 8 coding and 13 miRNA drivers in the list of known genes.

Availability and implementation
The source code can be accessed at https://github.com/mandarsc/NIBNA.

Supplementary information
Supplementary data are available at Bioinformatics online.
Monitoring of Chemical Markers in Extraction of Traditional Medicinal Plants (Piper nigrum, Curcuma longa) Using In Situ ReactIR
Authors: Sateesh Reddy K , Siva Bandi , Divya Reddy S , Kumar K , Pratap T V , Vidyasagar Reddy Konda , Venkateswara Rao B , Suresh Babu K 
Published: February 2021

Abstract

Background
The fingerprinting and quantification of marker compounds from medicinal plants is a domain of the herbal industry for quality/quantity control parameters.

Objective
The main objective of this study is the application of the in situ ReactIR technique for measuring the concentration of different components during the extraction process of different medicinal plants.

Method
In this study we have performed the extraction of two-marker compounds, viz. piperine from Piper nigrum and curcumin from Curcuma longa plants, using various solvents (dichloromethane and methanol). The progress of extraction was monitored using an in situ Fourier transform infrared (FTIR) probe instrument and an automated reactor.

Results
In this communication, using the in situ ReactIR technique we developed a method which demonstrates the relative quantification of marker analytes, optimizes extraction time and type of solvents to be used for different analytes during the extraction process.

Conclusions
To the best of our knowledge, this is the first report of relative quantification and structural information of marker compounds during the process of extraction using in situ FTIR.

Highlights
The present study highlights the real-time monitoring, in situ quantification, and structural information of marker compounds during the process of extraction of medicinal plants using in situ FTIR.
Structured water: effects on animals
Authors: Lindinger Michael I 
Published: February 2021

Abstract
This review focuses on the effects of structured water (SW) on animals when it is consumed on a daily basis. SW is liquid water that is given altered H-bonding structure by treatment with various forms of energy including magnetic fields and light. While most of the research has been conducted on ‘magnetized’ water, which has structure of short duration, recent research has examined effects of a SW with stability of at least 3.5 mo. A variety of laboratory and farm animals have been studied over the past 20 yr. Consistent (3 or more studies) responses among animals consuming SW for 1 mo or more include increased rate of growth, reduced markers of oxidative stress, improved glycemic and insulinemic responses in diabetics, improved blood lipid profile, improved semen and spermatozoa quality, and increased tissue conductivity as measured using bioelectrical impedance analysis. While it is known that fluids in and around cells and molecules are structured, it remains unknown if this endogenous water structuring is influenced by drinking SWs. The mechanisms by which SW affects biological systems are unknown and require investigation. Effects of SW, when taken up by biological systems, are likely associated with altered water structuring around biological surfaces, such as proteins and membranes.
Weaning causes a prolonged but transient change in immune gene expression in the intestine of piglets
Authors: de Groot Nienke , Fariñas Fernando , Cabrera-Gómez Carolina G , Pallares Francisco J , Ramis Guillermo 
Published: February 2021

AbstractControlling gut inflammation is important in managing gut disorders in the piglet after weaning. Establishing patterns of inflammation markers in the time subsequent to weaning is important for future research to determine whether interventions are effective in controlling gut inflammation. The objective of this study was to evaluate the intestinal inflammatory response during the postweaning period in piglets. A 45-d study included 108 piglets (weaned at 22 d, body weight 5.53 ± 1.19 kg), distributed in 12 pens with nine pigs per pen. Histomorphometry, gene expression of pro- and anti-inflammatory cytokines, and the quantity of immunoglobulin (Ig) A producing cells were measured in jejunum, ileum, and colon on days 0, 15, 30, and 45 postweaning. Cytokine gene expression in peripheral blood mononuclear cells and Ig quantities were analyzed in blood from piglets on days 0, 15, 30, and 45 postweaning. Histomorphometrical results showed a lower villus length directly after weaning. Results demonstrated a postweaning intestinal inflammation response for at least 15 d postweaning by upregulation of IgA producing cells and IFN-γ, IL-1α, IL-8, IL-10, IL-12α, and TGF-β in jejunum, ileum, and colon. IgM and IgA were upregulated at day 30 postweaning. IgG was downregulated at day 15 postweaning. The results indicate that weaning in piglets is associated with a prolonged and transient response in gene expression of pro- and anti-inﬂammatory cytokines and IgA producing cells in the intestine.
Limited Evidence for Parallel Evolution Among Desert-AdaptedPeromyscusDeer Mice
Authors: Colella Jocelyn P , Tigano Anna , Dudchenko Olga , Omer Arina D , Khan Ruqayya , Bochkov Ivan D , Aiden Erez L , MacManes Matthew D 
Published: February 2021

AbstractWarming climate and increasing desertification urge the identification of genes involved in heat and dehydration tolerance to better inform and target biodiversity conservation efforts. Comparisons among extant desert-adapted species can highlight parallel or convergent patterns of genome evolution through the identification of shared signatures of selection. We generate a chromosome-level genome assembly for the canyon mouse (Peromyscus crinitus) and test for a signature of parallel evolution by comparing signatures of selective sweeps across population-level genomic resequencing data from another congeneric desert specialist (Peromyscus eremicus) and a widely distributed habitat generalist (Peromyscus maniculatus), that may be locally adapted to arid conditions. We identify few shared candidate loci involved in desert adaptation and do not find support for a shared pattern of parallel evolution. Instead, we hypothesize divergent molecular mechanisms of desert adaptation among deer mice, potentially tied to species-specific historical demography, which may limit or enhance adaptation. We identify a number of candidate loci experiencing selective sweeps in the P. crinitus genome that are implicated in osmoregulation (Trypsin, Prostasin) and metabolic tuning (Kallikrein, eIF2-alpha kinase GCN2, APPL1/2), which may be important for accommodating hot and dry environmental conditions.
Influence of Holocene habitat availability on Pacific gray whale (Eschrichtius robustus) population dynamics as inferred from whole mitochondrial genome sequences and environmental niche modeling
Authors: Brüniche-Olsen Anna , Bickham John W , Godard-Codding Celine A , Brykov Vladimir A , Kellner Kenneth F , Urban Jorge , DeWoody J Andrew 
Published: February 2021

AbstractEnvironmental changes since the Pleistocene and commercial whaling in the last few centuries have drastically reduced many whale populations, including gray whales in the North Pacific. Herein we use complete mitogenome sequences from 74 individuals to evaluate gray whale phylogeography and historical demography, then use environmental niche modeling to assess how habitat availability has changed through time for Pacific gray whales. We identify a large degree of haplotype sharing between gray whales sampled in Russian and Mexican waters, coupled with very limited matrilineal population structure. Confirming previous studies, our environmental niche models showed a decrease in available habitat during the Last Glacial Maximum, but we find no genetic signals of recent population declines in mitochondrial genomes despite both sustained habitat loss and a commercial whaling bottleneck. Our results illustrate the complex dynamics of baleen whale biogeography since the Holocene as well as the difficulty in detecting recent demographic bottlenecks from mitochondrial DNA sequences.
Associations of sleep phenotypes with severe intentional self-harm: a prospective analysis of the UK Biobank cohort
Authors: Lei Binbin , Zhang Jihui , Chen Sijing , Chen Jie , Yang Lulu , Ai Sizhi , Chan Ngan Yin , Wang Jing , Dai Xi-jian , Feng Hongliang , Liu Yaping , Li Shirley Xin , Jia Fujun , Wing Yun-Kwok 
Published: February 2021

AbstractStudy objectivesWe aimed to investigate the prospective associations of sleep phenotypes with severe intentional self-harm (ISH) in middle-aged and older adults.MethodsA total of 499,159 participants (mean age: 56.55 ± 8.09 years; female: 54.4%) were recruited from the UK Biobank between 2006 and 2010 with follow-up until February 2016 in this population-based prospective study. Severe ISH was based on hospital inpatient records or a death cause of ICD-10 codes X60-X84. Patients with hospitalized diagnosis of severe ISH before the initial assessment were excluded. Sleep phenotypes, including sleep duration, chronotype, insomnia, sleepiness, and napping, were assessed at the initial assessments. Cox regression analysis was used to estimate temporal associations between sleep phenotypes and future risk of severe ISH.ResultsDuring a follow-up period of 7.04 years (SD: 0.88), 1,219 participants experienced the first hospitalization or death related to severe ISH. After adjusting for demographics, substance use, medical diseases, mental disorders, and other sleep phenotypes, short sleep duration (HR: 1.50, 95% CI: 1.23–1.83, p &lt; .001), long sleep duration (HR: 1.56, 95% CI: 1.15–2.12, p = .004), and insomnia (usually: HR: 1.57, 95% CI: 1.31–1.89, p &lt; .001) were significantly associated with severe ISH. Sensitivity analyses excluding participants with mental disorders preceding severe ISH yielded similar results.ConclusionThe current study provides the empirical evidence of the independent prediction of sleep phenotypes, mainly insomnia, short- and long-sleep duration, for the future risk of severe ISH among middle-aged and older adults.
A statewide analysis of SARS-CoV-2 transmission in New York
Authors: Lasek-Nesselquist Erica , Singh Navjot , Russell Alexis , Lamson Daryl , Kelly John , Plitnick Jonathan , Pfeiffer Ryan D. , Tucker Nathan , Schneider Erasmus , George Kirsten St. 
Published: February 2021

AbstractNew York State, in particular the New York City metropolitan area, was the early epicenter of the SARS-CoV-2 pandemic in the United States. Similar to initial pandemic dynamics in many metropolitan areas, multiple introductions from various locations appear to have contributed to the swell of positive cases. However, representation and analysis of samples from New York regions outside the greater New York City area were lacking, as were SARS-CoV-2 genomes from the earliest cases associated with the Westchester County outbreak, which represents the first outbreak recorded in New York State. The Wadsworth Center, the public health laboratory of New York State, sought to characterize the transmission dynamics of SARS-CoV-2 across the entire state of New York from March to September with the addition of over 600 genomes from under-sampled and previously unsampled New York counties and to more fully understand the breadth of the initial outbreak in Westchester County. Additional sequencing confirmed the dominance of B.1 and descendant lineages (collectively referred to as B.1.X) in New York State. Community structure, phylogenetic, and phylogeographic analyses suggested that the Westchester outbreak was associated with continued transmission of the virus throughout the state, even after travel restrictions and the on-pause measures of March, contributing to a substantial proportion of the B.1 transmission clusters as of September 30th, 2020.
Interpreting vaccine efficacy trial results for infection and transmission
Authors: Lipsitch Marc , Kahn Rebecca 
Published: February 2021

ABSTRACTRandomized controlled trials (RCTs) have shown high efficacy of multiple vaccines against SARS-CoV-2 disease (COVID-19), and recent studies have shown the vaccines are also effective against infection. Evidence for the effect of each of these vaccines on ability to transmit the virus is also beginning to emerge. We describe an approach to estimate these vaccines’ effects on viral positivity, a prevalence measure which under the reasonable assumption that vaccinated individuals who become infected are no more infectious than unvaccinated individuals forms a lower bound on efficacy against transmission. Specifically, we recommend separate analysis of positive tests triggered by symptoms (usually the primary outcome) and cross-sectional prevalence of positive tests obtained regardless of symptoms. The odds ratio of carriage for vaccine vs. placebo provides an unbiased estimate of vaccine effectiveness against viral positivity, under certain assumptions, and we show through simulations that likely departures from these assumptions will only modestly bias this estimate. Applying this approach to published data from the RCT of the Moderna vaccine, we estimate that one dose of vaccine reduces the potential for transmission by at least 61%, possibly considerably more. We describe how these approaches can be translated into observational studies of vaccine effectiveness.HighlightsSARS-CoV-2 vaccine trials did not directly estimate vaccine efficacy against transmission.We describe an approach to estimate a lower bound of vaccine efficacy against transmission.We estimate one dose of the Moderna vaccine reduces the potential for transmission by at least 61%.We recommend separate analysis of tests triggered by symptoms vs. cross-sectional tests.
Brazil Nut Effect Drives Pattern Formation in Early Mammalian Embryos
Authors: Guo Zheng , Yao Jie , Zheng Xu , Cao Jialing , Gao Zheng , Guo Shuyu , Qin Dandan , Tan Min , Wang Bo , Meng Fanzhe , Zhang Jing , Li Lei , Du Jing , Fan Yubo 
Published: February 2021

ABSTRACTThe formation of three-dimensional ordered spatial patterns, which is essential for embryonic development, tissue regeneration, and cancer metastasis, is mainly guided by the chemical concentration gradient of morphogens. However, since no chemical concentration gradient has been observed in the early embryonic development (pre-implantation) of mammals, the pattern formation mechanism has been unsolved for a long time. During the second cell fate decision of mouse embryos, the inner cell mass (ICM) segregates into topographically regionalized epiblast (EPI) and primitive endoderm (PrE) layers. Here, we report that the segregation process of PrE/EPI precursors coincides with an emerged periodic expansion-contraction vibration of the blastocyst cavity, which induces phase transition in the ICM compartment to a higher fluidity state and generates directional tissue flows. By experiments and modeling, we demonstrate that the spatial segregation of PrE and EPI precursors is mediated by a “Brazil nut effect”-like viscous segregation mechanism in which PrE precursors with low affinity gradually migrate to the surface of ICM along with the tissue flow, while EPI precursors with high affinity remains inside ICM under cavity vibration. Artificially manipulation of the frequency and amplitude of cavity vibration could control the process of spatial separation as well as lineage specification of PrE/EPI. Furthermore, disruption of the cavity vibration in the initial stage after segregation could reverse the ICM cells back to a mixed state. Therefore, this study reveals a fundamental mechanism that guarantees the robustness of cell segregation and pattern formation without specific morphogens in early mammalian embryos. Our model also emphasizes a conserved function of cavity structure that widely exists in organisms as an energy reservoir and converter between different forms, such as chemical and mechanical energy.
A unicellular walker controlled by a microtubule-based finite state machine
Authors: Larson Ben T. , Garbus Jack , Pollack Jordan B. , Marshall Wallace F. 
Published: February 2021

SummaryCells are complex biochemical systems whose behavior emerges from interactions among myriad molecular components. Computation is often invoked as a general framework for navigating this cellular complexity. However, it is unclear how cells might embody computational processes such that theories of computation, including finite state machine models, could be productively applied. Here, we demonstrate finite state machine-like processing embodied in cells using the walking behavior ofEuplotes eurystomus, a ciliate that walks across surfaces using fourteen motile appendages (cirri). We found that cellular walking entails regulated transitions between a discrete set of gait states. The set of observed transitions decomposes into a small group of high-probability, temporally irreversible transitions and a large group of low-probability time-symmetric transitions, thus revealing stereotypy in sequential patterns of state transitions. Simulations and experiments suggest that the sequential logic of the gait is functionally important. Taken together, these findings implicate a finite state machine-like process. Cirri are connected by microtubule bundles (fibers), and we found that the dynamics of cirri involved in different state transitions are associated with the structure of the fiber system. Perturbative experiments revealed that the fibers mediate gait coordination, suggesting a mechanical basis of gait control.
Quantitative consequences of protein carriers in immunopeptidomics and tyrosine phosphorylation MS2analyses
Authors: Stopfer Lauren E. , Conage-Pough Jason E. , White Forest M. 
Published: February 2021

ABSTRACTUtilizing a protein carrier in combination with isobaric labeling to “boost” the signal of other low-level samples in multiplexed analyses has emerged as an attractive strategy to enhance data quantity while minimizing protein input in mass spectrometry analyses. Recent applications of this approach include pMHC profiling and tyrosine phosphoproteomics, two applications that are often limited by large sample requirements. While including a protein carrier has been shown to increase the number of identifiable peptides in both applications, the impact of a protein carrier on quantitative accuracy remains to be thoroughly explored, particularly in relevant biological contexts where samples exhibit dynamic changes in abundance across peptides. Here, we describe two sets of analyses comparing MS2-based quantitation using a 20x protein carrier in pMHC analyses and a high (∼100x) and low (∼9x) protein carrier in pTyr analyses, using CDK4/6 inhibitors and EGF stimulation to drive dynamic changes in the immunopeptidome and phosphoproteome, respectively. In both applications, inclusion of a protein carrier resulted in an increased number of MHC peptide or phosphopeptide identifications, as expected. At the same time, quantitative accuracy was adversely affected by the presence of the protein carrier, altering interpretation of the underlying biological response to perturbation. Moreover, for tyrosine phosphoproteomics, the presence of high levels of protein carrier led to a large number of missing values for endogenous phosphopeptides, leading to fewer quantifiable peptides relative to the “no-boost” condition. These data highlight the unique limitations and future experimental considerations for both analysis types and provide a framework for assessing quantitative accuracy in protein carrier experiments moving forward.
Hyperspectral sensing of photosynthesis, stomatal conductance, and transpiration for citrus tree under drought condition
Authors: Zhou Jing-Jing , Zhang Ya-Hao , Han Ze-Min , Liu Xiao-Yang , Jian Yong-Feng , Hu Chun-Gen , Dian Yuan-Yong 
Published: February 2021

AbstractObtaining variation in water use and photosynthetic capacity is a promising route toward yield increases, but it is still too laborious for large-scale rapid monitoring and prediction. We tested the application of hyperspectral reflectance as a high-throughput phenotyping approach for early identification of water stress and rapid assessment of leaf photosynthetic traits in citrus trees. To this end, photosynthetic CO2assimilation rate (Pn), stomatal conductance (Cond) and transpiration rate (Trmmol) were measured with gas-exchange approaches alongside measurements of leaf hyperspectral reflectance from citrus grown across a gradient of soil drought levels. Water stress causedPn, CondandTrmmolrapid and continuous decreases in whole drought period. Upper layer was more sensitive to drought than middle and lower layers. Original reflectance spectra of three drought treatments were surprisingly of low diversity and could not track drought responses, whereas specific hyperspectral spectral vegetation indices (SVIs) and absorption features or wavelength position variables presented great potential. Performance of four machine learning algorithms were assessed and random forest (RF) algorithm yielded the highest predictive power for predicting photosynthetic parameters. Our results indicated that leaf hyperspectral reflectance was a reliable and stable method for monitoring water stress and yield increasing in large-scale orchards.HighlightAn efficient and stable methods using hyperspectral features for early and pre-visual identification of drought and machine learning techniques for predicting photosynthetic capacity.