bluuebunny/crossref_metadata_2025 huggingface dataset:
Reply to “Comments on ‘An Evaluation of Hurricane Superintensity in Axisymmetric Numerical Models’”
Authors: Emanuel Kerry , Rousseau-Rizzi Raphaël
Published: November 2020

We concur with Makarieva et al. that in our earlier work on the hurricane differential Carnot cycle, we neglected the work done in lifting water and the dissipation of kinetic energy in the outflow (we explicitly acknowledged neglecting these terms). Here, we relax those assumptions, affirm the conclusion of Makarieva et al. that the water lifting term is small, and show that the effect of outflow dissipation is negligible. We remind readers that the differential Carnot theory is not a closed theory for potential intensity as it does not specify the outflow temperature or the boundary layer moist enthalpy at the radius of maximum winds. The addition of enthalpy to the inflow can raise the boundary layer enthalpy, reducing subsequent surface fluxes, regardless of whether that addition comes from surface fluxes themselves or from dissipative heating. We show that while this may indeed reduce the effect of dissipative heating, it does not eliminate it. We disagree with Makarieva et al.’s assertions that dissipative heating does not increase potential intensity and that only latent heat fluxes can drive tropical cyclones when dissipative heating is included.
The Dependence of Internal Multidecadal Variability in the Southern Ocean on the Ocean Background Mean State
Authors: Zhang Liping , Delworth Thomas L. , Cooke William , Goosse Hugues , Bushuk Mitchell , Morioka Yushi , Yang Xiaosong
Published: November 2020

Previous studies have shown the existence of internal multidecadal variability in the Southern Ocean using multiple climate models. This variability, associated with deep ocean convection, can have significant climate impacts. In this work, we use sensitivity studies based on Geophysical Fluid Dynamics Laboratory (GFDL) models to investigate the linkage of this internal variability with the background ocean mean state. We find that mean ocean stratification in the subpolar region that is dominated by mean salinity influences whether this variability occurs, as well as its time scale. The weakening of background stratification favors the occurrence of deep convection. For background stratification states in which the low-frequency variability occurs, weaker ocean stratification corresponds to shorter periods of variability and vice versa. The amplitude of convection variability is largely determined by the amount of heat that can accumulate in the subsurface ocean during periods of the oscillation without deep convection. A larger accumulation of heat in the subsurface reservoir corresponds to a larger amplitude of variability. The subsurface heat buildup is a balance between advection that supplies heat to the reservoir and vertical mixing/convection that depletes it. Subsurface heat accumulation can be intensified both by an enhanced horizontal temperature advection by the Weddell Gyre and by an enhanced ocean stratification leading to reduced vertical mixing and surface heat loss. The paleoclimate records over Antarctica indicate that this multidecadal variability has very likely happened in past climates and that the period of this variability may shift with different climate background mean state.
Possible Cause of Seasonal Inhomogeneity in Interdecadal Changes of Tropical Cyclone Genesis Frequency over the Western North Pacific
Authors: Chang Minhee , Park Doo-Sun R. , Ho Chang-Hoi
Published: November 2020

An abrupt decrease in annual tropical cyclone genesis frequency (TCGF), which is statistically significant only from October to December (OND), has been noticed over the western North Pacific Ocean. However, the seasonal inhomogeneity of interdecadal changes in TCGF between OND and the other seasons (from January to September) and the associated mechanisms are not clearly documented. This study examines and compares the different interdecadal changes in OND and in January–September from 1979 to 2018. According to our analysis, the TCGF decrease in OND (2.2) accounts for 79% of the total decrease (2.8) in annual TCGF after 1998, whereas the TCGF in January to September remains unchanged. The key differences in large-scale environment are found from the extension of equatorial easterly wind anomalies and attendant anticyclone anomalies in the subtropics. Under similar sea surface temperature (SST) warming pattern in the tropical Indo-Pacific region (i.e., the La Niña–like SST warming), tropical precipitation is significantly enhanced over the area where its seasonal peak occurs: the tropical Indian Ocean in OND and the tropical western Pacific in January–September. Thus, the equatorial easterly wind anomalies extend westward to 110°E in OND and to 145°E in January–September. Different extension of easterly wind anomalies results in different expansion of attendant large-scale anticyclone anomaly over the subtropical western Pacific, which dominates the entire main development region in OND but not in January–September. To summarize, the different extensions of easterly wind anomalies under similar La Niña–like SST warming are responsible for the seasonal inhomogeneity of interdecadal changes in TCGF.
National Support for a Menthol Cigarette Sales Ban
Authors: Czaplicki Lauren , Schillo Barbara , Rose Shyanika W. , Zhou Yitong , Vallone Donna
Published: November 2020

Objectives

The US Food and Drug Administration (FDA) and local jurisdictions have different authorities to regulate menthol cigarettes, and a growing number of localities and the FDA are considering these policy options. The objective of this study was to update previous research on public support for a menthol ban, including examining differences in support by demographic factors, geographic region, and smoking status.

Methods

We assessed policy support among a cross-sectional sample of 2871 adults aged 18-64 from a nationally representative online panel. We calculated weighted estimates of support by demographic factors, political ideology, region (Northeast, Midwest, South, West), and smoking status (never, former, current nonmenthol, current menthol). We used weighted adjusted logistic regression analysis to examine correlates of support for a menthol ban.

Results

Overall, 56.4% (95% CI, 54.4%-58.3%) of participants supported a government policy to ban menthol cigarette sales. Support was significantly higher among women than among men (62.5% vs 50.1%; P < .001); among Hispanic/Latino (69.3%), non-Hispanic African American (60.5%), and non-Hispanic other (65.8%) people than among non-Hispanic White people (50.4%; P < .001); and among never (64.8%) and former (47.0%) smokers than among current nonmenthol cigarette smokers (30.1%; P < .001). A significant proportion (28.5%; P < .001) of current menthol cigarette smokers supported a ban. After controlling for other factors, geographic region was not significantly associated with support for a ban.

Conclusions

Efforts are needed to further increase support for a ban among current menthol cigarette smokers. These findings can be used to assist policy makers and communities in efforts to ban menthol cigarettes in their jurisdictions.
Does Shared Gender Group Membership Mitigate the Effect of Implicit Bias Attributions on Accountability for Gender-Based Discrimination?
Authors: Daumeyer Natalie M. , Onyeador Ivuoma N. , Richeson Jennifer A.
Published: November 2020

Attributing gender discrimination to implicit bias has become increasingly common. However, research suggests that when discrimination is attributed to implicit rather than explicit bias, the perpetrators are held less accountable and deemed less worthy of punishment. The present work examines (a) whether this effect replicates in the domain of gender discrimination, and (b) whether sharing a group membership with the victim moderates the effect. Four studies revealed that both men and women hold perpetrators of gender discrimination less accountable if their behavior is attributed to implicit rather than explicit bias. Moreover, women held male (Studies 1–3), but not female (Study 4), perpetrators of gender discrimination more accountable than did men. Together, these findings suggest that while shared gender group membership may inform judgments of accountability for gender discrimination, it does not weaken the tendency to hold perpetrators less accountable for discrimination attributed to implicit, compared with explicit, bias.
Hearing Outcomes and Complications in Stapes Surgery for Otosclerosis Performed Under General or Local Anesthesia
Authors: Luryi Alexander L. , Schettino Amy , Bojrab Dennis I. , Babu Seilesh C. , Michaelides Elias M. , Bojrab Dennis I. , Schutt Christopher A.
Published: November 2020

Objective

Stapes surgery is highly successful in reducing or eliminating the audiometric air‐bone gap (ABG) related to otosclerosis, and it can be performed under general anesthesia or local anesthesia with sedation. Literature on the relative outcomes of these 2 modalities is lacking. The purpose of this study was to compare hearing outcomes for these 2 modalities in a large patient population.

Study Design

Retrospective review.

Setting

Large otology referral center.

Methods

Patients undergoing primary stapes surgery for otosclerosis from 2005 to 2017 were grouped by anesthetic modality and their cases reviewed. Pre‐ and postoperative ABGs were primary outcomes.

Results

A total of 580 patients undergoing stapes surgery were included: 46% received local anesthesia and 54% received general anesthesia. These 2 groups were similar in demographic and disease characteristics. Mean preoperative ABGs were 25.6 and 26.6 dB for patients undergoing local and general anesthesia, respectively (P =. 2); mean postoperative ABGs were 9.5 and 9.7 dB (P =. 9). There were no significant differences in the rates of complications, the need for revision surgery, or the need to abort surgery intraoperatively between local and general anesthesia.

Conclusion

Consistent with limited prior data, in this cohort stapes surgery yielded similar hearing outcomes whether performed under general anesthesia or local anesthesia with sedation. While we report the largest sample size to date, this study, like previous work, carries the potential for sampling bias. Prospective study comparing local and general anesthesia for stapes surgery is needed.
Potential Influence of Olfactory, Gustatory, and Pharyngolaryngeal Sensory Dysfunctions on Swallowing Physiology in COVID‐19
Authors: Vergara José , Lirani‐Silva Camila , Brodsky Martin B. , Miles Anna , Clavé Pere , Nascimento Weslania , Mourão Lúcia Figueiredo
Published: November 2020

Persistent smell and taste disorders have been reported as some of the most common symptoms after COVID‐19 (coronavirus disease 2019). Sensory, olfactory, and gustatory functions perform an important role in the initiation and modulation of oropharyngeal swallow biomechanics and salivation as well as in mealtime enjoyment and appetite. Yet, the details of this interaction remain relatively unknown in patients who are infected with and recovering from COVID‐19. In this commentary, we discuss the possible impacts of SARS‐CoV‐2 on the central and peripheral nervous system and consider the pathophysiology of olfactory, gustatory, and pharyngolaryngeal sensory deficits and its influence on deglutition, describing hypotheses and offering guidance for future research.
The interplay of perceived parenting practices and bullying victimization among Hong Kong adolescents
Authors: Wong Tracy K. Y. , Konishi Chiaki
Published: November 2020

This study explored the interplay of adolescents’ perceived maternal and paternal practices and their associations with traditional and cyberbullying victimization experiences among adolescents. Participants included 439 Grades 7–11 adolescents (242 girls) from five secondary schools in Hong Kong. Moderation analyses were conducted controlling for adolescents sex. No strengthening effects were found between maternal × paternal control and maternal × paternal autonomy-support in relation to bullying victimization experiences. No buffering effect of parental autonomy-support was evident in the association between parental control and traditional bullying victimization. However, high levels of paternal autonomy-support were associated with more frequent reports of cyberbullying victimization at high levels of maternal control but not low levels. A similar pattern emerged for maternal autonomy-support and paternal control. These findings imply that inconsistent parenting might increase adolescents’ likelihood for cyberbullying victimization.
Venous thromboembolism in cancer patients: a population-based cohort study
Authors: Mulder F. I. , Horváth-Puhó E. , van Es N. , van Laarhoven H. W. M. , Pedersen L. , Moik F. , Ay C. , Büller H. R. , Sørensen H. T.
Published: November 2020

The incidence of venous thromboembolism (VTE) in cancer patients may have changed in the past decade, possibly due to novel cancer therapies, improved survival, and high-resolution imaging. Danish medical registries were used to identify 499 092 patients with a first-time cancer diagnosis between 1997 and 2017, who were matched to 1 497 276 comparison individuals without cancer from the general population. We computed cumulative incidences of VTE 6 and 12 months after the diagnosis/index date. Hazard ratios (HRs) were calculated using Cox regression. Risk factors were examined by computing subdistribution hazard ratios (SHRs) in a competing-risk analysis. Cumulative incidence of VTE 12 months after the cancer diagnosis/index date was 2.3% (95% confidence interval [CI], 2.2% to 2.3%) in the cancer cohort and 0.35% (95% CI, 0.34% to 0.36%) in the comparison cohort (HR, 8.5; 95% CI, 8.2-8.8). Important risk factors for cancer patients were prior VTE (SHR, 7.6; 95% CI, 7.2-8.0), distant metastasis (SHR, 3.2; 95% CI, 2.9-3.4), and use of chemotherapy (SHR, 3.4; 95% CI, 3.1-3.7), protein kinase inhibitors (SHR, 4.1; 95% CI, 3.4-4.9), antiangiogenic therapy (SHR, 4.4; 95% CI, 3.8-5.2), and immunotherapy (SHR, 3.6; 2.8-4.6). Twelve-month incidence in the cancer cohort increased from 1.0% (95% CI, 0.9% to 1.2%) in 1997 to 3.4% (95% CI, 2.9% to 4.0%) in 2017, which was paralleled by improved 12-month survival and increased use of computed tomography scans, chemotherapy, and targeted therapies. In conclusion, the risk of VTE in cancer patients is increasing steadily and is ninefold higher than in the general population.
Gene networks for three feed efficiency criteria reveal shared and specific biological processes
Authors: Taussat Sébastien , Boussaha Mekki , Ramayo-Caldas Yuliaxis , Martin Pauline , Venot Eric , Cantalapiedra-Hijar Gonzalo , Hozé Chris , Fritz Sébastien , Renand Gilles
Published: November 2020

Background

French beef producers suffer from the decrease in profitability of their farms mainly because of the continuous increase in feed costs. Selection for feed efficiency in beef cattle represents a relevant solution to face this problem. However, feed efficiency is a complex trait that can be assessed by three major criteria: residual feed intake (RFI), residual gain (RG) and feed efficiency ratio (FE), which involve different genetic determinisms. An analysis that combines phenotype and whole-genome sequence data provides a unique framework for genomic studies. The aim of our study was to identify the gene networks and the biological processes that are responsible for the genetic determinism that is shared between these three feed efficiency criteria.

Results

A population of 1477 French Charolais young bulls was phenotyped for feed intake (FI), average daily gain (ADG) and final weight (FW) to estimate RFI, RG and FE. A subset of 789 young bulls was genotyped on the BovineSNP50 single nucleotide polymorphism (SNP) array and imputed at the sequence level using RUN6 of the 1000 Bull Genomes Project. We conducted a genome-wide association study (GWAS) to estimate the individual effect of 8.5 million SNPs and applied an association weight matrix (AWM) approach to analyse the results, one for each feed efficiency criterion. The results highlighted co-association networks including 626 genes for RFI, 426 for RG and 564 for FE. Enrichment assessment revealed the biological processes that show the strongest association with RFI, RG and FE, i.e. digestive tract (salivary, gastric and mucin secretion) and metabolic processes (cellular and cardiovascular). Energetic functions were more associated with RFI and FE and cardio-vascular and cellular processes with RG. Several hormones such as apelin, glucagon, insulin, aldosterone, the gonadotrophin releasing hormone and the thyroid hormone were also identified, and these should be tested in future studies as candidate biomarkers for feed efficiency.

Conclusions

The combination of network and pathway analyses at the sequence level led to the identification of both common and specific mechanisms that are involved in RFI, RG and FE, and to a better understanding of the genetic determinism underlying these three criteria. The effects of the genes involved in each of the identified processes need to be tested in genomic evaluations to confirm the potential gain in reliability of using functional variants to select animals for feed efficiency.
Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks
Authors: Klamt Steffen , Mahadevan Radhakrishnan , von Kamp Axel
Published: November 2020

Background

The concept of minimal cut sets (MCS) has become an important mathematical framework for analyzing and (re)designing metabolic networks. However, the calculation of MCS in genome-scale metabolic models is a complex computational problem. The development of duality-based algorithms in the last years allowed the enumeration of thousands of MCS in genome-scale networks by solving mixed-integer linear problems (MILP). A recent advancement in this field was the introduction of the MCS2approach. In contrast to the Farkas-lemma-based dual system used in earlier studies, the MCS2approach employs a more condensed representation of the dual system based on the nullspace of the stoichiometric matrix, which, due to its reduced dimension, holds promise to further enhance MCS computations.

Results

In this work, we introduce several new variants and modifications of duality-based MCS algorithms and benchmark their effects on the overall performance. As one major result, we generalize the original MCS2approach (which was limited to blocking the operation of certain target reactions) to the most general case of MCS computations with arbitrary target and desired regions. Building upon these developments, we introduce a new MILP variant which allows maximal flexibility in the formulation of MCS problems and fully leverages the reduced size of the nullspace-based dual system. With a comprehensive set of benchmarks, we show that the MILP with the nullspace-based dual system outperforms the MILP with the Farkas-lemma-based dual system speeding up MCS computation with an averaged factor of approximately 2.5. We furthermore present several simplifications in the formulation of constraints, mainly related to binary variables, which further enhance the performance of MCS-related MILP. However, the benchmarks also reveal that some highly condensed formulations of constraints, especially on reversible reactions, may lead to worse behavior when compared to variants with a larger number of (more explicit) constraints and involved variables.

Conclusions

Our results further enhance the algorithmic toolbox for MCS calculations and are of general importance for theoretical developments as well as for practical applications of the MCS framework.
Inferring chromosome radial organization from Hi-C data
Authors: Das Priyojit , Shen Tongye , McCord Rachel Patton
Published: November 2020

Background

The nonrandom radial organization of eukaryotic chromosome territories (CTs) inside the nucleus plays an important role in nuclear functional compartmentalization. Increasingly, chromosome conformation capture (Hi-C) based approaches are being used to characterize the genome structure of many cell types and conditions. Computational methods to extract 3D arrangements of CTs from this type of pairwise contact data will thus increase our ability to analyze CT organization in a wider variety of biological situations.

Results

A number of full-scale polymer models have successfully reconstructed the 3D structure of chromosome territories from Hi-C. To supplement such methods, we explore alternative, direct, and less computationally intensive approaches to capture radial CT organization from Hi-C data. We show that we can infer relative chromosome ordering using PCA on a thresholded inter-chromosomal contact matrix. We simulate an ensemble of possible CT arrangements using a force-directed network layout algorithm and propose an approach to integrate additional chromosome properties into our predictions. Our CT radial organization predictions have a high correlation with microscopy imaging data for various cell nucleus geometries (lymphoblastoid, skin fibroblast, and breast epithelial cells), and we can capture previously documented changes in senescent and progeria cells.

Conclusions

Our analysis approaches provide rapid and modular approaches to screen for alterations in CT organization across widely available Hi-C data. We demonstrate which stages of the approach can extract meaningful information, and also describe limitations of pairwise contacts alone to predict absolute 3D positions.
A sequence embedding method for enzyme optimal condition analysis
Authors: Li Xiangjun , Dou Zhixin , Sun Yuqing , Wang Lushan , Gong Bin , Wan Lin
Published: November 2020

Background

An enzyme activity is influenced by the external environment. It is important to have an enzyme remain high activity in a specific condition. A usual way is to first determine the optimal condition of an enzyme by either the gradient test or by tertiary structure, and then to use protein engineering to mutate a wild type enzyme for a higher activity in an expected condition.

Results

In this paper, we investigate the optimal condition of an enzyme by directly analyzing the sequence. We propose an embedding method to represent the amino acids and the structural information as vectors in the latent space. These vectors contain information about the correlations between amino acids and sites in the aligned amino acid sequences, as well as the correlation with the optimal condition. We crawled and processed the amino acid sequences in the glycoside hydrolase GH11 family, and got 125 amino acid sequences with optimal pH condition. We used probabilistic approximation method to implement the embedding learning method on these samples. Based on these embedding vectors, we design a computational score to determine which one has a better optimal condition for two given amino acid sequences and achieves the accuracy 80% on the test proteins in the same family. We also give the mutation suggestion such that it has a higher activity in an expected environment, which is consistent with the previously professional wet experiments and analysis.

Conclusion

A new computational method is proposed for the sequence based on the enzyme optimal condition analysis. Compared with the traditional process that involves a lot of wet experiments and requires multiple mutations, this method can give recommendations on the direction and location of amino acid substitution with reference significance for an expected condition in an efficient and effective way.
Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes
Authors: Meyer Corentin , Scalzitti Nicolas , Jeannin-Girardon Anne , Collet Pierre , Poch Olivier , Thompson Julie D.
Published: November 2020

Background

Recent advances in sequencing technologies have led to an explosion in the number of genomes available, but accurate genome annotation remains a major challenge. The prediction of protein-coding genes in eukaryotic genomes is especially problematic, due to their complex exon–intron structures. Even the best eukaryotic gene prediction algorithms can make serious errors that will significantly affect subsequent analyses.

Results

We first investigated the prevalence of gene prediction errors in a large set of 176,478 proteins from ten primate proteomes available in public databases. Using the well-studied human proteins as a reference, a total of 82,305 potential errors were detected, including 44,001 deletions, 27,289 insertions and 11,015 mismatched segments where part of the correct protein sequence is replaced with an alternative erroneous sequence. We then focused on the mismatched sequence errors that cause particular problems for downstream applications. A detailed characterization allowed us to identify the potential causes for the gene misprediction in approximately half (5446) of these cases. As a proof-of-concept, we also developed a simple method which allowed us to propose improved sequences for 603 primate proteins.

Conclusions

Gene prediction errors in primate proteomes affect up to 50% of the sequences. Major causes of errors include undetermined genome regions, genome sequencing or assembly issues, and limitations in the models used to represent gene exon–intron structures. Nevertheless, existing genome sequences can still be exploited to improve protein sequence quality. Perspectives of the work include the characterization of other types of gene prediction errors, as well as the development of a more comprehensive algorithm for protein sequence error correction.
Uterine transcriptome analysis reveals mRNA expression changes associated with the ultrastructure differences of eggshell in young and aged laying hens
Authors: Feng Jia , Zhang Hai-jun , Wu Shu-geng , Qi Guang-hai , Wang Jing
Published: November 2020

Background

Lower eggshell quality in the late laying period leads to economic loss. It is a major threat to the quality and safety of egg products. Age-related variations in ultrastructure were thought to induce this deterioration. Eggshell formation is a highly complex process under precise regulation of genes and biological pathways in uterus of laying hens. Herein, we evaluated the physical, mechanical and ultrastructure properties of eggshell and conducted RNA sequencing to learn the transcriptomic differences in uterus between laying hens in the peak (young hens) and late phase (aged hens) of production.

Results

The declined breaking strength and fracture toughness of eggshell were observed in aged hen group compared to those in young hen group, accompanied with ultrastructure variations including the increased thickness of mammillary layer and the decreased incidence of early fusion. During the initial stage of eggshell formation, a total of 183 differentially expressed genes (DEGs; 125 upregulated and 58 downregulated) were identified in uterus of laying hens in the late phase in relative to those at peak production. The DEGs annotated to Gene Ontology terms related to antigen processing and presentation were downregulated in aged hens compared to young hens. The contents of proinflammatory cytokine IL-1β in uterus were higher in aged hens relative to those in young hens. Besides, the genes of some matrix proteins potentially involved in eggshell mineralization, such as ovalbumin, versican and glypican 3, were also differentially expressed between two groups.

Conclusions

Altered gene expression of matrix proteins along with the compromised immune function in uterus of laying hens in the late phase of production may conduce to age-related impairments of eggshell ultrastructure and mechanical properties. The current study enhances our understanding of the age-related deteriorations in eggshell ultrastructure and provides potential targets for improvement of eggshell quality in the late laying period.
Would large dataset sample size unveil the potential of deep neural networks for improved genome-enabled prediction of complex traits? The case for body weight in broilers
Authors: Passafaro Tiago L. , Lopes Fernando B. , Dórea João R. R. , Craven Mark , Breen Vivian , Hawken Rachel J. , Rosa Guilherme J. M.
Published: November 2020

Background

Deep neural networks (DNN) are a particular case of artificial neural networks (ANN) composed by multiple hidden layers, and have recently gained attention in genome-enabled prediction of complex traits. Yet, few studies in genome-enabled prediction have assessed the performance of DNN compared to traditional regression models. Strikingly, no clear superiority of DNN has been reported so far, and results seem highly dependent on the species and traits of application. Nevertheless, the relatively small datasets used in previous studies, most with fewer than 5000 observations may have precluded the full potential of DNN. Therefore, the objective of this study was to investigate the impact of the dataset sample size on the performance of DNN compared to Bayesian regression models for genome-enable prediction of body weight in broilers by sub-sampling 63,526 observations of the training set.

Results

Predictive performance of DNN improved as sample size increased, reaching a plateau at about 0.32 of prediction correlation when 60% of the entire training set size was used (i.e., 39,510 observations). Interestingly, DNN showed superior prediction correlation using up to 3% of training set, but poorer prediction correlation after that compared to Bayesian Ridge Regression (BRR) and Bayes Cπ. Regardless of the amount of data used to train the predictive machines, DNN displayed the lowest mean square error of prediction compared to all other approaches. The predictive bias was lower for DNN compared to Bayesian models, across all dataset sizes, with estimates close to one with larger sample sizes.

Conclusions

DNN had worse prediction correlation compared to BRR and Bayes Cπ, but improved mean square error of prediction and bias relative to both Bayesian models for genome-enabled prediction of body weight in broilers. Such findings, highlights advantages and disadvantages between predictive approaches depending on the criterion used for comparison. Furthermore, the inclusion of more data per se is not a guarantee for the DNN to outperform the Bayesian regression methods commonly used for genome-enabled prediction. Nonetheless, further analysis is necessary to detect scenarios where DNN can clearly outperform Bayesian benchmark models.
Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach
Authors: Qu Jinchan , Steppi Albert , Zhong Dongrui , Hao Jie , Wang Jian , Lung Pei-Yau , Zhao Tingting , He Zhe , Zhang Jinfeng
Published: November 2020

Background

Information on protein-protein interactions affected by mutations is very useful for understanding the biological effect of mutations and for developing treatments targeting the interactions. In this study, we developed a natural language processing (NLP) based machine learning approach for extracting such information from literature. Our aim is to identify journal abstracts or paragraphs in full-text articles that contain at least one occurrence of a protein-protein interaction (PPI) affected by a mutation.

Results

Our system makes use of latest NLP methods with a large number of engineered features including some based on pre-trained word embedding. Our final model achieved satisfactory performance in the Document Triage Task of the BioCreative VI Precision Medicine Track with highest recall and comparable F1-score.

Conclusions

The performance of our method indicates that it is ideally suited for being combined with manual annotations. Our machine learning framework and engineered features will also be very helpful for other researchers to further improve this and other related biological text mining tasks using either traditional machine learning or deep learning based methods.
Multi-omics analysis reveals that natural hibernation is crucial for oocyte maturation in the female Chinese alligator
Authors: Lin Jian-Qing , Yu Jun , Jiang Hua , Zhang Yi , Wan Qiu-Hong , Fang Sheng-Guo
Published: November 2020

Background

Hibernation in an appropriate environment not only is important for the survival of hibernators in winter, but also is crucial for breeding in the following season for many hibernating species. However, the genetic and epigenetic mechanism underlying this process remain unclear. In the current study, we performed an integrative multi-omics analysis of gonads collected from Chinese alligators that overwintered in wild cave and artificial warmroom to explore transcriptomic and epigenomic alternations in these organs.

Results

The data revealed that in the breeding season, female alligators were more strongly affected in terms of gene expression than males by non-hibernation because of overwintering in a warm room, especially for genes related to oocyte maturation, and this effect commenced in winter with the downregulation of STAR, which is the rate limiting factor of steroid biosynthesis. Further, miRNAs were found to play essential roles in this negative effect of overwintering in the warm room on hibernation. The upregulated miRNAs likely were responsible for the suppression of oocyte maturation in the breeding season. Finally, DNA methylome changes, especially hypomethylation, were found to play an important role in the alterations in ovarian function-related gene expression induced by non-hibernation.

Conclusions

Our study revealed the crucial role of hibernation quality for oocyte maturation in the Chinese alligator and the underlying genetic and epigenetic mechanisms, and highlights the importance of habitat, and especially, the overwintering site, in the conservation of not only the Chinese alligator, but also other endangered hibernators.
GWAS unveils features between early- and late-flowering pearl millets
Authors: Diack Oumar , Kanfany Ghislain , Gueye Mame Codou , Sy Ousmane , Fofana Amadou , Tall Hamidou , Serba Desalegn D. , Zekraoui Leila , Berthouly-Salazar Cécile , Vigouroux Yves , Diouf Diaga , Kane Ndjido Ardo
Published: November 2020

Background

Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distinguished in Senegal: early-flowering Souna and late-flowering Sanio. Phenotypic variabilities related to flowering time play an important role in the adaptation of pearl millet to climate variability. A better understanding of the genetic makeup of these variabilities would make it possible to breed pearl millet to suit regions with different climates. The aim of this study was to characterize the genetic basis of these phenotypic differences.

Results

We defined a core collection that captures most of the diversity of cultivated pearl millets in Senegal and includes 60 early-flowering Souna and 31 late-flowering Sanio morphotypes. Sixteen agro-morphological traits were evaluated in the panel in the 2016 and 2017 rainy seasons. Phenological and phenotypic traits related with yield, flowering time, and biomass helped differentiate early- and late-flowering morphotypes. Further, using genotyping-by-sequencing (GBS), 21,663 single nucleotide polymorphisms (SNPs) markers with more than 5% of minor allele frequencies were discovered. Sparse non-negative matrix factorization (sNMF) analysis confirmed the genetic structure in two gene pools associated with differences in flowering time. Two chromosomal regions on linkage groups (LG 3) (~ 89.7 Mb) and (LG 6) (~ 68.1 Mb) differentiated two clusters among the early-flowering Souna. A genome-wide association study (GWAS) was used to link phenotypic variation to the SNPs, and 18 genes were linked to flowering time, plant height, tillering, and biomass (P-value < 2.3E-06).

Conclusions

The diversity of early- and late-flowering pearl millet morphotypes in Senegal was captured using a heuristic approach. Key phenological and phenotypic traits, SNPs, and candidate genes underlying flowering time, tillering, biomass yield and plant height of pearl millet were identified. Chromosome rearrangements in LG3 and LG6 were inferred as a source of variation in early-flowering morphotypes. Using candidate genes underlying these features between pearl millet morphotypes will be of paramount importance in breeding for resilience to climatic variability.
Identification, evolution, expression, and docking studies of fatty acid desaturase genes in wheat (Triticum aestivum L.)
Authors: Hajiahmadi Zahra , Abedi Amin , Wei Hui , Sun Weibo , Ruan Honghua , Zhuge Qiang , Movahedi Ali
Published: November 2020

Backgrounds

Fatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids that have essential roles in plant development and response to biotic and abiotic stresses. Wheat germ oil, one of the important by-products of wheat, can be a good alternative for edible oils with clinical advantages due to the high amount of unsaturated fatty acids. Therefore, we performed a genome-wide analysis of the wheatFADgene family (TaFADs).

Results

68FADgenes were identified from the wheat genome. Based on the phylogenetic analysis, wheatFADsclustered into five subfamilies, includingFAB2,FAD2/FAD6,FAD4,DES/SLD, andFAD3/FAD7/FAD8. TheTaFADswere distributed on chromosomes 2A-7B with 0 to 10 introns. The Ka/Ks ratio was less than one for most of the duplicated pair genes revealed that the function of the genes had been maintained during the evolution. Several cis-acting elements related to hormones and stresses in theTaFADs promoters indicated the role of these genes in plant development and responses to environmental stresses. Likewise, 72 SSRs and 91 miRNAs in 36 and 47TaFADs have been identified. According to RNA-seq data analysis, the highest expression in all developmental stages and tissues was related toTaFAB2.5,TaFAB2.12,TaFAB2.15,TaFAB2.17,TaFAB2.20,TaFAD2.1,TaFAD2.6, andTaFAD2.8genes while the highest expression in response to temperature stress was related toTaFAD2.6,TaFAD2.8,TaFAB2.15,TaFAB2.17, andTaFAB2.20. Furthermore, docking simulations revealed several residues in the active site of TaFAD2.6 and TaFAD2.8 in close contact with the docked oleic acid that could be useful in future site-directed mutagenesis studies to increase the catalytic efficiency of them and subsequently improve agronomic quality and tolerance of wheat against environmental stresses.

Conclusions

This study provides comprehensive information that can lead to the detection of candidate genes for wheat genetic modification.
Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress
Authors: Chen Guodong , Wang Jizhong , Qiao Xin , Jin Cong , Duan Weike , Sun Xiaochuan , Wu Juyou
Published: November 2020

Background

The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptation. Because of their positive regulatory roles in response to adverse conditions, the genes encoding thes proteins are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family, and the function of these genes has not been explored in Rosaceae.

Results

A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear (Pyrus bretschneideri) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the primary forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assay results revealed that the distribution of PbrSnRK2s was very extensive, including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatment.

Conclusions

This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.
Membrane and lipid metabolism plays an important role in desiccation resistance in the yeast Saccharomyces cerevisiae
Authors: Ren Qun , Brenner Rebecca , Boothby Thomas C. , Zhang Zhaojie
Published: November 2020

Background

Anhydrobiotes, such as the yeast Saccharomyces cerevisiae, are capable of surviving almost total loss of water. Desiccation tolerance requires an interplay of multiple events, including preserving the protein function and membrane integrity, preventing and mitigating oxidative stress, maintaining certain level of energy required for cellular activities in the desiccated state. Many of these crucial processes can be controlled and modulated at the level of organelle morphology and dynamics. However, little is understood about what organelle perturbations manifest in desiccation-sensitive cells as a consequence of drying or how this differs from organelle biology in desiccation-tolerant organisms undergoing anhydrobiosis.

Results

In this study, electron and optical microscopy was used to examine the dynamic changes of yeast cells during the desiccation process. Dramatic structural changes were observed during the desiccation process, including the diminishing of vacuoles, decrease of lipid droplets, decrease in mitochondrial cristae and increase of ER membrane, which is likely caused by ER stress and unfolded protein response. The survival rate was significantly decreased in mutants that are defective in lipid droplet biosynthesis, or cells treated with cerulenin, an inhibitor of fatty acid synthesis.

Conclusion

Our study suggests that the metabolism of lipid droplets and membrane may play an important role in yeast desiccation tolerance by providing cells with energy and possibly metabolic water. Additionally, the decrease in mitochondrial cristae coupled with a decrease in lipid droplets is indicative of a cellular response to reduce the production of reactive oxygen species.
Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid
Authors: Brandt Katelyn , Barrangou Rodolphe
Published: November 2020

Background

Microbiome and metagenomic studies have given rise to a new understanding of microbial colonization of various human tissues and their ability to impact our health. One human microbiome growing in notoriety, the vaginal microbiome, stands out given its importance for women’s health, and is peculiar in terms of its relative bacterial composition, including its simplicity and typical domination by a small number ofLactobacillusspecies. The loss ofLactobacillusdominance is associated with disorders such as bacterial vaginosis, and efforts are now underway to understand the ability ofLactobacillusspecies to colonize the vaginal tract and adapt to this dynamic and acidic environment. Here, we investigate how variousLactobacillusspecies often isolated from the vaginal and intestinal cavities genomically and transcriptionally respond to iterative growth in simulated vaginal fluid.

Results

We determined the genomes and transcriptomes ofL. acidophilus, L. crispatus, L. fermentum, L. gasseri,andL. jenseniiand compared profiles after 50, 100, 500, and 1000 generations of iterative passages in synthetic vaginal fluid. In general, we identified relatively few genetic changes consisting of single nucleotide polymorphisms, with higher counts occurring more frequently in non-vaginal isolated species. Transcriptional profiles were more impacted over time and tended to be more extensive for species that typically do not dominate the vaginal tract, reflecting a more extensive need to adapt to a less familiar environment.

Conclusions

This study provides insights into how vaginal and non-vaginalLactobacillusspecies respond and adapt to a simulated vaginal environment. Overall, trends indicate high genomic stability for all species involved, with more variability in the transcriptome especially for non-dominant species of the vaginal tract.
Correction to: Weighted gene coexpression network analysis-based identification of key modules and hub genes associated with drought sensitivity in rice
Authors: Yu Baiyang , Liu Jianbin , Wu Di , Liu Ying , Cen Weijian , Wang Shaokui , Li Rongbai , Luo Jijing
Published: November 2020

An amendment to this paper has been published and can be accessed via the original article.
Cardiac damage in patients with the severe type of coronavirus disease 2019 (COVID-19)
Authors: Li Jing , Zhang Yinghua , Wang Fang , Liu Bing , Li Hui , Tang Guodong , Chang Zhigang , Liu Aihua , Fu Chunyi , Lv You , Gao Jing , Li Jing
Published: November 2020

Background

Coronavirus disease 2019 (COVID-19) has become a global pandemic. Studies showed COVID-19 affected not only the lung but also other organs. In this study, we aimed to explore the cardiac damage in patients with COVID-19.

Methods

We collected data of 100 patients diagnosed as severe type of COVID-19 from February 8 to April 10, 2020, including demographics, illness history, physical examination, laboratory test, and treatment. In-hospital mortality were observed. Cardiac damage was defined as plasma hypersensitive troponin I (hsTnI) over 34.2 pg/ml and/or N-terminal-pro brain natriuretic peptide (NTproBNP) above 450 pg/ml at the age < 50, above 900 pg/ml at the age < 75, or above 1800 pg/ml at the age ≥ 75.

Results

The median age of the patients was 62.0 years old. 69 (69.0%) had comorbidities, mainly presenting hypertension, diabetes, and cardiovascular disease. Fever (69 [69.0%]), cough (63 [63.0%]), chest distress (13 [13.0%]), and fatigue (12 [12.0%]) were the common initial symptoms. Cardiac damage occurred in 25 patients. In the subgroups, hsTnI was significantly higher in elder patients (≥ 60 years) than in the young (median [IQR], 5.2 [2.2–12.8] vs. 1.9 [1.9–6.2], p = 0.018) and was higher in men than in women (4.2 [1.9–12.8] vs. 2.9 [1.9–7.4], p = 0.018). The prevalence of increased NTproBNP was significantly higher in men than in women (32.1% vs. 9.1%, p = 0.006), but was similar between the elder and young patients (20.0% vs. 25.0%, p = 0.554). After multivariable analysis, male and hypertension were the risk factors of cardiac damage. The mortality was 4.0%.

Conclusions

Cardiac damage exists in patients with the severe type of COVID-19, especially in male patients with hypertension. Clinicians should pay more attention to cardiac damage.