bluuebunny/crossref_metadata_2025_split huggingface dataset:
NiPTUNE: an automated pipeline for noninvasive prenatal testing in an accurate, integrative and flexible framework
Authors: Duboc Véronique , Pratella David , Milanesio Marco , Boudjarane John , Descombes Stéphane , Paquis-Flucklinger Véronique , Bottini Silvia 
Published: September 2021

Abstract
Noninvasive prenatal testing (NIPT) consists of determining fetal aneuploidies by quantifying copy number alteration from the sequencing of cell-free DNA (cfDNA) from maternal blood. Due to the presence of cfDNA of fetal origin in maternal blood, in silico approaches have been developed to accurately predict fetal aneuploidies. Although NIPT is becoming a new standard in prenatal screening of chromosomal abnormalities, there are no integrated pipelines available to allow rapid, accurate and standardized data analysis in any clinical setting. Several tools have been developed, however often optimized only for research purposes or requiring enormous amount of retrospective data, making hard their implementation in a clinical context. Furthermore, no guidelines have been provided on how to accomplish each step of the data analysis to achieve reliable results. Finally, there is no integrated pipeline to perform all steps of NIPT analysis.
To address these needs, we tested several tools for performing NIPT data analysis. We provide extensive benchmark of tools performances but also guidelines for running them. We selected the best performing tools that we benchmarked and gathered them in a computational pipeline. NiPTUNE is an open source python package that includes methods for fetal fraction estimation, a novel method for accurate gender prediction, a principal component analysis based strategy for quality control and fetal aneuploidies prediction. NiPTUNE is constituted by seven modules allowing the user to run the entire pipeline or each module independently. Using two cohorts composed by 1439 samples with 31 confirmed aneuploidies, we demonstrated that NiPTUNE is a valuable resource for NIPT analysis.
The substitution spectra of coronavirus genomes
Authors: Forni Diego , Cagliani Rachele , Pontremoli Chiara , Clerici Mario , Sironi Manuela 
Published: September 2021

Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has triggered an unprecedented international effort to sequence complete viral genomes. We leveraged this wealth of information to characterize the substitution spectrum of SARS-CoV-2 and to compare it with those of other human and animal coronaviruses.
We show that, once nucleotide composition is taken into account, human and most animal coronaviruses display a mutation spectrum dominated by C to U and G to U substitutions, a feature that is not shared by other positive-sense RNA viruses. However, the proportions of C to U and G to U substitutions tend to decrease as divergence increases, suggesting that, whatever their origin, a proportion of these changes is subsequently eliminated by purifying selection. Analysis of the sequence context of C to U substitutions showed little evidence of apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC)-mediated editing and such contexts were similar for SARS-CoV-2 and Middle East respiratory syndrome coronavirus sampled from different hosts, despite different repertoires of APOBEC3 proteins in distinct species. Conversely, we found evidence that C to U and G to U changes affect CpG dinucleotides at a frequency higher than expected. Whereas this suggests ongoing selective reduction of CpGs, this effect alone cannot account for the substitution spectra. Finally, we show that, during the first months of SARS-CoV-2 pandemic spread, the frequency of both G to U and C to U substitutions increased. Our data suggest that the substitution spectrum of SARS-CoV-2 is determined by an interplay of factors, including intrinsic biases of the replication process, avoidance of CpG dinucleotides and other constraints exerted by the new host.
ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features
Authors: Hippe Kyle , Lilley Cade , William Berkenpas Joshua , Chandana Pocha Ciri , Kishaba Kiyomi , Ding Hui , Hou Jie , Si Dong , Cao Renzhi 
Published: September 2021

AbstractMotivationThe Estimation of Model Accuracy problem is a cornerstone problem in the field of Bioinformatics. As of CASP14, there are 79 global QA methods, and a minority of 39 residue-level QA methods with very few of them working on protein complexes. Here, we introduce ZoomQA, a novel, single-model method for assessing the accuracy of a tertiary protein structure/complex prediction at residue level, which have many applications such as drug discovery. ZoomQA differs from others by considering the change in chemical and physical features of a fragment structure (a portion of a protein within a radius $r$ of the target amino acid) as the radius of contact increases. Fourteen physical and chemical properties of amino acids are used to build a comprehensive representation of every residue within a protein and grade their placement within the protein as a whole. Moreover, we have shown the potential of ZoomQA to identify problematic regions of the SARS-CoV-2 protein complex.ResultsWe benchmark ZoomQA on CASP14, and it outperforms other state-of-the-art local QA methods and rivals state of the art QA methods in global prediction metrics. Our experiment shows the efficacy of these new features and shows that our method is able to match the performance of other state-of-the-art methods without the use of homology searching against databases or PSSM matrices.Availabilityhttp://zoomQA.renzhitech.com
Ferroptosis-related lncRNA pairs to predict the clinical outcome and molecular characteristics of pancreatic ductal adenocarcinoma
Authors: Tang Rong , Wu Zijian , Rong Zeyin , Xu Jin , Wang Wei , Zhang Bo , Yu Xianjun , Shi Si 
Published: September 2021

AbstractFerroptosis is a form of regulated cell death initiated by oxidative perturbations that can be blocked by iron chelators and lipophilic antioxidants, and ferroptosis may be the silver bullet treatment for multiple cancers, including immunotherapy- and chemotherapy-insensitive cancers such as pancreatic ductal adenocarcinoma (PDAC). Numerous studies have noted that long non-coding RNAs (lncRNAs) regulate the biological behaviour of cancer cells by binding to DNA, RNA and protein. However, few studies have reported the role of lncRNAs in ferroptosis processes and the function of ferroptosis-associated lncRNAs.The primary objective of the present study was to identify ferroptosis-related lncRNAs using bioinformatic approaches combined with experimental validation. The second objective was to construct a prognostic model to predict the overall survival of patients with PDAC. The present study identified ferroptosis-related lncRNAs using a bioinformatic approach and validated them in an independent pancreatic cancer cohort from Fudan University Shanghai Cancer Center. The lncRNA SLCO4A1-AS1 was identified as a novel molecule mediating ferroptosis resistance in vitro. A novel algorithm was used to construct a ‘0 or 1’ matrix-based prognosis model, which showed promising diagnostic accuracy for potential clinical translation (area under the curve = 0.89 for the 2-year survival rate). Notably, molecular subtypes classified by the risk scores of the model did not belong to any previously reported subtypes of PDAC. The immune microenvironment, metabolic activities, mutation landscape and ferroptosis sensitivity were significantly distinct between patients with different risk scores. Sensitivity (IC50) to 30 common anticancer drugs was analysed between patients with different risks, and imatinib and axitinib were found to be potential drugs for the treatment of patients with lower risk scores. Overall, we developed an accurate prognostic model based on the expression patterns of ferroptosis lncRNAs, which may contribute greatly to the evaluation of patient prognosis, molecular characteristics and treatment modalities and could be further translated into clinical applications.
A versatile and scalable single-cell data integration algorithm based on domain-adversarial and variational approximation
Authors: Hu Jialu , Zhong Yuanke , Shang Xuequn 
Published: September 2021

AbstractSingle-cell technologies provide us new ways to profile transcriptomic landscape, chromatin accessibility, spatial expression patterns in heterogeneous tissues at the resolution of single cell. With enormous generated single-cell datasets, a key analytic challenge is to integrate these datasets to gain biological insights into cellular compositions. Here, we developed a domain-adversarial and variational approximation, DAVAE, which can integrate multiple single-cell datasets across samples, technologies and modalities with a single strategy. Besides, DAVAE can also integrate paired data of ATAC profile and transcriptome profile that are simultaneously measured from a same cell. With a mini-batch stochastic gradient descent strategy, it is scalable for large-scale data and can be accelerated by GPUs. Results on seven real data integration applications demonstrated the effectiveness and scalability of DAVAE in batch-effect removing, transfer learning and cell-type predictions for multiple single-cell datasets across samples, technologies and modalities. Availability: DAVAE has been implemented in a toolkit package “scbean” in the pypi repository, and the source code can be also freely accessible at https://github.com/jhu99/scbean. All our data and source code for reproducing the results of this paper can be accessible at https://github.com/jhu99/davae_paper.
BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer
Authors: Huang Neng , Nie Fan , Ni Peng , Gao Xin , Luo Feng , Wang Jianxin 
Published: September 2021

AbstractLong-read sequencing technology enables significant progress in de novo genome assembly. However, the high error rate and the wide error distribution of raw reads result in a large number of errors in the assembly. Polishing is a procedure to fix errors in the draft assembly and improve the reliability of genomic analysis. However, existing methods treat all the regions of the assembly equally while there are fundamental differences between the error distributions of these regions. How to achieve very high accuracy in genome assembly is still a challenging problem. Motivated by the uneven errors in different regions of the assembly, we propose a novel polishing workflow named BlockPolish. In this method, we divide contigs into blocks with low complexity and high complexity according to statistics of aligned nucleotide bases. Multiple sequence alignment is applied to realign raw reads in complex blocks and optimize the alignment result. Due to the different distributions of error rates in trivial and complex blocks, two multitask bidirectional Long short-term memory (LSTM) networks are proposed to predict the consensus sequences. In the whole-genome assemblies of NA12878 assembled by Wtdbg2 and Flye using Nanopore data, BlockPolish has a higher polishing accuracy than other state-of-the-arts including Racon, Medaka and MarginPolish & HELEN. In all assemblies, errors are predominantly indels and BlockPolish has a good performance in correcting them. In addition to the Nanopore assemblies, we further demonstrate that BlockPolish can also reduce the errors in the PacBio assemblies. The source code of BlockPolish is freely available on Github (https://github.com/huangnengCSU/BlockPolish).
INTERCAAT: identifying interface residues between macromolecules
Authors: Grudman Steven , Fajardo J Eduardo , Fiser Andras 
Published: September 2021

Abstract

Summary
The Interface Contact definition with Adaptable Atom Types (INTERCAAT) was developed to determine the atomic interactions between molecules that form a known three dimensional structure. First, INTERCAAT creates a Voronoi tessellation where each atom acts as a seed. Interactions are defined by atoms that share a hyperplane and whose distance is less than the sum of each atoms’ Van der Waals radii plus the diameter of a solvent molecule. Interacting atoms are then classified and interactions are filtered based on compatibility. INTERCAAT implements an adaptive atom classification method; therefore, it can explore interfaces between a variety macromolecules.

Availability and implementation
Source code is freely available at: https://gitlab.com/fiserlab.org/intercaat.

Supplementary information
Supplementary data are available at Bioinformatics online.
Morphology of migration: associations between wing shape, bill morphology and migration in kingbirds (Tyrannus)
Authors: Macpherson Maggie P , Jahn Alex E , Mason Nicholas A 
Published: September 2021

Abstract
Morphology is closely linked to locomotion and diet in animals. In animals that undertake long-distance migrations, limb morphology is under selection to maximize mobility and minimize energy expenditure. Migratory behaviours also interact with diet, such that migratory animals tend to be dietary generalists, whereas sedentary taxa tend to be dietary specialists. Despite a hypothesized link between migration status and morphology, phylogenetic comparative studies have yielded conflicting findings. We tested for evolutionary associations between migratory status and limb and bill morphology across kingbirds, a pan-American genus of birds with migratory, partially migratory and sedentary taxa. Migratory kingbirds had longer wings, in agreement with expectations that selection favours improved aerodynamics for long-distance migration. We also found an association between migratory status and bill shape, such that more migratory taxa had wider, deeper and shorter bills compared to sedentary taxa. However, there was no difference in intraspecific morphological variation among migrants, partial migrants and residents, suggesting that dietary specialization has evolved independently of migration strategy. The evolutionary links between migration, diet and morphology in kingbirds uncovered here further strengthen ecomorphological associations that underlie long-distance seasonal movements in animals.
Phenotypic and genomic differences between biomes of the South America marsh rat,Holochilus brasiliensis
Authors: Prado Joyce R , Percequillo Alexandre R , Pirani Renata M , Thomaz Andrea T 
Published: September 2021

AbstractAbiotic factors can influence genetic and phenotypic divergence in several ways, and identifying the mechanisms responsible for generating this variation is challenging. However, when evaluated in combination, ecological characteristics and genetic and phenotypic information can help us to understand how habitat preferences can influence morphological and genetic patterns exhibited by taxa distributed between distinct biomes, such as the Atlantic Forest and Pampas biomes in South America. By combining distributional, environmental, phenotypic and genomic information from a habitat-specialist semi-aquatic rodent (Holochilus brasiliensis), we quantified the relationship between ecological niche differences and the phenotypic and genetic variation. The results demonstrate notable segregation among the ecological niches of H. brasiliensis within each biome, although we could not refute the hypothesis of niche similarity or equivalency. Such differences are consistent with a solid morphometric variation associated with the size of these rodents. However, the ecological and morphometric differentiation is not accompanied by the same pattern of genetic variation. Despite differences in the connectivity patterns in both biomes, the genetic differences corroborate a consistent level of migration history between biomes. Additionally, the association tests show that the environment explains a small and non- significant part of the genetic variation but a significant portion of the morphometric variation.
Genital coupling and copulatory wounding in the Drosophila auraria species complex (Diptera: Drosophilidae)
Authors: Onuma Moe , Kamimura Yoshitaka , Sawamura Kyoichi 
Published: September 2021

Abstract
Animal genitalia have changed substantially and rapidly during evolution, and functionally interacting anatomical structures complementarily match between the sexes. Several hypotheses have been proposed to explain how such structure-matching evolved. A test of these hypotheses would require a detailed analysis of male and female genitalia among closely related species and a comparison of the functional aspects of the interacting structures between the sexes. Therefore, here we document genital coupling and copulatory wounds in the four species of the Drosophila auraria complex. The position of the protrusion of the median gonocoxite of males relative to the female terminalia differed among the species, which may reflect differences in protrusion morphology. Species-specific female structures were discovered on the membrane between the genitalia and analia and on the vaginal wall. The former makes contact with the protrusion, and the latter makes contact with appendages of the aedeagus. Copulatory wounds, which are produced during copulation, were seen at three locations on females: depressions near the genital orifice, the membrane between the genitalia and analia, and the vaginal wall. Some of the copulatory wounds were located at sites that could potentially make contact with the species-specific structures that we identified. We speculate that the female structures that differ between species of the D. auraria complex evolved in concert with the genitalia of male conspecifics.
Prey preference of a wasp determined by nest size supports the role of natural selection in body size evolution in Cassidinae leaf beetles
Authors: Shinohara Tadashi , Takami Yasuoki 
Published: September 2021

Abstract
The prey preference of a predator can impose natural selection on prey phenotypes, including body size. Despite evidence that large body size protects against predation in insects, the determinants of body size variation in Cassidinae leaf beetles are not well understood. We examined the prey preference of the digger wasp Cerceris albofasciata, a specialist predator of adult Cassidinae leaf beetles, and found evidence for natural selection on prey body size. The wasp hunted prey smaller than the size of their nest entrance. However, the wasp preferred larger prey species among those that could be carried into their nest. Thus, the benefits of large prey and the cost associated with nest expansion might determine the prey size preference. As expected from the prey species preference, the wasp preferred small individuals of the largest prey species, Thlaspida biramosa, and large individuals of the smallest prey species, Cassida piperata, resulting in natural selection on body sizes. In intermediate-sized prey species, however, there was no evidence for selection on body size. Natural selection on body size might explain the variation of prey morphologies that increase body size, such as explanate margins, in this group.
Two distinct Sertoli cell states are regulated via germ cell crosstalk†
Authors: Gewiss Rachel L , Law Nathan C , Helsel Aileen R , Shelden Eric A , Griswold Michael D 
Published: September 2021

Abstract
Sertoli cells are a critical component of the testis environment for their role in maintaining seminiferous tubule structure, establishing the blood-testis barrier, and nourishing maturing germ cells in a specialized niche. This study sought to uncover how Sertoli cells are regulated in the testis environment via germ cell crosstalk in the mouse. We found two major clusters of Sertoli cells as defined by their transcriptomes in Stages VII–VIII of the seminiferous epithelium and a cluster for all other stages. Additionally, we examined transcriptomes of germ cell-deficient testes and found that these existed in a state independent of either of the germ cell-sufficient clusters. Altogether, we highlight two main transcriptional states of Sertoli cells in an unperturbed testis environment, and a germ cell-deficient environment does not allow normal Sertoli cell transcriptome cycling and results in a state unique from either of those seen in Sertoli cells from a germ cell-sufficient environment.
Understanding the Attraction: Prison Tourism and the Public Gaze
Authors: Urquhart Diane 
Published: September 2021

AbstractResearch undertaken in three decommissioned English prisons offers fresh insight into public attraction. Employing interviews with prison tourists, it reveals dark incentives rooted in historical and cultural representations of punishment, an inherent desire to look beyond the prison walls, and a fascination towards a concept I define as Abstract Death and Suffering.
GORD and Barrett’s oesophagus after bariatric procedures: multicentre prospective study
Authors: Genco Alfredo , Castagneto-Gissey Lidia , Gualtieri Loredana , Lucchese Marcello , Leuratti Luca , Soricelli Emanuele , Casella Giovanni 
Published: September 2021

Abstract

Introduction
Gastro-oesophageal reflux disease (GORD) after bariatric surgery is a debated topic. This study investigated the prevalence of GORD and associated oesophageal complications following bariatric procedures—namely, adjustable gastric banding (AGB), sleeve gastrectomy (SG), Roux-en-Y gastric bypass (RYGB), and one-anastomosis gastric bypass (OAGB).

Methods
This was a prospective multicentre study designed to evaluate the long-term effects of bariatric surgery on GORD. Patients were studied at baseline, at &gt;10 years following AGB, SG, and RYGB, and at &gt;3 years following OAGB (due to the more recent recognition of OAGB as a standard bariatric procedure). Patients were assessed by endoscopy and GORD symptom evaluation.

Results
A total of 241 patients were enrolled. A minimum follow-up of 10 years was completed by 193 patients following AGB (57 patients), SG (95 patients), and RYGB (41 patients), and of &gt;3 years by 48 subjects following OAGB. GORD symptoms increased following AGB and SG (from 14 to 31.6 per cent and from 26.3 to 58.9 per cent, respectively; P &lt; 0.0001), improved following RYGB (from 36.6 to 14.6 per cent; P &lt; 0.0001), and were unchanged following OAGB. The overall prevalence of erosive oesophagitis was greater in the SG group (74.7 per cent) than in the AGB (42.1 per cent), RYGB (22 per cent), and OAGB (22.9 per cent) groups (P &lt; 0.0001). Barrett’s oesophagus was found only in patients who had SG (16.8 per cent). Biliary-like gastric stagnation was found in a greater proportion of SG and OAGB patients (79.7 and 69.4 per cent, respectively) than in other treatment groups (P &lt; 0.0001). The prevalence of biliary-type reflux into the oesophagus was higher in patients who underwent SG (74.7 per cent), compared with other treatment groups.

Conclusion
Bariatric surgery leads to gastro-oesophageal complications of variable severity, particularly SG, which can result in a large proportion of patients developing Barrett’s oesophagus.