bluuebunny/crossref_metadata_2025_split huggingface dataset:
Age-related alterations in fertilization-induced Ca2+ oscillations depend on the genetic background of mouse oocytes†
Authors: Czajkowska Katarzyna , Walewska Agnieszka , Ishikawa Takao , Szczepańska Katarzyna , Ajduk Anna 
Published: August 2020

AbstractMaternal aging affects various aspects of oocytes’ physiology, including the functionality of their nuclear apparatus and mitochondria. In the present paper, we wished to investigate whether advanced reproductive age impacts oocytes’ ability to generate proper Ca2+ oscillations in response to monospermic fertilization. We examined three different mouse strains/crosses: inbred C57BL/6Tar, outbred Tar:SWISS, and hybrid F1 (C57BL/6Tar × CBA/Tar). The females were either 2–4 months old (young) or 13–16 months old (aged). We observed that the Ca2+ oscillatory pattern is altered in a strain-dependent manner and changes were more profound in aged C57BL/6Tar and F1 than in aged Tar:SWISS oocytes. We also showed that maternal aging differently affects the size of Ca2+ store and expression of Itpr1, Atp2a2, Erp44, and Pdia3 genes involved in Ca2+ homeostasis in oocytes of C57BL/6Tar, Tar:SWISS, and F1 genetic background, which may explain partially the differences in the extent of age-dependent changes in the Ca2+ oscillations in those oocytes. Maternal aging did not have any visible impact on the distribution of the ER cisterns in oocytes of all three genetic types. Finally, we showed that maternal aging alters the timing of the first embryonic interphase onset and that this timing correlates in C57BL/6Tar and Tar:SWISS oocytes with the frequency of fertilization-induced Ca2+ oscillations. Our results indicate that extreme caution is required when conclusions about oocyte/embryo physiological response to aging are made and complement an increasing amount of evidence that mammalian (including human) susceptibility to aging differs greatly depending on the genetic background of the individual.
Cerebrospinal fluid cytotoxicity in amyotrophic lateral sclerosis: a systematic review of in vitro studies
Authors: Ng Kee Kwong Koy Chong , Gregory Jenna M , Pal Suvankar , Chandran Siddharthan , Mehta Arpan R 
Published: August 2020

Abstract
Various studies have suggested that a neurotoxic cerebrospinal fluid profile could be implicated in amyotrophic lateral sclerosis. Here, we systematically review the evidence for cerebrospinal fluid cytotoxicity in amyotrophic lateral sclerosis and explore its clinical correlates. We searched the following databases with no restrictions on publication date: PubMed, Embase and Web of Science. All studies that investigated cytotoxicity in vitro following exposure to cerebrospinal fluid from amyotrophic lateral sclerosis patients were considered for inclusion. Meta-analysis could not be performed, and findings were instead narratively summarized. Twenty-eight studies were included in our analysis. Both participant characteristics and study conditions including cerebrospinal fluid concentration, exposure time and culture model varied considerably across studies. Of 22 studies assessing cell viability relative to controls, 19 studies reported a significant decrease following exposure to cerebrospinal fluid from patients with amyotrophic lateral sclerosis, while three early studies failed to observe any difference. Seven of eight studies evaluating apoptosis observed significant increases in the levels of apoptotic markers following exposure to cerebrospinal fluid from patients with amyotrophic lateral sclerosis, with the remaining study reporting a qualitative difference. Although five studies investigated the possible relationship between cerebrospinal fluid cytotoxicity and patient characteristics, such as age, gender and disease duration, none demonstrated an association with any of the factors. In conclusion, our analysis suggests that cerebrospinal fluid cytotoxicity is a feature of sporadic and possibly also of familial forms of amyotrophic lateral sclerosis. Further research is, however, required to better characterize its underlying mechanisms and to establish its possible contribution to amyotrophic lateral sclerosis pathophysiology.
Preventing Subsequent Teenage Pregnancy: A Multisite Analysis of Goal Orientation and Social Supports
Authors: Kan Marni L , Ramirez Derek D 
Published: August 2020

Abstract
Subsequent teenage births may present various challenges for teenage parents and their children. Evaluation of efforts to prevent subsequent teenage pregnancy and increase use of long-acting reversible contraception (LARC) have lacked investigation of the mechanisms—particularly, goal orientation and social supports—through which these efforts may be effective. Data were from a multisite evaluation of the Title XX Adolescent Family Life program, which involved 12 demonstration projects comparing enhanced and core services to pregnant and parenting teenagers. Data from 857 female teenagers at baseline and follow-up were used in analyses. Multivariate regression models examined associations between independent variables (study condition and effective project characteristics) and mediators (orientation toward goals and social supports) and between mediators and outcomes (subsequent pregnancy and use of LARC). Structural equation models tested mediation pathways. The program and selected project characteristics significantly predicted decreased coresidence with parents, and support from the child’s father was associated with higher LARC use. However, neither orientation toward goals nor social supports mediated program effects on LARC use or subsequent pregnancy. Programs to prevent subsequent teenage pregnancy may encourage teenagers’ independence from families of origin and should consider promoting supportive relationships with the child’s father.
Frailty and Prodromal Parkinson’s Disease: Results From the HELIAD Study
Authors: Ntanasi Eva , Maraki Maria , Yannakoulia Mary , Stamelou Maria , Xiromerisiou Georgia , Kosmidis Mary H , Dardiotis Efthimios , Hadjigeorgiou Georgios , Sakka Paraskevi , Gargalionis Antonios , Patas Kostas , Chatzipanagiotou Stylianos , Charisis Socrates , Stefanis Leonidas , Scarmeas Nikolaos 
Published: August 2020

Abstract

Background
To investigate the association between frailty, Parkinson’s disease (PD), and the probability of prodromal Parkinson’s disease (prodromal PD) in Greek community-dwelling older individuals.

Methods
Parkinson’s disease diagnosis was reached through standard clinical research procedures. Probability of prodromal PD was calculated according to the International Parkinson and Movement Disorder Society’s research criteria for PD-free participants. Frailty was evaluated according to definitions of the phenotypic and multidomain approach. Logistic and linear regression models were performed to investigate associations between frailty (predictor) and the probability of prodromal PD, either continuous or dichotomous (≥30% probability score), or PD (outcome).

Results
Data from 1765 participants aged 65 and older were included in the present analysis. Parkinson’s disease and prodromal PD prevalence were 1.9% and 3.0%, respectively. Compared to nonfrail participants, those who were frail, as identified with either the Fried frailty phenotype or Frailty Index had approximately 4 (odds ratio [OR] 4.09, 95% confidence interval [CI] 1.54–10.89) and 12 times (OR 12.16, 95% CI 5.46–27.09) higher odds of having a PD diagnosis, respectively. Moreover, compared to the nonfrail, frail participants as identified with either the Fried frailty phenotype or Frailty Index had 2.8 (OR 2.83, 95% CI 1.09–7.37) and 8.3 times (OR 8.39, 95% CI 4.56–15.42) higher odds of having possible/probable prodromal PD, respectively.

Conclusions
Frailty status was associated with prodromal PD and PD, suggesting common characteristics or underlying mechanisms of these conditions. Although prospective studies are warranted, acknowledging the possible association of frailty, PD, and prodromal PD may improve their clinical management.
VariantSpark: Cloud-based machine learning for association study of complex phenotype and large-scale genomic data
Authors: Bayat Arash , Szul Piotr , O'Brien Aidan R , Dunne Robert , Hosking Brendan , Jain Yatish , Hosking Cameron , Luo Oscar J , Twine Natalie , Bauer Denis C 
Published: August 2020

Abstract

Background
Many traits and diseases are thought to be driven by &gt;1 gene (polygenic). Polygenic risk scores (PRS) hence expand on genome-wide association studies by taking multiple genes into account when risk models are built. However, PRS only considers the additive effect of individual genes but not epistatic interactions or the combination of individual and interacting drivers. While evidence of epistatic interactions ais found in small datasets, large datasets have not been processed yet owing to the high computational complexity of the search for epistatic interactions.

Findings
We have developed VariantSpark, a distributed machine learning framework able to perform association analysis for complex phenotypes that are polygenic and potentially involve a large number of epistatic interactions. Efficient multi-layer parallelization allows VariantSpark to scale to the whole genome of population-scale datasets with 100,000,000 genomic variants and 100,000 samples.

Conclusions
Compared with traditional monogenic genome-wide association studies, VariantSpark better identifies genomic variants associated with complex phenotypes. VariantSpark is 3.6 times faster than ReForeSt and the only method able to scale to ultra-high-dimensional genomic data in a manageable time.
Genomic data imputation with variational auto-encoders
Authors: Qiu Yeping Lina , Zheng Hong , Gevaert Olivier 
Published: August 2020

Abstract

Background
As missing values are frequently present in genomic data, practical methods to handle missing data are necessary for downstream analyses that require complete data sets. State-of-the-art imputation techniques, including methods based on singular value decomposition and K-nearest neighbors, can be computationally expensive for large data sets and it is difficult to modify these algorithms to handle certain cases not missing at random.

Results
In this work, we use a deep-learning framework based on the variational auto-encoder (VAE) for genomic missing value imputation and demonstrate its effectiveness in transcriptome and methylome data analysis. We show that in the vast majority of our testing scenarios, VAE achieves similar or better performances than the most widely used imputation standards, while having a computational advantage at evaluation time. When dealing with data missing not at random (e.g., few values are missing), we develop simple yet effective methodologies to leverage the prior knowledge about missing data. Furthermore, we investigate the effect of varying latent space regularization strength in VAE on the imputation performances and, in this context, show why VAE has a better imputation capacity compared to a regular deterministic auto-encoder.

Conclusions
We describe a deep learning imputation framework for transcriptome and methylome data using a VAE and show that it can be a preferable alternative to traditional methods for data imputation, especially in the setting of large-scale data and certain missing-not-at-random scenarios.
Ruminal acidosis, bacterial changes, and lipopolysaccharides
Authors: Monteiro Hugo F , Faciola Antonio P 
Published: August 2020

AbstractAcute and subacute ruminal acidosis (SARA) are common nutritional problems in both beef and dairy cattle. Therefore, the objective of this review is to describe how ruminal Gram-negative bacteria could contribute to the pathogenesis of ruminal acidoses, by releasing lipopolysaccharides (LPS; a component of their cell wall) in the ruminal fluid. When cattle consume excessive amounts of highly fermentable carbohydrates without prior adaptation, normal fermentation become disrupted. The fermentation of these carbohydrates quickly decreases ruminal pH due to the accumulation of short-chain fatty acids and lactate in the rumen. As a consequence, ruminal epithelium may be damaged and tissue function could be impaired, leading to a possible translocation of pathogenic substances from the rumen into the bloodstream. Such changes in fermentation are followed by an increase in Gram-positive bacteria while Gram-negative bacteria decrease. The lyses of Gram-negative bacteria during ruminal acidosis increase LPS concentration in the ruminal fluid. Because LPS is a highly proinflammatory endotoxin in the circulatory system, past studies have raised concerns regarding ruminal LPS contribution to the pathogenesis of ruminal acidosis. Although animals that undergo these disorders do not always have an immune response, recent studies showed that different Gram-negative bacteria have different LPS composition and toxicity, which may explain the differences in immune response. Given the diversity of Gram-negative bacteria in the rumen, evaluating the changes in the bacterial community during ruminal acidosis could be used as a way to identify which Gram-negative bacteria are associated with LPS release in the rumen. By identifying and targeting ruminal bacteria with possible pathogenic LPS, nutritional strategies could be created to overcome, or at least minimize, ruminal acidosis.
RNA-recognition motifs and glycine and arginine-rich region cooperatively regulate the nucleolar localization of nucleolin
Authors: Okuwaki Mitsuru , Saotome-Nakamura Ai , Yoshimura Masashi , Saito Shoko , Hirawake-Mogi Hiroko , Sekiya Takeshi , Nagata Kyosuke 
Published: August 2020

AbstractNucleolin (NCL) is a nucleolar protein i.e. involved in the regulation of the nucleolar structure and functions, and consists of three distinct regions: the N-terminal region; the middle region, which contains four RNA-recognition motifs (RRMs); and the C-terminal glycine- and arginine-rich (GAR) region. The primary function of the RRMs and GAR is thought to be specific RNA binding. However, it is not well understood how these RNA-binding regions of NCL separately or cooperatively regulate its nucleolar localization and functions. To address this issue, we constructed mutant proteins carrying point mutations at the four RRMs individually or deletion of the C-terminal GAR region. We found that the GAR deletion and the mutations in the fourth RRM (RRM4) decreased the nucleolar localization of NCL. Biochemical analyses showed that NCL interacted directly with ribosomal RNAs (rRNAs) and G-rich oligonucleotides, and that this interaction was decreased by mutations at RRM1 and RRM4 and GAR deletion. Although GAR deletion decreased the rRNA-binding activity of NCL, the mutant was efficiently coprecipitated with rRNAs and nucleolar proteins from cell extracts. These contradictory results suggest that NCL stably localizes to the nucleoli via the interactions with rRNAs and nucleolar proteins via GAR, RRM1 and RRM4.
Acetabular cartilage repair: state of the art in surgical treatment
Authors: Bagheri Kian , Sierra Frank , Jamali Amir A 
Published: August 2020

AbstractHip preservation has emerged as a developing surgical subspecialty with a variety of tools to address hip joint pain and dysfunction. Cartilage tears and delamination are caused by injury to the hip and can ultimately progress to osteoarthritis. It has been established that the acetabulum is particularly at risk of cartilage injury secondary to trauma, hip dysplasia and hip impingement. In spite of the high frequency of acetabular cartilage lesions based on our experience and the literature, there is no consensus as to the optimal treatment of these lesions. This review article highlights the challenges in treating cartilage injuries of the acetabulum with a particular emphasis on published studies and technical considerations in performing these procedures.
Towards real-time DNA biometrics using GPU-accelerated processing
Authors: Reja Mario , Pungila Ciprian , Negru Viorel 
Published: August 2020

Abstract
Decoding the human genome in the past decades has brought into focus a computationally intensive operation through DNA profiling. The typical search space for these kinds of problems is extremely large and requires specialized hardware and algorithms to perform the necessary sequence analysis. In this paper, we propose an innovative and scalable approach to exact multi-pattern matching of nucleotide sequences by harnessing the massively parallel computing power found in commodity graphical processing units. Our approach places careful consideration on preprocessing of DNA datasets and runtime performance, while exploiting the full capabilities of the heterogeneous platform it runs on. Finally, we evaluate our models against real-world DNA sequences.
Attitudes Toward Collusion in Chile
Authors: Aydin Umut 
Published: August 2020

ABSTRACT
In the last two decades, competition agencies around the world have increasingly directed their attention to enforcement against cartels. With the encouragement of the antitrust authorities of the United States, and the Organization of Economic Cooperation and Development, various countries have introduced leniency programs, and sanctions for individuals found guilty of colluding. Critics are concerned, however, that these measures are not backed by broad public support, which could jeopardize their enforcement. This paper explores public attitudes toward cartels in Chile, an emerging economy that introduced a leniency program in 2009 and criminal sanctions in 2016, by presenting the results of a public opinion survey conducted in this country in August–September 2019. The results of the survey show high awareness of cartels and the harm they cause, and high public disapproval of cartel conduct among the Chilean respondents. In particular, up to 70 percent of the respondents support prison sentences against individuals found guilty of colluding. Such strong public support for anti-cartel measures could be considered positive from the perspective of enforcement. The results also emphasize the importance of continued competition advocacy directed at the society to explain and gain public support for the anti-cartel agenda.
Chronic pancreatitis with ductal stones in the pancreatic head treated by surgery: a case report
Authors: Meyer Alberto , Koszka Andreas Johann Molnar , Abreu Phillipe , Ferreira Raphaella , Fantauzzi Marcelo Callado , Segatelli Vanderlei , David Andre Ibrahim 
Published: August 2020

AbstractPancreatic duct stones are direct sequelae of chronic pancreatitis (CP) and can occur in ∼50% of patients. Selection of the appropriate treatment method for pancreatic duct stones depends on location, size and number of stones. We present a patient with upper abdominal pain and weight loss for the previous 3 months. Diagnostic workup detected a chronic inflammation of the pancreas with stone in the main pancreatic duct and a nodular lesion in the head of the pancreas. Endoscopic retrograde cholangiopancreatography was performed without success. Given the rise in incidence and prevalence of CP, the potential complications and high mortality rate, it is imperative that physicians understand the risk factors, disease process and management of this disease. Pancreaticoduodenectomy in patients with CP is a feasible option for the treatment of focal cystic lesions to the head of the pancreas associated to pancreatic stone in selected cases.
A 3D simulation of a neutrino-driven supernova explosion aided by convection and magnetic fields
Authors: Müller Bernhard , Varma Vishnu 
Published: August 2020

ABSTRACT
We study the impact of a small-scale dynamo in core-collapse supernovae using a 3D neutrino magnetohydrodynamics (MHD) simulation of a 15 M⊙ progenitor. The weak seed field is amplified exponentially in the gain region once neutrino-driven convection develops, and remains dominated by small-scale structures. About $250\, \mathrm{ms}$ after bounce, the field energy in the gain region reaches ${\sim } 50{{\ \rm per\ cent}}$ of kinetic equipartition. This supports the development of a neutrino-driven explosion with modest global anisotropy, which does not occur in a corresponding model without magnetic fields. Our results suggest that magnetic fields may play a beneficial subsidiary role in neutrino-driven supernovae even without rapid progenitor rotation. Further investigation into the nature of MHD turbulence in the supernova core is required.
Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data
Authors: Luu Phuc-Loi , Ong Phuc-Thinh , Dinh Thanh-Phuoc , Clark Susan J 
Published: August 2020

AbstractAs reference genome assemblies are updated there is a need to convert epigenome sequence data from older genome assemblies to newer versions, to facilitate data integration and visualization on the same coordinate system. Conversion can be done by re-alignment of the original sequence data to the new assembly or by converting the coordinates of the data between assemblies using a mapping file, an approach referred to as ‘liftover’. Compared to re-alignment approaches, liftover is a more rapid and cost-effective solution. Here, we benchmark six liftover tools commonly used for conversion between genome assemblies by coordinates, including UCSC liftOver, rtracklayer::liftOver, CrossMap, NCBI Remap, flo and segment_liftover to determine how they performed for whole genome bisulphite sequencing (WGBS) and ChIP-seq data. Our results show high correlation between the six tools for conversion of 43 WGBS paired samples. For the chromatin sequencing data we found from interval conversion of 366 ChIP-Seq datasets, segment_liftover generates more reliable results than USCS liftOver. However, we found some regions do not always remain the same after liftover. To further increase the accuracy of liftover and avoid misleading results, we developed a three-step guideline that removes aberrant regions to ensure more robust genome conversion between reference assemblies.