bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digestive Tract Development of Crossbreed Native Chickens due to Effect of Terminalia catappa Leaf (T. catappa L) Extract in Drinking Water
Authors: Suprijatna E , Ma’rifah B , Mahfudz L D , Sunarti D , Kismiati S , Sarjana T A , Muryani R 
Published: October 2023

Abstract
The purpose of the current study was to clarify the impact of drinking water extract from Terminalia catappa leaves on the development of the native chicken crossbreeds’ digestive systems. The study was set up with 4 treatments and 4 replications in a properly randomized design (5 bird for each replication). Water without Terminalia catappa leaf extract (T0), water with 3% of Terminalia catappa leaf extract for three days per week (T1), water with 3% of Terminalia catappa leaf extract for five days per week (T2), and water with 3% of Terminalia catappa extract for seven days per week (T3) were the study’s treatments (T3). Parameters observed are relative weight of digestive organs, length of digestive organs, and weight to length ratio of digestive organs. Results show that Terminalia catappa leaf extract in drinking water showed a significant effect in weight to length ratio of duodenum but had no effect in the other digestive organ. The use of Terminalia catappa leaf extract have a potensial effect to maintance digestive tract development.
LHC hadronic jet generation using convolutional variational autoencoders with normalizing flows
Authors: Orzari Breno , Chernyavskaya Nadezda , Cobe Raphael , Duarte Javier , Fialho Jefferson , Gunopulos Dimitrios , Kansal Raghav , Pierini Maurizio , Tomei Thiago , Touranakou Mary 
Published: October 2023

Abstract
In high energy physics, one of the most important processes for collider data analysis is the comparison of collected and simulated data. Nowadays the state-of-the-art for data generation is in the form of Monte Carlo (MC) generators. However, because of the upcoming high-luminosity upgrade of the Large Hadron Collider (LHC), there will not be enough computational power or time to match the amount of needed simulated data using MC methods. An alternative approach under study is the usage of machine learning generative methods to fulfill that task. Since the most common final-state objects of high-energy proton collisions are hadronic jets, which are collections of particles collimated in a given region of space, this work aims to develop a convolutional variational autoencoder (ConVAE) for the generation of particle-based LHC hadronic jets. Given the ConVAE’s limitations, a normalizing flow (NF) network is coupled to it in a two-step training process, which shows improvements on the results for the generated jets. The ConVAE+NF network is capable of generating a jet in

18.30
±
0.04

μ
s

, making it one of the fastest methods for this task up to now.
Allele detection using k-mer-based sequencing error profiles
Authors: Ashraf Hufsah , Ebler Jana , Marschall Tobias 
Published: October 2023

Abstract

Motivation
For genotype and haplotype inference, typically, sequencing reads aligned to a reference genome are used. The alignments identify the genomic origin of the reads and help to infer the absence or presence of sequence variants in the genome. Since long sequencing reads often come with high rates of systematic sequencing errors, single nucleotides in the reads are not always correctly aligned to the reference genome, which can thus lead to wrong conclusions about the allele carried by a sequencing read at the variant site. Thus, allele detection is not a trivial task, especially for single-nucleotide polymorphisms and indels.

Results
To learn the characteristics of sequencing errors, we introduce a method to create an error model in non-variant regions of the genome. This information is later used to distinguish sequencing errors from alternative alleles in variant regions. We show that our method, k-merald, improves allele detection accuracy leading to better genotyping performance as compared to the existing WhatsHap implementation using edit-distance-based allele detection, with a decrease of 18% and 24% in error rate for high-coverage Oxford Nanopore and PacBio CLR sequencing reads for sample HG002, respectively. We additionally observed a prominent improvement in genotyping performance for sequencing data with low coverage. For 3× coverage Oxford Nanopore sequencing data, the genotyping error rate reduced from 34% to 31%, corresponding to a 9% decrease.

Availability and implementation
https://github.com/whatshap/whatshap.
Multiple sequence alignment based on deep reinforcement learning with self-attention and positional encoding
Authors: Liu Yuhang , Yuan Hao , Zhang Qiang , Wang Zixuan , Xiong Shuwen , Wen Naifeng , Zhang Yongqing 
Published: October 2023

Abstract

Motivation
Multiple sequence alignment (MSA) is one of the hotspots of current research and is commonly used in sequence analysis scenarios. However, there is no lasting solution for MSA because it is a Nondeterministic Polynomially complete problem, and the existing methods still have room to improve the accuracy.

Results
We propose Deep reinforcement learning with Positional encoding and self-Attention for MSA, based on deep reinforcement learning, to enhance the accuracy of the alignment Specifically, inspired by the translation technique in natural language processing, we introduce self-attention and positional encoding to improve accuracy and reliability. Firstly, positional encoding encodes the position of the sequence to prevent the loss of nucleotide position information. Secondly, the self-attention model is used to extract the key features of the sequence. Then input the features into a multi-layer perceptron, which can calculate the insertion position of the gap according to the features. In addition, a novel reinforcement learning environment is designed to convert the classic progressive alignment into progressive column alignment, gradually generating each column’s sub-alignment. Finally, merge the sub-alignment into the complete alignment. Extensive experiments based on several datasets validate our method’s effectiveness for MSA, outperforming some state-of-the-art methods in terms of the Sum-of-pairs and Column scores.

Availability and implementation
The process is implemented in Python and available as open-source software from https://github.com/ZhangLab312/DPAMSA.
Privacy-preserving federated genome-wide association studies via dynamic sampling
Authors: Wang Xinyue , Dervishi Leonard , Li Wentao , Ayday Erman , Jiang Xiaoqian , Vaidya Jaideep 
Published: October 2023

Abstract

Motivation
Genome-wide association studies (GWAS) benefit from the increasing availability of genomic data and cross-institution collaborations. However, sharing data across institutional boundaries jeopardizes medical data confidentiality and patient privacy. While modern cryptographic techniques provide formal secure guarantees, the substantial communication and computational overheads hinder the practical application of large-scale collaborative GWAS.

Results
This work introduces an efficient framework for conducting collaborative GWAS on distributed datasets, maintaining data privacy without compromising the accuracy of the results. We propose a novel two-step strategy aimed at reducing communication and computational overheads, and we employ iterative and sampling techniques to ensure accurate results. We instantiate our approach using logistic regression, a commonly used statistical method for identifying associations between genetic markers and the phenotype of interest. We evaluate our proposed methods using two real genomic datasets and demonstrate their robustness in the presence of between-study heterogeneity and skewed phenotype distributions using a variety of experimental settings. The empirical results show the efficiency and applicability of the proposed method and the promise for its application for large-scale collaborative GWAS.

Availability and implementation
The source code and data are available at https://github.com/amioamo/TDS.
Coastal dwarf variants of the red swamp Banksia (Proteaceae) represent parallel ecotypic evolution rather than a divergent evolutionary lineage of single origin
Authors: Robins Timothy P , Binks Rachel M , Byrne Margaret , Hopper Stephen D 
Published: October 2023

Abstract
Morphological variation is common within widely distributed plant species and often raises interesting taxonomic and evolutionary questions. We sampled eight typical inland populations and two coastal dwarf populations of Banksia occidentalis to assess whether the coastal variant warrants taxonomic recognition. Genomic (single nucleotide polymorphisms) and morphometric analyses were undertaken to assess the variation within and between variants. Genetically, the coastal populations were more closely related to geographically adjacent populations of the typical variant than they were to each other, indicating that each coastal population has originated independently. Morphologically, the coastal populations also did not represent a cohesive phenotypic group, with both falling outside the range of variation for the typical variant, but also not overlapping each other. Wide morphological, but not genomic, variation was identified along a coastal–inland transect. Combined, these data indicate that the morphological variation in these coastal populations is the result of parallel ecotype evolution from experiencing similar environmental conditions and does not represent the diversification of a distinct evolutionary lineage that would have warranted taxonomic recognition. Our study highlights the consequences of strong selection pressures in marginal environments and provides fascinating insight to the long evolutionary history of the flora in this ancient Australian landscape.
Altered histone abundance as a mode of ovotoxicity during 7,12-dimethylbenz[a]anthracene exposure with additive influence of obesity
Authors: Rishi Jaspreet K , Timme Kelsey , White Hunter E , Kerns Karl C , Keating Aileen F 
Published: October 2023

AbstractHistones are slowly evolving chromatin components and chromatin remodeling can incorporate histone variants differing from canonical histones as an epigenetic modification. Several identified histone variants are involved with the environmental stress-induced DNA damage response (DDR). Mechanisms of DDR in transcriptionally inactive, prophase-arrested oocytes and epigenetic regulation are under-explored in ovarian toxicology. The study objective was to identify ovarian proteomic and histone modifications induced by DMBA exposure and an influence of obesity. Post-pubertal wildtype (KK.Cg-a/a; lean) and agouti (KK.Cg-Ay/J; obese) female mice, were exposed to either corn oil (control; CT) or DMBA (1 mg/kg) for 7d via intraperitoneal injection (n = 10/treatment). Ovarian proteome analysis (LC-MS/MS) determined that obesity altered 225 proteins (P &lt; 0.05) with histone 3 being the second least abundant (FC = −5.98, P &lt; 0.05). Histone 4 decreased by 3.33-fold, histone variant H3.3 decreased by 3.05-fold, and H1.2, H1.4 and H1.1(alpha) variants increased by 1.59, 1.90 and 2.01-fold, respectively (P &lt; 0.05). DMBA exposure altered 48 proteins in lean mice with no observed alterations in histones or histone variants. In obese mice, DMBA exposure altered 120 proteins and histone 2B abundance increased by 0.30-fold (P &lt; 0.05). In DMBA-exposed mice, obesity altered the abundance of 634 proteins. Histones 4, 3 and 2A type 1-F decreased by 4.03, 3.71, 0.43-fold, respectively, whereas histone variant H1.2 and linker histone, H15 increased by 2.72- and 3.07-fold, respectively (P &lt; 0.05). Thus, DMBA exposure alters histones and histone variants, and responsivity is more pronounced during obesity, potentially altering ovarian transcriptional regulation.
Left behind places in Brazil: the dynamics of regional inequalities and public policies in the early 21st century
Authors: Martins Humberto 
Published: October 2023

Abstract
This article aims to discuss left behind places in Brazil in the early 21st century. We conceptually debate the left behind places’ approach in dialogue with other contemporary theoretical perspectives. To evaluate regional inequalities in Brazil, we used the coefficient of variation, calculated at two different scales from 2002 to 2019 for GDP per capita, also considering social indicators. The results indicated a slow decline in regional inequalities. We debate the role of recently implemented public policies in this process, as well as the potentiality of these policies to identify left behind places and deal with them.
Analysis of Clinical Trial Screen Failures in Inflammatory Bowel Diseases [IBD]: Real World Results from the International Organization for the study of IBD
Authors: Vieujean Sophie , Lindsay James O , D’Amico Ferdinando , Ahuja Vineet , Silverberg Mark S , Sood Ajit , Yamamoto-Furusho Jesus K , Nagahori Masakazu , Watanabe Mamoru , Koutroubakis Ioannis E , Foteinogiannopoulou Kalliopi , Avni Biron Irit , Walsh Alissa , Outtier An , Nordestgaard Rie Louise Møller , Abreu Maria T , Dubinsky Marla , Siegel Corey , Louis Edouard , Dotan Iris , Reinisch Walter , Danese Silvio , Rubin David T , Peyrin-Biroulet Laurent 
Published: October 2023

AbstractBackgroundRecruitment for randomized controlled trials [RCTs] in inflammatory bowel diseases [IBD] has substantially dropped over time. This study aimed to assess reasons why IBD patients are not included in sponsored multicentre phase IIb–III RCTs.MethodsAll IOIBD members [n = 58] were invited to participate. We divided barriers to participation as follows: [1] reasons patients with active IBD were not deemed appropriate for an RCT; [2] reasons qualified patients did not wish to participate; and [3] reasons for screen failure [SF] in patients agreeing to participate. We assess these in a 4-week prospective study including, consecutively, all patients with symptomatic disease for whom a treatment change was required. In addition, we performed a 6-month retrospective study to further evaluate reasons for SF.ResultsA total of 106 patients (60 male [56.6%], 63 Crohn’s disease [CD] [59.4%]), from ten centres across the world, were included in the prospective study. An RCT has not been proposed to 65 of them [mainly due to eligibility criteria]. Of the 41 patients to whom an RCT was offered, eight refused [mainly due to reluctance to receive placebo] and 28 agreed to participate. Among these 28 patients, five failed their screening and 23 were finally included in an RCT. A total of 107 patients (61 male [57%], 67 CD [62.6%]), from 13 centres worldwide, were included in our retrospective study of SFs. The main reason was insufficient disease activity.ConclusionThis first multicentre study analysing reasons for non-enrolment in IBD RCTs shows that we lose patients at each step. Eligibility criteria, the risk of placebo assignment, and insufficient disease activity were part of the main barriers.
A comparison of excess deaths by UK country and region during the first year of the COVID-19 pandemic
Authors: Hopper Neil A , Campbell Annie , Roberts Cath , Ramsay Julie , IJpelaar Jos , Glickman Myer , Nafilyan Vahé , Islam Nazrul 
Published: October 2023

AbstractWe compare the impact of the first two waves of the COVID-19 pandemic on risk of age-standardized mortality by sex, UK country, and English region. Each wave is defined as lasting 26 weeks and are consecutive beginning in 2020 week 11. The expected rate is estimated from 2015 to 2019 mean and the projected mortality trend from the same period are used to estimate excess mortality. By both measures, excess mortality was highest and lowest in regions of England, London and the South-West, respectively. Excess mortality was consistently higher for males than females.
Teaching and Learning Reflexivity in the World Politics Classroom
Authors: Krystalli Roxani 
Published: October 2023

AbstractComplementing discussions of reflexivity as a research practice, this article turns its attention to the classroom. How does a pedagogy that invites students to practice reflexivity represent possibilities for thinking, writing, and imagining otherwise in scholarly engagements with world politics? In response to this question, I explore the dilemmas, challenges, and possibilities students encounter in practicing reflexivity. These include the challenge of meaningfully locating the self in relation to the workings of power, moving beyond a checkbox approach to vectors of identity, and learning to specifically analyze the manifestations of power in daily life. I argue that both the dilemmas and possibilities of practicing reflexivity are related to hierarchies of knowledge creation—and the opportunities to challenge those hierarchies—in the study of world politics. The aim is to illustrate how teachers and students of world politics alike can treat the invitation for reflexivity in the classroom as a potential site of experimentation and freedom that disrupts rigid frameworks of generating knowledge.
A two-component jet model for the optical plateau in the afterglow of GRB 191221B
Authors: Zhu Yi-Ming , Wang Yun , Zhou Hao , Lipunov Vladimir , Buckley David A H , Balanutsa Pavel , Jin Zhi-Ping , Wei Da-Ming 
Published: October 2023

ABSTRACT
The long gamma-ray burst GRB 191221B has abundant observations in X-ray, optical, and radio bands. In the literature, the observed optical light curve of GRB 191221B displays a plateau around 0.1 d, which is rather peculiar in gamma-ray bursts. Here, we performed detailed analysis of the observational data from Swift/UVOT, Very Large Telescope, and Las Cumbres Observatory, obtained the light curve of the multiband afterglow of GRB 191221B. By examining optical, ultraviolet, X-ray, and radio data for this event, we demonstrate that an on-axis two-component jet model can explain the observations. Our analysis suggests that the narrow component has an initial Lorentz factor of 400 and a jet opening half-angle of 1.4°, while the wide component has an initial Lorentz factor of 25 and a jet opening half-angle of 2.8°. The narrow jet dominates the early decay, whereas the wider jet causes the optical plateau and dominates late decay. According to this model, the reason for the absence of the X-ray plateau is due to the steeper spectral index of the wide component, resulting in a less significant flux contribution from the wide jet in the X-ray bands than in the optical bands. Moreover, we have explained the inconsistency in the decay indices of the UVOT- and Rc-band data around 2000 s using reverse shock emission.
Designing a Qualitative Study
Authors: Faulkner Sandra L. , Atkinson Joshua D. 
Published: October 2023

Abstract
In this chapter on designing a qualitative study, the authors cover some of the most common methods for qualitative research in communication and media, including ethnography, grounded theory, interviews, and arts-based research, including poetic portraiture and visual methods. They discuss sampling in qualitative work, including the importance of selecting appropriate texts and participants for research. The authors describe the key role of the institutional review board in helping researchers ensure that their research meets ethical standards. By the end of the chapter, readers should be able to design a qualitative study and describe what makes for a good qualitative interview.
Doing Qualitative Media Analysis (Part 2)
Authors: Faulkner Sandra L. , Atkinson Joshua D. 
Published: October 2023

Abstract
In this chapter the authors continue the discussion of qualitative media analysis that they began in the prior chapter. This chapter focuses on the difference between mass communication and mass self-communication by introducing a contemporary model of qualitative media analysis. The authors explain the rhizomatic metaphor used in new media networks, which is the idea that new, alternative forms of media create intersections between different parts of society that would otherwise be disconnected; such intersections are diffused and develop organically. They also discuss different approaches to studying online networks and have readers consider how they can work collaboratively with others in qualitative research.
Victims and Criminal Justice
Authors: Cox Pamela , Shoemaker Robert , Shore Heather 
Published: October 2023

Abstract
This unique book sets out how crime victims’ experiences of, and engagement with, the process of criminal justice changed dramatically between the late seventeenth and late twentieth centuries. At the start of our period, victims drove the English criminal justice system. They brought prosecutions as complainants and prosecutors, gave evidence as witnesses, and put up personal rewards for the recovery of lost goods or claimed rewards for securing convictions. By the end, victims had been firmly displaced as the state took virtually full responsibility for the process of prosecution. This book is the first of its kind to examine both the origins and impacts of key legal, procedural, and institutional changes introduced in England and Wales in order to encourage and govern prosecutions—moving from rewards to rights. Combining qualitative analysis of a range of textual sources with quantitative analysis of large datasets of over 235,000 criminal prosecutions, we explore how victims were defined in law, what the law allowed and encouraged them to do, who they were in social and economic terms, how they participated in the criminal justice system, why many were unwilling or unable to engage in that system, and why some campaigned for specific rights. Our account situates these shifts in victim participation in criminal trials in the context of broader political, social, and cultural changes. In doing so, it places current policy debates in a much-needed critical historical context.
Victims at the Old Bailey
Authors: Cox Pamela , Shoemaker Robert , Shore Heather 
Published: October 2023

Abstract
This chapter assesses the impact of the changing prosecution, policing, and support arrangements discussed in previous chapters on the participation of victims in arguably the most important criminal court in England, the Old Bailey. The chapter opens with a discussion of the major datasets analysed: reports of prosecutions from the published Old Bailey Proceedings and The Times newspapers. Subsequent sections chart the changing profile of victims according to social class, gender, age, and ethnicity. While the overwhelming majority of victims were white, adult, middle-class men, the chapter demonstrates that victims from marginalized groups, notably female and working-class victims, young and elderly victims, and minority ethnic victims, increased over time. In addition, from the late nineteenth century there were a growing number of institutional prosecutors, both public and private. In considering the causes of this broadening access to justice, the chapter assesses the impact of statutes and practices (including the use of counsel and the police) which facilitated victims’ appearances in court.
Trials and Outcomes
Authors: Cox Pamela , Shoemaker Robert , Shore Heather 
Published: October 2023

Abstract
This chapter considers the conduct of criminal trials, in terms of who participated, when, and how much they spoke in court, demonstrating that the growing role of the police and counsel in the courtroom had the effect of reducing the role of victims. It then offers an analysis of trial outcomes, starting with the growth of plea bargaining from the 1830s, which dramatically increased the number of cases which did not go to trial. Verdicts and punishment sentences are then considered, as measures of whether prosecutions might be deemed ‘successful’ by victims, and the chapter assesses the extent to which marginalized groups achieved poorer outcomes. It shows that this was particularly the case for young female victims of sexual offences.