bluuebunny/crossref_metadata_2025_split huggingface dataset:
Samurai: A Very Short Introduction
Authors: Wert Michael 
Published: April 2021

Abstract
A book about the samurai from their origins in the eighth and ninth centuries until their demise in the mid-nineteenth century. It describes samurai life, work, philosophy, and warfare as it changed over time and covers what samurai were doing when they weren’t fighting. The first half of the book tends to focus on warriors who were essentially aristocrats; warrior families who looked to non-warrior nobles for models of behaviour, lifestyle, and politics. It traces the early formation of a warrior regime, how it interacted with an emperor-centered noble court located permanently in Kyoto, and the political and cultural struggles within the warrior class. The second half of the book zeroes in on the details of warlord families, the struggles of “rank-and-file” samurai typically depicted in popular culture—warriors from the seventeenth through nineteenth centuries. It also shows how samurai history, culture, and values were consumed by non-samurai and, in so doing, contributed to an idealized warrior image that even samurai themselves tried to emulate.
Geology or biology?
Authors: Sheppard Charles 
Published: April 2021

Abstract
For centuries, reefs were used and valued for their food and shelter from storms, though for mariners they were a constant danger to be avoided because of their position at shallow depths in tropical seas. Scientific understanding started with European travellers trading with the Caribbean region and then with traders going eastwards to the Indian and Pacific oceans, especially when naturalists, commonly sponsored by patrons, accompanied the traders. The main questions included how the obviously living veneer could make the vast amounts of rock, as well as what the huge variety of sea creatures were. Darwin was the most famous naturalist who became intrigued by them and, following his Beagle voyage, he formed his theory of how they developed, which was proved true a century later. The basic underlying mechanism he proposed unified how they grew and why reefs around the world had so many common characteristics, especially why they nearly all had a similar depth and profile.
The resulting structure—a reef
Authors: Sheppard Charles 
Published: April 2021

Abstract
Reef profiles are remarkably consistent in general design because they are essentially biological constructions responding to environmental factors. All have reef flats, a horizontal expanse at low tide level that develops when the reef can no longer build upwards and extends horizontally. This is commonly the largest expanse and is the only part that early naturalists could examine until the advent of scuba diving relatively recently. However, it is always relatively depauperate because of the extremes of heat, salinity, and light that affect it. To seaward is the reef crest, commonly constructed by calcareous red algae that are the only form of life that can withstand the severe waves that pound the reef. To seaward of the crest, the reef slopes downwards, and is where environmental conditions are most benign and where the greatest biodiversity is found. The rugosity or 3-D structure of a reef is a key factor in reef biodiversity because it provides a vast number of niches for the huge diversity of life. Reefs are constantly subjected to erosion from burrowing and tunnelling forms, whose activity creates sand and sediment. This is then forced into crevices or pushed up onto the island behind it, so this erosion is also the starting point for further reef and island construction. Expanses of sand are associated with all reefs, and are home to another rich assemblage of species.
A multiple network-based bioinformatics pipeline for the study of molecular mechanisms in oncological diseases for personalized medicine
Authors: Dotolo Serena , Marabotti Anna , Rachiglio Anna Maria , Esposito Abate Riziero , Benedetto Marco , Ciardiello Fortunato , De Luca Antonella , Normanno Nicola , Facchiano Angelo , Tagliaferri Roberto 
Published: April 2021

Abstract

Motivation
Assessment of genetic mutations is an essential element in the modern era of personalized cancer treatment. Our strategy is focused on ‘multiple network analysis’ in which we try to improve cancer diagnostics by using biological networks. Genetic alterations in some important hubs or in driver genes such as BRAF and TP53 play a critical role in regulating many important molecular processes. Most of the studies are focused on the analysis of the effects of single mutations, while tumors often carry mutations of multiple driver genes. The aim of this work is to define an innovative bioinformatics pipeline focused on the design and analysis of networks (such as biomedical and molecular networks), in order to: (1) improve the disease diagnosis; (2) identify the patients that could better respond to a given drug treatment; and (3) predict what are the primary and secondary effects of gene mutations involved in human diseases.

Results
By using our pipeline based on a multiple network approach, it has been possible to demonstrate and validate what are the joint effects and changes of the molecular profile that occur in patients with metastatic colorectal carcinoma (mCRC) carrying mutations in multiple genes. In this way, we can identify the most suitable drugs for the therapy for the individual patient. This information is useful to improve precision medicine in cancer patients. As an application of our pipeline, the clinically significant case studies of a cohort of mCRC patients with the BRAF V600E-TP53 I195N missense combined mutation were considered.

Availability
The procedures used in this paper are part of the Cytoscape Core, available at (www.cytoscape.org). Data used here on mCRC patients have been published in [55].

Supplementary Information
A supplementary file containing a more detailed discussion of this case study and other cases is available at the journal site as Supplementary Data.
Interpretable principal component analysis for multilevel multivariate functional data
Authors: Zhang Jun , Siegle Greg J , Sun Tao , D’andrea Wendy , Krafty Robert T 
Published: April 2021

SummaryMany studies collect functional data from multiple subjects that have both multilevel and multivariate structures. An example of such data comes from popular neuroscience experiments where participants’ brain activity is recorded using modalities such as electroencephalography and summarized as power within multiple time-varying frequency bands within multiple electrodes, or brain regions. Summarizing the joint variation across multiple frequency bands for both whole-brain variability between subjects, as well as location–variation within subjects, can help to explain neural reactions to stimuli. This article introduces a novel approach to conducting interpretable principal components analysis on multilevel multivariate functional data that decomposes total variation into subject-level and replicate-within-subject-level (i.e., electrode-level) variation and provides interpretable components that can be both sparse among variates (e.g., frequency bands) and have localized support over time within each frequency band. Smoothness is achieved through a roughness penalty, while sparsity and localization of components are achieved by solving an innovative rank-one based convex optimization problem with block Frobenius and matrix $L_1$-norm-based penalties. The method is used to analyze data from a study to better understand reactions to emotional information in individuals with histories of trauma and the symptom of dissociation, revealing new neurophysiological insights into how subject- and electrode-level brain activity are associated with these phenomena. Supplementary materials for this article are available online.
The mitochondrial landscape of ovarian cancer: emerging insights
Authors: Shukla Pallavi , Singh Keshav K 
Published: April 2021

Abstract
Ovarian cancer (OC) is known to be the most lethal cancer in women worldwide, and its etiology is poorly understood. Recent studies show that mitochondrial DNA (mtDNA) content as well as mtDNA and nuclear genes encoding mitochondrial proteins influence OC risk. This review presents an overview of role of mitochondrial genetics in influencing OC development and discusses the contribution of mitochondrial proteome in OC development, progression and therapy. A role of mitochondrial genetics in racial disparity is also highlighted. In-depth understanding of role of mitochondria in OC will help develop strategies toward prevention and treatment and improving overall survival in women with OC.
Transmission Dynamics of the Rubella Virus Circulating in China During 2010–2019: 2 Lineage Switches Between Genotypes 1E and 2B
Authors: Zhu Zhen , Cui Aili , Zhang Yan , Mao Naiying , Liu Ying , Liu Li , Deng Lili , Chen Ying , Zhao Hua , Gong Tian , Zhou Shujie , Li Fangcai , Lei Yue , Yang Yuying , Wang Yan , Sun Zhaodan , Feng Daxing , Peng Xiaofang , Yuan Fang , Du Hui , Feng Yan , Wang Changyin , Guo Jun , Huang Fang , Gao Hui , Ma Yu , Chen Haiyun , Deng Xiuying , Zhang Ting , Li Liqun , Wang Shuang , Yang Xiuhui , Tian Xiaoling , Fan Lixia , Niu Dandan , Xu Wenbo 
Published: April 2021

Abstract

Background
To provide a better understanding of the progress on rubella control and elimination in China, a genetic analysis was conducted to examine the transmission pattern of the endemic rubella virus in China during 2010–2019.

Methods
A total of 4895 strains were obtained from 29 of the 31 provinces in mainland China during 2010–2019. The genotyping regions of the strains were amplified, determined, and assembled. Genotyping analysis and lineage division were performed by comparisons with the World Health Organization reference strains and reported lineage reference strains, respectively. Further phylogenetic analyses were performed to compare the genetic relationship.

Results
During 2010–2019, the domestic lineage 1E-L1 and multiple imported lineages of rubella viruses including 2B-L1, 1E-L2, and 2B-L2c were identified. Further analysis of the circulation trend of the different lineages indicated that 2 switches occurred among the lineages. The first shift was from lineage 1E-L1 to 2B-L1, which occurred around 2015–2016, followed by the lowest rubella incidence in 2017. The second shift was from lineage 2B-L1 to 1E-L2 and 2B-L2c, which occurred around 2018–2019, coinciding with rubella resurgence and the subsequent nationwide epidemic during 2018–2019. Insufficient genomic information worldwide made it impossible to trace the origin of the imported viruses.

Conclusions
China was moving toward rubella elimination, as evidenced by the fact that previous endemic lineages were not detected. However, rubella reemerged in 2018 2019 due to the newly imported rubella viruses. Therefore, to realize the rubella elimination goal, joint efforts are required for all countries worldwide.
Detection of Pathogenic Bacteria From Septic Patients Using 16S Ribosomal RNA Gene–Targeted Metagenomic Sequencing
Authors: Fida Madiha , Wolf Matthew J , Hamdi Ahmed , Vijayvargiya Prakhar , Esquer Garrigos Zerelda , Khalil Sarwat , Greenwood-Quaintance Kerryl E , Thoendel Matthew J , Patel Robin 
Published: April 2021

AbstractBackgroundConventional blood cultures were compared to plasma cell-free DNA–based 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR)/next-generation sequencing (NGS) for detection and identification of potential pathogens in patients with sepsis.MethodsPlasma was prospectively collected from 60 adult patients with sepsis presenting to the Mayo Clinic (Minnesota) Emergency Department from March through August 2019. Results of routine clinical blood cultures were compared to those of 16S rRNA gene NGS.ResultsNineteen (32%) subjects had positive blood cultures, of which 13 yielded gram-negative bacilli, 5 gram-positive cocci, and 1 both gram-negative bacilli and gram-positive cocci. 16S rRNA gene NGS findings were concordant in 11. For the remaining 8, 16S rRNA gene NGS results yielded discordant detections (n = 5) or were negative (n = 3). Interestingly, Clostridium species were additionally detected by 16S rRNA gene NGS in 3 of the 6 subjects with gastrointestinal sources of gram-negative bacteremia and none of the 3 subjects with urinary sources of gram-negative bacteremia. In the 41 remaining subjects, 16S rRNA gene NGS detected at least 1 potentially pathogenic organism in 17. In 15, the detected microorganism clinically correlated with the patient’s syndrome. In 17 subjects with a clinically defined infectious syndrome, neither test was positive; in the remaining 7 subjects, a noninfectious cause of clinical presentation was identified.Conclusions16S rRNA gene NGS may be useful for detecting bacteria in plasma of septic patients. In some cases of gram-negative sepsis, it may be possible to pinpoint a gastrointestinal or urinary source of sepsis based on the profile of bacteria detected in plasma.
Exposure to Diverse Plasmodium falciparum Genotypes Shapes the Risk of Symptomatic Malaria in Incident and Persistent Infections: A Longitudinal Molecular Epidemiologic Study in Kenya
Authors: Sumner Kelsey M , Freedman Elizabeth , Mangeni Judith N , Obala Andrew A , Abel Lucy , Edwards Jessie K , Emch Michael , Meshnick Steven R , Pence Brian W , Prudhomme-O’Meara Wendy , Taylor Steve M 
Published: April 2021

Abstract

Background
Repeated exposure to malaria infections could protect against symptomatic progression as people develop adaptive immunity to infections acquired over time.

Methods
We investigated how new, recurrent, and persistent Plasmodium falciparum infections were associated with the odds of developing symptomatic compared with asymptomatic malaria. Using a 14-month longitudinal cohort in Western Kenya, we used amplicon deep sequencing of 2 polymorphic genes (pfama1 and pfcsp) to assess overlap of parasite genotypes (represented by haplotypes) acquired within an individual’s successive infections. We hypothesized infections with novel haplotypes would increase the odds of symptomatic malaria.

Results
After excluding initial infections, we observed 534 asymptomatic and 88 symptomatic infections across 186 people. We detected 109 pfcsp haplotypes, and each infection was classified as harboring novel, recurrent, or persistent haplotypes. Incident infections with only new haplotypes had higher odds of symptomatic malaria when compared with infections with only recurrent haplotypes [odds ratio (OR): 3.24; 95% confidence interval (CI), 1.20–8.78], but infections with both new and recurrent haplotypes (OR: 0.64; 95% CI: 0.15–2.65) did not. Assessing persistent infections, those with mixed (persistent with new or recurrent) haplotypes (OR: 0.77; 95% CI: 0.21–2.75) had no association with symptomatic malaria compared with infections with only persistent haplotypes. Results were similar for pfama1.

Conclusions
These results confirm that incident infections with only novel haplotypes were associated with increased odds of symptomatic malaria compared with infections with only recurrent haplotypes but this relationship was not seen when haplotypes persisted over time in consecutive infections.
Non-bacterial thrombotic endocarditis manifested by ventricular fibrillation in a patient with low grade ovarian carcinoma: case report and literature review
Authors: Kuipers Remko S , Berghuis Meike A T , Ogilvie Aernout C , van Wissen Sanne A , Riezebos Robert K 
Published: April 2021

Abstract

Background
Non-bacterial thrombotic endocarditis (NBTE) is a rare form of endocarditis notably described in patients with advanced malignancy and auto-immune diseases. It is characterized by the formation of sterile, fibrin-containing vegetations on cardiac endothelium, in the absence of positive blood cultures. It is predominantly located on the mitral- and aortic valve (AV). Vegetations in NBTE are prone to embolize. Trousseau syndrome (TS) is defined as unexplained thrombotic events that precede the diagnosis of malignancy.

Case summary
A 49-year-old pre-menopausal woman with a history of visual disturbances, recurrent deep vein thrombosis (DVT) with concurrent pulmonary emboli (PE), and uterine myomas with dysfunctional uterine bleeding was resuscitated for ventricular fibrillation. While echocardiography revealed vegetations on the AV, blood cultures remained negative. Additional work-up for the aetiology of sterile vegetations revealed a low-grade ovarian carcinoma. Cardiac analysis showed evidence of myocardial infarction in the absence of coronary atherosclerosis as a cause for ventricular fibrillation.

Discussion
Unexplained thrombotic events (venous, arterial, or both) warrant further investigation, e.g., with regard to TS. NBTE is a potential source of thromboembolism in TS and a rare ante-mortem finding, which prompts additional investigation of the underlying cause. In our patient, a triad of (suspected) (i) arterial/systemic embolization (i.e. visual disturbances, splenic infarction, coronary embolism), (ii) peripheral thrombophlebitis/hypercoagulability (i.e. DVT and PE), and (iii) malignancy (i.e. gynaecological abnormalities) raised suspicion of NBTE in the setting of TS. Early diagnosis and treatment of NBTE is of importance due to the high incidence of embolization, with possible fatal outcome.
Paper-containing 1-methylcyclopropene treatment suppresses fruit decay of fresh Anxi persimmons by enhancing disease resistance
Authors: Zeng Lingzhen , Shi Lili , Lin Hetong , Lin Yuzhao , Lin Yixiong , Wang Hui 
Published: April 2021

Abstract

Objectives
The purpose of this work was to evaluate the potential application of papers containing 1-methylcyclopropene (1-MCP) postharvest treatment for suppressing fruit decay of fresh Anxi persimmons and its possible mechanism.

Materials and methods
Anxi persimmon fruit were treated with papers containing 1-MCP at the dosage of 1.35 μL/L and stored at 25 ± 1 °C and 85 per cent relative humidity for 35 days. During storage, the fruit decay rate and lignin content were evaluated, and the content of total phenolics, the activities of phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO), peroxidase (POD), chitinase (CHI), and β-1,3-glucanase (GLU) were determined by spectrophotometry.

Results
The 1-MCP–treated persimmons displayed a lower fruit decay rate, but higher contents of lignin and total phenolics, higher activities of PAL, PPO, POD, CHI, and GLU.

Conclusions
The treatment with 1-MCP could inhibit the fruit decay of postharvest Anxi persimmons, which might be because 1-MCP enhanced fruit disease resistance by increasing the activities of disease resistance-associated enzymes and retaining higher contents of disease resistance-related substances in postharvest fresh Anxi persimmons. These findings indicate that papers containing 1-MCP at the dosage of 1.35 μL/L have potential application in suppressing fruit decay and extending storage life of postharvest fresh Anxi persimmons.
INCIPIENT GENOME DIFFERENTIATION IN GOSSYPIUM. III. COMPARISON OF CHROMOSOMES OF G. HIRSUTUM AND ASIATIC DIPLOIDS USING HETEROZYGOUS TRANSLOCATIONS
Authors: Menzel Margaret Y , Hasenkampf Clare A , Stewart James McD 
Published: April 2021

ABSTRACT
Hybrids between upland cotton (G. hirsutum, genome constitution 2AhDh) and either A-genome or D-genome diploid species exhibit 26 paired and 13 unpaired chromosomes at metaphase I. The Ah and Dh genomes are therefore considered homoeologous with those of the respective diploids. Previous studies, nevertheless, revealed a low level of ("incipient") differentiation between Dh and various diploid D genomes. The diploid A genomes have been regarded as more closely homologous to Ah on the basis of low preferential pairing and autotetraploid segregation ratios in allohexaploids.—The present study addressed the following questions: Are the diploid A genomes differentiated from Ah in meiotic homology? If so, is the differentiation manifested equally by all 13 chromosomes or is it localized in certain chromosomes?—Three diploid A-genome lines representing G. herbaceum and G. arboreum were hybridized by in ovulo culture of embryos (1) with a standard line of G. hirsutum, which differs from G. herbaceum by two and from G. arboreum by three naturally occurring reciprocal translocations involving chromosomes 1—5, and (2) with six lines homozygous for experimental translocations involving chromosomes 6, 7, 10, 11, 12 and 13. Chiasma frequencies in hybrids were compared with those in appropriate G. hirsutum controls. In every comparison overall chiasma frequencies were slightly lower in the hybrids. Therefore Ah appears to be differentiated from the diploid A genomes. No localized differentiation was detected in chromosomes marked by experimental translocations. The differentiation may be localized mainly in chromosomes 4 and 5.
IDENTIFICATION OF A SECOND LOCUS IN DROSOPHILA MELANOGASTER REQUIRED FOR EXCISION REPAIR
Authors: Boyd J B , Snyder R D , Harris P V , Presley J M , Boyd S F , Smith P D 
Published: April 2021

ABSTRACT
The mus(2)201 locus in Drosophila is defined by two mutant alleles that render homozygous larvae hypersensitive to mutagens. Both alleles confer strong in vivo somatic sensitivity to treatment by methyl methanesulfonate, nitrogen mustard and ultraviolet radiation but only weak hypersensitivity to X-irradiation. Unlike the excision-defective mei-9 mutants identified in previous studies, the mus(2)201 mutants do not affect female fertility and do not appear to influence recombination proficiency or chromosome segregation in female meiocytes.—Three independent biochemical assays reveal that cell cultures derived from embryos homozygous for the mus(2) D1 allele are devoid of detectable excision repair. 1. Such cells quantitatively retain pyrimidine dimers in their DNA for 24 hr following UV exposure. 2. No measurable unscheduled DNA synthesis is induced in mutant cultures by UV treatment. 3. Single-strand DNA breaks, which are associated with normal excision repair after treatment with either UV or N-acetoxy-N-acetyl-2-aminofluorene,* are much reduced in these cultures. Mutant cells possess a normal capacity for postreplication repair and the repair of single-strand breaks induced by X-rays.
PRESENCE OF A BASE LINE LEVEL OF SISTER CHROMATID EXCHANGES IN SOMATIC CELLS OF DROSOPHILA MELANOGASTER IN VIVO AND IN VITRO
Authors: Tsuji Hideo 
Published: April 2021

ABSTRACT
Sister chromatid exchanges (SCEs) under in vivo and in vitro conditions were examined in ganglion cells of third-instar larvae of Drosophila melanogaster (Oregon-R). In the in vivo experiment, third-instar larvae were fed on synthetic media containing 5-bromo-2′-deoxyuridine (BrdUrd). After two cell cycles, ganglia were dissected and treated with colchicine. In the in vitro experiment, the ganglia were also incubated in media containing BrdUrd for two cell cycles, and treated with colchicine. SCEs were scored in metaphase stained with Hoechst 33258 plus Giemsa. The frequencies of SCEs stayed constant in the range of 25-150 vg/ml and 0.25-2.5 vg/ml of BrdUrd in vivo and in vitro, respectively. SCEs gradually increased at higher concentrations, strongly suggesting that at least a fraction of the detected SCEs are spontaneous. The constant levels of SCE frequency were estimated, on the average, at 0.103 per cell per two cell cycles for females and 0.101 for males in vivo and at 0.096 for females and 0.091 for males in vitro. No difference was found in the SCE frequency between sexes at any of the BrdUrd concentrations. The analysis for the distribution of SCEs within chromosomes revealed an extraordinarily high proportion of the SCEs at the junctions between euchromatin and heterochromatin; the remaining SCEs were preferentially localized in the euchromatic regions of the chromosomes and in the heterochromatic Y chromosome. These results were largely inconsistent with those of Gatti et al. (1979).