bluuebunny/crossref_metadata_2025_split huggingface dataset:
Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel
Authors: Gerdol Marco , Moreira Rebeca , Cruz Fernando , Gómez-Garrido Jessica , Vlasova Anna , Rosani Umberto , Venier Paola , Naranjo-Ortiz Miguel A. , Murgarella Maria , Greco Samuele , Balseiro Pablo , Corvelo André , Frias Leonor , Gut Marta , Gabaldón Toni , Pallavicini Alberto , Canchaya Carlos , Novoa Beatriz , Alioto Tyler S. , Posada David , Figueras Antonio 
Published: November 2020

AbstractBackgroundThe Mediterranean musselMytilus galloprovincialisis an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other bivalves. Although these traits have been recently linked with the maintenance of a high genetic variation within natural populations, the factors underlying the evolutionary success of this species remain unclear.ResultsHere, after the assembly of a 1.28-Gb reference genome and the resequencing of 14 individuals from two independent populations, we reveal a complex pan-genomic architecture inM. galloprovincialis, with acoreset of 45,000 genes plus a strikingly high number ofdispensablegenes (20,000) subject to presence-absence variation, which may be entirely missing in several individuals. We show that dispensable genes are associated with hemizygous genomic regions affected by structural variants, which overall account for nearly 580 Mb of DNA sequence not included in the reference genome assembly. As such, this is the first study to report the widespread occurrence of gene presence-absence variation at a whole-genome scale in the animal kingdom.ConclusionsDispensablegenes usually belong to young and recently expanded gene families enriched in survival functions, which might be the key to explain the resilience and invasiveness of this species. This unique pan-genome architecture is characterized by dispensable genes in accessory genomic regions that exceed by orders of magnitude those observed in other metazoans, including humans, and closely mirror the open pan-genomes found in prokaryotes and in a few non-metazoan eukaryotes.
Research and application of single-cell sequencing in tumor heterogeneity and drug resistance of circulating tumor cells
Authors: Dai Zhe , Gu Xu-yu , Xiang Shou-yan , Gong Dan-dan , Man Chang-feng , Fan Yu 
Published: November 2020

AbstractMalignant tumor is a largely harmful disease worldwide. The cure rate of malignant tumors increases with the continuous discovery of anti-tumor drugs and the optimisation of chemotherapy options. However, drug resistance of tumor cells remains a massive obstacle in the treatment of anti-tumor drugs. The heterogeneity of malignant tumors makes studying it further difficult for us. In recent years, using single-cell sequencing technology to study and analyse circulating tumor cells can avoid the interference of tumor heterogeneity and provide a new perspective for us to understand tumor drug resistance.
Oxidation resistance 1 functions in the maintenance of cellular survival and genome stability in response to oxidative stress-independent DNA damage
Authors: Matsui Ako , Hashiguchi Kazunari , Suzuki Masao , Zhang-Akiyama Qiu-Mei 
Published: November 2020

Abstract

Background
DNA damage is generated by various intrinsic and extrinsic sources such as reactive oxygen species (ROS) and environmental mutagens, and causes genomic alterations. DNA damage response (DDR) is activated to induce cell cycle arrest and DNA repair. Oxidation resistance 1 (OXR1) is a protein that defends cells against oxidative stress. We previously reported that OXR1 protein functions in the regulation of G2-phase cell cycle arrest in cells irradiated with gamma-rays, suggesting that OXR1 directly responds to DNA damage.

Purpose
To clarify the functions of OXR1 against ROS-independent DNA damage, HeLa and OXR1-depleted HeLa cells were treated with heavy-ion beams and the ROS-independent DNA-damaging agent methyl methanesulfonate (MMS).

Results
First, OXR1-depleted cells exhibited higher sensitivity to MMS and heavy-ion beams than control cells. Next, OXR1 depletion increased micronucleus formation and shortened the duration of G2-phase arrest after treatment with MMS or heavy-ion beams. These results suggest that OXR1 functions in the maintenance of cell survival and genome stability in response to DNA damage. Furthermore, the OXR1 protein level was increased by MMS and heavy-ion beams in HeLa cells.

Conclusions
Together with our previous study, the present study suggests that OXR1 plays an important role in the response to DNA damage, not only when DNA damage is generated by ROS.
Transcriptomic and Epigenetic Preservation of Genetic Sex Identity in Estrogen-feminized Male Chicken Embryonic Gonads
Authors: Shioda Keiko , Odajima Junko , Kobayashi Misato , Kobayashi Mutsumi , Cordazzo Bianca , Isselbacher Kurt J , Shioda Toshi 
Published: November 2020

Abstract
Whereas in ovo exposure of genetically male (ZZ) chicken embryos to exogenous estrogens temporarily feminizes gonads at the time of hatching, the morphologically ovarian ZZ-gonads (FemZZs for feminized ZZ gonads) are masculinized back to testes within 1 year. To identify the feminization-resistant “memory” of genetic male sex, FemZZs showing varying degrees of feminization were subjected to transcriptomic, DNA methylome, and immunofluorescence analyses. Protein-coding genes were classified based on their relative mRNA expression across normal ZZ-testes, genetically female (ZW) ovaries, and FemZZs. We identified a group of 25 genes that were strongly expressed in both ZZ-testes and FemZZs but dramatically suppressed in ZW-ovaries. Interestingly, 84% (21/25) of these feminization-resistant testicular marker genes, including the DMRT1 master masculinizing gene, were located in chromosome Z. Expression of representative marker genes of germline cells (eg, DAZL or DDX4/VASA) was stronger in FemZZs than normal ZZ-testes or ZW-ovaries. We also identified 231 repetitive sequences (RSs) that were strongly expressed in both ZZ-testes and FemZZs, but these RSs were not enriched in chromosome Z. Although 94% (165/176) of RSs exclusively expressed in ZW-ovaries were located in chromosome W, no feminization-inducible RS was detected in FemZZs. DNA methylome analysis distinguished FemZZs from normal ZZ- and ZW-gonads. Immunofluorescence analysis of FemZZ gonads revealed expression of DMRT1 protein in medullary SOX9+ somatic cells and apparent germline cell populations in both medulla and cortex. Taken together, our study provides evidence that both somatic and germline cell populations in morphologically feminized FemZZs maintain significant transcriptomic and epigenetic memories of genetic sex.
RAS-mediated suppression of PAR3 and its effects on SCC initiation and tissue architecture occur independently of hyperplasia
Authors: Ling Ji , Sckaff Maria , Tiwari Manisha , Chen Yifang , Li Jingting , Jones Jackson , Sen George L. 
Published: November 2020

ABSTRACT
Proper epithelial development and homeostasis depends on strict control of oriented cell division. Current evidence shows that this process is regulated by intrinsic polarity factors and external spatial cues. Owing to the lack of an appropriate model system that can recapitulate the architecture of the skin, deregulation of spindle orientation in human epithelial carcinoma has never been investigated. Here, using an inducible model of human squamous cell carcinoma (SCC), we demonstrate that RAS-dependent suppression of PAR3 (encoded by PARD3) accelerates epithelial disorganization during early tumorigenesis. Diminished PAR3 led to loss of E-cadherin-mediated cell adhesion, which in turn contributed to misoriented cell division. Pharmacological inhibition of the MAPK pathway downstream of RAS activation reversed the defects in PAR3 expression, E-cadherin-mediated cell adhesion and mitotic spindle orientation. Thus, temporal analysis of human neoplasia provides a powerful approach to study cellular and molecular transformations during early oncogenesis, which allowed identification of PAR3 as a critical regulator of tissue architecture during initial human SCC development.
Quality Disclosure Under Consumer Loss Aversion
Authors: Zhang Jianqiang , Li Krista J. 
Published: November 2020

Consumers experience a sense of loss when a product’s quality does not match their expectations. To alleviate consumer loss aversion (CLA), firms can disclose information to reduce consumers’ uncertainty about product quality and the resulting psychological loss. In this paper, we investigate the implications of CLA on firm profit, consumer surplus, and social welfare when firms endogenously make quality disclosure decisions. We find that CLA leads symmetric firms to disclose quality more often. Given that CLA weakly reduces consumers’ utility from buying a product and quality disclosure is costly, intuition suggests that CLA is detrimental to firms. We find that this intuition is true only in a monopoly. Surprisingly, CLA makes both firms in a competition better off. Moreover, CLA increases firms’ profit when they invest in quality disclosure instead of money-back guarantees to respond to CLA. We also find that CLA decreases consumer surplus and social welfare. Therefore, educating consumers to improve decision-making skills by deliberating on future outcomes and emotions can benefit firms at the cost of consumers and society. When firms disclose quality sequentially, CLA can discourage the follower from disclosing quality. A strong level of CLA increases the leader’s profit over the follower’s, thereby encouraging firms to be the first mover in quality disclosure.This paper was accepted by Juanjuan Zhang, marketing.
Identification of a 6-gene signature for the survival prediction of breast cancer patients based on integrated multi-omics data analysis
Authors: Mo Wenju , Ding Yuqin , Zhao Shuai , Zou Dehong , Ding Xiaowen 
Published: November 2020

Purpose
To identify a gene signature for the prognosis of breast cancer using high-throughput analysis.

Methods
RNASeq, single nucleotide polymorphism (SNP), copy number variation (CNV) data and clinical follow-up information were downloaded from The Cancer Genome Atlas (TCGA), and randomly divided into training set or verification set. Genes related to breast cancer prognosis and differentially expressed genes (DEGs) with CNV or SNP were screened from training set, then integrated together for feature selection of identify robust biomarkers using RandomForest. Finally, a gene-related prognostic model was established and its performance was verified in TCGA test set, Gene Expression Omnibus (GEO) validation set and breast cancer subtypes.

Results
A total of 2287 prognosis-related genes, 131 genes with amplified copy numbers, 724 gens with copy number deletions, and 280 genes with significant mutations screened from Genomic Variants were closely correlated with the development of breast cancer. A total of 120 candidate genes were obtained by integrating genes from Genomic Variants and those related to prognosis, then 6 characteristic genes (CD24, PRRG1, IQSEC3, MRGPRX, RCC2, and CASP8) were top-ranked by RandomForest for feature selection, noticeably, several of these have been previously reported to be associated with the progression of breast cancer. Cox regression analysis was performed to establish a 6-gene signature, which can stratify the risk of samples from training set, test set and external validation set, moreover, the five-year survival AUC of the model in the training set and validation set was both higher than 0.65. Thus, the 6-gene signature developed in the current study could serve as an independent prognostic factor for breast cancer patients.

Conclusion
This study constructed a 6-gene signature as a novel prognostic marker for predicting the survival of breast cancer patients, providing new diagnostic/prognostic biomarkers and therapeutic targets for breast cancer patients.
The Indecent Screen: Regulating Television in the Twenty-First Century, Cynthia Chris (2019)
Authors: Later Naja 
Published: November 2020

Review of: The Indecent Screen: Regulating Television in the Twenty-First Century, Cynthia Chris (2019)
New Brunswick: Rutgers University Press, 254 pp.,
ISBN 978-0-81359-406-4, p/bk, $29.95
Reformulasi Identitas Buddha Jawi Wisnu dan Sam Kaw Hwee Ke Dalam Buddhayana di Lampung Reformulating Identity of Buddha Jawi Wisnu and Sam Kaw Hwee Into Buddhayana in Lampung
Authors: Eko Putro Zaenal Abidin 
Published: November 2020

AbstractThe formulation of a social group identity is strongly influenced by the historical context and institutional site in which reformulation of social identity occurred. As a result, the group has a common understanding and categories that unite them into sameness identity. It is what we have seen on the Sam Kaw Hwee Buddhist sect group as well as Buddha Jawi Wisnu sect group who in early New Order regime changed their identity into becoming Buddhayana Buddhist sect in Lampung. At a glance, the Majelis Buddhayana Indonesia (MBI, or Indonesian Buddhayana Council) was a meeting point of which Javanese and Chinese are encountered. Furthermore, MBI is regarded as a shared identity for most Buddhists in Lampung. This paper wants to explain the background and the process of reformulating new social identity, as well as the impacts around it.The paper is based on a qualitative research that tries to understand the early formation of Buddhayana sect as the largest Buddhist sect in Lampung. MBI was as a new social identity resulting from interaction and negotiation its followers with external group who threatened the Buddhist group in Lampung in the past.Abstrak Terbentuknya identitas suatu kelompok sosial sangat dipengaruhi konteks sejarah dan situasi tertentu yang menyebabkan munculnya kesamaan pemahaman dan kategori yang menyatukan kelompok tersebut. Demikian pula terhadap kelompok penganut sekte Buddha Sam Kaw Hwee dan Buddha Jawi Wisnu yang kemudian, karena kesamaan-kesamaan yang ada, membentuk identitas baru menjadi sekte Agama Buddha Buddhayana di Lampung di awal Orde Baru. Saat ini Majelis Buddhayana Indonesia (MBI) diterima secara meluas dalam melakukan pembinaan dan pengorganisasian umat Buddha di Lampung, yang terdiri dari etnis Jawa dan Tionghoa. MBI hadir sebagai identitas bersama dan wadah bagi sebagian besar umat Buddha di Lampung. Tulisan ini hendak menjelaskan latar belakang dan proses reformulasi identitas tersebut, serta dampak yang muncul di sekitar itu. Tulisan hasil penelitian kualitatif ini menunjukkan bahwa Buddhayana sebagai aliran yang terbesar umat Buddha di Lampung, semakin kokoh sebagai identitas sosial yang dihasilkan dari interaksi dan negosiasi dengan pihak eksternal yang dilalui dengan cukup menegangkan pada masanya.
DEKONSTRUKSI MAKNA PELACUR DALAM ATAS NAMA MALAM KARYA SENO GUMIRA AJIDARMA
Authors: Manik Ricky Aptifive 
Published: November 2020

Prostitutes often get a negative meaning, not only in their profession but also in their identity markers. This stigma has put them in a low hierarchy compared to other professions as their opposite meaning. This research aims to find out various binary oppositions related to prostitute, dominant logic, and meaning invention of prostitute in a collection of short stories of Atas Nama Malam of Seno Gumira Ajidarma. The problem in this study is what is binary opposition, the dominant logic in the text and how the invention of the meaning of the prostitute after being deconstructed in SGAâ€™s short stories. This study used Derrida's deconstruction method with a comprehensive reading strategy in searching for binary oppositions of prostitute. Reconstruction of the text was also carried out to find the dominant logic contained in the text, including the interpretation of other assumptions to then be distorted from the hierarchical structure of the binary oppositions, that is finding the invention of meaning. This study found that there were seven binary oppositions of prostitute, namely a man, morning/afternoon worker, doctor, teacher, official wife, murderer, and harmonious family shaper. The meaning of prostitute finds its invention as the people who are responsible for her family, helper/hero, honest, and victim.
Novel Digital Gait Kinematic Solution to Improve Frailty
Authors: Rodgers Geraldine , Mottley Anne , Hodgins Diana 
Published: November 2020

Introduction: Frailty effects a person’s health and correlates with mobility and falls. Intervention studies that focus on exercise have demonstrated improved mobility and functional ability in some frailty groups. This study tested a personalised intervention programme automatically generated from digital gait data on frail older people under the care of the North East London Foundation Trust, Community Hospital setting.
Methods: One hundred and twenty one people, average age 79, who suffered an injurious fall and were under the care of the Community Hospital, completed the personalised intervention programme. Objective gait kinematic data, obtained using GaitSmartTM automatically generated a personalised exercise programme. Each participant received four tests, approximately 3 weeks apart and was provided with a copy of their report plus personalised exercises. Frailty was measured using the Edmonton Frailty Scale (EFS), fear of falling was measured using the Falls Efficacy Scale-International (FES-I) and speed was determined from the gait data (GS).
Results: Five parameters were analysed for all 121 participants at the start and end of the intervention: EFS; FES-I; GS; speed; walking aid. There was a statistically significance between the start and end (p<0.001) for all the parameters.
Conclusion: The results demonstrate that addressing frailty using a digital gait solution that sets exercises based on the gait kinematic data, did reverse frailty. This four session programme has shown to improve frailty levels and fear of falling. It also reduced the reliance on walking aids and increased average walking speed from 0.46 to 0.62 m/s.
Automatic EEG-based Alertness Classification using Sparse Representation and Dictionary Learning
Authors: Hadra Mohammad , Abdelrahman Iman 
Published: November 2020

Automation of human alertness identification has been widely investigated in recent decades. Many applications can benefit from automatic alertness state identification, such as driver fatigue detection, monotonous task workers' vigilance detection and sleep studies in the medical field. Many researchers have tried to exploit different types of behavioural aspects in vigilance detection, such as eye movement, head position and facial expression. On the other hand, some biomedical signals like ECG, EEG and heart rhythm are also exploited; however, there is a consensus of the superiority of EEG signal in alertness classification due to its close relation with different human vigilant states. In this paper, we propose an automatic method for vigilance detection using a single EEG channel along with sparse representation and dictionary learning. We used Discrete Wavelet Packet Transform to extract the features related to different human vigilance states. We use well-known other classifiers to compare the performance of our proposed method. Results of classification with sparse representation and dictionary learning produced better accuracy results than the other methods.
PEMAHAMAN TREN SAAT INI SEBAGAI LANGKAH AWAL PENGUATAN NILAI-NILAI PANCASILA
Authors: Kartoli Kartoli , Risman Helda 
Published: November 2020

Abstract. It is inevitable that Pancasila has become a unifier and guide to the life of the nation and state. In line with the dynamics of the era, of course, in its application needs continuous efforts in its adjustment and strengthening. For this reason, understanding the current situation and conditions is important to be a concern. This paper tries to explain the tendency of the current situation and conditions in the context of evaporation of the Pancasila values. The related literature study was used by the autor to compile the main idea points referring to the current situation and conditions and the need for a relevant mindset to contemporary times without losing the essence of strengthening the values of Pancasila. It was hoped that this paper may be a contribution of thought for stakeholders in relation to efforts to strengthen Pancasila as a unifying philosophy and life guide for elements of the Republic of Indonesia. Abstrak. Sudah tidak dapat dipungkiri bahwa Pancasila telah menjadi pemersatu dan panduan kehidupan berbangsa dan bernegara. Sejalan dengan dinamika perkembangan jaman, tentu dalam penerapannya perlu upaya berkelanjutan dalam penyesuaian dan penguatannya. Untuk itu, pemahaman terhadap situasi dan kondisi berjalan penting untuk menjadi perhatian. Tulisan ini mencoba memaparkan kecenderungan situasi dan kondisi saat ini dalam konteks penguapan nilai-nilai Pancasila. Kajian pustaka terkait digunakan penulis untuk merangkai pokok-pokok pikiran merujuk kepada trend situasi dan kondisi berjalan dan perlunya pola pikir yang relevan dengan masa kontemporer tanpa menghilangkan esensi penguatan nilai-nilai Pancasila. Harapannya adalah tulisan ini dapat menjadi sumbangsih pemikiran bagi pihak terkait dalam kaitannya dengan upaya penguatan Pancasila sebagai falsafah pemersatu dan pedoman kehidupan elemen dari NKRI.
Analisis Sistem Pemikiran Gender Berbasis Keagamaan di Pesantren Jawa Timur
Authors: Bosra Mustari , Umiarso Umiarso , Jamil Asyraf Isyraqi bin 
Published: November 2020

This research concentrates on the religious-based gender framework within the pesantren education system by which pesantren has an institutional vision to empower women and naturally participates in developing gender discourse with Islamic religious nuance. This research was conducted in East Java by taking the site of Pesantren Nurul Islam Antirogo, Pesantren Al-Falah Karangharjo Jember, and Pesantren Annuqayah Guluk-Guluk Sumenep. This research found that those pesantrens carried out reconstruction through theological-philosophical awareness that was designed from the dialogic process of re-interpretative religious normative texts with reality. The emergence of this awareness led the pesantren to direct their education system to feel egalitarian, non-discriminatory, and non-subordinate towards women inside and outside the pesantren. The axiology of the pesantren education system leads to the normative value of the unity of humanity. The realization of the education system ends up on peace values whether in the cultural, social, or even religious domains.
Emprendimiento colectivo juvenil en clave de Economía Social como una herramienta para la prevención de la violencia
Authors: Macías de la Torre Carolina , Reyes Cristóbal Verenice 
Published: November 2020

Objeto: el presente artículo tiene el propósito de hacer un ejercicio de sistematizar la experiencia de implementación de un programa diseñado para la prevención de las violencias en las juventudes en México, desde el enfoque de la Economía Social. El programa se implementa en diversos estados de la república impulsando emprendimientos colectivos con jóvenes en condiciones de riesgo, a partir de la metodología de acompañamiento e incubación de la Universidad Iberoamericana Puebla. El proyecto tiene como eje central el desarrollo de habilidades para que los jóvenes fortalezcan sus factores de protección ante el riesgo.
Metodología: en este artículo, se describen el objetivo y los fundamentos básicos del proyecto, así como la manera en que se opera desde los diferentes territorios en México, enfatizando en la metodología de acompañamiento utilizada para incubar a los emprendimientos colectivos.
Conclusiones: se concluye presentando la referencia de algunos casos de emprendimientos colectivos acompañados y se finaliza con algunas observaciones que se derivan del acompañamiento que se ha dado a estos colectivos en dos años de trabajo.