bluuebunny/crossref_metadata_2025_split huggingface dataset:
A case of dermatofibrosarcoma protuberans with neurofibromatous change
Authors: Kudoh Kazuhiro , Itabashi Chieko , Arai Eiichi , Ohshika Shusa , Mizukami Hiroki 
Published: September 2021

Abstract
A 31-year-old man with posterior neck mass visited a hospital. The mass recurred four times on the same location during the past 6 years. Needle biopsy diagnosis was suspicious for benign stromal tumor. Tumor excision was performed 3 months after the biopsy. The tumor size was 8.3 × 4.5 cm and was located at subcutaneous tissue. Histologically, main tumor cells showed comma-shaped nuclei, which are same as neurofibroma. Immunohistochemically, tumor cells were positive for vimentin, CD34, but were negative for S-100. Fluorescence in situ hybridization analysis disclosed a split signal of PDGFB gene. Reverse transcriptase-polymerase chain reaction clarified COL1A1 exon 47/PDGFB exon 2 chimeric gene. Final diagnosis was dermatofibrosarcoma protuberans (DFSP) with neurofibromatous change. DFSP with neurofibromatous change is rare and could be misdiagnosed as benign tumor, especially in a biopsy specimen. Molecular diagnosis is a promising aid in a challenging case and in biopsy specimens.
A rare case of multiple giant colonic diverticula successfully treated with laparoscopic sigmoidectomy
Authors: Merritt Clay M , Xing Chuheng , Schwartz Mary R , Bailey Harold R , Van Eps Jeffrey L 
Published: September 2021

Abstract
Colonic diverticulosis is pervasive in Western society, with over half of individuals over the age of 60 carrying the diagnosis. A Giant Colonic Diverticulum (GCD) is a rare presentation of diverticulosis, involving one or more colonic diverticula that measure 4 cm or greater. Less than 200 reports of GCD have been published in the literature. Almost all GCD patients present with symptoms, with abdominal pain being the most common. Diagnosis is usually made with CT imaging and recommended treatment is segmental colectomy. We present an atypical case of GCD with an asymptomatic presentation, initial diagnosis made during endoscopy and a minimally invasive resection of multiple GCD within the same patient.
The Discourse Marker מ ה ז ה (ma ze) to express Rebuking in Rabbinic Hebrew
Authors: Shemesh-Raiskin Rivka 
Published: September 2021

Abstract
The phrase מ ה ז ה (ma ze) is used in Rabbinic Hebrew to express a speech act of rebuking, for example: ? מהזה, עקיבא (‘What is this, ʿAqiba?’). A review of its occurrences reveals its various characteristics: a) it serves as a rhetorical question to express a rebuking; b) it appears in the spoken language; c) it is used especially by one sage when rebuking another sage; and d), syntactically, it appears at the beginning of the sentence and is followed by an address. It seems that its usage in Rabbinic Hebrew is not a continuation of the usage found in Biblical Hebrew, and that it has not continued into Modern Hebrew. This usage as described and exemplified in this article has apparently not been documented in dictionaries of Rabbinic Hebrew nor in the research literature. I suggest viewing מ ה ז ה Hebrew as a rebuking interactional discourse marker.
The Debate of Menaḥem and Dunash and a Frame-work for Non-Triliteral Hebrew Verbal Morphology
Authors: Dachman Joshua 
Published: September 2021

Abstract
This study presents a new suggestion as to the fundamental disagreement between the morphological theories of Menaḥem b. Saruq and Dunash b. Labraṭ, two tenth-century Hebraists with non-triliteral perspectives of the Hebrew root. A framework detailing the possible analyses of Hebrew verbal morphology without a priori assuming the triliteral perspective is first developed. It is noted that the multiplicity of possible analyses in this framework parallels the ‘Segmentation Problem’ of Romance languages due to thematic vowels. Based on analysis of their treatises it is then argued that Menaḥem generally follows one identified method of analysis, and Dunash another. Finally it is suggested that these different methods of analysis are rooted in two different models of morphology, with Menaḥem holding a morpheme-based model and Dunash holding a word-based model. An English translation of a lengthy relevant section of the introduction to Menaḥem’s treatise is given as an appendix.
The Faifi Arabic [St] Reflex of Ṣād: Proto-Semitic or Substrate?
Authors: Davis Stuart , Alfaifi Abdullah 
Published: September 2021

Abstract
This paper argues against the view that the unusual reflex of ṣād as [st] in Faifi Arabic stems from a metathesized version of the Proto-Semitic glottalized affricate * cʾ([tsʾ]), as in Alfaifi and Behnstedt (2010: 53–4), where [st] is assumed to pattern as monosegmental. Instead we propose that the [st] reflex of ṣād in Faifi Arabic reflects a South Arabian ejective or glottalized fricative *sʾ as a substrate feature. We first argue that Faifi Arabic [st] patterns as bisegmental based on linguistic argumentation internal to the dialect. We then discuss *s’as a feature of South Arabian varieties that can be considered as part of the Faifi substrate. We then detail how it is phonetically plausible for ejective sʾ to ‘break’ into a sequence of a fricative followed by a stop, such as [st], accounting for its bisegmental patterning and its realization as pharyngealized [ṣ] where [st] is phonotactically impossible.
CsMYB96 confers resistance to water loss in citrus fruit by simultaneous regulation of water transport and wax biosynthesis
Authors: Zhang Mingfei , Wang Jinqiu , Liu Ruilian , Liu Hai , Yang Hongbin , Zhu Zhifeng , Xu Rangwei , Wang Pengwei , Deng Xiuxin , Xue Shaowu , Zhu Feng , Cheng Yunjiang 
Published: September 2021

Abstract
A Citrus sinensis R2R3 MYB transcription factor (CsMYB96) has previously been shown to be strongly associated with the expression of many genes related to wax biosynthesis in the fruit. In this study, CsMYB96 was found to alleviate water loss by simultaneously regulating the expression of genes encoding plasma membrane intrinsic proteins (CsPIPs) and wax-related genes. Expression profiling indicated that CsPIP1;1 and CsPIP2;4 had high expression that was representative of other aquaporins, and they were down-regulated in the peel of post-harvest citrus fruit. CsPIP2;4 was further characterized as the predominant CsPIP, with high expression and high-water channel activity. Transient overexpression of CsPIP2;4 accelerated water loss in citrus fruit. In silico analysis further indicated that the expression of CsMYB96 had a significant negative correlation with that of CsPIPs. In vivo and in vitro experiments confirmed that CsMYB96 was able to directly repress the expression of CsPIPs. In addition, CsMYB96 was able to activate wax-related genes and promote wax biosynthesis for defense against water loss. Transient and stable overexpression of CsMYB96 reduced water loss from both citrus fruit and Arabidopsis.
Interactions among rooting traits for deep water and nitrogen uptake in upland and lowland ecotypes of switchgrass (Panicum virgatum L.)
Authors: Griffiths Marcus , Wang Xueyan , Dhakal Kundan , Guo Haichao , Seethepalli Anand , Kang Yun , York Larry M 
Published: September 2021

Abstract
The response of plant growth and development to nutrient and water availability is an important adaptation for abiotic stress tolerance. Roots need to intercept both passing nutrients and water while foraging into new soil layers for further resources. Substantial amounts of nitrate can be lost in the field when leaching into groundwater, yet very little is known about how deep rooting affects this process. Here, we phenotyped root system traits and deep 15N nitrate capture across 1.5 m vertical profiles of solid media using tall mesocosms in switchgrass (Panicum virgatum L.), a promising cellulosic bioenergy feedstock. Root and shoot biomass traits, photosynthesis and respiration measures, and nutrient uptake and accumulation traits were quantified in response to a water and nitrate stress factorial experiment for switchgrass upland (VS16) and lowland (AP13) ecotypes. The two switchgrass ecotypes shared common plastic abiotic responses to nitrogen (N) and water availability, and yet had substantial genotypic variation for root and shoot traits. A significant interaction between N and water stress combination treatments for axial and lateral root traits represents a complex and shared root development strategy for stress mitigation. Deep root growth and 15N capture were found to be closely linked to aboveground growth. Together, these results represent the wide genetic pool of switchgrass and show that deep rooting promotes nitrate capture, plant productivity, and sustainability.
Eight-carbon volatiles: prominent fungal and plant interaction compounds
Authors: Pennerman Kayla K , Yin Guohua , Bennett Joan W 
Published: September 2021

AbstractSignaling via volatile organic compounds (VOCs) has historically been studied mostly by entomologists; however, botanists and mycologists are increasingly aware of the physiological potential of chemical communication in the gas phase. Most research to date focuses on the observed effects of VOCs on different organisms such as differential growth or metabolite production. However, with the increased interest in volatile signaling, more researchers are investigating the molecular mechanisms for these effects. Eight-carbon VOCs are among the most prevalent and best-studied fungal volatiles. Therefore, this review emphasizes examples of eight-carbon VOCs affecting plants and fungi. These compounds display different effects that include growth suppression in both plants and fungi, induction of defensive behaviors such as accumulation of mycotoxins, phytohormone signaling cascades, and the inhibition of spore and seed germination. Application of ‘-omics’ and other next-generation sequencing techniques is poised to decipher the mechanistic basis of volatiles in plant–fungal communication.
Efficacy of POC Antibody Assays after COVID-19 Infection and Potential Utility for “Immunity Passports”
Authors: Shalaby Akram , Laharwani Hansini , Bates John T , Kyle Patrick B 
Published: September 2021

Abstract

Objective
Numerous manufacturers market lateral flow assays for the detection of SARS-CoV-2 antibodies, but there are many questions about the reliability and efficacy of these tests.

Materials and Methods
Serum specimens from 60 individuals were analyzed using 2 lateral flow antibody assays, an in-house enzyme-linked immunosorbent assay (ELISA), and the Abbott SARS-CoV-2 IgG chemiluminescent immunoassay.

Results
The BioMedomics and Premier Biotech lateral flow assays were positive for IgM in 73.3% and 70% and for IgG in 80% and 73.3% of specimens, respectively. The ELISA assay was positive for IgM and IgG in 73.3% and 86.7% of specimens from infected individuals, whereas the Abbott assay was positive in 80%. The specificities of the 4 assays ranged from 96.7% to 100% for IgM and from 93.3% to 100% for IgG.

Conclusion
Results of the 2 lateral flow assays were comparable to those of the ELISA and Abbott assays. Assay efficacy depended on length of time after SARS-CoV-2 infection.
medusa: Minkowski functionals estimated from Delaunay tessellations of the three-dimensional large-scale structure
Authors: Lippich Martha , Sánchez Ariel G 
Published: September 2021

ABSTRACT
Minkowski functionals (MFs) are a set of statistics that characterize the geometry and topology of the cosmic density field and contain complementary information to the standard two-point analyses. We present medusa, an implementation of an accurate method for estimating the MFs of three-dimensional point distributions. These estimates are inferred from triangulated isodensity surfaces that are constructed from the Delaunay tessellation of the input point sample. medusa can account for periodic boundary conditions, which is crucial for the analysis of N-body simulations. We validate our code against several test samples with known MFs, including Gaussian random fields with a ΛCDM power spectrum, and find excellent agreement with the theory predictions. We use medusa to measure the MFs of synthetic galaxy catalogues constructed from N-body simulations. Our results show clearly non-Gaussian signatures that arise from the non-linear gravitational evolution of the density field. We find that, although redshift-space distortions change our MFs estimates, their impact is considerably reduced if these measurements are expressed as a function of the volume-filling fraction. We also show that the effect of Alcock–Paczynski (AP) distortions on the MFs can be described by scaling them with different powers of the isotropic AP parameter q defined in terms of the volume-averaged distance DV(z). Thus the MFs estimates by medusa are useful probes of non-linearities in the density field, and the expansion and growth of structure histories of the Universe.
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
Authors: Cantalapiedra Carlos P , Hernández-Plaza Ana , Letunic Ivica , Bork Peer , Huerta-Cepas Jaime 
Published: September 2021

Abstract
Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de.
Oncogenic KRAS drives radioresistance through upregulation of NRF2-53BP1-mediated non-homologous end-joining repair
Authors: Yang Linlin , Shen Changxian , Estrada-Bernal Adriana , Robb Ryan , Chatterjee Moumita , Sebastian Nikhil , Webb Amy , Mo Xiaokui , Chen Wei , Krishnan Sunil , Williams Terence M 
Published: September 2021

Abstract
KRAS-activating mutations are oncogenic drivers and are correlated with radioresistance of multiple cancers, including colorectal cancer, but the underlying precise molecular mechanisms remain elusive. Herein we model the radiosensitivity of isogenic HCT116 and SW48 colorectal cancer cell lines bearing wild-type or various mutant KRAS isoforms. We demonstrate that KRAS mutations indeed lead to radioresistance accompanied by reduced radiotherapy-induced mitotic catastrophe and an accelerated release from G2/M arrest. Moreover, KRAS mutations result in increased DNA damage response and upregulation of 53BP1 with associated increased non-homologous end-joining (NHEJ) repair. Remarkably, KRAS mutations lead to activation of NRF2 antioxidant signaling to increase 53BP1 gene transcription. Furthermore, genetic silencing or pharmacological inhibition of KRAS, NRF2 or 53BP1 attenuates KRAS mutation-induced radioresistance, especially in G1 phase cells. These findings reveal an important role for a KRAS-induced NRF2-53BP1 axis in the DNA repair and survival of KRAS-mutant tumor cells after radiotherapy, and indicate that targeting NRF2, 53BP1 or NHEJ may represent novel strategies to selectively abrogate KRAS mutation-mediated radioresistance.
SomaMutDB: a database of somatic mutations in normal human tissues
Authors: Sun Shixiang , Wang Yujue , Maslov Alexander Y , Dong Xiao , Vijg Jan 
Published: September 2021

AbstractDe novo mutations, a consequence of errors in DNA repair or replication, have been reported to accumulate with age in normal tissues of humans and model organisms. This accumulation during development and aging has been implicated as a causal factor in aging and age-related pathology, including but not limited to cancer. Due to their generally very low abundance mutations have been difficult to detect in normal tissues. Only with recent advances in DNA sequencing of single-cells, clonal lineages or ultra-high-depth sequencing of small tissue biopsies, somatic mutation frequencies and spectra have been unveiled in several tissue types. The rapid accumulation of such data prompted us to develop a platform called SomaMutDB (https://vijglab.einsteinmed.org/SomaMutDB) to catalog the 2.42 million single nucleotide variations (SNVs) and 0.12 million small insertions and deletions (INDELs) thus far identified using these advanced methods in nineteen human tissues or cell types as a function of age or environmental stress conditions. SomaMutDB employs a user-friendly interface to display and query somatic mutations with their functional annotations. Moreover, the database provides six powerful tools for analyzing mutational signatures associated with the data. We believe such an integrated resource will prove valuable for understanding somatic mutations and their possible role in human aging and age-related diseases.
scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse
Authors: Yang Xiaoxiao , Tong Yang , Liu Gerui , Yuan Jiapei , Yang Yang 
Published: September 2021

Abstract
Alternative polyadenylation (APA) has been widely recognized as a crucial step during the post-transcriptional regulation of eukaryotic genes. Recent studies have demonstrated that APA exerts key regulatory roles in many biological processes and often occurs in a tissue- and cell-type-specific manner. However, to our knowledge, there is no database incorporating information about APA at the cell-type level. Single-cell RNA-seq is a rapidly evolving and powerful tool that enable APA analysis at the cell-type level. Here, we present a comprehensive resource, scAPAatlas (http://www.bioailab.com:3838/scAPAatlas), for exploring APA across different cell types, and interpreting potential biological functions. Based on the curated scRNA-seq data from 24 human and 25 mouse normal tissues, we systematically identified cell-type-specific APA events for different cell types and examined the correlations between APA and gene expression level. We also estimated the crosstalk between cell-type-specific APA events and microRNAs or RNA-binding proteins. A user-friendly web interface has been constructed to support browsing, searching and visualizing multi-layer information of cell-type-specific APA events. Overall, scAPAatlas, incorporating a rich resource for exploration of APA at the cell-type level, will greatly help researchers chart cell type with APA and elucidate the biological functions of APA.
VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes
Authors: Sun Qinglan , Shu Chang , Shi Wenyu , Luo Yingfeng , Fan Guomei , Nie Jingyi , Bi Yuhai , Wang Qihui , Qi Jianxun , Lu Jian , Zhou Yuanchun , Shen Zhihong , Meng Zhen , Zhang Xinjiao , Yu Zhengfei , Gao Shenghan , Wu Linhuan , Ma Juncai , Hu Songnian 
Published: September 2021

Abstract
The genomic variations of SARS-CoV-2 continue to emerge and spread worldwide. Some mutant strains show increased transmissibility and virulence, which may cause reduced protection provided by vaccines. Thus, it is necessary to continuously monitor and analyze the genomic variations of SARS-COV-2 genomes. We established an evaluation and prewarning system, SARS-CoV-2 variations evaluation and prewarning system (VarEPS), including known and virtual mutations of SARS-CoV-2 genomes to achieve rapid evaluation of the risks posed by mutant strains. From the perspective of genomics and structural biology, the database comprehensively analyzes the effects of known variations and virtual variations on physicochemical properties, translation efficiency, secondary structure, and binding capacity of ACE2 and neutralizing antibodies. An AI-based algorithm was used to verify the effectiveness of these genomics and structural biology characteristic quantities for risk prediction. This classifier could be further used to group viral strains by their transmissibility and affinity to neutralizing antibodies. This unique resource makes it possible to quickly evaluate the variation risks of key sites, and guide the research and development of vaccines and drugs. The database is freely accessible at www.nmdc.cn/ncovn.
PopHumanVar: an interactive application for the functional characterization and prioritization of adaptive genomic variants in humans
Authors: Colomer-Vilaplana Aina , Murga-Moreno Jesús , Canalda-Baltrons Aleix , Inserte Clara , Soto Daniel , Coronado-Zamora Marta , Barbadilla Antonio , Casillas Sònia 
Published: September 2021

Abstract
Adaptive challenges that humans faced as they expanded across the globe left specific molecular footprints that can be decoded in our today's genomes. Different sets of metrics are used to identify genomic regions that have undergone selection. However, there are fewer methods capable of pinpointing the allele ultimately responsible for this selection. Here, we present PopHumanVar, an interactive online application that is designed to facilitate the exploration and thorough analysis of candidate genomic regions by integrating both functional and population genomics data currently available. PopHumanVar generates useful summary reports of prioritized variants that are putatively causal of recent selective sweeps. It compiles data and graphically represents different layers of information, including natural selection statistics, as well as functional annotations and genealogical estimations of variant age, for biallelic single nucleotide variants (SNVs) of the 1000 Genomes Project phase 3. Specifically, PopHumanVar amasses SNV-based information from GEVA, SnpEFF, GWAS Catalog, ClinVar, RegulomeDB and DisGeNET databases, as well as accurate estimations of iHS, nSL and iSAFE statistics. Notably, PopHumanVar can successfully identify known causal variants of frequently reported candidate selection regions, including EDAR in East-Asians, ACKR1 (DARC) in Africans and LCT/MCM6 in Europeans. PopHumanVar is open and freely available at https://pophumanvar.uab.cat.
scMRMA: single cell multiresolution marker-based annotation
Authors: Li Jia , Sheng Quanhu , Shyr Yu , Liu Qi 
Published: September 2021

Abstract
Single-cell RNA sequencing has become a powerful tool for identifying and characterizing cellular heterogeneity. One essential step to understanding cellular heterogeneity is determining cell identities. The widely used strategy predicts identities by projecting cells or cell clusters unidirectionally against a reference to find the best match. Here, we develop a bidirectional method, scMRMA, where a hierarchical reference guides iterative clustering and deep annotation with enhanced resolutions. Taking full advantage of the reference, scMRMA greatly improves the annotation accuracy. scMRMA achieved better performance than existing methods in four benchmark datasets and successfully revealed the expansion of CD8 T cell populations in squamous cell carcinoma after anti-PD-1 treatment.