bluuebunny/crossref_metadata_2025_split huggingface dataset:
PIK3CA somatic alterations in invasive breast cancers: different spectrum from Caucasians to Chinese detected by next generation sequencing
Authors: Jia Minghan , Liao Ning , Chen Bo , Zhang Guochun , Wang Yulei , Li Xuerui , Cao Li , Mok Hsiaopei , Ren Chongyang , Li Kai , Li Cheukfai , Wen Lingzhu , Lin Jiali , Wei Guangnan , Balch Charles M. 
Published: January 2021

Abstract
Purpose
Somatic alteration of phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) is a crucial therapeutic target in breast cancer (BC) and PI3Kα-specific inhibitor Alpelisib has been used in clinics. This study investigates the PIK3CA alterations in Chinese and Caucasians BC patients for the purpose of selecting anti-PI3K therapy.

Methods
The molecular profile of the PIK3CA gene was analyzed in 412 Chinese patients with untreated invasive BC using a 540 gene next-generation sequencing panel. The results were compared with data of the Caucasian BC patients in The Cancer Genome Atlas (TCGA-white).

Results
PIK3CA alterations were frequently found in BC of estrogen receptor (ER) positive (49.3%, p = 0.024), low ki67 proliferation index (58.3%, p = 0.007) and low pathological grade (grade I/II/III 80%, 53.4%, 35.9%, p < 0.001). Compared to TCGA-white, Chinese BC patients had a higher alteration frequency (45.6% vs. 34.7%, p < 0.001) with larger proportion of p.H1047R mutation among three common mutation sites (p.E545K, p.E542K and p.H1047R) (66.1% vs. 43.7%, p = 0.01). Across four molecular subtypes, ER + /human epidermal growth factor receptor 2 positive (HER2 +) tumors harbored the most PIK3CA alterations (51.6%), while ER-/HER2- harbored the least alteration (30.0%) but the most copy number amplification (19.05%).

Conclusion
PIK3CA alterations prevail in Chinese BC patients and have different molecular features compared to that of Caucasians. The results provide precise annotations of PIK3CA genomic alterations of Chinese in the context of application of PIK3CA inhibitor.
Prenatal Diagnosis of Absent Right Superior Vena Cava in Referrals for Fetal Echocardiography
Authors: Acherman Ruben J. , Evans William N. , Restrepo Humberto 
Published: January 2021

AbstractA persistent LSVC with an absent right superior vena cava (RSVC) is unusual, encountered in about 10% of patients with persistent LSVC. We present 14 patients with a prenatal diagnosis of single LSVC and situs solitus, including prenatal findings and information on medium-term follow-up. We identified patients with situs solitus and a persistent LSVC born between March 2004 and March 2020, which had been diagnosed prenatally between December 2003 and November 2019. From this cohort, we identified those with absent RSVC. In the population of women undergoing fetal echocardiography, the prevalence of persistent LSVC in situs solitus was 0.43% (84/19,712). For the 84 identified patients and for the entire population respectively, 14/84 (17%) and 14/19,712 (0.07%) had a single LSVC (absent RSVC). Of 14 patients with a single LSVC, 8 (57%) were male. For the 84 identified patients and for the entire population respectively, 70/84 (83%) and 70/19,712 (0.36%) had bilateral SVCs. For a single LSVC (absent RSVC) and situs solitus, the majority had no associated cardiac, extracardiac, or syndromic abnormalities.
Active protection of work area against explosion of dust–gas mixture
Authors: Szkudlarek Zbigniew , Janas Sebastian 
Published: January 2021

AbstractPotentially explosive atmosphere can occur not only in the production systems of the food, energy, chemical and petrochemical industries but also in the production processes of the mining industry. Gases, vapours, mists and dusts arise can escape in an uncontrolled way during production, processing, transportation and storage of flammable substances. In combination with oxygen, they create explosive atmospheres that, if ignited, lead to an explosion causing catastrophic damage to people's lives and property. To protect against the results of hazardous dust–gas mixtures explosions in a confined work space, where employees can stay, various control and protection mechanisms are used in the form of an active explosion-proof system. The article presents the results of tests on an active system for limiting the effects of ignition of gas and/or dust based on a highly efficient explosion suppression system—equipped with an ignition detection system, high-pressure fire extinguisher and a power supply and trigger system. Smokeless powder was used as the explosive charge and sodium bicarbonate as the suppressive material. Tests of the effectiveness of the active explosion suppression system were carried out on two devices: a small-size dry dust collector and a zone extinguishing system adapted for direct explosion suppression in closed working spaces. In both cases, the explosion suppression process took place through the action of extinguishing powder blown out of the fire extinguisher after membrane perforation by compressed combustion products.
School-Based Mind–Body Interventions: A Research Review
Authors: Cozzolino Mauro , Vivo Deborah R. , Celia Giovanna 
Published: January 2021

AbstractThis paper contains a narrative review of the literature in the field of school-based mind–body interventions (MBIs). The aim of the current review is to verify whether the school-based MBI programs implemented in primary and secondary schools over the past 5 years are effective in helping schoolchildren cope with stress-related, behavioral, and affective issues, as well as improve stress response and school performance. All articles were retrieved using a number of databases. Inclusion criteria comprised qualitative and quantitative, English language, and peer-reviewed studies among third graders (8–9 years old) to twelfth graders (17–18 years old), including special needs pupils. Qualitative studies were limited to pupils’ experience only. Ten studies meeting the criteria for this review were assessed. The school-based interventions included yoga-based programs and mindfulness training. Evidence was evaluated and summarized. Across the reviewed studies, we found support for MBIs as part of school curricula to reduce negative effects of stress and promote overall well-being with caveats to consider in choosing specific programs. The practical implications of the current review include considerations related to the incorporation of MBIs in school curricula, which would likely benefit schoolchildren.
Origins of the long-range exciton diffusion in perovskite nanocrystal films: photon recycling vs exciton hopping
Authors: Giovanni David , Righetto Marcello , Zhang Qiannan , Lim Jia Wei Melvin , Ramesh Sankaran , Sum Tze Chien 
Published: January 2021

AbstractThe outstanding optoelectronic performance of lead halide perovskites lies in their exceptional carrier diffusion properties. As the perovskite material dimensionality is reduced to exploit the quantum confinement effects, the disruption to the perovskite lattice, often with insulating organic ligands, raises new questions on the charge diffusion properties. Herein, we report direct imaging of >1 μm exciton diffusion lengths in CH3NH3PbBr3 perovskite nanocrystal (PNC) films. Surprisingly, the resulting exciton mobilities in these PNC films can reach 10 ± 2 cm2 V−1 s−1, which is counterintuitively several times higher than the carrier mobility in 3D perovskite films. We show that this ultralong exciton diffusion originates from both efficient inter-NC exciton hopping (via Förster energy transfer) and the photon recycling process with a smaller yet significant contribution. Importantly, our study not only sheds new light on the highly debated origins of the excellent exciton diffusion in PNC films but also highlights the potential of PNCs for optoelectronic applications.
Bandwidth limits of luminescent solar concentrators as detectors in free-space optical communication systems
Authors: Portnoi Mark , Haigh Paul Anthony , Macdonald Thomas J. , Ambroz Filip , Parkin Ivan P. , Darwazeh Izzat , Papakonstantinou Ioannis 
Published: January 2021

AbstractLuminescent solar concentrators (LSCs) have recently emerged as a promising receiver technology in free-space optical communications due to their inherent ability to collect light from a wide field-of-view and concentrate it into small areas, thus leading to high optical gains. Several high-speed communication systems integrating LSCs in their detector blocks have already been demonstrated, with the majority of efforts so far being devoted to maximising the received optical power and the system’s field-of-view. However, LSCs may pose a severe bottleneck on the bandwidth of such communication channels due to the comparably slow timescale of the fluorescence events involved, a situation further aggravated by the inherent reabsorption in these systems, and yet, an in-depth study into such dynamic effects remains absent in the field. To fill this gap, we have developed a comprehensive analytical solution that delineates the fundamental bandwidth limits of LSCs as optical detectors in arbitrary free-space optical links, and establishes their equivalence with simple RC low-pass electrical circuits. Furthermore, we demonstrate a time-domain Monte Carlo simulation platform, an indispensable tool in the multiparameter optimisation of LSC-based receiver systems. Our work offers vital insight into LSC system dynamic behaviour and paves the way to evaluate the technology for a wide range of applications, including visible light communications, high-speed video recording, and real-time biological imaging, to name a few.
NAD+ metabolism, stemness, the immune response, and cancer
Authors: Navas Lola E. , Carnero Amancio 
Published: January 2021

AbstractNAD+ was discovered during yeast fermentation, and since its discovery, its important roles in redox metabolism, aging, and longevity, the immune system and DNA repair have been highlighted. A deregulation of the NAD+ levels has been associated with metabolic diseases and aging-related diseases, including neurodegeneration, defective immune responses, and cancer. NAD+ acts as a cofactor through its interplay with NADH, playing an essential role in many enzymatic reactions of energy metabolism, such as glycolysis, oxidative phosphorylation, fatty acid oxidation, and the TCA cycle. NAD+ also plays a role in deacetylation by sirtuins and ADP ribosylation during DNA damage/repair by PARP proteins. Finally, different NAD hydrolase proteins also consume NAD+ while converting it into ADP-ribose or its cyclic counterpart. Some of these proteins, such as CD38, seem to be extensively involved in the immune response. Since NAD cannot be taken directly from food, NAD metabolism is essential, and NAMPT is the key enzyme recovering NAD from nicotinamide and generating most of the NAD cellular pools. Because of the complex network of pathways in which NAD+ is essential, the important role of NAD+ and its key generating enzyme, NAMPT, in cancer is understandable. In the present work, we review the role of NAD+ and NAMPT in the ways that they may influence cancer metabolism, the immune system, stemness, aging, and cancer. Finally, we review some ongoing research on therapeutic approaches.
Mechanical force-driven TNFα endocytosis governs stem cell homeostasis
Authors: Yu Wenjing , Chen Chider , Kou Xiaoxing , Sui Bingdong , Yu Tingting , Liu Dawei , Wang Runci , Wang Jun , Shi Songtao 
Published: January 2021

AbstractMesenchymal stem cells (MSCs) closely interact with the immune system, and they are known to secrete inflammatory cytokines in response to stress stimuli. The biological function of MSC-derived inflammatory cytokines remains elusive. Here, we reveal that even under physiological conditions, MSCs produce and release a low level of tumor necrosis factor alpha (TNFα), which is unexpectedly required for preserving the self-renewal and differentiation of MSCs via autocrine/paracrine signaling. Furthermore, TNFα critically maintains MSC function in vivo during bone homeostasis. Mechanistically, we unexpectedly discovered that physiological levels of TNFα safeguard MSC homeostasis in a receptor-independent manner through mechanical force-driven endocytosis and that endocytosed TNFα binds to mammalian target of rapamycin (mTOR) complex 2 and restricts mTOR signaling. Importantly, inhibition of mTOR signaling by rapamycin serves as an effective osteoanabolic therapeutic strategy to protect against TNFα deficiency and mechanical unloading. Collectively, these findings unravel the physiological framework of the dynamic TNFα shuttle-based mTOR equilibrium that governs MSC and bone homeostasis.
Plant buffering against the high-light stress-induced accumulation of CsGA2ox8 transcripts via alternative splicing to finely tune gibberellin levels and maintain hypocotyl elongation
Authors: Liu Bin , Zhao Shuo , Li Pengli , Yin Yilu , Niu Qingliang , Yan Jinqiang , Huang Danfeng 
Published: January 2021

AbstractIn plants, alternative splicing (AS) is markedly induced in response to environmental stresses, but it is unclear why plants generate multiple transcripts under stress conditions. In this study, RNA-seq was performed to identify AS events in cucumber seedlings grown under different light intensities. We identified a novel transcript of the gibberellin (GA)-deactivating enzyme Gibberellin 2-beta-dioxygenase 8 (CsGA2ox8). Compared with canonical CsGA2ox8.1, the CsGA2ox8.2 isoform presented intron retention between the second and third exons. Functional analysis proved that the transcript of CsGA2ox8.1 but not CsGA2ox8.2 played a role in the deactivation of bioactive GAs. Moreover, expression analysis demonstrated that both transcripts were upregulated by increased light intensity, but the expression level of CsGA2ox8.1 increased slowly when the light intensity was >400 µmol·m−2·s−1 PPFD (photosynthetic photon flux density), while the CsGA2ox8.2 transcript levels increased rapidly when the light intensity was >200 µmol·m−2·s−1 PPFD. Our findings provide evidence that plants might finely tune their GA levels by buffering against the normal transcripts of CsGA2ox8 through AS.
Common bean SNP alleles and candidate genes affecting photosynthesis under contrasting water regimes
Authors: Leitão Susana Trindade , Bicho Maria Catarina , Pereira Priscila , Paulo Maria João , Malosetti Marcos , Araújo Susana de Sousa , van Eeuwijk Fred , Vaz Patto Maria Carlota 
Published: January 2021

AbstractWater deficit is a major worldwide constraint to common bean (Phaseolus vulgaris L.) production, being photosynthesis one of the most affected physiological processes. To gain insights into the genetic basis of the photosynthetic response of common bean under water-limited conditions, a collection of 158 Portuguese accessions was grown under both well-watered and water-deficit regimes. Leaf gas-exchange parameters were measured and photosynthetic pigments quantified. The same collection was genotyped using SNP arrays, and SNP-trait associations tested considering a linear mixed model accounting for the genetic relatedness among accessions. A total of 133 SNP-trait associations were identified for net CO2 assimilation rate, transpiration rate, stomatal conductance, and chlorophylls a and b, carotenes, and xanthophyll contents. Ninety of these associations were detected under water-deficit and 43 under well-watered conditions, with only two associations common to both treatments. Identified candidate genes revealed that stomatal regulation, protein translocation across membranes, redox mechanisms, hormone, and osmotic stress signaling were the most relevant processes involved in common bean response to water-limited conditions. These candidates are now preferential targets for common bean water-deficit-tolerance breeding. Additionally, new sources of water-deficit tolerance of Andean, Mesoamerican, and admixed origin were detected as accessions valuable for breeding, and not yet explored.
Chrysanthemum WRKY15-1 promotes resistance to Puccinia horiana Henn. via the salicylic acid signaling pathway
Authors: Bi Mengmeng , Li Xueying , Yan Xin , Liu Di , Gao Ge , Zhu Pengfang , Mao Hongyu 
Published: January 2021

AbstractChrysanthemum white rust disease, which is caused by the fungus Puccinia horiana Henn., severely reduces the ornamental quality and yield chrysanthemum. WRKY transcription factors function in the disease-resistance response in a variety of plants; however, it is unclear whether members of this family improve resistance to white rust disease in chrysanthemum. In this study, using PCR, we isolated a WRKY15 homologous gene, CmWRKY15-1, from the resistant chrysanthemum cultivar C029. Real-time quantitative PCR (RT-qPCR) revealed that CmWRKY15-1 exhibited differential expression patterns between the immune cultivar C029 and the susceptible cultivar Jinba upon P. horiana infection. In addition, salicylic acid (SA) treatment strongly induced CmWRKY15-1 expression. Overexpression of CmWRKY15-1 in the chrysanthemum-susceptible cultivar Jinba increased tolerance to P. horiana infection. Conversely, silencing CmWRKY15-1 via RNA interference (RNAi) in C029 increased sensitivity to P. horiana infection. We also determined that P. horiana infection increased both the endogenous SA content and the expression of salicylic acid biosynthesis genes in CmWRKY15-1-overexpressing plants, whereas CmWRKY15-1 RNAi plants exhibited the opposite effects under the same conditions. Finally, the transcript levels of pathogenesis-related (PR) genes involved in the SA pathway were positively associated with CmWRKY15-1 expression levels. Our results demonstrated that CmWRKY15-1 plays an important role in the resistance of chrysanthemum to P. horiana by influencing SA signaling.
Defining the ‘HoneySweet’ insertion event utilizing NextGen sequencing and a de novo genome assembly of plum (Prunus domestica)
Authors: Callahan Ann M. , Zhebentyayeva Tetyana N. , Humann Jodi L. , Saski Christopher A. , Galimba Kelsey D. , Georgi Laura L. , Scorza Ralph , Main Dorrie , Dardick Christopher D. 
Published: January 2021

Abstract‘HoneySweet’ plum (Prunus domestica) is resistant to Plum pox potyvirus, through an RNAi-triggered mechanism. Determining the precise nature of the transgene insertion event has been complicated due to the hexaploid genome of plum. DNA blots previously indicated an unintended hairpin arrangement of the Plum pox potyvirus coat protein gene as well as a multicopy insertion event. To confirm the transgene arrangement of the insertion event, ‘HoneySweet’ DNA was subjected to whole genome sequencing using Illumina short-read technology. Results indicated two different insertion events, one containing seven partial copies flanked by putative plum DNA sequence and a second with the predicted inverted repeat of the coat protein gene driven by a double 35S promoter on each side, flanked by plum DNA. To determine the locations of the two transgene insertions, a phased plum genome assembly was developed from the commercial plum ‘Improved French’. A subset of the scaffolds (2447) that were >10 kb in length and representing, >95% of the genome were annotated and used for alignment against the ‘HoneySweet’ transgene reads. Four of eight matching scaffolds spanned both insertion sites ranging from 157,704 to 654,883 bp apart, however we were unable to identify which scaffold(s) represented the actual location of the insertion sites due to potential sequence differences between the two plum cultivars. Regardless, there was no evidence of any gene(s) being interrupted as a result of the insertions. Furthermore, RNA-seq data verified that the insertions created no new transcriptional units and no dramatic expression changes of neighboring genes.
The methyl jasmonate-responsive transcription factor SmMYB1 promotes phenolic acid biosynthesis in Salvia miltiorrhiza
Authors: Zhou Wei , Shi Min , Deng Changping , Lu Sunjie , Huang Fenfen , Wang Yao , Kai Guoyin 
Published: January 2021

AbstractWater-soluble phenolic acids are major bioactive compounds in the medicinal plant species Salvia miltiorrhiza. Phenolic acid biosynthesis is induced by methyl jasmonate (MeJA) in this important Chinese herb. Here, we investigated the mechanism underlying this induction by analyzing a transcriptome library of S. miltiorrhiza in response to MeJA. Global transcriptome analysis identified the MeJA-responsive R2R3-MYB transcription factor-encoding gene SmMYB1. Overexpressing SmMYB1 significantly promoted phenolic acid accumulation and upregulated the expression of genes encoding key enzymes in the phenolic acid biosynthesis pathway, including cytochrome P450-dependent monooxygenase (CYP98A14). Dual-luciferase (dual-LUC) assays and/or an electrophoretic mobility shift assays (EMSAs) indicated that SmMYB1 activated the expression of CYP98A14, as well as the expression of genes encoding anthocyanin biosynthesis pathway enzymes, including chalcone isomerase (CHI) and anthocyanidin synthase (ANS). In addition, SmMYB1 was shown to interact with SmMYC2 to additively promote CYP98A14 expression compared to the action of SmMYB1 alone. Taken together, these results demonstrate that SmMYB1 is an activator that improves the accumulation of phenolic acids and anthocyanins in S. miltiorrhiza. These findings lay the foundation for in-depth studies of the molecular mechanism underlying MeJA-mediated phenolic acid biosynthesis and for the metabolic engineering of bioactive ingredients in S. miltiorrhiza.
Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars
Authors: Pérez de los Cobos Felipe , Martínez-García Pedro J. , Romero Agustí , Miarnau Xavier , Eduardo Iban , Howad Werner , Mnejja Mourad , Dicenta Federico , Socias i Company Rafel , Rubio-Cabetas Maria J. , Gradziel Thomas M. , Wirthensohn Michelle , Duval Henri , Holland Doron , Arús Pere , Vargas Francisco J. , Batlle Ignasi 
Published: January 2021

AbstractLoss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: “Tuono”, “Cristomorto”, and “Nonpareil”. Descendants from “Tuono” or “Cristomorto” number 76 (sharing 34 descendants), while “Nonpareil” has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying theSfallele for self-compatibility, the mean relatedness coefficient was 0.125, with “Tuono” as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.