bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping Cell Phenomics with Multiparametric Flow Cytometry Assays
Authors: Liu Yang , Zhao Haichu , Fu Boqiang , Jiang Shan , Wang Jing , Wan Ying 
Published: January 2022

AbstractPhenomics explores the complex interactions among genes, epigenetics, symbiotic microorganisms, diet, and environmental exposure based on the physical, chemical, and biological characteristics of individuals and groups. Increasingly efficient and comprehensive phenotyping techniques have been integrated into modern phenomics-related research. Multicolor flow cytometry technology provides more measurement parameters than conventional flow cytometry. Based on detailed descriptions of cell phenotypes, rare cell populations and cell subsets can be distinguished, new cell phenotypes can be discovered, and cell apoptosis characteristics can be detected, which will expand the potential of cell phenomics research. Based on the enhancements in multicolor flow cytometry hardware, software, reagents, and method design, the present review summarizes the recent advances and applications of multicolor flow cytometry in cell phenomics, illuminating the potential of applying phenomics in future studies.
Atmospheric Oxygen Abundance, Marine Nutrient Availability, and Organic Carbon Fluxes to the Seafloor
Authors: Cole Devon B. , Ozaki Kazumi , Reinhard Christopher T. 
Published: January 2022

AbstractThe global‐scale oxygenation of Earth's surface represents one of the most fundamental chemical transformations in our planet's history. There is empirical and theoretical evidence for at least two distinct and stable regimes of Earth surface oxygenation—a “low‐O2world” characterized by pervasively anoxic deep ocean waters, and a “high‐O2world” with dominantly well‐oxygenated deep ocean waters represented by our modern surface environment. Numerous biogeochemical processes and feedbacks control the redox state of the marine system, particularly when considered globally and on geologic timescales. It has therefore proven challenging to provide quantitative and internally consistent estimates of the atmospheric oxygen levels (and thereby, productivity, nutrient availability, and reductant consumption) necessary to oxygenate the deep seas. Here, we leverage an Earth‐system biogeochemical model that tracks the carbon, nitrogen, oxygen, phosphorus, and sulfur cycles to provide new quantitative constraints on this relationship. We explore ocean biogeochemistry and fluxes of reduced carbon to the seafloor across a wide range of atmospheric oxygen levels from 0.01% to 100% of the present atmospheric level (PAL), and implement a stochastic approach to provide formal estimates of uncertainty on our results. We find that deep ocean waters remain largely anoxic, and ocean productivity remains significantly muted relative to the modern marine biosphere, untilpO2levels reach ∼40% PAL. These results have major implications for quantitative constraints on atmosphericpO2levels during the latest Proterozoic and Paleozoic, both in terms of environmental habitability for early animals and with respect to potential energetic constraints on growing and diversifying benthic communities.
Increased Fire Activity in Alaska Since the 1980s: Evidence From an Ice Core‐Derived Black Carbon Record
Authors: Sierra‐Hernández M. Roxana , Beaudon Emilie , Porter Stacy E. , Mosley‐Thompson Ellen , Thompson Lonnie G. 
Published: January 2022

AbstractWildfires emit large quantities of particles that affect Earth's climate and human health. Black carbon (BC), commonly known as soot, is directly emitted to the atmosphere by wildfires and other processes and can be transported and deposited in remote regions including high‐altitude glaciers and the polar regions. Here, we present a continuous, high‐resolution record of BC and ammonium (NH4+) from 1933 to 2001 extracted from two ice cores retrieved in 2002 from the col between Mt. Bona and Mt. Churchill in the Wrangell‐St. Elias Mountain Range, southeast Alaska. Despite the substantial increase of BC from fossil fuels in the Arctic since the Industrial Revolution, BC at Bona‐Churchill originates primarily from biomass burning and thus provides a record reflecting a fire history for Alaska. The BC record from Bona‐Churchill reveals that high fire activity became more frequent after 1984 in agreement with Alaska fire records. Most years associated with high BC or high NH4+ before 1984 occurred during El Niño events when precipitation in Alaska was below “normal,” suggesting that precipitation played an important role in modulating fire activity in Alaska prior to the 1980s. Conversely, years with high BC or NH4+ after 1984 coincided with years with “normal” and low precipitation, but elevated temperatures, strongly suggesting that temperature became a more dominant factor influencing fire activity in Alaska after the 1980s as suggested by other studies. Recent Alaska fire records and temperatures indicate that this trend has continued in the 21st century.
Puf-A promotes cancer progression by interacting with nucleophosmin in nucleolus
Authors: Cho Huan-Chieh , Huang Yenlin , Hung Jung-Tung , Hung Tsai-Hsien , Cheng Kai-Chun , Liu Yun-Hen , Kuo Ming-Wei , Wang Sheng-Hung , Yu Alice L. , Yu John 
Published: January 2022

AbstractPreviously, we identified Puf-A as a novel member of Puf-family RNA-binding proteins; however, its biological functions remain obscure. Analysis of tumor samples of non-small cell lung cancer (NSCLC) showed that high Puf-A expression correlated with high histology grade and abnormal p53 status. Kaplan–Meier curve for overall survival revealed high expression of Puf-A to predict poor prognosis in stage I NSCLC. Among patients with colorectal cancer, high Puf-A expression also showed an adverse impact on overall survival. In lung cancer cell lines, downregulation of p53 increased Puf-A expression, and upregulation of p53 dampened its expression. However, luciferase reporter assays indicated that PUF-A locus harbored the p53-response element, but regulated Puf-A transcription indirectly. In vivo suppression of p53 in CCSP-rtTA/TetO-Cre/LSL-KrasG12D/p53flox/flox conditional mutant mice accelerated the progression of the KrasG12D-driven lung cancer, along with enhanced expression of Puf-A. Importantly, intranasal delivery of shPuf-A to the inducible KrasG12D/p53flox/flox mice suppressed tumor progression. Puf-A silencing led to marked decreases in the 80S ribosomes, along with decrease in S6 and L5 in the cytoplasm and accumulation in the nucleolus. Based on immunofluorescence staining and immunoprecipitation studies, Puf-A interacted with NPM1 in nucleolus. Puf-A silencing resulted in NPM1 translocation from nucleolus to nucleoplasm and this disruption of NPM1 localization was reversed by a rescue experiment. Mechanistically, Puf-A silencing altered NPM1 localization, leading to the retention of ribosomal proteins in nucleolus and diminished ribosome biogenesis, followed by cell-cycle arrest/cell death. Puf-A is a potential theranostic target for cancer therapy and an important player in cancer progression.
L‐band high power solid‐state power amplifier for aerospace usage
Authors: Yang Fei , Li Jun , Yu Hongxi , Yin Kang , Zhao Hengfei , Chen Xiaoming , Zhang Anxue , Jin Zhonghe 
Published: January 2022

AbstractThis work presents the design, implementation, and experimental results of an L‐band solid‐state power amplifier (SSPA) developed for the next generation high‐power transmitter for the space usage. The microwave frequency nircuit (MFC) is realized by cascading a channel amplifier, a drive power amplifier (PA) and a high PA section. By utilizing the gallium nitride (GaN) HEMTs, the efficiency of the drive PA and high PA are improved to more than 70% over the frequency range from 1.45 to 1.55 GHz, which ensures an overall efficiency of the MFC higher than 66%. Then a high efficiency power‐supply based on the phase‐array bridge topology is proposed for voltage conversion and output sequence control, which delivers a high efficiency of about 94% at the rated power range. In the 100‐MHz operating bandwidth, the SSPA delivers more than 200 W of output power with an associated 3rd order intermodulation product (IM3) and power added efficiency (PAE) better than −18 dBc and 60%, respectively. The gain can be varied from 25 to 56 dB with a minimal step of 0.5 dB through telecommand, whereas the phase can be adjusted within 360° range with a minimal step of 5.6°.
Upgrade of an integrated Langmuir probe system on the closed divertor target plates in the HL-2A tokamak
Authors: HUANG Zhihui , CHENG Jun , WU Na , YAN Longwen , XU Hongbing , WANG Weice , MIAO Xianggan , YI Kaiyang , XU Jianqiang , CAI Laizhong , SHI Zhongbing , DONG Jiaqi , LIU Yi , ZHONG Wulyu , YANG Qingwei , XU Min , DUAN Xuru 
Published: January 2022

Abstract
A newly designed divertor Langmuir probe diagnostic system has been installed in a rare closed divertor of the HL-2A tokamak and steadily operated for the study of divertor physics involved edge-localized mode mitigation, detachment and redistribution of heat flux, etc. Two sets of probe arrays including 274 probe tips were placed at two ports (approximately 180° separated toroidally), and the spatial and temporal resolutions of this measurement system could reach 6 mm and 1 μs, respectively. A novel design of the ceramic isolation ring can ensure reliable electrical insulation property between the graphite tip and the copper substrate plate where plasma impurities and the dust are deposited into the gaps for a long experimental time. Meanwhile, the condition monitoring and mode conversion between single and triple probe of the probe system could be conveniently implemented via a remote-control station. The preliminary experimental result shows that the divertor Langmuir probe system is capable of measuring the high spatiotemporal parameters involved the plasma density, electron temperature, particle flux as well as heat flux during the ELMy H-mode discharges.
Formation and destruction of striation plasmas in helium glow discharge at medium pressures
Authors: ZHU Hailong , HUANG Qixiang , WU Yifan , LI Yurui , REN Kechang 
Published: January 2022

Abstract
The striation plasmas are usually generated within a positive column of glow discharge, where rich and complex physical interactions are involved, especially, in the medium or high pressures. Along these lines, our work aims to thoroughly investigate the formation and destruction of helium striation plasmas at kPa level pressures. The characteristics of the helium striation plasmas, and especially the optical emission properties are explored. The emission lines of 706.52 nm and 391.44 nm related to the energetic electrons and the high-energy metastable helium atoms respectively, were focused on in this work. The formation of striation plasmas in a helium glow discharge, is mainly associated with the instability originating from the stepwise ionization of high-energy metastable state atoms, Maxwellization of the electron distribution functions and gas heating. Additionally, the destruction effect of helium striation plasmas is of great significance when a small amount of nitrogen or oxygen is mixed into the discharge plasmas. The reduction of the mean electron energy and the consumption of the high-energy metastable helium atoms are considered as the underlying reasons for the destruction of striation plasmas.
Diversity and Climatic Distribution of Moths in the Tribe Arctiini (Lepidoptera: Erebidae: Arctiinae) in Mexico
Authors: Montañez-Reyna M , León-Cortés J L , Infante F , Naranjo E J , Gómez-Velasco A 
Published: January 2022

AbstractThe Mexican lepidopteran fauna is particularly diverse, but many moth groups remain poorly documented. The tribe Arctiini is a species-rich group that has been used as a reliable indicator of environmental change. However, little is known about the fauna of the tribe Arctiini in Mexico, and there is no exhaustive review of its diversity and distribution patterns. Our aims were: 1) to account for the species diversity and distribution patterns of the tribe Arctiini; 2) to build spatial distributions and discuss possible changes in the distribution areas of the tribe Arctiini using conservative (RCP 2.6) and liberal (RCP 8.5) future climate scenarios; and 3) to discuss the conservation implications for key taxa that due to their life history characteristics and restricted distribution, might require particular conservation actions. We compiled a total of 16,385 records and 548 species in seven subtribes. Diversity profiles revealed higher cumulative species richness and diversity for the subtribes Phaegopterina, Ctenuchina, and Euchromiina, and we identified a pattern of decreasing species diversity with elevation. In addition, we estimated that 35% and 84% of modeled species in future conservative and liberal climatic scenarios, respectively, would result in significant losses of climatic suitability and shifts in spatial distribution. The endemic species, Virbia semirosea, Poliopastea jalapensis, and Pygoctenucha azteca would likely reduce their distribution by approximately 50% in both climatic scenarios. Maintaining a network of highly threatened habitats (e.g., cloud forests, tropical rain forests) will be essential to preserve persisting species populations and to increase likely (re)colonization events.
Thermometer: a webserver to predict protein thermal stability
Authors: Miotto Mattia , Armaos Alexandros , Di Rienzo Lorenzo , Ruocco Giancarlo , Milanetti Edoardo , Tartaglia Gian Gaetano 
Published: January 2022

Abstract

Motivation
Thermal properties of proteins are of great importance for a number of theoretical and practical implications. Predicting the thermal stability of a protein is a difficult and still scarcely addressed task.

Results
Here, we introduce Thermometer, a webserver to assess the thermal stability of a protein using structural information. Thermometer is implemented as a publicly available, user-friendly interface.

Availability and implementation
Our server can be found at the following link (all major browser supported): http://service.tartaglialab.com/new_submission/thermometer_file.

Supplementary information
Supplementary data are available at Bioinformatics online.
BioThings SDK: a toolkit for building high-performance data APIs in biomedical research
Authors: Lelong Sebastien , Zhou Xinghua , Afrasiabi Cyrus , Qian Zhongchao , Cano Marco Alvarado , Tsueng Ginger , Xin Jiwen , Mullen Julia , Yao Yao , Avila Ricardo , Taylor Greg , Su Andrew I , Wu Chunlei 
Published: January 2022

Abstract

Summary
To meet the increased need of making biomedical resources more accessible and reusable, Web Application Programming Interfaces (APIs) or web services have become a common way to disseminate knowledge sources. The BioThings APIs are a collection of high-performance, scalable, annotation as a service APIs that automate the integration of biological annotations from disparate data sources. This collection of APIs currently includes MyGene.info, MyVariant.info and MyChem.info for integrating annotations on genes, variants and chemical compounds, respectively. These APIs are used by both individual researchers and application developers to simplify the process of annotation retrieval and identifier mapping. Here, we describe the BioThings Software Development Kit (SDK), a generalizable and reusable toolkit for integrating data from multiple disparate data sources and creating high-performance APIs. This toolkit allows users to easily create their own BioThings APIs for any data type of interest to them, as well as keep APIs up-to-date with their underlying data sources.

Availability and implementation
The BioThings SDK is built in Python and released via PyPI (https://pypi.org/project/biothings/). Its source code is hosted at its github repository (https://github.com/biothings/biothings.api).

Supplementary information
Supplementary data are available at Bioinformatics online.
Human Visual System Guided Reversible Data Hiding Based On Multiple Histograms Modification
Authors: Zhang Cheng , Ou Bo , Li Xiaolong , Xiong Jianqin 
Published: January 2022

AbstractIn this paper, we propose a human visual system (HVS) guided reversible data hiding method based on multiple histograms modification. The proposed method utilizes the texture features of an image to adaptively modify the pixels, for a lower HVS quality distortion. The HVS quality is taken as the optimization objective and a new expansion-bin-selection strategy is given to solve the optimization. For the same HVS quality distortion, the proposed method can embed more secret bits and give higher priority for the modifications in texture regions. Besides, a better optimization rule is proposed to accelerate the speed and then consider more available solutions. In this way, a trade-off between the embedding performance and time complexity can be achieved. Experimental results show that the proposed method can achieve a better HVS quality than the conventional methods.
Integrative analysis of the transcriptome and metabolome reveals the mechanism of saline–alkali stress tolerance in Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge.) Hsiao
Authors: Liu Jie , Zhang Xiongjie , Sheng Jinhua 
Published: January 2022

Abstract
Saline–alkali stress is a major abiotic stress affecting the quality and yield of crops. Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge.) Hsiao (Astragalus mongholicus (A. mongholicus)) is a well-known medicine food homology species with various pharmacological effects and health benefits that can grow well in saline–alkali soil. However, the molecular mechanisms underlying the adaptation of A. mongholicus plants to saline–alkali stress have not yet been clarified. Here, A. mongholicus plants were exposed to long-term saline–alkali stress (200 mmol·L–1 mixed saline–alkali solution), which limited the growth of A. mongholicus. The roots of A. mongholicus could resist long-term saline–alkali stress by increasing the activity of antioxidant enzymes and the content of osmolytes. Transcriptome analysis (via the Illumina platform) and metabolome analysis (via the Nexera UPLC Series QE Liquid Mass Coupling System) revealed that saline–alkali stress altered the activity of various metabolic pathways (e.g. amino acid metabolism, carbohydrate metabolism, lipid metabolism, and biosynthesis of other secondary metabolites). A total of 3690 differentially expressed genes (DEGs) and 997 differentially accumulated metabolites (DAMs) were identified in A. mongholicus roots under saline–alkali stress, and flavonoid-related DEGs and DAMs were significantly upregulated. Pearson correlation analysis revealed significant correlations between DEGs and DAMs related to flavonoid metabolism. MYB transcription factors might also contribute to the regulation of flavonoid biosynthesis. Overall, the results indicate that A. mongholicus plants adapt to saline–alkali stress by upregulating the biosynthesis of flavonoids, which enhances the medicinal value of A. mongholicus.
Peddling Atrocity
Authors: Pizzi Jeremy 
Published: January 2022

Abstract
The contribution of corporations to the commission of international crimes has been profound in effect, but largely understated in actual criminal prosecutions. While the ability of the International Criminal Court to hold corporations accountable remains the subject of debate, national jurisdictions can play an important role. Canada could be a notable player in this regard, with many registered businesses operating abroad and sometimes in circumstances potentially linked to human rights violations or international crimes. This article addresses Canada’s ability to hold such corporations accountable. It first establishes the applicability of corporate criminal responsibility for international crimes in Canada. As an illustrative case study, it then applies this framework to a major arms deal between a Canadian corporation and Saudi Arabia and considers the potential link to war crimes allegedly committed by Saudi forces in Yemen. The article confirms that corporations may in principle be held criminally responsible in Canada for international crimes committed by third parties abroad, and urges close scrutiny of such matters, including in Yemen.
Study protocol for JCOG1807C (DEEP OCEAN): a interventional prospective trial to evaluate the efficacy and safety of durvalumab before and after operation or durvalumab as maintenance therapy after chemoradiotherapy against superior sulcus non-small cell lung cancer
Authors: Aokage Keiju , Tsuboi Masahiro , Zenke Yoshitaka , Horinouchi Hidehito , Nakamura Naoki , Ishikura Satoshi , Nishikawa Hiroyoshi , Kumagai Shogo , Koyama Shohei , Kanato Keisuke , Kataoka Tomoko , Wakabayashi Masashi , Fukutani Miki , Fukuda Haruhiko , Ohe Yuichiro , Watanabe Shun-ichi ,   the Lung Cancer Surgical Study Group of the Japan Clinical Oncology Group
Published: January 2022

Abstract

Background
Superior sulcus tumours (SSTs) are relatively uncommon and one of the most intractable lung cancers among non-small cell lung cancer (NSCLC). We planned a multicenter, single-arm confirmatory trial of new multidisciplinary treatment using immune-checkpoint inhibitor. The aim is to evaluate the safety and efficacy of new multidisciplinary treatment with perioperative durvalumab after chemoradiotherapy (CRT).

Methods
The primary endpoint is 3-year overall survival. Patients receive induction CRT with sequential two courses of durvalumab, followed by surgical resection for resectable SST. The regimen for CRT is two courses of cisplatin and S-1, and concurrent radiotherapy (66 Gy/33 Fr). After surgery, 22 courses of post-operative durvalumab therapy are administered. For unresectable SST, an additional 22 courses of durvalumab are administered after induction durvalumab.

Results
In two cases as a safety cohort, the safety of intervention treatment up to 30 days after surgery was examined, and there were no special safety signals. Patient enrollment has now resumed in the main cohort.

Conclusions
The results of this study may contribute to the establishment of a new standard of care for SST, which is an intractable NSCLC.
Forensically Relevant Flesh Flies (Diptera, Sarcophagidae, Sarcophaginae) of Southern Brazil
Authors: Madeira-Ott Tais , Souza Carina M , Bunde Paulo R S , Ries Ana C R , Blochtein Betina , Thyssen Patricia J 
Published: January 2022

AbstractFlesh flies comprise a large fly family distributed worldwide that has great importance for forensic entomology. A robust and updated checklist of Sarcophaginae flies recorded in Southern Brazil is presented, based on material collected in the Rio Grande do Sul state and on a literature review. The forensic importance (high, moderate, or none) of the recorded flesh flies for estimating the postmortem interval (PMI) or inferring cases of neglect was determined based on their ecological habits. A total of 2,831 specimens representing 38 taxa were collected from three studies. Oxysarcodexia was the most abundant and species-rich genus in all three studies. Dexosarcophaga carvalhoi (Lopes) was registered for the first time in Southern Brazil. The checklist for Southern Brazil comprises 91 species distributed in 19 genera, with Oxysarcodexia, Peckia, and Lepidodexia representing the richest genera. Considering the importance of species for PMI estimation, 10, 42, and 39 species were classified as having high, moderate, or no forensic relevance, respectively. Moreover, five myiasis-causing sarcophagine flies recorded in Southern Brazil were considered to have the potential to reveal cases of neglect or mistreatment. This study revealed that Microcerella halli (Engel) and Peckia (Euboettcheria) australis (Townsend) are the most important species for PMI estimation in Southern Brazil, as they are often found breeding in corpses in this region.