bluuebunny/crossref_metadata_2025_split huggingface dataset:
TCMPG: an integrative database for traditional Chinese medicine plant genomes
Authors: Meng Fanbo , Tang Qiang , Chu Tianzhe , Li Xianhai , Lin Yue , Song Xiaoming , Chen Wei 
Published: May 2022

Abstract
Because of their great therapeutic and economic value, medicinal plants have attracted increasing scientific attention. With the rapid development of high-throughput sequencing technology, the genomes of many medicinal plants have been sequenced. Storing and analyzing the increasing volume of genomic data has become an urgent task. To solve this challenge, we have proposed the Traditional Chinese Medicine Plant Genome database (TCMPG, http://cbcb.cdutcm.edu.cn/TCMPG/), an integrative database for storing the scattered genomes of medicinal plants. TCMPG currently includes 160 medicinal plants, 195 corresponding genomes, and 255 herbal medicines. Detailed information on plant species, genomes, and herbal medicines is also integrated into TCMPG. Popular genomic analysis tools are embedded in TCMPG to facilitate the systematic analysis of medicinal plants. These include BLAST for identifying orthologs from different plants, SSR Finder for identifying simple sequence repeats, JBrowse for browsing genomes, Synteny Viewer for displaying syntenic blocks between two genomes, and HmmSearch for identifying protein domains. TCMPG will be continuously updated by integrating new data and tools for comparative and functional genomic analysis.
DgbZIP3 interacts with DgbZIP2 to increase the expression ofDgPODfor cold stress tolerance in chrysanthemum
Authors: Bai Huiru , Liao Xiaoqin , Li Xin , Wang Bei , Luo Yunchen , Yang Xiaohan , Tian Yuchen , Zhang Lei , Zhang Fan , Pan Yuanzhi , Jiang Beibei , Jia Yin , Liu Qinglin 
Published: May 2022

AbstractThe bZIP transcription factor plays a very important role in abiotic stresses, e.g. drought, salt, and low-temperature stress, but the mechanism of action at low temperature is still unclear. In this study, overexpression of DgbZIP3 led to increased tolerance of chrysanthemum (Chrysanthemum morifolium Ramat.) to cold stress, whereas antisense suppression of DgbZIP3 resulted in decreased tolerance. Electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP), luciferase complementary imaging analysis (LCI), and dual-luciferase reporter gene detection (DLA) experiments indicated that DgbZIP3 directly bound to the promoter of DgPOD and activated its expression. DgbZIP2 was identified as a DgbZIP3-interacting protein using yeast two-hybrid, co-immunoprecipitation, LCI, and bimolecular fluorescence complementation assays. Overexpression of DgbZIP2 led to increased tolerance of chrysanthemum to cold stress, whereas antisense suppression of DgbZIP2 resulted in decreased tolerance. A ChIP–qPCR experiment showed that DgbZIP2 was highly enriched in the promoter of DgPOD, while DLA, EMSA, and LCI experiments further showed that DgbZIP2 could not directly regulate the expression of DgPOD. The above results show that DgbZIP3 interacts with DgbZIP2 to regulate the expression of DgPOD to promote an increase in peroxidase activity, thereby regulating the balance of reactive oxygen species and improving the tolerance of chrysanthemum to low-temperature stress.
Improved ginseng production under continuous cropping through soil health reinforcement and rhizosphere microbial manipulation with biochar: a field study ofPanax ginsengfrom Northeast China
Authors: Liu Cheng , Xia Rong , Tang Man , Chen Xue , Zhong Bin , Liu Xiaoyu , Bian Rongjun , Yang Li , Zheng Jufeng , Cheng Kun , Zhang Xuhui , Drosos Marios , Li Lianqing , Shan Shengdao , Joseph Stephen , Pan Genxing 
Published: May 2022

ABSTRACTThe production of ginseng, an important Chinese medicine crop, has been increasingly challenged by soil degradation and pathogenic disease under continuous cropping in Northeast China. In a field experiment, an Alfisol garden continuously cropped with Chinese ginseng (Panax ginseng C. A. Meyer) was treated with soil amendment at 20 t ha−1 with maize (MB) and wood (WB) biochar, respectively, compared to conventional manure compost (MC). Two years after the amendment, the rooted topsoil and ginseng plants were sampled. The changes in soil fertility and health, particularly in the soil microbial community and root disease incidence, and in ginseng growth and quality were portrayed using soil physico-chemical assays, biochemical assays of extracellular enzyme activities and gene sequencing assays as well as ginsenoside assays. Topsoil fertility was improved by 23% and 39%, ginseng root biomass increased by 25% and 27%, and root quality improved by 6% and 18% with WB and MB, respectively, compared to MC. In the ginseng rhizosphere, fungal abundance increased by 96% and 384%, with a significant and insignificant increase in bacterial abundance, respectively, under WB and MB. Specifically, the abundance of Fusarium spp. was significantly reduced by 19–35%, while that of Burkholderia spp. increased by folds under biochar amendments over MC. Relevantly, there was a significant decrease in the abundance proportion of pathotrophic fungi but a great increase in that of arbuscular mycorrhizal fungi, along with an enhanced microbial community network complexity, especially fungal community complexity, under biochar amendments. Thus, biochar, particularly from maize residue, could promote ginseng quality production while enhancing soil health and ecological services, including carbon sequestration, in continuously cropped fields.
Regulatory interaction of BcWRKY33A and BcHSFA4A promotes salt tolerance in non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]
Authors: Wang Huiyu , Li Zhubo , Ren Haibo , Zhang Changwei , Xiao Dong , Li Ying , Hou Xilin , Liu Tongkun 
Published: May 2022

Abstract
Salinity is a universal environmental stress that causes yield reduction in plants. WRKY33, which has been extensively studied in plant defense against necrotrophic pathogens, has recently been found to be important in salt-responsive pathways. However, the underlying molecular mechanisms controlling the involvement of WRKY33 in salt tolerance have not been fully characterized. Here, we explored the function of BcWRKY33A in non-heading Chinese cabbage (NHCC). Under salt stress, BcWRKY33A expression is significantly induced in roots. As a nuclear protein, BcWRKY33A has strong transcriptional activation activity. Overexpression of BcWRKY33A confers salt tolerance in Arabidopsis, whereas silencing of BcWRKY33A causes salt sensitivity in NHCC. Furthermore, BcHSFA4A, a protein that interacts with BcWRKY33A, could directly bind to the HSE motif within the promoters of BcZAT12 and BcHSP17.6A, which are involved in the plant response to salt stress. Finally, we found that BcWRKY33A could enhance the transcriptional activity of BcHSFA4A and affect its downstream genes (e.g. BcZAT12 and BcHSP17.6A), and co-overexpression of BcWRKY33A and BcHSFA4A could promote the expression of salt-related genes, suggesting that the regulatory interaction between BcWRKY33A and BcHSFA4A improves salt tolerance in plants. Overall, our results provide insight into the molecular framework of the BcWRKY33A-BcHSFA4A signaling pathway, which also aids in our understanding of the molecular mechanism of salt tolerance in plants.
Lessons From a Museum's Cabinet: DNA Barcoding and Collections-Based Life Stage Associations Reveals a Hidden Diversity in the Puerto Rican Bank Paedomorphic Lycidae (Coleoptera: Elateroidea: Leptolycini)
Authors: Ferreira Vinicius S , Ivie Michael A 
Published: May 2022

Abstract
The Leptolycini are a group of Lycidae endemic to the West Indies. Leptolycini adult females have been hypothesized to be extreme paedomorphic (i.e., larviform), however, females and larvae of the group are currently unknown. Here we provide the first association of adult male and immature life stages from the Puerto Rico using DNA barcoding, also collections-based associations and descriptions of immature Leptolycini and the first description of a paedomorphic female from the Virgin Islands. To carry out these life-stage associations we prepared an in-depth review of the Leptolycini fauna of the Puerto Rican bank (Puerto Rico and Virgin Islands). Several new taxa and taxonomic arrangements are proposed: Cessator crypticusnew species, Cessator tortolensisnew species, Cessator obrienorumnew species; Dracolycus chupacabranew genus and species, Dracolycus marshallinew species; Leptolycus falsoheterocornisnew species, and Leptolycus viensisnew species. Nanolycus gnomus Kazantsev is moved to Cessator gnomus (Kazantsev) new combination, rendering Nanolycus Kazantsev a new junior synonym of Cessator Kazantsev. The subgenus Baholycus Bocak is a new junior synonym of Leptolycus Leng and Mutchler. Leptolycus heterocornis var. flavicollis Leng and Mutchler is elevated to Leptolycus flavicollis Leng and Mutchler new status; Leptolycus (Leptolycus) albicauda Kazantsev is a new junior synonym of Leptolycus flavicollis Leng and Mutchler. An updated key to the adults and immature forms of Leptolycini from the Puerto Rican bank and a discussion on the importance of scientific collections in biodiversity studies is also provided.
High-z Sudoku: a diagnostic tool for identifying robust (sub)mm redshifts
Authors: Bakx Tom J L C , Dannerbauer Helmut 
Published: May 2022

ABSTRACT
We present methods to (i) graphically identify robust redshifts using emission lines in the (sub)mm regime, (ii) evaluate the capabilities of different (sub)mm practices for measuring spectroscopic redshifts, and (iii) optimize future (sub)mm observations towards increasing the fraction of robust redshifts. Using this publicly available code (https://github.com/tjlcbakx/redshift-search-graphs), we discuss scenarios where robust redshifts can be identified using both single- and multiple-line detections, as well as scenarios where the redshift remains ambiguous, even after the detection of multiple lines. Using the redshift distribution of (sub)mm samples, we quantify the efficiencies of various practices for measuring spectroscopic redshifts, including interferometers, as well as existing and future instruments specifically designed for redshift searches. Finally, we provide a method to optimize the observation strategy for future (sub)mm spectroscopic redshift searches with the Atacama Large Millimetre/submillimetre Array, where 2 mm proves indispensable for robust redshifts in the $\mathit{ z}$ = 2−4 region.
Starfall: a heavy rain of stars in ‘turning on’ AGN
Authors: McKernan B , Ford K E S , Cantiello M , Graham M , Jermyn A S , Leigh N W C , Ryu T , Stern D 
Published: May 2022

ABSTRACT
As active galactic nuclei (AGN) ‘turn on’, some stars end up embedded in accretion discs around supermassive black holes (SMBHs) on retrograde orbits. Such stars experience strong headwinds, aerodynamic drag, ablation, and orbital evolution on short time-scales. The loss of orbital angular momentum in the first ∼0.1 Myr of an AGN leads to a heavy rain of stars (‘starfall’) into the inner disc and on to the SMBH. A large AGN loss cone (θAGN, lc) can result from binary scatterings in the inner disc and yield tidal disruption events (TDEs). Signatures of starfall include optical/UV flares that rise in luminosity over time, particularly in the inner disc. If the SMBH mass is $M_{\rm SMBH} \gtrsim 10^{8}\, \mathrm{M}_{\odot }$, flares truncate abruptly and the star is swallowed. If $M_{\rm SMBH}\lt 10^{8}\, \mathrm{M}_{\odot }$, and if the infalling orbit lies within θAGN, lc, the flare is followed by a TDE that can be prograde or retrograde relative to the AGN inner disc. Retrograde AGN TDEs are overluminous and short-lived as in-plane ejecta collide with the inner disc and a lower AGN state follows. Prograde AGN TDEs add angular momentum to inner disc gas and so start off looking like regular TDEs but are followed by an AGN high state. Searches for such flare signatures test models of AGN ‘turn on’, SMBH mass, as well as disc properties and the embedded population.
Characteristics and evolution of Be-type high-mass X-ray binaries as potential ultraluminous X-ray sources
Authors: Karino Shigeyuki 
Published: May 2022

ABSTRACT
Some ultraluminous X-ray sources (ULXs) exhibit X-ray pulses, and their central sources are thought to be neutron stars. It has also been suggested that some are transient sources with Be-type donors. In this study, we use the mass accretion model of a Be-type high-mass X-ray binary (BeHMXB) to estimate the conditions under which a giant X-ray burst caused by a BeHMXB exceeds the Eddington luminosity. Moreover, we investigate the duration for which BeHMXBs can be observed as transient ULXs with bursts above the Eddington luminosity during binary evolutions. The results indicate that BeHMXBs could be ULXs for a typical duration of approximately 1 Myr. Comparisons with nearby observed BeHMXBs indicate that many binary systems have the potential to become ULXs during their evolution. Particularly, a BeHMXB system tends to become a ULX when the Be donor has a dense deccretion disc aligned with the orbital plane. Because BeHMXBs are very common objects and a significant number of them can become ULXs, we conclude that a reasonable fraction of the observed ULXs could consist of evolved BeHMXBs.
Lineage-specific insertions in T-box riboswitches modulate antibiotic binding and action
Authors: Giarimoglou Nikoleta , Kouvela Adamantia , Patsi Ioanna , Zhang Jinwei , Stamatopoulou Vassiliki , Stathopoulos Constantinos 
Published: May 2022

AbstractT-box riboswitches (T-boxes) are essential RNA regulatory elements with a remarkable structural diversity, especially among bacterial pathogens. In staphylococci, all glyS T-boxes synchronize glycine supply during synthesis of nascent polypeptides and cell wall formation and are characterized by a conserved and unique insertion in their antiterminator/terminator domain, termed stem Sa. Interestingly, in Staphylococcus aureus the stem Sa can accommodate binding of specific antibiotics, which in turn induce robust and diverse effects on T-box-mediated transcription. In the present study, domain swap mutagenesis and probing analysis were performed to decipher the role of stem Sa. Deletion of stem Sa significantly reduces both the S. aureus glyS T-box-mediated transcription readthrough levels and the ability to discriminate among tRNAGly isoacceptors, both in vitro and in vivo. Moreover, the deletion inverted the previously reported stimulatory effects of specific antibiotics. Interestingly, stem Sa insertion in the terminator/antiterminator domain of Geobacillus kaustophilus glyS T-box, which lacks this domain, resulted in elevated transcription in the presence of tigecycline and facilitated discrimination among proteinogenic and nonproteinogenic tRNAGly isoacceptors. Overall, stem Sa represents a lineage-specific structural feature required for efficient staphylococcal glyS T-box-mediated transcription and it could serve as a species-selective druggable target through its ability to modulate antibiotic binding.
Controllable Majorana vortex states in iron-based superconducting nanowires
Authors: Li Chuang , Luo Xun-Jiang , Chen Li , Liu Dong E , Zhang Fu-Chun , Liu Xin 
Published: May 2022

Abstract
To reveal the non-Abelian braiding statistics of Majorana zero modes (MZMs), it is crucial to design a Majorana platform, in which MZMs can be easily manipulated in a broad topological nontrivial parameter space. This is also an essential step to confirm their existence. In this study, we propose an iron-based superconducting nanowire system with Majorana vortex states to satisfy desirable conditions. This system has a radius-induced topological phase transition, giving a lower bound for the nanowire radius. In the topological phase, the iron-based superconducting nanowires have only one pair of MZMs over a wide range of radii, chemical potential and external magnetic fields. The wave function of MZMs has a sizable distribution at the side edge of the nanowires. This property enables the control of the interaction of MZMs in neighboring vortex nanowires and paves the way for Majorana fusion and braiding.
Preventing symptomatic vitamin D deficiency and rickets among Indigenous infants and children in Canada
Authors: Irvine James , Ward Leanne M 
Published: May 2022

Abstract
Vitamin D deficiency (VitDD) rickets and other manifestations of severe VitDD, such as cardiomyopathy and hypocalcemic seizures, continue to be diagnosed in Canada. Breastfed Indigenous infants, particularly those living in northern communities, are disproportionately impacted, although formula-fed infants are not exempt in cases where the mother’s vitamin D status is critically low. This statement deals with the prevention of rickets and hypocalcemia due to VitDD for Indigenous children, and revises an earlier document from the Canadian Paediatric Society. An assessment of the risk for VitDD is recommended for each maternal-infant dyad because of the link between maternal and infant VitDD. Along with supports for enhanced adherence, additional VitD supplementation is recommended for prenatal women and infants deemed at high risk and, in certain situations, intermittent higher dose supplementation may be required. Food insecurity can also contribute to rickets, so advocacy is required to prevent VitDD rickets in Indigenous children.
Can Laser-Assisted Indocyanine Green Angiography Be Used to Quantify Perfusion Changes During Staged Fixation of Pilon Fractures? A Pilot Study
Authors: Mitchell Brendon C. , Wall Pelle V. , Zak Taylor K. , Onodera Keenan M. , Gurusamy Pradyumna , Dwight Kathryn , Elsissy Joseph , Kent William T. 
Published: May 2022

Objective:
To quantify soft tissue perfusion changes in pilon fractures during staged treatment using laser-assisted indocyanine green angiography (LA-ICGA).

Setting:
Level 1 trauma center.

Design:
Prospective cohort study.

Patients/Participants:
Twelve patients with 12 pilon fractures participated in the study. Seven patients had OTA/AO classification of 43-C3, 3 had 43-C2, and 2 had 43-B2.

Main Outcome Measures:
LA-ICGA was performed with the SPY fluorescence imaging platform. Analysis via ImageJ was used to generate a fractional area of perfusion (FAP) based on fluorescent intensity to objectively quantify soft tissue perfusion. Anterior, medial, and lateral measurements were performed at the time of initial external fixation (EF) application and then at the time of definitive fixation.

Results:
FAP within the region of interest was on average 64% medially, 61% laterally, and 62% anteriorly immediately before EF placement. Immediately before definitive open reduction internal fixation, fractional region of interest perfusion was on average 86% medially, 87% laterally, and 86% anteriorly. FAP increased on average 24% medially (P = 0.0004), 26% laterally (P = 0.001), and 19% anteriorly (P = 0.002) from the time of initial EF to the time of definitive open reduction and internal fixation.

Conclusions:
Quantitative improvement in soft tissue perfusion was identified through the course of staged surgical management in pilon fractures. LA-ICGA potentially may be used to determine appropriate timing for definitive surgical intervention based on the readiness of the soft tissue envelope. Ultimately, these findings may influence clinical outcomes with respect to choice of surgical approach, soft tissue management, surgical timing, and wound healing.

Level of Evidence:
Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Detection of Hemodynamic Status Using an Analytic Based on an Electrocardiogram Lead Waveform
Authors: Schmitzberger Florian F. , Hall Ashley E. , Hughes Morgan E. , Belle Ashwin , Benson Bryce , Ward Kevin R. , Bassin Benjamin S. 
Published: May 2022

OBJECTIVES:
Delayed identification of hemodynamic deterioration remains a persistent issue for in-hospital patient care. Clinicians continue to rely on vital signs associated with tachycardia and hypotension to identify hemodynamically unstable patients. A novel, noninvasive technology, the Analytic for Hemodynamic Instability (AHI), uses only the continuous electrocardiogram (ECG) signal from a typical hospital multiparameter telemetry monitor to monitor hemodynamics. The intent of this study was to determine if AHI is able to predict hemodynamic instability without the need for continuous direct measurement of blood pressure.

DESIGN:
Retrospective cohort study.

SETTING:
Single quaternary care academic health system in Michigan.

PATIENTS:
Hospitalized adult patients between November 2019 and February 2020 undergoing continuous ECG and intra-arterial blood pressure monitoring in an intensive care setting.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
One million two hundred fifty-two thousand seven hundred forty-two 5-minute windows of the analytic output were analyzed from 597 consecutive adult patients. AHI outputs were compared with vital sign indications of hemodynamic instability (heart rate > 100 beats/min, systolic blood pressure < 90 mm Hg, and shock index of > 1) in the same window. The observed sensitivity and specificity of AHI were 96.9% and 79.0%, respectively, with an area under the curve (AUC) of 0.90 for heart rate and systolic blood pressure. For the shock index analysis, AHI’s sensitivity was 72.0% and specificity was 80.3% with an AUC of 0.81.

CONCLUSIONS:
The AHI-derived hemodynamic status appropriately detected the various gold standard indications of hemodynamic instability (hypotension, tachycardia and hypotension, and shock index > 1). AHI may provide continuous dynamic hemodynamic monitoring capabilities in patients who traditionally have intermittent static vital sign measurements.
TLR4 regulatory region variants reduce the susceptibility of small-cell lung cancer in Chinese population
Authors: Zhang Hongmei , Gao Hui , Li Ang , Wu Hongjiao , Xie Yuning , Zhang Zhi , Zhang Xuemei 
Published: May 2022

Objectives
Toll-like receptors (TLRs) participate in the induction and regulation of immune responses and are closely related to the occurrence and development of small-cell lung cancer (SCLC). This study aimed to investigate the impact of polymorphisms in the regulatory regions of TLRs on the susceptibility of SCLC.

Methods
The case–control study included 304 SCLC patients and 304 healthy controls. TLRs gene polymorphisms were genotyped by PCR-restrictive fragment length polymorphism analysis and TaqMan assay. Unconditional logistic regression was used to estimate odds ratio (OR) and its 95% confidence interval (95% CI).

Results
Our results showed that TLR4 rs1927914 GG genotype and TLR4 rs7869402 TT genotype reduced the risk of SCLC with OR (95% CI) of 0.54 (0.32–0.90) and 0.47 (0.28–0.80), respectively. Stratified analysis suggested that TLR4 rs1927914 GG genotypes significantly reduced the risk of SCLC among male (OR = 0.35; 95% CI, 0.18–0.69; P < 0.01), the younger patients (OR = 0.49; 95% CI, 0.26–0.94; P = 0.03) and non-drinkers (OR = 0.47; 95% CI, 0.24–0.89; P = 0.02). TLR4 rs7869402 CT or TT genotype significantly reduced the susceptibility to SCLC among male patients (OR = 0.37; 95% CI, 0.19–0.71, P < 0.01), the younger patients (OR = 0.41; 95% CI, 0.22–0.79; P < 0.01), smokers (OR = 0.25; 95% CI, 0.10–0.60; P < 0.01) and drinkers (OR = 0.31; 95% CI, 0.11–0.88; P = 0.03). TLR3 rs5743303, TLR4 rs11536891, TLR5 rs1640816 and TLR7 rs3853839 had no significant correlation with the risk of SCLC.

Conclusions
These findings emphasized the important role of TLR4 in the development of SCLC.