bluuebunny/crossref_metadata_2025_split huggingface dataset:
RiceNCexp: a rice non-coding RNA co-expression atlas based on massive RNA-seq and small-RNA seq data
Authors: Zhang Baoyi , Fei Yuhan , Feng Jiejie , Zhu Xueai , Wang Rui , Xiao Hanqing , Zhang Hongsheng , Huang Ji 
Published: June 2022

AbstractNon-coding RNAs (ncRNAs) play important roles in regulating expression of protein-coding genes. Although gene expression databases have emerged in a timely manner, a comprehensive expression database for ncRNAs is still lacking. Herein, we constructed a rice ncRNA co-expression atlas (RiceNCexp), based on 491 RNA-seq and 274 small RNA (sRNA)-seq datasets. RiceNCexp hosts four types of ncRNAs, namely lncRNAs, PHAS genes, miRNAs, and phasiRNAs. RiceNCexp provides comprehensive expression information for rice ncRNAs in 22 tissues/organs, an efficient tau-based mining tool for tissue-specific ncRNAs, and the robust co-expression analysis among ncRNAs or between ncRNAs and protein-coding genes, based on 116 pairs of RNA-seq and sRNA-seq libraries from the same experiments. In summary, RiceNCexp is a user-friendly and comprehensive rice ncRNA co-expression atlas and can be freely accessed at https://cbi.njau.edu.cn/RiceNCexp/.
Structured Curricular Change Fails to Combat Resident Burnout
Authors: Halista Courtney E , Dalton Heather A , Thornton Jennifer A 
Published: June 2022

ABSTRACT

Introduction
During the 2020-2021 academic year, the Family Medicine (FM) faculty at David Grant USAF Medical Center (DGMC) incorporated Clinic First principles into the resident educational experience. The faculty hypothesized that these changes could improve symptoms of resident burnout.

Materials and Methods
The study was conducted at a single United States Air Force (USAF) FM residency program in California and was approved by the DGMC Institutional Review Board. The validated Maslach Burnout Inventory Human Services Survey for Medical Personnel was used to assess (1) emotional exhaustion, (2) depersonalization, and (3) personal achievement both prior to and following implementation of the Clinic First-inspired curriculum. Descriptive and inferential statistics were used to summarize the data.

Results
There were 25 eligible FM residents who participated in the study. At baseline, the mean scores on the Maslach Burnout Inventory Human Services Survey for Medical Personnel indicated moderate burnout across all 3 domains. There was a statistically significant difference (P = .03) in the mean EE score over time, demonstrating worsening exhaustion. There was no statistically significant difference (P = .37 and P = .08, respectively) in the mean DP or PA score over time.

Conclusions
Residents in the DGMC FM residency program were experiencing moderate burnout at the beginning of the 2020-2021 AY. Due to unforeseen challenges, the Clinic First initiative was not realized in its full potential, and the curriculum changes did not definitively protect against burnout. Further study is indicated.
The ALMA REBELS Survey: dust continuum detections at z &gt; 6.5
Authors: Inami Hanae , Algera Hiddo S B , Schouws Sander , Sommovigo Laura , Bouwens Rychard , Smit Renske , Stefanon Mauro , Bowler Rebecca A A , Endsley Ryan , Ferrara Andrea , Oesch Pascal , Stark Daniel , Aravena Manuel , Barrufet Laia , da Cunha Elisabete , Dayal Pratika , De Looze Ilse , Fudamoto Yoshinobu , Gonzalez Valentino , Graziani Luca , Hodge Jacqueline A , Hygate Alexander P S , Nanayakkara Themiya , Pallottini Andrea , Riechers Dominik A , Schneider Raffaella , Topping Michael , van der Werf Paul 
Published: June 2022

ABSTRACT
We report 18 dust continuum detections (≥3.3σ) at ∼88 and 158 $\mu{\rm m}$ out of 49 ultraviolet (UV)-bright galaxies (MUV &lt; −21.3 mag) at $z$ &gt; 6.5, observed by the Cycle-7 Atacama Large Millimeter/submillimeter Array (ALMA) Large Program, Reionization-Era Bright Emission Line Survey (REBELS) and its pilot programs. This has more than tripled the number of dust continuum detections known at $z$ &gt; 6.5. Out of these 18 detections, 12 are reported for the first time as part of REBELS. In addition, 15 of the dust continuum detected galaxies also show a [C ii]$_{\rm 158\,{\rm \mu m}}$ emission line, providing us with accurate redshifts. We anticipate more line emission detections from six targets (including three continuum detected targets) where observations are still ongoing. We estimate that all of the sources have an infrared (IR) luminosity (LIR) in a range of $3\!-\!8 \times 10^{11}\, {\rm L_\odot }$, except for one with $L_{\rm IR} = 1.5^{+0.8}_{-0.5} \times 10^{12}\, \, {\rm L_{\odot }}$. Their fraction of obscured star formation is significant at ${\gtrsim} 50{{\ \rm per\ cent}}$, despite being UV-selected galaxies. Some of the dust continuum detected galaxies show spatial offsets (∼0.5–1.5 arcsec) between the rest-UV and far-IR emission peaks. These separations could imply spatially decoupled phases of obscured and unobscured star formation, but a higher spatial resolution observation is required to confirm this. REBELS offers the best available statistical constraints on obscured star formation in UV-luminous galaxies at $z$ &gt; 6.5.
Search for OB associations in Gaia Early Data Release 3
Authors: Chemel Alexander A , de Grijs Richard , Glushkova Elena V , Dambis Andrey K 
Published: June 2022

ABSTRACT
The distribution of young stars into OB associations has long been in need of updating. High-precision Gaia Early Data Release 3 astrometry, coupled with modern machine-learning methods, allows this to be done. We have compiled a well-defined sample which includes OB stars and young open clusters (OCs), in total comprising about 47 700 objects. To break the sample down into groupings resembling associations, we applied the HDBSCAN* clustering algorithm. We used a Monte Carlo method to estimate the kinematic ages of the resulting clusters and the Student’s t-test to assess the significance of the linear correlations between proper motions and coordinates, indicating the presence of possible cluster expansion signatures. The ages of the majority of clusters demonstrating a general expansion at a 1σ confidence level are several tens of Myr, which is in agreement with the expected ages of OB associations. We found 32 OCs which turned out to be members of the resulting groupings; their ages are consistent with one another within the uncertainties. Comparison of the clusters thus obtained with the historical composition of OB associations in the literature shows a correspondence between their positions in the Galaxy but an apparent absence of good one-to-one stellar matches. Therefore, we suggest that the historical composition of OB associations needs to be revised.
OCT4 activates aSuv39h1-repressive antisense lncRNA to couple histone H3 Lysine 9 methylation to pluripotency
Authors: Bernard Laure D , Dubois Agnès , Heurtier Victor , Fischer Véronique , Gonzalez Inma , Chervova Almira , Tachtsidi Alexandra , Gil Noa , Owens Nick , Bates Lawrence E , Vandormael-Pournin Sandrine , Silva José C R , Ulitsky Igor , Cohen-Tannoudji Michel , Navarro Pablo 
Published: June 2022

AbstractHistone H3 Lysine 9 (H3K9) methylation, a characteristic mark of heterochromatin, is progressively implemented during development to contribute to cell fate restriction as differentiation proceeds. Accordingly, in undifferentiated and pluripotent mouse Embryonic Stem (ES) cells the global levels of H3K9 methylation are rather low and increase only upon differentiation. How global H3K9 methylation levels are coupled with the loss of pluripotency remains largely unknown. Here, we identify SUV39H1, a major H3K9 di- and tri-methylase, as an indirect target of the pluripotency network of Transcription Factors (TFs). We find that pluripotency TFs, principally OCT4, activate the expression of Suv39h1as, an antisense long non-coding RNA to Suv39h1. In turn, Suv39h1as downregulates Suv39h1 transcription in cis via a mechanism involving the modulation of the chromatin status of the locus. The targeted deletion of the Suv39h1as promoter region triggers increased SUV39H1 expression and H3K9me2 and H3K9me3 levels, affecting all heterochromatic regions, particularly peri-centromeric major satellites and retrotransposons. This increase in heterochromatinization efficiency leads to accelerated and more efficient commitment into differentiation. We report, therefore, a simple genetic circuitry coupling the genetic control of pluripotency with the global efficiency of H3K9 methylation associated with a major cell fate restriction, the irreversible loss of pluripotency.
Rationale, Strengths, and Limitations of Real-World Evidence in Oncology: A Canadian Review and Perspective
Authors: Azoulay Laurent 
Published: June 2022

AbstractRandomized controlled trials (RCTs) continue to be the basis for essential evidence regarding the efficacy of interventions such as cancer therapies. Limitations associated with RCT designs, including selective study populations, strict treatment regimens, and being time-limited, mean they do not provide complete information about an intervention’s safety or the applicability of the trial’s results to a wider range of patients seen in real-world clinical practice. For example, recent data from Alberta showed that almost 40% of patients in the province’s cancer registry would be trial-ineligible per common exclusion criteria. Real-world evidence (RWE) offers an opportunity to complement the RCT evidence base with this kind of information about safety and about use in wider patient populations. It is also increasingly recognized for being able to provide information about an intervention’s effectiveness and is considered by regulators as an important component of the evidence base in drug approvals. Here, we examine the limitations of RCTs in oncology research, review the different types of RWE available in this area, and discuss the strengths and limitations of RWE for complementing RCT oncology data.
Coronitic and Symplectitic Textures in Meta-Troctolite Reveal the Transition from Magmatism to Granulite-Facies Metamorphism in the Early Paleozoic Tongbai Orogen, Central China
Authors: Wang Tingting , Zheng Jianping , Scott James M , Ping Xianquan , Ma Qiang , Xiong Qing , Zhang Sai 
Published: June 2022

AbstractNewly discovered meta-troctolite enclaves in Early Paleozoic Huanggang diorite within dominantly meta-volcaniclastic greenschist to amphibolite facies Erlangping unit in central China extends the known extent of granulite-facies metamorphism in the Tongbai Orogen. Evidence for this granulite facies event is preserved in coronitic and symplectitic textures developed in the meta-troctolites enclaves. The primary assemblage comprises olivine and plagioclase with minor orthopyroxene, clinopyroxene, spinel and amphibole. The late magmatic stage comprising an orthopyroxene (Opx1) corona around olivine and clinopyroxene corona around spinel formed by reaction of cumulus and intercumulus phases with trapped melt at around 1040–1060°C near the solidus. During troctolite cooling, metamorphic solid-state replacement of primary olivine and plagioclase produced orthopyroxene (Opx1)/clinopyroxene (Cpx1) + vermicular spinel (Sp1) symplectite, followed by an inclusion-free amphibole (Amp1) layer surrounded by amphibole + spinel symplectite (Amp2 + Sp2). Microstructural, pseudosection and mineral isopleth analysis coupled with prominent compositional zoning in the Opx1 corona and chrome-rich spinel (Cr-Sp) suggests that the symplectites formed by diffusion-controlled solid-state replacement at the interface of reactant minerals, probably during cooling to granulite-facies conditions of ~820–880°C and 6.7–7.0 kbar. U–Pb dates of rare metamorphic zircon, as indicated by growth zonation and identification of metamorphic minerals enclosed in grains by Raman probe, are ca. 450 Ma. The reaction textures record the transition from late magmatic to granulite-facies metamorphism with the heat supplied by magma upwelling at the base of Erlangping arc triggered by extension of Erlangping back-arc.
Chain or sphere? Perspectives on colony shapes and sizes in microalgae
Authors: Wang Xiaodong , Tang Kam W 
Published: June 2022

Abstract
Some microalgal species can increase their collective size by forming colonies; notable examples are chained colonies in diatoms and Scenedesmus sp., and spherical colonies in Phaeocystis globosa. For a given cell-specific growth rate, chain formation increases collective length quickly to fend off ciliates, but not against tube- and pallium-feeding heterotrophic dinoflagellates or metazoan grazers with ability to manipulate chains to aid ingestion. Sphere increases in volume relatively slowly but would be difficult to manipulate even for metazoan grazers. Diffusive nutrient supply to a chained colony would be a fixed proportion of that to solitary cells, regardless of chain length, whereas cells within a spherical colony would experience increasing nutrient limitation with increasing colony size. One hemisphere of a spherical colony would inevitably receive less irradiance, creating an auto-light limitation. Experimental data showed that light decreased substantially as it passed through a P. globosa colony, and the optical density of the colony increased linearly with colony diameter. However, neither in situ nutrient nor light limitation alone can explain an order-of-magnitude difference in colony size between the European and the Asian P. globosa populations. Instead, some evidence of different expression of gene(s) involved in colony formation and enlargement suggests genomic variations among the different populations.
Multigenerational Effects of an Environmentally Relevant Phthalate Mixture on Reproductive Parameters and Ovarian miRNA Expression in Female Rats
Authors: Gonsioroski Andressa V , Aquino Ariana M , Alonso-Costa Luiz G , Barbisan Luis F , Scarano Wellerson R , Flaws Jodi A 
Published: June 2022

Abstract
Phthalates are endocrine-disrupting chemicals used in many consumer products. Our laboratory previously developed an environmentally relevant phthalate mixture consisting of 6 phthalates and found that it disrupted female fertility in mice. However, it was unknown if maternal exposure to the mixture affects reproductive parameters and ovarian post-transcription in the F1 and F2 generation of female rats. Thus, we tested the hypothesis that maternal exposure to the phthalate mixture affects folliculogenesis, steroidogenesis, and ovarian microRNA (miRNA) in the F1 and F2 generations of female rats. Pregnant female rats were divided into 4 groups and orally dosed daily from gestational day 10 to postnatal day 21 with corn oil (control group), 20 μg/kg/day, 200 μg/kg/day, or 200 mg/kg/day of the phthalate mixture. Maternal exposure to the phthalate mixture impaired folliculogenesis in the F1 and F2 generations of female rats and affected steroidogenesis in the F1 generation of female rats compared to control. Further, the phthalate mixture altered ovarian expression of some genes related to the cell cycle and steroidogenesis compared to control in the F1 and F2 generations of female rats. The mixture also increased ovarian expression of rno-mir-184 that is involved with the oocyte maturation process. Collectively, our data show that maternal exposure to the phthalate mixture affects folliculogenesis and steroidogenesis in the F1 and F2 generations of female rats and alters ovarian miRNA expression in the F1 generation of female rats.
Transcriptomic Identification of a Unique Set of Nodule-Specific Cysteine-Rich Peptides Expressed in the Nitrogen-Fixing Root Nodule of Astragalus sinicus
Authors: Wei Feng , Liu Yuan , Zhou Donglai , Zhao Wenlong , Chen Zhennan , Chen Dason , Li Youguo , Zhang Xue-Xian 
Published: June 2022

Legumes in the inverted repeat-lacking clade (IRLC) each produce a unique set of nodule-specific cysteine-rich (NCR) peptides, which act in concert to determine the terminal differentiation of nitrogen-fixing bacteroid. IRLC legumes differ greatly in their numbers of NCR and sequence diversity. This raises the significant question how bacteroid differentiation is collectively controlled by the specific NCR repertoire of an IRLC legume. Astragalus sinicus is an IRLC legume that forms indeterminate nodules with its microsymbiont Mesorhizobium huakuii 7653R. Here, we performed transcriptome analysis of root and nodule samples at 3, 7, 14, 28 days postinoculation with M. huakuii 7653R and its isogenic ∆ bacA mutant. BacA is a broad-specificity peptide transporter required for the host-derived NCRs to target rhizobial cells. A total of 167 NCRs were identified in the RNA transcripts. Comparative sequence and electrochemical analysis revealed that A. sinicus NCRs (AsNCRs) are dominated by a unique cationic group (termed subgroup C), whose mature portion is relatively long (>60 amino acids) and phylogenetically distinct and possessing six highly conserved cysteine residues. Subsequent functional characterization showed that a 7653R variant harboring AsNCR083 (a representative of subgroup C AsNCR) displayed significant growth inhibition in laboratory media and formed ineffective white nodules on A. sinicus with irregular symbiosomes. Finally, bacterial two-hybrid analysis led to the identification of GroEL1 and GroEL3 as the molecular targets of AsNCR067 and AsNCR076. Together, our data contribute to a systematic understanding of the NCR repertoire associated with the A. sinicus and M. huakuii symbiosis. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Scaling up preexposure prophylaxis to maximize HIV prevention impact
Authors: Grulich Andrew E. , Bavinton Benjamin R. 
Published: June 2022

Purpose of review
Ten years since the first regulatory approval of oral HIV preexposure prophylaxis (PrEP), this review summarizes PrEP uptake, the role of ambitious PrEP targets, emerging evidence of impact on the HIV epidemic and innovative approaches to increasing PrEP uptake.

Recent findings
PrEP uptake among people at risk of HIV has been slow, but has accelerated in recent years, particularly in gay and bisexual men in a limited number of high-income settings and recently in heterosexuals at risk of HIV in sub-Saharan Africa. However, UNAIDS 2020 PrEP targets and HIV prevention targets were missed by large margins. Although UNAIDS testing and treatment targets have galvanised public health action, in contras, PrEP targets have been lower profile and insufficiently ambitious. Parts of the USA, Australia and the UK with high PrEP coverage have demonstrated striking reductions in HIV infection at the population level, as PrEP is introduced at scale. Scaling up PrEP uptake will require innovations in PrEP promotion, simplified models of care, improved adherence interventions, improved choice in the form of longer-acting PrEP and interventions to ensure that all those who can benefit from PrEP can access it.

Summary
PrEP is a revolutionary HIV prevention tool, which if ambitiously scaled up could drive HIV transmission towards elimination. Highly publicized and ambitious PrEP targets could help drive this.
HIV drug resistance in various body compartments
Authors: van Zyl Gert U. , Dorfman Jeffrey R. , Kearney Mary F. 
Published: June 2022

Purpose of review
HIV drug resistance testing using blood plasma or dried blood spots forms part of international guidelines. However, as the clinical utility of assessing drug resistance in other body compartments is less well established, we review this for blood cells and samples from other body compartments.

Recent evidence
Although clinical benefit is not clear, drug resistance testing in blood cells is often performed when patients with suppressed plasma viral loads require a treatment substitution. In patients with HIV neurocognitive disease, cerebral spinal fluid (CSF) drug resistance is rarely discordant with plasma but has nevertheless been used to guide antiretroviral drug substitutions. Cases with HIV drug resistance in genital fluids have been documented but this does not appear to indicate transmission risk when blood plasma viral loads are suppressed.

Summary
Drug-resistant variants, which may be selected in tissues under conditions of variable adherence and drug penetration, appear to disseminate quickly, and become detectable in blood. This may explain why drug resistance discordance between plasma and these compartments is rarely found. Partial compartmentalization of HIV populations is well established for the CSF and the genital tract but other than blood plasma, evidence is lacking to support drug resistance testing in body compartments.
Transcriptomics of angiotensin II-induced long noncoding and coding RNAs in endothelial cells
Authors: Bu Shuhan , Nguyen Hien C. , Michels David C.R. , Rasheed Berk , Nikfarjam Sepideh , Singh Rohan , Wang Lynn , Patel Darshil A. , Singh Shweta , Qadura Mohammad , Singh Krishna K. 
Published: June 2022

Objective:
Angiotensin II (Ang II)-induced endothelial dysfunction plays an important role in the pathogenesis of cardiovascular diseases such as systemic hypertension, cardiac hypertrophy and atherosclerosis. Recently, long noncoding RNAs (lncRNAs) have been shown to play an essential role in the pathobiology of cardiovascular diseases; however, the effect of Ang II on lncRNAs and coding RNAs expression in endothelial cells has not been evaluated. Accordingly, we sought to evaluate the expression profiles of lncRNAs and coding RNAs in endothelial cells following treatment with Ang II.

Methods:
Human umbilical vein endothelial cells (HUVECs) were cultured and treated with Ang II (10−6 mol/l) for 24 h. The cells were then profiled for the expression of lncRNAs and mRNAs using the Arraystar Human lncRNA Expression Microarray V3.0.

Results:
In HUVECs following Ang II treatment, from a total of 30 584 lncRNA targets screened, 25 targets were significantly upregulated, while 69 were downregulated. In the same HUVECs samples, from 26 106 mRNA targets screened, 28 targets were significantly upregulated and 67 were downregulated. Of the differentially expressed lncRNAs, RP11-354P11.2 and RP11-360F5.1 were the most upregulated (11-fold) and downregulated (three-fold) lncRNAs, respectively. Assigning the differentially regulated genes into functional groups using bioinformatics reveals numerous genes involved in the nucleotide excision repair and ECM-receptor interaction.

Conclusion:
This is the first study to profile the Ang II-induced differentially expressed lncRNAs and mRNAs in human endothelial cells. Our results reveal novel targets and substantially extend the list of potential candidate genes involved in Ang II-induced endothelial dysfunction and cardiovascular diseases.