bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adiabatic energy change in the inner heliosheath: how does it affect the distribution of pickup protons and energetic neutral atom fluxes?
Authors: Baliukin I I , Izmodenov V V , Alexashov D B 
Published: August 2023

ABSTRACT
The hydrogen atoms penetrate the heliosphere from the local interstellar medium, and while being ionized, they form the population of pickup protons. The distribution of pickup protons is modified by the adiabatic heating (cooling) induced by the solar wind plasma compression (expansion). In this study, we emphasize the importance of the adiabatic energy change in the inner heliosheath that is usually either neglected or considered improperly. The effect of this process on the energy and spatial distributions of pickup protons and energetic neutral atoms (ENAs), which originate in the charge exchange of pickup protons, has been investigated and quantified using a kinetic model. The model employs the global distributions of plasma and hydrogen atoms in the heliosphere from the simulations of a kinetic-magnetohydrodynamic model of solar wind interaction with the local interstellar medium. The findings indicate that the adiabatic energy change is responsible for the broadening of the pickup proton velocity distribution and the significant enhancement of ENA fluxes (up to ∼5 and ∼20 times in the upwind and downwind directions at energies ∼1–2 keV for an observer at 1 au). It sheds light on the role of adiabatic energy change in explaining the discrepancies between the ENA flux observations and the results of numerical simulations.
Pyoderma gangrenosum after surgery for forefoot deformity in a patient with rheumatoid arthritis: A case report
Authors: Mori Yu , Izumiyama Takuya , Otsuka Kazuaki , Kanabuchi Ryuichi , Yamamoto Jun , Sekine Mana , Mori Naoko , Asano Yoshihide , Aizawa Toshimi 
Published: August 2023

ABSTRACT
Pyoderma gangrenosum (PG) is a rare inflammatory skin disease characterised by skin ulcers that are associated with autoimmune diseases. Although the effectiveness of immunosuppression with glucocorticoids and tumour necrosis factor inhibitors in treating PG has been reported, the utility of negative-pressure wound therapy (NPWT) for severe ulcerative lesions in patients with PG remains controversial. Herein, we report the case of a 76-year-old woman with rheumatoid arthritis who developed PG after undergoing surgery for a forefoot deformity. The patient showed improvement in deep ulcer lesions through NPWT while receiving treatment with abatacept and systemic glucocorticoids. Subsequent topical glucocorticoid therapy led to the remission of the PG. This case suggests that NPWT, when used under immunosuppressive conditions, does not exacerbate the pathergy and may be beneficial for treating severe ulcerative PG.
tRNA queuosine modification is involved in biofilm formation and virulence in bacteria
Authors: Díaz-Rullo Jorge , González-Pastor José Eduardo 
Published: August 2023

AbstracttRNA modifications are crucial for fine-tuning of protein translation. Queuosine (Q) modification of tRNAs is thought to modulate the translation rate of NAU codons, but its physiological role remains elusive. Therefore, we hypothesize that Q-tRNAs control those physiological processes involving NAU codon-enriched genes (Q-genes). Here, we report a novel bioinformatic strategy to predict Q-genes, revealing a widespread enrichment in functions, especially those related to biofilm formation and virulence in bacteria, and particularly in human pathogens. Indeed, we experimentally verified that these processes were significantly affected by altering the degree of tRNA Q-modification in different model bacteria, representing the first report of a general mechanism controlling biofilm formation and virulence in Gram-positive and Gram-negative bacteria possibly through the coordination of the expression of functionally related genes. Furthermore, we propose that changes in Q availability in a microbiome would affect its functionality. Our findings open the door to the control of bacterial infections and biofilm formation by inhibition of tRNA Q-modification.
RAP80 phase separation at DNA double-strand break promotes BRCA1 recruitment
Authors: Qin Caolitao , Wang Yun-Long , Zhou Jin-Ying , Shi Jie , Zhao Wan-Wen , Zhu Ya-Xi , Bai Shao-Mei , Feng Li-Li , Bie Shu-Ying , Zeng Bing , Zheng Jian , Zeng Guang-Dong , Feng Wei-Xing , Wan Xiang-Bo , Fan Xin-Juan 
Published: August 2023

Abstract
RAP80 has been characterized as a component of the BRCA1-A complex and is responsible for the recruitment of BRCA1 to DNA double-strand breaks (DSBs). However, we and others found that the recruitment of RAP80 and BRCA1 were not absolutely temporally synchronized, indicating that other mechanisms, apart from physical interaction, might be implicated. Recently, liquid–liquid phase separation (LLPS) has been characterized as a novel mechanism for the organization of key signaling molecules to drive their particular cellular functions. Here, we characterized that RAP80 LLPS at DSB was required for RAP80-mediated BRCA1 recruitment. Both cellular and in vitro experiments showed that RAP80 phase separated at DSB, which was ascribed to a highly disordered region (IDR) at its N-terminal. Meanwhile, the Lys63-linked poly-ubiquitin chains that quickly formed after DSBs occur, strongly enhanced RAP80 phase separation and were responsible for the induction of RAP80 condensation at the DSB site. Most importantly, abolishing the condensation of RAP80 significantly suppressed the formation of BRCA1 foci, encovering a pivotal role of RAP80 condensates in BRCA1 recruitment and radiosensitivity. Together, our study disclosed a new mechanism underlying RAP80-mediated BRCA1 recruitment, which provided new insight into the role of phase separation in DSB repair.
Translocating RNA polymerase generates R-loops at DNA double-strand breaks without any additional factors
Authors: Lim Gunhyoung , Hwang Seungha , Yu Kilwon , Kang Jin Young , Kang Changwon , Hohng Sungchul 
Published: August 2023

Abstract
The R-loops forming around DNA double-strand breaks (DSBs) within actively transcribed genes play a critical role in the DSB repair process. However, the mechanisms underlying R-loop formation at DSBs remain poorly understood, with diverse proposed models involving protein factors associated with RNA polymerase (RNAP) loading, pausing/backtracking or preexisting transcript RNA invasion. In this single-molecule study using Escherichia coli RNAP, we discovered that transcribing RNAP alone acts as a highly effective DSB sensor, responsible for generation of R-loops upon encountering downstream DSBs, without requiring any additional factors. The R-loop formation efficiency is greatly influenced by DNA end structures, ranging here from 2.8% to 73%, and notably higher on sticky ends with 3′ or 5′ single-stranded overhangs compared to blunt ends without any overhangs. The R-loops extend unidirectionally upstream from the DSB sites and can reach the transcription start site, interfering with ongoing-round transcription. Furthermore, the extended R-loops can persist and maintain their structures, effectively preventing the efficient initiation of subsequent transcription rounds. Our results are consistent with the bubble extension model rather than the 5′-end invasion model or the middle insertion model. These discoveries provide valuable insights into the initiation of DSB repair on transcription templates across bacteria, archaea and eukaryotes.
New twists of a TAIL: novel insights into the histone binding properties of a highly conserved PHD finger cluster within the MLR family of H3K4 mono-methyltransferases
Authors: Zraly Claudia B , Schultz Richard , Diaz Manuel O , Dingwall Andrew K 
Published: August 2023

Abstract
Enhancer activation by the MLR family of H3K4 mono-methyltransferases requires proper recognition of histones for the deposition of the mono-methyl mark. MLR proteins contain two clusters of PHD zinc finger domains implicated in chromatin regulation. The second cluster is the most highly conserved, preserved as an ancient three finger functional unit throughout evolution. Studies of the isolated 3rd PHD finger within this cluster suggested specificity for the H4 [aa16–20] tail region. We determined the histone binding properties of the full three PHD finger cluster b module (PHDb) from the Drosophila Cmi protein which revealed unexpected recognition of an extended region of H3. Importantly, the zinc finger spacer separating the first two PHDb fingers from the third is critical for proper alignment and coordination among fingers for maximal histone engagement. Human homologs, MLL3 and MLL4, also show conservation of H3 binding, expanding current views of histone recognition for this class of proteins. We further implicate chromatin remodeling by the SWI/SNF complex as a possible mechanism for the accessibility of PHDb to globular regions of histone H3 beyond the tail region. Our results suggest a two-tail histone recognition mechanism by the conserved PHDb domain involving a flexible hinge to promote interdomain coordination.
scPlantDB: a comprehensive database for exploring cell types and markers of plant cell atlases
Authors: He Zhaohui , Luo Yuting , Zhou Xinkai , Zhu Tao , Lan Yangming , Chen Dijun 
Published: August 2023

Abstract
Recent advancements in single-cell RNA sequencing (scRNA-seq) technology have enabled the comprehensive profiling of gene expression patterns at the single-cell level, offering unprecedented insights into cellular diversity and heterogeneity within plant tissues. In this study, we present a systematic approach to construct a plant single-cell database, scPlantDB, which is publicly available at https://biobigdata.nju.edu.cn/scplantdb. We integrated single-cell transcriptomic profiles from 67 high-quality datasets across 17 plant species, comprising approximately 2.5 million cells. The data underwent rigorous collection, manual curation, strict quality control and standardized processing from public databases. scPlantDB offers interactive visualization of gene expression at the single-cell level, facilitating the exploration of both single-dataset and multiple-dataset analyses. It enables systematic comparison and functional annotation of markers across diverse cell types and species while providing tools to identify and compare cell types based on these markers. In summary, scPlantDB serves as a comprehensive database for investigating cell types and markers within plant cell atlases. It is a valuable resource for the plant research community.
Evaluation of Feasibility and Acceptability of a Text-Messaging Intervention for Tobacco Cessation in India
Authors: Nadkarni Abhijit , Gaikwad Leena , Sequeira Miriam , Velleman Richard , D'souza Joseline , Hoble Ankita , Haldankar Rajanish , Murthy Pratima , Naughton Felix 
Published: August 2023

Abstract

Introduction
The aim of our study was to assess the feasibility and acceptability of a brief behavioral intervention for tobacco cessation delivered via mobile phone text messaging in India.

Aims and Methods
We conducted an uncontrolled intervention cohort study in adult current users of tobacco. The participants received intervention messages on their mobile phones for eight weeks. We collected qualitative data about participants’ perceptions of intervention delivery and receipt, acceptability, and feasibility of the intervention. The outcomes measured at 3 months post-recruitment were self-reported 7- and 28-day point-prevalence abstinence, and Alcohol, Smoking, and Substance Involvement Screening Test (ASSIST) risk categories for tobacco—low (0–3), moderate (4–26), and high (≥27).

Results
We recruited 26 eligible participants, and 22 completed the outcome assessments. The participants generally perceived the intervention content to be simple to access and useful in facilitating a change in tobacco use. None of the participants indicated that they wanted to discontinue receiving the intervention messages. Some suggestions for enhancing acceptability included supplementing text messaging with more intensive counseling and the use of multimedia content. Eighteen percent of participants reported abstinence in the past 7 and 28 days. A greater proportion of those who used smokeless tobacco were abstinent at follow-up compared to those who smoked (42.9% vs. 6.7%; p = .04).

Conclusions
If effective, simple and low-cost mobile phone text messaging can be used to deliver interventions for tobacco use, and has the potential to be scaled up so it can be delivered to populations of smokers interested in receiving cessation support.

Implications
Our study is an important step towards the development of a contextually relevant intervention suited for low- and middle-income countries and which is responsive to the needs of both those who use smoked and smokeless tobacco. If found to be effective, our intervention would be a scalable solution to overcome the human resource related barrier to accessing tobacco cessation services in low resource settings.
MITOGEN-ACTIVATED PROTEIN KINASE3 enhances disease resistance of edr1 mutants by phosphorylating MAPKKK5
Authors: Wang Wei , Chen Shuling , Zhong Guitao , Gao Chenyang , Zhang Qin , Tang Dingzhong 
Published: August 2023

Abstract
Mitogen-activated protein kinase (MAPK/MPK) cascades are key signaling modules that regulate plant immunity. ENHANCED DISEASE RESISTANCE1 (EDR1) encodes a Raf-like MAPK kinase kinase (MAPKKK) that negatively regulates plant defense in Arabidopsis (Arabidopsis thaliana). The enhanced resistance of edr1 requires MAPK KINASE4 (MKK4), MKK5, and MPK3. Although the edr1 mutant displays higher MPK3/6 activation, the mechanism by which plants increase MAPK cascade activation remains elusive. Our previous study showed that MAPKKK5 is phosphorylated at the Ser-90 residue in edr1 mutants. In this study, we demonstrated that the enhanced disease resistance of edr1 required MAPKKK5. Phospho-dead MAPKKK5S90A partially impaired the resistance of edr1, and the expression of phospho-mimetic MAPKKK5S90D in mapkkk5-2 resulted in enhanced resistance to the powdery mildew Golovinomyces cichoracearum strain UCSC1 and the bacterial pathogen Pseudomonas syringae pv. tomato (Pto) strain DC3000. Thus, Ser-90 phosphorylation in MAPKKK5 appears to play a crucial role in disease resistance. However, MAPKKK5-triggered cell death was not suppressed by EDR1. Furthermore, activated MPK3 phosphorylated the N terminus of MAPKKK5, and Ser-90 was one of the phosphorylated sites. Ser-90 phosphorylation increased MAPKKK5 stability, and EDR1 might negatively regulate MAPK cascade activation by suppressing the MPK3-mediated feedback regulation of MAPKKK5. Taken together, these results indicate that MPK3 phosphorylates MAPKKK5 to enhance MAPK cascade activation and disease resistance in edr1 mutants.
Synthetic Communities Increase Microbial Diversity and Productivity of Agave tequilana Plants in the Field
Authors: Flores-Núñez Víctor M. , Camarena-Pozos David A. , Chávez-González J. Daniel , Alcalde-Vázquez Raúl , Vázquez-Sánchez M. Nélida , Hernández-Melgar Alan G. , Xool-Tamayo Jorge , Moreno-Ulloa Aldo , Martínez Laila P. Partida 
Published: August 2023

Agaves are plants native to North America that sustain life in arid and semiarid ecosystems. Previous studies revealed that cultivated plants of Agave tequilana had lower microbial diversity and functionality than wild Agave species. Here, we tested if synthetic communities (syncoms), based on microbial hubs or taxa with enriched microbial functions, could increase microbial diversity, plant health, and productivity in A. tequilana. We applied 10 syncoms to the phyllospheres of 6-month-old plants of A. tequilana in the field and monitored their development for 2 years. Amplicon sequencing of 16S-rRNA-V4 and ITS2 revealed that the inoculated syncoms played a negligible or minor role in the assembly of the prokaryotic and eukaryotic phyllospheric communities associated with A. tequilana, respectively. However, syncoms based on microbial hubs, particularly those observed in the phyllosphere associated with wild A. salmiana (PFCS), promoted microbial communities with higher alpha diversity. Some of these syncom-derived phyllospheric communities consumed a greater variety of carbon sources; had more complex co-occurrence networks; and increased the content of sugars (oBrix, a measure of productivity in agaves) in the stem and changed the leaf metabolome. Our work demonstrates that the application of syncoms formulated based on predicted microbe–microbe interactions and metagenomic analyses of microbial communities in cultivated and wild plant species represents an effective tool to improve the sustainability and productivity of crops in arid ecosystems. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Development of a qPCR Assay for Species-Specific Detection of the Tar Spot Pathogen Phyllachora maydis
Authors: Roggenkamp Emily M. , Check Jill C. , Biswal Akshaya K. , Floyd Crystal M. , Miles Laura A. , Nicolli Camila P. , Shim Sujoung , Salgado-Salazar Catalina , Alakonya Amos E. , Malvick Dean K. , Smith Damon L. , Telenko Darcy E. P. , Chilvers Martin I. 
Published: August 2023

Phyllachora maydis is a fungal plant pathogen that causes tar spot of corn ( Zea mays) in North and South America, causing devastating yield losses under favorable conditions. Although the causal agent is relatively easy to diagnose via macroscopic and microscopic observations, other diseases and conditions, such as insect frass, have been mistaken for tar spot of corn. Furthermore, conidia and ascospores in isolation can be difficult to visually distinguish from other fungi, and the development of signs and symptoms of the disease may not be observed until 12 to 20 days after infection. Therefore, we developed a TaqMan quantitative polymerase chain reaction (qPCR) assay for the detection and quantification of this pathogen to be used for diagnostics and airborne spore quantification. The assay was designed for the internal transcribed spacer region of P. maydis. The specificity of the assay was confirmed and tested against various nontarget Phyllachora species, corn pathogens, endophytes, and P. maydis samples from several states in the Midwest and from Mexico. The detection limit of this assay was determined to be 100 fg of genomic P. maydis DNA. To demonstrate the transferability of this technology, the assay was tested in different labs using various qPCR thermal cyclers. This assay can be used in downstream research involving latency period, disease prediction, and diagnostics. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Parental leave, childcare policies, and workplace bias for hepatology professionals: A national survey
Authors: Feld Lauren D. , Sarkar Monika , Au Jennifer S. , Flemming Jennifer A. , Gripshover Janet , Kardashian Ani , Muir Andrew J. , Nephew Lauren , Orloff Susan L. , Terrault Norah , Rabinowitz Loren , Volerman Anna , Arora Vineet , Farnan Jeanne , Villa Erica 
Published: August 2023

Background:
The presence of workplace bias around child-rearing and inadequate parental leave may negatively impact childbearing decisions and sex equity in hepatology. This study aimed to understand the influence of parental leave and child-rearing on career advancement in hepatology.

Methods:
A cross-sectional survey of physician members of the American Association for the Study of Liver Diseases (AASLD) was distributed through email listserv in January 2021. The 33-item survey included demographic questions, questions about bias, altering training, career plans, family planning, parental leave, and work accommodations.

Results:
Among 199 US physician respondents, 65.3% were women, and 83.4% (n = 166) were attendings. Sex and racial differences were reported in several domains, including paid leave, perceptions of bias, and child-rearing. Most women (79.3%) took fewer than the recommended 12 paid weeks of parental leave for their first child (average paid leave 7.5 wk for women and 1.7 for men). A majority (75.2%) of women reported workplace discrimination, including 83.3% of Black and 62.5% of Hispanic women. Twenty percent of women were asked about their/their partners’ pregnancy intentions or child-rearing plans during interviews for training. Women were more likely to alter career plans due to child-rearing (30.0% vs. 15.9%, p = 0.030). Women were also more likely to delay having children than men (69.5% vs.35.9%).

Conclusions:
Women reported sex and maternity bias in the workplace and during training interviews, which was more frequently experienced by Black and Hispanic women. As two-thirds of women had children during training, it is a particularly influential time to reevaluate programmatic support to address long-term gender disparities in career advancement.
Clinical Neurology in Practice
Authors: Mathis Stéphane , Solé Guilhem , Damon-Perrière Nathalie , Rouanet-Larrivière Marie , Duval Fanny , Prigent Julia , Nadal Louis , Péréon Yann , Le Masson Gwendal 
Published: August 2023

Background:
The tongue is an essential organ for the development of certain crucial functions, such as swallowing and language. The examination of the tongue can be very useful in neurology, as the various types of lingual alterations can lead to certain specific diagnoses, the tongue being a kind of “mirror” of some neurological function.

Review Summary:
In this study, we reviewed the literature on anatomy, physiology, and the various aspects of the examination of the tongue.

Conclusions:
Examination of the tongue should be an integral part of the clinical examination of the cranial nerves. This study aimed to demonstrate the importance of tongue motor and non-motor functions in neurological practice.
Thrombolysis Versus Nonthrombolyzed in Patients With Mild Strokes and Large Vessel Occlusions
Authors: Luo Xintong , Huo Tiantian , Cao Pengkai , Zhao Jingru , Zhang Yue , Tan Guojun 
Published: August 2023

Background
The safety and efficacy of intravenous thrombolysis (IVT) in acute ischemic stroke patients with large vessel occlusions and mild neurological deficits are controversial.

Methods:
Data of stroke patients presenting with mild initial stroke, which was defined as the National Institutes of Health Stroke Scale score (NIHSS) ≤5 and large vessel occlusion, were extracted from a large provincewide stroke registry.

Results:
A total of 619 IVT and 2170 non-IVT patients were identified in this study. IVT patients had higher rates of favorable functional outcome Modified Rankin Scale(mRS) ≤1 (74.6% vs. 70.6%; P=0.047), lower mRS scores (1 vs. 1, P=0.001), and higher NIHSS score decreased (1 vs. 0, P<0.001) at discharge compared with the non-IVT patients. The rates were similar in symptomatic intracranial hemorrhage (2.1% vs. 2.0%, P=0.853), severe systemic bleeding (0.8% vs. 0.6%, P=0.474), and mortality at discharge (0.2% vs. 0.2%, P=0.906) between the 2 groups. A multiple Logistic regression model found that age above 80 years [adjusted OR (aOR) 2.056 (95% CI, 1.125 to 3.756)], history of stroke [aOR 1.577 (95% CI, 1.303 to 1.910)], hyperlipidemia [aOR 2.156 (95% CI, 1.059 to 4.388)], high admission NIHSS score [aOR 1.564 (95% CI, 1.473 to 1.611)], and non-IVT [aOR 1.667 (95% CI, 1.337 to 2.077)] were independent risk factors for mRS >1.

Conclusions:
IVT administration is safe and effective in eligible acute ischemic stroke patients. Age above 80 years, with a history of stroke and hyperlipidemia, high admission NIHSS score, and non-IVT were independent risk factors for mRS >1 at discharge in these patients.