bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular basis for cell-wall recycling regulation by transcriptional repressor MurR in Escherichia coli
Authors: Zhang Ya , Chen Weizhong , Wu Di , Liu Yushi , Wu Zhaowei , Li Jian , Zhang Shu-Yu , Ji Quanjiang 
Published: May 2022

Abstract
The cell-wall recycling process is important for bacterial survival in nutrient-limited conditions and, in certain cases, is directly involved in antibiotic resistance. In the sophisticated cell-wall recycling process in Escherichia coli, the transcriptional repressor MurR controls the expression of murP and murQ, which are involved in transporting and metabolizing N-acetylmuramic acid (MurNAc), generating N-acetylmuramic acid-6-phosphate (MurNAc-6-P) and N-acetylglucosamine-6-phosphate (GlcNAc-6-P). Here, we report that both MurNAc-6-P and GlcNAc-6-P can bind to MurR and weaken the DNA binding ability of MurR. Structural characterizations of MurR in complex with MurNAc-6-P or GlcNAc-6-P as well as in the apo form revealed the detailed ligand recognition chemistries. Further studies showed that only MurNAc-6-P, but not GlcNAc-6-P, is capable of derepressing the expression of murQP controlled by MurR in cells and clarified the substrate specificity through the identification of key residues responsible for ligand binding in the complex structures. In summary, this study deciphered the molecular mechanism of the cell wall recycling process regulated by MurR in E. coli.
Twisting DNA by salt
Authors: Cruz-León Sergio , Vanderlinden Willem , Müller Peter , Forster Tobias , Staudt Georgina , Lin Yi-Yun , Lipfert Jan , Schwierz Nadine 
Published: May 2022

Abstract
The structure and properties of DNA depend on the environment, in particular the ion atmosphere. Here, we investigate how DNA twist -one of the central properties of DNA- changes with concentration and identity of the surrounding ions. To resolve how cations influence the twist, we combine single-molecule magnetic tweezer experiments and extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali and divalent alkaline earth cations. First, DNA twist increases monotonously with increasing concentration for all ions investigated. Second, for a given salt concentration, DNA twist strongly depends on cation identity. At 100 mM concentration, DNA twist increases as Na+ &lt; K+ &lt; Rb+ &lt; Ba2+ &lt; Li+ ≈ Cs+ &lt; Sr2+ &lt; Mg2+ &lt; Ca2+. Our molecular dynamics simulations reveal that preferential binding of the cations to the DNA backbone or the nucleobases has opposing effects on DNA twist and provides the microscopic explanation of the observed ion specificity. However, the simulations also reveal shortcomings of existing force field parameters for Cs+ and Sr2+. The comprehensive view gained from our combined approach provides a foundation for understanding and predicting cation-induced structural changes both in nature and in DNA nanotechnology.
Association of serum potassium with decline in residual kidney function in incident hemodialysis patients
Authors: Arif Yousif , Wenziger Cachet , Hsiung Jui Ting , Edward Amanda , Lau Wei Ling , Hanna Ramy M , Lee Yuji , Obi Yoshitsugu , Kovesdy Csaba P , Kalantar-Zadeh Kamyar , Streja Elani 
Published: May 2022

ABSTRACT

Background
Hyperkalemia is associated with kidney function decline in patients with non-dialysis dependent chronic kidney disease, but this relationship is unclear for residual kidney function (RKF) among hemodialysis (HD) patients.

Methods
We conducted a retrospective cohort study of 6655 patients, who started HD January 2007 and December 2011 and who had data on renal urea clearance (KRU). Serum potassium levels were stratified into four groups (i.e. ≤4.0, &gt;4.0 to ≤4.5, &gt;4.5 to ≤5.0 and &gt;5.0 mEq/L) and 1-year KRU slope for each group was estimated by a linear mixed-effects model.

Results
Higher serum potassium was associated with a greater decline in KRU, and the greatest decrease in KRU (–0.20, 95% confidence interval –0.50 to –0.06) was observed for baseline potassium &gt;5.0 mEq/L in the fully adjusted model. Mediation analysis showed that KRU slope mediated 1.78% of the association between serum potassium and mortality.

Conclusions
Hyperkalemia is associated with a decline in RKF amongst incident HD patients. These findings may have important clinical implications in the management of hyperkalemia in advanced CKD if confirmed in additional clinical trials.
Unraveling templated-regulated distribution of isolated SiO4 tetrahedra in silicoaluminophosphate zeolites with high-throughput computations
Authors: Li Yan , Shi Chao , Li Lin , Yang Guoju , Li Junyan , Xu Jun , Gu Qinfen , Wang Xingxing , Han Ji , Zhang Tianjun , Li Yi , Yu Jihong 
Published: May 2022

Abstract
Silicoaluminophosphate (SAPO) zeolites are well-known catalytic materials because of the mild acidity originating from the isolated SiO4 tetrahedra in their frameworks. Regulating the distribution of isolated SiO4 tetrahedra in SAPO zeolites is formidably challenging because SiO4 tetrahedra tend to agglomerate to form Si islands and the isolated SiO4 tetrahedra are difficult to determine using conventional characterization techniques. Here we synthesized Si-island-free SAPO-35 zeolites by using N-methylpiperidine as a new template, which exhibited excellent thermal stability compared to conventional SAPO-35 zeolites and a substantially improved methanol-to-olefins catalytic lifetime even comparable to that of commercial SAPO-34 zeolites. More strikingly, with the aid of high-throughput computations on 44 697 structure models combined with various state-of-the-art characterization techniques, for the first time, we reveal that the host–guest interactions between template molecules and SAPO frameworks determine the specific distributions of isolated SiO4 tetrahedra, which are responsible for the improvement in the chemical properties of zeolites. Our work provides an insight into the template-based regulation of isolated SiO4 tetrahedra in SAPO zeolites, which opens a new avenue in the discovery of promising zeolite catalysts with optimal SiO4 distribution.
Multiwavelength observations of the black hole X-ray binary MAXI J1820+070 in the rebrightening phase
Authors: Yoshitake Tomohiro , Shidatsu Megumi , Ueda Yoshihiro , Mineshige Shin , Murata Katsuhiro L , Adachi Ryo , Maehara Hiroyuki , Nogami Daisaku , Negoro Hitoshi , Kawai Nobuyuki , Niwano Masafumi , Hosokawa Ryohei , Saito Tomoki , Oasa Yumiko , Takarada Takuya , Shigeyoshi Takumi ,   OISTER Collaboration
Published: May 2022

Abstract
We report the results of quasi-simultaneous multiwavelength (near-infrared, optical, UV, and X-ray) observations of the Galactic X-ray black hole binary MAXI J1820+070 performed in 2019 May 10–13, ∼60 d after the onset of the first rebrightening phase. It showed a much larger optical-to-X-ray luminosity ratio (∼8) than in the initial outburst epoch. The primary components of the spectral energy distribution (SED) can be best interpreted by a radiatively inefficient accretion flow (RIAF) spectrum showing a luminosity peak in the optical band. By comparison with theoretical calculations, we estimate the mass accretion rate to be $\dot{M}/(8 L_{\rm Edd}/c^2) \sim 10^{-3}$, where c is the light speed and LEdd is the Eddington luminosity. In addition to the RIAF emission, a blue power-law component is detected in the optical–UV SED, which is most likely synchrotron radiation from the jet. The optical spectrum taken at the Seimei telescope shows a weak and narrow Hα emission line, the emitting region of which is constrained to be ≳2 × 104 times the gravitational radius. We suggest that the entire disk structure cannot be described by a single RIAF solution but cooler material responsible for the Hα emission must exist at the outermost region.
A serine-rich effector from the stripe rust pathogen targets a Raf-like kinase to suppress host immunity
Authors: Wan Cuiping , Liu Yan , Tian Shuxin , Guo Jia , Bai Xingxuan , Zhu Haochuan , Kang Zhensheng , Guo Jun 
Published: May 2022

Abstract
Puccinia striiformis f. sp. tritici (Pst) is an important obligate pathogen in wheat (Triticum aestivum L.) and secretes effectors into plant cells to promote infection. Identifying host targets of effector proteins and clarifying their roles in pathogen infection is essential for understanding pathogen virulence. In this study, we identified a serine-rich effector, Pst27791, from Pst that suppresses cell death in Nicotiana benthamiana. Stable overexpression of Pst27791 in wheat suppressed reactive oxygen species accumulation and the salicylic acid-dependent defense response. Transgenic wheat expressing the RNA interference construct of Pst27791 exhibited high resistance to Pst virulent isolate CYR31, indicating its importance in pathogenesis. Pst27791 interacting with wheat rapidly accelerated fibrosarcoma (Raf)-like kinase TaRaf46 in yeast and in planta. Knocking down TaRaf46 expression in wheat attenuated Pst infection and increased wheat immunity. The overexpression of TaRaf46 decreased wheat resistance to Pst and repressed MAPK activation in wheat. Pst27791 may stabilize TaRaf46 through the inhibition of proteasome-mediated degradation in N. benthamiana. The ability of Pst27791 to enhance Pst colonization was compromised when TaRaf46 was silenced, suggesting that the virulence of Pst27791 is mediated by TaRaf46. Overall, these results indicate that Raf-like kinase TaRaf46 is exploited by the Pst effector as a negative regulator of plant immunity to promote infection in wheat.
Heat shock-induced failure of meiosis I to meiosis II transition leads to 2n pollen formation in a woody plant
Authors: Zhou Qing , Cheng Xuetong , Kong Bo , Zhao Yifan , Li Zhiqun , Sang Yaru , Wu Jian , Zhang Pingdong 
Published: May 2022

Abstract
The formation of diploid gametes through chromosome doubling is a major mechanism of polyploidization, diversification, and speciation in plants. Unfavorable climate conditions can induce or stimulate the production of diploid gametes during meiosis. Here, we demonstrated that heat shock stress (38°C for 3 or 6 h) induced 2n pollen formation, and we generated 42 triploids derived from heat shock-induced 2n pollen of Populus canescens. Meiotic analysis of treated pollen mother cells revealed that induced 2n pollen originated from the complete loss of meiosis II (MII). Among the 42 triploids, 38 triploids derived from second division restitution (SDR)-type 2n pollen and 4 triploids derived from first division restitution-type 2n pollen were verified using simple sequence repeats (SSR) molecular markers. Twenty-two differentially expressed genes related to the cell cycle were identified and characterized by expression profile analysis. Among them was POPTR_0002s08020g (PtCYCA1;2), which encodes a type A Cyclin CYCA1;2 that is required for the meiosis I (MI) to MII transition. After male flower buds were exposed to heat shock, a significant reduction was detected in PtCYCA1;2 expression. We inferred that the failure of MI-to-MII transitions might be associated with downregulated expression of PtCYCA1;2, leading to the formation of SDR-type 2n pollen. Our findings provide insights into mechanisms of heat shock-induced 2n pollen formation in a woody plant and verify that sensitivity to environmental stress has evolutionary importance in terms of polyploidization.
Pit characters determine drought-induced embolism resistance of leaf xylem across 18 Neotropical tree species
Authors: Levionnois Sébastien , Kaack Lucian , Heuret Patrick , Abel Nina , Ziegler Camille , Coste Sabrina , Stahl Clément , Jansen Steven 
Published: May 2022

Abstract
Embolism spreading in xylem is an important component of plant drought resistance. Since embolism resistance has been shown to be mechanistically linked to pit membrane characters in stem xylem, we speculate that similar mechanisms account for leaf xylem. We conducted transmission electron microscopy to investigate pit membrane characters in leaf xylem across 18 Neotropical tree species. We also conducted gold perfusion and polar lipid detection experiments on three species covering the full range of leaf embolism resistance. We then related these observations to previously published data on embolism resistance of leaf xylem. We also incorporated previously published data on stem embolism resistance and stem xylem pit membranes to investigate the link between vulnerability segmentation (i.e. difference in embolism resistance) and leaf–stem anatomical variation. Maximum pit membrane thickness (Tpm,max) and the pit membrane thickness-to-diameter ratio (Tpm,max/Dpm) were predictive of leaf embolism resistance, especially when vestured pits were taken into account. Variation in Tpm,max/Dpm was the only trait predictive of vulnerability segmentation between leaves and stems. Gold particles of 5- and 10-nm infiltrated pit membranes in three species, while the entry of 50-nm particles was blocked. Moreover, polar lipids were associated with inner conduit walls and pits. Our results suggest that mechanisms related to embolism spreading are determined by Tpm, pore constrictions (i.e. the narrowest bottlenecks along pore pathways), and lipid surfactants, which are largely similar between leaf and stem xylem and between temperate and tropical trees. However, our mechanistic understanding of embolism propagation and the functional relevance of Tpm,max/Dpm remains elusive.
Tax Policy and Lumpy Investment Behaviour: Evidence from China’s VAT Reform
Authors: Chen Zhao , Jiang Xian , Liu Zhikuo , Serrato Juan Carlos Suárez , Xu Daniel Yi 
Published: May 2022

AbstractWe incorporate the lumpy nature of firm-level investment into the study of how tax policy affects investment behaviour. We show that tax policies can directly impact the lumpiness of investment. Extensive-margin responses to tax policy are key to understanding the effects of different tax reforms and to designing effective stimulus policies. We illustrate these results by studying China’s 2009 VAT reform, which lowered the tax cost of investment and reduced partial irreversibility—the price gap between new and used capital. Using comprehensive tax survey data and a difference-in-differences design, we estimate a 36$\%$ relative investment increase that is driven by investment spikes. Using a dynamic investment model that fits the reduced-form effects of the reform, we show that policies that directly reduce the likelihood of firm inaction are more effective at stimulating investment.
Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits
Authors: Grundler Michael C , Rabosky Daniel L , Zapata Felipe 
Published: May 2022

Abstract
Understanding phenotypic disparity across the tree of life requires identifying where and when evolutionary rates change on phylogeny. A primary methodological challenge in macroevolution is therefore to develop methods for accurate inference of among-lineage variation in rates of phenotypic evolution. Here, we describe a method for inferring among-lineage evolutionary rate heterogeneity in both continuous and discrete traits. The method assumes that the present-day distribution of a trait is shaped by a variable-rate process arising from a mixture of constant-rate processes and uses a single-pass tree traversal algorithm to estimate branch-specific evolutionary rates. By employing dynamic programming optimization techniques and approximate maximum likelihood estimators where appropriate, our method permits rapid exploration of the tempo and mode of phenotypic evolution. Simulations indicate that the method reconstructs rates of trait evolution with high accuracy. Application of the method to data sets on squamate reptile reproduction and turtle body size recovers patterns of rate heterogeneity identified by previous studies but with computational costs reduced by many orders of magnitude. Our results expand the set of tools available for detecting macroevolutionary rate heterogeneity and point to the utility of fast, approximate methods for studying large-scale biodiversity dynamics. [Brownian motion; continuous characters; discrete characters; macroevolution; Markov process; rate heterogeneity.]
A Wider Perspective on Data Validation: A Multiregion Collaboration
Authors: Houck Olivia C. , Harrison Kelly , Giambri Roxanna , Moore Deanah , Burt Joyce , Cookman Kathy , Graymire Vickie 
Published: May 2022

BACKGROUND:
Data validation is important in maintaining the high-quality data necessary for trauma programs and research. Most existing guidance focuses on trauma center-level data validation, but validation from a broader level (region, state) may also be a helpful tool.

OBJECTIVE:
The purpose of this project is to improve data collection and submission at the local, regional, and state levels by performing logic-based data validation.

METHODS:
Logic edits were identified and accuracy rates were tracked quarterly, as measures were taken to improve accuracy. Following completion of Phase 1 of validation, Phase 2 was initiated to include both new fields and fields from Phase 1 that did not meet the accuracy goal. Data from Phase 2 were then compared with data from the state trauma registry.

RESULTS:
In both Phase 1 and Phase 2, five of the seven data fields validated reached 90% accuracy by the end of the respective project phase. The project facilitated registrar education and pursuit of data collection solutions in registry software. Systemic issues were identified at a higher level that had not been noticed at the trauma center level.

DISCUSSION:
Robust data validation is critical for an accurate trauma registry. Engaging higher-level organizations, like trauma regions, provides new perspective in data validation.

CONCLUSION:
This regional data validation approach provided additional value beyond usual center-level data validation.
Systematic Review of Pelvic Anatomy iOS and Android Applications for Obstetricians and Gynecologists
Authors: Menhaji Kimia , Holtzman Sharonne , Roser Brittany , Hardart Anne , Chen Katherine T. 
Published: May 2022

Importance
Resources for learning and enhancing knowledge in medicine, such as mobile applications (apps), have dramatically increased in recent years; however, there is lack of a valid source for identifying the best and most reliable mobile apps.

Objectives
The goal of this study was to identify the highest scoring available pelvic anatomy apps based on quality, content, and functionality for obstetrician-gynecologists using a validated tool.

Study Design
This was a systematic evaluation of anatomy apps in the Apple iTunes (iOS) and Google Play (Android) stores. Exclusions included apps that had nonhuman, nonanatomy content, did not include female pelvic anatomy or were deemed inappropriate for postgraduate level. The validated Mobile App Rating Scale (MARS), a mobile-health (mHealth) app scoring system was used to evaluate apps based on both objective and subjective quality. The authors' MARS scores for each variable were compiled, and the objective, subjective, and overall scores were calculated.

Results
The search criteria yielded 2,432 apps: 952 (39%) Apple iTunes store and 1,480 (60.8%) Google Play Store apps. After applying the exclusion criteria, 35 (14 iOS, 8 Android, and 13 iOS/Android) apps were included for evaluation using the MARS system. “Complete Anatomy” app, available for both iOS and Android systems, obtained the highest objective, subjective, and overall MARS score.

Conclusions
Although there are numerous anatomy apps available, only a few meet prespecified criteria for functionality, content, quality, and are appropriate for obstetrician-gynecologists. Using a validated scoring system, we present a scored list of female pelvic anatomy apps most appropriate for obstetrician-gynecologists.
Prevalence of Pelvic Floor Disorders in United States Active-Duty Service Women Seeking Medical Care
Authors: Wheat Joy E. , Khan Munziba , Banaag Amanda , Vaccaro Christine , Greer Joy A. , P. Koehlmoos Tracey , Hamlin Lynette 
Published: May 2022

Importance
In the United States, pelvic floor disorders affect 25% of women. Despite facing unique occupational risk factors that may increase the risk of pelvic floor disorders, there is little research on the prevalence of these disorders in active-duty service women.

Objectives
This study sought to identify the prevalence of and risk factors for pelvic floor disorders in active-duty service women in the United States from diagnostic codes through service utilization.

Study Design
Utilizing the Military Health System Data Repository, a cross-sectional study was conducted of all active-duty service women in the United States Army, Air Force, Navy, and Marine Corps during fiscal years 2010 to 2019.

Results
This study identified 497,255 active-duty service women of whom 9.93% had pelvic floor disorders. Adjusted regression model analyses indicated increasing parity and body mass index significantly affect the risk of pelvic floor disorders. Active-duty women with 3 or more births were 3 times more likely to have pelvic floor disorders compared with the nulliparous group. Finally, subset analysis indicates the risk of pelvic floor disorders were increased 250% in obese women and decreased 20% for underweight women. The rate of pelvic floor disorders appears to be increasing among active-duty women.

Conclusions
Active-duty service women have significantly lower rates of pelvic floor disorders compared with the general population, possibly due to the protective effects of improved weight management and physical fitness requirements for their job performance. However, pelvic floor disorders may be uptrending and need continued monitoring.
Electroconvulsive Therapy in a Patient With Depression on Hemodialysis
Authors: Watanabe Shintaro , Yasuda Kazuyuki , Tada Teruo , Ishibashi Akifumi , Suzuki Takefumi 
Published: May 2022

Abstract
Evidence on electroconvulsive therapy (ECT) for people receiving chronic hemodialysis has been rather scarce in the literature. We report the case of a 74-year-old male patient with major depressive disorder on chronic hemodialysis for 14 years with numerous physical complications including abdominal aortic aneurysm, ossification of the posterior longitudinal ligament, and cerebral stroke. Several antidepressant drugs failed to improve the patient, but judicious implementation of a total of 6 ECT sessions under a close liaison with medical experts brought him into remission without any notable adverse effects. In particular, flumazenil, as well as rocuronium and sugammadex, was used together with a strict control of blood pressure. We thoroughly discuss the case and provide a literature review on such topics as assessment of physical complications, medications used for anesthesia, electrode placement, and timing of hemodialysis during ECT sessions, which identified a clear need for more research on this medically challenging issue.
Crystal structure and Hirshfeld surface analysis of 5-amino-5′-bromo-2′-oxo-2,3-dihydro-1H-spiro[imidazo[1,2-a]pyridine-7,3′-indoline]-6,8-dicarbonitrile dimethyl sulfoxide disolvate
Authors: Naghiyev Farid N. , Khrustalev Victor N. , Novikov Anton P. , Akkurt Mehmet , Rzayev Rovnag M. , Akobirshoeva Anzurat A. , Mamedov Ibrahim G. 
Published: May 2022

In the title compound, C16H11BrN6O·2C2H6OS, the 1,2,3,7-tetrahydroimidazo[1,2-a]pyridine ring system and the oxindole moiety are both nearly planar [maximum deviations = 0.042 (2) and 0.115 (2) Å, respectively] and their planes form a dihedral angle of 86.04 (5)° with each other. Intermolecular N—H...O, C—H...O and C—H...N hydrogen bonds link molecules in the crystal through the O atoms of the solvent molecules, generating a three-dimensional network. A Hirshfeld surface analysis was performed to further analyse the intermolecular interactions.