bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphoanatomy, Histochemistry, and Phytochemistry of Stem and Leaves ofCrateva tapiaL.
Authors: Magalhães Cledson dos Santos , da Silva Flávia Carolina Lins , Randau Karina Perrelli 
Published: February 2023

AbstractCrateva tapia L. occurs only in Brazil and belongs to the family Capparaceae. This study aimed to characterize the morphoanatomy and histochemistry of stem and leaves, and phytochemical tests of the leaf of C. tapia. Macroscopic characterization was performed with the aid of a pachymeter and a stereomicroscope. Cross-sections of the stem, petiole, petiolule, and leaf blade, as well as paradermal sections of the leaf blade were mounted on microscope slides. Analyzes were carried out with optical microscopy. For histochemical analysis, different reagents were useda ccording to the targeted metabolite. Phytochemical tests of the methanolic extracts of the leaves were performed using thin layer chromatography. Crateva tapia has a stem with a circular cross-section and smooth bark. The leaves are alternate spirally, compound 3-foliolate. The leaf blade is elliptical and has a reticulate dictiodromous nerve. Through anatomical characterization, it was possible to identify a hypostomatic leaf blade with anisocytic, tetracytic, and anomocytic stomata and the presence of secretory canals. Through histochemistry and phytochemical tests, it was possible to observe the presence of different metabolites. Thus, the results obtained in this study contribute to the quality control of C. tapia, a species only found in Brazil, increasing the taxonomic knowledge of the family Capparaceae.
Three-Dimensional Ultrastructural and Volume Analysis of the Redundant Nuclear Envelope of Developing and Matured Sperm in Mice
Authors: Uemura Kei-ichiro , Miyazono Yoshihiro , Hiroshige Tasuku , Ohta Keisuke , Ueda Kosuke , Nishihara Kiyoaki , Nakiri Makoto , Hirashima Shingo , Igawa Tsukasa , Nakamura Kei-ichiro 
Published: February 2023

AbstractThe ultrastructure of the nuclear envelope (NE) and redundant NE (RNE) of the spermatozoon cannot be observed in detail using conventional electron microscopy. Thus, this study aimed to employ transmission electron microscopy (TEM) and focused ion beam/scanning electron microscopy (FIB/SEM) tomography to fill this research gap. Male mice aged 13 weeks were deeply anesthetized, and the testes and vas deferens were extracted and processed for electron microscopy. In round spermatids, the acrosomal vesicle compressed the nucleus, and the acrosomal center was depressed. The nucleoli concentrated on the contralateral side of the acrosome formation site. In mature spermatozoa, the RNE accumulated in the neck with the residual bodies. The NE pores exhibited a hexagonal pattern. The body surface area and volume of the nuclei of spermatids and spermatozoa in each maturation phase were analyzed using FIB/SEM tomography. The body surface area and volume of the nuclei decreased during spermatid maturation into spermatozoa. The RNE converged at the sperm neck and possessed a honeycomb structure. The method used revealed that the nuclei of spermatids gradually condense as they mature into spermatozoa. This method may be used to analyze small tissues, such as RNE, and detect morphological abnormalities in microtissues, such as spermatozoa.
A Multidisciplinary Approach to Improvements in Perioperative Antibiotic Prophylaxis at a Military Treatment Facility
Authors: Baker Amelia L , McElrath Angela , Giancola Stephanie E , Schumaker Annabel L , Barsoumian Alice E 
Published: February 2023

ABSTRACT

Introduction
Surgical site infections complicate 2%-5% of surgeries. According to the Centers for Disease Control and Prevention, half of all surgical site infections are preventable. Adherence to published recommendations regarding perioperative antibiotic administration decreases the incidence of surgical site infections. Members of the Department of Anesthesia noticed casual observations of inaccurate prescribing of antibiotics at our institution, Brooke Army Medical Center, and approached the Antimicrobial Stewardship Program to collaborate on this issue.

Materials and Methods
A team of anesthesiologists, clinical pharmacists, and infectious disease specialists collaborated with the Department of Surgery to improve this effort as part of a multiyear project from 2018 to 2021. We first assessed adherence to recommended perioperative antibiotic use to establish a baseline and next, noticing gaps, created a project with the goal to improve compliance to &gt;90% across surveyed measures. Our key interventions included educational initiatives, creation of facility-specific guidelines, peer benchmarking, updating order sets, interdisciplinary collaboration, creation of intraoperative reminders and visual aids, and tailored presentations to selected services.

Results
Of 292 charts (2.3% of cases from January to October 2018) reviewed pre-intervention, compliance rates were 84% for antibiotic choice, 92% for dose, 65% for redosing, and 71% for postoperative administration. Of doses, 100% were timed correctly, and thus, this variable was not targeted. Post-intervention, our review of 387 charts (10% of cases from May to November 2020) showed no change in correct antibiotic choice (84%) and statistical improvement to 96% for correct dose, 95% for correct redosing, and 85% for correct postoperative administration (P &lt; .05 for all).

Conclusions
Our multidisciplinary approach of collaboration with multiple departments, creating guidelines and providing feedback, improved compliance with perioperative antibiotic administration recommendations.
Automated classification of Chandra X-ray point sources using machine learning methods
Authors: Kumaran Shivam , Mandal Samir , Bhattacharyya Sudip , Mishra Deepak 
Published: February 2023

ABSTRACT
A large number of unidentified sources found by astronomical surveys and other observations necessitate the use of an automated classification technique based on machine learning (ML) methods. The aim of this paper is to find a suitable automated classifier to identify the point X-ray sources in the Chandra Source Catalogue (CSC) 2.0 in the categories of active galactic nuclei (AGN), X-ray emitting stars, young stellar objects (YSOs), high-mass X-ray binaries (HMXBs), low-mass X-ray binaries (LMXBs), ultra luminous X-ray sources (ULXs), cataclysmic variables (CVs), and pulsars. The catalogue consists of ≈317 000 sources, out of which we select 277 069 point sources based on the quality flags available in CSC 2.0. In order to identify unknown sources of CSC 2.0, we use MW features, such as magnitudes in optical/ultraviolet bands from Gaia-EDR3, Sloan Digital Sky Survey, and GALEX, and magnitudes in infrared bands from 2MASS, WISE, and MIPS-Spitzer, in addition to X-ray features (flux and variability) from CSC 2.0. We find the Light Gradient Boosted Machine, an advanced decision tree-based ML classification algorithm, suitable for our purpose and achieve 93 per  cent precision, 93 per  cent recall score, and 0.91 Mathew’s Correlation coefficient score. With the trained classifier, we identified 54 770 (14 066) sources with more than 3σ (4σ) confidence, out of which there are 32 600 (8574) AGNs, 16,148 (5,166) stars, 5,184 (208) YSOs, 439 (46) HMXBs, 197 (71) LMXBs, 50 (0) ULXs, 89 (1) CVs, and 63 (0) pulsars. This method can also be useful for identifying sources of other catalogues reliably.
Pulsar scintillation studies with LOFAR: II. Dual-frequency scattering study of PSR J0826+2637 with LOFAR and NenuFAR
Authors: Wu Ziwei , Coles William A , Verbiest Joris P W , Ambalappat Krishnakumar Moochickal , Tiburzi Caterina , Grießmeier Jean-Mathias , Main Robert A , Liu Yulan , Kramer Michael , Wucknitz Olaf , Porayko Nataliya , Osłowski Stefan , Nielsen Ann-Sofie Bak , Donner Julian Y , Hoeft Matthias , Brüggen Marcus , Vocks Christian , Dettmar Ralf-Jürgen , Theureau Gilles , Serylak Maciej , Kondratiev Vladislav , McKee James W , Shaifullah Golam M , Kravtsov Ihor P , Zakharenko Vyacheslav V , Ulyanov Oleg , Konovalenko Olexandr O , Zarka Philippe , Cecconi Baptiste , Koopmans Léon V E , Corbel Stéphane 
Published: February 2023

ABSTRACT
Interstellar scattering (ISS) of radio pulsar emission can be used as a probe of the ionized interstellar medium (IISM) and causes corruptions in pulsar timing experiments. Two types of ISS phenomena (intensity scintillation and pulse broadening) are caused by electron density fluctuations on small scales (&lt; 0.01 au). Theory predicts that these are related, and both have been widely employed to study the properties of the IISM. Larger scales (∼1 – 100 au) cause measurable changes in dispersion and these can be correlated with ISS observations to estimate the fluctuation spectrum over a very wide scale range. IISM measurements can often be modelled by a homogeneous power-law spatial spectrum of electron density with the Kolmogorov (−11/3) spectral exponent. Here, we aim to test the validity of using the Kolmogorov exponent with PSR J0826+2637. We do so using observations of intensity scintillation, pulse broadening and dispersion variations across a wide fractional bandwidth (20–180 MHz). We present that the frequency dependence of the intensity scintillation in the high-frequency band matches the expectations of a Kolmogorov spectral exponent, but the pulse broadening in the low-frequency band does not change as rapidly as predicted with this assumption. We show that this behaviour is due to an inhomogeneity in the scattering region, specifically that the scattering is dominated by a region of transverse size ∼40 au. The power spectrum of the electron density, however, maintains the Kolmogorov spectral exponent from spatial scales of 5 × 10−6 au to ∼100 au.
Using X-ray continuum-fitting to estimate the spin of MAXI J1305–704
Authors: Feng Ye , Steiner James F , Ramirez Santiago Ubach , Gou Lijun 
Published: February 2023

ABSTRACT
MAXI J1305–704 is a transient X-ray binary with a black hole primary. It was discovered on 2012 April 9, during its only known outburst. MAXI J1305–704 is also a high inclination low-mass X-ray binary with prominent dip features in its light curves, so we check the full catalogue of 92 Swift/XRT continuous observations of MAXI J1305–704, focusing only on the stable spectra. We select 13 ‘gold’ spectra for which the rms &lt;0.075 and the coronal scattered fraction $f_{\mathrm{sc}} \lesssim 25$ per cent. These ‘gold’ data are optimal thermal-state observations for continuum-fitting modelling, in which the disc extends to the innermost stable circular orbit and is geometrically thin. The black hole spin was unknown for this object before. By utilizing the X-ray continuum fitting method with the relativistic thin disc model kerrbb2 and supplying the known dynamical binary system parameters, we find MAXI J1305–704 has a moderate spin ($a_{*}=0.87_{-0.13}^{+0.07}$) at a 68.3 per cent confidence level. This is the first determination of MAXI J1305–704’s spin.
Strand specificity of ribonucleotide excision repair inEscherichia coli
Authors: Łazowski Krystian , Faraz Mahmood , Vaisman Alexandra , Ashton Nicholas W , Jonczyk Piotr , Fijalkowska Iwona J , Clausen Anders R , Woodgate Roger , Makiela-Dzbenska Karolina 
Published: February 2023

AbstractIn Escherichia coli, replication of both strands of genomic DNA is carried out by a single replicase—DNA polymerase III holoenzyme (pol III HE). However, in certain genetic backgrounds, the low-fidelity TLS polymerase, DNA polymerase V (pol V) gains access to undamaged genomic DNA where it promotes elevated levels of spontaneous mutagenesis preferentially on the lagging strand. We employed active site mutants of pol III (pol IIIα_S759N) and pol V (pol V_Y11A) to analyze ribonucleotide incorporation and removal from the E. coli chromosome on a genome-wide scale under conditions of normal replication, as well as SOS induction. Using a variety of methods tuned to the specific properties of these polymerases (analysis of lacI mutational spectra, lacZ reversion assay, HydEn-seq, alkaline gel electrophoresis), we present evidence that repair of ribonucleotides from both DNA strands in E. coli is unequal. While RNase HII plays a primary role in leading-strand Ribonucleotide Excision Repair (RER), the lagging strand is subject to other repair systems (RNase HI and under conditions of SOS activation also Nucleotide Excision Repair). Importantly, we suggest that RNase HI activity can also influence the repair of single ribonucleotides incorporated by the replicase pol III HE into the lagging strand.
Transcriptional pause extension benefits the stand-by rather than catch-up Rho-dependent termination
Authors: Song Eunho , Hwang Seungha , Munasingha Palinda Ruvan , Seo Yeon-Soo , Kang Jin Young , Kang Changwon , Hohng Sungchul 
Published: February 2023

AbstractTranscriptional pause is essential for all types of termination. In this single-molecule study on bacterial Rho factor-dependent terminators, we confirm that the three Rho-dependent termination routes operate compatibly together in a single terminator, and discover that their termination efficiencies depend on the terminational pauses in unexpected ways. Evidently, the most abundant route is that Rho binds nascent RNA first and catches up with paused RNA polymerase (RNAP) and this catch-up Rho mediates simultaneous releases of transcript RNA and template DNA from RNAP. The fastest route is that the catch-up Rho effects RNA-only release and leads to 1D recycling of RNAP on DNA. The slowest route is that the RNAP-prebound stand-by Rho facilitates only the simultaneous rather than sequential releases. Among the three routes, only the stand-by Rho's termination efficiency positively correlates with pause duration, contrary to a long-standing speculation, invariably in the absence or presence of NusA/NusG factors, competitor RNAs or a crowding agent. Accordingly, the essential terminational pause does not need to be long for the catch-up Rho's terminations, and long pauses benefit only the stand-by Rho's terminations. Furthermore, the Rho-dependent termination of mgtA and ribB riboswitches is controlled mainly by modulation of the stand-by rather than catch-up termination.
The Ku complex promotes DNA end-bridging and this function is antagonized by Tel1/ATM kinase
Authors: Rinaldi Carlo , Pizzul Paolo , Casari Erika , Mangiagalli Marco , Tisi Renata , Longhese Maria Pia 
Published: February 2023

AbstractDNA double-strand breaks (DSBs) can be repaired by either homologous recombination (HR) or non-homologous end-joining (NHEJ). NHEJ is induced by the binding to DSBs of the Ku70–Ku80 heterodimer, which acts as a hub for the recruitment of downstream NHEJ components. An important issue in DSB repair is the maintenance of the DSB ends in close proximity, a function that in yeast involves the MRX complex and Sae2. Here, we provide evidence that Ku contributes to keep the DNA ends tethered to each other. The ku70-C85Y mutation, which increases Ku affinity for DNA and its persistence very close to the DSB ends, enhances DSB end-tethering and suppresses the end-tethering defect of sae2Δ cells. Impairing histone removal around DSBs either by eliminating Tel1 kinase activity or nucleosome remodelers enhances Ku persistence at DSBs and DSB bridging, suggesting that Tel1 antagonizes the Ku function in supporting end-tethering by promoting nucleosome removal and possibly Ku sliding inwards. As Ku provides a block to DSB resection, this Tel1 function can be important to regulate the mode by which DSBs are repaired.
Mousepost 2.0, a major expansion of the resource
Authors: Timmermans Steven , Vandewalle Jolien , Libert Claude 
Published: February 2023

AbstractThe Mousepost 1.0 online search tool, launched in 2017, allowed to search for variations in all protein-coding gene sequences of 36 sequenced mouse inbred strains, compared to the reference strain C57BL/6J, which could be linked to strain-specific phenotypes and modifier effects. Because recently these genome sequences have been significantly updated and sequences of 16 extra strains added by the Mouse Genomes Project, a profound update, correction and expansion of the Mousepost 1.0 database has been performed and is reported here. Moreover, we have added a new class of protein disturbing sequence polymorphisms (besides stop codon losses, stop codon gains, small insertions and deletions, and missense mutations), namely start codon mutations. The current version, Mousepost 2.0 (https://mousepost.be), therefore is a significantly updated and invaluable tool available to the community and is described here and foreseen by multiple examples.
Nutritional interventions for the prevention and treatment of cancer therapy-induced oral mucositis: an umbrella review of systematic reviews and meta-analysis
Authors: Amiri Khosroshahi Reza , Talebi Sepide , Zeraattalab-Motlagh Sheida , Imani Hossein , Rashidi Amirabbas , Travica Nikolaj , Mohammadi Hamed 
Published: February 2023

AbstractContextTo date, the efficacy of nutritional interventions on oral mucositis (OM) in patients with cancer, and the quality of this evidence have not been explored.ObjectiveThe goal of this umbrella review was to provide a comprehensive evaluation of nutritional interventions for patients with cancer with OM, as well as to assess the quality of this evidence.Data sourcesMeta-analyses were searched for using PubMed, Scopus, and ISI Web of Science databases until December 2021, with no time restrictions.Data extractionMeta-analyses of randomized control trials that evaluated the effects of nutritional interventions on the incidence of OM in patients with cancer had inclusion criteria for this umbrella review. Data extraction, quality assessment of meta-analyses, and primary studies were done independently by 2 authors. The Grading of Recommendations Assessment, Development, and Evaluation technique was used to grade the certainty of evidence.Data analysisA total of 26 meta-analyses were included in this umbrella review. The results showed that honey, glutamine, and propolis can reduce the incidence of severe OM, based on moderate evidence quality. In addition, zinc supplementation significantly reduced the incidence of OM, regardless of symptom severity; however, low certainty of the evidence was observed. The effects of vitamin E, curcumin, and probiotics on OM were not statistically significant.ConclusionThis umbrella review shows that honey, glutamine, and propolis can significantly reduce the incidence of severe OM. These findings need to be confirmed with well-designed, longitudinal randomized controlled trials.Systematic Review RegistrationPROSPERO registration no. CRD42022301010.
SCARECROW-like GRAS protein PES positively regulates petunia floral scent production
Authors: Shor Ekaterina , Ravid Jasmin , Sharon Elad , Skaliter Oded , Masci Tania , Vainstein Alexander 
Published: February 2023

AbstractEmission of scent volatiles by flowers is important for successful pollination and consequently, reproduction. Petunia (Petunia hybrida) floral scent is formed mainly by volatile products of the phenylpropanoid pathway. We identified and characterized a regulator of petunia scent production: the GRAS protein PHENYLPROPANOID EMISSION-REGULATING SCARECROW-LIKE (PES). Its expression increased in petals during bud development and was highest in open flowers. Overexpression of PES increased the production of floral volatiles, while its suppression resulted in scent reduction. We showed that PES upregulates the expression of genes encoding enzymes of the phenylpropanoid and shikimate pathways in petals, and of the core regulator of volatile biosynthesis ODORANT1 by activating its promoter. PES is an ortholog of Arabidopsis (Arabidopsis thaliana) PHYTOCHROME A SIGNAL TRANSDUCTION 1, involved in physiological responses to far-red (FR) light. Analyses of the effect of nonphotosynthetic irradiation (low-intensity FR light) on petunia floral volatiles revealed FR light as a scent-activating factor. While PHYTOCHROME A regulated scent-related gene expression and floral scent production under FR light, the influence of PES on volatile production was not limited by FR light conditions.
Tetratricopeptide repeat protein SlREC2 positively regulates cold tolerance in tomato
Authors: Zhang Ying , Peng Yinxia , Liu Juan , Yan Jiarong , Zhu Kangyou , Sun Xin , Bu Xin , Wang Xiujie , Ahammed Golam Jalal , Liu Yufeng , Sun Zhouping , Qi Mingfang , Wang Feng , Li Tianlai 
Published: February 2023

Abstract
Cold stress is a key environmental constraint that dramatically affects the growth, productivity, and quality of tomato (Solanum lycopersicum); however, the underlying molecular mechanisms of cold tolerance remain poorly understood. In this study, we identified REDUCED CHLOROPLAST COVERAGE 2 (SlREC2) encoding a tetratricopeptide repeat protein that positively regulates tomato cold tolerance. Disruption of SlREC2 largely reduced abscisic acid (ABA) levels, photoprotection, and the expression of C-REPEAT BINDING FACTOR (CBF)-pathway genes in tomato plants under cold stress. ABA deficiency in the notabilis (not) mutant, which carries a mutation in 9-CIS-EPOXYCAROTENOID DIOXYGENASE 1 (SlNCED1), strongly inhibited the cold tolerance of SlREC2-silenced plants and empty vector control plants and resulted in a similar phenotype. In addition, foliar application of ABA rescued the cold tolerance of SlREC2-silenced plants, which confirms that SlNCED1-mediated ABA accumulation is required for SlREC2-regulated cold tolerance. Strikingly, SlREC2 physically interacted with β-RING CAROTENE HYDROXYLASE 1b (SlBCH1b), a key regulatory enzyme in the xanthophyll cycle. Disruption of SlBCH1b severely impaired photoprotection, ABA accumulation, and CBF-pathway gene expression in tomato plants under cold stress. Taken together, this study reveals that SlREC2 interacts with SlBCH1b to enhance cold tolerance in tomato via integration of SlNCED1-mediated ABA accumulation, photoprotection, and the CBF-pathway, thus providing further genetic knowledge for breeding cold-resistant tomato varieties.
Computational models of dopamine release measured by fast scan cyclic voltammetry in vivo
Authors: Shashaank N , Somayaji Mahalakshmi , Miotto Mattia , Mosharov Eugene V , Makowicz Emily A , Knowles David A , Ruocco Giancarlo , Sulzer David L 
Published: February 2023

Abstract
Dopamine neurotransmission in the striatum is central to many normal and disease functions. Ventral midbrain dopamine neurons exhibit ongoing tonic firing that produces low extrasynaptic levels of dopamine below the detection of conventional extrasynaptic cyclic voltammetry (∼10–20 nanomolar), with superimposed bursts that can saturate the dopamine uptake transporter and produce transient micromolar concentrations. The bursts are known to lead to marked presynaptic plasticity via multiple mechanisms, but analysis methods for these kinetic parameters are limited. To provide a deeper understanding of the mechanics of the modulation of dopamine neurotransmission by physiological, genetic, and pharmacological means, we present three computational models of dopamine release with different levels of spatiotemporal complexity to analyze in vivo fast-scan cyclic voltammetry recordings from the dorsal striatum of mice. The models accurately fit to cyclic voltammetry data and provide estimates of presynaptic dopamine facilitation/depression kinetics and dopamine transporter reuptake kinetics, and we used the models to analyze the role of synuclein proteins in neurotransmission. The models’ results support recent findings linking the presynaptic protein α-synuclein to the short-term facilitation and long-term depression of dopamine release, as well as reveal a new role for β-synuclein and/or γ-synuclein in the long-term regulation of dopamine reuptake.