bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rate coefficients for rotational state-to-state transitions in H2O + H2O collisions for cometary and planetary applications, as predicted by mixed quantum-classical theory
Authors: Mandal Bikramaditya , Babikov Dmitri 
Published: January 2023

Aims. We present new calculations of collision cross sections for state-to-state transitions between the rotational states in an H2O + H2O system, which are used to generate a new database of collisional rate coefficients for cometary and planetary applications.
Methods. Calculations were carried out using a mixed quantum-classical theory approach that is implemented in the code MQCT. The large basis set of rotational states used in these calculations permits us to predict thermally averaged cross sections for 441 transitions in para- and ortho-H2O in a broad range of temperatures.
Results. It is found that all state-to-state transitions in the H2O + H2O system split into two well-defined groups, one with higher cross-section values and lower energy transfer, which corresponds to the dipole-dipole driven processes. The other group has smaller cross sections and higher energy transfer, driven by higher-order interaction terms. We present a detailed analysis of the theoretical error bars, and we symmetrized the state-to-state transition matrixes to ensure that excitation and quenching processes for each transition satisfy the principle of microscopic reversibility. We also compare our results with other data available from the literature for H2O + H2O collisions.
Gait is not Affected by Hemispherotomy—Case Report from Two Children
Authors: Alexander Nathalie , Cip Johannes , Müller Elisabeth , Lengnick-Lampadius Katrin , Broser Philip Julian 
Published: January 2023

AbstractIn children with therapy refractory epilepsy, the functional disconnection of one hemisphere (hemispherotomy) may be considered as a treatment option. The visual field defects and hand function effects associated with the procedure have been extensively studied. However, the effect of the hemispherotomy on gait pattern has thus far only been analyzed qualitatively, and there is limited quantitative data. At the Children's Hospital, we regularly perform standardized quantitative gait analysis studies and care for children with complex epilepsies. During the standard routine of care for two children with structural therapy refractory epilepsy, gait analysis was performed prior to and after hemispherotomy. Both patients had prenatal ischemic brain lesions, had developed severe epilepsy during the first 3 years of life, and were treated with the hemispherotomy at about 7 years of age. Interestingly, one patient did not show any changes in gait pattern, while for the other patient, differences could be observed by means of three-dimensional gait analysis. However, greater deviations to controls postoperatively may also be related to day-to-day variability.
Bioinspired Formal Synthesis of Pancracine via Selective Hydro­genation of an Indole Derivative
Authors: Qi Xiangbing , Han Shoule , Lou Mingliang 
Published: January 2023

AbstractA bioinspired formal synthesis of the montanine-type Amaryllidaceae alkaloid pancracine through selective hydrogenation of a 3-arylindole derivative is disclosed. The key features of this synthesis include a hexahydroindole synthesis by a chemoselective hydrogenation of an aryl-substituted indole and a diastereoselective silyl hydride reduction of an iminium intermediate generated from an enaminone through Tf2O activation. The eight-step assembly of the 5,11-methanomorphanthridine framework represents a novel and efficient strategy that permits one of the shortest syntheses of pancracine reported so far.
Investigations on Biomimetic Dimerization in Natural Product Synthesis
Authors: Hu Xiangdong , Zhang Fan , Chen Chongchong 
Published: January 2023

AbstractBiomimetic dimerization is a fascinating pathway to natural product synthesis. By using structurally inferior monomers, complex molecular architectures can be readily established with distinct efficiency and elegance. In this Account, our investigation on biomimetic dimerization in natural product synthesis has been summarized, which includes our synthetic exploration of linderaspirone A, bi-linderone, parvistemin A, (±)-diperezone, scabellone B, and spiroxins A/C/D.1	Introduction2	Biomimetic Dimerization in the Synthesis of Linderaspirone A and Bi-linderone3	Biomimetic Dimerization in the Synthesis of Parvistemin A and (±)-Diperezone4	Biomimetic Dimerization in the Synthesis of Scabellone B5	Dimerization Investigation in the Synthesis of Spiroxins A/C/D6	Conclusion
Endobronchial Inflammatory Myofibroblastic Tumor in a 3-Year-Old Child
Authors: Guanà Riccardo , Carpino Andrea , Miglietta Marta , Zambaiti Elisa , Cerrina Alessia , Lonati Luca , Guerrera Francesco , Vallero Stefano , Garofalo Salvatore , Bardessono Marco , Maletta Francesca , Shilly Steffi , Gennari Fabrizio 
Published: January 2023

AbstractInflammatory myofibroblastic tumor (IMT) is a mesenchymal tumor that can occur at any age. However, it is primarily seen in children, with the most common site being in the lung parenchyma, usually present with rare endobronchial lesions. This case reports the incidence in a 3-year-old girl diagnosed with pericardiac pneumonia treated with antibiotics with no clinical improvement. A chest computed tomography (CT) scan identified a 1.5-cm lesion in the left main bronchus. Bronchoscopy revealed complete obstruction of the left main stem bronchus. A left posterolateral thoracotomy was performed. Additionally, a left sleeve upper bronchial resection was conducted under fibroendoscopic control. Definitive histology confirmed IMT. After 2 years of endoscopic follow-up, there is no evidence of recurrence.
Dedicated Chalazion Clinic as a Tool for Early Surgical Education in Ophthalmology Residency
Authors: Lin Lisa Y. , Armstrong Grayson W. , Gardiner Matthew , Lorch Alice , Freitag Suzanne K. , Yadav Prashant 
Published: January 2023

Abstract
Objective Ophthalmology residency programs aim to improve resident surgical teaching through increased surgical exposure over a 4-year period. Resident-centric surgical clinics across various surgical specialties have been established to help develop surgical autonomy and experience. We present the first demonstration of a resident-centric chalazion incision and drainage clinic (chalazion clinic) in an ophthalmology residency with the goal of increasing early surgical exposure to residents.
Design The chalazion clinic was founded in July 2019. It is a once weekly procedure clinic conducted by an ophthalmology resident and supervised by an ophthalmology attending. Patients with chalazia were referred directly to this clinic for evaluation and management, rather than the oculoplastics clinic as they were in the past. Retrospective review of Accreditation Council for Graduate Medical Education (ACGME) case logs of all residents per academic year before and after establishment of the chalazion clinic was performed in order to assess the impact on residents' chalazion procedures numbers per academic year.
Setting The study involved a single academic ophthalmology department.
Participants Ophthalmology residents of all years were present.
Results A resident of any year performed an average of 3.0 chalazion procedures per year in the 2018 to 2019 academic year, 3.8 in 2019 to 2020, and 8.4 in the 2020 to 2021, which represents a 180% increase in procedure numbers per resident. Among post-graduate-year 2s (PGY)2s, the average number of chalazion procedures increased from 2.1 procedure per year to 22.3 per year (961.9% increase).
Conclusion To the best of our knowledge, this is the first description of a dedicated resident-centric chalazion clinic in an ophthalmology residency program. PGY2s demonstrated the largest increase in procedural numbers. While chalazion incision and drainage is a minor procedure, increased exposure to surgical procedures early in training could help improve residents' skills and confidence. This clinic provides a proof of concept of a dedicated minor procedure clinic for ophthalmology residents to increase early procedural volume.
The Association between Bleeding Disorders and Postoperative Complications Following Operative Treatment of Distal Radius Fracture
Authors: Quan Theodore , Chen Frank R. , Manzi Joseph E. , Mcdaniel Lea , Howard Peter , Marquardt Caillin , Ranson Rachel , Tabaie Sean 
Published: January 2023

Abstract
Background While previous studies have investigated the association between bleeding disorders and outcomes with hip or knee surgeries, no studies have investigated the association between bleeding disorders and outcomes in upper extremity surgery.
Questions/Purposes The purpose of this study was to investigate if a past history of bleeding disorders is associated with which, if any postoperative complications for patients receiving distal radius fracture open reduction internal fixation.
Patients and Methods Patients undergoing operative treatment for distal radius fracture from 2007 to 2018 were identified in the National Surgical Quality Improvement Program database. Patients were stratified into two cohorts: patients with a bleeding disorder and patients without a bleeding disorder. In this analysis, 30-day postoperative complications were assessed, as well as mortality, extended length of stay, reoperation, and readmission. Bivariate and multivariate analyses were performed.
Results Of the 16,489 total patients undergoing operative treatment for distal radius fracture, 16,047 patients (97.3%) did not have a bleeding disorder, whereas 442 (2.7%) had a bleeding disorder. Following adjustment on multivariate analyses, an increased risk of postoperative transfusion requirement (odds ratio [OR] 17.437; p = 0.001), extended length of hospital stay more than 3 days (OR 1.564; p = 0.038), and readmission (OR 2.515; p < 0.001) were seen in patients with a bleeding disorder compared to those without a bleeding disorder.
Conclusion History of bleeding disorders is an independent risk factor for transfusions, extended length of stay, and readmission. We recommend a multidisciplinary team approach to addressing bleeding disorders before patients receive distal radius fracture open reduction internal fixation.
Level of Evidence Level III, retrospective study.
A data selection method for matrix effects and uncertainty reduction for laser-induced breakdown spectroscopy
Authors: LONG Jie , SONG Weiran , HOU Zongyu , WANG Zhe 
Published: January 2023

Abstract
Severe matrix effects and high signal uncertainty are two key bottlenecks for the quantitative performance and wide applications of laser-induced breakdown spectroscopy (LIBS). Based on the understanding that the superposition of both matrix effects and signal uncertainty directly affects plasma parameters and further influences spectral intensity and LIBS quantification performance, a data selection method based on plasma temperature matching (DSPTM) was proposed to reduce both matrix effects and signal uncertainty. By selecting spectra with smaller plasma temperature differences for all samples, the proposed method was able to build up the quantification model to rely more on spectra with smaller matrix effects and signal uncertainty, therefore improving final quantification performance. When applied to quantitative analysis of the zinc content in brass alloys, it was found that both accuracy and precision were improved using either a univariate model or multiple linear regression (MLR). More specifically, for the univariate model, the root-mean-square error of prediction (RMSEP), the determination coefficients (R
2) and relative standard derivation (RSD) were improved from 3.30%, 0.864 and 18.8% to 1.06%, 0.986 and 13.5%, respectively; while for MLR, RMSEP, R
2 and RSD were improved from 3.22%, 0.871 and 26.2% to 1.07%, 0.986 and 17.4%, respectively. These results prove that DSPTM can be used as an effective method to reduce matrix effects and improve repeatability by selecting reliable data.
GMWI-webtool: a user-friendly browser application for assessing health through metagenomic gut microbiome profiling
Authors: Chang Daniel , Gupta Vinod K , Hur Benjamin , Cunningham Kevin Y , Sung Jaeyun 
Published: January 2023

Abstract

Summary
We recently introduced the Gut Microbiome Wellness Index (GMWI), a stool metagenome-based indicator for assessing health by determining the likelihood of disease given the state of one’s gut microbiome. The calculation of our wellness index depends on the relative abundances of health-prevalent and health-scarce species. Encouragingly, GMWI has already been utilized in various studies focusing on differences in the gut microbiome between cases and controls. Herein, we introduce the GMWI-webtool, a user-friendly browser application that computes GMWI, health-prevalent/-scarce species’ relative abundances, and α-diversities from stool shotgun metagenome taxonomic profiles. Users of our interactive online tool can visualize their results and compare them side-by-side with those from our pooled reference dataset of metagenomes, as well as export data in.csv format and high-resolution figures.

Availability and implementation
GMWI-webtool is freely available here: https://gmwi-webtool.github.io/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Efficient penalized generalized linear mixed models for variable selection and genetic risk prediction in high-dimensional data
Authors: St-Pierre Julien , Oualkacha Karim , Bhatnagar Sahir Rai 
Published: January 2023

AbstractMotivationSparse regularized regression methods are now widely used in genome-wide association studies (GWAS) to address the multiple testing burden that limits discovery of potentially important predictors. Linear mixed models (LMMs) have become an attractive alternative to principal components (PCs) adjustment to account for population structure and relatedness in high-dimensional penalized models. However, their use in binary trait GWAS rely on the invalid assumption that the residual variance does not depend on the estimated regression coefficients. Moreover, LMMs use a single spectral decomposition of the covariance matrix of the responses, which is no longer possible in generalized linear mixed models (GLMMs).ResultsWe introduce a new method called pglmm, a penalized GLMM that allows to simultaneously select genetic markers and estimate their effects, accounting for between-individual correlations and binary nature of the trait. We develop a computationally efficient algorithm based on penalized quasi-likelihood estimation that allows to scale regularized mixed models on high-dimensional binary trait GWAS. We show through simulations that when the dimensionality of the relatedness matrix is high, penalized LMM and logistic regression with PC adjustment fail to select important predictors, and have inferior prediction accuracy compared to pglmm. Further, we demonstrate through the analysis of two polygenic binary traits in a subset of 6731 related individuals from the UK Biobank data with 320K SNPs that our method can achieve higher predictive performance, while also selecting fewer predictors than a sparse regularized logistic lasso with PC adjustment.Availability and implementationOur Julia package PenalizedGLMM.jl is publicly available on github: https://github.com/julstpierre/PenalizedGLMM.Supplementary informationSupplementary data are available at Bioinformatics online.
Anex vivoovulation system enables the discovery of novel ovulatory pathways and nonhormonal contraceptive candidates
Authors: Zhang Jiyang , Goods Brittany A , Pattarawat Pawat , Wang Yingzheng , Haining Tessa , Zhang Qiang , Shalek Alex K , Duncan Francesca E , Woodruff Teresa K , Xiao Shuo 
Published: January 2023

AbstractOvulation is an integral part of women’s menstrual cycle and fertility. Understanding the mechanisms of ovulation has broad implications for the treatment of anovulatory diseases and the development of novel contraceptives. Now, few studies have developed effective models that both faithfully recapitulate the hallmarks of ovulation and possess scalability. We established a three-dimensional encapsulated in vitro follicle growth (eIVFG) system that recapitulates folliculogenesis and produces follicles that undergo ovulation in a controlled manner. Here, we determined whether ex vivo ovulation preserves molecular signatures of ovulation and demonstrated its use in discovering novel ovulatory pathways and nonhormonal contraceptive candidates through a high-throughput ovulation screening. Mature murine follicles from eIVFG were induced to ovulate ex vivo using human chorionic gonadotropin and collected at 0, 1, 4, and 8 hours post-induction. Phenotypic analyses confirmed key ovulatory events, including cumulus expansion, oocyte maturation, follicle rupture, and luteinization. Single-follicle RNA-sequencing analysis revealed the preservation of ovulatory genes and dynamic transcriptomic profiles and signaling. Soft clustering identified distinct gene expression patterns and new pathways that may critically regulate ovulation. We further used this ex vivo ovulation system to screen 21 compounds targeting established and newly identified ovulatory pathways. We discovered that proprotein convertases activate gelatinases to sustain follicle rupture and do not regulate luteinization and progesterone secretion. Together, our ex vivo ovulation system preserves molecular signatures of ovulation, presenting a new powerful tool for studying ovulation and anovulatory diseases as well as for establishing a high-throughput ovulation screening to identify novel nonhormonal contraceptives for women.
Differential responsiveness of spermatogonia to retinoic acid dictates precocious differentiation but not meiotic entry during steady-state spermatogenesis
Authors: Johnson Taylor A , Niedenberger Bryan A , Kirsanov Oleksandr , Harrington Ellen V , Malachowski Taylor , Geyer Christopher B 
Published: January 2023

AbstractThe foundation of mammalian spermatogenesis is provided by undifferentiated spermatogonia, which comprise of spermatogonial stem cells (SSCs) and transit-amplifying progenitors that differentiate in response to retinoic acid (RA) and are committed to enter meiosis. Our laboratory recently reported that the foundational populations of SSCs, undifferentiated progenitors, and differentiating spermatogonia are formed in the neonatal testis in part based on their differential responsiveness to RA. Here, we expand on those findings to define the extent to which RA responsiveness during steady-state spermatogenesis in the adult testis regulates the spermatogonial fate. Our results reveal that both progenitor and differentiating spermatogonia throughout the testis are capable of responding to exogenous RA, but their resulting fates were quite distinct—undifferentiated progenitors precociously differentiated and proceeded into meiosis on a normal timeline, while differentiating spermatogonia were unable to hasten their entry into meiosis. This reveals that the spermatogonia responding to RA must still complete the 8.6 day differentiation program prior to their entry into meiosis. Addition of exogenous RA enriched testes with preleptotene and pachytene spermatocytes one and two seminiferous cycles later, respectively, supporting recent clinical studies reporting increased sperm production and enhanced fertility in subfertile men on long-term RA analog treatment. Collectively, our results reveal that a well-buffered system exists within mammalian testes to regulate spermatogonial RA exposure, that exposed undifferentiated progenitors can precociously differentiate, but must complete a normal-length differentiation program prior to entering meiosis, and that daily RA treatments increased the numbers of advanced germ cells by directing undifferentiated progenitors to continuously differentiate.
Spontaneous activity in cortical neurons is stereotyped and non-Poisson
Authors: Swindale Nicholas V , Spacek Martin A , Krause Matthew , Mitelut Catalin 
Published: January 2023

Abstract
Neurons fire even in the absence of sensory stimulation or task demands. Numerous theoretical studies have modeled this spontaneous activity as a Poisson process with uncorrelated intervals between successive spikes and a variance in firing rate equal to the mean. Experimental tests of this hypothesis have yielded variable results, though most have concluded that firing is not Poisson. However, these tests say little about the ways firing might deviate from randomness. Nor are they definitive because many different distributions can have equal means and variances. Here, we characterized spontaneous spiking patterns in extracellular recordings from monkey, cat, and mouse cerebral cortex neurons using rate-normalized spike train autocorrelation functions (ACFs) and a logarithmic timescale. If activity was Poisson, this function should be flat. This was almost never the case. Instead, ACFs had diverse shapes, often with characteristic peaks in the 1–700 ms range. Shapes were stable over time, up to the longest recording periods used (51 min). They did not fall into obvious clusters. ACFs were often unaffected by visual stimulation, though some abruptly changed during brain state shifts. These behaviors may have their origin in the intrinsic biophysics and dendritic anatomy of the cells or in the inputs they receive.
Letting leaders spontaneously emerge yields better creative outcomes and higher leader–follower interbrain synchrony during creative group communication
Authors: He Yingyao , Wang Xinyue , Lu Kelong , Hao Ning 
Published: January 2023

AbstractThis study aimed to investigate how the ways leaders arise (appointed vs. emergent) affect the leader–follower interaction during creative group communication. Hyperscanning technique was adopted to reveal the underlying interpersonal neural correlates using functional near-infrared spectroscopy. Participants were assigned into 3-person groups to complete a creative problem-solving task. These groups were randomly split into conditions of appointed (condition A) and emergent (condition E) leaders. Creative group outcomes were better in condition E, accompanied by more frequent perspective-taking behaviors between leaders and followers. The interpersonal brain synchronization (IBS) increment for leader–follower pairs was significantly higher at the right angular gyrus (rAG), between the rAG and the right supramarginal gyrus (rSMG), and between the right middle temporal gyrus and the right motor cortex in condition E and positively correlated with perspective-taking behaviors between leaders and followers. The graph-based analysis showed higher nodal betweenness of the rAG and the rSMG in condition E. These results indicated the neural coupling of brain regions involved in mentalizing, semantic processing and motor imagery may underlie the dynamic information transmission between leaders and followers during creative group communication.