bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Systematic Review of the Efficacy and Safety of Tranexamic Acid in Facelift Surgery
Authors: Al-Hashimi Mustafa , Kaur Pawandeep , Charles Walton , Bhasta Mhafrin , Nahai Foad , Khajuria Ankur 
Published: July 2023

Abstract
Tranexamic acid (TXA) has become widely utilized in different specialities including facelift surgery. The aim of this review was to robustly evaluate the quality of available evidence on the efficacy and safety of TXA use in facelift surgery. We searched the MEDLINE (National Institutes of Health, Bethesda, MD), Embase (Elsevier, Amsterdam, the Netherlands), CINAHL (EBSCO Information Services, Ipswich, MA), Cochrane Central Register of Controlled Trials (CENTRAL; Wiley, Hoboken, NJ), Google Scholar (Alphabet Inc. Mountain View, CA), Science Citation Index (Clarivate, London, UK), and Latin American and Caribbean Center on Health Sciences Information (LILACS; São Paulo, Brazil) databases for randomized controlled trials (RCTs) and observational studies. Primary outcomes were blood loss, postoperative hematoma, ecchymosis, and swelling, in addition to technical considerations and complications. We assessed review quality with the AMSTAR 2 tool, study quality with Grading of Recommendations, Assessment, Development, and Evaluations approach (GRADE) tool, and the risk of bias with Cochrane's RoB 2.0 tool for RCTs and ROBINS-I for nonrandomized studies. Of the 368 articles, a total of 3 studies including 150 patients met the inclusion criteria. The RCT reported a significant reduction in postoperative serosanguineous collections in the TXA group (P &lt; .01), and in surgeon-rated postoperative ecchymosis and bruising. The prospective cohort study reported reduced drainage output in first 24 hours in the TXA group (P &lt; .01). The retrospective cohort study reported lower intraoperative blood loss, mean postoperative day 1 drain output, percentage of drain removal on postoperative day 1, and number of days to drain removal in the TXA group (all P &lt; .01). The quality of studies was moderate, and this review was the highest rated compared to previous reviews, as per the AMSTAR 2 tool. Based on limited literature, TXA improves clinical outcomes regardless of the route of administration. Topical TXA is an emerging route, expediting drain removal and reducing blood loss. Future Level I high-quality studies are required.
Gibberellin metabolism and signaling
Authors: Ueguchi-Tanaka Miyako 
Published: July 2023

ABSTRACT
Gibberellins (GAs) are plant hormones with a tetracyclic diterpenoid structure that are involved in various important developmental processes. Two GA-deficient mutants were isolated: a semidwarf mutant “sd1”, which was found to have a defective GA20ox2 gene and was introduced to the world in a green revolution cultivar, and a severe dwarf allele of “d18”, with a defective GA3ox2 gene. Based on the phenotypic similarity of d18, rice dwarf mutants were screened, further classifying them into GA-sensitive and GA-insensitive by applying exogenous GA3. Finally, GA-deficient rice mutants at 6 different loci and 3 GA signaling mutants (gid1, gid2, and slr1) were isolated. The GID1 gene encodes a GA nuclear receptor, and the GID1–DELLA (SLR1) system for GA perception is widely used in vascular plants. The structural characteristics of GID1 and GA metabolic enzymes have also been reviewed.
Difference in the ligand affinity among redundant plant hormone receptors of rice OsCOI1a/1b/2-OsJAZs
Authors: Okumura Taichi , Kitajima Tsumugi , Kaji Takuya , Urano Haruyuki , Matsumoto Kotaro , Inagaki Hideo , Miyamoto Koji , Okada Kazunori , Ueda Minoru 
Published: July 2023

ABSTRACT
(3R, 7S)-jasmonoyl-L-isoleucine (JA-Ile) is a lipid-derived plant hormone that regulates plant responses, including biotic/abiotic stress adaptation. In the plant cells, JA-Ile is perceived by COI1-JAZ co-receptor by causing protein-protein interaction between COI1 and JAZ proteins to trigger gene expressions. In this study, we focused on Oryza sativa, a model monocot and an important crop, with 45 possible OsCOI-OsJAZ co-receptor pairs composed of three OsCOI homologs (OsCOI1a, OsCOI1b, and OsCOI2) and 15 OsJAZ homologs. We performed fluorescein anisotropy and pull-down assays to examine the affinity between JA-Ile and OsCOI1a/1b/2-OsJAZ1-15 co-receptor pairs. The results revealed a remarkable difference in the modes of ligand perception by OsCOI1a/1b and OsCOI2. Recently, the unique function of OsCOI2 in some of the JA-responses were revealed. Our current results will lead to the possible development of OsCOI2-selective synthetic ligand.
iDRPro-SC: identifying DNA-binding proteins and RNA-binding proteins based on subfunction classifiers
Authors: Yan Ke , Feng Jiawei , Huang Jing , Wu Hao 
Published: July 2023

Abstract
Nucleic acid-binding proteins are proteins that interact with DNA and RNA to regulate gene expression and transcriptional control. The pathogenesis of many human diseases is related to abnormal gene expression. Therefore, recognizing nucleic acid-binding proteins accurately and efficiently has important implications for disease research. To address this question, some scientists have proposed the method of using sequence information to identify nucleic acid-binding proteins. However, different types of nucleic acid-binding proteins have different subfunctions, and these methods ignore their internal differences, so the performance of the predictor can be further improved. In this study, we proposed a new method, called iDRPro-SC, to predict the type of nucleic acid-binding proteins based on the sequence information. iDRPro-SC considers the internal differences of nucleic acid-binding proteins and combines their subfunctions to build a complete dataset. Additionally, we used an ensemble learning to characterize and predict nucleic acid-binding proteins. The results of the test dataset showed that iDRPro-SC achieved the best prediction performance and was superior to the other existing nucleic acid-binding protein prediction methods. We have established a web server that can be accessed online: http://bliulab.net/iDRPro-SC.
MSFP: undergraduate ‘collaborate-from-home’ research in macromolecular structure and function
Authors: Jeffery Constance J 
Published: July 2023

Abstract

Summary
When the COVID-19 crisis shut down most undergraduate research opportunities, the Macromolecular Structure and Function Research Experiences for Undergraduates Program provided a mentored research experience on the topic of Macromolecular Structure and Function and training in professional skills to assist the participants in pursuing a degree and a future career in STEM. The fully online, remote, computer-based program was funded by the USA National Science Foundation. It involved faculty at four geographically distributed institutions specializing in diverse but complementary approaches to study macromolecular structure and function. Importantly, its online ‘collaborate-from-home’ format made it accessible to students during the pandemic to participate fully in the research, professional development and other activities of the program. This project can also serve as an example for future remote, online projects that would especially be helpful for students who do not have access to similar programs at their universities, cannot travel to attend a summer program, have physical challenges that make it difficult for them to work in a lab or students whose research opportunities are limited due to the war in Ukraine. The lessons learned with the Macromolecular Structure and Function REU program can provide helpful information for ISCB members to set up similar programs to serve additional students.

Availability and implementation
More information and resources are available on the project web site http://jefferylab.moonlightingproteins.org.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
COVRECON: automated integration of genome- and metabolome-scale network reconstruction and data-driven inverse modeling of metabolic interaction networks
Authors: Li Jiahang , Waldherr Steffen , Weckwerth Wolfram 
Published: July 2023

Abstract

Motivation
One central goal of systems biology is to infer biochemical regulations from large-scale OMICS data. Many aspects of cellular physiology and organismal phenotypes can be understood as results of metabolic interaction network dynamics. Previously, we have proposed a convenient mathematical method, which addresses this problem using metabolomics data for the inverse calculation of biochemical Jacobian matrices revealing regulatory checkpoints of biochemical regulations. The proposed algorithms for this inference are limited by two issues: they rely on structural network information that needs to be assembled manually, and they are numerically unstable due to ill-conditioned regression problems for large-scale metabolic networks.

Results
To address these problems, we developed a novel regression loss-based inverse Jacobian algorithm, combining metabolomics COVariance and genome-scale metabolic RECONstruction, which allows for a fully automated, algorithmic implementation of the COVRECON workflow. It consists of two parts: (i) Sim-Network and (ii) inverse differential Jacobian evaluation. Sim-Network automatically generates an organism-specific enzyme and reaction dataset from Bigg and KEGG databases, which is then used to reconstruct the Jacobian’s structure for a specific metabolomics dataset. Instead of directly solving a regression problem as in the previous workflow, the new inverse differential Jacobian is based on a substantially more robust approach and rates the biochemical interactions according to their relevance from large-scale metabolomics data. The approach is illustrated by in silico stochastic analysis with differently sized metabolic networks from the BioModels database and applied to a real-world example. The characteristics of the COVRECON implementation are that (i) it automatically reconstructs a data-driven superpathway model; (ii) more general network structures can be investigated, and (iii) the new inverse algorithm improves stability, decreases computation time, and extends to large-scale models.

Availability and implementation
The code is available in the website https://bitbucket.org/mosys-univie/covrecon.
The origin and fate of fungal mitochondrial horizontal gene transferred sequences in orchids (Orchidaceae)
Authors: Valencia-D Janice , Neubig Kurt M , Clark David P 
Published: July 2023

Abstract
The transfer of DNA among distantly related organisms is relatively common in bacteria but less prevalent in eukaryotes. Among fungi and plants, few of these events have been reported. Two segments of fungal mitochondrial DNA have been recently discovered in the mitogenome of orchids. Here, we build on that work to understand the timing of those transfer events, which orchids retain the fungal DNA and the fate of the foreign DNA during orchid evolution. We update the content of the large DNA fragment and establish that it was transferred to the most recent common ancestor of a highly diverse clade of epidendroid orchids that lived ~28–43 Mya. Also, we present hypotheses of the origin of the small transferred fragment. Our findings deepen the knowledge of these interesting DNA transfers among organelles and we formulate a probable mechanism for these horizontal gene transfer events.
Women in cardiovascular imaging: a call for action to address ongoing challenges
Authors: Joshi Shruti S , Kadavath Sabeeda , Mandoli Giulia Elena , Gimelli Alessia , Gulati Martha , Thamman Ritu , Lundberg Gina , Mehran Roxana , Mulvagh Sharon L , Sade Leyla Elif , Shivalkar Bharati , Shaw Leslee J , Hristova Krasimira , Dweck Marc R , Almeida Ana G , Grapsa Julia 
Published: July 2023

Abstract

Aims
The EACVI Scientific Initiatives Committee and the EACVI women’s taskforce conducted a global survey to evaluate the barriers faced by women in cardiovascular imaging (WICVi).

Methods and results
In a prospective international survey, we assessed the barriers faced at work by WICVi. Three hundred fourteen participants from 53 countries responded. The majority were married (77%) and had children (68%), but most reported no flexibility in their work schedule during their pregnancy or after their maternity leave. More than half of the women reported experiencing unconscious bias (68%), verbal harassment (59%), conscious bias (51%), anxiety (70%), lack of motivation (60%), imposter syndrome (54%), and burnout (61%) at work. Furthermore, one in five respondents had experienced sexual harassment, although this was rarely reported formally. The majority reported availability of mentorship (73%), which was mostly rated as ‘good’ or ‘very good’. While more than two-thirds of respondents (69%) now reported being well trained and qualified to take on leadership roles in their departments, only one-third had been afforded that opportunity. Despite the issues highlighted by this survey, &gt;80% of the participating WICVi would still choose cardiovascular imaging if they could restart their career.

Conclusion
The survey has highlighted important issues faced by WICVi. While progress has been made in areas such as mentorship and training, other issues including bullying, bias, and sexual harassment are still widely prevalent requiring urgent action by the global cardiovascular imaging community to collectively address and resolve these challenges.
Periplasmic methionine sulfoxide reductase (MsrP)—a secondary factor in stress survival and virulence of Salmonella Typhimurium
Authors: Chandra Hari Balaji , Shome Arijit , Sahoo Raj , Apoorva S , Bhure Sanjeev Kumar , Mahawar Manish 
Published: July 2023

Abstract
Among others, methionine residues are highly susceptible to host-generated oxidants. Repair of oxidized methionine (Met-SO) residues to methionine (Met) by methionine sulfoxide reductases (Msrs) play a chief role in stress survival of bacterial pathogens, including Salmonella Typhimurium. Periplasmic proteins, involved in many important cellular functions, are highly susceptible to host-generated oxidants. According to location in cell, two types of Msrs, cytoplasmic and periplasmic are present in S. Typhimurium. Owing to its localization, periplasmic Msr (MsrP) might play a crucial role in defending the host-generated oxidants. Here, we have assessed the role of MsrP in combating oxidative stress and colonization of S. Typhimurium. ΔmsrP (mutant strain) grew normally in in-vitro media. In comparison to S. Typhimurium (wild type), mutant strain showed mild hypersensitivity to HOCl and chloramine-T (ChT). Following exposure to HOCl, mutant strain showed almost similar protein carbonyl levels (a marker of protein oxidation) as compared to S. Typhimurium strain. Additionally, ΔmsrP strain showed higher susceptibility to neutrophils than the parent strain. Further, the mutant strain showed very mild defects in survival in mice spleen and liver as compared to wild-type strain. In a nutshell, our results indicate that MsrP plays only a secondary role in combating oxidative stress and colonization of S. Typhimurium.
Chlamydia pneumoniae-immunoglobulin E antibody responses in serum from children with asthma
Authors: Smith-Norowitz Tamar A , Shulman Anastasiya , Abdelmajid Haram , Hammerschlag Margaret R , Joks Rauno , Weaver Diana , Kohlhoff Stephan 
Published: July 2023

Abstract
Chlamydia pneumoniae is an obligate intracellular bacterium that causes respiratory infections in humans. An association between persistent C. pneumoniae infection and asthma pathogenesis has been described. It is unknown whether specific immunoglobulin E (IgE) is a marker of persistent immune activation responses. Therefore, the association between C. pneumoniae-specific-IgE antibodies (Abs) and interferon (IFN)-gamma produced by C. pneumoniae-stimulated peripheral blood mononuclear cells (PBMC) was examined. Blood was collected and serum separated. PBMC from 63 children with or without stable asthma (N = 45 and 18, respectively) were infected or not infected with C. pneumoniae AR-39 and cultured for up to 7 days. Supernatants were collected, and IFN-gamma levels measured (ELISA). Serum C. pneumoniae-IgE Abs were detected by immunoblotting. C. pneumoniae-IgE Abs were detected in asthmatics (27%), compared with non-asthmatics (11%) (P = NS). IFN-gamma responses were more prevalent among asthmatics who had positive C. pneumoniae-IgE Abs (60%) compared with asthmatics without C. pneumoniae-IgE Abs (20%) (P = 0.1432). IFN-gamma responses in C. pneumoniae-stimulated PBMC from children with asthma were more frequent in children who had specific anti-C. pneumoniae-IgE Abs compared to those who did not. This immune response may reflect persistent infection, which may contribute to ongoing asthma symptoms.
Yeast population dynamics in Brazilian bioethanol production
Authors: Rego-Costa Artur , Huang I Ting , Desai Michael M , Gombert Andreas K 
Published: July 2023

Abstract
The large-scale and nonaseptic fermentation of sugarcane feedstocks into fuel ethanol in biorefineries represents a unique ecological niche, in which the yeast Saccharomyces cerevisiae is the predominant organism. Several factors, such as sugarcane variety, process design, and operating and weather conditions, make each of the ∼400 industrial units currently operating in Brazil a unique ecosystem. Here, we track yeast population dynamics in 2 different biorefineries through 2 production seasons (April to November of 2018 and 2019), using a novel statistical framework on a combination of metagenomic and clonal sequencing data. We find that variation from season to season in 1 biorefinery is small compared to the differences between the 2 units. In 1 biorefinery, all lineages present during the entire production period derive from 1 of the starter strains, while in the other, invading lineages took over the population and displaced the starter strain. However, despite the presence of invading lineages and the nonaseptic nature of the process, all yeast clones we isolated are phylogenetically related to other previously sequenced bioethanol yeast strains, indicating a common origin from this industrial niche. Despite the substantial changes observed in yeast populations through time in each biorefinery, key process indicators remained quite stable through both production seasons, suggesting that the process is robust to the details of these population dynamics.
Conjecture 𝒪 for Projective Complete Intersections
Authors: Ke Hua-Zhong 
Published: July 2023

Abstract
Conjecture ${{\mathcal{O}}}$ and Gamma conjectures for quantum cohomology of Fano manifolds were proposed by Galkin, Golyshev, and Iritani [ 16]. We prove Conjecture ${{\mathcal{O}}}$ for Fano complete intersections in projective spaces. The main tools to compute relevant genus-zero Gromov–Witten invariants with primitive insertions are the genus-one topological recursion relation and Zinger’s standard-versus-reduced formula. We also prove a related conjecture of Galkin [ 15] for projective Fano complete intersections.
Applying anti-racist approaches to informatics: a new lens on traditional frames
Authors: Platt Jodyn , Nong Paige , Merid Beza , Raj Minakshi , Cope Elizabeth , Kardia Sharon , Creary Melissa 
Published: July 2023

Abstract
Health organizations and systems rely on increasingly sophisticated informatics infrastructure. Without anti-racist expertise, the field risks reifying and entrenching racism in information systems. We consider ways the informatics field can recognize institutional, systemic, and structural racism and propose the use of the Public Health Critical Race Praxis (PHCRP) to mitigate and dismantle racism in digital forms. We enumerate guiding questions for stakeholders along with a PHCRP-Informatics framework. By focusing on (1) critical self-reflection, (2) following the expertise of well-established scholars of racism, (3) centering the voices of affected individuals and communities, and (4) critically evaluating practice resulting from informatics systems, stakeholders can work to minimize the impacts of racism. Informatics, informed and guided by this proposed framework, will help realize the vision of health systems that are more fair, just, and equitable.
Feeding 3-nitrooxypropanol reduces methane emissions by feedlot cattle on tropical conditions
Authors: Araújo Tiago L R , Rabelo Carlos H S , Cardoso Abmael S , Carvalho Victor V , Acedo Tiago S , Tamassia Luis F M , Vasconcelos Guilherme S F M , Duval Stephane M , Kindermann Maik , Gouvea Vinicius N , Fernandes Marcia H M R , Reis Ricardo A 
Published: July 2023

Abstract
Our objective was to evaluate the effects of feeding 3-nitrooxypropanol (3-NOP; Bovaer, DSM Nutritional Products) at two levels on methane emissions, nitrogen balance, and performance by feedlot cattle. In experiment 1, a total of 138 Nellore bulls (initial body weight, 360 ± 37.3 kg) were housed in pens (27 pens with either 4 or 5 bulls per pen) and fed a high-concentrate diet for 96 d, containing 1) no addition of 3-NOP (control), 2) inclusion of 3-NOP at 100 mg/kg dry matter (DM), and 3) inclusion of 3-NOP at 150 mg/kg DM. No adverse effects of 3-NOP were observed on DM intake (DMI), animal performance, and gain:feed (P &gt; 0.05). In addition, there was no effect (P &gt; 0.05) of 3-NOP on carcass characteristics (subcutaneous fat thickness and rib eye area). In experiment 2, 24 bulls (initial BW, 366 ± 39.6 kg) housed in 12 pens (2 bulls/pen) from experiment 1 were used for CH4 measurements and nitrogen balance. Irrespective of the level, 3-NOP consistently decreased (P &lt; 0.001) animals’ CH4 emissions (g/d; ~49.3%), CH4 yield (CH4/DMI; ~40.7%) and CH4 intensity (CH4/average daily gain; ~38.6%). Moreover, 3-NOP significantly reduced the gross energy intake lost as CH4 by 42.5% (P &lt; 0.001). The N retention: N intake ratio was not affected by 3-NOP (P = 0.19). We conclude that feeding 3-NOP is an effective strategy to reduce methane emissions, with no impairment on feedlot cattle performance.
Data-driven intelligent computational design for products: method, techniques, and applications
Authors: Yang Maolin , Jiang Pingyu , Zang Tianshuo , Liu Yuhao 
Published: July 2023

Abstract
Data-driven intelligent computational design (DICD) is a research hotspot that emerged under fast-developing artificial intelligence. It emphasizes utilizing deep learning algorithms to extract and represent the design features hidden in historical or fabricated design process data and then learn the combination and mapping patterns of these design features for design solution retrieval, generation, optimization, evaluation, etc. Due to its capability of automatically and efficiently generating design solutions and thus supporting human-in-the-loop intelligent and innovative design activities, DICD has drawn the attention of both academic and industrial fields. However, as an emerging research subject, many unexplored issues still limit the development and application of DICD, such as specific dataset building, engineering design-related feature engineering, systematic methods and techniques for DICD implementation in the entire product design process, etc. In this regard, a systematic and operable road map for DICD implementation from a full-process perspective is established, including a general workflow for DICD project planning, an overall framework for DICD project implementation, the common mechanisms and calculation principles during DICD, key enabling technologies for detailed DICD implementation, and three case scenarios of DICD application. The road map can help academic researchers to locate their specific research directions for the further development of DICD and provide operable guidance for the engineers in their specific DICD applications.