bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Automated Model Annotation System (AMAS) for SBML Models
Authors: Shin Woosub , Gennari John H. , Hellerstein Joseph L. , Sauro Herbert M. 
Published: July 2023

AbstractMotivationAnnotations of biochemical models provide details of chemical species, documentation of chemical reactions, and other essential information. Unfortunately, the vast majority of biochemical models have few, if any, annotations, or the annotations provide insufficient detail to understand the limitations of the model. The quality and quantity of annotations can be improved by developing tools that recommend annotations. For example, recommender tools have been developed for annotations of genes. Although annotating genes is conceptually similar to annotating biochemical models, there are important technical differences that make it difficult to directly apply this prior work.ResultsWe present AMAS, a system that predicts annotations for elements of models represented in the Systems Biology Markup Language (SBML) community standard. We provide a general framework for predicting model annotations for a query element based on a database of annotated reference elements and a match score function that calculates the similarity between the query element and reference elements. The framework is instantiated to specific element types (e.g., species, reactions) by specifying the reference database (e.g., ChEBI for species) and the match score function (e.g., string similarity). We analyze the computational efficiency and prediction quality of AMAS for species and reactions in BiGG and BioModels and find that it has sub-second response times and accuracy between 80% and 95% depending on specifics of what is predicted. We have incorporated AMAS into an open-source, pip-installable Python package that can run as a command-line tool that predicts and adds annotations to species and reactions to an SBML model.AvailabilityOur project is hosted athttps://github.com/sys-bio/AMAS, where we provide examples, documentation, and source code files. Our source code is licensed under the MIT open-source license.Contacthsauro@uw.eduSupplementary informationSupplementary data are available online.
Minero‐chemical and provenance analysis of Achaemenian lapis lazuli cylinders from Persepolis
Authors: Oudbashi Omid , Hessari Morteza , Shekofteh Atefeh 
Published: July 2023

AbstractFive archaeological plain cylinders made of lapis lazuli found in excavations at the Persepolis World Heritage Site (c.550–330 BCE) were analysed using wavelength‐dispersive X‐ray fluorescence spectroscopy, inductively coupled plasma‐mass spectroscopy, X‐ray powder diffraction, and scanning electron microscopy with energy‐dispersive X‐ray spectroscopy techniques with the goal of characterizing the chemical–mineralogical composition and identifying the possible provenance of raw materials. Results show that these objects are made of identical resources or mines. A comparison with available data from archaeological sites and ancient quarry sites shows that these finds may have been produced from lapis lazuli from east of the Iranian Plateau (Badakhshan in Afghanistan), as they resemble several ancient objects of Iran. The results of this study suggest that Persian artists also used the ancient East‐to‐West trade route for supplying raw material to produce decorative objects made of lapis lazuli.
Expectations of treatment outcome in complex cases of patients with chronic pain: A study on the DATAPAIN cohort
Authors: Waardenburg Sophie , de Meij Nelleke , van Kuijk Sander M. J. , Van Zundert Jan , Brouwer Brigitte A. 
Published: July 2023

AbstractBackgroundA better insight in how the biopsychosocial factors influence patient outcome(s) may provide information that helps selecting the optimal pain management for a specific group.MethodsCategorization was made in the prospective DATAPAIN registry, in which patients with pain severity (Numeric Rating Scale [NRS]: 7–10), depression or anxiety (Hospital Anxiety and Depression Scale: > 10), and pain catastrophizing (Pain Catastrophizing Scale: > 31) were identified as complex cases. Patient outcomes; treatment satisfaction on the Patient Global Impression of Change (PGIC), pain relief (NRS), pain interference on the Brief Pain Inventory (BPI) and quality of life indicator General Perceived Health (GPH) were evaluated. Logistic regression analyzed if belonging to the complex cases showed modification in the outcome of the PGIC and GPH. Linear regression was observed if complex cases differed in average reduction in pain relief and interference compared to non‐complex cases.Results1637 patients were included, of which 345 (21.08%) were considered complex cases. The changes in scores of pain relief and BPI active subscale were not significantly different between groups. The BPI affective subscale had a different change in score (−0.509; p: 0.002). The complex cases had an odds ratio (OR) of 0.59 (95% confidence interval [CI]: 0.36–0.77) on treatment satisfaction compared to non‐complex cases, and an OR of 0.28 (95% CI: 0.11–0.56) on the GPH.ConclusionWhen treating patients with complex cases, desired treatment outcome(s) should be recognized by specialists and patients, as these may be less likely to occur.
Natural variation of MS2 confers male fertility and drives hybrid breeding in soybean
Authors: Fang Xiaolong , Feng Xiangchi , Sun Xiaoyuan , Yang Xiangdong , Li Qing , Yang Xulei , Xu Jie , Zhou Minghui , Lin Chunjing , Sui Yi , Zhao Limei , Liu Baohui , Kong Fanjiang , Zhang Chunbao , Li Meina 
Published: July 2023

SummaryA complete and genetically stable male sterile line with high outcrossing rate is a prerequisite for the development of commercial hybrid soybean. It was reported in the last century that the soybean male sterile ms2 mutant has the highest record with seed set. Here we report the cloning and characterization of the MS2 gene in soybean, which encodes a protein that is specifically expressed in the anther. MS2 functions in the tapetum and microspore by directly regulating genes involved in the biosynthesis of secondary metabolites and the lipid metabolism, which is essential for the formation of microspore cell wall. Through comparison of the field performance with the widely used male sterile mutants in the same genetic background, we demonstrated that the ms2 mutant conducts the best in outcrossing rate and makes it an ideal tool in building a cost‐effective hybrid system for soybean.
RELIGION, SPIRITUALITY, AND MENTAL HEALTH AMONG SCIENTISTS DURING THE PANDEMIC: A FOUR‐COUNTRY STUDY
Authors: Di Di , Cranney Stephen , Vaidyanathan Brandon , Fitzgerald Caitlin Anne 
Published: July 2023

AbstractA vast body of research shows largely positive associations between religiosity/spirituality (R/S) and positive well‐being outcomes. Such research has examined religious communities and general populations, but little is known about the relationship between R/S and well‐being among scientists, who typically tend to be less religious than the general public. Drawing on nationally representative survey data on physicists and biologists in India, Italy, the United Kingdom, and the United States (N = 3442), this study examines whether the relationship between R/S and mental health holds for scientists, particularly during the COVID‐19 pandemic. We find that net of statistical controls, higher levels of religious and spiritual commitment are associated with significantly higher levels of well‐being and lower levels of psychological distress. Overall, the results indicate that a positive relationship between R/S and mental health holds even for scientists. The study's findings have implications for future analysis of the relationship between R/S and the well‐being of people working in other professions.
The First Systematic Meteorological Observations in the Americas (Recife, 1640–42)
Authors: Domínguez-Castro Fernando , Gallego María de la Cruz , Vaquero Jose M. , García Herrera Ricardo , Corral Victoria , Sáez Rosa M. Marina , Trigo Ricardo M. , Libonati Renata , Noguera Iván , El Kenawy Ahmed , Peña Angulo Dhais , Vicente-Serrano Sergio M. 
Published: July 2023

Abstract
In 1639, the German naturalist Georg Marcgraf established the first astronomical observatory in the Americas, located in Recife (Brazil). There, he made the first daily systematic meteorological observations of wind direction, precipitation, fog, and thunder and lightning from 1640 to 1642. We outline the circumstances that led to this observatory being established and analyze the observations. The range of values obtained from all the variables recorded by Marcgraf corresponds well with Recife’s current climate. However, wetter-than-normal conditions were recorded during 1640, while anomalous concentrations of foggy days occurred from May to December 1641. We hypothesize that these anomalous record foggy days could be associated with the highly explosive eruptions of the Komagatake and Parker volcanoes, both in 1640.
Efficacy of recombinant bovine basic fibroblast growth factor to reduce hemorrhage after cervical loop electrosurgical excision procedure
Authors: Weng Chongrong , Xu Jian , Yang Hua , Deng Panxia , Ou Honghui , Xu Yue , Zhuang Yuan , Nie Huilong 
Published: July 2023

Abstract
Objective
It has been reported that recombinant bovine basic fibroblast growth factor (rbFGF) may possess possible biological functions in promoting the process of wound healing. Consequently, our study aimed to investigate the hemostatic effect of topically applied rbFGF in patients who underwent a loop electrosurgical excision procedure (LEEP).

Methods
In this retrospective analysis, we meticulously examined clinicopathologic data from a cohort of 90 patients who underwent LEEP at our institution between 2020 and 2021. Subsequently, we conducted inquiries with the patients to ascertain the degree of vaginal bleeding experienced during the postoperative periods of 3 and 6 weeks, comparing it to their preoperative menstrual flow. The magnitude of the menstrual volume alteration was then quantified using a menstrual volume multiplier(MVM). The primary endpoints of our investigation were to assess the hemostatic effect of rbFGF by means of evaluating the MVM. Additionally, the secondary endpoints encompassed the assessment of treatment-related side effects of such as infection and dysmenorrhea.

Results
Our findings demonstrated a significant reduction in hemorrhage following cervical LEEP. Specifically, in the per-protocol analysis, the study group exhibited a statistically significantly decrease in MVM after 3 weeks (0 [0–0] vs. 1 [0–1], respectively; p < 0.001) and after 6 weeks (1 [1] vs. 2 [1–3], respectively; p < 0.001) of the procedure. No notable disparities were observed in the remaining outcomes between the two groups. Moreover, a logistic regression analysis was employed to explore the relationship between significant bleeding and rbFGF treatment (p < 0.001, OR = -2.47, 95% CI -4.07 ~-1.21), while controlling for confounding factors such as age, BMI, and surgical specimen.

Conclusions
In conclusion, our study findings highlight that the application of recombinant bovine basic fibroblast growth factorcan effectively mitigate hemorrhage subsequent to cervical loop electrosurgical excision procedure.
A community-based cross-sectional study of COVID-19 and psychological distress using the impact of event scale revised among recovered patients of COVID-19
Authors: Mushtaq Beenish , Jan Yasmeen , Bhat Ashfaq Ahmad , Deeba Farah 
Published: July 2023

COVID-19 infection is a potentially traumatic experience in terms of the risk of running a Severe Acute Respiratory Syndrome in addition to the social implications of the disease in terms of being isolated and follow up of strict quarantine measures of close contact. The purpose of this study was to assess the prevalence of psychological distress and its risk factors in patients who develop COVID-19 infection. There is scanty evidence regarding the magnitude of COVID-19-related psychological distress (PD) among the general population of India, and Post Traumatic Stress Disorder (PTSD) is a Mental Disorder that develops after a traumatic event that has a life-threatening impact.
The aim of this study was to assess COVID-19 infection.
Material and methods: This study was conducted among 672 COVID-19 survivors of district Budgam from (March to August 2020). They were contacted by telephone, and psychological distress in the post-COVID recovery period was assessed using the IES-R scale. This is a 22-item scale, and each item is rated on a scale ranging from 0-4. Suitable Statistical Analysis was done to analyze risk factors for the development of any psychological distress.
Methods: Descriptive cross-sectional study.
Study design: Cross-sectional study from District Budgam of Kashmir Division.
Study tool: using the IES-R scale for PTSD.
Result: In our study prevalence of psychological distress using IES –R was mild in (7.08 %) of the study participants and moderate in (1.06 %) of the study participants. Psychological distress in study participants was examined by age, sex, employment status, family history, COVID-19 disease status and history of hospitalization. No statistical significance between age, gender, days of hospitalization and PTSD was seen. However, statistical significance with the IES–R score was seen between family history and the presence and absence of symptoms in the study subjects.
Conclusion: As the pandemic crisis seems to be ebbing, the current findings help us to identify risk factors and devise pragmatic strategies to curtail the burden of mental issues and successfully meet the challenges that follow the pandemic
An Adaptive Fuzzy Control Method for Multi-joint Manipulator Based on Fuzzy Compensation
Authors: Zhang Biao , Yang Baoping , Wang Qiong 
Published: July 2023

Abstract
The manipulator is an important machine for assisting production and life and has been widely used in various fields. Aiming at the problem that the manipulator control system cannot realize fast and high precision trajectory tracking control when it is disturbed by random and non-linear factors, considering that the data information of the fuzzy system is known and the control variables of the system can be controlled and measured, an adaptive fuzzy control law based on fuzzy compensation is designed by using the approximation characteristics of the fuzzy system. This method can effectively suppress the external disturbance and friction disturbance in the process of manipulator motion, so that it can quickly and accurately track the position and speed of the manipulator. The simulation results of the proposed adaptive robust control method based on fuzzy compensation show that it can well suppress the influence of non-linear factors such as friction, disturbance and load variation, and improve the position tracking accuracy by 64.5% and the speed tracking accuracy by 67.3%.
Isolation and characterization of lytic bacteriophages infecting Pectobacterium atrosepticum
Authors: Wu Jian , Handique Utpal 
Published: July 2023

Abstract

Pectobacterium spp. cause blackleg and soft rot on potato worldwide. Potato is a staple crop in China, and blackleg and soft rot diseases caused by Pectobacterium spp. have increased significantly as potato cultivation expanded rapidly in the last decade. This study was conducted to isolate and characterize the lytic bacteriophages infecting the major pathogen causing potato blackleg and soft rot, Pectobacterium atrosepticum (P. a.), in water and soil samples collected in the cities Wuhan and Datong in China. Three lytic bacteriophages were obtained and named Pectobacterium Phages ZRIMU1, 2, and 7. Transmission electron microscopic analysis revealed that all three phages were similar in size, with a smooth head (diameter ca. 40–50 nm) and without a neck or tail. The adsorption of phages PP1, PP2, and PP7 to P. a. after 18, 27, and 18 min was 98, 99 and 98%, respectively. The latent periods for PP1, PP2, and PP7 were 20, 40, and 50 min, respectively. In vitro bacterial challenge assays showed that these three phages were able to infect P. a. 1 h after coinoculation. The potential of these bacteriophages to protect potato seedlings was tested. After 27 days of inoculation, seedlings inoculated with water and sprayed with or without phages developed well, and no symptoms developed. Seedlings inoculated with P. a. only had a significantly lower survival rate than the controls, and seedlings coinoculated with P. a. and phages significantly improved the survival rate by 40%. Recovery of symptomatic plants was observed in groups that were treated with either a single phage or a mixture of phages. More investigations are needed to clarify the mechanism by which phages can be used to cure symptomatic potato plants.
Identification of genetic loci and candidate genes underlying freezing tolerance in wheat seedlings
Authors: Pan Xu , Nie Xianlai , Gao Wei , Yan Shengnan , Feng Hansheng , Cao Jiajia , Lu Jie , Shao Hui , Ma Chuanxi , Chang Cheng , Zhang Haiping 
Published: July 2023

Abstract
Frost damage restricts wheat growth, development, and geographical distribution. However, the genetic mechanism of freezing tolerance (FT) remains unclear. Here, we evaluated FT phenotypes of 245 wheat varieties (lines) and genotyped them using a Wheat 90K array. The association analysis showed that ten stable loci were significantly associated with FT (P < 1 × 10-4), and explained 6.45-26.33% of the phenotypic variation. In particular, the major locus QFT.ahau-7B.2 was consistently related to all nine sets of FT phenotypic data. Based on five cleaved amplified polymorphic sequence (CAPS) markers closely linked to QFT.ahau-7B.2, we narrowed down the target region to the 566.13-566.63 Mb interval on chromosome 7B, in which four candidate genes were annotated. Of these, only TaRPM1-7BL exhibited consistent differential expression after low temperature treatment between freezing-tolerant and freezing-sensitive varieties. The results of cloning and whole-exome capture sequencing indicated that there were two main haplotypes for TaRPM1-7BL, including freezing-tolerant Hap1 and freezing-sensitive Hap2. Based on the representative SNP (+2556, A/G), leading to an amino acid change in the NBS domain, a CAPS marker (CAPS-TaRPM1-7BL) was developed and validated in 431 wheat varieties (lines) and 318 F2 lines derived from the cross of ‘Annong 9267’ (freezing-tolerant) × ‘Yumai 9’ (freezing-sensitive). Subsequently, the TaRPM1-7BL gene was silenced in ‘Yumai 9’ by virus-induced gene silencing (VIGS), and these silenced wheat seedlings exhibited enhanced FT phenotypes, suggesting that TaRPM1-7BL negatively regulates FT. These findings are valuable for understanding the complex genetic basis of FT in wheat.
The effect of social anxiety on prosocial behavior of college students: the mediating role of interpersonal security and the moderating role of basic psychological need satisfaction
Authors: Li Qiangqiang , Li Na 
Published: July 2023

Abstract
Background
The purpose of this study was to examine the impact of social anxiety on prosocial behavior and the role of interpersonal trust and basic psychological needs satisfaction in it.
Methods
The study utilizes a questionnaire (N = 458) to investigate the impact of social anxiety on prosocial behavior, as well as the mediating role of interpersonal security and the moderating role of basic psychological needs satisfaction.
Results
(1) the level of social anxiety negatively predicts prosocial behavior; (2) interpersonal security mediates the impact of social anxiety on prosocial behavior, as higher levels of social anxiety reduce interpersonal security, thereby decreasing prosocial behavior, (3) In the context of the negative prediction of social anxiety on prosocial behavior, the basic psychological needs satisfaction plays a moderating role. When an individual's level of satisfaction with basic psychological needs is low, the negative impact of social anxiety on prosocial behavior is significantly enhanced.
Conclusion
These findings reveal a relationship between social anxiety and pro-social behavior and provide strategies for socially anxious individuals to improve prosocial behavior.
Blackcurrant extract promotes the differentiation of MC3T3-E1 pre-osteoblasts
Authors: Nanashima Naoki , Horie Kayo , Oey Indrawati 
Published: July 2023

Abstract

Background
The risk of developing osteoporosis in menopausal women increases as estrogen secretion decreases. Blackcurrant extract (BCE) has been reported to ameliorate osteoporosis; however, the mechanisms underlying this phenomenon are unclear. Furthermore, although BCE has phytoestrogenic activity, its effects on osteoblasts are unknown. In this study, mouse pre-osteoblast MC3T3-E1 cells were used to investigate BCE-mediated attenuation of osteoporosis, with a focus on osteogenesis.
Methods and Results
After treating MC3T3-E1 cells with BCE for 48 h, the total number of cells was counted, and no conspicuous differences were observed. The levels of osteoblast differentiation markers, alkaline phosphatase activity, and total collagen content increased in BCE-treated cells on days 3–14. Additionally, the expression of genes encoding osteoblast differentiation markers, including collagen type I, alkaline phosphatase, osteocalcin, and runt-related transcription factor 2, increased in BCE-treated cells. At 21 days of treatment, calcified nodule levels were increased.
Conclusions
These findings show that BCE may promote osteogenesis by inducing osteoblast differentiation.
A Systematic Review and Meta-Analysis of the Consequences of Adolescent Pregnancy on Maternal and Neonatal Health
Authors: Islam Md Shahedul , Chowdhury Akibul Islam , Akhter Kazi Turjaun , Islam Md. Sayedul , Halima Oumma 
Published: July 2023

Abstract
Aims: Globally, both Human Nutritionists and Public Health Professionals are concerned about adolescent pregnancy. Maternal and neonatal morbidity and mortality are much greater among adolescent mothers than among adult mothers. This systematic review aimed to examine the effects of teenage pregnancy on Maternal and Neonate Health Status.
Methods: Three electronic databases (PubMed, the Cochrane library, and Google Scholar) were scoured for relevant articles between January 2015 and October 2021. All of the included studies were assessed for their methodological quality using the Joint Biomedical Investigations Handbook's (JBI) standards. To estimate the pooled outcomes, a random-effects model was applied.
Result: After examining the eligibility criteria, twelve papers were assessed for qualitative evaluation, and eight were selected for quantitative analysis. The pooled result of the analysis showed that the risk of preeclampsia [Odd (95% CI): 1.02 (0.79-1.32)] and anemia [Odd (95% CI): 1.11 (0.97-1.27)] was higher, and the risk of gestational diabetes [Odd (95% CI): 0.76 (0.51-1.13)], placental disruption [Odd (95% CI): 0.89 (0.5-1.56)], cesarean delivery [Odd (95% CI): 0.88 (0.51-1.52)] and premature rupture of the fetal membrane [Odd (95% CI): 0.95 (0.69-1.3)] were lower among adolescent mother compared with adult mother. Nevertheless, no significant differences existed across the groups. Adolescents had a significantly higher risk of having a premature baby [odds ratio (95% CI): 1.72, (1.03-2.85)]. whereas there is no significant difference observed in the risk of low birth weight and postpartum hemorrhage.
Conclusion: The current meta-analysis suggests that adolescent pregnancy might have a potential effect on maternal and neonatal health.