bluuebunny/crossref_metadata_2025 huggingface dataset:
Impaired Neuromuscular Efficiency and Symptom-Limited Aerobic Exercise Capacity 4 Weeks After Recovery From COVID-19 Appear to Be Associated With Disease Severity at Onset
Authors: Frazão Murillo , da Cruz Santos Amilton , Silva Paulo Eugênio , de Assis Pereira Cacau Lucas , Petrucci Tullio Rocha , Assis Mariela Cometki , de Almeida Leal Rômulo , Brasileiro Emanuella , de Moraes Forjaz Cláudia Lúcia , do Socorro Brasileiro-Santos Maria
Published: December 2022

Objective

The objectives of this study were to evaluate neuromuscular recruitment and efficiency in participants who recovered from COVID-19 and assess the association between neuromuscular efficiency and symptom-limited aerobic exercise capacity.

Methods

Participants who recovered from mild (n = 31) and severe (n = 17) COVID-19 were evaluated and compared with a reference group (n = 15). Participants underwent symptom-limited ergometer exercise testing with simultaneous electromyography evaluation after a 4-week recovery period. Activation of muscle fiber types IIa and IIb and neuromuscular efficiency (watts/percentage of root-mean-square obtained at the maximum effort) were determined from electromyography of the right vastus lateralis.

Results

Participants who had recovered from severe COVID-19 had lower power output and higher neuromuscular activity than the reference group and those who had recovered from mild COVID-19. Type IIa and IIb fibers were activated at a lower power output in participants who had recovered from severe COVID-19 than in the reference group and those who had recovered from mild COVID-19, with large effect sizes (0.40 for type IIa and 0.48 for type IIb). Neuromuscular efficiency was lower in participants who had recovered from severe COVID-19 than in the reference group and those who had recovered from mild COVID-19, with a large effect size (0.45). Neuromuscular efficiency showed a correlation with symptom-limited aerobic exercise capacity (r = 0.83). No differences were observed between participants who had recovered from mild COVID-19 and the reference group for any variables.

Conclusion

This physiological observational study supports the notion that more severe COVID-19 symptoms at disease onset appear to correspondingly impair neuromuscular efficiency in survivors over a short time frame of 4 weeks after recovery, potentially contributing to reduced cardiorespiratory capacity. Further studies are needed to replicate and extend these findings with respect to their clinical implications for assessment/evaluation and interventions.

Impact

After 4 weeks of recovery, neuromuscular impairment is particularly evident in severe cases; this problem may contribute to reduced cardiopulmonary exercise capacity.
Tuning macrophages for atherosclerosis treatment
Authors: Fang Fei , Xiao Crystal , Li Chunli , Liu Xiaoheng , Li Song
Published: December 2022

Atherosclerosis is a chronic inflammatory vascular disease and a leading cause of death worldwide. Macrophages play an important role in inflammatory responses, cell–cell communications, plaque growth and plaque rupture in atherosclerotic lesions. Here, we review the sources, functions and complex phenotypes of macrophages in the progression of atherosclerosis, and discuss the recent approaches in modulating macrophage phenotype and autophagy for atherosclerosis treatment. We then focus on the drug delivery strategies that target macrophages or use macrophage membrane-coated particles to deliver therapeutics to the lesion sites. These biomaterial-based approaches that target, modulate or engineer macrophages have broad applications for disease therapies and tissue regeneration.
Improved anti-Candida activity of hydrogel containing tea tree oil-loaded solid lipid nanoparticles for the treatment of oropharyngeal candidiasis
Authors: Mockdeci Hanny Reis , Junqueira Laura Andrade , Duarte Lucas Mattos , de Souza Moreira Carolina Paula , de Oliveira Marcone Augusto Leal , Brandão Marcos Antônio Fernandes , Tavares Guilherme Diniz , Raposo Nádia Rezende Barbosa
Published: December 2022

Objectives

Developing a hydrogel containing tea tree oil (TTO) encapsulated in solid lipid nanoparticles (SLNs) to treat oropharyngeal candidiasis.

Methods

Initially, the TTO chemical composition was evaluated. Next, SLNs containing TTO (TTO-SLNs) were produced and characterized. The TTO-SLNs were incorporated into a hydrogel, and the antifungal activity against Candida spp. was analysed. Finally, the ex vivo permeation was assessed.

Key findings

The chemical composition of TTO met ISO 4730:2017 standards. The TTO-SLNs were spherical and had a Z-average, PdI, ZP and entrapment efficiency of 135.90 ± 6.65 nm, 0.19 ± 0.04, −31.07 ± 1.05 mV and 92.74% ± 0.01%, respectively. Moreover, TTO-SLNs were stable (no changes in Z-average and PdI) for at least 120 days. In the cytotoxicity evaluation, the samples were considered cytotoxic at the following concentrations: TTO: 125–1000 µg/ml, TTO-SLN: 348–5568 µg/ml of TTO and the control nanoparticle was not cytotoxic. Both TTO-SLNs and the hydrogel containing TTO-SLNs demonstrated fungicidal action against all Candida spp., whilst for TTO, it was found only against C. albicans. The percentage of TTO permeation was 70.52%.

Conclusions

The hydrogel loaded with TTO-SLNs is a promising tool for TTO delivery, aiming at activity against C. albicans for the treatment of oropharyngeal candidiasis.
Bone Marrow Mesenchymal Stem Cells-Derived miR-21-5p Protects Grafted Islets Against Apoptosis by Targeting PDCD4
Authors: Wang Jingwen , Wang Jiale , Wang Ying , Ma Ruiyang , Zhang Shucong , Zheng Jin , Xue Wujun , Ding Xiaoming
Published: December 2022

The apoptosis of grafted islets is an urgent problem due to the high rate of islet loss soon after transplantation. MicroRNA-21-5p (miR-21-5p) is an essential mediator of bone marrow mesenchymal stem cells-derived exosomes (BMSCs-Exo) during anti-apoptosis, but its effect and the underlying molecular mechanism in islet transplantation remain partially understood. Here, we found that miR-21-5p could be delivered to islet cells via BMSCs-Exo. Subsequently, we demonstrated that miR-21-5p overexpression reduced apoptosis in islets and INS-1 cells, whereas miR-21-5p inhibition enhanced apoptosis. A mechanistic analysis involving RNA sequencing and bioinformatic analysis was performed to determine the interaction between miR-21-5p and its target gene programmed cell death 4 (PDCD4), which was further verified by a dual luciferase assay. In vivo, the grafted islets overexpressing miR-21-5p showed a higher survival rate, better insulin secretion function, and a lower apoptosis rate. In conclusion, these results demonstrated that miR‑21‑5p from BMSCs-Exo protects against the apoptosis of grafted islets by inhibiting PDCD4 expression. Hence, miR-21-5p can be used as a cell-free therapeutic agent to minimize β-cell apoptosis at the early stage of islet transplantation.
A randomized trial and multisite pooled trial analyses comparing effects of two hormonal implant programs and differing days-on-feed on carcass characteristics and feedlot performance of beef heifers
Authors: Horton Lucas M , Depenbusch Brandon E , Holland Ben P , Word Alyssa B , Streeter Marshall N , Hutcheson John P , Renter David G
Published: December 2022

Research objectives were to evaluate effects of two implant programs for beef heifers fed three different durations (days-on-feed; DOF) on carcass weight and composition (primary outcomes) and feedlot performance (secondary outcomes) at commercial feedlots. Data from a randomized trial in Kansas were analyzed separately and also pooled with data from two previously published trials conducted in Texas. Heifers were randomly allocated to pens within a block, and pens were randomized to treatments in a 2 × 3 factorial randomized complete block design. Implant programs were IH + 200 – an initial Revalor-IH implant [80 mg trenbolone acetate (TBA) and 8 mg estradiol (E2)] and a re-implant after a mean of 98-d (± 10.8 SD) with Revalor-200 (200 mg TBA and 20 mg E2), or XH – Revalor-XH, a single extended-release implant (200 mg TBA and 20 mg E2). Heifers were fed to a baseline endpoint (BASE; pooled mean 166-d ± 11.9 SD), +21, or +42 additional DOF. A total of 10,583 crossbred heifers with mean initial body weight (BW) 315 kg (± 20.1 SD) were enrolled in 144 pens in 24 blocks (treatment replications) across the three trials. General and generalized linear mixed models accounting for clustering of trials, blocks, and pens were used to test for effects of treatments, with significance set at α = 0.05. The only implant program × DOF interaction in pooled analyses was for dry matter intake (DMI; P < 0.01); IH + 200 heifers had lower mean DMI than XH when fed +42 DOF. Gain:feed was higher for IH + 200 compared to XH with dead and removed animals excluded (P < 0.01) or included (P = 0.03). For IH + 200, hot carcass weight (HCW) increased (P < 0.01), USDA Yield Grade (YG) distributions shifted towards lower numerical categories (P < 0.01), and Prime carcasses decreased while Select increased compared to XH (P < 0.01). For each incremental increase in DOF, final BW (P < 0.01) and HCW increased (P < 0.01), while daily gain (P < 0.01) and gain:feed (P < 0.01) decreased. Categories of YG were affected by DOF (P < 0.01); there were fewer YG 1 and 2 and more YG 4 and 5 carcasses for +42 compared to BASE and +21. USDA Quality Grade (QG) distributions differed by DOF (P < 0.01); each incremental increase in DOF resulted in more Prime and fewer Select carcasses. Without meaningful interactions, tested implant programs likely have a consistent effect when heifers are fed to similar DOF, while changes in HCW, QG, and YG may influence marketing decisions when extending DOF.
Association of maternal temperament and offspring disposition on growth performance
Authors: Sims Michael , Cauble Reagan N , Powell Jeremy , Kegley Beth , Foote Andrew P , Salak-Johnson Janeen L , Beck Paul
Published: December 2022

Animal behavior is complex and varies in definition, depending upon specific traits under observation. Temperament is one component of behavior, that in cattle, is described as the level of fearfulness to a novel or threatening environment. Temperament is a heritable trait which is important since aggressiveness and docility contribute to reproductive success, growth, and carcass quality. We observed maternal temperament at calving and the subsequent influence, if any, on offspring disposition at weaning and their effects collectively on growth performance and carcass traits. Maternal behaviors at calving were observed at four locations within the University of Arkansas system. Cows were assigned a maternal disposition score (MDS) at calving; a scale from 1 to 5 in which aggression decreases. At weaning, calves were assigned a chute score (CS); a scale from 1 to 6 in which aggression increases. Both scoring systems have been previously established. Blood was collected during the 56-d backgrounding period postweaning for blood glucose analysis. Data were analyzed using GLIMMIX procedures of SAS (α = 0.05). The relationship between the two scoring systems was determined with a Pearson correlation (P = 0.22). Animal was the experimental unit and blocked by location for all dependent variables. Location, sex, diet, and MDS were included in the class as covariables for all growth performance and carcass data related to CS. Cows that were more aggressive birthed heavier calves (P < 0.01) compared to indifferent cows. Calves born to cows with either very aggressive or very attentive (MDS of 2 or 3, respectively) scores were heavier upon feedlot entry (P = 0.03) compared to those from indifferent or apathetic cows (MDS of 4 or 5, respectively). Calves defined as nervous and restless (CS of 3 and 2, respectively) were heavier at weaning compared to docile calves (P < 0.01). Restless calves were heavier compared to nervous calves upon arrival and exiting the feedlot (P ≤ 0.01). Calves that were docile at weaning had greater marbling compared to calves that were restless (P ≤ 0.01). Calves that were restless at weaning had greater lean muscle area compared to calves that were nervous (P = 0.05). No definitive relationship was determined between dam and calf temperament. However, the results suggest temperament does impact growth performance and carcass traits but whether the influence comes from the dam or calf temperament, specifically, remains unanswered.
Genome Sequence Resource of Fusarium graminearum TaB10 and Fusarium avenaceum KA13, Causal Agents of Stored Apple Rot
Authors: Petreš Mladen , Hrustić Jovana , Vučinić Nataša , Ma Li-Jun , Ayhan Dilay Hazal , Grahovac Mila
Published: December 2022

The filamentous fungus Fusarium graminearum is a well-known cereal pathogen and F. avenaceum is a pathogen with a wide host range. Recently, both species were reported as causal agents of apple rot, raising concerns about postharvest yield losses and mycotoxin contamination. Here, we report genome assemblies of F. avenaceum KA13 and F. graminearum TaB10, both isolated from fruits with symptoms of apple rot. The final F. avenaceum KA13 genome sequence assembly of 41.7 Mb consists of 34 scaffolds, with an N50 value of 2.2 Mb and 15,886 predicted genes. The total size of the final F. graminearum TaB10 assembly is 36.76 Mb, consisting of 54 scaffolds with an N50 value of 1.7 Mb, and it consists of 14,132 predicted genes. These new genomes provide valuable resources to better understand plant-microbe interaction in stored apple rot disease.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Genetic Diversity and Fungicide Sensitivity of Cytospora plurivora on Peach
Authors: Baker Stephen T. , Froelich Martha H. , Boatwright Harriet , Wang Hehe , Schnabel Guido , Kerrigan Julia
Published: December 2022

Cytospora plurivora D.P. Lawr., L.A. Holland & Trouillas has been associated with recent premature peach tree decline in South Carolina, but very little is known about the pathogen or chemical control options. Ninety-three C. plurivora isolates were collected in 2016 and 2017 from 1-year-old peach wood and symptomatic scaffold limbs, respectively, from orchards in six towns in South Carolina. Six unique genotypes were identified based on substantial ITS1-5.8S-ITS2 sequence variability and classified G1 to G6. Three of the genotypes (G2, G3, and G6) were isolated in high frequency in multiple locations of both years. In addition to the genotypic variation, multiple phenotypes were observed between and within genotype groups. Species identity was determined using additional gene loci: ACT, TUB, and EF, and isolates were found to belong to C. plurivora for all genotype groups. All tested genotypes were sensitive to thiophanate-methyl (FRAC 1) but exhibited slightly lower sensitivity to propiconazole and difenoconazole (both FRAC 3). Boscalid, fluopyram (both FRAC 7s), azoxystrobin, and pyraclostrobin (both FRAC 11s) were ineffective in vitro at inhibiting mycelial growth of C. plurivora genotypes. Field inoculation of peach and nectarine trees revealed that all genotypes developed twig cankers with differences in virulence. G1 was most virulent, and G6 was least virulent. This study provides a link between the C. plurivora genetic variability and virulence and provides fungicide sensitivity information that could be used to improve disease management practices.
Puccinia coronatavar.coronata, a Crown Rust Pathogen of Two Highly Invasive Species, Is Detected Across the Midwest and Northeastern United States
Authors: Greatens Nicholas , Klejeski Nick , Szabo Les J. , Jin Yue , Olivera Pablo D.
Published: December 2022

Puccinia coronata var. coronata (Pcc) causes crown rust disease of glossy buckthorn (Frangula alnus) and reed canarygrass (Phalaris arundinacea), two highly invasive plant species in North America. Pcc is closely related to major pathogens of cereals, turfgrasses, and forage grasses. It occurs throughout Europe but was first recorded in North America in 2013. Where its hosts co-occur, such as in wetlands in the Twin Cities metro area in Minnesota, we have observed Pcc causing significant infection that results in defoliation and fruit loss in glossy buckthorns and premature leaf senescence in reed canarygrass. In this research, we mapped the distribution of this likely recently introduced rust fungus and provided a description of disease signs and symptoms and pathogen morphology. Samples were acquired by two primary means: by surveys in Minnesota and by correspondence with users of iNaturalist.org , a social network for nature enthusiasts and community scientists. With an Oxford Nanopore MinION, we sequenced two to four loci from 22 samples across 13 states and identified samples by phylogenetic analysis and sequence similarity. Notably, four pure isolates appear to have intragenomic variation of the ITS region. We found that Pcc is present throughout the range of glossy buckthorn in the eastern United States. In Minnesota, Pcc is not common outside the range of glossy buckthorn despite the presence of susceptible grass hosts.
High-Quality Genome Resource of Fusarium pseudograminearum Isolate Fp22-2 by Oxford Nanopore Long-Read Sequencing
Authors: Tai Jia , Zhang Xin , Gao Xinlong , Liu Huiquan , Xu Ming
Published: December 2022

Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, results in severe yield and quality losses of cereal crops in many arid and semiarid areas of the world. Limited information about the genome of F. pseudograminearum restricts the pathogenesis research and breeding of disease-resistant wheat varieties. In this study, a high-quality genome assembly of F. pseudograminearum isolate Fp22-2 was generated using Oxford Nanopore long-read sequencing technology. The assembled nuclear genome of Fp22-2 is 37.33 Mb with a repeat content of 3.69% and is divided into four contigs with a k-mer completeness score of 97.2% and a base quality accuracy of >99.99%. A total of 14,475 protein-coding genes (BUSCO completeness score, 99.9%) were predicted and functionally annotated. Moreover, genes encoding pathogenic proteins, including effector proteins and carbohydrate-active enzymes, and secondary metabolic gene clusters were identified. Overall, the high-quality genome assembly and gene annotation provided here will allow further investigation of the biology of F. pseudograminearum and lead to the development of new control options for FCR.
Nanopore/Illumina Hybrid Whole-Genome Sequence Resource of Plenodomus lindquistii Strain US01 Infecting Sunflower
Authors: Lei Rong , Duan Weijun , Wang Xinyi , Wu Pinshan
Published: December 2022

Plenodomus lindquistii (basionym: Leptosphaeria lindquistii) is the most prevalent fungus pathogen causing the black stem disease in sunflower. To date, only one whole-genome sequence is reported in NCBI, but no complete gene annotation has been submitted. Herein, we sequenced a Leptosphaeria lindquistii isolate from sunflower seeds imported from the United States using Oxford Nanopore long-read sequencing and Illumina short-read sequencing. We generated a 38.6-Mb genome assembly consisting of 29 contigs with an N50 of 1.689 Mb and a maximum length of 5.316 Mb. In the genome assembly, we identified 13,481 protein-coding genes, of which 12,531 were annotated. The high-quality assembly and annotation of the Leptosphaeria lindquistii genome will allow us to conduct further studies for the specific identification of pathogens causing sunflower black stem disease and provide a better understanding of the infection mechanisms of Leptosphaeria lindquistii.
Complete Genome Sequence of Xanthomonas citri subsp. citri CQ13, an Alternative Model Strain to Study Citrus Bacterial Canker in China
Authors: Wu Yonglin , Lv Weiwei , Chen Hongyu , Ge Yifei , Liu Chaoying , Ding Xiaojun , Zou Xiuping , Hu Junhua , Li Jingyu , Wang Jihua , Zhang Yunzeng , Zhou Xiaofeng
Published: December 2022

Xanthomonas citri subsp. citri is a quarantine organism causing citrus bacterial canker in many countries. Sharing research materials worldwide became difficult due to local administrative regulations, which hindered the continuity of studies on this disease. Here, we report a complete genome sequence of X. citri subsp. citri strain CQ13 achieved using a combination of Illumina and Nanopore platforms. The CQ13 genome comprises a circular chromosome (5,142,501 bp; G + C content 64.83%) and two circular plasmids, pXAC33 and pXAC64 (34,102 bp and 64,942 bp; G + C content 61.96 and 61.41%, respectively). Annotation revealed 4,243 protein-coding sequences, six rRNA genes, 53 tRNA genes, 40 ncRNA genes, and 168 pseudogenes. Notably, the analyses of average nucleotide identity, host range, pathogenicity, and type III effector repertoire suggest that CQ13 is particularly closely related to the current model strain 306. Therefore, strain CQ13 could serve as an alternative model strain, and its genome sequence could provide a valuable resource for citrus canker research in China.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Out-of-State Students at State Medical Schools and Increasing Medical Education Debt
Authors: Kraus Molly B. , Hasan Shaina H. , Buckner-Petty Skye A. , Files Julia A. , Hayes Sharonne N. , Habermann Elizabeth B. , LeMond Lisa M.
Published: December 2022

Purpose

Medical school tuition has increased at alarming rates ahead of inflation over the past 20 years. The authors investigated whether state-funded medical schools have had an increased number of out-of-state matriculants, which may create a diaspora of displaced in-state medical students matriculating to out-of-state programs and incurring substantial debt.

Method

Publicly available data from the Association of American Medical Colleges (AAMC) were accessed from 2004 through 2019 for applicants and matriculants at U.S. state-funded schools. Schools listed as public that reported tuition charges in the AAMC Tuition and Student Fees reports were included in this study. The numbers and trends of medical school applications and trends in tuition costs and average indebtedness were summarized for in-state and out-of-state matriculants. Values were analyzed by group as median and interquartile range (IQR). Group differences were assessed via t tests. P values less than .05 were considered statistically significant.

Results

From 2004 through 2019, the annual number of out-of-state matriculants in state-funded schools increased 7% (16%–23% [7,195–11,144]). Among 74 schools with data in 2004, the median percentage of out-of-state applications increased from 60% (IQR, 31%–74%) to 80% (IQR, 57%–85%; P < .001), and the median percentage of out-of-state matriculants increased from 13% (IQR, 5%–23%) to 17% (IQR, 11%–33%; P < .001). In 2004, the mean (standard error) debt upon completion of medical school (inflation adjusted to 2018 dollars) was $144,100 ($10,950); by 2016, the mean debt had increased to $251,600 ($32,040), a 75% increase over 12 years.

Conclusions

Since 2004, substantial increases have occurred in out-of-state matriculants at state-funded medical schools. This may displace residents from attending their in-state schools, causing them to attend out-of-state or private medical schools, where tuition is typically much higher.
Equal Pay for Equal Work in the Dean Suite: Addressing Occupational Gender Segregation and Compensation Inequities Among Medical School Leadership
Authors: Gottlieb Amy S. , Dandar Valerie M. , Lautenberger Diana M. , Best Cynthia , Jagsi Reshma
Published: December 2022

In 2022, the Association of American Medical Colleges published data from its annual Dean’s Office Staff Compensation and Dean’s Compensation Surveys in a new report addressing salary equity among medical school leadership. These data, disaggregated by gender and race/ethnicity, represent earnings of the senior most leaders in the dean suite and have historically been shared only with medical school Deans and principal business officers. The report shows that the highest-ranking decanal positions in U.S. medical schools are filled along the lines of traditional gender stereotypes (with men in clinical affairs and research affairs deanships and women in admissions, diversity affairs, faculty affairs, and student affairs deanships) and that the roles held mostly by men carry grander titles (e.g., senior associate dean vs assistant dean) and significantly higher salaries than those typically held by women. Additionally, within the same decanal positions, women earn lower median compensation than men.

In this commentary, the authors describe limited advancement and lower compensation as foregone conclusions for women in medicine and science due to a professional model that places a premium on activities traditionally pursued by men. They define and characterize the impact of this occupational gender segregation in the dean suite and offer a roadmap for an alternative value system that recognizes complementary leadership activities across the mission areas of academic medicine and ensures that the contributions of women in the profession are appropriately recognized, valued, and rewarded.
Predictors of Complications after Breast Reconstruction Surgery: A Systematic Review and Meta-analysis
Authors: Mrad Mohamed Amir , Al Qurashi Abdullah A. , Shah Mardan Qutaiba N.M. , Alqarni Mohammed D. , Alhenaki Ghazlan A. , Alghamdi Muath S. , Fathi Abdulaziz B. , Alobaidi Hussain A. , Alnamlah Abdulrahman A. , Aljehani Saif K. , Daghistani Ghadeer , Alsharif Thamer Hamad
Published: December 2022

Background:

Breast reconstruction (BR) is a unique surgical procedure that provides patients undergoing mastectomy with significant psychosocial and aesthetic benefits and has also become a crucial part of the treatment pathway for women with breast cancer. Due to methodological inadequacies and the absence of substantial risk factor analysis, no conclusion can be drawn about the correlation between risk variables and post-surgical complications in BR surgery. We aim to identify the potential risk factors associated with postoperative complications.

Methods:

We queried MEDLINE and Cochrane CENTRAL from their inception to March 2022, for published randomized controlled trials and observational studies that assessed complications post-reconstruction procedure in breast cancer patients following mastectomy or evaluated at least one of the following outcomes of major or reoperative complications. The results from the studies were presented as odds ratios with 95% confidence intervals and were pooled using a random-effects model.

Results:

Our pooled analysis demonstrated a significant correlation with BR postoperative complications and risk factors such as diabetes, hypertension, and obesity. Diabetes and the development of seroma were found to have a significant relationship. Risk variables such as age, radiotherapy, COPD, and smoking had no significant connection with 0-to-30-day readmission and 30-to-90-day readmission.

Conclusion:

This meta-analysis shows that risk factors like age, smoking history, high blood pressure, and body mass index (BMI) have a big effect on complications after BR, and patients with risk factors have a high rate of developing infection.
Matrix Metalloproteinases 2 and 9 and Their Tissue Inhibitors in the Diagnostics of Medullary Thyroid Carcinoma
Authors: Vázquez-Lorente Héctor , Dunđerović Duško M. , Tatić Svetislav B. , Radojević-Škodrić Sanja , Gomes Cláudio M. , Paunović Ivan R. , Dragutinović Vesna
Published: December 2022

Medullary Thyroid Carcinoma (MTC) is a tumor of the neuroendocrine system. In recent years, the need to assess the MTC diagnostic-related parameters has emerged with the aim to elucidate the mechanisms involved in this pathology. The objective of this study was to evaluate the role of Matrix Metalloproteinases (MMPs) 2 and 9, their tissue inhibitors of matrix metalloproteinases (TIMPs), S100 protein, and amyloid in the diagnostic of MTC. Thirty-two samples with MTC (72% women) were included in this cross-sectional study and divided by groups: T category 1 (T1)≤20 mm and T category 2 (T2) 20 to 40 mm of tumor size. MMPs 2 and 9, TIMPs 2 and 1, S100 protein, and calcitonin in tissues were obtained by immunohistochemical techniques. The presence of amyloid in tissue sections was detected on Thioflavin T–stained slides under fluorescent microscope. Percentage of positive cells (P) observed for MMP-2 was higher in those samples presenting T2 MTC with respect to those with T1 MTC (P<0.05). Moreover, P-MMP-2 showed a direct correlation with higher T category of MTC (Rho=0.439, P < 0.001), whereas P-MPP-9 was directly correlated with S100 protein and the intensity of calcitonin in tissues (Rho=0.419, P=0.017; Rho=0.422, P=0.016, respectively. Therefore, MMPs were directly correlated with some traditional biomarkers of MTC. In this regard, P-MMP-2 was more expressed in type 2 MTC. Combining the analysis of traditional and other useful biomarkers of MTC as MMPs 2 and 9 could be a useful strategy in the diagnostic of MTC.
Characterization, and in vitro antibacterial activity of sulfated polysaccharides from freshwater algae Cladophora crispata
Authors: jasem mohanad , Merai Abd- Alwahab , Nizam Adnan Ali
Published: December 2022

Barada River is characterized by an abundant growth of freshwater algae. In light of the increased interest in algae to find new sources of bioactive compounds, this research, aimed to extract sulfated Polysaccharides (SPs) from freshwater green algae Cladophoracrispata using ultrasonic-assisted extraction methods after cultivates it by the outdoor method. Also we determined and selected its compounds,and we investigation effect SPs as antibacterial agent  After extraction, Sephadex gel G-100 was used for the Purification of SPs, where the purifcation gave two fractions, namley F1 and F2. The chemical characterization of crud SPs and its fractions were investigated. The highest carbohydrate and protein contents were found in crude SPs with the ratios of 74.12%, and 4.02%, respectively, while the highest sulfate content 12.17% was found in fraction 2, and the higest uronic content 18.46% was found in fraction 1. Fourier transforms infrared Spectroscopy (FT-IR) used for confirmed the crud and fractions consist of sugar, uronic acids, protein unite, and sulfate groups. Both  F1, and F2 consist of rhamnose, galactose, xylose, and ribose based on separation on the High performance liquid chromatography (HPLC). Each fraction has inhibitory effect on bacteria negative and positive gram. F2 have the lowest minimization inhabit concentration (MIC) value against Enterobacteraerogenes and Staphylococcusaureus; where MIC were  28 and 10 mg/ml respectively. Polysaccharides had the most important interest because they have antibacterial properties, making them inter in pharmacy and food applications.
Estimating the epidemic reproduction number from temporally aggregated incidence data: a statistical modelling approach and software tool
Authors: Nash Rebecca K , Cori Anne , Nouvellet Pierre
Published: December 2022

Background

The time-varying reproduction number (Rt) is an important measure of epidemic transmissibility; it can directly inform policy decisions and the optimisation of control measures. EpiEstim is a widely used software tool that uses case incidence and the serial interval (SI, time between symptoms in a case and their infector) to estimate Rtin real-time. The incidence and the SI distribution must be provided at the same temporal resolution, which limits the applicability of EpiEstim and other similar methods, e.g. for pathogens with a mean SI shorter than the frequency of incidence reporting.

Methods

We use an expectation-maximisation algorithm to reconstruct daily incidence from temporally aggregated data, from which Rtcan then be estimated using EpiEstim. We assess the validity of our method using an extensive simulation study and apply it to COVID-19 and influenza data. The method is implemented in the opensource R package EpiEstim.

Findings

For all datasets, the influence of intra-weekly variability in reported data was mitigated by using aggregated weekly data. Rtestimated on weekly sliding windows using incidence reconstructed from weekly data was strongly correlated with estimates from the original daily data. The simulation study revealed that Rtwas well estimated in all scenarios and regardless of the temporal aggregation of the data. In the presence of weekend effects, Rtestimates from reconstructed data were more successful at recovering the true value of Rtthan those obtained from reported daily data.

Interpretation

Rtcan be successfully recovered from aggregated data, and estimation accuracy can even be improved by smoothing out administrative noise in the reported data.

Funding

MRC doctoral training partnership, MRC centre for global infectious disease analysis, the NIHR HPRU in Modelling and Health Economics, and the Academy of Medical Sciences Springboard, funded by the AMS, Wellcome Trust, BEIS, the British Heart Foundation and Diabetes UK.
Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes
Authors: Zhu Wensi , Shenoy Aditi , Kundrotas Petras , Elofsson Arne
Published: December 2022

Motivation

Despite near-experimental accuracy on single-chain predictions, there is still scope for improvement among multimeric predictions. Methods like AlphaFold-Multimer and FoldDock can accurately model dimers. However, how well these methods fare on larger complexes is still unclear. Further, evaluation methods of the quality of multimeric complexes are not well established.

Results

We analysed the performance of AlphaFold-Multimer on a homology-reduced dataset of homo- and heteromeric protein complexes. We highlight the differences between the pairwise and multi-interface evaluation of chains within a multimer. We describe why certain complexes perform well on one metric (e.g., TM-score) but poorly on another (e.g., DockQ). We propose a new score, Predicted DockQ version 2 (pDockQ2), to estimate the quality of each interface in a multimer. Finally, we modelled protein complexes (from CORUM) and identified two highly confident structures that do not have sequence homology to any existing structures.

Availability

All scripts, models, and data used to perform the analysis in this study are freely available athttps://gitlab.com/ElofssonLab/afm-benchmark.

Contact

arne@bioinfo.se

Supplementary information

Supplementary data are available atBioinformaticsonline.
In-silicoandin-vitromorphometric analysis of intestinal organoids
Authors: Montes-Olivas Sandra , Legge Danny , Lund Abbie , Fletcher Alexander G. , Williams Ann C. , Marucci Lucia , Homer Martin
Published: December 2022

Organoids offer a powerful model to study cellular self-organisation, the growth of specific tissue morphologiesin-vitro, and to assess potential medical therapies. However, the intrinsic mechanisms of these systems are not entirely understood yet, which can result in variability of organoids due to differences in culture conditions and basement membrane extracts used. Improving the standardisation of organoid cultures is essential for their implementation in clinical protocols. Developing tools to assess and predict the behaviour of these systems may produce a more robust and standardised biological model to perform accurate clinical studies. Here we developed an algorithm to automate crypt-like structure counting on intestinal organoids in bothin-vitroandin-silicoimages. In addition, we modified an existing two-dimensional agent-based mathematical model of intestinal organoids to better describe the system physiology, and evaluated its ability to replicate budding structures compared to new experimental data we generated. The crypt-counting algorithm proved useful in approximating the average budding structures found in ourin-vitrointestinal organoid culture images on days 3 and 7 after seeding. Our changes to thein-silicomodel maintain the potential to produce simulations that replicate the number of budding structures found on days 5 and 7 ofin-vitrodata. The present study aims to aid in quantifying key morphological structures and provide a method to compare bothin-vitroandin-silicoexperiments. Our results could be extended later to 3Din-silicomodels.
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
Authors: Cavlak Meryem Banu , Singh Gagandeep , Alser Mohammed , Firtina Can , Lindegger Joël , Sadrosadati Mohammad , Ghiasi Nika Mansouri , Alkan Can , Mutlu Onur
Published: December 2022

Basecalling is an essential step in nanopore sequencing analysis where the raw signals of nanopore sequencers are converted into nucleotide sequences, i.e., reads. State-of-the-art basecallers employ complex deep learning models to achieve high basecalling accuracy. This makes basecalling computationally-inefficient and memory-hungry; bottlenecking the entire genome analysis pipeline. However, for many applications, the majority of reads do no match the reference genome of interest (i.e., target reference) and thus are discarded in later steps in the genomics pipeline, wasting the basecalling computation.

To overcome this issue, we propose TargetCall, the first fast and widely-applicable pre-basecalling filter to eliminate the wasted computation in basecalling. TargetCall’s key idea is to discard reads that will not match the target reference (i.e., off-target reads) prior to basecalling. TargetCall consists of two main components: (1) LightCall, a lightweight neural network basecaller that produces noisy reads; and (2) Similarity Check, which labels each of these noisy reads as on-target or off-target by matching them to the target reference. TargetCall filters out all off-target reads before basecalling; and the highly-accurate but slow basecalling is performed only on the raw signals whose noisy reads are labeled as on-target.

Our thorough experimental evaluations using both real and simulated data show that TargetCall 1) improves the end-to-end basecalling performance of the state-of-the-art basecaller by 3.31 × while maintaining high (98.88%) sensitivity in keeping on-target reads, 2) maintains high accuracy in downstream analysis, 3) precisely filters out up to 94.71% of off-target reads, and 4) achieves better performance, sensitivity, and generality compared to prior works. We freely open-source TargetCall to aid future research in pre-basecalling filtering athttps://github.com/CMU-SAFARI/TargetCall.
Ventral Tegmental Area Glutamate Neurons establish a mu-opioid receptor gated circuit to mesolimbic dopamine neurons and regulate prescription opioid-seeking behavior
Authors: McGovern Dillon J. , Polter Abigail M. , Ly Annie , Prevost Emily D. , McNulty Connor , Root David H.
Published: December 2022

A two-neuron model of ventral tegmental area (VTA) opioid function classically involves VTA GABA neuron regulation of VTA dopamine neurons via a mu-opioid receptor dependent inhibitory circuit. However, this model predates the discovery of a third major type of neuron in the VTA: glutamatergic neurons. We find that about one-quarter of VTA neurons expressing the mu-opioid receptor are glutamate neurons without molecular markers of GABA co-release. Glutamate-Mu opioid receptor neurons are topographically distributed in the anterior VTA. The majority of remaining VTA mu-opioid receptor neurons are GABAergic neurons that are largely within the posterior VTA and do not express molecular markers of glutamate co-release. Optogenetic stimulation of VTA glutamate neurons results in monosynaptic excitatory currents recorded from VTA dopamine neurons that are reduced by presynaptic activation of the mu-opioid receptorex vivo, establishing a local mu-opioid receptor dependent excitatory circuit from VTA glutamate neurons to VTA dopamine neurons. This VTA glutamate to VTA dopamine pathway regulates dopamine release to the nucleus accumbens through mu-opioid receptor activityin vivo. Behaviorally, VTA glutamate calcium-related neuronal activity increased following oxycodone consumption and response-contingent oxycodone-associated cues during self-administration and abstinent reinstatement of drug-seeking behavior. Further, chemogenetic inhibition of VTA glutamate neurons reduced abstinent oxycodone-seeking behavior in male but not female mice. These results establish 1) a three-neuron model of VTA opioid function involving a mu-opioid receptor gated VTA glutamate neuron pathway to VTA dopamine neurons that controls dopamine release within the nucleus accumbens, and 2) that VTA glutamate neurons participate in prescription opioid-seeking behavior.
Examining the Role of Maternal Religiosity in Offspring Mental Health Using Latent Class Analysis in a UK Prospective Cohort Study
Authors: Halstead Isaac , Heron Jon , Svob Connie , Joinson Carol
Published: December 2022

Background

Previous research has examined the role of parental religious belief in offspring mental health, but has revealed inconsistent results, and suffered from a number of limitations. The aim of this study is to examine the prospective relationship between maternal religiosity and offspring mental health and psychosocial outcomes.

Methods

We used latent classes of religious belief (Highly religious, Moderately religious, Agnostic, Atheist) in mothers from the Avon Longitudinal Study of Parents and Children and examined their association with parent-reported mental health outcomes and self-reported psychosocial outcomes in their children at age 7-8 (n = 6079 for mental health outcomes and n = 5235 for psychosocial outcomes). We used inverse probability weighted multivariable logistic regression analysis adjusted for maternal mental health, adverse childhood experience, and socioeconomic variables.

Results

There was evidence for a greater risk of internalising problems among the offspring of the Highly religious and Moderately religious classes (e.g. for depression; OR = 1.51, 95% CI [1.24,1.77], OR = 1.50, 95% CI [1.26,1.73]), and greater risk of externalising problems in the offspring of the Atheist class (e.g. for ADHD; OR = 1.44, 95% CI [1.18,1.71]), compared to the offspring of the Agnostic class.

Conclusions

These novel findings provide evidence associations between maternal religiosity and offspring mental health differ when examined using a person-centred approach, compared to the previously used variable-centred approaches. Our findings also suggest that differences may exist in the relationship between religious (non)belief and mental health variables when comparing the UK and US.
Iclaprim mesylate displaying a hydrogen-bonded molecular tape
Authors: Neuner Sandro , Gelbrich Thomas , Wurst Klaus , Spreitz Josef , Nerdinger Sven , Griesser Ulrich J. , Stefinovic Marijan , Schottenberger Herwig
Published: December 2022

The title compound, 2,6-diamino-5-[(2-cyclopropyl-7,8-dimethoxy-2H-1-benzopyran-5-yl)methyl]pyrimidin-1-ium methanesulfonate, C19H23N4O3
+·CH3O3S−, is a salt made up from a protonated iclaprim molecule and a mesylate anion. The pyrimidine and chromene units of the iclaprim molecule form an orthogonal arrangement [interplanar angle of 89.67 (6)°], and the 3-nitrogen position of the pyrimidine ring is protonated. Four distinct N—H...O interactions and an additional N—H...N hydrogen bond connect iclaprim and mesylate molecules to one another, resulting in an infinite hydrogen-bonded molecular tape structure. The central section of the tape is formed by a sequence of fused hydrogen-bonded rings involving four distinct ring types.
Does female off-farm employment affect fertility desire? Evidence from rural China
Authors: Shen Zheng , Brown Derek S. , Yu Kang
Published: December 2022

Purpose

Off-farm employment is an important factor associated with fertility transition in many developing countries. The purpose of this paper is to investigate the impact of female off-farm employment on their fertility desire in rural China.

Design/methodology/approach

Based on the data from the China Labor-force Dynamics Survey, the authors adopt an instrumental variable approach to address the endogeneity issue. Desired number of children and desire for a second child are used to measure fertility desire.

Findings

The results show that off-farm employment participation significantly reduces women's desired number of children and the likelihood of their desire for a second child. Moreover, off-farm employment reduces women's fertility desire mainly through pathways including the weakening of son preference and a decrease in job autonomy, rather than the changes in leisure hours. Further evidence suggests that social health insurance plays an important role in moderating the adverse relationship between off-farm employment and the desire for a second child. The fertility-reducing effects are more pronounced among younger women, among those participating in off-farm wage employment and among families with only wives' participation in the off-farm labor market.

Originality/value

This paper contributes to the existing research by investigating the causal impact of off-farm employment on fertility desire in a rural developing context and the possible underlying mechanisms responsible for this relationship. This study provides important insights on this topic in developing countries and may have important implications for theory and practice.
Policy framework to apply artificial intelligence for the management of records at the Council for Scientific and Industrial Research
Authors: Modiba Mashilo
Published: December 2022

Purpose

This study aims to investigate how a policy framework can be applied in the use of artificial intelligence (AI) for the management of records at the Council for Scientific and Industrial Research (CSIR) in South Africa. A policy and legal framework enables the records divisions to protect, administer and make their records available in a safe and professional way. Policies play a crucial role in ensuring that records are properly managed.

Design/methodology/approach

Convergent mixed-methods research was conducted, and data were collected using interviews and questionnaires. Data were analysed thematically and statistically and presented in tables and figures.

Findings

The study reveals that the policy framework should also include the application of AI for the management of records. Therefore, this study further concludes that the CSIR should review their policy framework to ensure the application of AI for the management of records is accommodated.

Originality/value

The study proposed a framework to guide the application of the policy framework in using AI for the management of records at CSIR. It is hoped that the proposed framework will serve as a guideline for the implementation of a policy framework in the utilisation of AI in the archives and records management sector.