bluuebunny/crossref_metadata_2025 huggingface dataset:
Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars
Authors: Yang Yuyao , Lyu Mingjie , Liu Jun , Wu Jianjin , Wang Qian , Xie Tianyu , Li Haichao , Chen Rui , Sun Deling , Yang Yingxia , Yao Xingwei
Published: November 2022

Cauliflower is one of the most important vegetable crops grown worldwide. However, the lack of genetic diversity information and efficient molecular markers hinders efforts to improve cauliflower. This study aims to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. We developed a program for in silico simulations on 153 core germplasm samples to generate ideal SNP marker sets from the candidates. Finally, 41 highly polymorphic KASP markers were selected and applied to identify 329 cauliflower cultivars, mainly collected from the public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with the genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information about the current cauliflower cultivars.
Persistence of onchocerciasis in villages in Enugu and Ogun states in Nigeria following many rounds of mass distribution of ivermectin
Authors: Ekpo Uwem F. , Eneanya Obiora A. , Nwankwo Edith N. , Soneye Islamiat Y. , Weil Gary J. , Fischer Peter U. , Nwaorgu Obioma C.
Published: November 2022

Background

Onchocerciasis is endemic in most local government areas (LGAs) in Enugu and Ogun states. Most meso- and hyper-endemic LGAs have received many rounds of ivermectin mass drug administration (MDA). This study aimed to determine the current prevalence of onchocerciasis in villages in Enugu and Ogun states that were formerly highly endemic and to assess progress toward elimination of the infection in areas believed to be at high risk for persistence.

Methods

Cross-sectional community surveys were conducted 8 to 12 months after the last round of MDA in 16 villages (6 in Enugu state and 10 in Ogun state) in individuals aged ≥ 18 years. Study participants were examined for the presence of palpable subcutaneous nodules. Skin snips from the posterior iliac crests were used to assess microfiladermia (Mf) prevalence and density.

Results

643 subjects were palpated for nodules and 627 individuals (225 in Enugu state; 402 in Ogun state) provided skin snips. Nodule prevalence in the study villages ranged from 42 to 66.7% in Enugu state and from 0 to 25.0% in Ogun state. Mf prevalence in the Enugu and Ogun study villages ranged from 32 to 51.1% and 0 to 28.6%, respectively. Geometric mean skin Mf density in surveyed Enugu state villages ranged between 1 and 3.1 Mf/mg; these values were < 1 Mf/mg in all but one community in Ogun state villages.

Conclusion

Results from this study show that onchocerciasis persists in adults in many villages in Enugu and Ogun states despite many prior rounds of ivermectin MDA. Prevalence was higher in villages surveyed in Enugu than in Ogun. Low Mf densities suggest the MDA program is working well to reduce disease, but more time will be required to reach the elimination goal.
Pregnancy outcomes and risk factors for preeclampsia in dichorionic twin pregnancies after in vitro fertilization: a five-year retrospective study
Authors: Dai Fen , Pan Shuangjia , Lan Yehui , Tan Hongying , Li Jinman , Hua Ying
Published: November 2022

Background

Both in vitro fertilization (IVF) and preeclampsia (PE) were associated with placental dysfunction. Although IVF can increase the incidence of PE, the pregnancy outcomes and risk factors for preeclampsia in dichorionic twin pregnancies conceived via IVF remain unclear. This study aimed to investigate the pregnancy outcomes and the risk factors for preeclampsia in dichorionic twin pregnancies conceived through IVF compared to those conceived after natural conception (NC).

Methods

This retrospective observational study enrolled 181 dichorionic twin pregnancy women with preeclampsia from 2016 to 2020. According to the mode of conception, they were allocated into IVF (n = 117) and NC groups (n = 64). The clinical characteristics of preeclampsia and pregnancy outcomes between the two groups were compared by using Student’s t test, chi-square test, and Fisher’s exact test, and logistic regression models were used to obtain adjusted odds ratios (aOR) with 95% confidence intervals (CI) for risk factors of early-onset preeclampsia.

Results

The incidence of early-onset PE and growth discordance in dichorionic twin pregnancies with PE is significantly higher in IVF-PE group than in NC group (78.60% vs 43.80%, P < 0.001, 11.10% vs 25.00%, P = 0.015). We found that IVF (aOR = 4.635, 95% CI: 2.130–10.084, P < 0.001) and growth discordance (aOR = 3.288; 95% CI: 1.090–9.749, P < 0.05) increased the incidence of early-onset PE.

Conclusions

In preeclamptic dichorionic twin pregnancies, IVF and growth discordance were associated with the increased incidence of early-onset PE. The underlying mechanism for the relationship between IVF and early-onset PE or growth discordance may be placental dysfunction.
A comprehensive pan-cancer analysis of necroptosis molecules in four gynecologic cancers
Authors: Zheng Jianfeng , Cai Xintong , Zhang Yu , Wang Huihui , Liu Li , Tang Fengling , Liu Linying , Sun Yang
Published: November 2022

Background

In recent years, it has been proved that necroptosis plays an important role in the occurrence, development, invasion, metastasis and drug resistance of malignant tumors. Hence, further evaluation and targeting of necroptosis may be of clinical benefit for gynecologic cancers (GCs).

Methods

To compare consistency and difference, we explored the expression pattern and prognostic value of necroptosis-related genes (NRGs) in pan-GC analysis through Linear regression and Empirical Bayesian, Univariate Cox analysis, and public databases from TCGA and Genotype-Tissue Expression (GTEx), including CESC, OV, UCEC, and UCS. We explored the copy number variation (CNV), methylation level and enrichment pathways of NRGs in the four GCs. Based on LASSO Cox regression analysis or principal component analysis, we established the prognostic NRG-signature or necroptosis-score for the four GCs. In addition, we predicted and compared functional pathways, tumor mutational burden (TMB), somatic mutation features, immunity status, immunotherapy, chemotherapeutic drug sensitivity of the NRG-signature based on NRGs. We also examined the expression level of several NRGs in OV samples that we collected using Quantitative Real-time PCR.

Results

We confirmed the presence of NRGs in expression, prognosis, CNV, and methylation for four GCs, thus comparing the consistency and difference among the four GCs. The prognosis and independent prognostic value of the risk signatures based on NRGs were determined. Through the results of subclass mapping, we found that GC patients with lower risk score may be more sensitive to PDL1 response and more sensitive to immune checkpoint blockade therapy. Drug susceptibility analysis showed that, 51, 45, 64, and 29 drugs with differences between risk groups were yielded in CESC, OV, UCEC, and UCS respectively. For OV, the expression differences of several NRGs in the tissues we collected were similar to that in TCGA.

Conclusion

Our comprehensive analysis of NRGs and NRG-signature demonstrated their similarity and difference, as well as their potential roles in prognosis and could guide therapeutic strategies, thus improving the outcome of GC patients.
A novel focal adhesion-related risk model predicts prognosis of bladder cancer —— a bioinformatic study based on TCGA and GEO database
Authors: Hu Jiyuan , Wang Linhui , Li Luanfeng , Wang Yutao , Bi Jianbin
Published: November 2022

Background

Bladder cancer (BLCA) is the ninth most common cancer globally, as well as the fourth most common cancer in men, with an incidence of 7%. However, few effective prognostic biomarkers or models of BLCA are available at present.

Methods

The prognostic genes of BLCA were screened from one cohort of The Cancer Genome Atlas (TCGA) database through univariate Cox regression analysis and functionally annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The intersecting genes of the BLCA gene set and focal adhesion-related gene were obtained and subjected to the least absolute shrinkage and selection operator regression (LASSO) to construct a prognostic model. Gene set enrichment analysis (GSEA) of high- and low-risk patients was performed to explore further the biological process related to focal adhesion genes. Univariate and multivariate Cox analysis, receiver operating characteristic (ROC) curve analysis, and Kaplan–Meier survival analysis (KM) were used to evaluate the prognostic model. DNA methylation analysis was presented to explore the relationship between prognosis and gene methylation. Furthermore, immune cell infiltration was assessed by CIBERSORT, ESTIMATE, and TIMER. The model was verified in an external GSE32894 cohort of the Gene Expression Omnibus (GEO) database, and the Prognoscan database presented further validation of genes. The HPA database validated the related protein level, and functional experiments verified significant risk factors in the model.

Results

VCL, COL6A1, RAC3, PDGFD, JUN, LAMA2, and ITGB6 were used to construct a prognostic model in the TCGA-BLCA cohort and validated in the GSE32894 cohort. The 7-gene model successfully stratified the patients into both cohorts’ high- and low-risk groups. The higher risk score was associated with a worse prognosis.

Conclusions

The 7-gene prognostic model can classify BLCA patients into high- and low-risk groups based on the risk score and predict the overall survival, which may aid clinical decision-making.
Risk factors for Hirschsprung-associated enterocolitis following Soave: a retrospective study over a decade
Authors: Xie Chuanping , Yan Jiayu , Zhang Zhiyi , Kai Wang , Wang Zengmeng , Chen Yajun
Published: November 2022

Background

Hirschsprung-associated enterocolitis (HAEC), one of the most significant causes of morbidity and mortality for patients with Hirschsprung disease (HSCR), can occur before and after radical surgery. This study aims to identify the risk factors for HAEC before and after Soave. 

Methods

A retrospective study of 145 patients with HSCR treated by transanal or combination with laparoscopic or laparotomy Soave procedure between January 2011 and June 2021 was performed. Data were retrieved from the medical records. HAEC was defined as the presence of clinical signs of bowel inflammation and requiring treatment with intravenous antibiotics and rectal irrigation for at least two days in the outpatient or inpatient department. Univariate analysis and multivariate regression models were used to identify risk factors for developing pre-and postoperative HAEC.

Results

The incidence of pre-and postoperative HAEC was 24.1% and 20.7%, respectively. More than 90% of the patients with the first episode of postoperative HAEC occurred within the first year after Soave. Long-segment aganglionosis was the independent risk factor for developing preoperative HAEC ([OR] 5.8, Cl 2.4–14.2, p < 0.001), while the history of preoperative HAEC was significantly associated with developing postoperative HAEC ([OR] 4.2, Cl 1.6–10.8, p = 0.003).

Conclusions

Long-segment aganglionosis was the independent risk factor for the development of preoperative HAEC, and the history of preoperative HAEC was strongly associated with developing HAEC after Soave.

Level of Evidence

Level III
Greater muscle volume and muscle fat infiltrate in the deep cervical spine extensor muscles (multifidus with semispinalis cervicis) in individuals with chronic idiopathic neck pain compared to age and sex-matched asymptomatic controls: a cross-sectional study
Authors: Snodgrass Suzanne J , Stanwell Peter , Weber Kenneth A. , Shepherd Samala , Kennedy Olivia , Thompson Hannah J , Elliott James M
Published: November 2022

Muscle size and composition (muscle volume and muscle fat infiltrate [MFI]) may provide insight into possible mechanisms underpinning chronic idiopathic neck pain, a common condition with no definitive underlying pathology. In individuals with chronic idiopathic neck pain > 3 months and age- and sex-matched asymptomatic controls, muscle volumes of levator scapulae, multifidus including semispinalis cervicis (MFSS), semispinalis capitis, splenius capitis including splenius cervicis (SCSC), sternocleidomastoid and longus colli from C3 through T1 were quantified from magnetic resonance imaging. Between-group differences were determined using linear mixed models, accounting for side (left or right), muscle, spinal level, sex, age, and body mass index (BMI). Individuals with pain had greater muscle volume (mean difference 76.8mm3; 95% CI 26.6–127.0; p = .003) and MFI (2.3%; 0.2–4.5; p = .034) of the MFSS compared to matched controls with no differences in relative volume, accounting for factors associated with the outcomes: muscle, spinal level, side (left had smaller volume, relative volume and MFI than right), sex (females had less volume and relative volume than males), age (older age associated with less relative volume and greater MFI), and BMI (higher BMI associated with greater muscle volume and MFI). Greater MFI in individuals with chronic idiopathic neck pain suggests a possible underlying mechanism contributing to neck pain. Perspective: These findings suggest MFI in the MFSS may be radiologic sign, potentially identifying patients with a less favourable prognosis. Future studies are needed to confirm this finding and determine if MFI is a contributor to the development or persistence of neck pain, or consequence of neck pain.
High stone-free rate immediately after suctioning flexible ureteroscopy with Intelligent pressure-control in treating upper urinary tract calculi
Authors: Gao Xingjian , Zhang Zedong , Li Xinwei , Cai Weiping , Zheng Bin , Lu Yijin , Zhao Hualong , You Junhong , Zheng Gangfeng , Bao Weilong , Lai Yutong , Lv Yisong
Published: November 2022

Background

The retrospective observational study aimed to evaluate the safety and efficacy of suctioning flexible ureteroscopy with Intelligent pressure-control (SFUI) on treating upper urinary tract calculi in a large cohort.

Methods

Between July 2020 and August 2021, 278 patients with upper urinary tract calculi who underwent SFUI in our hospital were enrolled. Outcomes were stone-free rate (SFR) in one session and one-month after SFUI treatment, and complications scored by the Clavien-Dindo classification.

Results

A total of 310 kidneys underwent SFUI were included. The median surgery time was 75 min (ranged 60–110 min). One session and one-month SFRs were 80.65% and 82.26%, respectively. The one-session SFR was ≧ 87% in patients with Guy’s stone score of Grade I among stone size < 40 mm. Risk factors for unsuccessful stone-free in one session were stone history (adjusted odds ratio (aOR): 2.39, 95% confidence interval (CI): 1.21–4.73), stone size of 40–49 mm (aOR: 4.37, 95% CI: 1.16–16.45), Guy’s stone score ≧ Grade II (Grade II, aOR: 3.54, 95% CI: 1.18–10.59; Grade III, aOR: 10.95, 95% CI: 2.65–45.25). The incidence of Clavien-Dindo grade II-III complication was 3.26%. Complication is associated with Guy’s stone score III (aOR: 22.36, 95% CI: 1.81–276.36).

Conclusion

SFUI shows good safety and efficiency on treating upper urinary tract calculi. Patients with stone size < 40 mm or Guy’s stone score of Grade I have a high chance to reach stone-free after SFUI treatment.
Relationship between a novel non–insulin-based metabolic score for insulin resistance (METS‐IR) and coronary artery calcification
Authors: Wang Zhenwei , Hui Xiaofang , Huang Xu , Li Jingjie , Liu Naifeng
Published: November 2022

Background and aims

A novel non–insulin-based metabolic score for insulin resistance (METS‐IR) index has been proposed as a simple and reliable alternative insulin resistance (IR) marker, but its the predictive value in asymptomatic adults with coronary artery calcification (CAC) remains unclear.

Methods and results

We enrolled 1576 participants without cardiovascular disease (CVD), who underwent multidetector computed tomography. Logistic regression, restricted cubic spline models and receiver operating characteristic (ROC) curves were used to examine the association between METS-IR, the ratio of triglyceride to high-density lipoprotein cholesterol (TG/HDL-C) and triglyceride glucose index (TyG index) and CAC. In multivariate logistic regression analysis, the increase in METS-IR was independently associated with a higher prevalence of CAC (all P < 0.05 in Models 1–3). Furthermore, restricted cubic splines indicated that the significance of METS-IR in predicting CAC was higher than that of other IR indexes. In ROC curve analysis, without considering the P value, the area under the curve of CAC predicted by METS-IR was higher than that of other IR indexes (METS-IR, 0.607; TyG index, 0.603; TG/HDL-C, 0.577).

Conclusion

Compared with other IR indexes, METS-IR may have better discrimination ability in predicting the incidence of CAC in asymptomatic adults without CVD.
Characteristics of oral microbiome of healthcare workers in different clinical scenarios: a cross-sectional analysis
Authors: Zhang Zhixia , Yu Wenyi , Li Guangyao , He Yukun , Shi Zhiming , Wu Jing , Ma Xinqian , Zhu Yu , Zhao Lili , Liu Siqin , Wei Yue , Xue Jianbo , Guo Shuming , Gao Zhancheng
Published: November 2022

The environment of healthcare institutes (HCIs) potentially affects the internal microecology of medical workers, which is reflected not only in the well-studied gut microbiome but also in the more susceptible oral microbiome. We conducted a prospective cross-sectional cohort study in four hospital departments in Central China. Oropharyngeal swabs from 65 healthcare workers were collected and analyzed using 16S rRNA gene amplicon sequencing. The oral microbiome of healthcare workers exhibited prominent deviations in diversity, microbial structure, and predicted function. The coronary care unit (CCU) samples exhibited robust features and stability, with significantly higher abundances of genera such as Haemophilus, Fusobacterium, and Streptococcus, and a lower abundance of Prevotella. Functional prediction analysis showed that vitamin, nucleotide, and amino acid metabolisms were significantly different among the four departments. The CCU group was at a potential risk of developing periodontal disease owing to the increased abundance of F. nucleatum. Additionally, oral microbial diversification of healthcare workers was related to seniority. We described the oral microbiome profile of healthcare workers in different clinical scenarios and demonstrated that community diversity, structure, and potential functions differed markedly among departments. Intense modulation of the oral microbiome of healthcare workers occurs because of their original departments, especially in the CCU.
Assessing relational coordination and its impact on perceived mental health of students, teachers and staff in a clinical skills program during the COVID-19 pandemic
Authors: Alfazari Ali S. , Naim Ali Hebatallah A. , Alessa Awad , Magzoub Mohi Eldin
Published: November 2022

Background

The global spread of the COVID-19 virus caused unprecedented interruptions in medical education. This paper evaluates Relational Coordination (RC): communicating and relating for task integration; between the distinct stakeholders responsible for scheduling,delivering and receiving clinical teaching in the wake of the pandemic.

Methodology

Using a cross-sectional design, the level of Relational Coordination was assessed between twelve groups within a Clinical Skills Program at a Medical School in the United Arab Emirates. It also measures three relevant mental health factors: namely, Job satisfaction, Work Engagement, and Burnout.

Results

Overall, RC scores were moderate (3.65 out of 5.00). Controlling for participants' position, RC was found to positively and significantly increase both job satisfaction (β = 1.10, p < 0.001) and work engagement (β = 0.78, p < 0.01)., Additionally, RC was significantly associated with lower burnout (β = -0.56, p = 0.05). Fifty percent of participants experienced high job satisfaction, with a mean score of 5.0 out of 7.0, while 73% reported being enthusiastic about their job, with a mean score of 6.0 out of 7.0. About a third of participants (27%) reported feeling burnout.

Conclusions

During times of disruption and crisis, medical education can benefit from higher levels of relational coordination. Our study shows the significant impact of relational coordination on mental health measures like job satisfaction and work engagement. To achieve the full potential and benefits of excellent levels of relational coordination in this program, we recommend six interventions focusing on improving communication, work processes, regular meetings, education innovations, capacity building, and the establishment of coaching and counseling programs for students and faculty.
Development and evaluation of an e-learning course in oxygen therapy
Authors: Arabani Nezhad Maryam , Ayatollahi Haleh , Heidari Beigvand Hazhir
Published: November 2022

Background

Respiratory problems are among the most challenging situations in emergency care services. Different oxygen therapy methods are usually used to deal with these problems. In recent years, oxygen therapy has been recognized as one of the most widely used therapeutic processes in emergency departments (ED) mainly due to the Covid-19 pandemic. The aim of this study was to develop and evaluate an e-learning course in oxygen therapy for the ED clinicians.

Methods

This was a pre-post study conducted in three phases in 2021. Initially, the educational requirements of clinicians (n = 181) were investigated using a questionnaire, and in the second phase, an interactive e-learning course was developed. In the third phase, the course was assessed in terms of maintaining the principles of developing an e-learning course, affecting participants’ knowledge, and supporting usability requirements.

Results

The findings revealed that training in oxygen therapy was essential for the ED clinicians. Therefore, an e-learning course was developed. The content production experts and the participants evaluated the content and usability of the online course at a good level. In addition, there was a statistically significant difference between the nurses’ (p < 0.001) and general practitioners’ (p < 0.002) pre- and post-test scores suggesting that the course improved their knowledge.

Conclusion

It seems that the e-learning course developed in the current study can improve health care professionals’ knowledge and quality of care. However, more evaluation studies are needed to investigate the effectiveness of the course for other clinicians, such as nurses who work in intensive care units.
Medical research: what to expect in a student–supervisor relationship
Authors: Althubaiti Alaa , Althubaiti Suha M.
Published: November 2022

Background

A medical research supervisor is of crucial importance to the undergraduate student enrolled in a research methodology course. A solid relationship between the two is vital to the success of the research project and the overall well-being of the student. The structure of the relationship between a student and a research supervisor is seldom discussed in the context of undergraduate medical research. This study evaluates students’ expectations of their research contributions and their supervisors’ roles.

Methods

This was an observational study in a large health university in Saudi Arabia. A total of 320 medical students enrolled in a two-year medical research program completed an online survey, of a previously validated instrument, that is, Role Perceptions Rating Scale. Demographic questions such as the current level in the research program (junior or senior) were added.

Results

The results showed that most students expected the responsibility to be equally shared between the supervisor and student during the development and execution of the research project. Additionally, students expected the research supervisor to be responsible for the research themes and contents, ensuring access to facilities, and assisting in the actual writing of the final research manuscript. Furthermore, the results indicated differences in expectations between junior and senior students.

Conclusion

This study demonstrates that medical students expect their research supervisors to support them to a significant extent. Understanding medical students’ expectations in a supervisor–student relationship is essential to successful research and collaboration. The evidence gathered in this study has practical implications for educational institutes to base their research training program on these insights. Providing clarity on the expectations and responsibilities of those participating in the research program is crucial, as this would, in turn likely advance the output of the research program and encourage clinicians to join the program as research supervisors.
A novel autosomal dominant GREB1L variant associated with non-syndromic hearing impairment in Ghana
Authors: Adadey Samuel Mawuli , Aboagye Elvis Twumasi , Esoh Kevin , Acharya Anushree , Bharadwaj Thashi , Lin Nicole S. , Amenga-Etego Lucas , Awandare Gordon A. , Schrauwen Isabelle , Leal Suzanne M. , Wonkam Ambroise
Published: November 2022

Background

Childhood hearing impairment (HI) is genetically heterogeneous with many implicated genes, however, only a few of these genes are reported in African populations.

Methods

This study used exome and Sanger sequencing to resolve the possible genetic cause of non-syndromic HI in a Ghanaian family.

Results

We identified a novel variant c.3041G > A: p.(Gly1014Glu) in GREB1L (DFNA80) in the index case. The GREB1L: p.(Gly1014Glu) variant had a CADD score of 26.5 and was absent from human genomic databases such as TopMed and gnomAD. In silico homology protein modeling approaches displayed major structural differences between the wildtype and mutant proteins. Additionally, the variant was predicted to probably affect the secondary protein structure that may impact its function. Publicly available expression data shows a higher expression of Greb1L in the inner ear of mice during development and a reduced expression in adulthood, underscoring its importance in the development of the inner ear structures.

Conclusion

This report on an African individual supports the association of GREB1L variant with non-syndromic HI and extended the evidence of the implication of GREB1L variants in HI in diverse populations.
Dynamic modulations of urinary sphingolipid and glycerophospholipid levels in COVID-19 and correlations with COVID-19-associated kidney injuries
Authors: Kurano Makoto , Jubishi Daisuke , Okamoto Koh , Hashimoto Hideki , Sakai Eri , Morita Yoshifumi , Saigusa Daisuke , Kano Kuniyuki , Aoki Junken , Harada Sohei , Okugawa Shu , Doi Kent , Moriya Kyoji , Yatomi Yutaka
Published: November 2022

Background

Among various complications of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), renal complications, namely COVID-19-associated kidney injuries, are related to the mortality of COVID-19.

Methods

In this retrospective cross-sectional study, we measured the sphingolipids and glycerophospholipids, which have been shown to possess potent biological properties, using liquid chromatography-mass spectrometry in 272 urine samples collected longitudinally from 91 COVID-19 subjects and 95 control subjects without infectious diseases, to elucidate the pathogenesis of COVID-19-associated kidney injuries.

Results

The urinary levels of C18:0, C18:1, C22:0, and C24:0 ceramides, sphingosine, dihydrosphingosine, phosphatidylcholine, lysophosphatidylcholine, lysophosphatidic acid, and phosphatidylglycerol decreased, while those of phosphatidylserine, lysophosphatidylserine, phosphatidylethanolamine, and lysophosphatidylethanolamine increased in patients with mild COVID-19, especially during the early phase (day 1–3), suggesting that these modulations might reflect the direct effects of infection with SARS-CoV-2. Generally, the urinary levels of sphingomyelin, ceramides, sphingosine, dihydrosphingosine, dihydrosphingosine l-phosphate, phosphatidylcholine, lysophosphatidic acid, phosphatidylserine, lysophosphatidylserine, phosphatidylethanolamine, lysophosphatidylethanolamine, phosphatidylglycerol, lysophosphatidylglycerol, phosphatidylinositol, and lysophosphatidylinositol increased, especially in patients with severe COVID-19 during the later phase, suggesting that their modulations might result from kidney injuries accompanying severe COVID-19.

Conclusions

Considering the biological properties of sphingolipids and glycerophospholipids, an understanding of their urinary modulations in COVID-19 will help us to understand the mechanisms causing COVID-19-associated kidney injuries as well as general acute kidney injuries and may prompt researchers to develop laboratory tests for predicting maximum severity and/or novel reagents to suppress the renal complications of COVID-19.
Chemoradiation and consolidation chemotherapy for rectal cancer provides a high rate of organ preservation with a very good long-term oncological outcome: a single-center cohort series
Authors: Asoglu Oktar , Bulut Alisina , Aliyev Vusal , Piozzi Guglielmo Niccolò , Guven Koray , Bakır Barıs , Goksel Suha
Published: November 2022

Aim

To report long-term oncological outcomes and organ preservation rate with a chemoradiotherapy-consolidation chemotherapy (CRT-CNCT) treatment for locally advanced rectal cancer (LARC).

Method

Retrospective analysis of prospectively maintained database was performed. Oncological outcomes of mid-low LARC patients (n=60) were analyzed after a follow-up of 63 (50–83) months. Patients with clinical complete response (cCR) were treated with the watch-and-wait (WW) protocol. Patients who could not achieve cCR were treated with total mesorectal excision (TME) or local excision (LE).

Results

Thirty-nine (65%) patients who achieved cCR were treated with the WW protocol. TME was performed in 15 (25%) patients and LE was performed in 6 (10%) patients. During the follow-up period, 10 (25.6%) patients in the WW group had regrowth (RG) and 3 (7.7%) had distant metastasis (DM). Five-year overall survival (OS) and disease-free survival (DFS) were 90.1% and 71.6%, respectively, in the WW group. Five-year OS and DFS were 94.9% (95% CI: 88–100%) and 80% (95% CI: 55.2–100%), respectively, in the RG group. For all patients (n=60), 5-year TME-free DFS was 57.3% (95% CI: 44.3–70.2%) and organ preservation-adapted DFS was 77.5% (95% CI: 66.4–88.4%). For the WW group (n=39), 5-year TME-free DFS was 77.5% (95% CI: 63.2–91.8%) and organ preservation-adapted DFS was 85.0% (95% CI: 72.3–97.8%).

Conclusion

CRT-CNCT provides cCR as high as 2/3 of LARC patients. Regrowths, developed during follow-up, can be successfully salvaged without causing oncological disadvantage if strict surveillance is performed.
Gene flow and introgression are pervasive forces shaping the evolution of bacterial species
Authors: Diop Awa , Torrance Ellis L. , Stott Caroline M. , Bobay Louis-Marie
Published: November 2022

Background

Although originally thought to evolve clonally, studies have revealed that most bacteria exchange DNA. However, it remains unclear to what extent gene flow shapes the evolution of bacterial genomes and maintains the cohesion of species.

Results

Here, we analyze the patterns of gene flow within and between >2600 bacterial species. Our results show that fewer than 10% of bacterial species are truly clonal, indicating that purely asexual species are rare in nature. We further demonstrate that the taxonomic criterion of ~95% genome sequence identity routinely used to define bacterial species does not accurately represent a level of divergence that imposes an effective barrier to gene flow across bacterial species. Interruption of gene flow can occur at various sequence identities across lineages, generally from 90 to 98% genome identity. This likely explains why a ~95% genome sequence identity threshold has empirically been judged as a good approximation to define bacterial species. Our results support a universal mechanism where the availability of identical genomic DNA segments required to initiate homologous recombination is the primary determinant of gene flow and species boundaries in bacteria. We show that these barriers of gene flow remain porous since many distinct species maintain some level of gene flow, similar to introgression in sexual organisms.

Conclusions

Overall, bacterial evolution and speciation are likely shaped by similar forces driving the evolution of sexual organisms. Our findings support a model where the interruption of gene flow—although not necessarily the initial cause of speciation—leads to the establishment of permanent and irreversible species borders.
Great saphenous vein aneurysm mimicking inguinal hernia: a case report
Authors: Ghoddusi Johari Hamed , Malekhosseini Hamidreza , Erfani Amirhossein , Shahriarirad Reza
Published: November 2022

Background

Diagnosis of venous aneurysm may be difficult and can be misjudged as mass-like lesions, including hernias. Here we present the case of a patient with a great saphenous vein aneurysm misdiagnosed and operated as an inguinal hernia.

Case presentation

A 39-year-old Middle Eastern/Persian male presented with left inguinal bulging 15 years ago, which was misdiagnosed and operated on with a diagnosis of inguinal hernia. He was referred to our clinic, in which color Doppler sonography revealed left-sided saphenofemoral junction incompetence with severe flow reversal during the Valsalva maneuver, in favor of a great saphenous vein aneurysm. Ligation of left saphenofemoral junction and stripping of saphenous vein, and stab avulsion phlebotomy of left lower extremity varicose veins, were done. He was discharged the next day after the operation with an uneventful postoperative course or complication on follow-up.

Conclusion

Venous aneurysms can be misdiagnosed as other, more common, mass-like lesions, such as inguinal hernias. Therefore, our report emphasizes the consideration of thorough assessment and utilization of color duplex sonography to prevent further misdiagnosis and unnecessary intervention and operations.
Understanding the role of stress, personality and coping on learning motivation and mental health in university students during a pandemic
Authors: Gibbons Chris
Published: November 2022

The aims explored the associations between stress, personality and coping on student mental health and compared defensive-pessimism and optimism as influences on learning motivation. Most research construes ‘stress’ as ‘distress’, with little attempt to measure the stress that enhances motivation and wellbeing. Undergraduate psychology students (N = 162) were surveyed on student and pandemic-related stressors, personality, support, control, mental health and learning motivation. Overall, adverse mental health was high and the lack of motivation acute. While positive ratings of teaching and optimistic thinking were associated with good mental health, context control was key. Adverse ratings of teaching quality lowered learning motivation. Support and conscientiousness bolstered learning motivation and conscientiousness buffered against the adverse impact of stress on motivation. Openness was associated with the stress involved in learning. For those anxious-prone, defensive-pessimism was as effective as optimism was in stimulating learning motivation. Developing context control, support and strategies linked to personality could bolster student resilience during and post Covid-19.
Maladaptive personality traits as predictors of prosocial and trusting behavior in two economic games
Authors: Hepp Johanna , Mohr Melissa R. M. , Niedtfeld Inga
Published: November 2022

Background

Dimensional models of personality disorders postulate interpersonal dysfunction as the core feature of personality pathology, and describe maladaptive personality traits that characterize the specific pattern of dysfunction that is experienced. Herein, we examined whether maladaptive traits predict prosocial and trusting behavior, both of which are highly relevant behaviors for interpersonal functioning. Specifically, we examined antagonism as a predictor of prosocial behavior in a dictator game, and suspiciousness as a predictor of trust in the faith game.

Materials and methods

The study was preregistered and conducted online. The preregistration protocol is available athttps://osf.io/er43j. Data and code are available athttps://osf.io/2rvbg/. Participants (N = 445) completed the German version of the Personality Inventory for DSM-5 to measure antagonism and suspiciousness. Additionally, they played the dictator game (more money taken away from another person indicates less prosocial behavior) and the faith game (choosing the sure choice instead of the faith choice indicates less trust). We conducted a linear regression model to test whether antagonism is associated with prosocial behavior in the dictator game and a logistic regression model to test whether suspiciousness predicts selection of the sure choice in the faith game.

Results

As hypothesized, higher levels of antagonism were associated with less prosocial behavior in the dictator game. The remaining hypotheses were not supported, as suspiciousness was not significantly associated with the likelihood of choosing the sure choice in the faith game. Exploratory analyses on participants’ estimates of the sure choice amount suggest successful experimental manipulation in the faith game.

Conclusions

The results on antagonism and prosocial behavior are consistent with those of previous studies that used categorial classification systems of personality disorders or examined non-pathological personality traits. Potential explanations for the non-significant effects of suspiciousness are discussed, including the small size and range of the sure choice payoff and that the anonymity of the game may have precluded suspicious traits from expressing. Future research with higher stakes and known interaction partners is needed to further probe the effects of suspiciousness.
Does diabetes mellitus affect the safety profile of valproic acid for the treatment of status epilepticus? A retrospective cohort study
Authors: Müller Annekatrin , von Hofen-Hohloch Judith , Awissus Carolin , Przybilla Jens , Mrestani Achmed , Classen Joseph
Published: November 2022

Background

In the treatment of status epilepticus less is known about the influence of comorbidities on the safety profile of anticonvulsive drugs. Especially patients with diabetes mellitus may be predisposed to certain adverse events that have been related to therapy with valproic acid. In this single-center retrospective cohort study we examined if the complications of the intravenous treatment with valproic acid is different in patients with or without diabetes.

Methods

Patients who were treated for status epilepticus with intravenous valproic acid between 2008 and 2020 were identified. Primary endpoint was the discontinuation of therapy with valproic acid due to adverse events. Relevant secondary endpoints were the functional status at the time of discharge from hospital in comparison to the premorbid state and the in-hospital mortality. Both groups (patients with or without diabetes) were compared by Mann–Whitney U-Test or Pearson´s Chi2 test. To identify therapy with valproic acid as a risk factor of in-hospital mortality, a binary regression model was used.

Results

During the study period 408 patients and 482 episodes of status epilepticus were treated with intravenous valproic acid. Group comparisons did not reveal a significant difference in the rates of discontinuation of therapy. A difference was found in the rate of thrombocytopenia (p = 0.015), which occurred more often in patients with diabetes. In total, 36 hypoglycemic episodes could be identified, two occurred spontaneously under intravenous valproic acid. After correction for potential confounders, continuous therapy with valproic acid could not be confirmed as an independent risk factor for in-hospital mortality (p = 0.079). In patients with diabetes, the proportion of patients with a good functional state, indicated by the modified Rankin Scale, was significantly lower in both times (premorbid: 55% vs. 69%, p = 0.008; at discharge: 22% vs. 36%, p = 0.004).

Conclusions

Tolerability of the treatment with valproic acid was similar in patients with or without diabetes. Diabetes as a relevant comorbidity can signal a potentially increased risk of a poor outcome after status epilepticus.

Trial registration: The study was registered at the German Clinical Trials Register on 8 April 2022 (DRKS 00,027,836).
Sterol demethylation inhibitor fungicide resistance in Colletotrichum siamense from chili is caused by mutations in CYP51A and CYP51B
Authors: Chen Wenchan , Wei Lingling , Hou Rongxian , Zhao Yangyang , Zhao Yancun , Liu Fengquan
Published: November 2022

Anthracnose, caused by fungi of the genus Colletotrichum, is a serious disease of chili worldwide. Sterol 14α-demethylation inhibitors (DMIs) are a class of chemical fungicides that can effectively control anthracnose diseases. In this study, 22 Colletotrichum isolates collected from commercial chili fields in Zhangzhou, Fujian Province, China, were identified as Colletotrichum siamense. The sensitivities of the 22 C. siamense isolates to tebuconazole were determined based on the EC50 (50% effective inhibition concentration) value. The results showed that the EC50 values of the two isolates to tebuconazole were 0.039 ± 0.0036 and 0.042 ± 0.0012 mg/L, while the other 20 isolates showed significantly decreased sensitivities to tebuconazole, with EC50 values ranging from 0.61 ± 0.056 to 1.94 ± 0.11 mg/L. Sequence analysis of CYP51A and CYP51B revealed five genotype mutations (i. e., CYP51AV46L, D115V, P163S, R306K, E397D, CYP51AD115V, S164Y, R306K, E397D, CYP51AD115V, R306K, P339T, E397D, CYP51AD115V, R306K, E397D, S400N, and CYP51AD115V, R306K, E397DCYP51BR266H) in the resistant isolates. The tebuconazole-resistant isolates of five genotypes suffered a fitness penalty and exhibited cross-resistance to difenoconazole, prochloraz, and propiconazole. Additionally, the five genotype mutations were validated as being responsible for tebuconazole-resistance in C. siamense by construction of replacement mutants. Overexpression of CYP51A and CYP51B was not detected in the replacement mutants of the five genotypes. Overall, the present study is the first to report DMI resistance in C. siamense and provides significant information for rational use of DMIs to control chili anthracnose.
Physics-driven self-supervised learning system for seismic velocity inversion
Authors: Liu Bin , Jiang Peng , Wang Qingyang , Ren Yuxiao , Yang Senlin , Cohn Anthony G.
Published: November 2022

Seismic velocity inversion plays a vital role in various applied seismology processes. A series of deep learning methods have been developed that rely purely on manually provided labels for supervision; however, their performances depend heavily on using large training data sets with corresponding velocity models. Because no physical laws are used in the training phase, it is usually challenging to generalize trained neural networks to a new data domain. To mitigate these issues, we have embedded a seismic forward modeling step at the end of a network to remap the inversion result back to seismic data and thus train the neural network through self-supervised loss, i.e., the misfit between the network input and output. As a result, we eliminate the need for many labeled velocity models, and physical laws are introduced when back-propagating gradients through the seismic forward modeling step. We verify the effectiveness of our approach through comprehensive experiments on synthetic data sets, where self-supervised learning outperforms the fully supervised approach, which accesses much more labeled data. The superior performance is even more significant when compared with a new data domain that has velocity models with faults and more geologic layers. Finally, in case of unknown and more complex data types, we develop a network-constrained full-waveform inversion (FWI) method. This method refines the initial prediction of the network by iteratively optimizing network parameters other than the velocity model, as found with the conventional FWI method, and demonstrates clear advantages in terms of interface and velocity accuracy. With these measures (self-supervised learning and network-constrained FWI), our physics-driven self-supervised learning system successfully mitigates issues such as the dependence on large labeled data sets, the absence of physical laws, and the difficulty in adapting to new data domains.
Data-assimilated time-lapse visco-acoustic full-waveform inversion: Theory and application for injected CO2 plume monitoring
Authors: Huang Chao , Zhu Tieyuan , Xing Guangchi
Published: November 2022

Continuous seismic monitoring for quantifying CO2 plume migration and detection of any potential leakages in the subsurface is essential for the security of long-term anthropogenic carbon dioxide geologic storage. Traditional time-lapse full-waveform inversion (TLFWI) methods aim to map the CO2 distribution by estimating seismic velocity changes, but recent studies find that CO2-induced attenuation is an important complement to seismic velocity for tracking the CO2 plumes and even quantifying the CO2 saturation. We have developed a novel data-assimilated TLFWI method to construct high-resolution time-lapse velocity and attenuation changes from dense time-lapse monitoring data. This method consists of two theoretical developments: visco-acoustic full-waveform inversion (QFWI) and multiparameter hierarchical matrix-powered extended Kalman filter (mHiEKF). The method is capable of (1) posing temporal constraints to retrieve time-lapse information from dense monitoring data by using mHiEKF, (2) accurately recovering high-spatial-resolution velocity and attenuation perturbations using first-order equation system-based QFWI, and (3) providing the model uncertainty by estimating their model standard deviation. With numerical examples, we first find the effectiveness of the new QFWI on estimating accurate velocity and attenuation models simultaneously. Then, a CO2 leakage case and a realistic Frio-II CO2 monitoring case are presented to find the advantages and applicability of our data-assimilated QFWI method for estimating time-lapse changes using dense time-lapse monitoring surveys. By assimilating time-lapse seismic monitoring data over time, our data-assimilated QFWI method can improve the resolution of velocity and attenuation changes and decrease their model uncertainties.