bluuebunny/crossref_metadata_2025 huggingface dataset:
Negative supercoils regulate meiotic crossover patterns in budding yeast
Authors: Tan Taicong , Tan Yingjin , Wang Ying , Yang Xiao , Zhai Binyuan , Zhang Shuxian , Yang Xuan , Nie Hui , Gao Jinmin , Zhou Jun , Zhang Liangran , Wang Shunxin
Published: September 2022

Interference exists ubiquitously in many biological processes. Crossover interference patterns meiotic crossovers, which are required for faithful chromosome segregation and evolutionary adaption. However, what the interference signal is and how it is generated and regulated is unknown. We show that yeast top2 alleles which cannot bind or cleave DNA accumulate a higher level of negative supercoils and show weaker interference. However, top2 alleles which cannot religate the cleaved DNA or release the religated DNA accumulate less negative supercoils and show stronger interference. Moreover, the level of negative supercoils is negatively correlated with crossover interference strength. Furthermore, negative supercoils preferentially enrich at crossover-associated Zip3 regions before the formation of meiotic DNA double-strand breaks, and regions with more negative supercoils tend to have more Zip3. Additionally, the strength of crossover interference and homeostasis change coordinately in mutants. These findings suggest that the accumulation and relief of negative supercoils pattern meiotic crossovers.
The effect of probiotics on postsurgical complications in patients with colorectal cancer: a systematic review and meta-analysis
Authors: Araújo Maísa Miranda , Montalvão-Sousa Thaís Muniz , Teixeira Patrícia da Cruz , Figueiredo Ana Claudia Morais Godoy , Botelho Patrícia Borges
Published: September 2022

Context

Clinical trials have investigated the effect of probiotics on postsurgical complications in colorectal cancer (CRC). However, so far, there are no systematic reviews evaluating the effect of probiotics and synbiotics on the clinical or infectious postsurgical complications of colorectal cancer.

Objective

The objective of this review was to synthesize the best available evidence on the effects of the use of probiotics or synbiotics on pre-, peri-, and post-operative complications of CRC surgical resection.

Data Sources

A search of the PubMed, Embase, LILACS, Scopus, Cochrane, Web of Science, ProQuest, and Google Scholar databases was conducted for clinical trials published up until January 2022.

Data Extraction

The population characteristics, period and protocol of supplementation, and postoperative complications were extracted and reported. A random-effects model was used to estimate the effect of probiotic and synbiotic treatment on these variables.

Data Synthesis

In total, 2518 studies were identified, of which 16 were included in the qualitative synthesis and 13 in the meta-analysis. Overall, probiotic supplementation reduced the incidence of ileus (odds ratio [OR] = .13, 95% confidence interval [CI]: .02, .78), diarrhea (OR = .32, 95% CI: .15, .69), abdominal collection (OR: .35, 95% CI: .13, .92), sepsis (OR = .41, 95% CI: .22, .80), pneumonia (OR = .39, 95% CI: .19, .83), and surgical site infection (OR = .53, 95% CI: .36, .78). The results of the subgroup analysis indicated that lower dose (<109 colony-forming units), higher duration of supplementation (>14 days), and being administrated ≤5 days before and >10 days after surgery was more effective at reducing the incidence of surgical site infection.

Conclusion

Probiotics and synbiotics seem to be a promising strategy for the prevention of postoperative complications after CRC surgery. Larger, high-quality randomized controlled trials are needed to establish the optimal treatment protocol for the use of probiotics and synbiotics in preventing postoperative complications for CRC surgery.
Long-term relatedness and income distribution: understanding the deep roots of inequality
Authors: Vu Trung V
Published: September 2022

This article explores the role of long-term relatedness between countries, captured by an index of genetic distance, in driving worldwide differences in income inequality. The main hypothesis is that genetic distance gives rise to barriers to the international diffusion of redistributive policies and measures, and institutions, leading to greater income disparities. Using cross-country data, I consistently find that countries that are genetically distant to Denmark—the world frontier of egalitarian income distribution—tend to suffer from higher inequality, ceteris paribus. I also demonstrate that genetic distance is associated with greater bilateral differences in income inequality between countries. Employing data from the European Social Survey, I document that second-generation Europeans descending from countries with greater genetic distance to Denmark are less likely to exhibit positive attitudes towards equality. Further evidence suggests that effective fiscal redistribution is a key mechanism through which genetic distance to Denmark transmits to greater income inequality.
Why do states give refugees the right to work?
Authors: Betts Alexander , Sterck Olivier
Published: September 2022

This article explains the conditions under which countries allow refugees the right to work in accordance with Articles 17–19 of the 1951 Convention on the Status of Refugees. It explores variation in both the de jure and de facto rights to work through a mixed-methods approach. Qualitatively, it builds upon research in the East African region, in which there is significant variation in state practice relating to refugees’ socio-economic rights. Quantitatively, it draws upon an original dataset to examine the policies of low- and middle-income countries that host more than 1,000 refugees. Coding for the right to work was supplied by and triangulated across three different refugee organizations with relevant expertise. We argue that the de jure and de facto rights to work are shaped by distinctive actors and mechanisms. De jure rights are determined by pay-offs at the ‘national’ level; de facto rights by pay-offs at the ‘local’ level. While being a signatory of international norms is the most important variable for de jure commitment, the degree of decentralization is the most important variable underlying de facto rights. These findings suggest that promoting refugee norm compliance relies upon creating incentives at both national and local levels.
Association Between Childhood Adversity and Functional Outcomes in People With Psychosis: A Meta-analysis
Authors: Christy Angeline , Cavero Daniela , Navajeeva Sujeena , Murray-O’Shea Rachel , Rodriguez Victoria , Aas Monica , Trotta Giulia , Moudiab Socayna , Garrido Nathalia , Zamora Blanca , Sideli Lucia , Wrobel Anna L , Salazar de Pablo Gonzalo , Alameda Luis
Published: September 2022

Background and Hypothesis

Despite the accepted link between childhood adversity (CA) and psychotic disorders, evidence on the relationship between CA and poor functional outcome remains less consistent and has never been reviewed quantitatively. The aim of this meta-analysis was to systematically examine the association between CA and functional outcomes in people with psychotic disorders.

Study Design

The study protocol was registered on the International Prospective Register of Systematic Reviews (CRD42021254201). A search was conducted across EMBASE, MEDLINE, PsycINFO, and Cochrane Libraries (CENTRAL) using search terms related to psychosis; CA (general, sexual abuse, physical abuse, emotional abuse, physical neglect, and emotional neglect); and functional outcomes (social, occupational, and general functioning [GF]). We conducted random-effects models, sensitivity and heterogeneity analyses, meta-regressions, and we assessed quality.

Study Results

Our meta-analysis comprised 35 studies, including 10 568 cases with psychosis. General CA was negatively associated with GF (28 studies; r = −0.109, 95%CI = −0.161 to −0.05, P < .001), with greater effects in prospective data (10 studies; r = −0.151, 95% CI = −0.236 to −0.063, P = .001). General CA was also associated with social functioning (r = −0.062, 95% CI = −0.120 to −0.004, P = .018) but not occupational outcomes. All CA subtypes except sexual abuse were significantly associated with GF, with emotional and physical neglect showing the largest magnitudes of effect (ranging from r = −0.199 to r = −0.250).

Conclusions

This meta-analysis provides evidence for a negative association between general CA, specific subtypes, and general and social functional outcomes in people with psychosis.
Cannabis dosing and administration for sleep: a systematic review
Authors: Velzeboer Rob , Malas Adeeb , Boerkoel Pierre , Cullen Katie , Hawkins Michelle , Roesler Jordanna , Lai Wayne Wei-Ku
Published: September 2022

Study objectives

As cannabis is increasingly used to treat sleep disorders, we performed a systematic review to examine the effects of cannabis on sleep and to guide cannabis prescribers in their recommendations to patients, specifically focusing on dosing.

Methods

We searched EMBASE, Medline, and Web of Science and identified 4550 studies for screening. Five hundred sixty-eight studies were selected for full-text review and 31 were included for analysis. Study results were considered positive based on improvements in sleep architecture or subjective sleep quality. Bias in randomized controlled trials was assessed using Cochrane Risk of Bias tool 2.0.

Results

Sleep improvements were seen in 7 out of 19 randomized studies and in 7 out of 12 uncontrolled trials. There were no significant differences between the effects of tetrahydrocannabinol and cannabidiol. Cannabis showed most promise at improving sleep in patients with pain-related disorders, as compared to those with neurologic, psychiatric, or sleep disorders, and showed no significant effects on healthy participants’ sleep. While subjective improvements in sleep quality were often observed, diagnostic testing showed no improvements in sleep architecture. Adverse events included headaches, sedation, and dizziness, and occurred more frequently at higher doses, though no serious adverse events were observed.

Conclusion

High-quality evidence to support cannabis use for sleep remains limited. Heterogeneity in cannabis types, doses, timing of administration, and sleep outcome measures limit the ability to make specific dosing recommendations.
Neural activation underlying emotional interference of cognitive control in rotating shift workers: moderating effects of the prefrontal cortex response on the association between sleep disturbance and depressive symptoms
Authors: Kim Sun-Young , Lee Kyung Hwa , Lee Hayoung , Jeon Jeong Eun , Kim Soohyun , Lee Mi Hyun , Lee Jooyoung , Jeon Sehyun , Oh Seong-Min , Kim Seog Ju , Lee Yu Jin
Published: September 2022

Study Objectives

This study investigated the altered neural function involved in emotional interference and its role in linking sleep disturbance and depressive/anxiety symptoms in rotating shift workers.

Methods

Sixty rotating shift workers and 61 controls performed the emotional Stroop task in three blocks (emotional-related, sleep-related, and neutral words) during functional magnetic resonance imaging (fMRI) assessments. Sleep disturbance and depressive/anxiety symptoms were assessed using self-report measures and sleep diaries. Actigraphy was used to assess the sleep and circadian variables. fMRI scans were performed to compare brain activation during the emotional Stroop task. The proposed moderating models were tested using the PROCESS macro in SPSS software.

Results

A significant condition effect on reaction time was detected. Regardless of the group, reaction times were longer in the negative emotional word and sleep-related conditions than in the neutral word condition. Whole-brain analysis revealed that rotating shift workers show greater neural activation in the left dorsolateral prefrontal cortex (DLPFC) compared with controls while performing the emotional Stroop task with negative emotional words. Sleep disturbance was more strongly associated with depressive symptoms when activation of the left DLPFC was higher during the emotional Stroop task with negative words.

Conclusions

The left DLPFC may play important roles in increased sensitivity to emotional information, possibly due to circadian misalignment, and has moderating effects on the association between sleep disturbance and depressive symptoms in rotating shift workers. These findings will help to identify possible brain regions where interventions can be performed to correct sleep and mood problems in rotating shift workers.
Investigation of severe acute respiratory syndrome coronavirus 2 antibodies among the paediatric population in Mogadishu, Somalia
Authors: Orey Fartun Abdullahi H , Sodal Ali Mohamed , Mohamoud Jamal Hassan , Garba Bashiru , Mohamed Ifrah Hassan , Adam Mohamed Hussein , Dahie Hassan Abdullahi , Nur Maryan Abdullahi Sh , Dirie Najib Isse
Published: September 2022

Background

We undertook this cross-sectional study to determine the level of circulating anti-severe acute respiratory syndrome coronavirus 2 immunoglobulins (IgM and IgG) in children, as well as to evaluate other potential risk factors.

Methods

Children attending the outpatient department of the SOS and Benadir Hospitals in Mogadishu from 26 July to 8 August 2021 were selected following parental consent. The children (aged <18 y) were screened using the coronavirus disease 2019 (COVID-19) rapid test lateral flow immune-assay kit.

Results

Of the 500 children screened for COVID-19, 32 (6.4%) tested positive, out of which 26 (5.2%) had IgG antibodies, while five (1%) had IgM, with the other child (0.2%) having both circulating IgG and IgM antibodies. Also, 46.9% of the COVID-19–positive children were asymptomatic without any clinical signs of the disease. Children aged >6 y and those attending school were the most affected (p=0.002). The most common clinical features among positive children were fever (22.6%), cough (22.2%), shortness of breath (5.8%) and loss of smell (2.6%) and taste (2.2%). Similarly, not wearing a facemask as a preventive measure was found to be a significant risk factor (p=0.007).

Conclusions

This study shows that children are at risk of contracting COVID-19 infection. Our study also shows evidence of a high rate of IgG antibodies in school-aged children having close contact with infected adults, in those not wearing facemasks, as well as in those with a family history of comorbidities.
A novel chemotherapy strategy for advanced hepatocellular carcinoma: a multicenter retrospective study
Authors: Sun Juxian , Liu Chang , Shi Jie , Wang Nanya , Jiang Dafeng , Mao Feifei , Gu Jingwen , Zhou Liping , Shen Li , Lau Wan Yee , Cheng Shuqun
Published: September 2022

Background:

Chemotherapy is a common treatment for advanced hepatocellular carcinoma, but the effect is not satisfactory. The study aimed to retrospectively evaluate the effects of adding all-trans-retinoic acid (ATRA) to infusional fluorouracil, leucovorin, and oxaliplatin (FOLFOX4) for advanced hepatocellular carcinoma (HCC).

Methods:

We extracted the data of patients with advanced HCC who underwent systemic chemotherapy using FOLFOX4 or ATRA plus FOLFOX4 at the Eastern Hepatobiliary Surgery Hospital, First Hospital of Jilin University, and Zhejiang Sian International Hospital and retrospectively compared for overall survival. The Cox proportional hazards model was used to calculate the hazard ratios for overall survival and disease progression after controlling for age, sex, and disease stage.

Results:

From July 2013 to July 2018, 111 patients with HCC were included in this study. The median survival duration was 14.8 months in the ATRA plus FOLFOX4 group and 8.2 months in the FOLFOX4 only group (P < 0.001). The ATRA plus FOLFOX4 group had a significantly longer median time to progression compared with the FOLFOX4 group (3.6 months vs. 1.8 months, P < 0.001). Hazard ratios for overall survival and disease progression were 0.465 (95% confidence interval: 0.298–0.726; P = 0.001) and 0.474 (0.314–0.717; P < 0.001) after adjusting for potential confounders, respectively.

Conclusion:

ATRA plus FOLFOX4 significantly improves the overall survival and time to disease progression in patients with advanced HCC.
Analysis of risk factors associated with endoscopic retrograde cholangiopancreatography for patients with liver cirrhosis: a multicenter, retrospective, clinical study
Authors: Li Jielin , Hu Jiexuan , Li Peng , Wu Yongdong , Wang Yongjun , Ji Ming , Hua Haiyang , Ran Wenbin , Pan Yanglin , Zhang Shutian
Published: September 2022

Background:

Endoscopic retrograde cholangiopancreatography (ERCP) is the endoscopic modality of choice for the treatment of biliary and pancreatic diseases. However, patients with cirrhosis, particularly those with decompensated cirrhosis, are believed to be at increased risk for complications associated with ERCP. There is a paucity of literature describing the outcomes of ERCP for patients with cirrhosis. This study aimed to investigate the outcomes of ERCP for cirrhosis patients, especially adverse events, and evaluated its safety and efficacy.

Methods:

We performed a multicenter, retrospective study of all patients at Beijing Friendship Hospital affiliated to Capital Medical University, Xijing Hospital of Air Force Military Medical University, Beijing Youan Hospital affiliated to Capital Medical University, and the Fifth Medical Center of the People's Liberation Army General Hospital from June 2003 to August 2019. The adverse events of inpatient ERCP for patients with (n = 182) and without liver cirrhosis (controls; n = 385) were compared.

Results:

A total of 567 patients underwent ERCP between January 2003 and December 2019 were enrolled in this study. Compared to patients without cirrhosis, patients with cirrhosis were at higher risk for postoperative complications (odds ratio [OR], 4.172; 95% confidence interval [CI], 1.232–7.031; P < 0.001) such as postoperative pancreatitis (OR, 2.026; 95% CI, 1.002–4.378; P = 0.001) and cholangitis (OR, 3.903; 95% CI, 1.001–10.038; P = 0.036). The main indications for ERCP for patients with cirrhosis in this study included choledocholithiasis (101 cases; 55.5%), benign bile duct strictures (46 cases; 25.3%), and malignant bile duct strictures (28 cases; 15.4%). Among them, 23 patients (12.6%) underwent balloon dilation and 79 patients (43.4%) underwent sphincterotomy. Of the patients with cirrhosis, delayed bleeding occurred in ten patients (5.5%), postoperative pancreatitis occurred in 80 patients (44.0%), and postoperative cholangitis occurred in 25 patients (13.7%). An additional multivariate analysis showed that the total bilirubin (TBIL) level (OR, 4.58; 95% CI, 2.37–6.70) and Child-Pugh score of C (OR, 3.11; 95% CI, 1.04–5.37) were risk factors for postoperative complications in patients with cirrhosis.

Conclusions:

Compared with the general population of patients undergoing ERCP, patients with cirrhosis were more prone to postoperative pancreatitis and cholangitis. TBIL levels and Child-Pugh scores were risk factors for postoperative complications in patients with cirrhosis.
Encyclopedia of fecal microbiota transplantation: a review of effectiveness in the treatment of 85 diseases
Authors: Wang Yun , Zhang Sheng , Borody Thomas J. , Zhang Faming
Published: September 2022

Fecal microbiota transplantation (FMT) has been used as a core therapy for treating dysbiosis-related diseases by remodeling gut microbiota. The methodology and technology for improving FMT are stepping forward, mainly including washed microbiota transplantation (WMT), colonic transendoscopic enteral tubing (TET) for microbiota delivery, and purified Firmicutes spores from fecal matter. To improve the understanding of the clinical applications of FMT, we performed a systematic literature review on FMT published from 2011 to 2021. Here, we provided an overview of the reported clinical benefits of FMT, the methodology of processing FMT, the strategy of using FMT, and the regulations on FMT in global. A total of 782 studies were included for the final analysis. The present review profiled the effectiveness from all clinical FMT uses in 85 specific diseases as eight categories, including infections, gut diseases, microbiota–gut–liver axis, microbiota–gut–brain axis, metabolic diseases, oncology, hematological diseases, and other diseases. Although many further controlled trials will be needed, the dramatic increasing reports have shown the promising future of FMT for dysbiosis-related diseases in the gut or beyond the gut.
Global transmission of HIV-1 subtype C and its impact on the circulation of B/C recombination strains in China
Authors: Liu Zhanmou , Liang Yanling , Feng Yi , Li Kang , Shao Yiming
Published: September 2022

This study aimed to reconstruct the origin and worldwide epidemic history of human immunodeficiency virus (HIV)-1 subtype C, and comprehend how HIV-1 subtype C was introduced into and spread throughout China in the form of B/C recombinant strains. Envelope (env) sequences of HIV-1 subtype C and some other subtypes deposited before December 31, 2020 were downloaded from the Los Alamos HIV Database and the Chinese National Center for AIDS/STD Control and Prevention Database. The available sequences were screened for quality, and Bayesian analysis was used to build the maximum clade credibility evolutionary tree to analyze and judge the origin and spread of HIV-1 subtype C. HIV-1 subtype C originated in central Africa around 1952, then spread to southern Africa around 1969, and to eastern Africa around 1973. HIV-1 subtype C from southern Africa was introduced into India in 1977. HIV-1 subtype C of eastern Africa was introduced into Brazil in 1987. Indian HIV-1 subtype C was exported to China in three migration events during the period 1986-1989. The two predominant recombinants in China (CRF07_BC and CRF08_BC) emerged in 1988 and 1990, respectively. Other B/C recombinants, namely CRF64_BC, CRF61_BC, and CRF62_BC, originated in 1993, 2002, and 2000, respectively. Our study has reconstructed the global origin and evolutionary history of HIV-1 subtype C. Additionally, our study demonstrated that the Chinese HIV-1 subtype C originated from three related Indian lineages around the mid to late 1980s, and since then has formed some B/C recombinants with subtype B that caused a widespread epidemic in China.
Supporting an Inclusive Environment Through Correct Name Pronunciation
Authors: Najjar Rana , Noone Joanne , Reifenstein Karen
Published: September 2022

Background:

The Future of Nursing 2020-2030 Report recommends eliminating practices within nursing education that contribute to racism and discrimination.

Problem:

Name mispronunciation has been identified as a microaggression that can interfere with an inclusive learning environment and a sense of belonging.

Approach:

The faculty development approach used a TEDx talk of a story about personal naming, followed by a discussion on appropriate and inappropriate responses to name mispronunciation. Tools and strategies to promote correct name pronunciation were shared.

Outcomes:

Participants reported (1) the training and video were meaningful and impactful; (2) increased understanding that name mispronunciation may be considered a microaggression; and (3) increased awareness of their response to correct name pronunciation.

Conclusions:

A just and equitable learning environment free of discrimination is integral to achieving inclusion and belonging in nursing education. Correct name pronunciation tools and techniques can engender a sense of inclusion.
Factors Associated With Resilience During Long-Term Hemodialysis
Authors: García-Martínez Pedro , Ballester-Arnal Rafa , Gandhi-Morar Kavita , Temprado-Albalat María D. , Collado-Boira Eladio , Saus-Ortega Carlos , Castro-Calvo Jesús
Published: September 2022

Background

Resilience has been associated with greater adherence to treatment, better outcomes, and improved quality of life (QOL) in people with chronic health conditions. This study aimed to identify sociodemographic, treatment accessibility related, clinical, and psychological variables associated with resilience in advanced chronic kidney disease (CKD) patients undergoing long-term hemodialysis (> 6 months).

Methods

This was a multicenter, cross-sectional, and correlational study. The instruments used were the Spanish versions of the Connor–Davidson Resilience Scale, Perceived Stress Scale 10, and Kidney Disease Quality of Life 36. The participants were categorized as resilient (score greater than or equal to 49.37 on the resilience scale) or non-resilient. Binary logistic regression analysis was performed to identify variables with predictive power for the group with the resilient profile (RP).

Results

Perceived stress, general QOL, and subcomponents of QOL, such as the physical component and burden of kidney disease, were identified as factors related to RP.

Discussion

Identifying the factors related to resilient adjustment in patients with advanced CKD may assist health caregivers in improving adherence to treatment, treatment outcomes, and QOL.
Five-Year Prognosis of Complete Mesocolic Excision in Patients with Colon Cancer: A Prospective, Nonrandomized, Double-Blind Controlled Trial
Authors: Wang Chao , Gao Zhidong , Shen Zhanlong , Jiang Kewei , Zhou Jing , Wang Shan , Ye Yingjiang
Published: September 2022

BACKGROUND:

Previous studies on how complete mesocolic excision (CME) affects prognosis indicate fundamental limitations that prevent the procedure from being completely accepted in practice. This study evaluated 5-year survival in colon cancer patients who underwent CME in a strict quality-controlled trial.

STUDY DESIGN:

A prospective, nonrandomized, double-blind, controlled trial recruited patients who underwent open radical resection for colon cancer between November 2012 and November 2017. Third-party experts evaluated whether patients had undergone mesocolic dissection and/or central ligation by looking at photographs of both surgical field and specimen, and then divided patients into CME and non-CME (NCME) groups. The primary outcome was the 5-year local recurrence-free survival rate. Clinicopathological and follow-up data were recorded.

RESULTS:

There were 261 patients with a median follow-up time of 57 months assigned to the CME group, and 129 patients with a median follow-up time of 59 months were assigned to the NCME group. The 5-year local recurrence-free survival rate of patients with Union Internationale Contre le Cancer stage I to III cancer did not differ significantly between the groups. For stage I to III cancer and stage III cancer, the absolute risk reduction of 5-year cumulative death and disease progression after CME were 9.1% (95% CI 1% to 17%; p = 0.033) and 16.1% (95% CI 1% to 31%; p = 0.040), respectively. Meanwhile, CME also could reduce 14% 5-year cumulative incidence recurrence for Union Internationale Contre le Cancer stage III cancer compared with NCME (CME, 27.3% vs NCME, 41.3%; p = 0.042) after adjusting for the effect of non–cancer-related death.

CONCLUSIONS:

CME should be considered as a standard surgical procedure in affected patients.
Elevation of Clavibacter michiganensis subsp. californiensis to species level as Clavibacter californiensis sp. nov., merging and re-classification of Clavibacter michiganensis subsp. chilensis and Clavibacter michiganensis subsp. phaseoli as Clavibacter phaseoli sp. nov. based on complete genome in silico analyses
Authors: Arizala Dario , Dobhal Shefali , Alvarez Anne M. , Arif Mohammad
Published: September 2022

The Gram-positive genus

Clavibacter

is currently divided into seven species (

Clavibacter michiganensis

,

Clavibacter nebraskensis

,

Clavibacter capsici

,

Clavibacter sepedonicus

,

Clavibacter tessellarius

,

Clavibacter insidiosus

and

Clavibacter zhangzhiyongii

) and three subspecies (

C. michiganensis

subsp.

californiensis

,

C. michiganensis

subsp.

chilensis

and

C. michiganensis

subsp.

phaseoli

). Recent studies have indicated that the taxonomic rank of the subspecies must be re-evaluated. In this research, we assessed the taxonomic position of the three

C. michiganensis

subspecies and clarified the taxonomic nomenclature of other 75

Clavibacter

strains. The complete genomes of the type strains of the three

Clavibacter

subspecies, the type strain of

C. tessellarius

and

C. nebraskensis

A6096 were sequenced using PacBio RSII technology. Application of whole-genome-based computational approaches such as average nucleotide identity (ANI), digital DNA–DNA hybridization, multi-locus sequence analysis of seven housekeeping genes (acnA, atpD, bipA, icdA, mtlD, recA and rpoB), a phylogenomic tree reconstructed from 1 028 core genes, and ANI-based phylogeny provided sufficient justification for raising

C. michiganensis

subsp.

californiensis

to the species level. These results led us to propose the establishment of Clavibacter californiensis sp. nov. as a species with its type strain C55T (=CFBP 8216T=ATCC BAA-2691T). Moreover, the orthologous and in silico dot plot analyses, along with the above described bioinformatic strategies, revealed a high degree of similarity between

C. michiganensis

subsp.

chilensis

and

C. michiganensis

subsp.

phaseoli

. Based on these analyses, we propose that both subspecies be combined into a single taxon and elevated to the species level as Clavibacter phaseoli sp. nov., with LPPA 982T (= CECT 8144T= LMG 27667T) as the type strain.
Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations
Authors: Bhat Supriya V. , Maughan Heather , Cameron Andrew D. S. , Yost Christopher K.
Published: September 2022

Delftia

is a diverse betaproteobacterial genus with many strains having agricultural and industrial relevance, including plant-growth promotion, bioremediation of hydrocarbon-contaminated soils, and heavy metal immobilization.

Delftia

spp. are broadly distributed in the environment, and have been isolated from plant hosts as well as healthy and diseased animal hosts, yet the genetic basis of this ecological versatility has not been characterized. Here, we present a phylogenomic comparison of published

Delftia

genomes and show that the genus is divided into two well-supported clades: one ‘

Delftia acidovorans

’ clade with isolates from soils and plant rhizospheres, and a second ‘

Delftia lacustris

and

Delftia tsuruhatensis

’ clade with isolates from humans and sludge. The pan-genome inferred from 61

Delftia

genomes contained over 28 000 genes, of which only 884 were found in all genomes. Analysis of industrially relevant functions highlighted the ecological versatility of

Delftia

and supported their role as generalists.
Ex-PRESS implantation versus trabeculectomy for long-term maintenance of low intraocular pressure in patients with open angle glaucoma
Authors: Tokumo Kana , Okada Naoki , Onoe Hiromitsu , Komatsu Kaori , Masuda Shun , Okumichi Hideaki , Hirooka Kazuyuki , Asaoka Ryo , Kiuchi Yoshiaki
Published: September 2022

Purpose

To compare the efficacy of Ex-PRESS implantation to trabeculectomy with mitomycin C, for maintaining low target intraocular pressure (IOP) in patients with open angle glaucoma.

Materials and Methods

Patients were randomly assigned to receive Ex-PRESS implantation or trabeculectomy. Patients with IOP ≥ 15 mmHg were included in this study. Surgical success was defined according to three target mean IOP ranges (5 mmHg ≤ IOP ≤18 mmHg [criterion A], 5 mmHg ≤ IOP ≤15 mmHg [criterion B], and 5 mmHg ≤ IOP ≤12 mmHg [criterion C]) representing reductions of at least 20% below baseline on two consecutive follow-up visits 3 months post surgery.

Results

A total of 73 patients, including 30 in the Ex-PRESS implantation group and 43 in the trabeculectomy group, were included in the study. The baseline IOP was 20.4 ± 4.9 mmHg in the Ex-PRESS implantation group and 21.9 ± 7.9 mmHg in the trabeculectomy group. There were no significant differences in baseline ocular or demographic characteristics between the two groups. There was no statistical difference in IOP every 6 months. After the 3-year follow-up, success rates were A) 60.0% and 60.2%, B) 45.7% and 58.1%, and C) 31.5% and 40.5% for the Ex-PRESS implantation and trabeculectomy groups, respectively. A greater number of glaucoma medications before surgery was associated with a higher failure rate in the trabeculectomy group but not the Ex-PRESS implantation group.

Conclusions

Both procedures resulted in similar IOP reductions and success rates for low target IOP. The number of preoperative glaucoma medications was a risk factor for trabeculectomy failure.
Effect of inclusion education on the perceptions of sighted school children about the abilities of students living with severe visual impairment and blindness
Authors: Abraham Carl Halladay , Eshun Julian Daniel , Berchie Mercy Oforiwaa , Addo Naa Adjeley
Published: September 2022

Inclusion education was introduced to bridge the gap between access to education and individuals living with disabilities. In developing countries like Ghana, one of the primary reasons for the establishment of inclusion education was to improve the perceptions and attitudes of society from traditionally entrenched derogatory and condescending attitudes towards individuals living with disabilities, perceptions and attitudes which led to the establishment of special schools at the outskirts of towns and cities. Today, inclusion education is widely practiced and although the literature is buoyant with research on the implementation of inclusion education studies, no study has been conducted to identify the influence of inclusion education on the primary recipients, the students. Using structured interview questions exploring perceptions of sighted students in inclusion schools and sighted students in sighted only schools, we describe the differences in perceptions of these students about the abilities of individuals with visual impairment across educational prospects, leadership, participation in social activities, and routine activities. We also compared the perceptions of students living with visual impairment in inclusion schools to those in special schools. The results of the study, analyzed by Braun and Clarke’s thematic analysis showed that inclusion education has impacted and influenced positively the perceptions of the sighted students in inclusion schools about the abilities of individuals living with visual impairment compared to the perceptions held by sighted students in sighted only schools. Additionally, this study revealed that the perceptions about the abilities of students living with visual impairment in inclusion schools did not differ from those of the students living with visual impairment in special schools. This study has elucidated the need for public health education programs about the capabilities of individuals with visual impairment to foster and build healthy perceptions about them and enable a more inclusive society.
Cognitive status and rehabilitation outcomes of patients in acute rehabilitation post Covid-19
Authors: Vahtra Madli , Fahey Kyle , Malina Aaron , Dreyer Sean , Roth Elliot , Grafman Jordan , Jayabalan Prakash , Cohen-Zimerman Shira
Published: September 2022

Objective

This study aims to 1) characterize cognitive functioning in patients admitted for inpatient rehabilitation due to Covid-19 diagnosis and 2) examine how cognitive status at admission is associated with rehabilitation outcomes.

Design

Retrospective chart review.

Setting

An inpatient rehabilitation center located in Chicago, Illinois.

Participants

80 participants in acute rehabilitation due to Covid-19 disease

Intervention

Not applicable.

Main Outcome Measures

Cognitive functioning as measured by the Montreal Cognitive Assessment (MoCA) and rehabilitation outcomes as measured by Functional Index Measure (FIM) and Section GG items for self-care and mobility (GG-SC and GG-M respectively).

Results

On average, our sample presented with mild cognitive impairment as assessed by the (MoCA). The most significant deficits were demonstrated in executive function, attention, language, and delayed free recall measures. Higher levels of overall cognitive function were associated with higher cognitive measures of rehabilitation outcomes. Weaker associations were observed with outcome measures of self-care and motor functioning.

Conclusion

Cognitive impairments are common in patients in acute rehabilitation due to Covid-19 and cognitive performance may help predict rehabilitation outcomes.
Gender Relations, Women Empowerment and Maternal Health Care in sub-Saharan Africa: A Bayesian Multilevel Analysis
Authors: Simona Simona
Published: September 2022

Maternal health care utilization still remains crucial in ensuring good pregnancy outcomes and a reduction in maternal and child mortality especially in developing countries. Although several studies have been conducted to investigate determinants of maternal health care utilization, the innfluence of gender relations and women empowerment on maternal healthcare in cross-national context has received little attention. This paper sought out to examine the influence of gender relations and women empowerment on maternal healthcare utilization in sub-Saharan Africa. The analysis pools sample data of 245,955 respondents from the most recent Demographic and Health Surveys (DHS) and World Development Indicators of 35 sub-Saharan African countries. Separate Bayesian multilevel logistic regression models are fitted for adequate antenatal care and institutional delivery in relation to several factors indicating gender relations and women empowerment at three levels. Several components of gender relations and women empowerment were significantly associated with maternal health care after adjusting for covariates. In addition, significant between country and between community variations in the odds of maternal health care utilisation were observed. These results underscore the importance of prioritising contextual gender equity and women empowerment to achieve better utilisation of maternal healthcare services and subsequently, a reduction in maternal mortality in sub-Saharan Africa.
NCT Precision Oncology Thesaurus Drugs – a Curated Database for Drugs, Drug Classes, and Drug Targets in Precision Cancer Medicine
Authors: Kreutzfeldt Simon , Knurr Alexander , Hübschmann Daniel , Horak Peter , Fröhling Stefan
Published: September 2022

Implementation of precision cancer medicine requires structured reporting of clinical actionable molecular alterations. The growing number of targeted anticancer drugs in clinical use and development necessitates a hierarchical ontology that focuses on the interactions between drugs and their targets and the impact of drug classes. Here we report the development of NCT POT (National Center for Tumor Diseases Drug Precision Oncology Thesaurus) Drugs, a manually curated cancer drug class ontology that integrates multiple data sources. This easily accessible resource is part of the NCT POT framework and can be downloaded at https://github.com/TMO-HD/nct-thesaurus with detailed documentation.
Determinants of exposure to Aedes mosquitoes: a comprehensive geospatial analysis in peri-urban Cambodia
Authors: Parker Daniel M. , Medina Catalina , Bohl Jennifer , Lon Chanthap , Chea Sophana , Lay Sreyngim , Kong Dara , Nhek Sreynik , Man Somnang , Doehl Johannes S. P. , Leang Rithea , Kry Hok , Rekol Huy , Oliveira Fabiano , Minin Vladimir , Manning Jessica E.
Published: September 2022

Aedes mosquitoes are some of the most important and globally expansive vectors of disease. Public health efforts are largely focused on prevention of human-vector contact. A range of entomological indices are used to measure risk of disease, though with conflicting results (i.e. larval or adult abundance does not always predict risk of disease). There is a growing interest in the development and use of biomarkers for exposure to mosquito saliva, including for Aedes spp, as a proxy for disease risk. In this study, we conduct a comprehensive geostatistical analysis of exposure to Aedes mosquito bites among a pediatric cohort in a peri-urban setting endemic to dengue, Zika, and chikungunya viruses. We use demographic, household, and environmental variables (the flooding index (NFI), land type, and proximity to a river) in a Bayesian geostatistical model to predict areas of exposure to Aedes aegypti bites. We found that hotspots of exposure to Ae. aegypti salivary gland extract (SGE) were relatively small (< 500m and sometimes < 250m) and stable across the two-year study period. Age was negatively associated with antibody responses to Ae. aegypti SGE. Those living in agricultural settings had lower antibody responses than those living in urban settings, whereas those living near recent surface water accumulation were more likely to have higher antibody responses. Finally, we incorporated measures of larval and adult density in our geostatistical models and found that they did not show associations with antibody responses to Ae. aegypti SGE after controlling for other covariates in the model. Our results indicate that targeted house- or neighborhood-focused interventions may be appropriate for vector control in this setting. Further, demographic and environmental factors more capably predicted exposure to Ae. aegypti mosquitoes than commonly used entomological indices. Keywords: Aedes; saliva; geostatistical; environmental; dengue fever; Zika; chikungunya
Individualized fMRI connectivity defines signatures of antidepressant and placebo responses in major depression
Authors: Zhao Kanhao , Xie Hua , Fonzo Gregory A. , Tong Xiaoyu , Carlisle Nancy , Chidharom Matthieu , Etkin Amit , Zhang Yu
Published: September 2022

Though sertraline is commonly prescribed in patients with major depressive disorder (MDD), its superiority over placebo is only marginal. This is in part due to the neurobiological heterogeneity of the individuals. Characterizing individual-unique functional architecture of the brain may help better dissect the heterogeneity, thereby defining treatment-predictive signatures to guide personalized medication. In this study, we investigate whether individualized brain functional connectivity (FC) can define more predictable signatures of antidepressant and placebo treatment in MDD. The data used in the present work were collected by the Establishing Moderators and Biosignatures of Antidepressant Response in Clinical Care (EMBARC) study. Patients (N=296) was randomly assigned to antidepressant sertraline or placebo double-blind treatment for 8 weeks. The whole-brain FC networks were constructed from pre-treatment resting-state functional magnetic resonance imaging (rs-fMRI) at 4 clinical sites. Then, FC was individualized by removing the common components from the raw baseline FC to train regression-based connectivity predictive models. With individualized FC features, the established prediction models successfully identified signatures that explained 22% variance for the sertraline group and 31% variance for the placebo group in predicting HAMD17 change. Compared with the raw FC-based models, the individualized FC-defined signatures significantly improved the prediction performance, as confirmed by the 10×10-fold cross-validation. For sertraline treatment, predictive FC metrics were predominantly located in the left middle temporal cortex (MTC) and right insula. For placebo, predictive FC metrics were primarily located in the bilateral cingulate cortex and left superior temporal cortex (STC). Our findings demonstrated that individualization of FC metrics through removal of common FC components enhanced the prediction performance compared to the raw FC. Associated with previous MDD clinical studies, our identified predictive biomarkers provided new insights into the neuropathology of antidepressant and placebo treatment.
Antigen concentration, viral load, and test performance for SARS-CoV-2 in multiple specimen types
Authors: Golden Allison , Oliveira-Silva Michelle , Slater Hannah , Vieira Alexia Martines , Bansil Pooja , Gerth-Guyette Emily , Leader Brandon T. , Zobrist Stephanie , Braga Ferreira Alan Kennedy , Santos de Araujo Erika Crhistina , de Lucena Cruz Catherine Duran , Garbin Eduardo , Bizilj Greg T. , Carlson Sean J. , Sagalovsky Mariana , Pal Sampa , Gupta Vin , Wolansky Leo , Boyle David S. , Vieira Dall’Acqua Deusilene Souza , Naveca Felipe Gomes , do Nascimento Valdinete Alves , Villalobos Salcedo Juan Miguel , Drain Paul K. , Costa Alexandre Dias Tavares , Pereira Dhélio , Domingo Gonzalo J
Published: September 2022

The relationship between N-antigen concentration and viral load within a specimen and across different specimens is essential for interpretation of rapid diagnostic tests (RDT) clinical performance in different use cases. A prospective study was conducted in Porto Velho, Brazil, to investigate RDT performance in different specimen types as a function of the correlation between antigen concentration and viral load. The study included 214 close contacts with recent exposures to confirmed cases, aged 12 years and older and with various levels of vaccination. Antigen concentration was measured in nasopharyngeal swab (NPS), anterior nares swab (ANS), and saliva specimens. Reverse transcriptase (RT)–PCR was conducted on the NPS and saliva specimens, and two RDTs were conducted on ANS and one on saliva. Antigen concentration correlated with viral load when measured in the same specimen type but not across specimen types. Antigen levels were higher in symptomatic cases compared to asymptomatic/oligosymptomatic cases and lower in saliva compared to NPS and ANS samples. Discordant results between the RDTs conducted on ANS and the RT-PCR on NPS were resolved by antigen concentration values. The analytical limit-of-detection of RDTs can be used to predict the performance of the tests in populations for which the antigen concentration is known. The antigen dynamics across different sample types observed in SARS-CoV-2 disease progression support use of RDTs in nasal samples. Given lower antigen concentrations in saliva, tests using saliva is expected to require improved analytical sensitivity to achieve clinical sensitivity similar to testing of nasal samples.