bluuebunny/crossref_metadata_2025 huggingface dataset:
The correlation between Trichomonas vaginalis infection and reproductive system cancer: a systematic review and meta-analysis
Authors: Zhang Zhenchao , Li Dongxian , Li Yuhua , Zhang Rui , Xie Xianghuan , Yao Yi , Zhao Linfei , Tian Xiaowei , Yang Zhenke , Wang Shuai , Yue Xuejing , Mei Xuefang
Published: March 2023

Background

Trichomonas vaginalis (T. vaginalis) is a microaerophilic protozoan parasite which is responsible for trichomoniasis, the most common non-viral sexually transmitted infection in the world. The infection greatly damages the reproductive system. However, whether T. vaginalis infection can cause reproductive system cancer remains controversial.

Methods

This study systematically searched PubMed, EMBASE, Ovid and Google scholar, and 144 relevant articles were retrieved and classified into three categories: epidemiological investigations (68), reviews (30) and research articles (46). These three types of articles were verified according to their respective inclusion and exclusion criteria. Stata 16 was used to conduct a meta-analysis on the articles of epidemiological investigations for analysing the correlation between T. vaginalis infection and reproductive system cancer.

Results

The result of meta-analysis indicated that the rate of T. vaginalis infection in the cancer group was significantly higher than that in the non-cancer group (OR = 1.87, 95% CI 1.29–2.71, I2 = 52%). Moreover, the cancer rate of the population infected with T. vaginalis was significantly higher than that of the population without T. vaginalis infection (OR = 2.77, 95% CI 2.37–3.25, I2 = 31%). The review articles and most research articles stated that the infection of T. vaginalis could lead to cancer and the pathogenic mechanisms were as follows: T. vaginalis promoting inflammatory response, T. vaginalis infection changing the internal environment around parasitic sites and signal transduction pathway, the metabolites secreted by T. vaginalis inducing carcinogenesis and T. vaginalis increasing other pathogenic microbial infection to promote the occurrence of cancer.

Conclusions

Our study confirmed that there was a correlation between the infection of T. vaginalis and reproductive system cancer, and provided some possible research directions for clarifying the carcinogenic mechanisms caused by T. vaginalis infection.
A patient who recovered from post-COVID myalgic encephalomyelitis/chronic fatigue syndrome: a case report
Authors: Oka Takakazu
Published: March 2023

Background

Some patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) complain of persistent fatigue, dyspnea, pain, and cognitive dysfunction. These symptoms are often described as “long COVID”. Whether a patient with long COVID might develop myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is of interest, as is the treatment and management of ME/CFS in a post-COVID patient. Here I report a patient, who, after an infection with SARS-CoV-2, developed ME/CFS and recovered after treatment.

Case presentation

The patient was a previously healthy 55-year-old woman who worked as a nurse and became ill with COVID-19 pneumonia. She then presented with severe fatigue, post-exertional malaise, dyspnea, pain, cognitive dysfunction, tachycardia, and exacerbation of fatigue on physical exertion, which persisted for more than 6 months after her recovery from COVID-19 pneumonia. She was bedridden for more than half of each day. The patient was treated from multiple perspectives, which included (1) instructions on eating habits and supplements; (2) cognitive and behavioral modifications for coping with physical, emotional, and cognitive fatigue; (3) instructions on conditioning exercises to improve deconditioning due to fatigue and dyspnea; and (4) pharmacotherapy with amitriptyline and hochuekkito, a Japanese herbal (Kampo) medicine. The patient made a complete recovery after completing the prescribed regimen and was able to return to work as a nurse.

Conclusions

To the best of my knowledge, this is the first detailed report on a patient infected with SARS-CoV-2 followed by long COVID with the signs/symptoms of ME/CFS who recovered after treatment. I hope this case report will be helpful to health care practitioners by its presentation of some of the therapeutic options for alleviating disabling signs/symptoms in patients with post-COVID ME/CFS.
Targeting circulating high mobility group box-1 and histones by extracorporeal blood purification as an immunomodulation strategy against critical illnesses
Authors: Li Yupei , Chen Yu , Yang Tinghang , Chang Kaixi , Deng Ningyue , Zhao Weifeng , Su Baihai
Published: March 2023

Both high mobility group box-1 (HMGB1) and histones are major damage-associated molecular patterns (DAPMs) that mediate lethal systemic inflammation, activation of the complement and coagulation system, endothelial injury and multiple organ dysfunction syndrome in critical illnesses. Although accumulating evidence collectively shows that targeting HMGB1 or histones by their specific antibodies or inhibitors could significantly mitigate aberrant immune responses in multiple critically ill animal models, routine clinical use of such agents is still not recommended by any guideline. In contrast, extracorporeal blood purification, which has been widely used to replace dysfunctional organs and remove exogenous or endogenous toxins in intensive care units, may also exert an immunomodulatory effect by eliminating inflammatory mediators such as cytokines, endotoxin, HMGB1 and histones in patients with critical illnesses. In this review, we summarize the multiple immunopathological roles of HMGB1 and histones in mediating inflammation, immune thrombosis and organ dysfunction and discuss the rationale for the removal of these DAMPs using various hemofilters. The latest preclinical and clinical evidence for the use of extracorporeal blood purification to improve the clinical outcome of critically ill patients by targeting circulating HMGB1 and histones is also gathered.
correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes
Authors: Nyerki Emil , Kalmár Tibor , Schütz Oszkár , Lima Rui M. , Neparáczki Endre , Török Tibor , Maróti Zoltán
Published: March 2023

Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×–11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data.
Creating a best practice template for participant communication plans in global health clinical studies
Authors: Shelly Colleen E. , Logan Caroline , Skorochod Beth , Wiyeh Alison , Ndwandwe Duduzile , Choko Augustine , Valea Innocent , Titanji Boghuma K.
Published: March 2023

Background

Clinical trial participants have a right to be informed throughout the entire process of human subject research. As part of this pillar of research ethics, participants and other stakeholders should be made aware of research findings after a trial has been completed. Though participants have both a right, and a desire to be informed of research outcomes, studies show that they rarely receive communication about study findings. Our aim was (1) to understand what, if any, role communication plans play in current global health clinical research protocols and (2) to use our findings to develop a communication plan template tailored to clinical research carried out in low-and-middle-income countries (LMIC) while minimizing colonial assumptions. While the template was drafted in the LMIC context, the principles are universally applicable and should be considered best practices for all global health clinical trials.

Methods

We carried out a mixed-method study over a period of 6 months to understand the role of communication with study participants and other stakeholders in clinical trials. The semiquantitative analysis included mining publicly available clinical trial protocols for communication-related language. Qualitative interviews (n = 7) were used to gather knowledge and insight from clinical trial experts to inform the development of a communication plan template.

Results

None of the 48 mined clinical trial protocols included a communication plan. Of the 48, 21% (n = 21) protocols included communication-related language, and 10% (n = 5) described plans to share trial results with participants.

Conclusion

The use of communication plans in global health clinical trials is lacking. To our knowledge, this is the first in-depth analysis of communication plans in clinical trials to date. We recommend that researchers utilize the developed communication plan template throughout the entire research process to ensure a human-centered approach to participant communication. This communication plan should apply to all phases of a research trial, with a particular emphasis on plans to share results in an accessible and engaging manner once the trial has been completed.
Selenite as a dual apoptotic and ferroptotic agent synergizes with EGFR and KRAS inhibitors with epigenetic interference
Authors: Chan Lok Seng , Liu Johnson , Li Molly S. C. , Li Lili , Tao Qian , Mok Tony S. K.
Published: March 2023

Background

Selenium, an essential trace element, has previously been investigated as a pro-apoptotic and DNA demethylation agent. It sensitizes the response to chemotherapy in patients who were refractory to cytotoxic agents. Meanwhile, ferroptosis is a novel approach to cancer treatment by triggering cell death and reversing drug resistance. The role of selenium in treating cancer cells harboring druggable oncogenic alterations and its underlying mechanism are largely unknown.

Results

We treated lung adenocarcinoma cell lines—EGFR-mutant H1975 (H1975 EGFR p.L858R and p.T790M) and KRAS-mutant H358 (H358 KRAS p.G12C), with sodium selenite to examine its effect on cell apoptosis, ferroptosis, and DNA methylation, as well as its interaction with existing targeted therapy, osimertinib, and adagrasib. We observed selenite to be a dual apoptotic and ferroptotic agent on lung cancer cells, associated with the activation of p38-ATF4-DDIT3 axis in the unfolded protein response. Ferroptosis induction was more remarkable in H1975 than H358. Selenite also altered cellular DNA methylation machinery through downregulating DNMT1 and upregulating TET1, though not as a major mechanism of its activity. Low-dose selenite synergized with osimertinib in EGFR-mutant H1975, and with adagrasib in KRAS-mutant H358, with stronger synergism observed in H1975.

Conclusion

These results suggest that selenite is a potential apoptotic and ferroptotic drug candidate for the treatment of especially EGFR- and potentially KRAS-mutant lung cancer.
PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity
Authors: Ammar Ammar , Cavill Rachel , Evelo Chris , Willighagen Egon
Published: March 2023

Protein mutations, especially those which occur in the binding site, play an important role in inter-individual drug response and may alter binding affinity and thus impact the drug’s efficacy and side effects. Unfortunately, large-scale experimental screening of ligand-binding against protein variants is still time-consuming and expensive. Alternatively, in silico approaches can play a role in guiding those experiments. Methods ranging from computationally cheaper machine learning (ML) to the more expensive molecular dynamics have been applied to accurately predict the mutation effects. However, these effects have been mostly studied on limited and small datasets, while ideally a large dataset of binding affinity changes due to binding site mutations is needed. In this work, we used the PSnpBind database with six hundred thousand docking experiments to train a machine learning model predicting protein-ligand binding affinity for both wild-type proteins and their variants with a single-point mutation in the binding site. A numerical representation of the protein, binding site, mutation, and ligand information was encoded using 256 features, half of them were manually selected based on domain knowledge. A machine learning approach composed of two regression models is proposed, the first predicting wild-type protein-ligand binding affinity while the second predicting the mutated protein-ligand binding affinity. The best performing models reported an RMSE value within 0.5 $$-$$
-
 0.6 kcal/mol-1 on an independent test set with an R2 value of 0.87 $$-$$
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 0.90. We report an improvement in the prediction performance compared to several reported models developed for protein-ligand binding affinity prediction. The obtained models can be used as a complementary method in early-stage drug discovery. They can be applied to rapidly obtain a better overview of the ligand binding affinity changes across protein variants carried by people in the population and narrow down the search space where more time-demanding methods can be used to identify potential leads that achieve a better affinity for all protein variants.
A protein-based subunit vaccine with biological adjuvants provides effective protection against Pasteurella multocida in pigs
Authors: Wu Min-Chia , Wu Hsing-Chieh , Lee Jai-Wei , Chang Wan-Chen , Chu Chun-Yen
Published: March 2023

Streptococcus suis (S. suis) and Pasteurella multocida (P. multocida) are pathogens that can cause zoonotic diseases. P. multocida toxin (PMT) is an important virulence factor that causes atrophic rhinitis in pigs. Suilysin (Sly) is an extracellular protein of S. suis and has been shown to be a potential adjuvant. Previous studies have indicated that subunit vaccines containing several fragments of PMT as antigens are safer than traditional inactivated or live-attenuated vaccines. However, protein-based vaccines need strong adjuvants to enhance their immunogenicity. In this study, recombinant PMT-NC (rPMT-NC) protein antigen was formulated with either recombinant Sly (rSly) or CpG oligodeoxynucleotides (CpG) as the adjuvant. The immune responses elicited by these vaccines and the protective efficacy after challenge with live P. multocida were evaluated in piglets. In the dose-dependent test, piglets immunized with the low dose (100 µg) of rSly had increased antigen-specific total IgG, interferon (IFN)-γ gene expression, and CD4+ and CD8+ T-cell populations. Compared to piglets in the commercial (Al-gel) adjuvant and the control groups (p < 0.05), piglets in the biological adjuvant groups showed significantly reduced turbinate atrophy, nasal distortion, and lung lesion scores after challenge with P. multocida serotype A. Vaccines containing rSly or CpG adjuvant enhanced humoral and cellular immune responses and protection against P. multocida. This combination of a protein-based antigen formulated with a biological adjuvant showed synergistic and protective effects against atrophic rhinitis and has potential to be developed as part of a bivalent vaccine.
A cost-effective machine learning-based method for preeclampsia risk assessment and driver genes discovery
Authors: Wang Hao , Zhang Zhaoyue , Li Haicheng , Li Jinzhao , Li Hanshuang , Liu Mingzhu , Liang Pengfei , Xi Qilemuge , Xing Yongqiang , Yang Lei , Zuo Yongchun
Published: March 2023

Background

The placenta, as a unique exchange organ between mother and fetus, is essential for successful human pregnancy and fetal health. Preeclampsia (PE) caused by placental dysfunction contributes to both maternal and infant morbidity and mortality. Accurate identification of PE patients plays a vital role in the formulation of treatment plans. However, the traditional clinical methods of PE have a high misdiagnosis rate.

Results

Here, we first designed a computational biology method that used single-cell transcriptome (scRNA-seq) of healthy pregnancy (38 wk) and early-onset PE (28–32 wk) to identify pathological cell subpopulations and predict PE risk. Based on machine learning methods and feature selection techniques, we observed that the Tuning ReliefF (TURF) score hybrid with XGBoost (TURF_XGB) achieved optimal performance, with 92.61% accuracy and 92.46% recall for classifying nine cell subpopulations of healthy placentas. Biological landscapes of placenta heterogeneity could be mapped by the 110 marker genes screened by TURF_XGB, which revealed the superiority of the TURF feature mining. Moreover, we processed the PE dataset with LASSO to obtain 497 biomarkers. Integration analysis of the above two gene sets revealed that dendritic cells were closely associated with early-onset PE, and C1QB and C1QC might drive preeclampsia by mediating inflammation. In addition, an ensemble model-based risk stratification card was developed to classify preeclampsia patients, and its area under the receiver operating characteristic curve (AUC) could reach 0.99. For broader accessibility, we designed an accessible online web server (http://bioinfor.imu.edu.cn/placenta).

Conclusion

Single-cell transcriptome-based preeclampsia risk assessment using an ensemble machine learning framework is a valuable asset for clinical decision-making. C1QB and C1QC may be involved in the development and progression of early-onset PE by affecting the complement and coagulation cascades pathway that mediate inflammation, which has important implications for better understanding the pathogenesis of PE.
Effects of 12 mg vs. 6 mg dexamethasone on thromboembolism and bleeding in patients with critical COVID-19 - a post hoc analysis of the randomized, blinded COVID STEROID 2 trial
Authors: Jonmarker Sandra , Alarcón Felix , Litorell Jacob , Granholm Anders , Alm Eva Joelsson , Chew Michelle , Russell Lene , Weihe Sarah , Madsen Emilie Kabel , Meier Nick , Leistner Jens Wolfgang , Mårtensson Johan , Hollenberg Jacob , Perner Anders , Kjær Maj-Brit Nørregaard , Munch Marie Warrer , Dahlberg Martin , Cronhjort Maria , Wahlin Rebecka Rubenson
Published: March 2023

Background

Thromboembolism is more common in patients with critical COVID-19 than in other critically ill patients, and inflammation has been proposed as a possible mechanism. The aim of this study was to investigate if 12 mg vs. 6 mg dexamethasone daily reduced the composite outcome of death or thromboembolism in patients with critical COVID-19.

Methods

Using additional data on thromboembolism and bleeding we did a post hoc analysis of Swedish and Danish intensive care unit patients enrolled in the blinded randomized COVID STEROID 2 trial comparing 12 mg vs. 6 mg dexamethasone daily for up to 10 days. The primary outcome was a composite outcome of death or thromboembolism during intensive care. Secondary outcomes were thromboembolism, major bleeding, and any bleeding during intensive care.

Results

We included 357 patients. Whilst in intensive care, 53 patients (29%) in the 12 mg group and 53 patients (30%) in the 6 mg group met the primary outcome with an unadjusted absolute risk difference of − 0.5% (95% CI − 10 to 9.5%, p = 1.00) and an adjusted OR of 0.93 (CI 95% 0.58 to 1.49, p = 0.77). We found no firm evidence of differences in any of the secondary outcomes.

Conclusions

Among patients with critical COVID-19, 12 mg vs. 6 mg dexamethasone daily did not result in a statistically significant difference in the composite outcome of death or thromboembolism. However, uncertainty remains due to the limited number of patients.
Physiological and molecular mechanisms of insect appendage regeneration
Authors: Zhong Jiru , Jing Andi , Zheng Shaojuan , Li Sheng , Zhang Xiaoshuai , Ren Chonghua
Published: March 2023

Regeneration, as a fascinating scientific field, refers to the ability of animals replacing lost tissue or body parts. Many metazoan organisms have been reported with the regeneration phenomena, but showing evolutionarily variable abilities. As the most diverse metazoan taxon, hundreds of insects show strong appendage regeneration ability. The regeneration process and ability are dependent on many factors, including macroscopic physiological conditions and microscopic molecular mechanisms. This article reviews research progress on the physiological conditions and internal underlying mechanisms controlling appendage regeneration in insects.
The Neumann problem for a class of generalized Kirchhoff-type potential systems
Authors: Chems Eddine Nabil , Repovš Dušan D.
Published: March 2023

In this paper, we are concerned with the Neumann problem for a class of quasilinear stationary Kirchhoff-type potential systems, which involves general variable exponents elliptic operators with critical growth and real positive parameter. We show that the problem has at least one solution, which converges to zero in the norm of the space as the real positive parameter tends to infinity, via combining the truncation technique, variational method, and the concentration–compactness principle for variable exponent under suitable assumptions on the nonlinearities.
OpenStackDP: a scalable network security framework for SDN-based OpenStack cloud infrastructure
Authors: Krishnan Prabhakar , Jain Kurunandan , Aldweesh Amjad , Prabu P. , Buyya Rajkumar
Published: March 2023

Network Intrusion Detection Systems (NIDS) and firewalls are the de facto solutions in the modern cloud to detect cyberattacks and minimize potential hazards for tenant networks. Most of the existing firewalls, perimeter security, and middlebox solutions are built on static rules/signatures or simple rule matching, making them inflexible, susceptible to bugs, and difficult to introduce new services. This paper aims to improve network management in OpenStack Clouds by taking advantage of the combination of software-defined networking (SDN), Network Function Virtualization (NFV), and machine learning/artificial intelligence (ML/AI) and for making networks more predictable, reliable, and secure. Artificial intelligence is being used to monitor the behavior of the virtual machines and applications running in the OpenStack SDN cloud so that when any issues or degradations are noticed, the decision can be quickly made on how to handle that issue, being able to analyze data in motion, starting at the edge. The OpenStackDP framework comprises lightweight monitoring, anomaly-detecting intelligent sensors embedded in the data plane, a threat analytics engine based on ML/AI algorithms running inside switch hardware/network co-processor, and defensive actions deployed as virtual network functions (VNFs). This network data plane-based architecture makes high-speed threat detection and rapid response possible and enables a much higher degree of security. We have built the framework with advanced streaming analytics technologies, algorithms, and machine learning to draw knowledge from this data that is in motion before the malicious traffic goes to the tenant compute nodes or long-term data store. Cloud providers and users will benefit from improved Quality-of-Services (QoS) and faster recovery from cyber-attacks and compromised switches. The multi-phase collaborative anomaly detection scheme demonstrates an accuracy of 99.81%, average latencies of 0.27 ms, and response speed within 9 s. The simulations and analysis show that the OpenStackDP network analytics framework substantially secures and outperforms prior SDN-based OpenStack solutions for Cloud architectures.
Association between cognitive impairment and motor dysfunction among patients with multiple sclerosis: a cross-sectional study
Authors: Alharthi Hanadi Matar , Almurdi Muneera Mohammed
Published: March 2023

Background

Previous studies have shown that there is a relationship between cognitive impairment (CI) and motor dysfunction (MD) in neurological diseases, such as Alzheimer’s and Parkinson’s disease. However, there whether CI and MD are associated in patients with multiple sclerosis (MS) is unknown. Here we studied the association between CI and MD in patients with MS and examined if muscle weakness or incoordination, balance impairment, gait abnormalities, and/or increased fall risk are indicators of CI in patients with MS.

Methods

Seventy patients with MS were included in this cross-sectional study. Cognitive impairment was assessed using the Montreal Cognitive Assessment Scale (MoCA), muscle strength using a hand-held dynamometer, and balance, gait, and fall risk assessment using the Tinetti scale. Motor coordination was assessed using the timed rapid alternating movement test for the upper extremity and the timed alternate heel-to-knee test for the lower extremity.

Results

There was a significant association between CI and motor coordination, balance, gait, and risk of fall (p < 0.005) but not muscle strength. Stepwise multiple linear regression showed that 22.7% of the variance in the MoCA was predicted by the fall risk and incoordination of the upper extremities in the MS population.

Conclusions

CI is significantly associated with motor incoordination, balance impairment, gait abnormality, and increased fall risk. Furthermore, the risk of fall and upper extremity incoordination appeared to be best indicators of CI in patients with MS.
Considering the lip print patterns of Ibo and Hausa Ethnic groups of Nigeria: checking the wave of ethnically driven terrorism
Authors: Uzomba G. C. , Obijindu C. A. , Ezemagu U. K.
Published: March 2023

Introduction

Lip print of an individual is distinct and could be a useful form of evidence to identify the ethnicity of a terrorist.

Objectives

The study analyzed the distribution of lip print patterns of two major ethnic groups in Nigeria; Ibo and Hausa, to develop a strategic plan to check the wave of ethnically driven terrorism in Nigeria, carried out by groups such as Boko Haram and Indigeneous People of Biafra (IPOB).

Materials and methods

The study comprised 800 participants of Ibo and Hausa ethnic groups (400 males and 400 females). The study adopted a digital method of lip print analysis and followed the guidelines outlined by the Institute of Medicine (IOM) for anthropometric measurements. The lip was classified, using Tsuchihashi and Suzuki method of classification.

Results

The predominant lip print patterns of Ibo were Type I with complete vertical groove and Type III with intersect of groove for male and Type III for female. Type I’ with partial length groove was the predominant pattern for both male and female Hausa. The lip width and height of female Ibo were longer than that of the Hausa counterpart (P < 0.05), but none of the anthropometric variables could predict the lip print pattern.

Conclusion

The lip size and print could aid forensic investigation, though genetic diversity and heterogeneity of ethnic groups in Nigeria, especially that of Ibo, could setback use of lip print pattern to identify the ethnicity of an unknown individual in Nigeria to help determine the terrorist group to which they may belong.
Selection processes of Arctic seasonal glacier snowpack bacterial communities
Authors: Keuschnig Christoph , Vogel Timothy M. , Barbaro Elena , Spolaor Andrea , Koziol Krystyna , Björkman Mats P. , Zdanowicz Christian , Gallet Jean-Charles , Luks Bartłomiej , Layton Rose , Larose Catherine
Published: March 2023

Background

Arctic snowpack microbial communities are continually subject to dynamic chemical and microbial input from the atmosphere. As such, the factors that contribute to structuring their microbial communities are complex and have yet to be completely resolved. These snowpack communities can be used to evaluate whether they fit niche-based or neutral assembly theories.

Methods

We sampled snow from 22 glacier sites on 7 glaciers across Svalbard in April during the maximum snow accumulation period and prior to the melt period to evaluate the factors that drive snowpack metataxonomy. These snowpacks were seasonal, accumulating in early winter on bare ice and firn and completely melting out in autumn. Using a Bayesian fitting strategy to evaluate Hubbell’s Unified Neutral Theory of Biodiversity at multiple sites, we tested for neutrality and defined immigration rates at different taxonomic levels. Bacterial abundance and diversity were measured and the amount of potential ice-nucleating bacteria was calculated. The chemical composition (anions, cations, organic acids) and particulate impurity load (elemental and organic carbon) of the winter and spring snowpack were also characterized. We used these data in addition to geographical information to assess possible niche-based effects on snow microbial communities using multivariate and variable partitioning analysis.

Results

While certain taxonomic signals were found to fit the neutral assembly model, clear evidence of niche-based selection was observed at most sites. Inorganic chemistry was not linked directly to diversity, but helped to identify predominant colonization sources and predict microbial abundance, which was tightly linked to sea spray. Organic acids were the most significant predictors of microbial diversity. At low organic acid concentrations, the snow microbial structure represented the seeding community closely, and evolved away from it at higher organic acid concentrations, with concomitant increases in bacterial numbers.

Conclusions

These results indicate that environmental selection plays a significant role in structuring snow microbial communities and that future studies should focus on activity and growth.
Using strain-resolved analysis to identify contamination in metagenomics data
Authors: Lou Yue Clare , Hoff Jordan , Olm Matthew R. , West-Roberts Jacob , Diamond Spencer , Firek Brian A. , Morowitz Michael J. , Banfield Jillian F.
Published: March 2023

Background

Metagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating within the study itself remains underreported.

Results

Here, we applied high-resolution strain-resolved analyses to identify contamination in two large-scale clinical metagenomics datasets. By mapping strain sharing to DNA extraction plates, we identified well-to-well contamination in both negative controls and biological samples in one dataset. Such contamination is more likely to occur among samples that are on the same or adjacent columns or rows of the extraction plate than samples that are far apart. Our strain-resolved workflow also reveals the presence of externally derived contamination, primarily in the other dataset. Overall, in both datasets, contamination is more significant in samples with lower biomass.

Conclusion

Our work demonstrates that genome-resolved strain tracking, with its essentially genome-wide nucleotide-level resolution, can be used to detect contamination in sequencing-based microbiome studies. Our results underscore the value of strain-specific methods to detect contamination and the critical importance of looking for contamination beyond negative and positive controls.
Congenital hydrocephalus: new Mendelian mutations and evidence for oligogenic inheritance
Authors: Jacquemin Valerie , Versbraegen Nassim , Duerinckx Sarah , Massart Annick , Soblet Julie , Perazzolo Camille , Deconinck Nicolas , Brischoux-Boucher Elise , De Leener Anne , Revencu Nicole , Janssens Sandra , Moorgat Stèphanie , Blaumeiser Bettina , Avela Kristiina , Touraine Renaud , Abou Jaoude Imad , Keymolen Kathelijn , Saugier-Veber Pascale , Lenaerts Tom , Abramowicz Marc , Pirson Isabelle
Published: March 2023

Background

Congenital hydrocephalus is characterized by ventriculomegaly, defined as a dilatation of cerebral ventricles, and thought to be due to impaired cerebrospinal fluid (CSF) homeostasis. Primary congenital hydrocephalus is a subset of cases with prenatal onset and absence of another primary cause, e.g., brain hemorrhage. Published series report a Mendelian cause in only a minority of cases. In this study, we analyzed exome data of PCH patients in search of novel causal genes and addressed the possibility of an underlying oligogenic mode of inheritance for PCH.

Materials and methods

We sequenced the exome in 28 unrelated probands with PCH, 12 of whom from families with at least two affected siblings and 9 of whom consanguineous, thereby increasing the contribution of genetic causes. Patient exome data were first analyzed for rare (MAF < 0.005) transmitted or de novo variants. Population stratification of unrelated PCH patients and controls was determined by principle component analysis, and outliers identified using Mahalanobis distance 5% as cutoff. Patient and control exome data for genes biologically related to cilia (SYScilia database) were analyzed by mutation burden test.

Results

In 18% of probands, we identify a causal (pathogenic or likely pathogenic) variant of a known hydrocephalus gene, including genes for postnatal, syndromic hydrocephalus, not previously reported in isolated PCH. In a further 11%, we identify mutations in novel candidate genes. Through mutation burden tests, we demonstrate a significant burden of genetic variants in genes coding for proteins of the primary cilium in PCH patients compared to controls.

Conclusion

Our study confirms the low contribution of Mendelian mutations in PCH and reports PCH as a phenotypic presentation of some known genes known for syndromic, postnatal hydrocephalus. Furthermore, this study identifies novel Mendelian candidate genes, and provides evidence for oligogenic inheritance implicating primary cilia in PCH.
Investigating the correlation between perceived stress and health anxiety with obsessive–compulsive disorder and quality of life during COVID-19 pandemic
Authors: Homayuni Atefeh
Published: March 2023

Background and aims

The present study aimed to investigate the correlation between perceived stress and health anxiety with obsessive–compulsive symptoms and quality of life during COVID-19 pandemic.

Methods

This cross-sectional study was performed in the general public in Isfahan and Bandar Abbas. 559 citizens were selected by convenience sampling. An online questionnaire was used to collect the data, which consisted of: short health anxiety inventory, perceived stress scale, world health organization quality of life questionnaire and Padua inventory. Data analysis was performed using SPSS-24 and Amos-21.

Results

There were significant positive correlations between health anxiety and perceived stress (r = 0/338), obsessive–compulsive symptoms and perceived stress (r = 0/16), obsessive–compulsive symptoms and health anxiety (r = 0/344). Also there were significant negative correlations between obsessive–compulsive symptoms and quality of life (r = − 0/21), health anxiety and quality of life (r = − 0/366), perceived stress and quality of life (r = − 0/715).

Conclusion

health anxiety and perceived stress during COVID-19 affect the obsessive–compulsive symptoms and quality of life. Therefore, it is recommended to pay attention to these psychological disorders during this global crisis and take actions to prevent and treat them.
Body modifications in borderline personality disorder patients: prevalence rates, link with non-suicidal self-injury, and related psychopathology
Authors: Blay Martin , Hasler Roland , Nicastro Rosetta , Pham Eléonore , Weibel Sébastien , Debbané Martin , Perroud Nader
Published: March 2023

Background

Borderline Personality Disorder (BPD) is a potentially severe personality disorder, characterized by difficulties in emotion regulation and control of behaviors. It is often associated with non-suicidal self-injury (NSSI). Borderline personality features have also been linked to body modifications (BMs). However, the prevalence of BMs, the link between BMs and NSSI, and between BMs and several psychopathology dimensions (e.g. borderline severity, emotion regulation, impulsivity …) remains understudied in patients with BPD. This study aims to fill this gap, and to provide further evidence on the link between NSSI and BMs.

Methods

We used data from a psychiatric outpatient center located in Switzerland (n = 116), specialized in the assessment and treatment of BPD patients. Patients underwent several semi-structured interviews and self-report psychometric scales at the arrival, and the data were retrospectively analyzed.

Results

We found that 70.69% of the patients had one piercing or more, and 69.83% were tattooed. The total score of body modifications and the total number of piercings score of piercings were significantly positively associated with NSSI and the SCID BPD total score. The association with the SCID score was mainly driven by the “suicide and self-damaging behaviors” item and the “chronic feeling of emptiness” item. A significant association was found between total number of piercings and emotion dysregulation. On the other hand, the self-reported percentage of body covered by tattoos score was specifically associated with the sensation seeking subscale of the UPPS-P.

Conclusion

This study provides evidence on the prevalence of BMs in BPD patients, and on the link between BMs and NSSI in this population, suggesting a role of emotion regulation in the link between both constructs. These results also suggests that tattoos and piercings may be differentially linked to specific underlying psychological mechanisms. This calls for further considerations of body modifications in the assessment and care of BPD patients.
Heterogeneous rheology of Japan subduction zone revealed by postseismic deformation of the 2011 Tohoku-oki earthquake
Authors: Dhar Sambuddha , Muto Jun , Ohta Yusaku , Iinuma Takeshi
Published: March 2023

The 2011 Tohoku-oki earthquake produced the most well-recorded postseismic deformation of any megathrust earthquake in the world. Over the last decade, researchers have used a dense and widespread geodetic network of more than 1300 Global Navigation Satellite System (GNSS) stations inland, as well as the about 50 stations on the seafloor, to investigate the various deformation sources responsible for the observed crustal deformation. One of the contributing mechanisms to this crustal deformation is the stress relaxation of the viscoelastic mantle beneath the Japanese arc. As evident in experimental rock physics and geophysical observations, ambient mantle conditions and related rheology are expected to be heterogeneous in space. However, the contribution of such rheological heterogeneities to the postseismic deformation is still poorly understood. Here, we piece together several rheological heterogeneities inferred from the decade-long postseismic deformation of the 2011 Tohoku-oki earthquake. We reviewed more than twenty postseismic models to understand how viscoelastic earth can influence the postseismic surface deformation observed after the Tohoku-oki earthquake. Besides, we employed several synthetic models to tease out the contribution of individual rheological heterogeneities such as depth-dependent rheology of mantle wedge, oceanic asthenosphere, and low-viscosity zone beneath the volcanic front. We demonstrate that the vertical postseismic observation is the key to unravel rheological complexity beneath northeastern Japan. The broader vertical deformation pattern reveals the major viscosity contrast between backarc and forearc, and small-scale subsidence detects the presence of low-viscosity bodies related to arc magmatism. In short, this review paper provides a vista of three-dimensional heterogeneous rheology of viscoelastic earth. These rheological heterogeneities may play a crucial role in bridging the gap between our understanding of different phase of subduction zone earthquake cycle.
Adherence to anti-retroviral therapy, decisional conflicts, and health-related quality of life among treatment-naïve individuals living with HIV: a DEARS-J observational study
Authors: Sekine Yusuke , Kawaguchi Takashi , Kunimoto Yusuke , Masuda Junichi , Numata Ayako , Hirano Atsushi , Yagura Hiroki , Ishihara Masashi , Hikasa Shinichi , Tsukiji Mariko , Miyaji Tempei , Yamaguchi Takuhiro , Kinai Ei , Amano Kagehiro
Published: March 2023

Background

Supporting people living with HIV using anti-retroviral therapy (ART) is important due to the requirement for strict medication adherence. To date, no data from longitudinal studies evaluating adherence by treatment-naïve people living with HIV are currently available. We investigated the adherence of treatment-naïve people living with HIV over time and examined the relationships among decisional conflicts, adherence, and health-related quality of life (HRQL).

Methods

The survey items included adherence (visual analogue scale [VAS]), decisional conflict (decisional conflict scale [DCS]), and HRQL (Medical Outcomes Study HIV Health Survey [MOS-HIV]). The DCS and MOS-HIV scores and the VAS and MOS scores were collected electronically at the ART initiation time point and at 4-, 24-, and 48-week post-treatment time points.

Results

A total of 215 participants were enrolled. The mean DCS score was 27.3 (SD, 0.9); 23.3% of participants were in the high-score and 36.7% in the low-score groups. The mean adherence rates at 4, 24, and 48 weeks were 99.2% (standard error [SE], 0.2), 98.4% (SE, 0.4), and 96.0% (SE, 1.2), respectively. The least-square means of the MOS-HIV for the DCS (high vs. low scores) were 64.4 vs. 69.2 for general health perceptions and 57.7 vs. 64.0 for HRQL, respectively.

Conclusion

Adherence among treatment-naïve people living with HIV was maintained at a higher level, and HRQL tended to improve with ART. People with high levels of decisional conflict tended to have lower HRQL scores. Support for people living with HIV during ART initiation may be related to HRQL.
“My Body, My Rhythm, My Voice”: a community dance pilot intervention engaging breast cancer survivors in physical activity in a middle-income country
Authors: Rubio María Alejandra , Mejía-Arbeláez Carlos M. , Wilches-Mogollon Maria A. , Moreno Sergio , Finck Carolyn , Rosas Lisa G. , Romero Sol A. , Guevara Paula , Cabas Santiago , Rubiano Oscar , Flórez-Pregonero Alberto , León José G. , Alarcón Luis Fernando , Haile Robert , Sarmiento Olga L. , King Abby C.
Published: March 2023

Background

Interventions to promote physical activity among women breast cancer survivors (BCS) in low- to middle-income countries are limited. We assessed the acceptability and preliminary effectiveness of a theory-driven, group-based dance intervention for BCS delivered in Bogotá, Colombia.

Methods

We conducted a quasi-experimental study employing a mixed-methods approach to assess the 8-week, 3 times/week group dance intervention. The effect of the intervention on participants’ physical activity levels (measured by accelerometry), motivation to engage in physical activity, and quality of life were evaluated using generalized estimating equation analysis. The qualitative method included semi-structured interviews thematically analyzed to evaluate program acceptability.

Results

Sixty-four BCS were allocated to the intervention (n = 31) or the control groups (n = 33). In the intervention arm, 84% attended ≥ 60% of sessions. We found increases on average minutes of moderate-to-vigorous physical activity per day (intervention: +8.99 vs control: −3.7 min), and in ratings of motivation (intervention change score = 0.45, vs. control change score= −0.05). BCS reported improvements in perceived behavioral capabilities to be active, captured through the interviews.

Conclusions

The high attendance, behavioral changes, and successful delivery indicate the potential effectiveness, feasibility, and scalability of the intervention for BCS in Colombia.

Trial registration

ClinicalTrial.gov NCT05252780, registered on Dec 7th, 2021—retrospectively registered unique protocol ID: P20CA217199-9492018.
Adapted suicide safety plans to address self-harm, suicidal ideation, and suicide behaviours in autistic adults: protocol for a pilot randomised controlled trial
Authors: Rodgers Jacqui , Goodwin Jane , Nielsen Emma , Bhattarai Nawaraj , Heslop Phil , Kharatikoopaei Ehsan , O’Connor Rory C. , Ogundimu Emmanuel , Ramsay Sheena E. , Steele Katie , Townsend Ellen , Vale Luke , Walton Emily , Wilson Colin , Cassidy Sarah
Published: March 2023

Background

Suicide prevention is a national priority for the UK government. Autistic people are at greater risk of experiencing self-harm and suicidal thoughts and behaviours than the general population. Safety plans are widely used in suicide prevention but have not yet been designed with and for autistic people. We developed the first safety plan specifically targeting suicidality in autistic adults: the Autism Adapted Safety Plan (AASP). It consists of a prioritised list of hierarchical steps that can be used prior to or during a crisis to mitigate risk of self-harm and suicidal behaviour. This is a pilot study that aims to assess the feasibility and acceptability of the AASPs and the research processes, including the response rates, potential barriers and reach of AASPs, methods of recruitment, what comprises usual care, and economic evaluation methods/tools.

Methods

This is an external pilot randomised controlled trial of a suicide prevention tool aimed at mitigating the risk of self-harm and suicidal behaviour in autistic adults: AASPs. Participants will be assessed at baseline and followed up 1 month and 6 months later. Assessments include questions about self-harm, suicidality, service use, and their experience of the AASP/taking part in the study. Autistic adults who have a clinical autism diagnosis and self-reported history of self-harm, suicidal thoughts, or suicidal behaviours within the last 6 months will be invited to take part in the study. Informed consent will be obtained. Participants will be recruited via community and third sector services (including community settings, autism charities, and mental health charities). They may also “self-refer” into the study through social media recruitment and word of mouth. Ninety participants will be randomised to either develop an AASP or receive their usual care in a 1:1 ratio.

Discussion

The present study will provide an evaluation of the suitability of the processes that would be undertaken in a larger definitive study, including recruitment, randomisation, methods, questionnaires, outcome measures, treatment, and follow-up assessments.

Trial registration

ISRCTN70594445, Protocol v4: 8/2/22.
Impact of sexual intercourse on frozen-thawed embryo transfer outcomes: a randomized controlled trial
Authors: Hou Jin-Wei , Yuan Li-Hua , Cao Xian-Ling , Song Jing-Yan , Sun Zhen-Gao
Published: March 2023

Background

Exposure of the female reproductive tract to either seminal plasma or fluid component of the ejaculate is beneficial to achieving successful embryo implantation and normal embryo development. But whether the “physical” component of sexual intercourse during the peri-transfer period have any influence on frozen-thawed embryo transfer (FET) pregnancy outcomes is not clear.

Methods

We conducted a randomized trial that included 223 patients undergoing in vitro fertilization (IVF) treatment at a university-affiliated reproductive center from 19 July 2018 to 24 February 2019. Enrolled patients undergoing IVF treatment were randomized either to engage sexual intercourse using the barrier contraception (Group A, n = 116) or to abstain (Group B, n = 107) one night before FET. The primary outcome was clinical pregnancy rate.

Results

Patients having intercourse had higher clinical pregnancy rate (51.72% vs. 37.07%, P = 0.045) and implantation rate (38.31% vs. 24.77%, P = 0.005) compared to those did not engage intercourse. However, there was no significant difference of the spontaneous abortion rate between two groups (11.67% 33 vs. 14.63%, P = 0.662).

Conclusions

Sexual intercourse before embryo transfer may improve the clinical pregnancy and implantation rates during FET cycles. However, it should be noted that patients choose only one time for sexual intercourse, that is, the night before embryo transfer.

Trial registration

The present study was registered at the Chinese Clinical Trial Registry (http://www.chictr.org.cn/, ChiCTR1800017209).