bluuebunny/crossref_metadata_2025 huggingface dataset:
N18 The experience of the IBD patients with a permanent or temporary stoma: update of the literature
Authors: Povoli A , Grubissa S , Molino L , Marino M , Berretti D
Published: January 2024

Background

Surgery is indicated in selected patients with inflammatory bowel disease (IBD).Annually, 2000 (0.66%) of these individuals in the UK and an estimated 24,000 (1.5%) in the USA undergo surgery resulting in a permanent or temporary stoma. The audience of patients undergoing a stoma surgery is very broad and consists of not only elderly people, but also young adults, fertile or pregnant women.Fear of having a stoma is a major concern for people with IBD. And this aspect goes beyond the simple therapeutic aspect but it encroaches upon the psychological, occupational, relational, educational, financial and domestic area.This study aims to analyze the Quality of Life (QoL) outcomes of IBD patients with temporary or permanent stoma

Methods

To identify, evaluate and synthesis the lived experiences of IBD patients having a stoma, a meta-synthesis has been performed following the Sandelowski and Barroso guidelines (2007).Studies included: primary studies in English language, conducted using qualitative methodology that explore the subjective experience of IBD patients having a temporary or permanent stoma; studies that debated the experiences lived during the period of having a stoma; studies published from January 2013 to October 2023. The instrument Critical Appraisal Skills Program (CASP) has been used for the qualitative evaluation of the included studies (Image 1)

Results

Sixteen studies have been analyzed and the most of them involved more than one medical or research institution. The included studies described different areas of the perceived experience of 3046 IBD patients with a stoma. A total of 30 labels have been classified into 12 sub-themes, grouped in a total of five themes. (a) Surgery is a trigger for possible psychological disorders such as PTSD and (b) the positive perception of the stoma as an effective therapy in the management of IBD symptoms are the most frequent labels in the studies (Table 1)

Conclusion

The results of this study contributed to provide evidence about the experience of stoma-bearing IBD patients.Healthcare providers should offer improved interdisciplinary counselling earlier in the course of IBD so as to inform and enpower the patient and allow for shared decision-making. Patient information, education and support groups are crucial when managing IBD patients and optimizing patient-reported outcomes.This counts especially for young subjects that would be less prone to accept a stoma.Taken together, these findings provide further proof of the complex interplay between various psychological aspects.Our findings are consistent with previous research, which suggest, in terms of direction for psychological operations,that an increased focus in the educational and management of the disease is crucial
N31 HLA-DQA1*05 detection in saliva, an effective alternative in the monitoring and control of patients with Inflammatory Bowel Disease
Authors: Lavín Expósito C , Bouhmidi Assakali A , Rodríguez Romero V , Cabanillas Navarro M L , Vozmediano Sánchez P , Velasco del Burgo M , Alañon Barba M , Moraleda Cebrián F , Hidalgo Juárez M L , Bonillo Merino C , Pinilla Sánchez J , Laguna Laguna M T , Salueña Salueña I , Sánchez Pardo A M , Sánchez Alonso M , Barreto Suárez E
Published: January 2024

Background

The development of Inflammatory Bowel Disease (IBD) appears to be related to genetic susceptibility and an excessive immune response of the intestinal mucosa.

Tumour necrosis factor (anti-TNF) therapies are the most widely used biologic drugs to treat immune-mediated diseases, but repeated administration may induce the formation of anti-drug antibodies. The ability to identify patients at increased risk of developing anti-TNFα antibodies would facilitate the selection of therapy and the use of preventive strategies.

It has been shown that approximately 40% of the European population carries the HLA-DQA1*05 allele, and that its presence could have an important impact on treatment as it has been associated with:

- Increased risk of immunogenicity of anti-TNFα therapy, regardless of concomitant treatment or anti-TNFα drug selected.

- Decreased efficacy due to the formation of neutralising antibodies, leading to possible primary or secondary failures.

- Occurrence of adverse events such as infusion reactions or hypersensitivity reactions.

- Alterations in pharmacokinetics, so that drug clearance is accelerated regardless of whether the antibodies are neutralising.

In our hospital we have the possibility to request the determination of the HLA-DQA1*05 allele through a detection kit in saliva.

The main aim is to present a useful and effective tool for the detection of the HLA-DQA1*05 allele.

Methods

The methodology requires the inclusion of 30 newly diagnosed patients, patients naïve to biological treatment or patients on treatment with a first biological drug for no more than 24 months, by both the doctor and the nurse.The nurse will explain the previous preparation to the patient and will collect the sample using the saliva detection kit. Once the results have been received, the physician is notified.

Results

The detection of the HLA-DQA1*05 allele in our patients is 36.84%, a percentage similar to that detected in the European population through the detection of the HLA-DQA1*05 allele in blood.

Conclusion

- Having the ability to identify individuals at high risk of anti-TNF antibody formation and apply targeted combination therapy to these individuals is very valuable in clinical practice.

- Saliva determination of the HLA-DQA1*05 allele is an efficient and cheaper alternative in hospitals where HLA-DQA1*05 detection in blood is not available in the laboratory.

- The extraction and performance of the technique is simple, fast, obtaining the results within 5 days of submission, and convenient for both the patient and the healthcare professional.
ECCO Pioneer Award Functional assessment of the microbiome in persistent IBD-related psychological symptoms
Authors: Laukens D
Published: January 2024

Background and Aims

It is well established that patients with inflammatory bowel disease (IBD) experience psychological comorbidities, and that these symptoms persist upon remission of the IBD in more than 50% of patients. The mechanisms underlying this clinical association are unknown, which hampers to objectify the problem and limits the possibilities to intelligently consider targeted treatments. We recently observed behavioral anomalies and neuroinflammation in a mouse model of extinguished chronic colitis, enabling the fundamental study of psychological symptoms in IBD. Fueled by technical evolutions to characterize translationally active bacteria at the single-cell level, their importance in colitis, and a proof-of-concept stool transplantation experiment, the purpose of this project is to determine if specific bacterial functions drive persistent neuroinflammation upon IBD remission.

Methods

First, a state-of-the-art flow-cytometry based method will be used to temporally map translationally active bacteria during the course of extinguished chronic colitis. Second, the same functional microbial analysis will be achieved in human fecal samples of IBD patients in remission before and after treatment for fatigue, and results will be compared with persistent bacterial changes found in mouse flora. Finally, causality of associated bacteria to induce neuroinflammation will be tested by transplantation studies of bacterial communities isolated from the previous tasks.

Anticipated Impact

This research may impact the field in the short-term by creating solid scientific awareness that psychological comorbidities are intrinsically linked with IBD remission, and by more specifically attributing a role for specific bacterial functions in these symptoms. In addition, the technique applied may open novel insights for the IBD microbiome community. In the medium-term, this project aims to shed light on the actual bacterial mechanisms that lead to neuroinflammation and behavioral anomalies, which in the long-term could help identify biomarkers for diagnostic purposes or microbiome-related targets to design rational therapeutics for patients with IBD suffering from psychological comorbidities.
ECCO Grant Immune-epithelial crosstalk boosting intestinal repair in ulcerative colitis
Authors: Hausmann Annika
Published: January 2024

Background and Aims

1.3 million people in Europe suffer from inflammatory bowel disease (IBD). Its most prevalent subtype is ulcerative colitis (UC), a chronic colon inflammation of unknown etiology. The breakdown of intestinal epithelial barrier integrity is a key event initiating intestinal inflammation in UC, and remission requires epithelial repair. Repair is modulated by inflammatory signals which exert anti- but also pro-proliferative effects. It is unknown how the epithelium integrates inflammatory signals to finetune repair, limiting current therapeutic strategies in UC to symptomatic suppression of inflammation with potential detrimental effects on repair. With this project, I aim to gain a molecular understanding of immune cell-epithelial crosstalk in UC to inform targeted therapies that suppress detrimental inflammation and boost epithelial repair.

Methods

To this end, I propose a novel, interdisciplinary approach, venturing beyond traditional approaches by employing my host lab’s expertise on epithelial injury and repair in combination with my competence in mucosal immunology and a novel visual proteomics technique to decipher immune cell-epithelium crosstalk driving epithelial repair in UC. Specifically, I will generate a high-resolution proteome map of the repairing colonic mucosa of patients with UC to identify potential immune cell-epithelium crosstalk, validate candidates and assess the reparative potential of the identified crosstalk in human intestinal epithelial cells using organoid cultures.

Anticipated Impact

Current therapeutic strategies in UC, focused on immune suppression, still feature high rates of primary or secondary non-response, fueling disease progression and decreasing patient quality of life. This highlights a key unmet clinical need for alternative therapeutic approaches. I anticipate that the identified immune-mediated drivers of epithelial repair will provide novel molecular targets for future pharmacological interventions aiming to mitigate inflammation-induced epithelial barrier loss and to boost repair capacity. This will improve patient quality of life and reduce treatment costs.
N-ECCO Grant Spiritual needs of patients with inflammatory bowel disease and their caregivers: a European cross-sectional nursing study
Authors: Martinato M
Published: January 2024

Aims

Spirituality is the search for meaning or purpose in life (Delgado, 2005), not strictly from a religious perspective. Spiritual well-being is positively connected with physical and psychic well-being, and achieving the first is likely to help to maintain the latter (Bożek et al., 2020). Individuals with chronic disorders or experiencing a life-changing condition (e.g. Inflammatory Bowel Disease - IBD), may have gone through a spiritual quest of some sort that can produce spiritual anguish or 'spiritual distress', interpreting the disease as a punishment, feeling as a victim of 'superior injustice', losing faith in prayer (Klimasiński et al., 2022), but data on the spiritual needs (SpNs) of IBD patients are lacking.

The main objective of this project is to describe the SpNs of IBD patients to provide information to IBD nurses on how to address these needs.

Methods

A multilingual cross-sectional electronic survey will be carried on assessing the SpNs of patients using the Spiritual Needs Questionnaire (SpNQ). The tool is made up of items assessing the importance attributed by patients to SpNs using a 4-point Likert scale (Büssing et al., 2010), and is available in ten European languages, but it could be translated and validated in other European languages inside the project in case of anticipated participation by a country that need the questionnaire available in the local language if a collaboration with IBD clinicians and patients in that country will be possible.

Anticipated Impact

The findings of such a study can provide better consideration of SpNs in the treatment of IBD patients, emphasizing the importance of addressing SpNs for IBD nurses in managing IBD patients, adopting the tools to screen patients for these needs; furthermore, the results of this project can provide additional evidence of the importance of nursing in IBD patients’ care.
N-ECCO Grant Supporting psychosocial and emotional well-being and resilience in family members of people with IBD: an intervention co-design and feasibility study
Authors: Thapwong P , Norton C , Rowland E , Czuber Dochan W
Published: January 2024

Background and Aims

This ongoing PhD project seeks to develop a person-centred, evidence-based, theoretically informed prototype intervention to support psychosocial and emotional well-being and resilience in people with IBD’s family members (FMs). PhD project focuses on the intervention development and feasibility testing. The development phase has already been undertaken using a co-design approach informed by Design Thinking. A systematic review and qualitative research have been conducted and published, and co-design workshops have been held with people with IBD (n=4), FMs (n=9), and IBD nurses (n=2), revealing a preference for online-based intervention. Therefore, the aim of this study is to translate the paper-based intervention prototype into electronic format. The online prototype will be a) tested for acceptability and b) effect signal. The feasibility of the study design will be evaluated.

Methods

A sequential mixed methods approach, based on the UK Medical Research Council (MRC) Evaluation Framework. The intervention feasibility study will test the acceptability of content and delivery of the intervention and ascertain active feedback. The feasibility of the study design will be evaluated the recruitment, data collection, retention, and analysis strategies. A two-arm feasibility RCT with nested qualitative evaluation will be used to evaluate the newly developed intervention among 60 FMs. Participants will be recruited via Crohn’s & Colitis UK and Bowel Research UK charities. The 60 participants will be randomly allocated into intervention and control groups using 2:1 randomisation. The qualitative component will use purposive sampling from the intervention arm to elicit feedback on the content and format with up to 20 participants.

Anticipated Impact

Results from this intervention development and feasibility study will help revise the intervention, incorporate changes to the study protocol (if necessary), and develop a large-scale RCT for efficacy trailing of a complex intervention to benefit service users.
Disturbed atrial metabolism, shear stress, and cardiac load contribute to atrial fibrillation after ablation: AXAFA biomolecule study
Authors: Chua Winnie , Khashaba Alya , Canagarajah Hansel , Nielsen Jens Cosedis , di Biase Luigi , Haeusler Karl Georg , Hindricks Gerhard , Mont Lluis , Piccini Jonathan , Schnabel Renate B , Schotten Ulrich , Wienhues-Thelen Ursula-Henrike , Zeller Tanja , Fabritz Larissa , Kirchhof Paulus
Published: January 2024

Aims

Different disease processes can combine to cause atrial fibrillation (AF). Their contribution to recurrent AF after ablation in patients is not known. Cardiovascular processes associated with recurrent AF after AF ablation were determined by quantifying biomolecules related to inflammation, metabolism, proliferation, fibrosis, shear stress, atrial pressure, and others in the AXAFA biomolecule study.

Methods and results

Twelve circulating cardiovascular biomolecules (ANGPT2, BMP10, CA125, hsCRP, ESM1, FABP3, FGF23, GDF15, IGFBP7, IL6, NT-proBNP, and hsTnT) were quantified in plasma samples obtained prior to a first AF ablation using high-throughput, high-precision assays. Cox regression was used to identify biomolecules associated with recurrent AF during the first 3 months after AF ablation. In 433 patients (64 years [58, 70]; 33% women), baseline concentrations of ANGPT2, BMP10, hsCRP, FGF23, FABP3, GDF15, and NT-proBNP were elevated in patients with recurrent AF (120/433; 28%). After adjustment for 11 clinical features and randomized treatment, elevated NT-proBNP [hazard ratio (HR) 1.58, 95% confidence interval (1.29, 1.94)], ANGPT2 [HR 1.37, (1.12, 1.67)], and BMP10 [HR 1.24 (1.02, 1.51)] remained associated with recurrent AF. Concentrations of ANGPT2, BMP10, and NT-proBNP decreased in patients who remained arrhythmia free, but not in patients with recurrent AF, highlighting their connection to AF. The other eight biomarkers showed unchanged concentrations.

Conclusion

Elevated concentrations of ANGPT2, BMP10, and NT-proBNP are associated with recurrent AF after a first AF ablation, suggesting that processes linked to disturbed cardiomyocyte metabolism, altered atrial shear stress, and increased load contribute to AF after AF ablation in patients.
Cost-Effectiveness of Community-Based Active Case Finding Strategy for Tuberculosis: Evidence From Shenzhen, China
Authors: Pei Xingtong , Zhong Tao , Yang Chongguang , Sun Li , Chen Meiru , Xu Mingming
Published: January 2024

Background

Active case finding (ACF) is a potentially promising approach for the early identification and treatment of tuberculosis patients. However, evidence on its cost-effectiveness, particularly in low- and middle-income countries, remains limited. This study evaluates the cost-effectiveness of a community-based ACF practice in Shenzhen, China.

Methods

We employed a Markov model-based decision analytic method to assess the costs and effectiveness of 3 tuberculosis detection strategies: passive case finding (PCF), basic ACF, and advanced ACF. The analysis was conducted from a societal perspective on a dynamic cohort over a 20-year horizon, focusing on active tuberculosis (ATB) prevalence and the incremental cost-effectiveness ratio (ICER).

Results

Compared to the PCF strategy, the basic and advanced ACF strategies effectively reduced ATB cases by 6.8 and 10.2 per 100 000 population, respectively, by the final year of this 20-year period. The ICER for the basic and advanced ACF strategies were ¥14 757 and ¥8217 per quality-adjusted life-year, respectively. Both values fell below the cost-effectiveness threshold.

Conclusions

Our findings indicate that the community-based ACF screening strategy, which targets individuals exhibiting tuberculosis symptoms, is cost-effective. This underscores the potential benefits of adopting similar community-based ACF strategies for symptomatic populations in tuberculosis-endemic areas.
Unearthing New ccr Genes and Staphylococcal Cassette Chromosome Elements in Staphylococci Through Genome Mining
Authors: Huang Jianguo , Xiao Jinhe , Wang Xiaokun , Xue Xuemei , Ma Yadong , Zhang Ziqian , Zheng Liangjun , Zafir Muhammad , Liu Pilong , Zhao Xin , Larsen Anders Rhod , Xue Huping
Published: January 2024

Staphylococcal cassette chromosome mec (SCCmec) typing is crucial for investigating methicillin-resistant Staphylococcus aureus (MRSA), relying primarily on the combination of ccr and mec gene complexes. To date, 19 ccr genes and 10 ccr gene complexes have been identified, forming 15 SCCmec types. With the vast release of bacterial genome sequences, mining the database for novel ccr gene complexes and SCC/SCCmec elements could enhance MRSA epidemiological studies. In this study, we identified 12 novel ccr genes (6 ccrA, 3 ccrB, and 3 ccrC) through mining of the National Center for Biotechnology Information (NCBI) database, forming 12 novel ccr gene complexes and 10 novel SCC elements. Overexpression of 5 groups of novel Ccr recombinases (CcrA9B3, CcrA10B1, CcrC3, CcrC4, and CcrC5) in a mutant MRSA strain lacking the ccr gene and extrachromosomal circular intermediate (ciSCC) production significantly promoted ciSCC production, demonstrating their biological activity. This discovery provides an opportunity to advance MRSA epidemiological research and develop database-based bacterial typing methods.
Biotic interactions outweigh abiotic factors as drivers of bark microbial communities in Central European forests
Authors: Dreyling Lukas , Penone Caterina , Schenk Noëlle Valérie , Schmitt Imke , Dal Grande Francesco
Published: January 2024

Bark surfaces are extensive areas within forest ecosystems, which provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal, and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central, and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occur in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.
An analysis of muscle growth after proton beam therapy for pediatric cancer
Authors: Nitta Hazuki , Mizumoto Masashi , Li Yinuo , Oshiro Yoshiko , Fukushima Hiroko , Suzuki Ryoko , Hosaka Sho , Saito Takashi , Numajiri Haruko , Kawano Chie , Kamizawa Satoshi , Maruo Kazushi , Sakurai Hideyuki
Published: January 2024

Retardation of growth and development is a well-known late effect after radiotherapy for pediatric patients. The goal of the study was to examine the effect of proton beam therapy (PBT) on the growth of muscles included in the irradiated area. The subjects were 17 pediatric patients (age ≤ 5 years) who received PBT with a treatment field including a muscle on only one side out of a pair of symmetrical bilateral muscles and had imaging evaluations for at least 1 year after PBT. The thicknesses of the irradiated and non-irradiated (contralateral) muscles were measured retrospectively on CT or MRI axial images collected before and after PBT. The change of thickness divided by the period (years) for each muscle was compared between the irradiated and contralateral sides. Correlations of muscle growth with irradiation dose and age at the start of treatment were also evaluated. The median observation period was 39.2 months. The measurement sites included the erector spinae (n = 9), gluteus maximus (n = 5) and rhomboids + trapezius (n = 3) muscles. The average changes in muscle thickness were 0.24 mm/year on the irradiated side and 1.19 mm/year on the contralateral side, showing significantly reduced growth on the irradiated side (P = 0.001). Younger patients had greater muscle growth. Irradiation dose was not significant, but muscle growth tended to decrease as the dose increased, and muscles irradiated at >50 Gy (RBE) showed little growth. These results show that muscle growth is affected by PBT and that long-term follow-up is needed to evaluate muscle growth retardation.
Variants in the SARS2 gene cause HUPRA syndrome with atypical features: two case reports and review of the literature
Authors: Lahham Elias Edward , Hasassneh Juhina Jamal , Adawi Dua Osamah , Ismail Mohamad Khaled
Published: January 2024

Hyperuricemia, pulmonary hypertension, renal failure in infancy, and alkalosis (HUPRA syndrome) is a rare autosomal recessive mitochondrial disease with a prevalence of <1:1 000 000, due to variations in the seryl-tRNA synthetase (SARS2) gene encoding SARS on chromosome 19 (19q13.2). This study investigated two Palestinian girls from the same village who presented with progressive renal failure during infancy, with atypical clinical manifestations of HUPRA syndrome including leukopenia, anemia, salt wasting, renal failure, marked hyperuricemia, hypercholesterolemia, hyperlactatemia, and hypertriglyceridemia but without pulmonary hypertension or alkalosis. Instead, they showed acidosis on routine follow-up, distinguishing them from previous cases. Using single whole exome sequencing, we identified two homozygous pathogenic variants in the SARS2 gene (c.1175A>G (p.D392G)) and (c.1169A>G (p.D390G)). These cases with their unique phenotypes, expand the SARS2 pathogenic variant spectrum and describe clinical differences between homozygous and compound heterozygous variants.
Path Analysis of Factors Related to Burnout for Campus-Based Victim Advocates
Authors: Nightingale Sarah
Published: January 2024

Campus-based victim advocates provide support and assistance to victims of interpersonal violence in the college context. In this study of professional campus-based victim advocates, structural equation modeling (SEM) was used to assess the direct and indirect effects of factors related to burnout. A total of 208 full-time victim advocates employed at four-year college campuses across the United States participated in an online survey in the summer of 2021. SEM analysis found that secondary traumatic stress and organizational support had significant direct effects on the level of burnout in this population. Also, organizational support served as a mediating factor between perceptions of leadership and burnout, and secondary traumatic stress served as a mediating factor between organizational support and burnout. Higher education institutions can make changes at the organizational level to address burnout of victim advocates through manageable work hours, control over workload, fair compensation, and increased sense of community investment in interpersonal violence response.
Performance of risk prediction models for post-liver transplant patient and graft survival over time
Authors: Shaffer Lauren , Abu-Gazala Samir , Schaubel Douglas E. , Abt Peter , Mahmud Nadim
Published: January 2024

Given liver transplantation organ scarcity, selection of recipients and donors to maximize post-transplant benefit is paramount. Several scores predict post-transplant outcomes by isolating elements of donor and recipient risk, including the donor risk index, Balance of Risk, pre-allocation score to predict survival outcomes following liver transplantation/survival outcomes following liver transplantation (SOFT), improved donor-to-recipient allocation score for deceased donors only/improved donor-to-recipient allocation score for both deceased and living donors (ID2EAL-D/-DR), and survival benefit (SB) models. No studies have examined the performance of these models over time, which is critical in an ever-evolving transplant landscape. This was a retrospective cohort study of liver transplantation events in the UNOS database from 2002 to 2021. We used Cox regression to evaluate model discrimination (Harrell’s C) and calibration (testing of calibration curves) for post-transplant patient and graft survival at specified post-transplant timepoints. Sub-analyses were performed in the modern transplant era (post-2014) and for key donor-recipient characteristics. A total of 112,357 transplants were included. The SB and SOFT scores had the highest discrimination for short-term patient and graft survival, including in the modern transplant era, where only the SB model had good discrimination (C ≥ 0.60) for all patient and graft outcome timepoints. However, these models had evidence of poor calibration at 3- and 5-year patient survival timepoints. The ID2EAL-DR score had lower discrimination but adequate calibration at all patient survival timepoints. In stratified analyses, SB and SOFT scores performed better in younger (< 40 y) and higher Model for End-Stage Liver Disease (≥ 25) patients. All prediction scores had declining discrimination over time, and scores relying on donor factors alone had poor performance. Although the SB and SOFT scores had the best overall performance, all models demonstrated declining performance over time. This underscores the importance of periodically updating and/or developing new prediction models to reflect the evolving transplant field. Scores relying on donor factors alone do not meaningfully inform post-transplant risk.
The association between regional guidelines compliance and mortality in severe trauma patients: an observational, retrospective study
Authors: Duclos Gary , Heireche Fouzia , Siroutot Manon , Delamarre Louis , Sartorius Max-Antoine , Mergueditchian Celine , Velly Lionel , Carvelli Julien , Bordais Aurelia , Pilarczyk Estelle , Leone Marc
Published: January 2024

Background and importance

Trauma is a major cause of mortality and morbidity. Regional trauma systems are the cornerstones of healthcare systems, helping to improve outcomes and avoid preventable deaths in severe trauma patients.

Objectives

The goal of this study was to evaluate the association between compliance with the guidelines of a regional trauma management system and survival at 28 days of severe trauma patients.

Design, settings and participants

We conducted a retrospective observational study from 1 January 2019 to 31 December 2019. All adult patients admitted for trauma at the University Hospital of Marseille (France) and requiring a pre-hospital medical team were analysed. Compliance with a list of 30 items based on the regional guidelines for the trauma management was evaluated. Each item was classified as compliant, not compliant or not applicable. The global compliance was calculated for each patient as the ratio between the number of compliant items over the number of applicable items.

Outcome measures and analysis

The primary aim was to measure the association between compliance with the guidelines and survival at 28 days using a logistic regression. Secondary objectives were to measure the association between compliance with the guidelines and survival at 28 days and 6 months according to the severity of the patients, using a cut-off of the injury severity score at 24.

Main results

A total of 494 patients with a median age of 35.0 (25.0–50.0) years were analysed. Global compliance with guidelines was 63%. Mortality at 28 days and 6 months was assessed at 33 (6.7%) and 37 (7.5%) patients, respectively. The level of compliance was associated with reduced mortality at 28 days [odds ratio (OR) at 0.94 and 95% confidence interval (CI) at 0.89–0.98]. In the subgroup of 122 patients with an injury severity score above 23, the level of compliance was associated with reduced mortality at 28 days [OR: 0.93 (95% CI: 0.88–0.99)] and 6 months [OR: 0.93 (95% CI: 0.87–0.99)].

Conclusion

Increased levels of compliance with the guidelines in severe trauma patients were associated with an increase in survival, notably in the most severe patients.
Can modulation of gut microbiota affect anthropometric indices in patients with non-alcoholic fatty liver disease? An umbrella meta-analysis of randomized controlled trials
Authors: Amini-Salehi Ehsan , Samethadka Nayak Sandeep , Maddineni Gautam , Mahapatro Abinash , Keivanlou Mohammad-Hossein , Soltani Moghadam Saman , Vakilpour Azin , Aleali Maryam Sadat , Joukar Farahnaz , Hashemi Mohammad , Norouzi Naeim , Bakhshi Arash , Bahrampourian Ali , Mansour-Ghanaei Fariborz , Hassanipour Soheil
Published: January 2024

Background and aim:

Modulating the gut microbiota population by administration of probiotics, prebiotics, and synbiotics has shown to have a variety of health benefits in different populations, particularly those with metabolic disorders. Although the promising effects of these compounds have been observed in the management of patients with non-alcoholic fatty liver disease (NAFLD), the exact effects and the mechanisms of action are yet to be understood. In the present study, we aimed to evaluate how gut microbiota modulation affects anthropometric indices of NAFLD patients to achieve a comprehensive summary of current evidence-based knowledge.

Methods:

Two researchers independently searched international databases, including PubMed, Scopus, and Web of Science, from inception to June 2023. Meta-analysis studies that evaluated the effects of probiotics, prebiotics, and synbiotics on patients with NAFLD were entered into our umbrella review. The data regarding anthropometric indices, including body mass index, weight, waist circumference (WC), and waist-to-hip ratio (WHR), were extracted by the investigators. The authors used random effect model for conducting the meta-analysis. Subgroup analysis and sensitivity analysis were also performed.

Results:

A total number of 13 studies were finally included in our study. Based on the final results, BMI was significantly decreased in NAFLD patients by modulation of gut microbiota [effect size (ES): −0.18, 05% CI: −0.25, −0.11, P<0.001]; however, no significant alteration was observed in weight and WC (ES: −1.72, 05% CI: −3.48, 0.03, P=0.055, and ES: −0.24, 05% CI: −0.75, 0.26, P=0.353, respectively). The results of subgroup analysis showed probiotics had the most substantial effect on decreasing BMI (ES: −0.77, 95% CI: −1.16, −0.38, P<0.001) followed by prebiotics (ES: −0.51, 95% CI: −0.76, −0.27, P<0.001) and synbiotics (ES: -0.12, 95% CI: −0.20, −0.04, P=0.001).

Conclusion:

In conclusion, the present umbrella meta-analysis showed that although modulation of gut microbiota by administration of probiotics, prebiotics, and synbiotics had promising effects on BMI, no significant change was observed in the WC and weight of the patients. No sufficient data were available for other anthropometric indices including waist-to-hip ratio and waist-to-height ratio and future meta-analyses should be done in this regard.
Enhancing glycaemic control and promoting cardiovascular health: the therapeutic potential of Trigonella foenumgraecum in diabetic patients – a systematic review and meta-analysis
Authors: Shakil Saad , Akhtar Sareema E. , Ali Akhtar , Antony Meetty , Antony Ishan , Mansour Eyad , Khawar Farooqui Sabeeh , Akbar Absam , Alazazzi Hosam , Alsufyani Reema , Alsufyani Majid , Alawadhi Retaj , Ramtohul Rahul K. , Hadeed Sebastian , Tabassi Aysa , Tabassi Aylin , Almas Talal
Published: January 2024

Background:

The antidiabetic potential of fenugreek has been highlighted in past literature, and various in-vitro and in-vivo studies have validated its glucose-lowering effects; however, very limited data are available on its effects on diabetic patients.

Objective:

An updated systematic review and meta-analysis of randomized control trials that assessed patients who were administered fenugreek.

Methods:

The PRISMA guidelines (Supplemental Digital Content 1, http://links.lww.com/MS9/A361) were followed when conducting this meta-analysis. PubMed, Scopus, Google Scholar and MEDLINE were searched from inception until June 2023, for randomized control trials that compared fenugreek with control in patients with type 2 diabetes mellitus (DM) and reported the following outcomes of interest: fasting blood glucose, glycated haemoglobin A1c (HbA1c) and postprandial glucose levels. The findings were presented as mean difference (MD) with 95% confidence intervals (CIs) and were pooled using a random effects model.

Results:

Fenugreek significantly (P<0.001) reduced the fasting blood sugar (FBS), HbA1c levels and postprandial glucose levels in diabetic patients when compared to the control.

Conclusion:

Among patients with type 2 DM, our comparisons demonstrated a reduction in FBS, HbA1c levels and postprandial glucose levels with the administration of fenugreek seed at 2–5 mg dose in powder form.
Suppression of soliton collapses, modulational instability and rogue-wave excitation in two-Lévy-index fractional Kerr media
Authors: Zhong Ming , Chen Yong , Yan Zhenya , Malomed Boris A.
Published: January 2024

We introduce a generalized fractional nonlinear Schrödinger (FNLS) equation for the propagation of optical pulses in laser systems with two fractional-dispersion/diffraction terms, quantified by their Lévy indices,

α

1

 

α

2

∈
(
1
,
2
]

, and self-focusing or defocusing Kerr nonlinearity. Some fundamental solitons are obtained by means of the variational approximation, which are verified by comparison with numerical results. We find that the soliton collapse, exhibited by the one-dimensional cubic FNLS equation with only one Lévy index (LI)

α
=
1

, can be suppressed in the two-LI FNLS system. Stability of the solitons is also explored against collisions with Gaussian pulses and adiabatic variation of the system parameters. Modulation instability (MI) of continuous waves is investigated in the two-LI system too. In particular, the MI may occur in the case of the defocusing nonlinearity when two diffraction coefficients have opposite signs. Using results for the MI, we produce first- and second-order rogue waves on top of continuous waves, for both signs of the Kerr nonlinearity.
Caproicibacterium argilliputei sp. nov., a novel caproic acid producing anaerobic bacterium isolated from pit clay
Authors: Zeng Caiyu , Zeng Xiang , Xia Shangcao , Ye Guangbin
Published: January 2024

An anaerobic, Gram-positive, rod-shaped, motile and spore-forming bacterium, designated strain ZCY20-5T, was isolated from pit clay of Chinese strong-aroma type Baijiu (Chinese liquor). Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain ZCY20-5T belonged to the genus

Caproicibacterium

, family Oscillospiracheae, but it showed low similarity to the type species

Caproicibacterium amylolyticum

LBM18003T (98.00 %) and

Caproicibacterium lactatifermentans

LBM19010T (95.67 %). In anaerobic yeast extract medium, growth was observed at 20–45 °C (optimum, 35–40 °C), at pH 4.0–9.0 (optimum, pH 6.5–7.0) and with 0.0–2.0 % NaCl (w/v). The predominant fatty acids were C16 : 0, C14 : 0, C13 3-OH and C16 3-OH, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, three phospholipids of unknown structure containing glucosamine and two unidentified phospholipids. Strain ZCY20-5T exhibited an 81.32 % pairwise average nucleotide identity value, a 78.98 % average amino acid identity value and a 22.30 % digital DNA–DNA hybridization value compared to its closest relative

C. amylolyticum

LBM18003T. Based on morphological, physiological, biochemical, chemotaxonomic, genotypic and phylogenetic results, strain ZCY20-5T represents a novel species of

Caproicibacterium

, and the type strain is ZCY20-5T (=MCCC 1A19399T=KCTC 25590T).
Stability of BK polyomavirus DNA in urine over time and analytical evaluation of an automated BKV quantitative nucleic acid test
Authors: Lowe Christopher F. , Lawson Tanya , Young Matthew , Jang Willson , Ritchie Gordon , Romney Marc G. , Matic Nancy
Published: January 2024

Introduction. BK polyomavirus (BKPyV) quantitative testing is an important screening tool post-transplantation, although interpretation can be challenging due to lack of standardization, assay heterogeneity and variability of BKPyV DNA over time (in urine).

Methods. Remnant clinical EDTA plasma and urine samples were tested by the cobas BKV test and a validated laboratory-developed test (LDT). Accuracy [positive and negative percent agreement (PPA and NPA), Pearson’s correlation, Bland–Altman analysis] and reproducibility were evaluated. To assess BKPyV DNA stability in urine, prospective urine samples were maintained at two different storage temperatures and tested in triplicate over 7 days.

Results. Overall PPA was 95.6 % (43/45) and NPA was 94.4 % (170/180). For plasma, Pearson’s correlation (0.950) and Bland–Altman analysis (0.113±0.22 log10 IU ml–1) showed high agreement. For neat urine, Pearson’s correlation (0.842) and Bland–Altman analysis (0.326±0.80 log10 IU ml–1) showed somewhat higher variability. Reproducibility was high for the cobas BKV versus the LDT. BKPyV DNA levels in neat urine remained relatively stable over 7 days at both storage temperatures, although outlier results were intermittently detected.

Conclusion. The cobas BKV test showed high agreement and reproducibility compared to the reference LDT. BKPyV viral load testing in urine has known limitations, but neat urine can be processed by the cobas BKV.
Altruism pays off in group-structured populations
Authors: Steiner Klaus F.
Published: January 2024

The evolution of altruistic traits is a Darwinian puzzle that has not yet been satisfactorily solved. Using cost-benefit analyses and multi-agent simulations, I show here that there is a clear fitness advantage for the altruists in a mixed population of altruists and egoists if the following conditions are met:

(i) The population is segregated into groups that persist over time or several generations. (ii) The benefit achieved by altruists is only shared among the members of their own group. (iii) There is selection pressure on each individual, which is reduced by the benefit provided by altruists. (iv) The costs for an altruist are smaller than the total benefit achieved by him for all members of his group together. (v) There is already a high proportion of altruists in the population and/or the proportion of altruists varies greatly between groups.

I refer this kind of population dynamics as the grouping effect, or G-effect for short. This effect is made up of two biases, which basically come about through simple individual selection: the tendency to increase the variance among the groups (variation bias) and the tendency to increase fitness for altruistic traits when this variance is high (fitness bias).

In this context, selection only happens at the individual level. It does not require relationships between the group members, nor does it require competition among the groups. Extended multi-agent simulations with reproduction, mutation and migration also show that altruism can exist stably in a wide range of conditions due to this G-effect.
Haplotype phased genome of ‘Fairchild’ mandarin highlights influence of local chromatin state on gene expression
Authors: Diaz Isaac A. , Ostovar Talieh , Chen Jinfeng , Saddoris Sarah , Schmitz Robert J. , Wessler Susan R. , Stajich Jason , Seymour Danelle K.
Published: January 2024

Background

Cis-regulatory sequences control gene expression through the coordinated action of transcription factors and their associated partners. Both genetic and epigenetic perturbation of cis-regulatory sequences can lead to novel patterns of gene expression. Phased genome assemblies now enable the local dissection of linkages between cis-regulatory sequences, including their epigenetic state, and gene expression to further characterize gene regulation in heterozygous genomes.

Results

We assembled a locally phased genome for a mandarin hybrid named ‘Fairchild’ to explore the molecular signatures of allele-specific gene expression. With genome phasing, genes with allele-specific expression were paired with haplotype-specific chromatin states, including levels of chromatin accessibility, histone modifications, and DNA methylation. We found that 30% of variation in allele-specific expression could be attributed to haplotype associated factors, with allelic levels of chromatin accessibility and three histone modifications in gene bodies having the most influence. Structural variants in promoter regions were also associated with allele-specific expression, including specific enrichments of hAT and MULE-MuDR DNA transposon sequences. Mining of cis-regulatory sequences underlying regions with allelic variation in chromatin accessibility revealed a paternally-associated sequence motif bound by ERF48, a target of the Polycomb repressive complex 2 (PRC2), and sequence similarity of this motif corresponded to local levels of H3K27me3, a signature of PRC2 activity.

Conclusions

Using a locally phased assembly of a heterozygous citrus cultivar, we dissected the interplay between genetic variants and molecular phenotypes with the goal of revealing functional cis-regulatory sequences and exploring the evolution of gene regulation.
The variation landscape ofCYP2D6in a multi-ethnic Asian population
Authors: Maulana Yusuf , Jimenez Rodrigo Toro , Twesigomwe David , Sani Levana , Irwanto Astrid , Bertin Nicolas , Gonzalez-Porta Mar
Published: January 2024

Cytochrome P450 2D6 (CYP2D6) plays a crucial role in metabolizing approximately 20% of medications prescribed clinically. This enzyme is encoded by theCYP2D6gene, known for its extensive polymorphism with over 170 catalogued haplotypes or star alleles, which can have a profound impact on drug efficacy and safety. Despite its importance, a gap exists in the global genomic databases, which are predominantly representative of European ancestries, thereby limiting comprehensive knowledge ofCYP2D6variation in ethnically diverse populations. In an effort to bridge this knowledge gap, we focused on elucidating theCYP2D6variation landscape within a multi-ethnic Asian cohort, encompassing individuals of Chinese, Malay, and Indian descent. Our study comprised data analysis of 1,850 whole genomes from the SG10K_Health dataset using an in-house consensus algorithm, which integrates the capabilities of Cyrius, Aldy, and StellarPGx. This analysis unveiled distinct population-specific star-allele distribution trends, highlighting the unique genetic makeup of the Singaporean population. Significantly, 46% of our cohort harbored actionableCYP2D6variants—those with direct implications for drug dosing and treatment strategies. Furthermore, we identified 14 potential novelCYP2D6star-alleles, of which 7 were observed in multiple individuals, suggesting their broader relevance. Overall, our study contributes novel data onCYP2D6genetic variations specific to the Southeast Asian context. The findings are instrumental for the advancement of pharmacogenomics and personalized medicine, not only in Southeast Asia but also in other regions with comparable genetic diversity.
Rewinding the ratchet: rare recombination locally rescues neo-W degeneration and generates plateaus of sex-chromosome divergence
Authors: Decroly Thomas , Vila Roger , Lohse Konrad , Mackintosh Alexander
Published: January 2024

Natural selection is less efficient in the absence of recombination. As a result, non-recombining sequences, such as sex chromosomes, tend to degenerate over time. Although the outcomes of recombination arrest are typically observed after many millions of generations, recent neo-sex chromosomes can give insight into the early stages of this process. Here we investigate the evolution of neo-sex chromosomes in the Spanish marbled white butterfly,Melanargia ines, where a Z-autosome fusion has turned the homologous autosome into a non-recombining neo-W chromosome. We show that these neo-sex chromosomes are likely limited to the Iberian population ofM. ines, and that they arose around the time when populations in Iberia and North-Africa split, around 1.5 million years ago. Recombination arrest of the neo-W chromosome has led to an excess of premature stop codons and frameshift mutations, while levels of gene expression have remained similar for the neo-W and neo-Z chromosomes, even for genes with loss-of-function mutations. Surprisingly, we identified two regions of∼1 Mb at one end of the neo-W that are both less diverged from the neo-Z and less degraded than the rest of the chromosome, suggesting a history of rare but repeated genetic exchange between the two neo-sex chromosomes. These plateaus of neo-sex chromosome divergence suggest that neo-W degradation can be locally reversed by rare recombination between neo-W and neo-Z chromosomes.