bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical features, risk factors, and antimicrobial resistance of pseudomonas putida isolates
Authors: Baykal Hüsnü , Çelik Deniz , Ülger A. Füsun , Vezir Sedat , Güngör M. Ömür
Published: December 2022

Pseudomonas putida rarely results in infection, primarily in patients undergoing invasive procedures or immunocompromised hosts. We aimed to investigate the characteristics of Pseudomonas putida infections. This is a retrospectively designed cross-sectional observational study. We retrospectively scanned the data from our hospital for the 10 years before February 15, 2022. The patients with Pseudomonas putida growth in the microbiological cultures and with antibiotic susceptibility tests were included in the study. We recorded culture isolates types, age, gender, comorbidities, immunosuppressive factors, symptoms, invasive medical procedures, length of hospital stay, and radiological findings. The mean age of the patients was 66.2 ± 14.5 years, and the male patients predominated (76.3%, n = 58/76). There was growth in bronchial lavage in 33 patients, sputum in 28, pleural effusion fluid in 12, and tracheal aspirate in 3 patients. The rate of antibiotic-resistant strains was 56.6% (n = 43). All strains were sensitive to colistin (100%), and carbapenem, amikacin, and gentamicin sensitivity rates were high. We observed that the risk of antibiotic resistance increased 4.29 times in the patients in the intensive care unit (Cl:1.27–14.47, P = .01). The patients with Diabetes Mellitus had a higher risk (OR 4.33, Cl:1.11–16.77, P = .03), and in cancer cases, the risk was 3.31 times higher (Cl:1.06–10.32, P = .03). The risk of Pseudomonas putida infection should be considered, particularly in patients with comorbid disorders causing immunosuppression, including Diabetes Mellitus and Cancer.
Factors associated with falls in patients with knee osteoarthritis: A cross-sectional study
Authors: Rosadi Rakhmad , Jankaew Amornthaep , Wu Po-Ting , Kuo Li-Chieh , Lin Cheng-Feng
Published: December 2022

Falls represent an important adverse effect associated with knee osteoarthritis and result in a significant financial burden on the healthcare system. Therefore, identification of fall predictors is essential to minimize fall incidence. However, few studies have investigated falls and fall predictors, particularly focused on the fear of falls and proprioception. In this study, we investigated significant fall predictors in patients with knee osteoarthritis in Malang, Indonesia. Our findings may serve as useful guidelines to develop geriatric fall prevention programs. This cross-sectional survey using purposive sampling was performed between April and July 2021 and included 372 participants. We recorded the following data: sociodemographic and medical history questionnaire responses, visual analog scale scores, Hopkins falls grading scale scores, Fall Efficacy Scale-International scores, proprioception test findings, knee injury and osteoarthritis outcome score (KOOS), range of motion (ROM), chair stand test and the timed up and go test performance. Data were analyzed using the chi-square and t tests, and multivariate logistic regression to determine significant fall predictors. Multivariate logistic regression analysis showed a lower risk of falls in patients with better proprioception and ROM than in the other groups (odds ratio 0.55 vs 0.96). The risk of falls was higher in patients with higher KOOS symptoms, fear of falls, diagnosis of low back pain and diabetes mellitus, and increased body mass index than in the other groups (odds ratio 1.41, 2.65, 1.27, 3.45, and 1.10, respectively. Our study shows that knee proprioception and ROM serve as protective factors against falls, whereas KOOS symptoms, fear of falls, low back pain, diabetes mellitus, and body mass index were associated with a high risk of falls, with diabetes mellitus and fear of falls being the most significant risk factors. These findings may be useful to policy makers to develop a fall prevention program that can be implemented in community health care centers across Indonesia to deliver individualized, person-centered care and improve fall prevention strategies through a systematic process comprising evaluation, intervention, and monitoring to minimize fall risk.
Mass spectrometry-based identification of new serum biomarkers in patients with latent infection pulmonary tuberculosis
Authors: Li Yan-Xia , Zheng Kang-Di , Duan Yu , Liu Hua-Juan , Tang Yu-Qun , Wu Jun , Lin Dong-Zi , Zhang Zhao
Published: December 2022

Noninvasive and simple indicators for diagnosing latent tuberculosis (TB) infection (LTBI) and tracking progression from latent infection to active TB infection are still desperately needed. The aim of this study was to screen and identify possible biomarkers for diagnosing LTBI and monitoring the progression from latent infection to active TB infection, as well as to investigate the underlying processes and functions. To assess changes in metabolite composition associated with active tuberculosis infection in humans, whole blood supernatants were collected from patients with LTBI, drug-susceptible TB patients, drug-resistant TB patients, and healthy controls. The metabolites in all serum samples were extracted by oscillatory, deproteinization, and then detected by liquid chromatography-tandem mass spectrometry/MS analysis. Normalization by Pareto-scaling method, the difference analysis was carried out by Metaboanalyst 4.0 software, and 1-way analysis of variance analysis among groups showed that P-value < 0.05 was regarded as a different metabolite. To clarify the dynamic changes and functions of differential metabolites with disease progression, and explore its significance and mechanism as a marker by further cluster analysis, functional enrichment analysis, and relative content change analysis of differential metabolites. 65 metabolites were substantially different in four groups. Differential metabolites such as Inosine and Prostaglandin E1 may be important blood indicators for diagnosing mycobacterium tuberculosis latent infection, which were all tightly connected to amino acid metabolism, Biosynthesis of various secondary metabolites, Nucleotide metabolism, Endocrine system, Immune system, Lipid metabolism, and Nervous system. This study screened and identified Inosine, 16, 16-dimethyl-6-keto Prostaglandin E1, Theophylline, and Cotinine as potential serum biomarkers for diagnosing latent TB infection, and Cotinine as potential biomarkers for monitoring disease progression from healthy population to LTBI and then to active TB including drug-resistant TB infection and sensitive TB infection. Furthermore, this research provides a preliminary experimental basis to further investigate the development of metabolomics-based diagnosis of LTBI and monitoring the progress from latent infection to active TB infection.
Low-dose human chorionic gonadotropin supplementation initiated at the onset of ovarian stimulation can improve oocyte quality without impairing endometrial receptivity: Case series
Authors: Lin Huizhen , Huang Xiaona , Zhao Yue , Wang Yangyang , Wang Shasha , Hong Fang , Pan Mei , Liu Liu
Published: December 2022

Rationale:

Whether continuous low-dose human chorionic gonadotropin (hCG) supplementation during controlled ovarian hyperstimulation (COH) can improve oocyte and embryo quality is still controversial in clinical practice.

Patient concerns:

We report the first case series of inadvertent COH in luteal-phase stimulation in the presence of endogenous or exogenous low-dose hCG.

Diagnoses:

Patients were diagnosed with infertility.

Outcomes:

The first two cases had inadvertent COH during preexisting pregnancy, and one of which produced more high-quality embryos (5 vs 1) in the presence of low hCG. Both cases had a live birth. The third case had 7 repeated failures of IVF, during which a total of 55 oocytes were obtained, but only 3 developed into transferable embryo. However, supplementation of 330 IU hCG per day from the onset of COH resulted in the recovery of one high-quality embryo and subsequent delivery of a healthy baby following fresh embryo transfer in eighth attemption.

Lessons:

In conclude, supplementation with low-dose hCG from the onset of ovarian stimulation can improve oocyte quality without impairing endometrial receptivity.
Moxibustion for uterine contraction pain: A protocol for systematic review and meta-analysis
Authors: Zhao Xuewei , Liu Baiyan , Zhang Qi , Wang He , Tian Yu , Wang Fuchun
Published: December 2022

Background:

Uterine contraction pain is a common postpartum condition that often plagues mothers and can interfere with feeding and normal life for young children. Many investigations have demonstrated that moxibustion has certain advantages in the treatment of uterine contraction pain, but the effectiveness, safety, and advantages of various methods have not been confirmed by high-quality meta-analyses. This study will conduct a systematic review and meta-analysis to evaluate the safety and effectiveness in moxibustion, in order to provide a reference for further clinical treatment for uterine contraction pain.

Methods:

Nine electronic databases, including PubMed, Medline, Embase, Web of Science, Cochrane Central Register of Controlled Trials, China National Knowledge Infrastructure, Chinese Biomedical Literature Database, Chinese Scientific Journal Database, Wan-Fang Database and 1 clinical trial register platforms: ClinicalTrials.gov (www.ClinicalTrials.gov/) will be searched using English and Chinese search strategies. All eligible studies are randomized controlled trials of moxibustion treatment for uterine contraction pain, published on or before December 31, 2021. The screening process will be developed by 2 independent authors, and network meta-analysis will be performed with RevMan (V5.3) software.

Results:

This study will provide a high-quality review that will be used to evaluate the safety and effectiveness of moxibustion for the treatment of uterine contraction pain.

Conclusion:

The results of this study will provide evidence to support whether moxibustion can effectively intervene in uterine contraction pain.
Changes in Health Care Access by Race, Income, and Medicaid Expansion During the COVID-19 Pandemic
Authors: Auty Samantha G. , Aswani Monica S. , Wahbi Rafik N. , Griffith Kevin N.
Published: December 2022

Background:

The intersecting crises of the COVID-19 pandemic, job losses, and concomitant loss of employer-sponsored health insurance may have disproportionately affected health care access within minorized and lower-socioeconomic status communities.

Objective:

To describe changes in access to care during the COVID-19 pandemic, stratified by race/ethnicity, household income, and state Medicaid expansion status.

Research Design:

We used interrupted time series and difference-in-differences regression models, controlling for respondent characteristics and preexisting trends.

Subjects:

Data were extracted for all adults aged 18–64 surveyed in the 2015-2020 Behavioral Risk Factor Surveillance System (N=1,731,699) from all 50 states and the District of Columbia.

Measures:

Our outcomes included indicators for whether respondents had any health insurance coverage or avoided seeking care because of cost within the prior year. The primary exposure was the onset of the COVID-19 pandemic in the United States in March 2020.

Results:

The pandemic was associated with a 1.2 percentage point (pp) decline in uninsurance for Medicaid expansion states (95% CI, −1.8, −0.6); these reductions were concentrated among respondents who were Black, multiracial, or low income. The rates of uninsurance were generally stable in nonexpansion states. The rates of avoided care because of cost fell by 3.5 pp in Medicaid expansion states (95% CI, −3.9, −3.1), and by 3.6 pp (95% CI, 4.3–2.9) in nonexpansion states. These declines were concentrated among respondents who were Hispanic, Other Race, or low income.

Conclusions:

Our findings reinforce the value of Medicaid expansion as one tool to improve access to health insurance and care for marginalized and vulnerable populations.
Gender Differences in Connecting Veterans to Care Through the Veterans Crisis Line
Authors: Krishnamurti Lauren S. , Agha Aneeza , Denneson Lauren M. , Montgomery Ann E. , Chhatre Sumedha , Dichter Melissa E.
Published: December 2022

Background:

Suicide is a major public health crisis within the US military veteran community, with distinct gender differences in suicide risk and behavior. The Veterans Crisis Line (VCL) is a component of the Veterans Health Administration (VHA) suicide prevention program; through VCL, veterans may be referred to a VHA Suicide Prevention Coordinator (SPC) to arrange follow-up care. Research shows that engagement with an SPC is a strong protective factor in reducing veteran suicide risk.

Methods:

We evaluated SPC referral acceptance and assessed correlates of SPC referral decline using VCL administrative data for contacts: (1) made between January 1, 2018, through December 31, 2019; (2) by veterans contacting VCL on their own behalf; (3) with gender identified; and (4) current thoughts of suicide. Then, among a subsample of 200 veterans, evenly distributed by gender, we examined data from call synopsis notes to identify reasons given for veterans declining an SPC referral.

Results:

We found it was generally callers rated as lower risk by responders, and callers with loneliness as a reason for contacting VCL, who more frequently declined the SPC referral. An analysis of reasons given for declining SPC referral found that concerns with/about Veterans Affairs care were a key concern, particularly among women veterans articulating specific negative care experiences. Other reasons for referral decline included managing the veteran’s needs directly on the call or via alternative resources.

Conclusion:

The VCL as an intervention provides an important opportunity to re-engage vulnerable veterans into care, one that may be more challenging for women veterans.
Translation of Evidence-Based Interventions Into Oncology Care Settings
Authors: Cooley Mary E. , Biedrzycki Barbara , Brant Jeannine M. , Hammer Marilyn J. , Lally Robin M. , Tucker Sharon , Ginex Pamela K.
Published: December 2022

Background

Adoption of evidence remains slow, leading to variations in practices and quality of care. Examining evidence-based interventions implemented within oncology settings can guide knowledge translation efforts.

Objective

This integrative review aimed to (1) identify topics implemented for oncology-related evidence-based practice (EBP) change; (2) describe frameworks, guidelines, and implementation strategies used to guide change; and (3) evaluate project quality.

Methods

PubMed and CINAHL were searched to identify published practice change projects. PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines were followed. Fifty articles met the inclusion criteria. Data were extracted; content analysis was conducted. The Quality Improvement Minimum Quality Criteria Set guided quality assessment.

Results

Topics included infection control/prevention (n = 18), pain/palliative care (n = 13), psychosocial assessment (n = 11), and medication adherence (n = 8). Among the projects, Plan, Do, Study, Act (n = 8) and Lean Six Sigma (n = 6) frameworks were used most. Thirty-six projects identified guidelines that directed interventions. Multiple implementation strategies were reported in all articles with planning, education, and restructuring the most common. Reach, sustainability, and ability to be replicated were identified as quality gaps across projects.

Conclusion

The EBP topics that emerged are consistent with the oncology nursing priorities, including facilitating integration of EBP into practice. The studies identified used national guidelines and implementation strategies to move evidence into practice. Heterogeneity in measurement made synthesis of findings difficult across studies, although individual studies showed improvement in patient outcomes.

Implications for Practice

Development of an interprofessional oncology consortium could facilitate a standardized approach to implementation of high-priority topics that target improved patient outcomes, harmonize measures, and accelerate translation of evidence into practice.
Exploring Dyad-Based Communication During Cancer
Authors: Francis Martha E. , Mohindra Pranshu , Mooney-Doyle Kim
Published: December 2022

Background

For patients and intimate partners, the challenge of advanced cancer is often compounded by difficulties in effectively communicating about disease treatment. Relevant evidence-based data are limited, in part because of limitations in understanding the dynamics of dyad-based communication.

Objectives

This pilot study targeted development/feasibility testing of a practical model for assessment of these dynamics in a small group of cancer patients and their intimate partners, with a focus on communication before/after cancer diagnoses, including end-of-life discussions.

Methods

A descriptive phenomenological design was based on the Bodenmann systemic-transactional model of dyadic coping and on semistructured interviews with 7 dyads. Qualitative data analysis used the Colaizzi 7-step method for narrated text interpretation and identification of emergent themes.

Results

Patients (median age, 59 years; median intimate partner age, 52 years) had been given a diagnosis of cancer 0 to 6 months before enrollment and were receiving active therapy during participation. Of 534 significant statements analyzed, 2 emergent themes were identified: (1) vulnerable communication during advanced cancer is influenced by preexisting dynamics and complicated by balancing hope/positivity and uncertainty/fear, and (2) communications about end-of-life issues are emotional and influenced by dyad member perceptions about death. A study with a broader racial/demographic representation is planned.

Conclusion

It is feasible to study dyad communication in the advanced cancer setting, and preliminary data suggest the importance of these dynamics in expression of clinical preferences.

Implications for Practice

Structured interviews with dyads during advanced cancer care can be used to identify specific challenges and inform improved support approaches.
Social Support and Life Satisfaction in Women With Cervical Cancer
Authors: Li Hui , Lyu Mengmeng , Wang Anni , Yin Yizhen , Zhang Jingping , Li Pengcheng
Published: December 2022

Background

Although the number of studies focusing on life satisfaction in women with cervical cancer is increasing, there are limited studies on the pathway between social support and life satisfaction in this population.

Objective

This study explored the pathway between social support and life satisfaction in women with cervical cancer by examining the serial mediating effects of self-care self-efficacy, coping strategies, and depressive symptoms.

Methods

In this cross-sectional study, a total of 292 women with cervical cancer completed a questionnaire for assessing social support, self-efficacy, coping strategies, depressive symptoms, and life satisfaction. Structural equation modeling was used to test the direct and/or indirect effects of the variables on life satisfaction.

Results

Structural equation modeling analysis indicated that self-efficacy, coping strategies, and depressive symptoms mediates the effect of social support on life satisfaction. Direct paths from social support to life satisfaction, social support to self-efficacy, self-efficacy to coping strategies, coping strategies to depressive symptoms, and depressive symptoms to life satisfaction were significant (P< .05). Moreover, indirect paths from social support to life satisfaction, self-efficacy to life satisfaction, and coping strategies to life satisfaction were also significant (P< .05).

Conclusions

Self-care self-efficacy, coping strategies, and depressive symptoms are potential pathways through which social support may affect life satisfaction in women with cervical cancer.

Implication

Healthcare providers, family, and friends should offer more social support to the patients and make efforts to strengthen their self-care self-efficacy, facilitate active coping, and alleviate depressive symptoms to improve women’s life satisfaction.
How Does Health-Related Quality of Life Change Over Time in Cancer Survivors Following an Admission to the Intensive Care Unit?
Authors: Rourke Shalyn , Paterson Catherine
Published: December 2022

Background

Cancer survivors account for 15% to 20% of all intensive care unit (ICU) admissions. In general ICU populations, patients are known to experience reduced health-related quality of life (HRQoL). However, little is known about HRQoL impacts among cancer survivors following a critical illness in ICU.

Objective

The aim of this study was to critically synthesize the evidence to further understand the impact of a critical illness and ICU admission in cancer survivors.

Methods

An integrative review was conducted and reported according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analysis) guidelines. Three electronic databases were searched (MEDLINE, CINAHL, and EMBASE) using keywords and Boolean logic. Quality appraisal, data extraction, and a narrative synthesis were completed for all included studies by 2 reviewers.

Results

Eleven publications met inclusion criteria. Health-related quality-of-life domains most frequently reported in cancer survivors after discharge from ICU included the following: physical function limitations, physical symptoms, and anxiety/depression.

Conclusions

Health-related quality of life decreased immediately after the admission to ICU with a gradual increase in the 3 to 12 months following. Cancer survivors are vulnerable to physical limitations, pain, and social isolation after an admission to ICU.

Implications for Practice

Cancer survivors who have been affected by a critical illness are at risk of reduced HRQoL after an admission to ICU. This integrative review will help clinicians and researchers to develop patient-centered models of care during the recovery of critical illness, which are currently lacking in service delivery.
Community-Based Multidimensional Cancer Rehabilitation in Norway
Authors: Ahmedzai Hilde Hjelmeland , Oldervoll Line M. , Sweetmore Anne-Marte Hess , Hauken May Aasebø
Published: December 2022

Background

Cancer survival is often accompanied by late effects that can be mitigated by tailored rehabilitation. In Norway, this has traditionally been offered as residential programs, whereas community-based cancer rehabilitation programs are lacking.

Objective

This study aimed to assess the feasibility and acceptability of a newly developed community-based multidimensional cancer rehabilitation program in Norway.

Methods

A feasibility study with a mixed methods explanatory sequential design was implemented. The intervention was a 12-week group-based rehabilitation program comprising 5 components: goal setting, physical exercise, psychoeducation, individual follow-up consultations, and peer support. Feasibility was assessed through recruitment, retention, and intervention delivery. Acceptability was assessed through intervention adherence and participant evaluation. Qualitative data were generated from focus group interviews. Statistical analyses were descriptive, and qualitative data were transcribed and analyzed using framework analyses.

Results

Sixty participants started, and 55 completed the 12-week rehabilitation program. The majority were female (80%), and the mean age was 56 years. The largest diagnostic group was breast cancer (42%). Retention was high (92%), as were adherence rates for all intervention components. The exercise component was rated the most beneficial, followed by individual consultations and peer support. Qualitative findings contributed to explaining the high adherence and positive evaluation.

Conclusion

High retention, strong adherence, and positive evaluation imply that the community-based program was feasible and acceptable to cancer survivors.

Implication for Practice

The results will aid intervention refinement and contribute to a future randomized controlled trial to examine its effectiveness. If successful, the rehabilitation program could be implemented in the Norwegian Cancer Pathway “Home.”
The role of HIV/hepatitis B virus/hepatitis C virus RNA+ triple infection in end-stage liver disease and all-cause mortality in Europe
Authors: Mocroft Amanda , Geressu Adam , Beguelin Charles , Llibre Josep M. , Lazarus Jeffrey V. , Tomazic Janez , Smidt Jelena , Parczewski Milosz , Brännström Johanna , Sedlacek Dalibor , Degen Olaf , van der Valk Marc , Paduta Dzmitry , Flamholc Leo , Schmid Patrick , Orkin Chloe , Nielsen Lars N. , Hoffmann Christian , Beniowski Marek , Oprea Cristiana , Begovac Josip , Peters Lars
Published: December 2022

Background:

There are limited data on end-stage liver disease (ESLD) and mortality in people with HIV (PWH) coinfected with both hepatitis B virus (HBV) and hepatitis C virus (HCV).

Methods:

All PWH aged greater than 18 under follow-up in EuroSIDA positive for HBsAg (HBV), and/or HCVRNA+, were followed from baseline (latest of 1 January 2001, EuroSIDA recruitment, known HBV/HCV status) to ESLD, death, last visit, or 31 December 2020. Follow-up while HCVRNA- was excluded. In two separate models, Poisson regression compared three groups updated over time; HIV/HBV, HIV/HCV, and HIV/HBV/HCV.

Results:

Among 5733 included individuals, 4476 (78.1%) had HIV/HCV, 953 (16.6%) had HIV/HBV and 304 (5.3%) had HIV/HBV/HCV. In total, 289 (5%) developed ESLD during 34 178 person-years of follow-up (PYFU), incidence 8.5/1000 PYFU [95% confidence interval (CI) 7.5–9.4] and 707 deaths occurred during 34671 PYFU (incidence 20.4/1000 PYFU; 95% CI 18.9–21.9). After adjustment, compared with those with HIV/HCV, persons with HIV/HBV had significantly lower rates of ESLD [adjusted incidence rate ratio (aIRR) 0.53; 95% CI 0.34–0.81]. Those with HIV/HBV/HCV had marginally significantly higher rates of ESLD (aIRR 1.49; 95% CI 0.98–2.26). Those under follow-up in 2014 or later had significantly lower rates of ESLD compared with 2007–2013 (aIRR 0.65; 95% CI 0.47–0.89). Differences in ESLD between the three groups were most pronounced in those aged at least 40. After adjustment, there were no significant differences in all-cause mortality across the three groups.

Conclusion:

HIV/HBV-coinfected individuals had lower rates of ESLD and HIV/HBV/HCV had higher rates of ESLD compared with those with HIV/HCV, especially in those aged more than 40. ESLD decreased over time across all groups.

ClinicalTrials.gov Identifier:

NCT02699736.
In-utero HIV exposure and cardiometabolic health among children 5–8 years: findings from a prospective birth cohort in South Africa
Authors: Bengtson Angela M. , Pellowski Jennifer , McGarvey Stephen , McGinty Rae , Botha Maresa , Burd Tiffany , Burgner David , Mansell Toby , Zar Heather J.
Published: December 2022

Objective:

To evaluate if in-utero HIV exposure is associated with adverse cardiometabolic health outcomes at 5–8 years of age.

Design:

Prospective cohort study.

Methods:

We enrolled a random sample of HIV-exposed but uninfected (HEU) and HIV-unexposed children from the Drakenstein Child Health study, a longitudinal birth cohort study in Cape Town, South Africa, in a cardiometabolic health pilot study. Outcomes were assessed by trained study staff and included: anthropometry, body composition and size, blood pressure, fasting plasma glucose, HbA1c, lipids, and insulin resistance using HOMA-IR. We used multivariable linear and log-binomial regression to estimate associations between HIV-exposure and cardiometabolic outcomes, adjusted for child age, sex, height, body size, and maternal factors as appropriate.

Results:

We included 260 children (HEU n = 100, HIV-unexposed n = 160). HEU children had older mothers (median age 30 vs. 26 years), with minimal differences in gestational age and size at birth by HIV-exposure status. In multivariable analyses, HEU children had lower weight-for-age (mean difference −0.35, 95% confidence interval −0.66, −0.05), and height-for-age (mean difference −0.29, 95% confidence interval −0.56, −0.03; z-scores). There were no differences in adiposity, impaired glucose metabolism, or lipid levels by HIV-exposure status. Overall, 12% of children had blood pressure more than 90th percentile, with no differences by HIV-exposure status.

Conclusion:

Overall, there were few differences in cardiometabolic outcomes between HEU and HIV-unexposed children in this South African cohort. Although these findings are reassuring, monitoring of cardiometabolic health is important as HEU and HIV-unexposed children enter adolescence and cardiometabolic risk trajectories become established.
COVID-19 vaccine immunogenicity in people with HIV
Authors: Costiniuk Cecilia T. , Singer Joel , Lee Terry , Langlois Marc-André , Arnold Corey , Galipeau Yannick , Needham Judy , Kulic Iva , Jenabian Mohammad-Ali , Burchell Ann N. , Shamji Hasina , Chambers Catharine , Walmsley Sharon , Ostrowski Mario , Kovacs Colin , Tan Darrell H.S. , Harris Marianne , Hull Mark , Brumme Zabrina L. , Lapointe Hope R. , Brockman Mark A. , Margolese Shari , Mandarino Enrico , Samarani Suzanne , Vulesevic Branka , Lebouché Bertrand , Angel Jonathan B. , Routy Jean-Pierre , Cooper Curtis L. , Anis Aslam H.
Published: December 2022

Objectives:

Many vaccines require higher/additional doses or adjuvants to provide adequate protection for people with HIV (PWH). Our objective was to compare COVID-19 vaccine immunogenicity in PWH to HIV-negative individuals.

Design:

In a Canadian multi-center prospective, observational cohort of PWH receiving at least two COVID-19 vaccinations, we measured vaccine-induced immunity at 3 and 6 months post 2nd and 1-month post 3rd doses.

Methods:

The primary outcome was the percentage of PWH mounting vaccine-induced immunity [co-positivity for anti-IgG against SARS-CoV2 Spike(S) and receptor-binding domain proteins] 6 months post 2nd dose. Univariable and multivariable logistic regressions were used to compare COVID-19-specific immune responses between groups and within subgroups.

Results:

Data from 294 PWH and 267 controls were analyzed. Immunogenicity was achieved in over 90% at each time point in both groups. The proportions of participants achieving comparable anti-receptor-binding domain levels were similar between the group at each time point. Anti-S IgG levels were similar by group at month 3 post 2nd dose and 1-month post 3rd dose. A lower proportion of PWH vs. controls maintained vaccine-induced anti-S IgG immunity 6 months post 2nd dose [92% vs. 99%; odds ratio: 0.14 (95% confidence interval: 0.03, 0.80; P = 0.027)]. In multivariable analyses, neither age, immune non-response, multimorbidity, sex, vaccine type, or timing between doses were associated with reduced IgG response.

Conclusion:

Vaccine-induced IgG was elicited in the vast majority of PWH and was overall similar between groups. A slightly lower proportion of PWH vs. controls maintained vaccine-induced anti-S IgG immunity 6 months post 2nd dose demonstrating the importance of timely boosting in this population.
Update on treatments for anxiety-related disorders
Authors: Lee Hyun Jeong , Stein Murray B.
Published: December 2022

Purpose of review

This review examines recent evidence that informs the treatment of anxiety-related disorders.

Recent findings

In addition to selective serotonin reuptake inhibitors (SSRIs), serotonin and norepinephrine reuptake inhibitors (SNRIs), and benzodiazepines, agomelatine has demonstrated efficacy in treating generalized anxiety disorder (GAD). Other novel products, such as ketamine, psilocybin and cannabidiol, are in the process of gathering evidence in support of the treatment of anxiety disorders. In psychological therapy, various psychological treatments for anxiety disorders, such as mindfulness-based intervention, acceptance and commitment therapy, psychodynamic therapy, emotion-focused therapy and dialectical behavioural therapy, have been tried. Still, most therapies have not proven superior to cognitive behavioural therapy (CBT). In very preliminary findings: Repetitive transcranial magnetic stimulation (rTMS) was effective in GAD; transcranial direct current stimulation (tDCS) was effective for social anxiety disorder (SAD) and GAD and augmented exposure therapy for specific fears. Internet and mobile-based interventions have comparable efficacy to face-to-face therapy.

Pharmacotherapy of anxiety disorders is expanding to novel products. Despite trying other psychological therapies for anxiety disorders, most therapies were comparable to but not superior to CBT. rTMS and tDCS were also used and show early promise for GAD, but further studies are needed. Most internet or mobile app based psychological therapies were based on CBT, and some can be considered as alternatives to in-person face-to-face therapy.
Multi-omics analysis identifies drivers of protein phosphorylation
Authors: Zhang Tian , Keele Gregory R. , Gyuricza Isabela Gerdes , Vincent Matthew , Brunton Catherine , Bell Timothy A. , Hock Pablo , Shaw Ginger D. , Munger Steven C. , de Villena Fernando Pardo-Manuel , Ferris Martin T. , Paulo Joao A. , Gygi Steven P. , Churchill Gary A.
Published: December 2022

Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is determined by the abundance of its parent protein and the proportion of target sites that are phosphorylated. We quantified phosphopeptides, proteins, and transcripts in heart, liver, and kidney tissue samples of mice from 58 strains of the Collaborative Cross strain panel. We mapped ∼700 phosphorylation quantitative trait loci (phQTL) across the three tissues and applied genetic mediation analysis to identify causal drivers of phosphorylation. We identified kinases, phosphatases, cytokines, and other factors, including both known and potentially novel interactions between target proteins and genes that regulate site-specific phosphorylation. Our analysis highlights multiple targets of pyruvate dehydrogenase kinase 1 (PDK1), a regulator of mitochondrial function that shows reduced activity in the NZO/HILtJ mouse, a polygenic model of obesity and type 2 diabetes.
Random electrical noise drives non-deterministic computation in cortical neural networks
Authors: Stoll Elizabeth A
Published: December 2022

In cortical neurons, spontaneous membrane potential fluctuations affect the likelihood of firing an action potential. Yet despite retaining sensitivity to random electrical noise in gating signaling outcomes, these cells achieve highly accurate computations with extraordinary energy efficiency. A new approach models the inherently probabilistic nature of cortical neuron firing as a thermodynamic process of non-deterministic computation. Typically, the cortical neuron is modeled as a binary computational unit, in either an off-state or an on-state, but here, the cortical neuron is modeled as a two-state quantum system, with some probability of switching from an off-state to an on-state. This approach explicitly takes into account the contribution of random electrical noise in gating signaling outcomes, particularly during cortical up-states. In this model, the membrane potential is described as the mixed sum of all component microstates, or the quantity of von Neumann entropy encoded by the computational unit. This distribution of macrostates is given by a density matrix, which undergoes a unitary change of basis as each unit, ‘System A’, interacts with its surrounding environment, ‘System B’. Any linear correlations reduce the number of distinguishable pure states, leading to the selection of an optimal system state in the present context. This process of information compression is shown to be equivalent to the extraction of predictive value from a thermodynamic quantity of information. Calculations demonstrate that estimated coulomb scattering profiles and decoherence timescales in cortical neurons are consistent with a quantum system, with random electrical noise driving signaling outcomes.
Modeling electron interference at the neuronal membrane yields a holographic projection of representative information content
Authors: Stoll Elizabeth A
Published: December 2022

It has historically proven difficult to explain the relationship between neural activity and representative information content. A new approach focuses on the unique properties of cortical neurons, which allow both upstream signals and random electrical noise to affect the likelihood of reaching action potential threshold. Here, each electron is modeled as an electromagnetic point source, inter-acting in a probabilistic manner with each neuronal membrane. The electron is described as some set of probability amplitudes, distributed across five orthogonal axes:x, y, z, energy state, andtime. The membrane potential of each neuron is defined by the probabilistic spatial position and atomic orbital of each local electron, after some time evolution. The mixed sum of all probabilistic component pure states is the physical quantity of information held by the neural network, given by a complex-valued wavefunction. If the probabilistic trajectory of each electron over timetaffects the voltage state of multiple computational units, then the system state must be computed as a whole, with the state of each neuron being resolved as every component pure state is resolved. This computational process yields a defined system state at a defined location in time, which immediately becomes the past as a new probability density forms. If the membrane surface of each computational unit is also a charge-detecting polymer substrate that meets the criteria of a holographic recording surface, then this encoding process will generate a holographic projection of representative information content. The constructive and destructive interference of high-dimensional probability amplitudes yields a non-deterministic computational outcome for each neuron. That now-defined system state is paired with a multi-sensory percept, which is exclusively accessed by the encoding structure, with content limited by the range and sensitivity of the sensory apparatus. This model usefully offers a plausible explanation for both perceptual content and non-deterministic computational outcomes emerging from cortical neural network activity.
Assessment of Storm Impact on Coral Reef Structural Complexity
Authors: Yuval Matan , Pearl Naama , Tchernov Dan , Martinez Stephane , Loya Yossi , Bar-Massada Avi , Treibitz Tali
Published: December 2022

Extreme weather events are increasing in frequency and magnitude. Consequently, it is important to understand their effects and remediation. Resilience reflects the ability of an ecosystem to absorb change, which is important for understanding ecological dynamics and trajectories. To describe the impact of a powerful storm on coral reef structural complexity, we used novel computational tools and detailed 3D reconstructions captured at three time points over three years. Our data-setReefs4Dof 21 co-registered image-based models enabled us to calculate the differences at seven sites over time and is released with the paper. We employed six geometrical metrics, two of which are new algorithms for calculating fractal dimension of reefs in full 3D. We conducted a multivariate analysis to reveal which sites were affected the most and their relative recovery. We also explored the changes in fractal dimension per size category using our cube-counting algorithm. Three metrics showed a signicant difference between time points, i.e., decline and subsequent recovery in structural complexity. The multivariate analysis and the results per size category showed a similar trend. Coral reef resilience has been the subject of seminal studies in ecology. We add important information to the discussion by focusing on 3D structure through image-based modeling. The full picture shows resilience in structural complexity, suggesting that the reef has not gone through a catastrophic phase shift. Our novel analysis framework is widely transferable and useful for research, monitoring, and management.

Graphical Abstract

Highlights

The effect of storms on coral reef 3D structure is poorly understood.

We studied the impact of a storm on coral reefs using a novel 3D imaging framework.

We used geometrical metrics including new methods for calculating fractal dimension.

The reefs recovered in two years with regards to structural complexity.

Based on 3D analysis the reefs exhibit structural resilience.
Moderate High Temperature is Beneficial or Detrimental Depending on Carbon Availability in the Green AlgaChlamydomonas reinhardtii
Authors: Zhang Ningning , Venn Benedikt , Bailey Catherine E. , Xia Ming , Mattoon Erin M. , Mühlhaus Timo , Zhang Ru
Published: December 2022

High temperatures impair plant and algal growth and reduce food and biofuel production, but the underlying mechanisms remain elusive. The unicellular green algaChlamydomonas reinhardtiiis a superior model to study heat responses in photosynthetic cells due to its fast growth rate, many similarities in cellular processes to land plants, simple and sequenced genome, and ample genetic and genomics resources. Chlamydomonas grows in light by photosynthesis and/or with the externally supplied organic carbon source, acetate. Most of the published research about Chlamydomonas heat responses used acetate-containing medium. Understanding how organic carbon sources affect heat responses is important for the algal industry but understudied. We cultivated Chlamydomonas wild-type cultures under highly controlled conditions in photobioreactors at control of 25°C, moderate high temperature of 35°C, or acute high temperature of 40°C with and without constant acetate supply for 1- or 4-days. Our results showed that 35°C increased algal growth with constant acetate supply but reduced algal growth without sufficient acetate. The overlooked and dynamic effects of 35°C could be explained by induced carbon metabolism, including acetate uptake and assimilation, glyoxylate cycle, gluconeogenesis pathways, and glycolysis. Acute high temperature at 40°C for more than 2 days was lethal to algal cultures with and without constant acetate supply. Our research provides insights to understand algal heat responses and help improve thermotolerance in photosynthetic cells.

Highlight

We revealed the overlooked, dynamic effects of moderate high temperature in algae depending on carbon availability and demonstrated the importance of carbon metabolism in thermotolerance of photosynthetic cells.
Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data
Authors: Gopalakrishnan Saratram , Joshi Chintan J. , Valderrama Gomez Miguel , Icten Elcin , Rolandi Pablo , Johnson William , Kontoravdi Cleo , Lewis Nathan E.
Published: December 2022

Genome-scale metabolic models comprehensively describe an organism’s metabolism and can be tailored using omics data to model condition-specific physiology. The quality of context-specific models is impacted by (i) choice of algorithm and parameters and (ii) alternate context-specific models that equally explain the -omics data. Here we quantify the influence of alternate optima on microbial and mammalian model extraction using GIMME, iMAT, MBA, and mCADRE. We find that metabolic tasks defining an organism’s phenotype must be explicitly and quantitatively protected. The scope of alternate models is strongly influenced by algorithm choice and the topological properties of the parent genome-scale model with fatty acid metabolism and intracellular metabolite transport contributing much to alternate solutions in all models. mCADRE extracted the most reproducible context-specific models and models generated using MBA had the most alternate solutions. There were fewer qualitatively different solutions generated by GIMME inE. coli, but these increased substantially in the mammalian models. Screening ensembles using a receiver operating characteristic plot identified the best-performing models. A comprehensive evaluation of models extracted using combinations of extraction methods and expression thresholds revealed that GIMME generated the best-performing models inE. coli, whereas mCADRE is better suited for complex mammalian models. These findings suggest guidelines for benchmarking -omics integration algorithms and motivate the development of a systematic workflow to enumerate alternate models and extract biologically relevant context-specific models.
Megan Server: facilitating interactive access to metagenomic data on a server
Authors: Gautam Anupam , Zeng Wenhuan , Huson Daniel H.
Published: December 2022

Motivation

Metagenomic projects of large sequencing datasets (totaling hundreds of gigabytes of data). Thus, computational preprocessing and analysis are usually performed on a server rather than on a personal computer. The results of such analyses are then usually explored interactively. One approach is to use MEGAN, an interactive program that allows analysis and comparison of metagenomic datasets. Previous releases of MEGAN have required that the user first download the computed data from the server, an increasingly time-consuming process. Here we present Megan Server, a stand-alone program that serves MEGAN files to the web, using a RESTful API, facilitating interactive analysis without downloading the complete data. We describe a number of different application scenarios.

Availability

Megan Server is provided as a standalone program tools/megan-server in the Megan6 software suite, available athttps://software-ab.cs.uni-tuebingen.de/download/megan6.
Spatial frequency-based correction of the spherical aberration in living brain imaging
Authors: Gohma Aoi , Adachi Naoya , Horiba Daiki , Yonemaru Yasuo , Nishiwaki Daisuke , Yokoi Eiji , Higuchi Kaori , Ue Yoshihiro , Miyawaki Atsushi , Monai Hiromu
Published: December 2022

We previously developed a fully automated spherical aberration compensation microscope system, Deep-C, to obtain spherical aberration-free images, but the contrast-based algorithm (Peak-C) may limit applications for low signal-to-noise ratio images. Herein we propose a new spatial frequency-based algorithm called Peak-F and compared its performance to Peak-C. Unlike Peak-C, Peak-F is robust to any noise level since it is independent of the dynamic range of the images, and it does not suffer from image saturation. Finally, Peak-F was implemented in a two-photon microscope to observe living aged and young mouse brains. Consequently, the average refractive index of brain tissue was higher in old mice than in young mice. The Peak-F algorithm determines high-resolution microscopic images stably and robustly.