bluuebunny/crossref_metadata_2025 huggingface dataset:
DIY Flap Monitoring: The Glucose Index
Authors: Pérez Colman M.C. , Schauvinhold C.F. , Chavanne J.M. , Errea G.F. , Bou M. , Ernst G.
Published: September 2023

Background:

Flap loss is reduced by monitoring, which detects vascular compromise. Glucose levels vary in suffering flaps; therefore, we aimed to show that monitoring flaps with glucose pinprick test is a cheap, reliable, ubiquitous, and easy method.

Methods:

We reviewed a prospectively kept database. A pinprick test was performed to measure systemic and flap glucose levels. A glucose index (GI; flap glucose/systemic glucose) was calculated. Comparison between the groups (with occlusive event, and without occlusive event) was done.

Results:

In total, 32 flaps in 29 consecutive patients were included. Eleven (34%) were free flaps. Of these, one (9%) was explored twice. Initially, salvage was achieved. However, 36 hours later, a second exploration was needed but was unsuccessful. Of the 21 pedicled flaps (66%), one (5%) needed exploration (suture release), and three (14%) had partial losses that were not clinically relevant. On the ROC curve, we found a cut-off value for a GI of 0.49 or less with a sensitivity of 95% [95% confidence interval (CI): 75.1 to 99.9%] and a specificity of 100% (95% CI: 98.5 to 100%), with a positive predictive value of 100% (95% CI: 81.5 to 100%) and a negative predictive value of 99.6% (95% CI: 97.8 to 100%) for flap suffering.

Conclusions:

The GI, as a complement, assists in defining treatment approach. It is an easy, reliable, accessible method that can be performed by nonmedical personnel. Its main drawback is the inability to monitor buried or hard to reach flaps.
Combination of Fibrosis-4, liver-stiffness measurement, and Fibroscan-AST score to predict liver-related outcomes in nonalcoholic fatty liver disease
Authors: Wong Yu Jun , Urias Esteban , Song Michael W. , Goyal Tanvi , Tay Wei Xuan , Han Nicole Xinrong , Loo Jing Hong , Qiu Tian Yu , Wijarnpreecha Karn , Chan Yiong Huak , Chen Vincent L.
Published: September 2023

Introduction:

Noninvasive tests, such as Fibrosis-4 (FIB-4), liver-stiffness measurement (LSM) by vibration-controlled transient elastography, and Fibroscan-AST (FAST), are frequently used for risk stratification in NAFLD. The comparative performance of FIB-4 and LSM and FAST to predict clinical outcomes of patients with NAFLD remained unclear. We aim to evaluate the performance of FIB-4, LSM, and FAST scores to predict clinical outcomes in patients with NAFLD.

Methods:

We included consecutive adult patients with NAFLD with transient elastography performed between 2015 and 2022 from the United States and Singapore. Patients with NAFLD stratified based on baseline FIB-4, LSM, and FAST score were followed up until clinical outcomes notably liver-related events (LREs), LREs or death, death, and major adverse cardiac events.

Results:

A total of 1262 patients with NAFLD (63% with obesity and 37% with diabetes) with vibration-controlled transient elastography were followed up for median 3.5 years. FIB-4 stratified patients with NAFLD into low-risk (<1.3), intermediate-risk (1.3–2.67), and high-risk (>2.67) in 59.4%, 31.5%, and 9.1%, respectively. No LRE occurred with baseline FIB-4 <1.3, regardless of LSM and FAST score. Higher FIB-4 was associated with a higher risk of LREs within each LSM category. FIB-4 had a higher area under the received operating characteristic curve than LSM or FAST score to predict LRE.

Conclusions:

In this multicenter international study, FIB-4 and LSM synergistically predicted the risk of LRE. In patients with FIB-4 <1.3, vibration-controlled transient elastography may incorrectly classify up to 10% of the patients as high risk. FIB-4 should be incorporated into risk stratification in NAFLD even among patients who underwent VCTE.
Diagnostic performance of the fibrosis-4 index and the NAFLD fibrosis score for screening at-risk individuals in a health check-up setting
Authors: Park Huiyul , Yoon Eileen L. , Kim Mimi , Lee Jonghyun , Kim Hye-Lin , Cho Seon , Nah Eun-Hee , Jun Dae Won
Published: September 2023

Background:

The fibrosis-4 index (FIB-4) and the NAFLD fibrosis score (NFS) have been used as noninvasive screening methods for advanced fibrosis in patients with NAFLD. However, their diagnostic performance has not been evaluated in at-risk individuals regardless of hepatic steatosis. This study evaluated the performance of the FIB-4 and NFS in at-risk groups of health check-up examinees at mass screening centers.

Methods:

This retrospective, cross-sectional study included 8545 participants who underwent voluntary magnetic resonance elastography at a discounted fee during their regular health check-ups at 13 mass screening centers nationwide. The at-risk group was defined as those with any of the following conditions: NAFLD, 2 or more metabolic abnormalities, diabetes mellitus, or abnormal aminotransferase levels. A magnetic resonance elastography cutoff of ≥3.6 kPa was used to define conventional advanced fibrosis.

Results:

According to the proposed criteria, the proportion of at-risk individuals was 67.4%–80.2% in the health check-up cohort without viral or alcohol-associated liver disease. The prevalence of individuals with advanced hepatic fibrosis in each at-risk group was ~2.3%–2.8% according to various criteria. It was higher in patients without NAFLD than in those with NAFLD. A total of 28.2%–39.6% of those in each at-risk group did not show hepatic steatosis on ultrasonography. The performance of FIB-4 for advanced fibrosis in the at-risk group was comparable with that in the NAFLD group. FIB-4 showed a better area under the receiver operating characteristic curve and sensitivity than NFS in the at-risk group.

Conclusions:

FIB-4 demonstrated superior performance compared with the NFS, and its performance in at-risk individuals was similar to that observed for patients with NAFLD.
Exploring the Association Between Indicators of Socioeconomic Instability, Survival Sex, and Methamphetamine Use Among Young Adult Black Gay, Bisexual, and Other Men Who Have Sex With Men: A Cross-Sectional Study
Authors: Curtis Michael G. , Reed Marcus , Newman Antonio , Doraivelu Kamini , Patel Shivani A. , Crawford Natalie D. , Holland David P. , Hussen Sophia A.
Published: September 2023

Methamphetamine (Meth) use is a contributor to poor health outcomes among young Black American gay, bisexual, and other men who have sex with men (YB-GBMSM). Emerging research indicates that socioeconomic instability may be a salient antecedent of meth use as men may be encouraged to engage in health-eroding activities, such as survival sex, to care for themselves, and then cope with instability-related stress via use of substances. We examined the degree to which indicators of socioeconomic instability, including homelessness and food insecurity, would directly, and indirectly, predict increases in meth use, via survival sex engagement. Hypotheses were tested using mediated path analysis with data from 100 YB-GBMSM in Atlanta, Georgia. Preliminary analysis results demonstrated positive associations between engaging in survival sex, food insecurity, homelessness, and living with HIV. Findings demonstrated that homelessness and food insecurity were directly associated with increased survival sex engagement but were not directly associated with meth use. Homelessness and food insecurity were indirectly associated with increased severity of meth use, via increased engagement in survival sex. Socioeconomic instability and survival sex engagement may be important intervention targets for future meth use intervention/prevention programming. Integrating programmatic components that address homelessness and food insecurity may decrease YB-GBMSM's need to rely on survival sex to meet their needs and decrease their likelihood of using meth as a result.
Development of a continuously perfused ex vivo kidney training model for laparoscopic partial nephrectomy: validity and efficiency
Authors: Zhang Huijian , Wang Jun , Liu Chundong , Du Bingran , Xiao Jujiao , Qian Lei , Zhang Qun , Li Jianyi
Published: September 2023

Background:

Suture hemostasis is essential for laparoscopic partial nephrectomy (LPN). This study aimed to develop, validate, and test the efficacy of a continuously-perfused training model (CPTM) in LPN with high-level simulated bleeding.

Materials and Methods:

The CPTM was constructed using fresh porcine kidneys with renal arteries continuously perfused with red-dyed liquid gelatin. Twenty-nine participants with expert, intermediate, or novice laparoscopic experience levels were recruited. The expert and intermediate participants evaluated the CPTM, and the novice participants were randomly assigned to one of two groups to complete training on a CPTM or dry box training model (DBTM). Messick’s framework criteria were utilized to assess the validity and training efficacy of the model. The data were analyzed using the Mann–Whitney U, Kruskal–Wallis, and Friedman tests. A value of P<0.05 was considered statistically significant.

Results:

Positive comments were provided by all experts and intermediates for the Content. The Relationships with other variables demonstrated significant differences among novices, intermediates, and experts in all metrics (P<0.05). The Consequences showed that the CPTM helped novices acquire LPN skills. The training efficacy was significantly better than that of the DBTM (P<0.05). There were no significant differences between the final performances of the novices and initial performances of the experts (P>0.05). Synthesizing all metrics, the LPN skills learned using CPTMs were significantly improved in the 12th round of training.

Conclusion:

The CPTM offered high-level simulation of bleeding with realistic tissue texture for acquiring LPN skills. Training of no fewer than 12 rounds is recommended for a novice’s LPN training on the CPTM.
Endoscopic workup in pancreatic cancer
Authors: Valente Roberto , Coppola Alessandro , Scandavini Chiara Maria , Arnelo Urban
Published: September 2023

Pancreatic cancer is a highly lethal disease with a rising incidence. It is projected to become the second-leading cause of cancer-related mortality by 2030. The staging of pancreatic cancer can be broadly categorized into three groups: resectable cancers, locally advanced or borderline resectable cancers, and metastatic cancers. Endoscopy plays a crucial role in the management of pancreatic cancer for the establishment of the diagnosis, for the palliation of symptoms due to biliary and/or gastric outlet obstructions, and more recently, for the palliative ablation of cancer. The objective of this review is to provide an overview of the endoscopic evaluation and management of patients with pancreatic cancer. It will specifically cover the diagnostic approach utilizing endoscopic ultrasound, palliative interventions such as endoscopic retrograde cholangiopancreatography, and the emerging field of tumor debulking through radiofrequency ablation.
Mapping the landscape of immunonutrition and cancer research: A comprehensive bibliometric analysis on behalf of NutriOnc Research Group
Authors: De Felice Francesca , Cattaneo Carlo Guglielmo , Poto Gianmario Edoardo , Antropoli Carmine , Brillantino Antonio , Carbone Ludovico , Brunetti Oronzo , De Luca Raffaele , Desideri Isacco , Incorvaia Lorena , La Mendola Roberta , Marmorino Federica , Parini Dario , Rodriquenz Maria Grazia , Salvestrini Viola , Sebastiani Federica , Polom Karol , Marano Luigi
Published: September 2023

The ongoing global health challenge of cancer is driving the pursuit of innovative avenues for prevention, treatment, and enhanced outcomes. The convergence of nutrition and immune modulation, known as immunonutrition, is ready to act as a catalyst for transformative change in cancer research and therapy. Our study employs a bibliometric analysis to uncover the evolving trends within immunonutrition and cancer research across the past 25 years. Bibliometric data, including authors, journals, affiliations, and countries, were analyzed using the Bibliometrix R package. Clustering algorithms were applied to keywords to identify thematic areas and their evolution. A total of 489 documents were analyzed, showing an annual growth rate of 8.7%, with a collaboration index of 5.41, highlighting comprehensive multidisciplinary involvement within this landscape. Core authors demonstrated sustained productivity, while occasional authors indicated widespread interest. The Medical University of Warsaw led in institutional contributions. Country-wise, Italy, France, and the USA emerged as forerunners in fostering research productivity. Key journals like “Clinical Nutrition” served as beacons, emphasizing the multidimensional nature of this topic. The analysis highlighted growing research output and several collaborations, indicating the importance of immunoenriched nutrition in cancer treatment. The interplay of core authors and diversified engagement harmoniously accentuates the cross-disciplinary nature of this burgeoning field. International collaboration facilitated knowledge exchange. Prominent documents shaped the field, emphasizing the significance of nutritional interventions. Thematic clusters revealed varied focuses, including pharmaconutrients, surgical approaches, inflammation, and specific cancers. The expanding research output suggests further development, particularly in exploring immunoenriched nutrition’s impact on cancer types and patient populations. The multidisciplinary nature and international collaborations enhance the field’s progress. Gaps in research underscore the need for original studies and personalized approaches. This study guides future research, informing evidence-based nutritional interventions and advancing cancer care practices.
Diagnostic capability of 18F-PSMA PET-MRI and pelvic MRI plus bone scan in treatment-naive prostate cancer: A single-center paired validating confirmatory study
Authors: Qiao Ziyun , Wang Shuaidong , Wang Haiyan , He Biming , Shi Zhenkai , Zhou Hai , Yang Qiwei , Chen Xing , You Zhiwen , Zhao Jun , Wang Haifeng
Published: September 2023

Background:

Radical prostatectomy with pelvic lymph node dissection for the treatment of high-risk localized prostate cancer (PCa) results in long-term benefits in selected patients. But insufficient sensitivity of conventional examinations which are pelvic MRI and bone scan, limits the diagnosis of bone and lymph node metastasis of PCa. This affects the surgical management strategy of a large number of patients. The purpose of this study was to investigate whether 18F-prostate-specific membrane antigen (PSMA) positron emission tomography (PET)-magnetic resonance imaging (MRI) could improve the clinical detection of PCa metastases compared with the conventional pelvic MRI plus bone scan.

Materials and Methods:

From April 2020 to April 2023, we prospectively enrolled 472 patients with histologically proven PCa in our center, and 120 patients underwent 18F-PSMA PET-MRI, multiparametric MRI (mpMRI), and bone scan before laparoscopic radical prostatectomy plus lymph node dissection. The accuracy of imaging results in detecting lymph node and bone metastatic lesions was compared between PSMA PET-MRI and MRI plus bone scan.

Results:

In diagnosing lymph node metastasis, PSMA PET-MRI had an area under the curve (AUC) of 0.844 (95% confidence intervals [CI]: 0.738–0.949, P < 0.001), sensitivity and specificity of 75% and 96%, which performed apparently better than MRI (AUC=0.615 [95% CI: 0.480–0.750, P=0.073]). PSMA PET-MRI showed excellent expression in the diagnosis of bone metastases, with an AUC of 0.910 (95% CI: 0.840–0.981, P <0.001) compared to 0.700 (95% CI: 0.577–0.823, P =0.001) in bone scanning. PSMA PET-MRI also had higher sensitivity than bone scanning (90% vs. 43%), while lower specificity (92% vs. 97%).

Conclusion:

PSMA PET-MRI is superior to conventional imaging at diagnosing metastases in lymph nodes and bones in PCa and can provide a more accurate stagement.
Relationship-building, community-building, and security of the building: staff perspectives on tenant retention in permanent supportive housing
Authors: Evans Joshua , MacDonald Ariel
Published: September 2023

Objectives:

The objective of this article is to explore how housing practitioners navigate the challenge of tenant retention within Permanent Supportive Housing (PSH) programs and the practices they associate with program success.

Methods:

This article draws on semistructured interviews with 10 housing practitioners from 7 organizations operating 8 PSH programs in Edmonton, a city with roughly one million people in Alberta, Canada.

Results:

This article focuses on 3 specific challenges that have implications for the retention of residents: (1) interpersonal conflict, (2) property damage, and (3) guest management. It also focuses on 3 “promising practices” that practitioners have utilized to mitigate these challenges: (1) relationship-building, (2) community-building, and (3) security of the buildings.

Conclusions:

Tenant retention is integral to the realization of positive program outcomes in PSH. There are several factors affecting tenant retention. To address these challenges, the staff interviewed in this research found success in building programmatic elements that fostered positive interpersonal relationships, managed the behavior of guests on the property, and ensured the physical integrity of the buildings.
Examination of Participant Characteristics and Utilization Trends of a Web-Based Public Health Practice Training Curriculum
Authors: Sutphin Sarah , Dwelle Terry , Amos Kathleen , Harmon Jennifer
Published: September 2023

Context:

Public health workforce development has been an ongoing challenge. Understanding the needs, interests, and demographics of public health practice communities is essential for advancing the field of public health workforce development.

Program:

The North Dakota Public Health Training Network (NDPHTN) is addressing the needs of public health practice communities through virtual training curricula. The NDPHTN curriculum is based upon 7 domains of public health practice workforce development training, identified via reports, a job task analysis, and workforce competency and skill needs surveys. The curricula also align with the Council on Education for Public Health competencies, and courses offer registrants the opportunity to earn Certified Public Health Continuing Education credit.

Implementation:

The NDPHTN curriculum launched on August 1, 2019, is offered on the Public Health Foundation's TRAIN platform. The educational trainings are available as 6 “courses,” a group of related sessions on a public health workforce topic, or 72 Continuing Education Unit credits (“CEUs”), stand-alone sessions that are not part of a course. The courses were created to meet specialized certificate requirements, while CEUs present both overlapping materials with courses and unique “Special Topics,” such as education and training related to the COVID-19 pandemic. CEUs on “Special Topics” are regularly revised to provide up-to-date information on evolving topics. This research study period was August 1, 2019, to January 5, 2021.

Evaluation:

Using posttraining evaluations on quality and usefulness of NDPHTN sessions through the TRAIN platform, 96.71% of respondents reported that the sessions would be useful to their work.

Discussion:

The TRAIN platform is an excellent channel to provide public health practice workforce development training to a diverse workforce. This examination of learner characteristics and utilization trends provides indications of topics deemed valuable by members of the public health workforce who engage in continuing education and training opportunities.
Strengthening Public Health Capacity to Address Infectious Diseases: Lessons From 3 Centers of Excellence in Public Health and Homelessness
Authors: Bien Michael B. , Whitton Alaina , Meehan Ashley , Thornhill Lee , Ellis Karin , Leopold Josh , Borne Deborah , Vickery Katherine Diaz , Imbert Elizabeth , Twohey-Jacobs Lorraine , Perez Kenneth A. , Mosites Emily
Published: September 2023

People experiencing homelessness are disproportionately affected by infectious diseases and often face barriers to receiving appropriate medical treatment. Responding to the needs of people experiencing homelessness requires state and local health departments to integrate information sources and coordinate multisector efforts. From 2021 to 2023, the CDC Foundation, in cooperation with the Centers for Disease Control and Prevention, established pilot Centers of Excellence in Public Health and Homelessness in Seattle, Washington; San Francisco, California; and the state of Minnesota. These centers strengthened their capacity to address the needs of people experiencing homelessness by supporting cross-sector partnerships, assessing the interoperability of data systems, prioritizing infectious disease needs, and identifying health disparities. These programs demonstrated that health departments are heterogeneous entities with differing resources and priorities. They also showed the importance of employing dedicated public health staff focused on homelessness, establishing diverse partnerships and the need for support from local leaders to address homelessness.
Effect of Educational Video on Patient Adherence and Completeness of Voiding Diaries: A Randomized Trial
Authors: Mehta Shailja , Carmain Madeline , Dalal Shana , Lundsberg Lisbet , St. Martin Brad , Harmanli Oz
Published: September 2023

Importance

Voiding diaries are clinically useful tools for elucidating the etiology of lower urinary tract symptoms. The utility of voiding diaries is challenged by low return rate and incomplete or inaccurate data entry.

Objective

The objective was to determine the effect of the use of an educational video on patient adherence, completeness of intake and voiding diaries, and patient satisfaction.

Study Design

In this trial, patients who were asked to complete an intake and voiding diary in a urogynecology clinic were randomized to receive standard education or enhanced education with an instructional video on how to complete the diary. Patients returned the diaries at their follow-up visits in the clinic. The primary outcome was the return rate of the diaries. Upon follow-up, patients filled out a survey reporting their satisfaction with instructions received. Diaries were graded by 3 blinded experts.

Results

Eighty-five patients were enrolled, 42 in the standardized instructions arm and 43 in the video arm. A total of 26 patients (30.6%) filled out and returned an intake and voiding diary. Between groups, there was no difference in the rate of return of the diaries (P = 0.59) or in completeness of the returned voiding diaries (P = 0.60). The educational video did not change satisfaction between the groups; patients reported identical satisfaction between groups.

Conclusions

The addition of an instructional video on how to complete an intake and voiding diary did not increase patients’ rate of return, completeness of diaries, or satisfaction with instructions provided to complete the diary.
Patient Outcomes After Robotic Ventral Rectopexy With Sacrocolpopexy
Authors: Ross James H. , Yao Meng , Wallace Shannon L. , Paraiso Marie Fidela R. , Vogler Sarah A. , Propst Katie , Ferrando Cecile A.
Published: September 2023

Importance

As few studies exist examining postoperative functional outcomes in patients undergoing robotic sacrocolpopexy and ventral rectopexy, results from this study can help guide surgeons in counseling patients on their outcomes.

Objective

The aim of the study was to evaluate functional outcomes and overall postoperative satisfaction as measured by the Pelvic Floor Disability Index 20 (PFDI-20), Pelvic Organ Prolapse/Urinary Incontinence Sexual Questionnaire (PISQ-12), and Patient Global Impression of Improvement Scale (PGI-I) in patients who underwent combined robotic ventral rectopexy and sacrocolpopexy for concomitant pelvic organ prolapse (POP) and rectal prolapse or intussusception (RP/I).

Methods

This was a retrospective cohort and survey study of patients with combined POP and RP/I who underwent the previously mentioned surgical repair between January 2018 and July 2021. Each patient was contacted to participate in a survey evaluating postoperative symptoms related bother, sexual function, and overall satisfaction using the PFDI-20, PISQ-12, and PGI-I.

Results

A total of 107 patients met study inclusion criteria with 67 patients completing the surveys. The mean age and body mass index were 63.7 ± 11.5 years and 25.0 ± 5.4, respectively. Of the patients, 19% had a prior RP repair and 23% had a prior POP repair. Rectal prolapse or intussusception recurrence was reported in 10.4% of patients and objective POP recurrence was found in 7.5% of patients. Sixty-seven patients (62%) completed the surveys. The median time to survey follow-up was 18 (8.8–51.8) months. At the time of survey, the mean PFDI-20 score was 95.7 ± 53.7. The mean PISQ-12 score for all patients was 32.8 ± 7.2 and the median PGI-I score was 2.0 (interquartile range, 1.0–3.0).

Conclusions

In this cohort of patients who underwent a combined robotic ventral rectopexy and sacrocolpopexy, patient-reported postoperative symptom bother was low, sexual function was high, and their overall condition was much improved.
Virtual Assessment as a Way to Reduce Help-seeking Barriers in Older Adults With Subjective Cognitive Decline
Authors: Kann Michael R. , Zeiger Peter J. , Rizer Sandra J. , Cosentino Stephanie , Azar Martina
Published: September 2023

Subjective cognitive decline (SCD), a potential early marker for neurodegenerative disease such as Alzheimer’s disease, is common among older adults. Although it is often regarded as a personal health concern, most individuals with SCD do not seek help from a health care professional. Help-seeking (HS) is a complex, individualized process with significant life-course implications, and older adults often face several barriers to HS across personal, socioeconomic, and cultural domains. The pandemic exacerbated these barriers by imposing additional limitations on in-person care. In response, virtual assessment became a popular method to conduct remote care. We provide a narrative review of the challenges and triumphs that came with the transition from in-person, pen-paper cognitive assessments to virtual cognitive assessments. In addition, we address the impact virtual assessment had in tackling barriers that previously limited individuals with SCD from formal HS. We argue that virtual cognitive assessment helps alleviate health access barriers to HS (e.g., cost, transportation, and physician availability) and allows individuals with different coping styles to undergo assessment within more convenient environments. We hope the findings presented in this review inform health care practice, public education, and future research targeted towards the use of virtual assessment to facilitate HS in older adults with SCD.
Non-linear input-output relationships in the subthalamic nucleus of Parkinson’s patients
Authors: Liu Xiaowei , Glowinsky Stefanie , Abadi Hodaya , León Juan F , Wang Wei , Arkadir David , Israel Zvi , Bergman Hagai , Guang Jing
Published: September 2023

Both local field potentials (LFP) and spiking (SPK) activity in the subthalamic nucleus (STN) are related to Parkinson’s disease (PD) symptoms; however, their relationship is poorly understood. We explore it by separating STN signals of 146 PD patients (308 trajectories, >25,000 recording sites) into aperiodic and periodic components and whitening these signals using their corresponding aperiodic parameters. The LFP aperiodic exponents resemble Brown noise (α= 2.20 ± 0.40) and are significantly higher than SPK aperiodic exponents (α= 0.11 ± 0.22, White noise). The periodic oscillations of LFP are overwhelmingly distributed in the high beta frequency domain while those of SPK are in both low and high beta domains. Beta oscillation center frequencies were downshifted in SPK relative to simultaneously recorded LFP. This demonstrates that the STN synaptic input (LFP) undergoes significant modifications when transformed into STN output (SPK) of PD patients, and may explain the critical role of STN in PD physiology and STN-Deep-Brain-Stimulation therapeutic efficacy.
Coral species-specific loss and physiological legacy effects are elicited by extended marine heatwave
Authors: Strand E.L. , Wong K.H. , Farraj A. , Gray S. , McMenamin A. , Putnam H.M.
Published: September 2023

Marine heatwaves are increasing in frequency and intensity, with potentially catastrophic consequences for marine ecosystems such as coral reefs. An extended heatwave and recovery time-series that incorporates multiple stressors and is environmentally realistic can provide enhanced predictive capacity for performance under climate change conditions. We exposed common reef-building corals in Hawai‘i,Montipora capitataandPocillopora acuta, to a 2-month period of high temperature and high pCO2conditions or ambient conditions in a factorial design, followed by 2 months of ambient conditions. High temperature, rather than high pCO2, drove multivariate physiology shifts through time in both species, including decreases in respiration rates and endosymbiont densities.Pocillopora acutaexhibited more significantly negatively altered physiology, and substantially higher bleaching and mortality thanM. capitata. The sensitivity ofP. acutaappears to be driven by higher baseline rates of photosynthesis paired with lower host antioxidant capacity, creating an increased sensitivity to oxidative stress. Thermal tolerance ofM. capitatamay be partly due to harboring a mixture ofCladocopiumandDurusdiniumspp., whereasP. acutawas dominated by other distinctCladocopiumspp. OnlyM. capitatasurvived the experiment, but physiological state in heatwave exposedM. capitataremained significantly diverged at the end of recovery relative to individuals that experienced ambient conditions. In future climate scenarios, particularly marine heatwaves, our results indicate a species-specific loss of corals that is driven by baseline host and symbiont physiological differences as well as Symbiodiniaceae community compositions, with the surviving species experiencing physiological legacies that are likely to influence future stress responses.
GAUSS: A comprehensive R package for accurate estimation of linkage disequilibrium for variants, Gaussian imputation and TWAS analysis of cosmopolitan cohorts
Authors: Lee Donghyung , Bacanu Silviu-Alin
Published: September 2023

Motivation

As the availability of larger and more ethnically diverse reference panels grows, there is an increase in demand for ancestry-informed imputation of genome-wide association studies (GWAS), and other downstream analyses, e.g., fine-mapping. Performing such analyses at the genotype level is computationally challenging and necessitates access to individual-level genotype and phenotype data. Summary-statistics-based tools, not requiring individual-level data, provide an efficient alternative that streamlines computational requirements and promotes open science by simplifying the re-analysis and downstream analysis of existing GWAS summary data. However, existing tools perform only disparate parts of needed analysis, have only command-line interfaces and are difficult to extend/link by applied researchers.

Results

To address these challenges, we present GAUSS — a comprehensive and user-friendly R package designed to facilitate the re-analysis/downstream analysis of GWAS summary statistics. GAUSS offers an integrated toolkit for a range of functionalities, including i) estimating ancestry proportion of study cohorts, ii) calculating ancestry-informed linkage disequilibrium, iii) imputing summary statistics of unobserved variants, iv) conducting transcriptome-wide association studies, and v) correcting for “Winner’s Curse” biases. Notably, GAUSS utilizes an expansive, multi-ethnic reference panel consisting of 32,953 genomes from 29 ethnic groups. This panel enhances the range and accuracy of imputable variants, including the ability to impute summary statistics of rarer variants. As a result, GAUSS elevates the quality and applicability of existing GWAS analyses without requiring access to subject-level genotypic and phenotypic information.

Availability and implementation

The GAUSS R package, complete with its source code, is readily accessible to the public via our GitHub repository athttps://github.com/statsleelab/gauss. To further assist users, we provided illustrative use-case scenarios that are conveniently found athttps://statsleelab.github.io/gauss/.

Contact

leed13@miamioh.edu

Supplementary information

Supplementary data are available atBioinformaticsonline.
The Cost of Living Index as a Primary Driver of Homelessness: A Cross-State Analysis
Authors: Heston Thomas F.
Published: September 2023

Background

Homelessness persists as a critical global issue despite myriad interventions. This study analyzed state-level differences in homelessness rates across the United States to identify influential societal factors to help guide resource prioritization.

Methods

Homelessness rates for 50 states and Washington D.C. were compared using the most recent data from 2020-2023. Twenty-five variables representing potential socioeconomic and health contributors were examined. Given non-normal distributions, nonparametric statistical techniques, including correlation and predictive modeling, identified significant factors.

Results

The cost of living index, mainly influenced by housing, transportation, and grocery costs, showed the strongest positive correlation with homelessness rates (all p <0.001). Unemployment, alcohol binging, taxes, and poverty were also influential factors. Opioid prescription rates demonstrated an unexpected negative correlation. Random forest classification emphasized the cost of living index as the primary contributor, with housing costs presenting the largest influence.

Conclusion

This state-level analysis revealed the cost of living index, predominantly driven by housing expenses, as the foremost factor associated with homelessness rates, greatly outweighing other variables. These findings can help inform resource allocation to mitigate homelessness through targeted interventions.
Evidence for managing herbivores for reef resilience
Authors: Donovan Mary K. , Counsell Chelsie W.W. , Donahue Megan J. , Lecky Joey , Gajdzik Laura , Marcoux Stacia D. , Sparks Russell , Teague Christopher
Published: September 2023

Herbivore management is an important tool for resilience-based approaches to coral reef conservation. Yet, evidence-based science is needed to enact successful management. We synthesized data from multiple monitoring programs in Hawai’i to measure herbivore biomass and benthic condition over a 10-year period preceding any major coral bleaching. We analyzed data from 20,242 transects alongside data on 27 biophysical and human drivers and found herbivore biomass was highly variable throughout Hawai’i, with high values in remote locations and the lowest values near population centers. Both human and biophysical drivers explained variation in herbivore biomass, and among the human drivers both fishing and land-based pollution had negative effects on biomass. We also found evidence that herbivore functional group biomass is strongly linked to benthic condition, and that benthic condition is sensitive to changes in herbivore biomass associated with fishing. We show that when herbivore biomass is below 80% of potential biomass benthic condition is predicted to decline. We also show that a range of management actions, including area-specific fisheries regulations and gear restrictions, can increase parrotfish biomass. Together, these results provide lines of evidence to support managing herbivores as an effective strategy for maintaining or bolstering reef resilience in a changing climate.
Fishing for a reelGene: evaluating gene models with evolution and machine learning
Authors: Schulz Aimee J , Zhai Jingjing , AuBuchon-Elder Taylor , El-Walid Mohamed , Ferebee Taylor H , Gilmore Elizabeth H , Hufford Matthew B , Johnson Lynn C , Kellogg Elizabeth A , La Thuy , Long Evan , Miller Zachary R , Romay M Cinta , Seetharam Arun S. , Stitzer Michelle C , Wrightsman Travis , Buckler Edward S , Monier Brandon , Hsu Sheng-Kai
Published: September 2023

Assembled genomes and their associated annotations have transformed our study of gene function. However, each new assembly generates new gene models. Inconsistencies between annotations likely arise from biological and technical causes, including pseudogene misclassification, transposon activity, and intron retention from sequencing of unspliced transcripts. To evaluate gene model predictions, we developed reelGene, a pipeline of machine learning models focused on (1) transcription boundaries, (2) mRNA integrity, and (3) protein structure. The first two models leverage sequence characteristics and evolutionary conservation across related taxa to learn the grammar of conserved transcription boundaries and mRNA sequences, while the third uses conserved evolutionary grammar of protein sequences to predict whether a gene can produce a protein. Evaluating 1.8 million gene models in maize, reelGene found that 28% were incorrectly annotated or nonfunctional. By leveraging a large cohort of related species and through learning the conserved grammar of proteins, reelGene provides a tool for both evaluating gene model accuracy and genome biology.
Ventrointermediate thalamic stimulation improves motor learning in humans
Authors: Voegtle Angela , Terzic Laila , Farahat Amr , Hartong Nanna , Galazky Imke , Hinrichs Hermann , Nasuto Slawomir J. , de Oliveira Andrade Adriano , Knight Robert T. , Ivry Richard B. , Voges Jürgen , Deliano Matthias , Buentjen Lars , Sweeney-Reed Catherine M.
Published: September 2023

Ventrointermediate thalamic stimulation (VIM-DBS) modulates oscillatory activity in a cortical network including primary motor cortex, premotor cortex, and parietal cortex. Here we show that, beyond the beneficial effects of VIM-DBS on motor execution, this form of invasive stimulation facilitates production of sequential finger movements that follow a fixed sequence but not when the sequence is selected at random. These results highlight the role of thalamo–cortical activity in motor learning.
Virtual electrode or virtual scalpel? A cancellation-based approach to data analysis and source localization
Authors: de Cheveigné Alain
Published: September 2023

The “virtual electrode” is an appealing metaphor as it suggests that we can – with the right tools and skills – use macroscopic recording techniques such as EEG or MEG to place an electrode anywhere in the brain, and record from it as if it were a real, microscopic electrode. Like every good metaphor, it can sometimes lead us astray. This short paper reviews what we can, and cannot, expect of a “virtual electrode”. It is suggested that a more accurate metaphor – if less appealing – is that of a “virtual scalpel” by which activity from a source within the brain can be suppressed within the macroscopic recording. WithJchannels, up toJ− 1 sources can be suppressed while still retaining some information about other sources. In addition, with appropriate source and forward models, it may be possible to accurately localize any source that can be accurately suppressed. This paper sets out the possibilities and limits of what linear analysis applied to multichannel data can, or cannot, achieve.
Auditory selective attention during a working memory task with melodies: a MEG study
Authors: Aurélien de la Chapelle , Salomé Serres-Blain , Alma ElShafei , Denis Schwartz , Sébastien Daligault , Julien Jung , Perrine Ruby , Anne Caclin , Aurélie Bidet-Caulet
Published: September 2023

Working memory and attention are jointly needed in most everyday life tasks and activities. They have however mostly been studied separately. Here we investigate how auditory working memory and selective attention interact using a recently introduced paradigm (MEMAT) that combines a classic working memory paradigm, the delayed-matching-to-sample task, and selective attention, with distractors presented during the encoding phase. All stimuli are four-tone melodies. Twenty-two participants performed the MEMAT task during MEG recordings. We manipulate the difficulty of the memory task and of attentional filtering.When memory task difficulty increases, the amplitude of the CNV in anticipation of the melody to encode increases and the decrease in alpha power during encoding and maintenance in a left fronto-temporal network is reduced.When attentional filtering difficulty increases, the amplitude of the sustained evoked response during encoding increases, whereas the differential processing of relevant and irrelevant sounds in auditory areas is less pronounced, and frontal theta power during encoding and maintenance is higher. In the left auditory cortex, we could directly observe the result of the interaction between auditory memory and attention: the facilitation of relevant sound processing in the easy filtering condition was reduced when the memory task difficulty increased. This pattern mirrors the observed behavioral effects. Overall brain dynamics highlight reciprocal influences of working memory and selective attention processes, in keeping with shared cognitive resources between them.
Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation
Authors: Baron Maayan , Tagore Mohita , Wall Patrick , Zheng Fan , Barkley Dalia , Yanai Itai , Yang Jing , Kiuru Maija , White Richard M. , Ideker Trey
Published: September 2023

Desmosomes are transmembrane protein complexes that contribute to cell-cell adhesion in epithelia and other tissues. Here, we report the discovery of frequent genetic alterations in the desmosome in human cancers, with the strongest signal seen in cutaneous melanoma where desmosomes are mutated in >70% of cases. In primary but not metastatic melanoma biopsies, the burden of coding mutations in desmosome genes associates with a strong reduction in desmosome gene expression. Analysis by spatial transcriptomics and protein immunofluorescence suggests that these expression decreases occur in keratinocytes in the microenvironment rather than in primary melanoma cells. In further support of a microenvironmental origin, we find that desmosome gene knockdown in keratinocytes yields markedly increased proliferation of adjacent melanoma cells in keratinocyte/melanoma co-cultures. Similar increases in melanoma proliferation are observed in media preconditioned by desmosome-deficient keratinocytes. Thus, gradual accumulation of desmosome mutations in neighboring cells may prime melanoma cells for neoplastic transformation.
Postnatal maternal care moderates the effects of prenatal bisphenol exposure on offspring neurodevelopmental, behavioral, and transcriptomic outcomes
Authors: Lauby Samantha C. , Lapp Hannah E. , Salazar Melissa , Semyrenko Sofiia , Chauhan Danyal , Margolis Amy E. , Champagne Frances A.
Published: September 2023

Bisphenols (BPs), including BPA and “BPA-free” structural analogs, are commonly used plasticizers that are present in many plastics and are known endocrine disrupting chemicals. Prenatal exposure to BPA has been associated with negative neurodevelopmental and behavioral outcomes in children and rodent models. Prenatal BPA exposure has also been shown to impair postnatal maternal care provisioning, which can also affect offspring neurodevelopment and behavior. However, there is limited knowledge regarding the biological effects of prenatal exposure to bisphenols other than BPA and the interplay between prenatal BP exposure and postnatal maternal care on adult behavior. The purpose of the current study was to determine the interactive impact of prenatal BP exposure and postnatal maternal care on neurodevelopment and behavior. Our findings suggest that the effects of prenatal BP exposure on eye-opening, adult attentional set shifting and anxiety-like behavior in the open field are dependent on maternal care in the first five days of life. Interestingly, maternal care might also attenuate the effects of prenatal BP exposure on eye opening and adult attentional set shifting. Finally, transcriptomic profiles in male and female medial prefrontal cortex and amygdala suggest that the interactive effects of prenatal BP exposure and postnatal maternal care converge on estrogen receptor signaling and are involved in biological processes related to gene expression and protein translation and synthesis. Overall, these findings indicate that postnatal maternal care plays a critical role in the expression of the effects of prenatal BP exposure on neurodevelopment and adult behavior. Understanding the underlying biological mechanisms involved might allow us to identify potential avenues to mitigate the adverse effects of prenatal BP exposure and improve health and well-being in human populations.
Manifesto of Transparent Mathematical Modeling: From Ecology to General Science
Authors: Kalmykov V. L. , Kalmykov L. V.
Published: September 2023

Mathematical black box models, which hide the structure and behavior of the subsystems, currently dominate science. Errors and paradoxes, such as the biodiversity paradox and the limiting similarity hypothesis, often arise from subjective interpretations of these hidden mechanisms. To address these problems, we have developed transparent mathematical models of the white box type. Here we justify the hypothesis that transparent mathematical models of the white box type can be built by means of logical deterministic cellular automata whose rules are based on the general theory of the corresponding domain. Using white box models, we were able to directly identify the mechanisms of interspecific competition, test the principle of competitive exclusion and the hypothesis of limiting similarity, resolve the paradox of biodiversity, and formulate for the first time the general principle of competitive coexistence. As a basis for reproducing and further developing the method, we present two transparent mathematical models of an ecosystem with one and two competing species. C++ code for our models provided. Cellular automata thinking can be traced back from ancient cellular board games in the histories of all civilizations. The transparent mathematical modeling opens a rational approach to ensuring the safety, reliability, and trustworthiness of automatic decisions. A shift to transparency in the mathematical modeling paradigm has the potential to revolutionize scientific research and to advance knowledge and technology in a wide variety of domains.
Matrix Nanoscale Mechanics Regulates Exosome Production by Mesenchymal Stem Cells
Authors: Chrysanthou Alexandra , Gautrot Julien E.
Published: September 2023

Complex biotherapeutics such exosomes offer attractive opportunities for cell-free treatment of disease and conditions difficult to address with single, defined compounds. However their production remains challenging as adherent cells proposed to secrete therapeutic extra cellular vesicles require scalable platforms. In addition, the role of biomaterials design parameters on processes regulating vesicular secretory phenotypes is unclear. Here we propose the use of bioactive microdroplets, or bioemulsions, as microcarriers for the culture of mesenchymal stem cells and production of exosomes. We demonstrate 100% increase in the output of extracellular vesicles on bioemulsions. The impact of matrix mechanics on this process is then investigated, and in particular interfacial shear mechanical properties of corresponding liquid-liquid interfaces forming microdroplets. We find that such local nanoscale mechanics regulates not only cell adhesion, but also exosome output. We find that exosomes generated by cells cultured on bioemulsion microdroplets retain a high content of protein and RNA cargos. Finally, we demonstrate that the cold-shock protein YBox 1, previously associated with RNA packaging, is modulated by matrix mechanics and regulates exosome production. Together, these results demonstrate the impact of local interfacial mechanics on the adhesion and secretory machinery and provide a proof of concept for the application of bioemulsions for the production of complex biotherapeutics.