bluuebunny/crossref_metadata_2025 huggingface dataset:
Refractive Outcomes With New Generation Formulas for Intraocular Lens Power Calculation in Radial Keratotomy Patients
Authors: Ferrara Silvia , Crincoli Emanuele , Savastano Alfonso , Savastano Maria Cristina , Catania Fiammetta , Rizzo Stanislao
Published: May 2023

Purpose:

Radial keratotomies (RKs) are responsible for corneal irregularities resulting in biometric errors and lower best-corrected visual acuity (BCVA) due to lower-order and higher-order optical aberrations. The aim of the study was to compare performances of new and old generation formulas in a population of RK patients.

Methods:

RK patients who underwent phacoemulsification with intraocular lens (IOL) implantation were retrospectively recruited. Inclusion criteria were availability of preoperative and 6-month postoperative BCVA assessment, topography, and tomography. Documented refraction instability, corneal ectasia, and previous ocular surgery except for RK were exclusion criteria. Mean prediction error (ME), mean absolute prediction error (MAE), and incidence of MAE > 0.25D were calculated for SRK-T, Barrett True K, EVO 2.0, Kane, and PEARL-DGS.

Results:

Twenty-seven patients with a mean baseline BCVA of 0.32 ± 0.18 logMAR and a mean corneal root mean square (RMS) value of 1.59 ± 0.91 μm were included. EVO 2.0, Kane, and PEARL-DGS showed a significantly lower MAE and lower ME compared with all other formulas (P < 0.001 and P < 0.001) and a significant lower incidence of MAE >0.25D (P < 0.001). Significant differences were still detected when using 3-mm mean keratometry for IOL calculation.

Conclusions:

PEARL-DGS, Kane, and EVO 2.0 formulas show superior accuracy in IOL power calculation compared with SRK-T and Barrett True K in RK patients, with no significant differences between the 3.
Substance Use Among Physician Assistant Students: A National Study on the Prevalence of Alcohol, Tobacco, Illicit Substances, and Medication Use
Authors: Carim Charles A. , Keller Nicole E. , Greene Gabriel G. , Pitchford Kandi D. , Solh Tia M. , Miller Paul M.
Published: May 2023

Introduction

The purpose of this study was to discover the substance use prevalence among physician assistant students (PA-S) compared with the age-relevant general US population and to examine the frequency of stress, burnout, anxiety, and depression during the didactic and clinical phases, while accounting for the impact of the COVID-19 pandemic.

Methods

A 20-item survey instrument was created. Self-reported data included demographics, anxiety, burnout, tobacco, illicit substances, and prescription medication use. Outcome-based inventories included a modified Perceived Stress Scale, Patient Health Questionnaire-2 (PHQ-2), and Alcohol Use Disorder Identification Test–Concise. The survey was emailed to all US programs (∼270 programs; ∼25,000 students), with 54 programs approving dissemination to their students (n∼4,760).

Results

Of the 1432 responses (30% response rate, 96% completion rate), the final validated sample was 1378 students (56.1% didactic, 43.8% clinical). When compared with the national population, PA-S prevalence for tobacco (5.2%) and illicit substance use (9.9%) were notably lower; alcohol (53.5%) was comparable; and prescription medication (7.0%) is only reported for PA students due to the lack of a national comparison. A higher frequency of substance use was observed during the didactic (52.5%) vs clinical (47.5%) phases. Stress was the dominant factor in both phases (93.5% didactic, 86.1% clinical). Respondents reported that the COVID-19 pandemic had minimal impact on reported rates, other than alcohol.

Discussion

Although PA-S substance use prevalence is at or below the national population, PA programs are encouraged to review their policies and provide conversations and resources for students who may have one or more risk factors and experience a negative effect from current substance use.
The Role of Mentoring in Recruiting and Retaining Minority Physician Assistant Faculty
Authors: Radcliffe-Henry Erica , Obisesan Olawunmi
Published: May 2023

Introduction

The physician assistant profession (PA) is experiencing a proliferation of PA programs nationally, creating a demand for PA faculty to educate and train future PA clinicians. Current data show that the number of minority PA educators is insufficient to train a diverse PA workforce. Previous studies have explored the high turnover rate of minority PA faculty, their retention, and attrition. Guided by the social-ecological model (SEM), the purpose of this phenomenological study was to explore the lived experiences of Black and Hispanic minority PA faculty in PA education to gain further insights about the specific role that mentoring has played in their recruitment and retention.

Methods

Qualitative data were collected from a purposive sample of 6 minority PA faculty using semi-structured telephone interviews.

Results

This study's findings identified specific SEM constructs—specifically individual, interpersonal, and institutional levels of mentoring—that may influence minority PA faculty recruitment and retention efforts. The participants in this study identified several recruitment and retention factors, including formal and informal mentoring, support, and guidance. Challenges related to lack of pedagogical training and lack of administrative support for meaningful professional development were reportedly overcome by the assistance of colleagues within and outside of their programs.

Discussion

The findings of this study provide insights necessary to inform professional practice initiatives among PA program leaders and institutional leadership to engage in dialogue and coordinate efforts involving the implementation of effective professional development and mentoring structures.
Prevalence of and Risk Factors for Emergency Department Visits After Outpatient Gynecologic Surgery
Authors: Chaves Katherine F. , Novoa Victoria Arruga Novoa y , Apple Annie , Hassoun Jenine , Alamri Lamia A. , Zhao Zhiguo , Yunker Amanda
Published: May 2023

Outpatient gynecologic surgeries are very common; in 2014 alone, 500,000 procedures were performed with 70% and 85% of hysterectomies and oophorectomies, respectively, performed in the outpatient setting. Although risk factors for overnight or prolonged admission after outpatient hysterectomy have been studied, less is known about the postoperative emergency department (ED) burden generated by other outpatient gynecologic surgeries.

The objective of this retrospective cohort study was to identify the incidence of ED visits within 30 days of outpatient gynecologic surgery and to identify risk factors for these visits. This study included all adult patients undergoing scheduled outpatient gynecologic surgery for a benign condition at the Vanderbilt University Medical Center (VUMC), a tertiary academic medical institution, between January 2018 and September 2019. Demographic data, as well as comorbidities, surgical history, and surgical outcomes data, were obtained from the electronic medical record. Primary procedure performed was characterized into 1 of 4 categories: hysterectomy, other intra-abdominal nonprolapse surgery, prolapse surgery without hysterectomy, or other nonprolapse vulvovaginal procedure. The primary study outcome was evaluation in the VUMC ED within 30 days of surgery. Logistic regression models were used to evaluate associations between potential risk factors and the risk of an ED visit.

A total of 2373 surgeries met the inclusion criteria, with 109 patients (5%) visiting the VUMC ED for a total of 125 visits within 30 days of surgery. After adjustment for potential confounders, younger age (adjusted odds ratio [aOR], 1.2; 95% confidence interval [CI], 1.1–1.3; P < 0.001), history of abdominal surgery (aOR, 1.7; 95% CI, 1.1–2.6; P = 0.02), cardiopulmonary comorbidities (aOR, 1.9; 95% CI, 1.2–3.0; P = 0.004), undergoing hysterectomy (aOR, 2.0; 95% CI, 1.1–3.8; P = 0.03), and a vulvovaginal surgical route as opposed to abdominal surgical route (aOR, 2.4; 95% CI, 1.2–5.1; P = 0.02) were all related to an increased risk of visiting the emergency room. Patients who visited the ED were more likely to have undergone hysterectomy (26% vs 20%, P = 0.05) and less likely to have undergone prolapse surgery (4% vs 12%, P = 0.05). The median time to first ED presentation was 7 days following surgery and surgical site pain (n = 52 [42% of visits]), nausea and/or vomiting (n = 18 [14%]), and fever (n = 15 [12%]) were the most common chief complaints. Of the 125 visits, 45 (36%) resulted in admission, and 36 of these (80%) were surgery related.

The results of this study demonstrate that although ED visits after outpatient gynecologic surgery are uncommon, younger patients with underlying cardiopulmonary comorbidities and/or a history of abdominal surgery are at greater risk.
Trends in Long-Term Ventilation Care in U.K. Children and Young People—Further Consideration Required for Pediatric Critical Care Services
Authors: Wilkinson Kathy , Freeth Heather , Mahoney Nicholas , Iles Richard , Juniper Mark
Published: May 2023

OBJECTIVES:

The objective was to compare specific data from the 2020 National Confidential Enquiry into Patient Outcome and Death (NCEPOD) report “Balancing the Pressures” with two previous U.K. studies and to examine changes in the pediatric population requiring long-term ventilation (LTV) as well as the types delivered. We believe that the new data presented will facilitate future service planning.

DESIGN:

A subset of confidential enquiry data derived from a study by a nationally funded quality improvement organization (NCEPOD: www.ncepod.org.uk) was compared with two previous U.K. datasets.

SETTING:

Healthcare providers across England, Wales, and Northern Ireland—inpatient and community settings.

PATIENTS:

Children and young people (CAYP) 0–16 years old receiving LTV between April 1, 2016, and March 31, 2018.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

When comparing the NCEPOD data with that last published in the United Kingdom, the number of CAYP requiring LTV more than doubled between 2008 and 2018 (933–2,093). There has also been a particular increase in the proportion of children that were under two when they were commenced on LTV (26–39.2%). Children are now more likely than previously to be receiving LTV to manage upper airway obstruction and CNS conditions. There has also been an approximate doubling of those receiving LTV over the whole 24-hour period (9.4–18.4%).

CONCLUSIONS:

The increased numbers and changing characteristics of babies and children requiring LTV over the last 3 decades in the United Kingdom have implications for all healthcare sectors but particularly for providers of critical care services.
Whole blood transfusion in the treatment of acute hemorrhage, a systematic review and meta-analysis
Authors: van der Horst Robert A. , Rijnhout Tim W.H. , Noorman Femke , Borger van der Burg Boudewijn L.S. , van Waes Oscar J.F. , Verhofstad Michael H.J. , Hoencamp Rigo
Published: May 2023

BACKGROUND

Whole blood (WB) transfusion received renewed interest after recent armed conflicts. The effectiveness as compared with blood component transfusion (BCT) is, however, still topic of debate. Therefore, this study investigated the effect of WB ± BCT as compared with BCT transfusion on survival in trauma patients with acute hemorrhage.

METHODS

Studies published up to January 16, 2023, including patients with traumatic hemorrhage comparing WB ± BCT and BCT were included in meta-analysis. Subanalyses were performed on the effectiveness of WB in the treatment of civilian or military trauma patients, patients with massive hemorrhage and on platelet (PLT)/red blood cell (RBC), plasma/RBC and WB/RBC ratios. Methodological quality of studies was interpreted using the Cochrane risk of bias tool. The study protocol was registered in PROSPERO under number CRD42022296900.

RESULTS

Random effect pooled odds ratio (OR) for 24 hours mortality in civilian and military patients treated with WB as compared with BCT was 0.72 (95% confidence interval [CI], 0.53–0.97). In subanalysis of studies conducted in civilian setting (n = 20), early (4 hours, 6 hours, and emergency department) and 24 hours mortality was lower in WB groups compared with BCT groups (OR, 0.65; 95% CI, 0.44–0.96 and OR, 0.71; 95% CI, 0.52–0.98). No difference in late mortality (28 days, 30 days, in-hospital) was found. In military settings (n = 7), there was no difference in early, 24 hours, or late mortality between groups. The WB groups received significant higher PLT/RBC (p = 0.030) during early treatment and significant higher PLT/RBC and plasma/RBC ratios during 24 hours of treatment (p = 0.031 and p = 0.007). The overall risk of bias in the majority of studies was judged as serious due to serious risk on confounding and selection bias, and unclear information regarding cointerventions.

CONCLUSION

Civilian trauma patients with acute traumatic hemorrhage treated with WB ± BCT as compared to BCT had lower odds on early and 24-hour mortality. In addition, WB transfusion resulted in higher PLT/RBC and plasma/RBC ratios.

LEVEL OF EVIDENCE

Systematic Review and Meta-Analysis; Level III.
Genomic regions and candidate genes affect root anatomical traits in diverse rice accessions
Authors: Fonta Jenna E. , Vejchasarn Phanchita , Hanlon Meredith T. , McCouch Susan R. , Brown Kathleen M.
Published: April 2023

Root anatomical traits show significant variation among rice,Oryza sativaL., genotypes and are of interest for improving adaptation to a variety of edaphic, hydrological and nutritional environments in which rice is grown. However, they are difficult to measure and the genetic controls of these traits are not well understood in rice. We conducted genome-wide association (GWA) analyses using moderate- and high-density SNP panels on a diverse rice population to identify genomic regions and candidate genes that control root anatomical traits. We identified 28 genomic regions for metaxylem vessel area and number, root cross-sectional area, stele area, and aerenchyma area. One genomic region associated with metaxylem vessel number and two regions associated with three root thickness-related traits, stele area, root cross-sectional area and metaxylem vessel area, were supported by chromosome-specific GWA using a high-density SNP panel and are regarded as highly significant regions controlling trait variation. Candidate genes in these regions were related to cell differentiation, elongation and division, and secondary cell wall formation. For genomic regions identified in theindicasubpopulation, haplotype variation and root anatomical phenotypes were associated with geographic distributions of the accessions, notably the presence of alternate alleles conferring larger diameter roots, stele, and metaxylem vessels in accessions from theindica 2andindica 3subgroups originating largely in south and southeast Asia. The identification of genomic regions and candidate genes related to root anatomical traits in a diverse panel of rice varieties deepens our understanding of trait variation and genetic architecture and facilitates the incorporation of favorable alleles into breeding populations.

Key message

Genomic regions and candidate genes associated with root anatomical traits were identified inOryza sativausing genome-wide association analyses.
RNAvigate: Efficient exploration of RNA chemical probing datasets
Authors: Irving Patrick S. , Weeks Kevin M.
Published: April 2023

Chemical probing technologies enable high-throughput examination of diverse structural features of RNA including local nucleotide flexibility, RNA secondary structure, protein- and ligand-binding, through-space interaction networks, and multi-state structural ensembles. Performing these experiments, by themselves, does not directly lead to biological insight. Instead, deep understanding of RNA structure-function relationships typically requires evaluating a system under structure- and function-altering conditions, linking these data with additional information, and visualizing multi-layered relationships. Current platforms lack the broad accessibility, flexibility, and efficiency needed to iterate on integrative analyses of these diverse, complex data. Here, we share the RNA visualization and graphical analysis toolset RNAvigate, a straightforward and flexible Python library. RNAvigate currently automatically parses twenty-one standard file formats (primary sequence annotations, per- and inter-nucleotide data, and secondary and tertiary structures) and outputs eighteen plot types. These features enable efficient exploration of nuanced relationships between chemical probing data, RNA structure, and motif annotations across multiple experimental samples. Compatibility with Jupyter Notebooks enables non-burdensome, reproducible, transparent and organized sharing of multi-step analyses and data visualization strategies. RNAvigate simplifies examination of multi-layered RNA structure information and accelerates discovery and characterization of RNA-centric functions in biology.
Performance ofqpAdm-based screens for genetic admixture on admixture-graph-shaped histories and stepping-stone landscapes
Authors: Flegontova Olga , Işıldak Ulaş , Yüncü Eren , Williams Matthew P. , Huber Christian D. , Kočí Jan , Vyazov Leonid A. , Changmai Piya , Flegontov Pavel
Published: April 2023

qpAdmis a statistical tool that is often used for testing large sets of alternative admixture models for a target population. Despite its popularity,qpAdmremains untested on two-dimensional stepping-stone landscapes and in situations with low pre-study odds (low ratio of true to false models). We tested high-throughputqpAdmprotocols with typical properties such as number of source combinations per target, model complexity, model feasibility criteria, etc. Those protocols were applied to admixture-graph-shaped and stepping-stone simulated histories sampled randomly or systematically. We demonstrate that false discovery rates of high-throughputqpAdmprotocols exceed 50% for many parameter combinations since: 1) pre-study odds are low and fall rapidly with increasing model complexity; 2) complex migration networks violate the assumptions of the method, hence there is poor correlation betweenqpAdm p-values and model optimality, contributing to low but non-zero false positive rate and low power; 3) although admixture fraction estimates between 0 and 1 are largely restricted to symmetric configurations of sources around a target, a small fraction of asymmetric highly non-optimal models have estimates in the same interval, contributing to the false positive rate. We also re-interpret large sets ofqpAdmmodels from two studies in terms of source-target distance and symmetry and suggest improvements toqpAdmprotocols: 1) temporal stratification of targets and proxy sources in the case of admixture-graph-shaped histories; 2) focused exploration of few models for increasing pre-study odds; dense landscape sampling for increasing power and stringent conditions on estimated admixture fractions for decreasing the false positive rate.

Article Summary

Proliferation in the archaeogenetic literature of protocols for detection of admixed groups based a so-calledqpAdmalgorithm became disconnected from performance testing: the only extensive study ofqpAdmon simulated data showed that it performs well under an unrealistically simple demographic scenario. We found that false discoveries of gene flows byqpAdmon a collection of random admixture-graph-shaped histories and on complex stepping-stone landscapes are very common and provide guidelines for design ofqpAdmprotocols in archaeogenetic studies.
Spatial and temporal changes in microbial communities and greenhouse gas emissions in a denitrifying woodchip bioreactor at low water temperatures
Authors: Hellman Maria , Juhanson Jaanis , Herbert Roger , Hallin Sara
Published: April 2023

Nitrogen (N) pollution is a major threat to ecosystems and a driver of climate change through emissions of the greenhouse gas nitrous oxide (N2O). Mining activities are increasingly recognized for contributing to N pollution due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities in pore water and woodchips and their genetic potential for different N transformation processes, and how this affected the N removal capacity and possible production of undesired N species, like ammonium, nitrite and N2O. About 80 and 65 % of the nitrate was removed from the leachate the first and second operational year, respectively, which agreed with a decrease in dissolved organic carbon in the outlet water. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in the genetic potential for N cycling and ultimately also reactor performance. We conclude that DNRA had minimal impact on the overall N removal efficiency due to the low relative abundance of the key genenrfAinvolved in DNRA and the low production of ammonium. However, nitrite, ammonium, and N2O were formed in the bioreactor and released in the effluent water, although direct emissions of N2O from the surface was low. The N2O production in the reactor might be explained by the ratio between the genetic potential for overall denitrification and N2O reduction in the woodchip and pore water communities, as indicated by the low ratio between the abundance ofnirandnosZgenes. Altogether, the results indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length, and that unwanted reactive N species were produced at different time points and locations in the reactor. Thus, the succession of microbial communities in woodchip denitrifying bioreactors treating mining impacted water develops slowly at low temperature, which impacts the reactor performance.
Bcl-xL is translocated to the nucleus via CtBP2 to epigenetically promote metastasis
Authors: Zhang Tiantian , Li Sha , Tan Yingcai Adrian , Na Joseph HyungJoon , Chen Zhengming , Damle Priyadarshan , Chen Xiang , Choi Soyoung , Mishra Bikash , Wang Dunrui , Grossman Steven R. , Jiang Xuejun , Li Yi , Chen Yao-Tseng , Xiang Jenny Z. , Du Yi-Chieh Nancy
Published: April 2023

Besides its mitochondria-based anti-apoptotic role, Bcl-xL also travels to the nucleus to promote cancer metastasis by upregulating global histone H3 trimethyl Lys4 (H3K4me3) and TGFβ transcription. How Bcl-xL is translocated into the nucleus and how nuclear Bcl-xL regulates H3K4me3 modification are not understood. Here, we report that C-terminal Binding Protein 2 (CtBP2) binds Bcl-xL via its N-terminus and translocates Bcl-xL into the nucleus. Knockdown of CtBP2 by shRNA decreases the nuclear portion of Bcl-xL and reverses Bcl-xL-induced cell migration and metastasis in mouse models. Furthermore, knockout of CtBP2 suppresses Bcl-xL transcription. The binding between Bcl-xL and CtBP2 is required for their interaction with MLL1, a histone H3K4 methyltransferase. Pharmacologic inhibition of MLL1 enzymatic activity reverses Bcl-xL-induced H3K4me3 and TGFβ mRNA upregulation as well as cell invasion. Moreover, cleavage under targets and release using nuclease (CUT&RUN) coupled with next generation sequencing reveals that H3K4me3 modifications are particularly enriched in the promotor region of genes encoding TGFβ and its signaling pathway in the cancer cells overexpressing Bcl-xL. Altogether, the metastatic function of Bcl-xL is mediated by its interaction with CtBP2 and MLL1.
Integrated analysis of spatial multi-omics with SpatialGlue
Authors: Long Yahui , Ang Kok Siong , Liao Sha , Sethi Raman , Heng Yang , Zhong Chengwei , Xu Hang , Husna Nazihah , Jian Min , Ng Lai Guan , Chen Ao , Gascoigne Nicholas RJ , Xu Xun , Chen Jinmiao
Published: April 2023

Integration of multiple data modalities in a spatially informed manner remains an unmet need for exploiting spatial multi-omics data. We introduce SpatialGlue, a graph neural network with dual-attention mechanism, to learn each modality’s significance at cross-omics and intra-omics integration. We demonstrate that SpatialGlue can accurately aggregate cell types into spatial domains at a higher resolution on different tissue types and technology platforms, as well as gain insights into cross-modality spatial correlations.
Gene Expression and Splicing QTL Analysis of Blood Cells in African American Participants from the Jackson Heart Study
Authors: Wen Jia , Sun Quan , Huang Le , Zhou Lingbo , Doyle Margaret F. , Ekunwe Lynette , Olson Nels C. , Reiner Alexander P. , Li Yun , Raffield Laura M.
Published: April 2023

Most gene expression and alternative splicing quantitative trait loci (eQTL/sQTL) studies have been biased toward European ancestry individuals. Here, we performed eQTL and sQTL analysis using TOPMed whole genome sequencing-derived genotype data and RNA sequencing data from stored peripheral blood mononuclear cells in 1,012 African American participants from the Jackson Heart Study (JHS). At a false discovery rate (FDR) of 5%, we identified 4,798,604 significant eQTL-gene pairs, covering 16,538 unique genes; and 5,921,368 sQTL-gene-cluster pairs, covering 9,605 unique genes. About 31% of detected eQTL and sQTL variants with a minor allele frequency (MAF) > 1% in JHS were rare (MAF < 0.1%), and therefore unlikely to be detected, in European ancestry individuals. We also generated 17,630 eQTL credible sets and 24,525 sQTL credible sets for genes (gene-clusters) with lead QTL p < 5e-8. Finally, we created an open database, which is freely available online, allowing fast query and bulk download of our QTL results.
Surfaces: A software to quantify and visualize interactions within and between proteins and ligands
Authors: Teruel Natália , Borges Vinicius Magalhães , Najmanovich Rafael
Published: April 2023

Computational methods for the quantification and visualization of the relative contribution of molecular interactions to the stability of biomolecular structures and complexes are fundamental to understand, modulate and engineer biological processes. Here we present Surfaces, an easy to use, fast and customizable software for quantification and visualization of molecular interactions based on the calculation of surface areas in contact. Surfaces calculations shows equivalent levels of correlations with experimental data as computationally expensive methods based on molecular dynamics. All scripts are available athttps://github.com/nataliateruel/Surfaces

Documentation is available athttps://surfaces-tutorial.readthedocs.io/en/latest/index.html
Eccentric contraction response of stimulated skeletal muscle fascicle at the various strain rates and stimulation timing
Authors: Tran Dat Trong , Tsai Liren
Published: April 2023

Muscle injuries are the most common sports injuries, and it is often observed in eccentric contraction. There are many factors that could influence the severity of muscle injuries, including strain and strain rate. This study evaluated the interaction of these two factors on the biomechanical properties of the muscle-tendon bundle and their role in injuries. A Hopkinson bar system, an MTS machine and an electrical pulse generator were utilized to collect eccentric contraction response data of over 150 frog muscle-tendon samples at strain rates ranging from 0.01 to 300 s-1. The results have shown that the maximum stress has increased and peaked at about 150 s-1. That peak value has then maintained at the following strain rates. While Young’s modulus of stimulated samples reduced as the strain rate changed from 50 to 300 s-1. That trend was in contrast to unstimulated muscle bundles. In addition, strain rate has significantly influenced tendon-muscle bundle fracture. Samples tend to rupture at a minor strain of about 3.5 % with strain rates over 200 s-1. Because of the increasing stiffness of the muscle area at high strain rates, increased strain in the tendon region resulted in frequent injuries in the tendon area. On the other hand, a maximum-stress reduction was detected when the muscle bundles were stimulated at muscle strain greater than 0.2. The results showed that improper timing of stimulation could increase muscle injury.
Evaluation of the Pilot Wastewater Surveillance for SARS-CoV-2 in Norway, June 2022 – March 2023
Authors: Amato Ettore , Hyllestad Susanne , Heradstveit Petter , Langlete Petter , Moen Line Victoria , Rohringer Andreas , Pires João , Baz Lomba Jose Antonio , Bragstad Karoline , Feruglio Siri Laura , Aavitsland Preben , Madslien Elisabeth Henie
Published: May 2023

Background

During the COVID-19 pandemic, wastewater-based surveillance gained great international interest as an additional tool to monitor SARS-CoV-2. In autumn 2021, the Norwegian Institute of Public Health decided to pilot a national wastewater surveillance (WS) system for SARS-CoV-2 and its variants between June 2022 and March 2023. We evaluated the system to assess if it met its objectives and its attribute-based performance.

Methods

We adapted the available guidelines for evaluation of surveillance systems. The evaluation was carried out as a descriptive analysis and consisted of the following three steps: (i) description of the WS system, (ii) identification of users and stakeholders, and (iii) analysis of the system’s attributes and performance including sensitivity, specificity, timeliness, usefulness, representativeness, simplicity, flexibility, stability, and communication. Cross-correlation analysis was performed to assess the system’s ability to provide early warning signal of new wave of infections.

Results

The pilot WS system was a national surveillance system using existing wastewater infrastructures from the largest Norwegian municipalities. We found that the system was sensitive, timely, useful, representative, simple, flexible, acceptable, and stable to follow the general trend of infection. Preliminary results indicate that the system could provide an early signal of changes in variant distribution. However, challenges may arise with: (i) specificity due to temporary fluctuations of RNA levels in wastewater, (ii) representativeness when downscaling, and (iii) flexibility and acceptability when upscaling the system due to limited resources and/or capacity.

Conclusions

Our results showed that the pilot WS system met most of its surveillance objectives. The system was able to provide an early warning signal of 1-2 weeks, and the system was useful to monitor infections at population level and complement routine surveillance when individual testing activity was low. However, temporary fluctuations of WS values need to be carefully interpreted. To improve quality and efficiency, we recommend to standardise and validate methods for assessing trends of new waves of infection and variants, evaluate the WS system using a longer operational period particularly for new variants, and conduct prevalence studies in the population to calibrate the system and improve data interpretation.
Highly Potent Peptide Therapeutics To Prevent Protein Aggregation In Huntington’s Disease
Authors: Khan Anooshay , Yuca Esra , Özçelik Cemile Elif , Begli Ozge , Oguz Oguzhan , Kasırga Serkan , Seker Urartu Ozgur Safak
Published: April 2023

Huntington’s disease (HD) is a progressive, autosomal dominant neurodegenerative disorder resulting from a significant amplification of CAG repeats in exon 1 of the Huntingtin (Htt) gene. More than 36 CAG repeats result in the formation of mutant Htt (mHtt) protein. These amino-terminal mHtt fragments lead to the formation of misfolded proteins, which then form aggregates in relevant brain regions. Available treatments concentrate primarily on alleviating the disease’s symptoms. Therefore, therapies that can delay the progression of the disease are imperative to halt the course of the disease. Peptide-based drug therapies provide such a platform. Inhibitory peptides were screened against monomeric units of both wild type (Htt(Q25)) and mHtt fragments, including Htt(Q46)and Htt(Q103). It was accomplished by utilizing several display technologies. This study focuses on the in-vitro characterization of the screened peptides. Fibril kinetics was studied in real-time utilizing the Thioflavin T (ThT) assay. The impact of specific peptides on fibril formation was examined by observing the change in fluorescence signal. Atomic force microscopy was also used to study the influence of peptides on fibril formation. Three of the six chosen peptides (HHGANSLSLVSQD, HGLHSMHNKLTR, and WMFPSLKLLDYH) effectively inhibited aggregation. These experiments demonstrate that the chosen peptides suppress the formation of fibrils in mHtt proteins and can provide a therapeutic lead for further optimization and development.
Generation of parthenocarpic tomato plants in multiple elite cultivars using the CRISPR/Cas9 system
Authors: Nguyen Cam Chau , Vu Tien Van , Shelake Rahul Mahadev , Nguyen Nhan Thi , Khanh Tran Dang , Kim Jae-Yean
Published: April 2023

Tomato (Solanum lycopersicumL.) is one of the most important crops in the world for its fruit production. Advances in cutting-edge techniques have enabled the development of numerous critical traits related to the quality and quantity of tomatoes. Genetic engineering techniques, such as gene transformation and gene editing, have emerged as powerful tools for generating new plant varieties with superior traits. In this study, we induced parthenocarpic traits in a population of elite tomato (ET) lines. At first, the adaptability of ET lines to genetic transformation was evaluated to identify the best-performing lines by transforming theSlANT1gene overexpression cassette and then later used to produce theSlIAA9knockout lines using the CRISPR/Cas9 system. ET5 and ET8 emerged as excellent materials for these techniques and showed higher efficiency. Typical phenotypes of knockoutsliaa9were clearly visible in G0 and G1 plants, in which simple leaves and parthenocarpic fruits were observed. The high efficiency of the CRISPR/Cas9 system in developing new tomato varieties with desired traits in a short period was demonstrated by generating T-DNA-free homozygoussliaa9knockout plants in the G1 generation. Additionally, a simple artificial fertilization method was successfully applied to recover seed production from parthenocarpic plants, securing the use of these varieties as breeding materials.
Aging-associated Decline in Vascular Smooth Muscle Cell Mechanosensation is Mediated by Piezo1 Channel
Authors: Luu Ngoc , Bajpai Apratim , Li Rui , Park Seojin , Noor Mahad , Ma Xiao , Chen Weiqiang
Published: April 2023

Aging of the vasculature is associated with detrimental changes in vascular smooth muscle cell (VSMC) mechanosensitivity to extrinsic forces in their surrounding microenvironment. However, how chronological aging alters VSMCs’ ability to sense and adapt to mechanical perturbations remains unexplored. Here, we show defective VSMC mechanosensation in aging measured with ultrasound tweezers-based micromechanical system, force instantaneous frequency spectrum and transcriptome analyses. The mechanobiological study reveals that aged VSMCs adapt a relatively inert solid-like state with altered actin cytoskeletal integrity, resulting in an impairment in their mechanosensitivity and dynamic mechanoresponse to mechanical perturbations. The aging-associated decline in mechanosensation behaviors is mediated by hyperactivity of Piezo1-dependent calcium signaling. Inhibition of Piezo1 alleviates vascular aging and partially restores the loss in dynamic contractile properties in aged cells. Altogether, our study reveals the novel signaling pathway underlying aging-associated aberrant mechanosensation in VSMC and identifies Piezo1 as a potential therapeutic mechanobiological target to alleviate vascular aging.
Rapid appearance of negative emotion during oral fentanyl self-administration in male and female rats
Authors: Coffey Kevin R. , Nickelson William , Dawkins Aliyah J. , Neumaier John F.
Published: April 2023

Opioid use disorder has become an epidemic in the United States, fueled by the widespread availability of fentanyl, which produces rapid and intense euphoria followed by severe withdrawal and emotional distress. We developed a new preclinical model of fentanyl seeking in outbred male and female rats using volitional oral self-administration that can be readily applied in labs without intravascular access. Using a traditional two lever operant procedure, rats learned to take oral fentanyl vigorously, escalated intake across sessions, and readily reinstated responding to conditioned cues after extinction. Oral self-administration also revealed individual and sex differences that are essential to studying substance use risk propensity. During a behavioral economics task, rats displayed inelastic demand curves and maintained stable intake across a wide range of fentanyl concentrations. Oral SA was also neatly patterned, with distinct “ loading” and “ maintenance” phases of responding within each session. Using our software DeepSqueak, we analyzed thousands of ultrasonic vocalizations (USVs), which are innate expressions of current emotional state in rats. Rats produced 50 kHz USVs during loading then shifted quickly to 22 kHz calls despite ongoing maintenance oral fentanyl taking, reflecting a transition to negative reinforcement. Using fiber photometry, we found that the lateral habenula differentially processed drug-cues and drug-consumption depending on affective state, with potentiated modulation by drug cues and consumption during the negative affective maintenance phase. Together, these results indicate a rapid progression from positive to negative reinforcement occurs even within an active drug taking session, revealing a within-session opponent process.

Significance Statement

The United States opioid epidemic is defined by rampant and treatment resistant fentanyl use. Better understanding of neural substrates underlying this phenomenon is essential to slowing the opioid crisis. Intravenous and vapor self-administration (SA) are the standard models for studying fentanyl use in rodents, however they many carry pragmatic downsides. Here, we used a novel oral fentanyl self-administration model that provides key translational and technical benefits and can be readily applied in other labs to study the neurobiology of fentanyl SA. This method captured individual and sex differences necessary for studying substance use risk propensity and uncovered a rapid shift in affective state in rats, suggesting and shift from positive to negative reinforcement within each fentanyl taking session.
Homeostatic Regulation of Seizure Susceptibility and Cognitive Function by Derlin-1 through Maintenance of Adult Neurogenesis
Authors: Murao Naoya , Matsuda Taito , Kadowaki Hisae , Matsushita Yosuke , Tanimoto Kousuke , Katagiri Toyomasa , Nakashima Kinichi , Nishitoh Hideki
Published: April 2023

Dysfunction of organelle is closely associated with neurological diseases involving disruption of adult neurogenesis. However, the role of the endoplasmic reticulum (ER)-related molecules in this process remains largely unexplored. Here we show that Derlin-1, an ER quality controller, maintains adult neurogenesis in a spatiotemporal manner. Deletion of Derlin-1 in the mouse central nervous system induces ectopic localization of newborn neurons and impairs neural stem cells (NSCs) transition from active to quiescent states, resulting in early depletion of hippocampal NSCs. As a result, Derlin-1- deficient mice exhibit phenotypes of increased seizure susceptibility and impaired cognitive function. Reduced expression of signal transducer and activator of transcription 5b (Stat5b) was found to be responsible for the impairment of adult neurogenesis in Derlin-1-deficient NSCs. Remarkably, the inhibition of histone deacetylase activity ameliorated seizure susceptibility and cognitive dysfunction in Derlin-1-deficient mice by increasing Stat5b expression and restoring abnormal neurogenesis. Overall, our findings demonstrate that Derlin-1, as its characteristic function, plays an essential role in the homeostasis of adult neurogenesis via Stat5b expression, thus regulating seizure susceptibility and cognitive function.
Sex Differences in Sleep Phenotypes in the BACHD Mouse Model of Huntington’s Disease
Authors: Chiem Emily , Zhao Kevin , Stark Gemma , Ghiani Cristina A. , Colwell Christopher S. , Paul Ketema N.
Published: April 2023

Sleep and circadian rhythm disturbances are common features of Huntington’s disease (HD). HD is an autosomal dominant neurodegenerative disorder that affects men and women in equal numbers, but some epidemiological studies as well as preclinical work indicate there may be sex differences in disease progression. Since sex differences in HD could provide important insights to understand cellular and molecular mechanism(s), we used the bacterial artificial chromosome transgenic mouse model of HD (BACHD) to examine whether sex differences in sleep/wake cycles are detectable in an animal model of the disease. Electroencephalography/electromyography (EEG/EMG) was used to measure sleep/wake states and polysomnographic patterns in young adult (12 week-old) male and female wild-type and BACHD mice. Our findings show that male, but not female, BACHD mice exhibited increased variation in phases of the rhythms as compared to age and sex matched wild-types. For both Rapid-eye movement (REM) and Non-rapid eye movement (NREM) sleep, genotypic and sex differences were detected. In particular, the BACHD males spent less time in NREM and exhibited a more fragmented sleep than the other groups. Both male and female BACHD mice exhibited significant changes in delta but not in gamma power compared to wild-type mice. Finally, in response to a 6-hrs sleep deprivation, both genotypes and sexes displayed predicted homeostatic responses to sleep loss. These findings suggest that females are relatively protected early in disease progression in this HD model.

Significance Statement

Sleep and circadian rhythm disturbances are common features of Huntington’s disease (HD). Using an animal model of HD and EEG measures of sleep, we found that the males were more vulnerable to sleep/wake architecture alterations and sleep fragmentation. Homeostatic recovery from sleep loss did not appear to be altered at this stage of the disease. These findings raise the possibility that sex-specific factors play a role in the HD symptom progression and that hormone-based treatments may have therapeutic utility.
Chimeric Antigen Receptor Macrophages Target and Resorb Amyloid Plaques in a Mouse Model of Alzheimer’s Disease
Authors: Pan Qiuyun , Yan Ping , Kim Alexander B. , Xiao Qingli , Pandey Gaurav , Haecker Hans , Epelman Slava , Diwan Abhinav , Lee Jin-Moo , DeSelm Carl J.
Published: April 2023

Substantial evidence suggests a role for immunotherapy in treating Alzheimer’s disease (AD). Several monoclonal antibodies targeting aggregated forms of beta amyloid (Aβ), have been shown to reduce amyloid plaques and in some cases, mitigate cognitive decline in early-stage AD patients. We sought to determine if genetically engineered macrophages could improve the targeting and degradation of amyloid plaques. Chimeric antigen receptor macrophages (CAR-Ms), which show promise as a cancer treatment, are an appealing strategy to enhance target recognition and phagocytosis of amyloid plaques in AD. We genetically engineered macrophages to express a CAR containing the anti-amyloid antibody aducanumab as the external domain and the Fc receptor signaling domain internally. CAR-Ms recognize and degrade Aβin vitroand on APP/PS1 brain slicesex vivo;however, when injected intrahippocampally, these first-generation CAR-Ms have limited persistence and fail to reduce plaque load. We overcame this limitation by creating CAR-Ms that secrete M-CSF and self-maintain without exogenous cytokines. These CAR-Ms have greater survival in the brain niche, and significantly reduce plaque load locallyin vivo. These proof-of-principle studies demonstrate that CAR-Ms, previously only applied to cancer, may be utilized to target and degrade unwanted materials, such as amyloid plaques in the brains of AD mice.

Amyloid targeting CAR Macrophages engineered to secrete M-CSF promote their own local survival and expansion while resorbing amyloid plaques in the brains of Alzheimer’s disease APP/PS1 mice, resulting in significant local clearance of amyloid plaques of all sizes.
On the involvement of cell volume regulation mechanisms in post-hypertonic lysis and slow-freezing injury of human erythrocytes and its broader cryobiological significance
Authors: Klbik Ivan
Published: April 2023

An effort is made to explain the salt loading of hypertonicity-treated human red blood cells (RBC) and their post-hypertonic lysis, which occurs upon resuspension to isotonic media. It is recognized that the salt loading is consistent with the regulatory volume increase response - a physiological response applied by cells to adapt to hypertonic conditions. It is therefore hypothesized that salt loading occurs via physiological ion transport pathways, allowing passive dissipative fluxes across the plasma membrane with the preservation of membrane integrity. It is argued that post-hypertonic lysis is essentially a hypotonic lysis occurring already in an isotonic medium due to the excess salt in the cytoplasm. A simplified physiological model accounting for transmembrane ion fluxes was applied to simulate the RBC physiological state to address the problem quantitatively. Instead of assuming the plasma membrane to be impermeable to ions, the dynamic nature of cell physiological state and capacity of cells to perform acute cell volume regulation by increasing passive cation plasma membrane permeability is recognized. It is shown that the RBC plasma membrane contains ion pathways capable of supporting a several-order increase in catio permeability, facilitating overall salt loading. The obtained picture, consistent with general physiology, predicts the experimentally observed RBC behavior. Although treated in theory, evidence supporting the proposed theory is provided, and the high explanatory power of the proposed idea is demonstrated. While focused on human RBCs, this study offers a general mechanism for the osmotic injury of cells exposed to hypertonic solutions - conditions relevant to cell cryopreservation - since many cells possess cell volume regulation mechanisms. Implications of the proposed hypothesis explaining the cryoprotective mechanism of common cryoprotectants are discussed, and additives targeting ion transport pathways are suggested as novel cryoprotectants.
Disruption of aPlasmodium falciparumpatatin-like phospholipase delays male gametocyte exflagellation
Authors: Pietsch Emma , Niedermüller Korbinian , Gilberger Tim-Wolf , Burda Paul-Christian
Published: April 2023

An essential process in transmission of the malaria parasite to theAnophelesvector is the conversion of mature gametocytes into gametes within the mosquito gut, where they egress from the red blood cell (RBC). During egress, male gametocytes undergo exflagellation, leading to the formation of eight haploid motile microgametes, while female gametes retain their spherical shape. Gametocyte egress depends on sequential disruption of the parasitophorous vacuole membrane and the host cell membrane. In other life cycle stages of the malaria parasite, phospholipases have been implicated in membrane disruption processes during egress, however their importance for gametocyte egress is relatively unknown. Here, we performed comprehensive functional analyses of six putative phospholipases for their role during development and egress ofPlasmodium falciparumgametocytes. We localize two of them, the prodrug activation and resistance esterase (PF3D7_0709700) and the lysophospholipase 1 (PF3D7_1476700), to the parasite plasma membrane. Subsequently, we show that disruption of most of the studied phospholipase genes does neither affect gametocyte development nor egress. The exception is the putative patatin-like phospholipase PF3D7_0924000, whose gene deletion leads to a delay in male gametocyte exflagellation, indicating an important, albeit not essential, role of this enzyme in male gametogenesis.