bluuebunny/crossref_metadata_2025 huggingface dataset:
Considerations & challenges of mitral valve repair in females: diagnosis, pathology, and intervention
Authors: Deng Mimi Xiaoming , Barodi Batol , Elbatarny Malak , Yau Terrence M.
Published: December 2023

Purpose of review

Disparities in mitral valve (MV) repair outcomes exist between men and women. This review highlights sex-specific differences in MV disease aetiology, diagnosis, as well as timing and type of intervention.

Recent findings

Females present with more complicated disease: anterior or bileaflet prolapse, leaflet dysplasia/thickening, mitral annular calcification, and mixed mitral lesions. The absence of indexed echocardiographic mitral regurgitation (MR) severity parameters contributes to delayed intervention in women, resulting in more severe symptom burden at time of surgery. The sequelae of chronic MR also necessitate concomitant procedures (e.g. tricuspid repair, arrhythmia surgery) at the time of mitral surgery. Complex MV pathology, greater patient acuity, and more complicated procedures collectively pose challenges to successful MV repair and postoperative recovery. As a consequence, women receive disproportionately more MV replacement than men. In-hospital mortality after MV repair is also greater in women than men. Long-term outcomes of MV repair are comparable after risk-adjustment for preoperative status; however, women experience a greater incidence of postoperative heart failure.

To address the inequity in MV repair outcomes between sexes, indexed diagnostic measurements, diligent surveillance of asymptomatic MR, increased recruitment of women in large clinical trials, and mandatory reporting of sex-based subgroup analyses are recommended.
Entrectinib-induced tubulointerstitial nephritis: a case report
Authors: Stempler Márk , Dobi Deján , Ledó Nóra
Published: December 2023

Introduction and importance:

Entrectinib has been approved and increasingly administered for the treatment of non-small cell lung cancer, especially with intracranial metastasis. Although previous clinical studies have confirmed its safety, disproportionality analysis showed unusually high potential adverse renal effects.

Case presentation:

We present a case of a 71-year-old woman with pulmonary adenocarcinoma who developed severe renal function impairment during the treatment with entrectinib. Urinary sediment examination revealed leukocyte casts, while urinary culture was negative, suggesting the presence of possible tubulointerstitial nephritis (TIN). A kidney biopsy was performed, and the diagnosis of TIN was confirmed. The administration of oral methylprednisolone improved renal function.

Clinical discussion:

Protein kinase inhibitors might lead to renal function impairment in several different ways. It is of utmost importance to differentiate between the underlying pathomechanism, which is often challenging. TIN is a potentially reversible condition when treated appropriately.

Conclusion:

In the case of renal function impairment during entrectinib therapy, the possibility of TIN should be considered, and a kidney biopsy should be performed since corticosteroid therapy might improve renal function.
Radiation oncology for the rhinologist
Authors: Levyn Helena , Yang Fan , Lee Nancy Y.
Published: December 2023

Purpose of review

This comprehensive review explores evolving treatment strategies for sinonasal and nasopharyngeal malignancies. It analyzes the role of adjuvant radiotherapy, the potential of intensity-modulated proton therapy (IMPT), and the relevance of de-escalation strategies nasopharyngeal carcinoma (NPC). Additionally, it discusses hyperfractionation in re-irradiation in NPC.

Recent findings

Adjuvant radiotherapy remains pivotal for sinonasal tumors, improving locoregional control and survival, notably in squamous cell carcinomas, adenocarcinomas, and adenoid cystic carcinomas. IMPT promises enhanced outcomes by sparing healthy tissues, potentially improving patients’ quality of life. For select stage II/T3N0 NPC, radiotherapy alone offers comparable outcomes to concurrent chemoradiotherapy, with fewer adverse events and improved quality of life. Selective neck irradiation in NPC patients with uninvolved necks maintains oncologic outcomes while reducing late toxicity. Hyperfractionation in re-irradiation shows promise in lowering late toxicities and improving overall survival, particularly in undifferentiated sinonasal carcinomas.

This review underscores the significance of adjuvant radiotherapy and the potential of advanced radiation techniques in optimizing sinonasal and nasopharyngeal malignancy outcomes. It emphasizes evolving de-escalation methods and individualized, evidence-based approaches. Future research will further refine strategies for these challenging malignancies.
Machine learning in the evaluation of voice and swallowing in the head and neck cancer patient
Authors: Srinivasan Yashes , Liu Amy , Rameau Anaïs
Published: December 2023

Purpose of review

The purpose of this review is to present recent advances and limitations in machine learning applied to the evaluation of speech, voice, and swallowing in head and neck cancer.

Recent findings

Novel machine learning models incorporating diverse data modalities with improved discriminatory capabilities have been developed for predicting toxicities following head and neck cancer therapy, including dysphagia, dysphonia, xerostomia, and weight loss as well as guiding treatment planning. Machine learning has been applied to the care of posttreatment voice and swallowing dysfunction by offering objective and standardized assessments and aiding innovative technologies for functional restoration. Voice and speech are also being utilized in machine learning algorithms to screen laryngeal cancer.

Machine learning has the potential to help optimize, assess, predict, and rehabilitate voice and swallowing function in head and neck cancer patients as well as aid in cancer screening. However, existing studies are limited by the lack of sufficient external validation and generalizability, insufficient transparency and reproducibility, and no clear superior predictive modeling strategies. Algorithms and applications will need to be trained on large multiinstitutional data sets, incorporate sociodemographic data to reduce bias, and achieve validation through clinical trials for optimal performance and utility.
Host-related indexes in head and neck cancer
Authors: Valero Cristina , León Xavier , Quer Miquel
Published: December 2023

Purpose of review

Peripheral blood host-related indexes have been widely studied in cancer patients. Several authors have shown the prognostic capacity of these indexes in head and neck cancer. Therefore, there has been an increasing interest in this topic recently.

Recent findings

The main variables analyzed and used to create these host-related indexes are peripheral blood leukocytes – including neutrophils, monocytes and lymphocytes – albumin and hemoglobin levels. Other factors with proven prognostic capacity in some studies are: platelets, C-reactive protein, and BMI. Among all the combined indexes, the neutrophil-to-lymphocyte ratio has been the most accepted and used worldwide. Nonetheless, there are other indexes which group multiple of these factors that have shown better prognostic capacity, and are promising in the near future.

Host-related indexes are ideal biomarkers to be used on our daily-basis. There is enough evidence to start considering them when assessing patients with head and neck cancer.
The differences between palliative care and hospice care
Authors: Moseley Kelly , Hammond Lori
Published: December 2023

It's essential for the nurse to be knowledgeable in palliative and hospice care in order to answer questions from the patient or family.
Seven strategies for optimizing end-of-life skin and wound care
Authors: Krasner Diane L.
Published: December 2023

These seven strategies may help the interdisciplinary healthcare team optimize the care of patients at the end of life with skin and wound concerns.
Health System and University Leader Learning Collaboratives
Authors: Kapu April
Published: December 2023

This month's column proposes advanced practice nurse (APN), health system, and university leader roundtable discussions to understand and address global healthcare challenges and the evolving role of the APN. Forming international learning collaboratives focused on gaining a comprehensive understanding of the use of APNs and related education, regulatory frameworks, and models for practice can lead to greater utilization and impact to global healthcare. The “PEPPA” framework is discussed as 1 tool to enhance discussion in these collaboratives.
Leveraging the Hawai'i Nurse Residency Collaborative to Optimize Statewide Workforce Goals
Authors: Reichhardt Laura , Kuwabara Brianne , Loos Joanne R.
Published: December 2023

This article describes the planning and implementation of the Hawai'i Nurse Residency Program (HNRP). The HNRP provides a shared, adaptable nurse residency program model. Through the HNRP, Hawai'i achieved high new-graduate retention and addressed other state initiatives. Since 2012, more than 1666 new-graduate nurses have participated, leading to an average 1st-year retention rate of 96.77%. Statewide nurse residency collaboratives are adaptable, may cost less than other alternatives, and may save on lost funds due to nurse attrition, resulting in an enhanced nursing workforce.
Increasing Medicare Annual Wellness Visit Utilization
Authors: McMurry Christie , Cline Brian P. , Miller Katherine , Padilla Blanca Iris
Published: December 2023

Annual wellness visits (AWVs) are an important component of primary care as they provide preventive services and an opportunity to identify safety and health risk factors for Medicare beneficiaries. However, primary care practices are facing unprecedented demands with high patient volumes, multimorbidity, a rapidly growing aging population, and primary care provider (PCP) shortages. RN-led models of care are increasingly recognized as a major key to providing quality care while relieving PCP demands. This article describes the implementation of an RN-led model of care pilot in an urban family practice to increase Medicare AWV completion and alleviate PCP burden.
Estimated Costs of Drug-Related Problems Prevented by Pharmacist Prescription Reviews Among Hospitalized Internal Medicine Patients
Authors: Zheng Xiaoying , Shan Xuefeng , Liu Weichu , Gao Diansa , Jiang Huiming , Xue Lifen , Hu Lei , Qiu Feng
Published: December 2023

Background and Objectives:

Data are lacking on the estimated costs of pharmacist prescription reviews (PPRs) for hospitalized internal medicine patients. This study investigates the estimated costs of drug-related problems (DRPs) prevented by PPRs among hospitalized internal medicine patients.

Methods:

We reviewed all medication orders for patients at an academic teaching hospital in China for 2 years. DRPs were categorized using the Pharmaceutical Care Network Europe classification. The severity of the potential harm of DRPs was assessed by the Harm Associated with Medication Error Classification (HAMEC) tool. The estimated cost of PPRs was calculated.

Results:

A total of 162426 medication orders for 4314 patients were reviewed, and 1338 DRPs were identified by pharmacists who spent 2230 hours performing PPRs. Among the 1080 DRPs that were prospectively intervened upon, 703 were resolved. The HAMEC tool showed that 47.1% of DRPs were assessed as level 2, 30.4% as level 3, 20.6% as level 1, and 0.6% carried a life-threatening risk. Pharmacist interventions contributed to the prevention of DRP errors and a reduction of $339 139.44. This resulted in a mean cost saving of $482.42 per patient at an input cost of $21 495.06 over the 2 years. The benefit-cost ratio was 15.8.

Conclusion:

PPRs are beneficial for detecting potential DRPs and creating potential cost savings among hospitalized internal medicine patients.
Use of an Escape Room to Enhance Nutrition Care Process Skills and Self-efficacy
Authors: Wright Lauri , Asare Irene , Harris Michel , Colin Casey
Published: December 2023

Application of the Nutrition Care Process (NCP) is a fundamental concept for students preparing to become registered dietitian nutritionists (RDNs). Adequate practice, within pedagogical methods designed to mimic actual dietetics practice scenarios as realistically as possible, is necessary to increase student NCP skill proficiency and confidence. This study assessed the impact of a virtual escape room experience compared with a traditional case study on both NCP skills and confidence in a senior didactic program in dietetics for undergraduate students. Results indicate that the escape room experience improved both NCP documentation (P < .001) and student self-efficacy (P < .001).
Food Insecurity in College Students
Authors: Cuy Castellanos Diana , Holcomb Jeanne
Published: December 2023

Using a mixed-methods approach, the purpose of this study was to identify contributing factors and their relationship to food insecurity at a midsize, private university. During semistructured interviews (N = 23), students discussed social and environmental factors related to food insecurity, as well as the individual factors of food-related time, stress, and skill. A short questionnaire measuring the individual factors was developed and implemented with the US Department of Agriculture food security survey (N = 270). Between the food secure and insecure groups, there were significant differences in relation to food-related time, stress, and skill (P < .01). Identifying specific factors can inform campus-specific interventions to address food insecurity.
A Nationwide Survey of Clinical Dietitians' Perceptions of Precepting
Authors: Hernandez Jennifer L. , Lopez Nanette V. , Clifford Dawn E. , Ross Vicki D.
Published: December 2023

Clinical preceptor shortages are a limiting factor for programs in dietetics. Perceptions on precepting were obtained from 378 registered dietitian nutritionists. The top benefits of precepting included improved teaching skills, staying current/stimulated in the profession, and increased awareness of practice area. Frequently reported barriers included inadequate compensation, time, and reward. People who had not precepted in the past year indicated higher perceived benefits of precepting. Those who indicated they would discontinue precepting reported significantly fewer benefits and more barriers than those who would continue. Finding and addressing barriers among a program's preceptor pool may be key to promoting preceptorship.
Food Addiction and Consumption of Ultraprocessed Foods Among Undergraduate Nutrition and Dietetics Students
Authors: Ünal Gökçe , Uçar Aslı
Published: December 2023

The aim of this study was to determine food addiction and consumption of ultraprocessed foods among undergraduate nutrition and dietetics students according to academic year. A total of 238 students participated in this cross-sectional study. The ultraprocessed food consumption frequency was assessed and the Yale Food Addiction Scale was applied. The overall prevalence of food addiction was 10.5%. The mean symptom count for food addiction was lower in the fourth year than in the first and second years (P = .002). The frequency of processed meat (r = −0.441, P < .001) and donut consumption (r = −0.309, P < .001) showed a moderate negative linear relationship with the increase in academic years.
Higher Intakes of Soft Drinks Are Associated With Anxiety, Depression, and Bone Mineral Density Among University Students
Authors: Ikram Mashta , Shahbaz Hafiz Muhammad , Ahmed Waqas , Khan Zahra , Tahir Sajid Khan , Akram Kashif
Published: December 2023

This cross-sectional study was used to investigate the association of carbonated soft drink (CSD) intake with symptoms of anxiety, depression, and bone health in university students in Pakistan. Daily intake of CSDs was significantly correlated with an increased risk of anxiety, depression, and low bone mineral density (BMD) (P-trend = .000) compared with consumption of less than 1 CSD per week. About one-third of participants reported a moderate anxiety level, 26.4% reported a moderate depression level, and 7.8% reported a severe depression level. Furthermore, 67.2% of participants classified with osteopenia and 8.6% classified with osteoporosis. University students having high consumption of CSDs had significantly higher levels of anxiety, depression, and low BMD.
Asian elephants distinguish sexual status and identity of unfamiliar elephants using urinary odours
Authors: LaDue Chase A. , Snyder Rebecca J.
Published: December 2023

Despite the ubiquity of odours in mammals, few studies have documented the natural olfactory abilities of many ‘non-model’ species such as the Asian elephant. As Asian elephants are endangered, we may apply odours to more effectively manage threatened populations. We implemented a habituation–discrimination paradigm for the first time in Asian elephants to test the ability of elephants to discriminate between unfamiliar male elephant urine, hypothesizing that elephants would successfully distinguish non-musth from musth urine and also distinguish identity between two closely related individuals. We conducted two bioassay series, exposing three female and three male zoo-housed elephants to the same urine sample (non-musth urine in the first series, and urine from an unfamiliar individual in the second) over 5 days. On the sixth day, we simultaneously presented each elephant with a novel sample (either musth urine or urine from a second unfamiliar individual) alongside the habituated urine sample, comparing rates of chemosensory response to each sample to indicate discrimination. All elephants successfully discriminated non-musth from musth urine, and also urine from two unfamiliar half-brothers. Our results further demonstrate the remarkable olfactory abilities of elephants with promising implications for conservation and management.
Spatiotemporal evolution of SARS-CoV-2 in the Bangkok metropolitan region, Thailand, 2020–2022: implications for future outbreak preparedness
Authors: Aiewsakun Pakorn , Jamsai Bharkbhoom , Phumiphanjarphak Worakorn , Sawaengdee Waritta , Palittapongarnpim Prasit , Mahasirimongkol Surakameth
Published: December 2023

Thailand experienced five waves of coronavirus disease 2019 (COVID-19) between 2020 and 2022, with the Bangkok Metropolitan Region (BMR) being at the centre of all outbreaks. The molecular evolution of the causative agent of the disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has previously been characterized in Thailand, but a detailed spatiotemporal analysis is still lacking. In this study, we comprehensively reviewed the development and timelines of the five COVID-19 outbreaks in Thailand and the public health responses, and also conducted a phylogenetic analysis of 27 913 SARS-CoV-2 genomes from Thailand, together with 7330 global references, to investigate the virus’s spatiotemporal evolution during 2020 and 2022, with a particular focus on the BMR. Limited cross-border transmission was observed during the first four waves in 2020 and 2021, but was common in 2022, aligning well with the timeline of change in the international travel restrictions. Within the country, viruses were mostly restricted to the BMR during the first two waves in 2020, but subsequent waves in 2021 and 2022 saw extensive nationwide transmission of the virus, consistent with the timeline of relaxation of disease control measures employed within the country. Our results also suggest frequent epidemiological connections between Thailand and neighbouring countries during 2020 and 2021 despite relatively stringent international travel controls. The overall sequencing rate of the viruses circulating in the BMR was ~0.525 %, meeting the recommended benchmark, and our analysis supports that this is sufficient for tracking of the trend of the virus burden and genetic diversity. Our findings reveal insights into the local transmission dynamics of SARS-CoV-2 in Thailand, and provide a valuable reference for planning responses to future outbreaks.
A joint embedding of protein sequence and structure enables robust variant effect predictions
Authors: Blaabjerg Lasse M. , Jonsson Nicolas , Boomsma Wouter , Stein Amelie , Lindorff-Larsen Kresten
Published: December 2023

The ability to predict how amino acid changes may affect protein function has a wide range of applications including in disease variant classification and protein engineering. Many existing methods focus on learning from patterns found in either protein sequences or protein structures. Here, we present a method for integrating information from protein sequences and structures in a single model that we term SSEmb (Sequence Structure Embedding). SSEmb combines a graph representation for the protein structure with a transformer model for processing multiple sequence alignments, and we show that by integrating both types of information we obtain a variant effect prediction model that is more robust to cases where sequence information is scarce. Furthermore, we find that SSEmb learns embeddings of the sequence and structural properties that are useful for other downstream tasks. We exemplify this by training a downstream model to predict protein-protein binding sites at high accuracy using only the SSEmb embeddings as input. We envisage that SSEmb may be useful both for zero-shot predictions of variant effects and as a representation for predicting protein properties that depend on protein sequence and structure.
VoltRon: A Spatial Omics Analysis Platform for Multi-Resolution and Multi-omics Integration using Image Registration
Authors: Manukyan Artür , Bahry Ella , Wyler Emanuel , Becher Erik , Pascual-Reguant Anna , Plumbom Izabela , Dikmen Hasan Onur , Elezkurtaj Sefer , Conrad Thomas , Altmüller Janine , Hauser Anja E. , Hocke Andreas , Radbruch Helena , Schmidt Deborah , Landthaler Markus , Akalin Altuna
Published: December 2023

The growing number of spatial omic technologies have created a demand for computational tools capable of managing, storing, and analyzing spatial datasets with multiple modalities and spatial resolutions. Meanwhile, computer vision is becoming an integral part of processing spatial data readouts where image registration and spatial data alignment of tissue sections are essential prior to data integration. Hence, there is a need for computational platforms that analyze data across spatial datasets with diverse resolutions as well as those that manipulate and process images of microanatomical tissue structures. To this end, we have developed VoltRon, a novel R package for spatial omics analysis with a unique data structure that accommodates data readouts with many levels of spatial resolutions (i.e., multi-resolution) including regions of interest (ROIs), spots, single cells, and even subcellular entities such as molecules. To connect and integrate these spatially diverse omic profiles, VoltRon accounts for spatial organization of tissue blocks (samples), layers (sections) and assays given a multi-resolution collection of spatial data readouts. An easy-to-use computer vision toolbox, OpenCV, is fully embedded in VoltRon that allows users to both automatically and manually register spatial coordinates across adjacent layers for data transfer without the need for external software tools. VoltRon is implemented in the R programming language and is freely available athttps://github.com/BIMSBbioinfo/VoltRon.
Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies
Authors: Henderson Rory , Anasti Kara , Manne Kartik , Stalls Victoria , Saunders Carrie , Bililign Yishak , Williams Ashliegh , Bubphamala Pimthada , Montani Maya , Kachhap Sangita , Li Jingjing , Jaing Chuancang , Newman Amanda , Cain Derek , Lu Xiaozhi , Venkatayogi Sravani , Berry Madison , Wagh Kshitij , Korber Bette , Saunders Kevin O. , Tian Ming , Alt Fred , Wiehe Kevin , Acharya Priyamvada , Alam S. Munir , Haynes Barton F.
Published: December 2023

Vaccine development targeting rapidly evolving pathogens such as HIV-1 requires induction of broadly neutralizing antibodies (bnAbs) with conserved paratopes and mutations, and, in some cases, the same Ig-heavy chains. The current trial-and-error search for immunogen modifications that improve selection for specific bnAb mutations is imprecise. To precisely engineer bnAb boosting immunogens, we used molecular dynamics simulations to examine encounter states that form when antibodies collide with the HIV-1 Envelope (Env). By mapping how bnAbs use encounter states to find their bound states, we identified Env mutations that were predicted to select for specific antibody mutations in two HIV-1 bnAb B cell lineages. The Env mutations encoded antibody affinity gains and selected for desired antibody mutationsin vivo. These results demonstrate proof-of-concept that Env immunogens can be designed to directly select for specific antibody mutations at residue-level precision by vaccination, thus demonstrating the feasibility of sequential bnAb-inducing HIV-1 vaccine design.
Characterizing the viscoelastic properties of different fibroblasts in 2D and 3D collagen gels
Authors: Pérez-Domínguez Sandra , Sanz-Fraile Héctor , Vidal Laura Martínez , Alfano Massimo , Otero Jorge , Radmacher Manfred
Published: December 2023

We assessed cell mechanical properties in both 2D and 3D environments employing compliant type I collagen matrices. Firstly, collagen gels of varying stiffness were prepared using a photocrosslinker to increase gel stiffness. Using methacrylic anhydride and UV light, a 10-fold increase in apparent Young’s modulus with respect to the soft collagen gel was achieved (0.2 kPa to 2 kPa). In addition, cells were plated onto the different collagen gels and hard Petri dishes (as a super stiff substrate) and their mechanical properties were evaluated. An increase in apparent Young’s modulus was observed in Dupuytren fibroblasts behavior when increasing substrate stiffness, supporting its myofibroblast phenotype (3.8 kPa to 5.2 kPa from soft collagen gels to hard Petri dishes). Secondly, gel’s mechanics, in which fibroblasts were embedded, were evaluated over time to assess cells contraction properties. Gel’s apparent Young’s modulus increased over time regardless of fibroblasts type and cells presented dendritic protrusions. Rheological properties of both cells and gels were extracted using AFM sweep frequency scheme and power law structural damping model for data analysis. As a summary, we have found that fibroblasts contractile properties, related to myofibroblast differentiation and development are highly influenced on the mechanical properties of the surrounding environment, being stiffer environments those that favor the increase in fibroblast mechanical tension.
Functional implication of the homotrimeric multidomain vacuolar sorting receptor 1 (VSR1) fromArabidopsis thaliana
Authors: Park HaJeung , Youn BuHyun , Park Daniel J. , Puthanveettil Sathyanarayanan V. , Kang ChulHee
Published: December 2023

The vacuolar sorting receptors (VSRs) are specific to plants and are responsible for sorting and transporting particular proteins from thetrans-Golgi network to the vacuole. This process is critically important for various cellular functions, including storing nutrients during seed development. Despite many years of intense studies on VSRs, a complete relation between function and structure has not yet been revealed. For the first time, the crystal structure of the full-length luminal part of glycosylated VSR1 fromArabidopsis thaliana(AtVSR1) has been determined. The structure provides insights into the tertiary and quaternary structures of VSR1, which are composed of an N-terminal protease-associated (PA) domain, a unique central region, and one epidermal growth factor (EGF) domain followed by two disordered EGF domains. The structure of VSR1 exhibits unique characteristics, the significance of which is yet to be fully understood.
Downscaling global reference points to assess the sustainability of local fisheries
Authors: Zamborain-Mason Jessica , Connolly Sean R. , MacNeil M. Aaron , Barnes Michele L. , Bauman Andrew G. , Feary David A. , Huertas Victor , Januchowski-Hartley Fraser A. , Lau Jacqueline D. , Mihalitsis Michalis , Cinner Joshua E.
Published: December 2023

Multispecies coral reef fisheries are typically managed by local communities who often lack research and monitoring capacity, which prevents estimation of well-defined sustainable reference points to perform locally relevant fishery assessments. Recent global advances in modelling coral reef fisheries have developed pathways to use environmental indicators to estimate multispecies sustainable reference points. These global reference points are a promising tool for assessing data-poor reef fisheries but need to be downscaled to be relevant to resource practitioners. Here, using a small-scale multispecies reef fishery from Papua New Guinea, we estimate sustainable reference points and assess the sustainability of the fishery by integrating global-scale analyses with local-scale environmental conditions, fish catch, reef area, standing biomass estimates, and fishers’ perceptions. We found that assessment results from global models applied to the local context of our study location provided results consistent with local fishers’ perceptions. Specifically, our downscaled results suggest that the fishing community is overfishing their reef fish stocks (i.e., catching more than can be sustained) and stocks are below BMMSY(i.e., below biomass levels that maximize production), making the overall reef fishery unsustainable. These results were consistent with fisher perceptions that reef fish stocks were declining in abundance and mean fish length, and that they had to spend more time finding fish. Our downscaled site-level assessment reveals severe local resource exploitation, whose dynamics are masked in national-scale assessments, emphasizing the importance of matching assessments to the scale of management. More broadly, our study shows how global reference points can be applied locally when long-term data are not available, providing baseline assessments for sustainably managing previously un-assessed multispecies reef fisheries around the globe.
Predicting the First Steps of Evolution in Randomly Assembled Communities
Authors: McEnany John D , Good Benjamin H
Published: December 2023

Microbial communities can self-assemble into highly diverse states with predictable statistical properties. However, these initial states can be disrupted by rapid evolution of the resident strains. When a new mutation arises, it competes for resources with its parent strain and with the other species in the community. This interplay between ecology and evolution is difficult to capture with existing community assembly theory. Here, we introduce a mathematical framework for predicting the first steps of evolution in large randomly assembled communities that compete for substitutable resources. We show how the fitness effects of new mutations and the probability that they coexist with their parent depends on the size of the community, the saturation of its niches, and the metabolic overlap between its members. We find that successful mutations are often able to coexist with their parent strains, even in saturated communities with low niche availability. At the same time, these invading mutants often cause extinctions of metabolically distant species. Our results suggest that even small amounts of evolution can produce distinct genetic signatures in natural microbial communities.
In vitro antimicrobial mechanism of diacerein and potential to reverse MRSE resistance to β-lactams
Authors: Fu Chunyan , Xu Yi , Mao Liping , Zheng Chengzhi , Shen Yangyang , Ling Xinyi , Zhou Yumei , Yin Yiling , Lou Yongliang , Zheng Meiqin
Published: December 2023

Staphylococcus epidermidisis the most common pathogens causing ocular infection. With the increase of drug resistance rate, it poses a new challenge to anti-infection treatment. In this study, we analyzed the drug resistance ofS. epidermidisisolated from the eye in the past 5 years to guide empirical antibiotics treatment. Then, the MIC and MBC of diacerein against MRSE were detected, and continuous induced resistance experiments confirmed that MRSE not easily induce resistance to diacerein. In addition, it was observed that diacerein induced MRSE cell lysis, increased membrane permeability and resulted in intracellular ROS accumulation. Diacerein does not have toxic effects to HCEC at effective bacteriostatic concentrations. The results of checkerboard assay indicated that the combination of diacerein and β-lactams had additive effect on MRSE. We also observed that diacerein may reverse MRSE resistance to β-lactam drugs by affecting the active efflux system. In conclusion, our results provide strong evidence for the high therapeutic potential of diacerein against MRSE.
An RXLR effector targets ER-Golgi interface to induce ER stress and necrotic cell death
Authors: Kim Jihyun , Kaleku Jesse , Woo Jongchan , Jin Hongshi , Kang Hui Jeong , Kang Minji , Kim Haeun , Jung Seungmee , Segonzac Cecile , Park Eunsook , Choi Doil
Published: December 2023

To achieve successful colonization, the pathogen secretes hundreds of effectors into host cells to manipulate the host’s immune response. Despite numerous studies, the molecular mechanisms underlying effector-induced necrotic cell death remain elusive. In this study, we identified a novel virulent RXLR effector named Pc12 fromP. capsici.Pc12 induces necrosis by triggering a distinct ER stress response through its interaction with Rab13-2. Unlike conventional hypersensitive response cell death associated with effector-triggered immunity, Pc12-induced cell death does not coincide with defense gene expression. Instead, it induces the aggregation of ER-resident proteins and confines secretory proteins within the ER. Pc12 interacts with Rab13-2, exhibiting a specific affinity for the active form of Rab13-2. Thus, the complex of Pc12 and Rab13-2 mimics the conformation of the inactive state of Rab13-2, subsequently recruiting the Rab-escort protein (REP). This process results in disruptions in vesicle formation within the ER-Golgi trafficking pathway. Furthermore, the substitution of a single amino acid of Rab13-2 structurally predicted to be crucial for the Pc12 interaction decreased the interaction with Pc12 while maintaining the interaction with REP1. These findings offer valuable insights into the ER stress-mediated cell death as well as a potential strategy for enhancing resistance against pathogens.
The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA
Authors: Hardikar Swanand , Ren Ren , Ying Zhengzhou , Horton John R. , Bramble Matthew D. , Liu Bin , Lu Yue , Liu Bigang , Dan Jiameng , Zhang Xing , Cheng Xiaodong , Chen Taiping
Published: December 2023

CDCA7, encoding a protein with a C-terminal cysteine-rich domain (CRD), is mutated in immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, a disease related to hypomethylation of juxtacentromeric satellite DNA. How CDCA7 directs DNA methylation to juxtacentromeric regions is unknown. Here, we show that the CDCA7 CRD adopts a unique zinc-binding structure that recognizes a CpG dyad in a non-B DNA formed by two sequence motifs. CDCA7, but not ICF mutants, preferentially binds the non-B DNA with strand-specific CpG hemi-methylation. The unmethylated sequence motif is highly enriched at centromeres of human chromosomes, whereas the methylated motif is distributed throughout the genome. At S phase, CDCA7, but not ICF mutants, is concentrated in constitutive heterochromatin foci, and the formation of such foci can be inhibited by exogenous hemi-methylated non-B DNA bound by the CRD. Binding of the non-B DNA formed in juxtacentromeric regions during DNA replication provides a mechanism by which CDCA7 controls the specificity of DNA methylation.
Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel
Authors: Tross Michael C. , Grzybowski Marcin W. , Jubery Talukder Z. , Grove Ryleigh J. , Nishimwe Aime V. , Torres-Rodriguez J Vladimir , Sun Guangchao , Ganapathysubramanian Baskar , Ge Yufeng , Schnable James C.
Published: December 2023

Hyperspectral reflectance data can be collected from large plant populations in a high-throughput manner in both controlled and field environments. The efficacy of using hyperspectral leaf reflectance as a proxy for traits that typically require significant labor and time to collect has been evaluated in a number of studies. Commonly, estimating plant traits using hyperspectral reflectance involves collecting substantial amounts of ground truth data from plant populations, which may not be feasible for many researchers. In this study, we explore the potential of data-driven approaches to analyze hyperspectral reflectance data with little to no ground truth phenotypic measurements. Evaluations were performed using data on the reflectance of 2,151 individual wavelengths of light from the leaves of maize plants harvested from 1,658 field plots of a replicated trial including representatives of 752 maize genotypes from the Wisconsin Diversity Panel. We reduced the dimensionality of this dataset using an autoencoder neural network and principal component analyses, producing 10 latent variables and principal components, respectively. A subset of these principal components and latent variables demonstrated significant repeatability, indicating that a substantial proportion of the total variance in these variables was explained by genetic factors. Moreover, correlations were observed between variables derived from the autoencoder network and principal components with molecular traits. Notably, the most relevant latent variable (LV8) showed a much stronger correlation with chlorophyll content (R2= 0.59) compared to the most correlated principal component (PC2;R2= 0.31). Furthermore, one latent variable exhibited modestly better performance than a partial least squares regression model in estimating leaf chlorophyll content (PLSR;R2= 0.58, LV8;R2= 0.59). A number of genetic markers in the maize genome were significantly correlated with variation in different latent variables in genome wide association studies. In a number of cases, significant signals in genome wide association studies were adjacent to genes with plausible links to traits expected to influence leaf hyperspectral reflectance patterns.
AVM: a manually curated database of aerosol-transmitted virus mutations, human diseases, and drugs
Authors: Mei Lan , Hou Yaopan , Zhou Jiajun , Chang Yetong , Liu Yuwei , Wang Di , Zhang Yunpeng , Ning Shangwei , Li Xia
Published: December 2023

Aerosol-transmitted viruses, with aerosol particles floating in the air to long distances, have the characteristics of strong infectivity and wide spread that is difficult to control. They cause various human diseases, posing a huge threat to human health. Some mutations can increase the transmissibility and virulence of the strain, which can reduce the protection of vaccines and weaken efficacy of antiviral drugs. Here, we established a manually curated database, AVM, to store this information. The current version of the AVM contains a total of 42,041 virus mutations, including 2613 immune escape mutations, 45 clinical information datasets, and 407 drugs, antibodies, or vaccines. In addition, we recorded 88 human diseases associated with viruses, and we found that the same virus can attack multiple target organs in the body and lead to diversified diseases. Further, the AVM database offers a straightforward user interface to expediently browse, retrieve, and download details. The AVM database is a comprehensive resource that provides timely and valuable assistance regarding the transmission, treatment, and related diseases of aerosol-transmitted viruses (http://bio-bigdata.hrbmu.edu.cn/AVMorhttp://www.bio-bigdata.center/AVM).
Proliferation in malaria parasites: how resource limitation can prevent evolution of greater virulence
Authors: Pak Damie , Kamiya Tsukushi , Greischar Megan A.
Published: December 2023

For parasites, robust proliferation within hosts is crucial for establishing the infection and creating opportunities for onward transmission. While faster proliferation enhances transmission rates, it is often assumed to curtail transmission duration by killing the host (virulence), a tradeoff constraining parasite evolution. Yet in many diseases, including malaria, the preponderance of infections with mild or absent symptoms suggests that host mortality is not a sufficient constraint, raising the question of what restrains evolution towards faster proliferation. In malaria infections, the maximum rate of proliferation is determined by the burst size, the number of daughter parasites produced per infected red blood cell. Larger burst sizes should expand the pool of infected red blood cells that can be used to produce the specialized transmission forms needed to infect mosquitoes. We use a within-host model parameterized for rodent malaria parasites (Plasmodium chabaudi) to project the transmission consequences of burst size, focusing on initial acute infection where re-source limitation and risk of host mortality are greatest. We find that resource limitation restricts evolution towards higher burst sizes below the level predicted by host mortality alone. Our results suggest resource limitation could represent a more general constraint than virulence-transmission tradeoffs, preventing evolution towards faster proliferation.
Sociodemographic correlates of parent and youth-reported eating disorder symptoms in the Adolescent Brain Cognitive Development Study
Authors: Makowski Carolina , Westwater Margaret L. , Rhee Kyung E. , Zou Jingjing , Bischoff-Grethe Amanda , Wierenga Christina E.
Published: December 2023

Purpose

Eating Disorders (EDs) often start in adolescence, though ED-related concerns in diverse youth samples remain understudied. We leveraged data from the Adolescent Brain Cognitive Development□(ABCD) Study to identify the prevalence of parent- and youth-reported ED symptoms and their sociodemographic characteristics.

Methods

Data were drawn from baseline (ages 9-11 years, n=11,868) and 2-year follow-up (ages 11-14 years; n=10,908) from the ABCD Study. A tetrachoric factor analysis summarized clusters of ED symptoms, which were compared between parent and youth reports and across sociodemographic variables.

Results

Three factors emerged reflecting “weight distress”, “weight control”, and “binge eating” (prevalence range: 1.5-7.3%). Symptoms loaded onto similar factors between reporters. Rates of symptom endorsement were similar between sexes, with disproportionately higher endorsement rates for youth who self-identified as sexual minority, Hispanic, Black, or Mixed race participants, and those from a disadvantaged socioeconomic background, compared to the reference ABCD sample. Youth and parent reports at 2-year showed ∼12% overlap.

Conclusions

ED-related concerns among historically understudied racial and sexual minority groups call for greater attention to the detection and treatment of these symptoms in these groups. Applying a transdiagnostic approach to ED symptoms can inform effective detection and intervention efforts.

Public health statement

Our work depicts the sociodemographic breadth of disordered eating behaviors in a large diverse sample of American youth, and underscores the importance of including multiple reporters when assessing ED symptoms in community samples of children and adolescents. Taking into consideration the diverse sociodemographic landscape of disordered eating behaviors is imperative to ensure access to care is equitable across the sexes, and racial, ethnic and socioeconomic groups.
Short-term and Mid-term Blood Pressure Variability and long-term Mortality: evidence from the Third National Health and Nutrition Examination Study
Authors: Steinsaltz David , Patten Hamish , Bester D W , Rehkopf David H.
Published: December 2023

In considering the impact of blood-pressure variability on health outcomes, two methodological challenges arise: The presence of multiple timescales of variability that may act independently and interactively, and the fairly large stochastic uncertainty that is inevitable in estimates of individual variability based on modest numbers of observations. Here we present an application of Bayesian hierarchical modeling to the problem of estimating the effect of blood pressure (BP) variability on all-cause and cardiovascular mortality with two timescales – short-term variation among multiple measures at one visit, and medium-term variation between the measures at two visits several months apart. We use data from the Third National Health and Nutrition Examination Survey linked with up to 27 years of mortality follow-up. We find that medium-term systolic BP variability had a very significant predictive value for CV and all-cause mortality, around one-third as large as the well-established impact of mean systolic BP. Medium-term diastolic variability had an additional, though smaller, predictive effect. Short-term variability, on the other hand, had little or no measurable predictive value. The medium-term variability effect persisted when controlling for Framingham risk score.