bluuebunny/crossref_metadata_2025 huggingface dataset:
Gaps in the prevention of mother-to-child transmission of syphilis: a review of reported cases, South Africa, January 2020–June 2022
Authors: de Voux Alex , Maruma Wellington , Morifi Mabore , Maduma Modiehi , Ebonwu Joy , Sheikh Khadeejah , Dlamini-Nqeketo Sithembile , Kufa Tendesayi
Published: May 2024

Introduction

Congenital syphilis (CS) is preventable through timely antenatal care (ANC), syphilis screening and treatment among pregnant women. Robust CS surveillance can identify gaps in this prevention cascade. We reviewed CS cases reported to the South African notifiable medical conditions surveillance system (NMCSS) from January 2020 to June 2022.

Methods

CS cases are reported using a case notification form (CNF) containing limited infant demographic and clinical characteristics. During January 2020–June 2022, healthcare workers supplemented CNFs with a case investigation form (CIF) containing maternal and infant testing and treatment information. We describe CS cases with/without a matching CIF and gaps in the CS prevention cascade among those with clinical information.

Findings

During January 2020–June 2022, 938 CS cases were reported to the NMCSS with a median age of 1 day (interquartile range: 0–5). Nine percent were diagnosed based on clinical signs and symptoms only. During January 2020–June 2022, 667 CIFs were reported with 51% (343) successfully matched to a CNF. Only 57% of mothers of infants with a matching CIF had an ANC booking visit (entry into ANC). Overall, 87% of mothers were tested for syphilis increasing to 98% among mothers with an ANC booking visit. Median time between first syphilis test and delivery was 16 days overall increasing to 82 days among mothers with an ANC booking visit.

Discussion

Only 37% of CS cases had accompanying clinical information to support evaluation of the prevention cascade. Mothers with an ANC booking visit had increased syphilis screening and time before delivery to allow for adequate treatment.
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii
Authors: Gupta Purav , Hiller Aiden , Chowdhury Jawad , Lim Declan , Lim Dillon Yee , Saeij Jeroen P J , Babaian Artem , Rodriguez Felipe , Pereira Luke , Morales-Tapia Alejandro
Published: May 2024

We are entering a ‘Platinum Age of Virus Discovery’, an era marked by exponential growth in the discovery of virus biodiversity, and driven by advances in metagenomics and computational analysis. In the ecosystem of a human (or any animal) there are more species of viruses than simply those directly infecting the animal cells. Viruses can infect all organisms constituting the microbiome, including bacteria, fungi, and unicellular parasites. Thus the complexity of possible interactions between host, microbe, and viruses is unfathomable. To understand this interaction network we must employ computationally assisted virology as a means of analyzing and interpreting the millions of available samples to make inferences about the ways in which viruses may intersect human health. From a computational viral screen of human neuronal datasets, we identified a novel narnavirus Apocryptovirus odysseus (Ao) which likely infects the neurotropic parasite Toxoplasma gondii. Previously, several parasitic protozoan viruses (PPVs) have been mechanistically established as triggers of host innate responses, and here we present in silico evidence that Ao is a plausible pro-inflammatory factor in human and mouse cells infected by T. gondii. T. gondii infects billions of people worldwide, yet the prognosis of toxoplasmosis disease is highly variable, and PPVs like Ao could function as a hitherto undescribed hypervirulence factor. In a broader screen of over 7.6 million samples, we explored phylogenetically proximal viruses to Ao and discovered nineteen Apocryptovirus species, all found in libraries annotated as vertebrate transcriptome or metatranscriptomes. While samples containing this genus of narnaviruses are derived from sheep, goat, bat, rabbit, chicken, and pigeon samples, the presence of virus is strongly predictive of parasitic Apicomplexa nucleic acid co-occurrence, supporting the fact that Apocryptovirus is a genus of parasite-infecting viruses. This is a computational proof-of-concept study in which we rapidly analyze millions of datasets from which we distilled a mechanistically, ecologically, and phylogenetically refined hypothesis. We predict that this highly diverged Ao RNA virus is biologically a T. gondii infection, and that Ao, and other viruses like it, will modulate this disease which afflicts billions worldwide.
‘Birds’ of two feathers: Avicranium renestoi and the paraphyly of bird-headed reptiles (Diapsida: ‘Avicephala’)
Authors: Buffa Valentin , Frey Eberhard , Steyer J-Sébastien , Laurin Michel
Published: May 2024

The anatomy of Late Triassic drepanosauromorphs is re-examined, with a focus on the previously published surface models of the holotype of Avicranium renestoi from the Norian of North America. We comment on the cranial anatomy of this taxon and propose a new reconstruction of the skull and mandible. Contrary to previous interpretations, the entire rostrum and most of the palate are not preserved in this specimen. We also suggest that some proposed plesiomorphic characters may result from incomplete ossification due to immaturity. These new observations are compiled into a new morphological phylogenetic dataset designed to address the monophyly of ‘Avicephala’, the group comprising the Late Permian gliding reptiles Weigeltisauridae, and the Late Triassic chameleon-like Drepanosauromorpha. We recover Weigeltisauridae as stem-saurian diapsids and Drepanosauromorpha as sister-group to Trilophosauridae among archosauromorphs, thus implying the paraphyly of ‘Avicephala’. Drepanosauromorphs and trilophosaurids are recovered as sister-taxa for the first time, as supported by several cranial and postcranial synapomorphies. This new phylogenetic position of Drepanosauromorpha reduces the group’s ghost lineage that now does not necessarily cross the Permian–Triassic boundary. However, much remains unknown of the early history of trilophosaurids and drepanosauromorphs, and of the evolution of arboreality in Triassic archosauromorph reptiles.
FGF13 enhances the function of TRPV1 by stabilizing microtubules and regulates acute and chronic itch
Authors: Dong Zi‐shan , Zhang Xue‐rou , Xue Da‐zhong , Liu Jia‐hui , Yi Fan , Zhang Yi‐yi , Xian Fu‐yu , Qiao Ruo‐yang , Liu Bo‐yi , Zhang Hai‐lin , Wang Chuan
Published: May 2024

Itching is an aversive somatosensation that triggers the desire to scratch. Transient receptor potential (TRP) channel proteins are key players in acute and chronic itch. However, whether the modulatory effect of fibroblast growth factor 13 (FGF13) on acute and chronic itch is associated with TRP channel proteins is unclear. Here, we demonstrated that conditional knockout of Fgf13 in dorsal root ganglion neurons induced significant impairment in scratching behaviors in response to acute histamine‐dependent and chronic dry skin itch models. Furthermore, FGF13 selectively regulated the function of the TRPV1, but not the TRPA1 channel on Ca2+ imaging and electrophysiological recordings, as demonstrated by a significant reduction in neuronal excitability and current density induced by TRPV1 channel activation, whereas TRPA1 channel activation had no effect. Changes in channel currents were also verified in HEK cell lines. Subsequently, we observed that selective modulation of TRPV1 by FGF13 required its microtubule‐stabilizing effect. Furthermore, in FGF13 knockout mice, only the overexpression of FGF13 with a tubulin‐binding domain could rescue TRP channel function and the impaired itch behavior. Our findings reveal a novel mechanism by which FGF13 is involved in TRPV1‐dependent itch transduction and provide valuable clues for alleviating pathological itch syndrome.
Qualitative Insights Into Enhancing Neonatal Resuscitation in Post-Pandemic Vietnam
Authors: Kain Victoria J. , Nguyen Thi Thanh Binh , Nguyen Thi Thanh Binh , Fatth Waleed , Kelly Patty , Larbah Amina R. , Patel Divya
Published: May 2024

Background:

The neonatal phase is vital for child survival, with a substantial portion of deaths occurring in the first month. Neonatal mortality rates differ significantly between Vietnam (10.52/1000 live births) and the United States (3.27/1000). In response to these challenges, interventions such as the Helping Babies Breathe (HBB) program have emerged, aiming to enhance the quality of care provided during childbirth, and the postpartum period in low-resource settings.

Purpose:

The purpose of this study was to explore stakeholder perceptions of the HBB program in Vietnam postpandemic, aiming to identify requisites for resuming training.

Methods:

Utilizing qualitative content analysis, 19 in-person semistructured interviews were conducted with diverse stakeholders in 2 provinces of Central Vietnam.

Results:

The content analysis revealed following 5 main themes: (1) the pandemic’s impact on HBB training; (2) resource needs for scaling up HBB training as the pandemic abates; (3) participants’ perceptions of the pandemic’s effect on HBB skills and knowledge; (4) the pandemic’s influence on a skilled neonatal resuscitation workforce; and (5) future prospects and challenges for HBB training in a postpandemic era.

Implications for Practice and Research:

This research highlights the importance of sustainable post-HBB training competencies, including skill assessment, innovative knowledge retention strategies, community-based initiatives, and evidence-based interventions for improved healthcare decision-making and patient outcomes. Healthcare institutions should prioritize skill assessments, refresher training, and collaborative efforts among hospitals, authorities, non-government organizations, and community organizations for evidence-based education and HBB implementation.
Advancements in AMA Guides Musculoskeletal Impairment Evaluations
Authors: Melhorn J. Mark , Gelinas Barry , Martin Douglas W. , Hegmann Kurt T. , Thiese Matthew S.
Published: May 2024

Objective

Describe and evaluate methodological improvements in AMA Guides to the Evaluation of Permanent Impairment (Guides) Sixth Edition 2024, including an updated sequential method and enhanced diagnosis-based impairment tables, compared to the Guides Sixth 2008.

Methods

Three physician experts and 3 premedical students, respectively, completed 2 rounds of impairment ratings using the AMA Guides Sixth 2008 versus 2024 methods. Impairment values and completion times using each method were compared for both groups.

Results

Time to complete an impairment rating by experts averaged 3.5 minutes using Guides 2024 compared with 13.9 minutes using Guides 2008, with 100% accuracy and reliability for both. Students' time averaged 5.3 and 15.9 minutes, respectively, with increased accuracy and reliability with Guides 2024.

Conclusions

The Guides Sixth 2024 allowed more efficient impairment ratings while retaining accuracy, consistency, reliability, and reproducibility.
Factors contributing to weight loss success after bariatric procedures in patient over 65 years old: a multicenter retrospective cohort study
Authors: Karpińska Izabela , Dowgiałło-Gornowicz Natalia , Franczak Paula , Orłowski Michał , Lech Paweł , Kowalski Grzegorz , Major Piotr ,   Collaborative Study Group
Published: May 2024

Background:

Although bariatric surgery in patients over 65 years of age gives comparable results to treatment in the younger population, there are still controversies regarding the indications for surgery, risk assessment, and choice between different types of surgery. The study aimed to identify the factors contributing to weight loss success after bariatric surgery in patients over 65 years of age.

Material and Methods:

This is a retrospective, multicenter cohort study of patients with obesity aged over 65 years undergoing primary laparoscopic bariatric surgery in the years 2008–2022. Data came from 11 bariatric centers. Patients were divided into two groups: responders (R) who achieved more than 50% EWL and nonresponders (NR) who achieved less than 50% EWL. Both groups were compared. Uni- and multivariate logistic regression was used to identify predictors of weight loss success.

Results:

Out of 274 analyzed patients, the average BMI before surgery was 42.9 kg/m2. The most common obesity-related diseases were hypertension (85.1%) and type 2 diabetes (53.3%). Sleeve gastrectomy was the most frequently performed procedure (85.4%). Uni- and multivariate logistic regression analysis confirmed preoperative BMI (OR=0.9, 95% CI: 0.82–0.98, P=0.02), duration of diabetes >10 years (OR=0.3, 95% CI: 0.09–0.82, P=0.02), balloon placement (OR=10.6, 95% CI: 1.33–84.83, P=0.03), time since first visit (OR=0.9, 95% CI: 0.84–0.99, P=0.04), preoperative weight loss (OR=0.9, 95% CI: 0.86–0.98, P=0.01), and OAGB (OR=15.7, 95% CI: 1.71–143.99, P=0.02) to have a significant impact on weight loss success 1 year after bariatric surgery.

Conclusions:

Patients with higher preoperative weight loss may have a poorer response to surgery. OAGB emerged as the most beneficial type of surgery in terms of weight loss. Intragastric balloon placement before surgery may be effective in patients above 65 years of age and may be considered as a two-stage approach.
Omission of Antiplatelet Therapy in Patients With HeartMate 3 Left Ventricular Assist Devices: A Systematic Review and Meta-Analysis
Authors: Tscharre Maximilian , Mutschlechner David , Schlöglhofer Thomas , Wiedemann Dominik , Zimpfer Daniel , Gremmel Thomas
Published: May 2024

The HeartMate 3 (HM3) left ventricular assist device has decreased thromboembolic events and minimized the risk of pump thrombosis. However, bleeding complications due to combined antithrombotic therapy with a vitamin K antagonist (VKA) and aspirin remain high. Only limited data on the safety of VKA monotherapy in HM3 patients are available. A systematic search on the main databases was performed. Observational data and randomized trials were eligible for this analysis. As primary endpoint, we analyzed hemocompatibility-related adverse events (HRAE). As secondary endpoints, we investigated the individual components of the primary endpoint. The analysis was carried out using the odds ratio (OR) as outcome measure. A random-effects model was fitted to the data. Five manuscripts fulfilled the inclusion criteria. These trials included 785 patients (381 on VKA monotherapy, 404 on VKA and aspirin). VKA monotherapy significantly reduced HRAE (OR: 0.11 [95% confidence interval {CI}: 0.02–0.59], p = 0.01, I
2 = 87%). The reduction was driven by a decrease in bleeding complications (OR: 0.12 [95% CI: 0.02–0.62], p = 0.01, I
2 = 86%) without increasing the rates of thromboembolic events (OR: 0.69 [95% CI: 0.26–1.81], p = 0.45, I = 0%). Vitamin K antagonist monotherapy is associated with a significant reduction of bleeding events without increasing the risk of thromboembolic complications in HM3 patients.
National Overview of Nonprofit Hospitals’ Community Benefit Programs to Address Housing
Authors: Celano Annalise , Keselman Pauline , Barley Timothy , Schnautz Ryan , Piller Benjamin , Nunn Dylan , Scott Maliek , Cronin Cory , Franz Berkeley
Published: May 2024

Background:

Housing is a critical social determinant of health that can be addressed through hospital-supported community benefit programming.

Objectives:

To explore the prevalence of hospital-based programs that address housing-related needs, categorize the specific actions taken to address housing, and determine organizational and community-level factors associated with investing in housing.

Research Design:

This retrospective, cross-sectional study examined a nationally representative dataset of administrative documents from nonprofit hospitals that addressed social determinants of health in their federally mandated community benefit implementation plans. We conducted descriptive statistics and bivariate analyses to examine hospital and community characteristics associated with whether a hospital invested in housing programs. Using an inductive approach, we categorized housing investments into distinct categories.

Measures:

The main outcome measure was a dichotomous variable representing whether a hospital invested in one or more housing programs in their community.

Results:

Twenty percent of hospitals invested in one or more housing programs. Hospitals that addressed housing in their implementation strategies were larger on average, less likely to be in rural communities, and more likely to be serving populations with greater housing needs. Housing programs fell into 1 of 7 categories: community partner collaboration (34%), social determinants of health screening (9%), medical respite centers (4%), community social determinants of health liaison (11%), addressing specific needs of homeless populations (16%), financial assistance (21%), and targeting high-risk populations (5%).

Conclusions:

Currently, a small subset of hospitals nationally are addressing housing. Hospitals may need additional policy support, external partnerships, and technical assistance to address housing in their communities.
Trends in HCAHPS Survey Scores, 2008–2019
Authors: Beckett Megan K. , Quigley Denise D. , Cohea Christopher W. , Lehrman William G. , Russ Chelsea , Giordano Laura A. , Goldstein Elizabeth , Elliott Marc N.
Published: May 2024

Background:

HCAHPS’ 2008 initial public reporting, 2012 inclusion in the Hospital Value-Based Purchasing Program (HVBP), and 2015 inclusion in Hospital Star Ratings were intended to improve patient experiences.

Objectives:

Characterize pre-COVID-19 (2008–2019) trends in hospital consumer assessment of healthcare providers and systems (HCAHPS) scores.

Research Design:

Describe HCAHPS score trends overall, by phase: (1) initial public reporting period (2008–2013), (2) first 2 years of HVBP (2013–2015), and (3) initial HCAHPS Star Ratings reporting (2015–2019); and by hospital characteristics (HCAHPS decile, ownership, size, teaching affiliation, and urban/rural).

Subjects:

A total of 3909 HCAHPS-participating US hospitals.

Measures:

HCAHPS summary score (HCAHPS-SS) and 9 measures.

Results:

The mean 2007–2019 HCAHPS-SS improvement in most-positive-category (“top-box”) responses was +5.2 percentage points/pp across all hospitals (where differences of 5pp, 3pp, and 1pp are “large,” “medium,” and “small”). Improvement rate was largest in phase 1 (+0.8/pp/year vs. +0.2pp/year and +0.1pp/year for phases 2 and 3, respectively). Improvement was largest for Overall Rating of Hospital (+8.5pp), Discharge Information (+7.3pp), and Nurse Communication (+6.5pp), smallest for Doctor Communication (+0.8pp). Some measures improved notably through phases 2 and 3 (Nurse Communication, Staff Responsiveness, Overall Rating of Hospital), but others slowed or reversed in Phase 3 (Communication about Medicines, Quietness). Bottom-decile hospitals improved more than other hospitals for all measures.

Conclusions:

All HCAHPS measures improved rapidly 2008–2013, especially among low-performing (bottom-decile) hospitals, narrowing the range of performance and improving scores overall. This initial improvement may reflect widespread, general quality improvement (QI) efforts in lower-performing hospitals. Subsequent slower improvement following the introduction of HVBP and Star Ratings may have reflected targeted, resource-intensive QI in higher-performing hospitals.
Philadelphia Latine Immigrant Birthing People’s Perspectives on Mitigating the Chilling Effect on Prenatal Care Utilization
Authors: Montoya-Williams Diana , Barreto Alejandra , Laguna-Torres Alicia , Worsley Diana , Wallis Kate , Peña Michelle-Marie , Palladino Lauren , Salva Nicole , Levine Lisa , Rivera Angelique , Hernandez Rosalinda , Fuentes-Afflick Elena , Yun Katherine , Lorch Scott , Virudachalam Senbagam
Published: May 2024

Research Design:

Community-engaged qualitative study using inductive thematic analysis of semistructured interviews.

Objective:

To understand Latine immigrants’ recent prenatal care experiences and develop community-informed strategies to mitigate policy-related chilling effects on prenatal care utilization.

Background:

Decreased health care utilization among immigrants due to punitive immigration policies (ie, the “chilling effect”) has been well-documented among Latine birthing people both pre and postnatally.

Patients and Methods:

Currently or recently pregnant immigrant Latine people in greater Philadelphia were recruited from an obstetric clinic, 2 pediatric primary care clinics, and 2 community-based organization client pools. Thematic saturation was achieved with 24 people. Participants’ pregnancy narratives and their perspectives on how health care providers and systems could make prenatal care feel safer and more comfortable for immigrants.

Results:

Participants’ recommendations for mitigating the chilling effect during the prenatal period included training prenatal health care providers to sensitively initiate discussions about immigrants’ rights and reaffirm confidentiality around immigration status. Participants suggested that health care systems should expand sources of information for pregnant immigrants, either by partnering with community organizations to disseminate information or by increasing access to trusted individuals knowledgeable about immigrants’ rights to health care. Participants also suggested training non-medical office staff in the use of interpreters.

Conclusion:

Immigrant Latine pregnant and birthing people in greater Philadelphia described ongoing fear and confusion regarding the utilization of prenatal care, as well as experiences of discrimination. Participants’ suggestions for mitigating immigration-related chilling effects can be translated into potential policy and programmatic interventions which could be implemented locally and evaluated for broader applicability.
Is Electronic Information Exchange Associated With Lower 30-Day Readmission Charges Among Medicare Beneficiaries?
Authors: Turbow Sara D. , Chehal Puneet K. , Culler Steven D. , Vaughan Camille P. , Offutt Christina , Rask Kimberly J. , Perkins Molly M. , Clevenger Carolyn K. , Ali Mohammed K.
Published: May 2024

Objective:

Fragmented readmissions, when admission and readmission occur at different hospitals, are associated with increased charges compared with nonfragmented readmissions. We assessed if hospital participation in health information exchange (HIE) was associated with differences in total charges in fragmented readmissions.

Data Source:

Medicare Fee-for-Service Data, 2018.

Study Design:

We used generalized linear models with hospital referral region and readmission month fixed effects to assess relationships between information sharing (same HIE, different HIEs, and no HIE available) and total charges of 30-day readmissions among fragmented readmissions; analyses were adjusted for patient-level clinical/demographic characteristics and hospital-level characteristics.

Data Extraction Methods:

We included beneficiaries with a hospitalization for acute myocardial infarction, congestive heart failure, chronic obstructive pulmonary disease, syncope, urinary tract infection, dehydration, or behavioral issues with a 30-day readmission for any reason.

Principal Findings:

In all, 279,729 admission-readmission pairs were included, 27% of which were fragmented (n=75,438); average charges of fragmented readmissions were $64,897-$71,606. Compared with fragmented readmissions where no HIE was available, the average marginal effects of same-HIE and different-HIE admission-readmission pairs were -$2329.55 (95% CI: −7333.73, 2674.62) and −$3905.20 (95% CI: −7592.85, −307.54), respectively. While the average marginal effects of different-HIE pairs were lower than those for no-HIE fragmented readmissions, the average marginal effects of same-HIE and different-HIE pairs were not significantly different from each other.

Conclusions:

There were no statistical differences in charges between fragmented readmissions to hospitals that share an HIE or that do not share an HIE compared with hospitals with no HIE available.
Health Care Access and COVID-19 Vaccination in the United States
Authors: De Guzman Charles , Thomas Chloe A. , Wiwanto Lynn , Hu Dier , Henriquez-Rivera Jose , Gage Lily , Perreault Jaclyn C. , Harris Emily , Rastas Charlotte , McCormick Danny , Gaffney Adam
Published: May 2024

Background:

Although federal legislation made COVID-19 vaccines free, inequities in access to medical care may affect vaccine uptake.

Objective:

To assess whether health care access was associated with uptake and timeliness of COVID-19 vaccination in the United States.

Design:

A cross-sectional study.

Setting:

2021 National Health Interview Survey (Q2-Q4).

Subjects:

In all, 21,532 adults aged≥18 were included in the study.

Measures:

Exposures included 4 metrics of health care access: health insurance, having an established place for medical care, having a physician visit within the past year, and medical care affordability. Outcomes included receipt of 1 or more COVID-19 vaccines and receipt of a first vaccine within 6 months of vaccine availability. We examined the association between each health care access metric and outcome using logistic regression, unadjusted and adjusted for demographic, geographic, and socioeconomic covariates.

Results:

In unadjusted analyses, each metric of health care access was associated with the uptake of COVID-19 vaccination and (among those vaccinated) early vaccination. In adjusted analyses, having health coverage (adjusted odds ratio [AOR] 1.60; 95% CI: 1.39, 1.84), a usual place of care (AOR 1.58; 95% CI: 1.42, 1.75), and a doctor visit within the past year (AOR 1.45, 95% CI: 1.31, 1.62) remained associated with higher rates of COVID-19 vaccination. Only having a usual place of care was associated with early vaccine uptake in adjusted analyses.

Limitations:

Receipt of COVID-19 vaccination was self-reported.

Conclusions:

Several metrics of health care access are associated with the uptake of COVID-19 vaccines. Policies that achieve universal coverage, and facilitate long-term relationships with trusted providers, may be an important component of pandemic responses.
Modulation ofIdeonella sakaiensisPETase active site flexibility and activity on morphologically distinct substrates by surface charge engineering
Authors: Ding Ke , Levitskaya Zarina , Sana Barindra , Pasula Rupali Reddy , Kannan Srinivasaraghavan , Adam Abdurrahman , Sundaravadanam Vishnu Vadanan , Verma Chandra , Lim Sierin , Ghadessy John F.
Published: May 2024

Enzymatic hydrolysis of polyethylene terephthalate (PET) waste is a compelling strategy for environmentally friendly recycling of a major pollutant. Here, we investigate the effects of surface charge point mutations both proximal and distal to the active site of the mesophilic PET-degrading enzyme fromIdeonella sakaienses(IsPETase) and an engineered thermostable variant with superior activity, STAR PETase. The vicinal K95A mutation significantly inhibitedIsPETase activity on mechanically processed PET powder. Conversely, this mutation significantly increased hydrolysis of PET powder in the STAR PETase background. Activity of both enzymes on PET film was inhibited by the K95A mutation, highlighting complex interplay between mutation context and substrate morphology. Further installing the distal R132N and R280A surface charge mutations potentiated activity of STAR on all substrates tested. This variant afforded 100% degradation of bottle-grade PET powder in 3 days at 40°C reaction temperature, a 3-fold improvement overIsPETase. Molecular dynamics simulations reveal modulation of active site flexibility in mutants, which differentially impacts both hydrolysis of morphologically distinct PET substrates and the concentration-dependent inhibition phenomenon observed for PETase.
Brassinosteroids function as the plant male and female reproductive hormone coordinating gene expression
Authors: Matsuura-Tokita Kumi , Suzuki Takamasa , Kimata Yusuke , Takebayashi Yumiko , Ueda Minako , Nakano Takeshi , Sakakibara Hitoshi , Nakano Akihiko , Higashiyama Tetsuya
Published: May 2024

Brassinosteroids (BRs) are steroid hormones identified in plants. Besides promoting cell elongation and division, BRs facilitate the development of both male and female reproductive tissues. In animals, reproductive steroid hormones play an essential role in reproductive tissue development by regulating gene expression. Here, we focused on the function of BRs during fertilization. We measured the content of biologically active BRs, brassinolide (BL) and castasterone (CS), in the reproductive tissues ofArabidopsis thaliana. Both BL and CS accumulated abundantly in pollen grains and in larger amounts in pistils than in leaves. To evaluate BL function during fertilization, we used anin vitroguidance assay with exogenously applied BL. Although pollen tubes need to be elongated through the pistils for efficient capacitation, BL treatment promoted pollen tube capacitation and improved attraction to ovulesin vitro. Transcriptome analysis demonstrated that BL treatment induced the expression of half of the genes expressed in pollen tubes that elongated through the pistils. These results indicated that BL supplied from pistils is a key factor for pollen tube capacitation. However, using thebri1mutant for the guidance assay resulted in reduced pollen tube capacitation, suggesting that BRI1-signaling in pistils is also important. Furthermore, BRs act on ovules. Exogenous BL application to ovules maintained guidance capacity by promoting the expression of small secreted proteins involved in pollen tube attraction and gamete fusion. Overall, BRs play a significant role as male and female reproductive hormones throughout the plant fertilization process.
Mechanical control of the splicing factor PTBP1 regulates extracellular matrix stiffness-induced cell proliferation and mechanomemory
Authors: Tseng Pei-Li , Sun Weiwei , Salem Ahmed , Macfarlane Sarah , Gad Annica K. B. , Collins Mark O. , Erdmann Kai S.
Published: May 2024

Cells sense and respond to mechanical cues from their environment. Mechanical cues are important for many biological processes, including embryonic development, ageing, cellular homeostasis, and diseases. Cells translate mechanical cues into cellular biochemical signals that govern cellular behaviour, like cell proliferation or migration, via a process called mechanotransduction. However, this process and the proteins involved remain incompletely understood. Here, we present an unbiased and large-scale approach to identify proteins involved in mechanotransduction. The screen revealed that the splicing factor PTBP1 is a novel mechanotransducer. We show that the nuclear localisation of PTBP1 depends on extracellular matrix stiffness, cell density, and the actomyosin-based contractility of the cell. Furthermore, we demonstrate that PTBP1 promotes the mechanosensitive splicing of the adapter protein Numb and that alternative splicing of Numb is crucial for matrix stiffness-induced cell proliferation and mechanomemory. Our results support the idea that changes in alternative splicing are an integral part of mechanotransduction and provide a mechanism by which matrix stiffness regulates cell proliferation and the formation of a mechanomemory in cells.
Accurate single domain scaffolding of three non-overlapping protein epitopes using deep learning
Authors: Castro Karla M. , Watson Joseph L. , Wang Jue , Southern Joshua , Ayardulabi Reyhaneh , Georgeon Sandrine , Rosset Stéphane , Baker David , Correia Bruno E.
Published: May 2024

De novoprotein design has seen major success in scaffolding single functional motifs, however, in nature most proteins present multiple functional sites. Here we describe an approach to simultaneously scaffold multiple functional sites in a single domain protein using deep learning. We designed small single domain immunogens, under 130 residues, that simultaneously present three distinct and irregular motifs from respiratory syncytial virus. These motifs together comprise nearly half of the designed proteins, and hence the overall folds are quite unusual with little global similarity to proteins in the PDB. Despite this, X-ray crystal structures confirm the accuracy of presentation of each of the motifs, and the multi-epitope design yields improved cross-reactive titers and neutralizing response compared to a single-epitope immunogen. The successful presentation of three distinct binding surfaces in a small single domain protein highlights the power of generative deep learning methods to solve complex protein design problems.
High-resolution disease phenotyping reveals distinct resistance strategies of wild tomato crop wild relatives againstSclerotinia sclerotiorum
Authors: Einspanier Severin , Tominello-Ramirez Christopher , Hasler Mario , Barbacci Adelin , Raffaele Sylvain , Stam Remco
Published: May 2024

Besides the well-understood qualitative disease resistance, plants possess a more complex quantitative form of resistance: quantitative disease resistance (QDR). QDR is commonly defined as a partial but more durable form of resistance and, therefore, might display a valuable target for resistance breeding. The characterization of QDR phenotypes, especially of wild crop relatives, displays a major bottleneck in deciphering QDR’s genomic and regulatory background. Moreover, the relationship between QDR parameters, such as infection frequency, lag phase duration, and lesion growth rate, remains elusive. High hurdles for applying modern phenotyping technology, such as the low availability of phenotyping facilities or complex data analysis, further dampen progress in understanding QDR. Here, we applied a low-cost phenotyping system to measure lesion growth dynamics of wild tomato species (e.g.,S. pennelliiorS. pimpinellifolium). We provide insight into QDR diversity of wild populations and derive specific QDR strategies and their crosstalk. We show how temporally continuous observations are required to dissect end-point severity into functional resistance strategies. The results of our study show how QDR can be maintained by facilitating different defense strategies during host-parasite interaction and that the capacity of the QDR toolbox highly depends on the host’s genetic context. We anticipate that the present findings display a valuable resource for more targeted functional characterization of the processes involved in QDR. Moreover, we show how modest phenotyping technology can be leveraged to help answer highly relevant biological questions.
Clinicogenomic characterization of inflammatory breast cancer
Authors: Priedigkeit Nolan , Harrison Beth , Shue Robert , Hughes Melissa , Li Yvonne , Kirkner Gregory J. , Spurr Liam F. , Remolano Marie Claire , Strauss Sarah , Files Janet , Feeney Anne-Marie , Grant Libby , Mohammed-Abreu Ayesha , Garrido-Castro Ana , Sousa Romualdo Barroso , Bychkovsky Brittany , Nakhlis Faina , Bellon Jennifer R. , King Tari A. , Winer Eric P. , Lindeman Neal , Johnson Bruce E. , Sholl Lynette , Dillon Deborah , Overmoyer Beth , Tolaney Sara M. , Cherniack Andrew , Lin Nancy U. , Lynce Filipa
Published: May 2024

Background

Inflammatory breast cancer (IBC) is a rare and poorly characterized type of breast cancer with an aggressive clinical presentation. The biological mechanisms driving the IBC phenotype are relatively undefined—partially due to a lack of comprehensive, large-scale genomic studies and limited clinical cohorts.

Patients and Methods

A retrospective analysis of 2457 patients with metastatic breast cancer who underwent targeted tumor-only DNA-sequencing was performed at Dana-Farber Cancer Institute. Clinicopathologic, single nucleotide variant (SNV), copy number variant (CNV) and tumor mutational burden (TMB) comparisons were made between clinically confirmed IBC cases within a dedicated IBC center versus non-IBC cases.

Results

Clinicopathologic differences between IBC and non-IBC cases were consistent with prior reports—including IBC being associated with younger age at diagnosis, higher grade, and enrichment with hormone receptor (HR)-negative and HER2-positive tumors. The most frequent somatic alterations in IBC involvedTP53(72%),ERBB2(32%),PIK3CA(24%),CCND1(12%),MYC(9%),FGFR1(8%) andGATA3(8%). A multivariate logistic regression analysis revealed a significant enrichment inTP53SNVs in IBC; particularly in HER2-positive and HR-positive disease which was associated with worse outcomes. Tumor mutational burden (TMB) did not differ substantially between IBC and non-IBC cases and a pathway analysis revealed an enrichment in NOTCH pathway alterations in HER2-positive disease.

Conclusion

Taken together, this study provides a comprehensive, clinically informed landscape of somatic alterations in a large cohort of patients with IBC. Our data support higher frequency ofTP53mutations and a potential enrichment in NOTCH pathway activation—but overall; a lack of major genomic differences. These results both reinforce the importance ofTP53alterations in IBC pathogenesis as well as their influence on clinical outcomes; but also suggest additional analyses beyond somatic DNA-level changes are warranted.
Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations
Authors: Tenthorey Jeannette L. , del Banco Serena , Ramzan Ishrak , Klingenberg Hayley , Liu Chang , Emerman Michael , Malik Harmit S.
Published: May 2024

Antiviral proteins often evolve rapidly at virus-binding interfaces to defend against new viruses. We investigated whether antiviral adaptation via missense mutations might face limits, which insertion or deletion mutations (indels) could overcome. We report one such case of a nearly insurmountable evolutionary challenge: the human anti-retroviral protein TRIM5α requires more than five missense mutations in its specificity-determining v1 loop to restrict a divergent simian immunodeficiency virus (SIV). However, duplicating just one amino acid in v1 enables human TRIM5α to potently restrict SIV in a single evolutionary step. Moreover, natural primate TRIM5α v1 loops have evolved indels that confer novel antiviral specificities. Thus, indels enable antiviral proteins to overcome viral challenges inaccessible by missense mutations, revealing the potential of these often-overlooked mutations in driving protein innovation.
Amyloid β Induces Hormetic-Like Effects Through Major Stress Pathways in aC. elegansModel of Alzheimer’s Disease
Authors: Lichty James D. , San Miguel Adriana
Published: May 2024

Amyloid β (Aβ) is a peptide known for its characteristic aggregates in Alzheimer’s Disease and its ability to induce a wide range of detrimental effects in various model systems. However, Aβ has also been shown to induce some beneficial effects, such as antimicrobial properties against pathogens. In this work, we explore the influence of Aβ in stress resistance in aC. elegansmodel of Alzheimer’s Disease. We found thatC. elegansthat express human Aβ exhibit increased resistance to heat and hypoxia, but not to oxidative stress. This beneficial effect of Aβ was driven from Aβ in neurons but not muscles, and the abundance of Aβ in neurons correlated with stress resistance levels. Transcriptomic analysis revealed that this selective stress resistance was mediated by the Heat Shock Protein (HSPs) family of genes. Furthermore, neuropeptide signaling was necessary for Aβ to induce stress resistance, suggesting neuroendocrine signaling plays a major role in activating organismal stress response pathways. These results highlight the potential beneficial role of Aβ in cellular function, as well as its complex effects on cellular and organismal physiology that must be considered when usingC. elegansas a model for Alzheimer’s Disease.
Interplay of condensate material properties and chromatin heterogeneity governs nuclear condensate ripening
Authors: Banerjee Deb Sankar , Chigumira Tafadzwa , Lackner Rachel M. , Kratz Josiah C. , Chenoweth David M. , Banerjee Shiladitya , Zhang Huaiying
Published: May 2024

Nuclear condensates play many important roles in chromatin functions, but how cells regulate their nucleation and growth within the complex nuclear environment is not well understood. Here, we report how condensate properties and chromatin mechanics dictate condensate growth dynamics in the nucleus. We induced condensates with distinct properties using different proteins in human cell nuclei and monitored their growth. We revealed two key physical mechanisms that underlie droplet growth: diffusion-driven or ripening-dominated growth. To explain the experimental observations, we developed a quantitative theory that uncovers the mechanical role of chromatin and condensate material properties in regulating condensate growth in a heterogeneous environment. By fitting our theory to experimental data, we find that condensate surface tension is critical in determining whether condensates undergo elastic or Ostwald ripening. Our model also predicts that chromatin heterogeneity can influence condensate nucleation and growth, which we validated by experimentally perturbing the chromatin organization and controlling condensate nucleation. By combining quantitative experimentation with theoretical modeling, our work elucidates how condensate surface tension and chromatin heterogeneity govern nuclear condensate ripening, implying that cells can control both condensate properties and the chromatin organization to regulate condensate growth in the nucleus.
Enhancing Whole Slide Image Classification with Discriminative and Contrastive Learning
Authors: Liang Peixian , Zheng Hao , Li Hongming , Gong Yuxin , Fan Yong
Published: May 2024

Whole slide image (WSI) classification plays a crucial role in digital pathology data analysis. However, the immense size of WSIs and the absence of fine-grained sub-region labels, such as patches, pose significant challenges for accurate WSI classification. Typical classification-driven deep learning methods often struggle to generate compact image representations, which can compromise the robustness of WSI classification. In this study, we address this challenge by incorporating both discriminative and contrastive learning techniques for WSI classification. Different from the extant contrastive learning methods for WSI classification that primarily assign pseudo labels to patches based on the WSI-level labels, our approach takes a different route to directly focus on constructing positive and negative samples at the WSI-level. Specifically, we select a subset of representative and informative patches to represent WSIs and create positive and negative samples at the WSI-level, allowing us to better capture WSI-level information and increase the likelihood of effectively learning informative features. Experimental results on two datasets and ablation studies have demonstrated that our method significantly improved the WSI classification performance compared to state-of-the-art deep learning methods and enabled learning of informative features that promoted robustness of the WSI classification.
Single particle cryo-electron microscopy with an enhanced 200 kV cryo-TEM configuration achieves near-atomic resolution
Authors: Jia Lijia , Ruben Eliza A. , Suarez Humberto J. , Olsen Shaun K. , Wasmuth Elizabeth V.
Published: May 2024

Single particle cryogenic electron microscopy (cryo-EM) as a structural biology methodology has become increasingly attractive and accessible to investigators in both academia and industry as this ever-advancing technology enables successful structural determination of a wide range of protein and nucleic acid targets. Although data for many high resolution cryo-EM structures are still obtained using a 300 kV cryogenic transmission electron microscope (cryo-TEM), a modern 200 kV cryo-TEM equipped with an advanced direct electron detector and energy filter is a cost-effective choice for most single particle applications, routinely achieving sub 3 angstrom (Å) resolution. Here, we systematically evaluate performance of one such high-end configuration - a 200 kV Glacios microscope coupled with a Falcon 4 direct electron detector and Selectris energy filter (Glacios-F4-S). First, we evaluated data quality on the standard benchmarking sample, rabbit muscle aldolase, using three of the most frequently used cryo-EM data collection software: SerialEM, Leginon and EPU, and found that – despite sample heterogeneity – all final reconstructions yield same overall resolutions of 2.6 Å and map quality when using either of the three software. Furthermore, comparison between Glacios-F4-S and a 300 kV cryo-TEM (Titan Krios with Falcon 4) revealed nominal resolution differences in overall reconstructions of a reconstituted human nucleosome core particle, achieving 2.8 and 2.5 Å, respectively. Finally, we performed comparative data analysis on the human RAD51 paralog complex, BCDX2, a four-protein complex of approximately 150 kilodaltons, and found that a small dataset (≤1,000 micrographs) was sufficient to generate a 3.3 Å reconstruction, with sufficient detail to resolve co-bound ligands, AMP-PNP and Mg+2. In summary, this study provides evidence that the Glacios-F4-S operates equally well with all standard data collection software, and is sufficient to obtain high resolution structural information of novel macromolecular complexes, readily acquiring single particle data rivaling that of 300 kV cryo-TEMs.
Spatial Transcriptomic Sequencing of a DIPG-infiltrated Brainstem reveals Key Invasion Markers and Novel Ligand-Receptor Pairs contributing to Tumour to TME Crosstalk
Authors: Kordowski Anja , Mulay Onkar , Tan Xiao , Vo Tuan , Baumgartner Ulrich , Maybury Mellissa K. , Hassall Timothy E. G. , Wainwright Brandon J. , Harris Lachlan , Nguyen Quan , Day Bryan W.
Published: May 2024

Emerging spatially-resolved sequencing technologies offer unprecedented possibilities to study cellular functionality and organisation, transforming our understanding of health and disease. The necessity to understand healthy and diseased tissues in its entirety becomes even more evident for the human brain, the most complex organ in the body. The brain’s cellular architecture and corresponding functions are tightly regulated. However, when intercellular communications are altered by pathologies, such as brain cancer, these microenvironmental interactions are disrupted.

DIPG is a brainstem high-grade glioma arising in young children and is universally fatal. Major disease obstacles include intratumoural genetic and cellular heterogeneity as well as a highly invasive phenotype. Recent breakthrough studies have highlighted the vital oncogenic capacity of brain cancer cells to functionally interact with the central nervous system (CNS). This CNS-crosstalk crucially contributes to tumour cell invasion and disease progression. Ongoing worldwide efforts seek to better understand these cancer-promoting CNS interactions to develop more effective DIPG anti-cancer therapies.

In this study, we performed spatial transcriptomic analysis of a complete tumour-infiltrated brainstem from a single DIPG patient. Gene signatures from ten sequential tumour regions were analysed to assess disease progression and to study DIPG cell interactions with the tumour microenvironment (TME). We leveraged this unique DIPG dataset to evaluate genes significantly correlated with invasive tumour distal regions versus the proximal tumour initiation site. Furthermore, we assessed novel ligand-receptor pairs that actively promote DIPG tumour progression via crosstalk with endothelial, neuronal and immune cell communities, which can be utilised to support future research efforts in this area of high unmet need.