bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA
Authors: de Oliveira Eliezyer Fermino , Garg Pranjal , Hjerling-Leffler Jens , Batista-Brito Renata , Sjulson Lucas
Published: August 2024

High-dimensional data have become ubiquitous in the biological sciences, and it is often desirable to compare two datasets collected under different experimental conditions to extract low-dimensional patterns enriched in one condition. However, traditional dimensionality reduction techniques cannot accomplish this because they operate on only one dataset. Contrastive principal component analysis (cPCA) has been proposed to address this problem, but it has seen little adoption because it requires tuning a hyperparameter resulting in multiple solutions, with no way of knowing which is correct. Moreover, cPCA uses foreground and background conditions that are treated differently, making it ill-suited to compare two experimental conditions symmetrically. Here we describe the development of generalized contrastive PCA (gcPCA), a flexible hyperparameter-free approach that solves these problems. We first provide analyses explaining why cPCA requires a hyperparameter and how gcPCA avoids this requirement. We then describe an open-source gcPCA toolbox containing Python and MATLAB implementations of several variants of gcPCA tailored for different scenarios. Finally, we demonstrate the utility of gcPCA in analyzing diverse high-dimensional biological data, revealing unsupervised detection of hippocampal replay in neurophysiological recordings and heterogeneity of type II diabetes in single-cell RNA sequencing data. As a fast, robust, and easy-to-use comparison method, gcPCA provides a valuable resource facilitating the analysis of diverse high-dimensional datasets to gain new insights into complex biological phenomena.
Aspergillusspecies in Iceland: species distribution andcyp51Amutation testing in a 7.5-year clinical isolate collection
Authors: Hilmarsdottir Ingibjorg , Alcanzo Ervin Martien , Gerrits van den Ende Bert , Houbraken Jos , Hagen Ferry
Published: August 2024

Introduction.

Among challenges in diagnosing and treating aspergillosis areAspergillusspecies identification, which can inform therapeutic choices, and detection of antifungal resistance. Increasing rates of triazole resistance have been reported for the most common species,Aspergillus fumigatus.

Methods.

A collection of clinicalAspergillusisolates cultured during 2014–2021, previously identified morphologically, were tested with the AsperGenius qPCR-kit for identification ofA. fumigatusandAspergillus flavusand the presence of acyp51Amutation encoding azole resistance (TR34/L98H and Y121F/T289A); other species were identified with calmodulin sequencing.

Results.

Identification of the 312 isolates (224 patients) tested revealed 19 species in nineAspergillussections. Rare or cryptic species were identified in 48 isolates (44 patients). Thirty-one isolates had been assigned an incorrect species name when initially cultured. The TR34/L98H and Y121F/T289A mutations were not found in any of the 202A. fumigatusisolates tested.

Discussion.

In this first study on clinicalAspergillusisolates in Iceland the proportion of cryptic and rare species was on par with findings from other countries. In contrast, unlike other studies we did not find the most common azole resistance-related mutations inA. fumigatus, possibly due to the absence of significant environmental antifungal pressure in the local agriculture.
Modulation of inhibitory synaptic plasticity for restoration of basal ganglia dynamics in Parkinson’s disease
Authors: Spencer KA , Boogers A , Sumarac S , Crompton DJ , Steiner LA , Zivkovic L , Buren Y , Lozano AM , Kalia SK , Hutchison WD , Fasano A , Milosevic L
Published: August 2024

Introduction

Parkinson’s disease is characterized, in part, by hypoactivity of both direct pathway inhibitory projections from striatum to the globus pallidus internus (GPi) and indirect pathway inhibitory projections from globus pallidus externus (GPe) to the subthalamic nucleus (STN), giving rise to disrupted basal ganglia circuit activity. In this study, we explored the use of intracranial stimulation for eliciting long-term potentiation (LTP) of each of these pathologically underactive inhibitory projections for the restoration of basal ganglia circuit dynamics and amelioration of motor symptoms.

Methods

Data were collected from a total of 31 people with Parkinson’s disease (42 hemispheres). During deep brain stimulation (DBS) surgery, we assessed microelectrode stimulation-induced changes to inhibitory evoked field potentials (fEP) and hand kinematics before versus after a 40-second train of high-frequency stimulation (HFS) in the GPi (n = 7, 11 sites at 100 Hz) and STN (n = 10, 14 sites at 100 Hz; n = 4, 7 sites at 180 Hz). Additionally, we assessed changes to beta oscillations and hand kinematics in people with chronic DBS implants in the GPi (n = 6 at 125 Hz) and STN (n = 4 at 180 Hz).

Results

Intraoperatively, increases in fEP amplitude (p = 0.002) and improved motor performance (p = 0.003) were observed after 100 Hz HFS in the GPi; while in STN, HFS did not potentiate fEPs (p = 0.589) or improve motor performance (p = 0.460) (similar results yielded for 180 Hz in STN). Similarly, extraoperative GPi-DBS produced suppression of beta power (p=0.096) and motor improvement (p = 0.077) before versus after HFS at 125 Hz; while STN-DBS at 180 Hz did not significantly affect beta power (p = 0.267) or motor performance (p=0.850).

Interpretation

Our findings support that LTP-like effects in GPi may produce motor improvements that extend beyond stimulation cessation, aligning with optogenetic studies showing long-lasting motor recovery through periodic D1-striatal activation in rodents. The lack of effects in STN suggests that stimulation paradigms may require optimization for effective LTP induction. These findings nevertheless highlight the potential of LTP-based strategies for sustained therapeutic benefits in Parkinson’s disease, warranting further investigation into periodic stimulation paradigms for optimizing DBS efficacy and side effect profiles.
Whole genome sequencing improves tissue of origin diagnosis and treatment options for cancer of unknown primary
Authors: Rebello Richard J. , Posner Atara , Dong Ruining , Prall Owen W.J. , Sivakumaran Tharani , Mitchell Camilla B. , Flynn Aidan , Caneborg Alex , Mitchell Catherine , Kanwal Sehrish , Fedele Clare , Webb Samantha , Fisher Krista , Wong Hui-Li , Balachander Shiva , Zhu Wenying , Nicolson Shannon , Dimitriadis Voula , Wilcken Nicholas , DeFazio Anna , Gao Bo , Singh Madhu , Collins Ian , Steer Christopher , Warren Mark , Karanth Narayan , Xu Huiling , Fellowes Andrew , Hicks Rodney J. , Stewart Kym Pham , Shale Charles , Priestley Peter , Dawson Sarah-Jane , Vissers Joseph H.A. , Fox Stephen B. , Schofield Penelope , Bowtell David , Hofmann Oliver , Grimmond Sean M. , Mileshkin Linda , Tothill Richard W.
Published: August 2024

Genomics holds promise for precision treatment and identifying the primary tissue of origin (TOO) in cases of cancer of unknown primary (CUP). We evaluated the feasibility and diagnostic superiority of whole genome and transcriptome sequencing (WGTS) over conventional panel testing in 72 patients using routine pathology samples. WGTS not only detected all reportable mutations identified by panel testing but also uncovered additional clinically relevant features in 76% of cases. Utilizing a CUP prediction algorithm (CUPPA) trained on WGTS data of known primary cancers, WGTS informed TOO in 77% of cases. Importantly, WGTS suggested potential treatment options for 79% of patients, a significant improvement over the 62% informed by panel testing. Additionally, WGTS and CUPPA applied to 22 cell-free DNA samples yielded high-likelihood TOO predictions in 41% of cases. These findings demonstrate that WGTS is diagnostically superior to panel testing, broadens treatment options, and is feasible using archived tissues and cell-free DNA.
Genome-Wide Association Study Meta-Analysis Uncovers Novel Genetic Variants Associated with Olfactory Dysfunction
Authors: Imtiaz Mohammed Aslam , Melas Konstantinos , Tin Adrienne , Talevi Valentina , Chen Honglei , Fornage Myriam , Shrestha Srishti , Gögele Martin , Emmert David , Pattaro Cristian , Pramstaller Peter , Förster Franz , Horn Katrin , Mosley Thomas H. , Fuchsberger Christian , Scholz Markus , Breteler Monique M.B. , Aziz N. Ahmad
Published: August 2024

IMPORTANCE

Olfactory dysfunction is among the earliest signs of many age-related neurodegenerative diseases and has been associated with increased mortality in older adults; however, its genetic basis remains largely unknown.

OBJECTIVE

To identify the genetic loci associated with olfactory dysfunction in the general population.

DESIGN, SETTING AND PARTIICIPANTS

This genome-wide association study meta-analysis (GWMA) included participants of European ancestry (N = 22,730) enrolled in four different large population-based studies, followed by a multi-ancestry GWMA including participants of African ancestry (N = 1,030). The data analysis was performed from March 2023 through June 2024.

EXPOSURES

Genome-wide single nucleotide polymorphisms.

MAIN OUTCOMES AND MEASURES

Olfactory dysfunction was the outcome and assessed using a 12-item smell identification test.

RESULTS

GWMA revealed a novel genome-wide significant locus (tagged by rs11228623 at 11q12) associated with olfactory dysfunction. Gene-based analysis revealed a high enrichment for olfactory receptor genes in this region. Phenome-wide association studies demonstrated associations between genetic variants related to olfactory dysfunction and blood cell counts, kidney function, skeletal muscle mass, cholesterol levels and cardiovascular disease. Using individual-level data, we also confirmed and quantified the strength of these associations on a phenotypic level. Moreover, employing two-sample Mendelian Randomization analyses, we found evidence for causal associations between olfactory dysfunction and these phenotypes.

CONCLUSIONS

These findings provide novel insights into the genetic architecture of the sense of smell and highlight its importance for many aspects of human health.

Key Points

Question

What is the genetic basis of olfactory dysfunction, and is it causally related to adverse health outcomes?

Findings

This genome-wide association study meta-analysis (GWMA) of 22,730 European and 1,030 African participants identified a novel genomic locus, enriched for olfactory receptor genes, robustly associated with olfactory dysfunction. Two-sample Mendelian Randomization analyses provided evidence for causal associations of olfactory dysfunction with biochemical, anthropometric and cardiovascular health outcomes.

Meaning

These findings provide new insights into the genetic architecture of olfaction and implicate olfactory dysfunction as a causal risk factor for many aspects of human health.
Empowering Refugee Voices: Using Nominal Group Technique with a Diverse Refugee Patient Advisory Committee (PAC) to Identify Health and Research Priorities
Authors: Altahsh Deyana , Holdbrook Linda , Norrie Eric , Sahilie Adanech , Essar Mohammad Yasir , Grewal Rabina , Horbach Olha , Abdaly Fawzia , Santana Maria , Talavlikar Rachel , Aucoin Michael , Coakley Annalee , Fabreau Gabriel E.
Published: August 2024

Background

Despite rising forced displacement globally, refugees’ health and research priorities are largely unknown. We investigated whether a diverse refugee committee could utilize participatory methods to identify health priorities and a research agenda to address them.

Methods

We conducted a qualitative study with focus groups of current and former refugees, asylum claimants and evacuees from a specialized refugee clinic over a year. We collected sociodemographic data using standardized instruments, then utilized a four-step nominal group technique process (idea generation, recording, discussion, and voting) to identify and rank participants’ health and research priorities. Participants ranked their top five priorities across three time periods: Pre-migration/early arrival (0–3 months), post-migration (3 months–2 years), and long-term health (>2 years). Participants created overarching priorities and corroborated findings via a member checking step.

Findings

Twenty-three participants (median age 35 years) attended one or more of five focus groups. Twenty-one completed sociodemographic surveys: 16/21 (76%) were women, representing 8 countries of origin. Participants identified “more family physicians” and “improving health system navigation” (11/60 votes each) as top health and research priorities respectively across all resettlement periods. Participants also prioritized pre-departure healthcare system orientation and improved post-arrival and long-term mental health services. Twelve participants completed the member checking process, affirming the results with minor clarifications.

Interpretation

This proof-of-concept study illustrates how refugees can use a rigorous consensus process without external influence to prioritize their healthcare needs, direct a health research agenda to address those needs, and co-produce research. These low-cost participatory methods should be replicated elsewhere.

Funding

Funded by the O’Brien Institute for Public Health at the University of Calgary.
Factors Associated with the Ability of Adolescent Girls and Young Women (AGYW) in Sexual Unions to Negotiate for Safer Sex. An Analysis of Data from the 2018 Zambia Demographic and Health Survey (ZDHS)
Authors: Zulu Teebeny , Musukuma Mwiche , Jacobs Choolwe , Musonda Patrick
Published: August 2024

The ability of AGYW to negotiate for safer sex is key in the fight against the Human Immunodeficiency Virus (HIV). We determined the prevalence of safer sex negotiation among AGYW in sexual unions aged 15–24 and its associated factors in Zambia. Of 1879 respondents, 78.0% (1466) had the ability to negotiate for safer sex (ANSS). While adjusting for other variables in the model, condom use at last sex with the most recent partner (AOR 4.08, 95% CI 1.74-9.60, p=0.001), experiencing any sexual violence by husband or partner (AOR 1.74, 95% CI 1.17-2.59, p=0.006), listening to the radio at least once a week (AOR 2.03, 95% CI 1.32-3.13, p=0.001), secondary or higher education (AOR1.77, 95% CI 1.04-2.99, p=0.034), being in the richest wealth quintile (AOR 2.70, 95% CI 1.30-5.60, p=0.008), and living in Eastern Province (AOR 2.75, 95% CI 1.53-4.93 p=0.001), Northwestern (AOR 2.31, 95% CI 1.15-4.65, p=0.019) and Southern (AOR 3.11, 95% CI 1.58-6.09, p=0.001) was associated with a significant increase in the odds of ANSS among AGYW aged 15-24 years in sexual unions. On the other hand, being in Muchinga province (AOR 0.48, 95% CI 0.28–0.81, p = 0.006) decreased the odds of ANSS. In conclusion, safer sex negotiation is crucial in combating HIV; hence, tailor-made interventions that promote condom use, frequency of listening to health programmes on the radio, education, and wealth acquisition should be implemented to build and sustain safer sex negotiation, particularly among AGYW in sexual unions.
What is the relationship between viral prospecting in animals and medical countermeasure development?
Authors: Aatresh Aishani V. , Lipsitch Marc
Published: August 2024

In recent decades, surveillance in nonhuman animals has aimed to detect novel viruses before they “spill over” to humans. However, the extent to which these viral prospecting efforts have enhanced preparedness for disease outbreaks remains poorly characterized, especially in terms of whether they are necessary, sufficient, or feasible ways to spur medical countermeasure development. We find that several viruses which pose known threats to human health lack approved vaccines and that known viruses discovered in human patients prior to 2000 have caused most major 21st-century outbreaks. WithFiloviridaeas a case study, we show there is little evidence to suggest that viral prospecting has accelerated countermeasure development or that systematically discovering novel zoonotic viruses in animal hosts before they cause human outbreaks has been feasible. These results suggest that prospecting for novel viral targets does not accelerate a rate-limiting step in countermeasure development and underscore questions about the importance of zoonotic viral discovery for outbreak preparedness. We consider limitations to these conclusions and alternative but related approaches to preparedness and response.
Changes in prediction modelling in biomedicine – do systematic reviews indicate whether there is any trend towards larger data sets and machine learning methods?
Authors: Lusa Lara , Kappenberg Franziska , Collins Gary S. , Schmid Matthias , Sauerbrei Willi , Rahnenführer Jörg
Published: August 2024

The number of prediction models proposed in the biomedical literature has been growing year on year. In the last few years there has been an increasing attention to the changes occurring in the prediction modeling landscape. It is suggested that machine learning techniques are becoming more popular to develop prediction models to exploit complex data structures, higher-dimensional predictor spaces, very large number of participants, heterogeneous subgroups, with the ability to capture higher-order interactions.

We examine these changes in modelling practices by investigating a selection of systematic reviews on prediction models published in the biomedical literature. We selected systematic reviews published since 2020 which included at least 50 prediction models. Information was extracted guided by the CHARMS checklist. Time trends were explored using the models published since 2005.

We identified 8 reviews, which included 1448 prediction models published in 887 papers. The average number of study participants and outcome events increased considerably between 2015 and 2019, but remained stable afterwards. The number of candidate and final predictors did not noticeably increase over the study period, with a few recent studies using very large numbers of predictors. Internal validation and reporting of discrimination measures became more common, but assessing calibration and carrying out external validation were less common. Information about missing values was not reported in about half of the papers, however the use of imputation methods increased. There was no sign of an increase in using of machine learning methods. Overall, most of the findings were heterogeneous across reviews.

Our findings indicate that changes in the prediction modeling landscape in biomedicine are less dramatic than expected and that poor reporting is still common; adherence to well established best practice recommendations from the traditional biostatistics literature is still needed. For machine learning best practice recommendations are still missing, whereas such recommendations are available in the traditional biostatistics literature, but adherence is still inadequate.
Leveraging Pretrained Models for Multimodal Medical Image Interpretation: An Exhaustive Experimental Analysis
Authors: Fagbola Temitayo Matthew , Success Igwebuike
Published: August 2024

Artificial intelligence (AI) in radiology, particularly pretrained machine learning models, holds promise for overcoming image interpretation complexities and improving diagnostic accuracy. Although extensive research highlights their potential, challenges remain in adapting these models for generalizability across diverse medical image modalities, such as Magnetic Resonance Imaging (MRI), Computed Tomography (CT), and X-rays. Most importantly, limited generalizability across image modalities hinders their real-world application in diverse medical settings. This study addresses this gap by investigating the effectiveness of pretrained models in interpreting diverse medical images. We evaluated ten state-of-the-art convolutional neural network (CNN) models, including ConvNeXtBase, EfficientNetB7, VGG architectures (VGG16, VGG19), and InceptionResNetV2, for their ability to classify multimodal medical images from brain MRI, kidney CT, and chest X-ray (CXR) scans. Our evaluation reveals VGG16’s superior generalizability across diverse modalities, achieving accuracies of 96% for brain MRI, 100% for kidney CT, and 95% for CXR. Conversely, EfficientNetB7 excelled in brain MRI with 96% accuracy but showed limited generalizability to kidney CT (56% accuracy) and CXR (33% accuracy), suggesting its potential specialization for MRI tasks. Future research should enhance the generalizability of pretrained models across diverse medical image modalities. This includes exploring hybrid models, advanced training techniques, and utilizing larger, more diverse datasets. Integrating multimodal information, such as combining imaging data with patient history, can further improve diagnostic accuracy. These efforts are crucial for deploying robust AI systems in real-world medical settings, ultimately improving patient outcomes.
Safety and Efficacy of Cardiac Sympathetic Denervation for Ventricular Arrhythmias: An Updated Review and Meta-Analysis
Authors: Hanna Daniel B. , Karimianpour Ahmadreza , Mamprejew Nicole , Fiechter Chris , Verghese Dhiran , Sierra Juan , Navas Viviana , Sharma Dinesh
Published: August 2024

Introduction

The role of sympathetic nervous system in the initiation and continuation of ventricular tachyarrhythmias (VTA) is well established. However, whether CSD reduces implantable cardioverter defibrillator (ICD) shocks and recurrent VTA is still uncertain.

Objective

To explore long-term arrhythmic outcomes, safety, and efficacy of CSD by measuring event rates of recurrent VTA and ICD shocks after CSD.

Methods

A comprehensive literature search was performed at Medline and Embase until March 2023. Our primary outcome was event rate of ICD shocks and VTA. Analyses were conducted using Comprehensive Meta-Analysis software.

Results

Initial search yielded 1,324 scientific studies with a total of 15 studies fitting our inclusion criteria. ICD shocks at 1 year post CSD revealed an event rate of 69.8% (95% CI, 56.4% – 80.4% with 50% heterogeneity) (I2statistic)). ICD shocks at 6 months had an event rate of 59.1% (95% CI 46.9% - 70.4%, 47 I2). Freedom of VTA 1 year post CSD revealed an event rate of 64.3% (95% CI, 42.3% - 81.5%, 26% I2). Freedom from VTA at 6 months revealed an event rate of of 62.3% (95% CI, 51.2% - 72.2%, 40% I2). Reported mortality due to VTA was subdivided into short-term (0-30 days), intermediate-term (31-364 days) and long-term (32-364 days). The event rate for the short-term tertile was 8.9% (95% CI, 5.0% - 15.4%, 0% I2), medium-term was 5.3% (95% CI, 2.4% - 11.3%, 0% I2) and long-term 5.2% (95% CI, 2.4% - 10.9%, 0% I2).

Conclusion

CSD seems to be promising as an acceptable treatment strategy for recurrent VTA refractory to traditional pharmacological or ablation therapy.
Mechanism of recurrent outbreak of the scarlet fever epidemics in mainland China
Authors: Sun Meirong , Li Meijia , Haihambo Naem , Zhang Huiwen , Zhang Zhizhen , Zhao Xixi , Wang Bin , Guo Mingrou , Han Chuanliang
Published: August 2024

In mainland China, most infectious diseases occur once a year, except for scarlet fever, which has been steadily breaking out twice a year in recent years. Over the years, the recurrence of scarlet fever, a contagious disease characterized by a distinctive red rash, has been a focus of attention. However, the oscillatory mechanism of scarlet fever remains unclear. This study aimed to uncover how meteorological factors contribute to the recrudescence of scarlet fever in mainland China. The study used a longitudinal public dataset covering 31 provinces in mainland China, containing 14 years of monthly scarlet fever infections, along with available local meteorological data. Power spectrum analysis was conducted on time series data, and correlation analyses were performed to assess the relationship between the oscillatory nature of epidemics and meteorological factors. We found that the scarlet fever epidemics generally occur twice a year in various provinces of China, and the timing of these outbreaks’ peaks progressively from southern to northern regions. Furthermore, we established an atlas that shows the relationship between scarlet fever oscillation and meteorological factors. Our findings indicated a significant correlation between the oscillation characteristics of scarlet fever in 50% of provinces and each natural meteorological factor. Our study presents a detailed description of the temporal and spatial changes in the oscillatory characteristics of scarlet fever for the first time and explores the oscillatory characteristics of natural meteorological conditions and their correlation with the number of scarlet fever infections. These findings could serve as a valuable guide for government prevention and control measures for the scarlet fever epidemic.
Ultrastructure of immature synaptic inputs in the lateral superior olive of rodent brainstem
Authors: Ma Siyi , Watanabe Shigeki , Gillespie Deda C.
Published: August 2024

Neurons of the lateral superior olive (LSO), which compute intensity differences between the two ears, receive two primary inputs, an ipsilaterally arising excitatory input and a contralaterally arising inhibitory input, that are precisely matched for stimulus frequency. Circuit refinement to establish this precise match takes place within the first few postnatal weeks through elimination of single-fiber inputs and concomitant strengthening of the remaining inputs. However, little is known about the ultrastructure of these young synapses and about how changes in physical features of these synapses could contribute to refinement. To characterize pre-hearing postnatal development of somatic synapses in the LSO, we performed transmission electron microscopy and examined synapses in the rodent LSO from birth to hearing onset at postnatal day 13. Synaptic vesicles and mitochondria in putative synaptic boutons were surprisingly scarce at birth. During the second week, bouton enlargement was accompanied by an increase in the number of vesicles and mitochondria. The size of mitochondria also increased, pointing to changes in functional and metabolic needs of synapses. Our results reveal extensive remodeling at individual presynaptic terminals that could strengthen single-fiber inputs and contribute to the development of robust synaptic transmission.
A qMRI approach for mapping microscopic water populations and tissue relaxivity in thein vivohuman brain
Authors: Shir Filo , Cohen Lee , Yahalom Gilad , Mezer Aviv A.
Published: August 2024

Quantitative magnetic resonance imaging (qMRI) enables non-invasive mapping of brain tissue microstructure and is widely used for monitoring various physiological and pathological brain processes. Here, we introduce a qMRI approach for enriching the microstructural characterization of the sub-voxel environment. Inspired by pioneering magnetization transfer (MT) models, this approach employs MT saturation to differentiate between various water populations within each voxel. Ourin vivoresults align well with theoretical predictions and are reproducible using standard qMRI protocols. We present an array of new quantitative maps, highlighting different aspects of the tissue’s water. Furthermore, by manipulating the effective water content and relaxation rate with MT, we approximate within the voxel the tissue relaxivity. This property reflects the dependency of R1 on the macromolecular tissue volume (MTV) and is associated with the lipid and macromolecular composition of the brain. Our approach also enables biophysically-informed modulation of the R1 contrast, resulting in a set of unique cortical profiles. Finally, we demonstrate the effectiveness of our technique in imaging the common pathology of white matter hyperintensities (WMH), revealing tissue degradation and molecular alterations.
Genetically and Functionally Distinct Immunoglobulin Heavy Chain Locus Duplication in Bats
Authors: Pursell Taylor , Reers Ashley , Mikelov Artem , Kotagiri Prasanti , Ellison James A. , Hutson Christina L. , Boyd Scott D. , Frank Hannah K.
Published: August 2024

The genetic locus encoding immunoglobulin heavy chains (IgH) is critical for vertebrate humoral immune responses and diverse antibody repertoires. Immunoglobulin and T cell receptor loci of most bat species have not been annotated, despite the recurrent role of bats as viral reservoirs and sources of zoonotic pathogens. We investigated the genetic structure and function of IgH loci across the largest bat family, Vespertilionidae, focusing on big brown bats(Eptesicus fuscus). We discovered thatE. fuscusand ten other species within Vespertilionidae have two complete, functional, and distinct immunoglobulin heavy chain loci on separate chromosomes. This locus organization is previously unknown in mammals, but is reminiscent of more limited duplicated loci in teleost fish. Single cell transcriptomic data validate functional rearrangement and expression of immunoglobulin heavy chains of both loci in the expressed repertoire ofEptesicus fuscus, with maintenance of allelic exclusion, bias of usage toward the smaller and more compact IgH locus, and evidence of differential selection of antigen-experienced B cells and plasma cells varying by IgH locus use. This represents a unique mechanism for mammalian humoral immunity and may contribute to bat resistance to viral pathogenesis.
Evidence for S331-G-S-L within the amyloid core of myocilin olfactomedin domain fibrils based on low-resolution 3D solid-state NMR spectra
Authors: Saccuzzo Emily G. , Robang Alicia S. , Gao Yuan , Chen Bo , Lieberman Raquel L. , Paravastu Anant K.
Published: August 2024

Myocilin-associated glaucoma is a protein-conformational disorder associated with formation of a toxic amyloid-like aggregate. Numerous destabilizing single point variants, distributed across the myocilin olfactomedin β-propeller (OLF, myocilin residues 245-504, 30 kDa) are associated with accelerated disease progression.In vitro, wild type (WT) OLF can be promoted to form thioflavin T (ThT)-positive fibrils under mildly destabilizing (37°C, pH 7.2) conditions. Consistent with the notion that only a small number of residues within a protein are responsible for amyloid formation, 3D13C-13C solid-state NMR spectra show that OLF fibrils are likely to be composed of only about one third of the overall sequence. Here, we probe the residue composition of fibrils formedde novofrom purified full-length OLF. We were able to make sequential assignments consistent with the sequence S331-G-S-L334. This sequence appears once within a previously identified amyloid-prone region (P1, G326AVVYSGSLYFQ) internal to OLF. Since nearly half of the pairs of adjacent residues (di-peptides) in OLF occur only once in the primary structure and almost all the 3-residue sequences (tri-peptides) are unique, remarkably few sequential assignments are necessary to uniquely identify specific regions of the amyloid core. This assignment approach could be applied to other systems to expand our molecular comprehension of how folded proteins undergo fibrillization.

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The SH Protein of Mumps Virus is a Druggable Pentameric Viroporin
Authors: Devantier Kira , Toft-Bertelsen Trine L. , Prestel Andreas , Kjær Viktoria M. S. , Sahin Cagla , Giulini Marco , Louka Stavroula , Spiess Katja , Manandhar Asmita , Qvortup Katrine , Ulven Trond , Bentzen Bo H. , Bonvin Alexandre MJJ , MacAulay Nanna , Kragelund Birthe B. , Rosenkilde Mette M.
Published: August 2024

Viral infections are on the rise and drugs targeting viral proteins are needed. Viroporins constitute a growing group of virus-encoded transmembrane oligomeric proteins that allow passage of small molecules across the membrane. Despite sparsity in viroporin structures, recent work has revealed diversity in both the number of transmembrane helices and oligomeric states. Here we provide evidence that the small hydrophobic protein (SH) from mumps virus is a pentameric viroporin. From extensive biophysical data, a HADDOCK model of full-length SH shows its intracellular C-terminal region to form an extended structure crucial to stabilization of the pentamer. Heterologous expression of wild type SH and variants inXenopus laevisoocytes reveals the viroporin as a chloride channel, facilitated by conserved hydroxyl-carrying residues lining the pore. The channel function of SH is inhibited by the small-molecule BIT225, highlighting the potential for antiviral targeting through SH.
The Rad52 superfamily as seen by AlphaFold
Authors: Al-Fatlawi Ali , Hossen Md. Ballal , de Paula Lopes Stella , Stewart A. Francis , Schroeder Michael
Published: August 2024

1

Rad52, a highly conserved eukaryotic protein, plays a crucial role in DNA repair, especially in double-strand break repair. Recent findings reveal that its distinct structural features, including a characteristicβ-sheet andβ-hairpin motif, are shared with the lambda phage single-strand annealing proteins, Redβ, indicating a common superfamily. Our analysis of over 10,000 single-strand annealing proteins (SSAPs) across all kingdoms of life supports this hypothesis, confirming their possession of the characteristic motif despite variations in size and composition. We found that archaea, representing only 1% of the studied proteins, exhibit most of these variations. Through the examination of four representative archaeal SSAPs, we elucidate the structural relationship between eukaryotic and bacterial SSAPs, highlighting differences inβ-sheet size andβ-hairpin complexity. Furthermore, we identify an archaeal SSAP with a structure nearly identical to the human variant and screen over 100 million unannotated proteins for potential SSAP candidates. Our computational analysis complements existing sequence with structural evidence supporting the suggested orthology among five SSAP families across all kingdoms: Rad52, Redβ, RecT, Erf, and Sak3.
A survey of duckweed species in Southern Italy provided first distribution records of the hybridLemna×mediterraneain nature
Authors: Romano Leone Ermes , Braglia Luca , Iannelli Maria Adelaide , Lee Yuri , Gianì Silvia , Gavazzi Floriana , Morello Laura
Published: August 2024

Interspecific hybridisation and polyploidization are two main driving forces in plant evolution, shaping genomes and favouring evolutionary novelty and ecological adaptation. Recent studies have demonstrated hybridisation within the genusLemna(Lemnaceae Martinov) as well as triploid.L. ×mediterranea, a recently described hybrids betweenLemna minorandLemna gibbawas identified among only long lasting germplasm collections ofin vitropropagated plants, originally collected at different times in the Mediterranean area.

We report the first distribution record ofL. × mediterraneain the nature, in the Campania region of Southern Italy, the same area whereLemna symmeterwas described as a new species about 50 years ago, confirming their synonymy. Eight specimens isolated from five different sampling sites over an area of about 4200 Km2showed identical genetic profiles by Tubulin-Based Polymorphism (TBP) analysis, suggesting their common origin from the same hybridisation event, followed by clonal dispersal. TheL. × mediterraneapopulation of Campania is genetically different from any of the previously analysed clones, suggesting that recurrent hybridisation between the parental species may occur. The natural hybrid clone is triploid, withL.gibbaas the plastid donor, and remarkably similar to it by morphology, although the typical gibbosity of this species becomes evident only uponin vitroflower induction. Flowers are protogynous and self-sterile. Ecological factors including competition with parental and invasive species, niche and climate change adaptation, stability in time and space likely played a role in the successful establishment ofL. × mediterranea.

Highlights

Interspecific hybridisation within the genus Lemna documented in nature

β-tubulin intron length polymorphism for tracking duckweed species distribution

Flower induction in Lemna × mediterranea
Spatial transcriptomic data reveals pure cell types via the mosaic hypothesis
Authors: Wang Yiliu , Koch Christof , Sümbül Uygar
Published: August 2024

Neurons display remarkable diversity in their anatomical, molecular, and physiological properties. Although observed stereotypy in subsets of neurons is a pillar of neuroscience, clustering in high-dimensional feature spaces, such as those defined by single cell RNA-seq data, is often inconclusive and cells seemingly occupy continuous, rather than discrete, regions. In the retina, a layered structure, neurons of the same discrete type avoid spatial proximity with each other. While this principle, which is independent of clustering in feature space, has been a gold standard for retinal cell types, its applicability to the cortex has been only sparsely explored. Here, we provide evidence for such a mosaic hypothesis by developing a statistical point process analysis framework for spatial transcriptomic data. We demonstrate spatial avoidance across many excitatory and inhibitory neuronal types. Spatial avoidance disappears when cell types are merged, potentially offering a gold standard metric for evaluating the purity of putative cell types.
Prediction of symptomatic and asymptomatic bacteriuria in spinal cord injury patients using machine learning
Authors: Hoque M. Mozammel , Noorian Parisa , Espinoza-Vergara Gustavo , To Joyce , Leo Dominic , Chari Priyadarshini , Weber Gerard , Pryor Julie , Duggin Iain G. , Lee Bonsan B. , Rice Scott A. , McDougald Diane
Published: August 2024

Background

Individuals with spinal cord injuries (SCI) frequently rely on urinary catheters to drain urine from the bladder, making them susceptible to asymptomatic and symptomatic catheter-associated bacteriuria and urinary tract infections (UTI). Proper identification of these conditions lacks precision, leading to inappropriate antibiotic use which promotes selection for drug-resistant bacteria. Since infection often leads to dysbiosis in the microbiome and correlates with health status, this study aimed to develop a machine learning-based diagnostic framework to predict potential UTI by monitoring urine and/or catheter microbiome data, thereby minimising unnecessary antibiotic use and improving patient health.

Results

Microbial communities in 609 samples (309 catheter and 300 urine) with asymptomatic and symptomatic bacteriuria status were analysed using 16S rRNA gene sequencing from 27 participants over 18 months. Microbial community compositions were significantly different between asymptomatic and symptomatic bacteriuria, suggesting microbial community signatures have potential application as a diagnostic tool. A significant decrease in local (alpha) diversity was noted in symptomatic bacteriuria compared to the asymptomatic bacteriuria (P< 0.01). Beta diversity measured in weighted unifrac also showed a significant difference (P< 0.05) between groups. Supervised machine learning models trained on amplicon sequence variant (ASVs) counts and bacterial taxonomic abundances (Taxa) to classify symptomatic and asymptomatic bacteriuria with a 10-fold cross-validation approach. Combining urine and catheter microbiome data improved the model performance during cross-validation, yielding a mean area under the receiver operating characteristic curve (AUROC) of 0.91-0.98 (Interquartile range, IQR 0.93-0.96) and 0.78-0.91 (IQR 0.86-0.88) for ASVs and taxonomic features, respectively. ASVs and taxa features achieve a mean AUROC of 0.85-1 (IQR 0.93-0.98) and 0.69-0.99 (IQR 0.78-0.88) in the independent held-out test set, respectively, signifying their potential in differentiating symptomatic and asymptomatic bacteriuria states.

Conclusions

Our findings demonstrate that signatures within catheter and urine microbiota could serve as tools to monitor the health status of SCI patients. Establishing an early warning system based on these microbial signatures could equip physicians with alternative management strategies, potentially reducing UTI episodes and associated hospital costs, thus significantly improving patient quality of life while mitigating the impact of drug-resistant UTI.
Optimized LC-MS/MS method for Doxorubicin quantification: validating drug uptake and tumor reduction in zebrafish xenograft model of breast cancer
Authors: Rahman Ghazala , Pramanik Atanu , Das Susmita , Roy Anindya , Bhargava Anamika
Published: August 2024

Doxorubicin, a potent chemotherapeutic drug, is widely used against various cancers, notably breast cancer. While its efficacy is well-documented, precise dosage determination in experimental models remains challenging. Zebrafish xenografts of various cancers confirm doxorubicin’s anti-cancerous effect; however, since doxorubicin treatment of zebrafish larva is done by adding doxorubicin to fish water, the precise chemotherapeutic dosage for zebrafish larva remains unknown. In this study, we provide a liquid chromatography tandem mass-spectrometry (LC-MS/MS) method for quantifying doxorubicin uptake in zebrafish larvae and thus provide a direct estimate of doses required for the therapeutic effect. Alongside quantification, we measured the therapeutic effect of doxorubicin in zebrafish larvae xenografted with triple negative breast cancer cell line, MDA-MB-231. LD50value of doxorubicin was first determined by incubating 3-days post fertilization (dpf) larvae with different doses of doxorubicin for 72 h. Doxorubicin was quantified both from zebrafish larval homogenate and treatment solution. Analysis was performed by selected-reaction monitoring (SRM) scans in positive ionization mode. LD50value for 72 h calculated to be 35.95 mg/L. As expected, doxorubicin-treated xenografts exhibited a significant reduction in tumor growth. The range of limit of detection (LOD) and limit of quantification (LOQ) for doxorubicin were 2 and 5 μg/L respectively. Intra- and inter-day accuracy was within the range of 82-114%. Overall, in this study we describe a reliable method for quantifying doxorubicin in zebrafish larvae. Our study facilitates precise dosage estimation, enhancing the relevance of zebrafish xenograft model in cancer research and potentially improving translational applications of chemotherapeutic treatments.
Outcome of H5N1 clade 2.3.4.4b virus infection in calves and lactating cows
Authors: Halwe Nico Joel , Cool Konner , Breithaupt Angele , Schön Jacob , Trujillo Jessie D. , Nooruzzaman Mohammed , Kwon Taeyong , Ahrens Ann Kathrin , Britzke Tobias , McDowell Chester D. , Piesche Ronja , Singh Gagandeep , dos Reis Vinicius Pinho , Kafle Sujan , Pohlmann Anne , Gaudreault Natasha N. , Corleis Björn , Ferreyra Franco Matias , Carossino Mariano , Balasuriya Udeni B.R. , Hensley Lisa , Morozov Igor , Covaleda Lina M. , Diel Diego , Ulrich Lorenz , Hoffmann Donata , Beer Martin , Richt Juergen A.
Published: August 2024

In March 2024, highly pathogenic avian influenza virus (HPAIV) clade 2.3.4.4b H5N1 infections in dairy cows were first reported from Texas, USA. Rapid dissemination to more than 190 farms in 13 states followed. Here, we provide results of two independent clade 2.3.4.4b experimental infection studies evaluating (i) oronasal susceptibility and transmission in calves to a US H5N1 bovine isolate genotype B3.13 (H5N1 B3.13) and (ii) susceptibility of lactating cows following direct mammary gland inoculation of either H5N1 B3.13 or a current EU H5N1 wild bird isolate genotype euDG (H5N1 euDG). Inoculation of the calves resulted in moderate nasal replication and shedding with no severe clinical signs or transmission to sentinel calves. In dairy cows, infection resulted in no nasal shedding, but severe acute mammary gland infection with necrotizing mastitis and high fever was observed for both H5N1 genotypes/strains. Milk production was rapidly and drastically reduced and the physical condition of the cows was severely compromised. Virus titers in milk rapidly peaked at 108TCID50/mL, but systemic infection did not ensue. Notably, adaptive mutation PB2 E627K emerged after intramammary replication of H5N1 euDG. Our data suggest that in addition to H5N1 B3.13, other HPAIV H5N1 strains have the potential to replicate in the udder of cows and that milk and milking procedures, rather than respiratory spread, are likely the primary routes of H5N1 transmission between cattle.
Extraction-free colorimetric RT-LAMP for SARS-CoV-2 RNA detection from saliva
Authors: Yang Yuying , Liu Xing , Tie Songyan , Li Xin , Yang Xin , Cao Jianzhong
Published: August 2024

Aim

To develop a rapid and easy diagnostic assay for detection of SARS-CoV-2 RNA presented in saliva samples.

Method

The color-based RT-LAMP was used to detect nucleocapsid (N) gene of SARS-CoV-2 without RNA extraction from saliva.

Results

RNA spiked saliva can be used directly for cDNA synthesis after heat inactivation of the saliva and diluted 2-fold with either water or PBS. For both PCR and LAMP, 20% of saliva did not have obvious effect on the reaction. Saliva did not interfere with RT-LAMP when the volume of saliva was less than 20% of the total volume. The sensitivity of the RT-LAMP reached to 1.034×10-5ng/µl (475 copies/μl). The RT-LAMP assay was validated by testing 20 RNA spiked saliva samples. The assay specificity was similar to that of data without saliva.

Conclusions

The RT-LAMP colorimetric assay can be used as a screening method with the advantages of being rapid, easy to use than the qRT-PCR.
A Refined Analysis of Neanderthal-Introgressed Sequences in Modern Humans with a Complete Reference Genome
Authors: Liang Shen-Ao , Ren Tianxin , Zhang Jiayu , He Jiahui , Wang Xuankai , Jiang Xinrui , He Yuan , McCoy Rajiv , Fu Qiaomei , Akey Joshua M. , Mao Yafei , Chen Lu
Published: August 2024

Background

Leveraging long-read sequencing technologies, the first complete human reference genome, T2T-CHM13, corrects the assembly errors in prior references and addresses the remaining 8% of the genome. While the studies on archaic admixture in modern humans so far have been relying on the GRCh37 reference due to the archaic genome data, the impact of T2T-CHM13 in this field remains unknown.

Results

We remapped the sequencing reads of the high-quality Altai Neanderthal and Denisovan genomes onto GRCh38 and T2T-CHM13 respectively. Compared with GRCh37, we found T2T-CHM13 has a significant improvement of read mapping quality in archaic samples. We then applied IBDmix to identify Neanderthal introgressed sequences in 2,504 individuals from 26 geographically diverse populations in different references. We observed different pre-phasing filtering strategies prevalently used in public data can largely impact determination of archaic ancestry, calling for consideration on the choice of filters. We discovered ~51Mb T2T-CHM13 unique Neanderthal sequences, which are predominantly located in regions where the variants distinct between the GRCh38 and T2T-CHM13 assemblies emerge. Besides, we unfolded new instances of population-specific archaic introgression in diverse populations, covering genes involved in metabolism, olfactory-related, and icon-channel. Finally, we integrated the introgressed sequences and adaptive signals with all references into a visualization database website, called ASH (www.arcseqhub.com), to facilitate the utilization of archaic alleles and adaptive signals in human genomics and evolutionary research.

Conclusions

Our study refines the detection of archaic variations in modern humans, highlights the importance of T2T-CHM13 reference utility, and provides novel insights into functional consequences of archaic hominin admixture.