bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary dynamics of pigmentary grey and non-iridescent structural blue colouration in Tanagers (family: Thraupidae)
Authors: Babarovic Frane , Cooney Christopher R , Guillerme Thomas , Nadeau Nicola J , Thomas Gavin Huw
Published: September 2023

3.1

Birds are one of the most colourful animal groups in the world and there are multiple ways by which they achieve this feature. Mechanisms of colour production range from pigmentary (pigment deposition) to structural (nanostructural arrangements), or the combination of both. Despite the hugebreadthof colour gamut, the basic components of feathers are shared across all of them (keratin, air and presence of pigments in accordance with the colour produced). It has been shown that in some instances, colour evolution between pigmentary and structural colours can proceed by rearrangement of the nano-structural elements of feathers. Here, we investigated evolutionary transitions between pigmentary grey and non-iridescent structural blue. We focus on the Thraupidae (tanagers and allies) that display a variety of blues and greys including a potential transition state that we refer to as slate. We used digitally calibrated images of birds to quantify colour and determine the distinctiveness of slate colour in colourspace. Following, we identify the most likely pathway for the evolution of the colour blue: from grey via slate colour. Our research reveals a new pathway in the evolution of blue colour.
Local field potentials in human motor and non-motor brain areas encode the direction of upcoming movements: An intracerebral EEG classification study
Authors: Combrisson Etienne , Di Rienzo Franck , Saive Anne-Lise , Perrone-Bertolotti Marcela , Soto Juan LP , Kahane Philippe , Lachaux Jean-Philippe , Guillot Aymeric , Jerbi Karim
Published: September 2023

Limb movement direction can be inferred from motor cortex activity. In humans, such decoding has been predominantly demonstrated using the spectral power of electrophysiological signals recorded in sensorimotor areas during movement execution. Yet, it remains unclear to what extent intended hand movement direction can be predicted from brain signals recorded during movement planning. Furthermore, whether other oscillatory features beyond power are also involved in direction encoding is not fully understood. Here, we set out to probe the directional-tuning of oscillatory phase, amplitude and Phase-Amplitude Coupling (PAC) during motor planning and execution, using a machine learning framework on multi-site local field potentials (LFPs) in humans. To this end, we recorded intracranial EEG data from implanted epilepsy patients as they performed a four-direction delayed center-out motor task. We found that LFP power significantly predicted hand-movement direction at execution but also during planning. While successful classification during planning primarily involved low-frequency power in a fronto-parietal circuit, decoding during execution was largely mediated by higher frequency activity in motor and premotor areas. Interestingly, LFP phase at very low frequencies (<1.5 Hz) led to significant decoding in premotor brain regions during execution. The machine learning framework also showed PAC to be uniformly modulated across directions through the task. Cross-temporal generalization analyses revealed that several stable brain patterns in prefrontal and premotor brain regions encode directions across both planning and execution. Finally, multivariate classification led to an increase in overall decoding accuracy (>80%) during both planning and execution. The novel insights revealed here extend our understanding of the role of neural oscillations in encoding motor plans.
A model for the dynamics of expanded CAG repeat alleles:ATXN2andATXN3as prototypes
Authors: Sena Lucas Schenatto , Lemes Renan , Furtado Gabriel Vasata , Saraiva-Pereira Maria Luiza , Jardim Laura Bannach
Published: September 2023

Spinocerebellar ataxia types 2 (SCA2) and 3 (SCA3/MJD) are diseases due to dominant unstable expansions of CAG repeats (CAGexp). Age of onset of symptoms (AO) correlates with the CAGexp length. Repeat instability leads to new expansions, to important AO anticipations and to the eventual extinction of lineages. Because of that, compensatory forces are expected to act on the maintenance of expanded alleles, but they are poorly understood. Here, we described the CAGexp dynamics, adapting a classical equation and aiming to estimate for how many generations will the descendants of ade novoexpansion last. A mathematical model was adapted to encompass anticipation, fitness, and allelic segregation; and empirical data fed the model. The arbitrated ancestral mutations included in the model had the lowest CAGexp and the highest AO described in the literature. One thousand generations were simulated until the alleles were eliminated, fixed, or 650 generations had passed. All SCA2 lineages were eliminated in a median of 10 generations. In SCA3/MJD lineages, 593 were eliminated in a median of 29 generations. The other ones were eliminated due to anticipation after the 650th generation or remained indefinitely with CAG repeats transitioning between expanded and unexpanded ranges. Therefore, the model predicted outcomes compatible with empirical data - the very old ancestral SCA3/MJD haplotype, and thede novoSCA2 expansions -, which previously seemed to be contradictory. This model accommodates these data into understandable dynamics and might be useful for other CAGexp disorders.
Population genomics ofAspergillus sojaeis shaped by the food environment
Authors: Acevedo Kimberly L. , Eaton Elizabeth , Zhao Shu , Chacon-Vargas Katherine , McCarthy Colin M. , Choi Dasol , Yu Jae-Hyuk , Gibbons John G.
Published: September 2023

Traditional fermented foods often contain specialized microorganisms adapted to the unique food environment. For example, the filamentous moldAspergillus oryzae, used in saké fermentation, has evolved to thrive in starch-rich conditions compared to its wild ancestor,Aspergillus flavus. Similarly,Aspergillus sojaeis used in soybean-based food fermentations (e.g.miso and shochu) and is closely related toAspergillus parasiticus. Here, we investigated the impact of long-termA. sojaeusage in soybean fermentation on population structure, genome variation, and phenotypic traits. We analyzed 12A. sojaeand 10A. parasiticusgenomes, along with phenotypic characteristics of 15 isolates. Our results revealed thatA. sojaeisolates formed a distinct population separate fromA. parasiticusand displayed remarkably low levels of genetic diversity, indicative of a recent clonal expansion. Genome comparisons revealed numerous loss-of-function mutations inA. sojae, notably in genes responsible for secondary metabolite production, including genes in the aflatoxin encoding gene cluster. Consequently,A. sojaelacked aflatoxin production, while it varied amongA. parasiticusisolates. No other significant differences were observed in growth rates or other measured phenotypic traits betweenA. sojaeandA. parasiticus. These findings suggest thatA. sojaemay have evolved from a population ofA. parasiticusand lost the ability to produce some secondary metabolites. To elucidate the phenotypic differences betweenA. sojaeandA. parasiticus, future work should focus on the influence of wild and food-associated strains on the sensory aspects and microbial community dynamics of fermented soy products.

Significance Statement

Like plants and animals, microbes were also domesticated by humans, however relatively little is known about how the process of domestication shapes microbial genomes and traits. We found that isolates ofAspergillus sojae, a mold used in the production of miso and soy sauce, makeup a less toxic group that is genetically distinct from its closely related wild ancestorAspergillus parasiticus. Our analyses shed new light on commonalities observed across filamentous molds adapted to the food environment.
OxLDL/LOX-1 Mediated Sex, Age, and Cell Dependent Alterations in Mouse Thoracic Aortic Vascular Reactivity
Authors: Wendt Trevor S. , Gonzales Rayna J.
Published: September 2023

Elevated oxidized low-density lipoprotein (oxLDL) is a risk factor and component that worsens cardiovascular disease states. OxLDL can elicit its detrimental action, via lectin-like oxLDL receptor 1 (LOX-1) and has been shown to disrupt vascular function. In this study, we determined whether oxLDL, via LOX-1, alters aortic vascular reactivity and determined if sex differences exist. Thoracic aortic endothelium-intact or -denuded ring segments were isolated from intact C57BL/6J female and male mice and incubated with oxLDL ex vivo (50ug/dL; 2h). Using wire myography, cumulative concentration-response curves to phenylephrine (PE) were generated to determine contractile responses. From these curves, the EC50 was determined and used to contract rings to assess acetylcholine (ACh) dependent relaxation. Calculated aortic stiffness and remodeling, as well as mRNA expression of vasoactive and pro-inflammatory mediators were assessed. BI-0115 (10μM; selective LOX-1 inhibitor) was used to determine LOX-1 dependence. We observed differential sex, age, endothelial cell, and LOX-1 dependent alterations to the efficacy of PE-induced contractile responses and ACh-mediated vasorelaxation in the thoracic aortic rings following oxLDL exposure. Additionally, we observed a distinct sex and age effect on thoracic aortic stiffness following exposure to oxLDL. There was also a sex effect on calculated vessel diameter, as well as an age effect on oxLDL-mediated inward remodeling that was LOX-1 dependent. Thus, LOX-1 inhibition and the resulting attenuation of oxLDL/endothelial-mediated alterations in aortic function suggests that there are differential sex differences in the role of oxLDL/LOX-1 in the thoracic aorta of male and female mice.

NEW & NOTEWORTHY

We investigated the effects of oxidized low-density lipoprotein (oxLDL) via the LOX-1 receptor on murine thoracic aortic vasoreactivity, stiffness, and remodeling across age and sex. Acute exposure to oxLDL led to altered vasoreactivity, endothelial dysfunction, and changes in aortic stiffness and remodeling. These effects were in-part age, sex, endothelial, and LOX-1 dependent. This study reveals potential complex interactions in oxLDL/LOX-1-mediated vascular responses that could serve as potential therapeutic intervention for vascular diseases such as atherosclerosis.
Deep Learning Model for Tumor Type Prediction using Targeted Clinical Genomic Sequencing Data
Authors: Darmofal Madison , Suman Shalabh , Atwal Gurnit , Chen Jie-Fu , Chang Jason C. , Toomey Michael , Vakiani Efsevia , Varghese Anna M , Rema Anoop Balakrishnan , Syed Aijazuddin , Schultz Nikolaus , Berger Michael , Morris Quaid
Published: September 2023

Tumor type guides clinical treatment decisions in cancer, but histology-based diagnosis remains challenging. Genomic alterations are highly diagnostic of tumor type, and tumor type classifiers trained on genomic features have been explored, but the most accurate methods are not clinically feasible, relying on features derived from whole genome sequencing (WGS), or predicting across limited cancer types. We use genomic features from a dataset of 39,787 solid tumors sequenced using a clinical targeted cancer gene panel to develop Genome-Derived-Diagnosis Ensemble (GDD-ENS): a hyperparameter ensemble for classifying tumor type using deep neural networks. GDD-ENS achieves 93% accuracy for high-confidence predictions across 38 cancer types, rivalling performance of WGS-based methods. GDD-ENS can also guide diagnoses on rare type and cancers of unknown primary, and incorporate patient-specific clinical information for improved predictions. Overall, integrating GDD-ENS into prospective clinical sequencing workflows has enabled clinically-relevant tumor type predictions to guide treatment decisions in real time.
Pre-dominance of dengue non-cross-reacting SARS-CoV-2 spike antibodies during the Omicron era and their role in the ADE-mediated surge of Dengue virus serotype 3
Authors: Sarker Supratim , Dutta Chiroshri , Mallick Abinash , Das Sayantan , Chowdhury Chandrika Das , De Abhishek , Gorai Surajit , Biswas Subhajit
Published: September 2023

In India, the SARS-CoV-2 Delta wave (2020-21) gradually faded away with the advent of the Omicron variants (2021-present). Dengue incidences were observably less in Southeast Asia during the active years of the pandemic (2020-21). However, Dengue virus type 3 (DV3) cases were increasingly reported in India and many other dengue-endemic countries concurrent with the progression of the Omicron wave since 2022. This observation prompted us to investigate the current state of cross-reactivity between prevalent SARS-CoV-2 variants and different DV serotypes.

Fifty-five COVID-19 serum samples (collected between January-September, 2022) and three pre-pandemic healthy serum samples were tested for DV or SARS-CoV-2 Immunoglobulin G/Immunoglobulin M (IgG/IgM) using the lateral flow immunoassays (LFIAs). The SARS-CoV-2 antibody (Ab)-positive samples were further tested for their ability to cross-neutralize DV types 1-4 (DV1-4) in Huh7 cell lines.

Cross-reactivity between SARS-CoV-2 and DV diminished with the shift from Delta to Omicron prevalence. COVID-19 serum samples that were DV cross-reactive neutralized all DV serotypes, including DV3. However, Omicron wave serum samples were predominantly DV non-cross-reactive (about 70%) in LFIAs and coincided with the prevalence of BA.2 Omicron variant. They also cross-neutralized DV1, 2 and 4 but enhanced DV3 infectivity as evident from increased DV3 titres in virus neutralization test (VNT) compared to control serum samples.

In conclusion, DV non-cross-reactive COVID-19 serum samples are becoming increasingly prominent in the present times. These non-cross-reactive serums could neutralize DV1, 2 and 4 but they are contributing to the surge in DV3 cases worldwide by means of ADE.
Change in body weight of older adults before and during the COVID-19 pandemic: Longitudinal results from the Berlin Aging Study II
Authors: Vetter Valentin Max , Drewelies Johanna , Düzel Sandra , Homann Jan , Meyer-Arndt Lil , Braun Julian , Pohrt Anne , Kendel Friederike , Wagner Gert G. , Thiel Andreas , Bertram Lars , Regitz-Zagrosek Vera , Gerstorf Denis , Demuth Ilja
Published: September 2023

Background

Change in body weight during the COVID-19 pandemic as an unintended side effect of lockdown measures has been predominantly reported for younger and middle-aged adults. However, information on older adults for which weight loss is known to result in adverse outcomes, is scarce.

Aims

Describe body weight change in older adults before, during, and after the COVID-19 lockdown measures and explore putative associated factors with a focus on the period that includes the first six months of the COVID-19 containment measures.

Methods

In this study, we analyzed the longitudinal weight change of 472 participants of the Berlin Aging Study II (mean age of 67.5 years at baseline, average follow-up time 10 years). Additionally, differences between subgroups characterized by socio-economic, cognitive, and psychosocial variables as well as morbidity burden, biological age markers (epigenetic clocks, telomere length), and frailty were compared.

Results

On average, women and men lost 0.87% (n=227) and 0.5% (n=245) of their body weight per year in the study period covering the first six months of the COVID-19 pandemic. Weight loss among men was particularly pronounced among groups characterized by change in physical activity due to COVID-19 lockdown, low positive affect, premature epigenetic age (7-CpG clock), diagnosed metabolic syndrome, and a more masculine gender score (all variables: p<0.05, n=245).

Conclusions

Older participants lost weight with a 2.5-times (women) and 2-times (men) higher rate than what is expected in this age.
A Nanopore sequencing-based pharmacogenomic panel to personalize tuberculosis drug dosing
Authors: Verma Renu , Esther da Silva Kesia , Rockwood Neesha , Wasmann Roeland E. , Yende Nombuso , Song Taeksun , Kim Eugene , Denti Paolo , Wilkinson Robert J. , Andrews Jason R.
Published: September 2023

Rationale

Standardized dosing of anti-tubercular (TB) drugs leads to variable plasma drug levels, which are associated with adverse drug reactions, delayed treatment response, and relapse. Mutations in genes affecting drug metabolism explain considerable interindividual pharmacokinetic variability; however, pharmacogenomic (PGx) assays that predict metabolism of anti-TB drugs have been lacking.

Objectives

To develop a Nanopore sequencing panel and validate its performance in active TB patients to personalize treatment dosing.

Measurements and Main Results

We developed a Nanopore sequencing panel targeting 15 single nucleotide polymorphisms (SNP) in 5 genes affecting the metabolism of isoniazid (INH), rifampin (RIF), linezolid and bedaquiline. For validation, we sequenced DNA samples (n=48) from the 1000 genomes project and compared variant calling accuracy with Illumina genome sequencing. We then sequenced DNA samples from patients with active TB (n=100) from South Africa on a MinION Mk1C and evaluated the relationship between genotypes and pharmacokinetic parameters for INH and RIF.

Results

The PGx panel achieved 100% concordance with Illumina sequencing in variant identification for the samples from the 1000 Genomes Project. In the clinical cohort, coverage was >100x for 1498/1500 (99.8%) amplicons across the 100 samples. One third (33%) of participants were identified as slow, 47% were intermediate and 20% were rapid isoniazid acetylators. Isoniazid clearance was significantly impacted by acetylator status (p<0.0001) with median (IQR) clearances of 11.2 L/h (9.3-13.4), 27.2 L/h (22.0-31.7), and 45.1 L/h (34.1-51.1) in slow, intermediate, and rapid acetylators. Rifampin clearance was 17.3% (2.50-29.9) lower in individuals with homozygousAADACrs1803155 G>A substitutions (p=0.0015).

Conclusion

Targeted sequencing can enable detection of polymorphisms influencing TB drug metabolism on a low-cost, portable instrument to personalize dosing for TB treatment or prevention.

This manuscript describes the development and validation of Nanopore sequencing panel to detect host pharmacogenomic markers to guide personalized drug dosing for treatment or prevention of tuberculosis.

This article has an online data supplement, which is accessible from this issue’s table of content online atwww.atsjournals.org
Advancing Drug Development with aiHumanoid Simulations: A Virtual Phase 1 Comparative Study of Standard Chemotherapy versus Standard Chemotherapy plus COTI-2 for Pancreatic Adenocarcinoma
Authors: Danter WR
Published: September 2023

Background

Traditional Phase 1 trials often provide important drug development insights, which can be limited by ethical issues, costs, and lengthy timelines. Advancements in AI based simulations offer a potential avenue for mitigating these challenges. The present study used the aiHumanoid platform, specifically the upgraded DeepNEU database v8.1, to design and conduct a virtual Phase 1 trial, to assess the comparative efficacy and toxicity of standard chemotherapy with gemcitabine plus Taxol vs a combination of standard chemotherapy plus COTI-2 for treating Pancreatic Adenocarcinoma (PAC).

Methods

Applying the updated DeepNEU database of 7267 genotypic and phenotypic concepts linked through 67491 relationships, the study used aiHumanoid simulations to predict outcomes from 30 virtual patients. Data from the standard chemotherapy arm and the standard treatment plus COTI2 arm were analyzed at 25%, 50%, 75%, and 100% of maximal dose. Estimates of efficacy and potential toxicities were based on a combination of the paired 2 tailed T test and Cohen’s d values as a true estimate of treatment effects.

Results

The novel combined treatment regimen, especially at 100% dosage, showed medium to large treatment effects on the entire Pancreatic Adenocarcinoma disease profile. Notably, a significant decrease was observed in all disease profile components, bolstered by p-values less than 8.68E-5 and Cohen’s d values >=0.335. While evidence hinted at an increased bone marrow toxicity in the novel treatment arm, no individual organoid toxicity exceeded one standard deviation above predicted values. Importantly, COTI-2 treatment demonstrated a dose-dependent increase in p53 levels, significant at p < 0.006.

Conclusion

This aiHumanoid’s virtual Phase 1 trial emphasizes the potential of computational simulations in the drug development process. Our findings indicate a promising treatment pathway combining COTI-2 with standard chemotherapy for Pancreatic Adenocarcinoma. Ongoing development and validation of the aiHumanoid based virtual Phase 1 clinical trial methodology is warranted.
Characterizing spinal reflexes evoked by spinal cord stimulation to restore sensation in people with lower-limb amputation
Authors: Bose Rohit , Dalrymple Ashley N , Sarma Devapratim , Petersen Bailey A , Barra Beatrice , Nanivadekar Ameya C , Madonna Tyler J , Liu Monica F , Levy Isaiah , Helm Eric R , Miele Vincent J , Capogrosso Marco , Fisher Lee E , Weber Douglas J
Published: September 2023

Background

People with lower-limb amputations lack sensory inputs from their missing limb, which increases their risk of falling. We recently demonstrated that spinal cord stimulation (SCS) can restore sensation in the missing lower limb. Previous studies have shown that SCS can affect motor control by exciting spinal reflex pathways after stroke or spinal cord injury. The effects of SCS on spinal reflex activation have not been studied in people with lower-limb amputation. Furthermore, it is unknown if SCS-evoked spinal reflex activation would perturb walking. Therefore, the goal of this study was to characterize SCS-evoked spinal reflexes in people with lower-limb amputation and quantify effects on gait parameters, including step cycle duration and limb alternation symmetry.

Methods

We implanted percutaneous SCS electrodes over the lumbosacral enlargement in 3 people with trans-tibial amputation (2 diabetic neuropathy; 1 traumatic) for 28 or 84 days. SCS was delivered to restore sensation in the missing limb during walking based on signals from a pressure-sensing insole in the shoe under the prosthesis. We used electromyography (EMG) to record posterior root-muscle (PRM) reflexes in the residual limb while participants were seated, standing, or walking. We characterized rate-dependent depression and recruitment properties of the PRM reflexes. We used pressure data from instrumented insoles to measure the step cycle duration and limb alternation symmetry with and without SCS.

Results

SCS evoked PRM reflexes in the residual limb muscles in all participants, which was confirmed by the presence of rate-dependent depression at stimulation frequencies ≥2Hz. Overall, there was broad activation of residual limb muscles with SCS that varied with the position of the stimulating electrode relative to the lumbar spinal cord. PRM reflexes were also activated during walking, as confirmed by the presence of rate-dependent depression. However, SCS-evoked PRM reflexes did not disrupt gait, with similar step cycle duration or limb alternation symmetry with and without SCS.

Conclusions

Restoring sensation in the missing limb using SCS excites spinal reflexes according to the expected rostral-caudal myotomes but does not disrupt the step cycle duration or limb alternation symmetry in people with trans-tibial amputation.
Polygenic Scores for Longitudinal Prediction of Incident Type 2 Diabetes in an Ancestrally and Medically Diverse Primary Care Network
Authors: Mandla Ravi , Schroeder Philip , Porneala Bianca , Florez Jose C. , Meigs James B. , Mercader Josep M. , Leong Aaron
Published: September 2023

OBJECTIVE

The clinical utility of genetic information for type 2 diabetes (T2D) prediction with polygenic score (PGS) in ancestrally diverse, real-world US healthcare systems is unclear, especially for those at low clinical phenotypic risk for T2D.

RESEARCH DESIGN AND METHODS

We tested the association of PGS with T2D incidence in patients followed within a primary care practice network over 16 years in four hypothetical scenarios that varied by clinical data availability (N = 14,712): 1) age and sex, 2) age, sex, BMI, systolic blood pressure, and family history of diabetes; 3) all variables in (2) and random glucose; 4) all variables in (3), HDL, total cholesterol, and triglycerides, combined in a clinical risk score (CRS). To determine whether genetic effects differed by baseline clinical risk, we tested for interaction with the CRS.

RESULTS

PGS was associated with incident diabetes in all models. Adjusting for age and sex only, the Hazard Ratio (HR) per PGS standard deviation (SD) was 1.76 (95% CI 1.68, 1.84) and the HR of top 5% of PGS vs interquartile range (IQR) was 2.80 (2.39, 3.28). Adjusting for the CRS, the HR per SD was 1.48 (1.40, 1.57) and HR of top 5% of PGS vs IQR was 2.09 (1.72, 2.55). Genetic effects differed by baseline clinical risk [(PGS-CRS interactionp=0.05; CRS below the median: HR 1.60 (1.43, 1.79); CRS above the median: HR 1.45 (1.35, 1.55)].

CONCLUSIONS

Genetic information can help identify high-risk patients even among those perceived to be low risk in a clinical evaluation.
Use of SGLT2i and ARNi in patients with atrial fibrillation and heart failure in 2021-2022: an analysis of real-world data
Authors: Alonso Alvaro , Morris Alanna A. , Naimi Ashley I. , Alam Aniqa B. , Li Linzi , Subramanya Vinita , Chen Lin Yee , Lutsey Pamela L.
Published: September 2023

Objective

To evaluate utilization of sodium-glucose cotransporter-2 inhibitors (SGLT2i) and angiotensin receptor neprilysin inhibitors (ARNi) in patients with atrial fibrillation (AF) and heart failure (HF).

Methods

We analyzed the MarketScan databases for the period 1/1/2021 to 6/30/2022. Validated algorithms were used to identify patients with AF and HF, and to classify patients into HF with reduced ejection fraction (HFrEF) or preserved ejection fraction (HFpEF). We assessed the prevalence of SGLT2i and ARNi use overall and by HF type. Additionally, we explored correlates of lower utilization, including demographics and comorbidities.

Results

The study population included 60,927 patients (mean age 75, 43% female) diagnosed with AF and HF (85% with HFpEF, 15% with HFrEF). Prevalence of ARNi use was 11% overall (30% in HFrEF, 8% in HFpEF), while the corresponding figure was 6% for SGLT2i (13% in HFrEF, 5% in HFpEF). Use of both medications increased over the study period: ARNi from 9% to 12% (from 22% to 29% in HFrEF, from 6% to 8% in HFpEF), and SGLT2i from 3% to 9% (from 6% to 16% in HFrEF, from 2% to 7% in HFpEF). Female sex, older age, and specific comorbidities were associated with lower utilization of these two medication types overall and by HF type.

Conclusion

Use of ARNi and SGLT2i in patients with AF and HF is suboptimal, particularly among females and older individuals, though utilization is increasing. These results underscore the need for understanding reasons for these disparities and developing interventions to improve adoption of evidence-based therapies among patients with comorbid AF and HF.
Antibiotic pharmacokinetics in infected pleural effusions
Authors: Arnold David T , Read Liam , Waddington Oliver , Hamilton Fergus W , Patole Sonia , Hughes Jessica , Milne Alice , Noel Alan , Bayliss Mark , Maskell Nick A , MacGowan Alasdair
Published: September 2023

Pleural infection is usually treated with empirical broad-spectrum antibiotics but limited data exists around their penetrance into the infected pleural space. We performed a pharmacokinetic study analysing the concentration of 5 intravenous antibiotics across 146 separate timepoints in 35 patients (amoxicillin, metronidazole, piperacillin-tazobactam, clindamycin and cotrimoxazole). All antibiotics tested, apart from co-trimoxazole, reach pleural fluid levels equivalent to levels within blood, and well above the relevant minimum inhibitory concentrations. The results demonstrate that concerns around the penetration of commonly used antibiotics, apart from co-trimoxazole, into the infected pleural space are unfounded.
LVING Reveals the Intracellular Structure of Cell Growth
Authors: Pradeep Soorya , Zangle Thomas A.
Published: September 2023

The continuous balance of growth and degradation inside cells maintains homeostasis. Disturbance of the balance by internal or external factors cause state of disease. Effective disease treatments seek to restore this balance. Here, we present a method based on quantitative phase imaging (QPI) based measurements of cell mass and the velocity of mass transport to quantify the balance of growth and degradation within intracellular control volumes. The result, which we call Lagrangian velocimetry for intracellular net growth (LVING), provides high resolution maps of intracellular biomass production and degradation. We use LVING to quantify the growth in different regions of the cell during phases of the cell cycle. LVING can also be used to quantitatively compare the effect of range of chemotherapy drug doses on subcellular growth processes. Finally, we applied LVING to characterize the effect of autophagy on the growth machinery inside cells. Overall, LVING reveals both the structure and distribution of basal growth within cells, as well as the disruptions to this structure that occur during alterations in cell state.
KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells
Authors: Mays Joseph C. , Mei Sally , Kogenaru Manjunatha , Quysbertf Helberth M. , Bosco Nazario , Zhao Xin , Bianchi Joy J. , Goldberg Aleah , Kidiyoor Gururaj Rao , Holt Liam J. , Fenyö David , Davoli Teresa
Published: September 2023

Investigating chromosomal instability and aneuploidy within tumors is essential for understanding tumorigenesis and developing diagnostic and therapeutic strategies. Single-cell DNA sequencing technologies have enabled such analyses, revealing aneuploidies specific to individual cells within the same tumor. However, it has been difficult to scale the throughput of these methods to detect rare aneuploidies while maintaining high sensitivity. To overcome this deficit, we developed KaryoTap, a method combining custom targeted DNA sequencing panels for the Tapestri platform with a computational framework to enable detection of chromosome- and chromosome arm-scale aneuploidy (gains or losses) and copy number neutral loss of heterozygosity in all human chromosomes across thousands of single cells simultaneously. KaryoTap allows detecting gains and losses with an average accuracy of 83% for arm events and 91% for chromosome events. Importantly, together with chromosomal copy number, our system allows us to detect barcodes and gRNAs integrated into the cells’ genome, thus enabling pooled CRISPR- or ORF-based functional screens in single cells. As a proof of principle, we performed a small screen to expand the chromosomes that can be targeted by our recently described CRISPR-based KaryoCreate system for engineering aneuploidy in human cells. KaryoTap will prove a powerful and flexible approach for the study of aneuploidy and chromosomal instability in both tumors and normal tissues.
Visualizing interactions of VDAC1 in live cells using a tetracysteine tag
Authors: Pilic Johannes , Oflaz Furkan E. , Gottschalk Benjamin , Erdogan Yusuf C. , Graier Wolfgang F. , Malli Roland
Published: September 2023

The voltage-dependent anion channel 1 (VDAC1) is a crucial gatekeeper in the outer mitochondrial membrane, controlling metabolic and energy homeostasis. The available methodological approaches fell short of accurate visualization of VDAC1 in living cells. To permit precise VDAC1 imaging, we used the tetracysteine (TC)-tag approach and visualized VDAC1 dynamics in living cells. TC-tagged VDAC1 had a cluster-like distribution on mitochondria. The majority of VDAC1-clusters were localized at endoplasmic reticulum (ER)-mitochondria contact sites. Notably, VDAC1 colocalized with BCL-2 Antagonist/Killer (BAK)-clusters upon apoptotic stimulation. Additionally, VDAC1 was found at mitochondrial fission sites, likely promoting mitochondrial fragmentation. These findings highlight the suitability of the TC-tag for live-cell imaging of VDAC1, shedding light on the roles of VDAC1 in multiple cellular processes.
Genetic manipulation of anIxodes scapulariscell line
Authors: Singh Nisha , Rolandelli Agustin , O’Neal Anya J. , Butler L. Rainer , Samaddar Sourabh , Laukaitis-Yousey Hanna J. , Butnaru Matthew , Mohr Stephanie E. , Perrimon Norbert , Pedra Joao H. F.
Published: September 2023

Although genetic manipulation is one of the hallmarks in model organisms, its applicability to non-model species has remained difficult due to our limited understanding of their fundamental biology. For instance, manipulation of a cell line originated from the blacklegged tickIxodes scapularis,an arthropod that serves as a vector of several human pathogens, has yet to be established. Here, we demonstrate the successful genetic modification of the commonly used tick ISE6 line through ectopic expression and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing. We performed ectopic expression using nucleofection and attained CRISPR-Cas9 editing via homology dependent recombination. Targeting the E3 ubiquitin ligase X-linked inhibitor of apoptosis (xiap) and its substratep47led to alteration in molecular signaling within the immune deficiency (IMD) network and increased infection of the rickettsial agentAnaplasma phagocytophiluminI. scapularisISE6 cells. Collectively, our findings complement techniques for genetic engineering of ticksin vivoand aid in circumventing the long-life cycle ofI. scapularis,of which limits efficient and scalable molecular genetic screens.

Importance

Genetic engineering in arachnids has lagged compared to insects, largely because of substantial differences in their biology. This study unveils the implementation of ectopic expression and CRISPR-Cas9 gene editing in a tick cell line. We introduced fluorescently tagged proteins in ISE6 cells and edited its genome via homology dependent recombination. We ablated the expression ofxiapandp47, two signaling molecules present in the immune deficiency (IMD) pathway ofI. scapularis. Impairment of the tick IMD pathway, an analogous network of the tumor necrosis factor receptor in mammals, led to enhanced infection of the rickettsial agentA. phagocytophilum. Altogether, our findings provide a critical technical resource to the scientific community to enable a deeper understanding of biological circuits in the blacklegged tickIxodes scapularis.
No model to rule them all: a systematic comparison of 83 thermal performance curve models across traits and taxonomic groups
Authors: Kontopoulos Dimitrios - Georgios , Sentis Arnaud , Daufresne Martin , Glazman Natalia , Dell Anthony I. , Pawar Samraat
Published: September 2023

In ectotherms, the performance of physiological, ecological and life-history traits universally increases with temperature to a maximum before decreasing again. Identifying the most appropriate thermal performance model for a specific trait type has broad applications, from metabolic modelling at the cellular level to forecasting the effects of climate change on population, ecosystem and disease transmission dynamics. To date, numerous mathematical models have been designed, but a thorough comparison among them is lacking. In particular, we do not know if certain models consistently outperform others and how factors such as sampling resolution and trait or organismal identity influence model performance. To fill this knowledge gap, we compile 2,739 thermal performance datasets from diverse traits and taxa, to which we fit a comprehensive set of 83 existing mathematical models. We detect remarkable variation in model performance that is not primarily driven by sampling resolution, trait type, or taxonomic information. Our results reveal a surprising lack of well-defined scenarios in which certain models are more appropriate than others. To aid researchers in selecting the appropriate set of models for any given dataset or research objective, we derive a classification of the 83 models based on the average similarity of their fits.
Ultrasensitive quantification of HIV-1 cell-to-cell transmission in primary human CD4+T cells measures viral sensitivity to broadly neutralizing antibodies
Authors: Mazurov Dmitriy , Herschhorn Alon
Published: September 2023

HIV-1 efficiently replicatesin vivoby direct transmission from infected to uninfected CD4+T cells at confined local sites designated virological synapses (VSs). VSs are formed by cell junctions between HIV-1 envelope glycoproteins (Envs) on an infected cell and CD4 on an uninfected cell. These sites facilitate highly efficient viral transmission and contribute to HIV-1 evasion from neutralizing antibodies, but accurate quantification of the efficiency of cell-cell transmission is still challenging. Here, we developed an ultrasensitive HIV-1 cell- to-cell transmission assay that triggers the expression of thenanoluciferase (nluc)gene in target cells upon transmission and after reverse transcription of the HIV-1 RNA genome. The assay is based on insertion of thenlucgene in an antisense orientation into HIV-1 provirus; Nluc expression is blocked in virus-producing cells because thenlucgene contains an intron that can be efficiently spliced out only when mRNA is transcribed from the opposite (sense) strand. Thus, only sense mRNA that is spliced and subsequently reversed transcribed during transmission to target cells will support Nluc expression. Assay optimization resulted in a very low background, >99% splicing efficiency, high sensitivity and wide dynamic range for detection of cell-cell transmission in T cell lines and primary CD4+T cells. The new reporter vector can detect cell-cell transmission using single-round viral vectors and HIV-1 molecular clones, which provide viral proteins of different HIV-1 strains, and reproducibly measures sensitivity of HIV-1 transmission to antibody neutralizationin vitro. This assay will contribute to understanding fundamental mechanisms of HIV-1 cell-to-cell transmission, allow evaluation of pre-existing or acquired HIV-1 resistance in clinical trials, and can be adapted to study other retroviruses.
Discovering Disease Genes in PPI Networks: A Bridge from Centrality to Communities
Authors: Khan Mehwish Wahid , Shams Malick Rauf Ahmed , Cherifi Hocine
Published: September 2023

Targeted therapies have become pivotal in modern clinical oncology, driven by a molecularlevel understanding of cancer’s intricacies, its progression, and innovative research and technology. Personalized and targeted treatments hinge on identifying key genes, hub genes, or biomarkers. Protein-protein interaction (PPI) networks are instrumental in understanding the molecular basis of diseases. While existing literature has identified significant genes based on network centrality, investigations based on community-aware centrality have been notably absent. This omission matters because disease networks frequently display modular structures, necessitating a new perspective. This study bridges the gap between network centrality and community-based investigations. Indeed, in modular networks, node influence can be categorized into two types: local impact within its community, determined by intra-community connections, and global effect on nodes in other communities, established through inter-community links. This concept extends conventional centrality measures to networks with a community structure. Initially, we performed a comparative analysis of seven PPI networks related to cancer and noncancerous conditions. We explore the correlation between classical network centralities and their equivalents at the global (inter-community) and local (intra-community) levels. Notably, we consistently observed a high correlation between network degree and local degree centrality in all PPIs, leading us to select local degree centrality for further investigation. Pronounced modularity characterizes prostate and cervical disease networks. Consequently, we investigate these networks to identify key genes at the local community level and validate them by examining their expression levels. Variations in gene expression between cancerous and non-cancerous tissues bolster our findings. We identify a novel set of genes as potential key players in prostate and cervical cancer. Specifically, in cervical cancer, the top genes at the mesoscopic level include AKT1, CDK2, BRCA1, VEGFA, SRC, PSMD14, MRPL3, TP53, and NUP37. Meanwhile, the top genes identified in prostate cancer are FOS, TP53, UBA52, HLA-B, TSPO, and CD19. Although we focus on cancer data, our methodology’s versatility makes it applicable to other disease networks, opening avenues to identify key genes as potential drug targets.
CCR3 inhibition suppresses inflammation-driven recruitment of peripheral immune cells to the eye
Authors: Lopez Yesenia , Caryotakis Sofia , Raina Sharda , Rege Sanket V. , Harish Reema , Ray Rebecca , Kosti Idit , Teichert Arnaud , Minami S. Sakura , Dhande Onkar S.
Published: September 2023

C-C chemokine receptor type 3 (CCR3) has been linked with age-related macular degeneration (AMD) pathologies. Specifically, its function as an immune modulator in AMD remains unclear. To address this question, we investigated the impact of CCR3 inhibition on inflammation, a key driver of AMD pathologies, by assessing inflammatory cytokines and infiltrating immune cells in two models of ocular inflammation.

Mice were orally dosed twice a day with AKST4290, a CCR3 small molecular inhibitor, in the sodium iodate (NaIO3) and myelin oligodendrocyte glycoprotein (MOG) models. A combination of autoradiography and analytical chemistry techniques were used to assess drug concentration and distribution. Bead-based multiplexing technology was used to determine cytokine concentrations, and flow cytometry and immunohistochemistry was used to ascertain ocular immune-cell composition.

CCR3 expression was detected in the retinal pigment epithelium (RPE)/choroid complex where AKST4290 was found to preferentially accumulate at sustained levels. In the NaIO3model, inhibition of CCR3 with AKST4290 significantly decreased both the concentration of specific chemokines and the number of multiple populations of infiltrating peripheral immune cell. Furthermore, effects of CCR3 inhibition on immune cell infiltration were confirmed in the MOG model.

These data demonstrate that CCR3 inhibition strongly modulates local inflammation by impacting both cytokine concentrations and immune cell composition in ocular diseases.

Moreover, these findings together with the known role of CCR3 in promoting pathologic angiogenesis implicate a pleiotropic role for CCR3 in AMD.
Machine learning to identify clinically relevantCandidayeast species
Authors: Shankarnarayan Shamanth A. , Charlebois Daniel A.
Published: September 2023

Background

Fungal infections, especially due toCandidaspecies, are on the rise. Multi-drug resistant organism such asCandida aurisare difficult and time consuming to identify accurately.

Machine learning is increasingly being used in health care, especially in medical imaging. In this study, we evaluated the effectiveness of six convolutional neural networks (CNNs) to identify four clinically importantCandidaspecies.

Materials and Methods

Wet-mounted images were captured using bright field live-cell microscopy followed by separating single cells, budding cells, and cell group images which were then subjected to different machine learning algorithms (custom CNN, VGG16, ResNet50, InceptionV3, EfficientNetB0, and EfficientNetB7) to learn and predictCandidaspecies.

Results

Among the six algorithms tested, the InceptionV3 model performed best in predictingCandidaspecies from microscopy images. All models performed poorly on raw images obtained directly from the microscope. The performance of all models increased when trained on single and budding cell images. The InceptionV3 model identified budding cells ofC. albicans, C. auris,C. glabrata(Nakaseomyces glabrata), andC. haemuloniiin 97.0%, 74.0%, 68.0%, and 66.0% cases, respectively. For single cells ofC. albicans, C. auris,C. glabrata, andC. haemuloniiInceptionV3 identified 97.0%, 73.0%, 69.0%, and 73.0% cases, respectively. The sensitivity and specificity of InceptionV3 were respectively 77.1% and 92.4%.

Conclusion

This study provides proof of concept that microscopy images from wet mounted slides can be used to identifyCandidayeast species using machine learning quickly and accurately.
Integrative Genomic Analyses Reveal Putative Cell Type-specific Targets of theDrosophilaEts Transcription Factor Pointed
Authors: Bollepogu Raja Komal Kumar , Yeung Kelvin , Shim Yoon-Kyung , Mardon Graeme
Published: September 2023

The Ets domain transcription factors direct diverse biological processes throughout all metazoans and are implicated in development as well as in tumor initiation, progression and metastasis. TheDrosophilaEts transcription factor Pointed (Pnt) is required for several aspects of eye development and regulates cell cycle progression, specification, and differentiation. Despite its critical role in development, very few targets of Pnt have been reported previously. Here, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine the genome-wide occupancy of Pnt in late larval eye discs. We identified enriched regions that mapped to an average of 6,941 genes, the vast majority of which are novel putative Pnt targets. Integrating ChIP-seq data with two other larval eye single cell genomics datasets (scRNA-seq and snATAC-seq) reveals genes that may be putative cell type-specific genes regulated by Pnt. Finally, our ChIP-seq data predict cell type-specific functional enhancers that were not reported previously. Our study provides a greatly expanded list of putative Pnt targets in the eye and is a resource for future studies that will allow mechanistic insights into complex developmental processes regulated by Pnt.
Mitonuclear effects on sex ratio persist across generations in interpopulation hybrids
Authors: Edmands Suzanne , Denova Jacob R. , Flanagan Ben A. , Jah Murad , Applebaum Scott L.
Published: September 2023

Eukaryotic energy production requires tight coordination between gene products from both the nuclear and mitochondrial genomes. Because males and females often have different energetic strategies, this mitonuclear coordination can be expected to differentially impact the two sexes. Previous work found evidence for sex-specific mitonuclear effects in the copepodTigriopus californicusby comparing two parental lines and their reciprocal F1 crosses. However, an alternative hypothesis is that the patterns could instead be driven by the parental source of nuclear alleles. Here we test this alternative hypothesis by extending the same cross to F2 hybrids, who receive both maternal and paternal nuclear alleles from F1 hybrids. Results confirm mitonuclear effects on sex ratio, with distorted ratios persisting from the F1 to F2 generations, despite reduced fitness in F2 hybrids. No sex by cross interactions were found for other phenotypic traits measured. Mitochondrial DNA content was shown to be higher in females, the more stress-tolerant sex. Both routine metabolic rate and oxidative DNA damage were found to be lower in F2 hybrids than in parentals. Confirmation of sex-biased mitonuclear effects inT. californicusis notable, given that the species lacks sex chromosomes, which can confound interpretations of sex-specific mitochondrial effects.