bluuebunny/crossref_metadata_2025 huggingface dataset:
Postacute/Long COVID in Pediatrics
Authors: Morrow Amanda K. , Ng Rowena , Vargas Gray , Jashar Dasal Tenzin , Henning Ellen , Stinson Nika , Malone Laura A.
Published: October 2021

The long-term sequelae after SARS-CoV-2 infections in children is unknown. Guidance is needed on helpful models of care for an emerging subset of pediatric patients with postacute/long COVID who continue to experience persistent symptoms after initial COVID-19 diagnosis. Here, we describe a pediatric multidisciplinary post–COVID-19 rehabilitation clinic model as well as a case series of the initial cohort of patients who presented to this clinic. A consecutive sample of nine patients (pediatric patients <21 yrs of age) who presented to our clinic are included. The most common presenting symptoms were fatigue (8 of 9 patients), headaches (6 of 9), difficulty with schoolwork (6 of 8), “brain fog” (4 of 9), and dizziness/lightheadedness (4 of 9). Most patients had decreased scores on self-reported quality-of-life measures compared with healthy controls. In the patients who participated in neuropsychological testing, a subset demonstrated difficulties with sustained auditory attention and divided attention; however, most of these patients had preexisting attention and/or mood concerns. There were also some who self-reported elevated depression and anxiety symptoms. Pediatric patients with postacute/long COVID may present with a variety of physical, cognitive, and mood symptoms. We present a model of care to address these symptoms through a multidisciplinary rehabilitation approach.
Brief Report: Polymorphisms in CAMKK2 may Influence Domain-Specific Neurocognitive Function in HIV+ Indonesians Receiving ART
Authors: Gaff Jessica , Estiasari Riwanti , Diafiri Dinda , Halstrom Samuel , Kamerman Peter , Price Patricia
Published: October 2021

Background:

Despite effective antiretroviral therapy (ART), milder forms of HIV-associated neurocognitive disorders remain prevalent and are characterized by neuroinflammation, synaptic dysfunction, and neuronal loss.

Methods:

We explore associations between neurocognitive impairment in HIV+ Indonesians and 17 polymorphisms in adjacent genes involved in inflammation and neuronal growth/repair pathways, P2X4R and CAMKK2. HIV+ Indonesians (n = 59) who had received ART for 12 months were assessed to derive Z-scores for the attention, fluency, memory, executive, and motor speed domains relative to local control subjects. These were used to determine total cognitive scores.

Results:

No alleles of P2X4R displayed significant associations with neurocognition in bivariate or multivariable analyses. In CAMKK2, rs2686344 influenced total cognitive scores in bivariate analyses (P = 0.04). Multivariable linear regression modeling independently associated rs2686344 with higher executive function Z-scores (P = 0.05) after adjusting for CD4 T-cell counts (adjusted R2 = 0.103, model P = 0.034), whereas rs1653588 associated with lower and rs1718120 (P = 0.05) with higher fluency Z-scores (P = 0.05) after adjusting for education and log10 HIV RNA copies/mL (adjusted R2 = 0.268, model P = 0.001).

Conclusions:

Polymorphisms in CAMKK2 may influence neurocognitive outcomes in specific domains in HIV+ Indonesians receiving ART for 12 months.
Forecasting HIV-1 Genetic Cluster Growth in Illinois,United States
Authors: Ragonnet-Cronin Manon , Hayford Christina , D'Aquila Richard , Ma Fangchao , Ward Cheryl , Benbow Nanette , Wertheim Joel O.
Published: October 2021

Background:

HIV intervention activities directed toward both those most likely to transmit and their HIV-negative partners have the potential to substantially disrupt HIV transmission. Using HIV sequence data to construct molecular transmission clusters can reveal individuals whose viruses are connected. The utility of various cluster prioritization schemes measuring cluster growth have been demonstrated using surveillance data in New York City and across the United States, by the Centers for Disease Control and Prevention (CDC).

Methods:

We examined clustering and cluster growth prioritization schemes using Illinois HIV sequence data that include cases from Chicago, a large urban center with high HIV prevalence, to compare their ability to predict future cluster growth.

Results:

We found that past cluster growth was a far better predictor of future cluster growth than cluster membership alone but found no substantive difference between the schemes used by CDC and the relative cluster growth scheme previously used in New York City (NYC). Focusing on individuals selected simultaneously by both the CDC and the NYC schemes did not provide additional improvements.

Conclusion:

Growth-based prioritization schemes can easily be automated in HIV surveillance tools and can be used by health departments to identify and respond to clusters where HIV transmission may be actively occurring.
Characterization of the Population Affected by the 6-Month Recertification Criterion of the Ryan White HIV/AIDS Program's AIDS Drug Assistance Program in Washington State, 2017–2019
Authors: Erly Steven , Khosropour Christine M. , Hajat Anjum , Sharma Monisha , Reuer Jen , Grimm Martha , Kwaiser Kelse , Dombrowski Julia C.
Published: October 2021

Introduction:

AIDS Drug Assistance Programs (ADAPs) provide financial support for medical care for people living with HIV (PLWH) in the United States. Federal policy requires that clients recertify for the program every 6 months, which has been described as a barrier to care access. Our objective was to describe the prevalence of and factors associated with ADAP disenrollment in Washington State.

Methods:

Between 2017 and 2019, we categorized ADAP clients by the success of their recertification applications as follows: (1) continuously enrolled, (2) ruled ineligible, or (3) disenrolled if they failed to recertify. We compared individuals who were disenrolled with those who were continuously enrolled by demographic and socioeconomic characteristics and engagement with case management using data from the Washington State HIV Surveillance and Ryan White data systems.

Results:

From 2017 to 2019, 5480 clients were enrolled in ADAP, of whom 1423 (26%) were disenrolled and 984 (18%) were ruled ineligible at least once. Compared with those who were continuously enrolled, disenrolled PLWH were more likely to be Black [unadjusted prevalence ratio (PR) vs White 1.31, 95% confidence interval (CI): 1.17 to 1.46], uninsured (PR vs private insurance 1.24, 95% CI: 1.10 to 1.40), and younger (PR 25–34 vs 35–44 years 1.23, 95% CI: 1.08 to 1.41). The median time to return after disenrollment was 12 months (95% CI: 8 to 19 months).

Conclusions:

Disenrollment after failure to recertify was the most common reason why PLWH lost ADAP coverage in Washington State. ADAP recertification procedures disproportionately affect Black, young, and uninsured PLWH and may contribute to disparities in HIV outcomes.
Tranexamic Acid in Craniosynostosis Surgery: A Systematic Review and Meta-Analysis
Authors: Varidel Alistair , Marucci Damian
Published: October 2021

Blood loss is a potential cause of morbidity and mortality in craniosynostosis surgery. Recent reports have suggested that the use of tranexamic acid (TXA), an antifibrinolytic agent, mitigates this blood loss. A comprehensive systematic review and subsequent meta-analysis was undertaken, with the view to clarify the effectiveness of TXA in reducing blood loss and transfusion requirements in craniosynostosis surgery. Medline and PubMed databases were searched using the preferred reporting items for systematic reviews and meta-analyses technique, and 7003 articles were assessed based on predefined selection criteria. Seven trials were identified, of which 2 were randomized controlled trials and the remainder retrospective cohort studies. All trials were assessed using the Jadad and strengthening the reporting of observational studies in epidemiology scores. The meta-analysis found a clear statistical reduction in blood loss in those patients who received TXA perioperatively, with a combined blood loss reduction of 7.06 ml/kg (95% confidence interval −8.97 to −5.15, P < 0.00001). The blood loss reduction was found to extrapolate to a reduction in perioperative transfusion requirements by 8.47 ml/kg in this cohort (95% confidence interval −10.9 to −6.04, P < 00001). There were no TXA-related adverse outcomes recorded in the 258 patients who received TXA across all trials. The trials included in this meta-analysis were limited by underpowered population sizes and significant heterogeneity in blood loss recording techniques. Further, there was significant heterogeneity amongst operations performed. The current literature appears to support the use of TXA in craniosynostosis surgery, but further high quality randomized controlled trials are indicated, ideally including a subgroup analysis between the operations performed.
Relationship Between Blood Glucose Level and Prevalence and Frequency of Stress Urinary Incontinence in Women
Authors: Ying Youyou , Xu Linlin , Huang Ruofei , Chen Tianxi , Wang Xinghong , Li Ke , Tang Lixia
Published: October 2021

Objectives

The purpose of this study was to evaluate the relationship between blood glucose level and the prevalence and frequency of stress urinary incontinence (SUI) in women.

Methods

We conducted a cross-sectional study of female participants in the National Health and Nutrition Examination Survey database between 2007 and 2016. Dose-response analysis curves and univariate and multivariate logistic regressions were used to determine the relationship between blood glucose level and the prevalence and frequency of SUI.

Results

A total of 10,771 participants were included in this study, of which 6,466 (60.0%) reported no SUI, 4,305 (31.1%) reported monthly SUI, and 953 (8.8%) reported weekly SUI. We found that the blood glucose levels were higher in the weekly SUI group than in the monthly SUI and no SUI groups. Based on blood glucose levels, participants were divided into 3 groups: ≤86.0 mg/dL group, >86.0 to 98.0 mg/dL group, and >98.0 mg/dL group. Dose-response curves showed a nonlinear positive correlation between blood glucose levels and the prevalence and extent of SUI, and participants in the glucose >98.0 mg/dL group had a 15.2% higher risk (adjusted odds risk, 1.152; 95% confidence interval, 1.027–1.293; P = 0.016) of SUI prevalence and 12.5% higher risk (adjusted odds risk 1.125; 95% confidence interval, 1.009–1.255; P = 0.034) of SUI frequency than participants in the glucose ≤86.0 mg/dL group.

Conclusions

We found that the prevalence and frequency of SUI in women were positively correlated with blood glucose levels, and these findings warrant further study and application to clinical practice to control SUI in women.
Anoxybacillus karvacharensis sp. nov., a novel thermophilic bacterium isolated from the Karvachar geothermal spring in Nagorno-Karabakh
Authors: Panosyan Hovik , Margaryan Armine , Birkeland Nils-Kåre
Published: October 2021

Twelve thermophilic

Anoxybacillus

strains were isolated from sediment and water samples from a Karvachar hot spring located in the northern part of Nagorno-Karabakh. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, one of the isolates, designated strain K1T, was studied in detail. The cells are straight, motile rods that are 0.2–0.4×2.3–7.2 µm in size. The strain is a Gram-stain-positive, moderately thermophilic facultative anaerobe with an optimum growth temperature of 60–65 °C and a growth temperature range of 45–70 °C. Growth of strain K1T was observed at pH 6–11 (optimum, pH 8–9) and was inhibited in the presence of NaCl concentrations above 2.5 % (optimum, 1–1.5 %). The isolate could utilize a wide variety of carbon sources, including d-arabinose, d-ribose, d-galactose, d-fructose, d-mannitol, maltose, aesculin, melibiose, sucrose, trehalose, raffinose, amidone, glycogen, turanose, d-lyxose, d-tagatose, potassium gluconate and 2-keto-gluconate. The strain was able to hydrolyse starch, casein and gelatin, was positive for oxidase and catalase, and reduced nitrate to nitrite, but was negative for H2S production. Production of urease and indole was not observed. The major cellular fatty acids were C15 : 0 iso, C16 : 0 and C17 : 0 iso (52.5, 13.6 and 19.6 % of total fatty acids, respectively). Strain K1T shares >99 % 16S rRNA sequence similarity and a genomic average nucleotide identity value of 94.5 % with its closest relative,

Anoxybacillus flavithermus

DSM 2641T, suggesting that it represents a separate and novel species, for which the name Anoxybacillus karvacharensis sp. nov. is proposed. The type strain of Anoxybacillus karvacharensis is K1T (=DSM 106524T=KCTC 15807T).
Microbe Profile: Xylella fastidiosa – a devastating agricultural pathogen with an endophytic lifestyle
Authors: Burbank Lindsey P. , Roper M. Caroline
Published: October 2021

Xylella fastidiosa

is a vector-borne plant vascular pathogen that has caused devastating disease outbreaks in diverse agricultural crops worldwide. A major global quarantine pathogen,

X. fastidiosa

can infect hundreds of plant species and can be transmitted by many different xylem sap-feeding insects. Several decades of research have revealed a complex lifestyle dependent on adaptation to the xylem and insect environments and interactions with host plant tissues.
Natural statistics support a rational account of confidence biases
Authors: Webb Taylor W. , Miyoshi Kiyofumi , So Tsz Yan , Rajananda Sivananda , Lau Hakwan
Published: October 2021

Previous work has sought to understand decision confidence as a prediction of the probability that a decision will be correct, leading to debate over whether these predictions are optimal, and whether they rely on the same decision variable as decisions themselves. This work has generally relied on idealized, low-dimensional models, necessitating strong assumptions about the representations over which confidence is computed. To address this, we used deep neural networks to develop a model of decision confidence that operates directly over high-dimensional, naturalistic stimuli. The model accounts for a number of puzzling dissociations between decisions and confidence, reveals a rational explanation of these dissociations in terms of optimization for the statistics of sensory inputs, and makes the surprising prediction that, despite these dissociations, decisions and confidence depend on a common decision variable.
Nanometer-Scale Imaging of Compartment-Specific Localization and Dynamics of Voltage-Gated Sodium Channels
Authors: Liu Hui , Wang Hong-Gang , Pitt Geoffrey S. , Liu Zhe J.
Published: October 2021

Membrane excitability and cell-to-cell communication in the brain are tightly regulated by diverse ion channels and receptor proteins localized to distinct membrane compartments. Currently, a major technical barrier in cellular neuroscience is lack of reliable methods to label these membrane proteins and image their sub-cellular localization and dynamics. To overcome this challenge, we devised optical imaging strategies that enable systematic characterization of subcellular composition, relative abundances and trafficking dynamics of membrane proteins at nanometer scales in cultured neurons as well as in the brain. Using these methods, we revealed exquisite developmental regulation of subcellular distributions of voltage-gated sodium channel (VGSC) Nav1.2 and Nav1.6, settling a decade long debate regarding the molecular identity of sodium channels in dendrites. In addition, we discovered a previously uncharacterized trafficking pathway that targets Nav1.2 to unmyelinated fragments in the distal axon. Myelination counteracts this pathway, facilitating the installment of Nav1.6 as the dominant VGSC in the axon. Together, these imaging approaches unveiled compartment-specific trafficking mechanisms underpinning differential membrane distributions of VGSCs and open avenues to decipher how membrane protein localization and dynamics contribute to neural computation in the brain.
The extended Price equation: migration and sex
Authors: Brown Jake , Field Jared M.
Published: October 2021

The Price equation provides a general partition of evolutionary change into two components. The first is usually thought to represent natural selection and the second, transmission bias. Here, we provide a new derivation of the generalised equation, which contains a largely ignored third term. Unlike the original Price equation, this extension can account for migration and mixed asexual and sexual reproduction. The notation used here expresses the generalised equation explicitly in terms of fitness, rendering this otherwise difficult third term more open to biological interpretation and use. This re-derivation also permits fundamental results, derived from the Price equation, to be more easily generalised. We take Hamilton’s rule as a case study, and provide an exact, total expression that allows for population structures like haplodiploidy. Our analysis, more generally, makes clear the previously hidden assumptions in similar fundamental results, highlighting the caution that must be taken when interpreting them.
Delineation and birth of a layered intestinal stem cell niche
Authors: McCarthy Neil , Tie Guodong , Madha Shariq , Kraiczy Judith , Maglieri Adrianna , Shivdasani Ramesh A.
Published: October 2021

Wnt and Rspondin (RSPO) signaling drives proliferation, and bone morphogenetic protein inhibitors (BMPi) impede differentiation, of intestinal stem cells (ISCs). Here we identify the adult mouse ISC niche as a complex, multi-layered structure that encompasses distinct mesenchymal and smooth muscle cell populations. Diverse sub-cryptal cells provide redundant supportive factors, with certain BMPi and the most potent Wnt co-factor, RSPO2, restricted to single cell types. Niche functions refine during a critical period of postnatal crypt morphogenesis, in part to oppose dense aggregation of BMP-expressing sub-epithelial myofibroblasts that promote epithelial differentiation. A specialized muscle layer, the muscularis mucosae, first appears during this period and supplements neighboring RSPO and BMPi sources. In vivo ablation of smooth muscle raises BMP activity and potently limits a pre-weaning burst of crypt fission. Thus, distinct and progressively specialized mesenchymal components together create the milieu required to propagate crypts during rapid organ growth and to sustain adult ISCs.
Robust W1282X-CFTR rescue by a small molecule GSPT1 degrader
Authors: Lee Rhianna E. , Lewis Catherine A. , He Lihua , Gallant Samuel C. , Mascenik Teresa M. , Dang Hong , Morton Lisa C. , Minges John T. , Theile Jonathan W. , Castle Neil A. , Knowles Michael R. , Kimple Adam J. , Randell Scott H.
Published: October 2021

With the approval of elexacaftor/tezacaftor/ivacaftor (trade name Trikafta), the vast majority of people with cystic fibrosis (CF) are eligible for CF transmembrane conductance regulator (CFTR) modulator therapy. Remaining individuals have premature termination codons or rareCFTRvariants with limited treatment options. Although clinical modulator response can be reliably predicted using primary airway epithelial cells, primary cells carrying rareCFTRvariants are scarce. To overcome this obstacle, these cells can be expanded by overexpression of mouseBmi-1and humanTERT(hTERT). We therefore used this approach to develop two non-CF and three CF (F508del/F508del, F508del/S492F, W1282X/W1282X) nasal cell lines and two W1282X/W1282X bronchial cell lines. Bmi-1/hTERT cell lines recapitulated primary cell morphology and ion transport function. The F508del/F508del and F508del/S492F cell lines robustly responded to Trikafta, which was mirrored in the parent primary cells and the cell donors’ clinical response. CC-90009, a novel cereblon E3 ligase modulator targeting the GSPT1 protein, rescued ~20% of wildtype CFTR function in our panel of W1282X/W1282X cell lines and primary cells. Intriguingly, CC-90009 also diminished epithelial sodium channel function. These studies demonstrate that Bmi-1/hTERT cell lines faithfully mirror primary cell responses to CFTR modulators and illustrate novel therapeutic approaches for the W1282X CFTR variant.
Extracellular Electron Transfer Enables Cellular Control of Cu(I)-catalyzed Alkyne-Azide Cycloaddition
Authors: Partipilo Gina , Graham Austin J. , Belardi Brian , Keitz Benjamin K.
Published: October 2021

Extracellular electron transfer (EET) is an anaerobic respiration process that couples carbon oxidation to the reduction of metal species. In the presence of a suitable metal catalyst, EET allows for cellular metabolism to control a variety of synthetic transformations. Here, we report the use of EET from the model electroactive bacterium Shewanella oneidensis for metabolic and genetic control over Cu(I)-catalyzed Alkyne-Azide Cycloaddition (CuAAC). CuAAC conversion under anaerobic and aerobic conditions was dependent on live, actively respiring S. oneidensis cells. In addition, reaction progress and kinetics could be further manipulated by tailoring the central carbon metabolism of S. oneidensis. Similarly, CuAAC activity was dependent on specific EET pathways and could be manipulated using inducible genetic circuits controlling the expression of EET-relevant proteins including MtrC, MtrA, and CymA. EET-driven CuAAC also exhibited modularity and robustness in ligand tolerance and substrate scope. Furthermore, the living nature of this system could be exploited to perform multiple reaction cycles without requiring regeneration, something inaccessible to traditional chemical reductants. Finally, S. oneidensis enabled bioorthogonal CuAAC membrane labelling on live mammalian cells without affecting cell viability, suggesting that S. oneidensis can act as a dynamically tunable biocatalyst in complex environments. In summary, our results demonstrate how EET can expand the reaction scope available to living systems by enabling cellular control of CuAAC.
TACI: an ImageJ plugin for 3D calcium imaging analysis
Authors: Omelchenko Alisa A. , Bai Hua , Hussain Sibtain , Tyrrell Jordan J. , Ni Lina
Published: October 2021

Research in the field of neuroscience has evolved to use complex imaging and computational tools to extract comprehensive information from data sets. Calcium imaging is a widely used technique that requires sophisticated software to obtain reproducible results, but many laboratories struggle to adopt computational methods when updating protocols to meet modern standards. Difficulties arise due to the lack of computational knowledge and paywalls for software. In addition, most calcium imaging analysis approaches ignore motion on the z-axis. Here, we described a workflow to use ImageJ to analyze 3D calcium imaging. We applied TrackMate, an open-source ImageJ plugin, to track neurons in the lateral (x/y) direction, detect regions of interest (ROIs), and extract fluorescence intensities. To track motion on the z-axis, we developed a new ImageJ plugin, TrackMate Analysis of Calcium Imaging (TACI). For neurons appearing on multiple z-positions, maximum fluorescence values were identified to represent neurons’ intensities of corresponding z-stacks. This workflow does not require coding ability, avoids human bias, and increases reproducibility. We validated this workflow using fly larval thermosensitive neurons that displayed movements in all directions during temperature fluctuation and a 3D calcium imaging dataset acquired from the fly brain.
Social framing effects in decision making
Authors: Piray Payam , Cools Roshan , Toni Ivan
Published: October 2021

Human decisions are known to be strongly influenced by the manner in which options are presented, the “framing effect”. Here, we ask whether decision-makers are also influenced by how advice from other knowledgeable agents are framed, a “social framing effect”. For example, do students learn better from a teacher who often frames advice by emphasizing appetitive outcomes, or do they learn better from another teacher who usually emphasizes avoiding options that can be harmful to their progress? We study the computational and neural mechanisms by which framing of advice affect decision-making, social learning, and trust. We found that human participants are more likely to trust and follow an adviser who often uses an appetitive frame for advice compared with another one who often uses an aversive frame. This social framing effect is implemented through a modulation of the integrative abilities of the ventromedial prefrontal cortex. At the time of choice, this region combines information learned via personal experiences of reward with social information, but the combination differs depending on the social framing of advice. Personally-acquired information is weighted more strongly when dealing with an adviser who uses an aversive frame. The findings suggest that social advice is systematically incorporated into our decisions, while being affected by biases similar to those influencing individual value-based learning.
Evaluation of Vicinity-based Hidden Markov Models for Genotype Imputation
Authors: Wang Su , Kim Miran , Jiang Xiaoqian , Harmanci Arif
Published: October 2021

The decreasing cost of DNA sequencing has led to a great increase in our knowledge about genetic variation. While population-scale projects bring important insight into genotype-phenotype relationships, the cost of performing whole-genome sequencing on large samples is still prohibitive. In-silico genotype imputation coupled with genotyping-by-arrays is a cost-effective and accurate alternative for genotyping of common and uncommon variants. Imputation methods compare the genotypes of the typed variants with the large population-specific reference panels and estimate the genotypes of untyped variants by making use of the linkage disequilibrium patterns. Most accurate imputation methods are based on the Li-Stephens hidden Markov model, HMM, that treats the sequence of each chromosome as a mosaic of the haplotypes from the reference panel. Here we assess the accuracy of local-HMMs, where each untyped variant is imputed using the typed variants in a small window around itself (as small as 1 centimorgan). Locality-based imputation is used recently by machine learning-based genotype imputation approaches. We assess how the parameters of the local-HMMs impact the imputation accuracy in a comprehensive set of benchmarks and show that local-HMMs can accurately impute common and uncommon variants and can be relaxed to impute rare variants as well. The source code for the local HMM implementations is publicly available at https://github.com/harmancilab/LoHaMMer.
A genetic bottleneck of mitochondrial DNA during human lymphocyte development
Authors: Tang Zhongjie , Lu Zhaolian , Chen Baizhen , Zhang Weixing , Chang Howard Y. , Hu Zheng , Xu Jin
Published: October 2021

Mitochondria are essential organelles in eukaryotic cells that provide critical support for energetic and metabolic homeostasis. Mutations that accumulate in mitochondrial DNA (mtDNA) in somatic cells have been implicated in cancer, degenerative diseases, and the aging process. However, the mechanisms used by somatic cells to maintain proper functions despite their mtDNA mutation load are poorly understood. Here, we analyzed somatic mtDNA mutations in more than 30,000 human single peripheral and bone marrow mononuclear cells and observed a significant overrepresentation of homoplastic mtDNA mutations in B, T and NK lymphocytes despite their lower mutational burden than other hematopoietic cells. The characteristic mutational landscape of mtDNA in lymphocytes were validated with data from multiple platforms and individuals. Single-cell RNA-seq and computational modeling demonstrated a stringent mitochondrial bottleneck during lymphocyte development likely caused by lagging mtDNA replication relative to cell proliferation. These results illuminate a potential mechanism used by highly metabolically active immune cells for quality control of their mitochondrial genomes.
A Pre-Processing Pipeline to Quantify, Visualize and Reduce Technical Variation in Protein Microarray Studies
Authors: Bérubé Sophie , Kobayashi Tamaki , Wesolowski Amy , Norris Douglas E. , Ruczinski Ingo , Moss William J. , Louis Thomas A.
Published: October 2021

Technical variation, or variation from non-biological sources, is present in most laboratory assays. Correcting for this variation enables analysts to extract a biological signal that informs questions of interest. However, each assay has different sources and levels of technical variation and the choice of correction methods can impact downstream analyses. Compared to similar assays such as DNA microarrays, relatively few methods have been developed and evaluated for protein microarrays, a versatile tool for measuring levels of various proteins in serum samples. Here, we propose a pre-processing pipeline to correct for some common sources of technical variation in protein microarrays. The pipeline builds upon an existing normalization method by using controls to reduce technical variation. We evaluate our method using data from two protein microarray studies, and by simulation. We demonstrate that pre-processing choices impact the fluorescent-intensity based ranks of proteins, which in turn, impact downstream analysis.

1

Impact Statement

Protein microarrays are in wide use in cancer research, infectious disease diagnostics and biomarker identification. To inform research and practice in these and other fields, technical variation must be corrected using normalization and pre-processing. Current protein microarray studies use a variety of normalization methods, many of which were developed for DNA microarrays, and therefore are based on assumptions and data that are not ideal for protein microarrays. To address this issue, we develop, evaluate, and implement a pre-processing pipeline that corrects for technical variation in protein microarrays. We show that pre-processing and normalization directly impact the validity of downstream analysis, and protein-specific approaches are essential.
Non-parametric Functional Muscle Network as a Robust Biomarker of Fatigue
Authors: O’Keeffe Rory , Shirazi Seyed Yahya , Yang Jinghui , Mehrdad Sarmad , Rao Smita , Atashzar S. Farokh
Published: October 2021

The possibility of muscle fatigue detection using surface electromyography has been explored and multiple biomarkers, such as median frequency, have been suggested. However, there are contradictory reports in the literature which results in an inconsistent understanding of the biomarkers of fatigue. Thus, there is an unmet need for a statistically robust sEMG-based biomarker for fatigue detection. This paper, for the first time, demonstrates the superior capability of a non-parametric muscle network to reliably detect fatigue-related changes. Seven healthy volunteers completed a lower limb exercise protocol, which consisted of 30s of a sit-to-stand exercise before and after the completion of fatiguing leg press sets. A non-parametric muscle network was constructed, using Spearman’s power correlation and showed a very reliable decrease in network metrics associated with fatigue (degree, weighted clustering coefficient (WCC)). The network metrics displayed a significant decrease at the group level (degree, WCC: p < 0.001), individual subject level (degree: p < 0.035 WCC: p < 0.004) and particular muscle level (degree: p < 0.017). Regarding the decrease in mean degree connectivity at particular muscles, all seven subjects followed the group trend. In contrast to the robust results achieved by the proposed non-parametric muscle network, classical spectrotemporal measurements showed heterogeneous trends at the particular muscle and individual subject levels. Thus, this paper for the first time shows that non-parametric muscle network is a reliable biomarker of fatigue and could be used in a broad range of applications.
Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation
Authors: Wang Jiankang , Bando Masashige , Shirahige Katsuhiko , Nakato Ryuichiro
Published: October 2021

Cohesin, an essential protein complex for chromosome segregation, regulates transcription through a variety of mechanisms. It is not a trivial task to genome-widely assign the diverse cohesin functions. Moreover, the context-specific roles of cohesin-mediated interactions, especially on intragenic regions, have not been thoroughly investigated. Here we performed a comprehensive characterization of cohesin binding sites in several human cell types. We integrated epigenomic, transcriptomic and chromatin interaction data with and without transcriptional stimulation, to explore context-specific functions of intragenic cohesin related to gene activation. We identified a new subset of cohesin binding sites, decreased intragenic cohesin sites (DICs), which have a different function from previously known ones. The intron-enriched DICs were negatively correlated with transcriptional regulation: a subgroup of DICs were related to enhancer markers and paused RNA polymerase II, whereas others contributed to chromatin architecture. We implemented machine learning and successfully isolated DICs with distinct genomic features. We observed DICs in various cell types, including cells from cohesinopathy patients. These results suggest a previously unidentified function of cohesin at intragenic regions for transcription regulation.
Reduced motivation for social contact in Disrupted-in-schizophrenia transgenic rats
Authors: Seidisarouei Mohammad , van Wingerden Marijn , Schäble Sandra , Trossbach Svenja V. , Korth Carsten , Kalenscher Tobias
Published: October 2021

The Disrupted-in-schizophrenia 1 (DISC1) signaling pathway is considered to play a key role in schizophrenia, depression, autism and other psychiatric disorders. DISC1 is involved in regulating the dopaminergic neurotransmission in, among others, the mesolimbic reward system. A transgenic rat line tgDISC1 has been introduced as a model system to study behavioral phenotypes associated with abnormal DISC1 pathways. Here, we evaluated the impact of impaired DISC1 signaling on social (social interaction) and non-social (sucrose) reward preferences in the tgDISC1 animal model. In a plus-maze setting, rats chose between the opportunity for social interaction with an unfamiliar juvenile conspecific (social reward) or drinking sweet solutions with variable sucrose concentrations (non-social reward). tgDISC1 rats differed from wild-type rats in their social, but not in their non-social reward preferences. Specifically, DISC1 rats showed a lower interest in interaction with the juvenile conspecific, but did not differ from wild-type rats in their preference for higher sucrose concentrations. These results suggest that disruptions of the DISC1 pathway that is associated with altered dopamine transmission in the brain result in selective deficits in social motivation seen in neuropsychiatric illness.
Convergent mosaic brain evolution is associated with the evolution of novel electrosensory systems in teleost fishes
Authors: Schumacher Erika L. , Carlson Bruce A.
Published: October 2021

Brain region size generally scales allometrically with total brain size, but mosaic shifts in brain region size independent of brain size have been found in several lineages and may be related to the evolution of behavioral novelty. African weakly electric fishes (Mormyroidea) evolved a mosaically enlarged cerebellum and hindbrain, yet the relationship to their behaviorally novel electrosensory system remains unclear. We addressed this by studying South American weakly electric fishes (Gymnotiformes) and weakly electric catfishes (Synodontis spp.), which evolved varying aspects of electrosensory systems, independent of mormyroids. If the mormyroid mosaic increases are related to evolving an electrosensory system, we should find similar mosaic shifts in gymnotiforms and Synodontis. Using micro-computed tomography scans, we quantified brain region scaling for multiple electrogenic, electroreceptive, and non-electrosensing species. We found mosaic increases in cerebellum in all three electrogenic lineages relative to non-electric lineages and mosaic increases in torus semicircularis and hindbrain associated with the evolution of electrogenesis and electroreceptor type. These results show that evolving novel electrosensory systems is repeatedly and independently associated with changes in the sizes of individual brain regions independent of brain size, which suggests that selection can impact structural brain composition to favor specific regions involved in novel behaviors.
A deep learning algorithm for potato tuber hollow heart classification
Authors: Abbasi Arash , Feldman Max J. , Park Jaebum , Greene Katelyn , Novy Richard G. , Liu Huaping
Published: October 2021

A novel deep learning algorithm is proposed for hollow heart detection which is an internal tuber defect. Hollow heart is one of many internal defects that decrease the market value of potatoes in the fresh market and food processing sectors. Susceptibility to internal defects like the hollow heart is influenced by genetic and environmental factors so elimination of defect-prone material in potato breeding programs is important. Current methods of evaluation utilize human scoring which is limiting (only collects binary data) relative to the data collection capacity afforded by computer vision or are based upon X-ray transmission techniques that are both expensive and can be hazardous. Automation of defect classification (e.g. hollow heart) from data sets collected using inexpensive, consumer-grade hardware has the potential to increase throughput and reduce bias in public breeding programs. The proposed algorithm consists of ResNet50 as the backbone of the model followed by a shallow fully connected network (FCN). A simple augmentation technique is performed to increase the number of images in the data set. The performance of the proposed algorithm is validated by investigating metrics such as precision and the area under the curve (AUC).
Drop of Prevalence after Population Expansion: A lower prevalence for recessive disorders in a random mating population is a transient phenomenon during and after a growth phase
Authors: Rocca Luis La , Frank Julia , Bentzen Heidi Beate , Pantel Jean-Tori , Gerischer Konrad , Bovier Anton , Krawitz Peter M.
Published: October 2021

Despite increasing data from population-wide sequencing studies, the risk for recessive disorders in consanguineous partnerships is still heavily debated. An important aspect that has not sufficiently been investigated theoretically, is the influence of inbreeding on mutation load and incidence rates when the population sizes change. We therefore developed a model to study these dynamics for a wide range of growth and mating conditions. In the phase of population expansion and shortly afterwards, our simulations show that there is a drop of diseased individuals at the expense of an increasing mutation load for random mating, while both parameters remain almost constant in highly consanguineous partnerships. This explains the empirical observation in present times that a high degree of consanguinity is associated with an increased risk of autosomal recessive disorders. However, it also states that the higher frequency of severe recessive disorders with developmental delay in inbred populations is a transient phenomenon before a mutation-selection balance is reached again.

Author summary

What determines the recessive disease burden? The empirical observation that the proportion of intellectual disability of autosomal recessive cause is usually higher in offspring of consanguineous partnerships may lead to a misunderstanding about the mechanisms at work. In any population, selection removes pathogenic alleles from the gene pool while the de novo mutation rate adds novel pathogenic alleles. For comparable mutation rates, the incidence of severe recessive disease should be comparable in mutation-selection balance, regardless of the mating scheme. Different incidences can therefore only be explained by population dynamics that are not in equilibrium. We studied in simulated populations the time scales in which mutation-selection balance is reached after a growth phase and found that the mating scheme has a big impact on this lag time. When cousins mate preferentially with cousins, a few generations after a ten-fold increase in size the new equilibrium is established. In contrast, for random-mating, the transient advantage of a lower incidence may last for hundreds of generations, while the mutation load increases. By this means, our findings also highlight the importance of better carrier screens in the future for genetic consultations.
Revisiting the role of beta-tubulin inDrosophiladevelopment: beta-tubulin60D is not an essential gene, and its novelPin1allele has a tissue-specific dominant-negative impact
Authors: Krishnan Ramesh Kumar , Halachmi Naomi , Baskar Raju , Anna Bakhrat , Salzberg Adi , Abdu Uri
Published: October 2021

Diversity in cytoskeleton organization and function may be achieved through alternative tubulin isotypes and by a variety of post-translational modifications. TheDrosophilagenome contains five different β-tubulin paralogs, which may play an isotype tissue-specific functionin vivo. One of these genes, thebeta-tubulin60Dgene, which is expressed in a tissue-specific manner, was found to be essential for fly viability and fertility. To further understand the role of the beta-tubulin60D gene, we generated newbeta-tubulin60Dnull alleles (beta-tubulin60DM)using the CRISPR/Cas9 system and found that the homozygous flies were viable and fertile. Moreover, using a combination of genetic complementation tests, rescue experiments, and cell biology analyses, we identifiedPin1, an unknown dominant mutant with bristle developmental defects, as a dominant-negative allele ofbeta-tubulin60D. We also found a missense mutation in thePin1mutant that results in an amino acid replacement from the highly conserved glutamate at position 75 to lysine (E75K). Analyzing the β-tubulin structure suggests that this E75K alteration destabilizes the alpha-helix structure and may also alter the GTP-Mg2+complex binding capabilities. Our results revisited the credence thatbeta-tubulin60Dis required for fly viability and revealed for the first time inDrosophila, a novel dominant-negative function of missensebeta-tubulin60Dmutation in bristle morphogenesis.

Author summary

Diversity in cell microtubule cytoskeleton organization and function may be achieved through alternative tubulin isotypes and by a variety of post-translational modifications. The expression pattern of different tubulin isotypes (both α and β subunits) can vary according to cell type and stage of development, which contribute significantly to cell-specific MT organization and function. In this study, we revisited the role of one of the beta-tubulin isotopes inDrosophila, namely, beta-tubulin60D. This is the first study where a well molecularly defined protein null allele ofβTub60Dwas generated and characterized. This well-characterizedβTub60Dallele demonstrated unambiguity thatβTub60Dis not an essential gene, as was described before. Moreover, we identifiedPin1, an unknown dominant mutant with bristle developmental defects, as a dominant-negative allele ofbeta-tubulin60D. We also found a missense mutation in thePin1mutant that results in an amino acid (E75K). Analyzing the β-tubulin structure suggests that this E75K alteration destabilizes the alpha-helix structure and may also alter GTP-Mg2+complex binding capabilities. Thus, our results also revealed for the first time inDrosophila, a novel dominant-negative function of a missensebeta-tubulin60Dmutation, which has a tissue-specific function.
Repression of the Hox gene abd-A by ELAV-mediated Transcriptional Interference
Authors: Castro Alvarez Javier J. , Revel Maxime , Cléard Fabienne , Pauli Daniel , Karch François , Maeda Robert K.
Published: October 2021

Intergenic transcription is a common feature of eukaryotic genomes and performs important and diverse cellular functions. Here, we investigate the iab-8 ncRNA from the Drosophila Bithorax Complex and show that this RNA is able to repress the transcription of genes located at its 3’ end by a sequence-independent, transcriptional interference mechanism. Although this RNA is expressed in the early epidermis and CNS, we find that its repressive activity is limited to the CNS, where in wild-type embryos, it acts on the Hox gene, abd-A located immediately downstream of it. The CNS specificity is achieved through a 3’ extension of the transcript, mediated by the neuronal-specific, RNA-binding protein, ELAV. Loss of ELAV activity eliminates the 3’ extension and results in the ectopic activation of abd-A. Thus, a tissue-specific change in the length of a ncRNA is used to generate a precise pattern of gene expression in a higher eukaryote.
Genome-wide identification of protein binding sites in mammalian cells
Authors: Liu Fenglin , Ma Tianyu , Zhang Yu-Xiang
Published: October 2021

We present GWPBS-Cap, a method to capture genome-wide protein binding sites (PBSs) without using antibodies. Using this technique, we identified many protein binding sites with different binding strengths between proteins and DNA. The PBSs can be useful to predict transcription binding sites and the co-localization of multiple transcription factors in the genome. The results also revealed that active promoters contained more protein binding sites with lower NaCl tolerances. Taken together, GWPBS-Cap can be used to efficiently identify protein binding sites and reveal genome-wide landscape of DNA-protein interactions.
Balancing selection at a wing pattern locus is associated with major shifts in genome-wide patterns of diversity and gene flow
Authors: Rodríguez de Cara María Ángeles , Jay Paul , Rougemont Quentin , Chouteau Mathieu , Whibley Annabel , Huber Barbara , Piron-Prunier Florence , Ramos Renato Rogner , Freitas André V. L. , Salazar Camilo , Silva-Brandão Karina Lucas , Torres Tatiana Teixeira , Joron Mathieu
Published: October 2021

Selection shapes genetic diversity around target mutations, yet little is known about how selection on specific loci affects the genetic trajectories of populations, including their genome-wide patterns of diversity and demographic responses. Here we study the patterns of genetic variation and geographic structure in a neotropical butterfly,Heliconius numata, and its closely related allies in the so-called melpomene-silvaniform clade.H. numatais known to have evolved an inversion supergene which controls variation in wing patterns involved in mimicry associations with distinct groups of co-mimics whereas it is associated to disassortative mate preferences and heterozygote advantage at this locus. We contrasted patterns of genetic diversity and structure 1) among extant polymorphic and monomorphic populations ofH. numata, 2) betweenH. numataand its close relatives, and 3) between ancestral lineages. We show thatH. numatapopulations which carry the inversions as a balanced polymorphism show markedly distinct patterns of diversity compared to all other taxa. They show the highest genetic diversity and effective population size estimates in the entire clade, as well as a low level of geographic structure and isolation by distance across the entire Amazon basin. By contrast, monomorphic populations ofH. numataas well as its sister species and their ancestral lineages all show lower effective population sizes and genetic diversity, and higher levels of geographical structure across the continent. One hypothesis is that the large effective population size of polymorphic populations could be caused by the shift to a regime of balancing selection due to the genetic load and disassortative preferences associated with inversions. Testing this hypothesis with forward simulations supported the observation of increased diversity in populations with the supergene. Our results are consistent with the hypothesis that the formation of the supergene triggered a change in gene flow, causing a general increase in genetic diversity and the homogenisation of genomes at the continental scale.