bluuebunny/crossref_metadata_2025 huggingface dataset:
A rara case of concurrent chromophobe renal cell cancer with lung neuroendocrine tumor: a case report and literature review
Authors: Zeer Zahraa M. M. , Noman Mahmoud , Zeer Almotazbellah M. M. , Mahamid Yamama Hasan , Arafat Hasan , Abomoch Malak , Abu Aqeel Bashir
Published: February 2024

Introduction:

Multiple primary malignances may be in one organ or in multiple separate organs. They are categorized into synchronous and metachronous according to the time interval between the two malignancies. Multiple risk factors could be attributed to the development of second primary malignancy.

Case Presentation:

we report a case of a 51-year-old male patient with renal cell carcinoma. During his evaluation, he seemed to have a lung mass which revealed to be a carcinoid tumor. As the patient had two primary malignancies, he was managed according to the treatment options for each tumor.

Discussion:

Although multiple primary malignancies (MPM) have been reported increasingly in the past decade, overall incidence is still very rare. Appropriate management and survival depend on distinguishing between dual primary tumors from metastatic disease.

Conclusion:

Multidisciplinary approach is very crucial for diagnosis and management such rare cases.
Effect of an Evaluation Algorithm on CT Utilization in Identifying Appendicitis in Children
Authors: Sikes Kendra L. , Hart Rebecca J. , Feygin Yana , Penrod Cody H.
Published: February 2024

Objective

Our objective was to determine if there was a significant change in computed tomography (CT) utilization or length of stay (LOS) among patients evaluated for acute appendicitis after implementation of an appendicitis evaluation algorithm.

Methods

We conducted a retrospective chart review of patients aged 3–18 years in an urban, tertiary pediatric emergency department with acute abdominal pain, evaluated for appendicitis. Data were collected for 6 months preimplementation and postimplementation of the evaluation algorithm with a 3-month washout period between September 2018 and November 2019. Main outcomes were rate of CT utilization and LOS preimplementation and postimplementation and were analyzed using χ2 test and Mann-Whitney U test, respectively. Descriptive analysis of demographics was performed, in addition to logistic regression to assess differences between the 2 study periods.

Results

A total of 2872 charts were identified with a chief complaint inclusive of “abdominal pain.” Of these, 1510 met age requirements but did not meet at least 1 inclusion criteria; 229 more were excluded upon chart review for a final study sample of 1133 patients. Of these, 648 (57.2%) were female, 747 (65.9%) were White, and 988 (87.2%) were non-Hispanic. The majority of patients (770, 68%) were discharged home from the emergency department without a diagnosis of acute appendicitis. Neither CT (25.7% to 24.8%; P = 0.794) nor ultrasound (59.5% to 59.7%; P = 1.000) utilization significantly changed postimplementation. Total ED median LOS increased significantly (333.50 to 362.00 minutes; P = 0.011). Significant factors associated with CT utilization included fever, migration of pain, and right lower quadrant tenderness. Significant factors associated with appendicitis diagnosis included right lower quadrant pain, nausea/vomiting, migration of pain, and peritoneal signs.

Conclusions

Overall, the appendicitis evaluation algorithm did not significantly decrease CT utilization or LOS. Equivocal grade 2 or 3 ultrasound finding rates were high, likely leading to higher rates of CT utilization and increasing LOS.
Sex differences in immune function and disease risk are not easily explained by an evolutionary mismatch
Authors: Arner Audrey M , Muhoya Benjamin , Rozado Mitchell Sanchez , Gurven Michael R , Kahumbu John , Kamau Joseph , Kinyua Patriciah , Lotukoi Francis , Martins Dino J. , Miano Charles , Montague Michael J , Njeru Sospeter , Peng Julie , Straub Peter , Watowich Marina M , Davis Lea K , Snyder-Mackler Noah , Ayroles Julien F , Lea Amanda J
Published: February 2024

The Pregnancy Compensation Hypothesis (PCH) posits that sex differences in the mammalian immune system reflect the effects of selection on female immunity during pregnancy, during which increased immunomodulation is required to reduce immune responses to the fetus, while maintaining the ability to respond to pathogens. In humans, fewer pathogens and lower parity in urban, industrialized environments has been suggested to leave female immune systems under-stimulated, creating an evolutionary mismatch which exacerbates sex differences in immunity and increases female autoimmune disease risk. Yet, robust tests of this mismatch hypothesis have not been conducted. Here, we first confirmed a sex-bias in autoimmune disease prevalence in a large dataset of individuals from the United Kingdom (UK Biobank). Second, we asked whether sex differences in immune function are affected by shifts toward urban, lower-parity lifestyles in a single population (the Turkana people of northwest Kenya). We found that lifestyle alters sex differences in immune cell type proportions, but not in gene expression levels. Contrary to expectations from the PCH, parity did not predict immune physiology. We then tested for generalizable trends across natural fertility mammalian populations versus urban humans (data from Turkana, NHANES, GTEx, Batwa and Bakiga, yellow baboons, and macaques). We did not find consistent relationships between lifestyle and sex-biases in immune biomarkers or between parity and the same immune outcomes. Indeed, we found that parity predicts autoimmune disease risk in the opposite direction than expected from the PCH, with higher parity associated with higher autoimmune disease risk while adjusting for relevant socioeconomic variables in the UK Biobank. Taken together, our work suggests that while sex clearly influences immune physiology and disease risk in urban settings, these effects are not easily explained by an evolutionary mismatch. Future work addressing how sex interacts with lifestyle change to generate disease is needed.
Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations
Authors: Kobren Shilpa Nadimpalli , Moldovan Mikhail A. , Reimers Rebecca , Traviglia Daniel , Li Xinyun , Barnum Danielle , Veit Alexander , Corona Rosario I , Carvalho George de V. , Willett Julian , Berselli Michele , Ronchetti William , Nelson Stanley F. , Martinez-Agosto Julian A , Sherwood Richard , Krier Joel , Kohane Isaac S ,   Undiagnosed Diseases Network, Sunyaev Shamil R
Published: February 2024

Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform "N-of-1" analyses on individual patients with ultra-rare diseases. The increasing sizes of ultra-rare disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development. The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale N-of-1 analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We further release a software package, RaMeDiES, enabling automated cross-analysis of deidentified sequenced cohorts for new diagnostic and research discoveries. Gene-level findings and variant-level information across the cohort are available in a public-facing browser (https://dbmi-bgm.github.io/udn-browser/). These results show that N-of-1 efforts should be supplemented by a joint genomic analysis across cohorts.
Investigating altered limbic reward system in Huntington's Disease: Implications for apathy
Authors: Bikou Vasiliki , de Vicente Inigo , De Paepe Audrey E. , Garcia-Gorro Clara , Rodriguez-Dechicha Nadia , Vaquer Irene , Calopa Matil , de Diego-Balaguer Ruth , Camara Estela
Published: February 2024

Huntington's disease (HD) is an inherited neurodegenerative condition characterized by motor, cognitive, and behavioral impairments. Apathy, marked by reduced motivation and goal-directed behavior, is the most prevalent psychiatric symptom in HD, impacting both patients and caregivers. Traditionally linked to executive dysfunction within the dorsolateral prefrontal cortex (dlPFC)-dorsal striatum loop in HD, the role of limbic regions in the basal ganglia and their impact on reward processing deficits remains poorly understood. This study sought to dissociate the functional correlates that are altered in reward valuation and may underlie apathy in HD. We aimed to tease apart whether apathy is associated with insensitivity to processing rewards, hypersensitivity to losses, or both, leading to the observed lack of motivation in apathetic individuals. Thirty-nine HD gene-expansion carriers (HDGEC) and 26 non-apathetic control participants underwent functional magnetic resonance imaging during a gambling task. The goal was to identify disrupted reward-related regions in HDGEC and their association with apathetic symptoms. Whole-brain analysis of gains and losses separately showed a significant reduction in activity, when HD group was compered to controls, within the left ventral striatum (VS), including the nucleus accumbens. The effect observed in the VS remained when clinically apathetic HDGEC were compared with controls. Conversely, non-apathetic HDGEC did not show any significant differences from controls. Interestingly, these group differences appeared exclusively during the processing of the reward. Additionally, higher levels of apathy were associated with especially decreased activity related with the processing of gains in this region. Our findings highlight the vulnerability of the left VS in HD and its association with the altered processing of gains, particularly in apathetic individuals, while preserving the valuation of losses. This suggests that reward insensitivity associated with VS dysfunction may be an important component of apathy in HD. Understanding the underlying mechanisms of reward processing and apathy in HD may help elucidate the implications of limbic regions as opposed to frontal executive dysfunction in apathy.
TARGETED STIMULATION OF THE SENSORY AFFERENTS IMPROVES MOTONEURON FUNCTION IN HUMANS WITH A DEGENERATIVE MOTONEURON DISEASE
Authors: Prat-Ortega G. , Ensel S. , Donadio S. , Borda L. , Boos A. , Yadav P. , Verma N. , Ho J. , Frazier-Kim S. , Fields D.P. , Fisher LE , Weber DJ , Duong T. , Weinstein S. , Eliasson M. , Montes J , Chen K.S. , Clemens P , Gerszten P. , Mentis G.Z. , Pirondini E , Friedlander R. M. , Capogrosso M
Published: February 2024

Spinal Muscular Atrophy (SMA) is an inherited neurodegenerative disease causing motoneuron dysfunction, muscle weakness and early mortality1,2. Three therapies can slow disease progression enabling people to survive albeit with lingering motoneuron dysfunction and severe motor impairments3,4. Here we introduce a neurotechnological approach that improved spinal motoneuron function, muscle strength and walking in three adults with SMA. Starting from preclinical evidence showing that motoneuron dysfunction in SMA originates from the loss of excitatory inputs from primary afferents5,6, we hypothesized that augmentation of sensory neural activity with targeted electrical stimulation could compensate for this loss thereby improving motoneuron function. To test this hypothesis we implanted three adults with SMA with epidural electrodes over the lumbosacral spinal cord to stimulate the sensory axons of the legs7,8. We stimulated participants for 4 weeks 2 hours per day while they executed walking and strength tasks. Remarkably, our neurostimulation regime led to robust improvements in strength, walking and fatigue paralleled by reduced neuronal hyperexcitability, increased sensory inputs and higher motoneuron firing rates. Our data indicate that targeted neurostimulation can reverse degenerative processes of circuit dysfunction thus promoting disease modifying effects in a human neurodegenerative disease.
PIMENTA: PIpeline for MEtabarcoding through Nanopore Technology used for Authentication
Authors: van der Vorst Valerie , Thijssen Marijke , Fronen Bas J. , de Groot Arjen , Maathuis Margot A.M. , Nijhuis Els , Polling Marcel , Stassen Joost , Voorhuijzen-Harink Marleen M , Jak Robbert
Published: February 2024

DNA metabarcoding has become a cost-effective method to assess species composition of mixed samples. Developments such as advances in sequencing technology and increased species coverage of reference databases can be leveraged to gain more insights from metabarcoding experiments, given suitable tools. To this end, we introduce PIMENTA, a new pipeline that streamlines the analysis of Nanopore DNA metabarcoding sequencing data. PIMENTA consists of four phases: pre-processing, clustering per sample, reclustering of all samples, and taxonomic identification. PIMENTA expands a workflow created by Voorhuijzen-Harink et al. Multiple updates have been made, including parallelization of the analysis of multiple samples with the use of high-performance computing (HPC), implementation of a local taxonomy database, and expansion of the taxonomic results summary. Settings have been optimized to process higher quality nanopore reads, for an increased accuracy of taxonomic identification. We evaluated the pipeline with mock samples of zooplankton species, incorporating COI, 18SV4, and 18SV9 marker sequences. The performance and runtime have been benchmarked against two other existing pipelines. PIMENTA was able to quickly identify species with a high resolution and minimal misidentifications.
Novel approach for carbon-wise utilization of lignin-related compounds by synergistically employing anaerobic and aerobic bacteria
Authors: Meriläinen Ella , Efimova Elena , Santala Ville , Santala Suvi
Published: February 2024

Lignin is a highly abundant but strongly underutilized natural resource that could serve as a sustainable feedstock to produce chemicals by microbial cell factories. However, the production from lignin-related aromatics is hindered by limited substrate range and inefficient catabolism of the production hosts. Particularly, the aerobic demethylation reactions are energy-limited and cause growth inhibition and loss of CO2. Here, we present a novel approach for carbon-wise utilization of lignin-related aromatics by the integration of anaerobic and aerobic metabolisms. In practice, we employed an acetogenic bacteriumAcetobacterium woodiifor anaerobic O-demethylation of aromatic compounds, which distinctively differs from the aerobic demethylation; in the process, the carbon from the methoxyl groups is fixated together with CO2 to form acetate while the aromatic ring remains unchanged. These accessible end-metabolites were then utilized by an aerobic bacteriumAcinetobacter baylyiADP1. Finally, we demonstrated the production of muconic acid from guaiacol, an abundant but inaccessible substrate to most microbes, with a nearly equimolar yield with only a minor genetic engineering and without the need for additional organic carbon source. This study highlights the power of synergistic integration of distinctive metabolic features of bacteria, thus unlocking new opportunities for harnessing microbial cocultures in upgrading challenging feedstocks.
Engineering the cyanobacterial ATP-driven BCT1 bicarbonate transporter for functional targeting to C3plant chloroplasts
Authors: Rottet Sarah , Rourke Loraine M. , Pabuayon Isaiah C.M. , Phua Su Yin , Yee Suyan , Weerasooriya Hiruni N. , Wang Xiaozhuo , Mehra Himanshu S. , Nguyen Nghiem D. , Long Benedict M. , Moroney James V. , Price G. Dean
Published: February 2024

The ATP-driven bicarbonate transporter 1 (BCT1), a four-component complex in the cyanobacteria CO2concentrating mechanism, could enhance photosynthetic CO2assimilation in plant chloroplasts. However, directing its subunits (CmpA, CmpB, CmpC and CmpD) to three chloroplast sub-compartments is highly complex. Investigating BCT1 integration intoNicotiana benthamianachloroplasts revealed promising targeting strategies using transit peptides from the intermembrane space protein Tic22 for correct CmpA targeting, while the transit peptide of the chloroplastic ABCD2 transporter effectively targeted CmpB to the inner envelope membrane. CmpC and CmpD were targeted to the stroma by RecA and recruited to the inner envelope membrane by CmpB. Despite successful targeting, expression of this complex in CO2-dependentEscherichia colifailed to demonstrate bicarbonate uptake. We then used rational design and directed evolution to generate new BCT1 forms that were constitutively active. Several mutants were recovered, including a CmpCD fusion. Selected mutants were further characterized and stably expressed inArabidopsis thaliana, but the transformed plants did not have higher carbon assimilation rates or decreased CO2compensation points in mature leaves. While further analysis is required, this directed evolution and heterologous testing approach presents potential for iterative modification and assessment of CO2concentrating mechanism components to improve plant photosynthesis.
Locomotion-dependent auditory gating to the parietal cortex guides multisensory decisions
Authors: Choi Ilsong , Lee Seung-Hee
Published: February 2024

Decision-making in mammals fundamentally relies on integrating multiple sensory inputs, with conflicting information resolved flexibly based on a dominant sensory modality. However, the neural mechanisms underlying state-dependent changes in sensory dominance remain poorly understood. Our study demonstrates that locomotion in mice shifts auditory-dominant decisions toward visual dominance during audiovisual conflicts. Using circuit-specific calcium imaging and optogenetic manipulations, we found that weakened visual representation in the posterior parietal cortex (PPC) leads to auditory-dominant decisions in stationary mice. Prolonged locomotion, however, promotes visual dominance by inhibiting auditory cortical neurons projecting to the PPC (ACPPC). This shift is mediated by secondary motor cortical neurons projecting to the auditory cortex (M2AC), which specifically inhibit ACPPCneurons without affecting auditory cortical projections to the striatum (ACSTR). Our findings reveal the neural circuit mechanisms underlying auditory gating to the association cortex depending on locomotion states, providing insights into the state-dependent changes in sensory dominance during multisensory decision-making.
Exploitation of CD3ζ to enhance TCR expression levels and antigen-specific T cell function
Authors: Degirmencay Abdullah , Thomas Sharyn , Holler Angelika , Stauss Hans
Published: February 2024

The expression levels of TCRs on the surface of human T cells define the avidity of TCR-HLA/peptide interactions. In this study, we have explored which components of the TCR-CD3 complex are involved in determining the surface expression levels of TCRs in primary human T cells. The results show that there is a surplus of endogenous TCR α/β chains that can be mobilised by providing T cells with additional CD3γ,δ,ε,ζ chains, which leads to a 5-fold increase in TCR α/β surface expression. The analysis of individual CD3 chains revealed that provision of additional ζ chain alone was sufficient to achieve a 3-fold increase in endogenous TCR expression. Similarly, CD3ζ also limits the expression levels of exogenous TCRs transduced into primary human T cells. Interestingly, transduction with TCR plus CD3ζ not only increased surface expression of the introduced TCR, but it also reduced mispairing with endogenous TCR chains, resulting in improved antigen-specific function. TCR reconstitution experiments in HEK293 cells that do not express endogenous TCR or CD3 showed that TCRα/β and all four CD3 chains were required for optimal surface expression, while in the absence of CD3ζ the TCR expression was reduced by 50%. Together, the data show that CD3ζ is a key regulator of TCR expression levels in human T cells, and that gene transfer of exogenous TCR plus CD3ζ improved TCR surface expression, reduced TCR mispairing and increased antigen-specific function.
VICTree - a Variational Inference method for Clonal Tree reconstruction
Authors: Melin Harald , Zampinetti Vittorio , McPherson Andrew , Lagergren Jens
Published: February 2024

Clonal tree inference brings crucial insights to the analysis of tumor heterogeneity and cancer evolution. Recent progress in single cell sequencing has prompted a demand for more advanced probabilistic models of copy number evolution, coupled with inference methods which can account for the noisy nature of the data along with dependencies between adjacent sites in copy number profiles. We present VICTree, a Variational Inference based algorithm for joint Bayesian inference of clonal trees, together with a novel Tree-structured Mixture Hidden Markov Model (TSMHMM) which combines HMMs related through a tree with a mixture model. For the tree inference, we introduce a new algorithm, LARS, for sampling directed labeled multifurcating trees. To evaluate our proposed method, we conduct experiments on simulated data and on samples of multiple myeloma and breast cancer. We demonstrate VICTree's capacity for reliable clustering, clonal tree reconstruction, copy number evolution and the utility of the ELBO for model selection. Lastly, VICTree's results are compared in terms of quality and speed of inference to other state-of-the art methods. The code for VICTree is available on GitHub: github.com/Lagergren-Lab/victree.
Circadian rhythms of macrophages are altered by the acidic pH of the tumor microenvironment
Authors: Knudsen-Clark Amelia M. , Mwangi Daniel , Cazarin Juliana , Morris Kristina , Baker Cameron , Hablitz Lauren M. , McCall Matthew N. , Kim Minsoo , Altman Brian J.
Published: February 2024

Macrophages are prime therapeutic targets due to their pro-tumorigenic and immunosuppressive functions in tumors, but the varying efficacy of therapeutic approaches targeting macrophages highlights our incomplete understanding of how the tumor microenvironment (TME) can influence regulation of macrophages. The circadian clock is a key internal regulator of macrophage function, but how circadian rhythms of macrophages may be influenced by the tumor microenvironment remains unknown. We found that conditions associated with the TME such as polarizing stimuli, acidic pH, and elevated lactate concentrations can each alter circadian rhythms in macrophages. Circadian rhythms were enhanced in pro-resolution macrophages but suppressed in pro-inflammatory macrophages, and acidic pH had divergent effects on circadian rhythms depending on macrophage phenotype. While cyclic AMP (cAMP) has been reported to play a role in macrophage response to acidic pH, our results indicate that pH-driven changes in circadian rhythms are not mediated solely by the cAMP signaling pathway. Remarkably, clock correlation distance analysis of tumor-associated macrophages (TAMs) revealed evidence of circadian disorder in TAMs. This is the first report providing evidence that circadian rhythms of macrophages are altered within the TME. Our data further suggest that heterogeneity in circadian rhythms at the population level may underlie this circadian disorder. Finally, we sought to determine how circadian regulation of macrophages impacts tumorigenesis, and found that tumor growth was suppressed when macrophages had a functional circadian clock. Our work demonstrates a novel mechanism by which the tumor microenvironment can influence macrophage biology through altering circadian rhythms, and the contribution of circadian rhythms in macrophages to suppressing tumor growth.
Exploring anterior thalamus functional connectivity with cortical regions in prospective memory with ultra-high-field fMRI
Authors: Flanagan Luke , Mansur Bruno de Matos , Reichert Christoph , Richter Anni , Golbabaei Soroosh , Kizilirmak Jasmin M. , Sweeney-Reed Catherine M.
Published: February 2024

Prospective memory, or memory for future intentions, engages particular cortical regions. Lesion studies also implicate the thalamus, with prospective memory deterioration following thalamic stroke. Neuroimaging, anatomical, and lesion studies suggest the anterior nuclei of the thalamus (ANT) in particular are involved in episodic memory, with electrophysiological studies suggesting an active role in selecting neural assemblies underlying particular memory traces. Here we hypothesized that the ANT are engaged in realizing prospectively-encoded intentions, detectable using ultra-high field strength functional MRI. Using a within-subject design, participants (N = 14; age 20-35 years) performed an ongoing n-back working memory task with two cognitive loads, each with and without a prospective memory component, during 7-Tesla functional MRI. Seed-to-voxel whole brain functional connectivity analyses were performed to establish whether including a prospective memory component in an ongoing task results in greater connectivity between ANT and cortical regions known to be engaged in prospective memory. Repeated measures ANOVAs were applied to behavioral and connectivity measures, with the factorsTask Type(with prospective memory or not) andN-Back(2-back or 3-back). Response accuracy was greater and reaction times faster without the prospective memory component, and accuracy was higher in the 2- than 3-back condition. We observed a main effect ofTask Typeon connectivity with an ANT seed, with greater ANT–DLPFC (dorsolateral prefrontal cortex) and ANT–STG (superior temporal gyrus) connectivity when including a prospective memory component. Post hoc testing based on a significant interaction showed greater ANT–DLPFC connectivity (p-FWE = 0.007) when prospective memory was included with the low and ANT–STG connectivity (p-FWE = 0.019) with the high cognitive load ongoing task. These locations showed no main effect ofN-Back. Connectivity based on a dorsomedial nucleus of the thalamus (DMNT) seed did not differ according toTask Typeat these locations. Enhanced connectivity between the ANT and the DLPFC, a brain region with an established role in strategic monitoring for prospective memory cues, arose with a low cognitive load ongoing task that enabled monitoring. This pattern was absent on directly increasing the cognitive load of the ongoing task without prospective memory, suggesting specificity for prospective memory. Greater ANT–STG connectivity on prospective memory inclusion in the higher cognitive load ongoing task condition fits with reports of STG activation on prospective memory through spontaneous retrieval. Differing connectivity based on a DMNT seed suggests ANT specificity. The findings fit with a coordinating role for the ANT in prospective remembering.
In bacterial membranes lipid II changes the stability of pores formed by the antimicrobial peptide nisin
Authors: Sheridan Miranda S. , Pandey Preeti , Hansmann Ulrich H. E.
Published: February 2024

Resistance to available antibiotics poses a growing challenge to modern medicine as this often disallows infections to be controlled. This problem can only be alleviated by developing new drugs. Nisin, a natural lantibiotic with broad antimicrobial activity, has shown promise as a potential candidate for combating antibiotic-resistant bacteria. However, nisin is poorly soluble and barely stable at physiological pH, which, despite attempts to address these issues through mutant design, has restricted its use as a antibacterial drug. Therefore, gaining a deeper understanding of the antimicrobial effectiveness, which relies in part on its ability to form pores, is crucial for finding innovative ways to manage infections caused by resistant bacteria. Using large-scale molecular dynamics simulations we find that the bacterial membrane specific lipid II increases the stability of pores formed by nisin, and that the interplay of nisin and lipid II reduces the overall integrity of bacterial membranes by changing local thickness and viscosity.
Initial Characterization of Canine T-cell Receptor Repertoires Using RNA-seq Data from Different Diseases and Tissues
Authors: Zhang Mengyuan , Ho Kun-Lin , Zhao Shaying
Published: February 2024

The dog serves as a key translational model in cancer immunotherapy. Understanding the T cell receptor (TCR) repertoire is needed for various cancer immunotherapies. Compared to humans where >300 million TCRs have been identified, <100 canine TCRs are reported. To address this deficiency, we assembled >200,000 complete TCR complementarity-determining region 3 (CDR3) sequences from RNA-seq data published for ~2,000 canine samples of blood, lymph node, and other tissues, of which 613 are tumors. We collected 1,324 human RNA-seq samples to compare the similarities and differences in T-cell repertoires between humans and dogs. Notably, our analysis revealed distinct variable gene usage patterns between blood samples and solid tissues in both canine and human samples for TRA and TRB loci. Moreover, our investigation led to the discovery of novel V gene and allele candidates in the canine genome. Our findings also revealed that the canine CDR3 resembled human CDR3 in terms of length and motifs. Additionally, our study unveiled shared traits in cancer TCRs between dogs and humans, including longer lengths and higher hydrophobicity of private CDR3s. Our results indicated the diversity of canine to be more comparable to that of humans than mice. Our study provides an initial landscape of the canine TCR repertoire, highlighting both its similarities and differences with the human counterpart, thus laying the groundwork for future research in comparative immunology and vaccine development.
DOPAMINE D4 RECEPTOR DOWN-REGULATES RENAL SODIUM CHLORIDE COTRANSPORTER VIA UBIQUITINATION-ASSOCIATED LYSOSOME DEGRADATION
Authors: Zhang Mingzhuo , Liu Mingda , Ren Zhiyun , Wang Weiwan , Upadhyay Kiran , Asico Laureano Asico , Armando Ines , Jia Yutao , Wang Ping , Xue Ying , Wang Xiaoyan
Published: February 2024

Background: The thiazide-sensitive sodium chloride cotransporter (NCC) is the major apical sodium transporter located in the mammalian renal distal convoluted tubule (DCT). The amount of sodium reabsorbed in the DCT through NCC plays an important role in the regulation of extracellular fluid volume and blood pressure. Dopamine and its receptors constitute a renal antihypertensive system in mammals. The disruption of Drd4 in mice causes kidney-related hypertension. However, the pathogenesis of D4R-deficiency associated hypertension is not well documented. Method: We assessed the effects of D4R on NCC protein abundances and activities of DCT in mice with renal or global Drd4-deficiencies and expressing human D4.7 variant and in cultured mouse DCT cells, and explored the molecular mechanism. Results: NCC inhibitor hydrochlorothiazide enhanced the natriuresis in Drd4-/- mice. Renal NCC protein was greater while ubiquitination of NCC was less in Drd4-/- than Drd4+/+ mice. Silencing of D4R in cultured mouse DCT cells increased NCC protein but decreased NCC ubiquitination. D4R agonist had opposite effects that were blocked by the antagonist. In mouse kidneys and DCT cells D4R and NCC colocalized and co-immunoprecipitated. Moreover, D4R-agonist promoted the binding between the two proteins demonstrated by fluorescence resonance energy transfer. D4R agonism internalized NCC, decreased NCC in the plasma membrane, increased NCC in lysosomes and reduced NCC-dependent-intracellular-sodium transport. The lysosomal inhibitor chloroquine prevented the D4R-induced NCC-reduction. A shortened NCC half-life was suggested by its decay under cycloheximide-chase. Ubiquitin-specific-protease 48 (USP48, a deubiquitinating enzyme) was increased in the kidneys and cells with Drd4-deficiency while D4R stimulation decreased it in vitro and reduction of USP48 with siRNA decreased NCC expression. The mice carrying human D4.7 variant or with renal supcapsular-Drd4-siRNA-delivery developed hypertension with increased NCC. Conclusion: Our data demonstrates that D4R downregulates NCC by promoting USP48-associated deubiquitination and subsequent internalization, lysosome relocation and degradation.
Barriers in accessing healthcare during the COVID-19 pandemic: analysis of the Virus Watch community cohort study
Authors: Menezes Dee , Siegele-Brown Chloe , Yavlinsky Alexei , Nguyen Vincent , Braithwaite Isobel , Burns Rachel , Tweed Sam , Oskrochi Youssof , Kovar Jana , Fong Wing Lam Erica , Hayward Andrew , Aldridge Robert W
Published: February 2024

Background: Differential barriers to accessing healthcare contribute to inequitable health outcomes. This study aims to describe the characteristics of individuals who experienced barriers, and what those barriers were, during the COVID-19 pandemic. Methods: We analysed data from Virus Watch: an online survey-based community study of households in England and Wales. The primary outcome was reported difficulty accessing healthcare in the previous year. Results: Minority ethnic participants reported difficulty accessing healthcare more than White British participants (41.6% vs 37%), while for migrants this was at broadly similar levels to non-migrants. Those living in the most deprived areas reported difficulty more than those living in the least deprived quintile (45.5% vs. 35.5%). The most frequently reported barrier was cancellation/disruption of services due to the COVID-19 pandemic (72.0%) followed by problems with digital or telephone access (21.8%). Ethnic minority participants, migrants, and those from deprived areas more commonly described 'insufficient flexibility of appointments' and 'not enough time to explain complex needs' as barriers. Conclusions: Minority ethnic individuals and those living in deprived areas were more likely to experience barriers to healthcare during the COVID-19 pandemic, and it is essential they are addressed as services seek to manage backlogs of care.
Establishing Reference Ranges for Vitamin D Levels in a Representative Population of Peshawar, Pakistan
Authors: Usama  , Rehman Zeeshan , Ali Aktar
Published: February 2024

Background

Vitamin D deficiency is prevalent in Pakistan, yet there is no consensus on the optimal range for 25-hydroxyvitamin D (25(OH)D) levels. Establishing reference ranges specific to the population is essential due to variations in age, sex, race, and diet. Parathyroid hormone (PTH) serves as a surrogate marker for vitamin D deficiency. This study aims to determine the reference range for plasma vitamin D in a healthy population in Peshawar, considering various demographic and biochemical factors.

Methods

A population-based cross-sectional study was conducted in four union councils of District Peshawar. Participants (n=200) aged 18-54 years underwent serum vitamin D and PTH analysis using ELISA kits. Data on sun exposure, anthropometric measurements, and dietary habits were collected.

Results

The majority of participants (92%) reported daily sun exposure of 15-30 minutes and had a mean BMI of 23.598±3.988 kg/m2. Only 28% of participants were vitamin D sufficient, while 72% were deficient. test results obtained for the reference values were 6.43–45.0 ng/mL for the percentile range of 2.5–97.5.

Conclusion

The high prevalence of vitamin D deficiency underscores the need for governmental and educational interventions to promote awareness and address this issue. Additionally, tailored nutrition plans are crucial to mitigate vitamin D deficiency in the local population.
Systematic evaluation of multifactorial causal associations for Alzheimer's disease and an interactive platform based on Mendelian randomization analysis——MRAD
Authors: Zhao Tianyu , Li Hui , Zhang Meishuang , Xu Yang , Zhang Ming , Chen Li
Published: February 2024

Alzheimer's disease (AD) is a complex degenerative disease of the central nervous system. Traditional epidemiological studies have reported several risk factors for AD. However, most epidemiological studies are insufficient to draw definitive conclusions on causal association due to the potential for reverse causality and confounding bias. Therefore, elucidating its pathogenesis remains challenging. Mendelian randomization (MR) was developed for assessing causality using genetic variants as a new approach in epidemiological research. In this study, we used MR analysis to investigate potential AD risk factors to support extensive AD research. We used the inverse-variance weighted (IVW) model as the major analysis method to perform hypothesis-free Mendelian randomization analysis on the data from MRC IEU OpenGWAS (18,097 exposure traits and 16 AD outcome traits), and conducted sensitivity analysis with six models, to assess the robustness of the IVW results, to identify various classes of risk or protective factors for AD, early-onset AD, and late-onset AD. We generated 400,274 data entries in total, among which the major analysis method of IVW model consists of 73,129 records with 4840 exposure traits, which fall into 10 categories: Disease (n=17,168), Medical laboratory science (n=15,416), Imaging (n=4,896), Anthropometric (n=4,478), Treatment (n=4,546), Molecular trait (n=17,757), Gut microbiota (n=48), Past history (n=668), Family history (n=1,114), and Lifestyle trait (n=7,038). For the convenience of display and operation, an online platform called MRAD has been developed using the Shiny package with MR analysis results. MRAD can be freely accessed online at https://gwasmrad.com/mrad/. Moreover, novel potential AD therapeutic targets (CD33, TBCA, VPS29, GNAI3, PSME1) are identified, among which CD33 was positively associated with the main outcome traits of AD, as well as with both EOAD and LOAD. TBCA and VPS29 were negatively associated with the main outcome traits of AD, as well as with both EOAD and LOAD. GNAI3 and PSME1 were negatively associated with the main outcome traits of AD, as well as with LOAD, but had no significant causal association with EOAD. This is one of the most comprehensive studies in this field. The findings of our research advance understanding of the etiology of AD.
Rare Diseases Clinical Trials Toolbox - Public resources and main considerations to set up a clinical trial on medicinal products for humans in Europe
Authors: del Álamo Marta , Zafirova Biljana , Esdaile Martina , Karam Sarah , Klager Sabine , Kubiak Christine
Published: February 2024

Background

Drug development programmes in rare diseases have many challenges, some of which differ from those facing researchers working on common diseases, like the scarcity of patients.

Over the past years, research and regulatory initiatives, as well as resources have been implemented to expedite drug development for rare diseases. Nevertheless, these tools have been developed in the context of different projects and with diverse aims. Therefore, they have not yet been structured to encompass the conduct of clinical trials as a whole. To address this issue, the EJP RD (European Joint Program for Rare Diseases) has developed the Rare Diseases Clinical Trial Toolbox.

Purpose

This toolbox collates the accumulated knowledge, experience, and resources (collectively termed ‘tools’) generated by projects, research infrastructures and/or other organizations into a structured, practical and guided instrument to help clinical trialists and trial managers understand the regulations and requirements for conducting trials, with a special focus on investigator-initiated trials for rare diseases.

Methods

The toolbox is organized into five domains: research question, plan, execution, analysis, and end of trial. Each domain describes one or several activities to be considered in this step and indicate at what stage of the trial pathway these activities should take place, regardless of the therapeutic area. Each activity is further linked to specific resources (the tools) that are relevant for those activities. Associated resources are in the public domain developed in the context of research projects or by relevant clinical research stakeholders. Selected tools must be of fundamental importance to clinical trials and be applicable torare diseases clinical research. Rare-diseases specific resources are highlighted as such and include those specially relevant to paediatric clinical research, considering than one half of rare disorders affect children and some 60% of designated orphan medicines are intended for paediatric use.

Results

The current version of the Toolbox includes 111 resources tagged as relevant for any of the 18 activities within the clinical trial outline. Overall, 75 % of all resources are relevant to any clinical trial while 25 % are tagged as “rare disease specific”.

Conclusion

Access to public resources relevant to the development of clinical trials for rare diseases is sometimes challenged by limited awareness and/or the absence of an adequate framework that enables their findability. This Toolbox aims at building a framework supporting the optimal use of existing tools.
Screening Accuracy and Age-based Scoring Procedures of the Polish Version of Communication and Symbolic Behavior Scales-Developmental Profile Infant-Toddler Checklist
Authors: Sobieski Mateusz , Kopszak Anna , Wrona Sylwia , Bujnowska-Fedak Maria Magdalena
Published: February 2024

Background

The first stage of diagnosing autism spectrum disorders usually involves population screening to detect children at risk. The aim of this study was to develop cut-off points and assess diagnostic properties for the Polish version of the Communication and Symbolic Behavior Scales-Developmental Profile – Infant-Toddler Checklist for the possibility of using this questionnaire in population screening.

Method

The study was conducted among 602 children from the general population who had previously participated in the earlier phase of validation of the questionnaire for Polish conditions. The collected data were statistically processed to calculate the accuracy (i.e. sensitivity, specificity) of the questionnaire.

Results

In individual age groups, the sensitivity of the questionnaire varies from 0.667 to 0.750, specificity from 0.854 to 0.939, positive predictive value from 0.261 to 0.4 and negative predictive value - from 0.979 to 0.981.

Conclusions

These results indicate that the Polish version of the Communication and Symbolic Behavior Scales-Developmental Profile – Infant-Toddler Checklist can be used as an effective tool for ASD universal screening.
Enhancing Semantic Segmentation in Chest X-Ray Images through Image Preprocessing: ps-KDE for Pixel-wise Substitution by Kernel Density Estimation
Authors: Wang Yuanchen , Guo Yujie , Wang Ziqi , Yu Linzi , Yan Yujie , Gu Zifan
Published: February 2024

Background

Deep-learning-based semantic segmentation algorithms, in combination with image preprocessing techniques, can reduce the need for human annotation and advance disease classification. Among established preprocessing techniques, CLAHE has demonstrated efficacy in enhancing the segmentations algorithms across various modalities.

Method

This study proposes a novel preprocessing technique, ps-KDE, to investigate its impact on deep learning algorithms to segment major organs in posterior-anterior chest X-rays. Ps-KDE augments image contrast by substituting pixel values based on their normalized frequency across all images. Our approach employs a U-Net architecture with ResNet34 (pre-trained on ImageNet) serving as the decoder. Five separate models are trained to segment the heart, left lung, right lung, left clavicle, and right clavicle.

Results

The model trained to segment the left lung using ps-KDE achieved a Dice score of 0.780 (SD=0.13), while that trained on CLAHE achieved a Dice score of 0.717 (SD=0.19),p<0.01. ps-KDE also appears to be more robust as CLAHE-based models misclassified right lungs in select test images for the left lung model.

Discussion

Our results suggest that ps-KDE offers advantages over current preprocessing techniques when segmenting certain lung regions. This could be beneficial in subsequent analysis such as disease classification and risk stratification.
Effectiveness of Omicron XBB.1.5 vaccine against SARS-CoV-2 Omicron XBB and JN.1 infection in a prospective cohort study in the Netherlands, October 2023 to January 2024
Authors: Huiberts Anne J. , Hoeve Christina E. , de Gier Brechje , Cremer Jeroen , van der Veer Bas , de Melker Hester E. , van de Wijgert Janneke H.H.M. , van den Hof Susan , Eggink Dirk , Knol Mirjam J.
Published: February 2024

We estimated vaccine effectiveness (VE) of SARS-CoV-2 Omicron XBB.1.5 vaccination against self-reported infection between 9 October 2023 and 9 January 2024 in 23,895 XBB.1.5 vaccine-eligible adults who had previously received at least one booster. VE was 41% (95%CI:23-55) in 18-59-year-olds and 50% (95%CI:44-56) in 60-85-year-olds. Sequencing data in a subset of infections suggests immune escape of the emerging BA.2.86 (JN.1) variant from recent prior infection (OR:2.6; 95%CI:1.1-6.3) and, although not statistically significant, from XBB.1.5 vaccination (OR:1.6; 95%CI:0.9-2.9).

A monovalent mRNA vaccine targeting the SARS-CoV-2 Omicron XBB.1.5 subvariant (Comirnaty) was used in the 2023 Dutch COVID-19 vaccination campaign that started on October 2, 2023. Individuals aged ≥60 years, medical risk groups, pregnant women and healthcare workers were eligible for vaccination. Since September 2023, a new Omicron BA.2.86 sub-variant named JN.1 has emerged and quickly became dominant in the Netherlands and globally [1, 2]. BA.2.86 is genetically divergent from the previously circulating XBB variants, indicating potential for immune escape [3].

We estimated vaccine effectiveness (VE) of XBB.1.5 vaccination against self-reported SARS-CoV-2 infection between 9 October 2023 and 9 January 2024 among adults aged 18-85 years who had previously received primary vaccination and at least one booster vaccination before 2 October 2023 and were eligible for XBB.1.5 vaccination. To assess potential immune escape by JN.1, we analyzed whether there was an association between XBB.1.5 vaccination or prior infection and the Omicron variant causing the infection (XBB vs. BA.2.86, including JN.1). The variant was determined by sequencing of viral genetic material present in positive lateral flow antigen self-tests.