bluuebunny/crossref_metadata_2025 huggingface dataset:
Is Cervical Disk Arthroplasty a Suitable Alternative to Treat Degenerative Cervical Myelopathy?
Authors: Schupper Alexander J , Boylan Arianne J , Houten John K
Published: September 2023

Study Design:

Systemic review

Objective:

To understand the role of cervical disk arthroplasty in the treatment of cervical myelopathy.

Summary of Background Data:

The surgical management of degenerative cervical myelopathy (DCM) most frequently involves decompression and fusion, but stiffness introduced by the fusion and adjacent segment degeneration remain problems that can result in significant morbidity. Cervical disk arthroplasty (CDA) is a newer procedure that has been demonstrated to be safe and effective for the management of cervical spine degenerative disk disease, but it has not been traditionally considered as a treatment option for DCM and the use for this indication has not been extensively studied.

Materials and Methods:

A systematic review was undertaken using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines using a search strategy to query all relevant articles on the use of cervical disk arthroplasty in the setting of cervical myelopathy over a 20-year period (2004–2023). This review examines the literature to assess our current understanding of the appropriateness, safety, and value of CDA in the treatment of DCM.

Results:

A total of 844 patients received CDA across the 14 studies that met inclusion criteria, with an average of 60.3±40.4 patients per study (range: 11–152 subjects). Featured studies included 5 (35.7%) prospective studies, of which 2 were randomized. All studies had primary outcome measures of disability and/or pain scores, with the Japanese Orthopedic Association myelopathy score and neck disability index as the most commonly assessed. Four (26.7%) studies compared arthroplasty with arthrodesis. Safety of CDA for DCM was found in all studies with improvement in clinical outcome measurements.

Conclusion:

Cervical disk arthroplasty appears to be a safe and effective surgical option in the management of degenerative cervical myelopathy. Further study is needed to assess if arthroplasty provides clinical improvement in DCM of comparable magnitude and durability as traditional fusion strategies.
Reference Managers
Authors: Meade Matthew , DiCiurcio William , Radack Tyler , Michael Mark , Woods Barrett
Published: September 2023

Reference Managers (RMs) are software applications designed to build web-based libraries to organize, annotate, and reference literature when compiling a research study. With an ever-increasing volume of literature, RMs not only serve to centralize information but also allow seamless in-text citation and 1-click bibliography creation, with the ability to format each citation based on target journal specifications. There are many different RMs available for utilization; some of the most popular are EndNote, Zotero, Mendeley, and Paperpile. Each of these aforementioned applications has its own pros and cons, which this paper aims to summarize, though authors should take their individual research needs into consideration when deciding on their preferred reference manager.
PEG 400 Ion Suppression in Busulfan Detection by High-Performance Liquid Chromatography—Tandem Mass Spectrometry
Authors: De Gregori Simona , Capone Mara , De Silvestri Annalisa , Albertini Riccardo
Published: September 2023

Background:

Busulfan (Bu), an alkylating agent commonly used in chemotherapy and transplantation, exhibits high intraindividual pharmacokinetic variability and possible time-dependent variations in clearance, which complicate therapeutic drug monitoring. Numerous analytical methods have been developed to reduce analysis time and facilitate timely decision-making regarding treatment changes; however, the validation procedures rarely involve analysis of potentially interfering excipients. Macrogol 400 (PEG 400) should be considered as a possible interfering agent in the detection of plasma Bu levels, especially as an ionization suppressor.

Methods:

Six intravenous formulations of Bu were compared with identify at least 1 common excipient (PEG 400). During the 176 therapeutic drug monitoring analyses of Bu, one of the PEG 400 specific mass-to-charge ratio transitions was determined using an instrumental method. After coelution with Bu and its internal standard (Bu-d8) was confirmed, all analyses were repeated using a different experimental setup free of ion suppression induced by PEG. The concentration–time profile of PEG 400 was also analyzed.

Results:

The area under the curve obtained from the 2 data sets was compared and analyzed using Lin concordance correlation coefficient and Bland–Altman plot analysis. The results from the 2 analytical methods were comparable: PEG 400 negatively affected the Bu-d8 coefficient of variation but not the Bu/Bu-d8 ratio.

Conclusions:

The possible interference of PEG 400 should be thoroughly investigated, especially with respect to analytical methods that cannot be supported by correction of the stable isotopically labeled internal standard analog.
3-Methylmethcathinone Intoxication: Discrepancies Between Blood Concentrations and Clinical Outcomes—A Short Communication
Authors: Drevin Guillaume , Baudriller Antoine , Ferec Severine , Beloncle François , Briet Marie , Abbara Chadi
Published: September 2023

Background:

The absence of a correlation between the blood concentration of 3-methylmethcathinone (3-MMC) and clinical outcomes in intoxication cases has been attributed to stability issues. Indeed, a loss of more than 50%, 70%, and even 95% of 3-MMC in whole blood after 2 weeks of storage at 20°C, 4°C, and room temperature, respectively, has been reported in the past. Here, the authors report the case of a 43-year-old man who was hospitalized with generalized convulsive status epilepticus related to 3-MMC use with a plasma concentration of 9600 ng/mL (delay between sampling and analysis <72 hours). The stability of 3-MMC was evaluated in several biological specimens.

Methods:

Three quality control samples (human plasma, whole blood, and postmortem blood) spiked with 3-MMC were stored at −20°C and 4°C for 14 days. The initial analysis was performed on day 1 to establish the initial concentration of 3-MMC in each specimen type, and the samples were divided into 2 aliquots for storage under both conditions. Further analyses were performed on days 7 and 14 for each specimen, and the results were compared with those obtained on day 1.

Results:

3-MMC appeared relatively stable in whole and postmortem blood when stored at −20°C for 1 week, with losses of <3% in both matrices (0% and 2.5%, respectively). At +4°C, 3-MMC losses ranged from 25% to 53%.

Conclusions:

These results differ from others reported in the literature. Hence, it may be hypothesized that other elements should be considered to explain the discrepancy between the concentration and toxicity pointed out by the Toxicology community, especially the development of tolerance.
Simultaneous Quantification of Psychotropic Drugs in Human Plasma and Breast Milk and Its Application in Therapeutic Drug Monitoring and Peripartum Treatment Optimization
Authors: Le Marois Marguerite , Doudka Natalia , Tzavara Eleni , Delaunay Laurence , Quaranta Sylvie , Blin Olivier , Belzeaux Raoul , Guilhaumou Romain
Published: September 2023

Background:

Therapeutic drug monitoring is recommended for several psychotropic drugs, particularly in sensitive situations such as the peripartum period. This study aimed to develop an ultra-high-performance liquid chromatography–tandem spectrometry method for the simultaneous quantification of 14 psychotropic drugs in human plasma and 4 in breast milk.

Methods:

The samples were precipitated with methanol containing the stable isotope-labeled analogs. Chromatographic separation was performed using a Phenomenex Luna Omega Polar C18 column. Detection was performed using a triple-quadrupole mass spectrometer equipped with an electrospray ionization interface. The method was fully validated in plasma according to the European Guidelines on Bioanalytical Method Validation and partially validated in breast milk by determining the intraday precision and accuracy, linearity, lower limit of quantification, and matrix effect.

Results:

The correlation coefficients of the calibration curves were greater than 0.99. Coefficients of variation ranged from 3.05% to 14.66% and 0.62%–14.90% for internal standard-normalized matrix effect, 1.4%–14.1% and 2.1%–10.4% for intraday precision, and 3.2%–13.9% and 4.1%–9.6% for interday precision, in plasma and milk, respectively. The relative error in accuracy did not exceed ±15% for any analyte. The method was successfully applied clinically to measure the concentrations of psychotropic drugs in 952 plasma samples, among which 43% of the concentrations were out of the therapeutic range, and 13 breast milk samples, with calculated relative infant doses ranging from 0.32% to 8.18%.

Conclusions:

To the best of the authors' knowledge, this is the first routine technique validated for the quantification of psychotropic drugs in both plasma and breast milk, allowing for treatment optimization and prevention of adherence issues, including those in breastfeeding patients.
Direct Immunofluorescence Findings and Factors Affecting Conjunctival Biopsy Positivity in Ocular Mucous Membrane Pemphigoid
Authors: Jain Neha , Jakati Saumya , Shanbhag Swapna S. , Basu Sayan
Published: September 2023

Purpose:

The aim of this study was to describe the direct immunofluorescence (DIF) findings and factors affecting conjunctival biopsy positivity in patients clinically diagnosed with ocular mucous membrane pemphigoid (OMMP).

Methods:

This retrospective observational case series included patients with clinical OMMP who underwent conjunctival biopsy for DIF in at least 1 eye between 2018 and 2021 in an institutional setting. The primary outcome measures were association of age and chronic ocular complications with biopsy positivity.

Results:

Of 61 patients, DIF positivity was seen in 33 (54.1%) clinically suspected cases of OMMP. Of 39 patients who underwent bilateral biopsy, 23 (59%) were positive, of which 12 (52%) were positive in both eyes while 11 (48%) were positive in 1 eye. Of 22 patients who underwent unilateral biopsy, 10 (45%) were positive. Of the 100 biopsied eyes, 45 (45%) were DIF positive. Among the immunoreactants studied, linear deposition of C3 was seen in all 45 positive eyes (100%). Increasing age was significantly associated with higher likelihood of biopsy negativity (P = 0.032), whereas a greater Sotozono chronic ocular complication score, indicative of disease severity, was associated with low likelihood of biopsy positivity (P = 0.0042) and lower overall expression of immunoreactants on DIF (P = 0.0007).

Conclusions:

Older patients and patients with more severe ocular surface disease sequelae are likely to have negative DIF results. To optimize the chances of confirming the diagnosis of OMMP by DIF, both eyes should be biopsied early in the disease course. If 1 eye is being biopsied, the less affected eye must be chosen.
Leukemia circulation kinetics revealed through blood exchange method
Authors: Miller Alex B. , Langenbucher Adam , Rodriguez Felicia H. , Lin Lin , Bray Christina , Duquette Sarah , Zhang Ye , Goulet Dan , Lane Andrew A. , Weinstock David M. , Hemann Michael T. , Manalis Scott R.
Published: September 2023

Leukemias and their bone marrow microenvironment are known to undergo dynamic changes over the course of disease. However, relatively little is known about the circulation kinetics of leukemia cells, nor the impact of specific factors on the clearance of circulating leukemia cells (CLCs) from the blood. To gain a basic understanding of leukemia cell dynamics over the course of disease progression and therapeutic response, we apply a blood exchange method to mouse models of acute leukemia. We find that CLCs circulate in the blood for 1-2 orders of magnitude longer than solid tumor circulating tumor cells. We further observe that: i) leukemia presence in the marrow can limit the clearance of CLCs in a model of acute lymphocytic leukemia (ALL), and ii) CLCs in a model of relapsed acute myeloid leukemia (AML) can clear faster than their untreated counterparts. Our approach can also directly quantify the impact of microenvironmental factors on CLC clearance properties. For example, data from two leukemia models suggest that E-selectin, a vascular adhesion molecule, alters CLC clearance. Our research highlights that clearance rates of CLCs can vary in response to tumor and treatment status and provides a strategy for identifying basic processes and factors that govern the kinetics of circulating cells.
ParSE-seq: A Calibrated Multiplexed Assay to Facilitate the Clinical Classification of Putative Splice-altering Variants
Authors: O’Neill Matthew J. , Yang Tao , Laudeman Julie , Calandranis Maria , Solus Joseph , Roden Dan M. , Glazer Andrew M.
Published: September 2023

Background

Interpreting the clinical significance of putative splice-altering variants outside 2-base pair canonical splice sites remains difficult without functional studies.

Methods

We developed Parallel Splice Effect Sequencing (ParSE-seq), a multiplexed minigene-based assay, to test variant effects on RNA splicing quantified by high-throughput sequencing. We studied variants in SCN5A, an arrhythmia-associated gene which encodes the major cardiac voltage-gated sodium channel. We used the computational tool SpliceAI to prioritize exonic and intronic candidate splice variants, and ClinVar to select benign and pathogenic control variants. We generated a pool of 284 barcoded minigene plasmids, transfected them into Human Embryonic Kidney (HEK293) cells and induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), sequenced the resulting pools of splicing products, and calibrated the assay to the American College of Medical Genetics and Genomics scheme. Variants were interpreted using the calibrated functional data, and experimental data were compared to SpliceAI predictions. We further studied some splice-altering missense variants by cDNA-based automated patch clamping (APC) in HEK cells and assessed splicing and sodium channel function in CRISPR-edited iPSC-CMs.

Results

ParSE-seq revealed the splicing effect of 224SCN5Avariants in iPSC-CMs and 244 variants in HEK293 cells. The scores between the cell types were highly correlated (R2=0.84). In iPSCs, the assay had concordant scores for 21/22 benign/likely benign and 24/25 pathogenic/likely pathogenic control variants from ClinVar. 43/112 exonic variants and 35/70 intronic variants with determinate scores disrupted splicing. 11 of 42 variants of uncertain significance were reclassified, and 29 of 34 variants with conflicting interpretations were reclassified using the functional data. SpliceAI computational predictions correlated well with experimental data (AUC = 0.96). We identified 20 uniqueSCN5Amissense variants that disrupted splicing, and 2 clinically observed splice-altering missense variants of uncertain significance had normal function when tested with the cDNA-based APC assay. A splice-altering intronic variant detected by ParSE-seq, c.1891-5C>G, also disrupted splicing and sodium current when introduced into iPSC-CMs at the endogenous locus by CRISPR editing.

Conclusions

ParSE-seq is a calibrated, multiplexed, high-throughput assay to facilitate the classification of candidate splice-altering variants.
A Systematic Review on the Effects of Exercise on Gut Microbial Diversity, Taxonomic Composition, and Microbial Metabolites: Identifying Research Gaps and Future Directions
Authors: Cullen John M.A. , Shahzad Shahim , Dhillon Jaapna
Published: September 2023

The gut microbiome, hosting a diverse microbial community, plays a pivotal role in metabolism, immunity, and digestion. While the potential of exercise to influence this microbiome has been increasingly recognized, findings remain incongruous. This systematic review examined the effects of exercise on the gut microbiome of human and animal models. Databases (i.e., PubMed, Cochrane Library, Scopus, and Web of Science) were searched up to June 2022. Thirty-two exercise studies, i.e., 19 human studies, and 13 animal studies with a minimum of two groups that discussed microbiome outcomes, such as diversity, taxonomic composition, or microbial metabolites, over the intervention period, were included in the systematic review (PROSPERO registration numbers: CRD42023394223 and CRD42023394485). Results indicated that over 50% of studies found no significant exercise effect on human microbial diversity. When evident, exercise often augmented the Shannon index, reflecting enhanced microbial richness and evenness, irrespective of disease status. Changes in beta-diversity metrics were also documented with exercise but without clear directionality. A larger percentage of animal studies demonstrated shifts in diversity compared to human studies, but without any distinct patterns, mainly due to the varied effects of predominantly aerobic exercise on diversity metrics. In terms of taxonomic composition, in humans, exercise usually led to a decrease in the Firmicutes/Bacteroidetes ratio, and consistent increases withBacteroidesandRoseburiagenera. In animal models,Coprococcus, a SCFA producer, consistently rose with exercise. Generally, SCFA producers were found to increase with exercise in animal models. With regard to metabolites, SCFAs emerged as the most frequently measured metabolite. However, due to limited human and animal studies examining exercise effects on microbial-produced metabolites, including SCFAs, clear patterns did not emerge. The overall risk of bias was deemed neutral. In conclusion, this comprehensive systematic review underscores that exercise can potentially impact the gut microbiome with indications of changes in taxonomic composition. The significant variability in study designs and intervention protocols demands more standardized methodologies and robust statistical models. A nuanced understanding of the exercise-microbiome relationship could guide individualized exercise programs to optimize health.
A beneficial synonymous substitution in EF-Tu is contingent on genetic background
Authors: McGrath Kaitlyn M. , Russell Steven J. , Fer Evrim , Garmendia Eva , Hosgel Ali , Baltrus David A. , Kaçar Betül
Published: September 2023

Synonymous mutations are changes to DNA sequence that occur within translated genes but which do not affect the protein sequence. Although often referred to as silent mutations, evidence suggests that synonymous mutations can affect gene expression, mRNA stability, and even translation efficiency. A collection of both experimental and bioinformatic data has shown that synonymous mutations can impact cell phenotype, yet less is known about the molecular mechanisms and potential of beneficial or adaptive effects of such changes within evolved populations. Here, we report a beneficial synonymous mutation acquired via experimental evolution in an essential gene variant encoding the translation Elongation Factor protein EF-Tu. We demonstrate that this particular synonymous mutation increases EF-Tu mRNA and protein levels, as well as the polysome abundance on global transcripts. Although presence of the synonymous mutation is clearly causative of such changes, we also demonstrate that fitness benefits are highly contingent on other potentiating mutations present within the genetic background in which the mutation arose. Our results underscore the importance of beneficial synonymous mutations, especially those that affect levels of proteins that are key for cellular processes.

Importance

This study explores the degree to which synonymous mutations in essential genes can influence adaptation in bacteria. An experimental system whereby anEscherichia colistrain harboring an engineered translation protein Elongation Factor-Tu (EF-Tu) was subjected to laboratory evolution. We find that a synonymous mutation acquired on the gene encoding for EF-Tu is conditionally beneficial for bacterial fitness. Our findings provide insight into the importance of the genetic background when a synonymous substitution is favored by natural selection and how such changes have the potential to impact evolution when critical cellular processes are involved.
Short-latency preference for faces in the primate superior colliculus
Authors: Yu Gongchen , Katz Leor N. , Quaia Christian , Messinger Adam , Krauzlis Richard J.
Published: September 2023

Face processing is fundamental to primates and has been extensively studied in higher-order visual cortex. Here we report that visual neurons in the midbrain superior colliculus (SC) display a preference for faces, that the preference emerges within 50ms of stimulus onset – well before “face patches” in visual cortex – and that this activity can distinguish faces from other visual objects with accuracies of ∼80%. This short-latency preference in SC depends on signals routed through early visual cortex, because inactivating the lateral geniculate nucleus, the key relay from retina to cortex, virtually eliminates visual responses in SC, including face-related activity. These results reveal an unexpected circuit in the primate visual system for rapidly detecting faces in the periphery, complementing the higher-order areas needed for recognizing individual faces.

One-Sentence Summary

An unexpected circuit through the primate midbrain reports the presence of a face in peripheral vision in 1/20thof a second.
Hippo-deficient cardiac fibroblasts differentiate into osteochondroprogenitors
Authors: Tsai Chang-Ru , Kim Jong , Li Xiao , Czarnewski Paulo , Li Rich , Meng Fansen , Zheng Mingjie , Zhao Xiaolei , Steimle Jeffrey , Grisanti Francisco , Wang Jun , Samee Md. Abul Hassan , Martin James
Published: September 2023

Cardiac fibrosis, a common pathophysiology associated with various heart diseases, occurs from the excess deposition of extracellular matrix (ECM)1. Cardiac fibroblasts (CFs) are the primary cells that produce, degrade, and remodel ECM during homeostasis and tissue repair2. Upon injury, CFs gain plasticity to differentiate into myofibroblasts3and adipocyte-like4,5and osteoblast-like6cells, promoting fibrosis and impairing heart function7. How CFs maintain their cell state during homeostasis and adapt plasticity upon injury are not well defined. Recent studies have shown that Hippo signalling in CFs regulates cardiac fibrosis and inflammation8–11. Here, we used single-nucleus RNA sequencing (snRNA-seq) and spatially resolved transcriptomic profiling (ST) to investigate how the cell state was altered in the absence of Hippo signaling and how Hippo-deficient CFs interact with macrophages during cardiac fibrosis. We found that Hippo-deficient CFs differentiate into osteochondroprogenitors (OCPs), suggesting that Hippo restricts CF plasticity. Furthermore, Hippo-deficient CFs colocalized with macrophages, suggesting their intercellular communications. Indeed, we identified several ligand-receptor pairs between the Hippo-deficient CFs and macrophages. Blocking the Hippo-deficient CF-induced CSF1 signaling abolished macrophage expansion. Interestingly, blocking macrophage expansion also reduced OCP differentiation of Hippo-deficient CFs, indicating that macrophages promote CF plasticity.
SNPred outperforms other ensemble-based SNV pathogenicity predictors and elucidates the challenges of using ClinVar for evaluation of variant classification quality
Authors: Molotkov Ivan , Koboldt Daniel C. , Artomov Mykyta
Published: September 2023

Background

Current single nucleotide variants (SNVs) pathogenicity prediction tools assess various properties of genetic variants and provide a likelihood of causing a disease. This information aids in variant prioritization – the process of narrowing down the list of potential pathogenic variants, and, therefore, facilitating diagnostics. Assessing the effectiveness of SNV pathogenicity tools using ClinVar data is a widely adopted practice. Our findings demonstrate that this conventional method tends to overstate performance estimates.

Methods

We introduce SNPred, an ensemble model specifically designed for predicting the pathogenicity of nonsynonymous single nucleotide variants (nsSNVs). To evaluate its performance, we conducted assessments using six distinct validation datasets derived from ClinVar andBRCA1Saturation Genome Editing (SGE) data.

Results

Across all validation scenarios, SNPred consistently outperformed other state-of-the-art tools, particularly in the case of rare and cancer-related variants, as well as variants that are classified with low confidence by mostin silicotools. To ensure convenience, we provide precalculated scores for all possible nsSNVs.

We proved that the exceptionally high accuracy scores of the best models achieved for ClinVar variants are only attainable if the models learn to replicate misclassifications found in ClinVar. Additionally, we conducted a comparison of predictor performance on two distinct sets of BRCA1 variants that did not overlap: one sourced from ClinVar and the other from the SGE study. Across allin silicopredictors, we observed a significant trend where ClinVar variants were classified with notably higher accuracy.

Conclusions

We provide a powerful variant pathogenicity predictor that enhances the quality of clinical variant interpretation and highlights important challenges of using ClinVar for SNV pathogenicity predictors evaluation.
Early combination with remdesivir, nirmatrelvir/ritonavir and sotrovimab for the treatment of COVID-19 in immunocompromised hosts
Authors: Gentile Ivan , Foggia Maria , Silvitelli Maria , Sardanelli Alessia , Cattaneo Letizia , Viceconte Giulio ,   Federico II COVID team
Published: September 2023

Background

Immunocompromised patients with COVID-19 have higher morbidity and mortality than general population. Some authors have successfully used antiviral combination, but never in the early phase of the infection.

Methods

Retrospective cohort study to describe efficacy and safety of the combination of 2 antivirals, with or without a mAb, both in early (within 10 days from symptoms) and in later phase (after 10 days) of SARS-CoV-2 infection in immunocompromised patients admitted to our facility.

Results

We treated 11 patients (7 in early phase and 4 in later phase of COVID-19) with 10 days of intravenous remdesivir plus 5 days of oral nirmatelvir/ritonavir, also combined with sotrovimab in 10/11 cases.

Notably, 100% of the “early” patients reached virological clearance at day 30 from the end of the therapy and were alive and well at follow-up, whereas corresponding figures in the “late” patients were 50% and 75%. Patients in late group more frequently needed oxygen supplementation (p=0.015) and steroid therapy (p=0.045) during admission and reached higher a COVID-19 severity (p=0.017).

Discussion

The combination of antiviral and sotrovimab in early phase of COVID-19 in immunocompromised patients is well tolerated and associated with 100% of virological clearance. Patients treated later have lower response rate and higher disease severity, but a causative role of the therapy in such finding is yet to be demonstrated.
Prevalence and Associated Factors of Chronic Illness among Adults in Somalia: Findings from the Somali Health and Demographic Survey 2018-2019
Authors: Jayte Mohamed
Published: September 2023

Background

The distribution and related determinants of chronic diseases remain poorly characterized in Somalia, despite an emerging burden. The 2018-2019 Somali Health and Demographic Survey (SHDS) offers an opportunity to address evidence gaps regarding chronic conditions in Somalia.

Objectives

This study aimed to determine the prevalence of chronic illnesses and analyze related sociodemographic factors among adults aged ≥18 years in Somalia using data from the SHDS.

Methods

The analysis was conducted using cross-sectional SHDS data gathered from 31,198 households. Prevalence of self-reported chronic diseases was evaluated for the adult sample (n=23,485). Multivariable logistic regression examined sociodemographic factors associated with having a chronic condition.

Results

Approximately one in twelve adults (8.3%, 95% CI 7.9-8.6) had at least one chronic condition, with greater prevalence among women, urban dwellers, older individuals, and those having secondary education or higher. The most prevalent conditions were hypertension (26%), arthritis (15%), diabetes (11%), and asthma (8%). Advanced age, female gender, urban residence, and elevated wealth status were associated with higher likelihood of having a chronic disease.

Conclusions

Chronic diseases affect a substantial proportion of Somali adults, with heightened prevalence among growing urban populations. Integrative policies and programs are crucial for addressing the increasing burden of chronic conditions in conjunction with demographic changes
Gestures Of Hunger: Uncovering Intentional Gestural Communication In Free-Ranging Hanuman Langurs
Authors: Dasgupta Dishari , Banerjee Arnab , Dutta Akash , Mitra Shohini , Banerjee Debolina , Karar Rikita , Karmakar Srijita , Bhattacharya Aparajita , Ghosh Swastika , Bhattacharjee Pritha , Paul Manabi
Published: September 2023

Contrary to previous beliefs, intentional gestural communication (IGC) is not exclusive to the hominoid lineage but is also present in other non-human primates. Here, we report the presence of IGC among free-ranging Hanuman langur troop in Dakshineswar, West Bengal, India. These langurs exhibit a food-requesting behaviour wherein they use several gestures to communicate with the humans nearby. Moreover, they can also assess the recipient’s mental state and persistently check if the signal (food request) has been received, waiting until they receive the desired food item. We have identified eight begging gestures used by langurs of all ages, except infants. The most common gesture is by holding cloth (BGc), but provocation-initiated begging (BGpi) and begging by embracing legs (BGe) efficiently direct these events to its success. The frequency of successful begging events is higher in the evening due to increased human interactions. Our findings suggest that ontogenetic ritualization might be at play here among these troop members as this gestural communication has been learned through imitation and reinforced by the reward of receiving food. Moreover, these successful begging events serve as an effective foraging strategy for urban-adapted langurs, allowing them to acquire high-calorie processed food items within a human-modified urban ecosystem.
A common Alu element insertion in the 3’UTR ofTMEM106Bis associated with an increased risk of dementia
Authors: Rodney Alana , Karanjeet Kul , Benzow Kellie , Koob Michael D.
Published: September 2023

Sequence variants inTMEM106Bhave been associated with an increased risk of developing several different types of dementia. As part of our efforts to generate a set of mouse lines in which we replaced the mouseTmem106bgene with a humanTMEM106Bgene comprised of either a risk or protective haplotype, we conducted an in-depth sequence analysis of these alleles. We identified an AluYb8 insertion in the 3’ untranslated region (3’UTR) of theTMEM106Brisk haplotype. We analyzed transcribedTMEM106Bsequences using RNA-seq data available through the AD Knowledge portal and full genome sequences from the 1000Genomes databases and found that every risk allele analyzed shares this same AluYb8 insertion. The allele frequency of the risk haplotype ranges from 26% to 60% in the populations examined, and the balance of the alleles in each population is the protective haplotype. The primary sequence features of both haplotypes are distinct from the variants found in other primates. We conclude that the risk haplotype arose early in human development with a single Alu-insertion event within a unique haplotype context. Together these two non-ancestral allele variant types now appear to constitute the vast majority of theTMEM106Balleles but neither has come to fully predominate in any modern human population.
A soybean rust effector protease suppresses host immunity and cleaves a 3-deoxy-7-phosphoheptulonate synthase
Authors: Chicowski Aline Sartor , Qi Mingsheng , Variz Haris , Bredow Melissa , Montes Christian , Caiazza Francesco , Dong Haili , Margets Alexandra , Mejias Joffrey , Walley Justin W. , Craik Charles S. , Pedley Kerry F. , Aung Kyaw , Innes Roger , Whitham Steven A.
Published: September 2023

The devastating soybean rust (SBR) pathogen,Phakopsora pachyrhizi, encodes many secreted proteins, but only two have been functionally characterized for their roles in rust virulence. Here, we demonstrate that transient expression ofP. pachyrhizieffector candidate 15 (PpEC15), an aspartic protease, leads to enhanced bacterial growthin planta, suppression of callose deposition, reduced expression of plant defense-related marker genes and suppression of pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species (ROS). Stable expression ofPpEC15 in soybean suppresses PAMP-induced ROS production and enhances bacterial growth, indicating that, collectively,PpEC15 suppresses host and non-host innate immune responses. Yeast-two-hybrid and proximity labeling identified putativePpEC15 interacting partners including a peptide-chain release factor (PCRF), a NAC83 (NAM, ATAF, and CUC) transcription factor, and a DAHP (3-deoxy-7-phosphoheptulonate) synthase. We further show thatPpEC15 can cleave DAHP but does not cleave PCRF or NAC83. Virus-induced gene silencing of NAC83, PCRF and DAHP altered PAMP-induced ROS production and salicylic acid production, indicating that these proteins may be involved in immune signaling. Collectively, our data show thatPpEC15 is conserved acrossP. pachyrhiziisolates and other economically important rust species and is involved in the suppression of plant basal defense responses. Understanding the role ofPpEC15 inP. pachyrhizivirulence will provide a foundation for designing targeted intervention strategies to generate rust-resistant crops.
Association of secondary metabolite gene clusters with host-specific lineages of the cereal blast fungusPyricularia oryzae
Authors: Mehta Khyati , Navarro-Muñoz Jorge C. , Bakore Sayali , Collemare Jérôme , Patkar Rajesh
Published: September 2023

Fungal plant pathogens constantly evolve and deploy novel peptide and metabolite effectors to break down plant resistance and adapt to new host plants. The blast fungal pathogenPyricularia oryzaeis a single species subdivided into multiple host-specific lineages that have evolved through gain and/or loss of virulence and/or effector related genes through chromosomal rearrangement. Here, we mined 68 genomes ofP. oryzae, belonging to six host-specific lineages, to identify secondary metabolite (SM) biosynthetic gene clusters (BGCs) likely associated with potential metabolite effectors involved in host specialization. A similarity network analysis grouped a total of 4501 BGCs into 283 gene cluster families (GCFs), based on the content and architecture of the BGCs. While most of the GCFs were present in all theP. oryzaelineages, two (BGC-O1 and BGC-O2) were found specifically in theOryzalineage and one (BGC-TLE) was found in the lineage specific toTriticum, LoliumandEleusinehosts. Further analysis of the phylogenetic relationships between core biosynthetic genes confirmed that BGC-O1, which comprises a reducing polyketide synthase gene (MGG_08236) and four putative tailoring genes, was present only in theOryzalineage. Importantly, most genes, including MGG_08236, from the BGC-O1 were expressed specifically during pathogenesis. We propose that theOryzalineage-specific BGC-O1 produces a metabolite effector likely involved in specialization ofP. oryzaeto the rice host. In addition, we identified five SM genes under positive or balancing selection only in theOryzalineage, suggesting a role in the interaction with rice specifically. Our findings highlight the importance of further mining novel metabolite effectors in specialization and virulence of the blast fungus to different cereal hosts.
The crystal and cryo-EM structures of PLCγ2 reveal dynamic inter-domain recognitions in autoinhibition
Authors: Shin Young-Cheul , Plummer-Medeiros Ashlee Marie , Mungenast Alison , Choi Hyeong-wook , TenDyke Karen , Zhu Xiaojie , Shepard Jennifer , Zhuang Ningning , Hu Liang , Qian Dongming , Song Kangkang , Xu Chen , Wang John , Poda Suresh B , Liao Maofu , Chen Yu
Published: September 2023

Abstract/Summary

Phospholipase C gamma 2 (PLCγ2) plays important roles in cell signaling downstream of various membrane receptors. PLCγ2 contains a multi-domain inhibitory region critical for its regulation, while it has remained unclear how these domains contribute to PLCγ2 activity modulation. Here we determined three structures of human PLCγ2 in autoinhibited states, which reveal dynamic interactions at the autoinhibition interface, involving the conformational flexibility of the SH3 domain in the inhibitory region, and its previously unknown interaction with a C-terminal helical domain in the core region. We also determined a structure of PLCγ2 bound to the kinase domain of fibroblast growth factor receptor 1 (FGFR1), which demonstrates the recognition of FGFR1 by the nSH2 domain in the inhibitory region of PLCγ2. Our results provide new structural insights into PLCγ2 regulation that will facilitate future mechanistic studies to understand the entire activation process.
TRPM2-CaMKII signaling drives excessive GABAergic synaptic inhibition following ischemia
Authors: Burch Amelia M. , Garcia Joshua D. , O’Leary Heather , Haas Ami , Orfila James E. , Tiemeier Erika , Chalmers Nicholas , Smith Katharine R. , Quillinan Nidia , Herson Paco S.
Published: September 2023

Following an ischemic insult to the brain, there is an acute loss of GABAergic inhibitory synapses and an increase in excitatory/ inhibitory (E/I) imbalance that drives neuronal hyperexcitability. It is unknown whether this E/I imbalance persists at delayed timepoints and contributes to chronic impairments in memory and long-term potentiation (LTP) in the hippocampus following ischemic brain injury. Here, we reveal a shift to reduced E/I ratio in hippocampal CA1 neurons via a persistent increase in postsynaptic GABAAreceptor mediated inhibitory responses and clustering days after a global ischemic insult. This enhancement of postsynaptic inhibitory function and clustering required activation of the Ca2+-permeable TRPM2 ion channel and the Ca2+-dependent kinase, CaMKII. Thus, we propose a mechanism in which acute downregulation of GABAAreceptors is followed by a strengthening of inhibitory synapses at delayed periods after ischemia. Targeting this mechanism has therapeutic potential to recover hippocampal plasticity and cognitive function post-ischemia.

GRAPHICAL ABSTRACT
Temporally resolved single cell transcriptomics in a human model of amniogenesis
Authors: Sekulovski Nikola , Carleton Amber E , Rengarajan Anusha A , Lin Chien-Wei , Juga Lauren L , Whorton Allison E , Kropp Schmidt Jenna , Golos Thaddeus , Taniguchi Kenichiro
Published: September 2023

Amniogenesis is triggered in a collection of pluripotent epiblast cells as the human embryo implants. To gain insights into the critical but poorly understood transcriptional machinery governing amnion fate determination, we examined the evolving transcriptome of a developing human pluripotent stem cell-derived amnion model at the single cell level. This analysis revealed several continuous amniotic fate progressing states with state-specific markers, which include a previously unrecognized CLDN10+ amnion progenitor state. Strikingly, we found that expression of CLDN10 is restricted to the amnion-epiblast boundary region in the human post-implantation amniotic sac model as well as in a peri-gastrula cynomolgus macaque embryo, bolstering the growing notion that, at this stage, the amnion-epiblast boundary is a site of active amniogenesis. Bioinformatic analysis of published primate peri-gastrula single cell sequencing data further confirmed that CLDN10 is expressed in cells progressing to amnion. Additionally, our loss of function analysis shows that CLDN10 promotes amniotic but suppresses primordial germ cell-like fate. Overall, this study presents a comprehensive amniogenic single cell transcriptomic resource and identifies a previously unrecognized CLDN10+ amnion progenitor population at the amnion-epiblast boundary of the primate peri-gastrula.
Identification of an H-Ras nanocluster disrupting peptide
Authors: Manoharan Ganesh babu , Steffen Candy Laura , Pavic Karolina , Yeste-Vázquez Alejandro , Knuuttila Matias , Arora Neha , Zhou Yong , Härmä Harri , Gaigneaux Anthoula , Grossmann Tom N. , Abankwa Daniel Kwaku
Published: September 2023

The Ras-MAPK pathway is critical to regulate cell proliferation and differentiation. Its dysregulation is implicated in the onset and progression of numerous types of cancers. To be active, Ras proteins are membrane anchored and organized into nanoclusters, which realize high-fidelity signal transmission across the plasma membrane. Nanoclusters therefore represent potential drug targets. However, targetable protein components of signalling nanoclusters are poorly established.

We previously proposed that the nanocluster scaffold galectin-1 (Gal1) enhances H-Ras nanoclustering by stabilizing stacked dimers of H-Ras and Raf via a direct interaction of dimeric Gal1 with the Ras binding domain (RBD) in particular of B-Raf. Here, we provide further supportive evidence for this model. We establish that the B-Raf preference emerges from divergent regions of the Raf RBDs that were proposed to interact with Gal1. We then identify the L5UR peptide, which disrupts this interaction by binding with low micromolar affinity to the B-Raf-RBD. Its 23-mer core fragment is thus sufficient to interfere with Gal1-enhanced H-Ras nanocluster, reduce MAPK-output and cell viability inHRAS-mutant cancer cell lines.

Our data therefore suggest that the interface between Gal1 and the RBD of B-Raf can be targeted to disrupt Gal1-enhanced H-Ras nanoclustering. Collectively, our results support that Raf-proteins are integral components of active Ras nanoclusters.
Genome-wide Perturbation Analysis Screening System for Exosomes-Related Genes Based on the CRISPR/Cas9 Platform
Authors: Lu Lu , Yin Jianxin , Chen Ning , Guo Xiaofei , Han Chunle , Wang Miao , Du Huanqing , Li Huifang , Pan Xingang , Gao Mengya , Wang Na , Qi Dongli , Wang Jianhong , Dong Fengwei , Li Tianshi , Ge Xiaohu
Published: September 2023

As reported previously, exosomes have significant impacts on the physiological and pathological statein vivo. Exosomes have been extensively studied as a drug delivery carrier and some exosomes drugs have been undergoing clinical research. The mechanisms of exosome production, transport, and secretion remain to be studied in depth. Thus, here, we developed a novel CRISPR-UMI-based gene screening system, with which we can reveal the exosomes biogenesis, transport, and uptake mechanisms on a genome-wide scale. This system consists of two parts: one is a gene knockout component; the other part is a unique molecular identifiers (UMI) labeling component that can label the exosomes produced by the knockout cells, in which each sgRNA corresponds to a specific UMI. In this way, by detecting the UMI loaded in the exosomes, we can trace the knockout gene. In this study, we first verified the function of each component using plasmids and lentiviruses respectively. Next, we simulated the infection of cells with lentiviral libraries using a single lentivirus to validate the functionality of the screening system. Finally, we constructed a CRISPR-UMI-based library targeting 15 genes (genes with clear effects on exosomes biogenesis) to further validate the reliability of the screening system. The development of this screening system is of indispensable importance for the in-depth study of the mechanisms of exosome production and secretion, as well as for the improvement of exosomes production and the advancement of exosomes industrialization.
Does the stress axis mediate behavioural flexibility in a social cichlid,Neolamprologus pulcher?
Authors: Fischer Stefan , Ferlinc Zala , Hirschenhauser Katharina , Taborsky Barbara , Fusani Leonida , Tebbich Sabine
Published: September 2023

Behavioural flexibility plays a major role in the way animals cope with novel situations, and physiological stress responses are adaptive and highly efficient mechanisms to cope with unpredictable events. Previous studies investigating the role of stress responses in mediating behavioural flexibility were mostly done in laboratory rodents using stressors and cognitive challenges unrelated to the ecology of the species. To better understand how stress mediates behavioural flexibility in a natural context, direct manipulations of the stress response and cognitive tests in ecologically relevant contexts are needed. To this aim, we pharmacologically blocked glucocorticoid receptors (GR) in adultNeolamprologus pulcherusing a minimally invasive application of a GR antagonist. GR blockade prevents the recovery after a stressful event, which we predicted to impair behavioural flexibility. After the application of the GR antagonist, we repeatedly exposed fish to a predator and tested their behavioural flexibility using a detour task, i.e. fish had to find a new, longer route to the shelter when the shortest route was blocked. While the latencies to find the shelter were not different between treatments, GR blocked fish showed more failed attempts during the detour tasks than control fish. Furthermore, weak performance during the detour tasks was accompanied by an increase of fear related behaviours. This suggests that blocking GR changed the perception of fear and resulted in an impaired behavioural flexibility. Therefore, our results support a causal link between the capacity to recover from stressors and behavioural flexibility inN. pulcherwith potential consequences for an effective and adaptive coping with changing environments.
Novel laminarin-binding CBMs in multimodular proteins of marineBacteroidotafeature prominently in phytoplankton blooms
Authors: Zühlke Marie-Katherin , Ficko-Blean Elizabeth , Bartosik Daniel , Terrapon Nicolas , Jeudy Alexandra , Jam Murielle , Wang Fengqing , Welsch Norma , Larocque Robert , Jouanneau Diane , Eisenack Tom , Thomas François , Trautwein-Schult Anke , Teeling Hanno , Becher Dörte , Schweder Thomas , Czjzek Mirjam
Published: September 2023

The ß-(1,3)-glucan laminarin functions as storage polysaccharide in marine stramenophiles such as diatoms. Laminarin is abundant, water-soluble and structured simply, making it an attractive substrate for marine bacteria. As a consequence, many marine bacteria have developed competitive strategies to scavenge and decompose laminarin, which involves carbohydrate-binding modules (CBMs) as key players. We therefore functionally and structurally characterized two yet unassigned domains as laminarin-binding CBMs in multimodular proteins from our model bacteriumChristiangramia forsetiiKT0803T, hereby unveiling the novel laminarin-binding CBM families CBMxx and CBMyy (official CAZy numbering will be provided upon acceptance of the manuscript in a peer-reviewed journal). We discovered four CBMxx repeats in a surface glycan-binding protein (SGBP) and a single CBMyy combined with a glycoside hydrolase module from family 16 (GH16_3). Our analyses revealed that both modular proteins have an elongated shape, and that the GH16_3 displayed a higher flexibility than the SGBP. While motility of both polypeptide chains may facilitate recognition and/or degradation of laminarin, constraints in the SGBP may support docking of laminarin onto the bacterial surface. The exploration of bacterial metagenome-assembled genomes (MAGs) from phytoplankton blooms in the North Sea revealed that both laminarin-binding CBM families are widely distributed among marineBacteroidota, illustrating the high adaptability of modularity in sugar-binding and -degrading proteins. High expression of CBMxx- and CBMyy-containing proteins during phytoplankton blooms further underpins their importance in marine laminarin usage.