Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk factors for vitamin D deficiency in Abu Dhabi Emirati population

Objective There have been concerns regarding the high prevalence of vitamin D deficiency in the United Arab Emirates and the association between this prevalence and cardiovascular risk. Vitamin D deficiency is a global public health problem, with a high prevalence in the Abu Dhabi national population. This cross-sectional retrospective observational study aimed to elucidate vitamin D deficiency symptoms and contributing factors in this context. Method and sampling Among 12346 participants presenting for their Weqaya population comprehensive cardiovascular risk factor screening, 700 were randomly selected and telephoned, among whom 400 completed a questionnaire that elicited information on dietary intake, sun exposure, clothing, physical activity, and symptoms related to vitamin D deficiency. Results Higher vitamin D levels were noted in participants who consumed extra servings of cod liver oil, tuna, salmon, and eggs; who wore clothes with their arms and legs exposed; and who performed daily physical activity. Symptoms of hypovitaminosis D (bone pain) were more frequently found in females. Fatigue is significantly associated with low vitamin D and younger participants. Strategies focusing on health promotion and lifestyle interventions should be implemented to address vitamin D deficiency.
Exploration of Prognostic Immune-Related Genes and lncRNAs Biomarkers in Kidney Renal Clear Cell Carcinoma and Its Crosstalk with Acute Kidney Injury

Kidney renal clear cell carcinoma (KIRC) has a poor prognosis and a high death rate globally. Cancer prognosis is strongly linked to immune-related genes (IRGs), according to numerous research. We utilized KIRC RNA-seq data from the TCGA database to build a prognostic model incorporating seven immune-related (IR) lncRNAs, and we constructed the model using LASSO regression. Additionally, we calculated a risk score for each patient using a prognostic model that divided patients into high-risk and low-risk groups. The ESTIMATE and CIBERSORT methodologies were then used to analyze the differences in the tumor microenvironment of the two groups of patients. Finally, we predicted three small molecule drugs that may have potential therapeutic effects for high-risk patients. We combined the acute kidney injury dataset to obtain differential genes that may serve standard biological functions with two risk groups. Our study shows that the model we constructed for IR-lncRNAs has reliable predictive efficacy for patients with KIRC.
The global gap in treatment coverage for major depressive disorder in 84 countries from 2000–2019: A systematic review and Bayesian meta-regression analysis

Background The treatment coverage for major depressive disorder (MDD) is low in many parts of the world despite MDD being a major contributor to disability globally. Most existing reviews of MDD treatment coverage do not account for potential sources of study-level heterogeneity that contribute to variation in reported treatment rates. This study aims to provide a comprehensive review of the evidence and analytically quantify sources of heterogeneity to report updated estimates of MDD treatment coverage and gaps by location and treatment type between 2000 and 2019. Methods and findings A systematic review of the literature was conducted to identify relevant studies that provided data on treatment rates for MDD between January 1, 2000, and November 26, 2021, from 2 online scholarly databases PubMed and Embase. Cohort and cross-sectional studies were included if treatment rates pertaining to the last 12 months or less were reported directly or if sufficient information was available to calculate this along with 95% uncertainty intervals (UIs). Studies were included if they made use of population-based surveys that were representative of communities, countries, or regions under study. Studies were included if they used established diagnostic criteria to diagnose cases of MDD. Sample and methodological characteristics were extracted from selected studies. Treatment rates were modeled using a Bayesian meta-regression approach and adjusted for select covariates that quantified heterogeneity in the data. These covariates included age, sex, treatment type, location, and choice of MDD assessment tool. A total of 149 studies were included for quantitative analysis. Treatment coverage for health service use ranged from 51% [95% UI 20%, 82%] in high-income locations to 20% [95% UI 1%, 53%] in low- and lower middle-income locations. Treatment coverage for mental health service use ranged from 33% [95% UI 8%, 66%] in high-income locations to 8% [95% UI <1%, 36%] in low- and lower middle-income countries. Minimally adequate treatment (MAT) rates ranged from 23% [95% UI 2%, 55%] in high-income countries to 3% [95% UI <1%, 25%]) in low- and lower middle-income countries. A primary methodological limitation was the lack of sufficient data from low- and lower middle-income countries, which precluded our ability to provide more detailed treatment rate estimates. Conclusions In this study, we observed that the treatment coverage for MDD continues to be low in many parts of the world and in particular in low- and lower middle-income countries. There is a continued need for routine data collection that will help obtain more accurate estimates of treatment coverage globally.
Unraveling the Expression Patterns of Immune Checkpoints Identifies New Subtypes and Emerging Therapeutic Indicators in Lung Adenocarcinoma

Immune checkpoint genes (ICGs) play pivotal roles in tumor immune microenvironment (TIME), and thus, targeting them represents a promising strategy for cancer immunotherapy. However, the genetic landscape of ICGs in lung adenocarcinoma (LUAD) is still unknown. Herein, we comprehensively evaluated the ICG expression profiles of 1439 LUAD samples and linked ICG expression patterns with infiltration of immune cells, clinical features, and response to immune checkpoint blockade (ICB). The ICGscore was developed to quantify ICG expression patterns of individual patient by principal component analysis algorithms. Three distinct ICG expression patterns and three ICG-related genomic clusters were determined, which were implicated in different clinical outcomes, level of immune infiltrates, and biological process. LUAD patients were subdivided into high- and low-ICGscore subgroups. Patients with higher ICGscore were characterized by favorable survival outcomes, increased immune cell infiltration, and enhanced expression of ICGs. Further analysis revealed that lower ICGscore was associated with greater tumor mutation loads and higher mutation rates of TTN, KEAP1, and ZFHX4. High ICGscore has the potential to be a robust indicator in clinical benefit of immunotherapy. Taken together, unraveling the ICG expression patterns will advance our understanding of heterogeneity of TIME and guides more effective immunotherapeutic strategies in LUAD.
Live and video observations of scapular dyskinesis in individuals with nonspecific neck pain: A reliability study

ABSTRACT Background Scapular dyskinesis (SD) has been demonstrated in neck pain patients, however reliability of SD test in this population is still lacking. Objective To investigate inter-rater and intra-rater (live versus video) reliability of SD by observation in neck pain patients. Methods Sixty-nine participants with nonspecific neck pain (31.7 ± 14.3 years) were recruited. SD was tested on the ipsilateral side of neck pain during unilateral and bilateral arm elevation. Two examiners categorized SD using two classification systems: simple (yes/no) and specific type (winging, dysrhythmia, mixed abnormality or normal). Video recordings were reviewed by one examiner. Results For inter-rater reliability, agreement and kappa (κ) values for unilateral test were 94.20%, 0.82 by simple classification and 72.46%, 0.59 by specific type. Agreement and κ values for bilateral test were 91.30%, 0.68 by simple classification and 65.22%, 0.52 by specific type. For intra-rater reliability, agreement and κ values for unilateral test were 92.75%, 0.77 by simple classification and 71.01%, 0.57 by specific type. Agreement and κ values for bilateral test were 91.30%, 0.65 by simple classification and 65.22%, 0.52 by specific type. Conclusion Observation assessment demonstrated good-to-very good inter-rater and moderate-to-good intra-rater (live versus video) reliability for assessing SD in neck pain patients.
Considerations before the decision-making including fluvoxamine as a treatment option in guidelines on the management of COVID-19

Unit of Psychiatry, Department of Public Health and Medicinal Administration, & Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SAR, China; Centre for Cognitive and Brain Sciences, University of Macau, Macao SAR, China; Institute of Advanced Studies in Humanities and Social Sciences, University of Macau, Macao SAR, China; College of Education for the Future, Beijing Normal University, Beijing, China; The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital & the Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China; Center on Smart and Connected Health Technologies, Mays Cancer Center, School of Nursing, UT Health San Antonio, San Antonio, Texas, USA; School of Nursing, Hong Kong Polytechnic University, Hong Kong SAR, China; The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, China and Department of Psychiatry, The Melbourne Clinic and St Vincent’s Hospital, University of Melbourne, Richmond, Victoria, Australia
Influence of target-distractor neural similarity on working memory performance in older and younger adults

ABSTRACT According to the inhibitory deficit hypothesis, older adults often fail to selectively inhibit distractors and attend to relevant information in working memory, leading to poorer memory of target items but better recall of irrelevant distractors compared to younger adults. Here, we explored how neural similarity of activity patterns between relevant and irrelevant stimulus categories impacts memory performance. We found evidence that older adults may benefit from failing to inhibit distractors that are similar to targets, perhaps because sustained neural activation of distractors partially supports maintenance of targets when they share neural resources, allowing for better subsequent recognition of studied target items. We also found increased category-specific multivoxel pattern activity in medial temporal regions in younger compared to older adults as category similarity increased. We propose that this reduced category-specific activation in medial temporal regions in older adults may reflect more blended representations of all the information available in working memory.
Early Hearing Preservation Outcomes Following Cochlear Implantation With New Slim Lateral Wall Electrode Using Electrocochleography

Objective: Describe early hearing preservation (HP) cochlear implantation (CI) outcomes using a new slim lateral wall electrode (SLWE). Study Design: Prospective cohort study. Setting: Tertiary referral center. Patients: Adult CI candidates with preoperative low-frequency pure-tone average (LFPTA; 125, 250, 500 Hz) ≤60 dB HL. Intervention: CI with and without intracochlear real-time electrocochleography (RT-ECochG). Main Outcome Measure: HP (LFPTA ≤80 dB HL), LFPTA shift, speech-perception performance measures, postoperative CT reconstruction. Results: Forty-two subjects were implanted with the SLWE. Thirty patients underwent full insertion without RT-ECochG feedback, and HP was maintained at 3-months postactivation for 7 (23.3%) patients with mean LFPTA shift of 57.5 ± 25.6 dB HL. RT-ECochG feedback was utilized on 12 patients, of whom 6 patients had full insertions and 6 patients had anywhere from 1 to 3 electrodes left outside of the cochlea based on RT-ECochG feedback. At 3 months postoperatively, HP was achieved on 10 (83.3%) patients and mean LFPTA shift was 18.9 c 11.7 dB HL. Mean difference between LFPTA threshold shift at 3-months postactivation with and without RT-ECochG was 38.6 dB HL (95% CI, 25.6–51.67). There was an improvement in delta CNC from preoperative to 3-months postactivation when using RT-ECochG, with mean difference 20.7% (95% CI, 3.3–38.1). Conclusions: Use of RT-ECochG monitoring during SLWE placement results in fewer full electrode insertions and significantly better HP rates and speech-perception outcomes when compared with unmonitored insertions. Further investigation is needed to evaluate long-term audiologic outcomes to better understand the relationships among ECochG, cochlear trauma, functional outcomes, and HP.
Correction methods for noncontact intraocular pressure measurement in patients with keratoconus and healthy individuals.

PURPOSE The objective of this study was to investigate the usefulness of four different algorithms to correct noncontact intraocular pressure measurement errors in keratoconus patients and normal individuals. METHODS Noncorrected intraocular pressure and corrected intraocular pressures were measured in one eye of 34 patients with keratoconus and 34 age- and gender-matched healthy controls using Corvis Scheimpflug Technology. The correlation of noncorrected intraocular pressure and corrected intraocular pressures with age, axial length, corneal shape, thickness, and biomechanics was calculated. Corrected intraocular pressures were compared with noncorrected intraocular pressure using paired t test and Bland-Altman plots (95% limits of agreement). RESULTS The noncorrected intraocular pressure correlated with corneal thickness and biomechanical parameters in both groups (all p≤0.047), and front and back mean keratometry in the keratoconus group (r=-0.39, p=0.02, and r=0.39, p=0.02, respectively). After adjustment with different intraocular pressure correction algorithms, biomechanically corrected intraocular pressure showed a minimal correlation with corneal features and a nonsignificant difference with noncorrected intraocular pressure in the healthy group (-0.1 ± 1.1 mmHg, p=0.58; 95% limits of agreement: -2.3 to 2.1 mmHg). CONCLUSIONS Measuring intraocular pressure using noncontact tonometry and its corrected forms with a corneal thickness-based simple linear formula in patients with keratoconus is associated with many errors. Using more complex formulas that take into consideration more corneal stiffness parameters in addition to corneal thickness, such as biomechanically corrected intraocular pressure formula, may be more reliable and beneficial in this group of patients.
AMIGO1 Promotes Axon Growth and Territory Matching in the Retina

Dendrite and axon arbor sizes are critical to neuronal function and vary widely between different neuron types. The relative dendrite and axon sizes of synaptic partners control signal convergence and divergence in neural circuits. The developmental mechanisms that determine cell-type-specific dendrite and axon size and match synaptic partners' arbor territories remain obscure. Here, we discover that retinal horizontal cells express the leucine-rich repeat domain cell adhesion molecule AMIGO1. Horizontal cells provide pathway-specific feedback to photoreceptors—horizontal cell axons to rods and horizontal cell dendrites to cones. AMIGO1 selectively expands the size of horizontal cell axons. When Amigo1 is deleted in all or individual horizontal cells of either sex, their axon arbors shrink. By contrast, horizontal cell dendrites and synapse formation of horizontal cell axons and dendrites are unaffected by AMIGO1 removal. The dendrites of rod bipolar cells, which do not express AMIGO1, shrink in parallel with horizontal cell axons in Amigo1 knockout (Amigo1 KO) mice. This territory matching maintains the function of the rod bipolar pathway, preserving bipolar cell responses and retinal output signals in Amigo1 KO mice. We previously identified AMIGO2 as a scaling factor that constrains retinal neurite arbors. Our current results identify AMIGO1 as a scaling factor that expands retinal neurite arbors and reveal territory matching as a novel homeostatic mechanism. Territory matching interacts with other homeostatic mechanisms to stabilize the development of the rod bipolar pathway, which mediates vision near the threshold. SIGNIFICANCE STATEMENT Neurons send and receive signals through branched axonal and dendritic arbors. The size of these arbors is critical to the function of a neuron. Axons and dendrites grow during development and are stable at maturity. The mechanisms that determine axon and dendrite size are not well understood. Here, we identify a cell surface protein, AMIGO1, that selectively promotes axon growth of horizontal cells, a retinal interneuron. Removal of AMIGO1 reduces the size of horizontal cell axons without affecting the size of their dendrites or the ability of both arbors to form connections. The changes in horizontal cell axons are matched by changes in synaptic partner dendrites to stabilize retinal function. This identifies territory matching as a novel homeostatic plasticity mechanism.
The evolution and role of eukaryotic-like domains in environmental intracellular bacteria: the battle with a eukaryotic cell.

Intracellular pathogens that are able to thrive in different environments, such as Legionella spp. which preferentially live in protozoa in aquatic environments or environmental Chlamydiae which replicate either within protozoa or a range of animals, possess a plethora of cellular biology tools to influence their eukaryotic host. The host manipulation tools that evolved in the interaction with protozoa, confer these bacteria the capacity to also infect phylogenetically distinct eukaryotic cells, such as macrophages and thus they can also be human pathogens. To manipulate the host cell, bacteria use protein secretion systems and molecular effectors. Although these molecular effectors are encoded in bacteria, they are expressed and function in a eukaryotic context often mimicking or inhibiting eukaryotic proteins. Indeed, many of these effectors have eukaryotic-like domains. In this review we propose that the main pathways environmental intracellular bacteria need to subvert in order to establish the host eukaryotic cell as a replication niche are chromatin remodelling, ubiquitination signalling, and modulation of protein-protein interactions via tandem repeat domains. We then provide mechanistic insight into how these proteins might have evolved as molecular weapons. Finally, we highlight that in environmental intracellular bacteria the number of eukaryotic-like domains and proteins is considerably higher than in intracellular bacteria specialised to an isolated niche, such as obligate intracellular human pathogens. As mimics of eukaryotic proteins are critical components of host pathogen interactions, this distribution of eukaryotic-like domains suggests that the environment has selected them.
Familiar Infections in Novel Anatomy: Patient Reports of Sexually Transmitted Infections After Gender-Affirming Penile Reconstruction

Survey respondents report sexually transmitted infection after gender-affirming phalloplasty and metoidioplasty. There were no infections in the penile urethra and several infections localized to the unaltered vaginal orifice. Background Sexually transmitted infections (STIs) after penile reconstruction in transgender, nonbinary, and other gender expansive (T/GE) populations have not previously been described, despite known risk factors in the population. After T/GE penile reconstruction, care providers may underdiagnose STI without anatomically appropriate guidelines. Methods A detailed anonymous online survey of experiences of T/GE penile reconstruction patients was constructed with community input. Respondents were recruited from online support groups. Results A total of 128 T/GE people with experience of penile reconstruction responded to an anonymous survey posted in online support groups from January to May 2020. Seven respondents (5.5%) self-reported 1 or more of the listed STIs at any point after penile reconstruction. All respondents with neourethras were diagnosed with localized STIs in nonurethral (extrapenile) locations only, and lack of vaginectomy was correlated with STI (P = 0.002). Sexually transmitted infections were correlated with reporting sex with cisgender men (P = 0.001), transgender men (P = 0.009), and transgender women (P = 0.012). Of health care access variables, only receiving health care at a community health center was correlated with STI history (P = 0.003). Conclusions This exploratory survey indicates that STI occurs after penile reconstruction in T/GE patients. Clinical confirmation is needed to identify specific risk factors and relative susceptibility of postreconstruction anatomy to STIs. Given no previous surveillance recommendations for this population and the correlation of health care provider location with STI prevalence, underdiagnoses are likely. Based on the authors' clinical experience, we describe a urogenital screening algorithm after gender-affirming penile reconstruction.
Clinical significance of pancreatic ductal metaplasia

Pancreatic ductal metaplasia (PDM) is the stepwise replacement of differentiated somatic cells with ductal or ductal‐like cells in the pancreas. PDM is usually triggered by cellular and environmental insults. PDM development may involve all cell lineages of the pancreas, and acinar cells with the highest plasticity are the major source of PDM. Pancreatic progenitor cells are also involved as cells of origin or transitional intermediates. PDM is heterogeneous at the histological, cellular, and molecular levels and only certain subsets of PDM develop further into pancreatic intraepithelial neoplasia (PanIN) and then pancreatic ductal adenocarcinoma (PDAC). The formation and evolution of PDM is regulated at the cellular and molecular levels through a complex network of signaling pathways. The key molecular mechanisms that drive PDM formation and its progression into PanIN/PDAC remain unclear, but represent key targets for reversing or inhibiting PDM. Alternatively, PDM could be a source of pancreas regeneration, including both exocrine and endocrine components. Cellular aging and apoptosis are obstacles to PDM‐to‐PanIN progression or pancreas regeneration. Functional identification of the cellular and molecular events driving senescence and apoptosis in PDM and its progression would help not only to restrict the development of PDM into PanIN/PDAC, but may also facilitate pancreatic regeneration. This review systematically assesses recent advances in the understanding of PDM physiology and pathology, with a focus on its implications for enhancing regeneration and prevention of cancer. © 2022 The Pathological Society of Great Britain and Ireland.