Miracle-dz/UniFAR-FTUs huggingface dataset:
Chest Computed Tomography Features of Nontuberculous Mycobacterial Pulmonary Disease Versus Asymptomatic Colonization

Background: Asymptomatic colonization by nontuberculous mycobacteria (NTM) found in sputum isolates are commonly encountered and clinicians lack a biomarker for prognosticating the risk of transition asymptomatic colonization to active clinical disease. Chest computed tomography (CT) imaging is commonly obtained in this patient population and may serve a role for this purpose. Methods: We conducted a single-center, cross-sectional study of patients followed in the NTM clinic at our center between August 2019 and August 2020. All patients had a history of NTM isolated from their airways and were cohorted as either nontuberculous mycobacteria-pulmonary disease (NTM-PD) if they met ATS/IDSA guidelines for treatment or as nontuberculous mycobacteria-colonized (NTM-C) if they did not meet ATS/IDSA criteria for NTM treatment. Patients with a chest CT were included in the analysis and CT scans were assessed for features including bronchiectasis, nodules, and cavities. Bronchiectasis severity was calculated using the modified Reiff scoring system. Univariate analyses were conducted to compare patients with NTM-C and NTM-PD. Results: Eighty-four patients were included in the analysis and 27 were classified as NTM-C and 57 as NTM-PD. NTM-PD patients had a greater median number of lung lobes affected by bronchiectatic airways (6 [1] NTM-PD vs. 5 [3] NTM-C P=0.005) and a greater frequency of cystic bronchiectasis (17.5% NTM-PD vs. 0% NTM-PD, P=0.016). Bronchiectasis severity was higher for NTM-PD patients (7 [9] NTM-PD vs. 5 [1.5] NTM-C, P<0.001). Conclusions: Patients with NTM-PD have greater bronchiectatic airway involvement and the forms of bronchiectasis present are more severe compared with NTM-C patients. In addition, cavitation of lung parenchyma was a radiographic feature solely associated with NTM-PD. Features identified on chest CT may be useful as a prognostic biomarker for the risk of transition from NTM-C to NTM-PD.
CCR5-Δ32 polymorphism: a possible protective factor for post-stroke depressive symptoms

Background: A naturally occurring loss-of-function mutation in the gene for C-C chemokine receptor type 5 (CCR5-Δ32) has recently been reported as a protective factor in post-stroke motor and cognitive recovery. We sought to examine whether this mutation also prevented the development of depressive symptoms up to 2 years after a stroke. Methods: Participants were survivors of a first-ever mild to moderate ischemic stroke or transient ischemic attack from the TABASCO prospective study who underwent a 3 T MRI at baseline and were examined by a multiprofessional team 6, 12 and 24 months after the event, including an evaluation of depressive symptoms using the Geriatric Depression Scale. Results: CCR5-Δ32 status and a baseline depression evaluation were available for 435 patients. Compared with noncarriers, CCR5-Δ32 carriers (16.1%) had fewer depressive symptoms at admission (p = 0.035) and at 6 months (p < 0.001), 12 months (p < 0.001) and 24 months (p = 0.006) after the index event. This association remained significant at 6 and 12 months after adjustment for age, sex, education, antidepressant use, ethnicity and the presence of cortical infarcts. These findings were more robust in women. Compared to baseline, depressive symptoms in CCR5-Δ32 noncarriers tended to remain stable or grow worse over time, but in CCR5-Δ32 carriers, symptoms tended to improve. Limitations: A limitation of this study was the exclusion of patients who had a severe stroke or who had pre-stroke depression. Conclusion: Carriers of the CCR5-Δ32 allele had a lower tendency to develop depressive symptoms post-stroke, and this phenomenon was more prominent in women. These findings could have clinical implications; they suggest a mechanism-based treatment target for post-stroke depression. Drugs mimicking this loss-of-function mutation exist and could serve as a novel antidepressant therapy.
Computational modeling of falling liquid film free surface evaporation

A computational model is developed to investigate fundamental flow physics and transport phenomena of evaporating wavy-laminar falling liquid films of water and black liquor. The computational model is formulated from first principles based on the conservation laws for mass, momentum, energy and species in addition to a phase transport equation for capturing interface deformation and evolution. Free surface waves are generated by monochromatic perturbation of velocity. Continuum models for interfacial evaporation define source terms for liquid vaporization and species enrichment in the conservation laws. A phenomenological crystallization model is derived to account for species depletion due to salt precipitation during black liquor falling film evaporation. Using highly resolved numerical grids on parallel computers, the computational model is implemented to analyze the dynamics of capillary separation eddies in low Reynolds number falling films, investigate the dominant mechanisms of heat transfer enhancement in falling films at moderately high Reynolds numbers and study the fundamental wave structures and wave induced transport in black liquor falling films on flat and cylindrical walls. From simulation results, a theory based on the dynamics of wavefront streamwise pressure gradient is proposed to explain interfacial waves interaction that give rise to multiple backflow regions in films dominated by solitary-capillary waves. The study shows that the mechanism of heat transfer enhancement in moderately high Reynolds number films follows from relatively lower conduction thermal resistance and higher crosswise convective transport at newly formed intermediate wavefronts. Interfacial phenomena such as wave-breaking and vapor entrainment observed in black liquor falling films is explained in terms of a mechanistic theory based on evolution of secondary instabilities and large amplitude wave force imbalances.
Gastrointestinal tissue as a “new” target of pollution exposure

Airborne pollution has become a leading cause of global death in industrialized cities and the exposure to environmental pollutants has been demonstrated to have adverse effects on human health. Among the pollutants, particulate matter (PM) is one of the most toxic and although its exposure has been more commonly correlated with respiratory diseases, gastrointestinal (GI) complications have also been reported as a consequence to PM exposure. Due to its composition, PM is able to exert on intestinal mucosa both direct damaging effects, (by reaching it either via direct ingestion of contaminated food and water or indirect inhalation and consequent macrophagic mucociliary clearance) and indirect ones via generation of systemic inflammation. The relationship between respiratory and GI conditions is well described by the lung‐gut axis and more recently, has become even clearer during coronavirus disease 2019 (COVID‐19) pandemic, when respiratory symptoms were associated with gastrointestinal conditions. This review aims at pointing out the mechanisms and the models used to evaluate PM induced GI tract damage.
Variability in microcystin quotas during a Microcystis bloom in a eutrophic lake

Microcystis is a bloom-forming genus of cyanobacteria with some genotypes that produce highly toxic microcystin hepatotoxins. In waterbodies where biological and physical factors are relatively homogenous, toxin quotas (the average amount of toxin per cell), at a single point in time, are expected to be relatively constant. In this study we challenged this assumption by investigating the spatial distribution of microcystin quotas at a single point in time on two separate occasions in a lake with a major Microcystis bloom. Microcystis cell concentrations varied widely across the lake on both sampling occasions (730- and 137-fold) together with microcystin quotas (148- and 362-fold). Cell concentrations and microcystin quotas were strongly positively correlated (R2 = 0.89, P < 0.001, n = 28; R2 = 0.67, P < 0.001, n = 25). Analysis of Microcystis strains using high-throughput sequencing of the 16S-23S rRNA intergenic spacer region showed no relationship between microcystin quota and the relative abundance of specific sequences. Collectively, the results of this study indicate an association between microcystin production and cell density that magnifies the potential for bloom toxicity at elevated cell concentrations.
Group-level human values estimated with web search data and archival data explain the geographic variation in COVID-19 severity in the United States

Abstract Objectives Personal Focus values (PF = Openness to change values + Self-enhancement values) motivate self-centred behaviours, and Social Focus values (SF = Conservation values + Self-transcendence values) promote self-sacrificial counterparts. This research investigated how a state-level PF-SF value-continuum would explain the geographic variation in COVID-19 severity in the United States. Design This research estimated state-level values by Google search data (from 2004 to 2019) on value-related words (e.g. family for conservation values) (Study 1a) and archival indicators (e.g. gun ownership rate for security values) (Study 1b). COVID-19 severity was measured by shorter time delay of first documented cases, shorter overall doubling times, higher reproductive ratio and higher case fatality ratio. Hierarchical and multilevel analyses examined how state-level values would predict COVID-19 severity across U.S. states (Studies 1a and 1b) and 3,135 counties (Study 2). Results State-level analyses accounting for spatial autocorrelation and covariates (e.g. COVID-19 testing rate, airport traffic, personality, etc.) revealed that the PF-SF value-continuums measured with different methods positively and significantly predicted COVID-19 severity, and the effects of state-level values on county-level COVID-19 severity were significant when county- and state-level covariates were controlled. Conclusion Social focus values may mitigate the devastating effect of COVID-19 in the United States.
Post-thaw culture has no beneficial effect on frozen embryos transfer outcomes comparing to same embryonal age non-cultured frozen-thawed embryos

Abstract Purpose To assess the impact of post-thawing embryo culture on frozen embryo transfer (FET) outcomes. Methods A retrospective cohort study including 678 consecutive FET cycles performed between the years 2004 and 2017 was conducted. Patients older than 45 years old were excluded. FET cycles were stratified as follows: (1) two-day (2d) embryos thawed and cultured to three-day (3d) versus 3d embryos thawed and transferred; (2) 2d or 3d embryos thawed and cultured to blastocysts versus blastocysts thawed and transferred. A p-value <. 05 was considered statistically significant. Results Maternal age, BMI, smoking, and basal FSH of the 2d and 3d cultured embryo group (n = 110) and the 3d non-cultured embryo group (n = 189) were comparable. Endometrium preparation protocols and the achieved endometrial thickness did not differ between groups. Pregnancy rate, implantation rate, clinical pregnancy, live birth rate, abortions, multiple pregnancies, perinatal outcomes, and birth weight were comparable. The 2d and 3d embryos cultured to blastocyst (n = 41) compared to non-cultured blastocyst (n = 338) showed that the non-cultured blastocyst patients had higher smoking rates and longer follicular phase. Endometrial thickness was comparable. The 2d and 3d embryos cultured to blastocyst stage had higher multiple pregnancies rate compared to the blastocyst non-cultured group, whereas pregnancy rate, implantation rate, live birth rate, miscarriages, perinatal outcomes, and birth weight were comparable. Conclusion We could not demonstrate that the post-thaw culture had a significant impact on the outcome of FET cycles.
Ascending myelopathy after intrathecal methotrexate

Methotrexate (MTX) is an anti-metabolite medication that inhibits deoxyribonucleic acid synthesis. Due to poor drug penetration through the blood–brain barrier, it is often administered intrathecally to attain higher cerebrospinal fluid (CSF) concentration. However, intrathecal (IT) administration of MTX is generally concomitant with higher neurotoxicity. MTX myelopathy is defined as the development of isolated spinal cord dysfunction following the IT administration of MTX. Documented manifestations vary from vacuolar degeneration of the lateral and posterior funiculi to complete transverse necrosis of the spinal cord. Here, we present the clinical presentations and image findings of a women with bilateral paresthesia after IT administration of MTX. A 31-year-old woman presented with bilateral lower limb numbness. The numbness was symmetric without shooting pain. In the following 2 weeks, weakness of the lower extremities developed from the distal and gradually progressed upwards. She also experienced urinary incontinence and severe low back pain. On admission, physical examination revealed decreased pain and proprioception below L4 level and absence below S3. Deep tendon reflexes were hyperactive over bilateral lower extremities, accompanied with bilateral ankle clonus. Muscle power of bilateral proximal and distal legs was 2 and 1 on a scale of 1 to 5, respectively. She had been diagnosed with acute myeloid leukemia 10 months before the onset of weakness. Two days after the diagnosis, induction chemotherapy with idarubicin and cytarabine (I3A7) was initiated. Subsequent bone marrow and CSF studies showed positive central nervous system involvement. Therefore, IT MTX was given for therapeutic purposes, and the total accumulative dose of IT MTX during the following 10 months since the initial diagnosis of acute myeloid leukemia was 120 mg (12 mg 10 sessions). After the eradication of blast cells in CSF, she received haploidentical bone marrow transplantation, followed by haploidentical peripheral blood stem cell transplantation. She had complete remission and achieved successful trilineage engraftment. Six weeks after the last dose of IT MTX administration, ascending weakness developed. Magnetic resonance imaging disclosed bilateral symmetrical signal change in spinal cord, predominately in the posterior and lateral columns (Figure 1). MTX-induced myelopathy was diagnosed. Leucovorin, prednisone and vitamins B12 were administered for rescue treatment. Physical therapy was also arranged. Before discharge, she was able to walk over 100 m without device assistance. Myelopathy is an uncommon complication after IT administration of MTX. The reported incidence was around 3%. An observation study showed that median number of weeks from the first day of IT MTX to the first neurotoxicity event was 51 weeks (ranging from 4 to 127 weeks). As
Intraoperative fluorescence angiography as an independent factor of anastomotic leakage and a nomogram for predicting leak for colorectal anastomoses

Purpose Colorectal anastomotic leakage (AL) is a life-threatening complication, which increases morbidity, hospital stay and cost of treatment. The aim of this study is to identify risk factors, including intraoperative indocyanine green fluorescence angiography (ICG FA), associated with the leak of stapled colorectal anastomosis. Methods Four hundred twenty-nine consecutive patients underwent surgery between 2017 and 2019 for benign (n=10, 2.3%) or malignant (n=419, 97.7%) and rectal (n=349, 81.4%) or distal sigmoid (n=80, 18.6%) lesions with double-stapling technique reconstruction were included into retrospective study. Univariate analysis and multivariate logistic regression of the tumor-, patient- and treatment-related risk factors of AL was performed. Results An AL developed in 52 patients (12.1%). In multivariate analysis following variables were independently associated with AL; male sex (odds ratio [OR], 3.8; 95% confidence interval [CI], 1.9−7.7; P<0.01), anastomosis at ≤6.5 cm from anal verge (OR, 3.1; 95% CI, 1.3−7.5; P=0.01), and age of ≤62.5 years (OR, 2.1; 95% CI, 1.1−4.1; P=0.03). ICG FA was found as independent factor reducing colorectal AL rate (OR, 0.4; 95% CI, 0.2−0.8; P=0.02). A nomogram with high discriminative ability (concordance index, 0.81) was created. Conclusion ICG FA is a modifiable surgery-related risk factor associated with a decrease of colorectal AL rate. A suggested nomogram, which takes into consideration ICG FA, might be helpful to identify the individual risk of AL.
Learning Binary Hash Codes Based on Adaptable Label Representations

The goal of supervised hashing is to construct hash mappings from collections of images and semantic annotations such that semantically relevant images are embedded nearby in the learned binary hash representations. Existing deep supervised hashing approaches that employ classification frameworks with a classification training objective for learning hash codes often encode class labels as one-hot or multi-hot vectors. We argue that such label encodings do not well reflect semantic relations among classes and instead, effective class label representations ought to be learned from data, which could provide more discriminative signals for hashing. In this article, we introduce Adaptive Labeling Deep Hashing (AdaLabelHash) that learns binary hash codes based on learnable class label representations. We treat the class labels as the vertices of a $K$ -dimensional hypercube, which are trainable variables and adapted together with network weights during the backward network training procedure. The label representations, referred to as codewords, are the target outputs of hash mapping learning. In the label space, semantically relevant images are then expressed by the codewords that are nearby regarding Hamming distances, yielding compact and discriminative binary hash representations. Furthermore, we find that the learned label representations well reflect semantic relations. Our approach is easy to realize and can simultaneously construct both the label representations and the compact binary embeddings. Quantitative and qualitative evaluations on several popular benchmarks validate the superiority of AdaLabelHash in learning effective binary codes for image search.
Tryptophan metabolites modulate inflammatory bowel disease and colorectal cancer by affecting immune system

Abstract Tryptophan is an essential amino acid, going through three different metabolic pathways in the intestines. Indole pathway in the gut microbiota, serotonin system in the enterochromaffin cells and kynurenine pathway in the immune cells and intestinal lining are the three arms of tryptophan metabolism in the intestines. Clinical, in vivo and in vitro studies showed that each one of these arms has a significant impact on IBD. This review explains how different metabolites of tryptophan are involved in the pathophysiology of IBD and colorectal cancer, as a major complication of IBD. Indole metabolites alleviate colitis and protect against colorectal cancer while serotonin arm follows a more complicated and receptor-specific pattern. Indole metabolites and kynurenine interact with aryl hydrocarbon receptor (AHR) to induce T regulatory cells differentiation, confine Th17 and Th1 response and produce anti-inflammatory mediators. Kynurenine decreases tumor-infiltrating CD8+ cells and mediates tumor cells immune evasion. Serotonin system also increases colorectal cancer cells proliferation and metastasis while, indole metabolites can profoundly decrease colorectal cancer growth. Targeted therapy for tryptophan metabolites may improve the management of IBD and colorectal cancer, e.g. supplementation of indole metabolites such as indole-3-carbinol (I3C), inhibition of kynurenine monooxygenase (KMO) and selective stimulation or inhibition of specific serotonergic receptors can mitigate colitis. Furthermore, it will be explained how indole metabolites supplementation, inhibition of indoleamine 2,3-dioxygenase 1 (IDO1), KMO and serotonin receptors can protect against colorectal cancer. Additionally, extensive molecular interactions between tryptophan metabolites and intracellular signaling pathways will be thoroughly discussed.
Multicenter Postimplementation Assessment of the Positive Predictive Value of SARS-CoV-2 Antigen-Based Point-of-Care Tests Used for Screening of Asymptomatic Continuing Care Staff

Frequent screening of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among asymptomatic populations using antigen-based point-of-care tests (APOCTs) is occurring globally with limited clinical performance data. The positive predictive value (PPV) of two APOCTs used in the asymptomatic screening of SARS-CoV-2 among health care workers (HCWs) at continuing care (CC) sites across AB, Canada, was evaluated. Between 22 February and 2 May 2021, CC sites implemented SARS-CoV-2 voluntary screening of their asymptomatic HCWs. On-site testing with Abbott Panbio or BD Veritor occurred on a weekly or twice-weekly basis. ABSTRACT Frequent screening of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among asymptomatic populations using antigen-based point-of-care tests (APOCTs) is occurring globally with limited clinical performance data. The positive predictive value (PPV) of two APOCTs used in the asymptomatic screening of SARS-CoV-2 among health care workers (HCWs) at continuing care (CC) sites across AB, Canada, was evaluated. Between 22 February and 2 May 2021, CC sites implemented SARS-CoV-2 voluntary screening of their asymptomatic HCWs. On-site testing with Abbott Panbio or BD Veritor occurred on a weekly or twice-weekly basis. Positive APOCTs were confirmed with a real-time reverse transcriptase PCR (rRT-PCR) reference method. A total of 71,847 APOCTs (17,689 Veritor and 54,158 Panbio) were performed among 369 CC sites. Eighty-seven (0.12%) APOCTs were positive, of which 39 (0.05%) were confirmed as true positives using rRT-PCR. Use of the Veritor and Panbio resulted in 76.6% and 30.0% false-positive detection, respectively (P < 0.001). This corresponded to PPVs of 23.4 and 70.0% for the Veritor and Panbio, respectively. Frequent screening of SARS-CoV-2 among asymptomatic HCWs in CC, using APOCTs, resulted in a very low detection rate and a high rate of detection of false positives. Careful assessment of the risks versus benefits of APOCT programs and the prevalence of infection in this population needs to be thoroughly considered before implementation.
Analysis of trans‐sacral corridors in stabilization of fractures of the pelvic ring

Percutaneous screw fixation combined with pelvic reduction is a surgical technique used to stabilize fractures of the posterior pelvic ring. This is the standard surgical treatment of unstable posterior pelvic ring injuries. The primary goal of this treatment is an anatomic reduction and stable fixation. This has been shown to reduce pain and improve the patients' long‐term well‐being. The aim of this analysis was to determine the possible screw lengths and the positioning of the screws in the S1 and S2 sacral segments. A population of 697 pelvises from the Stryker Orthopaedic Modeling and Analytics database were analyzed. The dimensions of the S1 and S2 screw corridors were determined and after assessing for sacral dysmorphism, the correct screw placement was chosen to determine the necessary screw length for surgical treatment. The measurements of the screw lengths show a Gaussian distribution for the analyzed population. The percentage of dysmorphic pelvises for the S1 screw corridor was 31.3% and for the S2 corridor 8%. Average screw length for S1 was 163.8 ± 16.2 mm and for the S2 137.3 ± 9.5 mm. The results show that the S1/S2 axis cannot be used for a trans‐sacral screw placement in every patient. The study shows that intraosseous screw corridors are present in 68.7% of the patients in the S1 position and in 92% at the S2 level where an intended implant can be placed fully intraosseous.