Miracle-dz/UniFAR-FTUs huggingface dataset:
Perceived Discrimination, Racial Identity, and Multisystem Stress Response to Social Evaluative Threat Among African American Men and Women

Objective Understanding individual differences in the psychobiology of the stress response is critical to grasping how psychosocial factors contribute to racial and ethnic health disparities. However, the ways in which environmentally sensitive biological systems coordinate in response to acute stress is not well understood. We used a social-evaluative stress task to investigate coordination among the autonomic nervous system, hypothalamic-pituitary-adrenal axis, and immune/inflammatory system in a community sample of 85 healthy African American men and women. Methods Six saliva samples, 2 at each of baseline, event, and recovery phases of the stressor task, were assayed for cortisol, dehydroepiandrosterone-sulfate, salivary alpha-amylase, and salivary C-reactive protein. Individual differences in perceived discrimination and racial identity were also measured. Results Factor analysis demonstrated that stress systems were largely dissociated before stressor exposure but became aligned during event and recovery phases into functional biological stress responses (factor loadings ≥ .58). Coordinated responses were related to interactions of perceived discrimination and racial identity: when racial identity was strong, highly perceived discrimination was associated with low hypothalamic-pituitary-adrenal axis activity at baseline (B's = .68–.72, p < .001), low stress mobilization during the task (B's = .46–.62, p < .049), and a robust inflammatory response (salivary C-reactive protein) during recovery (B's = .72–.94, p < .002). Conclusion Culturally relevant social perceptions may be linked to a specific pattern of changing alignment in biological components of the stress response. Better understanding these links may significantly advance understanding of stress-related illnesses and disparities.
Alterations of atrial electrophysiology induced by electrolyte variations: combined computational and P-wave analysis.

AIMS Haemodialysis (HD) therapy represents a unique model to test in vivo, in humans, the effects of changes in plasma ionic concentrations. Episodes of paroxysmal atrial fibrillation (AF) often occur during the treatment. We investigated the effects of HD-induced electrolyte variations on atrial electrophysiology by analysing ECG P-wave duration (PWd), which reflects atrial conduction velocity (CV), and simulated atrial action potential (AP). METHODS AND RESULTS In 20 end-stage renal disease patients PWd (signal-averaged ECG), heart rate (HR), blood pressure, Na(+), K(+), Ca(2+), and Mg(2+) plasma concentrations were measured before and after HD session. The Courtemanche computational model of human atrial myocyte was used to simulate the atrial AP. AP upstroke duration (AP(ud)), AP duration and atrial cell effective refractory period (ERP) were computed. Extracellular electrolyte concentrations and HR were imposed to the average values measured in vivo. HD decreased K(+) (from 4.9 +/- 0.5 to 3.9 +/- 0.4 mmol/L, P < 0.001) and Mg(2+) (0.92 +/- 0.08 to 0.86 +/- 0.05 mmol/L, P < 0.05), and increased Na(+) (139.8 +/- 3.4 to 141.6 +/- 3.1 mmol/L, P < 0.05) and Ca(2+) (1.18 +/- 0.09 to 1.30 +/- 0.07 mmol/L, P < 0.001) plasma concentrations. PWd systematically increased in all the patients after HD (131 +/- 11 to 140 +/- 12 ms, P < 0.001), indicating an intra-atrial conduction slowing. PWd increments were inversely correlated with K(+) variations (R = 0.73, P < 0.01). Model-based analysis indicated an AP(ud) increase (from 2.58 to 2.94 ms) after HD, coherent with experimental observations on PWd, and a reduction of ERP by 12 ms. CONCLUSION Changes of plasma ionic concentrations may lead to modifications of atrial electrophysiology that can favour AF onset, namely a decrease of atrial CV and a decrease of atrial ERP.
Measurement Properties of the Center for Epidemiologic Studies Depression Scale (CES-D 10): Findings From HCHS/SOL

The Center for Epidemiologic Studies Depression Scale (CES-D) is a widely used self-report measure of depression symptomatology. This study evaluated the reliability, validity, and measurement invariance of the CES-D 10 in a diverse cohort of Hispanics/Latinos from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). The sample consisted of 16,415 Hispanic/Latino adults recruited from 4 field centers (Miami, FL; San Diego, CA; Bronx, NY; Chicago, IL). Participants completed interview administered measures in English or Spanish. The CES-D 10 was examined for internal consistency, test–retest reliability, convergent validity, and measurement invariance. The total score for the CES-D 10 displayed acceptable internal consistencies (Cronbach’s alpha’s = .80–.86) and test–retest reliability (r values = .41–.70) across the total sample, language group and ethnic background group. The total CES-D 10 scores correlated in a theoretically consistent manner with the Spielberger State–Trait Anxiety Inventory, r = . 72, p < . 001, the Patient Health Questionnaire-9 depression measure, r = . 80, p < . 001, the Short Form-12’s Mental Component Summary, r = −. 65, p < . 001, and Physical Component Summary score, r = −. 25, p < . 001. A confirmatory factor analysis showed that a 1-factor model fit the CES-D 10 data well (CFI = .986, RMSEA = .047) after correlating 1 pair of item residual variances. Multiple group analyses showed the 1-factor structure to be invariant across English and Spanish speaking responders and partially invariant across Hispanic/Latino background groups. The total score of the CES-D 10 can be recommended for use with Hispanics/Latinos in English and Spanish.
Making a meaningful impact: modelling simultaneous frictional collisions in spatial multibody systems

Impacts are instantaneous, computationally efficient approximations of collisions. Current impact models sacrifice important physical principles to achieve that efficiency, yielding qualitative and quantitative errors when applied to simultaneous impacts in spatial multibody systems. We present a new impact model that produces behaviour similar to that of a detailed compliant contact model, while retaining the efficiency of an instantaneous method. In our model, time and configuration are fixed, but the impact is resolved into distinct compression and expansion phases, themselves comprising sliding and rolling intervals. A constrained optimization problem is solved for each interval to compute incremental impulses while respecting physical laws and principles of contact mechanics. We present the mathematical model, algorithms for its practical implementation, and examples that demonstrate its effectiveness. In collisions involving materials of various stiffnesses, our model can be more than 20 times faster than integrating through the collision using a compliant contact model. This work extends the use of instantaneous impact models to scientific and engineering applications with strict accuracy requirements, where compliant contact models would otherwise be required. An open-source implementation is available in Simbody, a C++ multibody dynamics library widely used in biomechanical and robotic applications.
The effect of noise and lipid signals on determination of Gaussian and non‐Gaussian diffusion parameters in skeletal muscle

This work characterizes the effect of lipid and noise signals on muscle diffusion parameter estimation in several conventional and non‐Gaussian models, the ultimate objectives being to characterize popular fat suppression approaches for human muscle diffusion studies, to provide simulations to inform experimental work and to report normative non‐Gaussian parameter values. The models investigated in this work were the Gaussian monoexponential and intravoxel incoherent motion (IVIM) models, and the non‐Gaussian kurtosis and stretched exponential models. These were evaluated via simulations, and in vitro and in vivo experiments. Simulations were performed using literature input values, modeling fat contamination as an additive baseline to data, whereas phantom studies used a phantom containing aliphatic and olefinic fats and muscle‐like gel. Human imaging was performed in the hamstring muscles of 10 volunteers. Diffusion‐weighted imaging was applied with spectral attenuated inversion recovery (SPAIR), slice‐select gradient reversal and water‐specific excitation fat suppression, alone and in combination. Measurement bias (accuracy) and dispersion (precision) were evaluated, together with intra‐ and inter‐scan repeatability. Simulations indicated that noise in magnitude images resulted in <6% bias in diffusion coefficients and non‐Gaussian parameters (α, K), whereas baseline fitting minimized fat bias for all models, except IVIM. In vivo, popular SPAIR fat suppression proved inadequate for accurate parameter estimation, producing non‐physiological parameter estimates without baseline fitting and large biases when it was used. Combining all three fat suppression techniques and fitting data with a baseline offset gave the best results of all the methods studied for both Gaussian diffusion and, overall, for non‐Gaussian diffusion. It produced consistent parameter estimates for all models, except IVIM, and highlighted non‐Gaussian behavior perpendicular to muscle fibers (α ~ 0.95, K ~ 3.1). These results show that effective fat suppression is crucial for accurate measurement of non‐Gaussian diffusion parameters, and will be an essential component of quantitative studies of human muscle quality.
Video Representation Learning Using Discriminative Pooling

Popular deep models for action recognition in videos generate independent predictions for short clips, which are then pooled heuristically to assign an action label to the full video segment. As not all frames may characterize the underlying action-indeed, many are common across multiple actions-pooling schemes that impose equal importance on all frames might be unfavorable. In an attempt to tackle this problem, we propose discriminative pooling, based on the notion that among the deep features generated on all short clips, there is at least one that characterizes the action. To this end, we learn a (nonlinear) hyperplane that separates this unknown, yet discriminative, feature from the rest. Applying multiple instance learning in a large-margin setup, we use the parameters of this separating hyperplane as a descriptor for the full video segment. Since these parameters are directly related to the support vectors in a max-margin framework, they serve as robust representations for pooling of the features. We formulate a joint objective and an efficient solver that learns these hyperplanes per video and the corresponding action classifiers over the hyperplanes. Our pooling scheme is end-to-end trainable within a deep framework. We report results from experiments on three benchmark datasets spanning a variety of challenges and demonstrate state-of-the-art performance across these tasks.
Laparoscopic partial cholecystectomy: A safe and effective alternative surgical technique in "difficult cholecystectomies".

OBJECTIVE Laparoscopic cholecystectomy has become the "gold standard" for benign gallbladder diseases due to its advantages. In the presence of inflammation or fibrosis, the risk of bleeding and bile duct injury is increased during dissection. Laparoscopic partial cholecystectomy (LPC) is a feasible and safe method to prevent bile duct injuries and decrease the conversion (to open cholecystectomy) rates in difficult cholecystectomies where anatomical structures could not be demonstrated clearly. MATERIAL AND METHODS The feasibility, efficiency, and safety of LPC were investigated. The data of 80 patients with cholelithiasis who underwent LPC (n=40) and conversion cholecystectomy (CC) (n=40) were retrospectively examined. Demographic characteristics, ASA scores, operating time, drain usage, requirement for intensive care, postoperative length of hospital stay, surgical site infection, antibiotic requirement and complication rates were compared. RESULTS The median ASA value was 1 in the CC group and 2 in the LPC group. Mean operation time was 123 minutes in the CC group, and 87.50 minutes in the LPC group. Surgical drains were used in 16 CC patients and 4 LPC patients. There was no significant difference between groups in postoperative length of intensive care unit stay (p=0.241). When surgical site infections were compared, the difference was at the limit of statistical significance (p=0.055). Early complication rates were not different (p=0.608) but none of the patients in the LPC group suffered from late complications. CONCLUSION LPC is an efficient and safe way to decrease the conversion rate. LPC seems to be an alternative procedure to CC with advantages of shorter operating time, lower rates of surgical site infection, shorter postoperative hospitalization and fewer complications in high-risk patients.
Evaluation of oxidative stress via protein expression of glutathione S-transferase and cytochrome p450 (CYP450) ısoenzymes in psoriasis vulgaris patients treated with methotrexate

Abstract Introduction: Oxidative stress is the imbalance between oxidant-antioxidant systems and may play a major role in the psoriasis pathogenesis. Cytochrome (CYP) is a family of enzymes that are responsible for the metabolism of various endogenous and exogenous substances such as drug metabolism. Most importantly, the antioxidant system is the glutathione S-transferases (GST), which decrease oxidative stress by reducing oxidative products. Aim: We aimed to evaluate the expressions of isoenzymes of GST and CYP families and the beneficial role of metotrexate (MTX) in this process. Material and methods: This study included 21 patients with psoriasis and 22 healthy subjects. We treated all the patients with 10–15 mg/week of MTX for minimum 12 weeks. Expressions of GST and CYP enzymes were assessed by immunohistochemical staining. Results: GSTK1, GSTM1 and GSTT1 expressions were significantly higher in the psoriasis tissues than in the control tissues (p < 0.05; p < 0.05; p < 0.05, respectively). In the psoriasis patients, GSTO1 expression was similar the control group. CYP1B1 and CYP2E1 expressions were significantly higher in the pre-treatment and post-treatment psoriasis tissues than in the control tissues (p < 0.05; p < 0.05; p < 0.05; p < 0.05, respectively). Conclusion: We found a significant increase in the tissue levels of, either expression of GST, or CYP, which has important role in drug metabolism and oxidative stress. MTX treatment resulted in marked clinical improvement, yet we found that MTX did not have any significant effect on these parameters. CYP2E1 is especially the most important enzyme for MTX metabolism since it is the primarily responsible of the toxic metabolism of various drugs. The other experimental studies involving greater number of patients and other different drug are needed to enlighten the role of oxidant and antioxidant systems and the other possible mechanisms for the pathogenesis of psoriasis.
Spontaneous and Vaccine-Induced Clearance of Mus Musculus Papillomavirus 1 Infection

ABSTRACT Mus musculus papillomavirus 1 (MmuPV1/MusPV1) induces persistent papillomas in immunodeficient mice but not in common laboratory strains. To facilitate the study of immune control, we sought an outbred and immunocompetent laboratory mouse strain in which persistent papillomas could be established. We found that challenge of SKH1 mice (Crl:SKH1-Hrhr) with MmuPV1 by scarification on their tail resulted in three clinical outcomes: (i) persistent (>2-month) papillomas (∼20%); (ii) transient papillomas that spontaneously regress, typically within 2 months (∼15%); and (iii) no visible papillomas and viral clearance (∼65%). SKH1 mice with persistent papillomas were treated by using a candidate preventive/therapeutic naked-DNA vaccine that expresses human calreticulin (hCRT) fused in frame to MmuPV1 E6 (mE6) and mE7 early proteins and residues 11 to 200 of the late protein L2 (hCRTmE6/mE7/mL2). Three intramuscular DNA vaccinations were delivered biweekly via in vivo electroporation, and both humoral and CD8 T cell responses were mapped and measured. Previously persistent papillomas disappeared within 2 months after the final vaccination. Coincident virologic clearance was confirmed by in situ hybridization and a failure of disease to recur after CD3 T cell depletion. Vaccination induced strong mE6 and mE7 CD8+ T cell responses in all mice, although they were significantly weaker in mice that initially presented with persistent warts than in those that spontaneously cleared their infection. A human papillomavirus 16 (HPV16)-targeted version of the DNA vaccine also induced L2 antibodies and protected mice from vaginal challenge with an HPV16 pseudovirus. Thus, MmuPV1 challenge of SKH1 mice is a promising model of spontaneous and immunotherapy-directed clearances of HPV-related disease. IMPORTANCE High-risk-type human papillomaviruses (hrHPVs) cause 5% of all cancer cases worldwide, notably cervical, anogenital, and oropharyngeal cancers. Since preventative HPV vaccines have not been widely used in many countries and do not impact existing infections, there is considerable interest in the development of therapeutic vaccines to address existing disease and infections. The strict tropism of HPV requires the use of animal papillomavirus models for therapeutic vaccine development. However, MmuPV1 failed to grow in common laboratory strains of mice with an intact immune system. We show that MmuPV1 challenge of the outbred immunocompetent SKH1 strain produces both transient and persistent papillomas and that vaccination of the mice with a DNA expressing an MmuPV1 E6E7L2 fusion with calreticulin can rapidly clear persistent papillomas. Furthermore, an HPV16-targeted version of the DNA can protect against vaginal challenge with HPV16, suggesting the promise of this approach to both prevent and treat papillomavirus-related disease.
An Image-Domain Contrast Material Extraction Method for Dual-Energy Computed Tomography

Objectives Conventional material decomposition techniques for dual-energy computed tomography (CT) assume mass or volume conservation, where the CT number of each voxel is fully assigned to predefined materials. We present an image-domain contrast material extraction process (CMEP) method that preferentially extracts contrast-producing materials while leaving the remaining image intact. Materials and Methods Image processing freeware (Fiji) is used to perform consecutive arithmetic operations on a dual-energy ratio map to generate masks, which are then applied to the original images to generate material-specific images. First, a low-energy image is divided by a high-energy image to generate a ratio map. The ratio map is then split into material-specific masks. Ratio intervals known to correspond to particular materials (eg, iodine, calcium) are assigned a multiplier of 1, whereas ratio values in between these intervals are assigned linear gradients from 0 to 1. The masks are then multiplied by an original CT image to produce material-specific images. The method was tested quantitatively at dual-source CT and rapid kVp-switching CT (RSCT) with phantoms using pure and mixed formulations of tungsten, calcium, and iodine. Errors were evaluated by comparing the known material concentrations with those derived from the CMEP material-specific images. Further qualitative evaluation was performed in vivo at RSCT with a rabbit model using identical CMEP parameters to the phantom. Orally administered tungsten, vascularly administered iodine, and skeletal calcium were used as the 3 contrast materials. Results All 5 material combinations—tungsten, iodine, and calcium, and mixtures of tungsten-calcium and iodine-calcium—showed distinct dual-energy ratios, largely independent of material concentration at both dual-source CT and RSCT. The CMEP was successful in both phantoms and in vivo. For pure contrast materials in the phantom, the maximum error between the known and CMEP-derived material concentrations was 0.9 mg/mL, 24.9 mg/mL, and 0.4 mg/mL for iodine, calcium, and tungsten respectively. Mixtures of iodine and calcium showed the highest discrepancies, which reflected the sensitivity of iodine to the image-type chosen for the extraction of the final material-specific image. The rabbit model was able to clearly show the 3 extracted material phases, vascular iodine, oral tungsten, and skeletal calcium. Some skeletal calcium was misassigned to the extracted iodine image; however, this did not impede the depiction of the vasculature. Conclusions The CMEP is a straightforward, image-domain approach to extract material signal at dual-energy CT. It has particular value for separation of experimental high-Z contrast elements from conventional iodine contrast or calcium, even when the exact attenuation coefficient profiles of desired contrast materials may be unknown. The CMEP is readily implemented in the image-domain within freeware, and can be adapted for use with images from multiple vendors.
Inhibition of matrix metalloproteinase‐9 by a barbiturate‐nitrate hybrid ameliorates dextran sulphate sodium‐induced colitis: effect on inflammation‐related genes

Matrix metalloproteinase‐9 (MMP‐9) is up‐regulated in ulcerative colitis and implicated in the pathology of the disease. In this study, we have examined the effects of a barbiturate‐based MMP inhibitor incorporating a nitric oxide donor/mimetic group (dinitrate‐barbiturate) on the intestinal injury induced by dextran sulphate sodium (DSS).
Validation of measurement‐guided 3D VMAT dose reconstruction on a heterogeneous anthropomorphic phantom

3DVH software (Sun Nuclear Corp., Melbourne, FL) is capable of generating a volumetric patient VMAT dose by applying a volumetric perturbation algorithm based on comparing measurement‐guided dose reconstruction and TPS‐calculated dose to a cylindrical phantom. The primary purpose of this paper is to validate this dose reconstruction on an anthropomorphic heterogeneous thoracic phantom by direct comparison to independent measurements. The dosimetric insert to the phantom is novel, and thus the secondary goal is to demonstrate how it can be used for the hidden target end‐to‐end testing of VMAT treatments in lung. A dosimetric insert contains a 4 cm diameter unit‐density spherical target located inside the right lung (0.21g/cm3 density). It has 26 slots arranged in two orthogonal directions, milled to hold optically stimulated luminescent dosimeters (OSLDs). Dose profiles in three cardinal orthogonal directions were obtained for five VMAT plans with varying degrees of modulation. After appropriate OSLD corrections were applied, 3DVH measurement‐guided VMAT dose reconstruction agreed 100% with the measurements in the unit density target sphere at 3%/3 mm level (composite analysis) for all profile points for the four less‐modulated VMAT plans, and for 96% of the points in the highly modulated C‐shape plan (from TG‐119). For this latter plan, while 3DVH shows acceptable agreement with independent measurements in the unit density target, in the lung disagreement with experiment is relatively high for both the TPS calculation and 3DVH reconstruction. For the four plans excluding the C‐shape, 3%/3mm overall composite analysis passing rates for 3DVH against independent measurement ranged from 93% to 100%. The C‐shape plan was deliberately chosen as a stress test of the algorithm. The dosimetric spatial alignment hidden target test demonstrated the average distance to agreement between the measured and TPS profiles in the steep dose gradient area at the edge of the 2 cm target to be 1.0±0.7,0.3±0.3, and 0.3±0.3mm for the IEC X, Y, and Z directions, respectively. PACS number: 87.55Qr