Miracle-dz/UniFAR-FTUs huggingface dataset:
In Search of Complex Disease Risk through Genome Wide Association Studies

The identification and characterisation of genomic changes (variants) that can lead to human diseases is one of the central aims of biomedical research. The generation of catalogues of genetic variants that have an impact on specific diseases is the basis of Personalised Medicine, where diagnoses and treatment protocols are selected according to each patient’s profile. In this context, the study of complex diseases, such as Type 2 diabetes or cardiovascular alterations, is fundamental. However, these diseases result from the combination of multiple genetic and environmental factors, which makes the discovery of causal variants particularly challenging at a statistical and computational level. Genome-Wide Association Studies (GWAS), which are based on the statistical analysis of genetic variant frequencies across non-diseased and diseased individuals, have been successful in finding genetic variants that are associated to specific diseases or phenotypic traits. But GWAS methodology is limited when considering important genetic aspects of the disease and has not yet resulted in meaningful translation to clinical practice. This review presents an outlook on the study of the link between genetics and complex phenotypes. We first present an overview of the past and current statistical methods used in the field. Next, we discuss current practices and their main limitations. Finally, we describe the open challenges that remain and that might benefit greatly from further mathematical developments.
Brown Tumor of Lower Right Limb in Patients With Primary Hyperparathyroidism: A Case Report

Background.Brown tumor of Hyperparathyroidism is a metabolic disorder that can affect the entire skeleton and reactive process due to bone resorption caused by primary or secondary hyperparathyroidism (HPT). Brown tumors can occur as solitary or multiple lesions in any bone, most often in the pelvis, ribs, clavicle, mandibula, and extremities. Here, we report the Brown tumor in the lower right limb in patients with primary HPT, and the literature is reviewed. Case presentation. Patients was women 30 years old had married and come with main complains of difficulty walking. This condition has been experienced by patients since diagnosis with lunb of tibia last 8 months and caused pain from hip to lower leg. On laboratory results, it showed elevated PTH 1.249 (normal 15-65) pg/dL, elevated phosphatase alkali 1156 (normal 40-150) u/dL, elevated Ca 10,8 (n:8,6 -10,3) mg/dL, phosphor 2,1 (3–4,5) mg/dL. Histology examination of tibia lump was a benign lesion of bone (Brown Tumor). Ultrasonography transabdominal result revealed kidney stones with bilateral renal pelvis dilation, nephrolithiasis non-obstructive was found with size 1 cm & left kidney cyst with size 0.6 cm. On Neck USG showed giant cyst lesion on parathyroid glands. Radiologist pelvic examination results showed bone metastasis disease. Head CT Scan examination concluded as suspect metastatic bone. Body bone scans examination showed pathological bone metastatic process. Conclusion. Brown tumor in right lower limb caused by primary HPT
Sandbur Drought Tolerance Reflects Phenotypic Plasticity Based on the Accumulation of Sugars, Lipids, and Flavonoid Intermediates and the Scavenging of Reactive Oxygen Species in the Root

The perennial grass Cenchrus spinifex (common sandbur) is an invasive species that grows in arid and semi-arid regions due to its remarkable phenotypic plasticity, which confers the ability to withstand drought and other forms of abiotic stress. Exploring the molecular mechanisms of drought tolerance in common sandbur could lead to the development of new strategies for the protection of natural and agricultural environments from this weed. To determine the molecular basis of drought tolerance in C. spinifex, we used isobaric tags for relative and absolute quantitation (iTRAQ) to identify proteins differing in abundance between roots growing in normal soil and roots subjected to moderate or severe drought stress. The analysis of these proteins revealed that drought tolerance in C. spinifex primarily reflects the modulation of core physiological activities such as protein synthesis, transport and energy utilization as well as the accumulation of flavonoid intermediates and the scavenging of reactive oxygen species. Accordingly, plants subjected to drought stress accumulated sucrose, fatty acids, and ascorbate, shifted their redox potential (as determined by the NADH/NAD ratio), accumulated flavonoid intermediates at the expense of anthocyanins and lignin, and produced less actin, indicating fundamental reorganization of the cytoskeleton. Our results show that C. spinifex responds to drought stress by coordinating multiple metabolic pathways along with other adaptations. It is likely that the underlying metabolic plasticity of this species plays a key role in its invasive success, particularly in semi-arid and arid environments.
Health Power Resources Theory: A Relational Approach to the Study of Health Inequalities

Link and Phelan’s pioneering 1995 theory of fundamental causes urged health scholars to consider the macro-level contexts that “put people at risk of risks. ” Allied research on the political economy of health has since aptly demonstrated how institutions contextualize risk factors for health. Yet scant research has fully capitalized on either fundamental cause or political economy of health’s allusion to power relations as a determinant of persistent inequalities in population health. I address this oversight by advancing a theory of health power resources that contends that power relations distribute and translate the meaning (i.e., necessity, value, and utility) of socioeconomic and health-relevant resources. This occurs through stratification, commodification, discrimination, and devitalization. Resurrecting historical sociological emphases on power relations provides an avenue through which scholars can more fully understand the patterning of population health and better connect the sociology of health and illness to the central tenets of the discipline.
Endometrial Surveillance in Tamoxifen and Letrozole Treated Breast Cancer Patients

Background: Our study aimed to assess the risk of endometrial pathologies after tamoxifen and aromatase inhibitors (AIs) adjuvant treatment for female breast cancer patients treated at Sultan Qaboos University Hospital in Oman. Materials and Methods: A total of 457 patients diagnosed with estrogen positive breast cancer between January 2011 and December 2018 were screened. Two hundred and four patients met the inclusion criteria, and their detailed clinicopathological and endometrial surveillance data were collected from their electronic health records. Results: All patients underwent endometrial assessment during tamoxifen or letrozole therapy. The mean diagnostic age of breast cancer patients is 43.6 years, ranging from 27-84 years. Eighty-three percent of those patients are premenopausal, and 17% are postmenopausal. The mean tamoxifen use duration was 33 months. The majority of patients, 123 (60.3%), have had tamoxifen for three years or less, 47 (23.1%) for 3-5 years, and only 22 (10.8%) were on tamoxifen for more than five years. Increased endometrial thickness was reported in 8% of the premenopausal and 14% of the postmenopausal group. Other endometrial pathologies that were detected are inactive endometrium three (1.47%), atrophic endometrium three (1.47%), serous carcinoma one (0.50%), endometrial cancer two (0.98%), and chronic endometritis one (0.50%), which were not significantly associated with tamoxifen or letrozole therapy duration. Two patients have developed endometrial cancer, and both are postmenopausal and > 60 years old. Conclusions: Tamoxifen and letrozole did not increase the risk of endometrial cancer in premenopausal patients. Breast Cancer (BC) patients on tamoxifen or letrozole might need a pre-treatment endometrial evaluation and explanation of alarming symptoms to guide further endometrial surveillance.
GaN/AlGaN high electron mobility transistors with f τ of 110 GHz

The performance of 50 nm gate length GaN/AlGaN HEMTs is reported. The device layers were grown by MBE directly onto an SiC substrate. Devices exhibit a maximum drain current density of 1.2 A/mm, an extrinsic fτ of 110 GHz and an fmax of over 140 GHz. The fτ of 110 GHz is the highest reported to date for a GaN/AlGaN HEMT, a nearly 50% increase over the previous record.
Surface aerodynamic temperature modeling over rainfed cotton.

Evapotranspiration (ET) or latent heat flux (LE) can be spatially estimated as an energy balance (EB) residual for land surfaces using remote sensing inputs. The EB equation requires the estimation of net radiation (Rn), soil heat flux (G), and sensible heat flux (H). Rn and G can be estimated with an acceptable accuracy. In computing H, radiometric surface temperature (Ts) is often used instead of surface aerodynamic temperature (To), as To is neither measured nor easily estimated. This may cause an underestimation of ET because H will be overestimated as Ts is typically larger than To for unstable atmospheric conditions. The objectives of this study were to (1) model To to improve the estimation of H and consequently ET for advective environments in the semi-arid Texas High Plains, and (2) assess the accuracy of the To model using three different methods (aerodynamic profile, lysimeter, and eddy covariance). A 6.5 m tower platform was used to measure profiles of wind speed, air temperature, and relative humidity in and above cotton canopy near a large weighing lysimeter managed under rainfed conditions at the USDA-ARS Conservation and Production Research Laboratory, Bushland, Texas. The To was modeled using H as a residual from the EB at the lysimeter location. Results indicated that To was better modeled as a linear function of Ts, air temperature, and surface aerodynamic resistance. Modeled To showed a very small estimation error (0.1% mean bias error and 3.8% root mean square error) when compared to To values measured using the aerodynamic profile data. Even though excellent results were found in this study, the model is only valid for dryland cotton with a leaf area index ranging from 0.2 to 1.3 m2 m-2. Furthermore, more research is needed to expand the To model to cover cotton grown under irrigated conditions and showing larger crop percent cover and leaf area index values, and under different environmental and atmospheric conditions.
Detailed characterisation of an indoor MIMO channel in the double directional spatial domain

The spatial domain characteristics of an indoor multiple-input multiple-output (MIMO) communication system are examined in detail. Using a high-resolution algorithm, the authors were able to effectively estimate multipath parameters on the joint azimuth of arrival/azimuth of departure (AoA/AoD) domain. The analysis showed dense clustering phenomena at the vast majority of considered locations and a strong correlation between the azimuth spreads of the two angular domains with the presence of line-of-sight (Los) specular components or when the distance between the transmitter (Tx) and the receiver (Rx) is low. The authors also noticed higher azimuth dispersions, compared with those reported in the literature, which can be attributed to low antenna heights and local scattering interactions in the vicinity of both the transmit and receive arrays. Finally, the impact of the spatial global parameters on the ergodic MIMO capacity was tested revealing a direct relation between them.
Psychosocial Implications of Limb Lengthening and Reconstruction Orthopedic Surgery: A Literature Review

A fervent interest in improving patient care, quality of life, and outcomes in adolescent patients undergoing limb Lengthening/ Reconstruction Surgeries (LLRS) has guided the exploration of how psychosocial markers in adolescence may be viewed as crucial to achieving enhanced healthcare delivery. This systematic literature review stems from a retrospective pilot study which investigated the importance of psychosocial aspects in the care of children, adolescents, and young adults who have undergone multiple LLRS. It was determined that such patients value psychosocial support given by their surgeons and caregivers, further promoting psychosocial maturation [1]. Currently, prospective investigation is in the process of being explored as yet another outgrowth of this seminal pilot study. Specifically, the current review seeks to explore the literature relevant to aspects of psychosocial development fundamental to enhancing outcomes of a chronic, orthopedic medical condition. The dearth of studies applying a biosocial lens to this subspecialized field of orthopedic surgery and care supports the need for such expanded investigation.
PET-Based Imaging with 18F-FDG and 18F-NaF to Assess Inflammation and Microcalcification in Atherosclerosis and Other Vascular and Thrombotic Disorders

Positron emission tomography (PET) imaging with 18F-fluorodeoxyglucose (FDG) represents a method of detecting and characterizing arterial wall inflammation, with potential applications in the early assessment of vascular disorders such as atherosclerosis. By portraying early-stage molecular changes, FDG-PET findings have previously been shown to correlate with atherosclerosis progression. In addition, recent studies have suggested that microcalcification revealed by 18F-sodium fluoride (NaF) may be more sensitive at detecting atherogenic changes compared to FDG-PET. In this review, we summarize the roles of FDG and NaF in the assessment of atherosclerosis and discuss the role of global assessment in quantification of the vascular disease burden. Furthermore, we will review the emerging applications of FDG-PET in various vascular disorders, including pulmonary embolism, as well as inflammatory and infectious vascular diseases.
Performance and torque-ripple characterization in induction motor adjustable-speed drives using time-stepping coupled finite-element state-space techniques

In this paper, the time-stepping coupled finite-element state-space (TSCFE-SS) model developed in an earlier companion paper is applied here for assessments of effects of machine geometry and magnetic circuit design modifications, and effects of pulsewidth modulation (PWM) carrier frequency on performance characteristics of induction motor drives. Namely, this has been accomplished through analysis of developed torque profile ripples and harmonic spectra of mid-air-gap radial flux density waveforms of the case-study motor. Furthermore, consequent effects of design modifications pertaining to geometry and/or magnetic circuit modifications and PWM carrier frequency on ohmic and iron core losses are investigated. The investigation has been performed on a case-study motor, which is a Y-connected single-layer three-phase two-pole 1.2-hp 208-V squirrel-cage induction motor with 24 stator slots and a cage with 34 rotor bars.
Deep Learning Predicts EBV Status in Gastric Cancer Based on Spatial Patterns of Lymphocyte Infiltration

Simple Summary EBV infection represents a distinct subtype in gastric cancer, so determining infection status is important in guiding treatment decisions. Currently, EBV infection in gastric cancer is most often determined using PCR and in situ hybridization, which requires multiple steps and nucleic acid preservation. On the other hand, histopathology images are widely available and included in the course of diagnosis for patients. Thus, our development of an approach to determine EBV status from these histopathology images could save costs and time associated with making EBV diagnoses for gastric cancer patients or independently validate the results from traditional methods. Additionally, our model’s predictions are able to classify patients into EBV infection categories that are significantly correlated with prognosis. This may serve to better inform clinicians’ decisions in prescribing immunotherapy, as both EBV infection status and prognosis are critical factors in whether immunotherapy is effective or worth the costs and side effects. Abstract EBV infection occurs in around 10% of gastric cancer cases and represents a distinct subtype, characterized by a unique mutation profile, hypermethylation, and overexpression of PD-L1. Moreover, EBV positive gastric cancer tends to have higher immune infiltration and a better prognosis. EBV infection status in gastric cancer is most commonly determined using PCR and in situ hybridization, but such a method requires good nucleic acid preservation. Detection of EBV status with histopathology images may complement PCR and in situ hybridization as a first step of EBV infection assessment. Here, we developed a deep learning-based algorithm to directly predict EBV infection in gastric cancer from H&E stained histopathology slides. Our model can not only predict EBV infection in gastric cancers from tumor regions but also from normal regions with potential changes induced by adjacent EBV+ regions within each H&E slide. Furthermore, in cohorts with zero EBV abundances, a significant difference of immune infiltration between high and low EBV score samples was observed, consistent with the immune infiltration difference observed between EBV positive and negative samples. Therefore, we hypothesized that our model’s prediction of EBV infection is partially driven by the spatial information of immune cell composition, which was supported by mostly positive local correlations between the EBV score and immune infiltration in both tumor and normal regions across all H&E slides. Finally, EBV scores calculated from our model were found to be significantly associated with prognosis. This framework can be readily applied to develop interpretable models for prediction of virus infection across cancers.
An experimental investigation of the propulsive thrust of oscillating foils of different planforms

A second design loop in the development of the computer controlled oscillating motion apparatus was completed as a part of this research. Specifically, work was concentrated in two areas: first, modifications to the existing motion control software with the aim to produce a continuous sinusoidal motion, and second, design of a dynamometer to measure more accurately the thrust developed by the oscillating foil. -- Bench tests conducted with the changes in the motion control indicated that the limitations to produce true sinusoidal oscillatory motion were due to the oscillating apparatus drive system. A single degree of freedom dynamometer consisted of two flexible vertical sheets to which a rigid plate was connected forming a U frame. This design allowed for sensitivity in the fore and aft direction, but was very rigid in the transverse direction. The oscillating apparatus was supported by the frame, and thrust or drag forces developed by the oscillating foil were transmitted through this frame to the load cell. -- An experimental study to measure developed thrust from a series of rigid foils subjected to unsteady, oscillatory motion has been conducted in the towing tank at Memorial University of Newfoundland. The foils tested consisted of a rectangular planform, a straight tapered and swept back planform, as well as the planform with curved leading edge, similar to the flukes of a fin whale. The foils had the same aspect ratio of 6. Two foils were fabricated out of brass, and another was made out of wood. The brass foils had a span of 200 mm, while the wooden foil had a span of 400 mm. In the experiment the heave amplitude to chord ratio was large (of order 1) and the pitch amplitudes tested were :6, 13, 17.5 and 21 deg. The pitching axis position was fixed at chord/2, and pitch led heave by 90 deg. -- Results of developed thrust from different planforms are presented and examined with respect to four areas of interest: large amplitude motion, effects of different planforms on developed thrust, foil performance at large angles of attack, and a comparison of an existing 3D unsteady flow panel code to predict developed thrust with the experimental results. -- Comparison of experimental results with the panel method showed that for small reduced frequencies and angles of attack, agreement in the magnitude of the thrust coefficient was good. At large reduced frequencies and angles of attack results from the panel method underpredicted the developed thrust. This discrepancy in results was due to separation and dynamic stall which occurred in the range of 33 to 40 deg. angle of attack. The combination of a leading edge sweep and taper of the foil's planform has a marked difference in developed thrust compared to the foil with a straight leading edge. This was due to different stall behaviour over foils with leading edge sweep compared to the stall of foils with a straight leading edge.
Brain Substrates for Distinct Spatial Processing Components Contributing to Hemineglect in Humans

Several cortical and sub-cortical regions in the right hemisphere, particularly in parietal and frontal lobe, but also in temporal lobe and thalamus, are part of neural networks critically implicated in spatial and attentional functions. Damage to different sites within these networks can cause hemispatial neglect. The aim of this study was to identify the neural substrates of different spatial processing components that are known to contribute to neglect symptoms. First, three different spatial tasks (visual search, bisection, and visual memory) were tested in 27 patients with focal right brain-damage. Voxel-based lesion–symptom mapping was used to determine the relationships between specific sites of damage and severity of deficits in these three spatial tasks. Secondly, fMRI was used in 26 healthy controls who performed the same tasks. In the healthy group, fMRI results showed a differential activation of regions within the parietal and frontal lobes during bisection and visual search, respectively. In the patients, we confirmed a critical role of right lateral parietal cortex in bisection, but lesions in frontal and temporal lobe were more critical for visual search. These data support the existence of distinct components in spatial attentional processes that might be damaged to different degrees in neglect patients.
DFT Analysis of Mechanical and Dynamic Properties of CuBe

In this study, we have presented a comprehensive theoretical calculation to analyze the mechanical, and dynamic properties of the CuBe with the Density Functional Theory (DFT). Hardness, plasticity, and Poisson’s ratio are calculated. The ductile nature of the compound was demonstrated by mechanical properties. Also, the melting temperature (Tm) of this material was 1581 ± 300 K. Debye temperature was found to be 489.17 K, estimated from the acoustic velocity. The anisotropy properties of CuBe were evaluated in three dimensions and the presence of anisotropy in all other forms was revealed, except for Linner compression. The charge density plots show that the bonds between Cu-Be are more ionic. As a final word, the absence of negative phonon frequencies of the CuBe intermetallic compound showed its dynamical stability. Received: 13 Apr 2021 Accepted: 26 Oct 2021