gebhart/patrepeval huggingface dataset:
Avoiding COVID-19 complications with diabetic patients could be achieved by multi-dose Bacillus Calmette-Guérin vaccine: a case study of beta cells regeneration. (2020)

Diabetes mellitus (DM) is one of the major risk factors for COVID-19 complications as it is one of the chronic immune-compromising conditions especially if patients have uncontrolled diabetes, poor HbA<sub>1c</sub> and/or irregular blood glucose levels. Diabetic patients' mortality rates with COVID-19 are higher than those of cardiovascular or cancer patients. Recently, Bacillus Calmette-Guérin (BCG) vaccine has shown successful results in reversing diabetes in both rats and clinical trials based on different mechanisms from aerobic glycolysis to beta cells regeneration. BCG is a multi-face vaccine that has been used extensively in protection from tuberculosis (TB) and leprosy and has been repositioned for treatment of bladder cancer, diabetes and multiple sclerosis. Recently, COVID-19 epidemiological studies confirmed that universal BCG vaccination reduced morbidity and mortality in certain geographical areas. Countries without universal policies of BCG vaccination (Italy, Nederland, USA) have been more severely affected compared to countries with universal and long-standing BCG policies that have shown low numbers of reported COVID-19 cases. Some countries have started clinical trials that included a single dose BCG vaccine as prophylaxis from COVID-19 or an attempt to minimize its side effects. This proposed research aims to use BCG vaccine as a double-edged weapon countering both COVID-19 and diabetes, not only as protection but also as therapeutic vaccination. The work includes a case study of regenerated pancreatic beta cells based on improved C-peptide and PCPRI laboratory findings after BCG vaccination for a 9 year old patient. The patient was re-vaccinated based on a negative tuberculin test and no scar at the site of injection of the 1<sup>st</sup> BCG vaccination at birth. The authors suggest and invite the scientific community to take into consideration the concept of direct BCG re-vaccination (after 4 weeks) because of the reported gene expressions and exaggerated innate immunity consequently. As the diabetic MODY-5 patient (mutation of <i>HNF1B,</i> Val2Leu) was on low dose Riomet<sup>®</sup> while eliminating insulin gradually, a simple analytical method for metformin assay was recommended to ensure its concentration before use as it is not approved yet by the Egyptian QC labs.
Organic photosensitive devices using subphthalocyanine compounds (2023)

An organic photosensitive optoelectronic device, having a donor-acceptor heterojunction of a donor-like material and an acceptor-like material and methods of making such devices is provided. At least one of the donor-like material and the acceptor-like material includes a subphthalocyanine, a subporphyrin, and/or a subporphyrazine compound; and/or the device optionally has at least one of a blocking layer or a charge transport layer, where the blocking layer and/or the charge transport layer includes a subphthalocyanine, a subporphyrin, and/or a subporphyrazine compound.
Novel vitamin D photoproducts and their precursors in the skin (2013)

Novel metabolic pathways initiated by the enzymatic action of CYP11A1 on 7DHC (7-dehydrocholesterol), ergosterol, vitamins D3 and D2 were characterized with help of chemical synthesis, UV and mass spectrometry and NMR analyses. The first pathway follows the sequence 7DHC→22(OH)7DHC → 20,22(OH)27DHC → 7DHP (7-dehydropregnenolone), which can further be metabolized by steroidogenic enzymes. The resulting 5,7-dienes can be transformed by UVB to corresponding, biologically active, secosteroids. Action of CYP11A1 on vitamin D3 and D2 produces novel hydroxyderivatives with OH added at positions C17, C20, C22, C23 and C24, some of which can be hydroxylated by CYP27B1 and/or by CYP27A1 and/ or by CYP24A1.The main products of these pathways are biologically active with a potency related to their chemical structure and the target cell type. Main products of CYP11A1-mediated metabolism on vitamin D are non-calcemic and non-toxic at relatively high doses and serve as partial agonists on the vitamin D receptor. New secosteroids are excellent candidates for therapy of fibrosing, inflammatory or hyperproliferative disorders including cancers and psoriasis.
Length-adaptive graph search for automatic segmentation of pathological features in optical coherence tomography images (2016)

We introduce a metric in graph search and demonstrate its application for segmenting retinal optical coherence tomography (OCT) images of macular pathology. Our proposed “adjusted mean arc length” (AMAL) metric is an adaptation of the lowest mean arc length search technique for automated OCT segmentation. We compare this method to Dijkstra’s shortest path algorithm, which we utilized previously in our popular graph theory and dynamic programming segmentation technique. As an illustrative example, we show that AMAL-based length-adaptive segmentation outperforms the shortest path in delineating the retina/vitreous boundary of patients with full-thickness macular holes when compared with expert manual grading.
Gut microbiota analysis reveals a marked shift to bifidobacteria by a starter infant formula containing a synbiotic of bovine milk‐derived oligosaccharides and B ifidobacterium animalis subsp. lactis   CNCM I ‐3446 (2015)

Summary Non‐digestible milk oligosaccharides were proposed as receptor decoys for pathogens and as nutrients for beneficial gut commensals like bifidobacteria. Bovine milk contains oligosaccharides, some of which are structurally identical or similar to those found in human milk. In a controlled, randomized double‐blinded clinical trial we tested the effect of feeding a formula supplemented with a mixture of bovine milk‐derived oligosaccharides ( BMOS ) generated from whey permeate, containing galacto‐oligosaccharides and 3'‐ and 6'‐sialyllactose, and the probiotic B ifidobacterium animalis subsp. lactis ( B . lactis ) strain CNCM I ‐3446. Breastfed infants served as reference group. Compared with a non‐supplemented control formula, the test formula showed a similar tolerability and supported a similar growth in healthy newborns followed for 12 weeks. The control, but not the test group, differed from the breast‐fed reference group by a higher faecal pH and a significantly higher diversity of the faecal microbiota. In the test group the probiotic B . lactis increased by 100‐fold in the stool and was detected in all supplemented infants. BMOS stimulated a marked shift to a bifidobacterium‐dominated faecal microbiota via increases in endogenous bifidobacteria ( B . longum , B . breve , B . bifidum , B . pseudocatenulatum ).
Wideband monolithic millimeter-wave phase shifter with minimum insertion loss variation (2002)

A novel MM-wave monolithic phase shifter is described which achieves wide bandwidth and minimum insertion loss variation. The circuit employs a dual-varactor reflection termination which behaves like a tunable L-C resonator. The circuit operates at 50 GHz center frequency with 100 degrees of control range and /spl plusmn/0.4 dB maximum amplitude variation.
Methods, systems and apparatus for adjusting duty cycle of pulse width modulated (PWM) waveforms (2023)

Embodiments of the present invention relate to methods, systems and apparatus for controlling operation of a multi-phase machine in a vector controlled motor drive system when the multi-phase machine operates in an overmodulation region. The disclosed embodiments provide a mechanism for adjusting a duty cycle of PWM waveforms so that the correct phase voltage command signals are applied at the angle transitions. This can reduce variations/errors in the phase voltage command signals applied to the multi-phase machine so that phase current may be properly regulated thus reducing current/torque oscillation, which can in turn improve machine efficiency and performance, as well as utilization of the DC voltage source.
Effects of Different Early Experiences on the Development of Spatial Cognition (2022)

By looking carefully at the methods, results, and discussions of a variety of studies using different populations, suggestions can be raised and theories synthesized which may add to our understanding of the development of spatial cognition. This chapter addresses three main issues within the brain bases and development of spatial cognition: the rationalist/empiricist question, autonomy, and brain organization. The rationalist/empiricist question focuses on whether innate principles exist which shape the development of a particular domain of cognition. The second issue is that of modularity, or autonomy of various cognitive functions. The third issue is that of brain organization and plasticity for these various functions. Although the behavioral manifestations of the development of spatial cognition was found to be dissociated from linguistic abilities and environmental factors in the Williams children and the blind, cerebral lateralization for some spatial functions was found to be affected by congenital deafness and by the acquisition of a spatial language.
Multi Gbit/s bit parallel WDM transmission using dispersion managed fibers (2000)

This paper demonstrates the feasibility of a bit parallel WDM (BP-WDM) system using dispersion managed fibers. An expression for the total bit skew as a function of the fiber dispersion and system bandwidth is derived and compared with experimental results. A 4 bit/spl times/10 Gbit/s-per bit BP-WDM transmission experiment over 30 km DMF is used and an aggregate bite rate/spl times/distance product of 1.2 Tbit/s-km is obtained. The total bit skew of the system is reduced to one half of the bit period. We believe that systems using BPWDM will be useful for computer interconnects in high-speed parallel systems and ring networks.
Initial Safety and Feasibility of Steerable Ureteroscopic Renal Evacuation: A Novel Approach for the Treatment of Urolithiasis (2022)

<b><i>Background:</i></b> There is a need to reliably render urolithiasis patients completely stone free with minimal morbidity. We report on the initial safety and feasibility with steerable ureteroscopic renal evacuation (SURE) in a prospective study using basket extraction as a comparison. <b><i>Materials and Methods:</i></b> A pilot randomized controlled study was conducted comparing SURE with basket extraction postlaser lithotripsy. SURE is performed using the CVAC™ Aspiration System, a steerable catheter (with introducer). The safety and feasibility of steering CVAC throughout the collecting system under fluoroscopy and aspirating stone fragments as it was designed to do were evaluated. Fluoroscopy time, change in hemoglobin, adverse events through 30 days, total and proportion of stone volume removed at 1 day, intraoperative stone removal rate, and stone-free rate (SFR) at 30 days through CT were compared. <b><i>Results:</i></b> Seventeen patients were treated (<i>n</i> = 9 SURE, <i>n</i> = 8 Basket). Baseline demographics and stone parameters were not significantly different between groups. One adverse event occurred in each group (self-limiting ileus for SURE and urinary tract infection for Basket). No mucosal injury and no contrast extravasation were observed in either group. The CVAC catheter was steered throughout the collecting system and aspirated fragments. There was no significant difference in fluoroscopy time, procedure time, change in hemoglobin, or stone removal rate between groups. SURE removed more and a greater proportion of stone volume at day 1 <i>vs</i> baskets (202 mm<sup>3</sup> <i>vs</i> 91 mm<sup>3</sup>, <i>p</i> < 0.01 and 84% <i>vs</i> 56%, <i>p</i> = 0.022). SURE achieved 100% SFR at 30 days <i>vs</i> 75% for baskets, although this difference was not statistically significant (<i>p</i> = 0.20). <b><i>Conclusions:</i></b> This initial study suggests SURE is safe, feasible, and may be more effective in stone removal postlaser lithotripsy compared to basketing. More development is needed, and larger clinical studies are underway.
Clinical, pathological, and molecular correlations of necrosis in the primary tumor of patients with renal cell carcinoma (2004)

4643 Background: Presence of histologic necrosis in the primary tumor of patients with renal cell carcinoma (RCC) has been demonstrated to be an important predictor of survival. We investigated the relationship of necrosis to other histologic and clinical factors known to be important prognostic indicators for patients with RCC. Methods: The records of 300 patients undergoing treatment for RCC at UCLA were evaluated for basic clinical information including TNM stage, Eastern Cooperative Oncology Group performance status (ECOG-PS), nuclear grade, and survival. Pathologic slides of the primary tumors were reviewed by a single pathologist. Presence and amount of necrosis were correlated with clinical factors, carbonic anhydrase IX (CAIX) expression, and survival. Results: Patents with necrosis presented with higher T stage (p < 0.0001), metastases (p < 0.0001), greater mean tumor size (p < 0.001) and higher grade (p < 0.0001) compared to patients without necrosis. Extent of necrosis in the primary tumor significantly correlated with T stage, nodal status, metastasis, ECOG-PS, grade, tumor size, and UCLA Integrated Staging System (UISS) (p < 0.01). Patients with necrosis demonstrated a significantly lower 5-year disease specific survival compared to patients without necrosis (36% vs. 75%; p < 0.0001). Multivariate analysis demonstrated grade (p = 0.002), T stage (p < 0.0001), and ECOG-PS (p < 0.0001) to be independent predictors of disease specific survival, while necrosis approached significance (p = 0.07). Presence and extent of necrosis were independent predictors of survival in patients with localized (p < 0.05), but not metastatic (p > 0.05) disease. In patients with clear cell histology, necrosis was also an independent predictor of survival for localized (p = 0.04), but not metastatic (p = 0.49) disease. Conclusions: Presence of necrosis in the primary tumor of patients with RCC is associated with large size, high stage, high grade, and poor ECOG-PS, as well as the presence of distant metastases. The presence of this histologic variant is an independent predictor of poor survival in patients with localized, but not metastatic disease. No significant financial relationships to disclose.
Preparation of Uniform-sized Polymer Nanofibers by Extrusive Spinning Using Ordered Anodic Porous Alumina (2010)

Abstract Uniform-sized polymer nanofibers were fabricated by the extrusive spinning of a photocurable monomer under UV irradiation using ordered anodic porous alumina as a nozzle for the spinning. The size of the resulting polymer nanofibers could be controlled by adjusting the pore size of the anodic porous alumina membrane.
Strain Measurement (2023)

This chapter begins with a review of the fundamental definitions of strain and ways it can be measured. This is followed by a review of the many types of strain sensors and their application, and sources for strain sensors and signal conditioners. Next, a more detailed look is taken at operating principles of various strain measurement techniques and the associated signal conditioning. These include piezoresistive gages (foil or wire strain gages and semiconductor strain gages), piezoelectric gages (polyvinylidene fluoride film and quartz), fiber optic gages, bircfringent films and materials, and Moire grids. The longitudinal strain sensitivity is given as sensor output per unit longitudinal strain in the sensor direction. This is divided by the viewing length to obtain the strain resolution. Strain gages are mounted to test specimens with adhesives using a procedure that is suitable for bonding most types of strain sensors.
Phage Shock Protein PspA of Escherichia coli Relieves Saturation of Protein Export via the Tat Pathway (2003)

Overexpression of either heterologous or homologous proteins that are routed to the periplasm via the twin-arginine translocation (Tat) pathway results in a block of export and concomitant accumulation of the respective protein precursor in the cytoplasm. Screening of a plasmid-encoded genomic library for mutants that confer enhanced export of a TorA signal sequence (ssTorA)-GFP-SsrA fusion protein, and thus result in higher cell fluorescence, yielded the pspA gene encoding phage shock protein A. Coexpression of pspA relieved the secretion block observed with ssTorA-GFP-SsrA or upon overexpression of the native Tat proteins SufI and CueO. A similar effect was observed with the Synechocystis sp. strain PCC6803 PspA homologue, VIPP1, indicating that the role of PspA in Tat export may be phylogenetically conserved. Mutations in Tat components that completely abolish export result in a marked induction of PspA protein synthesis, consistent with its proposed role in enhancing protein translocation via Tat.
Modeling the Binding Mechanism of Remdesivir, Favilavir, and Ribavirin to SARS-CoV-2 RNA-Dependent RNA Polymerase (2021)

Recent efforts to repurpose drugs to combat COVID-19 have identified Remdesivir as a candidate. It acts on the RNA-dependent, RNA polymerase (RdRp) of the SARS-CoV-2 virus, a protein complex responsible for mediating replication of the virus's genome. However, its exact action mechanism, and that of other nucleotide analogue inhibitors, is not known. In this study, we examine at the molecular level the interaction of this drug and that of similar nucleotide analogue inhibitors, ribavirin and favilavir, by relying on atomistic molecular simulations and advanced sampling. By analyzing the binding free energies of these different drugs, it is found that all of them bind strongly at the active site. Surprisingly, however, ribavirin and favilavir do not bind the nucleotide on the complementary strand as effectively and seem to act by a different mechanism than remdesivir. Remdesivir exhibits similar binding interactions to the natural base adenine. Moreover, by analyzing remdesivir at downstream positions of the RNA, we also find that, consistent with a "delayed" termination mechanism, additional nucleotides can be incorporated after remdesivir is added, and its highly polar 1'-cyano group induces a set of conformational changes that can affect the normal RdRp complex function. By analyzing the fluctuations of residues that are altered by remdesivir binding, and comparing them to those induced by lethal point mutations, we find a possible secondary mechanism in which remdesivir destabilizes the protein complex and its interactions with the RNA strands.
Magnetic compression for treatment of large oesophageal diverticula: a new endoscopic approach for a risky surgical disease? (2015)

SCOPUS: no.j
Image Segmentation of the Ventricular Septum in Fetal Cardiac Ultrasound Videos Based on Deep Learning Using Time-Series Information (2020)

Image segmentation is the pixel-by-pixel detection of objects, which is the most challenging but informative in the fundamental tasks of machine learning including image classification and object detection. Pixel-by-pixel segmentation is required to apply machine learning to support fetal cardiac ultrasound screening; we have to detect cardiac substructures precisely which are small and change shapes dynamically with fetal heartbeats, such as the ventricular septum. This task is difficult for general segmentation methods such as DeepLab v3+, and U-net. Hence, here we proposed a novel segmentation method named Cropping-Segmentation-Calibration (CSC) that is specific to the ventricular septum in ultrasound videos in this study. CSC employs the time-series information of videos and specific section information to calibrate the output of U-net. The actual sections of the ventricular septum were annotated in 615 frames from 421 normal fetal cardiac ultrasound videos of 211 pregnant women who were screened. The dataset was assigned a ratio of 2:1, which corresponded to a ratio of the training to test data, and three-fold cross-validation was conducted. The segmentation results of DeepLab v3+, U-net, and CSC were evaluated using the values of the mean intersection over union (mIoU), which were 0.0224, 0.1519, and 0.5543, respectively. The results reveal the superior performance of CSC.
The Infrared Spectrum of the Matrix-Isolated Phenyl Radical (2001)

We have measured the infrared absorption spectrum of C(6)H(5), /X (2)A(1), in an Ar matrix at 10 K. The experimental frequencies (cm(-)(1)) and polarizations follow. a(1) modes: 3086, 3072, 3037, 1581, 1441, 1154, 1027, 997, 976, 605; b(1) modes: 972, 874, 706, 657, 416; b(2) modes: 3071, 3060, 1624, 1432, 1321, 1283, 1159, 1063, and 587. Three different methods have been used for the production of the phenyl radicals. Infrared absorption spectra of five deuterated isotopomers, C(6)D(5), p-C(6)H(4)D, p-C(6)HD(4), o-C(6)H(4)D, and m-C(6)H(4)D, were recorded to compare experimental frequency shifts with calculated (UB3LYP/cc-pVDZ) harmonic frequency shifts. The use of CO(2) or NO as internal standards enabled the experimental determination of absolute infrared intensities. The linear dichroism was measured with photooriented samples to establish experimental polarizations of each vibrational band. True gas-phase vibrational frequencies were estimated by considering the gas-to-matrix shifts and matrix inhomogeneous line broadening. The phenyl radical matrix frequencies listed above are within +/-1% of the gas-phase vibrational frequencies. The C(6)H(5) frequencies from this paper supersede our earlier values reported in J. Am. Chem. Soc. 1996, 118, 7400-7401. See also: http://ellison.colorado.edu/phenyl.
Interaction Between the Distribution of Diabetic Retinopathy Lesions and the Association of Optical Coherence Tomography Angiography Scans With Diabetic Retinopathy Severity (2020)

These results suggest that central retinal vessel density is associated with DR severity in eyes without, but not with, PPL. These findings suggest a potential need to stratify future optical coherence tomography angiography studies of eyes with DR by the presence or absence of PPL. If DR onset and worsening are associated with the location of retinal nonperfusion, assessment of global retinal nonperfusion using widefield angiography may improve the ability to evaluate DR severity and risk of DR worsening over time.
Activation of a c-K- ras Oncogene by Somatic Mutation in Mouse Lymphomas Induced by Gamma Radiation (1984)

Mouse tumors induced by gamma radiation are a useful model system for oncogenesis. DNA from such tumors contains an activated K-ras oncogene that can transform NIH 3T3 cells. This report describes the cloning of a fragment of the mouse K-ras oncogene containing the first exon from both a transformant in rat-2 cells and the brain of the same mouse that developed the tumor. Hybrid constructs containing one of the two pieces were made and only the plasmid including the first exon from the transformant gave rise to foci in NIH 3T3 cells. There was only a single base difference (G----A) in the exonic sequence, which changed glycine to aspartic acid in the transformant. By use of a synthetic oligonucleotide the presence of the mutation was demonstrated in the original tumor, ruling out modifications during DNA-mediated gene transfer and indicating that the alteration was present in the thymic lymphoma but absent from other nonmalignant tissue. The results are compatible with gamma radiation being a source of point mutations.
The absolute configuration of sulphoxides: 3-thiacholestane oxides and 1,8,8-trimethyl-3-thiabicyclo[3,2,1]octane oxides (1967)

R. Nagarajan, B. H. Chollar and R. M. Dodson, Chem. Commun. (London), 1967, 550 DOI: 10.1039/C19670000550