gebhart/patrepeval huggingface dataset:
Efficiently cleaved HIV-1 envelopes: can they be important for vaccine immunogen development? (2020)

The enormous diversity of HIV-1 is a significant impediment in selecting envelopes (Envs) that can be suitable for designing vaccine immunogens. While tremendous progress has been made in developing soluble, trimeric, native-like Env proteins, those that have elicited neutralizing antibodies (Abs) in animal models are relatively few. A strategy of selecting naturally occurring Envs suitable for immunogen design by studying the correlation between efficient cleavage on the cell surface and their selective binding to broadly neutralizing Abs (bNAbs) and not to non-neutralizing Abs (non-NAbs), properties essential in immunogens, may be useful. Here we discuss some of the challenges of developing an efficacious HIV-1 vaccine and the work done in generating soluble immunogens. We also discuss the study of naturally occurring, membrane-bound, efficiently cleaved (naturally more sensitive to furin) Envs and how they may positively add to the repertoire of HIV-1 Envs that can be used for vaccine immunogen design. However, even with such Envs, the challenges of developing well-folded, native-like trimers as soluble proteins or using other immunogen strategies such as virus-like particles with desirable antigenic properties remain, and are formidable. In spite of the progress that has been made in the HIV-1 vaccine field, an immunogen that elicits neutralizing Abs with significant breadth and potency in vaccines has still not been developed. Efficiently cleaved Envs may increase the number of available Envs suitable for immunogen design and should be studied further.
FDG‐PET subtypes of Alzheimer’s disease and their association with distinct biomarker profiles and clinical trajectories (2020)

Abstract Background PET with the glucose analog FDG is a sensitive marker of neuronal dysfunction/degeneration. The aim of this study was to identify distinct metabolic subtypes in prodromal and dementia stages of AD by a data‐driven exploration of FDG‐PET and to compare the subtypes with respect to molecular biomarkers and clinical trajectory. Method First, we used hierarchical clustering of voxel‐wise FDG‐PET from 177 biomarker‐confirmed AD dementia patients from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort to identify distinct subtypes of hypometabolism in AD. The AD subtypes were then characterized with respect to clinical and molecular biomarker characteristics. Subsequently, we classified FDG‐PET scans of 217 amyloid‐positive MCI patients (‘prodromal AD’) according to the subtypes identified in AD patients, and examined their prognostic value for predicting domain‐specific cognitive decline and conversion to dementia over a follow‐up interval of up to 72 months. Result Four main AD subtypes characterized by differential hypometabolism patterns were identified (Fig. 1): (i) “AD‐typical” (48.6%), showing a classic posterior temporo‐parietal hypometabolic pattern with intermediate cognitive decline and biomarker characteristics, (ii) “minimal limbic” (24.9%), showing least impaired cognitive performance but comparable amyloid and tau biomarker profiles, (iii) “limbic‐frontal” (19.8%), characterized by old age and most severe hippocampal atrophy, and (iv) a “frontal” subtype (6.8%), characterized by younger age, more severe executive dysfunction, and least severe hippocampal atrophy. The subtypes observed in the prodromal AD sample demonstrated similar characteristics as in the AD dementia sample, and further showed differential courses of cognitive decline and progression to dementia. Specifically, the “AD‐typical” and the “limbic‐frontal” subtypes demonstrated a higher risk of progressing to AD dementia, as well as a faster decline of memory and executive function performance compared to the “minimal limbic” subtype. Conclusion Data‐driven clustering of FDG‐PET identified distinct hypometabolic subtypes in AD that were readily detectable at prodromal disease stages and associated with differential clinical courses and biomarker characteristics. The convergence of these hypometabolic subtypes with previously described MRI‐derived atrophy subtypes remains to be determined.
Blood Viscosity in Broilers: Influence on Pulmonary Hypertension Syndrome (1996)

Elevation in apparent blood viscosity may enhance the pulmonary hypertension that leads to pulmonary hypertension syndrome (PHS) and 1ascites in fast-growing broilers. We investigated the importance of packed cell volume (PCV) and shear rate in modifying apparent viscosity of the blood from broilers assigned to normal, preascites, and ascites groups. Apparent viscosity of broiler blood increased at all shear rates as PCV increased; the increase in apparent viscosity became greater as the shear rate decreased at PCV above 0.30. At the PCV of normal broilers (0.30 or below), apparent viscosity was nearly shear rate independent, at least down to 11.25 per second, the lowest shear rate studied. Apparent viscosity, at any given PCV and shear rate, was significantly lower in the blood of birds with ascites than in normal birds; however, the relative viscosity was not different between those groups, indicating that lower plasma viscosity in the birds with PHS was responsible for the finding. The results show that the principal factor responsible for increased apparent viscosity of blood in birds with PHS is the increase in PCV. The increased resistance to flow of blood as the result of higher blood viscosity may contribute to the pulmonary hypertension.
The modified HSINFET using the trenched JBS injector (2002)

A Hybrid Schottky INjector Field Effect Transistor (HSINFET) which increases the forward conduction current without sacrificing the latch-up capability and turn-off characteristics, is proposed. The feature of the structure is that the hybrid Schottky injector is implemented by the trench sidewall Schottky contact and p-n junction injector at the bottom of a trench. The device characteristics of the proposed HSINFET are numerically simulated and compared with conventional devices. The proposed HSINFET exhibits a lower forward voltage drop than the conventional HSINFET by 0.4 V at 100 A/cm/sup 2/.
A Novel Functional Soy‐based Food Fermented by Lactic Acid Bacteria: Effect of Heat Treatment (2004)

ABSTRACT: The development of a novel fermented soymilk product using selected lactic acid bacteria was performed. The immunomodulatory properties of strains able to grow in soymilk were evaluated in a murine model using inbred BALB/c mice. Lactobacillus acidophilus CRL 43 and CRL 1064 and Lactobacillus paracasei CRL 75 and CRL 208 were all able to significantly increase the phagocytic index (41 ± 4) compared with the control group (16 ± 3) when given individually. These strains were then used in the elaboration of multicultured fermented soymilks that were able to stimulate an innate immune response (peritoneal macrophage activation). However, these novel fermented products sometimes caused undesired secondary effects such as microbial translocation and animal weight loss. When the same fermented products were subjected to heat treatment, they were still able to stimulate the innate immune response without causing secondary effects. These results clearly show that it is not always necessary for lactic acid bacteria to be alive to exert a beneficial physiological effect. This study could thus be used as a model in the design and future evaluation of novel fermented vegetable products.
Fatty acid specificity of T1 lipase and its potential in acylglycerol synthesis (2013)

DAGs and MAGs were synthesised in good yields although C18:1 (a much poorer substrate) was used. Our work demonstrates that T1 lipase, which was discovered to show 1,3-regio-selectivity, is a promising biocatalyst for lipids modification.
Heterotopic transcatheter tricuspid valve implantation: first-in-man application of a novel approach to tricuspid regurgitation (2011)

Transcatheter treatment of severe TR by caval valve implantation is feasible resulting in an immediate abolition of IVC regurgitation and mid-term clinical improvement. Thus, in selected non-surgical patients, caval valve implantation may become a therapeutic option to treat venous regurgitation and improve associated non-cardiac diseases. Further confirmatory experience with longer follow-up is required to evaluate the long-term clinical benefit of the procedure as well as potential deleterious effects.
Profiling Heterogeneous Computing Performance with VTune Profiler (2021)

Programming of heterogeneous platforms requires deep understanding of system architecture on all levels, which help applications design to leveraging the best data and work decomposition between CPU and an accelerating hardware like GPUs. However, in many cases the applications are being converted form a conventional CPU programming language like C++, or from accelerator friendly but still low level languages like OpenCL, and the main problem is to determine which part of the application is leveraging from being offloaded to GPU. Another problem is to estimate, how much performance increase one might gain due to the accelerating in the particular GP GPU device. Each platform has its unique limitations that are affecting performance of offloaded computing tasks, e.g. data transfer tax, task initialization overhead, memory latency and bandwidth limitations. In order to take into account those constraints, software developers need tooling for collecting right information and producing recommendations to make the best design and optimization decisions. In this presentation we will introduce two new GPU performance analysis types in Intel® VTune™ Profiler, and a methodology of heterogeneous applications performance profiling supported by the analyses. VTune Profiler is a well-known tool for performance characterization on CPUs, now it includes GPU Offload Analysis and GPU Hotspots Analysis of applications written on most offloading models with OpenCL, SYCL/Data Parallel C++, and OpenMP Offload. The GPU Offload analysis helps to identify how CPU is interacting with GPU(s) by creating and submitting tasks to offload queues. It provides metrics and performance data such as GPU Utilization, Hottest GPU Computing Tasks, Tasks instance count and timing, kernel Data Transfer Size, SIMD Width measurements, GPU Execution Units (EU) threads occupancy, and Memory Utilization. All together the metrics are providing a systematic picture on how effectively tasks were offloaded and executed on GPUs.
Metabolic responsiveness to training depends on insulin sensitivity and protein content of exosomes in insulin-resistant males (2021)

High-intensity interval training (HIIT) improves cardiorespiratory fitness (VO<sub>2</sub>max), but its impact on metabolism remains unclear. We hypothesized that 12-week HIIT increases insulin sensitivity in males with or without type 2 diabetes [T2D and NDM (nondiabetic humans)]. However, despite identically higher VO<sub>2</sub>max, mainly insulin-resistant (IR) persons (T2D and IR NDM) showed distinct alterations of circulating small extracellular vesicles (SEVs) along with lower inhibitory metabolic (protein kinase Cε activity) or inflammatory (nuclear factor κB) signaling in muscle of T2D or IR NDM, respectively. This is related to the specific alterations in SEV proteome reflecting down-regulation of the phospholipase C pathway (T2D) and up-regulated antioxidant capacity (IR NDM). Thus, SEV cargo may contribute to modulating the individual metabolic responsiveness to exercise training in humans.
Strong Ditkin algebras without bounded relative units (1999)

In a previous note the author gave an example of a strong Ditkin algebra which does not have bounded relative units in the sense of Dales. In this note we investigate a certain family of Banach function algebras on the one point compactification of ℕ , and see that within this family are many easier examples of strong Ditkin algebras without bounded relative units in the sense of Dales.
Bandwidth of Crossbar and Multiple-Bus Connections for Multiprocessors (1982)

In this paper we compare the effective bandwidth in a multiprocessor with shared memory using as interconnection networks the crossbar or the multiple-bus. We consider a system with N processors and N memory modules, in which the processor requests to the memory modules are independent and uniformly distributed random variables. We consider two cases: in the first the processor makes another request immediately after a memory service, and in the second there is some internal processing time.
Quantification of Metal Atom Ordering in Engineered W1-xMoxS2 Monolayers (2022)

Journal Article Quantification of Metal Atom Ordering in Engineered W1-xMoxS2 Monolayers Get access Danielle Reifsnyder Hickey, Danielle Reifsnyder Hickey Department of Chemistry, The Pennsylvania State University, University Park, PA, United StatesDepartment of Materials Science and Engineering, The Pennsylvania State University, University Park, PA, United States Search for other works by this author on: Oxford Academic Google Scholar Leixin Miao, Leixin Miao Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA, United States Search for other works by this author on: Oxford Academic Google Scholar Mikhail Chubarov, Mikhail Chubarov 2D Crystal Consortium-Materials Innovation Platform, Materials Research Institute, The Pennsylvania State University, University Park, PA, United States Search for other works by this author on: Oxford Academic Google Scholar Saiphaneendra Bachu, Saiphaneendra Bachu Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA, United States Search for other works by this author on: Oxford Academic Google Scholar Tanushree H Choudhury, Tanushree H Choudhury 2D Crystal Consortium-Materials Innovation Platform, Materials Research Institute, The Pennsylvania State University, University Park, PA, United StatesDepartment of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Powai, Mumbai, India Search for other works by this author on: Oxford Academic Google Scholar Joan M Redwing, Joan M Redwing 2D Crystal Consortium-Materials Innovation Platform, Materials Research Institute, The Pennsylvania State University, University Park, PA, United States Search for other works by this author on: Oxford Academic Google Scholar Nasim Alem Nasim Alem Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA, United States Corresponding author: nua10@psu.edu Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 28, Issue S1, 1 August 2022, Pages 2506–2507, https://doi.org/10.1017/S1431927622009588 Published: 01 August 2022
Expression of cytoplasmic retinoic acid-binding proteins and nuclear receptors in squamous-cell carcinomasin vitro (1997)

Retinoids have been described to be potent modulators of cell proliferation, differentiation and apoptosis in various types of squamous-cell carcinoma (SCC) and myeloid cancer cells in vitro (Bollag and Holdener, 1992;Lotan et al., 1995).It has also been demonstrated that treatment of cells with retinoic acid (RA) in combination with ionizing radiation resulted in significantly enhanced radiation cytotoxicity.In these studies, the reduction of cell survival could be attributed to a supra-additive inhibition of clonogenic activity and concomitantly to a stimulation of differentiation processes induced either by retinoids and or interferon-a in combination with irradiation (Hoffmann et al., 1994).The underlying molecular mechanism of these effects is not understood.It is thought that the cell biological activities of retinoids, and especially the radiosensitizing effect of RA, result from changes in gene expression mediated via the binding of RA to CRABP I/II and the transport of RA into the nucleus.It then can bind to the nuclear receptors RAR or RXR or to the dimer forms of these subunits (Mangelsdorf et al., 1995).Subsequently, the nuclear receptor is able to bind to specific RA-response elements of specific genes which are involved in the regulation of cell proliferation and differentiation.To study the underlying mechanism of the growthinhibitory and radiosensitizing effects of RA, we analyzed in various SCC lines the basal level as well as the RA-and/or irradiation-modulated gene expression of RAR, RXR and CRABP I/II.To increase the level of sensitivity, we therefore established the method of semi-quantitative RT-PCR.
Effects of a Bleaching Technic on the Labial Enamel of Human Teeth Stained with Endemic Dental Fluorosis (1970)

Enamel removal was studied in 54 permanent maxillary anterior teeth of people from high fluoride and unknown fluoride areas after the teeth were bleached by a standardized technic. A single 20-minute treatment was not excessively destructive, because it removed only about 0.1 mm of labial enamel in most specimens tested, regardless of fluoride background.
Autoimmune, Atopic, and Mental Health Comorbid Conditions Associated With Alopecia Areata in the United States (2013)

<h3>Objective</h3> To evaluate the prevalence of comorbid conditions among patients with alopecia areata (AA) seen at tertiary care hospitals in Boston, Massachusetts, during an 11-year period. <h3>Design</h3> Retrospective cross-sectional study. <h3>Setting</h3> Tertiary care hospitals in Boston, including Brigham and Women’s Hospital and Massachusetts General Hospital. <h3>Participants</h3> We identified 3568 individuals with AA seen in the Partners health care system in Boston between January 1, 2000, and January 1, 2011. We performed comprehensive searches of the Research Patient Data Repository using<i>International Classification of Diseases, Ninth Revision</i>code 704.01. We randomly selected 350 patients and manually reviewed their medical records to train and validate a novel artificial intelligence program. This program then used natural language processing to review free-text medical records and confirm a diagnosis of AA. To confirm the algorithm, we manually reviewed a subset of records and found 93.9% validity. <h3>Main Outcomes and Measures</h3> The prevalence of comorbid conditions was assessed. <h3>Results</h3> Common comorbid conditions included autoimmune diagnoses (thyroid disease in 14.6%, diabetes mellitus in 11.1%, inflammatory bowel disease in 2.0%, systemic lupus erythematosus in 4.3%, rheumatoid arthritis in 3.9%, and psoriasis and psoriatic arthritis in 6.3%), atopy (allergic rhinitis, asthma, and/or eczema in 38.2% and contact dermatitis and other eczema in 35.9%), and mental health problems (depression or anxiety in 25.5%). We also found high prevalences of hyperlipidemia (24.5%), hypertension (21.9%), and gastroesophageal reflux disease (17.3%). This profile was different from that seen in a comparison psoriasis and psoriatic arthritis group. <h3>Conclusions and Relevance</h3> We found a high prevalence of comorbid conditions among individuals with AA presenting to academic medical centers in Boston. Physicians caring for patients with AA should consider screening for comorbid conditions.
Antifungal effect of bean endochitinase on Rhizoctonia solani: ultrastructural changes and cytochemical aspects of chitin breakdown (1993)

A chitinase, purified to homogeneity from ethylene-treated bean leaves, was applied to actively growing mycelial cells of Rhizoctonia solani to evaluate a potential antifungal activity. Light microscopic investigations at 30-min intervals following enzyme exposure revealed the induction of morphological changes such as swelling of hyphal tips and hyphal distortions. More precise information concerning fungal cell alteration was obtained by ultrastructural observation and cytochemical detection of chitin distribution in fungal cell walls. Chitin breakdown was found to be an early event preceding wall disruption and cytoplasm leakage. The large amounts of chitin present in the walls of control R. solani cells and the rapid chitin hydrolysis upon chitinase treatment lead us to suggest that this polysaccharide is one of the main components of this fungal cell wall and is readily accessible to chitinase, especially in the apical zone. By 60 min after enzyme treatment, labeled molecules were observed in the vicinity of some fungal cells, suggesting the release of chitin oligosaccharides from fungal cell walls. The antifungal activity of the bean chitinase on cells of R. solani grown in culture is discussed in relation to the potential of genetically modified transgenic plants to resist attack by R. solani through an antimicrobial activity in planta.
Reduced-complexity widely linear adaptive estimation (2010)

Widely linear filters play an important role in signal processing applications where the circularity properties on the complex data do not hold. They are able to achieve smaller mean-square error (MSE) than linear complex filters, but at a significantly higher computational cost. In this paper, we propose a modified version of widely linear filters with a reduced computational complexity. In the proposed version, the data vector is real, being constituted by the real and imaginary parts of the complex data separately. We prove that the new scheme achieves the same minimum MSE of standard widely linear estimators. We exemplify this idea for the least-mean squares (LMS) algorithm and also for the recursive least-squares (RLS) algorithm.
ChemInform Abstract: Solid‐Phase Syntheses of Glycopeptides: Glycosylation of Resin‐Bound Serine‐Peptides by 3,4,6‐Tri‐O‐acetyl‐D‐glucoseoxazoline. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Microbial accumulation of neptunium (1988)

Resting cells of several species of microorganisms removed neptunium (Np) from an aqueous solution. Concentrations of up to 15 mg Np per g cells (dry weight) were obtained. Maximum uptake byMicrococcus luteus occurred in less than 10 min.
NMR Measurements of chemical theory equilibrium constants for hydrogen‐bonded solutions (1986)

Abstract Although various chemical theories have often been used to characterize hydrogen‐bonded systems with some success, they have been limited by the fact that the equilibrium constants were adjustable parameters. This paper reports a method to measure directly these constants by proton nuclear magnetic resonance spectroscopy. Results are reported for several systems and are used with a chemical‐physical theory to predict vapor‐liquid equilibria.
Detail-preserving Fluorescence Microscopy Image Deconvolution (2016)

We propose a detail-preserving image deconvolution method which outperforms state-of-the-art methods, and can further improve image quality in the super-resolution optical fluctuation imaging and other diffraction-limited/superresolution imaging modalities. Article not available.
Three-halves harmonic emission from femtosecond laser produced plasmas with steep density gradients (2004)

Detailed measurements of the angular distribution of 3 ω0/2 radiation are presented in short scale length plasmas (0.8–7 μm) generated by laser radiation at intensities reaching the relativistic level (1016–6×1018 W/cm2). The experimental results are in very good agreement with theoretical predictions based on two-plasmon decay and stimulated Raman scattering instabilities. New three-halves harmonic generation mechanisms are an identified characteristic of femtosecond laser induced parametric instabilities. These are the joint interaction of incident and reflected laser beams as well as stimulated Raman scattering. It is shown both experimentally and theoretically that the three-halves harmonic radiation is a useful preplasma diagnostic tool.