gebhart/patrepeval huggingface dataset:
A novel anti-Ia monoclonal antibody which specifically enhances the corresponding T cell alloreactivity. (1984)

An anti-I-Ab monoclonal antibody, designated K14.83-11, was produced in a fusion between SP 2/0 Ag-14 myeloma cells and spleen cells from a B10.D2/n mouse primed in vivo against C57BL/10. Unlike other anti-I-Ab monoclonal antibodies thus far described, K14.83-11 was found to have a combination of features involving specificity, isotype, and function, unique among existing anti-I-A reagents. K14.83-11 exhibited a strong binding to the I-Ab gene product, with only slight cross-reactivity to the I-Ap/q family of allelic products and no reactivity towards I-Ak,d. When analyzed for isotype, K14.83-11 was found to be of a rare IgG3 isotype. With respect to biologic activity, K14.83-11 not only failed to produce the expected inhibition of specific anti-I-Ab T cell reactivity in vitro, but instead produced a striking enhancement of T cell responses against the I-Ab gene product. The possible relationship of IgG isotype and function was suggested when the immunoenhancing effect of K14.83-11 on reactive T lymphocytes was reversed to that of suppression with highly purified F(ab)2 fragments obtained by pepsin digestion.
Identification of a novel percent mammographic density locus at 12q24 (2012)

Percent mammographic density adjusted for age and body mass index (BMI) is one of the strongest risk factors for breast cancer and has a heritable component that remains largely unidentified. We performed a three-stage genome-wide association study (GWAS) of percent mammographic density to identify novel genetic loci associated with this trait. In stage 1, we combined three GWASs of percent density comprised of 1241 women from studies at the Mayo Clinic and identified the top 48 loci (99 single nucleotide polymorphisms). We attempted replication of these loci in 7018 women from seven additional studies (stage 2). The meta-analysis of stage 1 and 2 data identified a novel locus, rs1265507 on 12q24, associated with percent density, adjusting for age and BMI (P = 4.43 × 10(-8)). We refined the 12q24 locus with 459 additional variants (stage 3) in a combined analysis of all three stages (n = 10 377) and confirmed that rs1265507 has the strongest association in the 12q24 region (P = 1.03 × 10(-8)). Rs1265507 is located between the genes TBX5 and TBX3, which are members of the phylogenetically conserved T-box gene family and encode transcription factors involved in developmental regulation. Understanding the mechanism underlying this association will provide insight into the genetics of breast tissue composition.
Fast switching and long retention Fe-O ReRAM and its switching mechanism (2007)

A novel iron oxide (Fe-O) ReRAM is proposed and its high-speed resistance-switching of 10 ns is demonstrated. The switching mechanism is confirmed as a redox reaction between Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> and y-Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> . Based on this model, we have achieved long-retention characteristics by introducing Zn atoms to suppress the reduction process.
Prognostic Value of Histologic Subtypes in Renal Cell Carcinoma: A Multicenter Experience (2005)

The stratification in three main renal cell carcinoma histologic subtypes as defined by the 1997 UICC-American Joint Committee on Cancer consensus should not be considered a major prognostic variable comparable to TNM stage, Fuhrman grade and ECOG PS.
Contactless power delivery system for mining applications (2002)

The authors present the application of a power delivery system design unifying power electronics and a coaxial-winding transformer for devices that require contactless connection and/or relative motion while delivering large amounts of power. The transformer's unique characteristics and how they might be used to advantage in combination with power electronics are emphasized. Applications which have near-term realizability are flexible power distribution, material handling, autonomous electric vehicles, and battery opportunity recharge. Test results on a scale prototype are presented to verify the concepts.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Optimized Tooling Design Algorithm for Sheet Metal Forming over Reconfigurable Compliant Tooling (2004)

New forming technologies based on compliant “discrete‐die” reconfigurable tooling are available for production of sheet metal parts, but there is a need for a formalism that can accurately predict the three‐dimensional shape of the required tooling, a priori. An optimized tooling design algorithm has been developed based on a methodology that uncouples the effects due to springback and those due to the compliance of the polymeric layer. A springback compensated die shape is initially predicted for the case of stretch forming over smooth rigid dies based on an iterative approach using the finite element method. The tooling design algorithm is based on an inverse springback approach that uses the elastic‐plastic stress state prior to unloading to elastically deform the sheet in a direction opposite to springback. A procedure has been developed to improve the convergence behavior of the inverse springback approach utilizing an interpolation scheme. The interpolation scheme uses prior iterations to predict the desired die shape by fitting spatially varying quadratic relationships between the tool shape and the part shape error histories. The optimized tooling design algorithm is extended to compliant dies by developing a method that corrects the die shape for polymer through the thickness compression. The algorithm is applied to stretch forming of large‐scale airframe skin parts commonly found in aerospace structures. Two shapes are investigated, a 90‐inch radius cylindrical cap and a 90‐inch radius spherical cap.
Supplementary Fig. S5 from A selective small-molecule nuclear factor-κB inhibitor from a high-throughput cell-based assay for “activator protein-1 hits” (2023)

Supplementary Fig. S5 from A selective small-molecule nuclear factor-κB inhibitor from a high-throughput cell-based assay for “activator protein-1 hits”
Enantioselectivity of Pseudomonas cepacia Lipase towards 2-Methyl-3(or 4)-arylalkanols: An Approach Based on the Stereoelectronic Theory and Molecular Modeling (2001)

For a better understanding of the previously reported enantioselectivity of Pseudomonas cepacia lipase (PCL) in acylation of racemic primary alcohols, 2-methyl-3(or 4)-arylalkanols, molecular modeling of tetrahedral intermediates (TIs) at the active site was performed.The most probable conformers of TIs were elucidated and their interactions with the amino acid residues of the binding pockets at the enzyme active site were studied.The free energy difference between TIs of two enantiomers was approximated by the differences in potential energy and the solvent accesible surface area.Correlation between the He(His286) Og(Ser87) hydrogen bond differences of diastereomeric, low energy gauche-TIs, and experimentally determined enantiomeric ratios was found.In agreement with the stereoelectronic theory, the gauche-TI precedes ester release.
DNA repair mutations and treatment-emergent small cell neuroendocrine prostate cancer (t-SCNC) as hallmarks of distinct subgroups of metastatic castration resistant prostate cancer (mCRPC): Data from the West Coast Prostate Cancer Dream Team. (2018)

5039 Background: Genomic alterations in DNA repair genes are present in approximately 20-30% of patients with mCRPC. t-SCNC may be increasing in prevalence and is associated with adverse clinical outcomes. Potential overlap between these two subsets of mCRPC was assessed. Methods: Eligible patients (pts) underwent a metastatic tumor core needle biopsy at one of 5 centers. Tumor tissue was sent for consensus pathology call (JH, GT, LT) and targeted next-generation DNA sequencing. Chi-square test was used to compare the frequency of genomic alterations in select DNA repair genes (BRCA1, BRCA2, ATM, CDK12, RAD51, PALB2, FANCA, CHEK2, MLH1, MSH2, MLH3, and MSH6) between tumors with versus those without small cell histology. Frozen tissue from the same metastatic tumor underwent RNA sequencing (RNA-seq). Pts were prospectively followed for overall survival (OS). Results: 119 consecutive biopsies with sufficient tumor to permit histologic assessment and targeted NGS were included, including 14 biopsies (13%) with t-SCNC. In the overall cohort, DNA repair mutations were present in 41 biopsies (34%). By histologic subtype, mutations were present in 40/105 (38%) of adenocarcinoma tumors vs. only 1 of 14 (7%) biopsies with t-SCNC histology (p = 0.047). In contrast, TP53 and/or RB1 loss were enriched in the t-SCNC cohort (83% vs. 34%, p = 0.0015). Unsupervised hierarchical analysis of the transcriptome identified small cell-enriched cluster of biopsies (N = 12) that were mutually exclusive of DNA repair mutations and enriched for E2F transcriptional targets on RNA-seq. The presence of t-SCNC histologic differentiation was associated with worse OS from date of mCRPC (median OS 44.5 vs. 36.6 months; log-rank p = 0.027); the presence of DNA repair mutations was not (p = 0.734). Conclusions: Tumors harboring DNA repair pathway mutations or t-SCNC differentiation may represent distinct disease subsets of mCRPC with differing clinical outcomes. Added together, the two subsets account for approximately 40% of mCRPC pts. Independent prospective validation of these findings is warranted. Clinical trial information: NCT02432001.
Facial Recognition Using Simulated Prosthetic Pixelized Vision (2003)

These findings suggest that reliable face recognition with crude pixelized grids can be learned and may be possible, even with a crude visual prosthesis.
The role of restricted food intake in the pathogenesis of cachexia in severe combined immunodeficient beige mice infected with Mycobacterium paratuberculosis. (1995)

A paired feeding experiment was conducted to investigate if reduced food intake is a reason for the body weight loss previously observed in severe combined immunodeficient beige (SCID bg) mice infected with Mycobacterium paratuberculosis. Mice were paired on the basis of age, litter and sex. One of each pair was injected intraperitoneally with 10(5) viable M. paratuberculosis organisms. The remainder served as uninfected pairfed mates. Each uninfected mouse was restricted to the amount of food (per gram body weight) that its infected paired mate ate in the previous 24 hour period starting at four weeks postinfection until 12 weeks postinfection when the mice were necropsied. The mean body weights of the two groups were not significantly different (p < 0.05) at the start of the experiment (infected 27.6 +/- 2.1 g, pairfed 27.3 +/- 3.4 g) but the pairfed group weighed less after 12 weeks of restricted food intake. Mycobacterium paratuberculosis was isolated from the spleen, liver, gut and fecal pellets of the infected but not the uninfected mice. Acid-fast bacilli were seen histologically in the liver, spleen and intestines of the infected mice only. Analysis of carcass compositions indicated that both infected and pairfed mice lost dry matter. Despite the loss in dry matter, the infected mice appeared to have maintained their body weights due to an increased retention of body water (presumably due to edema of inflammation). These results suggest that infection of SCID bg mice with M. paratuberculosis causes a reduction in their food intake (presumably due to reduced appetite) which, in turn, contributes to a loss in dry matter. We suggest that this loss in dry matter is one of the initial events that eventually lead to cachexia, and that it precedes the body weight loss that inevitably occurs in SCID bg mice chronically affected with M. paratuberculosis.
Cataract Surgery and the 6-year Incidence of Age-Related Macular Degeneration in a Multiethnic Asian Cohort (2020)

Our data are consistent with findings in population-based Caucasian studies that cataract surgery may be associated with incidence of late AMD. However, the absolute risk of late AMD development remains low and physicians should continue to balance the benefits and risks of cataract surgery in elderly patients.
Unprecedented crystallization and X-ray crystal structure of racemicN?-(t-butyloxycarbonyl)-L-L-phenylalanineN-methoxy-N-methylamide (2000)

Weinreb amide 3 was synthesized using isobutyl chloroformate, carbonyldiimidazole, or ethylcarbodiimide as the coupling agent in the reaction of Boc-phenylalanine with O,N-dimethylhydroxylamine hydrochloride. An optically active oil was isolated along with an optically inactive solid irrespective of the type of coupling agent used. Single crystal X-ray analysis of the solid revealed that it is a racemate. The molecular packing of the crystals reflect the stability of the racemate as opposed to an enantiomerically pure solid.
O1‐12‐02: Retinal vascular imaging markers are associated with cognitive decline (2015)

Retinal microvascular changes, measured easily and objectively by retinal vascular imaging, are likely to be markers of concomitant changes in the cerebral microvasculature, which may play an important role in the development and progression of Alzheimer's Disease (AD). We examined prospectively the association of a range of retinal microvascular parameters with cognitive decline in a cohort with mild cognitive impairment (MCI) and AD. Patients with AD and MCI were recruited from dementia/memory clinics, with follow up over a 1-year interval. Patients were administered the Mini Mental State Examination (MMSE) and the Clinical Dementia Rating (CDR) at baseline and follow-up visits. Cognitive decline was defined as a drop of at least 2 points on the MMSE or an increase of >= 0.5 points on the CDR global score at the follow-up visit. Baseline retinal photographs were analyzed using a computer program (Singapore I Vessel Assessment, SIVA) and a spectrum of quantitative retinal microvascular parameters (fractal dimension, caliber, tortuosity and bifurcation) were measured. Logistic regression models were used to compute odds ratio (OR) and 95% confidence interval for cognitive decline adjusting for age, gender, ethnicity, smoking, hypertension, diabetes and hypercholesterolemia. We included 55 patients with MCI and 56 patients with AD at baseline. 36.4% of MCI patients and 41.1% of AD patients had cognitive decline over 1-year follow-up. Greater retinal vascular fractal dimension (OR per standard deviation [SD] increase, 1.73 [1.10-2.73], p-value=0.018), reflecting a higher retinal vascular branching complexity, was independently associated with cognitive decline, after adjusting for age, gender, ethnicity, smoking, hypertension, diabetes and hypercholesterolemia at baseline. Retinal arteriolar branching asymmetry ratio (OR per SD increase, 0.64 [0.41-0.99], p-value=0.047) and retinal arteriolar junctional exponent deviation (OR per SD increase, 1.51 [0.97-2.37], p-value=0.071), reflecting a suboptimal retinal arteriolar bifurcation, were also independently associated with cognitive decline in the multivariate models. Other retinal microvascular parameters were not associated with cognitive decline. Retinal vascular imaging may be of additional value in predicting MCI and AD patients’ risk of developing progression of cognitive impairment.
Bending Fatigue Life Analysis of Carburized Components Using Strain Life and Fracture Mechanics Approaches (2003)

&lt;div class="htmlview paragraph"&gt;Axle primary gearing is normally carburized for high and balanced resistance to contact fatigue, wear, bending fatigue, and impact loading. The focus of this work is on bending fatigue which is a key design consideration of automotive and commercial vehicle axle gearing. Since a carburized component is basically a composite material with steep gradients in carbon content, hardness, tensile strength and microstructure from surface to the middle of the cross section combined with non-linear residual stress, its bending fatigue life prediction is a complex and challenging task. Many factors affect the bending fatigue performance of axle gearing, such as gear design, gear manufacturing, loading history during service, residual stress distribution, steel grade, and heat treatment.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;In this paper, the general methodology for bending fatigue life prediction of a carburized component is investigated. Carburized steel composites are treated as two homogeneous materials: case and core. Materials properties are evaluated separately with simulated case and simulated core samples. Two fatigue life analysis approaches are applied for bending fatigue life analysis: the strain-life approach and the crack growth fracture mechanics approach. The fundamental materials fatigue properties needed include strain controlled axial fatigue test data, crack growth rates and fracture toughness. Residual stress distributions are characterized and their effect on bending fatigue life is included in both fatigue life analysis approaches. Bending fatigue tests are conducted on carburized U-Notch bar samples, and the test results are compared with the life prediction results. Several important factors in bending fatigue life analysis of carburized components are discussed and included in the life prediction, such as bending stress gradient, mean stress, initial defect size, and residual stress. Finally the pros and cons of the two fatigue life analysis approaches are compared and summarized.&lt;/div&gt;
Spectral splitting photovoltaics using perovskite and wideband dye-sensitized solar cells (2015)

The extension of the light absorption of photovoltaics into the near-infrared region is important to increase the energy conversion efficiency. Although the progress of the lead halide perovskite solar cells is remarkable, and high conversion efficiency of >20% has been reached, their absorption limit on the long-wavelength side is ∼800 nm. To further enhance the conversion efficiency of perovskite-based photovoltaics, a hybridized system with near-infrared photovoltaics is a useful approach. Here we report a panchromatic sensitizer, coded DX3, that exhibits a broad response into the near-infrared, up to ∼1100 nm, and a photocurrent density exceeding 30 mA cm(-2) in simulated air mass 1.5 standard solar radiation. Using the DX3-based dye-sensitized solar cell in conjunction with a perovskite cell that harvests visible light, the hybridized mesoscopic photovoltaics achieved a conversion efficiency of 21.5% using a system of spectral splitting.
Kinematic Analysis of a Variable-Speed Transmission Mechanism (2007)

This paper presents a kinematic analysis and a redesign of a variable-speed transmission mechanism. The mechanism is a seven-bar linkage where the rotation of the input crank is converted into the oscillation of the output link. The input crank rotates at a constant speed and the output link consists of an overrunning clutch mounted on the output shaft. The angle through which the clutch oscillates, for each revolution of the input crank, can be adjusted by a control arm. This arm allows a fixed pivot to be temporarily released and moved along a circular arc about a permanent ground pivot. The paper shows how to determine the angle of oscillation of the clutch for a specified position of the fixed pivot. The paper also investigates the extreme positions of the clutch corresponding to the extreme positions of a point on the coupler link. For this reason, the paper investigates the geometry of the path traced by a coupler point. The work shows how to determine the location of the ground pivot of the control arm which will cause the clutch to remain stationary during a complete rotation of the input crank. Then the paper shows how to design the control arm by using these conditions; i.e., the conditions for a redesign of the mechanism are investigated. A novel technique, in which kinematic coefficients are obtained with respect to an independent variable, is presented. This technique decouples the position equations and gives additional insight into the geometry of the mechanism.
Scalable Synthesis of 6,6-Dimethylbicyclo[3.1.0]hexan-3-one (2017)

A simple five-step process for the conversion of technical grade (+)-3-carene into 6,6-dimethylbicyclo[3.1.0]hexan-3-one was developed. A robust process was required that delivered the 6,6-dimethylbicyclo[3.1.0]hexan-3-one, minimized chromatography, reduced the excess of silver salts, and avoided toxic chromium oxidants. A simple and scalable process that relies on crystallization and distillation was developed and demonstrated to produce hundreds of grams of 6,6-dimethylbicyclo[3.1.0]hexan-3-one.
Loss-of-function mutations in RAB39B are associated with typical early-onset Parkinson disease. (2015)

Rab proteins are small molecular weight guanosine triphosphatases involved in the regulation of vesicular trafficking.(1) Three of 4 X-linked RAB genes are specific to the brain, including RAB39B. Recently, Wilson et al.(2) reported that mutations in RAB39B cause X-linked intellectual disability (ID) and pathologically confirmed Parkinson disease (PD). They identified a ∼45-kb deletion resulting in the complete loss of RAB39B in an Australian kindred and a missense mutation in a large Wisconsin kindred. Here, we report an additional affected man with typical PD and mild mental retardation harboring a new truncating mutation in RAB39B.
Ethanol extract of Kalopanax septemlobus leaf induces caspase-dependent apoptosis associated with activation of AMPK in human hepatocellular carcinoma cells (2015)

The Kalopanax septemlobus leaf (Thunb.) Koidz. has been used as a traditional medicine herb for the treatment of various human diseases for hundreds of years. In this study, we investigated the mechanism underlying the inhibitory effects of an ethanol extract of K. septemlobus leaf (EEKS) on proliferation of HepG2 hepatocellular carcinoma cells. For this study, cell viability and apoptosis were evaluated using the MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay, DAPI (4,6-diamidino-2-phenylindole) staining, agarose gel electrophoresis, and flow cytometry. Measurements of the mitochondrial membrane potential (MMP), caspase activity assays and western blots were conducted to determine whether HepG2 cell death occurred by apoptosis. Treatment of HepG2 cells with EEKS concentration-dependently reduced cell survival while significantly increasing the ratio of apoptotic cells. EEKS treatment increased the levels of the death receptors (DRs), DR4 and DR5, and activated caspases, as well as promoting proteolytic degradation of poly(ADP-ribose)-polymerase associated with the downregulation of protein expression of members of the inhibitor of apoptosis protein family. Treatment with EEKS also caused truncation of Bid, translocation of pro-apoptotic Bax to the mitochondria, and loss of mitochondrial membrane permeabilization, thereby inducing the release of cytochrome c into the cytosol. However, treatment of HepG2 cells with a pan-caspase inhibitor reversed EEKS-induced apoptosis and growth suppression, indicating that EEKS appears to induce apoptosis though a caspase-dependent mechanism involving both intrinsic and extrinsic apoptotic pathways. In addition, the phosphorylation level of AMP-activated protein kinase (AMPK) was elevated when cells were exposed to EEKS. A specific inhibitor for AMPK attenuated the EEKS-induced activation of caspases, and consequently prevented the EEKS-induced apoptosis and reduction in cell viability. Overall, our findings suggest that EEKS inhibits the growth of HepG2 cells by inducing AMPK-mediated caspase-dependent apoptosis, suggesting the potential therapeutic application of EEKS in the treatment or prevention of cancers.