gebhart/patrepeval huggingface dataset:
Mass spectroscopy-based cancer genotyping of 800 patients enrolled in a personalized cancer medicine registry. (2010)

10503 Background: A challenge in delivering personalized cancer care to the clinic is identifying tumor genotypes that predict response to targeted therapeutics. Methods: In 2008, we established a Personalized Cancer Medicine Registry (PCMR) and began consenting patients for the following: 1) prospective genotyping of their cancer; 2) storing their tumor material for future research; and 3) permission to re-contact them if their tumor genotype fits the profile for a new therapeutic. As of the end of 2009, more than 800 patients were enrolled in the PCMR, including cases of colorectal carcinoma (CRC, n = 199), endometrioid carcinoma (EC, n = 95), thyroid carcinoma (TC, n = 276), bladder carcinoma (n = 80), and malignant melanoma (MM, n = 163 ). Tumor DNA from archival tissue was genotyped using a Sequenom MassArray system. Each sample was analyzed using a panel (320 assays) that detects known mutations in 29 genes. Clinical and genotyping data are stored in a web-interfaced, customized SQL database. Results: 95% of approached patients consented to registry enrollment. Archival tumor suitable for analysis was obtained in 95% of cases. Mutations in EC include PIK3CA (21%), CTNNB1 (13%), KRAS (11%), FBXW7 (5%), TP53 (5%), AKT1 (4%), FGFR2 (3%), NRAS (1%) and PDGFRA (1%); 14 cases harbor 2 or more mutations. Among cutaneous MM we found mutations in BRAF (47%; 10.8% other than V600E), NRAS (13%), CTNNB1 (3%), PIK3CA (2%), AKT1 (1%) and MEK2 (1%). In CRC we found mutations in KRAS (30%), TP53 (16%), PIK3CA (12%), NRAS / BRAF / FBXW7 (3% each), CTNNB1 (2%), and MEK1 / AKT1 / AKT2 / RET (1% each). Remarkably, 10 of 14 CRC tumors (71%) with a PIK3CA mutation also have a KRAS mutation. In TC, we found mutations of BRAF (63%), RET-PTC (7%), and PIK3CA/KRAS/NRAS/HRAS (1.5% each). Conclusions: Prospective tumor genotyping for PCMR patients reveals a remarkable diversity of potentially druggable mutations, knowledge of which will help in clinical trial enrollment. While rare in the examined tumors, mutations in FGFR2, MEK1/2, AKT1/2, PDGFRA and RET could be targeted as part of individualized cancer treatments. In CRC, the common overlap of PIK3CA mutations with KRAS mutations may negatively impact response to inhibitors of the PI3 kinase pathway. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Novartis, Sequenom MolecularMD Novartis, Sequenom Novartis
Battery-Based Energy Storage Systems for Catenary-Free Electric Trains (2018)

This paper focuses on three alternative railway systems (i.e., railway, urban metro and city tram). An approach to assess the size of an on-board energy storage unit is proposed. The unit is designed to supply the three trains along a catenary-free track. The equations of motion are formulated in a common case. The approach solves the system of equations by means of an optimization procedure where a set of constraints on the representative variables is assigned. Service duty cycle and energy requirements are characteristics of the three alternative systems. The results of the numerical simulations focus on the design of a battery-based storage unit to be equipped in the rolling stock vehicles. Specifically, the performance required to the storage units in the three alternative configurations are investigated and compared. Some final notes pointed out the impact of the design constraints on the unit sizing.
Integrated Weed Management in Direct Seeded Spring Sown Rice under Rainfed Low Valley Situation of Uttaranchal (2001)

Pendimethalin at 1.0 kg ha−1+fann wastes as mulch (7.5 t ha−1) supplemented with one hand weeding at 45 days after sowing (DAS) decreased weed density, dry matter production and gave highest weed control efficiency (91.3%) which was comparable to farmers' practice of hand weeding at 30, 60 and 90 DAS. This treatment also produced the highest grain (2439 kg ha−1) and straw yields (3740 kg ha−1). Pre-emergence application of pendimethalin at 1.0 kg ha−1 supplemented with post-emergence application of 2, 4–0 was economically most beneficial for controlling the weeds as it gave highest net return (Rs. 6967 ha−1) and benefit: cost ratio (1.9).
Hyperlipidemia, Diabetes and the Heart (2002)

Diabetes mellitus is a common health problem throughout the world. According to the World Health Organization statistics, the global prevalence of diabetes mellitus is approximately 155 million, which is expected to increase to 300 million in the year 2025 (1). The prevalence of diabetes is increasing signiﬁcantly in the United States (2). According to the Third National Health and Nutrition Examination Survey (NHANES III), which was conducted between 1988 and 1994, there are 10.2 million diagnosed and 5.4 million undiagnosed diabetic adult patients in the United States based on American Diabetes Association criteria (3). Diabetes is even more common in certain ethnic groups. African Americans, Native Americans, and Hispanic Americans have a two-to sixfold greater prevalence of diabetes when compared with white non-Hispanic Americans (3,4).
Characterization Analytic Method Specifying the Steel X10CRNITI18-10 Cylinder Surface Layer Quality Hardened by a Traveling Sphere (2016)

A traveling sphere by an elastic cylinder surface boundary problem is considered. At a contact zone the friction force and adhesive bond areas are supposed. The received solution enabled to estimate a plastic deformation area. The experimental and calculation data comparison found the acceptable accuracy of plastic deformation depth estimation. The devised methodology makes it possible to estimate the radius joining points depth of the plastic deformation by sphere.
The implications of first-order risk aversion for asset market risk premiums (1997)

In an effort to explain simultaneously the excess return predictability observed in equity, bond and foreign exchange markets, we incorporate preferences exhibiting first-order risk aversion into a general equilibrium two-country monetary model. When we calibrate the model to US and Japanese data, we find that first-order risk aversion substantially increases excess return predictability. However, this increased predictability is insufficient to match the data. We conclude that the observed patterns of excess return predictability are unlikely to be explained purely by time-varying risk premiums generated by highly risk averse agents in a complete markets economy.
Induction of a Secondary Structure in the N-Terminal Pentadecapeptide of Human Protamine HP2 through Ni(II) Coordination. An NMR Study (2000)

A solution structure of the Ni(II) complex with the N-terminal pentadecapeptide of human protamine HP2 (HP2(1)(-)(15)) was elucidated with the use of a range of one- and two-dimensional (1)H NMR techniques and molecular modeling. A striking double-loop conformation was found, exhibiting the interactions of the aromatic ring of the Tyr(8) residue with the Ni(II) coordination site at Arg(1), Thr(2), and His(3) residues and the side chain of the Arg(15) residue. In such a conformation, a tendency was found for all five positively charged arginine side chains to locate on one side of the molecule, making possible efficient contacts with the DNA double helix. These structural features, induced indirectly by Ni(II) coordination, are discussed in terms of a possible physiological function of the N-terminus of HP2 as a metal-binding site.
[Alzheimer's disease and trace elements]. (1996)

The etiology of Alzheimer's disease (AD) still remains unknown in spite of intensive research efforts. Recent genetic linkage studies have been reported regarding some candidate genes for familial Alzheimer's disease, such as amyloid precursor protein (APP) gene and apolipoprotein E gene. On the other hand, several risk factors of AD have been revealed by epidemiological studies, including age, family history, head trauma, thyroid dysfunctions and aluminum (Al). Our study of bulk sample analysis in AD brain using neutron activation analysis showed a significant increase of Al and iron (Fe) concentrations, especially in the cerebral cortices compared with age-matched controls. Based on these results, the possible role of trace elements on the etiopathogenesis of AD is discussed.
Higher hospitalization and mortality rates among SARS‐CoV‐2‐infected persons in rural America (2022)

Hospitalization, inpatient mortality, and other adverse outcomes are higher among rural persons with COVID-19, even after adjusting for demographic differences and comorbidities. Further research is needed to understand the factors that drive health disparities in rural populations.
Supplementary material from "The formation of methanol from glycerol bio-waste over doped ceria-based catalysts" (2020)

A series of ceria-based solid solution metal oxides were prepared by co-precipitation and evaluated as catalysts for glycerol cleavage, principally to methanol. The catalyst activity and selectivity to methanol were investigated with respect to the reducibility of the catalysts. Oxides comprising of Ce-Pr and Ce-Zr were prepared, calcined and compared to CeO<sub>2</sub>, Pr<sub>6</sub>O<sub>11</sub> and ZrO<sub>2</sub>. The oxygen storage capacity of the catalysts was examined with analysis of Raman spectroscopic measurements and a temperature programmed reduction, oxidation and reduction cycle. The incorporation of Pr resulted in significant defects, as evidenced by Raman spectroscopy. The materials were evaluated as catalysts for the glycerol to methanol reaction, and it was found that an increased defect density or reducibility was beneficial. The space–time yield of methanol normalized to surface area over CeO<sub>2</sub> was found to be 0.052 mmol<sub>MeOH </sub>m<sup>−2 </sup>h<sup>−1</sup>, and over CeZrO<sub>2</sub> and CePrO<sub>2</sub>, this was to 0.029 and 0.076 mmol<sub>MeOH </sub>m<sup>−2 </sup>h<sup>−1</sup>, respectively. The inclusion of Pr reduced the surface area; however, the carbon mole selectivity to methanol and ethylene glycol remained relatively high, suggesting a shift in the reaction pathway compared to that over ceria. This article is part of a discussion meeting issue ‘Science to enable the circular economy'.This article is part of the discussion meeting issue ‘Science to Enable the Circular Economy'.
NADH: Ubiquinone Oxidoreductase Inhibitors Block Induction of Ornithine Decarboxylase Activity in MCF‐7 Human Breast Cancer Cells* (1998)

Rotenone is the classical inhibitor of NADH: ubiquinone oxidoreductase and its analogue deguelin is a potent inhibitor of 12-O-tetradecanoylphorbol 13-acetate (TPA)-induced ornithine decarboxylase mRNA steady state level and enzyme activity in mouse 308 cells (Gerhäuser et al. 1995). In MCF-7 human breast cancer cells, rotenone, deguelin and two structurally-unrelated miticides (pyridaben and fenazaquin) inhibit not only NADH: ubiquinone oxidoreductase but also induced ornithine decarboxylase activity with IC50 values of < 1 to 70 nM. Rotenone inhibits ornithine decarboxylase activity equally well as induced by TPA, insulin-like growth factor I and 17 beta-oestradiol. Pyridaben is the most potent of the four inhibitors not only for NADH: ubiquinone oxidoreductase activity (bovine heart enzyme) and TPA-induced ornithine decarboxylase activity and mRNA steady state level but also for TPA-induced reactive oxygen species. It is therefore proposed that NADH: ubiquinone oxidoreductase inhibitors block multiple and possibly reactive oxygen species-modulated pathways which regulate ornithine decarboxylase activity.
Automated Tubule Nuclei Quantification and Correlation with Oncotype DX risk categories in ER+ Breast Cancer Whole Slide Images (2016)

Early stage estrogen receptor positive (ER+) breast cancer (BCa) treatment is based on the presumed aggressiveness and likelihood of cancer recurrence. Oncotype DX (ODX) and other gene expression tests have allowed for distinguishing the more aggressive ER+ BCa requiring adjuvant chemotherapy from the less aggressive cancers benefiting from hormonal therapy alone. However these tests are expensive, tissue destructive and require specialized facilities. Interestingly BCa grade has been shown to be correlated with the ODX risk score. Unfortunately Bloom-Richardson (BR) grade determined by pathologists can be variable. A constituent category in BR grading is tubule formation. This study aims to develop a deep learning classifier to automatically identify tubule nuclei from whole slide images (WSI) of ER+ BCa, the hypothesis being that the ratio of tubule nuclei to overall number of nuclei (a tubule formation indicator - TFI) correlates with the corresponding ODX risk categories. This correlation was assessed in 7513 fields extracted from 174 WSI. The results suggests that low ODX/BR cases have a larger TFI than high ODX/BR cases (p < 0.01). The low ODX/BR cases also presented a larger TFI than that obtained for the rest of cases (p < 0.05). Finally, the high ODX/BR cases have a significantly smaller TFI than that obtained for the rest of cases (p < 0.01).
Author response: Kinesin-1, -2, and -3 motors use family-specific mechanochemical strategies to effectively compete with dynein during bidirectional transport (2022)

The motility of three different kinesin-dynein pairs were analyzed and found to be strikingly similar, suggesting that bidirectional transport is not regulated by motor type, but rather by scaffold, adapter, and regulatory proteins.
Rate and Performance Enhancement of LDPC Codes Using Collection of Punctured Codes Decoding (CPCD) (2021)

Background: Low-Density Parity-Check (LDPC) codes have received significant interest in a variety of communication systems due to their superior performance and reasonable decoding complexity. Methods: A novel Collection of Punctured Codes Decoding (CPCD) technique that considers a code as a collection of its punctured codes is proposed. Two forms of CPCD, serial CPCD that decodes each punctured code serially and parallel CPCD that decodes each punctured code in parallel, are discussed. In contrast to other modifications of LDPC decoding documented in the literature, the proposed CPCD technique views a LDPC code as a collection of punctured LDPC codes, where all punctured codes are derived from the original LDPC code by removing different portions of its parity bits. CPCD technique decodes each punctured code separately and exchanges extrinsic information obtained from that decoding among all other punctured codes for their decoding. Hence, as the iterations increase, the information obtained in the decoding of punctured codes improve making CPCD perform better than standard decoding. Results: It is demonstrated that both serial and parallel CPCD have about the same decoding complexity compared with standard Sum Product Algorithm (SPA) decoding. It is also demonstrated that while serial CPCD has about the same decoding delay compared with standard SPA decoding, parallel CPCD can decrease the decoding delay, however, at the expense of processing power. Conclusion: Numerical results demonstrate that CPCD can either significantly improve the performance, or significantly increase the code rate of LDPC codes.
Ytterbium-doped large-core fibre laser with 1 kW of continuous-wave output power (2004)

A ytterbium-doped fibre laser with up to 1 kW of continuous-wave output power at 1.09 µm with a slope efficiency of 80% and a good beam quality (M2=3.4) is reported. The fibre was pumped by two diode-stack sources launched through opposite ends. No undesirable roll-over was observed in output power with increasing pump power.
ChemInform Abstract: Synthesis and Cytotoxicity Studies of New Analogues of Polyamines. (1998)

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.
P2-30-04 - Peptides derived from cereal albumins prevent postprandial hyperglycemia (2019)

[Introduction]Diabetes mellitus is a life-threatening disease because it often leads to various complications such as retinopathy, neuropathy, nephropathy, arteriosclerosis obliterans, and cerebral infarction. The symptoms do not appear until the damage of organs is in a serious stage. Most of the patients are categorized into type 2 diabetes that shows a symptom of insulin resistance and/or deficiency. In order to prevent type 2 diabetes, it is important to control the postprandial hyperglycemia by an appropriate food intake. Wheat albumin that inhibits the activity of mammalian u03b1-amylase suppresses the increase in blood glucose level after starch administration. It has been used as a functional component in Food for Specified Health Uses (FoSHU) in Japan. We have already reported that buckwheat and rice albumins effectively suppress the elevation in blood glucose level. The present study examines if peptides derived from cereal albumins retain the function to prevent postprandial hyperglycemia. [Materials and Methods]Albumins were extracted from buckwheat and rice and purified by ammonium-sulfate precipitation and gel-filtration chromatography. The obtained albumins were hydrolyzed by digestive enzymes. The inhibitory activity of albumins and hydrolysates against u03b1-amylase was measured. The hydrolysates were administered to rats together with starch or glucose. After the administration, the blood was collected from the tail vein at certain intervals. Then, the blood glucose and insulin levels were measured.[Results and Discussion] Buckwheat albumin inhibited the activity ofu03b1-amylase from human and porcine pancreas, but rice albumin did not have the inhibitory activity against mammalian u03b1-amylase. Buckwheat albumin was hydrolyzed to small peptides by digestive enzymes, while rice albumin of 16 kDa was hydrolyzed to a high-molecular peptide of 14 kDa (HMP) and low-molecular peptides (LMP). The peptides from buckwheat retained high inhibitory activity against u03b1-amylase in vitro, and buckwheat-albumin hydrolysates suppressed postprandial hyperglycemia after starch administration in vivo. As intraperitoneal glucose tolerance test (IPGTT) showed that there was no difference in blood glucose level between rice-albumin-administered group and water-administered group, rice albumin would exert its function not in the blood but in the gut. Both HMP and LMP derived from rice albumin prevented the increase in blood glucose level after glucose administration. [Conclusions] Buckwheat and rice albumins retain their function to prevent postprandial hyperglycemia even after digestion. As these albumins are odorless and tasteless, and easily dissolve in water, they can be used as bioactive components in functional foods to prevent diabetes.
Peripheral deletion of T cells in haemodialysis patients (1998)

Many patients with end-stage renal disease have altered host defenses against infectious agents. We have demonstrated that T cells, which play an important role in the immunological response, may undergo apoptosis by the Fas system in uraemia. To elucidate whether gammadelta T cells, which function as a first defense against intracellular pathogens, are altered in number or characteristics in dialysis patients, surface expressions of TCR, LFA-1 and Fas antigen on peripheral T cells were examined by immunofluorescence analysis. We demonstrated that the proportions of peripheral gammadelta T cells are altered significantly in haemodialysis (HD) patients. Interestingly, there were marked differences in the levels of expression of LFA-1 and Fas antigen between the two types of T cells. Moreover, both the expression of LFA-1 and that of Fas antigen were enhanced significantly in HD patients compared with normal controls. These results suggest that circulating gammadelta T cells may be susceptible to activation-induced cell death in comparison with alphabeta T cells in uraemic environments.
Quantitative differential phase contrast (DPC) microscopy with computational aberration correction (2018)

Differential Phase Contrast (DPC) microscopy is a practical method for recovering quantitative phase from intensity images captured with different source patterns in an LED array microscope. Being a partially coherent imaging method, DPC does not suffer from speckle artifacts and achieves 2× better resolution than coherent methods. Like all imaging systems, however, DPC is susceptible to aberrations. Here, we propose a method of algorithmic self-calibration for DPC where we simultaneously recover the complex-field of the sample and the spatially-variant aberrations of the system, using 4 images with different illumination source patterns. The resulting phase reconstructions are digitally aberration-corrected.
Improved inhaled air quality at reduced ventilation rate by control of airflow interaction at the breathing zone with lobed jets (2013)

Inhaled air quality at a reduced supply of clean air was studied by controlling the airflow interaction at the breathing zone of a person using lobed jets as part of personalized ventilation (PV). Experiments were performed in a full-scale test room at 23°C (73.4°F) with a breathing thermal manikin seated at a workstation, with realistic free-convection flow around the body and a normal breathing cycle. The air in the room was mixed with tracer gas R134a. Clean air was supplied isothermally from three nozzles with circular, four-leafed clover, and six-edged star openings of 0.025 m (0.08 ft) equivalent diameter. The nozzles were positioned frontally at the face within the boundary layer and centered to the mouth. The enhancement of inhaled air quality by changing the initial velocity (0.2–0.6 m/s, 0.66–1.97 fps) and the distance from the mouth (0.02–0.06 m, 0.07–0.20 ft) was studied. The control over the interaction between the inserted jets and the free convection flow was efficient. Over 80% clean PV air was measured in inhalation. The worst performing nozzle was the four-leafed clover: its best performance yielded 23% clean air inhalation, at the shortest distance and the highest velocity. The other lobed nozzle, the six-edged star, performed similarly to the circular nozzle.