gebhart/patrepeval huggingface dataset:
Human papillomavirus testing and molecular markers of cervical dysplasia and carcinoma (2007)

Cervical cancer is the second most common cancer in women worldwide. Human papillomavirus (HPV) is the etiologic agent for the vast majority of premalignant and malignant lesions, and high-risk HPV types can be detected in almost all cases of cervical dysplasia and carcinoma. HPV testing has been widely adopted for the triage of patients after a cervical cytology screening test (Papanicolaou smear or liquid-based cervical cytology such as ThinPrep or SurePath) interpretation of atypical squamous cells of undetermined significance (ASCUS), and HPV testing is increasingly used for screening in conjunction with cervical cytology. Although cervical cytology is a highly effective screening test for cancer, it has limited specificity for clinically significant lesions in cases with low-grade cytologic abnormalities. Up to a quarter of all patients may have a false-negative result on the basis of cervical cytology testing alone. This review focuses on HPV testing methods and molecular markers and their clinical relevance. HPV testing and surrogate molecular markers of HPV infection (p16INK4a) may help identify cases that are associated with underlying high-grade premalignant or malignant lesions and may also reduce aggressive treatment of patients with low-grade lesions.
Branched-Chain Amino Acid Ingestion Stimulates Muscle Myofibrillar Protein Synthesis following Resistance Exercise in Humans (2017)

The ingestion of intact protein or essential amino acids (EAA) stimulates mechanistic target of rapamycin complex-1 (mTORC1) signaling and muscle protein synthesis (MPS) following resistance exercise. The purpose of this study was to investigate the response of myofibrillar-MPS to ingestion of branched-chain amino acids (BCAAs) only (i.e., without concurrent ingestion of other EAA, intact protein, or other macronutrients) following resistance exercise in humans. Ten young (20.1 ± 1.3 years), resistance-trained men completed two trials, ingesting either 5.6 g BCAA or a placebo (PLA) drink immediately after resistance exercise. Myofibrillar-MPS was measured during exercise recovery with a primed, constant infusion of L-[ring<sup>13</sup>C<sub>6</sub>] phenylalanine and collection of muscle biopsies pre and 4 h-post drink ingestion. Blood samples were collected at time-points before and after drink ingestion. Western blotting was used to measure the phosphorylation status of mTORC1 signaling proteins in biopsies collected pre, 1-, and 4 h-post drink. The percentage increase from baseline in plasma leucine (300 ± 96%), isoleucine (300 ± 88%), and valine (144 ± 59%) concentrations peaked 0.5 h-post drink in BCAA. A greater phosphorylation status of S6K1<sup>Thr389</sup> (<i>P</i> = 0.017) and PRAS40 (<i>P</i> = 0.037) was observed in BCAA than PLA at 1 h-post drink ingestion. Myofibrillar-MPS was 22% higher (<i>P</i> = 0.012) in BCAA (0.110 ± 0.009%/h) than PLA (0.090 ± 0.006%/h). Phenylalanine Ra was ~6% lower in BCAA (18.00 ± 4.31 μmol·kgBM<sup>-1</sup>) than PLA (21.75 ± 4.89 μmol·kgBM<sup>-1</sup>; <i>P</i> = 0.028) after drink ingestion. We conclude that ingesting BCAAs alone increases the post-exercise stimulation of myofibrillar-MPS and phosphorylation status mTORC1 signaling.
Porosity Tailored Growth of Black Anodic Layers on Magnesium in an Organic Electrolyte (2008)

Thick anodic layers on pure Mg were produced by anodization in a nonaqueous electrolyte. The most promising systems for growth of thick, uniform anodic layers were nominally water-free methanol or ethanol electrolytes containing nitrate ions. The layer thickness shows a linear dependence on the applied voltage and on the anodization time. This nonlimited layer growth, leading to a very high thickness with time (e.g., up to with at for the methanol system), suggests a porous nature of the layer. Scanning electron microscopy examination of the surface morphology indeed reveals nanopores/flakes in the layer. In addition, the porosity of the layer can be tuned by the use of ethanol and methanol mixtures as an anodization bath. The chemical composition of the films was examined by using X-ray photoelectron spectroscopy and energy-dispersive X-ray analysis, which reveals that the anodic layer consists of mainly Mg, O, and C (without toxic or environmentally hazardous species). Furthermore, the layers can be converted into crystalline MgO upon annealing without significant loss in morphology. This type of thick nanoporous layer is a promising candidate for the functionalization of Mg surfaces for different applications.
Alzheimer's disease cells exhibit defective repair of alkylating agent—induced DNA damage (1987)

The most common cause of senile and presenile dementia is Alzheimer's disease, a disorder with an undetermined cause. A number of studies have indicated that neurons from patients with Alzheimer's disease have decreased ribonucleic acid levels and reduced protein synthesis. Recent studies using lymphoblasts from patients with Alzheimer's disease have indicated that these cells are more sensitive to deoxyribonucleic acid (DNA)-alkylating agents. We have used cell survival, unscheduled DNA synthesis, and alkaline elution to assess the capacity for DNA repair in skin fibroblasts from normal control subjects, control subjects with central nervous system disease, and patients with Alzheimer's disease. Our results indicate that the Alzheimer's disease cells, unlike normal cells, fail to repair methylmethane sulfonate-induced DNA damage. Both normal and Alzheimer's disease cells are able to ameliorate the effects of ultraviolet light. These results indicate that a specific pathway for DNA repair is affected in Alzheimer's disease. The repair defect may be related to the cause of the disease or may be the cause of the disease.
Computationally designed libraries for rapid enzyme stabilization (2014)

The ability to engineer enzymes and other proteins to any desired stability would have wide-ranging applications. Here, we demonstrate that computational design of a library with chemically diverse stabilizing mutations allows the engineering of drastically stabilized and fully functional variants of the mesostable enzyme limonene epoxide hydrolase. First, point mutations were selected if they significantly improved the predicted free energy of protein folding. Disulfide bonds were designed using sampling of backbone conformational space, which tripled the number of experimentally stabilizing disulfide bridges. Next, orthogonal in silico screening steps were used to remove chemically unreasonable mutations and mutations that are predicted to increase protein flexibility. The resulting library of 64 variants was experimentally screened, which revealed 21 (pairs of) stabilizing mutations located both in relatively rigid and in flexible areas of the enzyme. Finally, combining 10-12 of these confirmed mutations resulted in multi-site mutants with an increase in apparent melting temperature from 50 to 85°C, enhanced catalytic activity, preserved regioselectivity and a >250-fold longer half-life. The developed Framework for Rapid Enzyme Stabilization by Computational libraries (FRESCO) requires far less screening than conventional directed evolution.
Thermoluminescence of Solids (1985)

McKeever gives us a comprehensive survey of thermoluminescence, an important, versatile, and widely used experimental technique. Bringing together previously isolated specialized approaches, he stresses the importance of the solid state aspects of the phenomenon. The book contains chapters on analysis and special properties, on instrumentation, and on the variety of defect reaction - using the alkali halides and SiO2 as examples - that can take place within a material to yield thermoluminescence. Three chapters concerning applications discuss the features of the solid state reactions to expain some of the properties observed in practice.
Optimization of Fracture Cleanup Using Flowback Analysis (1998)

Abstract A field study in north-central Texas shows how flowback procedures can be optimized to improve fracture cleanup and well productivity in low-permeability formations. Load water and polymer returns from 15 Barnett shale hydraulic fractures were analyzed and quantified. These were massive hydraulic fracturing treatments (1.4 million lbm of sand and 10,000 to 15,000 bbl of fluid) in an ultra-low-permeability (0.001 md) formation. These wells were fractured using low gel loading borate-crosslinked fluid. Well productivity is correlated with fracture cleanup. Aggressive flowback procedures improved fracture cleanup and well productivity. The maximum flowback rate was increased from 0.6 bbl/min at the beginning of the field test, to as high as 6 bbl/min. Polymer returns at conservative flowback rates, &amp;lt; 3 bbl/min, averaged 31 ± 6% of the total amount pumped on the job. Polymer returns from wells aggressively flowed back, &amp;gt;3 bbl/min, averaged 46 ± 9%. Aggressively flowed back wells produced on average 19% more gas over the first 180 days of production than conservatively flowed back offsets. Recovery of polymer continued throughout the early stages of production in addition to the polymer returned during flowback. Significant polymer concentrations were recorded in produced water samples collected up to five months following the treatment. Recovery during production can yield 10 to 13 % of the polymer pumped during the job in addition to the amount recovered during flowback. Similar patterns of polymer recovery are observed when the Barnett shale results are compared with those from the Codell formation (0.010 md) in Colorado. This is in spite of differences in treatment size, job design, and fluid selection. Therefore, it is plausible that the results from these two studies can be generalized, and applied to many other low-permeability formations. Significant differences are observed when the Barnett results are compared with those from the Cotton Valley formation in east Texas. These differences are primarily due to the production of water by the latter formation.
Thrombospondin‐1 inhibits VEGF levels in the ovary directly by binding and internalization via the low density lipoprotein receptor‐related protein‐1 (LRP‐1) (2006)

VEGF is a potent pro-angiogenic factor whose effects are opposed by a host of anti-angiogenic proteins, including thrombospondin-1 (TSP-1). We have previously shown that VEGF has important extravascular roles in the ovary and that VEGF and TSP-1 are inversely expressed throughout the ovarian cycle. To date, however, a causal interaction between TSP-1 and VEGF has not been identified. Here, we show that TSP-1 has a direct inhibitory effect on VEGF by binding the growth factor and internalizing it via LRP-1. Mice lacking TSP-1 are subfertile and exhibited ovarian hypervascularization and altered ovarian morphology. Treatment of ovarian cells with TSP-1 decreased VEGF levels and rendered the cells more susceptible to TNFalpha-induced apoptosis. Knockdown of TSP-1, through RNA interference, resulted in overexpression of VEGF and reduced cytokine-induced apoptosis. In conclusion, we demonstrate a direct inhibitory effect of TSP-1 on VEGF in the ovary. TSP-1's regulation of VEGF appears to be an important mediator of ovarian angiogenesis and follicle development.
IL‐1 receptor antagonist in metabolic diseases: Dr Jekyll or Mr Hyde? (2006)

Interleukin-1 receptor antagonist (IL-1ra) has been shown to play a crucial role in the prevention of various inflammatory diseases. There is also convincing evidence that IL-1ra is able to counteract inflammatory effects of IL-1 members implicated in insulin resistance and diabetes. However, the use of knock-out animal models provides evidence to the contrary and the role of IL-1ra in obesity-linked anomalies remains controversial. This minireview gets an insight into recent findings on the implication of IL-1ra and its gene polymorphism in diabetes and obesity, discusses the potential dual effects of IL-1ra observed in different models, and comments on future directions.
RAC1 P29S is a spontaneously activating cancer-associated GTPase (2013)

RAC1 is a small, Ras-related GTPase that was recently reported to harbor a recurrent UV-induced signature mutation in melanoma, resulting in substitution of P29 to serine (RAC1(P29S)), ranking this the third most frequently occurring gain-of-function mutation in melanoma. Although the Ras family GTPases are mutated in about 30% of all cancers, mutations in the Rho family GTPases have rarely been observed. In this study, we demonstrate that unlike oncogenic Ras proteins, which are primarily activated by mutations that eliminate GTPase activity, the activated melanoma RAC1(P29S) protein maintains intrinsic GTP hydrolysis and is spontaneously activated by substantially increased inherent GDP/GTP nucleotide exchange. Determination and comparison of crystal structures for activated RAC1 GTPases suggest that RAC1(F28L)--a known spontaneously activated RAC1 mutant--and RAC1(P29S) are self-activated in distinct fashions. Moreover, the mechanism of RAC1(P29S) and RAC1(F28L) activation differs from the common oncogenic mutations found in Ras-like GTPases that abrogate GTP hydrolysis. The melanoma RAC1(P29S) gain-of-function point mutation therefore represents a previously undescribed class of cancer-related GTPase activity.
CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer (2015)

Cancer is a heterogeneous disease with different combinations of genetic alterations driving its development in different individuals. We introduce CoMEt, an algorithm to identify combinations of alterations that exhibit a pattern of mutual exclusivity across individuals, often observed for alterations in the same pathway. CoMEt includes an exact statistical test for mutual exclusivity and techniques to perform simultaneous analysis of multiple sets of mutually exclusive and subtype-specific alterations. We demonstrate that CoMEt outperforms existing approaches on simulated and real data. We apply CoMEt to five different cancer types, identifying both known cancer genes and pathways, and novel putative cancer genes.
Purine-Rich Foods, Dairy and Protein Intake, and the Risk of Gout in Men (2004)

Higher levels of meat and seafood consumption are associated with an increased risk of gout, whereas a higher level of consumption of dairy products is associated with a decreased risk. Moderate intake of purine-rich vegetables or protein is not associated with an increased risk of gout.
Studies on the mechanism of action of halofenate (1977)

This paper reviews most of the clinical studies on the mode of action of halofenate, an established hypolipidemichypouricemic agent in man. In yeast cutlures and in isolated rat adipocytes, halofenate was found to inhibit the conversion of pyruvate to acetyl CoA. While pyruvate dehydrogenase was inhibited in vitro, halofenate also inhibited the activety of various other isolated enzymes. In rats maintained on halofenate in the diet (0.02-0.10%) for 2-14 days, there were 20-40% decreases in plasma cholesterol, trigly cerides, phospholipids, and free fatty acids. Inhibition of liver HMG-CoTA reductase does not appear to account for the hypocholesterolemic effect, and activation of mitochondrial alpha-glycerophosphate dehydrogenase does not explain the hypotriglyceridemic action. Kinetic measurements of the serum appearance and disappearance of triglycerides in drug-treated rats suggest that the hypotriglyceridemic activity is due to a net inhibition of hepatic triglyceride synthesis. Reduction of very low density lipoprotein (VLDL) and high density lipoprotein (HDL) levels in rats with sucrose-induced hyperlipidemia and normalization of the altered apolipoprotein profiles are in accord with the effects of halofenate on plasma triglyceride and cholesterol levels. The reduced insulin-to-glucagon ratio observed in Zucker obese hyperlipemic rats is also consistent with halofenat's hypotriglyceridemic activity. Preliminary experiments in rats on the mechanism of its hypoglycemic activity, observed in some diabetic hyperlipidemic patients, indicate that halofenate acts differently than conventional oral hypoglycemic agents. Some, but not all, of the effects of halofenate were observed with clofibrate at two to ten times higher levels.
Reaction Mechanism of Monoacyl- and Bisacylphosphine Oxide Photoinitiators Studied by 31P-, 13C-, and 1H-CIDNP and ESR (1996)

31P-NMR-CIDNP (CIDNP = chemically induced dynamic nuclear polarization) spectroscopy was applied for the first time to investigate the formation and reaction of phosphorus-centered radicals obtained from phosphorus-containing photoinitiators. 13C-NMR- and 1H-NMR-CIDNP and ESR spectroscopies were used as complementary experimental techniques for the elucidation of the photochemistry of these compounds. The large hyperfine coupling constants of the 31P-nucleus results in a violation of Kaptein's rules, which is the only observation of this kind in 13C-NMR-CIDNP spectra reported so far. Interpretation of the CIDNP spectra, using a modification of Kaptein's rules for the 13C-NMR- and 1H-NMR-CIDNP, consistently shows that all compounds investigated undergo a photoinduced cleavage of the carbonyl−phosphinoyl bond from a triplet state. The fate of the primary radicals is discussed, and it is unambiguously shown by trapping experiments that the novel bisacylphosphine oxide photoinitiators give four radicals in a stepwise process.
Insulin-Like Growth Factor Binding Protein-3 Leads to Insulin Resistance in Adipocytes (2005)

IGFBP-3 may contribute to insulin resistance in adipocytes.
Recent advances and developments in the treatment of acute renal failure (2002)

Acute renal failure is commonly encountered in contemporary medical practice. The most severe form of acute renal failure is often referred to as acute tubular necrosis (ATN). The ATN syndrome results in loss of most kidney function for a period of several days to a few weeks. The current mortality rate of ATN is ~ 50% and has not changed significantly in recent decades. Most ATN results from either ischaemic or nephrotoxic damage to the kidney. Subsequently, either apoptosis or necrosis results in death of renal tubular epithelium and loss of most renal function. This review will focus on several patents that exhibit diverse strategies to prevent, attenuate or hasten recovery from ATN.
LSOM: A Link State protocol Over MAC addresses for metropolitan backbones using Optical Ethernet switches (2003)

This paper presents a new protocol named "Link State Over MAC" (LSOM) for Optical Ethernet switches to allow the use of active loop topologies, like meshes, in Metropolitan Area Networks (MAN) or even Wide Area Networks (WAN) backbone. In this respect, LSOM is an alternative to a ring topology as proposed in draft IEEE 802.17 Resilient Packet Ring (RPR) or a tree topology using IEEE802. 1D Rapid Spanning Tree Protocol (RSTP). LSOM provides higher scalability and is able to achieve better bandwidth utilization and lower latency than RSTP and RPR. Simulation results for 4-node and 9-node topologies show that LSOM can improve throughput over RPR by a factor of up to 1.7. Furthermore, full freedom to choose any MAN active topology allows an effective use of the available dark fiber resources.
Multifunctional Magnetic Nanoparticles: Design, Synthesis, and Biomedical Applications (2009)

The combination of nanotechnology and molecular biology has developed into an emerging research area: nanobiotechnology. Magnetic nanoparticles are well-established nanomaterials that offer controlled size, ability to be manipulated externally, and enhancement of contrast in magnetic resonance imaging (MRI). As a result, these nanoparticles could have many applications in biology and medicine, including protein purification, drug delivery, and medical imaging. Because of the potential benefits of multimodal functionality in biomedical applications, researchers would like to design and fabricate multifunctional magnetic nanoparticles. Currently, there are two strategies to fabricate magnetic nanoparticle-based multifunctional nanostructures. The first, molecular functionalization, involves attaching antibodies, proteins, and dyes to the magnetic nanoparticles. The other method integrates the magnetic nanoparticles with other functional nanocomponents, such as quantum dots (QDs) or metallic nanoparticles. Because they can exhibit several features synergistically and deliver more than one function simultaneously, such multifunctional magnetic nanoparticles could have unique advantages in biomedical applications. In this Account, we review examples of the design and biomedical application of multifunctional magnetic nanoparticles. After their conjugation with proper ligands, antibodies, or proteins, the biofunctional magnetic nanoparticles exhibit highly selective binding. These results indicate that such nanoparticles could be applied to biological medical problems such as protein purification, bacterial detection, and toxin decorporation. The hybrid nanostructures, which combine magnetic nanoparticles with other nanocomponents, exhibit paramagnetism alongside features such as fluorescence or enhanced optical contrast. Such structures could provide a platform for enhanced medical imaging and controlled drug delivery. We expect that the combination of unique structural characteristics and integrated functions of multicomponent magnetic nanoparticles will attract increasing research interest and could lead to new opportunities in nanomedicine.
The Annexins and Exocytosis (1992)

The annexins are a group of homologous proteins that bind phospholipids in the presence of calcium. They may provide a major pathway for communication between cellular membranes and their cytoplasmic environment. Annexins have a characteristic "bivalent" activity in the sense that they can draw two membranes together when activated by calcium. This has led to the hypothesis that certain members of this protein family may initiate contact and fusion between a secretory vesicle membrane and the plasma membrane during the process of exocytosis.
Data-driven face cartoon stylization (2014)

This paper presents a data-driven framework for generating cartoon-like facial representations from a given portrait image. We solve our problem by an optimization that simultaneously considers a desired artistic style, image-cartoon relationships of facial components as well as automatic adjustment of the image composition. The stylization operation consists of two steps: a face parsing step to localize and extract facial components from the input image; a cartoon generation step to cartoonize the face according to the extracted information. The components of the cartoon are assembled from a database of stylized facial components. Quantifying the similarity between facial components of input and cartoon is done by image feature matching. We incorporate prior knowledge about photo-cartoon relationships and the optimal composition of cartoon facial components extracted from a set of cartoon faces to maintain a natural and attractive look of the results.
Near‐Infrared‐Resonant Gold/Gold Sulfide Nanoparticles as a Photothermal Cancer Therapeutic Agent (2010)

The development and optimization of near-infrared (NIR)-absorbing nanoparticles for use as photothermal cancer therapeutic agents has been ongoing. This work exploits the properties of gold/gold sulfide NIR-absorbing nanoparticles (approximately 35-55 nm) that provide higher absorption (98% absorption and 2% scattering for gold/gold sulfide versus 70% absorption and 30% scattering for gold/silica nanoshells) as well as potentially better tumor penetration. The ability to ablate tumor cells in vitro and efficacy for photothermal cancer therapy is demonstrated, and an in vivo model shows significantly increased long-term, tumor-free survival. Furthermore, enhanced circulation and biodistribution is observed in vivo. This class of NIR-absorbing nanoparticles has the potential to improve upon photothermal tumor ablation for cancer therapy.