gebhart/patrepeval huggingface dataset:
Hydrothermal synthesis, structure determination from powder data of a three-dimensional zirconium diphosphonate with an exceptionally high thermal stability: Zr(O3P-(CH2)-PO3) or MIL-57 (2002)

Zr(O3P-(CH2)-PO3) or MIL-57 was prepared in a pure form under hydrothermal conditions (3 days, 493 K, autogenous pressure). Its structure was solved ab initio from laboratory powder X-ray diffraction data. This compound is monoclinic (space group P21 (no. 14)) with a = 7.589(1), b = 8.110(1), c = 5.056(1) Å, β = 103.934(1)°, V = 302.14(1) Å3 and Z = 2. Its three-dimensional structure is built up from zirconium(IV) octahedra linked together via diphosphonate groups. This delimits a three-dimensional network with three and seven-member-ring tunnels along the c axis. The thermal behaviour, deduced from TGA and X-ray thermodiffractometry has been investigated and reveals that MIL-57 is stable under air atmosphere up to 1023 K, which is the highest temperature reported to date for a hybrid inorganic–organic solid. A brief comparison between structures of MIL-57 and ZrP2O7 is also reported.
Three Dimensional Imaging Using T-ray (2002)

For over a decade it has been known that terahertz time-domain spectroscopy systems can be used to determine the frequency dependent optical properties of materials in the submillimeter wavelength regime. More recently 2 dimensional (2D) THz imaging systems’,’ have been demonstrated for a diverse range of applications. However, using these imaging techniques the three-dimensional structure of the object has been unavailable until now. In particular the effects of variations in topography and the far-infrared optical properties of the sample have been indistinguishable. T-ray computed tomography (T-ray CT) draws inspiration from the now ubiquitous X-ray CT system. The T-ray CT system hardware is a relatively simple extension of modern transmission mode THz imaging systems. A 2D image is obtained at a number of projection angles. This data can then be used to reconstruct the object in 3D. The mathematical field of inverse problems
Suppression of HIV Type 1 Replication by a Dominant-Negative Ets-1 Mutant (2000)

Activity of the distal region of the human immunodeficiency virus (HIV-1) long terminal repeat (LTR), which contains binding sites for the Ets-1 and USF-1 proteins, is integral for HIV-1 replication. The Ets-1 and USF-1 proteins play a critical role in the activity of the HIV-1 LTR distal enhancer region, as indicated by the potent dominant negative effect of a mutant Ets-1 lacking trans-activation domains on the transcriptional activity of the LTR. To determine the biological relevance of the Ets-1 and USF-1 proteins in HIV-1 replication, we examined the effect of expression of the dominant-negative mutant of Ets-1 (dnEts-1) on HIV-1 infection of T cells. We demonstrated that expression of dnEts markedly suppressed HIV-1 infection of a T cell line. This finding indicates that formation of a transcriptionaly active USF-1/Ets-1 complex is important in the productive infection of cells by HIV-1, and suggests that inhibition of the interaction between USF-1 and Ets-1 with the HIV-1 LTR may provide a new target for anti-HIV-1 gene therapy.
Wet oxidation of GeSi at 700 °C (1992)

About 500-nm-thick films of Ge0.36Si0.64 and Ge0.28Si0.72 grown epitaxially on (100)Si have been oxidized at 700 °C in wet ambient. A uniform GexSi1−xO2 oxide layer forms with a smooth interface between it and the unoxidized GexSi1−x layer below. The composition and structure of that layer remains unchanged as monitored by backscattering spectrometry or cross-sectional transmission electronic microscopy. The oxide of both samples grows as square root of oxidation duration. The parabolic rate constant increases with the Ge content and is larger than that for wet oxidation of pure Si at the same temperature. The absence of a regime of linear growth at this relatively low temperature indicates a much enhanced linear rate constant.
Exercise Inhibits Epithelial Sodium Channels in Patients with Cystic Fibrosis (2001)

The aim of this study was to determine the effects of a single exercise bout on luminal Cl(-) and Na(+) conductance in the respiratory epithelium of patients with cystic fibrosis (CF). In nine patients with CF and nine healthy control subjects, the transepithelial electrical potential difference (PD) of the nasal respiratory epithelium was recorded, first at rest and then during moderate-intensity exercise. Under both conditions, PD was first measured while superfusing the epithelium with isotonic saline. Then, the effects of amiloride and amiloride plus low chloride plus isoproterenol were determined. Exercise resulted in a significant lower PD compared with rest in patients with CF (-6.6 +/- 16.6 mV versus -33.6 +/- 10.0 mV, p < 0.0001) and control subjects (0.1 +/- 8.7 mV versus -7.1 +/- 5.1 mV, p < 0.01). The effects of amiloride on PD were reduced during exercise compared with rest in patients with CF (+15.8 +/- 9.5 mV versus +26.1 +/- 11.0 mV, p < 0.01) and control subjects (+5.8 +/- 4.8 mV versus +10.0 +/- 3.1 mV, p < 0.01). There was no effect of exercise on chloride conductance in patients with CF and control subjects. We conclude that moderate-intensity exercise partially blocks the amiloride-sensitive sodium conductance in the respiratory epithelium. The inhibition of luminal sodium conductance could increase water content of the mucus in the CF lung during exercise and may, in part, explain the beneficial effects of exercise in patients with CF.
Dietary restriction reduces insulin-like growth factor I levels, which modulates apoptosis, cell proliferation, and tumor progression in p53-deficient mice. (1997)

Diet contributes to over one-third of cancer deaths in the Western world, yet the factors in the diet that influence cancer are not elucidated. A reduction in caloric intake dramatically slows cancer progression in rodents, and this may be a major contribution to dietary effects on cancer. Insulin-like growth factor I (IGF-I) is lowered during dietary restriction (DR) in both humans and rats. Because IGF-I modulates cell proliferation, apoptosis, and tumorigenesis, the mechanisms behind the protective effects of DR may depend on the reduction of this multifaceted growth factor. To test this hypothesis, IGF-I was restored during DR to ascertain if lowering of IGF-I was central to slowing bladder cancer progression during DR. Heterozygous p53-deficient mice received a bladder carcinogen, p-cresidine, to induce preneoplasia. After confirmation of bladder urothelial preneoplasia, the mice were divided into three groups: (a) ad libitum; (b) 20% DR; and (c) 20% DR plus IGF-I (IGF-I/DR). Serum IGF-I was lowered 24% by DR but was completely restored in the IGF-I/DR-treated mice using recombinant IGF-I administered via osmotic minipumps. Although tumor progression was decreased by DR, restoration of IGF-I serum levels in DR-treated mice increased the stage of the cancers. Furthermore, IGF-I modulated tumor progression independent of changes in body weight. Rates of apoptosis in the preneoplastic lesions were 10 times higher in DR-treated mice compared to those in IGF/DR- and ad libitum-treated mice. Administration of IGF-I to DR-treated mice also stimulated cell proliferation 6-fold in hyperplastic foci. In conclusion, DR lowered IGF-I levels, thereby favoring apoptosis over cell proliferation and ultimately slowing tumor progression. This is the first mechanistic study demonstrating that IGF-I supplementation abrogates the protective effect of DR on neoplastic progression.
Gene Therapy for Diabetic Retinopathy – Targeting the Renin-Angiotensin System (2013)

acterized by pathological neovascularization. Vision loss can occur from vitreous hemorrhage or from tractional retinal detachment Despite recent developments in the pharmacotherapy of DR, treatment options for patients with DR are still limited. Laser photocoagulation, the primary treatment option for patients with PDR, is still considered gold standard therapy for the treatment of PDR. Although this treatment slows the loss of vision in those with PDR, it does not represent a cure, and is in itself a cell destructive therapy. Corticosteroids and anti-VEGF agents have shown promising results with regard to prevention of neovascularization, but remain limited in use due to their short-duration effects. More importantly, none of these agents have been able to substitute for the durability and effectiveness of laser mediated panretinal photocoagulation in preventing vision loss in the late stages of DR.
Subcellular localization of CD80 receptors is dependent on an intact cytoplasmic tail and is required for CD28-dependent T cell costimulation (1996)

CD28 provides a major costimulatory signal to T cells when it is cross-linked with mAb, immobilized recombinant ligand (CD80Ig or CD86Ig), or ligand-bearing cells but not when it is bound by specific Fab fragments or monomeric ligand. We wanted to determine how monomeric CD80 could cross-link CD28 since CD80 is expressed as a monomer on the surface of APC. We found that CD80 may interact with the actin-based cytoskeleton. To test whether the interaction of CD80 with the cytochalasin B-sensitive cytoskeleton was necessary for T cell costimulation through CD28, we constructed a tailless form of CD80 and generated stable transfectants of Chinese hamster ovary epithelial cells and Reh B cells expressing either the tailless or wild-type CD80 molecules. Unlike control cells expressing wild-type CD80, the tailless CD80 transfectants expressing equivalent levels of surface CD80 were not able to provide a costimulatory signal for anti-CD3-induced T cell proliferation, up-regulation of CD25 (IL-2Ralpha) expression, or the induction of IL-2 secretion. Thus, the cytoplasmic tail of CD80 apparently is required to signal T cells. Confocal microscopic studies revealed that wild-type CD80 and tailless CD80 have different patterns of subcellular distribution in both epithelial and lymphoid cells. Furthermore, T cell contact induces more patching and capping of CD80 in wild-type CD80-expressing cells than in tailless CD80-expressing cells. This suggests that the cytoplasmic region of CD80 functions to localize CD80 in complexes required for effective T cell costimulation.
Conditional ROCK Activation In vivo Induces Tumor Cell Dissemination and Angiogenesis (2004)

Progression of tumors to invasive and metastatic forms requires that tumor cells undergo dramatic morphologic changes, a process regulated by Rho GTPases. Elevated expression of RhoA and RhoC, as well as the Rho effector proteins ROCK I and ROCK II, are commonly observed in human cancers and are often associated with more invasive and metastatic phenotypes. To examine how ROCK contributes to the progression of solid tumors, we established a conditionally activated form of ROCK II by fusing the kinase domain to the estrogen receptor hormone-binding domain (ROCK:ER). ROCK:ER-expressing colon carcinoma cells grown as tumors in immunocompromised nude mice organized into discrete clusters surrounding blood vessels. However, ROCK:ER activation resulted in the aggressive dissemination of tumor cells into the surrounding stroma, indicating that increased ROCK signaling is sufficient to promote invasion from solid tumors. In addition, tumors in which ROCK:ER was activated were more highly vascularized, indicating that ROCK contributes to tumor angiogenesis. ROCK:ER activation resulted in changes to epithelial morphology and organization that facilitated motility in vitro, likely by inducing the redistribution of proteins such as ezrin, as well as adherens junction and extracellular matrix-binding proteins. These results suggest that ROCK inhibitors would be useful antimetastatic and antiangiogenic chemotherapeutic agents in tumors associated with elevated RhoA, RhoC, ROCK I, or ROCK II expression.
Kinetics of furfural production by dehydration of xylose in a biphasic reactor with microwave heating (2010)

In this paper we report a kinetic model for the dehydration of xylose to furfural in a biphasic batch reactor with microwave heating. There are four key steps in our kinetic model: (1) xylose dehydration to form furfural; (2) furfural reaction to form degradation products; (3) furfural reaction with xylose to form degradation products, and (4) mass transfer of furfural from the aqueous phase into the organic phase (methyl isobutyl ketone - MIBK). This kinetic model was used to fit experimental data collected in this study. The apparent activation energy for xylose dehydration is higher than the apparent activation energy for the degradation reactions. The biphasic system does not alter the fundamental kinetics in the aqueous phase. The organic layer, which serves as “storage” for the extracted furfural, is crucial to maximize product yield. Microwave heating does not change the kinetics compared to heating by conventional means. We use our model to describe the optimal reaction conditions for furfural production. These conditions occur in a biphasic regime at higher temperatures (i.e. 170 °C) and short reaction times. We estimate that at these conditions furfural yields in a biphasic system can reach 85%. At these same conditions in a monophase system furfural yields are only 30%.
miR-34a repression of SIRT1 regulates apoptosis (2008)

MicroRNA 34a (miR-34a) is a tumor suppressor gene, but how it regulates cell proliferation is not completely understood. We now show that the microRNA miR-34a regulates silent information regulator 1 (SIRT1) expression. MiR-34a inhibits SIRT1 expression through a miR-34a-binding site within the 3' UTR of SIRT1. MiR-34 inhibition of SIRT1 leads to an increase in acetylated p53 and expression of p21 and PUMA, transcriptional targets of p53 that regulate the cell cycle and apoptosis, respectively. Furthermore, miR-34 suppression of SIRT1 ultimately leads to apoptosis in WT human colon cancer cells but not in human colon cancer cells lacking p53. Finally, miR-34a itself is a transcriptional target of p53, suggesting a positive feedback loop between p53 and miR-34a. Thus, miR-34a functions as a tumor suppressor, in part, through a SIRT1-p53 pathway.
Risk Factors for Prostate Cancer (1993)

It appears that prostate cancer results from an interplay between endogenous hormones and environmental influences that include, most prominently, dietary fat.
“Artificial Lotus Leaf” Prepared Using a 1945 Patent and a Commercial Textile (2006)

Two polyester textiles, conventional polyester and microfiber polyester fabrics, were hydrophobized using a simple, patented water-repellent silicone coating procedure. Water contact angles on these two surfaces are theta(A)/theta(R) = 151 degrees/140 degrees and theta(A)/theta(R) = 170 degrees/165 degrees, respectively. A smooth surface of this of this coating exhibits theta(A)/theta(R) = 110 degrees/100 degrees. The binary length scale topography (approximately 2 microm/ approximately 50 microm) of the microfiber polyester is responsible for relieving receding contact line pinning and promoting water repellency that is superior to that of the lotus leaf. The recent literature on superhydrophobic surfaces is criticized for neglecting literature of the 1940s.
Prospective investigation of positron emission tomography in lung nodules. (1998)

FDG-PET can accurately characterize indeterminate SPNs. PET imaging provides a noninvasive method to evaluate indeterminate SPNs, which can reduce the need for invasive tissue biopsy.
Assessment of major histocompatibility complex class I interaction with Epstein‐Barr virus and human immunodeficiency virus peptides by elevation of membrane H‐2 and HLA in peptide loading‐deficient cells (1992)

Earlier findings indicate that peptides can affect the expression of major histocompatibility complex (MHC) class I molecules on the surface of cells with defective peptide loading mechanism. We have used peptide induced increase of class I antigen expression to assess peptide interaction with MHC class I molecules. A panel of 41 overlapping synthetic peptides derived from the human immunodeficiency virus-1 (HIV-1) gag protein and 33 nonoverlapping peptides from Epstein-Barr virus (EBV) proteins EBNA-1, 2, 3, 4, 5, 6, LMP, BZLF2, BILF2, BSLF2, BALF4 and BcLF1 was assessed for the ability to enhance the expression of HLA-A2.1, H-2Db, Kb and Dd on the murine RMA-S and human 721.174/T2 (.174/T2) lines by indirect immunofluorescence. Considering doubling of the fluorescence intensity in the peptide-treated samples as positivity, 6 of 39 HIV and 1 of 32 EBV peptides were found to bind to A2.1, 6 of 39 HIV gag and 7 of 16 EBV peptides to Db, 8 of 39 HIV gag and 5 of 16 EBV peptides to Kb and 2 of 39 HIV gag and 1 of 17 EBV peptides to Dd. The sensitivity of the method is comparable to the in vitro class I assembly assay with conformation-dependent monoclonal antibody and is more discriminating than the solid-phase assay. Due to its simplicity this method can also serve for testing large peptide panels for binding capacity to various class I molecules. Moreover, the method provides information about the relevance of in vitro tests for class I assembly in living cells.
ATP‐Independent Formation of Hydrocarbons Catalyzed by Isolated Nitrogenase Cofactors (2012)

Reduce to produce: Molybdenum- and vanadium-nitrogenase cofactors have been isolated and shown to reduce carbon monoxide and cyanide ions to a mixture of alkanes and alkenes in the presence of a strong reductant, europium(II) diethylenetriaminepentaacetate (see scheme). Various hydrocarbons of up to seven carbon atoms in length are detected as products in these ATP-free reactions.
A Highly Selective Catalytic Method for the Oxidative Functionalization of C−H Bonds (2004)

This communication describes a new and highly practical Pd(II)-catalyzed method for the regio- and chemoselective oxidative functionalization of arenes and alkanes. Carbon-hydrogen bonds of substrates that contain a variety of directing groups (e.g., pyridine, azobenzene, pyrazole, and imine derivatives) are selectively transformed into esters, ethers, and aryl-halides under mild conditions. The scope of this reaction in terms of substrate, directing group, and oxidant is described, and a preliminary catalytic cycle is proposed.
FGF-4 increasesin vitroexpansion rate of human adult bone marrow-derived mesenchymal stem cells (2007)

Human bone marrow-derived mesenchymal stem cells (MSCs) exhibit limited in vitro growth. Fibroblast growth factors (FGFs) elicit a variety of biological responses, such as cell proliferation, differentiation and migration. FGF-4 represents one of the FGFs with the highest cell mitogenic activity. We studied the effect of FGF-4 on MSCs growth and pluripotency. MSCs duplication time (Td) was significantly reduced with FGF-4 compared to controls (2.2 +/- 0.2 vs. 4.1 +/- 0.2 days, respectively; p = 0.03) while BMP-2 and SCF-1 did not exert a significant growth effect. MSC expression of surface markers, differentiation into adipogenic and osteogenic lineages, and baseline expression of cardiomyogenic genes were unaffected by FGF-4. In summary, exogenous FGF-4 increases the rate at which MSC proliferate and has no significant effect on MSC pluripotency.
Control of the specificity of T cell-mediated anti-idiotype immunity by natural regulatory T cells (2010)

The idiotypes of B cell lymphomas represent tumor-specific antigens. T cell responses induced by idiotype vaccination in vivo are directed predominantly against CDR peptides, whereas in vitro T cells also recognize framework-derived epitopes. To investigate the mechanisms regulating the specificity of idiotype-specific T cells, BALB/c or B10.D2 mice were immunized with mature dendritic cells loaded with H-2K(d)-restricted peptides from influenza hemagglutinin, or from shared (J region) or unique (CDR3) structures of the A20 lymphoma idiotype. Antigen-specific T cells were induced in vivo by the CDR3 and influenza epitopes, but not by the J peptide. Gene expression profiling of splenic regulatory T cells revealed vaccination-induced Treg activation and proliferation. Treg activity involved J epitope-dependent IL-10 secretion and functional suppression of peptide-specific effector T cells. Vaccination-induced in vivo proliferation of transgenic hemagglutinin-specific T cells was suppressed by co-immunization with the J peptide and was restored in CD25-depleted animals. In conclusion, Treg induced by a shared idiotype epitope can systemically suppress T cell responses against idiotype-derived and immunodominant foreign epitopes in vivo. The results imply that tumor vaccines should avoid epitopes expressed by normal cells in the draining lymph node to achieve optimal anti-tumor efficacy.
Role of Glycogen Synthase Kinase-3 in Insulin Resistance and Type 2 Diabetes (2006)

A reduced ability of insulin to activate glucose transport in skeletal muscle, termed insulin resistance, is a primary defect leading to the development of impaired glucose tolerance and type 2 diabetes. Glycogen synthase kinase-3 (GSK-3) is a serine/threonine kinase with important roles in the regulation of glycogen synthesis, protein synthesis, gene transcription, and cell differentiation in various cell types. An emerging body of evidence has implicated GSK-3 in the multifactorial etiology of skeletal muscle insulin resistance in obese animal models and in obese human type 2 diabetic subjects. Overexpression and overactivity of GSK-3 in skeletal muscle of rodent models of obesity and obese type 2 diabetic humans are associated with an impaired ability of insulin to activate glucose disposal and glycogen synthase. New insights into the importance of GSK-3 as a regulator of insulin action on glucose transport activity in muscle have come from studies utilizing selective and sensitive inhibitors of GSK-3. These studies have demonstrated that selective inhibition of GSK-3 in insulin-resistant skeletal muscle causes improvements in insulin-stimulated glucose transport activity that are likely caused by enhanced post-insulin receptor insulin signaling and GLUT-4 glucose transporter translocation. An additional important action of these GSK-3 inhibitors in the context of obese-associated type 2 diabetes is a reduction of hepatic glucose production, likely via downregulation of genes associated with gluconeogensis. It is clear from these studies that selectively targeting GSK-3 in skeletal muscle may be an important new strategy for the treatment of obesity-associated insulin-resistant states characterized by GSK-3 overactivity in insulin-sensitive tissues.
Inhibition of Poly(ADP-Ribose) Polymerase-1 Enhances Temozolomide and Topotecan Activity against Childhood Neuroblastoma (2009)

These data show enhancement of temozolomide and topotecan efficacy by PARP inhibition in neuroblastoma. Coupled with the acceptable pharmacokinetic, pharmacodynamic, and toxicity profiles of AG014699, our findings provide strong rationale for investigation of PARP inhibitors in pediatric early clinical studies.