gebhart/patrepeval huggingface dataset:
A Microworld for Developing Learning Design Strategies (1992)

This article describes a beginner's programming environment. It is similar to Turtle graphics in that it operates on a simple concrete domain, that of Darel, a robot. Darel can move around a simple world, trying to avoid running into walls as it goes about its tasks that involve picking up and putting down beepers and bricks. Central to the design of the environment is the use of predicates that define the state of Darel's world. These serve as statements of program goals, subgoals, and assumptions. The Darel environment was designed to encourage students to use the formulation of these predicates as a strategy to design algorithms.
Three-dimensional probe reconstruction for atomic force microscopy (1994)

Colloidal gold particles are used as hard, spherical imaging targets to assist in the three-dimensional reconstruction of the atomic force probe apex. Probe reconstructions are shown to be accurate to 1 nm resolution and dynamically change as the sample is scanned, emphasizing the utility of colloidal gold particles as in situ calibration standards for image reconstruction of a coadsorbed specimen.
Exceptionally potent inhibitors of fatty acid amide hydrolase: The enzyme responsible for degradation of endogenous oleamide and anandamide (2000)

The development of exceptionally potent inhibitors of fatty acid amide hydrolase (FAAH), the enzyme responsible for the degradation of oleamide (an endogenous sleep-inducing lipid), and anandamide (an endogenous ligand for cannabinoid receptors) is detailed. The inhibitors may serve as useful tools to clarify the role of endogenous oleamide and anandamide and may prove to be useful therapeutic agents for the treatment of sleep disorders or pain. The combination of several features-an optimal C12-C8 chain length, pi-unsaturation introduction at the corresponding arachidonoyl Delta(8,9)/Delta(11,12) and oleoyl Delta(9,10) location, and an alpha-keto N4 oxazolopyridine with incorporation of a second weakly basic nitrogen provided FAAH inhibitors with K(i)s that drop below 200 pM and are 10(2)-10(3) times more potent than the corresponding trifluoromethyl ketones.
Molecular cloning and expression of Campylobacter pylori species-specific antigens in Escherichia coli K-12 (1989)

A gene bank of Campylobacter pylori DNA in Escherichia coli was constructed by cloning Sau3A-cleaved DNA fragments into the bacteriophage vector lambda EMBL3. The expression of C. pylori antigens was determined by screening the gene library with adsorbed C. pylori whole-cell rabbit antisera. One recombinant clone which reacted positively (lambda CP2) was studied further. Immunoblot analysis with lambda CP2 showed a polypeptide band of 66 kilodaltons (kDa) reacting antigenically with the adsorbed antiserum. Extraction of DNA from lambda CP2 and digestion with SalI revealed a DNA insert of 17 kilobases (kb). Subcloning with SalI and the E. coli vector pUC18 showed that the DNA also encoded a 31-kDa antigen. The cloned antigens were shown by immunoblotting to have the same molecular weight in E. coli as in C. pylori and to be present in all C. pylori strains. Antiserum was raised against the cloned polypeptides and found to react only with C. pylori when analyzed by dot blotting and indirect immunofluorescence. The cloned antigens were determined to be expressed from the pUC18 lac promoter. The DNA encoding these antigens was radiolabeled with 32P and found to hybridize only to C. pylori strains. Immunoblotting with affinity-purified polyclonal antibody to the urease enzyme of C. pylori revealed that the cloned antigens may be part of the urease enzyme.
Complete pathological remission is possible with systemic combination chemotherapy for inoperable hepatocellular carcinoma. (1999)

The purpose of this Phase II study was to determine the response rate, the toxicity, and the effect on survival of the combination of cisplatin, doxorubicin, 5-fluorouracil, and alpha-IFN (PIAF) in advanced unresectable hepatocellular carcinoma. Fifty patients with either unresectable or metastatic disease were treated with PIAF: cisplatin (20 mg/m2 i.v., days 1-4), doxorubicin (40 mg/m2 i.v., day 1), 5-fluorouracil (400 mg/m2 i.v., days 1-4), and alpha-IFN (5 MU/m2 s.c., days 1-4). Treatment was repeated every 3 weeks to a maximum of six cycles. All patients were evaluable for response, toxicity, and survival. As assessed by conventional imaging criteria, there were no complete responses, but 13 patients (26%) had a partial response. Among the 36 patients who had an initially high alpha-fetoprotein level (>500 ng/ml), 15 (42%) had a >50% fall after therapy. Nine patients underwent surgical resection after achieving partial response and, in 4 of these patients, histological examination of the resected specimens revealed no viable tumor cells. All these nine patients are alive, and eight patients remain in complete remission at between 7.6 and 25.8 months at the time of analysis. The overall median survival was 8.9 months. Toxicity was mainly myelosuppression and mucositis. There were two treatment-related deaths due to neutropenic sepsis. PIAF is active in hepatocellular carcinoma despite considerable hematological toxicity. Complete pathological remission is possible with this systemic combination. Apparently, persistent radiological lesions may still represent complete pathological resolution of active disease.
Post-translational Modifications of Proteins (2024)

Hydroxylation of Proline and Lysine Residues in Collagens and Other Animal and Plant Proteins (K.I. Kivirikko, R. Myllyla and T. Pihlajaniemi). Advanced Glycosylation Endproducts (R. Bucala, H. Vlassara and A. Cerami). Rabbit Muscle Glycogen Phosphorylase b. The Structural Basis of Activation and Catalysis (N.G. Oikonomakos, K.R. Acharya and L.N. Johnson). Mono-ADP-Ribosylation of Proteins (S. van Heyningen). Glycan Structures in Glycoproteins and Their Analysis by Fast Atom Bombardment Mass Spectrometry (A. Dell, R.A. McDowell and M.E. Rogers). Glycoproteins of Mammalian and Avian Cells (F.W. Hemming). FEATURES:
Concurrent knock‐out of at least 20 transporter genes is required to block uptake of hexoses in Saccharomyces cerevisiae (1999)

The hexose transporter family of Saccharomyces cerevisiae comprises 18 proteins (Hxt1-17, Gal2). Here, we demonstrate that all these proteins, except Hxt12, and additionally three members of the maltose transporter family (Agt1, Ydl247, Yjr160) are able to transport hexoses. In a yeast strain deleted for HXT1-17, GAL2, AGT1, YDL247w and YJR160c, glucose consumption and transport activity were completely abolished. However, as additional deletion of the glucose sensor gene SNF3 partially restored growth on hexoses, our data indicate the existence of even more proteins able to transport hexoses in yeast.
Increased Expression of thehPim-2Gene In Human Chronic lymphocytic Leukemia and Non-Hodgkin Lymphoma (2004)

Pim-1 and Pim-2 are murine proto-oncogenes implicated in lymphomagenesis. The aim of this study was to investigate whether the human Pim-2 (hPim-2) expression is altered in chronic lymphocytic leukemia (B-CLL) and non-Hodgkin's lymphomas (NHL). We analyzed hPim-2 expression in 48 patients with NHL and CLL by quantitative in-situ hybridization, quantitative RT-PCR and FACS analysis. In-situ hybridization revealed a 5.5 +/- 2.2 times higher expression of hPim-2 in NHL over normal lymphocytes (P < 0.001). Similarly, with quantitative RT-PCR, expression in NHL was 1.5 to 2.6 times higher in involved splenic foci compared to nearby uninvolved regions (n = 3). hPim-2 mRNA was increased 3-folds in B-CLL over normal B-cells (P < 0.006). The increased hPim-2 levels correlated with lymphocyte doubling time (DT), in that mRNA levels were two times greater in patients with rapid DT (P < 0.006). Moreover, a significant correlation was found between hPim-2 expression and the Binet staging system of CLL (P < 0.022). The hPIM-2-protein expression was also upregulated in CLL, as assessed by FACS analysis. Therefore, this report provides direct evidence for a linkage of hPim-2 upregulation to NHL and CLL in man. This relationship between hPim-2 and NHL and CLL raises a number of novel mechanistic options for the genesis and/or progression of some types of human lymphomas.
The relationship between glandular kallikrein and growth factor-processing proteases of mouse submaxillary gland. (1979)

Three highly specific trypsin-like proteases from mouse submaxillary gland; nerve growth factor gamma subunit, beta nerve growth factor-endopeptidase, and epidermal growth factor-binding protein were tested for kallikrein activity. Low molecular weight kininogen was purified from mouse plasma and used as substrate for the three enzymes, and the kinin released by the enzymes was assayed by its ability to induce contraction of isolated rat uterus. All three enzymes were found to have significant kininogenase activity, and the most active enzyme, beta nerve growth factor-endopeptidase, has activity comparable to authentic kallikreins from other glandular sources. Essentially all of the kininogenase activity of submaxillary gland co-purifies with beta nerve growth factor-endopeptidase. Hence, beta nerve growth factor-endopeptidase appears to be identical with submaxillary gland kallikrein. Nerve growth factor gamma subunit, epidermal growth factor-binding protein, and beta nerve growth factor-endopeptidase have similar amino acid compositions and molecular weights, and are immunologically similar. Comparison of published partial primary sequence data confirms our conclusion that nerve growth factor gamma subunit, epidermal growth factor-binding protein, and kallikrein are very closely related enzymes. It is postulated that these three enzymes are members of a larger family of similar enzymes, all of which are involved in the processing of precursors to polypeptide hormones and growth factors.
Use of Molecular Tools to Identify Patients With Indolent Breast Cancers With Ultralow Risk Over 2 Decades (2017)

The ultralow-risk threshold of the 70-gene MammaPrint assay can identify patients whose long-term systemic risk of death from breast cancer after surgery alone is exceedingly low.
Inhibition of endothelial cell migration by thrombospondin-1 type-1 repeats is mediated by β1 integrins (2005)

The anti-angiogenic effect of thrombospondin-1 has been shown to be mediated through binding of the type-1 repeat (TSR) domain to the CD36 transmembrane receptor. We now report that the TSR domain can inhibit VEGF-induced migration in human umbilical vein endothelial cells (HUVEC), cells that lack CD36. Moreover, we identified beta1 integrins as a critical receptor in TSR-mediated inhibition of migration in HUVEC. Using pharmacological inhibitors of downstream VEGF receptor effectors, we found that phosphoinositide 3-kinase (PI3k) was essential for TSR-mediated inhibition of HUVEC migration, but that neither PLCgamma nor Akt was necessary for this response. Furthermore, beta1 integrins were critical for TSR-mediated inhibition of microvascular endothelial cells, cells that express CD36. Together, our results indicate that beta1 integrins mediate the anti-migratory effects of TSR through a PI3k-dependent mechanism.
Amino acid limitation regulates the expression of genes involved in several specific biological processes through GCN2‐dependent and GCN2‐independent pathways (2008)

Evidence has accumulated that amino acids play an important role in controlling gene expression. Nevertheless, two components of the amino acid control of gene expression are not yet completely understood in mammals: (a) the target genes and biological processes regulated by amino acid availability, and (b) the signaling pathways that mediate the amino acid response. Using large-scale analysis of gene expression, the objective of this study was to gain a better understanding of the control of gene expression by amino acid limitation. We found that a 6 h period of leucine starvation regulated the expression of a specific set of genes: 420 genes were up-regulated by more than 1.8-fold and 311 genes were down-regulated. These genes were involved in the control of several biological processes, such as amino acid metabolism, lipid metabolism and signal regulation. Using GCN2-/- cells and rapamycin treatment, we checked for the role of mGCN2 and mTORC1 kinases in this regulation. We found that (a) the GCN2 pathway was the major, but not unique, signaling pathway involved in the up- and down-regulation of gene expression in response to amino acid starvation, and (b) that rapamycin regulates the expression of a set of genes that only partially overlaps with the set of genes regulated by leucine starvation.
Tropical Dairy Farming: Feeding Management for Small Holder Dairy Farmers in the Humid Tropics (2005)

Tropical Dairy Farming is a manual designed for use by dairy production advisors working in tropical areas, especially in South-East Asia. It aims to increase the productivity of small holder dairy farmers in the humid tropics by improving the feeding management of their livestock. It shows how to provide dairy cows with cost-effective feeds that match small holder farming systems and discusses the major obstacles to improving feeding management in the humid tropics.

The author shows the benefits and drawbacks of various feed components and the calculation of balanced diets based mainly on forages combined with some supplementary feeding. Diseases and problems associated with unbalanced diets are also covered, as well as important information on growing and conserving quality forages as silage.

The book draws on examples from a variety of countries including Indonesia, Malaysia, Thailand, Vietnam, China, East Timor and the Philippines.
Comparison of Propofol with Lidocaine Pretreatment Versus Propofol Formulated with Long- and Medium-Chain Triglycerides or Confounding Effect of Tourniquet (2005)

In Response: We would like to thank Drs. Eghtesadi-Araghi and Marashi for their interest in our randomized clinical trial. They have raised some concerns regarding tourniquet use and the potential for an interaction between ischemia/reperfusion injury and the pain triggered by the injection of propofol. First, the tourniquet used on the forearm of our patients in this trial was not a “surgical tourniquet” whereby two cuffs are inflated to a pressure of 300 mm Hg to prevent arterial flow to provide a bloodless surgical field during microsurgery, to minimize blood loss during orthopedic surgery, or to perform distal limb anesthesia with prilocaine. As is our routine practice when using standard propofol with pretreatment with lidocaine and as has been described by others (1), we used a rubber tourniquet that was held in place on the forearm for <1 min. It is most unlikely that any ischemia would result from such a procedure with low compression applied for a short time. Therefore, we do not consider that neutrophil-mediated endothelial cytotoxicity and activation or generation of free radicals and kinines provide an explanation for the increased pain observed after injection of the long- and medium-chain triglyceride propofol. Furthermore, both formulations of propofol were administered with a rubber tourniquet, so if the tourniquet were to have a confounding effect, this would have been seen in both groups. Although the solvent might be key in producing the pain (2), it is most unlikely that the different lipid contents in the two propofol formulations react in such a different way to a 30-s tourniquet application as to result in an exaggerated free radicals and cytokines release with the long- and medium-chain triglyceride formulation. Finally, a recent randomized trial comparing long- and medium-chain triglycerides with standard propofol mixed with lidocaine without using a tourniquet also described a trend towards more pain in patients receiving the long- and medium-chain triglyceride formulation (3). E. Schaub, MD C. Kern, MD Ruth Landau, MD Service d’ Anesthesiologie Hopitaux Universitaires de Geneve Geneva, Switzerland [email protected]
Kerr-gated time-resolved Raman spectroscopy of equine cortical bone tissue (2005)

Picosecond time-resolved Raman spectroscopy in equine cortical bone tissue is demonstrated. Using 400-nm pulsed laser excitation (1 ps at 1 kHz) it is shown that Kerr cell gating with a 4-ps window provides simultaneously time-resolved rejection of fluorescence and time-resolved Raman scatter enabling depth profiling through tissue. The Raman shifts are the same as those observed by conventional cw Raman spectroscopy using deep-red or near-infrared lasers. The time decay of Raman photons is shown to fit an inverse square root of time function, suggesting propagation by a diffusive mechanism. Using polystyrene behind a bone specimen, it is shown that the 400-nm laser light penetrates at least 0.31 mm below the surface of a fully mineralized bone tissue specimen and generates observable bone Raman scatter (approximately 415 to 430 nm) through most of this depth. These novel results demonstrate great promise for in vivo applications for studying diseased bone tissue, and ways to optimize the setup are discussed.
Presence and Quality of Navigational Landmarks: Effect on Driver Performance and Implications for Design (2006)

The design of future vehicle navigation systems should not rely on distance-to turn information alone to enable a driver to locate forthcoming maneuvers but, rather, should incorporate good landmarks within the navigation instructions they present to drivers.
Interferon alpha2b inhibits the murine melanoma cell line Cloudman S91 in vivo but not in vitro: a model for studying tumor cell-cytokine interactions. (2001)

Interferon alpha2b has recently been shown to improve outcome in patients with metastatic malignant melanoma. The high-dose interferon therapy used is however associated with significant systemic adverse effects. These adverse effects are likely related to the multitude of actions of interferon which in addition to its antineoplastic effects also possesses antiviral and immunomodulating properties. Elucidation of the mechanism of the antiproliferative effects of interferon may allow for the development of agents that possess the antineoplastic properties while being devoid of the other effects that make interferon toxic. In the animal model developed for this study tumors in mice receiving interferon alpha2b grew at a slower rate and achieved a small final tumor volume (3040 +/- 690 vs 1400 +/- 314 mm3 for the control and treated groups respectively, P < 0.05). Furthermore the final tumor weight in the treated group was significantly smaller (1.50 +/- 0.21 g vs 2.76 +/- 0.46 g for the treated and control groups respectively; P = 0.036). The (3-[4,5-Dimethylthiazol-2-y]-2,5-diphenyltetrazolium bromide) (MTT) colorimetric assay failed to reveal any direct effects of interferon alpha2b on this murine melanoma cell line. This antiproliferative effect of interferon alpha2b was in addition found to be independent of alterations in the expression of the angiogenic cytokines vascular endothelial growth factor, basic fibroblast growth factor, and transforming growth factor beta.
Identification and initial characterization of five Cryptosporidium parvum sporozoite antigen genes (1992)

Cryptosporidium parvum, an Apicomplexan parasite of gastrointestinal epithelial cells, causes severe disease in persons with AIDS and is a common cause of self-limited diarrhea in children, animal handlers, and residents of developing countries. No approved therapy exists; in research studies, however, hyperimmune bovine colostrum raised to Cryptosporidium oocysts and sporozoites has eradicated disease or decreased parasite burden in some AIDS patients. Although the protective antigens recognized by bovine hyperimmune colostrum have not been defined, protective antigens of other Apicomplexan parasites frequently have been associated with two unique structures of invasive forms, the trilaminar pellicle and the apical complex. In order to identify immunogenic Cryptosporidium proteins that may be protective antigens for use as recombinant immunogens in passive and/or active immunotherapy, we screened two genomic DNA expression libraries with polyspecific anti-Cryptosporidium antibodies. We used an approach to cloning apical complex and pellicle protein antigens that succeeded despite the lack of large numbers of organisms that would be necessitated for conventional biochemical approaches requiring organelle or membrane purification. We report here the molecular cloning of five C. parvum genes and the characterization of the cognate sporozoite proteins having molecular masses of greater than 500, 68/95, 45, 23, and 15/35 kDa. The light microscopic immunofluorescence pattern of antibodies recognizing these protein antigens suggest that they are located in the pellicle or apical complex of Cryptosporidium sporozoites.
Evaluation of the porcine intestinal collagen layer as a biomaterial (2000)

The submucosal layer of the small intestine has been investigated as a source of collagenous tissue with the potential to be used as a biomaterial because of its inherent strength and biocompatibility. In this study we utilized a novel method for processing the tissue to generate an acellular intestinal collagen layer (ICL). This nondetergent, nonenzymatic chemical cleaning protocol removes cells and cellular debris without damaging the native collagen structure. Multilayer laminates of ICL crosslinked with a water-soluble carbodiimide (EDC) were evaluated as a tissue repair material in a rabbit abdominal hernia model. The ICL laminates provided the requisite physical properties and did not lead to adhesion formation. No immune response to the porcine collagen was detectable, and this material did not show any calcification in either the rabbit model or in the juvenile rat model. © 2000 John Wiley & Sons, Inc. J Biomed Mater Res, 51, 442–452, 2000.
Effects of substituted elements into the Cr layer on a CoNiCr/Cr sputtered hard disk (1990)

A study was made on the effects of elements substituted into the Cr layer on a CoNiCr/Cr sputtered hard disk. Among the various elements tried, Si, Gd, Ce, and Cu were found to increase the coercive force in the film. For Si and Gd, alloy targets of Cr-Si and Cr-Gd were prepared, and the deposited films indicated an increase of the coercive force by about 150 Oe over those without Si or Gd element.
Las llamadas “comparativas relativas” y la selección de-que (1999)

En español se puede establecer un subtipo de estructura comparativa, llamada “comparativa relativa” (más…de+artículo+que). La dividimos en la “relativa neutra” (más…de lo que) y la “relativa concordante” (más…de el/los/la/las que). Podemos considerar la relativa como una clase de “comparativa prepositiva”.Por otra parte existen estructuras que aparentemente presentan la misma secuencia que la relativa (más…artículo+que) pero no lo son. Las denominamos “pseudo-relativas”.En la relativa el elemento que sigue a de debe ser una oración de cantidad. Se podría interpretar como estructura enfática o oracion de relativo con un verbo parentético, mientras que en la pseudo-relativa no hay condición especial.En la pseudo-relativa existe la elipsis de los elementos comunes (fondo común), mientras que en la relativa no hay elipsis de este tipo, aunque la hay de otra índole: la elipsis del elemento que sigue al verbo parentetico.En cuanto a la selección de particula de la comparación hay que analizarla distinguiendo en tres estructuras: que-de el que-que el que (esto es, correlativa, relativa y pseudo-relativa respectivamente). La clave de la selección, según nuestro análisis, está más bien en la grámatica que en la llamada cacofonía.