gebhart/patrepeval huggingface dataset:
Developmental regulation of biglycan expression in muscle and tendon (2006)

Biglycan is an extracellular ligand for the dystrophin-associated protein complex (DAPC) that is upregulated in both dystrophic and regenerating muscle. Biglycan also binds to collagen VI, mutations of which cause a congenital muscular dystrophy (Ullrich's; UCMD) that is also characterized by connective tissue abnormalities. The expression of biglycan in early development and postnatal ages has not been well characterized. Here we show that biglycan transcript levels peak at approximately 21 weeks' gestation in human fetal muscle. Immunocytochemical analysis of developing mouse muscle shows that biglycan can be detected in muscle as early as embryonic day (E)16 and is most abundant between postnatal day (P)1 and P7. Biglycan is also highly expressed in developing tendon, with maximal levels observed at E16-18. This robust tendon expression is correlated with a sharp peak in biglycan transcript levels in the hindlimb. Finally, at E18 collagen VI colocalizes with biglycan in tendon. These results suggest that biglycan has a particularly important function during muscle and connective tissue development. Moreover, biglycan may play a role in the pathogenesis of collagen VI-associated congenital muscular dystrophies.
[Differentiation of bone marrow stem cells in rat hepatic fibrogenesis environment]. (2003)

Bone marrow stem cells in hepatic fibrogenesis environment can differentiate into hepatocytes, but can't differentiate into myofibroblasts
Autoradiographic studies of glial proliferation in different areas of the brain of the 14-day-old rat. (1983)

Cell cycle parameters, as well as the mode of proliferation of glial cells, in four different areas of the brain of the 14-day-old rat (cortex, corpus callosum, nucleus caudatus putamen and commissura anterior) were studied using different cell kinetic methods after injection of [3H]TdR and/or [14C]TdR. The duration of the S phase (tS) was found to be about 10 hr and that of the cycle time (tC) about 20 hr, tG2 is less than 2 hr and t(G2 + M) about 4 hr. These values are valid for glial cells in all four brain areas studied. However, the labelling index (LI) of the glial cells differs by a factor of 3, between 1.8 and 5.4% in the different brain areas. Accordingly, the growth fraction of the glial cell population in the four areas varies between 0.04 and 0.12. Glial cells (astrocytes as well as oligodendrocytes) proliferate according to a steady state system. Furthermore, the proliferation of glial cells is associated with continuous cell loss. After each mitosis about 3% of the daughter cells become pyknotic and die. In addition, a permanent exchange of glial cells occurs between the proliferating and non-proliferating pool.
Clustering of Genes Dispensable for Growth in Culture in the S Component of the HSV-1 Genome (1987)

The herpes simplex virus 1 genome consists of one long and one short stretch of unique sequences flanked by inverted repeat sequences. The nucleotide sequence and RNA map predict 12 open reading frames designated as US1 through US12 within the short stretch of unique sequences. This paper reports the construction of virus mutants from which US2, US3, or US4 had been deleted that are capable of growth in cell culture. One of the three deleted genes, US4, specifies the viral envelope glycoprotein G. Mutants with deletions in US1, US8, US9, US10, US11, and US12 have been previously reported. The nine genes deleted from this region form two clusters, US1 through US4 and US8 through US12, and encode at least two and possibly more structural proteins. The presence of so many genes dispensable for growth in cell culture suggests several hypotheses regarding their function and evolution.
Mechanism of Inhibition of LDL Phospholipase A2 by Monocyclic-β-lactams. Burst Kinetics and the Effect of Stereochemistry (1998)

Investigation of the inhibition of LDL-associated phospholipase A2 by monocyclic beta-lactams has shown that LDL phospholipase A2 is capable of hydrolyzing monocyclic-beta-lactams by a mechanism which shares many similarities to the hydrolysis of beta-lactams by beta-lactamases. We believe that this is the first demonstration of a serine-dependent lipase being able to hydrolyze an amide bond. Although 4-(phenylthio)-N-(4-phenyl-2-oxobutyl)azetidin-2-one, SB-216477, and its enantiomers are relatively modest covalent inactivators with kobs/[I] = 46 M-1 s-1 for the R enantiomer, analysis of the kinetics of inactivation and reactivation shows that these compounds act as slow-turnover substrates, presumably via an acylation-deacylation mechanism. The detection of a suprastoichiometric burst indicates that the pathway must be branched with the branching giving rise to the slow reactivation via a more stable covalent intermediate. Study of the two enantiomers of SB-216477 shows that LDL-associated phospholipase A2 is sensitive to the beta-lactam stereochemistry at C4. However, a common achiral intermediate is formed along the turnover pathway, and this must be at or immediately prior to the branch point.
Bovine beta 1----4-galactosyltransferase: two sets of mRNA transcripts encode two forms of the protein with different amino-terminal domains. In vitro translation experiments demonstrate that both the short and the long forms of the enzyme are type II membrane-bound glycoproteins. (1990)

We have used S1 and primer extension analysis to demonstrate that the gene for bovine beta 1----4-galactosyltransferase specifies two sets of mRNA transcripts of different lengths. The longer mRNA transcripts initiate upstream of two in-frame ATG codons and encode a protein of 402 amino acids (long form). The shorter mRNA transcripts initiate between the two in-frame ATG codons and encode a protein of 389 amino acids (short form). These two related forms of beta 1----4-galactosyltransferase have an identical large (358 amino acids), potentially glycosylated, COOH-terminal catalytic domain, and an identical single transmembrane domain. The only difference in primary structure between the two forms is that the long form contains an NH2-terminal extension of 13 amino acids. Thus, bovine beta 1----4-galactosyltransferase fits the pattern established for murine beta 1----4-galactosyltransferase (Shaper, N. L., Hollis, G. L., Douglas, J. G., Kirsch, I. R., and Shaper, J. H. (1988) J. Biol. Chem. 263, 10420-10428). Inspection of the NH2-terminal domain suggests that the long form of the bovine enzyme, like its murine counterpart, has a functional cleavable signal sequence which would dictate that the two forms of the membrane-bound enzyme are oriented in opposite directions. We have tested this hypothesis by in vitro translation in the absence or presence of dog pancreas microsomes. In vitro translation of RNA transcripts for the long and short form of beta 1----4-galactosyltransferase in the absence of microsomes results in the synthesis of polypeptides with apparent Mr of 44,500 and 43,000, respectively. In vitro translation of each transcript in the presence of microsomes results in the synthesis of two glycosylated, endoglycosidase H-sensitive proteins with apparent Mr of 47,500 and 46,000. These experiments and additional protease protection experiments demonstrate that the COOH-terminal domain of both the short and the long form of bovine beta 1----4-galactosyltransferase are translocated into the microsomal lumen. By extrapolation, both forms of the enzyme are oriented in vivo as Type II membrane-bound glycoproteins.
Molecular cloning and characterization of the genomes of nine newly recognized human papillomavirus types associated with epidermodysplasia verruciformis (1984)

The genomes of 11 human papillomaviruses (HPVs) found in benign lesions of eight patients suffering from epidermodysplasia verruciformis were cloned in Escherichia coli after insertion into plasmid pBR322. The study of the sensitivity of the cloned HPV DNAs to 14 restriction endonucleases permitted the construction of physical maps. DNA-DNA hybridization experiments, performed under stringent conditions, showed that these viruses represent nine new types, HPVs 14 (with subtypes a and b), 15, 17 (with subtypes a and b), 19, 20, 21, 22, 23, and 24. These HPVs were divided into three groups based on an absent or very weak cross-hybridization among the genomes of the viruses belonging to different groups.
Soluble Polymer-Supported Synthesis of N,N-di(Boc)-Protected Guanidines (1998)

A novel method for soluble, inexpensive polymer-supported synthesis of internal guanidines with piperazine and piperidine scaffolds has been developed. We carried out a preliminary study on the reactivity of N,N-bis-Boc-1-guanylpyrazole 1, N,N-bis-Boc-thiourea 2 and N,N-di-(tert-butoxycarbonyl)-S-methylisothiourea 3 with resin bound diamines in liquid phase. Guanidines are liberated from the polymer support in high yields and good purity by simple precipitation and washing. This liquid-phase method proves to be a useful tool for constructing guanidine libraries containing a diamine moiety.
Behavioral Stochastic Resonance within the Human Brain (2003)

We provide the first evidence that stochastic resonance within the human brain can enhance behavioral responses to weak sensory inputs. We asked subjects to adjust handgrip force to a slowly changing, subthreshold gray level signal presented to their right eye. Behavioral responses were optimized by presenting randomly changing gray levels separately to the left eye. The results indicate that observed behavioral stochastic resonance was mediated by neural activity within the human brain where the information from both eyes converges.
Prognostic markers in triple‐negative breast cancer (2006)

The authors concluded that assessment of androgen receptor and basal phenotype, in addition to the established pathologic variables, mainly lymph node status and tumor size, can be used to select high-risk and low-risk patients at the time of primary surgery and can provide valuable information on treatment options in these triple-negative tumors.
Improving chemotherapeutic efficiency in acute myeloid leukemia treatments by chemically synthesized peptide interfering with CXCR4/CXCL12 axis (2015)

Bone marrow stroma can protect acute myeloid leukemia (AML) cells against chemotherapeutic agents and provide anti-apoptosis and chemoresistance signals through secreting chemokine CXCL12 to activate its receptor CXCR4 on AML cells, resulting in minimal residual leukemia and relapse. Therefore disrupting the CXCR4/CXCL12 axis with antagonists is of great significance for improving chemosensitivity and decreasing relapse rate. In a previous study, we reported a novel synthetic peptide E5 with its remarkable effect on inhibiting CXCR4/CXCL12-mediated adhesion and migration of AML cells. Here we presented E5's capacity of enhancing the therapeutic efficiency of various chemotherapeutics on AML in vitro and in vivo. Results showed that E5 can diminish bone marrow stromal cell-provided protection to leukemia cells, significantly increasing the apoptosis induced by various chemotherapeutics in multiple AML cell lines. In an AML mouse xenograft model, E5 induced 1.84-fold increase of circulating AML cells out of protective stroma niche. Combined with vincristine or cyclophosphamide, E5 inhibited infiltration of AML cells into bone marrow, liver and spleen, as well as prolonged the lifespan of AML mice compared with mice treated with chemotherapy alone. In addition, E5 presented no toxicity in vivo according to the histological analysis and routine clinical parameters of serum analysis.
A Novel Breast/Ovarian Cancer Peptide Vaccine Platform That Promotes Specific Type-1 but not Treg/Tr1-type Responses (2010)

In light of lack of efficacy associated with current cancer vaccines, we aimed to develop a novel vaccine platform called DepoVax as a therapeutic vaccine for breast/ovarian cancer. This study was designed to examine the efficacy of this novel platform over conventional emulsion vaccine using human class I MHC transgenic mice. We have developed a water-free depot vaccine formulation (DPX-0907) with high immune activating potential. Naturally processed peptides bound to HLA-A2 molecules isolated from independent breast and ovarian tumor cell lines, but not normal cells, were isolated and used as antigens in DPX-0907 along with a proprietary adjuvant and a T helper peptide epitope. Efficacy of vaccine was tested in immunized HLA-A*0201/H2Dd transgenic mice by measuring the frequency of IFN-gamma secreting cells in the draining lymph nodes, and regulatory T-cell frequencies in the spleen. Compared with a water-in-oil emulsion vaccine, DPX-0907 enhanced IFN-gamma+CD8+ T cells in vaccine site-draining lymph nodes, as seen by immunofluorescence staining and increased the frequency of IFN-gamma+ lymph node cells as seen by enzyme-linked immunosorbent spot assay. Notably, while conventional vaccine formulations elicited elevated levels of splenic Foxp3+CD4+ and IL10-secreting T cells, this was not the case for DPX-0907-based vaccines, with treated animals exhibiting normal levels of regulatory T cells. These data support the unique capabilities of a vaccine formulation containing novel tumor peptides and DPX-0907 to elicit type-1 dominated, specific immunity that may represent a potent clinical therapeutic modality for patients with breast or ovarian carcinoma.
Assembly of viruslike particles by recombinant structural proteins of adeno-associated virus type 2 in insect cells (1992)

The three capsid proteins VP1, VP2, and VP3 of the adeno-associated virus type 2 (AAV-2) are encoded by overlapping sequences of the same open reading frame. Separate expression of these proteins by recombinant baculoviruses in insect cells was achieved by mutation of the internal translation initiation codons. Coexpression of VP1 and VP2, VP2 and VP3, and all three capsid proteins and the expression of VP2 alone in Sf9 cells resulted in the production of viruslike particles resembling empty capsids generated during infection of HeLa cells with AAV-2 and adenovirus. These results suggest a requirement for VP2 in the formation of empty capsids. Individual expression of the AAV capsid proteins in HeLa cells showed that VP1 and VP2 accumulate in the cell nucleus and VP3 is distributed between nucleus and cytoplasm. Coexpression of VP3 with the other structural proteins also led to nuclear localization of VP3, indicating that the formation of a complex with VP1 or VP2 is required for accumulation of VP3 in the nucleus.
Shared Sanitation versus Individual Household Latrines: A Systematic Review of Health Outcomes (2014)

Evidence to date does not support a change of existing policy of excluding shared sanitation from the definition of improved sanitation used in international monitoring and targets. However, such evidence is limited, does not adequately address likely confounding, and does not identify potentially important distinctions among types of shared facilities. As reliance on shared sanitation is increasing, further research is necessary to determine the circumstances, if any, under which shared sanitation can offer a safe, appropriate and acceptable alternative to individual household latrines.
Fundamentals of Natural Gas Processing (2006)

Fundamentals of Natural Gas Processing explores the natural gas industry from the wellhead to the marketplace. It compiles information from the open literature, meeting proceedings, and experts to accurately depict the state of gas processing technology today and highlight technologies that could become important in the future.This book cov
Augmented production of chemokines (monocyte chemotactic protein-1 (MCP-1), macrophage inflammatory protein-1α (MIP-1α) and MIP-1β) in patients with systemic sclerosis: MCP-1 and MIP-1α may be involved in the development of pulmonary fibrosis (1999)

To determine the role of chemokines in the pathogenesis of systemic sclerosis (SSc), we examined serum levels, spontaneous production by peripheral blood mononuclear cells (PBMC), and histological distribution in the affected skin, of MCP-1, MIP-1alpha and MIP-1beta in SSc patients. Serum levels of these chemokines were examined by ELISA in 58 patients with SSc and 20 normal controls. The levels of these chemokines in culture supernatants from PBMC were also measured by ELISA. Serum levels and spontaneous production levels by PBMC of MCP-1, MIP-1alpha, and MIP-1beta were significantly elevated in patients with SSc compared with normal controls. Elevated serum levels of MCP-1 and MIP-1alpha significantly correlated with the presence of pulmonary fibrosis. MCP-1 expression in the skin of SSc was immunohistochemically examined using anti-MCP-1 MoAb. MCP-1 was strongly expressed in the epidermis, inflammatory mononuclear cells, and vascular endothelial cells in the sclerotic skin of SSc patients, but not expressed in any control skin. Furthermore, the MCP-1 expression in inflammatory mononuclear cells and endothelial cells significantly correlated with earlier onset of SSc. Thus, MCP-1, MIP-1alpha and MIP-1beta may be involved in the disease process, possibly by augmenting leucocyte migration into the affected tissues in SSc. Furthermore, MCP-1 and MIP-1alpha may play an important role in the development of pulmonary fibrosis in SSc.
Probabilistic Neural Network Model for the In Silico Evaluation of Anti-HIV Activity and Mechanism of Action (2006)

A theoretical model has been developed that discriminates between active and nonactive drugs against HIV-1 with four different mechanisms of action for the active drugs. The model was built up using a probabilistic neural network (PNN) algorithm and a database of 2720 compounds. The model showed an overall accuracy of 97.34% in the training series, 85.12% in the selection series, and 84.78% in an external prediction series. The model not only correctly classified a very heterogeneous series of organic compounds but also discriminated between very similar active/nonactive chemicals that belong to the same family of compounds. More specifically, the model recognized 96.02% of nonactive compounds, 94.24% of active compounds that inhibited reverse transcriptase, 97.24% of protease inhibitors, 97.14% of virus uncoating inhibitors, and 90.32% of integrase inhibitors. The results indicate that this approach may represent a powerful tool for modeling large databases in QSAR with applications in medicinal chemistry.
Controlling the Surface Chemistry of Graphite by Engineered Self-Assembled Peptides (2012)

The systematic control over surface chemistry is a long-standing challenge in biomedical and nanotechnological applications for graphitic materials. As a novel approach, we utilize graphite-binding dodecapeptides that self-assemble into dense domains to form monolayer-thick long-range-ordered films on graphite. Specifically, the peptides are rationally designed through their amino acid sequences to predictably display hydrophilic and hydrophobic characteristics while maintaining their self-assembly capabilities on the solid substrate. The peptides are observed to maintain a high tolerance for sequence modification, allowing control over surface chemistry via their amino acid sequence. Furthermore, through a single-step coassembly of two differently designed peptides, we predictably and precisely tune the wettability of the resulting functionalized graphite surfaces from 44° to 83°. The modular molecular structures and predictable behavior of short peptides demonstrated here give rise to a novel platform for functionalizing graphitic materials that offers numerous advantages, including noninvasive modification of the substrate, biocompatible processing in an aqueous environment, and simple fusion with other functional biological molecules.
A Ribonuclease A Variant with Low Catalytic Activity but High Cytotoxicity (2000)

Onconase, a homolog of ribonuclease A (RNase A) with low ribonucleolytic activity, is cytotoxic and has efficacy as a cancer chemotherapeutic. Here variants of RNase A were used to probe the interplay between ribonucleolytic activity and evasion of the cytosolic ribonuclease inhibitor protein (RI) in the cytotoxicity of ribonucleases. K41R/G88R RNase A is a less active catalyst than G88R RNase A but, surprisingly, is more cytotoxic. Like Onconase, the K41R/G88R variant has a low affinity for RI, which apparently compensates for its low ribonucleolytic activity. In contrast, K41A/G88R RNase A, which has the same affinity for RI as does the K41R/G88R variant, is not cytotoxic. The nontoxic K41A/G88R variant is a much less active catalyst than is the toxic K41R/G88R variant. These data indicate that maintaining sufficient ribonucleolytic activity in the presence of RI is a requirement for a homolog or variant of RNase A to be cytotoxic. This principle can guide the design of new chemotherapeutics based on homologs and variants of RNase A.
Optimal positioning of right-sided internal jugular venous catheters: Comparison of intra-atrial electrocardiography versus Peres′ formula (2008)

Central venous catheters are routinely placed in patients undergoing major surgeries where expected volume and hemodynamic disturbances are likely consequences. The incorrect positioning may give false central venous pressure (CVP) readings leading to incorrect volume replacement and other serious complications. 50 American Society of Anaesthesiologists grade II-IV patients aged 18-60 years were selected for right-sided internal jugular vein (IJV) catheterization using Seldinger's technique. In group A, central venous catheterization was done under electrocardiography (ECG) guidance. In group B, the catheter was inserted blindly using Peres' formula of "height (in cm)/10". The position of the tip of central venous catheter was confirmed radiologically by postoperative chest X-ray. 92% of patients in group A had radiologically correct positioning of catheter tip i.e. above the carina, while in group B 48% patients had over-insertion of the catheter in to the right atrium. Intra-atrial ECG technique to judge correct tip positioning is simple and economical. It can determine the exact position intraoperatively and can justify a delayed postoperative chest X-ray to confirm CVC line tip placement.
30-GHz bandwidth 1.55-μm strain-compensated InGaAlAs-InGaAsP MQW laser (1997)

High-speed 1.55 μm laser diodes with a 3-dB modulation bandwidths of 30 GHz were fabricated by using short-cavity mushroom structures with undoped, strain-compensated InGaAlAs-InGaAsP twenty-quantum-well active regions. The bandwidths were achieved at low bias current of 100 mA. The laser exhibited a high differential gain of 1.54×10/sup -15/ cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and a small K factor of 0.135 ns. These results were achieved by using an In/sub 0.386/Ga/sub 0.465/AlAs barrier with 0.83% tensile strain to reduce the thermal emission time of holes from wells and hence the hole transport time.