gebhart/patrepeval huggingface dataset:
An N-acetylglucosaminyltransferase of the Golgi apparatus of the yeast Saccharomyces cerevisiae that can modify N-linked glycans (2003)

The yeast Saccharomyces cerevisiae is widely regarded as being only capable of producing N-linked glycans with high-mannose structures. To investigate the glycan structures made in different mutant strains, we made use of a reporter protein consisting of a version of hen egg lysozyme that contains a single site for N-linked glycosylation. Mass spectrometry analysis of the attached glycans revealed that a large proportion contained an unexpected extra mass corresponding to a single N-acetylhexosamine residue. In addition, the glycosylated lysozyme was recognized by an N-acetylglucosamine specific lectin. The genome of S. cerevisiae contains an uncharacterized open reading frame, YOR320c, that is related to a known N-acetylglucosaminyltransferase. Deletion of this ORF resulted in the disappearance of the extra mass on the N-linked glycans and loss of lectin binding. We show that the protein encoded by YOR320c (which we term Gnt1p) is localized to the Golgi apparatus and has GlcNAc-transferase activity in vitro. The physiological role of Gnt1p is unclear because mutants lacking the protein show no obvious growth or cell wall defects. Nonetheless, these results indicate that heterologous glycoproteins expressed in yeast can receive N-glycans with structures other than high mannose. In addition, they indicate that the lumen of the yeast Golgi contains UDP-GlcNAc, which may facilitate reconstitution of higher eukaryotic N-glycan processing.
Experience With Wound VAC and Delayed Primary Closure of Contaminated Soft Tissue Injuries in Iraq (2006)

This series of 88 cases is the first report of the use of a negative pressure dressing (wound VAC) as part of the definitive management of high-energy soft tissue wounds in a deployed wartime environment. Our experience with these patients suggests that conventional wound management doctrine may be improved with the wound VAC, resulting in earlier more reliable primary closure of wartime injuries.
5-(Trimethylstannyl)-2H-pyran-2-one and 3-(Trimethylstannyl)-2H-pyran-2-one:  New 2H-Pyran-2-one Synthons (1996)

5-(Trimethylstannyl)-2H-pyran-2-one (11) and 3-(trimethylstannyl)-2H-pyran-2-one (30), readily prepared from the corresponding bromo-2H-pyran-2-ones, undergo Pd(0)-catalyzed coupling reactions with a variety of enol triflates to give 5- and 3- substituted 2H-pyran-2-ones, respectively. This reaction is applicable to the enol triflates of 14beta-hydroxy-17-ketosteroids, and therefore may prove useful in convergent syntheses of lucibufagins and bufadienolides.
Growth Hormone (GH) Insensitivity Due to Primary GH Receptor Deficiency (1994)

As demonstrated in Table 2, the differential diagnosis of growth hormone insensitivity (GHI) includes a number of discrete disorders that can be broadly classified as primary or secondary forms. We have selected GHRD (Laron syndrome) as the prototypic disorder of GHI, in part because such dramatic and rapid progress has been made in this clinical condition over the last 6 yr. These advances represent the fortunate convergence of: 1) the cloning of the GHR gene and the identification of deletions and mutations of this gene in GHRD; 2) the development of assay methods for measurement of the GHBP, IGF peptides, and binding proteins; 3) the discovery of a larger number of affected individuals than had been previously suspected, including the recognition and description of a large genetically homogeneous population of GHRD patients in Ecuador; and 4) the production of recombinant IGF-I for therapeutic trials in GHRD. Although we are still in the early phases of clinical trials of recombinant hIGF-I in GHRD, preliminary results have been encouraging. Whether this promise translates into genuine improvements in height and body composition, without significant clinical toxicity, remains to be determined. Similarly, the suitability of IGF-I therapy for other, particularly secondary, forms of GHI is still uncertain, although the responsiveness of GHD-IA patients seems to parallel that seen in GHRD (66, 78). The next few years should provide exciting and potentially important new data on the clinical spectrum, biochemical and molecular characteristics, and responsiveness to therapy of syndromes of GHI.
Hypermethylated RASSF1A in Maternal Plasma: A Universal Fetal DNA Marker that Improves the Reliability of Noninvasive Prenatal Diagnosis (2006)

Hypermethylated RASSF1A is a universal marker for fetal DNA and is readily detectable in maternal plasma. When applied to prenatal RhD genotyping, this marker allows the detection of false-negative results caused by low fetal DNA concentrations in maternal plasma. This new marker can also be applied to many other prenatal diagnostic and monitoring scenarios.
Supervised Latent Semantic Indexing for Document Categorization (2005)

Latent semantic indexing (LSI) is a successful technology in information retrieval (IR) which attempts to explore the latent semantics implied by a query or a document through representing them in a dimension-reduced space. However, LSI is not optimal for document categorization tasks because it aims to find the most representative features for document representation rather than the most discriminative ones. In this paper, we propose supervised LSI (SLSI) which selects the most discriminative basis vectors using the training data iteratively. The extracted vectors are then used to project the documents into a reduced dimensional space for better classification. Experimental evaluations show that the SLSI approach leads to dramatic dimension reduction while achieving good classification results.
Misfolded human chorionic gonadotropin beta subunits are secreted from transfected Chinese hamster ovary cells. (1994)

There are six intramolecular disulfide (S-S) bonds that form during intracellular folding of the human chorionic gonadotropin (hCG)-beta subunit. Site-directed mutagenesis of every pair of Cys residues involved in the formation of each S-S bond was used to examine the roles that S-S bonds play in beta subunit folding and secretion. Tryptic maps of secreted hCG-beta showed that only one S-S bond formed in all S-S bond mutants that failed to fold from the earliest detectable beta folding intermediate, p beta 1, into a second major intermediate, p beta 2 (C34A-C88A, C38A-C57A or C9A-C90A mutants), whereas all 5 remaining S-S bonds formed in mutants when p beta 1-->p beta 2 conversion occurred (C23A-C72A, C93A-C100A, or C26A-C110A mutants). Nonreducing SDS-polyacrylamide gel electrophoresis showed that beta multimers were secreted from cells expressing S-S bond mutations where the folding of p beta 1-->p beta 2 was blocked. However, for mutations where p beta 1-->p beta 2 conversion was efficient, beta monomers rather than multimers were secreted. For all cell lines studied, secreted hCG-beta migrated as monomeric beta during reducing SDS-polyacrylamide gel electrophoresis, indicating that hCG-beta multimers formed via intermolecular cross-linking of unpaired thiols. Tryptic maps of hCG-beta isolated from mutants lacking the 34-88 bond, where > 80% turnover occurs, showed that only the 38-57 S-S bond formed. beta Subunits lacking the 9-90 linkage also have only S-S bond 38-57 formed, but < 10% turnover of C9A-C90A hCG-beta occurs. Thus, subtle conformational differences between partially folded or misfolded beta subunits may determine whether hCG-beta is degraded, or undergoes intracellular translocation and secretion.
Standard Reference for the Six-Minute-Walk Test in Healthy Children Aged 7 to 16 Years (2007)

These 6MWD standards will provide useful references for the care of pediatric patients.
The somatostatin analogue, octreotide, modifies both steroidogenesis and IGFBP-1 secretion in human luteinizing granulosa cells (1998)

The effect of the somatostatin analogue octreotide on the secretion of progesterone and insulin-like growth factor binding protein-1 (IGFBP-1) from human granulosa-luteal cells was investigated. Octreotide (10(-11), 10(-10) and 10(-9) M) alone induced a significant decrease in progesterone secretion (maximum suppression 69 +/- 5% of control: P < 0.0001). In contrast, treatment with octreotide in combination with human chorionic gonadotrophin (HCG), at 1 IU/ ml potentiated the stimulatory effect of HCG on progesterone secretion (HCG alone 201 +/- 3% of control: HCG + octreotide 10(-9) M 318 +/- 16%: P < 0.001). Treatment with octreotide increased the secretion of IGFBP-1 (maximum stimulation 254 +/- 25% of control: P < 0.01). No effect of HCG was seen on secretion of IGFBP-1. These findings raise the possibility that somatostatin may have a modulatory role in regulating steroidogenesis by the human corpus luteum. Further studies are required to establish the physiological significance of any such function.
Tissue microarray technology for high-throughput molecular profiling of cancer (2001)

Tissue microarray (TMA) technology allows rapid visualization of molecular targets in thousands of tissue specimens at a time, either at the DNA, RNA or protein level. The technique facilitates rapid translation of molecular discoveries to clinical applications. By revealing the cellular localization, prevalence and clinical significance of candidate genes, TMAs are ideally suitable for genomics-based diagnostic and drug target discovery. TMAs have a number of advantages compared with conventional techniques. The speed of molecular analyses is increased by more than 100-fold, precious tissues are not destroyed and a very large number of molecular targets can be analyzed from consecutive TMA sections. The ability to study archival tissue specimens is an important advantage as such specimens are usually not applicable in other high-throughput genomic and proteomic surveys. Construction and analysis of TMAs can be automated, increasing the throughput even further. Most of the applications of the TMA technology have come from the field of cancer research. Examples include analysis of the frequency of molecular alterations in large tumor materials, exploration of tumor progression, identification of predictive or prognostic factors and validation of newly discovered genes as diagnostic and therapeutic targets.
The RET/PTC-RAS-BRAF linear signaling cascade mediates the motile and mitogenic phenotype of thyroid cancer cells (2005)

In papillary thyroid carcinomas (PTCs), rearrangements of the RET receptor (RET/PTC) and activating mutations in the BRAF or RAS oncogenes are mutually exclusive. Here we show that the 3 proteins function along a linear oncogenic signaling cascade in which RET/PTC induces RAS-dependent BRAF activation and RAS- and BRAF-dependent ERK activation. Adoptive activation of the RET/PTC-RAS-BRAF axis induced cell proliferation and Matrigel invasion of thyroid follicular cells. Gene expression profiling revealed that the 3 oncogenes activate a common transcriptional program in thyroid cells that includes upregulation of the CXCL1 and CXCL10 chemokines, which in turn stimulate proliferation and invasion. Thus, motile and mitogenic properties are intrinsic to transformed thyroid cells and are governed by an epistatic oncogenic signaling cascade.
A large-vocabulary continuous speech recognition algorithm and its application to a multi-modal telephone directory assistance system (1994)

This paper describes an accurate and efficient algorithm for very-large-vocabulary continuous speech recognition based on an HMM-LR algorithm. The HMM-LR algorithm uses a generalized LR parser as a language model and hidden Markov models (HMMs) as phoneme models. To reduce the search space without pruning the correct candidate, we use forward and backward trellis likelihoods, an adjusting window for choosing only the probable part of the trellis for each predicted phoneme, and an algorithm for merging candidates that have the same allophonic phoneme sequences and the same context-free grammar states. Candidates are also merged at the meaning level. This algorithm is applied to a telephone directory assistance system that recognizes spontaneous speech containing the names and addresses of more than 70,000 subscribers (vocabulary size is about 80,000). The experimental results show that the system performs well in spite of the large perplexity. This algorithm was also applied to a multi-modal telephone directory assistance system, and the system was evaluated from the human-interface point of view. To cope with the problem of background noise, an HMM composition technique which combines a noise-source HMM and a clean phoneme HMM into a noise-added phoneme HMM was investigated and incorporated into the system.
Biofouling and Design of a Biomimetic Hull-Grooming Tool (2007)

Abstract : Biofouling, the accumulation of biological detritus on a hard substrate, has plagued the United Navy. Fouling causes increased hydrodynamic drag, resulting in increased fuel consumption and decreased speed and range. The purpose of this investigation was to research the formation of fouling, mechanisms of prevention, and tools for its removal. The Navy currently uses a copper-based antifouling coating that releases copper into the water, killing the fouling organisms. There is new research in biomimetic polymers that deter fouling, but are non-toxic. These polymers are rigidly attached to the hull surface extending their lifetime. Removal mechanisms have included water jets and abrasive brushes, yet no tool has concentrated on grooming the hull to remove the initial layer of microfouling. Removing the initial layer will deter the development of macrofouling, such as barnacles, which are more difficult to remove. The mechanisms that marine animals use to de-foul themselves were also examined and several concepts for a biomimetic hull-grooming tool were developed. These tools include novel brush designs; in addition, ultraviolet light was explored as another tool to remove microfouling.
Mechanistic insight into the dominant mode of the Parkinson's disease-associated G2019S LRRK2 mutation (2007)

Pathogenic mutations in the leucine-rich repeat kinase-2 (LRRK2) gene cause autosomal-dominant and certain cases of sporadic Parkinson's disease (PD). The G2019S substitution in LRRK2 is the most common genetic determinant of PD identified so far, and maps to a specific region of the kinase domain called the activation segment. Here, we show that autophosphorylation of LRRK2 is an intermolecular reaction and targets two residues within the activation segment. The prominent pathogenic G2019S mutation in LRRK2 results in altered autophosphorylation, and increased autophosphorylation and substrate phosphorylation, through a process that seems to involve reorganization of the activation segment. Our results suggest a molecular mechanistic explanation for how the G2019S mutation enhances the catalytic activity of LRRK2, thereby leading to pathogenicity. These findings have important implications for therapeutic strategies in PD.
Protocadherins and diversity of the cadherin superfamily (1996)

Recent cadherin studies have revealed that many cadherins and cadherin-related proteins are expressed in various tissues of different multicellular organisms. These proteins are characterized by the multiple repeats of the cadherin motif in their extracellular domains. The members of the cadherin superfamily are divided into two groups: classical cadherin type and protocadherin type. The current cadherins appear to have evolved from a protocadherin type. Recent studies have proved the cell adhesion role of classical cadherins in embryogenesis. In contrast, the biological role of protocadherins is elusive. Circumstantial evidence, however, suggests that protocadherins are involved in a variety of cell-cell interactions. Since protocadherins, and many other new cadherins as well, have unique properties, studies of these cadherins may provide insight into the structure and biological role of the cadherin superfamily.
Prostate Cancer Screening Perceptions, Knowledge and Behaviors among African American Men: Focus Group Findings (2005)

The purpose of the study was to explore, using focus groups, the knowledge, perceptions, attitudes, and behavior of African American men concerning prostate cancer and screening for the disease using the prostate specific antigen and the digital rectal examination. Twelve focus groups (n=104) were conducted among African American men 40 years of age and older, residing in three counties in the metropolitan area of Baltimore, Maryland. The results of the study show various barriers to screening among the target population, which include limited knowledge about the disease, lack of access to screening services, embarrassment and fear of a positive diagnosis. Additional barriers reported were distrust of medical professionals and the government, reluctance to talk about sex-related health problems, complacency about the possibility of having the disease, and belief that prostate cancer is related to sexual behavior. Positive beliefs, hope, and familiarity with the disease were enabling factors for prostate cancer screening. The focus groups served to open doors to communities from the research and medicine world, and heightened awareness of prostate cancer.
Integrated-optic dispersion compensator that uses chirped gratings (1995)

An integrated-optic dispersion compensator that uses chirped waveguide gratings is designed and fabricated. The 7-mm-long chirped grating is realized by a recently proposed method of curving a waveguide through a uniform grating. At 800 nm, the fabricated device exhibits a reflection bandwidth in excess of 0.5 nm and a nearly quadratic phase response corresponding to a fiber dispersion–length product of 58 ps/nm. The phase response reported is measured interferometrically with a narrow-band, tunable Ti:sapphire laser. Extending this technology to 5-cm-long gratings should permit dispersion compensation of 50-km-long fiber lengths at 1.55 μm.
Mitochondria in Neurodegeneration: Bioenergetic Function in Cell Life and Death (1999)

The biochemical pathways to cell death in chronic and acute forms of neurodegeneration are poorly understood, limiting the ability to develop effective therapeutic approaches. As details of the apoptotic and necrotic pathways have been revealed, an appreciation for the decisive role that mitochondria play in life-death decisions for the cell has grown. As a result, the need has arisen to reevaluate the significance to cell viability of mitochondrial Ca2+ sequestration, reactive oxygen species generation, and the membrane permeability transition. This review provides basic information on these mitochondrial functions as they relate to control over cell death.
Rewritable Full-Color Recording in a Photon Mode (2000)

The recording of stable and reversible full-color images in the photon mode is reported here. The material is composed of the dicholesteryl ester shown in the Figure, which, when mixed with a small amount of an azobenzene derivative known to be photochemically isomerizable, is able to record full-color images (see also cover) in the liquid-crystalline phase (at increased temperature) but not in the solid phase (room temperature), where images are stable for at least a year.
Dopamine in schizophrenia: a review and reconceptualization (1991)

The possible co-occurrence of high and low dopamine activity in schizophrenia has implications for the conceptualization of dopamine's role in schizophrenia. It would explain the concurrent presence of negative and positive symptoms. This hypothesis is testable and has important implications for treatment of schizophrenia and schizophrenia spectrum disorders.
The Switch between Latency and Replication of Epstein-Barr Virus (1990)

Latency is characteristic behavior of many viruses that persist in their hosts. During latency an intact viral genome resides in the cell, but most viral genes are silent. Diverse inducing stimuli, by which the environment interacts with the host cell, trigger the latent viral genome into replication. Experiments are described that led to the identification of a crucial Epstein-Barr virus (EBV) gene, called ZEBRA, which acts as a switch between latency and replication of this herpes virus. During latency of EBV, ZEBRA expression is repressed. Inducing stimuli cause synthesis of ZEBRA which, in turn, activates expression of several individual EBV early genes. The ZEBRA polypeptide is a site-specific DNA binding protein that is likely to function as a transcriptional transactivator. The recognition that a single viral product may control the latency-to-replication switch offers promise of a detailed understanding of a central process in virology.
Lupus autoantibodies target ribosomal P proteins. (1985)

All nine SLE (systemic lupus erythematosus) sera with antiribosomal antibody activity targeted the same three ribosomal protein antigens, of molecular masses 38 and 17/19 kD when analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting. One serum reacted with an additional protein of approximately kD. Ribosomal subunit fractionation by composite gel electrophoresis and sucrose density ultracentrifugation showed that these proteins were part of the large subunit. Isoelectric focusing in agarose, and two-dimensional polyacrylamide gel electrophoresis revealed that the antigens had pI between 4.5 and 6.5, but that the 17/19 kD antigens were more acidic than the 38 kD antigen. Similarities in the molecular masses, charges, as well as the presence of highly conserved crossreactive epitopes, failure to bind to carboxymethylcellulose at pH 4.2, and extractability of the 17/19 kD proteins by 400 mM NH4Cl-ethanol at 0 degrees C indicated that these antigens were analogous to the proteins P0 (38 kD) and P1/P2 (17/19 kD) described previously (25, 36). Co-identity was confirmed using reference antibodies and antigen. Although antibodies to these proteins were only found in 5-10% of more than 50 sera screened by radioimmunoassay or Western blotting, the selective production of antibodies to epitopes on three (out of a total of more than 80) ribosomal proteins may provide further clues to autoantibody induction of SLE.
Singlet energy transfer and singlet-singlet annihilation in light-emitting blends of organic semiconductors (2009)

Excitation energy transfer from host to guest is studied in spin-cast blends of 4,4′-bis(N-carbazolyl)biphenyl (CBP) and a phosphorescent fac-tris(2-phenylpyridyl)iridium(III)-cored dendrimer using time resolved fluorescence. The kinetics of energy transfer are consistent with homogeneous dispersion of the dendrimers in the CBP host. Diffusion-controlled singlet-singlet exciton annihilation is observed in the CBP host at moderate excitation densities, similar to those encountered in high brightness light-emitting devices and organic lasers. The results are important for organic lighting and the understanding of exciton diffusion in guest-host systems for electrophosphorescence.
Porous bioactive glass and hydroxyapatite ceramic affect bone cell functionin vitro along different time lines (1997)

We describe the effects on cell function of treating porous bioactive glass (BG) such that its surface is a composite of carbonated hydroxyapatite and serum protein. The effects on bone cell function of porous hydroxyapatite (HA) ceramic and porous glass treated to become amorphous calcium phosphate only also were studied subsequent to their having adsorbed a serum protein layer. Substrates treated for different durations were seeded with MC3T3-E1 cells and cultured for 3-17 days. Whereas cells seeded on any substrates, BG and HA produced collagen types I and III, bone sialoprotein, and osteopontin, there were significant differences between HA and BG, and among the various surface conditions created on BG. Covering the glass surface with hydroxyapatite and serum protein enhanced expression of high alkaline phosphatase activity, high rates of cell proliferation, and production of mineralized extracellular matrix. The enhancement may be due to the adsorption of a high quantity of fibronectin from the serum onto the reacted bioactive glass surface.