gebhart/patrepeval huggingface dataset:
Identification of Metal Ligands in the Clostridium histolyticum ColH Collagenase (1999)

A Clostridium histolyticum 116-kDa collagenase has an H415EXXH motif but not the third zinc ligand, as found in already characterized zinc metalloproteinases. To identify its catalytic site, we mutated the codons corresponding to the three conserved residues in the motif to other amino acid residues. The mutation affecting His415 or His419 abolished catalytic activity and zinc binding, while that affecting Glu416 did the former but not the latter. These results suggest that the motif forms the catalytic site. We also mutated the codons corresponding to other amino acid residues that are likely zinc ligands. The mutation affecting Glu447 decreased markedly both the enzymatic activity and the zinc content, while that affecting Glu446 or Glu451 had smaller effects on activity and zinc binding. These mutations caused a decrease in kcat but no significant change in Km. These results are consistent with the hypothesis that Glu447 is the third zinc ligand. The spacing of the three zinc ligands is the same in all known clostridial collagenases but not in other known gluzincins, indicating that they form a new gluzincin subfamily. The effects of mutations affecting Glu446 and Glu451 suggest that the two residues are also involved in catalysis, possibly through an interaction with the two zinc-binding histidine residues.
Inhibition of Ras–effector interactions by cyclic peptides (2012)

A combinatorial library of 6 × 10<sup>6</sup> cyclic peptides was synthesized in the one bead-two compound format, with each bead displaying a unique cyclic peptide on its surface and a linear peptide encoding tag in its interior. Screening of the library against K-Ras identified compounds that bound K-Ras with submicromolar affinity and disrupted its interaction with effector proteins.
A Survey of Cloud Storage Facilities (2011)

There are many applications such as software for processing customer records in telecom, patient records in hospitals, email processing software accessing a single email in a mailbox etc. which require to access a single record in a database consisting of millions of records. A basic feature of these applications is that they need to access data sets which are very large but simple. Cloud computing provides computing requirements for these kinds of new generation of applications involving very large data sets which cannot possibly be handled efficiently using traditional computing infrastructure. In this paper, we describe storage services provided by three well-known cloud service providers and give a comparison of their features with a view to characterize storage requirements of very large data sets as examples and we hope that it would act as a catalyst for the design of storage services for very large data set requirements in future. We also give a brief overview of other kinds of storage that have come up in the recent past for cloud computing.
Amdahl multiple-domain architecture (1988)

A description is given of extensions to the architecture of Amdahl's first mainframe computers, which were hard-wired implementations of the IBM System/370 architecture, and the why's and how's of their development are examined. The latest architecture helps maintain compatibility with a changing standard. Its multiple-domain facility allows multiple operating systems to share one mainframe system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Physiologic Oxygen Enhances Human Embryonic Stem Cell Clonal Recovery and Reduces Chromosomal Abnormalities (2006)

Human embryonic stem cells (hESC) have great potential in regenerative medicine, provided that culture systems are established that maintain genomic integrity. Here we describe a comparison of the effects of culture in either physiologic oxygen (2%) or room oxygen (21%) on the hESC lines, H1, H9, and RH1. Physiologic oxygen enabled an average sixfold increase in clone recovery across the hESC lines tested (p < 0.001). FACS analysis showed that cells cultured in physiologic oxygen were significantly smaller and less granular. No significant changes had occurred in levels of SSEA4, SSEA1, TRA-1-60, or TRA-1-81. While karyotypic normalcy was maintained in both H1 and H9, the frequency of spontaneous chromosomal aberrations was significantly increased in room oxygen. This increase was not observed in physiologic oxygen. These results clearly demonstrate that physiologic oxygen culture conditions are indispensable for robust hES clone recovery and may enhance the isolation of novel hES lines and transgenic clones.
Activation of ARF6 by ARNO stimulates epithelial cell migration through downstream activation of both Rac1 and phospholipase D (2001)

Migration of epithelial cells is essential for tissue morphogenesis, wound healing, and metastasis of epithelial tumors. Here we show that ARNO, a guanine nucleotide exchange factor for ADP-ribosylation factor (ARF) GTPases, induces Madin-Darby canine kidney epithelial cells to develop broad lamellipodia, to separate from neighboring cells, and to exhibit a dramatic increase in migratory behavior. This transition requires ARNO catalytic activity, which we show leads to enhanced activation of endogenous ARF6, but not ARF1, using a novel pulldown assay. We further demonstrate that expression of ARNO leads to increased activation of endogenous Rac1, and that Rac activation is required for ARNO-induced cell motility. Finally, ARNO-induced activation of ARF6 also results in increased activation of phospholipase D (PLD), and inhibition of PLD activity also inhibits motility. However, inhibition of PLD does not prevent activation of Rac. Together, these data suggest that ARF6 activation stimulates two distinct signaling pathways, one leading to Rac activation, the other to changes in membrane phospholipid composition, and that both pathways are required for cell motility.
Neonatal neutrophil dysfunction. (1989)

Functional as well as quantitative abnormalities of neutrophilic granulocytes have been implicated in the pathogenesis of neonatal septicemia and other infectious complications in human neonates. Despite considerable previous investigation, the molecular basis for observed abnormalities of inflammatory functions of neonatal neutrophils is not well understood. The development of novel preventative or therapeutic strategies for high-risk neonatal populations will depend upon further investigations to delineate the fundamental basis of abnormal cellular events.
Hierarchical Self-Assembly of Poly(γ-benzyl-l-glutamate)−Poly(ethylene glycol)−Poly(γ-benzyl-l-glutamate) Rod−Coil−Rod Triblock Copolymers (2003)

The self-assembly mechanism has been studied in poly(γ-benzyl-l-glutamate)−poly(ethylene glycol)−poly(γ-benzyl-l-glutamate) (PBLG−PEG−PBLG) triblock copolymer melts using X-ray scattering, polarizing optical microscopy, differential scanning calorimetry, and FTIR spectroscopy. Intrinsic competing interactions (crystallization, hydrogen bonding, liquid crystallinity, microphase separation) give rise to different levels of organization. Depending on the peptide volume fraction f, two cases can be discussed: for low peptide volume fractions, microphase separation results in PBLG and PEG phases rich in all secondary structures (α-helices, β-sheets, and chain-folded PEG) notwithstanding the large undercooling necessary to induce PEG crystallization. For f > 0.4, interfacial mixing results in the destruction of the less coherent peptide secondary structures (β-sheet). Interfacial mixing may prove to be a key factor in controlling the appearance of β-sheets in low molecular weight peptides.
Development of Monocytes, Macrophages, and Dendritic Cells (2010)

Monocytes and macrophages are critical effectors and regulators of inflammation and the innate immune response, the immediate arm of the immune system. Dendritic cells initiate and regulate the highly pathogen-specific adaptive immune responses and are central to the development of immunologic memory and tolerance. Recent in vivo experimental approaches in the mouse have unveiled new aspects of the developmental and lineage relationships among these cell populations. Despite this, the origin and differentiation cues for many tissue macrophages, monocytes, and dendritic cell subsets in mice, and the corresponding cell populations in humans, remain to be elucidated.
Germinal Center Marker GL7 Probes Activation-Dependent Repression of N -Glycolylneuraminic Acid, a Sialic Acid Species Involved in the Negative Modulation of B-Cell Activation (2007)

Sialic acid (Sia) is a family of acidic nine-carbon sugars that occupies the nonreducing terminus of glycan chains. Diversity of Sia is achieved by variation in the linkage to the underlying sugar and modification of the Sia molecule. Here we identified Sia-dependent epitope specificity for GL7, a rat monoclonal antibody, to probe germinal centers upon T cell-dependent immunity. GL7 recognizes sialylated glycan(s), the alpha2,6-linked N-acetylneuraminic acid (Neu5Ac) on a lactosamine glycan chain(s), in both Sia modification- and Sia linkage-dependent manners. In mouse germinal center B cells, the expression of the GL7 epitope was upregulated due to the in situ repression of CMP-Neu5Ac hydroxylase (Cmah), the enzyme responsible for Sia modification of Neu5Ac to Neu5Gc. Such Cmah repression caused activation-dependent dynamic reduction of CD22 ligand expression without losing alpha2,6-linked sialylation in germinal centers. The in vivo function of Cmah was analyzed using gene-disrupted mice. Phenotypic analyses showed that Neu5Gc glycan functions as a negative regulator for B-cell activation in assays of T-cell-independent immunization response and splenic B-cell proliferation. Thus, Neu5Gc is required for optimal negative regulation, and the reaction is specifically suppressed in activated B cells, i.e., germinal center B cells.
Preneoplastic Prostate Lesions (2001)

Environmental factors, especially the diet, play a prominent role in the epidemic of prostate cancer (PCA), in the United States. Many candidate dietary components have been proposed to influence human prostatic carcinogenesis, including fat, calories, fruits and vegetables, anti-oxidants, and various micronutrients, but the specific roles dietary agents play in promoting or preventing PCA remain controversial. We have collected evidence to suggest that GSTP1, the gene encoding the pi-class glutathione S-transferase (GST), may serve a "caretaker" function for prostatic cells. Although GSTP1 can be detected in normal prostatic epithelium, in almost all PCA cases, PCA cells fail to express GSTP1 polypeptides, and lack of GSTP1 expression most often appears to be the result of somatic "CpG island" DNA methylation changes. Loss of GSTP1 function also appears to be characteristic of prostatic epithelial neoplasia (PIN) lesions, thought to represent PCA precursors. We have recently learned that a new candidate early PCA precursor lesion, proliferative inflammatory atrophy (PIA), characterized by proliferating prostatic cells juxtaposed to inflammatory cells, contains epithelial cells that express high levels of GSTP1. These findings have formed the basis for a new model of prostatic carcinogenesis, in which prostatic cells in PIA lesions, subjected to a barrage of inflammatory oxidants, induce GSTP1 expression as a defense against oxidative genome damage. When cells with defective GSTP1 genes appear amongst the PIA cells, such cells become vulnerable to oxidants and electrophiles that inflict genome damage that tends to promote neoplastic transformation to PIN and PCA cells. Subsequently, PIN and PCA cells with defective GSTPI genes remain vulnerable to similar stresses tending to promote malignant progression. This new model for prostatic carcinogenesis has implications for the design of new prostate cancer prevention strategies. Rational prevention approaches might include: (i) restoration of GSTPI expression via treatment with inhibitors of CpG methylation, (ii) compensation for inadequate GSTPI activity via treatment with inducers of general GST activity, and (iii) abrogation of genome-damaging stresses via avoidance of exogenous carcinogens and/or reduction of endogenous carcinogenic (particularly oxidant) stresses.
Catabolism in uremia: the impact of metabolic acidosis. (1998)

Chronic metabolic acidosis stimulates the catabolism of bone and muscle in experimental animals and humans. The toxicity caused by acidosis involves changes in endocrine function and toxicity arising from the homeostatic responses that are activated by the body to maintain pH near normal levels. Glucocorticoids, insulin, insulin-like growth factor-1, and parathyroid hormone play important roles in the homeostatic responses of bone and muscle to acid. Bone buffering of acid and the resulting increase in renal calcium excretion leads to negative calcium balance. Activation of the ubiquitin-proteasome proteolytic system and branched-chain ketoacid dehydrogenase in muscle, along with hepatic glutamine synthesis in the liver and renal glutamine uptake, are homeostatic mechanisms that cause negative nitrogen balance and loss of muscle mass. Treating the acidosis of chronic renal insufficiency improves both bone and muscle metabolism by reducing the loss of calcium and protein and amino acids in the two organs, respectively. Thus, treating acidosis suppresses both bone and muscle catabolism in patients with normal and reduced renal function.
The indoor radio propagation channel (1993)

In this tutorial survey the principles of radio propagation in indoor environments are reviewed. The channel is modeled as a linear time-varying filter at each location in the three-dimensional space, and the properties of the filter's impulse response are described. Theoretical distributions of the sequences of arrival times, amplitudes and phases are presented. Other relevant concepts such as spatial and temporal variations of the channel, large-scale path losses, mean excess delay and RMS delay spread are explored. Propagation characteristics of the indoor and outdoor channels are compared and their major differences are outlined. Previous measurement and modeling efforts are surveyed, and areas for future research are suggested.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characterization of Antibodies that Detect Human GFAP after Traumatic Brain Injury (2012)

After traumatic brain injury (TBI), glial fibrillary acidic protein (GFAP) and other brain-derived proteins and their breakdown products are released into biofluids such as CSF and blood. Recently, a sandwich ELISA was constructed that measured GFAP concentrations in CSF or serum from human mild-moderate TBI patients. The goals of the present study were to characterize the same two antibodies used in this ELISA, and to determine which GFAP bands are detected by this antibody combination. Here, both antibodies recognized GFAP specifically in human brain and post-TBI CSF in a cluster of bands ranging from 50-38 kDa, that resembled bands from calpain-cleaved GFAP. By immunoprecipitation, the anti-GFAP Capture antibody recovered full length GFAP and its breakdown products from human brain lysate and post-TBI CSF. These findings demonstrate that the anti-GFAP ELISA antibodies non-preferentially detect intact GFAP and GFAP breakdown products, underscoring their utility for detecting brain injury in human patients.
Production of superoxide anions by a CNS macrophage, the microglia (1987)

Microglia have been implicated in both physiological and pathological processes of the brain. Their possible roles have been compared to those of macrophages and granulocytes. Here we demonstrate that specific ability of microglia to secrete the superoxide radical ion in response to a complement activated agent, opsonized zymosan, and to phorbol myristate acetate. As in other organs, this endogenously produced reactive oxygen intermediate could have both beneficial and deleterious effects.
The Structure of the Potassium Channel: Molecular Basis of K + Conduction and Selectivity (1998)

The potassium channel from Streptomyces lividans is an integral membrane protein with sequence similarity to all known K+ channels, particularly in the pore region. X-ray analysis with data to 3.2 angstroms reveals that four identical subunits create an inverted teepee, or cone, cradling the selectivity filter of the pore in its outer end. The narrow selectivity filter is only 12 angstroms long, whereas the remainder of the pore is wider and lined with hydrophobic amino acids. A large water-filled cavity and helix dipoles are positioned so as to overcome electrostatic destabilization of an ion in the pore at the center of the bilayer. Main chain carbonyl oxygen atoms from the K+ channel signature sequence line the selectivity filter, which is held open by structural constraints to coordinate K+ ions but not smaller Na+ ions. The selectivity filter contains two K+ ions about 7.5 angstroms apart. This configuration promotes ion conduction by exploiting electrostatic repulsive forces to overcome attractive forces between K+ ions and the selectivity filter. The architecture of the pore establishes the physical principles underlying selective K+ conduction.
A motif in human histidyl-tRNA synthetase which is shared among several aminoacyl-tRNA synthetases is a coiled-coil that is essential for enzymatic activity and contains the major autoantigenic epitope. (1994)

In myositis, disease-specific autoantibodies may be directed against an aminoacyl-tRNA synthetase, usually histidyl-tRNA synthetase. To explore the basis for this phenomenon, we have made recombinant histidyl-tRNA synthetase in the baculovirus system. It was enzymatically active and recognized by human autoantibodies. A truncated protein lacking the first 60 amino acids was inactive as an antigen and as an enzyme. This region is within the first two exons, is predicted to have a coiled-coil configuration, and is found in some other synthetases but not in Escherichia coli or yeast histidyl-tRNA synthetase. Circular dichroism showed that the peptides from this region (amino acids 1-60 and 1-47) have the predicted high alpha-helical content, but smaller fragments (1-30, 14-45, and 31-60) do not. The peptides with a high alpha-helical content could inhibit autoantibodies almost completely, whereas the smaller peptides were unable to do so. The amino acid sequence of this coiled-coil domain in human histidyl-tRNA synthetase resembles the sequence of the extended this coiled-coil arm near the NH2 terminus of bacterial seryl-tRNA synthetase as well as similar regions in some eukaryotic aminoacyl-tRNA synthetases, raising the possibility that this domain serves a similar tRNA-stabilizing role and has been preserved from a common ancestor.
Supporting application-tailored grid file system sessions with WSRF-based services (2005)

This paper presents novel service-based grid data management middleware that leverages standards defined by WSRF specifications to create and manage dynamic grid file system sessions. A unique aspect of the service is that the sessions it creates can be customized to address application data transfer needs. Application-tailored configurations enable selection of both performance-related features (block-based partial file transfers and/or whole-file transfers, cache parameters and consistency models) and reliability features (file system copy-on-write checkpointing to aid recovery of client-side failures; replication, autonomous failure detection and data access redirection for server-side failures). These enhancements, in addition to cross-domain user identity mapping and encrypted communication, are implemented via user level proxies managed by the service, requiring no changes to existing kernels. Sessions established using the service is mounted as distributed file systems and can be used transparently by unmodified binary applications. The paper analyzes the use of the service to support virtual machine based grid systems and workflow execution, and also reports on the performance and reliability of service managed wide-area file system sessions with experiments based on scientific applications (NanoMOS/Matlab, CHID, GAUSS and SPECseis).
Formation of Enantiopure 5-Substituted Oxazolidinones through Enzyme-Catalysed Kinetic Resolution of Epoxides (2008)

Halohydrin dehalogenase from Agrobacterium radiobacter catalyzed the enantioselective ring opening of terminal epoxides with cyanate as a nucleophile, yielding 5-substituted oxazolidinones in high yields and with high enantiopurity (69-98% ee). This is the first example of the biocatalytic conversion of a range of epoxides to the corresponding oxazolidinones.
In Vivo Near-Infrared Spectroscopy of Rat Skin Tissue with Varying Blood Glucose Levels (2005)

We have performed in vivo measurements of near-infrared rat skin absorption in the 4000-5000-cm(-1) spectral range (2.0-2.5-microm wavelength) during a glucose clamp experiment in order to identify the presence of glucose-specific spectral information. Spectra were collected during an initial 3-h period where the animal's blood glucose concentration was held at its normal value. The blood glucose level was then increased above 30 mM by venous infusion of glucose and held for 2 h, after which it was allowed to return to normal. Spectra were recorded continuously during the procedure and are analyzed to identify spectral changes associated with changes in glucose concentration. Because the change in absorbance due to an increase in glucose concentration is small compared to changes due to other variations (e.g., the thickness of the skin sample), a simple subtraction of absorbance spectra from the hyperglycemic and euglycemic phases is not instructive. Instead, a set of principal components is established from the euglycemic period where the glucose concentration is constant. We then examine the change in absorbance during the hyperglycemic period that is orthogonal to these principal components. We find that there are significant similarities between these orthogonal variations and the net analyte signal of glucose, which suggests that glucose spectral information is present. The analysis described here provides a procedure by which the analytical significance of a multivariate calibration can be evaluated.
Challenges to increasing targeting efficiency in genome engineering (2015)

Gene targeting technologies are essential for the analysis of gene functions. Knockout mouse generation via genetic modification of embryonic stem cells (ESCs) is the commonest example, but it is a time-consuming and labor-intensive procedure. Recently, a novel genome editing technology called CRISPR/Cas has enabled the direct production of knockout mice by non-homologous end joining (NHEJ)-mediated mutations. Unexpectedly, however, it generally exhibits a low efficiency in homologous recombination (HR) and is prone to high mosaicism. Meanwhile, gene targeting using ESCs is still being improved, as reported by Fukuda et al. in this issue. Here, we outline current gene targeting technologies with special emphasis on HR-mediated technologies, which are currently being performed using these two major strategies.