gebhart/patrepeval huggingface dataset:
A High Resolution Broad Spectral Range Spatial Heterodyne Spectrometer for UV Laboratory Astrophysics (2007)

A high resolving power (&gt;500,000) Spatial Heterodyne Spectrometer with spectral coverage across the VUV - UV region is being built for laboratory spectroscopy including emission branching fractions, improved level energies, and hyperfine/isotopic parameters.
Misacylation of Yeast Amber Suppressor tRNATyr by E. coli Lysyl-tRNA Synthetase and Its Effective Repression by Genetic Engineering of the tRNA Sequence (2006)

Through an exhaustive search for Escherichia coli aminoacyl-tRNA synthetase(s) responsible for the misacylation of yeast suppressor tRNA(Tyr), E. coli lysyl-tRNA synthetase was found to have a weak activity to aminoacylate yeast amber suppressor tRNA(Tyr) (CUA) with L-lysine. Since our protein-synthesizing system for site-specific incorporation of unnatural amino acids into proteins is based on the use of yeast suppressor tRNA(Tyr)/tyrosyl-tRNA synthetase (TyrRS) pair as the "carrier" of unusual amino acid in E. coli translation system, this misacylation must be repressed as low as possible. We have succeeded in effectively repressing the misacylation by changing several nucleotides in this tRNA by genetic engineering. This "optimized" tRNA together with our mutant TyrRS should serve as an efficient and faithful tool for site-specific incorporation of unnatural amino acids into proteins in a protein-synthesizing system in vitro or in vivo.
DNA Unwinding Is the Primary Determinant of CRISPR-Cas9 Activity (2018)

Bacterial adaptive immunity utilizes RNA-guided surveillance complexes comprising Cas proteins together with CRISPR RNAs (crRNAs) to target foreign nucleic acids for destruction. Cas9, a type II CRISPR-Cas effector complex, can be programed with a single-guide RNA that base pairs with the target strand of dsDNA, displacing the non-target strand to create an R-loop, where the HNH and the RuvC nuclease domains cleave opposing strands. While many structural and biochemical studies have shed light on the mechanism of Cas9 cleavage, a clear unifying model has yet to emerge. Our detailed kinetic characterization of the enzyme reveals that DNA binding is reversible, and R-loop formation is rate-limiting, occurring in two steps, one for each of the nuclease domains. The specificity constant for cleavage is determined through an induced-fit mechanism as the product of the equilibrium binding affinity for DNA and the rate of R-loop formation.
Myelin Gene Expression after Experimental Contusive Spinal Cord Injury (1998)

After incomplete traumatic spinal cord injury (SCI), the spared tissue exhibits abnormal myelination that is associated with reduced or blocked axonal conductance. To examine the molecular basis of the abnormal myelination, we used a standardized rat model of incomplete SCI and compared normal uninjured tissue with that after contusion injury. We evaluated expression of mRNA for myelin proteins using in situ hybridization with oligonucleotide probes to proteolipid protein (PLP), the major protein in central myelin; myelin basic protein (MBP), a major component of central myelin and a minor component of peripheral myelin; and protein zero (P0), the major structural protein of peripheral myelin, as well as myelin transcription factor 1 (MYT1). We found reduced expression of PLP and MBP chronically after SCI in the dorsal, lateral, and ventral white matter both rostral and caudal to the injury epicenter. Detailed studies of PLP at 2 months after injury indicated that the density of expressing cells was normal but mRNA per cell was reduced. In addition, P0, normally restricted to the peripheral nervous system, was expressed both at the epicenter and in lesioned areas at least 4 mm rostral and caudal to it. Thus, after SCI, abnormal myelination of residual axons may be caused, at least in part, by changes in the transcriptional regulation of genes for myelin proteins and by altered distribution of myelin-producing cells. In addition, the expression of MYT1 mRNA and protein seemed to be upregulated after SCI in a pattern suggesting the presence of undifferentiated progenitor cells in the chronically injured cord.
The heterogeneity of mononuclear phagocytes in lymphoid organs: distinct macrophage subpopulations in the rat recognized by monoclonal antibodies ED1, ED2 and ED3. (1985)

In the present study, a set of three monoclonal antibodies is described, each of which recognizes cells of the monocyte-macrophage lineage in the rat. The tissue distribution, in particular in lymphoid organs, of each of the three monoclonals is determined by immunoenzyme histochemistry on cryostat sections, as well as on cell suspensions. Results show that ED1 recognizes a cytoplasmic antigen in monocytes and in most macrophages, free and fixed. ED2 and ED3 recognize membrane antigens of tissue macrophages, discriminating between distinct subpopulations of macrophages, each with a characteristic localization in the compartments of lymphoid organs. No other cell types except cells of the mononuclear phagocyte system are positive for any of the three monoclonals. Possible relations between the macrophages recognized by this set of monoclonals and dendritic cells are discussed.
Medial–Frontal Stimulation Enhances Learning in Schizophrenia by Restoring Prediction Error Signaling (2015)

When there is a difference between what we expect to happen and what we actually experience, our brains generate a prediction error signal, so that we can map stimuli to responses and predict outcomes accurately. Theories of schizophrenia implicate abnormal prediction error signaling in the cognitive deficits of the disorder. Here, we combine noninvasive brain stimulation with large-scale electrophysiological recordings to establish a causal link between faulty prediction error signaling and learning deficits in schizophrenia. We show that it is possible to improve learning rate, as well as the neural signature of prediction error signaling, in patients to a level quantitatively indistinguishable from that of healthy subjects. The results provide mechanistic insight into schizophrenia pathophysiology and suggest a future therapy for this condition.
A facile route to imidazol-4-yl anions and their reaction with carbonyl compounds (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA facile route to imidazol-4-yl anions and their reaction with carbonyl compoundsRichard M. Turner, Stephen D. Lindell, and Steven V. LeyCite this: J. Org. Chem. 1991, 56, 20, 5739–5740Publication Date (Print):September 1, 1991Publication History Published online1 May 2002Published inissue 1 September 1991https://pubs.acs.org/doi/10.1021/jo00020a002https://doi.org/10.1021/jo00020a002research-articleACS PublicationsRequest reuse permissionsArticle Views712Altmetric-Citations64LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Practical free-space quantum key distribution over 10 km in daylight and at night (2002)

We have demonstrated quantum key distribution (QKD) over a 10-km, 1-airmass atmospheric range during daylight and at night. Secret random bit sequences of the quality required for the cryptographic keys used to initialize secure communications devices were transferred at practical rates with realistic security. By identifying the physical parameters that determine the system's secrecy efficiency, we infer that free-space QKD will be practical over much longer ranges under these and other atmospheric and instrumental conditions.
Automatic registration of microarray images. I. Rectangular grid (2003)

http://fleece.ucsd.edu/~vit/Registration_Supplement.pdf
Regulation of Cell Cycle in Hematopoietic Stem Cells by the Niche (2004)

The quiescent state is thought to be an indispensable property for the maintenance of hematopoietic stem cells (HSCs). Interaction of HSCs with their particular microenvironments, known as the stem cell niches, is critical for cell cycle regulation of HSCs. Monitoring of the quiescence of HSCs using by a new stem cell marker, Side Population (SP), revealed that the cell cycle status of HSCs is dynamically controlled by the microenvironments. We have recently revealed a molecular mechanism in which cell cycle of HSCs is regulated by the niche. HSCs expressing the receptor tyrosine kinase Tie2 are adhere to osteoblasts (OBs) in the BM niche. The interaction of Tie2 and its ligand Angiopoietin-1 (Ang-1) leads to tight adhesion of HSCs to stromal cells, resulting in maintainance of long-term repopulating activity of HSCs. Thus, Tie2/Ang-1 signaling pathway plays a critical role in the maintenance of HSCs in a quiescent state in the BM niche. The understanding of cell cycle control in stem cells leads to development of new strategy for progress in regenerative medicine.
Determination of intrinsic hydrophilicity/hydrophobicity of amino acid side chains in peptides in the absence of nearest‐neighbor or conformational effects (2005)

Understanding the hydrophilicity/hydrophobicity of amino acid side chains in peptides/proteins is one the most important aspects of biology. Though many hydrophilicity/hydrophobicity scales have been generated, an "intrinsic" scale has yet to be achieved. "Intrinsic" implies the maximum possible hydrophilicity/hydrophobicity of side chains in the absence of nearest-neighbor or conformational effects that would decrease the full expression of the side-chain hydrophilicity/hydrophobicity when the side chain is in a polypeptide chain. Such a scale is the fundamental starting point for determining the parameters that affect side-chain hydrophobicity and for quantifying such effects in peptides and proteins. A 10-residue peptide sequence, Ac-X-G-A-K-G-A-G-V-G-L-amide, was designed to enable the determination of the intrinsic values, where position X was substituted by all 20 naturally occurring amino acids and norvaline, norleucine, and ornithine. The coefficients were determined by reversed-phase high-performance liquid chromatography using six different mobile phase conditions involving different pH values (2, 5, and 7), ion-pairing reagents, and the presence and absence of different salts. The results show that the intrinsic hydrophilicity/hydrophobicity of amino acid side chains in peptides (proteins) is independent of pH, buffer conditions, or whether C(8) or C(18) reversed-phase columns were used for 17 side chains (Gly, Ala, Cys, Pro, Val, nVal, Leu, nLeu, Ile, Met, Tyr, Phe, Trp, Ser, Thr, Asn, and Gln) and dependent on pH and buffer conditions, including the type of salt or ion-pairing reagent for potentially charged side chains (Orn, Lys, His, Arg, Asp, and Glu).
Animal Models Used in Spinal Cord Regeneration Research (2002)

Animal models will continue to play a critical role in the development of experimental therapies for spinal cord injuries. Both sharp and blunt spinal cord injury paradigms have unique characteristics that make them useful in addressing slightly different neurobiologic problems.
Decrease in Serum Hepatitis C Viral RNA during Alpha-Interferon Therapy for Chronic Hepatitis C (1991)

These results indicate that the clinical and serum biochemical response to alpha-interferon in chronic hepatitis C is associated with a loss of detectable HCV genome from serum.
PaDDMAS: parallel and distributed data mining application suite (2002)

Discovering complex associations, anomalies and patterns in distributed data sets is gaining popularity in a range of scientific, medical and business applications. Various algorithms are employed to perform data analysis within a domain, and range from statistical to machine learning and AI based techniques. Several issues need to be addressed however to scale such approaches to large data sets, particularly when these are applied to data distributed at various sites. As new analysis techniques are identified, the core tool set must enable easy integration of such analytical components. Similarly, results from an analysis engines must be sharable, to enable storage, visualisation or further analysis of results. We describe the architecture of PaDDMAS, a component based system for developing distributed data mining applications. PaDDMAS provides a tool set for combining pre-developed or custom components using a dataflow approach, with components performing analysis, data extraction or data management and translation. Each component is wrapped as a Java/CORBA object, and has an interface defined in XML. Components can be serial or parallel objects, and may be binary or contain a more complex internal structure. We demonstrate a prototype using a neural network analysis algorithm.
Provocative pattern of rearrangements of the genes for the gamma and beta chains of the T-cell receptor in human leukemias. (1987)

To examine the distribution of rearrangements of the gamma- and beta-chain T-cell receptor (TCR) genes in T- and non-T acute lymphoblastic leukemias (ALLs), and potentially to determine which genes rearrange first in ontogeny, we analyzed high molecular weight DNA from 102 patients with acute leukemia. Rearranged gamma- and beta-chain genes were found in all T-cell ALLs (22/22) examined. Overall, 27% (18/66) of B-lineage ALLs had beta-chain gene rearrangements, and 41% (24/58) had gamma-chain gene rearrangements, but the distribution of rearranged genes varied according to the stage of B-cell differentiation. The gamma-chain genes were rearranged in 11% (1/9) of the B-lineage patients negative for the common acute lymphoblastic leukemia antigen (cALLA) and 50% (23/46) of cALLA+ ALL patients, while the beta-chain genes were not rearranged in any of the 7 cALLA- ALL patients examined but were rearranged in 32% (18/56) of the cALLA+ patients. Neither TCR gene was found to be rearranged in acute nonlymphoid leukemia patients (0/12) or in patients with B-cell (surface immunoglobulin-positive) leukemia (0/3). Of the 44 cALLA+ patients in which a direct comparison of gamma- and beta-chain gene rearrangements could be made, 34% had both genes rearranged, 16% had only gamma-chain gene rearrangements, and the remaining 50% had both genes in the germ-line configuration. beta-Chain rearrangements have not been found in the absence of gamma-chain rearrangements, thus supporting a proposed hierarchy of TCR gene rearrangements. A provocative finding was that only a small percentage (11%) of the patients with cALLA- B precursor cell ALLs had rearranged TCR genes, while 50% of the cALLA+ leukemia patients had at least gamma-chain rearrangement, raising a question as to whether indeed cALLA- cells are precursors to cALLA+ cells. Interestingly, 18% (2/11) of the cytoplasmic immunoglobulin (cIg)-positive cALLA+ (pre-B) ALLs involved TCR gene rearrangements, compared to 60% (21/35) of the cIg-negative cases, suggesting the possibility that the majority of functional B cells are derived from the cALLA+ pool that contains immunoglobulin but not TCR gene rearrangements.
Somatic Mutations and Immunotherapy Outcome with CTLA-4 Blockade in Melanoma (2014)

One of the greatest challenges in the study and treatment of cancer has been that the disease is too heterogeneous: too many tissue types, too many etiologic factors, too much genetic diversity. After the discovery of oncogenes, it was thought that a limited number of genes, the proto-oncogenes, might turn a normal cell into a cancerous one. But soon it was discovered that tumor-suppressor genes antagonize the action of oncogenes, thus increasing genetic diversity in the context of cancer pathogenesis. To date, about 140 genes have been identified that can drive cancer growth when genetically altered.1 The discovery that driver . . .
Clinical Impact of Checkpoint Inhibitors as Novel Cancer Therapies (2014)

Immune responses are tightly regulated via signaling through numerous co-stimulatory and co-inhibitory molecules. Exploitation of these immune checkpoint pathways is one of the mechanisms by which tumors evade and/or escape the immune system. A growing understanding of the biology of immune checkpoints and tumor immunology has led to the development of monoclonal antibodies designed to target co-stimulatory and co-inhibitory molecules in order to re-engage the immune system and restore antitumor immune responses. Anti-cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) antibodies were among the first to be tested in the clinic, and ipilimumab was the first immune checkpoint inhibitor approved for an anticancer indication. Agents targeting the programmed death 1 (PD-1) pathway, either PD-1 or one of its ligands, programmed death ligand 1, are in active clinical development for numerous cancers, including advanced melanoma and lung cancer. Understanding the different mechanisms of action, safety profiles, and response patterns associated with inhibition of the CTLA-4 and PD-1 pathways may improve patient management as these therapies are moved in to the clinical practice setting and may also provide a rationale for combination therapy with different inhibitors. Additional immune checkpoint molecules with therapeutic potential, including lymphocyte activation gene-3 and glucocorticoid-induced tumor necrosis factor receptor-related gene, also have inhibitors in early stages of clinical development. Clinical responses and safety data reported to date on immune checkpoint inhibitors suggest these agents may have the potential to markedly improve outcomes for patients with cancer.
Identification of regions of bovine factor VII essential for binding to tissue factor. (1994)

Initiation of the extrinsic blood coagulation pathway is mediated by a complex formed between plasma-derived factor VII/VIIa and cell-derived tissue factor (TF). To identify the site(s) of interaction, zymogen VII and VIIa were enzymatically and chemically modified, and their affinities for TF were estimated by measuring their inhibitory effects on the amidolytic activity enhanced after formation of the VIIa-TF complex. We found that the VIIa-light chain (Ki = 3.5 x 10(-7) M) and its fragment consisting of the gamma-carboxyglutamic acid (Gla)-domain and the first epidermal growth factor (EGF)-like domain (Gla-EGF1 peptide; Ki = 1.0 x 10(-6) M) have an affinity for TF. Therefore, one of the binding sites of VII with TF is probably located in the Gla-EGF1 region. On the other hand, a dansyl-Glu-Gly-Arg chloromethyl ketone-treated Gla-domainless VIIa (Ki = 0.7 x 10(-7) M) showed a high affinity for TF, whereas the corresponding Gla-domainless VII similarly treated showed no binding potential, thereby indicating that binding site(s) other than in the Gla-EGF1 region are present in VIIa but not in VII. Acetylation or carbamylation of the alpha-amino group of the NH2-terminal Ile-153 of VIIa resulted in the loss of binding affinity for TF; such modifications convert VIIa into a zymogen-like inactive form by destroying the salt bridge between Ile-153 and Asp-343 in VIIa. The rate of carbamylation of VIIa was reduced in the presence of TF. Protection of the alpha-amino group of Ile-153 from carbamylation after complex formation was consistent with salt bridge formation between Ile-153 and Asp-343 in the VIIa-TF complex. Therefore, binding of TF with the heavy chain of VIIa may induce a conformational change that brings the alpha-amino group of Ile-153 close to the beta-carboxyl group of Asp-343 to make a stable salt bridge.
Architecture for interoperability of services between an ACAP receiver and home networked devices (2006)

As digital convergence of home networking and broadcasting technologies is being accelerated, it becomes increasingly important to achieve interoperability of not only heterogeneous devices but also various types of services. Therefore, in this paper, we describe the design and implementation of architecture for interoperability of data broadcasting and home networking services based on the ACAP middleware and the UMB stack. The proposed architecture provides a TV-centric user interface capable of managing home networking services using TV sets, by applying Java TV Xlet interface and HAVi user interface APIs for home networking sendees such as data broadcasting services. In addition, it provides data broadcasting services through metadata and media streaming for home networked devices without ACAP middleware.
Inhibitors of myosin light chain kinase and phosphodiesterase reduce ventilator-induced lung injury (2000)

Alveolar overdistension due to high peak inflation pressures (PIP) is associated with an increased capillary filtration coefficient (K(fc)). To determine which signal pathways contribute to this injury, we perfused isolated rat lungs with 5% bovine albumin in Krebs solution and measured K(fc) after successive 30-min periods of ventilation with peak inflation pressures (PIP) of 7, 20, 30, and 35 cmH(2)O. In a high-PIP control group, K(fc) increased significantly after ventilation with 30 and 35 cmH(2)O PIP, but significant increases were prevented by treatment with 100 microM trifluoperazine, an inhibitor of Ca(2+)/calmodulin, 500 nM ML-7, an inhibitor of myosin light chain kinase (MLCK), a combination of isoproterenol (20 microM) and rolipram (10 microM) to enhance intracellular cAMP levels, and a dose of KT-5720 (2 microM), which inhibits MLCK and protein kinase C. These studies suggest that the Ca(2+)/calmodulin-MLCK pathway augments capillary fluid leak after a modest high-PIP injury and that this is attenuated by kinase inhibition and increased intracellular cAMP.
In Vivo Inhibition of CC and CX3C Chemokine–induced Leukocyte Infiltration and Attenuation of Glomerulonephritis in Wistar-Kyoto (WKY) Rats by vMIP-II (1998)

Chemokines play a central role in immune and inflammatory responses. It has been observed recently that certain viruses have evolved molecular piracy and mimicry mechanisms by encoding and synthesizing proteins that interfere with the normal host defense response. One such viral protein, vMIP-II, encoded by human herpesvirus 8, has been identified with in vitro antagonistic activities against CC and CXC chemokine receptors. We report here that vMIP-II has additional antagonistic activity against CX3CR1, the receptor for fractalkine. To investigate the potential therapeutic effect of this broad-spectrum chemokine antagonist, we studied the antiinflammatory activity of vMIP-II in a rat model of experimental glomerulonephritis induced by an antiglomerular basement membrane antibody. vMIP-II potently inhibited monocyte chemoattractant protein 1-, macrophage inflammatory protein 1beta-, RANTES (regulated on activation, normal T cell expressed and secreted)-, and fractalkine-induced chemotaxis of activated leukocytes isolated from nephritic glomeruli, significantly reduced leukocyte infiltration to the glomeruli, and markedly attenuated proteinuria. These results suggest that molecules encoded by some viruses may serve as useful templates for the development of antiinflammatory compounds.