gebhart/patrepeval huggingface dataset:
Annexin IV inhibits calmodulin-dependent protein kinase II-activated chloride conductance. A novel mechanism for ion channel regulation. (1994)

Ca(2+)-activated Cl- current (ICl,Ca) in colonic T84 cells is inhibited by the specific peptide inhibitor of Ca2+/calmodulin-dependent kinase II (CaM KII). Annexin IV, a Ca(2+)-dependent phospholipid binding protein also inhibits Ca(2+)-dependent anion current activation (Kaetzel, M.A., Chan, H.-C., Dubinsky, W.P., Dedman, J.R., and Nelson, D.J. (1994) J. Biol. Chem. 269, 5297-5302). Intracellular injection of antibodies against annexin IV enhances current activation; this activation is inhibited by the peptide inhibitor of CaM KII. Intracellular application of autonomously active CaM KII in the presence of ATP induced a Cl- current similar to that activated by the Ca2+ ionophore A23187. Current activation by the exogenous kinase was completely inhibited in the presence of purified annexin IV. In vitro, annexin IV does not inhibit CaM KII activity nor does it act as a substrate for CaM KII. Thus, it appears that annexin IV inhibits phosphorylation-dependent anion conductance activation by preventing CaM KII-ion channel interaction rather than by direct interaction with the enzyme itself. These findings suggest a novel mechanism by which Ca(2+)-dependent membrane binding proteins, cytoplasmic kinases, and ion channels interact to regulate membrane conductance. The characterization of unique channel regulatory pathways in Cl- transporting epithelia may identify potential avenues of alternate therapy to compensate for the loss of functional Cl- channels in the disease of cystic fibrosis.
Learning-Based SMT Processor Resource Distribution via Hill-Climbing (2006)

The key to high performance in Simultaneous Multithreaded (SMT) processors lies in optimizing the distribution of shared resources to active threads. Existing resource distribution techniques optimize performance only indirectly. They infer potential performance bottlenecks by observing indicators, like instruction occupancy or cache miss counts, and take actions to try to alleviate them. While the corrective actions are designed to improve performance, their actual performance impact is not known since end performance is never monitored. Consequently, potential performance gains are lost whenever the corrective actions do not effectively address the actual bottlenecks occurring in the pipeline. We propose a different approach to SMT resource distribution that optimizes end performance directly. Our approach observes the impact that resource distribution decisions have on performance at runtime, and feeds this information back to the resource distribution mechanisms to improve future decisions. By evaluating many different resource distributions, our approach tries to learn the best distribution over time. Because we perform learning on-line, learning time is crucial. We develop a hill-climbing algorithm that efficiently learns the best distribution of resources by following the performance gradient within the resource distribution space. This paper conducts an in-depth investigation of learningbased SMT resource distribution. First, we compare existing resource distribution techniques to an ideal learning-based technique that performs learning off-line. This limit study shows learning-based techniques can provide up to 19.2% gain over ICOUNT, 18.0% gain over FLUSH, and 7.6% gain over DCRA across 21 multithreaded workloads. Then, we present an on-line learning algorithm based on hill-climbing. Our evaluation shows hill-climbing provides a 12.4% gain over ICOUNT, 11.3% gain over FLUSH, and 2.4% gain over DCRA across a larger set of 42 multiprogrammed workloads.
Generation of the germline peripheral B cell repertoire: VH81X-lambda B cells are unable to complete all developmental programs. (1998)

The generation of VH81X heavy chain lambda-light chain-expressing B cells (VH81X-lambda+ B cells) was studied in VH81X heavy chain transgenic mice as well as in VH81X JH (-/-) and VH81X JH (-/-) Ck (-/-) mice, in which competition resulting from expression of heavy and light chains from the endogenous heavy and kappa light chain loci was prevented. We show that although lambda light chain gene rearrangements occur normally and give rise to light chains that associate with the transgenic heavy chain to form surface and soluble IgM molecules, further B cell development is almost totally blocked. The few VH81X-lambda+ B cells that are generated progress into a mature compartment (expressing surface CD21, CD22, CD23, and low CD24 and having a relatively long life span) but they also have reduced levels of surface Ig receptor and express higher amounts of Fas Ag than VH81X-kappa+ B cells. These VH81X-lambda+ B cells reach the peripheral lymphoid organs and accumulate in the periarteriolar lymphoid sheath but are unable to generate primary B cell follicles. In other heavy chain transgenic mice (MD2, M167, and M54), lambda+ B cells are generated. However, they seem to be preferentially selected in the peripheral repertoire of some transgenic heavy chain mice (M54) but not in others (MD2, M167). These studies show that a crucial selection step is necessary for B cell survival and maintenance in which B cells, similar to T cells, receive signals depending on their clonal receptors.
Hypoxic Regulation of Vascular Endothelial Growth Factor mRNA Stability Requires the Cooperation of Multiple RNA Elements (1999)

Vascular endothelial growth factor (VEGF) is a key regulator of developmental, physiological, and tumor angiogenesis. Upregulation of VEGF expression by hypoxia appears to be a critical step in the neovascularization of solid cancers. The VEGF mRNA is intrinsically labile, but in response to hypoxia the mRNA is stabilized. We have systematically analyzed the regions in the VEGF mRNA that are responsible for its lability under normoxic conditions and for stabilization in response to hypoxia. We find that the VEGF mRNA not only contains destabilizing elements in its 3' untranslated region (3'UTR), but also contains destabilizing elements in the 5'UTR and coding region. Each region can independently promote mRNA degradation, and together they act additively to effect rapid degradation under normoxic conditions. Stabilization of the mRNA in response to hypoxia is completely dependent on the cooperation of elements in each of the 5'UTR, coding region, and 3'UTR. Combinations of any of two of these three regions were completely ineffective in responding to hypoxia, whereas combining all three regions allowed recapitulation of the hypoxic stabilization seen with the endogenous VEGF mRNA. We conclude that multiple regions in the VEGF mRNA cooperate both to ensure the rapid degradation of the mRNA under normoxic conditions and to allow stabilization of the mRNA in response to hypoxia. Our findings highlight the complexity of VEGF gene expression and also reveal a mechanism of gene regulation that could become the target for strategies of therapeutic intervention.
A fully integrated micromachined magnetic particle separator (1996)

A prototype micromachined magnetic particle separator that can separate magnetic particles from suspended liquid solutions has been realized on a silicon wafer. The requisite magnetic field gradients are generated by integrated inductive components in place of permanent magnets, which yields several advantages in design flexibility, compactness, electrical and optical monitoring, and integration feasibility (thus enabling mass production). Preliminary experiments have been performed on aqueous suspensions of magnetic beads. At 500 mA of dc current, approximately 0.03 Tesla of magnetic flux density is achieved at the gap between the quadrupoles, and the magnetic particles rapidly move toward the quadrupoles, separate from the buffer solution, and clump on the poles. The magnetic particles clumped on the poles are also easily released when the dc current is removed, achieving the primary purpose of a separator. The device shows that micromachined magnetic components have a high potential in biological or biomedical applications, especially in separating small amounts of cells or DNA that are marked with magnetic beads, especially when close monitoring and control of the process is important.
Recent advances in augmented reality (2001)

In 1997, Azuma published a survey on augmented reality (AR). Our goal is to complement, rather than replace, the original survey by presenting representative examples of the new advances. We refer one to the original survey for descriptions of potential applications (such as medical visualization, maintenance and repair of complex equipment, annotation, and path planning); summaries of AR system characteristics (such as the advantages and disadvantages of optical and video approaches to blending virtual and real, problems in display focus and contrast, and system portability); and an introduction to the crucial problem of registration, including sources of registration error and error-reduction strategies.
Proinflammatory Cytokines and Early Neurological Worsening in Ischemic Stroke (2000)

In addition to participating in the acute-phase response that follows focal cerebral ischemia, IL-6 levels on admission are associated with early clinical deterioration. The association between IL-6 and early neurological worsening prevails without regard to the initial size, topography, or mechanism of the ischemic infarction.
Three-dimensional Assessment of Femoral Head Coverage in Normal and Dysplastic Hips: A Novel Method. (2014)

The acetabular coverage of the femoral head has been assessed in two-dimensions as the projected covered area or the covered angle on plain radiographs. We present a novel method of the three-dimensional assessment of femoral head coverage obtained by evaluating the covered volume of the femoral head in both normal and dysplastic hips. We also assessed the covered angles on the vertical slices passing through the center of the femoral head. The mean covered volume of the femoral head was 57.4% in normal hips and 26.6% in dysplastic hips. In dysplastic hips, the L-CE, A-CE, and P-CE angles were 7.7°, 21.8°, and 95.8°, respectively, while the acetabular angle was 27.5°. In normal hips, the CE angles were 34.0°, 56.8°, and 109.4°, respectively, while the acetabular angle was 7.2°. Our study suggests the usefulness of a novel 3D assessment for acetabular coverage of the femoral head. This assessment provided the precise 3D information necessary to diagnose hip dysplasia and assess the deficiency of acetabular coverage in these patients. Moreover, we may detect a cut-off between normal and dysplastic hips in the 3D assessment by assessing a large number of dysplastic hips both morphologically and using the new assessment.
Five quantum register error correction code for higher spin systems (1997)

I construct a quantum error correction code (QECC) in higher spin systems using the idea of multiplicative group character. Each $N$-state quantum particle is encoded as five $N$-state quantum registers. By doing so, this code can correct any quantum error arising from any one of the five quantum registers. This code generalizes the well-known five qubit perfect code in spin-1/2 systems and is shown to be optimal for higher spin systems. I also report a simple algorithm for encoding. The importance of multiplicative group character in constructing QECCs will be addressed.
Structure-Function Analysis of the mRNA Cap Methyltransferase of Saccharomyces cerevisiae (1997)

The Saccharomyces cerevisiae mRNA cap methylating enzyme is a 436-amino acid protein encoded by the essential ABD1 gene. To identify structural features of ABD1 required for enzyme function, we introduced alanine mutations at 19 positions within a 205-amino acid region of similarity to the methyltransferase domain of the vaccinia capping enzyme. Three new recessive lethal mutations, E170A, D194A, and R206A, were identified. Structure-function relationships were clarified by introducing conservative substitutions at Glu-170, Asp-194, and Arg-206, and at Tyr-254 (an essential residue identified previously). Alleles E170D and D194E were viable, whereas E170Q and D194N were lethal; hence, acidic side chains were critical at both positions. R206K was viable, suggesting that a basic residue sufficed. Y254S was lethal, whereas Y254F was viable, albeit slow growing; thus, an aromatic side chain was important. The ABD1 mutations that were deleterious in vivo elicited catalytic defects in vitro. By studying the effects of amino- and carboxyl-terminal deletions, we defined a fully active catalytic domain of ABD1 from residues 130 to 426. Residues 110-129 were dispensable for methyltransferase activity in vitro, but essential for function in vivo. This analysis allowed us to delineate a subfamily of ABD1-like proteins within the superfamily of AdoMet-dependent methyltransferases. In addition, we identify a candidate Caenorhabditis elegans gene encoding a putative cap methyltransferase. All residues essential for ABD1 activity are conserved in the C. elegans homologue.
Metal–Organic Frameworks Stabilize Solution-Inaccessible Cobalt Catalysts for Highly Efficient Broad-Scope Organic Transformations (2016)

New and active earth-abundant metal catalysts are critically needed to replace precious metal-based catalysts for sustainable production of commodity and fine chemicals. We report here the design of highly robust, active, and reusable cobalt-bipyridine- and cobalt-phenanthroline-based metal-organic framework (MOF) catalysts for alkene hydrogenation and hydroboration, aldehyde/ketone hydroboration, and arene C-H borylation. In alkene hydrogenation, the MOF catalysts tolerated a variety of functional groups and displayed unprecedentedly high turnover numbers of ∼2.5 × 10(6) and turnover frequencies of ∼1.1 × 10(5) h(-1). Structural, computational, and spectroscopic studies show that site isolation of the highly reactive (bpy)Co(THF)2 species in the MOFs prevents intermolecular deactivation and stabilizes solution-inaccessible catalysts for broad-scope organic transformations. Computational, spectroscopic, and kinetic evidence further support a hitherto unknown (bpy(•-))Co(I)(THF)2 ground state that coordinates to alkene and dihydrogen and then undergoing σ-complex-assisted metathesis to form (bpy)Co(alkyl)(H). Reductive elimination of alkane followed by alkene binding completes the catalytic cycle. MOFs thus provide a novel platform for discovering new base-metal molecular catalysts and exhibit enormous potential in sustainable chemical catalysis.
Myocardial ischemia and infarction can be detected by microwave spectroscopy. II. Biophysical reconstruction (2002)

Cross sectional static and dynamic images of the canine explanted heart have been reconstructed in microwave tomography. Our hypothesis is that microwave spectroscopy (multifrequency probing) is a sensitive indicator of the myocardial ischemia and infarction. This hypothesis has been experimentally proven. It is known, that myocardial ischemia and infarction relate to the changes of the ion environment, tissue water content, extracellular, intracellular resistances, cells coupling, etc. Therefore, some mechanism of determining the tissue water, ion content, etc., based on the measured values of the tissue dielectric spectroscopic properties can be found. We called the "biophysical reconstruction" this mechanism and it is the specific aim of this report. The remarkable correlation between reconstructed and known values of the myocardial DC resistance and water content in the dynamic of the ischemic injury and infarction have been reached.
[The new x-ray ordinance]. (1988)

The new ordinance on X-ray irradiation, which was passed on 8 January 1987 and comes into force on 1 January 1988, is designed to keep radiation exposure during X-ray examinations to the minimum absolutely necessary. This is to be achieved not only by improving the specialist qualifications of the personnel concerned, but also by improved quality control. Substantial changes in X-ray diagnosis procedures will be introduced with the expected guidelines on implementation of the new decree.
AMRIS: a multicast protocol for ad hoc wireless networks (2003)

This paper introduces AMRIS, a new multicast routing protocol for ad hoc wireless networks. AMRIS (Ad hoc Multicast Routing protocol utilizing Increasing id-numberS) is designed to operate independently of underlying unicast protocols. The idea behind AMRIS is to dynamically assign every node (on demand) in a multicast session with an id-number. The ordering between id-numbers is used to direct the multicast flow, and the sparseness among them used for quick connectivity repair. A multicast delivery tree rooted at a special node called Sid joins up the nodes participating in the multicast session. The relationship between the id-numbers (and the nodes that own them) and Sid is that the id-numbers increase in numerical value as they radiate from Sid in the delivery tree. These id-numbers help the nodes dynamically leave and join a session, as well as adapt rapidly to changes in link connectivity (due to mobility etc.). Messages to repair a link breakage are confined to the region where it occurs. AMRIS is simulated with PARSEC and the results reported.
Hepatitis C virus replication is directly inhibited by IFN-α in a full-length binary expression system (2001)

Hepatitis C virus (HCV) is a leading cause of chronic hepatitis, cirrhosis, and hepatocellular carcinoma. The absence of culture systems permissive for HCV replication has presented a major bottleneck to antiviral development. We sought to recapitulate the early steps in the life cycle of HCV by means of DNA-based expression of viral genomic sequences. Here we report expression of replicating HCV RNA by using a, to our knowledge, novel binary expression system in which cells were transfected with a T7 polymerase-driven full-length HCV cDNA plasmid containing a cis-acting hepatitis Delta ribozyme to control 3' cleavage, and infected with vaccinia-T7 polymerase. HCV genomic and replicative strand synthesis, in addition to protein synthesis, was detectable and depended on full-length HCV sequences. Moreover, the system was capable of generating HCV RNA quasispecies, consistent with the action of the low-fidelity HCV NS5B RNA polymerase. IFN-alpha, but not ribavirin, directly inhibited the viral replicative cycle in these cells, identifying the virus itself and not solely the immune system as a direct target of IFN action. The availability of a cell-based test for viral replication will facilitate screening of inhibitory compounds, analysis of IFN-resistance mechanisms, and analysis of virus-host cell interactions.
Isolating short-lived operands for energy reduction (2004)

A mechanism for reducing the power requirements in processors that use a separate (architectural) register file (ARF) for holding committed values is proposed. We exploit the notion of short-lived operands-values that target architectural registers that are renamed by the time the instruction producing the value reaches the writeback stage. Our simulations of the SPEC 2000 benchmarks show that as much as 71 percent to 97 percent of the results are short-lived. Our technique avoids unnecessary writebacks into the result repository (a slot within the reorder buffer or a physical register) as well as writes into the ARF from unnecessary commitments by caching (and isolating) short-lived operands within a small dedicated register file. Operands are cached in this manner till they can be safely discarded without jeopardizing the recovery from possible branch mispredictions or reconstruction of the precise state in case of interrupts or exceptions. Additional energy savings are achieved by limiting the number of ports used for instruction commitment. The power/energy savings are validated using SPICE measurements of actual layouts in a 0.18 micron CMOS process. The energy reduction in the ROB and the ARF is about 20 percent (translating into the overall chip energy reduction of about 5 percent) and this is achieved with no increase in cycle time, little additional complexity, and no degradation in the number of instructions committed per cycle.
Peptide TFP5/TP5 derived from Cdk5 activator P35 provides neuroprotection in the MPTP model of Parkinson’s disease (2015)

Parkinson's disease (PD) is a chronic neurodegenerative disorder characterized by the loss of dopamine neurons in the substantia nigra, decreased striatal dopamine levels, and consequent extrapyramidal motor dysfunction. Recent evidence indicates that cyclin-dependent kinase 5 (Cdk5) is inappropriately activated in several neurodegenerative conditions, including PD. To date, strategies to specifically inhibit Cdk5 hyperactivity have not been successful without affecting normal Cdk5 activity. Previously we reported that TFP5 peptide has neuroprotective effects in animal models of Alzheimer's disease. Here we show that TFP5/TP5 selective inhibition of Cdk5/p25 hyperactivation in vivo and in vitro rescues nigrostriatal dopaminergic neurodegeneration induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP/MPP+) in a mouse model of PD. TP5 peptide treatment also blocked dopamine depletion in the striatum and improved gait dysfunction after MPTP administration. The neuroprotective effect of TFP5/TP5 peptide is also associated with marked reduction in neuroinflammation and apoptosis. Here we show selective inhibition of Cdk5/p25 -hyperactivation by TFP5/TP5 peptide, which identifies the kinase as a potential therapeutic target to reduce neurodegeneration in Parkinson's disease.
Hypoxia-Induced Signaling in the Cardiovascular System (2007)

Low oxygen (O2) levels are a naturally occurring feature of embryonic development, adult physiology, and diseases such as those of the cardiovascular system. Although many responses to O2 deprivation are mediated by hypoxia-inducible factors (HIFs), researchers are finding a growing number of HIF-independent pathways that promote O2 conformance and hypoxia tolerance. Here, we describe HIF-independent responses and how they impact cardiovascular tissue homeostasis.
ChemInform Abstract: Homocamptothecins: Synthesis and Antitumor Activity of Novel E‐Ring‐Modified Camptothecin Analogues. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Strategies for nonradioactive methods in the localization of phosphorylated amino acids in proteins 1 (1993)

Identification of O-phosphorylated amino acids within the primary structure of regulatory proteins is important in understanding the mechanisms by which their functions are regulated. In many cases radioactive labeling with [32P]phosphate is tedious or sometimes impossible. Therefore, we have established a series of new non-radioactive methods that permit the localization of phosphoserine, phosphothreonine, and phosphotyrosine. After partial hydrolysis of a phosphopeptide or phosphoprotein, phosphoserine, phosphothreonine, or phosphotyrosine are determined by capillary electrophoresis as their dabsyl-derivatives. Chemical modification transforms phosphoserine or phosphothreonine to S-ethyl-cysteine or beta-methyl-S-ethyl-cysteine, respectively, allowing their localization during sequence analysis. We apply solid-phase sequencing to overcome the limitations of the gas-phase sequenator in the case of phosphotyrosine-containing peptides. Liquid chromatography on-line connected to an electrospray mass spectrometer is a powerful new method of increasing importance in the protein chemistry field. It is especially well suited for identification of phosphoserine- or phosphothreonine-containing peptides in a proteolytic digest of a phosphoprotein. In this article we will describe how to work with these new methods practically.