gebhart/patrepeval huggingface dataset:
Synthesis of the Glycopeptide Partial Sequence A80–A84 of Human Fibroblast Interferon (1985)

Abstract The glycopentapeptide H‐(GlcNAcβ1‐)Asn‐Glu‐Thr‐Ile‐Val‐OH ( 10 ) representing the partial sequence A 80 –A 84 of human fibroblast interferon was synthesized using the newly developed allyl‐ester protection of carboxy functions. The allyl esters, which are stable to acids and to bases, can be cleaved under very mild, neutral conditions using tris(triphenylphosphine)rhodium(I) chloride or tetrakis(triphenylphosphine)palladium(0) as a catalyst. This synthetic method opens up a preparative route to glycopeptide model structures of glycoproteins of high biological interest.
Toward a Practical Face Recognition System: Robust Alignment and Illumination by Sparse Representation (2011)

Many classic and contemporary face recognition algorithms work well on public data sets, but degrade sharply when they are used in a real recognition system. This is mostly due to the difficulty of simultaneously handling variations in illumination, image misalignment, and occlusion in the test image. We consider a scenario where the training images are well controlled and test images are only loosely controlled. We propose a conceptually simple face recognition system that achieves a high degree of robustness and stability to illumination variation, image misalignment, and partial occlusion. The system uses tools from sparse representation to align a test face image to a set of frontal training images. The region of attraction of our alignment algorithm is computed empirically for public face data sets such as Multi-PIE. We demonstrate how to capture a set of training images with enough illumination variation that they span test images taken under uncontrolled illumination. In order to evaluate how our algorithms work under practical testing conditions, we have implemented a complete face recognition system, including a projector-based training acquisition system. Our system can efficiently and effectively recognize faces under a variety of realistic conditions, using only frontal images under the proposed illuminations as training.
Complement Receptor 2Is Expressed in Neural Progenitor Cells and Regulates Adult Hippocampal Neurogenesis (2011)

Injury and inflammation are potent regulators of adult neurogenesis. As the complement system forms a key immune pathway that may also exert critical functions in neural development and neurodegeneration, we asked whether complement receptors regulate neurogenesis. We discovered that complement receptor 2 (CR2), classically known as a coreceptor of the B-lymphocyte antigen receptor, is expressed in adult neural progenitor cells (NPCs) of the dentate gyrus. Two of its ligands, C3d and interferon-α (IFN-α), inhibited proliferation of wild-type NPCs but not NPCs derived from mice lacking Cr2 (Cr2(-/-)), indicating functional Cr2 expression. Young and old Cr2(-/-) mice exhibited prominent increases in basal neurogenesis compared with wild-type littermates, whereas intracerebral injection of C3d resulted in fewer proliferating neuroblasts in wild-type than in Cr2(-/-) mice. We conclude that Cr2 regulates hippocampal neurogenesis and propose that increased C3d and IFN-α production associated with brain injury or viral infections may inhibit neurogenesis.
Cloning of Nrf1, an NF-E2-related transcription factor, by genetic selection in yeast. (1993)

We have devised a complementation assay in yeast to clone mammalian transcriptional activators and have used it to identify a human basic leucine-zipper transcription factor that we have designated Nrf1 for NF-E2-related factor 1. Nrf1 potentially encodes a 742-aa protein and displays marked homology to the mouse and human NF-E2 transcription factors. Nrf1 activates transcription via NF-E2 binding sites in yeast cells. The ubiquitous expression pattern of Nrf1 and the range of promoters containing the NF-E2 binding motif suggest that this gene may play a role in the regulation of heme synthesis and ferritin genes.
Planar 2-pass texture mapping and warping (1987)

The 2-pass tranformation replaces a 2-D (2-dimensional) transformation with a sequence of orthogonal, simpler 1-D transformation. It may be used for the closely related processes of texture mapping and warping in computer graphics and image processing. First, texture maps onto planar quadric and superquadric surfaces and, second, planar bicubic and biquadratic warps of images are shown to be 2-pass transformable. A distinction between serial and parallel warps is introduced to solve a confusion in terms between computer graphics and image processing. It is shown that an n -th order serial polynomial warp is equivalent to an ( n 2 + n )-th order parallel polynomial warp. It is also shown that the serial equivalent to a parallel polynomial warp is generally not a polynomial warp, being more complicated than a polynomial. The unusual problem of bottlenecking and the usual one of antialiasing are discussed in the 2-pass context.
The metabolic syndrome (2003)

May be a guidepost or detour to preventing type 2 diabetes and cardiovascular disease 

Type 2 diabetes mellitus is becoming extremely common; its prevalence worldwide is expected to reach 5-7.6% by 2025.1 Atherosclerotic cardiovascular disease is the principal cause of death, disability, and excess healthcare costs in diabetes. Cardiovascular disease may already be present at the time when diabetes is diagnosed,w1 and patients with diabetes are more likely than their non-diabetic counterparts to die from a first event of cardiovascular disease.w2 These realities point to prevention of type 2 diabetes as the route to prevention of its costliest complications. The close association of type 2 diabetes with cardiovascular disease led to the hypothesis that the two arise from a common antecedent;w3 this concept has been codified by the World Health Organization and others as “the metabolic syndrome.”2

The diagnosis of the metabolic syndrome in patients might hold promise for enhanced prevention of diabetes and cardiovascular disease. However, substantial uncertainties remain about the clinical definition of the syndrome and whether risk factor clusters collectively indicate a discrete, unifying disorder. Most importantly, it is unclear whether diagnosing …
Mutational analysis of upstream AUG codons of poliovirus RNA (1988)

The 5' untranslated region of poliovirus type 2 Lansing RNA consists of 744 nucleotides containing seven AUG codons which are followed by in-frame termination codons, thus forming short open reading frames (ORFs). To determine the biological significance of these small ORFs, all of the upstream AUG codons were mutated to UUG. The point mutations were introduced into an infectious poliovirus cDNA clone, and RNA transcribed in vitro from the altered cDNA was transfected into HeLa cells to recover the virus. Mutation of AUG 7 resulted in a virus (called R2-5NC-14) with a small-plaque phenotype, whereas mutation of the other six AUG codons produced virus with a wild-type plaque morphology. To determine whether the small-plaque phenotype of R2-5NC-14 was due to altered translational efficiency of the viral mRNA, we constructed chimeric mRNAs containing the 5' noncoding region of poliovirus mRNA fused to the chloramphenicol acetyltransferase (CAT) coding sequence. mRNA containing a mutated AUG 7 codon showed decreased translational efficiency in vitro. The results indicate that the upstream ORFs of poliovirus RNA are not essential for viral replication and do not act as barriers to the translation of poliovirus mRNA. AUG 7 and flanking sequences may play a positive acting role in poliovirus RNA translation.
Activity-induced recovery of excitability in K+-depressed rat soleus muscle (2001)

Increased extracellular K(+) concentration ([K(+)](o)) can reduce excitability and force in skeletal muscle. Here we examine the effects of muscle activation on compound muscle action potentials (M waves), resting membrane potential, and contractility in isolated rat soleus muscles. In muscles incubated for 60 min at 10 mM K(+), tetanic force and M wave area decreased to 23 and 24%, respectively, of the control value. Subsequently, short (1.5 s) tetanic stimulations given at 1-min intervals induced recovery of force and M wave area to 81 and 90% of control levels, respectively, within 15 min (P < 0.001). The recovery of force and M wave was associated with a partial repolarization of the muscle fibers. Experiments with tubocurarine suggest that the force recovery was related to activation of muscle Na(+)-K(+) pumps caused by the release of some compound from sensory nerves in response to muscle activity. In conclusion, activity produces marked recovery of excitability in K(+)-depressed muscle, and this may protect muscles against fatigue caused by increased [K(+)](o) during exercise.
Immunomagnetic removal of B-lymphoma cells from human bone marrow: a procedure for clinical use. (1988)

B-lymphoma cells were purged from human bone marrow by incubating the cell suspension with a cocktail of three different pan-B cell mouse IgG1 monoclonal antibodies, and then with immunobeads charged with sheep anti-mouse antibody, followed by magnetic separation. The primary antibodies used, HD37 (CD19), HD6 (CD22), and HH1 (CD37), bind to a very high percentage of the cells in non-Hodgkin's lymphomas of poor prognosis. The secondary antibody is directed against the Fc portion of the IgG antibodies. In model experiments Burkitt's lymphoma cells (Rael) were admixed to mononuclear bone marrow cells in the ratio 1/9. With a ratio of immunobeads/total antibody-binding B cells of 50/1 in a first treatment cycle and repeating the procedure with the same number of beads in a second cycle, a tumor cell depletion of more than 5 logs was achieved, as judged by a clonogenic assay. The concomitant reduction of CFU-GM and CFU-GEMM was about 20%. The purging procedure has been scaled up to clinical use. Equipment suitable for purging patients' marrow specimens, employing standard transfusion facilities, is described. With this equipment the efficacy of tumor cell removal was the same as in the model experiments, and the whole magnetic separation could be completed in 2 hours.
Analog and digital circuits using organic thin-film transistors on polyester substrates (2000)

We have fabricated and characterized analog and digital circuits using organic thin-film transistors on polyester film substrates. These are the first reported dynamic results for organic circuits fabricated on polyester substrates. The high-performance pentacene transistors yield circuits with the highest reported clock frequencies for organic circuits.
Weighted least squares algorithm for continuous-time model (2002)

In this paper we discuss a weighted least squares algorithm for the following continuous-time model: A(S)y/sub t/=SB(S)u/sub t/+C(S)v/sub t/ where S denotes the integral operator, i.e. Sy/sub t/=/spl int//sub 0//sup t/y/sub s/ds and A(S), B(S) and C(S) are matrix polynomials in the integral operator S. Similar to discrete WLS, the almost sure boundedness and convergence are established for continuous-time weighted least squares (CWLS) algorithm. The simulation results for the discrete WLS and the discrete extended least squares (ELS), the CWLS and the continuous ELS algorithms are given in this paper. Our techniques of proofs are totally different from those in discrete case. The results presented can be extended to state-space models with continuous time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
In-Datacenter Performance Analysis of a Tensor Processing Unit (2017)

Many architects believe that major improvements in cost-energy-performance must now come from domain-specific hardware. This paper evaluates a custom ASIC---called a Tensor Processing Unit (TPU) --- deployed in datacenters since 2015 that accelerates the inference phase of neural networks (NN). The heart of the TPU is a 65,536 8-bit MAC matrix multiply unit that offers a peak throughput of 92 TeraOps/second (TOPS) and a large (28 MiB) software-managed on-chip memory. The TPU's deterministic execution model is a better match to the 99th-percentile response-time requirement of our NN applications than are the time-varying optimizations of CPUs and GPUs that help average throughput more than guaranteed latency. The lack of such features helps explain why, despite having myriad MACs and a big memory, the TPU is relatively small and low power. We compare the TPU to a server-class Intel Haswell CPU and an Nvidia K80 GPU, which are contemporaries deployed in the same datacenters. Our workload, written in the high-level TensorFlow framework, uses production NN applications (MLPs, CNNs, and LSTMs) that represent 95% of our datacenters' NN inference demand. Despite low utilization for some applications, the TPU is on average about 15X -- 30X faster than its contemporary GPU or CPU, with TOPS/Watt about 30X -- 80X higher. Moreover, using the CPU's GDDR5 memory in the TPU would triple achieved TOPS and raise TOPS/Watt to nearly 70X the GPU and 200X the CPU.
Employer-specific versus community-wide report cards: is there a difference? (1996)

This article describes preliminary results from a natural experiment that tested the impact of report cards on employees. As part of the 1995 enrollment process, some members of the State of Minnesota Employee Group Insurance Program received report cards on the plans offered to them, and others did not. Both groups of employees had a chance to review a second community-wide report card covering all Minnesota plans that had been distributed by an independent organization through local newspapers. Both groups were surveyed before and after they made their health plan selections. We compare the likelihood of seeing, the intensity of reading, and the perceived helpfulness of the first, employer-specific report card with the second, community-wide report card for consumers who make plan selections.
Reducing Cardiac Filling Pressure Lowers Norepinephrine Spillover in Patients With Chronic Heart Failure (2000)

Background —We studied the cardiac sympathetic response to selective unloading of cardiopulmonary baroreceptors in subjects with normal left ventricular (LV) function and congestive heart failure (CHF). Methods and Results —Eight patients with normal LV function (age 57±5 years, ejection fraction 58±2%) and 8 patients with CHF (age 60±2 years; ejection fraction 19±2%) were studied. Instrumentation consisted of an arterial line, a pulmonary artery catheter, and a coronary sinus thermodilution catheter. The radiotracer technique was used for measurement of cardiac norepinephrine spillover (CANESP) and total-body norepinephrine spillover. Lower-body negative pressure (LBNP) was applied at 2 levels: nonhypotensive and hypotensive LBNP. Nonhypotensive LBNP reduced filling pressures significantly in both groups. Arterial pressure did not change. This reduction in filling pressures caused a significant reduction in CANESP in the CHF group (from 167±53 to 125±37 pmol/min, P &lt;0.05) but no change in the normal LV function group. Hypotensive LBNP caused a significant increase in CANESP in the normal group (73±13 vs 122±27 pmol/min, P &lt;0.05) but no significant change in those with CHF. Conclusions —We conclude that selective reduction in filling pressures lowers cardiac norepinephrine spillover in patients with CHF. These findings suggest that a goal of CHF management should be to reduce cardiac filling pressures while avoiding systemic hypotension.
Igβ(CD79b) mRNA expression in chronic lymphocytic leukaemia cells correlates with immunoglobulin heavy chain gene mutational status but does not serve as an independent predictor of clinical severity (2007)

The etiology of chronic lymphocytic leukemia (CLL) is poorly understood and its course is highly variable. Somatic hypermutation (SHM) of the immunoglobulin heavy chain (IgV(H)) gene and ZAP70 protein expression have been reported as prognostic indicators. However, these assays are not widely available and their concordance is imperfect. Thus a need exists to identify additional molecular determinants of CLL. The Igbeta (CD79b) subunit of the B cell antigen receptor is essential for B lymphocyte function. Defects in Igbeta expression are implicated in CLL pathogenesis. We have analyzed Igbeta mRNA expression in CLL cells in 40 consecutive patient samples. About 75% of the samples showed the expected decrease of Igbeta surface staining. Igbeta mRNA levels covered a wider range, did not correlate with Igbeta surface staining, but clearly distinguished the normal and CLL lymphocyte populations. Remarkably, Igbeta mRNA levels correlated strongly with SHM; Igbeta mRNA levels in CLL cells were significantly higher in patients with an unmutated IgV(H) gene when compared with those in whom IgV(H) was hypermutated (P = 0.008). In contrast, no correlation was observed between Igbeta mRNA levels and ZAP70 expression. Multiple parameters abstracted from chart reviews were used to estimate severity of CLL in each case. While severity correlated strongly with ZAP70 staining, and to a lesser extent with SHM status, there was no correlation with Igbeta mRNA levels. These data establish a strong linkage between Igbeta mRNA expression and SHM in CLL and highlight the complex relationships between biochemical parameters and clinical status in this disease.
[Prevention and treatment of acute graft-versus host disease]. (1991)

Graft-versus host disease (GvHD) is a major and at times lethal complication of allogeneic bone marrow transplantation, particularly in case of genetic disparity. Although T-cell depletion of the marrow graft is the most effective prophylaxis, its use is controverted because of the role it plays in the increase of failed transplantations and leukaemia relapses, but the overall survival rate remains unchanged. The fact that patients without GvHD have a much better quality of life justifies the current clinical research on partial or selective T-cell depletion, aimed at reducing the GvHD effect while preserving the antileukaemic effect. Biological response modifiers (haemotopoietic growth factors, lymphokins, monoclonal antibodies) are recent tools issued from biotechnology, which can act at 3 levels in the prevention and treatment of GvHD: they can reduce the undesirable effects of T-cell depletion, intervene in the antileukaemic reaction and act on GvHD effectors.
Haem binding to horse spleen ferritin (1990)

Horse spleen ferritin, a spherical protein shell of 24 subunits, contains no haem when extracted. This contrasts with ferritins isolated from bacterial sources which have the capacity to bind up to 24 haem groups [(1990) FEBS Lett. 271, 141-143] via two methionine residues [(1990) Nature 341, 771]. Here it is shown that horse spleen ferritin can bind between 15 and 17 haems per 24 subunits with an apparent association constant of 2.2-3.2 x 10(4) M-1. The strength of haem binding appears to be unaffected either by the presence of the core or by the oxidation state of the haem. The demonstration of the ability of animal ferritin to bind haem strengthens the similarity between it and bacterioferritin and could have major consequences for its mechanism of action in physiological iron uptake and release processes.
Analysis of a recombinant dengue-2 virus-dengue-3 virus hybrid envelope protein expressed in a secretory baculovirus system. (1997)

In a step towards a tetravalent dengue virus subunit vaccine which is economical to produce, highly immunogenic and stable, a hybrid dengue virus envelope (E) protein molecule has been constructed. It consists of 36 amino acids from the membrane protein, the N-terminal 288 amino acids of the dengue-2 virus E protein plus amino acids 289-424 of the dengue-3 virus E protein. It has been engineered for secretory expression by fusion to a mellitin secretory signal sequence and truncation of the hydrophobic transmembrane segment. Using the baculovirus expression system and serum-free conditions, more than 95% of recombinant dengue-2 virus-dengue-3 virus hybrid E protein (rD2D3E) was secreted into the cell culture supernatant in a stable form with multiple features indicative of preserved conformation. The hybrid molecule reacted with a panel of dengue virus- and flavivirus-specific MAbs which recognize linear or conformational epitopes on dengue virions. Human dengue virus-specific antisera also reacted with the protein. The hybrid rD2D3E protein was able to inhibit the in vitro binding of dengue-2 and dengue-3 viruses to human myelomonocytic cells, suggesting that the receptor-binding epitope(s) was preserved. Adjuvant-free immunization with the hybrid protein induced an antibody response to both dengue-2 and dengue-3 virus in outbred mice, comparable in strength to that of individual rD2E and rD3E proteins. Notably, these antibody responses were primarily of the IgG2a and IgG2b isotype. A strong dengue virus cross-reactive T cell response was also induced in the mice, suggesting that dengue virus hybrid E proteins could form the basis of an efficacious multivalent dengue virus vaccine.
Single-molecule approach to dispersed kinetics and dynamic disorder: Probing conformational fluctuation and enzymatic dynamics (2002)

This article reviews our efforts in understanding dynamical fluctuations of both conformation and enzymatic reactivity in single biomolecules. The single-molecule approach is shown to be particularly powerful for studies of dispersed kinetics and dynamic disorder. New single-molecule observations have revealed conformational transitions occurring on a broad range of timescales, 100 μs–10 s, offering new clues for understanding energy landscape of proteins, as well as the structural and chemical dynamics therein.
Expression of latent human immunodeficiency type 1 is induced by novel and selective histone deacetylase inhibitors (2020)

A family of histone deacetylases (HDACs) mediates chromatin remodeling, and repression of gene expression. Deacetylation of histones within the HIV-1 long terminal repeat (LTR) by HDACs plays a key role in the maintenance of latency, whereas acetylation of histones about the LTR is linked to proviral expression and escape of HIV from latency. Global HDAC inhibition may adversely affect host gene expression, leading to cellular toxicities. Potent inhibitors selective for HDACs that maintain LTR repression could be ideal antilatency therapeutics.
A multi-period design model for survivable network architecture selection for SONET interoffice networks (1991)

The authors propose a multi-period design model to select a best mix of SONET survivable network architectures. These include: (1) point-to-point/hubbing architectures with diverse protection and (2) ring architectures. The algorithm can be used to study growth strategies, for networks incorporating the ring architecture, that minimize the network evolution cost. Numerical examples show that the algorithm can generate a good solution quickly, using a VAX 6000-420 computer for most practical applications. A case study suggests that a particular well accepted engineering rule can work well. This engineering rule is: use direct point-to-point systems in conjunction with self-heating rings and hubbing/diverse protection architectures only when a few demand pairs have appreciably higher demand requirements than other demand pairs. When demand is fairly even, then use self-healing rings or hubbing/diverse protection without direct point-to-point systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>