gebhart/patrepeval huggingface dataset:
Malaria — Resurgence, Resistance, and Research (1983)

If we take as our standard of importance the greatest harm to the greatest number, then there is no question that malaria is the most important of all infectious diseases.— Sir Macfarlane Burnet Natural History of Infectious Disease In the 16 years since malaria was reviewed in this section of the Journal,1 major developments have occurred that have begun a new chapter in the 3500-year-old recorded history of malaria. There has been a worldwide resurgence in disease transmission, and the concept that malaria could be eradicated through a program of dichlorodiphenyl trichloroethane (DDT) spraying and chemoprophylaxis has been . . .
A monolithic optoelectronic receiver in standard 0.7-μm CMOS operating at 180 MHz and 176-fJ light input energy (1997)

A novel monolithic optoelectronic receiver/converter system is presented in standard 0.7-μm N-well CMOS technology. Differential light input incident on enlarged drains of two MOS transistors of a sense amplifier induces latching in either the digital HIGH state or the digital LOW state. The enlarged drains serve as photodiodes, circumventing hybridization techniques like flip-chip and/or solderbumping necessary when using III-V photodiodes. The first receivers of this type have photodetector areas of 15×15 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and demonstrate bitrates of 180 Mb/s with a differential light input of 176 fJ. The electrical power dissipation is of the order of the dissipation of one CMOS logic gate. The very small total receiver area makes the receiver further perfectly suited for use in massive parallel optical interconnects between VLSI chips.
Replacement therapy with plasma-derived factor VIII concentrates induces skew in T-cell receptor usage and clonal expansion of CD8+ T-cell in HIV-seronegative hemophilia patients (2003)

Replacement therapy with factor VIII (FVIII) products causes immune abnormalities in human immunodeficiency virus (HIV)-seronegative hemophilia patients. However, the question remains why an absolute increase in the number of CD8+ T-cells and diminished proliferation responses of lymphocytes to antigen stimulation in vitro occurs in HIV-seronegative hemophilia patients. To examine whether the FVIII products induce skewing of T-cell receptor (TCR) repertoires, TCR variable region alpha-chain and beta-chain repertoires were analyzed for peripheral blood mononuclear cells (PBMCs) from 15 hemophilia patients treated with heated and/or non-heated plasma-derived FVIII concentrates and 10 age-matched healthy adults. Also, T-cell clonality was compared between these groups using complementarity-determining region 3 (CDR3) size spectratyping. The skewing of TCR repertoires was significantly greater for hemophilia patients than healthy controls. The extent of T-cell clonality was greater for hemophilia patients than the controls, indicating that clonal T-cells frequently expanded in hemophilia patients. The skew in TCR usage and clonal expansion were primarily observed in patients treated with non-heated plasma-derived products. The spectratyping and sequencing of CDR3 regions revealed that the clonal expansion of T-cells was observed for CD8+ T-cells, but not CD4+ T-cells. These results suggest that extensive expansion of CD8+ T-cells is induced by some viruses other than HIV present in FVIII preparations, and the resulting accumulation of CD8+ T-cells is responsible for changes in peripheral T-cell population in HIV-seronegative hemophilia patients.
Conversion of Residual Organics in Corn Stover-Derived Biorefinery Stream to Bioenergy via a Microbial Fuel Cell (2012)

A biorefinery process typically uses about 4-10 times more water than the amount of biofuel generated. The wastewater produced in a biorefinery process contains residual sugars, 5-furfural, phenolics, and other pretreatment and fermentation byproducts. Treatment of the wastewater can reduce the need for fresh water and potentially add to the environmental benefits of the process. Use of microbial fuel cells (MFCs) for conversion of the complete range of phenolic compounds and furan aldehyde derivatives present in a postfermentation biorefinery stream is reported here. The consortium was capable of removing the molecules simultaneously with sugars, which were present at 2 orders of magnitude higher concentrations. Organic loading in a fed-batch MFC affected Coulombic efficiency, which decreased from 40% at 0.66 g/L loading to 1.8% at 66.4 g/L loading. Power density increased with loading reaching 1180 mW/m(2) at 5.3 g/L (8% dilution), but decreased thereafter. Excessive loading leads to poor electrogenic performance; therefore, operation of an MFC at an intermediate loading using dilution and recirculation of the process stream can enable effective treatment with bioenergy recovery.
Influence of substratum on corneal epithelial cell growth and protein synthesis. (1988)

To evaluate the effect of substratum on corneal epithelial cell growth and on protein synthesis, bacteriological dishes were coated with laminin, fibronectin, Type I collagen or Type IV collagen. Cell growth was enhanced by day 6 on both laminin and Type I collagen substrata. Adhesion sites and parallel microfilament arrays were present only on cells cultured on laminin coated substratum. The synthesis of connective tissue and cytoskeletal proteins was influenced by the four different substrata. Both the time course and the amount synthesized was affected. The results of this study indicate that the substratum plays a significant role in regulating the synthesis of specific proteins.
Occurrence of Multiple Genomovars of Burkholderia cepacia in Cystic Fibrosis Patients and Proposal of Burkholderia multivorans sp. nov. (1997)

We performed an integrated genotypic and phenotypic analysis of 128 strains of the genera Burkholderia, Ralstonia, and Pseudomonas in order to study the taxonomic structure of Burkholderia cepacia and its relationships with other Burkholderia species. Our data show that presumed B. cepacia strains isolated from cystic fibrosis patients belong to at least five distinct genomic species, one of which was identified as Burkholderia vietnamiensis. This group of five phenotypically similar species is referred to as the B. cepacia complex. The name Burkholderia multivorans is proposed for one of these genomic species, which was formerly referred to as B. cepacia genomovar II; the remaining B. cepacia groups are referred to as genomovars I, III, and IV, pending additional differential phenotypic tests. The role and pathogenic potential of each of these taxa, particularly in view of the potentially fatal infections in cystic fibrosis patients, need further evaluation. The data presented also demonstrate that Pseudomonas glathei and Pseudomonas pyrrocinia should be reclassified as Burkholderia species.
Endonuclease substrate selectivity characterized with full-length PA of influenza A virus polymerase (2012)

The influenza A polymerase is a heterotrimer which transcribes viral mRNAs and replicates the viral genome. To initiate synthesis of mRNA, the polymerase binds a host pre-mRNA and cleaves a short primer downstream of the 5′ end cap structure. The N-terminal domain of PA has been demonstrated to have endonuclease activity in vitro. Here we sought to better understand the biochemical nature of the PA endonuclease by developing an improved assay using full-length PA protein. This full-length protein is active against both RNA and DNA in a cap-independent manner and can use several different divalent cations as cofactors, which affects the secondary structure of the full-length PA. Our in vitro assay was also able to demonstrate the minimal substrate size and sequence selectivity of the PA protein, which is crucial information for inhibitor design. Finally, we confirmed the observed endonuclease activity of the full-length PA with a FRET-based assay.
High-performance linear algebra algorithms using new generalized data structures for matrices (2003)

We present a novel way to produce dense linear algebra factorization algorithms. The current state-of-the-art (SOA) dense linear algebra algorithms have a performance inefficiency, and thus they give suboptimal performance for most LAPACK factorizations. We show that using standard Fortran and C two-dimensional arrays is the main source of this inefficiency. For the other standard format (packed one-dimensional arrays for symmetric and/or triangular matrices), the situation is much worse. We show how to correct these performance inefficiencies by using new data structures (NDS) along with so-called kernel routines. The NDS generalize the current storage layouts for both standard formats. We use the concept of Equivalence and Elementary Matrices along with coordinate (linear) transformations to prove that our method works for an entire class of dense linear algebra algorithms. Also, we use the Algorithms and Architecture approach to explain why our new method gives higher efficiency. The simplest forms of the new factorization algorithms are a direct generalization of the commonly used LINPACK algorithms. On IBM platforms they can be generated from simple, textbook-type codes by the XLF Fortran compiler. On the IBM POWER3 processor, our implementation of Cholesky factorization achieves 92% of peak performance, whereas conventional SOA full-format LAPACK DPOTRF achieves 77% of peak performance. All programming for our NDS can be accomplished in standard Fortran through the use of three- and four-dimensional arrays. Thus, no new compiler support is necessary. Finally, we describe block hybrid formats (BHF). BHF allow one to use no additional storage over conventional (full and packed) matrix storage. This means that new algorithms based on BHF can be used as a backward-compatible replacement for LAPACK or LINPACK algorithms.
A Stiffer and Safer Light Pipe for 25-Gauge Vitrectomy (2007)

Adrawback of the 25-gauge vitrectomy system is the flexibility of the instruments. It can be difficult to perform precise maneuvers such as removing the internal limiting membrane because it is difficult to prevent saccadic eye movements. We designed a new, less flexible, safer light pipe (compared with the standard light pipes) for 25-gauge vitrectomy. The length of the light pipe is 15 mm, making the instrument much less flexible compared with the 32-mm-long standard light pipes. The new instrument also can prevent retinal damage caused by illumination and mechanical retinal damage associated with the longer light pipe. The new short light pipe is useful for the 25-gauge sutureless vitrectomy system.
Coupled Gaussian processes for pose-invariant facial expression recognition (2012)

We propose a method for head-pose invariant facial expression recognition that is based on a set of characteristic facial points. To achieve head-pose invariance, we propose the Coupled Scaled Gaussian Process Regression (CSGPR) model for head-pose normalization. In this model, we first learn independently the mappings between the facial points in each pair of (discrete) nonfrontal poses and the frontal pose, and then perform their coupling in order to capture dependences between them. During inference, the outputs of the coupled functions from different poses are combined using a gating function, devised based on the head-pose estimation for the query points. The proposed model outperforms state-of-the-art regression-based approaches to head-pose normalization, 2D and 3D Point Distribution Models (PDMs), and Active Appearance Models (AAMs), especially in cases of unknown poses and imbalanced training data. To the best of our knowledge, the proposed method is the first one that is able to deal with expressive faces in the range from -45° to +45° pan rotation and -30° to +30° tilt rotation, and with continuous changes in head pose, despite the fact that training was conducted on a small set of discrete poses. We evaluate the proposed method on synthetic and real images depicting acted and spontaneously displayed facial expressions.
Blockade of Cannabinoid Receptor 1 Improves Insulin Resistance, Lipid Metabolism, and Diabetic Nephropathy in db/db Mice (2012)

The endocannabinoid system is important in the pathogenesis of obesity-related metabolic disorders. However, the effect of inhibiting the endocannabinoid system in type 2 diabetic nephropathy is unclear. Therefore, we examined the effect of the cannabinoid (CB)1 receptor antagonist, SR141716, on insulin resistance and diabetic nephropathy in db/db mice. Six-week-old db/db mice were treated with the CB1-specific antagonist SR141716 (10 mg/kg · d) for 3 months. Treatment with SR141716 significantly improved insulin resistance and lipid abnormalities. Concomitantly, CB1 antagonism improved cardiac functional and morphological abnormality, hepatic steatosis, and phenotypic changes of adipocytes into small differentiated forms, associated with increased adiponectin expression and decreased lipid hydroperoxide levels. CB1 receptor was overexpressed in diabetic kidneys, especially in podocytes. Treatment with the SR141716 markedly decreased urinary albumin excretion and mesangial expansion and suppressed profibrotic and proinflammatory cytokine synthesis. Furthermore, SR141716 improved renal lipid metabolism and decreased urinary 8-isoprostane levels, renal lipid hydroperoxide content, and renal lipid content. In cultured podocytes, high-glucose stimulation increased CB1 receptor expression, and SR141716 treatment abolished high-glucose-induced up-regulation of collagen and plasminogen activator inhibitor-1 synthesis. Additionally, knockdown of CB1 receptor expression by stealth small interfering RNA abolished high-glucose-induced sterol-regulatory element-binding protein-1 expression in podocytes. These findings suggest that CB1 blockade improves insulin resistance and protect against renal injury through both metabolic and antifibrotic effects in type 2 diabetic nephropathy. Targeting CB1 blockade could therefore provide a new therapeutic target to prevent type 2 diabetic nephropathy.
Substitution rate of the hepatitis B virus surface gene (2008)

Molecular epidemiology of hepatitis B virus (HBV) often relies on the comparison of HBV surface (S) gene sequences, although little is known about the substitution rate of the HBV S-gene. In this study, we compared HBV S-gene sequences in longitudinal sample pairs of 40 untreated, chronically HBV-infected patients, spanning 210 years of cumulative follow-up. The 40 patients included HBV e-antigen positive and negative persons; with HBV DNA levels ranging from 10(3) to 10(9) cps/mL and belonging to HBV genotypes A, B, C, D and E. In the 40 sample pairs, 70 nucleotide changes occurred in the HBV S-gene (0-8 per patient), resulting in an average substitution rate of 5.1 x 10(-4) nucleotide changes/site/year (range: 0-1.3 x 10(-2)). Surprisingly, the number of substitutions was strongly associated with the inverse level of viremia; and only weakly with the duration of follow-up: in 11 highly viremic patients (HBV DNA > or =10(8) cps/mL), only four substitutions occurred despite a cumulative observation period of 56 years (substitution rate: 1.1 x 10(-4)), while in the 10 patients with viremia below 10(4) cps/mL, 29 substitutions occurred during 30 years of follow-up (substitution rate: 14.6 x 10(-4)). We conclude that in chronic hepatitis B virus infection the rate of nucleotide substitution in the HBV S-gene is inversely related to the level of viremia and thus varies widely from person to person; hampering the phylogenetic analysis of possible chains of HBV infection.
Suppression of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="italic">T</mml:mi></mml:mrow><mml:mrow><mml:mi mathvariant="italic">c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math>in Superconducting Amorphous Wires (1999)

The suppression of the mean field temperature of the superconducting transition, ${T}_{c}$, in homogeneous amorphous wires is studied. We develop a theory that gives ${T}_{c}$ in situations when the dynamically enhanced Coulomb repulsion competes with the contact attraction. The theory accurately describes recent experiments on ${T}_{c}$ suppression in superconducting wires, after a procedure that minimizes the role of nonuniversal mechanisms influencing ${T}_{c}$ is applied.
Intensive treatment and survival outcomes in NUT midline carcinoma of the head and neck (2016)

HNNMC portends a poor prognosis. Aggressive initial surgical resection with or without postoperative chemoradiation or radiation is associated with significantly enhanced survival. Chemotherapy or radiation alone is often inadequate. Cancer 2016;122:3632-40. © 2016 American Cancer Society.
Approaches to layered coding for dual-rate wireless video transmission (2002)

Visual communications over wireless networks require the efficient and robust coding of video signals for transmission over wireless links having time-varying channel capacity. The authors compare several schemes for encoding video data into two priority streams, thereby enabling the transmission of video data over wireless links to be switched between two bit rates. An H.261 (p/spl times/64) algorithm is modified to implement each candidate scheme. The algorithms are evaluated for a microcellular wireless environment and a clear-channel bit rate of 65 kb/s. The results show that by combining layering with automatic-repeat request (wireless-)link control, almost-wireline visual quality can be achieved. >
Painful Plantar Heel, Plantar Fasciitis, and Calcaneal Spur: Etiology and Treatment (1987)

Painful plantar heel is a relatively common clinical entity encountered by the health care professional who treats patients with foot complaints. Plantar fasciitis and calcaneal spurs are frequently associated with this condition. The most common etiology involves abnormal pronation with resultant increased tension forces developed in the structures attaching in the region of the calcaneal tuberosity. This article reviews the relevant anatomy, pathomechanics, pathophysiology, and clinical presentation of the painful plantar heel patient. A course of treatment is suggested. J Ortho Sports Phys Ther 1987;9(1):17-24.
Islet Amyloid Polypeptide in Human Insulinomas: Evidence for Intracellular Amyloidogenesis (1994)

Amyloid deposits that characteristically form in the pancreatic islets of patients with non-insulin-dependent diabetes mellitus (NIDDM) and in insulinomas are both derived from islet amyloid polypeptide (IAPP). Evidence from previous studies has suggested that deposition of IAPP-derived amyloid is related to inherent amyloidogenic sequences present within normal human IAPP, together with an increased production and local concentration of IAPP. However, whether the aggregation of IAPP to form amyloid fibrils is primarily an intra- or extracellular event is not clear. To address this question, we studied 20 human insulinomas by light and electron microscopy. By light microscopy, amyloid deposits were demonstrated in 13 of 20 (65%) human insulinomas. Furthermore, evaluation of Congo red-stained tumor sections showed small, globular or irregular, congophilic amyloid deposits within the cytoplasm of many tumor cells in 10 of 13 (77%) amyloid-containing insulinomas. Dense, punctate areas of IAPP immunoreactivity within tumor cells corresponded with the congophilic intracellular deposits. Ubiquitin immunoreactivity also was observed as punctate intracellular labeling and within large extracellular amyloid deposits. Among the 10 insulinomas available for electron microscopic evaluation, pathological IAPP-immunoreactive (immunogold) deposits were found in 3 of 5 insulinomas in which amyloid was demonstrated by light microscopy and in none of 5 tumors found negative for amyloid by light microscopy. Morphology of IAPP-immunoreactive deposits varied from those with the classical distinct 7- to 10-nm diameter nonbranching fibrils to those with distinct but faint fibrillarity to those without discernable fibrils.(ABSTRACT TRUNCATED AT 250 WORDS)
Three-Dimensional Self-Assembly of Metallic Rods with Submicron Diameters Using Magnetic Interactions (2003)

Metallic rods with submicron diameters that contain disklike ferromagnetic sections self-assemble into highly stable, hexagonally close-packed arrays of rods. The rods were fabricated by electrodeposition in porous alumina membranes and comprised alternating sections of gold and nickel. The thicknesses of the ferromagnetic nickel sections were approximately one-half the diameter of the rods (400 nm); this geometry orients the "easy" axis of magnetization perpendicular to the long axis of the rod. After magnetization of the rods with a rare-earth magnet, followed by sonication of the suspension, the rods spontaneously assembled into three-dimensional (3D) bundles that, on average, contained 15-30 rods. A macroscopic model of the rods suggests that the most stable orientation of the magnetic dipoles for rods in a defect-free, hexagonally close-packed arrangement is in concentric rings with the dipoles oriented head-to-tail. This configuration minimizes the energy of the bundle and does not generate a net dipole for the structure. This work provides a simple demonstration that magnetic interactions between ferromagnetic objects can direct and stabilize the formation of ordered, 3D structures by self-assembly.
Rocaglamide, silvestrol and structurally related bioactive compounds from Aglaia species (2014)

Covering: 2006 to 2013. Investigations on the chemistry and biology of rocaglamide, silvestrol and structurally related bioactive compounds from Aglaia species during the period 2006-2013 are reviewed. Included are new phytochemical studies of naturally occurring rocaglamide derivatives, an update on synthetic methods for cyclopenta[b]benzofurans, and a description of the recent biological evaluation and mechanism-of-action studies on compounds of this type.
Brownian Motion of an Ellipsoid (2006)

We studied the Brownian motion of isolated ellipsoidal particles in water confined to two dimensions and elucidated the effects of coupling between rotational and translational motion. By using digital video microscopy, we quantified the crossover from short-time anisotropic to long-time isotropic diffusion and directly measured probability distributions functions for displacements. We confirmed and interpreted our measurements by using Langevin theory and numerical simulations. Our theory and observations provide insights into fundamental diffusive processes, which are potentially useful for understanding transport in membranes and for understanding the motions of anisotropic macromolecules.