gebhart/patrepeval huggingface dataset:
[Three patterns of interaction between soil and non-point source P-pollutants in agricultural watershed]. (2004)

Typical agricultural watershed was selected to study the interactions between soil matrix and non-point source P-pollutants in surface runoff under simulative conditions. The soil samples were taken in different spatial locations in this watershed and were under different degree of human disturbance. The results showed that the interactions between different soil matrix and phosphorus could be divided into three patterns:retention, release and combination of retention and release. Soil of retention pattern has strong adsorption capacity of phosphate and will retain phosphorus from polluted runoff. Soil of release pattern has significant desorption capacity of phosphate and will release phosphorus to the runoff. Soil of retention and release combination pattern will retain or release phosphorus according to the phosphate concentration in the polluted runoff. These results showed that soil matrix in different spatial locations in the agricultural watershed have different ecological functions and environmental values under the processing of natural conditions and human disturbance. From the view of occurrence of non-point source pollution, these soils could become the sink of pollutants as well as the source of pollutants. Under some conditions, there has a conversion between sink and source of them. These results are valuable for control of non-point source pollution on watershed level, identification of key source area of pollutants and improvement of efficiency of control measures.
Noninvasive Magnetic Resonance Imaging of Microvascular Changes in Type 1 Diabetes (2007)

Based on these observations, we conclude that in the STZ model of type 1 diabetes, changes in vascular volume and permeability associated with early stages of the disease can be monitored noninvasively and semiquantitatively by MRI.
Role of Endothelial Nitric Oxide Generation and Peroxynitrite Formation in Reperfusion Injury After Focal Cerebral Ischemia (2000)

These data support the hypothesis that in addition to the detrimental action of NO formed by neuronal NOS during ischemia, NO generation at reperfusion plays a significant role in reperfusion injury, possibly through peroxynitrite formation. Contrary to L-NA, failure of 7-NI to protect against reperfusion injury suggests that the source of NO is the cerebrovascular compartment.
Psychopharmacology of ADHD: children and adolescents. (1998)

Medications can provide significant salutary effects for children and adolescents with attention-deficit/hyperactivity disorder (ADHD). Due to their well-established safety and efficacy, psychostimulants are generally considered first-line pharmacotherapy for most young patients with ADHD. Since psychostimulant treatment often requires frequent dosing and may be associated with unacceptable side effects and risks, other classes of medication have been studied as possible treatment alternatives. The most extensively researched nonstimulant medications are the tricyclic antidepressants. In addition, alpha2 agonists have also been shown to reduce symptoms of ADHD. However, concerns regarding potential cardiotoxicity have tempered the enthusiasm for both of these classes of medication. Newer antidepressants such as bupropion and venlafaxine may hold promise as treatments for ADHD.
Suppression of solid tumor growth by immunoneutralizing monoclonal antibody against human basic fibroblast growth factor. (1991)

Basic fibroblast growth factor (bFGF) is a potent angiogenic mitogen. To elucidate the effect of bFGF inhibitors in vivo, anti-bFGF immunoneutralizing monoclonal antibody was prepared. One monoclonal antibody against human bFGF, obtained by cell fusion and designated 3H3, completely inhibited bFGF-induced proliferation of human umbilical vein endothelial cells at a concentration of 100 ng/ml. 3H3 did not bind to acidic fibroblast growth factor or HST1 protein, indicating high specificity for bFGF. Furthermore, the immunoneutralizing activity of 3H3 was examined in vivo. K1000 cells (a BALB/c 3T3 transformant in which the leader sequence-fused bFGF gene was transfected) were transplanted s.c. into BALB/c nude mice. Growth of the tumor cells was inhibited by i.v. treatment with 3H3 at a concentration of 200 micrograms/mouse. Histological observation showed that the antitumor effect of 3H3 was due to the inhibition of bFGF-induced angiogenesis. This experiment provides direct causal evidence for the hypothesis that tumor growth is angiogenesis dependent. This finding could also have implications for the development of novel therapeutic approaches to angiogenic solid tumors.
Scissors-Grip Model for DNA Recognition by a Family of Leucine Zipper Proteins (1989)

C/EBP is a sequence-specific DNA binding protein that regulates gene expression in certain mammalian cells. The region of the C/EBP polypeptide required for specific recognition of DNA is related in amino acid sequence to other regulatory proteins, including the Fos and Jun transforming proteins. It has been proposed that these proteins bind DNA via a bipartite structural motif, consisting of a dimerization interface termed the "leucine zipper" and a DNA contact surface termed the "basic region." An evaluation of the properties of conserved amino acids within the basic region of 11 deduced protein sequences, coupled with the observation that they are located at an invariant distance from the leucine zipper, has led to the formulation of a "scissors-grip" model for DNA binding. The architectural features of this model are well suited for interaction with directly abutted, dyadsymmetric DNA sequences. Data supportive of the model were obtained with chemical probes of protein: DNA complexes.
The macrophage scavenger receptor CD163: endocytic properties of cytoplasmic tail variants (2006)

CD163 is the monocyte/macrophage-specific receptor for haptoglobin-hemoglobin (Hp-Hb) complexes. The cytoplasmic tail of human CD163 exists as a short tail variant and two long tail variants. Reverse transcriptase-polymerase chain reaction analysis indicated that all three CD163 variants are substantially expressed in blood, liver, and spleen, and the short tail variant is the predominant mRNA species. Using cell transfectants in which cDNA encoding the CD163 variants was inserted at the same site in the genome, we evaluated the expression and endocytic properties of the tail variants. Ligand uptake analysis showed that cells expressing the CD163 short tail variant exhibited a higher capacity for ligand endocytosis than cells expressing the CD163 long tail variants. The difference in endocytic activity was explained by confocal microscopic analysis, showing marked deviations in subcellular distribution. Surface expression was far most pronounced for the CD163 short tail variant, whereas the long tail variants were most abundant in the Golgi region/endosomes. Mutational change of a putative signal for endocytosis (Tyr-Arg-Glu-Met), present in a common part of the cytoplasmic tail of the variants, almost completely inactivated the endocytic activity of the short tail variant. In conclusion, the three physiological tail variants of CD163 may contribute to Hp-Hb endocytosis by means of the common ligand-binding region and endocytic signal. However, the high mRNA expression level and relatively high endocytic capacity of the short tail variant suggest that it accounts for the majority of Hp-Hb uptake from the circulation, whereas the long tail variants may have yet-unknown intracellular roles.
The relevance of the Lewy body to the pathogenesis of idiopathic Parkinson's disease. (1988)

The Lewy body is a distinctive neuronal inclusion that is always found in the substantia nigra and other specific brain regions in Parkinson's disease. It is mainly composed of structurally altered neurofilament, and occurs wherever there is excessive loss of neurons. It occurs in some elderly individuals and rarely in other degenerative diseases of the central nervous system. In 273 brains of patients dying from disorders other than Parkinson's disease, the age-specific prevalence of Lewy bodies increased from 3.8% to 12.8% between the sixth and ninth decades. Associated pathological findings suggest that these cases of incidental Lewy body disease are presymptomatic cases of Parkinson's disease, and confirm the importance of age (time) in the evolution of the disease. In view of the common and widespread occurrence of this disorder we propose that endogenous mechanisms operating in early life may be more important than environmental agents in the pathogenesis of Lewy bodies and Parkinson's disease.
Thin Film Materials: Stress, Defect Formation and Surface Evolution (2004)

Thin film mechanical behavior and stress presents a technological challenge for materials scientists, physicists and engineers. This book provides a comprehensive coverage of the major issues and topics dealing with stress, defect formation, surface evolution and allied effects in thin film materials. Physical phenomena are examined from the continuum down to the sub-microscopic length scales, with the connections between the structure of the material and its behavior described. Theoretical concepts are underpinned by discussions on experimental methodology and observations. Fundamental scientific concepts are embedded through sample calculations, a broad range of case studies with practical applications, thorough referencing, and end of chapter problems. With solutions to problems available on-line, this book will be essential for graduate courses on thin films and the classic reference for researchers in the field
A new macrophage differentiation antigen which is a member of the scavenger receptor superfamily (1993)

The antibodies Ki-M8, Ber-Mac3, GHI/61 and SM4 define a human macrophage-associated antigen with a relative molecular mass of 130,000 which we designate M130. The protein was purified by immunoaffinity chromatography and an N-terminal and three internal amino acid sequences were obtained. A cDNA fragment was initially obtained by polymerase chain reaction (PCR) using reverse-translated primers. Several variant cDNA clones, derived from alternative spliced messages, were obtained from a lipopolysaccharide-stimulated human monocyte library and were sequenced. The relative abundance of these variants was evaluated by a series of overlapping PCR reactions. The size of the most representative cDNA is 3.7 kb and closely agrees with the mRNA size of 3.8 kb determined by Northern blot analysis. The membrane protein encoded contains a leader peptide of 40 residues, a putative extracellular domain of 1003 residues, followed by a hydrophobic segment of 24 residues and a cytoplasmic domain of 49 residues. The extracellular domain was found to contain nine repeating elements, of about 110 residues, which are similar to those of the scavenger receptor superfamily.
InGaP/GaAs power HBTs with a low bias voltage (2002)

This paper describes InGaP/GaAs heterojunction bipolar transistors (HBTs) for L-band power amplifiers with low bias voltage. A fabricated HBT with an emitter size of 2 /spl mu/m/spl times/20 /spl mu/m/spl times/64 fingers offers an output power, Pout, of 34.3 dBm and a power added efficiency, /spl eta//sub add/, of 57.7 % at 1.5 GHz with a collector bias of 3.5 V under class AB operation. The power HBT indicates an output power of over 31 dBm at a bias of as low as 2.5 V. Adjacent channel power leakage of the power HBT according to the Japanese standards of personal digital cellular phone (PDC) is -49 dBc when Pout is 31.4 dBm and /spl eta//sub add/ is 50.3% with collector bias of 3.5 V. This performance shows that InGaP/GaAs HBT is a useful device with a low bias voltage.
Inflammatory cytokines compromise programmed cell death-1 (PD-1)-mediated T cell suppression in inflammatory arthritis through up-regulation of soluble PD-1 (2017)

The programmed cell death 1 (PD-1) receptor plays a major role in regulating T cell activation. Our aim was to determine how inflammation influences PD-1-mediated T cell suppression. Flow cytometry analysis of rheumatoid arthritis (RA) and psoriatic arthritis (PsA) synovial fluid (SF) mononuclear cells showed an increase in the percentage of PD-1<sup>+</sup> cells within the CD4<sup>+</sup> and CD8<sup>+</sup> T cell compartment compared to paired peripheral blood (PB). Upon in-vitro T cell receptor (TCR) stimulation of healthy control (HC) CD4<sup>+</sup> T cells in the presence of plate-bound PD-L1fc chimera, significantly decreased proliferation and interferon (IFN)-γ secretion was observed. In contrast, CD4<sup>+</sup> T cells from RA and PsA PB and SF appeared resistant to such PD-1-mediated inhibition. Addition of the proinflammatory cytokines tumour necrosis factor (TNF)α, interleukin (IL)-6 and IL-1β, which were increased in RA and PsA SF compared to osteoarthritis (OA) SF, consistently abrogated PD-1-mediated suppression in HC CD4<sup>+</sup> T cell cultures. This effect was reversed by inhibitors of these cytokines. Soluble PD-1 (sPD-1) levels were increased in cell culture supernatants from TNFα and IL-6-stimulated cultures compared to untreated controls, and also in RA and PsA, but not in OA, serum and SF. Functionally, addition of sPD-1fc counteracted PD-1-mediated suppression of HC CD4<sup>+</sup> T cells, and increased T cell proliferation in HC CD4<sup>+</sup> T cell/monocyte co-cultures. These in-vitro findings indicate that CD4<sup>+</sup> T cells from patients with RA and PsA show increased resistance to PD-1-mediated suppression, which may be explained in part by the presence of soluble PD-1 in the inflammatory environment.
FDG-PET imaging in mild traumatic brain injury: a critical review (2014)

Traumatic brain injury (TBI) affects an estimated 1.7 million people in the United States and is a contributing factor to one third of all injury related deaths annually. According to the CDC, approximately 75% of all reported TBIs are concussions or considered mild in form, although the number of unreported mild TBIs (mTBI) and patients not seeking medical attention is unknown. Currently, classification of mTBI or concussion is a clinical assessment since diagnostic imaging is typically inconclusive due to subtle, obscure, or absent changes in anatomical or physiological parameters measured using standard magnetic resonance (MR) or computed tomography (CT) imaging protocols. Molecular imaging techniques that examine functional processes within the brain, such as measurement of glucose uptake and metabolism using [(18)F]fluorodeoxyglucose and positron emission tomography (FDG-PET), have the ability to detect changes after mTBI. Recent technological improvements in the resolution of PET systems, the integration of PET with magnetic resonance imaging (MRI), and the availability of normal healthy human databases and commercial image analysis software contribute to the growing use of molecular imaging in basic science research and advances in clinical imaging. This review will discuss the technological considerations and limitations of FDG-PET, including differentiation between glucose uptake and glucose metabolism and the significance of these measurements. In addition, the current state of FDG-PET imaging in assessing mTBI in clinical and preclinical research will be considered. Finally, this review will provide insight into potential critical data elements and recommended standardization to improve the application of FDG-PET to mTBI research and clinical practice.
Use of Gene-Expression Profiling to Identify Prognostic Subclasses in Adult Acute Myeloid Leukemia (2004)

The use of gene-expression profiling improves the molecular classification of adult AML.
Cancer monitoring by FTIR spectroscopy. (2006)

Evidence for balanced cell growth where protein and RNA content rise at a constant relative rate with respect to DNA content with increasing grade of cancer and with malignant transformation, is derived from analysis of infrared spectra of malignant lymphoma and transformed fibroblasts within the literature. This evidence is consistent with flow cytometry derived RNA-protein relationships, and supports the biosynthetic connection proposed here between the RNA/DNA ratio as calculated from the absorbance pulse at 1121 cm(-1), and the protein/nucleic acid ratio as measured by the absorbance ratio A1650 cm(-1)/A1084 cm(-1). The present analysis is the first to explain and show evidence for a simple unifying biomolecular content theory for interdependent changes seen within the fingerprint region (900 cm(-1)-1750 cm(-1)) of the infrared spectrum of cells. Structural changes to lipids and proteins in the wavenumber range 2800 cm(-1)-3000 cm(-1), seen as increasing CH3/CH2 ratio and decreasing symmetric CH2/asymmetric CH2 ratio, are found for the first time to occur with increasing cancer (lymphoma) grade as well. These lipid/protein structural changes (2800-3000 cm(-1)) may reflect an increasing protein/lipid content ratio with malignant grade, and are the same as those shown recently for benign to malignant transformation, further supporting their cellular metabolic basis. Rising ribose content (1121 cm(-1)) is seen to correlate with rising 996 cm(-1)/966 cm(-1) ratio (another index of RNA/DNA) with increasing malignant lymphoma grade as well, The proposed spectral connections have a high signal/noise ratio with respect to clinically meaningful information. They may potentially be applied to clinical cancer grading, or in vitro cancer treatment sensitivity testing.
Regulation of intracranial pressure in rat, dog, and man (1978)

Abstract Intracranial resistance and compliance were assessed in the cerebrospinal fluid system of rat, dog, and man by means of low‐volume, short‐duration infusions of artificial CSF into the subarachnoid space. A family of pressure/time response curves was obtained for each species: at low flow rates, steady‐state pressure elevations were associated with marked neurological dysfunction. From these curves a mathematical model was developed which describes transport and pressure‐dependent valvelike characteristics of the CSF outflow resistance. This resistance. This resistance shows a progressive phylogenetic change in rat, dog, and man which increasingly enhances the species' abilities to vent fluid from the intracranial cavity into the venous circulation. Arachnoid villi appear to be the major structures modulating sustained, nonlethal elevations of intracranial pressure.
Learning to Linearize Under Uncertainty (2015)

Training deep feature hierarchies to solve supervised learning tasks has achieved state of the art performance on many problems in computer vision. However, a principled way in which to train such hierarchies in the unsupervised setting has remained elusive. In this work we suggest a new architecture and loss for training deep feature hierarchies that linearize the transformations observed in unlabeled natural video sequences. This is done by training a generative model to predict video frames. We also address the problem of inherent uncertainty in prediction by introducing latent variables that are non-deterministic functions of the input into the network architecture.
Crystal Structure of the Escherichia coli Peptide Deformylase, (1997)

Protein synthesis in bacteria involves the formylation and deformylation of the N-terminal methionine. As eukaryotic organisms differ in their protein biosynthetic mechanisms, peptide deformylase, the bacterial enzyme responsible for deformylation, represents a potential target for antibiotic studies. Here we report the crystallization and 2.9 A X-ray structure solution of the zinc containing Escherichia coli peptide deformylase. While the primary sequence, tertiary structure, and use of coordinated cysteine suggest that E. coli deformylase belongs to a new subfamily of metalloproteases, the environment around the metal appears to have strong geometric similarity to the active sites of the thermolysin family. This suggests a possible similarity in their hydrolytic mechanisms. Another important issue is the origin of the enzyme's specificity for N-formylated over N-acetylated substrates. Based on the structure, the specificity appears to result from hydrogen-bonding interactions which orient the substrate for cleavage, and steric factors which physically limit the size of the N-terminal carbonyl group.
Nuclear Localization of Ataxin-3 Is Required for the Manifestation of Symptoms in SCA3:In VivoEvidence (2007)

Spinocerebellar ataxia type 3 (SCA3) is an autosomal dominantly inherited neurodegenerative disorder caused by the expansion of a CAG repeat in the MJD1 gene resulting in an expanded polyglutamine repeat in the ataxin-3 protein. To study the course of the disease, we generated transgenic mice for SCA3 using full-length ataxin-3 constructs containing 15, 70, or 148 CAG repeats, respectively. Control mice (15 CAGs) were phenotypically normal and had no neuropathological findings. However, mice transgenic for ataxin-3 with expanded polyglutamine repeats were severely affected by a strong neurological phenotype with tremor, behavioral deficits, strongly reduced motor and exploratory activity, a hunchback, and premature death at 3 to 6 months of age. Neuropathological examination by immunohistochemical staining revealed ubiquitin- and ataxin-3-positive intranuclear inclusion bodies in a multitude of neurons. Directing ataxin-3 with 148 CAGs to the nucleus revealed an even more pronounced phenotype with more inclusions and earlier death, whereas mice transgenic with the same construct but attached to a nuclear export signal developed a milder phenotype with less inclusions. These studies indicate that nuclear localization of ataxin-3 is required for the manifestation of symptoms in SCA3 in vivo.
Structure-based assignment of the biochemical function of a hypothetical protein: A test case of structural genomics (1998)

Many small bacterial, archaebacterial, and eukaryotic genomes have been sequenced, and the larger eukaryotic genomes are predicted to be completely sequenced within the next decade. In all genomes sequenced to date, a large portion of these organisms' predicted protein coding regions encode polypeptides of unknown biochemical, biophysical, and/or cellular functions. Three-dimensional structures of these proteins may suggest biochemical or biophysical functions. Here we report the crystal structure of one such protein, MJ0577, from a hyperthermophile, Methanococcus jannaschii, at 1.7-A resolution. The structure contains a bound ATP, suggesting MJ0577 is an ATPase or an ATP-mediated molecular switch, which we confirm by biochemical experiments. Furthermore, the structure reveals different ATP binding motifs that are shared among many homologous hypothetical proteins in this family. This result indicates that structure-based assignment of molecular function is a viable approach for the large-scale biochemical assignment of proteins and for discovering new motifs, a basic premise of structural genomics.
End-to-end videotext recognition for multimedia content analysis (2001)

Videotext refers to text superimposed on still images and video frames, and a videotext based Multimedia Description Scheme has recently been adopted into the MPEG-7 standard as one of the normative media content description interfaces. While much of the previous work including ours concentrates on the task of locating and extracting text from the video frames automatically, very little research has focused on reliably recognizing segmented text. The low resolution of videotext, unconstrained font styles and sizes, poor separation of characters often resulting from video compression and decoding, all pose severe problems even to commercial OCRs in recognizing videotext accurately. This paper describes novel end-to-end video character recognition system featuring new character attributes emphasizing macro shapes, a Support Vector Machine-based character classifier, videotext object synthesis, font context analysis, and temporal contiguity analysis, to successfully address the issues confounding accurate videotext recognition. We present results from our experiments with real video data that demonstrate the strengths of this system.