gebhart/patrepeval huggingface dataset:
Factor H family proteins: on complement, microbes and human diseases (2002)

At present, the human Factor H protein family represents seven multidomain, multifunctional serum proteins. This group includes the complement and immune regulators Factor H, the Factor H-like protein 1 (FHL-1) and five Factor H-related proteins proteins (FHR-1, -2, -3, -4 and -5). Each is exclusively composed of individually folded protein domains, termed short consensus repeats (SCRs) or complement control modules. Structure-function analyses allowed the localization of the complement regulatory domain of Factor H and FHL-1 in the N-terminal region within SCRs 1-4. In addition, multiple binding sites for C3b, heparin and microbial surface proteins were localized in the N-terminus, within the middle region and also in the C-terminus of Factor H and FHL-1. Recent results show a central role for the C-terminus of Factor H, i.e. SCRs 19-20. These particular domains are conserved in all FHRs identified so far, include contact points for C3b, heparin and microbial surface proteins and represent a 'hot-spot' for gene mutations in patients that suffer from the Factor H-associated form of haemolytic uraemic syndrome.
Microanalysis of cardiolipin in small biopsies including skeletal muscle from patients with mitochondrial disease (1999)

Cardiolipin is a specific mitochondrial phospholipid that is present in mammalian tissues in low concentration. To measure cardiolipin in small biopsies from patients with mitochondrial disease, we developed a new technique that can detect subnanomolar levels of well-resolved molecular species, the most abundant of which are tetralinoleoyl-cardiolipin (L(4)) and trilinoleoyl-oleoyl-cardiolipin (L(3)O). To this end, a fluorescence-labeled derivative of cardiolipin (2-[naphthyl-1'-acetyl]-cardiolipin dimethyl ester) was formed and analyzed by high performance liquid chromatography. Cardiolipin was measured in skeletal muscle biopsies from 8 patients with mitochondrial disease and in 17 control subjects. In 5 patients with mitochondrial disease, cardiolipin content was higher than normal (2. 4;-7.0 vs. 0.4;-2.2 nmol/mg protein). In 3 patients with mitochondrial disease, the L(4)/L(3)O ratio was lower than normal (2;-4 vs. 4;-6). Cardiolipin was also measured in various rat and dog muscle tissues. The L(4)/L(3)O ratio was higher in condensed "muscle" type mitochondria (heart ventricle, skeletal muscle, ratios 4;-7) than in orthodox "liver" type mitochondria (liver, smooth muscle, heart auricular appendage, H9c2 myoblasts, ratios 0.4;-3), suggesting that the L(4)/L(3)O proportion is important for cristae membrane structure. We concluded that the L(4)/L(3)O ratio is a tissue-specific variable that may change in the presence of mitochondrial disease. The new method is suitable to measure cardiolipin in muscle biopsies in order to estimate concentration of mitochondria.
The endothelin system in pulmonary arterial hypertension (2004)

Endothelin-1 (ET-1), a peptide produced primarily by vascular endothelial cells, was discovered in 1980 and it was characterized as a powerful vasoconstrictor and mitogen for smooth muscle. ET-1 binds to two types of receptors, ETA and ETB: ETA-receptors are found in smooth muscle cells, whereas ETB-receptors are localized on both endothelial cells and in smooth muscle cells. Activation of ETA- and ETB-receptors on smooth muscle cells mediates the vasoconstrictive and mitogenic effects of ET-1. Stimulation of endothelial ETB-receptors promotes ET-1 clearance and activation of NO and prostacyclin release. Pulmonary arterial hypertension (PAH) is a severe condition characterized by a progressive increase in pulmonary vascular resistance leading to right ventricular failure and death. An activation of the ET-1 system has been demonstrated in both plasma and lung tissues of PAH patients as well as in animal models of PAH. The most efficient way to antagonize the ET-1 system is the use of ET-1 receptor antagonists that can block either ETA- or ETA- and ETB-receptors. These drugs are effective in animal models of PAH and have been tested in multiple clinical trials in patients with PAH. Bosentan, an orally active, dual ET-1 receptor antagonist has been shown to improve symptoms, exercise capacity, hemodynamics, echocardiographic parameters and the outcome of patients with severe PAH, and it has been approved for clinical use in many countries. The selective ETA-receptor antagonist sitaxentan has improved exercise capacity and hemodynamics of PAH patients in two preliminary studies. The main side effect of ET-1 antagonists is the increase of liver enzymes likely due to an accumulation of bile salts cytotoxic to hepatocytes. Additional trials with these drugs are currently ongoing. In conclusion, the hypothesis that the ET-1 system over-activation can be successfully antagonised in patients with PAH has been clearly demonstrated.
Reduction of diffusion barriers in isolated rat islets improves survival, but not insulin secretion or transplantation outcome (2010)

For people with type 1 diabetes and severe hypoglycemic unawareness, islet transplants offer hope for improving the quality of life. However, islet cell death occurs quickly during or after transplantation, requiring large quantities of islets per transplant. The purpose of this study was to determine whether poor function demonstrated in large islets was a result of diffusion barriers and if removing those barriers could improve function and transplantation outcomes. Islets were isolated from male DA rats and measured for cell viability, islet survival, glucose diffusion and insulin secretion. Modeling of diffusion barriers was completed using dynamic partial differential equations for a sphere. Core cell death occurred in 100% of the large islets (diameter >150 µm), resulting in poor survival within 7 days after isolation. In contrast, small islets (diameter <100 µm) exhibited good survival rates in culture (91%). Glucose diffusion into islets was tracked with 2-NBDG; 4.2 µm/min in small islets and 2.8 µm/min in large islets. 2-NBDG never permeated to the core cells of islets larger than 150 µm diameter. Reducing the diffusion barrier in large islets improved their immediate and long-term viability in culture. However, reduction of the diffusion barrier in large islets failed to improve their inferior in vitro insulin secretion compared to small islets, and did not return glucose control to diabetic animals following transplantation. Thus, diffusion barriers lead to low viability and poor survival for large islets, but are not solely responsible for the inferior insulin secretion or poor transplantation outcomes of large versus small islets.
Tag-Encoded FLX Amplicon Pyrosequencing for the Elucidation of Microbial and Functional Gene Diversity in Any Environment (2011)

Comprehensive evaluation of microbial diversity in almost any environment is now possible. Questions such as "Does the addition of fiber to the diet of humans change the gastrointestinal microbiota?" can now be answered easily and inexpensively. Tag-encoded FLX-amplicon pyrosequencing (TEFAP) has been utilized to evaluate bacterial, archaeal, fungal, algal, as well as functional genes. Using the new tag-encoded FLX amplicon pyrosequencing (bTEFAP) approach, we have evaluated the microbial diversity using a more cost-effective and largely reproducible method that would allow us to sequence the ribosomal RNA genes of microorganisms (hereafter focused on bacteria), without the need for the inherent bias of culture methods. These developments have ushered in a new age of microbial ecology studies, and we have utilized this technology to evaluate the microbiome in a wide range of systems in almost any conceivable environment.
A Chloroplast Light-Regulated Oxidative Sensor for Moderate Light Intensity in Arabidopsis (2012)

The transition from dark to light involves marked changes in the redox reactions of photosynthetic electron transport and in chloroplast stromal enzyme activity even under mild light and growth conditions. Thus, it is not surprising that redox regulation is used to dynamically adjust and coordinate the stromal and thylakoid compartments. While oxidation of regulatory proteins is necessary for the regulation, the identity and the mechanism of action of the oxidizing pathway are still unresolved. Here, we studied the oxidation of a thylakoid-associated atypical thioredoxin-type protein, ACHT1, in the Arabidopsis thaliana chloroplast. We found that after a brief period of net reduction in plants illuminated with moderate light intensity, a significant oxidation reaction of ACHT1 arises and counterbalances its reduction. Interestingly, ACHT1 oxidation is driven by 2-Cys peroxiredoxin (Prx), which in turn eliminates peroxides. The ACHT1 and 2-Cys Prx reaction characteristics in plants further indicated that ACHT1 oxidation is linked with changes in the photosynthetic production of peroxides. Our findings that plants with altered redox poise of the ACHT1 and 2-Cys Prx pathway show higher nonphotochemical quenching and lower photosynthetic electron transport infer a feedback regulatory role for this pathway.
MBone provides audio and video across the Internet (1994)

Researchers have produced the Multicast Backbone (MBone), which provides audio and video connectivity from outer space to under water/spl minus/and virtually everyplace in between. MBone is a virtual network that has been in existence since early 1992. It originated from an effort to multicast audio and video from meetings of the Internet Engineering Task Force. Today. hundreds of researchers use MBone to develop protocols and applications for group communication. Multicast provides one-to-many and many-to-many network delivery services for applications such as videoconferencing and audio where several hosts need to communicate simultaneously. This article describes the network concepts underlying MBone, the importance of bandwidth considerations, various application tools, MBone events, interesting MBone uses, and provides guidance on how to connect your Internet site to the MBone.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Testosterone Deficiency: A Key Factor in the Increased Cardiovascular Risk to Women Following Hysterectomy or with Natural Aging? (1998)

The ovaries are a critical source not only of estrogen but also of testosterone. On removal of the uterus, even in instances where ovaries have been spared, their function can be compromised. Women who have had a simple hysterectomy (ovaries remaining intact), even if treated postsurgically with supplementary estrogen, have three times the risk of cardiovascular disease compared with women who have not had a hysterectomy. In men, testosterone has been demonstrated to have beneficial fibrinolytic effects and beneficial effects on blood vessel endothelium, in blood sugar and insulin metabolism, and in maintaining coronary artery circulation. Studies on the potential cardiovascular protective effects of physiologic levels of testosterone in women are critically needed. Restoring a physiologic level of testosterone to women after hysterectomy not only can improve quality of life in terms of sexual libido, sexual pleasure, and sense of well-being but also can build bones--and may be a key to protecting cardiovascular health. Women developing testosterone deficiency as a consequence of natural aging/menopause may similarly benefit from physiologic testosterone supplementation.
The Switch from Fetal to Adult Hemoglobin (2012)

The fetal-to-adult hemoglobin switch and silencing of fetal hemoglobin (HbF) have been areas of long-standing interest among hematologists, given the fact that clinical induction of HbF production holds tremendous promise to ameliorate the clinical symptoms of sickle cell disease (SCD) and β-thalassemia. In this article, we discuss historic attempts to induce HbF that have resulted in some therapeutic approaches to manage SCD and β-thalassemia. We then go on to discuss how more recent molecular studies that have identified regulators, including BCL11A, MYB, and KLF1, hold great promise to develop targeted and more effective approaches for HbF induction. We go on to discuss strategies by which such approaches may be developed. Older studies in this field can provide important lessons for future studies aimed at developing more effective strategies for HbF induction, and we therefore chronologically cover the work accomplished as this field has evolved over the course of the past four decades.
Bulk flow of brain interstitial fluid under normal and hyperosmolar conditions (1980)

Although bulk flow of brain interstitial fluid (ISF) occurs with changes in hydrostatic and osmotic pressures, under normal conditions only diffusion of molecules in the ISF has been reported. Extrachoroidal cerebrospinal fluid (CSF) production and intracerebral injection studies, however, provide indirect evidence for the bulk flow of ISF under normal conditions. We studied tissue penetration profiles of an extracellular molecule in gray and white matter after 1-, 2-, 3-, and 4-h ventriculocisternal perfusions. Gray matter apparent diffusion coefficients were similar at different times as expected with diffusion; however, white matter coefficients decreased significantly with time, suggesting bulk flow of ISF. White matter data was reanalyzed for both bulk flow and diffusion; we calculated a diffusion coefficient of 3.00 x 10(-6) cm2/s and a velocity for ISF of 10.5 micrometers/min toward the ventricle. Additional animals were given 20% mannitol (1.5--3 g/kg) intravenously prior to a /-h ventriculocisternal perfusion. Mannitol produced a significant bulk flow of ISF away from the ventricle in gray matter. We estimate that 30% of extrachoroidal CSF production is from flow of ISF in white matter.
Rapid sequencing of the p53 gene with a new automated DNA sequencer (1998)

p53 is the most commonly mutated gene in human cancers. Approximately 90% of the p53 gene mutations are localized between domains encoding exons 5 to 8. Sequencing methods currently available are tedious and time-consuming and are not suitable for routine laboratory testing. In an effort to identify a simple and rapid sequencing method, we analyzed 16 preselected breast tumors and 18 preselected ovarian tumors, using a newly developed automated DNA sequencer. p53 gene mutations had been previously identified in these tumors, using a conventional automated sequencing procedure. Exons 5 to 8 were amplified by PCR, and the PCR products were subsequently subjected to cycle sequencing with the Sanger chain termination method, using Cy5.5-labeled primers. The sequencing mixture was then resolved on a newly developed automated DNA sequencer that can sequence approximately 300 bases of DNA in 30 min. Of these 16 breast tumors, two had mutations in exon 5, four in exon 6, three in exon 7, and three in exon 8. Of the 18 ovarian tumors, two had mutations in exon 5, five in exon 6, two in exon 7, and three in exon 8. In all cases, we identified the same mutations by both the new and the conventional sequencing procedures. Most mutations affected an arginine codon. These data demonstrate that the new method has the capability to provide accurate sequencing information in a fraction of the time and labor in comparison with current automated sequencing techniques. When such procedures are used, DNA sequencing may become a routine tool for identifying clinically important mutations for diagnosis and prognosis of patients with genetic, malignant, infectious, and other diseases.
Purification and staining of intact yeast DNA chromosomes and real-time observation of their migration during gel electrophoresis (1997)

In the past few years, fluorescence microscopy has been used successfully to characterize the motion of intermediate-size DNA molecules (50-500 kbp) during steady- and pulsed-field gel electrophoresis. However, experimental difficulties had prevented the application of this technique to the direct observation of longer DNA chromosomes (1-2 Mbp). In the present study a particular procedure was followed for the purification and staining of chromosomal yeast DNA to protect it from shear forces. Also, a new highly fluorescent DNA-labelling dye, YOYO-1, was employed to improve brightness and contrast. Finally, the motion of such long DNA molecules (1-2 Mbp) was characterized under steady-field electrophoresis conditions. An accurate description of the molecular mechanisms of motion of such long molecules should provide the basis for a detailed analysis of the mechanisms responsible for DNA trapping.
Tracking multiple humans in complex situations (2004)

Tracking multiple humans in complex situations is challenging. The difficulties are tackled with appropriate knowledge in the form of various models in our approach. Human motion is decomposed into its global motion and limb motion. In the first part, we show how multiple human objects are segmented and their global motions are tracked in 3D using ellipsoid human shape models. Experiments show that it successfully applies to the cases where a small number of people move together, have occlusion, and cast shadow or reflection. In the second part, we estimate the modes (e.g., walking, running, standing) of the locomotion and 3D body postures by making inference in a prior locomotion model. Camera model and ground plane assumptions provide geometric constraints in both parts. Robust results are shown on some difficult sequences.
FasGene Mutations in the Canale–Smith Syndrome, an Inherited Lymphoproliferative Disorder Associated with Autoimmunity (1996)

Patients with the Canale-Smith syndrome have mutations in Fas, which implicates this gene in the accumulation of lymphocytes and the autoimmunity characteristic of the syndrome.
Joint damage and inflammation in c‐Jun N‐terminal kinase 2 knockout mice with passive murine collagen‐induced arthritis (2002)

JNK-2 is a determinant of matrix degradation, but it has little effect on inflammation in arthritis. Complete inhibition of MMP expression and joint destruction will likely require combined JNK-1 and JNK-2 inhibition.
Effect of Capillary Force on Friction Force Microscopy : A Scanning Hydrophilicity Microscope (1996)

Abstract The effect of capillary force due to surface water on friction force microscopy (FFM) was examined by comparing FFM images on oxidized Si surfaces partially covered with chemically bound hydrocarbon (HC) monolayers in vacuo and in an ambient atmosphere. It was found also from force-distance curves and FFM under various relative humidities that adhesive and friction forces observed on the hydrophobic HC covered surface were almost independent of the humidity, while those on the hydrophilic bare oxidized Si surface increased with an increase in the humidity. The higher friction observed on the oxidized Si in the higher humidity was interpreted by the higher effective normal load due to the higher capillary force which originated from a surface water film formed by adsorption of water vapor in the humid air. The results suggest a novel scanning hydrophilicity microscope under a controlled humidity which can be used to map local hydrophilicities of a sample surface in a x-y plane.
Disentangled Image Matting (2019)

Most previous image matting methods require a roughly-specificed trimap as input, and estimate fractional alpha values for all pixels that are in the unknown region of the trimap. In this paper, we argue that directly estimating the alpha matte from a coarse trimap is a major limitation of previous methods, as this practice tries to address two difficult and inherently different problems at the same time: identifying true blending pixels inside the trimap region, and estimate accurate alpha values for them. We propose AdaMatting, a new end-to-end matting framework that disentangles this problem into two sub-tasks: trimap adaptation and alpha estimation. Trimap adaptation is a pixel-wise classification problem that infers the global structure of the input image by identifying definite foreground, background, and semi-transparent image regions. Alpha estimation is a regression problem that calculates the opacity value of each blended pixel. Our method separately handles these two sub-tasks within a single deep convolutional neural network (CNN). Extensive experiments show that AdaMatting has additional structure awareness and trimap fault-tolerance. Our method achieves the state-of-the-art performance on Adobe Composition-1k dataset both qualitatively and quantitatively. It is also the current best-performing method on the alphamatting.com online evaluation for all commonly-used metrics.
Effect of Spatial Attention on the Responses of Area MT Neurons (1999)

This study examines the influence of spatial attention on the responses of neurons in the middle temporal visual area (MT or V5) of extrastriate cortex. Two monkeys were trained to perform a direction-discrimination task. On each trial, two apertures of random-dot stimuli appeared simultaneously at two spatially separated locations; the monkeys were required to discriminate the direction of stimulus motion at one location while ignoring the stimulus at the other location. After extensive training, we recorded the responses of MT neurons in two configurations: 1) Both apertures placed "within" the neuron's receptive field (RF) and 2) one aperture covering the RF while the other was presented at a "remote" location. For each unit we compared the responses to identical stimulus displays when the monkey was instructed to attend to one or the other aperture. The responses of MT neurons were 8.7% stronger, on average, when the monkey attended to the spatial location that contained motion in the "preferred" direction. Attentional effects were equal, on average, in the within RF and remote configurations. The attentional modulations began approximately 300 ms after stimulus onset, gradually increased throughout the trial, and peaked near stimulus offset. An analysis of the neuronal responses on error trials suggests that the monkeys failed to attend to the appropriate spatial location on these trials. The relatively weak attentional effects that we observed contrast strikingly with recent results of Treue and Maunsell, who demonstrated very strong attentional modulations (median effect >80%) in MT in a task that shares many features with ours. Our results suggest that spatial attention alone is not sufficient to induce strong attentional effects in MT even when two competing motion stimuli appear within the RF of the recorded neuron. The difference between our results and those of Treue and Maunsell suggests that the magnitude of the attentional effects in MT may depend critically on how attention is directed to a particular stimulus and on the precise demands of the task.
Structure of endogenous murine leukemia virus DNA in mouse genomes. (1980)

By using molecularly cloned ecotropic AKR murine leukemia virus (MuLV) DNA, a 400-base-pair ecotropic type-specific segment in the env region has been identified. This DNA segment and other defined viral subgenomic fragments have been used as 32P-labeled probes to identify and analyze the structure of integrated ecotropic viral DNA sequences in uninfected mouse genomes. Those mice from which endogenous ecotropic MuLV of the AKR type have been isolated contained at least one virtually complete linear copy of the viral genome. Strains from which ecotropic MuLV has not been isolated lacked ecotropic-specific sequences. All inbred mouse strains tested also contained MuLV DNAs of genomic length whose restriction endonuclease digestion pattern was characteristic of xenotropic viruses.
Improved Transplant-Free Survival in Patients with Systemic Sclerosis-Associated (2014)

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