gebhart/patrepeval huggingface dataset:
KANK deficiency leads to podocyte dysfunction and nephrotic syndrome (2015)

Steroid-resistant nephrotic syndrome (SRNS) is a frequent cause of progressive renal function decline and affects millions of people. In a recent study, 30% of SRNS cases evaluated were the result of monogenic mutations in 1 of 27 different genes. Here, using homozygosity mapping and whole-exome sequencing, we identified recessive mutations in kidney ankyrin repeat-containing protein 1 (KANK1), KANK2, and KANK4 in individuals with nephrotic syndrome. In an independent functional genetic screen of Drosophila cardiac nephrocytes, which are equivalents of mammalian podocytes, we determined that the Drosophila KANK homolog (dKank) is essential for nephrocyte function. RNAi-mediated knockdown of dKank in nephrocytes disrupted slit diaphragm filtration structures and lacuna channel structures. In rats, KANK1, KANK2, and KANK4 all localized to podocytes in glomeruli, and KANK1 partially colocalized with synaptopodin. Knockdown of kank2 in zebrafish recapitulated a nephrotic syndrome phenotype, resulting in proteinuria and podocyte foot process effacement. In rat glomeruli and cultured human podocytes, KANK2 interacted with ARHGDIA, a known regulator of RHO GTPases in podocytes that is dysfunctional in some types of nephrotic syndrome. Knockdown of KANK2 in cultured podocytes increased active GTP-bound RHOA and decreased migration. Together, these data suggest that KANK family genes play evolutionarily conserved roles in podocyte function, likely through regulating RHO GTPase signaling.
Characterization of the Polarity of Natural Organic Matter under Ambient Conditions by the Polarity Rapid Assessment Method (PRAM) (2007)

The polarity rapid assessment method (PRAM) characterizes the polarity of aqueous natural organic matter (NOM) by quantifying the amount of material adsorbed onto different solid-phase extraction (SPE) sorbents. The analysis is performed under ambient conditions resulting in the elimination of pretreatment steps that may alterthe chemical characteristics of the NOM, allowing an accurate representation of its polarity as it exists in the environment. Additionally, analysis only requires 200 mL of sample and can be performed in 2 h. In this paper, the underlying theory of the method is presented, followed by its optimization, with emphasis on the development of conditions for the analysis of NOM in natural waters. A series of organic probe compounds showed that the most important physicochemical property describing the interaction between the NOM and the SPE sorbents was the hydrophobic surface area, allowing for the estimation of the hydrophobic character under ambient conditions. Evaluation of the effects of chemical concentration, pH, and ionic strength show that (1) concentration did not have an effect on PRAM characterization as long as the pH and ionic strength remained constant; (2) changes in pH and ionic strength resulted in considerable changes in PRAM characterization, as a result of the changes in configuration of the NOM; and (3) PRAM characterization of NOM can be completed in the concentration range of < 10 mg C/L, although this range could be expanded by evaluating the effect of concentration on a site-specific basis. Results indicate that measurement of both ultraviolet absorption and dissolved organic carbon show complementary results as they measure different aspects of NOM.
A High‐Throughput Screening Method for Identification of Inhibitors of the Deubiquitinating Enzyme USP14 (2012)

Deubiquitinating enzymes (DUBs) reverse the process of ubiquitination, and number nearly 100 in humans. In principle, DUBs represent promising drug targets, as several of the enzymes have been implicated in human diseases. The isopeptidase activity of DUBs can be selectively inhibited by targeting the catalytic site with drug-like compounds. Notably, the mammalian 26S proteasome is associated with three major DUBs: RPN11, UCH37, and USP14. Because the ubiquitin 'chain-trimming' activity of USP14 can inhibit proteasome function, inhibitors of USP14 can stimulate proteasomal degradation. We recently established a high-throughput screening (HTS) method to identify small-molecule inhibitors specific for USP14. The protocols in this article cover the necessary procedures for preparing assay reagents, performing HTS for USP14 inhibitors, and carrying out post-HTS analysis. Curr. Protoc. Chem. Biol. 4:311-330 © 2012 by John Wiley & Sons, Inc.
Summarizing and Searching Sequential Semistructured Sources (2000)

this paper, we focus on the impact of ordered subelements on two important technologies associated with semistructured data: DataGuides [GW97] and proximitysearch [GSVGM98].
Experimental measurements of the temporal evolution of cluster size distributions for high-functionality antigens cross-linked by antibody (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExperimental measurements of the temporal evolution of cluster size distributions for high-functionality antigens cross-linked by antibodyGustav K. Von Schulthess, George B. Benedek, and Ralph W. De BloisCite this: Macromolecules 1983, 16, 3, 434–440Publication Date (Print):March 1, 1983Publication History Published online1 May 2002Published inissue 1 March 1983https://pubs.acs.org/doi/10.1021/ma00237a019https://doi.org/10.1021/ma00237a019research-articleACS PublicationsRequest reuse permissionsArticle Views62Altmetric-Citations27LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Review Gene therapy for lipid disorders (2000)

Lipid disorders are associated with atherosclerotic vascular disease, and therapy is associated with a substantial reduction in cardiovascular events. Current approaches to the treatment of lipid disorders are ineffective in a substantial number of patients. New therapies for refractory hypercholesterolemia, severe hypertriglyceridemia, and low levels of highdensity lipoprotein cholesterol are needed: somatic gene therapy is one viable approach. The molecular etiology and pathophysiology of most of the candidate diseases are well understood. Animal models exist for the diseases and in many cases preclinical proof-ofprinciple studies have already been performed. There has been progress in the development of vectors that provide long-term gene expression. New clinical gene therapy trials for lipid disorders are likely to be initiated within the next few years.
Deformable GANs for Pose-Based Human Image Generation (2018)

In this paper we address the problem of generating person images conditioned on a given pose. Specifically, given an image of a person and a target pose, we synthesize a new image of that person in the novel pose. In order to deal with pixel-to-pixel misalignments caused by the pose differences, we introduce deformable skip connections in the generator of our Generative Adversarial Network. Moreover, a nearest-neighbour loss is proposed instead of the common L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> and L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> losses in order to match the details of the generated image with the target image. We test our approach using photos of persons in different poses and we compare our method with previous work in this area showing state-of-the-art results in two benchmarks. Our method can be applied to the wider field of deformable object generation, provided that the pose of the articulated object can be extracted using a keypoint detector.
The HealthDoc Sentence Planner (1996)

This paper describes the Sentence Planner (sP) in the HealthDoc project, which is concerned with the production of customized patienteducation material from a source encoded in terms of plans.The task of the sP is to transform selected, not necessarily consecutive, plans (which may vary in detail, from text plans specifying only content and discourse organization to fine-grained but incohesive, sentence plans) into completely specified specifications for the surface generator.The paper identifies the sentence planning tasks, which are highly interdependent and partially parallel, and argues, in accordance with [Nirenburg et al., 1989], that' a blackboard architecture with several independent modules is most suitable to deal with them.The architecture is presented, and the interaction of the sentence planning modules within this architecture is shown.The first implementation of the sP is discussed; examples illustrate the planning process in action.
Microhardness of SiO <sub>2</sub> Glass in Various Environments (1987)

It was shown in earlier studies that the crack initiation stress of SiO 2 glass was stressing‐time dependent only in water while it was time independent in nonaqueous liquids. In order to clarify the roles that various liquids play in the crack initiation of SiO 2 glass, Knoop microhardness measurements were made on SiO 2 glass in various liquids and FTIR spectroanalysis was performed on the indented SiO 2 glass. The microhardness measurements showed a similar loading‐time dependence to the crack initiation stress. The microhardness was separated into two parts: the surface contribution and the volume contribution. The results showed that the volume (or bulk) component was a nearly constant value for glass measured in nonaqueous liquids and that it was lower for glass measured in water. Consistent with these results, FTIR analysis showed that water entered the glass during indentation while nonaqueous liquids did not. The surface component showed a good correlation with the crack initiation stress.
Revolutionizing the evolution of the CGIAR 2001 to 2007 : a contribution to the institutional memoir and some thoughts for the future (2007)

On May 19, 1971, a small group of policymakers endowed with unusual foresight inaugurated the Consultative Group on International Agricultural Research (CGIAR). The CGIAR was created against the background of looming famine in Asia. Increasing food production in the tropics was therefore the dominant preoccupation of the CGIAR at its founding. The main objectives of the CGIAR were to focus international agricultural research on developing country problems, to ensure that the products of research will be freely available as public goods across national boundaries, and to promote the conservation and international mobility of germplasm. Some changes were the result of recommendations by the three 'external system reviews' that were undertaken during the 1972-2007 period. Some, such as the increase in Southern membership and the initial demolition of barriers between the CGIAR and others in the agricultural research community, took place as a result of the renewal program to which reference is made above. Changes in the research agenda of CGIAR Centers came about as a result of initiatives within the Centers and pressure from CGIAR Members. Funding did not grow in a linear fashion but faced many fluctuations, mostly as a result of domestic trends within Member countries or institutions. If change did occur over the 30 years of its existence, was a reform program that dramatically changed the outlook and conduct of the CGIAR really necessary? Why a major reform program was considered necessary, how it was launched, how it differs from past changes within the CGIAR, and what the reform program has achieved, are the focus of this report which also outlines a vision for the CGIAR in 2015.
The Future: In Vivo CAR T Cell Gene Therapy (2019)

International audience
Hydrogen sulphide as inhibitor and substrates for the cytochrome c-cytochrome c oxidase system / (1981)

It has previously been recognized that the major biochemical toxicity\ninduced by sulphide is due to an inhibition of cytochrome ~ oxidase.\nInhibition of this enzyme occurs at 30°C and pH 7.4 with a Ki of approximately\n0.2 ~M, and a kon of 104 M-1 s-l, under catalytic conditions. However, the\nequimo1ar mixture of sulphide and the enzyme shows identical catalytic\nbehaviour to that of the native enzyme. This cannot readily be attributed\nto rapid dissociation of sulphide, as both spectroscopic and plot analysis\nindicate the koff value is low. The addition of stoichiometric sulphide to\nthe resting oxidized enzyme gives rise to the appearance of a low-spin\nferric-type spectrum not identical with that seen on the addition of excess\nsulphide to the enzyme aerobically. Sulphide added to the enzyme anaerobically\ngives rise to another low-spin, probably largely ferric, form which upon\nadmission of oxygen is then converted into a 607 nm species closely resembling\nCompound C. The 607 nm form is probably the precursor of oxyferricytochrome\naa3. The addition of successive a1iquots of Na2S solution to the enzyme\ninduces initial uptake of approximately 3 moles of oxygen per mole of the\nenzyme. Thus, it is concluded that:\n1. the initial product of sulphide-cytochrome c oxidase interaction is not\nan inhibited form of the enzyme, but the low-spin (oxyferri) ~3+~+ species;\n2. a subsequent step in which sulphide reduces cytochrome ~ occurs;\n3. the final inhibitory step, in which a further molecule of sulphide binds\nto the cytochrome ~ iron centre in the cytochrome ~2+~+ species, gives the\ncytochrome a2+~+-H2S form which is a half-reduced fully inhibited species;4. a 607 run form of the enzyme is produced which may be converted into a\ncatalytically active low-spin (oxyferri) state; and therefore\n5. liganded sulphide may be able to reduce the cytochrome 33 -Cu centre\nwithout securing the prior reduction of the cytochrome a_ haem group or the\nCud centre associated with it.
Production of Carbon from Carbon Dioxide with Iron Oxides and High-Temperature Solar Energy (1997)

We demonstrate from both a theoretical and experimental point of view that CO2 can be thermally reduced to carbon with concentrated solar energy. The concept involves reactions between CO2 and iron oxides. Thus, we experimentally studied the thermochemical reactivity of iron oxides for splitting CO2 into C(gr) and O2 using high-temperature powder X-ray diffraction, gas chromatography, and mass spectrometry. Emphasis was given to the dependence of the gaseous and solid reaction products on the structural change of wustite (Fe1-yO). The CO2 decomposition occurs in two steps at temperatures near 773 K: First wustite reacts with CO2 to form CO and magnetite (Fe3O4); then CO disproportionates to C(gr) and CO2. Fe3O4 can be recycled to Fe1-yO by thermal dissociation above 2200 K using highly concentrated solar radiation as the only energy source for process heat.
Dose reduction for kilovotage cone-beam computed tomography in radiation therapy (2008)

Kilovotage cone-beam computed tomography (kV-CBCT) has shown potentials to improve the accuracy of a patient setup in radiotherapy. However, daily and repeated use of CBCT will deliver high extra radiation doses to patients. One way to reduce the patient dose is to lower mAs when acquiring projection data. This, however, degrades the quality of low mAs CBCT images dramatically due to excessive noises. In this work, we aim to improve the CBCT image quality from low mAs scans. Based on the measured noise properties of the sinogram, a penalized weighted least-squares (PWLS) objective function was constructed, and the ideal sinogram was then estimated by minimizing the PWLS objection function. To preserve edge information in the projection data, an anisotropic penalty term was designed using the intensity difference between neighboring pixels. The effectiveness of the presented algorithm was demonstrated by two experimental phantom studies. Noise in the reconstructed CBCT image acquired with a low mAs protocol was greatly suppressed after the proposed sinogram domain image processing, without noticeable sacrifice of the spatial resolution.
Nucleoside Derived Antibiotics to Fight Microbial Drug Resistance: New Utilities for an Established Class of Drugs? (2016)

Novel antibiotics are urgently needed to combat the rise of infections due to drug-resistant microorganisms. Numerous natural nucleosides and their synthetically modified analogues have been reported to have moderate to good antibiotic activity against different bacterial and fungal strains. Nucleoside-based compounds target several crucial processes of bacterial and fungal cells such as nucleoside metabolism and cell wall, nucleic acid, and protein biosynthesis. Nucleoside analogues have also been shown to target many other bacterial and fungal cellular processes although these are not well characterized and may therefore represent opportunities to discover new drugs with unique mechanisms of action. In this Perspective, we demonstrate that nucleoside analogues, cornerstones of anticancer and antiviral treatments, also have great potential to be repurposed as antibiotics so that an old drug can learn new tricks.
eExpense: A Smart Approach to Track Everyday Expense (2018)

Tracking regular expense is a key factor to maintain a budget. People often track expense using pen and paper method or take notes in a mobile phone or a computer. These processes of storing expense require further computations and processing for these data to be used as a trackable record. In this work, we are proposing an automated system named as eExpense to store and calculate these data. eExpnese is an application that runs on Android smartphones. By using this application, users can save their expense by simply scanning the bills or receipt copies. This application extracts the textual information from the receipts and saves the amount and description for further processing. It also monitors user's income by tracking the received SMS's from the user's saving accounts. By calculating income and expense it produces the user's balance in monthly and yearly basis. Overall, this is a smart automated solution for tracking expense.
Decoder for an enhanced serial generalized bit flipping algorithm (2012)

An enhanced serial generalized bit-flipping algorithm is proposed in this paper. This new algorithm includes method to compute the extrinsic information during all the iterations, improving the performance of the algorithm in the waterfall region compared to the direct serial description. In addition, the algorithm allow us to reduce the storage resources the derived architecture. The decoder was implemented on a Virtex-VI FPGA device for the (837,723) non-binary code over GF(2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> ), achieving 439 Mbps at 10 iterations.
Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome (2016)

The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics.
Structural and Optical Studies of Magnesium Doped Zinc Oxide Thin Films (2013)

The paper describes the structural and optical properties of Magnesium doped Zinc Oxide (Mg  3.5 %, 6 %, 9 %, 12 % by weight) thin films prepared by pulsed laser deposition technique. The samples are characterized by X-ray diffraction technique, Ultra-violet visible absorption spectroscopy, X-ray photoelectron spectroscopy. X-ray diffraction results reveal the polycrystalline nature of samples with no impurity or secondary phase formation. Ultra-violet visible absorption spectroscopy studies show the blue shift in the optical band gap subsequent to Mg doping. X-ray photoelectron spectroscopy results reveal the replacement of Zn2+ cation by Mg2+ ion.\nWhen you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/31019
Nereis cuticle collagen. Isolation and properties of a large fragment resistant to proteolysis by bacterial collagenase. (1977)

Native cuticle collagen, obtained from Nereis virens, was incubated with purified bacterial collagenase (EC 3.4.4.19). The kinetics of proteolysis were monitored by viscometry, in parallel with similar digestions of calf skin collagen. Comparison of the kinetics of digestion of the two collagens, at similar enzyme to substrate ratios (w/w), showed that the native cuticle collagen was relatively refractory to digestion by bacterial collagenase. Characterization of the cuticle collagen digest by sodium dodecyl sulfate-polyacrylamide electrophoresis and agarose gel filtration in CaCl2 showed a large polypeptide, of about 300,000 daltons, to be a major product. The native form of this product, a unique fragment, was isolated from the digest by ethanol precipitation. It was found to have an intrinsic viscosity of 120 dl/g, to have an optical rotary dispersion curve characteristic of collagen, to undergo a typical collagenous thermal transition with a Tm of 23.2 degrees, and to have a calculated molar mass of 900,000 g with molecular dimensions of 9,000 X 13 A. It had an amino acid composition which was similar, but not identical with the native cuticle collagen. Although the original substrate contained two dissimilar chains, A and B, in a molar ratio of 1:2, the collagenase-resistant product appeared to be composed of only one type of polypeptide fragment. Possibly, the original subunits contain similar, if not identical collagenase-resistant regions.