gebhart/patrepeval huggingface dataset:
Nephrogenic Systemic Fibrosis, Kidney Disease, and Gadolinium (2007)

Nephrogenic systemic fibrosis (NSF), formerly known as nephrogenic fibrosing dermopathy (NFD), is now a major concern for nephrologists. This entity was first described in 1997 in renal transplant recipients with poor graft function (1). More than 215 cases of NSF have subsequently been described in the NFD/NSF registry, with increasing numbers of cases being reported (2). NSF is a fibrosing disorder that involves predominantly the skin but also affects systemic organs such as the liver, heart, lungs, diaphragm, and skeletal muscle (3). It is associated with severe physical disability and death when multisystem disease supervenes (3). The cause of NSF is unknown; however, underlying kidney dysfunction is present in all cases. Approximately 90% of the patients described in the registry have ESRD and are on either hemodialysis or peritoneal dialysis (2). The rest have chronic kidney disease (CKD) or developed NSF in the setting of acute kidney injury (AKI). Thus, underlying kidney disease is a requisite for NSF to occur. Because not all patients with kidney disease develop NSF, one must hypothesize that a trigger is required to set the “fibrosing process” into motion.

What do we know about the histology of tissue fibrosis in NSF? Dermal spindle cells, the predominant cell type found in NSF biopsies, have an immunologic profile (CD34/procollagen I) that is identical to blood-borne cells, circulating fibrocytes (cF), which participate in normal wound healing (4). In the setting of tissue/endothelial injury, they enter tissues and engage in wound healing and scar formation. In NSF, however, this process differs from normal wound healing in that cF engage in this activity in the absence of a clinically evident wound. The disturbed environment of kidney disease may supply abnormal signals, which result in cF entry into normal tissues and induction of fibrosis (4).

A logical first step to …
Edward: A library for probabilistic modeling, inference, and criticism (2016)

Probabilistic modeling is a powerful approach for analyzing empirical information. We describe Edward, a library for probabilistic modeling. Edward's design reflects an iterative process pioneered by George Box: build a model of a phenomenon, make inferences about the model given data, and criticize the model's fit to the data. Edward supports a broad class of probabilistic models, efficient algorithms for inference, and many techniques for model criticism. The library builds on top of TensorFlow to support distributed training and hardware such as GPUs. Edward enables the development of complex probabilistic models and their algorithms at a massive scale.
The immunoglobulin mu enhancer core establishes local factor access in nuclear chromatin independent of transcriptional stimulation. (1993)

Factor access in chromatin has been proposed to be facilitated by transcriptional enhancers. With the aim of uncoupling factor access from transcriptional stimulation by protein-protein contacts, we analyzed the potential of enhancer fragments to confer accessibility upon a linked promoter for prokaryotic T7 RNA polymerase. Access to the T7 promoter in pre-B cells from transgenic mice was examined by transcribing chromatin of isolated nuclei with T7 RNA polymerase. A 95-bp immunoglobulin mu enhancer core element was necessary and sufficient to confer accessibility upon the T7 promoter independent of its chromosomal position. This enhancer-dependent factor access could be uncoupled from an active transcriptional state of the transgene and was not accompanied by the formation of pronounced DNase I hypersensitive sites. Additional mu enhancer sequences comprising previously identified matrix attachment regions and a cryptic promoter were required to induce DNase I hypersensitivity. Together, these data provide evidence that the 95-bp mu enhancer core can establish localized factor access in nuclear chromatin independent of detectable transcription by endogenous polymerases and suggest that multiple steps are involved in the alteration of chromatin structure.
Genotoxicity of 255 chemicals in the Salmonella microsome test (Ames test) and 8-hydroxyguanine (8-OH-Gua) assay for the detection of carcinogens (2003)

A program of cancer prevention, which aimed at identifying and minimizing human exposure to hazardous chemicals, requires the development of a rapid inexpensive screening assay as a complement to expensive long-term animal tests. Among thousands of hazardous chemicals to which humans are exposed, very few have been tested for genotoxicity. This report presents 255 chemicals (mutagens, non-mutagens, etc.) of a wide variety of chemical types which have been tested for genotoxicity, both in the Salmonella microsome test (Ames test) and in 8-hydroxyguanine (8-OH-Gua) assay, in order to detect carcinogens. Of the 255 chemicals tested, 83 chemicals (32.5%) were mutagenic in S. Typhimurium YG1041, YG1042, YG3003 and/or YG7108 strain, and 21 chemicals (8.2%) formed 8-OH-Gua in the rat hepatocytes oxidized DNA. These results may demonstrate the utility and limitation of both the Ames test and 8-OH-Gua assay in detecting chemicals likely to be toxic.
Nonrigid retrospective respiratory motion correction in whole‐heart coronary MRA (2011)

A nonrigid retrospective respiratory motion correction scheme is presented for whole-heart coronary imaging with interleaved acquisition of motion information. The quasi-periodic nature of breathing is exploited to populate a 3D nonrigid motion model from low-resolution 2D imaging slices acquired interleaved with a segmented 3D whole-heart coronary scan without imposing scan time penalty. Reconstruction and motion correction are based on inversion of a generalized encoding equation. Therein, a forward model describes the transformation from the motion free image to the motion distorted k-space data, which includes nonrigid spatial transformations. The effectiveness of the approach is demonstrated on 10 healthy volunteers using free-breathing coronary whole-heart scans. Although conventional respiratory-gated acquisitions with 5-mm gating window resulted in an average gating efficiency of 51% ± 11%, nonrigid motion correction allowed for gate-free acquisitions, and hence scan time reduction by a factor of two without significant penalty in image quality. Image scores and quantitative image quality measures for the left coronary arteries showed no significant differences between 5-mm gated and gate-free acquisitions with motion correction. For the right coronary artery, slightly reduced image quality in the motion corrected gate-free scan was observed as a result of the close vicinity of anatomical structures with different motion characteristics. Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.
Structural and electrostatic effects on binding of trivalent cations to double‐stranded and single‐stranded poly[d (AT)] (1990)

We have measured the thermal melting profile for poly[d(AT)].poly[d(TA)] as a function of concentration of three trivalent cations: spermidine, me8spermidine, and hexammine cobalt(III). Using McGhee's (1976) theory of DNA melting in the presence of ligands, we have estimated association constants Kh, Kc and binding site sizes nh, nc for binding to double-helical (h) and single-stranded (c) polynucleotide. The results are as follows: (table; see text) The binding parameters for spermidine and hexammine cobalt(III) to double helical molecules agree fairly well with direct equilibrium dialysis measurements, and are in reasonable accord with predictions of counterion condensation theory. However, despite their identical charges, the three ligands bind to single-stranded DNA with quite different affinities. Estimates of the charge spacing of single-stranded DNA suggest that poly[d(AT)] is less elongated in the presence of spermidine and hexammine cobalt(III) than it is when complexed with me8spermidine.
Shape-controlled growth of one-dimensional Sb2O3nanomaterials (2004)

This paper describes a simple surfactant-assisted solvothermal approach to the large-scale synthesis of one-dimensional Sb2O3 nanorods, needle-like fibres, nanobelts and nanotubes. The shape of Sb2O3 nanomaterials can be controlled by the concentration of the reactants and CTAB. The growth mechanism and the factors that affect the shapes of 1D Sb2O3 nanomaterials are briefly discussed.
Development of coded-aperture imaging with a compact gamma camera (2004)

In the 1990s, CEA has developed a very compact operational gamma camera, CARTOGAM, capable of mapping the surrounding radioactivity and representing it superimposed onto a visible-light image. Since then, the camera has been successfully industrialized and commercialized. In the same time, the Kurchatov Institute has developed a coded-aperture gamma camera. Both teams have joined their efforts to develop a compact coded-aperture gamma camera. This paper presents the first results obtained with a coded mask adapted to the existing CARTOGAM camera. Simulations have been carried out to design small-sized coded masks for high-energy gamma imaging (/sup 137/Cs or /sup 60/Co). Innovative tungsten-alloy masks have been achieved that lead to the following results: a significant increase in the sensitivity (up to 10 times), an improved angular resolution (2/spl deg/ to 3/spl deg/) and a large field of view (about 30/spl deg/). The laboratory results of /sup 137/Cs and /sup 60/Co imaging, including shadowgrams and reconstructed images for point sources, are presented.
La autonomía moral en el horizonte de la educación social (1995)

En este artículo se analiza algunas de las constantes más frecuentes en la personalidad del sujeto inadaptado y se propone un conjunto de metodologías que pueden ayudar en el tratamiento de las mismas. Así mismo se insiste en el ambiente institucional como elemento básico en el proceso de socialización y en el logro de la autonomía personal de cada individuo.
Deubiquitination of FANCD2 Is Required for DNA Crosslink Repair (2007)

Monoubiquitination of FANCD2 and PCNA promotes DNA repair. It causes chromatin accumulation of FANCD2 and facilitates PCNA's recruitment of translesion polymerases to stalled replication. USP1, a protease that removes monoubiquitin from FANCD2 and PCNA, was thought to reverse the DNA damage response of these substrates. We disrupted USP1 in chicken cells to dissect its role in a stable genetic system. USP1 ablation increases FANCD2 and PCNA monoubiquitination but unexpectedly results in DNA crosslinker sensitivity. This defective DNA repair is associated with constitutively chromatin-bound, monoubiquitinated FANCD2. In contrast, persistent PCNA monoubiquitination has negligible impact on DNA repair or mutagenesis. USP1 was previously shown to autocleave after DNA damage. In DT40, USP1 autocleavage is not stimulated by DNA damage, and expressing a noncleavable mutant in the USP1 knockout strain partially rescues crosslinker sensitivity. We conclude that efficient DNA crosslink repair requires FANCD2 deubiquitination, whereas FANCD2 monoubiquitination is not dependent on USP1 autocleavage.
Molecular analysis of the human beta-globin locus activation region. (1989)

Recently, DNA sequences containing four erythroid-specific DNase I hypersensitive sites within 20 kilobases 5' of the human epsilon-globin gene have been identified as an important cis-acting regulatory element, the locus activation region (LAR). Subfragments of the LAR, containing either all or only the two 5' or two 3' hypersensitive sites were linked to the human beta-globin gene and analyzed for their effect on globin gene expression in stably transformed mouse erythroleukemia (MEL) cells. Constructs containing all four of the hypersensitive sites increase beta-globin mRNA levels 8- to 13-fold, while constructs with only the 5' or 3' sites increase globin expression to a lesser extent. No effect was seen when the constructs were assayed in 3T3 fibroblasts. All of the LAR derivatives form hypersensitive sites at the corresponding sequence position in MEL cells prior to and after induction of MEL cell differentiation. However, in 3T3 fibroblasts only the hypersensitive site corresponding to the previously described erythroid-specific -10.9 site was formed.
Chasing Mutations in the Epidermal Growth Factor in Lung Cancer (2005)

Non–small-cell lung cancer is the leading cause of death from cancer in men and women in the United States, and worldwide it kills more than 1 million people annually. Approximately two thirds of patients with non–small-cell lung cancer present with locally advanced or metastatic disease that requires systemic therapy in addition to surgery or radiation therapy. The good news is that the results of systemic therapy are improving: chemotherapy prolongs survival and improves the quality of life for patients with non–small-cell lung cancer. The bad news is that systemic therapy is still woefully inadequate: only 30 to 40 percent of . . .
Sequencing DNA Amplified Directly from a Bacterial Colony (2003)

We show that PCR product asymmetrically amplified directly from a bacterial colony can be sequenced to yield results as good as those obtained when purified template DNA is used for the PCR amplification step. With either template, greater than 300 nucleotides can be read from a typical sequencing reaction. Taq DNA polymerase was used for both the PCR amplification and sequencing reactions.
Fluorescent Amino Acids: Modular Building Blocks for the Assembly of New Tools for Chemical Biology (2013)

Fluorescence spectroscopy is a powerful tool for probing complex biological processes. The ubiquity of peptide-protein and protein-protein interactions in these processes has made them important targets for fluorescence labeling, and to allow sensitive readout of information concerning location, interactions with other biomolecules, and macromolecular dynamics. This review describes recent advances in design, properties and applications in the area of fluorescent amino acids (FlAAs). The ability to site-selectively incorporate fluorescent amino acid building blocks into a protein or peptide of interest provides the advantage of closely retaining native function and appearance. The development of an array of fluorescent amino acids with a variety of properties, such as environment sensitivity, chelation-enhanced fluorescence, and profluorescence, has allowed researchers to gain insights into biological processes, including protein conformational changes, binding events, enzyme activities, and protein trafficking and localization.
Dense Decoder Shortcut Connections for Single-Pass Semantic Segmentation (2018)

We propose a novel end-to-end trainable, deep, encoder-decoder architecture for single-pass semantic segmentation. Our approach is based on a cascaded architecture with feature-level long-range skip connections. The encoder incorporates the structure of ResNeXt's residual building blocks and adopts the strategy of repeating a building block that aggregates a set of transformations with the same topology. The decoder features a novel architecture, consisting of blocks, that (i) capture context information, (ii) generate semantic features, and (iii) enable fusion between different output resolutions. Crucially, we introduce dense decoder shortcut connections to allow decoder blocks to use semantic feature maps from all previous decoder levels, i.e. from all higher-level feature maps. The dense decoder connections allow for effective information propagation from one decoder block to another, as well as for multi-level feature fusion that significantly improves the accuracy. Importantly, these connections allow our method to obtain state-of-the-art performance on several challenging datasets, without the need of time-consuming multi-scale averaging of previous works.
A single fragment of a malaria merozoite surface protein remains on the parasite during red cell invasion and is the target of invasion-inhibiting antibodies. (1990)

A complex of polypeptides derived from a precursor is present on the surface of the malaria merozoite. During erythrocyte invasion only a small fragment from this complex is retained on the parasite surface and carried into the newly infected red cell. Antibodies to this fragment will interrupt invasion.
Overview of citric acid production from Aspergillus niger (2015)

Citric acid has high economic potential owing to its numerous applications. It is mostly produced by microbial fermentation using Aspergillus niger. In view of surges in demand and growing markets, there is always a need for the discovery and development of better production techniques and solutions to improve production yields and the efficiency of product recovery. To support the enormous scale of production, it is necessary and important for the production process to be environmentally friendly by utilizing readily available and inexpensive agro-industrial waste products, while maintaining high production yields. This article reviews the biochemistry of citric acid formation, choices of citric-acid producing microorganisms and raw materials, fermentation strategies, the effects of various fermentation conditions, citric acid recovery options and the numerous applications of citric acid, based on information drawn from the literature over the past 10 years.
Rapid, Transient Phosphatidylserine Externalization Induced in Host Cells by Infection withChlamydiaspp (2001)

Chlamydia organisms are obligate intracellular bacterial pathogens responsible for a range of human diseases. Persistent infection or reinfection with Chlamydia trachomatis leads to scarring of ocular or genital tissues, and Chlamydia pneumoniae infection is associated with the development of atherosclerosis. We demonstrate that C. trachomatis and C. pneumoniae infection in vitro elicits the externalization of the lipid phosphatidylserine on the surface of human epithelial, endothelial, granulocytic, and monocytic cells. Phosphatidylserine externalization is associated with cellular development, differentiation, and death. Infection-induced phosphatidylserine externalization was immediate, transient, calcium dependent, and infectious dose dependent and was unaffected by a broad-spectrum caspase inhibitor. Chlamydia-infected cells accelerated plasma clotting and increased the macrophage phagocytosis of infected cells that was phosphatidylserine dependent. The rapid externalization of phosphatidylserine by infected cells may be an important factor in the pathogenesis of chlamydial infections.
Cytotoxicity against human peripheral blood mononuclear cells and T cell lines mediated by anti-T cell immunotoxins in the absence of added potentiator (1991)

Several in vitro assays have indicated that anti-T cell immunotoxins (IT), composed of monoclonal antibodies (MoAbs) conjugated to ricin A chain (RTA), are maximally effective against T cells only in the presence of potentiators. It was thought that such IT might not be sufficiently cytotoxic to deplete T cells in vivo upon administration to patients. Therefore, we have re-evaluated the in vitro assays and report herein that even with a short exposure time (2 h), the two anti-T cell IT, H65-RTA (anti-CD5 MoAb coupled to RTA) and 4MRTA (anti-CD7 MoAb coupled to RTA30), were specifically cytotoxic for peripheral blood mononuclear cells (PBMC) in the absence of potentiators. Moreover, as has been reported for IT when tested against T cell lines, prolonging the exposure time of the IT with PBMC from 2 h to as long as 90 h, without added potentiators, enhanced their cytotoxicity from 2- to 40-fold. In contrast, most T cell lines were more sensitive to IT in the presence of potentiator, and IT cytotoxicity was much less enhanced by prolonging the exposure time. Thus, T cell lines may not serve as accurate models to determine the efficacy of IT against PBMC in vitro or in vivo. We conclude that IT-induced cytotoxicity of PBMC can be demonstrated in vitro at pharmacologically achievable concentrations in the absence of added potentiators.
Integrated electrical and SEM-based defect characterization for rapid yield ramp (2004)

Challenges of the new nanometer processes have complicated the yield enhancement process. The systematic yield loss component is increasing, due to the complexity and density of the new processes and the designs that are developed for them. High product yields can now only be achieved when process failure rates are on the order of a few parts per billion structures. Traditional yield ramping techniques cannot ramp yields to these levels and new methods are required. This paper presents a new systematic approach to yield loss pareto generation. The approach uses a sophisticated Design-of-Experiments (DOE) approach to characterize systematic and random yield loss mechanisms in the Back End Of the Line (BEOL). Sophisticated Characterization Vehicle (CV)<sup>TM</sup> test chips, fast electrical test and Automatic Defect Localization (ADL) are critical components of the method. Advanced statistical analysis and visualization of the detected and localized electrical defects provides a comprehensive view of the yield loss mechanisms. In situations where the defects are not visible in a SEM of the structure surface, automated FIB and imaging is used to characterize the defect. The combined approach provides the required resolution to appropriately characterize parts per billion failure rates.
Molecular Cloning and Restriction Endonuclease Mapping of Two Strains of Canine Adenovirus Type 2 (1989)

The DNA of a field isolate and of a vaccine strain of canine adenovirus type 2 (CAV-2) were analysed by digestion with several restriction endonucleases. The PstI restriction fragments of the field isolate (CAV-2 Glasgow) and the vaccine strain were cloned into the plasmid pBR322. Physical maps of the two viral genomes were constructed by molecular hybridization of PstI, EcoRI, SmaI, BamHI and KpnI digests of the viral DNA with the cloned PstI fragments. The restriction profile of CAV-2 Glasgow was shown to be virtually identical to those of the two prototype CAV-2 strains, Toronto A26/61 and Manhattan. However, the restriction fragment pattern of the vaccine strain of CAV-2 showed characteristic alterations, in particular additional sequences at or near the genome termini.
A colourimetric screening test for evaluation of the buffer capacity of saliva. (1980)

A colourimetric method for screening buffer capacity of mixed paraffin stimulated saliva in general practice is described. Mixed paraffin stimulated saliva (1.00 ml) is pipetted into a standard tube belonging to a commercial "saliva kit" (Dentobuff, Orion Diagnostics Ltd). The tube is sealed with a plastic stopper and vigorously shaken for 10 seconds. The stopper is then removed and carbon dioxide is allowed to evaporate for 2--5 minutes. The colour is compared with a scale graded from pH 3 to pH 6. The method was evaluated using 136 dental patients and dental students, and a number of dentists and nurses, and the results were compared with the generally accepted clinical method developed by Ericsson (1959). Several different nurses, dentists and dental students took part in registering the results. In four cases the results differed by more than +/- 2.0 pH units between the two methods and in another 18 by more than +/- 1.0 units. Of the 80 tests performed on no occasion was a person with a "low" salivary buffer capacity evaluated as "normal" or "good". There was no obvious systematic deviation between the two methods, provided carbon dioxide was allowed to evaporate for 2--5 minutes before reading the colour. A thorough examination revealed that at a final pH over 5.5 the method gives lower values than Ericsson's method because of retained carbonic acid, a fact which was considered to be of minor importance, clinically. The method was found to be easy to handle and rapid and the accuracy was considered adequate. It is advisable, however, to repeat the test once or twice because of biological variation and in doubtful cases if "intermediate" results are repeatedly found to send the patient to a clinic with facilities for a complete test.