gebhart/patrepeval huggingface dataset:
Transmission of Swine Dysentery by Carrier Pigs (1978)

SUMMARY Swine dysentery ( sd ) was transmitted to healthy pigs by contact with experimentally-induced carrier pigs. Carrier pigs were produced by exposure of specific pathogen-free ( spf ) swine to swine acutely affected with sd . When carrier pigs became acutely affected with sd , they were allowed to recover naturally or were treated with dimetridazole or ronidazole. Recovery was based on disappearance of clinical signs of sd . At a given time after recovery, normal spf swine were housed with the carriers in a disinfected isolation unit to determine the ability of carriers to transmit sd . In each of 3 experiments, carriers that had recovered and remained asymptomatic for 11 to 25 days transmitted sd to contacts in 14 to 51 days. In 2 experiments, pathogenic Treponema hyodysenteriae was isolated from carriers 12 days before clinical sd was observed in contacts. Carriers which had recovered and remained asymptomatic for 70 to 90 days transmitted sd to contacts in 1 of 3 experiments. Treponema hyodysenteriae was isolated only from contacts with clinical signs of sd . In 4 experiments, carriers that had been treated with nitroimidazole compounds and subsequently recovered for 19 to 44 days failed to transmit sd . Culture of fecal samples on trypticase soy agar with 5% bovine blood and 400 μg of spectinomycin/ml was helpful in predicting the carrier state, but phase contact microscopy of wet fecal smears was not.
Simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested‐PCR assays (2004)

There is a need for rapid, sensitive, and accurate diagnosis of lower respiratory tract infections in children, elderly, and immunocompromised patients, who are susceptible to serious complications. The multiplex RT-nested PCR assay has been used widely for simultaneous detection of non-related viruses involved in infectious diseases because of its high specificity and sensitivity. A new multiplex RT-PCR assay is described in this report. This approach includes nested primer sets targeted to conserve regions of human parainfluenza virus haemagglutinin, human coronavirus spike protein, and human enterovirus and rhinovirus polyprotein genes. It permits rapid, sensitive, and simultaneous detection and typing of the four types of parainfluenza viruses (1, 2, 3, 4AB), human coronavirus 229E and OC43, and the generic detection of enteroviruses and rhinoviruses. The testing of 201 clinical specimens with this multiplex assay along with other one formerly described by our group to simultaneously detect and type the influenza viruses, respiratory syncytial viruses, and a generic detection of all serotypes of adenovirus, covers the detection of most viruses causing respiratory infectious disease in humans. The results obtained were compared with conventional viral culture, immunofluorescence assay, and a third multiplex RT-PCR assay for all human parainfluenza viruses types described previously. In conclusion, both multiplex RT-PCR assays provide a system capable of detecting and identifying simultaneously 14 different respiratory viruses in clinical specimens with high sensitivity and specificity, being useful for routine diagnosis and survey of these viruses within the population.
Confocal Direct Imaging Raman Microscope: Design and Applications in Biology (1998)

A confocal direct imaging Raman microscope (CDIRM) based on two synchronized scanning mirrors, a monochromator, and two charge-coupled device (CCD) cameras has been developed. With this system it is possible to make both Raman spectra of a small measurement volume and images of a larger sample area in one specific Raman band. The spatial resolution of the system was determined for two limiting situations: a small sphere and a thin layer. The image of a 0.282 μm sphere appeared to have a full width at half-maximum (FWHM) of 1.2 μm in the axial and 0.37 μm in the lateral direction, whereas the image of a 275 nm layer showed an FWHM of 1.4 μm in the axial direction. Confocal Raman images were made of the DNA and protein distribution in polytene chromosomes with a relatively weak Raman signal [0.1 photons/(second·pixel)]. Further, a three-dimensional Raman image of the drug distribution in a phthalocyanine-incubated fixed cell is presented. These examples show that the CDIRM can be used to image samples with a weak Raman signal and that three-dimensional images of the distribution of specific molecules in a sample can be made.
Guidelines on the use of therapeutic apheresis in clinical practice—Evidence‐based approach from the apheresis applications committee of the American Society for Apheresis (2010)

Abstract The American Society for Apheresis (ASFA) Apheresis Applications Committee is charged with a review and categorization of indications for therapeutic apheresis. Beginning with the 2007 ASFA Special Issue (fourth edition), the subcommittee has incorporated systematic review and evidence‐based approach in the grading and categorization of indications. This Fifth ASFA Special Issue has further improved the process of using evidence‐based medicine in the recommendations by refining the category definitions and by adding a grade of recommendation based on widely accepted GRADE system. The concept of a fact sheet was introduced in the Fourth edition and is only slightly modified in this current edition. The fact sheet succinctly summarizes the evidence for the use of therapeutic apheresis. The article consists of 59 fact sheets devoted to each disease entity currently categorized by the ASFA as category I through III. Category IV indications are also listed. J. Clin. Apheresis, 2010. © 2010 American Society for Apheresis
Confocal laser scanning microscopy of apoptosis in organogenesis-stage mouse embryos (1998)

Confocal laser scanning microscopy combined with a vital stain has been used to study apoptosis in organogenesis-stage mouse embryos. In order to achieve optical sectioning through embryos, it was necessary to use low power objectives and to prepare the sample appropriately. Mouse embryos were harvested on gestation day 8 or 9 and stained with the vital lysosomal dye, LysoTracker Red. Following incubation in the stain, embryos were fixed in 2% paraformaldehyde overnight, dehydrated in a graded methanol series, and cleared in benzyl alcohol/benzyl benzoate. The resulting embryo is almost transparent and retains specific LysoTracker Red staining. The entire embryo can be optically sectioned and reconstructed in three dimensions to reveal areas of dye staining. To test this approach, the chemotherapeutic drug hydroxyurea was added to day 8 embryos in vitro to induce apoptosis. Our results demonstrated specific regions undergoing programmed cell death in normal development and increased apoptosis in embryos exposed to hydroxyurea. The observed patterns of LysoTracker Red staining correlate well with previous studies of cell death using other lysosomotropic dyes such as Nile blue sulfate, acridine orange, or neutral red. LysoTracker Red has the advantages of being aldehyde-fixable and highly fluorescent (bleaching was not observed even after multiple scans). This procedure allows for the optical imaging of whole day 9 (approximately 22 somites) embryos that were greater than 500 microns thick in the Z-axis.
Primary C utaneous B -Cell L ymphoma: R eview a nd C urrent Concepts (2000)

Purpose: Primary cutaneous B-cell lymphoma (PCBCL) has only recently been recognized as a distinct clinical entity. With the advent of improved immunophenotyping and immunogenotyping, increasing numbers of PCBCL cases are being diagnosed. However, there is much confusion regarding the classification, treatment, and prognosis of these patients. The purpose of this article is to review and analyze the available data to provide the clinician with a concise summary of the diagnosis, prognosis, and treatment of PCBCL. Design: We conducted a thorough review of the medical literature on PCBCL, with a focus on classification, prognosis, and treatment trials. Results and Conclusion: PCBCL is defined as a B-cell lymphoma originating in the skin. There is no evidence of extracutaneous disease at presentation and for 6 months after diagnosis, as assessed by adequate staging procedures. Currently, the European Organization for Research and Treatment of Cancer classification is the most concise disease classification scheme, dividing the subtypes of PCBCL by clinical behavior and histopathologic findings. Based on this classification, the most common subtype of PCBCL is follicular center cell lymphoma. PCBCL is generally an indolent form of lymphoma with a good prognosis. Although local cutaneous recurrences are observed in 25% to 68% of patients, dissemination to internal organs is rare. Fiveyear survival rates typically range from 89% to 96%. A specific subtype, large B-cell lymphoma of the leg, is noted to have a poorer prognosis, with a 5-year survival rate of 58%. Overly aggressive treatment of PCBCL has not been shown to improve survival or prevent relapse. The treatment of choice usually varies depending on the type of PCBCL, the body surface area, and the location of the involvement, as well as the age and general health condition of the patient. The majority of studies indicate that PCBCL is highly responsive to radiation therapy. Polychemotherapy should be reserved for involvement of noncontiguous anatomic sites or those with extracutaneous spread. J Clin Oncol 18:2152-2168. © 2000 by American Society of Clinical Oncology.
Lumbar Adhesive Arachnoiditis (1978)

The etiologic factors and pathologic findings in 38 patients with lumbar arachnoiditis are presented. Lumbar spine surgery and the injection of contrast materials prior to the diagnosis of this condition are considered the most important factors in its genesis. In this series, there was microscopic evidence of arachnoiditis ossificans in 3 patients and arachnoiditis calcificans in 1 patient.
Fas- and Tumor Necrosis Factor-induced Apoptosis Is Inhibited by the Poxvirus crmA Gene Product (1995)

crmA is a cowpox virus gene that encodes a protease inhibitor of the serpin family. The only reported target for the CrmA protein is the cysteine protease interleukin-1 beta converting enzyme (ICE). ICE, by virtue of its homology to the Caenorhabditis elegans cell death protein Ced-3, has been suggested to play a fundamentally important role in mammalian apoptosis. We hypothesized that a function of crmA may be to inhibit cell death, since a major mechanism of viral clearance is the immune system-mediated induction of apoptosis of infected cells. The tumor necrosis factor receptor and the Fas antigen are two cytokine receptors which, by engaging and activating the death pathway, can eliminate virus-infected cells. Remarkably, crmA was found to be an exceptionally potent inhibitor of apoptosis induced by both these receptors, capable of blocking the cell death program even at pharmacological doses of the death stimulus. Therefore, an important new function for crmA is the inhibition of cytokine-induced apoptosis. Further, the data suggest that a protease, either ICE or a related crmA-inhibitable protein, is a component of the Fas- and tumor necrosis factor-induced cell death pathways.
Direct Inhibition of GSK3β by the Phosphorylated Cytoplasmic Domain of LRP6 in Wnt/β-Catenin Signaling (2008)

Wnt/beta-catenin signaling plays a central role in development and is also involved in a diverse array of diseases. Binding of Wnts to the coreceptors Frizzled and LRP6/5 leads to phosphorylation of PPPSPxS motifs in the LRP6/5 intracellular region and the inhibition of GSK3beta bound to the scaffold protein Axin. However, it remains unknown how GSK3beta is specifically inhibited upon Wnt stimulation. Here, we show that overexpression of the intracellular region of LRP6 containing a Ser/Thr rich cluster and a PPPSPxS motif impairs the activity of GSK3beta in cells. Synthetic peptides containing the PPPSPxS motif strongly inhibit GSK3beta in vitro only when they are phosphorylated. Microinjection of these peptides into Xenopus embryos confirms that the phosphorylated PPPSPxS motif potentiates Wnt-induced second body axis formation. In addition, we show that the Ser/Thr rich cluster of LRP6 plays an important role in LRP6 binding to GSK3beta. These observations demonstrate that phosphorylated LRP6/5 both recruits and directly inhibits GSK3beta using two distinct portions of its cytoplasmic sequence, and suggest a novel mechanism of activation in this signaling pathway.
Polymorphisms in TBX21 and STAT4 increase the risk of systemic sclerosis: Evidence of possible gene–gene interaction and alterations in Th1/Th2 cytokines (2009)

The present results, from studies of 2 independent cohorts, indicate that SNPs in TBX21 and STAT4 contribute uniquely and interactively to SSc susceptibility, leading to altered cytokine balance and immune dysregulation.
Structure-Function Relationships of Cellular Retinoic Acid-binding Proteins (1997)

It has been suggested that electrostatic interactions are critical for binding of retinoic acid by cellular retinoic acid-binding proteins (CRABP-I and CRABP-II). However, the roles of two conserved arginine residues (Arg-111 and Arg-131 in CRABP-I; Arg-111 and Arg-132 in CRABP-II) that interact with the carboxyl group of retinoic acid have not been evaluated. A novel competitive binding assay has been developed for measuring the relative dissociation constants of the site-directed mutants of CRABPs. Arg-111 and Arg-132 of CRABP-II were replaced with methionine by site-directed mutagenesis. The relative dissociation constants of R111M and R132M (Kd (R111M)/Kd (CRABP-II) and Kd (R132M)/Kd(CRABP-II)) were determined to be 40-45 and 6-8, respectively. The ring protons of the aromatic residues of the wild-type CRABP-II and the two mutants were sequentially assigned by two-dimensional homonuclear NMR in conjunction with three-dimensional heteronuclear NMR. Detailed analysis of the nuclear Overhauser effect spectroscopy spectra of the proteins indicated that the conformations of the two mutants are highly similar to that of the wild-type CRABP-II. These results taken together showed that Arg-111 and Arg-132 are important for binding retinoic acid but contribute to the binding energy only by approximately 2.2 and 1.2 kcal/mol, respectively. In addition, the relative dissociation constant of CRABP-II and CRABP-I (Kd (CRABP-II)/Kd (CRABP-I)) was determined to be 2-3, in close agreement with that calculated using the apparent Kd values determined under the same conditions by fluorometric titrations.
Pulsed Field Ablation of Paroxysmal Atrial Fibrillation (2021)

PVI with a "single-shot" PFA catheter results in excellent PVI durability and acceptable safety with a low 1-year rate of atrial arrhythmia recurrence. These data mitigate concern that the nonthermal ablative mechanism of PFA might mask undiscovered compromises to clinical success. (IMPULSE: A Safety and Feasibility Study of the IOWA Approach Endocardial Ablation System to Treat Atrial Fibrillation, NCT03700385; A Safety and Feasibility Study of the FARAPULSE Endocardial Ablation System to Treat Paroxysmal Atrial Fibrillation, NCT03714178; PEFCAT II Expanded Safety and Feasibility Study of the FARAPULSE Endocardial Multi Ablation System to Treat Paroxysmal Atrial Fibrillation [PEFCAT II], NCT04170608).
Association of Antibiotics in Infancy With Early Childhood Obesity (2014)

Repeated exposure to broad-spectrum antibiotics at ages 0 to 23 months is associated with early childhood obesity. Because common childhood infections were the most frequent diagnoses co-occurring with broad-spectrum antibiotic prescription, narrowing antibiotic selection is potentially a modifiable risk factor for childhood obesity.
Association between wild type and mutant APC gene products. (1993)

Germline mutations of the APC gene are responsible for familial adenomatous polyposis, an autosomal dominant inherited predisposition to colorectal tumors. Mutation of the APC gene is also an early, if not initiating, event for sporadic colorectal tumorigenesis. In both cases, almost all of the currently identified mutations of APC result in the truncation of the protein. In this study, we demonstrate that truncated APC proteins can associate with the wild type APC in vivo. Using in vitro expression and immunoprecipitation, we show that the first 171 residues of APC are sufficient for APC oligomerization and that the first 45 amino acids of APC is necessary for this interaction. These results indicate that most mutant APC proteins should be able to bind to wild type APC protein and perhaps inactivate it in a dominant negative manner.
TAP-independent, beta 2-microglobulin-dependent surface expression of functional mouse CD1.1. (1995)

CD1 molecules consist of beta 2-microglobulin (beta 2m) noncovalently complexed to a non-major histocompatibility complex (MHC)-encoded monomorphic integral membrane protein homologous to MHC class I alpha chains. Little is known about the requirements for cell surface expression and T cell recognition of CD1. We inserted the mouse CD1.1 gene into vaccinia virus to create a recombinant virus expressing CD1.1 under the control of a viral promoter. Using this recombinant virus to infect normal or mutant cell lines, we found that the expression of molecules reactive with the CD1.1-specific monoclonal antibody 3C11 requires the expression of beta 2m but was not affected by the absence of the MHC-encoded peptide transporter (TAP). Consistent with these results, IL-2 production by the mCD1.1-specific T cell hybridoma DN32.D3 was induced by thymocytes from normal mice or mice with a homozygous deletion of the TAP1 gene, but not by thymocytes from mice with a homozygous deletion of the beta 2m gene. These results indicate that expression of functional mCD1.1 occurs in a beta 2m-dependent, TAP-independent manner.
Fine pitch probing and wirebonding and reliability of aluminum capped copper bond pads (2002)

The requirement for improved electrical performance and reduced silicon area has driven Copper to replace Aluminum interconnection as silicon technology is scaled beyond 0.25 /spl mu/m. The front-end change, in turn, pushes wirebond pad pitch from above 100 /spl mu/m to 80 /spl mu/m-66 /spl mu/m range. This creates challenges for back-end to probe and wire bond at fine pitch geometry onto a readily oxidized Copper surface. After several re-metallization structures and types of metallurgy were evaluated, capping Copper bond pads with Aluminum was selected as the primary approach for probing and wirebonding Copper devices. Aluminum re-metallization structure offers many advantages that help leverage existing tooling and knowledge in fab, probing and wire bonding processes. This paper will describe probe and wirebond experiments used to select the proper adhesion and diffusion barrier between Copper and Aluminum, and Aluminum thickness that can withstand the mechanical stress during probing and wire bonding. Probe mark depth and the impact of probe marks to the underlying barrier and Copper pad were examined. Ball shear, wire rip and corresponding failure modes, intermetallic coverage and cratering analysis were evaluated at various readpoints of thermal aging study to evaluate the integrity of the re-metallization structure as well as the quality of ball bonds onto the new structure. Contact resistance measurement and reliability assessment were also performed. One re-metallization structure was recommended for Copper High Performance wire bonded devices.
Plant growth promoting and phytostimulatory potential of Bacillus subtilis and Bacillus amyloliquefaciens. (2012)

Root colonizing bacteria that exert beneficial effects on plant growth have been defined as plant growth promoting rhizobacteria (PGPR). The present study aimed to the production of indole-3-acetic acid (IAA) and siderophore in WR-W2 and MR-AI strains under in vitro condition. Synthesis of IAA and siderophore was checked in presence of different carbon sources in JNFb - medium amended with L-tryptophan (100 µg/ml) and iron limited M9 medium, respectively. Time course study and simultaneous production of IAA and siderophore was performed in the strain MR-AI and WR-W2. Malate followed by acetate was found as the most suitable sole carbon source for both the IAA and siderophore production by the strain. Siderophore production was inhibited above 20µM concentration of Fe (III). Catecholate type of siderophore production was identified in the culture supernatant of both the strain. Furthermore, significant increase in rice plant (Pusa sugandha III) growth response was observed, when the strains were used as bioinoculum under gnotobiotic condition, in presence of L-tryptophan (100µg/ml). 16S rRNA gene sequence reveals strains MR-AI as Bacillus amyloliquefaciens and WR-W2 as Bacillus subtilis. Strain WR-W2 was found to be more efficient as compared to MR-AI in terms of its capability to produce IAA and siderophore. Therefore, strain MR-AI and WR-W2 could be further applied as bioinnoculum in different formulation in seeds or crop fields for sustainable agricultural systems.
Shaping Gene Expression in Activated and Resting Primary Macrophages by IL-10 (2002)

IL-10 regulates inflammation by reducing cytokine and chemokine production from activated macrophages. We performed microarray experiments to identify possible effector molecules of IL-10 and to investigate the global effect of IL-10 on the transcriptional response induced in LPS-activated macrophages. To exclude background effects of endogenous IL-10, macrophages from IL-10-deficient mice were used. IL-10 up-regulated expression of a small number of genes (26 and 37 after 45 min and 3 h, respectively), including newly identified and previously documented targets such as suppressor of cytokine signaling-3 and IL-1 receptor antagonist. However, the activation program triggered by LPS was profoundly affected by IL-10. IL-10 repressed 62 and further increased 15 of 259 LPS-induced genes. For all genes examined, the effects of IL-10 were determined to be STAT3-dependent. These results suggest that IL-10 regulates STAT3-dependent pathways that selectively target a broad component of LPS-induced genes at the mRNA level.
Towards computing with proteins (2006)

Can proteins be used as computational devices to address difficult computational problems? In recent years there has been much interest in biological computing, that is, building a general purpose computer from biological molecules. Most of the current efforts are based on DNA because of its ability to self-hybridize. The exquisite selectivity and specificity of complex protein-based networks motivated us to suggest that similar principles can be used to devise biological systems that will be able to directly implement any logical circuit as a parallel asynchronous computation. Such devices, powered by ATP molecules, would be able to perform, for medical applications, digital computation with natural interface to biological input conditions. We discuss how to design protein molecules that would serve as the basic computational element by functioning as a NAND logical gate, utilizing DNA tags for recognition, and phosphorylation and exonuclease reactions for information processing. A solution of these elements could carry out effective computation. Finally, the model and its robustness to errors were tested in a computer simulation.
Preferential Nucleosome Assembly at DNA Triplet Repeats from the Myotonic Dystrophy Gene (1994)

The expansion of CTG repeats in DNA occurs in or near genes involved in several human diseases, including myotonic dystrophy and Huntington's disease. Nucleosomes, the basic structural element of chromosomes, consist of 146 base pairs of DNA coiled about an octamer of histone proteins and mediate general transcriptional repression. Electron microscopy was used to examine in vitro the nucleosome assembly of DNA containing repeating CTG triplets. The efficiency of nucleosome formation increased with expanded triplet blocks, suggesting that such blocks may repress transcription through the creation of stable nucleosomes.