gebhart/patrepeval huggingface dataset:
Validation of sperm sexing in the cattle (Bos taurus) by dual colour fluorescence in situ hybridization (2005)

Separation of X- and Y-bearing sperm cells, together with artificial insemination using sex-specific semen, makes it possible to pre-determine the sex of calves. This has the potential to considerably improve cattle breeding, genetic resource management and particularly the efficiency of dairy and meat production. However, the broad use of sexed semen will depend on availability, price, fertilizability and in particular the actual sorting purity of sperm doses. To validate the accuracy of sperm sexing in Bos taurus, we have developed a simple, fast and reliable dual colour fluorescence in situ hybridization (FISH) test, where Y-bearing spermatozoa are identified by a DNA fragment hybridizing to a large pericentromeric repetitive DNA block on the bovine Y chromosome (locus DYZI, Yp13-q12). To avoid an underestimation of Y signals, we used a second DNA probe identifying a large subcentromeric block of complex repetitive DNA on the bovine autosome 6 (locus D6Z1, 6q12-15) as a positive control. Bovine sperm were fixed with methanol:acetic acid and denatured by simply immersing in 3 M NaOH, yielding consistent hybridization results and good preservation of sperm morphology. The FISH protocol was evaluated on unsorted sperm as well as on sperm samples sexed using the Beltsville technology, which separates X- and Y-bearing spermatozoa by staining with Hoechst 33342 and flow sorting according to their DNA content (Johnson et al. 1987).
Ultrasound-based navigation for minimally invasive surgical atrial fibrillation treatment: workflow and application prototype (2005)

Atrial fibrillation (AF) is the most common arrhythmia and results in an increased risk of ischemic stroke. Recently, a european consortium has developed a new minimally invasive device for surgical AF treatment. It consists of a micro-robot holding an end-effector called "umbrella" containing 22 radiofrequency powered electrodes. Surgery using this new device can only be performed having an appropriate navigation technique. Therefore, we have developed an image-based navigation workflow and a prototypic navigation application. First, a navigation workflow including an appropriate intra-operative image-modality was defined. Intraoperative ultrasound became the imaging modality of choice. Once the umbrella is unfolded inside the left atrium, data is acquired and segmented. Using a reliable communication protocol, mobility values are transferred from the control software to the navigation system. A deformation model predicts the behavior of the umbrella during repositioning. Prior to surgery, desired ablation lines can be interactively planned and actually made ablation lines are visualized during surgery. Several in-vitro tests were performed. The navigation prototype has been integrated and tested within the overall system successfully. Image acquisitions of the umbrella showed the feasibility of the navigation procedure. More in-vitro and in-vivo tests are currently performed to make the new device and the described navigation procedure ready for clinical use.
Macrophage Colony-stimulating Factor Augments β-Amyloid-induced Interleukin-1, Interleukin-6, and Nitric Oxide Production by Microglial Cells (1998)

In Alzheimer's disease (AD), a chronic cerebral inflammatory state is thought to lead to neuronal injury. Microglia, intrinsic cerebral immune effector cells, are likely to be key in the pathophysiology of this inflammatory state. We showed that macrophage colony-stimulating factor, a microglial activator found at increased levels in the central nervous system in AD, dramatically augments beta-amyloid peptide (betaAP)-induced microglial production of interleukin-1, interleukin-6, and nitric oxide. In contrast, granulocyte macrophage colony-stimulating factor, another hematopoietic cytokine found in the AD brain, did not augment betaAP-induced microglial secretory activity. These results indicate that increased macrophage colony-stimulating factor levels in AD could magnify betaAP-induced microglial inflammatory cytokine and nitric oxide production, which in turn could intensify the cerebral inflammatory state by activating astrocytes and additional microglia, as well as directly injuring neurons.
Streptococcal protein G. Gene structure and protein binding properties. (1991)

Protein G was solubilized from 31 human group C and G streptococcal strains with the muralytic enzyme mutanolysin. As judged by the mobility in sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the binding patterns of the solubilized protein G molecules in Western blot experiments, the strains could be divided into three groups, represented by the group G streptococcal strains G148 and G43 and the group C streptococcal strain C40. The 65-kDa G148 protein G and the 58-kDa C40 protein G showed affinity for both immunoglobulin G (IgG) and human serum albumin (HSA), whereas the 40-kDa G43 protein G bound only IgG. Despite the different molecular patterns, the three protein G species had identical NH2-terminal amino acid sequences. Apart from the 65-kDa peptide, digestion of G148 streptococci with mutanolysin also produced a 52-kDa IgG- and HSA-binding peptide and a 14-kDa HSA-binding peptide. It was demonstrated that these peptides resulted from cleavage of 65-kDa protein G by proteolytic components in the mutanolysin preparation. The protein G genes of the C40 and G43 strains were cloned and sequenced, and their structure was compared to the previously published sequence of the G148 protein G gene. As compared to G148, both the C40 and G43 genes lacked a 210-base pair fragment in the IgG-binding region, accounting for the 10-fold lower affinity of these proteins for IgG. The G43 gene also lacked a 450-base pair fragment in the 5'-end of the gene, explaining why the G43 protein G did not bind HSA. The differences in protein G structure did not correlate with the clinical origin of the strains used in this study. The IgG-binding region of protein G was further mapped. Thus, a peptide corresponding to a single IgG-binding unit was obtained by the cloning and expression of a 303-base pair polymerase chain reaction-generated DNA fragment. The affinity of this 11.5-kDa peptide for human IgG was 8.0 x 10(7) M-1, as determined by Scatchard plots. Finally, a 55-amino acid-long synthetic peptide, corresponding to one of the three repeated domains in the COOH-terminal half of strain G148 protein G, effectively blocked binding of protein G to IgG.
Validation of the protective Ostertagia ostertagi ES‐thiol antigens with different adjuvantia (2004)

Intramuscular immunization of calves with an excretory-secretory antigen fraction enriched for cysteine proteinase activity (ES-thiol) and QuilA as adjuvant induces a protective immune response against the abomasal nematode Ostertagia ostertagi. The objectives of the present study were to confirm the protective capacity of ES-thiol in combination with QuilA, to test Al(OH)(3) as adjuvant for vaccination against O. ostertagi and to look for correlations between protection and immunological effector responses. Calves(seven animals/group) were vaccinated three times intramuscularly with 100 micro g antigen and/or adjuvant (ES-thiol with QuilA, ES-thiol with Al(OH)(3), QuilA alone and Al(OH)(3) alone) and subsequently challenged with a trickled oral infection of 25 000 infective larvae in total over 25 days. Faecal egg counts in the ES-thiol QuilA group were reduced by 56% during the two-month period of the trial compared to the QuilA control group (P < 0.002). Calves immunized with ES-thiol QuilA had significantly smaller adult worms (P < 0.002) and less eggs/female worm (P < 0.05) compared to the QuilA control group. No differences in egg output, worm counts or parameters of worm fitness were observed in the ES-thiol Al(OH)(3) group compared to the Al(OH)(3) control group. Although the protective immune mechanism against O. ostertagi remains unknown, protection in the ES-thiol QuilA group was associated with high levels of parasite-specific antibodies in the abomasal mucosa.
Prognostic value of interleukin-8 in AIDS-associated Pneumocystis carinii pneumonia. (1995)

i) IL-8 in BAL fluid correlates to the clinical severity of the pneumonia, and ii) is a predictor of mortality and severe respiratory compromise.
Identification of the vaccinia virus mRNA guanyltransferase active site lysine. (1993)

The vaccinia virus mRNA capping enzyme is a heterodimeric protein containing subunits of 97 and 33 kDa, the products of genes D1R and D12L, respectively. The enzyme catalyzes the first three reactions in the mRNA cap formation pathway: mRNA triphosphatase, guanyltransferase and (guanine-7-)methyltransferase. The guanyltransferase reaction proceeds by way of a covalent enzyme GMP (E-GMP) intermediate (Shuman, S. and Hurwitz, J. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 187-191) in which the GMP is linked to the large subunit through a lysine residue (Toyama, R., Mizumoto, K., Nakahara, Y., Tatsuno, T., and Kaziro, Y. (1983) Eur. J. Biochem. 2, 2195-2201; Roth, M. J., and Hurwitz, J. (1984) J. Biol Chem. 259, 13488-13494). In order to identify the map position of the guanyltransferase active site lysine residue, high specific activity [32P]E-GMP was prepared. Digestion of the E-GMP with hydroxylamine at pH 9.5 yielded a 31-kDa radioactive fragment derived from amino acids 1-273. Cleavage of E-GMP with cyanogen bromide produced a radioactive peptide of 14 kDa corresponding to amino acids 242-365. Lysine residues are found at positions 244 and 260. Staphylococcus aureus V8 protease digestion of cyanogen bromide-cleaved E-GMP yields a radioactive product of about 5 kDa in molecular mass corresponding to the peptide generated by cleavage at glutamic acid residues 253 and 297, demonstrating that lysine 260 is the site of linkage of GMP.
Protein Design of an HIV-1 Entry Inhibitor (2001)

Human immunodeficiency virus type-1 (HIV-1) membrane fusion is promoted by the formation of a trimer-of-hairpins structure that brings the amino- and carboxyl-terminal regions of the gp41 envelope glycoprotein ectodomain into close proximity. Peptides derived from the carboxyl-terminal region (called C-peptides) potently inhibit HIV-1 entry by binding to the gp41 amino-terminal region. To test the converse of this inhibitory strategy, we designed a small protein, denoted 5-Helix, that binds the C-peptide region of gp41. The 5-Helix protein displays potent (nanomolar) inhibitory activity against diverse HIV-1 variants and may serve as the basis for a new class of antiviral agents. The inhibitory activity of 5-Helix also suggests a strategy for generating an HIV-1 neutralizing antibody response that targets the carboxyl-terminal region of the gp41 ectodomain.
The Escritoire: A personal projected display for interacting with documents (2021)

The Escritoire is a horizontal desk interface that uses two projectors to create a foveal display. Items such as images, documents, and the interactive displays of other conventional computers, can be manipulated on the desk using pens in both hands. The periphery covers the desk, providing ample space for laying out the objects relevant to a task, allowing them to be identified at a glance and exploiting human spatial memory for rapid retrieval. The fovea is a high resolution focal area that can be used to view any item in detail. The projected images are continuously warped with commodity graphics hardware before display, to reverse the effects of misaligned projectors and ensure registration between fovea and periphery. The software is divided into a hardware-specific client driving the display, and a platform-independent server imposing control.
The ontogeny of a 57-Kd cationic antimicrobial protein of human polymorphonuclear leukocytes: localization to a novel granule population (1990)

The ontogeny of a 57-Kd cationic antimicrobial protein (CAP57) that has substantial similarities to bactericidal permeability increasing protein (BPI) has been determined immunocytochemically. CAP57 was detected in the granules of mature peripheral blood neutrophils. However, it was absent from other cells of the peripheral blood: eosinophils, red blood cells (RBCs), and mononuclear cells. In human bone marrow, CAP57 was confined to the neutrophilic series. The earliest stage of development of the myeloid cells at which CAP57 was demonstrated was the promyelocyte. Double immunofluorescent labeling showed that CAP57 was detected in cells positive for myeloperoxidase. The absence of lactoferrin in certain cells (promyelocytes) containing CAP57 indicated that CAP57 was synthesized and packaged in a population of granules prior to the development of granules that contain lactoferrin. CAP57 could not be demonstrated in HL60 cells either by enzyme-linked immunosorbent assay (ELISA) or by immunocytochemistry. However, the presence of another granule-associated cationic antimicrobial protein of molecular weight 37 Kd (CAP37) was readily detected in undifferentiated HL60 cells. Amino acid sequence analysis showed that CAP57 and BPI were identical. Further indication of the identity between CAP57 and BPI was that monoclonal anti-CAP57 antibodies cross reacted with BPI. Sucrose density-gradient centrifugations showed CAP57 was confined to a granule population that exhibited a buoyant density intermediate of the previously described light and heavy azurophil granules. Further resolution of the individual azurophil granule populations by Percoll density-gradient centrifugation revealed that CAP57 was most concentrated in the density range of 1.093 to 1.100 g/cc. These results strongly suggest the unique finding that CAP57 may be associated with a heretofore unreported granule type.
Visualization of clustered directed acyclic graphs with node interleaving (2009)

Graph drawing and visualization represent structural information as diagrams of abstract graphs and networks. An important subset of graphs is directed acyclic graphs (DAGs). E-Spring algorithm, extended from the popular spring embedder model, eliminates node overlaps in clustered DAGs by modeling nodes as charged particles whose repulsion is controlled by edges modeled as springs. The drawing process needs to reach a stable state when the average distances of separation between nodes are near optimal. This paper presents an enhancement to E-Spring to introduce a stopping condition, which reduces equilibrium distances between nodes and therefore results in a significantly reduced area for DAG visualization. It imposes an upper bound on the repulsive forces between nodes based on graph geometry. The algorithm employs node interleaving to eliminate any residual node overlaps. These new techniques have been validated by visualizing eBay buyer-seller relationships and resulted in overall area reductions in the range of 45% to 79%.
In vitro susceptibility testing of nonsporing anaerobes to ten antimicrobial agents. (2000)

Antibiotic Susceptibility was performed on sixty clinical isolates of nonsporing anaerobes against ten antimicrobial agents. The test was performed on Muller Hinton Agar and Wilkins Chalgren blood agar by preparing suspension of freshly isolated colonies in BHI broth. Apart from Metronidazole and Chloramphenicol newer antibiotics like Minocycline, Secnidazole, Tinidazole, Clarithromycin, Roxithromycin were also tried. Antimicrobial agents like metronidazole, Secnidazole, Tinidazole and Minocycline were 100% sensitive, followed by Chloramphenicol, Clarithromycin and Roxithromycin. These newer agents can be good alternatives for the treatment of non sporing anaerobes.
Accuracy of B-Type Natriuretic Peptide Tests to Exclude Congestive Heart Failure (2006)

The use of BNP tests to rule out CHF in primary care settings could reduce demand for echocardiography. The advantages of rapid ELISA tests need to be balanced against their higher cost.
Electrochemically Enabled Sustainability (2014)

Electroreduction of Carbon Dioxide Daniel A. Lowy and Maria Jitaru Microbial Fuel Cells and Other Bio-Electrochemical Conversion Devices Shaoan Cheng and Weifeng Liu Lithium Batteries: Status and Future Bruno Scrosati and Jusef Hassoun Hollow Mesoporous Carbon with Hierarchical Nanoarchitecture in Electrochemical Energy Storage and Conversion Min-Sik Kim, Dae-Soo Yang, Min Young Song, Jung Ho Kim, and Jong-Sung Yu Layer-Structured Cathode Materials for Energy Storage Bohang Song, Man On Lai and Li Lu First-Principles Approach for Cathode Design and Characterisation Dong-Hwa Seo, Inchul Park and Kisuk Kang Advanced Batteries and Improvements in Electrode Materials Ashok Kumar Shukla, Vedam Ganesh Kumar and Musuwathi Krishnamoorthy Ravikumar Lead-Carbon Hybrid Ultracapacitors and Their Applications Ashok Kumar Shukla, Anjan Banerjee and Musuwathi Krishnamoorthy Ravikumar Vanadium Flow Batteries: From Materials to Large-Scale Prototypes Huamin Zhang Physical Properties of Negative Half-Cell Electrolytes in the Vanadium Redox Flow Battery Asem Mousa and Maria Skyllas-Kazacos pH Differential Power Sources with Electrochemical Neutralisation Huanqiao Li, Chi-Ying Vanessa Li, Guo-Ming Weng and Kwong-Yu Chan
The "primary" antiphospholipid syndrome: major clinical and serological features. (1989)

The antiphospholipid syndrome--the association of venous and/or arterial thromboses, often accompanied by thrombocytopenia in the presence of the antiphospholipid antibodies ("lupus anticoagulant" antibodies to cardiolipin)--is seen mainly in patients with systemic lupus erythematosus (SLE) and the closely related "lupus-like" disease, i.e., lupus patients not conforming to the 1982 revised American Rheumatism Association classification for SLE. It is also seen in a group of patients who do not manifest any of the major clinical or serologic features of SLE, the majority of whom do not appear to progress to classical lupus. A multicenter study of 70 of these patients is documented and their major clinical and serologic characteristics examined: They have been characterized as suffering from a "primary" antiphospholipid syndrome and present typically with a history of deep vein thromboses, often accompanied by pulmonary thromboembolism, which in a few is complicated by thromboembolic pulmonary hypertension, arterial occlusions (most commonly strokes), or fetal loss. The events are often recurrent and may be accompanied by hemocytopenias (thrombocytopenia and less frequently Coombs positivity and/or hemolytic anemia). They are often antinuclear antibody-negative and are always negative for antibodies to dsDNA and to ENA, typical serologic features of SLE. There may be a family history of SLE or a familial clotting tendency in a minority. The group of patients presented appears to be closely related, but distinctly separate from SLE.
Tissue characterization using magnetic resonance elastography: preliminary results* (2000)

The well-documented effectiveness of palpation as a diagnostic technique for detecting cancer and other diseases has provided motivation for developing imaging techniques for noninvasively evaluating the mechanical properties of tissue. A recently described approach for elasticity imaging, using propagating acoustic shear waves and phase-contrast MRI, has been called magnetic resonance elastography (MRE). The purpose of this work was to conduct preliminary studies to define methods for using MRE as a tool for addressing the paucity of quantitative tissue mechanical property data in the literature. Fresh animal liver and kidney tissue specimens were evaluated with MRE at multiple shear wave frequencies. The influence of specimen temperature and orientation on measurements of stiffness was studied in skeletal muscle. The results demonstrated that all of the materials tested (liver, kidney, muscle and tissue-simulating gel) exhibit systematic dependence of shear stiffness on shear rate. These data are consistent with a viscoelastic model of tissue mechanical properties, allowing calculation of two independent tissue properties from multiple-frequency MRE data: shear modulus and shear viscosity. The shear stiffness of tissue can be substantially affected by specimen temperature. The results also demonstrated evidence of shear anisotropy in skeletal muscle but not liver tissue. The measured shear stiffness in skeletal muscle was found to depend on both the direction of propagation and polarization of the shear waves.
Prognostic Value of Nonobstructive and Obstructive Coronary Artery Disease Detected by Coronary Computed Tomography Angiography to Identify Cardiovascular Events (2014)

Among patients with nonobstructive CAD, those with extensive plaque experienced a higher rate of cardiovascular death or myocardial infarction, comparable with those who have nonextensive disease. Even among patients with obstructive CAD, greater extent of nonobstructive plaque was associated with higher event rate. Our findings suggest that regardless of whether obstructive or nonobstructive disease is present, the extent of plaque detected by coronary computed tomography angiography enhances risk assessment.
The Histone Code Regulating Expression of the Imprinted MouseIgf2rGene (2003)

The mouse IGF-II receptor (Igf2r) and its antisense transcript Air are reciprocally imprinted in most normal tissues. Several mechanisms have been hypothesized to explain Igf2r-Air imprinting, including Igf2r silencing by Air, and transcriptional repression of Igf2r-Air by two differentially methylated regions (DMR1 and DMR2). We employed Mus musculus x Mus spretus interspecific mice and chromatin immunoprecipitation (ChIP) to investigate allele-specific histone modifications in the two DMRs. We show that, in both DMRs, the active alleles of both Igf2r, and Air are associated with acetylated histones (H3, and H4), acetyl lysine 9 of histone H3 (H3 K9-Ac), and methyl lysine 4 of histone H3 (H3 K4-Me). The silenced alleles are associated with methylated DNA, deacetylated H3 K9, and unmethylated H3 K4. Allele-specific histone modifications are present in the DMR2 that is established in the gametes and represents the DNA gametic-imprint of the Igf2r. In the DMR2 from liver, kidney, and central nervous system tissues, H3 K9 methylation is associated exclusively with the silenced allele, and H3 S10 phosphorylation with the active alleles. Treatment of fibroblast cells with 5-aza-deoxycytidine and/or Trichostatin A led to partial reactivation of the silenced allele, which correlates with biallelic histone acetylation. In central nervous system, despite the presence of imprinted Air transcripts, biallelic expression of Igf2r occurs. The tissue-specific relaxation of Igf2r imprinting correlates with biallelic histone acetylation, and biallelic H3 K4 methylation in the promoter region of Igf2r (DMR1). We propose a model of the histone code for Igf2r, and Air imprinting that defines histone modifications specific for the putative gametic imprint DMR2, and explains the tissue-specific imprinting of Igf2r in the mouse and the absence of IGF2R imprinting in human.
Cytokines in Sjögren's syndrome. (1995)

This review discusses the respective role in Sjögren's syndrome of pro-inflammatory cytokines, such as interleukin (IL)-1 beta and tumour-necrosis factor-alpha, and anti-inflammatory cytokines, such as transforming growth factor-beta, interferon-alpha and IL-10. The former products are secreted by lymphocytes as well as epithelial cells. Th 1 cell cytokines predominate within the focal infiltrates. Increased levels of circulating IL2 receptors correlate to the progression of the ongoing disease.