gebhart/patrepeval huggingface dataset:
Immunohistochemical evaluation of urokinase plasminogen activator receptor in noninvasive and early invasive urothelial papillary neoplasia. (2004)

Detection of immunoreactivity for uPAR was associated with high grade UP carcinomas. These data indicate that uPAR is potentially an important prognostic factor in bladder carcinoma.
A New Combination of Blood Test and Fibroscan for Accurate Non-Invasive Diagnosis of Liver Fibrosis Stages in Chronic Hepatitis C (2011)

The association of new fibrosis indexes combining FibroMeter and Fibroscan provides a new fibrosis stage classification. This classification is significantly more accurate than Fibrotest, FibroMeter, or Fibroscan classifications, and improves the accuracy of the non-invasive diagnosis of liver fibrosis stages to 86% without any liver biopsy.
Regular exercise and branched‐chain amino acids prevent ischemic acute kidney injury‐related muscle wasting in mice (2020)

Acute kidney injury (AKI) causes glucose and protein metabolism abnormalities that result in muscle wasting, thereby affecting the long-term prognosis of critical illness survivors. Here, we examined whether early intervention with treadmill exercise and branched-chain amino acids (BCAA) can prevent AKI-related muscle wasting and reduced physical performance in mice. Unilateral 15 min ischemia-reperfusion injury was induced in contralateral nephrectomized mice, and muscle histological and physiological changes were assessed and compared with those of pair-fed control mice, since AKI causes severe anorexia. Mice exercised for 30 min each day and received oral BCAA for 7 days after AKI insult. By day 7, ischemic AKI significantly decreased wet weight, myofiber cross-sectional area, and central mitochondrial volume density of the anterior tibialis muscle, and significantly reduced maximal exercise time. Regular exercise and BCAA prevented AKI-related muscle wasting and low physical performance by suppressing myostatin and atrogin-1 mRNA upregulation, and restoring reduced phosphorylated Akt and PGC-1α mRNA expression in the muscle. Ischemic AKI induces muscle wasting by accelerating muscle protein degradation and reducing protein synthesis; however, we found that regular exercise and BCAA prevented AKI-related muscle wasting without worsening kidney damage, suggesting that early rehabilitation with nutritional support could prevent AKI-related muscle wasting.
A Massive Outbreak in Milwaukee of Cryptosporidium Infection Transmitted through the Public Water Supply (1994)

This massive outbreak of watery diarrhea was caused by cryptosporidium oocysts that passed through the filtration system of one of the city's water-treatment plants. Water-quality standards and the testing of patients for cryptosporidium were not adequate to detect this outbreak.
Enhancing cellular multicast performance using ad hoc networks (2005)

Although multicast communication is well-suited to shared wireless links, receiver heterogeneity impedes the use of multicast in wireless networks. In this paper, we examine an approach that addresses the receiver heterogeneity problem in cellular multicast with the help of an additional IEEE 802.11 ad hoc network. The basic idea is to allow the cellular receivers experiencing poor channel conditions to use the ad hoc network to connect to those cellular receivers that are experiencing good cellular channel conditions. The good receivers (called proxies) relay multicast data to the poor receivers through the ad hoc network. We specifically consider the third generation cellular high data rate (HDR) broadcast/multicast services (BCMCS). We develop a new routing algorithm to find efficient ad hoc paths from the proxies to the cellular multicast receivers. Unlike existing algorithms (Luo et al. (2003)), our routing algorithm considers the effect of ad hoc path interference. Using simulations of an HDR BCMCS network in conjunction with an IEEE ad hoc network, we show that our algorithm improves the receiver goodput by up to 280% compared to that obtained without using ad hoc paths. We also show that our algorithm achieves up to 98% higher receiver goodput in comparison to the greedy algorithm proposed in Luo.
Separation of hyaluronidase from a strain of anaerobic corynebacteria (1971)

abstract – Separation of hyaluronidase from a strain of anaerobic corynebacteria has been carried out. The separation procedure made use of precipitation with ammonium sulfate, ion‐exchange chromatography on CM‐Sephadex C‐50, and gelfiltration on Bio‐Gel A–0.5 m. The separation resulted in a 2,300‐fold increase in specific activity of the enzyme which was obtained in about 33% yield. The isoelectric point was found at pH 8.0±0.5. pH optimum for activity was 5.1–6.2. The hyaluronidase was stable over a wide pH range. Temperature stability determinations showed that the enzyme was rather heat labile.
Peptide and Small Molecule Microarray for High Throughput Cell Adhesion and Functional Assays (2001)

A novel class of chemical microchips consisting of glass microscope slides was prepared for the covalent attachment of small molecule ligands and peptides through site-specific oxime bond or thiazolidine ring ligation reaction. Commercially available microscope slides were thoroughly cleaned and derivatized with (3-aminopropyl)triethoxysilane (APTES). The amino slides were then converted to glyoxylyl derivatives via two different routes: (1) coupling of Fmoc-Ser followed by deprotection and oxidation, or (2) coupling with protected glyoxylic acid and final deprotection with HCl. Biotin or peptide ligands derivatized at the carboxyl terminus with a 4,7,10-trioxa-1,13-tridecanediamine succinimic acid linker and an amino-oxy group or a 1,2-amino-thiol group (e.g., cysteine with a free N(alpha)-amino group) were printed onto these slides using a DNA microarray spotter. After chemical ligation, the microarray of immobilized ligands was analyzed with three different biological assays: (1) protein-binding assay with fluorescence detection, (2) functional phosphorylation assay using [gamma(33)P]-ATP and specific protein kinase to label peptide substrate spots, and (3) adhesion assay with intact cells. In the cell adhesion assay, not only can we determine the binding specificity of the peptide against different cell lines, we can also determine functional cell signaling of attached cells using immunofluorescence techniques in situ on the microchip. This chemical microchip system enables us to rapidly analyze the functional properties of numerous ligands that we have identified from the "one-bead one-compound" combinatorial library method.
Ribozyme-Catalyzed Excision of Targeted Sequences from within RNAs (2002)

We demonstrate that a group I intron-derived ribozyme from the opportunistic pathogen Pneumocystis carinii can bind an RNA in trans and excise from within it an internal segment, resulting in the splicing of the remaining ends of the RNA back together (the trans excision-splicing reaction). The reaction is intramolecular with regard to substrate. The ribozyme targets its substrate by base pairing with two or three noncontiguous regions on the substrate, and the reaction occurs through a nucleotide cofactor independent mechanism. The excised segment can be as long as 28 nucleotides, or more, and as little as one nucleotide. The potential usefulness of this reaction is demonstrated by engineering a ribozyme that excises the triplet-repeat expansion region from a truncated myotonic dystrophy protein kinase transcript mimic in vitro.
An ancestral oomycete locus contains late blight avirulence gene <i>Avr3a</i> , encoding a protein that is recognized in the host cytoplasm (2005)

The oomycete Phytophthora infestans causes late blight, the potato disease that precipitated the Irish famines in 1846 and 1847. It represents a reemerging threat to potato production and is one of >70 species that are arguably the most devastating pathogens of dicotyledonous plants. Nevertheless, little is known about the molecular bases of pathogenicity in these algae-like organisms or of avirulence molecules that are perceived by host defenses. Disease resistance alleles, products of which recognize corresponding avirulence molecules in the pathogen, have been introgressed into the cultivated potato from a wild species, Solanum demissum, and R1 and R3a have been identified. We used association genetics to identify Avr3a and show that it encodes a protein that is recognized in the host cytoplasm, where it triggers R3a-dependent cell death. Avr3a resides in a region of the P. infestans genome that is colinear with the locus containing avirulence gene ATR1(NdWsB) in Hyaloperonospora parasitica, an oomycete pathogen of Arabidopsis. Remarkably, distances between conserved genes in these avirulence loci were often similar, despite intervening genomic variation. We suggest that Avr3a has undergone gene duplication and that an allele evading recognition by R3a arose under positive selection.
FIFO-Based Multicast Scheduling Algorithm for Virtual Output Queued Packet Switches (2005)

Many networking/computing applications require high speed switching for multicast traffic at the switch/router level to save network bandwidth. However, existing queuing-based packet switches and scheduling algorithms cannot perform well under multicast traffic. While the speedup requirement makes the output queued switch difficult to scale, the single input queued switch suffers from head of line (HOL) blocking, which severely limits the network throughput. An efficient yet simple buffering strategy to remove the HOL blocking is to use the virtual output queued (VOQ) switch structure, which has been shown to perform well under unicast traffic. However, the traditional VOQ switch is impractical for multicast traffic because a VOQ switch for multicast traffic has to maintain an exponential number of queues in each input port (i.e., 2/sup N/-1 queues for a switch with N output ports). In this paper, we give a novel queue structure for the input buffers of a multicast VOQ switch by separately storing the address information and data information of a packet so that an input port only needs to manage a linear number (N) of queues. In conjunction with the multicast VOQ switch, we present a first-in-first-out based multicast scheduling algorithm, FIFO multicast scheduling (FIFOMS), and conduct extensive simulations to compare FIFOMS with other popular scheduling algorithms. Our results fully demonstrate the superiority of FIFOMS in both multicast latency and queue space requirement.
The Descriptor Differential Scale: applying psychophysical principles to clinical pain assessment (1988)

The Descriptor Differential Scale (DDS) applies psychophysical principles to clinical pain assessment. It contains 12 descriptor items for each pain dimension assessed. For each item, subjects indicate if their pain either is equal in magnitude to that implied by the anchoring descriptor, or how much greater or lesser on a 10-point graphic scale. The method permits collection of multiple responses, reducing scaling error, and assess both pain magnitude and scaling consistency. Ninety-one patients completed the sensory intensity and unpleasantness forms of the DDS at both 1 and 2 h after surgical extraction of a lower third molar. Results show that the DDS satisfies standard psychometric criteria for reliability, objectivity and item homogeneity. The coefficients found satisfy standard psychometric criteria and improve after elimination of inconsistent profiles.
Representational Power of Restricted Boltzmann Machines and Deep Belief Networks (2008)

Deep belief networks (DBN) are generative neural network models with many layers of hidden explanatory factors, recently introduced by Hinton, Osindero, and Teh (2006) along with a greedy layer-wise unsupervised learning algorithm. The building block of a DBN is a probabilistic model called a restricted Boltzmann machine (RBM), used to represent one layer of the model. Restricted Boltzmann machines are interesting because inference is easy in them and because they have been successfully used as building blocks for training deeper models. We first prove that adding hidden units yields strictly improved modeling power, while a second theorem shows that RBMs are universal approximators of discrete distributions. We then study the question of whether DBNs with more layers are strictly more powerful in terms of representational power. This suggests a new and less greedy criterion for training RBMs within DBNs.
CCD Charge Density Study on Crystals with Large Unit Cell Parameters: The Case of Hexagonal<scp>l</scp>-Cystine (1999)

The electron density of l-cystine has been analyzed using 110 K single-crystal Mo Kα X-ray diffraction data to a resolution of (sin θ/λ)max = 1.123 Å-1 with a CCD area detector. Due to the large c-parameter (55.9 Å), a discussion is made for choosing the best experimental data collection strategy and data reduction. A multipolar pseudo-atom density model was fitted against the 2309 observed data with I > 3σ(I), [R(F) = 0.014, RW(F) = 0.019, S = 0.73]. The deformation density distribution and topological analysis of charge density clearly reveals disulfide bridge characteristic features and sulfur lone pair electron regions which validate high-level ab initio calculations. The valence shell charge concentration (VSCC) suggests sp3 hybridization of sulfur atoms.
Tumor Vaccines Expressing Flt3 Ligand Synergize with CTLA-4 Blockade to Reject Preimplanted Tumors (2009)

The transformation of a healthy cell into a malignant neoplasm involves numerous genetic mutations and aberrations in gene expression. As few of these changes are shared between individuals or types of cancer, the best source for eliciting broad-spectrum tumor immunity remains each patient's own tumor. Previously, we have shown that combining blockade of the T-cell-negative costimulatory molecule CTL-associated antigen 4 (CTLA-4) and vaccination with irradiated B16 tumor expressing granulocyte macrophage colony-stimulating factor (GM-CSF; Gvax) promotes rejection of established murine melanomas. Here we show that, like GM-CSF, the cytokine Flt3 ligand (Flt3L) expressed in B16 and coupled with CTLA-4 blockade promotes both prophylactic and therapeutic rejection of B16. When administered at the site of growing tumor, Gvax fails to prevent tumor outgrowth in any mice, whereas the B16-Flt3L vaccine (Fl3vax) induces the rejection of 75% of melanomas implanted 3 days before vaccination. Relative to Gvax, Fl3vax promotes greater infiltration of both the vaccine site and the tumor site by CD8+ T cells and "sentinel" and plasmacytoid dendritic cells. Gvax and Fl3vax did not synergize when used in combination in treating B16 melanoma even in the context of CD25+ regulatory T-cell depletion. Further, we show that a combination of Flt3L expression and CTLA-4 blockade can also promote the rejection of established TRAMP prostate adenocarcinomas, proving that the utility of this treatment extends beyond melanoma. Engineering Flt3L to be constitutively secreted and attaching an IgG2a tail yielded a B16 vaccine that, when combined with CTLA-4 blockade, prevented the outgrowth of significantly more 5-day implanted B16-BL6 tumors than did Gvax.
Crystallographic and Solution Studies of <i>N</i>-Lithocholyl Insulin:  A New Generation of Prolonged-Acting Human Insulins (2004)

The addition of specific bulky hydrophobic groups to the insulin molecule provides it with affinity for circulating serum albumin and enables it to form soluble macromolecular complexes at the site of subcutaneous injection, thereby securing slow absorption of the insulin analogue into the blood stream and prolonging its half-life once there. N-Lithocholic acid acylated insulin [Lys(B29)-lithocholyl des-(B30) human insulin] has been crystallized and the structure determined by X-ray crystallography at 1.6 A resolution to explore the molecular basis of its assembly. The unit cell in the crystal consists of an insulin hexamer containing two zinc ions, with two m-cresol molecules bound at each dimer-dimer interface stabilizing an R(6) conformation. Six covalently bound lithocholyl groups are arranged symmetrically around the outside of the hexamer. These form specific van der Waals and hydrogen-bonding interactions at the interfaces between neighboring hexamers, possibly representing the kinds of interactions which occur in the soluble aggregates at the site of injection. Comparison with an equivalent nonderivatized native insulin hexamer shows that the addition of the lithocholyl group disrupts neither the important conformational features of the insulin molecule nor its hexamer-forming ability. Indeed, binding studies show that the affinity of N-lithocholyl insulin for the human insulin receptor is not significantly diminished.
A GALOIS THEORY FOR THE FIELD EXTENSION <i>K</i>((<i>X</i>))/<i>K</i> (2010)

Abstract Let K be a field of characteristic 0, which is algebraically closed to radicals. Let F = K (( X )) be the valued field of Laurent power series and let G = Aut ( F / K ). We prove that if L is a subfield of F , K ≠ L , such that L / K is a sub-extension of F / K and F / L is a Galois algebraic extension ( L / K is Galois coalgebraic in F / K ), then L is closed in F , F / L is a finite extension and Gal ( F / L ) is a finite cyclic group of G . We also prove that there is a one-to-one and onto correspondence between the set of all finite subgroups of G and the set of all Galois coalgebraic sub-extensions of F / K . Some other auxiliary results which are useful by their own are given.
Localization of carcinoembryonic antigen in uterine cervical neoplasia. (1990)

Tissues for 74 uterine cervical lesions including 64 invasive squamous cell carcinomas, 4 adenocarcinomas and 6 cervical intraepithelial neoplasia (CIN) were studied by peroxidase-antiperoxidase (PAP) method for presence of carcinoembryonic antigen (CEA). CEA was absent in normal squamous and endocervical epithelium. The antigen was demonstrated in all the cases of CIN (100%) and in 48 invasive carcinomas (70.6%). A heterogeneous pattern of staining was noted in different cases and also within a tumour. None of the 6 endometrial carcinomas showed CEA reactivity while all sections from endocervical carcinomas were positive for CEA. Carcinoembryonic antigen may be a useful tumour marker in the diagnosis of cervical neoplasia and helpful in differentiating endocervical carcinoma from endometrial carcinoma.
Mouse sialoadhesin is not responsible for Candida albicans yeast cell binding to splenic marginal zone macrophages (1994)

Candida albicans hydrophilic yeast cells specifically adhere to mouse macrophages in the splenic marginal zone and in lymph node subcapsular and medullary sinuses. These macrophages express sialoadhesin that binds erythrocytes, but binding of yeast cells is not mediated by sialoadhesin because (i) erythrocytes did not block yeast cell binding, (ii) yeast cell adherence was unaffected by sialoadhesin-specific monoclonal antibodies, (iii) the purified sialoadhesin did not bind to yeast cells, and (iv) an Fc-sialoadhesin chimera immobilized on plastic did not bind yeast cells. These data give further support for a unique macrophage adhesion system that binds C. albicans.
Self-Assembled Gold Nanoparticle/Alkanedithiol Films:  Preparation, Electron Microscopy, XPS-Analysis, Charge Transport, and Vapor-Sensing Properties (2003)

Gold nanoparticle/alkanedithiol films were prepared via layer-by-layer self-assembly. For the assembly process, dodecylamine-stabilized Au nanoparticles with an average size of 4 nm and alkanedithiols with different alkylene chain lengths (C6, C9, C12, C16) were used. The thickness of the films was determined by AFM and ranged between 26 and 34 nm. FE-SEM and TEM images indicate that the particle size within the film materials was similar to that of the dodecylamine-stabilized particles used for film preparation. The composition of the films was analyzed by XPS. The absence of the nitrogen signal indicated that the dodecylamine ligands were quantitatively exchanged by alkanedithiol molecules during film assembly. Two sulfur signals were observed, which could be assigned to sulfur bound to gold (S−Au) and to free thiol groups (S−H). As indicated by the relative signal intensities, about 60% of the alkanedithiol molecules were bound with both ends to the nanoparticles, whereas 40% were bound with only one thiol group. The C/S ratio was in good agreement with the stoichiometry of the alkanedithiol molecules. All films showed linear current−voltage characteristics. Conductivity measurements at variable temperature were consistent with an Arrhenius-type activation of charge transport. Using an activated tunneling model for describing the charge transport properties, we obtained an electron tunneling decay constant of βN = 0.61 or 0.71, depending on the method used for data analysis. When the films were dosed with vapors of toluene and tetrachloroethylene, the resistance of the films increased reversibly. This response increased exponentially with increasing length of the alkanedithiol molecules. The chemical selectivity of the films corresponded essentially to the solubility properties of the alkanedithiol molecules.
Tumor Necrosis Factor-α Signaling in Macrophages (2010)

Tumor necrosis factor-α (TNFα) was cloned over 2 decades ago and its identification in part led to the discovery of a super family of tumor necrosis factors (TNFs) and their receptors. TNFα signals through two transmembrane receptors, TNFR1 and TNFR2, and regulates a number of critical cell functions including cell proliferation, survival, differentiation, and apoptosis. Macrophages are the major producers of TNFα and interestingly are also highly responsive to TNFα. Aberrant TNFα production and TNF receptor signaling have been associated with the pathogenesis of several diseases, including rheumatoid arthritis, Crohn's disease, atherosclerosis, psoriasis, sepsis, diabetes, and obesity. TNFα has been shown to play a pivotal role in orchestrating the cytokine cascade in many inflammatory diseases and because of this role as a "master-regulator" of inflammatory cytokine production, it has been proposed as a therapeutic target for a number of diseases. Indeed anti-TNFα drugs are now licensed for treating certain inflammatory diseases including rheumatoid arthritis and inflammatory bowel disease. In this review we discuss the discovery of TNFα and its actions especially in regulating macrophage biology. Given its importance in several human diseases, we also briefly discuss the role of anti-TNFα therapeutics in the treatment of inflammatory diseases.