gebhart/patrepeval huggingface dataset:
Cloning and characterization of IL-17B and IL-17C, two new members of the IL-17 cytokine family (2000)

IL-17 is a T cell-derived cytokine that may play an important role in the initiation or maintenance of the proinflammatory response. Whereas expression of IL-17 is restricted to activated T cells, the IL-17 receptor is found to be widely expressed, a finding consistent with the pleiotropic activities of IL-17. We have cloned and expressed two novel human cytokines, IL-17B and IL-17C, that are related to IL-17 ( approximately 27% amino acid identity). IL-17B mRNA is expressed in adult pancreas, small intestine, and stomach, whereas IL-17C mRNA is not detected by RNA blot hybridization of several adult tissues. No expression of IL-17B or IL-17C mRNA is found in activated T cells. In a survey of cytokine induction, IL-17B and IL-17C stimulate the release of tumor necrosis factor alpha and IL-1beta from the monocytic cell line, THP-1, whereas IL-17 has only a weak effect in this system. No induction of IL-1alpha, IL-6, IFN-gamma, or granulocyte colony-stimulating factor is found in THP-1 cells. Fluorescence-activated cell sorter analysis shows that IL-17B and IL-17C bind to THP-1 cells. Conversely, IL-17B and IL-17C are not active in an IL-17 assay or the stimulation of IL-6 release from human fibroblasts and do not bind to the human IL-17 receptor extracellular domain. These data show that there is a family of IL-17-related cytokines differing in patterns of expression and proinflammatory responses that may be transduced through a cognate set of cell surface receptors.
Solving Partially Monotone Problems With Neural Networks (2007)

In many applications, it is a priori known that the target function should satisfy certain constraints imposed by, for example, economic theory or a human-decision maker. Here we consider partially monotone problems, where the target variable depends monotonically on some of the predictor variables but not all. We propose an approach to build partially monotone models based on the convolution of monotone neural networks and kernel functions. The results from simulations and a real case study on house pricing show that our approach has significantly better performance than partially monotone linear models. Furthermore, the incorporation of partial monotonicity constraints not only leads to models that are in accordance with the decision maker's expertise, but also reduces considerably the model variance in comparison to standard neural networks with weight decay.
Growth habits and defects in ZnO nanowires grown on GaN/sapphire substrates (2005)

Growth habits and defects in epitaxial ZnO nanowires grown from Au catalyst on (00.1) GaN/sapphire substrate using the vapor-liquid-solid (VLS) technique were studied using electron microscopy and x-ray diffraction. The results revealed presence of both horizontal (crawling-like) and vertical nanowires having similar orientation relationship to the substrate (00.1)ZnO‖(00.1)GaN, [11.0]ZnO‖[11.0]GaN. The crawling-like growth precedes the vertical growth, and the coalescence and overgrowth of the crawling nanowires produce a highly defective layer which separates the substrate and vertical nanorods. Transmission electron microscopy revealed a high density of planar defects in this interfacial layer. A significant density of stacking faults residing on the (0001) planes was also observed in the shorter vertical nanorods. The crawling nanowires are under residual compressive strain, whereas the vertical nanorods grow strain-free.
Protospacer Adjacent Motif (PAM)-Distal Sequences Engage CRISPR Cas9 DNA Target Cleavage (2014)

The clustered regularly interspaced short palindromic repeat (CRISPR)-associated enzyme Cas9 is an RNA-guided nuclease that has been widely adapted for genome editing in eukaryotic cells. However, the in vivo target specificity of Cas9 is poorly understood and most studies rely on in silico predictions to define the potential off-target editing spectrum. Using chromatin immunoprecipitation followed by sequencing (ChIP-seq), we delineate the genome-wide binding panorama of catalytically inactive Cas9 directed by two different single guide (sg) RNAs targeting the Trp53 locus. Cas9:sgRNA complexes are able to load onto multiple sites with short seed regions adjacent to 59 NGG 39 protospacer adjacent motifs (PAM). Yet among 43 ChIP-seq sites harboring seed regions analyzed for mutational status, we find editing only at the intended ontarget locus and one off-target site. In vitro analysis of target site recognition revealed that interactions between the 59 end of the guide and PAM-distal target sequences are necessary to efficiently engage Cas9 nucleolytic activity, providing an explanation for why off-target editing is significantly lower than expected from ChIP-seq data.
Seizure anticipation: from algorithms to clinical practice (2006)

Prediction algorithms must be proven to perform better than a random predictor before prospective clinical trials involving seizure intervention techniques in patients can be justified.
Changes in antigenic reactivity of Borrelia burgdorferi, the Lyme disease spirochete, during persistent infection in mice (1991)

Adult laboratory mice, Mus musculus, were shown to be suitable experimental animals for studying infectivity, persistent infection, and in vivo antigenic changes of Borrelia burgdorferi. Sixteen mice were inoculated intraperitoneally with a low-passage culture of an uncloned strain of B. burgdorferi and 16 months later spirochetes were reisolated from the urinary bladder of 15 (94%) of the mice. Spirochetes recovered from the urinary bladder of one persistently infected mouse were tested for infectivity and found to be infectious when passaged into four laboratory mice. Western blot analysis of immune serum from each of the persistently infected mice demonstrated that spirochetes used to infect the mice reacted differently when compared with the spirochetes subsequently reisolated from the mice, demonstrating for the first time that changes in antigenic reactivity had occurred in the spirochete populations during persistent infection.
ACE2-Ang-(1-7)-Mas Axis in Brain: A Potential Target for Prevention and Treatment of Ischemic Stroke (2013)

The renin-angiotensin system (RAS) in brain is a crucial regulator for physiological homeostasis and diseases of cerebrovascular system, such as ischemic stroke. Overactivation of brain Angiotensin-converting enzyme (ACE) - Angiotensin II (Ang II) - Angiotensin II type 1 receptor (AT1R) axis was found to be involved in the progress of hypertension, atherosclerosis and thrombogenesis, which increased the susceptibility to ischemic stroke. Besides, brain Ang II levels have been revealed to be increased in ischemic tissues after stroke, and contribute to neural damage through elevating oxidative stress levels and inducing inflammatory response in the ischemic hemisphere via AT1R. In recent years, new components of RAS have been discovered, including ACE2, Angiotensin-(1-7) [Ang-(1-7)] and Mas, which constitute ACE2-Ang-(1-7)-Mas axis. ACE2 converts Ang II to Ang-(1-7), and Ang-(1-7) binds with its receptor Mas, exerting benefical effects in cerebrovascular disease. Through interacting with nitric oxide and bradykinin, Ang-(1-7) could attenuate the development of hypertension and the pathologic progress of atherosclerosis. Besides, its antithrombotic activity also prevents thrombogenic events, which may contribute to reduce the risk of ischemic stroke. In addition, after ischemia insult, ACE2-Ang-(1-7)-Mas has been shown to reduce the cerebral infarct size and improve neurological deficits through its antioxidative and anti-inflammatory effects. Taken together, activation of the ACE2-Ang-(1-7)-Mas axis may become a novel therapeutic target in prevention and treatment of ischemia stroke, which deserves further investigations.
The effect of levetiracetam on essential tremor (2005)

The effect of a single dose of 1,000 mg of levetiracetam on essential tremor was investigated in 24 patients in a double-blind, placebo-controlled trial. There was a significant reduction of hand tremor for at least 2 hours as measured by accelerometry and functional tests.
Syntheses of Alternating Oligo-2‘-O-Methylribonucleoside Methylphosphonates and Their Interactions with HIV TAR RNA (1999)

Oligonucleotide analogues 15-20 nucleotides in length have been prepared, whose sequences are complementary to nucleotides in the upper hairpin of HIV TAR RNA. These alternating oligonucleoside methylphosphonates, mr-AOMPs, contain 2'-O-methylribonucleosides and alternating methylphosphonate and phosphodiester internucleotide linkages. The methylphosphonate and phosphodiester linkages of these oligomers are highly resistant to hydrolysis by exonuclease activity found in mammalian serum and to endonucleases, such as S1 nuclease. The oligomers were prepared using automated phosphoramidite chemistry and terminate with a 5'-phosphate group, which provides an affinity handle for purification by strong anion exchange HPLC. A 15-mer mr-AOMP, 1676, that is complementary to the 5'-side of the TAR RNA hairpin, including the 3-base bulge and 6-base loop region, forms a 1:1 duplex with a complementary RNA 18-mer, mini-TAR RNA. The T(m) of this duplex is 71 degrees C, which is similar to that of the duplex formed by the corresponding all phosphodiester 15-mer. Introduction of two mismatched bases reduces the T(m) by 17 degrees C. The apparent dissociation constant, K(d), for the 1676/mini-TAR RNA duplex as determined by an electrophoretic mobility shift assay at 37 degrees C is 0.3 nM. Oligomer 1676 also binds tightly to the full length TAR RNA target under physiological conditions (K(d) = 20 nM), whereas no binding was observed by the mismatched oligomer. A 19-mer that is complementary to the entire upper hairpin also binds to TAR RNA with a K(d) that is similar to that of 1676, a result that suggests only part of the oligomer binds. When two of the methylphosphonate linkages in the region complementary to the 6-base loop are replaced with phosphodiester linkages, the K(d) is reduced by approximately a factor of 10. This result suggests that interactions between TAR RNA and the oligomer occur initially with nucleotides in the 6-base loop, and that these interactions are sensitive to presence and possibly the chirality of the methylphosphonate linkages in the oligomer. The high affinities of mr-AOMPs for TAR RNA and their resistance to nuclease hydrolysis suggests their potential utility as antisense agents in cell culture.
Therapeutic effects of Clostridium butyricum on experimental colitis induced by oxazolone in rats (2009)

In our experimental colitis model, treatment with C. butyricum CGMCC0313, a probiotic supplement, is at least as efficient as treatment with mesalamine.
The amino-acid sequence of copper/zinc superoxide dismutase from swordfish liver. Comparison of copper/zinc superoxide dismutase sequences (1984)

The amino acid sequence of copper/zinc superoxide dismutase from swordfish (Xiphias gladius) liver has been determined by alignment of the tryptic peptides according to the known sequence of bovine erythrocyte copper/zinc superoxide dismutase. This alignment has resulted in the ligands to the copper (His-47, 49, 76 and 94) and the zinc (His-76, 85, 134 and Asp-97) being conserved in all the copper/zinc superoxide dismutases sequenced so far. Also conserved in the sequences are the cysteines forming the intrachain disulphide bridge (Cys-58 and 160) and the essential arginine (Arg-157). Comparison of the amino acid sequence of swordfish liver copper/zinc superoxide dismutase with the bovine, human, horse, yeast and Photobacterium leiognathi indicates that the swordfish enzyme has a high homology with the other eukaryotic enzymes. Low homology is, however, observed with the P. leiognathi enzyme.
Toroidal structures from brush amphiphiles (2013)

The self-assembly of macromolecular brushes of varying amphiphilic character from homogeneous solution under rapid assembly conditions results in unique morphologies, distinct from equilibrium structures. Kinetic features of the assembly process enabled the formation of toroid structures, the sizes of which were readily tuned according to solvent quality.
Role of serum-derived hyaluronan-associated protein-hyaluronan complex in ovarian cancer (2008)

The objective of this study was to determine if the level of serum hyaluronan (HA), serum-derived HA-associated protein (SHAP)-HA complex, and urinary trypsin inhibitor (UTI) correlate with the clinical outcome of ovarian cancer patients. The relationship of metalloproteinase and its inhibitor with HA and the SHAP-HA complex was also examined. Serum and urine samples were obtained from 45 patients with ovarian cancer, 22 patients with benign ovarian tumors and 50 healthy women. Concentrations of serum HA and UTI were measured by an inhibitory sandwich enzyme-linked immunosorbent assay, and concentrations of the serum SHAP-HA complex were measured by a sandwich enzyme-linked immunosorbent assay. Concentrations of MMP-2, MMP-9 and TIMP-1 were measured by a one-step enzyme immunoassay. The levels of HA, SHAP-HA complex, MMP-9 and TIMP-1 were higher in the ovarian cancer group than in the benign ovarian tumor group. In ovarian cancer patients, the levels of HA, SHAP-HA complex and MMP-9 were higher in the stage III/IV group than in the stage I/II group, and the levels of SHAP-HA complex, MMP-9 and TIMP-1 were higher in the non-responder group than in the responder group. The serum concentration of SHAP-HA complex had a significant correlation with HA, MMP-9 and TIMP-1 in ovarian cancer patients. The patients with elevated SHAP-HA complex had a shorter disease-free survival compared with those with normal levels of SHAP-HA complex. The multiple regression analysis revealed that SHAP-HA complex is the significant independent variable for progression-free survival. The elevated level of SHAP-HA complex may indicate the prognosis of recurrence and reflect the tumor metastasis associated with MMP-9 in ovarian cancer patients.
11: Generalized maps showing distribution, lithology, and age of Cenozoic igneous rocks in the Western United States (1978)

Two maps (Pls. 11-1 and 11-2, in pocket) have been prepared to show the general distribution, lithology, and age of Cenozoic igneous rocks in the Western United States. Plate 11-1 shows igneous rocks that range in age from 65 m.y. (start of the Cenozoic Era) to 17 m.y., and Plate 11-2 shows rocks that are 17 m.y. or younger. The 17-m.y. age is a geologically significant division point. This age is approximately the low point of the mid-Miocene lull in igneous activity that has been recognized in the Great Basin (McKee and others, 1970), in the Basin and Range province...
Report of an International Workshop to Standardize Response Criteria for Non-Hodgkin's Lymphomas (1999)

Standardized guidelines for response assessment are needed to ensure comparability among clinical trials in non-Hodgkin's lymphomas (NHL). To achieve this, two meetings were convened among United States and international lymphoma experts representing medical hematology/oncology, radiology, radiation oncology, and pathology to review currently used response definitions and to develop a uniform set of criteria for assessing response in clinical trials. The criteria that were developed include anatomic definitions of response, with normal lymph node size after treatment of 1.5 cm in the longest transverse diameter by computer-assisted tomography scan. A designation of complete response/unconfirmed was adopted to include patients with a greater than 75% reduction in tumor size after therapy but with a residual mass, to include patients-especially those with large-cell NHL-who may not have residual disease. Single-photon emission computed tomography gallium scans are encouraged as a valuable adjunct to assessment of patients with large-cell NHL, but such scans require appropriate expertise. Flow cytometric, cytogenetic, and molecular studies are not currently included in response definitions. Response rates may be the most important objective in phase II trials where the activity of a new agent is important and may provide support for approval by regulatory agencies. However, the goals of most phase III trials are to identify therapies that will prolong the progression-free survival, if not the overall survival, of the treated patients. We hope that these guidelines will serve to improve communication among investigators and comparability among clinical trials until clinically relevant laboratory and imaging studies are identified and become more widely available.
Preliminary results of an absorbable interference screw (1995)

A randomized, prospective multicenter comparison was done of a bioabsorbable interference screw (Bioscrew; Linvatec Corp, Largo, FL) made from poly L-lactic acid and a metal interference screw produced by the same company. Assignment was randomized by sealed envelopes. A total of 110 patients underwent arthroscopic patellar tendon autografts. A minimum 12 months follow-up is available on 85 patients (mean 19 months, range 12 to 33) including 42 with Bioscrews and 43 with metal screws. There were 56 male and 29 female patients. The average age was 29 years (16 to 50 years). Tourniquet times and associated surgical findings were similar for the two groups. Postoperative Tegner and Lysholm scores were not statistically different between the two groups. KT tests at 1 year showed an average 20-lb laxity of 1.8 mm for the Bioscrew and 1.2 mm for the metal screw groups. The average 1-year KT maximum manual side-to-side difference was 1.6 mm for Bioscrews and 1.6 mm for metal screws. A pivot shift was absent in 83% of Bioscrews and 90% of metal screws at follow-up. Six of 85 Bioscrews inserted (7%) broke on insertion (all were 7-mm diameter screws at the femoral site). No additional fixation was required in four cases. In two, the broken screw was replaced. No lytic bone changes or tunnel widening were found with any Bioscrew. One metal screw had tibial tunnel widening. No statistical difference was found between the Bioscrew and the metal screw groups. Short-term data support the conclusion that the Bioscrew is a reasonable alternative to metal interference screws.
Robert L. Bogomolny: A Colleague and Friend (1988)

A Tribute to Dean Robert L. Bogomolny
Thermometer Encoding: One Hot Way To Resist Adversarial Examples (2018)

It is well known that it is possible to construct examples for neural networks: inputs which are misclassified by the network yet indistinguishable from true data. We propose a simple modification to standard neural network architectures, thermometer encoding, which significantly increases the robustness of the network to adversarial examples. We demonstrate this robustness with experiments on the MNIST, CIFAR-10, CIFAR-100, and SVHN datasets, and show that models with thermometer-encoded inputs consistently have higher accuracy on adversarial examples, without decreasing generalization. State-of-the-art accuracy under the strongest known white-box attack was increased from 93.20% to 94.30% on MNIST and 50.00% to 79.16% on CIFAR-10. We explore the properties of these networks, providing evidence that thermometer encodings help neural networks to find more-non-linear decision boundaries.
Hydrodynamic shear stress and mass transport modulation of endothelial cell metabolism (1991)

Mammalian cells responds to physical forces by altering their growth rate, morphology, metabolism, and genetic expression. We have studied the mechanism by which these cells detect the presence of mechanical stress and convert this force into intracellular signals. As our model systems, we have studied cultured human endothelial cells, which line the blood vessels and forms the interface between the blood and the vessel wall. These cell responds within minutes to the initiation of flow by increasing their arachidonic acid metabolism and increasing the level of the intracellular second messengers inositol trisphosphate and calcium ion concentration. With continued exposure to arterial levels of wall shear stress for up to 24 h, endothelial cells increase the expression of tissue plasminogen activator (tPA) and tPA messenger RNA (mRNA) and decrease the expression of endothelin peptide and endothelin mRNA. Since the initiation of flow also causes enhanced convective mass transfer to the endothelial cell monolayer, we have investigated the role of enhanced convection of adenosine trisphosphate (ATP) to the cell surface in eliciting a cellular response by monitoring cytosolic calcium concentrations on the single cell level and by computing the concentration profile of ATP in a parallel-plate flow geometry. Our result demonstrate that endothelial cells respond in very specific ways to the initiation of flow and that mass transfer and fluid shear stress can both play a role in the modulation of intracellular signal transduction and metabolism.
The Yeast Saccharomyces cerevisiae Is Not an Efficient Tool for in Vivo Studies of Plant Vacuolar Sorting Receptors (2005)

Previously, we demonstrated a specific interaction between the vacuolar sorting receptor PS1 (VSRPS-1, also named BP-80) and the petunia aleurain vacuolar sorting determinant (VSD) fused to a green fluorescent protein (aleu-GFP) in vivo in the yeast Saccharomyces cerevisiae ([Humair et al., 2001][1
Incidence and risk factors for thrombotic complications in a historical cohort of 100 patients with essential thrombocythemia. (1990)

The purpose of this study was to determine which factors were associated with an increased risk of thrombo-hemorrhagic complications in a historical cohort of 100 consecutive and unselected patients with essential thrombocythemia (ET) in whom busulfan treatment was given when platelets were more than 1,000 x 10(9)/L and/or a major thrombotic or hemorrhagic event occurred. The incidence of major hemorrhagic complications was very low (0.33%/person-time at risk [pt-yr]) in comparison with that of thrombotic episodes (6.6%/pt-yr). In an adequate and appropriate control historical group of 200 patients, no severe hemorrhages were recorded and the incidence of thrombotic events was 1.2% pt-yr. Thus, the analysis of risk factors was restricted to this latter group of events. Age, a previous thrombotic event, and long duration of thrombocytosis were identified as major risk factors for thrombosis, while smoking, diabetes mellitus, hyperlipidemia, and hypertension did not influence the rate of thrombotic episodes.
Pathogenesis of Foreign Body Infection: Description and Characteristics of an Animal Model (1982)

An animal model involving the subcutaneous implantation of tissue cages into guinea pigs and subsequent infection with Staphylococcus aureus was used for study factors pertinent to foreign body infection. Whereas 10(8) colony-forming units (cfu) of S. aureus strain Wood 46 did not produce any abscesses in the absence of foreign material, 10(2) cfu was sufficient to infect 95% of the tissue cages despite the presence of polymorphonuclear leukocytes (PMNLs) in sterile tissue cage fluid. Opsonization of S. aureus by tissue cage fluid was adequate during the first hour of infection, but opsonic coating of the organisms decreased at 20 hr after the induction of infection. PMNLs from sterile tissue cage fluid showed decreased phagocytic and bactericidal activities when compared with PMNLs from either blood or peritoneal exudate obtained after short- or long-term stimulation (P less than 0.001).