gebhart/patrepeval huggingface dataset:
The effects of reactive nitrogen intermediates on gene expression in<i>Mycobacterium tuberculosis</i> (2003)

Nitric oxide (NO) and related reactive nitrogen intermediates (RNI) are effective antimycobacterial agents and signal-transducing molecules. The present study uses microarray analysis to examine the effects of RNI on Mycobacterium tuberculosis gene expression. A common set of 53 genes was regulated by two chemically distinct nitric oxide donors. For a subset of the RNI-inducible genes, evidence exists suggesting that they may play a role in promoting survival of the tubercle bacillus in the host. Results obtained from studies based on a murine experimental tuberculosis model involving nos2-deficient mice suggest that RNI could regulate M. tuberculosis gene expression in vivo. Finally, there is a remarkable overlap between the RNI-inducible regulon and that previously reported to be regulated by hypoxia; and both reactive nitrogen species and anaerobicity upregulate the expression of one and the same putative two-component regulatory response system. Together, the results of this study provide evidence suggesting that (i) RNI play a role in regulating M. tuberculosis gene expression in vivo; (ii) the reactive nitrogen species upregulate genes that may be conducive to the survival of the tubercle bacillus in the infected host; and (iii) RNI and hypoxia may regulate mycobacterial gene expression via overlapping signal transduction pathways.
Comorbidity of attention deficit hyperactivity disorder with conduct, depressive, anxiety, and other disorders (1991)

Subgroups of children with attention deficit hyperactivity disorder might be delineated on the basis of the disorder's comorbidity with other disorders. These subgroups may have differing risk factors, clinical courses, and pharmacological responses. Thus, their proper identification may lead to refinements in preventive and treatment strategies. Investigation of these issues should help to clarify the etiology, course, and outcome of attention deficit hyperactivity disorder.
Generation of synthetic training data for an HMM-based handwriting recognition system (2004)

A perturbation model for generating synthetic text lines from existing cursively handwritten lines of text produced by human writers is presented. Our purpose is to improve the performance of an HMM-based off-line cursive handwriting recognition system by providing it with additional synthetic training data. Two kinds of perturbations are applied, geometrical transformations and thinning/thickening operations. The proposed perturbation model is evaluated under different experimental conditions.
Intravesical administration of bacillus Calmette-Guérin in patients with recurrent superficial carcinoma of the urinary bladder: report of a prospective, randomized trial. (1985)

In an attempt to prevent, delay, or reduce further tumor occurrence, 88 patients with recurrent, superficial carcinoma of the urinary bladder were randomly assigned to receive either standard therapy (cystoscopy with fulguration) or standard therapy and bacillus Calmette-Guérin (BCG). BCG was administered intravesically and percutaneously once weekly for 6 weeks. No serious toxicity was seen. There were 43 evaluable patients in each of the two groups. Results in the BCG group versus the control group were as follows: reduction in the number of recurrent tumors (43 vs 27 patients [P less than 0.001] ); conversion to negative cytology (11 of 33 vs three of 34 patients [P less than 0.05] ); and tumor progression requiring cystectomy (three vs 15 patients [P less than 0.001] ). Disease-free interval (P less than 0.001), time with negative cytology (P less than 0.001), and time to progression of disease (P less than 0.003) were longer in patients treated with BCG. These results indicate that the combination of standard therapy and BCG is more effective than standard therapy alone in patients with recurrent superficial bladder tumors.
<i>RAS</i> gene mutations in childhood acute myeloid leukemia: A pediatric oncology group study (1990)

Mutations at codon 12, 13, and 61 of the HRAS, KRAS, and NRAS genes were evaluated in 99 cases of pediatric acute myeloid leukemia (AML) using oligonucleotide hybridization to polymerase chain reacted derived products. Twenty-four mutations were identified in the NRAS gene, 13 in the KRAS gene, and none in the HRAS gene. The mutations occurred in a broad spectrum of cases, and there was no specific association of RAS gene mutations with patient subsets defined on the basis of clinical or hematologic features. These data demonstrate that RAS gene mutations are at least as common in childhood AML as in adult AML and suggest that RAS gene mutations play a role in myeloid neoplasia in both age groups.
Combined model for text entry rate development (2003)

We combine the power law of learning and theoretical upper limit predictions to describe the development of text entry rates from users' first contact to asymptotic expert usage. The combined model makes comparing text entry methods easier. We present the rationale for the model and two candidate implementations. The first is a simple regression model with a reasonable fit to the data. The second fits measured data better, but is more complicated.
A lightweight framework for cross-application user monitoring (2002)

The human-computer interaction community has often focused on the face applications present to the user. The authors present a new framework that monitors higher-level events to learn how people access, create, and modify information rather than how they use applications. By associating information sources with tasks and processes and monitoring user actions, the system can offer task-specific help.
Sclerostin and Dickkopf-1 as Therapeutic Targets in Bone Diseases (2012)

The processes of bone growth, modeling, and remodeling determine the structure, mass, and biomechanical properties of the skeleton. Dysregulated bone resorption or bone formation may lead to metabolic bone diseases. The Wnt pathway plays an important role in bone formation and regeneration, and expression of two Wnt pathway inhibitors, sclerostin and Dickkopf-1 (DKK1), appears to be associated with changes in bone mass. Inactivation of sclerostin leads to substantially increased bone mass in humans and in genetically manipulated animals. Studies in various animal models of bone disease have shown that inhibition of sclerostin using a monoclonal antibody (Scl-Ab) increases bone formation, density, and strength. Additional studies show that Scl-Ab improves bone healing in models of bone repair. Inhibition of DKK1 by monoclonal antibody (DKK1-Ab) stimulates bone formation in younger animals and to a lesser extent in adult animals and enhances fracture healing. Thus, sclerostin and DKK1 are emerging as the leading new targets for anabolic therapies to treat bone diseases such as osteoporosis and for bone repair. Clinical trials are ongoing to evaluate the effects of Scl-Ab and DKK1-Ab in humans for the treatment of bone loss and for bone repair.
Interferon gamma-resistant mutants are defective in the induction of indoleamine 2,3-dioxygenase. (1989)

Several mutants of the human cell line ME-180 resistant to the cytotoxic effect of interferon gamma (IFN-gamma) were isolated after mutagenesis with nitrosoguanidine. Two of the mutant lines (ME-IR3b and ME-IR6g) examined had significantly lower induction levels of the L-tryptophan (L-Trp) degradative enzyme indoleamine 2,3-dioxygenase activity in response to IFN-gamma. Moreover, culture medium supplemented with low concentrations of L-Trp reversed the cytotoxic effect of IFN-gamma, whereas higher concentrations of L-Trp in the medium were extremely toxic to both parental and mutant cells. These mutants were still protected against herpes simplex virus infection by IFN-gamma and expressed the HLA-DR alpha gene normally in the presence of this lymphokine. Thus, the mutation in these cells is specific to indoleamine 2,3-dioxygenase and not a global effect of an IFN-gamma-induced gene. This genetic evidence indicates that the major pathway of IFN-gamma cytotoxicity in this cell line is mediated primarily by induction of indoleamine 2,3-dioxygenase and deprivation of L-Trp.
Dependence analysis for pointer variables (1989)

Our concern is how to determine data dependencies between program constructs in programming languages with pointer variables. We are particularly interested in computing data dependencies for languages that manipulate heap-allocated storage, such as Lisp and Pascal. We have defined a family of algorithms that compute safe approximations to the flow, output, and anti-dependencies of a program written in such a language. Our algorithms account for destructive updates to fields of a structure and thus are not limited to the cases where all structures are trees or acyclic graphs; they are applicable to programs that build cyclic structures. Our technique extends an analysis method described by Jones and Muchnick that determines an approximation to the actual layouts of memory that can arise at each program point during execution. We extend the domain used in their abstract interpretation so that the (abstract) memory locations are labeled by the program points that set their contents. Data dependencies are then determined from these memory layouts according to the component labels found along the access paths that must be traversed during execution to evaluate the program's statements and predicates. For structured programming constructs, the technique can be extended to distinguish between loop-carried and loop-independent dependencies, as well as to determine lower bounds on minimum distances for loop-carried dependencies.
A “pile” metaphor for supporting casual organization of information (1992)

A user study was conducted to investigate how people deal with the flow of information in their workspaces. Subjects reported that, in an attempt to quickly and informally manage their information, they created piles of documents. Piles were seen as complementary to the folder filing system, which was used for more formal archiving. A new desktop interface element–the pile– was developed and prototyped through an iterative process. The design includes direct manipulation techniques and support for browsing, and goes beyond physical world functionality by providing system assistance for automatic pile construction and reorganization. Preliminary user tests indicate the design is promising and raise issues that will be addressed in future work.
Monitoring and control for extractive fermentation of Clostridium acetobutylicum (1985)

Le butanol est elimine du milieu de culture au cours de la fermentation par extraction liquide liquide in situ. Developpement d'un systeme de culture en semi continu pour controler la concentration en butanol au dessous du seuil toxique en utilisant le volume de gaz emis pendant la fermentation comme indicateur
Visual Control of Robots Using Range Images (2010)

In the last years, 3D-vision systems based on the time-of-flight (ToF) principle have gained more importance in order to obtain 3D information from the workspace. In this paper, an analysis of the use of 3D ToF cameras to guide a robot arm is performed. To do so, an adaptive method to simultaneous visual servo control and camera calibration is presented. Using this method a robot arm is guided by using range information obtained from a ToF camera. Furthermore, the self-calibration method obtains the adequate integration time to be used by the range camera in order to precisely determine the depth information.
AC losses in a type II superconductor strip with inhomogeneous critical current distribution (2005)

Analytical formulae derived by Brandt and Indenbom (1993 Phys. Rev. B 48 12893–906) and Norris (1970 J. Phys. D: Appl. Phys. 3 489–507) are often used to calculate the magnetization and AC transport current losses in HTS strip conductors, respectively. In these formulae, homogeneous distribution of critical sheet current density σc in the strip is assumed. However, it is considered that σc distributions are inhomogeneous in actual HTS strips and that the inhomogeneous σc distributions cause deviations of the measured AC loss data of actual HTS strips from those formulae. A semi-analytical method to calculate AC transport current and magnetization losses is derived for a type II superconductor strip with inhomogeneous distribution of σc in the direction of the strip width. The method is derived modifying the analysis of Brandt et al. The validity of the semi-analytical method is shown by comparing the results calculated by this method with those calculated by the Norris and Brandt formulae and by a different method of our previous work and also with experimental data. Moreover, it is shown that the deviation of the measured data from the Norris and Brandt models can be estimated by assuming proper σc distributions.
Inhibition of protein synthesis alters the subcellular distribution of mRNA in neurons but does not prevent dendritic transport of RNA. (1993)

This study evaluates whether protein synthesis plays a role in targeting RNA molecules to different subcellular domains within neurons. Transport of newly synthesized RNA (labeled with [3H]uridine) was examined in the presence of the protein synthesis inhibitors puromycin and cycloheximide. In situ hybridization was used to determine whether inhibition of protein synthesis altered the subcellular distribution of mRNAs. Transport of recently synthesized RNA was not disrupted after prolonged exposure to either inhibitor. However, inhibition of protein synthesis caused several mRNAs that are normally confined to the cell body to appear in dendrites. The distribution of mRNAs that are normally present in dendrites was unaffected. These findings suggest that protein synthesis is not required to translocate RNA into the dendrites but may play a role in restricting particular mRNAs to the neuronal cell body.
Performance analysis of very-small-aperture lasers (2005)

The fabrication of very-small-aperture lasers is demonstrated, and their performance is analyzed. Because of strong optical feedback caused by a gold film on the front facet of the laser, its behavior changes: The threshold current decreases, the density of light inside the laser diode and the redshift effect of the spectra are enhanced, and the laser diode's lifetime is shorter than that of common laser diodes with large driving current.
Asthma and Rhinitis (1995)

Part 1: Disease Classification Part 2: Epidemiology Part 3: Normal Anatomy, Development and Physiology Part 4: Pathology Part 5: Mast Cells And Basophils Part 6: Eosinophils Part 7: Neutrophils Part 8: Lymphocytes Part 9: Macrophages And Monocytes Part 10: Platelets Part 11: Fibroblasts Part 12: Epithilial Cells Part 13: Mediators Of Inflammation Part 14: Role Of Allergans In Airways Disease Part 15: Physiology Of The Airways Part 16: Smooth Muscle Response Part 17: Exercise Induced Asthma Part 18: Viral Mechanisms In Asthma And Related Disease Part 19: Clinical And Therapeutic Implications
4-Amino-1-hydroxy-2-oxo-1,8-naphthyridine-Containing Compounds Having High Potency against Raltegravir-Resistant Integrase Mutants of HIV-1 (2014)

There are currently three HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) approved by the FDA for the treatment of AIDS. However, the emergence of drug-resistant mutants emphasizes the need to develop additional agents that have improved efficacies against the existent resistant mutants. As reported herein, we modified our recently disclosed 1-hydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamides IN inhibitors to develop compounds that have improved efficacies against recombinant IN in biochemical assays. These new compounds show single-digit nanomolar antiviral potencies against HIV vectors that carry wild-type (WT) IN in a single round replication assay and have improved potency against vectors harboring the major forms of drug resistant IN mutants. These compounds also have low toxicity for cultured cells, which in several cases, results in selectivity indices (CC50/EC50) of greater than 10000. The compounds have the potential, with additional structural modifications, to yield clinical agents that are effective against the known strains of resistant viruses.
Demographic, neurological and behavioural characteristics and brain perfusion SPECT in frontal variant of frontotemporal dementia (2006)

We conducted a French multicentric cross-sectional study to describe in detail the demographic, neurological and behavioural characteristics of the frontal variant of frontotemporal dementia (fvFTD) and to characterize the pattern of brain perfusion SPECT in comparison to a healthy control group. A total of 68 fvFTD patients had technetium-99m-ECD brain perfusion SPECT at inclusion, 61 of which also underwent an in-depth evaluation including 70 items assessing behaviour, language and affect/emotion at onset and at inclusion. The mean age-at-onset was 60.4 +/- 7.8 years (35-75). Twenty-six per cent of the patients were older than 65 at onset. A positive familial history consistent with an autosomal dominant inheritance was found in 18% of the patients. At onset, the behavioural profile was predominantly inert in 25% of the patients, disinhibited in 18% and mixed in others. The behavioural features progressed to predominantly mixed or inert forms. Although, inertia was associated with predominant medial frontal and cingulate hypoperfusion, and patients with disinhibition exhibited predominant ventromedial prefrontal and temporal hypoperfusion, there were no major clinical differences between disinhibited and inert patients. Forty-five per cent of the deceased patients survived <6 years (short survival), and 34% of the patients survived >8 years (long survival). This shows that the final outcome of fvFTD is highly variable. No clinical factors predictive of short or long survival were identified. Unexpected, however, was the finding that brainstem hypoperfusion distinguished patients with a short survival from patients with long survival. In conclusion, this study shows that fvFTD is clinically a rather homogeneous entity. It also provides evidence that different behavioural presentations at onset are related to different anatomical localizations of degenerative damage. Finally, it demonstrates the prognostic value of brainstem hypoperfusion in a subgroup of patients with a short survival.
The cytoplasmic domain of neuropilin‐1 regulates focal adhesion turnover (2013)

Though the vascular endothelial growth factor coreceptor neuropilin-1 (Nrp1) plays a critical role in vascular development, its precise function is not fully understood. We identified a group of novel binding partners of the cytoplasmic domain of Nrp1 that includes the focal adhesion regulator, Filamin A (FlnA). Endothelial cells (ECs) expressing a Nrp1 mutant devoid of the cytoplasmic domain (nrp1(cyto)(Δ/Δ)) migrated significantly slower in response to VEGF relative to the cells expressing wild-type Nrp1 (nrp1(+/+) cells). The rate of FA turnover in VEGF-treated nrp1(cyto)(Δ/Δ) ECs was an order of magnitude lower in comparison to nrp1(+/+) ECs, thus accounting for the slower migration rate of the nrp1(cyto)(Δ/Δ) ECs.
Local Convolutional Features with Unsupervised Training for Image Retrieval (2015)

Patch-level descriptors underlie several important computer vision tasks, such as stereo-matching or content-based image retrieval. We introduce a deep convolutional architecture that yields patch-level descriptors, as an alternative to the popular SIFT descriptor for image retrieval. The proposed family of descriptors, called Patch-CKN, adapt the recently introduced Convolutional Kernel Network (CKN), an unsupervised framework to learn convolutional architectures. We present a comparison framework to benchmark current deep convolutional approaches along with Patch-CKN for both patch and image retrieval, including our novel "RomePatches" dataset. Patch-CKN descriptors yield competitive results compared to supervised CNN alternatives on patch and image retrieval.
Pulmonary clearance of circulating endothelin-1 in dogs in vivo: exclusive role of ET<sub>B</sub>receptors (1996)

The pulmonary circulation plays an important role in the removal of circulating endothelin-1 (ET-1). Plasma ET-1 levels are increased in pulmonary hypertensive states of various etiologies (e.g., idiopathic, heart failure, and congenital anomalies) in proportion to the severity of pulmonary hypertension. It is possible that reduced pulmonary clearance of this peptide contributes to the hyperendothelinemia of those pathologies. The ETA and ETB receptors are abundant in lung tissues: on the vascular endothelium, the ETB receptor is predominant and may contribute to ET-1 extraction through receptor-mediated endocytosis. We designed experiments to determine and quantify the importance of the ETA and ETB receptors in the pulmonary extraction of circulating ET-1 in anesthetized dogs. The single-pass cumulative tracer ET-1 extraction by the lung was measured with the indicator-dilution technique before and 5 min after intrapulmonary injection of the specific ETA antagonist BQ-123 (n = 5, 120-960 nmol) and the specific ETB antagonist BQ-788 (n = 6, 1,000 nmol). The inhibitors had no significant effect on pulmonary and systemic hemodynamics. Mean cumulative pulmonary ET-1 extraction was not modified by BQ-123 [control (C): 36 +/- 4%, antagonist (A): 34 +/- 6%] but was completely abolished by BQ-788 (C: 34 +/- 6%, A: 0 +/- 2%, P < 0.001). The pulmonary rate constant (K) for ET-1 removal was also unaffected by BQ-123 (C: 0.050 +/- 0.0085 s-1, A: 0.047 +/- 0.012 s-1) but significantly decreased and became close to zero after BQ-788 (C: 0.058 +/- 0.014 s-1, A: 0.009 +/- 0.007 s-1, P < 0.1). We conclude that the ETB receptor is completely and exclusively responsible for pulmonary ET-1 removal in vivo. Future studies are needed to show whether desensitization or downregulation of the ETB receptor may contribute to the increase in circulating ET-1 levels in conditions associated with pulmonary hypertension. This novel pulmonary endothelial cell function may play a protective role by modulating circulating ET-1 levels in the systemic circulation.
Estimates of the prevalence of arthritis and other rheumatic conditions in the United States: Part I (2007)

Arthritis and other rheumatic conditions continue to be a large and growing public health problem. Estimates for many specific rheumatic conditions rely on a few, small studies of uncertain generalizability to the US population. This report provides the best available prevalence estimates for the US, but for most specific conditions, more studies generalizable to the US or addressing understudied populations are needed.
On the infeasibility of modeling polymorphic shellcode (2007)

Polymorphic malcode remains a troubling threat. The ability formal code to automatically transform into semantically equivalent variants frustrates attempts to rapidly construct a single, simple, easily verifiable representation. We present a quantitative analysis of the strengths and limitations of shellcode polymorphism and consider its impact on current intrusion detection practice.