gebhart/patrepeval huggingface dataset:
A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis (2015)

Mycobacterium tuberculosis (MTB) is a pathogenic bacterium responsible for 12 million active cases of tuberculosis (TB) worldwide. The complexity and critical regulatory components of MTB pathogenicity are still poorly understood despite extensive research efforts. In this study, we constructed the first systems-scale map of transcription factor (TF) binding sites and their regulatory target proteins in MTB. We constructed FLAG-tagged overexpression constructs for 206 TFs in MTB, used ChIP-seq to identify genome-wide binding events and surveyed global transcriptomic changes for each overexpressed TF. Here we present data for the most comprehensive map of MTB gene regulation to date. We also define elaborate quality control measures, extensive filtering steps, and the gene-level overlap between ChIP-seq and microarray datasets. Further, we describe the use of TF overexpression datasets to validate a global gene regulatory network model of MTB and describe an online source to explore the datasets.
The Effect of Back Belt Use on Isometric Lifting Force and Fatigue of the Lumbar Paraspinal Muscles (1998)

These findings do not support the use of back belts for the purpose of minimizing either lumbar paraspinal muscle fatigue or a loss in isometric lifting force production.
Iterative asymptotic inversion in the acoustic approximation (1992)

Abstract We propose an iterative method for the linearized prestack inversion of seismic profiles based on the asymptotic theory of wave propagation. For this purpose, we designed a very efficient technique for the downward continuation of an acoustic wavefield by ray methods. The different ray quantities required for the computation of the asymptotic inverse operator are estimated at each diffracting point where we want to recover the earth image. In the linearized inversion, we use the background velocity model obtained by velocity analysis. We determine the short wavelength components of the impedance distribution by linearized inversion of the seismograms observed at the surface of the model. Because the inverse operator is not exact, and because the source and station distribution is limited, the first iteration of our asymptotic inversion technique is not exact. We improve the images by an iterative procedure. Since the background velocity does not change between iterations, there is no need to retrace rays, and the same ray quantities are used in the iterations. For this reason our method is very fast and efficient. The results of the inversion demonstrate that iterations improve the spatial resolution of the model images since they mainly contribute to the increase in the short wavelength contents of the final image. A synthetic example with one-dimensional (1-D) velocity background illustrates the main features of the inversion method. An example with two-dimensional (2-D) heterogeneous background demonstrates our ability to handle multiple arrivals and a nearly perfect reconstruction of a flat horizon once the perturbations above it are known. Finally, we consider a seismic section taken from the Oseberg oil field in the North Sea off Norway. We show that the iterative asymptotic inversion is a reasonable and accurate alternative to methods based on finite differences. We also demonstrate that we are able to handle an important amount of data with presently available computers.
Leptin-induced satiation mediated by abdominal vagal afferents (2004)

Leptin is a hormone secreted into the systemic blood primarily by white adipose tissue. However, leptin also is synthesized and stored by cells in the gastric mucosa. Because gastric mucosal leptin is secreted in response to ingestion of a meal, we hypothesized that it might contribute to satiation (meal termination) by acting on gastrointestinal vagal afferent neurons. To test whether leptin is capable of acutely reducing short-term food intake, we measured consumption of a liquid meal (15% sucrose) following low-dose leptin administration via the celiac artery, which perfuses the upper gastrointestinal tract. Leptin (1, 3, 10 mug) was infused via a chronically implanted, nonocclusive celiac arterial catheter or via a jugular vein catheter with its tip in the right cardiac atrium. Fifteen percent sucrose intake was then measured for 30 min. We found that leptin dose dependently inhibited sucrose intake when infused through the celiac catheter but not when infused into the general circulation via a jugular catheter. Plasma leptin concentrations in the general circulation following celiac arterial or jugular leptin infusions were not significantly different. Celiac arterial leptin infusion did not reduce meal size in vagotomized or capsaicin-treated rats. Finally, we also found that reduction of meal size by celiac leptin infusion was markedly enhanced when coinfused with cholecystokinin, a gastrointestinal satiety peptide whose action depends on vagal afferent neurons. Our results support the hypothesis that leptin contributes to satiation by a mechanism dependent on gastrointestinal vagal afferent innervation of the upper gastrointestinal tract.
AIM2 inflammasome in infection, cancer, and autoimmunity: Role in DNA sensing, inflammation, and innate immunity (2015)

Recognition of DNA by the cell is an important immunological signature that marks the initiation of an innate immune response. AIM2 is a cytoplasmic sensor that recognizes dsDNA of microbial or host origin. Upon binding to DNA, AIM2 assembles a multiprotein complex called the inflammasome, which drives pyroptosis and proteolytic cleavage of the proinflammatory cytokines pro-IL-1β and pro-IL-18. Release of microbial DNA into the cytoplasm during infection by Francisella, Listeria, Mycobacterium, mouse cytomegalovirus, vaccinia virus, Aspergillus, and Plasmodium species leads to activation of the AIM2 inflammasome. In contrast, inappropriate recognition of cytoplasmic self-DNA by AIM2 contributes to the development of psoriasis, dermatitis, arthritis, and other autoimmune and inflammatory diseases. Inflammasome-independent functions of AIM2 have also been described, including the regulation of the intestinal stem cell proliferation and the gut microbiota ecology in the control of colorectal cancer. In this review we provide an overview of the latest research on AIM2 inflammasome and its role in infection, cancer, and autoimmunity.
A heart sound segmentation and feature extraction algorithm using wavelets (2006)

A heart sound segmentation and feature extraction algorithm, which separates the heart sound signal into four parts: the first heart sound S1, the systolic period, the second heart sound S2, and the diastolic period. A features extraction algorithm has been developed. The algorithm uses discrete wavelet decomposition and reconstruction to produce approximations and details of the original phonocardiographic signal.
Heterogeneity of histones. I. A quantitative analysis of calf histones in very long polyacrylamide gels (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHeterogeneity of histones. I. A quantitative analysis of calf histones in very long polyacrylamide gelsSakol Panyim and Roger ChalkleyCite this: Biochemistry 1969, 8, 10, 3972–3979Publication Date (Print):October 1, 1969Publication History Published online1 May 2002Published inissue 1 October 1969https://pubs.acs.org/doi/10.1021/bi00838a013https://doi.org/10.1021/bi00838a013research-articleACS PublicationsRequest reuse permissionsArticle Views106Altmetric-Citations283LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Lithography with Self‐Assembled Block Copolymer Microdomains (2004)

This chapter contains sections titled: Introduction Self-assembled Structures Imaging Microdomains in Thin Films Mechanisms to Control Orientation Metallic Incorporation or Modifications to the Copolymer Template Lithographic Use of Templates Current Applications of Block Copolymer Lithography Summary and Future Directions Acknowledgements References
The Exacerbation of Pancreatic Endocrine Dysfunction by Potent Pancreatic Exocrine Supplements in Patients with Chronic Pancreatitis (2001)

In conclusion, high-dose pancreatin mini-microspheres improved, but did not normalize, fat absorption, possibly because of the residual influence of diabetes and malnutrition on absorptive function. In view of the brittle nature of blood glucose control in malnourished insulin-dependent patients, enzyme adjustment should be carefully supervised in-hospital.
L'Europe et les Etats-Unis entre la discorde et l'harmonie (1981)

L'Europe et les Etats-Unis entre la discorde et l'harmonie, par Stanley Hoffmann La plus grave menace qui pèse sur l'Alliance aujourd'hui n'est pas celle qui émane des Soviétiques, pour sérieuse que soit celle-ci, par l'ampleur des moyens militaires qu'elle met en oeuvre et par l'envergure planétaire qu'elle revêt. Le danger réside plutôt dans les forces centrifuges potentielles qu'engendre la situation présente avec une Amérique qui tente de réaffirmer son leadership en prêchant de façon militante et quasi obsessionnelle ses vues anti soviétiques ; avec un allié allemand de plus en plus insatisfait des options américaines et désireux de conserver ses possibilités d'entente avec Moscou ; avec une France qui tente, de manière parfois acrobatique, de préserver ses liens avec Bonn, lesquels constituent le moteur de la coopération européenne et de restaurer en même temps l'harmonie entre Paris et Washington à un moment où ses relations avec les Soviétiques semblent se révéler plutôt stériles. Le besoin se fait désormais sentir d'un effort de grande envergure qui permettrait de parvenir aux compromis politiques, à l'intégration stratégique et aux innovations institutionnelles qui font actuellement défaut. Seule une tentative de ce genre peut contribuer à parfaire la coopération européenne et à préserver l'Alliance atlantique. Mais il faudra, chez les Américains, un abandon radical de leur penchant pour l'action unilatérale et, chez les Européens, une volonté nouvelle, non pas simplement de revendiquer mais de jouer un rôle d'envergure planétaire et de commencer par s'occuper de la défense de leurs propres frontières.
Visual Function Tests as Potential Biomarkers in Age-Related Macular Degeneration (2011)

All the visual function tests had good diagnostic capacity. Combination of the 14-Hz flicker thresholds and dynamics of the PSR test provided optimal quantitative assessment of retinal function in early AMD, suggesting that this set is a potentially useful clinical tool for following progression of early AMD and assessing the efficacy of interventions.
Resistance of keratinocytes to TGFβ-mediated growth restriction and apoptosis induction accelerates re-epithelialization in skin wounds (2002)

The pleiotropic growth factor TGFbeta plays an important role in regulating responses to skin injury. TGFbeta targets many different cell types and is involved in all aspects of wound healing entailing inflammation, re-epithelialization, matrix formation and remodeling. To elucidate the role of TGFbeta signal transduction in keratinocytes during cutaneous wound healing, we have used transgenic mice expressing a dominant negative type II TGFbeta receptor exclusively in keratinocytes. We could demonstrate that this loss of TGFbeta signaling in keratinocytes led to an accelerated re-epithelialization of full thickness excisional wounds accompanied by an increased proliferation in keratinocytes at the wound edge. Furthermore, we show that impaired TGFbeta signaling in keratinocytes reduces apoptosis in re-epithelialized wounds of transgenic animals. A cDNA array identified the transcription factor early growth response factor 1 (Egr1) as a target gene for TGFbeta in late phases of the wound healing process. As a member of the immediate-early gene family, Egr1 is upregulated shortly after injury and induces the expression of growth factor genes. We could demonstrate that Egr1 expression is also upregulated in skin wounds which have already undergone re-epithelialization. In conclusion, we attribute the enhanced re-epithelialization in our transgenics to the resistance of keratinocytes to TGFbeta-mediated growth restriction and apoptosis induction. We also propose a new role for TGFbeta induced Egr1 in late phase wound repair.
A Personal Light-Treatment Device for Improving Sleep Quality in the Elderly: Dynamics of Nocturnal Melatonin Suppression at Two Exposure Levels (2009)

Light treatment has been used as a non-pharmacological tool to help mitigate poor sleep quality frequently found in older people. In order to increase compliance to non-pharmacological light treatments, new, more efficacious light-delivery systems need to be developed. A prototype personal light-treatment device equipped with low brightness blue light-emitting diodes (LEDs) (peak wavelength near 470 nm) was tested for its effectiveness in suppressing nocturnal melatonin, a measure of circadian stimulation. Two levels of corneal irradiance were set to deliver two prescribed doses of circadian light exposure. Eleven older subjects, between 51 and 80 yrs of age who met the selection criteria, were exposed to a high and a low level of light for 90 min on separate nights from the personal light-treatment device. Blood and saliva samples were collected at prescribed times for subsequent melatonin assay. After 1 h of light exposure, the light-induced nocturnal melatonin suppression level was about 35% for the low-light level and about 60% for the high-light level. The higher level of blue light suppressed melatonin more quickly, to a greater extent over the course of the 90 min exposure period, and maintained suppression after 60 min. The constant exposure of the low-light level resulted in a decrease in nocturnal melatonin suppression for the last sampling time, whereas for the high-light level, suppression continued throughout the entire exposure period. The present study performed with healthy adults suggests that the tested personal light-treatment device might be a practical, comfortable, and effective way to deliver light treatment to those suffering from circadian sleep disorders; however, the acceptance and effectiveness of personal light-treatment devices by older people and by other segments of the population suffering from sleep disorders in a real-life situation need to be directly tested.
SPECIES: A spreadsheet program for modeling speciation of soil solution (1990)

ABSTRACT The SPECIES program is a solution equilibrium model to teach concepts of ion activity and ion speciation as applied to soil solutions. The program is written as a spreadsheet file that may be used with Lotus 1–2‐3 or compatible spreadsheet software. The spreadsheet format provides a user‐friendly computer environment and leaves the computational portions of the program transparent to the user. Results are easily manipulated on screen, exported to disk, or output as hard copy using standard spreadsheet functions.
Knudsen forces on microcantilevers (2002)

When two surfaces at two different temperatures are separated by a distance comparable to a mean-free path of the molecules of the ambient medium, the surfaces experience Knudsen force. This mechanical force can be important in microelectromechanical systems and in atomic force microscopy. A theoretical discussion of the magnitude of the forces and the conditions where they can be encountered is discussed. A potential application of the Knudsen force in designing a cantilever-based vacuum gauge is discussed.
<title>Review Of Fiber Optic Gyroscopes</title> (1983)

The fiber optic gyroscope is now within the high sensitivity predicted by theoretical studies. We review the different steps involved in the progresses realized over the last five years by the various research teams working on this subject around the world. Measurement of rotation rates of 10-2 deg/h have been demonstrated. That corresponds to measurement of phase shift of 10-7 rad in this interferometric system, five orders of magnitude better than the earliest results. The first major breakthrough was the detailled analysis of the effects of fiber birefringence and of mechanical stability of the system, using the fundamental principle of reciprocity of modal propagation. The need for single mode filtering has led to a so-called minimum reciprocal configuration which improves dramatically the sensitivity of the system when it is used in addition of biasing detection techniques. We present the various technological approaches which have been used (bulk optics, all-fiber optics and integrated optics) and we analyse the residual parasitic phenomena which had to be reduced (thermal and acoustic noise, Faraday and optical Kerr effects). Experimental data of an all-fiber system and of a brass board using a single multifunction integrated optic circuit are reported. Finally we discuss the current problems and the future directions of research which should lead to an actual navigation instrument.
Neural network modeling and optical information processing (1986)

We discuss how the understanding that exists of the way neural networks process information can provide useful insights that can help us find effective ways to use optical interconnections. Optical realization of simple neural network models are described.
Condensation-Enhanced Self-Assembly as a Route to High Surface Area α-Aluminas (2013)

High surface area nanosized α-alumina has been obtained by thermally treating a sol–gel-derived mesophase at 1200 °C; the mesophase was synthesized by a sol–gel route involving evaporation induced self-assembly (EISA) of a hydrolyzed gel from Al-tri-sec-butoxide in s-BuOH in the presence of a nonionic surfactant (EO20PO70EO20), HCl as catalyst, and water (H2O/Al = 6). The activated material renders moderate surface areas of about 8.4–10 m2 g–1, associated with significant crystallite coarsening. The key aspect to produce smaller crystallites is making the mesophase more resistant to coarsening. This was achieved by enhancing the condensation step by treating the hydrolyzed gel with tetrabutyl ammonium hydroxide (TBAOH) before evaporation. The characteristics of the mesophase indicate condensation of the primary particles with less AlO5 unsaturated sites, at the expense of a lower solid yield due to small crystallites dissolution. The activated TBAOH condensed EISA material is composed of α-alumina aggregated crystallites of about 60–100 nm, and the material possesses surface areas ranging from 16 to 24 m2 g–1 due to the improved resistance to coarsening. At least two aspects are suggested to play a role in this. The worm-hole morphology of the mesophase aggregates yields high particle coordination, which favors densification rather than coarsening. Furthermore, the decrease of the AlO5 defect sites by the TBAOH condensation makes the mesophase less reactive and consequently more resistant to coarsening.
Lifetime RC time delay of on-chip copper interconnect (2002)

Increasing resistance and RC time delay induced by an oxidation in a copper line during its lifetime may limit copper-based metallization for technologies with critical dimension. Based on the mechanisms of resistance, constriction resistance and material diffusion, two dynamic models to access lifetime behavior of resistance and RC time delay were developed and discussed. These models also provide a means to gain insight into the correlation between the resistance and RC time delay of copper interconnect and such key variables as feature dimension, operating condition, and oxidation.
One-step synthesis of peptide conjugated gold nanoclusters for the high expression of FGFR2 tumor targeting and imaging (2016)

An effective method to synthesize gold nanoclusters that can specifically recognize fibroblast growth factor receptor2 (FGFR2) was reported.
Detecting Attacks That Exploit Application-Logic Errors Through Application-Level Auditing (2005)

Host security is achieved by securing both the operating system kernel and the privileged applications that run on top of it. Application-level bugs are more frequent than kernel-level bugs, and, therefore, applications are often the means to compromise the security of a system. Detecting these attacks can be difficult, especially in the case of attacks that exploit application-logic errors. These attacks seldom exhibit characterizing patterns as in the case of buffer overflows and format string attacks. In addition, the data used by intrusion detection systems is either too low-level, as in the case of system calls, or incomplete, as in the case of syslog entries. This paper presents a technique to enforce nonbypassable, application-level auditing that does not require the recompilation of legacy systems. The technique is implemented as a kernel-level component, a privileged daemon, and an offline language tool. The technique uses binary rewriting to instrument applications so that meaningful and complete audit information can be extracted. This information is then matched against application-specific signatures to detect attacks that exploit application-logic errors. The technique has been successfully applied to detect attacks against widely-deployed applications, including the Apache Web server and the OpenSSH server.
Pancreatic-Specific Inactivation of IGF-I Gene Causes Enlarged Pancreatic Islets and Significant Resistance to Diabetes (2004)

The dogma that IGF-I stimulates pancreatic islet growth has been challenged by combinational targeting of IGF or IGF-IR (IGF receptor) genes as well as β-cell–specific IGF-IR gene deficiency, which caused no defect in islet cell growth. To assess the physiological role of locally produced IGF-I, we have developed pancreatic-specific IGF-I gene deficiency (PID) by crossing Pdx1-Cre and IGF-I/loxP mice. PID mice are normal except for decreased blood glucose level and a 2.3-fold enlarged islet cell mass. When challenged with low doses of streptozotocin, control mice developed hyperglycemia after 6 days that was maintained at high levels for at least 2 months. In contrast, PID mice only exhibited marginal hyperglycemia after 12 days, maintained throughout the experiment. Fifteen days after streptozotocin, PID mice demonstrated significantly higher levels of insulin production. Furthermore, streptozotocin-induced β-cell apoptosis (transferase-mediated dUTP nick-end labeling [TUNEL] assay) was significantly prevented in PID mice. Finally, PID mice exhibited a delayed onset of type 2 diabetes induced by a high-fat diet, accompanied by super enlarged pancreatic islets, increased insulin mRNA levels, and preserved sensitivity to insulin. Our results suggest that locally produced IGF-I within the pancreas inhibits islet cell growth; its deficiency provides a protective environment to the β-cells and potential in combating diabetes.