gebhart/patrepeval huggingface dataset:
Role of Deleted in Breast Cancer 1 (DBC1) Protein in SIRT1 Deacetylase Activation Induced by Protein Kinase A and AMP-activated Protein Kinase (2012)

The NAD(+)-dependent deacetylase SIRT1 is a key regulator of several aspects of metabolism and aging. SIRT1 activation is beneficial for several human diseases, including metabolic syndrome, diabetes, obesity, liver steatosis, and Alzheimer disease. We have recently shown that the protein deleted in breast cancer 1 (DBC1) is a key regulator of SIRT1 activity in vivo. Furthermore, SIRT1 and DBC1 form a dynamic complex that is regulated by the energetic state of the organism. Understanding how the interaction between SIRT1 and DBC1 is regulated is therefore essential to design strategies aimed to activate SIRT1. Here, we investigated which pathways can lead to the dissociation of SIRT1 and DBC1 and consequently to SIRT1 activation. We observed that PKA activation leads to a fast and transient activation of SIRT1 that is DBC1-dependent. In fact, an increase in cAMP/PKA activity resulted in the dissociation of SIRT1 and DBC1 in an AMP-activated protein kinase (AMPK)-dependent manner. Pharmacological AMPK activation led to SIRT1 activation by a DBC1-dependent mechanism. Indeed, we found that AMPK activators promote SIRT1-DBC1 dissociation in cells, resulting in an increase in SIRT1 activity. In addition, we observed that the SIRT1 activation promoted by PKA and AMPK occurs without changes in the intracellular levels of NAD(+). We propose that PKA and AMPK can acutely activate SIRT1 by inducing dissociation of SIRT1 from its endogenous inhibitor DBC1. Our experiments provide new insight on the in vivo mechanism of SIRT1 regulation and a new avenue for the development of pharmacological SIRT1 activators targeted at the dissociation of the SIRT1-DBC1 complex.
Facial Landmark Detection and Tracking for Facial Behavior Analysis (2016)

The face is the most dominant and distinct communication tool of human beings. Automatic analysis of facial behavior allows machines to understand and interpret a human's states and needs for natural interactions. This research focuses on developing advanced computer vision techniques to process and analyze facial images for the recognition of various facial behaviors. Specifically, this research consists of two parts: automatic facial landmark detection and tracking, and facial behavior analysis and recognition using the tracked facial landmark points. In the first part, we develop several facial landmark detection and tracking algorithms on facial images with varying conditions, such as varying facial expressions, head poses and facial occlusions. First, to handle facial expression and head pose variations, we introduce a hierarchical probabilistic face shape model and a discriminative deep face shape model to capture the spatial relationships among facial landmark points under different facial expressions and face poses to improve facial landmark detection. Second, to handle facial occlusion, we improve upon the effective cascade regression framework and propose the robust cascade regression framework for facial landmark detection, which iteratively predicts the landmark visibility probabilities and landmark locations.
Allele-Specific Isothermal Amplification Method Using Unmodified Self-Stabilizing Competitive Primers (2018)

Rapid and specific detection of single nucleotide polymorphisms (SNPs) related to drug resistance in infectious diseases is crucial for accurate prognostics, therapeutics and disease management at point-of-care. Here, we present a novel amplification method and provide universal guidelines for the detection of SNPs at isothermal conditions. This method, called USS-sbLAMP, consists of SNP-based loop-mediated isothermal amplification (sbLAMP) primers and unmodified self-stabilizing (USS) competitive primers that robustly delay or prevent unspecific amplification. Both sets of primers are incorporated into the same reaction mixture, but always targeting different alleles; one set specific to the wild type allele and the other to the mutant allele. The mechanism of action relies on thermodynamically favored hybridization of totally complementary primers, enabling allele-specific amplification. We successfully validate our method by detecting SNPs, C580Y and Y493H, in the Plasmodium falciparum kelch 13 gene that are responsible for resistance to artemisinin-based combination therapies currently used globally in the treatment of malaria. USS-sbLAMP primers can efficiently discriminate between SNPs with high sensitivity (limit of detection of 5 × 10<sup>1</sup> copies per reaction), efficiency, specificity and rapidness (<35 min) with the capability of quantitative measurements for point-of-care diagnosis, treatment guidance, and epidemiological reporting of drug-resistance.
Autoantibodies to DEK oncoprotein in human inflammatory disease (2000)

Anti-DEK autoantibodies are less specific for JRA than previously believed. They are produced in association with a variety of inflammatory conditions, many of which are associated with granuloma formation and/or predominant Thl cytokine production. Anti-DEK antibodies may be a marker for a subset of autoimmunity associated with interferon-gamma production rather than a particular disease subset.
Enhanced Sensitivity of a Surface Acoustic Wave Gyroscope (2009)

In this paper, we present an optimal design and performance evaluation of a surface acoustic wave (SAW) gyroscope. It consists of a two-port SAW resonator (SAWR) and a SAW sensor (SAWS) structured using a delay line pattern. The SAW resonator provides a stable reference vibration and creates a standing wave, and the vibrating metallic dot array at antinodes of the standing wave induces the second SAW in the normal direction by the Coriolis force, and the SAW sensor is used to detect the secondary SAW. By using the coupling of modes (COM), the SAW resonator was simulated, and the effects of the design parameters on the frequency response of the device were investigated. Also, a theoretical analysis was performed to investigate the effect of metallic dots on the frequency response of the SAW device. The measured frequency response S21 of the fabricated 80 MHz two-port SAW resonator agrees well with the simulated result, that is, a low insertion loss (∼5 dB) and a single steep resonance peak were observed. In the gyroscopic experiments using a rate table, optimal metallic dot thickness was determined, and the sensitivity of the fabricated SAW gyroscope with an optimal metallic dot thickness of ∼350 nm was determined to be 3.2 µV deg-1 s-1.
Efficient Minimal Perfect Hash Language Models (2010)

The recent availability of large collections of text such as the Google 1T 5-gram corpus (Brants and Franz, 2006) and the Gigaword corpus of newswire (Graff, 2003) have made it possible to build language models that incorporate counts of billions of n-grams. This paper proposes two new methods of efficiently storing large language models that allow O(1) random access and use significantly less space than all known approaches. We introduce two novel data structures that take advantage of the distribution of n-grams in corpora and make use of various numbers of minimal perfect hashes to compactly store language models containing full frequency counts of billions of n-grams using 2.5 Bytes per n-gram and language models of quantized probabilities using 2.26 Bytes per n-gram. We show that our approaches are simple to implement and can easily be combined with pruning and quantization to achieve additional reductions in the size of the language model. 1.
Expression of Th1-mediated immunity in mouse lungs induces a <i>Mycobacterium tuberculosis</i> transcription pattern characteristic of nonreplicating persistence (2002)

The lung is the primary target of infection with Mycobacterium tuberculosis. It is well established that, in mouse lung, expression of adaptive, Th1-mediated host immunity inhibits further multiplication of M. tuberculosis. Here, real-time RT-PCR was used to define the pattern of expression against time of lung infection of key genes involved in Th1-mediated immunity and of selected genes of M. tuberculosis. Inhibition of bacterial multiplication was preceded by increased mRNA synthesis for IFN-gamma and inducible NO synthase (NOS2) and by NOS2 protein synthesis in infected macrophages. Concurrently, the pattern of transcription of bacterial genes underwent dramatic changes. mRNA synthesis increased for alpha-crystallin (acr), rv2626c, and rv2623 and decreased for superoxide dismutase C (sodC), sodA, and fibronectin-binding protein B (fbpB). This pattern of M. tuberculosis transcription is characteristic of the nonreplicating persistence [Wayne, L. G. & Sohaskey, C. D. (2001) Annu. Rev. Microbiol. 55, 139-163] associated with adaptation of tubercle bacilli to hypoxia in vitro. Based on this similarity, we infer that host immunity induces bacterial growth arrest. In IFN-gamma gene-deleted mice, bacterial growth was not controlled; NOS2 protein was not detected in macrophages; sodC, sodA, and fbpB transcription showed no decrease; and acr, rv2626c, and rv2623 transcription increased only at the terminal stages of lung pathology. These findings define the transcription signature of M. tuberculosis as it transitions from growth to persistence in the mouse lung. The bacterial transcription changes measured at onset of Th1-mediated immunity are likely induced, directly or indirectly, by nitric oxide generated by infected macrophages.
Risk of infection associated with anti-TNF-α therapy (2018)

The advent, more than two decades ago, of monoclonal antibodies and soluble receptors targeting tumor necrosis factor (TNF)-α has revolutionized the therapeutic approach to otherwise difficult-to-treat autoimmune and inflammatory diseases. However, due to the pleiotropic functions played by this pro-inflammatory cytokine (with particular relevance in granuloma maintenance), TNF-α blockade may increase the incidence of serious infections. Areas covered: The present review summarizes the biological rationale supporting the impact of anti-TNF-α therapy on the host's susceptibility to infection. The structure, mode of action, and indications of available agents are reviewed, as well as the clinical evidence coming from clinical trials and observational registries. We discuss the impact of patient- and disease-related factors influencing the occurrence of infection. Finally, strategies for risk minimization are also covered, with particular attention to recommendations for screening of latent tuberculosis infection and management of chronic hepatitis B infection. Expert commentary: Methodological limitations (confounding by indication bias, patient dropout, or switching therapies) should be considered when interpreting observational data. Clinicians must individualize the infection risk assessment not only on the basis of the specific anti-TNF-α agent used or the expected duration of therapy, but also by taking into account the baseline susceptibility of a given patient.
Predictable Paco<sub>2</sub>, with two different flow settings using the Mapleson D system (1990)

Two different settings of fresh gas flow (VFG) and minute ventilation (VE) used with the coaxial Mapleson D system (Bain), were evaluated in 59 adults (ASA I-III) during controlled ventilation and different types of surgical procedures. The two flow settings (alternatives A and B) were VFG of 75 and 110 ml.min-1.kg-1 and VE of 150 and 175 ml.min-1.kg-1, aiming to generate normocapnea and mild hypocapnea, respectively. The PaCO2 obtained with alternative A was 5.5 +/- 0.5 kPa (mean +/- s.d.), with 92% of the patients within the range 4.7-6.1 kPa. With alternative B, the PaCO2 was 4.4 +/- 0.5 kPa, with 82% of the patients within the range 3.5-4.9 kPa. It is concluded that these two flow regimes are suitable for clinical use when either normocapnea or mild hypocapnea is desired.
Neuraminidase induces capacitation and acrosome reaction in mammalian spermatozoa (1988)

The treatment of epididymal spermatozoa of guinea pig and ejaculated spermatozoa of rabbit with neuraminidase from Arthrobacter ureafaciens induced significant acrosome reaction while the neuraminidase from Cl. perfringens failed to do so. The addition of the neuraminidase inhibitors kept the enzyme induced acrosome reaction to the control level. The zona-free hamster ova test showed that the treatment of spermatozoa with Arthrobacter neuraminidase rendered 82% of the guinea pig and 69% of the rabbit spermatozoa capable of fertilization. Thus, neuraminidase seems to enhance the rate of acrosome reaction by first capacitating spermatozoa in vitro.
Treatment of genital warts: an overview (1998)

Traditional treatments for human papillomavirus-associated lesions may be categorised into chemical, surgical and immunological therapies. Among chemical treatments, podophyllotoxin and trichloroacetic acid are the most commonly used. Cryotherapy, electrocautery and laser ablation constitute the main surgical approaches, while in the past decade interferons have been prescribed as an immunological treatment. The majority of current treatments are directed at lesion ablation. This clearly represents an insufficient treatment approach and should be replaced by, or used in conjunction with, a treatment which stimulates the host immunity in order to eradicate the virus. This would remove the source of re-occurrence and might also establish a stable immunity which would protect the patient from reinfection.
ChemInform Abstract: SYNTHESIS OF ALL‐L CONFIGURATION CYCLOHEXADEPSIPEPTIDE CYCLO‐(L‐VAL‐L‐LAC)3 USING THE PEOC/ACID CHLORIDE METHOD (1985)

Abstract Ausgehend von Peoc‐geschütztem L‐Valin (Ia) und L‐Milchsäure‐tert.‐butylester (II) wird auf dem im Formelschema skizzierten Weg das geschützte l‐lexadepsipeptid (VIa) hergestellt, das in den aktivierten Ester (VIc) übergeführt wird.
Hyaluronic acid production with <i>Corynebacterium glutamicum</i>: effect of media composition on yield and molecular weight (2014)

Corynebacterium glutamicum has a great potential as an alternative production host for HA. The fact that Coryne. glutamicum produces no distinct HA capsule facilitates HA isolation and improves overall yield.
Enhanced photoacoustic spectroscopy sensitivity through intra-cavity OPO excitation (2018)

We report an optical molecular gas sensor exhibiting high levels of selectivity and sensitivity. The outstanding sensitivity demonstrated by our technology is rooted in a novel combination of photoacoustic spectroscopy (PAS) operated within the cavity of a continuous-wave, intra-cavity Optical Parametric Oscillator (OPO). We exploit the very high circulating field present within the resonant down-converted cavity as the excitation source of the photoacoustic effect, conferring orders-of-magnitude improvement in optical excitation power. Additionally, the wide selectivity of the system arises from the inherent broad tunability and narrow optical linewidth of an OPO. Here we report the use of this technology for the detection of ammonia (NH<sub>3</sub>) as a simulant target molecule. A 3-D printed miniature PAS cell with microelectromechanical systems based (MEMS) microphone is used for the gas detection. The resonance frequency of the cell was measured at 17.9 kHz with a Q-factor of 9. The down-converted signal wave resonating within its optical cavity was tuned to 6605.6cm<sup>-1</sup> (corresponding to a strong local NH<sub>3</sub> absorption line) through a combination of phase matching and intra-cavity etalon control. The laser was amplitude modulated at the resonance frequency of the PAS cell, producing an average optical excitation power of ~10W in the signal arm of the OPO, to induce the photoacoustic effect for only 4W of primary diode pump power. In this work we show detection limit at the level of single parts-per-billion (ppb). Additionally, we will discuss how this technology could be readily refined to potentially demonstrate a sensitivity of tens parts-per-quadrillion.
Fundamental Properties of a Synthetic Cation Exchange Resin (1947)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFundamental Properties of a Synthetic Cation Exchange ResinW. C. Bauman and J. EichhornCite this: J. Am. Chem. Soc. 1947, 69, 11, 2830–2836Publication Date (Print):November 1, 1947Publication History Published online1 May 2002Published inissue 1 November 1947https://doi.org/10.1021/ja01203a065Request reuse permissionsArticle Views1303Altmetric-Citations134LEARN 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 InReddit PDF (580 KB) Get e-Alertsclose Get e-Alerts
Melting and Premelting Transitions of an Oligomer Measured by DNA Base Fluorescence and Absorption (1994)

Incorporation of 2-aminopurine (2AP) in place of adenine gives an optical probe of local and global DNA conformation. The temperature dependence of the absorption of the duplex d[CTGA(2AP)-TTCAG]2 DNA decamer shows that the helix has approximately an all-or-none melting transition. Absorbance at wavelengths of 260 and 330 nm monitors the average normal base conformation and the 2AP base local conformation, respectively. From this measure, the 2AP base melts less than 1 degree C below the other bases. Temperature-dependent lifetime measurements of 2AP also mirror the melting transition. Absorption spectra show that below Tm most 2AP's are H-bonded. Fluorescence intensity and excitation spectra measurements show, on the other hand, that the most highly-fluorescent states correspond to non-H-bonded 2AP's which sense conformational changes of the helix. The temperature dependence of the fluorescence spectral shift shows the conformation and/or dynamics of the 2AP base changes 10 degrees C or more below Tm. The data suggest a premelting transition which is purely dynamic in nature--transient exposure of most 2AP's to water increases, while the average conformation remains B-helical.
Blood Brain Barrier Compromise with Endothelial Inflammation may Lead to Autoimmune Loss of Myelin during Multiple Sclerosis (2009)

Multiple sclerosis is an autoimmune disease characterized by multifocal areas of inflammation and demyelination within the central nervous system. The mechanism that triggers the disease remains elusive. However, recent findings may indicate that multiple sclerosis, at its source, could be a hemodynamic disorder. It has been found that multiple sclerosis patients exhibit significant stenoses in extracranial veins draining the central nervous system (in azygous and internal jugular veins), which are associated with significant pressure gradients measured across strictures. Such anatomic venous abnormalities were not found in the control group of healthy subjects. In this review, it is hypothesized that pathological refluxing venous flow in the cerebral and spinal veins increases the expression of adhesion molecules, particularly intercellular adhesion molecule-1 (ICAM-1), by the cerebrovascular endothelium. This, in turn, could lead to the increased permeability of the blood-brain barrier. Inflamed and activated endothelium could secrete proinflammatory cytokines, including GM-CSF and TGF-beta In these settings, monocytes could transform into antigen-presenting cells and initiate an autoimmune attack against myelin-containing cells. Consequently, a potential therapeutic option for multiple sclerosis could be pharmacotherapy with either substances that strengthen the tight-junctions barrier, or with agents that reduce the expression of adhesion molecules. In addition, surgical correction could be an option in some anatomical variants of pathologic venous outflow. We are optimistic that a hemodynamic approach to the multiple sclerosis pathogenesis can open a new chapter of investigations and treatment of this debilitating neurologic disease.
Ubit Field Rejuvenation: A Case History of Reservoir Management of a Giant Oil Field, Offshore Nigeria (1998)

Abstract Ubit field is an example of a successful application of integrated reservoir management to an old field, which has resulted in a total change in the development strategy, an increase in recoverable reserves by a half billion barrels and a production uplift of 110 MBD. The key was an improved understanding of the reservoir hydraulics. Unlocking the genesis of elements that defined the fluid flow units identified their connectivity and distribution as related to their depositional facies, led to rejuvenating this field so completely. New data and techniques in 3-D seismic, core interpretation, computer mapping, 3-D visualization, and advanced reservoir simulation prediction capabilities were brought together to optimize recovery and production. Through the integration of the new reservoir model, horizontal drilling, and surface facilities, this old field is now producing an all-time high of 140 MBD, with ultimate recovery expected to exceed 1 billion barrels. The techniques and methodologies developed at Ubit are being leveraged in other assets. Ubit has a STOIIP of 2.1 billion. The reservoir is cut by 3500 feet of dipping, unconsolidated sands and shales. Production is from a thin oil column, with an associated thick gas cap. Gravity-stable gas expansion is the primary recovery mechanism. For 25 years, Ubit averaged only 30 MBD with a high gas-oil ratio. Gas breakthrough in conventional directionally-drilled production wells has been problematic. Previous reservoir interpretations described the chaotic nature and poor quality reservoir properties in the eastern two-thirds of the field. Poor historical production performance seemed to confirm these observations. A new horizontally-layered, hydraulic-focused geologic model combined with advanced reservoir simulation techniques yielded a substantially improved interpretation. The reservoir model is the primary focus of this paper. Predicted performance has guided the management of the re-development of Ubit. New technology applications and conventional techniques were brought together in the reservoir model design to capture the geologic elements controlling flow, and the dynamic processes controlling recovery. This paper describes some of the significant reservoir engineering, geoscience, infrastructure challenges, and the technical resolutions during the development and management of this complex reservoir system. Key reservoir management strategies were applied to maximize performance and ultimate recoveries. They include: 1) implementing horizontal well drilling, 2) full-field full-life reservoir simulation results defining well placement / timing, 3) balancing a non-uniform gas cap, 4) maintaining stable gas cap movement and pressure throughout, 5) establishing a field plateau rate and 6) minimizing free-gas production.