gebhart/patrepeval huggingface dataset:
Global Effects of Inactivation of the Pyruvate Kinase Gene in the <i>Mycobacterium tuberculosis</i> Complex (2009)

To better understand the global effects of "natural" lesions in genes involved in the pyruvate metabolism in Mycobacterium bovis, null mutations were made in the Mycobacterium tuberculosis H37Rv ald and pykA genes to mimic the M. bovis situation. Like M. bovis, the M. tuberculosis DeltapykA mutant yielded dysgonic colonies on solid medium lacking pyruvate, whereas colony morphology was eugonic on pyruvate-containing medium. Global effects of the loss of the pykA gene, possibly underlying colony morphology, were investigated by using proteomics on cultures grown in the same conditions. The levels of Icd2 increased and those of Icl and PckA decreased in the DeltapykA knockout. Proteomics suggested that the synthesis of enzymes involved in fatty acid and lipid biosynthesis were decreased, whereas those involved in beta-oxidation were increased in the M. tuberculosis DeltapykA mutant, as confirmed by direct assays for these activities. Thus, the loss of pykA from M. tuberculosis results in fatty acids being used principally for energy production, in contrast to the situation in the host when carbon from fatty acids is conserved through the glyoxylate cycle and gluconeogenesis; when an active pykA gene was introduced into M. bovis, the opposite effects occurred. Proteins involved in oxidative stress-AhpC, KatG, and SodA-showed increased synthesis in the DeltapykA mutant, and iron-regulated proteins were also affected. Ald levels were decreased in the DeltapykA knockout, explaining why an M. tuberculosis DeltapykA Deltaald double mutant showed little additional phenotypic effect. Overall, these data show that the loss of the pykA gene has powerful, global effects on proteins associated with central metabolism.
Unemployment and mortality (1987)

bearing in mind that no delay could be attributed to efforts to provide advanced trauma or cardiac life support.It would be a blow to the care of the seriously ill and injured if the impressions put forward in this article, which are based on theoretical supposition from an area with no experience of extended training, were allowed to override the experience of others who have produced hard data to the contrary.
Efficacy of Monotherapy with Either Bimatoprost or Travoprost in Patients with Primary Open-Angle Glaucoma Resistant to Latanoprost Therapy (2011)

Pur po se: This prospective study aimed to evaluate the efficacy of monotherapy with either bimatoprost or travoprost in patients with primary open-angle glaucoma (POAG) resistant to latanoprost therapy. Patients and Methods: Forty patients with POAG who received therapy with topical latanoprost at Gaziantep University Hospital, Department of Ophthalmology between March 2009 and March 2010 were chosen to participate in this study. The decision to stop latanoprost therapy in these patients was made either due to the fact that they were resistant to therapy or due to the necessity to further decrease the intraocular pressure (IOP); 20 subjects were chosen to receive monotherapy with bimatoprost and 20 were chosen to receive monotherapy with travoprost. The patients were observed for 6 months with follow-up visits at 1 week, 1 month, 3 months and 6 months. Results: For the group of patients receiving therapy with bimatoprost, the average decrease in IOP was measured to be 2.05 mmHg at 1 week, 2.25 mmHg at 1 month, 1.90 mmHg at 3 months and 2.40 mmHg at 6 months. For the group of patients receiving therapy with travoprost, the average decrease in IOP was measured to be 1.47 mmHg at 1 week, 1.75 mmHg at 1 month, 1.42 mmHg at 3 months and 1.27 mmHg at 6 months. At the end of 6 months, there were no significant changes observed in the mean deviation and central corneal thickness in both therapy groups. Conjunctival hyperemia and ocular irritation were the most common side effects observed in both groups, with the bimatoprost therapy group showing higher values than the travoprost group. Discussion: For patients resistant to latanoprost therapy, prior to any adjuvant therapy, monotherapy with either bimatoprost, which is a prostamide, or travoprost, a prostaglandin analogue, has been shown to be effective at lowering IOP. (Turk J Ophthalmol 2011; 41: 295-8)
Important Role of Erythropoietin Receptor to Promote VEGF Expression and Angiogenesis in Peripheral Ischemia in Mice (2007)

We have recently demonstrated that endogenous erythropoietin (Epo)/Epo receptor (EpoR) system plays an important protective role in hypoxia-induced pulmonary hypertension. However, it remains to be examined whether vascular EpoR system contributes to angiogenesis in response to ischemia. We examined angiogenesis in EpoR(-/-)-rescued mice that lack EpoR in most organs including cardiovascular system except erythroid-lineage cells. Two weeks after femoral artery ligation, blood flow recovery, activation of VEGF/VEGF receptor system, and mobilization of endothelial progenitor cells were all impaired in EpoR(-/-)-rescued mice as compared with wild-type (WT) mice. Bone marrow (BM) transplantation with WT-BM cells in EpoR(-/-)-rescued mice partially but significantly improved blood flow recovery after hindlimb ischemia. The extent of VEGF upregulation and the number of BM-derived cells in ischemic tissue were significantly less in EpoR(-/-)-rescued mice compared with WT mice even after BM reconstitution with WT-BM cells. Similarly, the recovery of blood flow was significantly impaired in recipient EpoR(-/-)-rescued mice that had been transplanted with WT-BM or EpoR(-/-)-rescued-BM as compared with recipient WT mice. Furthermore, the Matrigel implantation assay and aortic ring assay showed that microvessel growth in vitro was significantly reduced in EpoR(-/-)-rescued mice as compared with WT mice. These results indicate that vascular EpoR system also plays an important role in angiogenesis in response to hindlimb ischemia through upregulation of VEGF/VEGF receptor system, both directly by enhancing neovascularization and indirectly by recruiting endothelial progenitor cells and BM-derived proangiogenic cells.
Anisotropic-Medium PML for Vector FETD With Modified Basis Functions (2006)

A novel anisotropic-medium perfectly matched layer (PML) implementation is presented for boundary truncation in the three-dimensional vector finite-element time-domain (FETD) method. This approach utilizes a complex set of vector test and basis functions in the PML region, that recover the usual basis functions in the non-PML region. Numerical examples show that the proposed PML-FETD approach has small reflection errors and no observed late-time instabilities for simulations involving up to 10/sup 6/ time steps.
New X-ray Patent Specifications (1934)

The following abridgements of recent Patent Specifications has been compiled from the Official Patents Journal by permission of the Controller of H.M. Stationery Office. Printed copies of the full Specifications can, when accepted, be obtained from the Patent Office, 25 Southampton Buildings, London, W.C.2, at 1s. each.
Using Deep Neural Network for Android Malware Detection (2019)

The pervasiveness of the Android operating system, with the availability of applications almost for everything, is readily accessible in the official Google play store or a dozen alternative third-party markets. Additionally, the vital role of smartphones in modern life leads to store significant information on devices, not only personal information but also corporate information, which attract malware developers to develop applications that can infiltrate user's devices to steal information and perform harmful tasks. This accompanied with the limitation of currently defenses techniques such as ineffective screening in Google play store, weak or no screening in third-party markets. Antiviruses software that still relies on a signature-based database that is effective only in identifying known malware. To contrive with malicious applications that are increased in volume and sophistication, we propose an Android malware detection system that applies deep learning technique to face the threats of Android malware. Extensive experiments on a real-world dataset contain benign and malicious applications uncovered that the proposed system reaches an accuracy of 95.31%.
EGFR Protein Expression in Non–Small Cell Lung Cancer Predicts Response to an EGFR Tyrosine Kinase Inhibitor—A Novel Antibody for Immunohistochemistry or AQUA Technology (2011)

EGFR protein expression using an ID-specific antibody specifically predicts response to gefitinib in NSCLC patients, including in EGFR-mutated patients, and increased PFS/OS from gefitinib. These data suggest that the choice of diagnostic antibody and methodology matters to predict response and outcome to specific therapies. The potential clinical application needs further validation. Clin Cancer Res; 17(24); 7796-807. ©2011 AACR.
Effect of Clotting in Stomachs of Infants on Protein Digestibility of Milk (1987)

Differences in clotting between human and cow's milk in the stomachs of infants are discussed. Gastric pH, after ingesting milk, of an infant up to 6 months of age stays at a pH range of 4-5, near the isoelectric point of casein, and never reaches the value of 2, which is found in adults. Pepsin C (or gastricsin) can hydrolyze proteins at this pH range. Gastric emptying time is shorter with human milk than with cow's milk which appears to be correlated to the smaller size of human milk clots. Elimination of a readily coagulable fraction of casein from cow's milk by restricted rennet action produced B-casein rich milk with similar coagulating properties to that of human milk. Although pepsin digestibility at pH 2 was greater for bovine whole casein than bovine B-casein-rich fraction or human casein, this difference was minimized or even reversed at pH4. This was ascribred to the difference in clotting behavior of s1-casein and B-casein, namely a harder clot of the former. Therefore, the difference in clotting and proteolytic properties between human milk and cow's milk in an infant's stomach can be explained from the difference in chemical properties of their major caseins, i.e., B-caseins and s1-case-ins in human milk and cow's milk, respectively.
Cocaine‐induced ventricular fibrillation: protection afforded by the calcium antagonist verapamil (1988)

There is increasing evidence that the use of cocaine can trigger lethal cardiac events, including ventricular fibrillation. The mechanism responsible for these lethal cardiac arrhythmias remains to be determined. Therefore, 13 mongrel dogs were instrumented so that heart rate, left ventricular pressure (LVP), and d(LVP)/dt could be measured. After a 3- to 4-wk recovery period, the left circumflex coronary artery was occluded for 2 min, beginning with the last minute of an exercise stress test and continuing for 1 min after the cessation of exercise. None of the dogs developed cardiac arrhythmias during the control exercise plus ischemia test. On a subsequent day, the test was repeated after the injection of cocaine HCl (1.0 mg/kg). Cocaine significantly (P less than 0.01) elevated heart rate, systolic LVP, and d(LVP)/dt, and it elicited cardiac arrhythmias in 12 of the 13 animals during the exercise plus test. In fact, 11 animals developed ventricular fibrillation. Verapamil, a calcium channel antagonist (250 micrograms/kg), attenuated the hemodynamic effects of cocaine and prevented the development of ventricular arrhythmias. These data suggest that cocaine can induce ventricular fibrillation during myocardial ischemia and that these lethal arrhythmias may be prevented by a calcium channel antagonist.
Gaseous emissions and toxic hazards associated with plastics in fire situations: A literature review (1976)

The hazards of plastics in fire situations, the gases emitted, the factors influencing the nature of these emissions, the characteristics of toxic gases, and the results of laboratory studies, are discussed. The literature pertaining to the pyrolysis and oxidation of plastics was reviewed. An effort was made to define the state of the art for determining the toxic gases emitted by plastics under fire conditions. Recommendations are made and research needs defined as a result of this review.
A Colchicine, Hypotonic Citrate, Squash Sequence for Mammalian Chromosomes (1956)

The method was developed for bone marrow of mice but is applicable to other tissues and other species of small mammals. Mice are injected intraperitoneally with 0.5 ml of 0.025% colchicine solution and killed 1 hr afterwards. The femurs are dissected out rapidly, the epiphyses are removed, and the marrow is washed out of the shafts by warm hypotonic sodium citrate solution from a hypodermic syringe. Gentle aspiration of the marrow into and out of the syringe converts it into a fine suspension. The suspension is kept in the citrate solution at 37°C for 10 min. Connective tissue and bony spicules are removed by centrifuging through Nylon bolting cloth in a bacterial filtration tube, before fixing in acetic-alcohol (1:3) and staining by the standard Feulgen procedure. The cells are concentrated for each change of reagent by centrifuging slowly. The advantages of colchicine pretreatment and of working with cell suspensions are emphasized.
Repression of human immunodeficiency virus type 1 long terminal repeat-driven gene expression by binding of the virus to its primary cellular receptor, the CD4 molecule (1996)

We have previously postulated that the binding of the human immunodeficiency virus type 1 (HIV-1) to cell surface CD4 induces signal transduction pathways that down-modulate production of progeny virions in acutely infected T cells (M. Tremblay, S. Meloche, S. Gratton, M. A. Wainberg, and R.-P. Sékaly, EMBO J. 13:774-783, 1994). To evaluate the possibility that CD4 cross-linking might indeed affect viral gene expression, we have introduced a molecular construct made of the luciferase reporter gene placed under the control of the regulatory elements of HIV-1 in several CD4-positive T-cell lines. We found that cross-linking of CD4 with defective HIV-1 particles and heat-inactivated viruses inhibits long terminal repeat-dependent luciferase expression. Experiments revealed that the gp120-CD4 interaction was necessary to repress HIV-1 long terminal repeat-dependent luciferase activity. The cytoplasmic domain of CD4 was also found to be required for this effect to occur. The virus-mediated signal transduction was shown to be mediated via p56lck-dependent and -independent pathways. These results indicate that the earliest event in the HIV-1 replicative cycle, namely, the binding of the virus to its cellular receptor, can lead to signal transduction culminating in down-modulation of viral gene expression. Thus we propose that defective viruses could regulate the pathogenesis of HIV disease as they constitute the vast majority of circulating HIV-1 particles.
<i>Ab‐initio</i>simulations of materials using VASP: Density‐functional theory and beyond (2008)

During the past decade, computer simulations based on a quantum-mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid-state physics and chemistry and on materials science-promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of electronic many-body effects within density-functional theory (DFT) and the upcoming post-DFT methods. (ii) The implementation of the new functionals and many-body techniques within highly efficient, stable, and versatile computer codes, which allow to exploit the potential of modern computer architectures. In this review, I discuss the implementation of various DFT functionals [local-density approximation (LDA), generalized gradient approximation (GGA), meta-GGA, hybrid functional mixing DFT, and exact (Hartree-Fock) exchange] and post-DFT approaches [DFT + U for strong electronic correlations in narrow bands, many-body perturbation theory (GW) for quasiparticle spectra, dynamical correlation effects via the adiabatic-connection fluctuation-dissipation theorem (AC-FDT)] in the Vienna ab initio simulation package VASP. VASP is a plane-wave all-electron code using the projector-augmented wave method to describe the electron-core interaction. The code uses fast iterative techniques for the diagonalization of the DFT Hamiltonian and allows to perform total-energy calculations and structural optimizations for systems with thousands of atoms and ab initio molecular dynamics simulations for ensembles with a few hundred atoms extending over several tens of ps. Applications in many different areas (structure and phase stability, mechanical and dynamical properties, liquids, glasses and quasicrystals, magnetism and magnetic nanostructures, semiconductors and insulators, surfaces, interfaces and thin films, chemical reactions, and catalysis) are reviewed.
Measuring SO <sub>2</sub> ship emissions with an ultraviolet imaging camera (2014)

Abstract. Over the last few years fast-sampling ultraviolet (UV) imaging cameras have been developed for use in measuring SO2 emissions from industrial sources (e.g. power plants; typical emission rates ~ 1–10 kg s−1) and natural sources (e.g. volcanoes; typical emission rates ~ 10–100 kg s−1). Generally, measurements have been made from sources rich in SO2 with high concentrations and emission rates. In this work, for the first time, a UV camera has been used to measure the much lower concentrations and emission rates of SO2 (typical emission rates ~ 0.01–0.1 kg s−1) in the plumes from moving and stationary ships. Some innovations and trade-offs have been made so that estimates of the emission rates and path concentrations can be retrieved in real time. Field experiments were conducted at Kongsfjord in Ny Ålesund, Svalbard, where SO2 emissions from cruise ships were made, and at the port of Rotterdam, Netherlands, measuring emissions from more than 10 different container and cargo ships. In all cases SO2 path concentrations could be estimated and emission rates determined by measuring ship plume speeds simultaneously using the camera, or by using surface wind speed data from an independent source. Accuracies were compromised in some cases because of the presence of particulates in some ship emissions and the restriction of single-filter UV imagery, a requirement for fast-sampling (> 10 Hz) from a single camera. Despite the ease of use and ability to determine SO2 emission rates from the UV camera system, the limitation in accuracy and precision suggest that the system may only be used under rather ideal circumstances and that currently the technology needs further development to serve as a method to monitor ship emissions for regulatory purposes. A dual-camera system or a single, dual-filter camera is required in order to properly correct for the effects of particulates in ship plumes.
Do Grain Boundaries Affect Microwave Dielectric Loss in Oxides? (2009)

Reducing loss in microwave dielectrics is critical to improving performance in wireless communications systems. Grain boundaries in polycrystalline microwave dielectric ceramics have long been suspected of increasing dielectric loss. They are often cited as the main contributor to the observed difference in dielectric losses between single crystals and polycrystalline ceramics. The exact configuration of grain boundaries is problematic to quantify in practice and their influence on the dielectric loss difficult to distinguish from other defects such as porosity, oxygen vacancies, impurities, and dislocations. Here we measure the sensitivity of a single grain boundary in a magnesium oxide bi‐crystal to the polarization of an applied microwave field as a function of temperature.
Specific aromatic foldamers potently inhibit spontaneous and seeded Aβ42 and Aβ43 fibril assembly (2014)

Amyloid fibrils are self-propagating entities that spread pathology in several devastating disorders including Alzheimer's disease (AD). In AD, amyloid-β (Aβ) peptides form extracellular plaques that contribute to cognitive decline. One potential therapeutic strategy is to develop inhibitors that prevent Aβ misfolding into proteotoxic conformers. Here, we design specific aromatic foldamers, synthetic polymers with an aromatic salicylamide (Sal) or 3-amino benzoic acid (Benz) backbone, short length (four repetitive units), basic arginine (Arg), lysine (Lys) or citrulline (Cit) side chains, and various N- and C-terminal groups that prevent spontaneous and seeded Aβ fibrillization. Ac-Sal-(Lys-Sal)3-CONH2 and Sal-(Lys-Sal)3-CONH2 selectively inhibited Aβ42 fibrillization, but were ineffective against Aβ43, an overlooked species that is highly neurotoxic and frequently deposited in AD brains. By contrast, (Arg-Benz)4-CONH2 and (Arg-Sal)3-(Cit-Sal)-CONH2 prevented spontaneous and seeded Aβ42 and Aβ43 fibrillization. Importantly, (Arg-Sal)3-(Cit-Sal)-CONH2 inhibited formation of toxic Aβ42 and Aβ43 oligomers and proteotoxicity. None of these foldamers inhibited Sup35 prionogenesis, but Sal-(Lys-Sal)3-CONH2 delayed aggregation of fused in sarcoma (FUS), an RNA-binding protein with a prion-like domain connected with amyotrophic lateral sclerosis and frontotemporal dementia. We establish that inhibitors of Aβ42 fibrillization do not necessarily inhibit Aβ43 fibrillization. Moreover, (Arg-Sal)3-(Cit-Sal)-CONH2 inhibits formation of toxic Aβ conformers and seeding activity, properties that could have therapeutic utility.
Reductions in Occipital Cortex GABA Levels in Panic Disorder Detected With 1H-Magnetic Resonance Spectroscopy (2001)

Panic disorder is associated with reductions in total occipital cortex GABA levels. This abnormality might contribute to the pathophysiology of panic disorder.
Distributed compression of the plenoptic function (2005)

In this paper, we consider the problem of distributed compression in camera sensor networks. Due to the spatial proximity of the different cameras, acquired images can be highly dependent. The correlation in the visual information retrieved is related to the structure of the plenoptic function and can be estimated using geometrical information such as the position of the cameras and some bounds on the location of the objects. We propose a distributed compression scheme that takes advantage of this geometrical information in order to reduce the overall transmission rate from the sensors to a common central receiver. This new approach allows for a flexible repartition of the transmission bit-rates amongst the encoders and is optimal in many cases. Moreover, we show that our coding scheme can be made resilient to a fixed number of occlusions and that perfect reconstruction and interpolation are possible at the receiver.