gebhart/patrepeval huggingface dataset:
Carrier dynamics and spin–valley–layer effects in bilayer transition metal dichalcogenides (2018)

Transition metal dichalcogenides are an interesting class of low dimensional materials in mono- and few-layer form with diverse applications in valleytronic, optoelectronic and quantum devices. Therefore, the general nature of the band-edges and the interplay with valley dynamics is important from a fundamental and technological standpoint. Bilayers introduce interlayer coupling effects which can have a significant impact on the valley polarization. The combined effect of spin-orbit and interlayer coupling can strongly modify the band structure, phonon interactions and overall carrier dynamics in the material. Here we use first-principles calculations of electron-electron and electron-phonon interactions to investigate bilayer MoS<sub>2</sub> and WSe<sub>2</sub> in both the AA' and AB stacking configurations. We find that in addition to spin-orbit coupling, interlayer interactions present in the two configurations significantly alter the near-band-edge dynamics. Scattering lifetimes and dynamic behavior are highly material-dependent, despite the similarities and typical trends in TMDCs. Additionally, we capture significant differences in dynamics for the AA' and AB stacking configurations, with lifetime values differing by up to an order of magnitude between them for MoS<sub>2</sub>. Further, we evaluate the valley polarization times and find that maximum lifetimes at room temperature are of the scale of 1 picosecond for WSe<sub>2</sub> in the AB orientation. These results present a pathway to understanding complex heterostructure configurations and 'magic angle' physics in TMDCs.
Binding of Thyrotropin-Releasing Hormone to Plasma Membranes of Bovine Anterior Pituitary Gland (1972)

An assay for the binding of [(3)H]thyrotropin-releasing hormone ([(3)H]TRH) is described. Plasma membranes isolated from bovine anterior pituitary gland bind about 600 femtomoles of this hormone per mg of protein, as compared to 15 femtomoles per mg of protein in the total adenohypophyseal homogenate (40-fold purification). The equilibrium constant of membrane receptor-[(3)H]TRH binding at 0 degrees C is 4.3 x 10(7) L.M(-1), or a half-maximal binding of this hormone at 23 nM. The binding is time-dependent; addition of unlabeled hormone induces dissociation of the receptor-[(3)H]TRH complex with a half-life of 14 min. The binding of TRH is not altered by 10 muM melanocyte-stimulating hormone-release inhibiting hormone, lysine-vasopressin, adrenocorticotropin, growth hormone, prolactin, luteinizing hormone, insulin, glucagon, L-thyroxine, or L-triiodothyronine. K(+) and Mg(++) increase formation of the receptor-TRH complex at optimal concentrations of 5-25 mM and 0.5-2.5 mM, respectively, with inhibition at higher concentrations. Ca(++) inhibits binding of TRH at all concentrations tested.
Longitudinal control of automated CHVs with significant actuator delays (2001)

One of the most critical obstacles in the automated operation of commercial heavy vehicles (CHVs) is the presence of significant delays in the fuel and brake actuators. These delays are especially important in longitudinal control of vehicle platoons that do not employ intervehicle communication, because their effect becomes cumulative as it propagates upstream, resulting in considerably degraded performance. Our objective in this paper is to design autonomous controllers which, in the presence of large delays, recover the good performance achieved when the delays are negligible. We propose two different approaches which are tailored to different performance requirements and computational resources. A backstepping-based nonlinear scheme with prediction almost recovers the original "delay-free" performance at the cost of additional controller complexity, while a simpler PID-based nonlinear scheme yields nearly as good performance.
Scalable transaction processing through data-oriented execution: OLTP on highly parallel hardware with DORA (2012)

Data management technology changes the world we live in by providing efficient access to huge volumes of constantly changing data and by enabling sophisticated analysis of those data. In parallel, we witness a tremendous shift in the underlying hardware technology toward highly parallel multicore processors. Data management systems need to fully exploit the abundantly available hardware parallelism. Transaction processing is one of the most important and challenging database workloads and this dissertation contributes to the quest for scalable transaction processing software. It shows that conventional transaction processing has inherent scalability limitations due to the unpredictable access patterns caused by the request-oriented execution model it follows. Instead, it proposes adopting a data-oriented execution model, and shows that transaction processing systems designed around data-oriented execution break the inherent limitations of conventional execution. The data-oriented design paves the way for transaction processing systems to maintain scalability as parallelism increases for the foreseeable future; as hardware parallelism increases, the benefits will only increase.
p53 Adenoviral vector (Ad-CMV-p53) induced prostatic growth inhibition of primary cultures of human prostate and an experimental rat model (2000)

The results suggest that further investigation of molecular gene therapy with recombinant wt-p53 adenovirus for the treatment of BPH is warranted.
Staphostatins: an expanding new group of proteinase inhibitors with a unique specificity for the regulation of staphopains, Staphylococcus spp. cysteine proteinases (2003)

A novel type of cysteine proteinase inhibitor (SspC) has been recently recognized in Staphylococcus aureus (Massimi, I., Park, E., Rice, K., Muller-Esterl, W., Sauder, D.N., and McGavin, M.J. (2002) J Biol Chem 277: 41770-41777). In this paper we have identified homologous proteins encoded in the genome of S. aureus and other coagulase-negative Staphylococci. Collectively we refer to these proteins as staphostatins as they specifically inhibit cysteine proteinases (staphopains) from Staphylococcus spp. The primary structure of staphostatins seems to be unique, although they resemble cystatins in size (105-108 residues). Recombinant staphostatin A, a product of the scpB gene and staphostatin B (SspC) from S. aureus have been characterized in details. Similar to the cystatins, the staphostatins interact specifically with their target proteinases forming tight and stable non-covalent complexes, staphostatin A with staphopain A and staphostatin B with staphopain B. However, in contrast to the cystatins, each of which inhibits broad range of cathepsins, complex formation between staphostatin and staphopain appears to be exclusive, with no cross interaction observed. In addition, the activities of several tested cysteine proteinases of prokaryotic- and eukaryotic-origin were not affected by staphostatins. Such narrow specificity limited to staphopains is presumed to be required to protect staphylococcal cytoplasmic proteins from being degraded by prematurely activated/folded prostaphopains. This function is guaranteed through the unique co-expression of the secreted proteinase and the intracellular inhibitor from the same operon, and represents a unique mechanism of regulation of proteolytic activity in Gram-positive bacteria.
ChemInform Abstract: Synthesis from D‐Lyxonolactone of 1,4‐Dideoxy‐1,4‐imino‐L‐arabinitol, a Glucosidase Inhibitor with in vitro Antiviral Activity. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Integrin αvβ3acts downstream of insulin in normalization of interstitial fluid pressure in sepsis and in cell-mediated collagen gel contraction (2008)

The administration of insulin is recommended to patients with severe sepsis and hyperglycemia. Previously, we demonstrated that insulin may have direct anti-inflammatory properties and counteracted fluid losses from the circulation by normalizing the interstitial fluid pressure (P(IF)). P(IF) is one of the Starling forces determining fluid flux over the capillary wall, and a lowered P(IF) is one of the driving forces in early edema formation in inflammatory reactions. Here we demonstrate that insulin restores a lipopolysaccharide (LPS)-lowered P(IF) via a mechanism involving integrin alpha(v)beta(3). In C57 black mice (n = 6), LPS lowered P(IF) from -0.2 +/- 0.2 to -1.6 +/- 0.3 (P < 0.05) and after insulin averaged -0.8 +/- 0.2 mmHg (P = 0.098 compared with after LPS). Corresponding values in wild-type BALB/c mice (n = 5) were -0.8 +/- 0.1, -2.1 +/- 0.3 (P < 0.05), and -0.8 +/- 0.3 mmHg (P < 0.05 compared with LPS) after insulin administration. In BALB/c integrin beta(3)-deficient (beta(3)(-/-)) mice (n = 6), LPS lowered P(IF) from -0.1 +/- 0.2 to -1.5 +/- 0.3 mmHg (P < 0.05). Insulin did not, however, restore P(IF) in these mice (averaged -1.7 +/- 0.3 mmHg after insulin administration). Cell-mediated collagen gel contraction can serve as an in vitro model for in vivo measurements of P(IF). Insulin induced alpha(v)beta(3)-integrin-dependent collagen gel contraction mediated by C2C12 cells. Our findings suggest a beneficiary effect of insulin for patients with sepsis with regard to the fluid balance, and this effect may in part be due to a normalization of P(IF) by a mechanism involving the integrin alpha(v)beta(3).
Lithium Rechargeable Batteries as Electromechanical Actuators (2006)

An electromechanical actuation concept utilizing the reversible dilation of ion storage compounds is demonstrated, using prismatic cells based on the couple as the test vehicle. Under zero stress, reversible linear strains of were obtained. At 10 MPa stress, 1.5% strain ( mechanical work) was achievable. In tests of maximum actuation speed, cells rated for 20C discharge capability reached actuation strain in 80–100 s. This electrochemical actuation approach provides a low-voltage electrically operated mechanism with mechanical energy density exceeding that of high strain polycrystalline piezoelectrics, and may be useful in high strain, high force, moderate bandwidth actuator applications.
Functional and morphological differences following Monarc and TVT‐O procedures (2011)

At short-term follow-up, Monarc and TVT-O procedures are comparable in both functional outcome of the lower urinary tract and morphology on ultrasound as assessed by parameters representing tape location, tape tension and urethral mobility.
Protein assembly for the design of new materials: characterization of interactions at amino-acid level betweenalpha-lactalbumin and lysozyme (2010)

The final structure and stability of supramolecular objects result from interactions between proteins at amino-acid level. Their characterizatio n is the basis for the design of new protein- based biomaterials. In this study we focus on the i nteractions and assembly of bovine alpha- lactalbumin (LAC) with hen egg white lysozyme (LYS) . While LYS interacts with the apo and holo forms of LAC (Ca 2+ depleted and loaded form respectively), these inte ractions lead to the formation of micro-spheres with apoLAC only. Our objectives are to identify the amino-acids involved in the interactions and to est ablish the mechanism of such self-assembly into suprastructures. The early step of the process is most probably the formation of hetero- dimers. A structural characterization of both holoL AC-LYS and apoLAC-LYS dimers was performed in order to understand why micro-spheres are formed with apoLAC only. The surfaces of interaction of holoLAC with LYS and LYS with the holo and apo forms of LAC were determined using ( 1 H, 15 N) Nuclear Magnetic Resonance. Interacting amino-ac ids were identified according to the chemical shift perturba tions measured during titration of one 15 N- labelled protein by its non-labelled partner. The t itration of 15 N-holoLAC by LYS indicates that holoLAC interacts with LYS through its beta-do main (beta-sheet and flexible loop). The reverse titration indicates that LYS interacts with holoLAC mainly through its alpha-domain, including amino-acids of helices B and D and C- and N-terminal regions. Few residues of its beta-domain are also involved. In both cases the su rfaces of interaction are localized on one side of the proteins and are composed of contiguous surface patches. LYS interacts with the apo form of LAC mainly through its alpha-domain and this surface patch is larger than with the holo form. This difference could be explained b y the increased flexibility of the apoLAC which is in its molten globule state at the working temperature (45°C). In order to know how proteins interact on an atom-to-atom basis, docking experiments were performed using the HADDOCK program. The interacting amino-acids were t ransformed into ambiguous intermolecular distance restraints to calculate het ero-dimers structures. This characterization is a prerequisite for the use of LAC and LYS micro- spheres as biomaterials, such as bioactive compound carrier. These findings give key elements to understand protein interaction and self-assembly process in mixed systems. in assembly for the design of new materials: characterization of interactions at amino acids levels between a-lactalbumin and lysozyme
11 femtosecond pulses from a modelocked Ti:sapphire laser (1992)

Cubic dispersion in a self-modelocked Ti:sapphire laser has been reduced, allowing us to generate sub-11 femtosecond pulses, with average power of 0.6W.
Oxidation of 7,8-Dihydro-8-oxoguanine Affords Lesions That Are Potent Sources of Replication Errors in Vivo (2001)

Three single-stranded DNA genomes have been constructed that contain the 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) oxidation products oxaluric acid, oxazalone, and cyanuric acid. Oligonucleotides containing each lesion were synthesized by treating an oligonucleotide containing a single 8-oxodG with peroxynitrite, and the desired products were isolated by HPLC. The modified oligonucleotides were ligated into M13mp7L2 bacteriophage DNA in such a way that the lesion was situated at a known site in the lacZ gene fragment of the viral genome. The circular genomes were transfected into wild-type AB1157 Escherichia coli. The relative efficiency of lesion bypass by DNA polymerase was determined by counting the number of initial independent infections produced by each genome relative to that of an unmodified DNA control. Viral progeny were analyzed for mutation frequency and type by PCR amplification of the insert region followed by a recently developed post-labeling assay. All three secondary lesions were readily bypassed, causing G --> T transversions at frequencies at least an order of magnitude higher than 8-oxodG. These data establish a model whereby the modestly mutagenic primary lesion 8-oxodG is oxidized in vivo to much more highly mutagenic secondary lesions.
Evaluation of Mitochondrial Function in CHCHD10 Mutation (P5.001) (2016)

Background: Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron degenerative disorder. We found R15L mutation in five FALS out of 308 FALS families. The causative mechanism of CHCHD10 mutation is unknown. Objectives: To evaluate the effect of CHCHD10 mutation on mitochondria. Methods: Mitochondria was enriched by centrifugation at 17,000g for 30 mins. Myc tagged various CHCHD10 constructs including that lacked amino acid 2-16 of CHCHD10 were generated by Site-Directed Mutagenesis. Cell lines cultured were Neuro-2a, NSC-34, lymphocytes and fibroblast . mtDNA copy was determined using primers for tRNALeu(UUR) gene, normalized against nuclear β-2-microglobulin. DNA was digested with BamH1 and BMgBI for Southern. Oxygen consumption assay was done with SeaHorse. Mitochondria complex IV, V and Citrate Synthase activity were determined using Microplate Assay Kits Results: Confocal microscopy showed both wild type and R15L CHCHD10 mutant were expressed diffusely in the cytoplasm as well as the extended neuronal processes and mostly colocalized with mitochondria. Deletion of amino acid 2-16 did not prevent entry of CHCHD10 into mitochondria as shown on Western blot. EM of R15L skin fibroblast showed abnormal mitochondria morphology. Southern blot of R15L fibroblast showed mitochondria DNA fragmentation. R15L fibroblast had significantly less mitochondria DNA copies than controls. The mitochondria movement was analyzed in 137 mitochondria of 9 motor neurons expressing wild type CHCHD10 and 180 mitochondria of 12 motor neurons expressing R15L CHCHD10. The backward moving frequency of R15L mitochondria was 16.9[percnt] ±0.92 (mean ±SEM), significantly less than 32.2[percnt]±4.30 in wild type. Mitochondria oxygen consumption rate and Complex IV and V activity were significantly decreased in fibroblast with R51L CHCHD10 mutation than in control fibroblast without mutation. Conclusions: CHCHD10 gene mutation damaged mitochondrial morphology, DNA stability, respiration and dynamics, suggesting mitochondria dysfunction played key role in its pathogenesis. Study Supported by: Les Turner ALS Foundation & NIH grants
DNA polymerase with modified processivity (2023)

Chimeric DNA polymerase having a DNA polymerase domain and processivity factor binding domain not naturally associated with DNA polymerase domain.
654. Core Antibiotic-Induced Transcriptional Signatures Reflect Susceptibility to All Members of an Antibiotic Class (2020)

Abstract Background Current growth-based antibiotic susceptibility testing (AST) is too slow to guide key clinical decisions. We previously demonstrated a combined Genotypic and Phenotypic AST assay using RNA detection (GoPhAST-R) that can provide AST in &amp;lt; 4h directly from blood culture, 24-36h faster than standard growth-based methods. GoPhAST-R quantifies specific mRNA expression signatures using the multiplexed hybridization RNA-detection platform, NanoString. After brief antibiotic exposure, susceptible cells become stressed, eliciting transcriptional changes that distinguish them from unharmed resistant cells. Here, we assess the generalizability of transcriptional signatures of susceptibility within an antibiotic class. Methods For Escherichia coli and Klebsiella pneumoniae, we assessed the ability of the top ten antibiotic-responsive genes previously identified for ciprofloxacin, gentamicin, and meropenem to predict susceptibility to two other fluoroquinolones (FQ), two other aminoglycosides (AG), and six other beta-lactams (BL), respectively, across 6-8 clinical isolates for each drug for a total of 184 pathogen-drug pairs. After standardized antibiotic exposure (60m for FQs and AGs, 120m for BLs, each at its CLSI breakpoint MIC), samples were mechanically lysed and used as input for NanoString assays as previously described (Bhattacharyya, Nat Med 2019). Results In both species, the top ten genes identified for AST of ciprofloxacin, gentamicin, and meropenem showed similar normalized fold-induction upon treatment with three FQs, three AGs, and seven BLs, respectively, allowing robust distinction of susceptible and resistant isolates (Fig 1). Figure 1 Conclusion We show that a shared set of genes optimized for AST of one antibiotic can predict susceptibility to all members of that drug class, consistent with a conserved core transcriptional response related to mechanism of action. We demonstrate this phenomenon for two common pathogens with propensity for multidrug resistance treated with multiple members of three major antibiotic classes in common clinical use. This unified set of genes for susceptibility prediction would streamline GoPhAST-R implementation, in turn facilitating efficient deployment of antibiotics and reducing unnecessary broad-spectrum use. Disclosures All Authors: No reported disclosures
Area spectral efficiency performance comparison between VLC and RF femtocell networks (2013)

In this paper the average area spectral efficiency (ASE) of indoor visible light communication (VLC) wireless network is investigated for various room geometries (2.5m×5m×3m, 5m×5m×3m and 10m×10m×3m). A comparison is made against state-of-the-art radio frequency (RF) systems employing femtocells indoors. A modified version of the wireless world initiative new radio (WINNER) indoor deployment scenario (office building) is used as the common setup where femtocell access points (APs) and VLC APs are installed alternatively. For the RF system the minimum number of femtocell APs per floor area is four as specified. The requirement for the VLC system is to fulfill the lighting conditions inside the room, characterized by the illuminance distribution in rooms with several possible dimensions. The ASE gains of the VLC system compared to the femtocell network range between 12 and 924 (depending on the number of femtocell APs and floor geometry).
Cellular Stresses and Cytokines Activate Multiple Mitogen‐Activated‐Protein Kinase Kinase Homologues in PC12 and KB Cells (1996)

The identities of the upstream activators of the mitogen-activated protein (MAP) kinase homologues termed stress-activated-protein (SAP) kinase-1 (also known as JNK or SAPK) and SAP kinase-2 (also known as p38, RK and CSBP) were investigated in rat PC12 cells and human KB cells after exposure to cellular stresses and cytokines. In PC12 cells, the same two upstream activators, SAP kinase kinase-1 (SAPKK-1) and SAPKK-2 were activated after exposure to osmotic shock, ultraviolet irradiation or the protein synthesis inhibitor anisomycin, and more weakly in response to sodium arsenite. SAPKK-1 was capable of activating both SAP kinase-1 and SAP kinase-2 and was similar, if not identical, to the previously described MAP kinase kinase homologue MKK4, as judged by immunological criteria and by its ability to be activated by MEK kinase in vitro. In contrast, SAPKK-2 activated SAP kinase-2, but not SAP kinase-1 in vitro. In KB cells, five distinct upstream activators of SAP kinase-1 and SAP kinase-2 were induced, namely SAPKK-1, SAPKK-2, SAPKK-3, SAPKK-4 and SAPKK-5, whose appearance depended on the nature of the stimulus. SAPKK-3, which was strongly induced by every stimulus tested (osmotic shock, ultraviolet irradiation, anisomycin or IL-1), accounted for about 95% of the SAP kinase-2 activator activity in these cells, did not activate SAP kinase-1 and eluted from Mono S at a lower salt concentration than SAPKK-2. SAPKK-4 and SAPKK-5 were also eluted from Mono S at higher NaC1 concentrations than SAPKK-3 and these enzymes activated SAP kinase-1 but not SAP kinase-2. SAPKK-4 was the only SAP kinase-1 activator induced by interleukin-1 or ultraviolet irradiation, while two SAP kinase-1 activators, SAPKK-1 and SAPKK-5, were induced by osmotic shock or anisomycin. SAPKK-2, SAPKK-3, SAPKK-4 and SAPKK-5, were not activated by MEK kinase in vitro, were separable from the major activator(s) of p42 MAP kinase, and were not recognised by anti-MKK4 antibodies. At least two of these enzymes are likely to be novel MAP kinase kinase homologues. Our results demonstrate unexpected complexity in the upstream regulation of stress and cytokine-stimulated kinase cascades and indicate that the selection of the appropriate SAPKK varies with both the stimulus and the cell type.