gebhart/patrepeval huggingface dataset:
SIRT3 is a Mitochondrial Tumor Suppressor and Genetic Loss Results in a Murine Model for ER/PR Positive Mammary Tumors Connecting Metabolism and Carcinogenesis (2011)

Abstract : The last year, which was funded by the DOD collaborative Breast Cancer Idea Award, has resulted in several important translational and basic science findings. Specifically, the most significant finding during the research period were: (1) the identification of MnSOD as a legitimate Sirt3 deacetylation target that for the first time shows that post-translation modifications of mitochondrial proteins plays a role in mitochondrial function (published in Molecular Cell); (2) that Sirt3 is first mitochondrial tumor suppressor protein that may play a role in the development of human luminal B breast malignancies; (3) that Sirt3 regulates the ATP synthase complex and the aberrant regulation of ATP synthase may play a role, at least in part, in breast carcinogenesis; (4) that tumors lacking Sirt3 may require the dysregulation of HIF-1 suggesting that there may be a subgroup of human tumors that may response to HIF-1 inhibitors in both chemoprevention as potentially as anti-cancer agents; and (5) that MnSOD function as both a molecular mechanism in breast cancers as well as the suggestion that agents that activate MnSOD may be agents for chemoprevention.
First-Principles Study of the Ligand Substituent Effect on ORR Catalysis by Metallocorroles (2020)

Metallocorroles (M-N-C) and especially Co-corroles are some of the best molecular catalyst alternatives to the expensive platinum-group metals (PGM) for oxygen reduction reaction (ORR) catalysis in polymer electrolyte membrane (PEM) fuel cells. In this work, we study the M-N-C corroles (M = Mn, Fe, Co) and the ligand (L) substitution (L-M-N-C, L = H, CH3, CF3, and imidazole) on the metal site as ORR catalysts based on the free energies of the *OOH, *O, and *OH ORR pathway intermediates. We also examine the influence of the basis set size, density functional theory exchange-correlation functional, and solvent environment on the calculated energies for the *OOH, *O, and *OH intermediates. We find that improved catalytic performance is expected in the ligand-substituted Mn-N-C that can be further fine-tuned by changing the nature of the ligand and the substituent group on the corrole. By contrast, the catalytic activity of the Co-corrole is decreased by the ligand substitution. The obtained ORR energetics are sensitive to basis set size, exchange-correlation functional, and solvent environment with the best agreement with the experiment obtained for large (6-311++G**) basis set, PBE functional, and gas-phase ORR intermediate calculations.
A modular tracking system for far infrared pedestrian recognition (2005)

This paper describes a modular tracking system designed to improve the performance of a pedestrian detector. The tracking system consists of two modules, a labeler and a predictor. The former associates a tracking identifier to each pedestrian, keeping memory of the past history; this is achieved by merging the detector and predictor outputs combined with data about vehicle motion. The predictor, basically a Kalman filter, estimates the new pedestrian position by observing his previous movements. Its output helps the labeler to improve the match between the pedestrians detected in the new frame and those observed in the previous shots (feedback). If a pedestrian is occluded by some obstacle for a short while, the system continues tracking its movement using motion parameters. Moreover, it is able to reassign the same tracking ID in case the occlusion disappears in a short time. This behavior helps to correct temporary mis-recognitions that occur when the detector fails. The system has been tested using a quantitative performance evaluation tool, giving promising results.
Imperfect information flow (2002)

The view that computers are information processors is commonplace. They are used, for the most part successfully, throughout our society, as reliable links in the transmission of information and knowledge. Yet the formulation of a precise, qualitative conception of information and a theory of the transmission of information has proved elusive, despite the many other successes of computer science. The authors set out the motivation for and a skeleton of a new mathematical model of information flow, one that is compatible with less than perfect flow.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Optical Dielectric Function Modeling and Electronic Band Lineup Estimation of Amorphous High-k LaGdO3Films (2012)

Optical constants of pulsed laser ablated amorphous high-k LaGdO3 (a-LGO) thin films on quartz (0001) substrates were measured and analyzed. Refractive index (n ∼ 2.05–2.29) and extinction coefficient (k ∼ 0.004–0.017) were parameterized by analysis of the UV/Visible transmission spectra employing a Cauchy-Urbach dispersion model in the 300–750 nm spectral window and confirmed the applicability of this model in this wavelength region. The composition and chemistry of these dielectric films were studied by utilizing ATR-FTIR spectroscopy. The deduced pinning factor (S), 0.5 suggests that LGO/Si is an interacting interface. The parameter S was applied in the Cowley-Sze relation to estimate the interface trap density (Dit) to be 1.08 × 1013 states cm−2 eV−1. As grown LGO/p-Si heterojunction showed a downward Fermi-level (FL) pinning of 0.39 ± 0.02 eV. A complete Type I straddled band lineup of this gate dielectric/semiconductor heterostructure was determined by applying the charge neutrality level (CNL) model. The CNL of LGO was deduced to be 2.11 ± 0.05 eV above valence band maximum.
Differences in SARS-CoV-2 Vaccine Response Dynamics Between Class-I- and Class-II-Specific T-Cell Receptors in Inflammatory Bowel Disease (2022)

T-cells specifically bind antigens to induce adaptive immune responses using highly specific molecular recognition, and a diverse T-cell repertoire with expansion of antigen-specific clones can indicate robust immune responses after infection or vaccination. For patients with inflammatory bowel disease (IBD), a spectrum of chronic intestinal inflammatory diseases usually requiring immunomodulatory treatment, the T-cell response has not been well characterized. Understanding the patient factors that result in strong vaccination responses is critical to guiding vaccination schedules and identifying mechanisms of T-cell responses in IBD and other immune-mediated conditions. Here we used T-cell receptor sequencing to show that T-cell responses in an IBD cohort were influenced by demographic and immune factors, relative to a control cohort of health care workers (HCWs). Subjects were sampled at the time of SARS-CoV-2 vaccination, and longitudinally afterwards; TCR Vβ gene repertoires were sequenced and analyzed for COVID-19-specific clones. We observed significant differences in the overall strength of the T-cell response by age and vaccine type. We further stratified the T-cell response into Class-I- and Class-II-specific responses, showing that Ad26.COV2.S vector vaccine induced Class-I-biased T-cell responses, whereas mRNA vaccine types led to different responses, with mRNA-1273 vaccine inducing a more Class-I-deficient T-cell response compared to BNT162b2. Finally, we showed that these T-cell patterns were consistent with antibody levels from the same patients. Our results account for the surprising success of vaccination in nominally immuno-compromised IBD patients, while suggesting that a subset of IBD patients prone to deficiencies in T-cell response may warrant enhanced booster protocols.
High density bump-less Cu-Cu bonding with enhanced quality achieved by pre-bonding temporary passivation for 3D wafer stacking (2011)

Face-to-face stacking of wafer-on-wafer is demonstrated successfully using bump-less Cu-Cu bonding. Using self-assembled monolayer passivation and in-situ desorption, Cu-Cu bond is enhanced in shear strength and bonding uniformity. Excellent specific contact resistance of 0.30 Ω.μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> is obtained. Continuous daisy chain of at least 6,000 contacts at 15μm pitch is connected successfully. This provides inter-IC connection density of 4.4 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> suitable for wafer level 3D integration to augment Moore Law's scaling.
Genetic organization of methylamine utilization genes from Methylobacterium extorquens AM1 (1991)

An isolated 5.2-kb fragment of Methylobacterium extorquens AM1 DNA was found to contain a gene cluster involved in methylamine utilization. Analysis of polypeptides synthesized in an Escherichia coli T7 expression system showed that five genes were present. Two of the genes encoded the large and small subunits of methylamine dehydrogenase, and a third encoded amicyanin, the presumed electron acceptor for methylamine dehydrogenase, but the function of the other two genes is not known. The order on the 5.2-kb fragment was found to be large-subunit gene, the two genes of unknown function, small-subunit gene, amicyanin gene. The gene for azurin, another possible electron acceptor in methylamine oxidation, does not appear to be present within this cluster of methylamine utilization genes.
Smooth vanadium-nitride layers created on silicon substrates by pulse laser deposition method (1998)

Pulsed Laser Deposition (PLD) of vanadium-nitride (V<SUB>2</SUB>N, V<SUB>10</SUB>N<SUB>7</SUB>) films on Si substrates have been carried out under influence of series of UV (excimer) laser pulses ((lambda) equals 308 nm, (tau) <SUB>FWHM</SUB> equals 25 ns) in NH<SUB>3</SUB> atmosphere of a few mbars. In the reaction cell the Si target has been placed to be parallel to V sheet at angle of 45 degree(s) to the incident laser beam, and the plasma plume induced by laser pulse reached the target close perpendicularly. The number of shots at fluxes of 30 J/cm<SUP>2</SUP> were varied between 100 and 5000. Rutherford Back- Scattering studies revealed that under influence of laser pulses at Si layer V<SUB>2</SUB>N layers of 100 nm thickness were formed, while the composition of the layer closer atmosphere was V<SUB>10</SUB>N<SUB>7</SUB> of 50 nm thickness (in average). In some cases we observed layers of VNCO and V<SUB>10</SUB>N<SUB>7</SUB>C<SUB>5</SUB>. Atomic Force Microscopy measurements revealed a formation of quite smooth surfaces with roughness of less than 10 nm. A characteristic wave-like structure with period of 3 - 5 nm was able to be observed in some cases. XPS examinations showed the existence of well defined peaks of V(2p) lines at 516 eV and 513 eV. Also we observed lines of N(1s) at 397 eV, O(1s) at 529 eV and C(1s) at 284 eV. From these investigations it might be concluded that PLD technique allows growing smooth VN layers on Si with a little, but measurable contamination of carbon and oxygen.
Supplementary Figure 2 from Epigenetic Deregulation Across Chromosome 2q14.2 Differentiates Normal from Prostate Cancer and Provides a Regional Panel of Novel DNA Methylation Cancer Biomarkers (2023)

Supplementary Figure 2 from Epigenetic Deregulation Across Chromosome 2q14.2 Differentiates Normal from Prostate Cancer and Provides a Regional Panel of Novel DNA Methylation Cancer Biomarkers
Verification of communication protocols using data flow analysis (1996)

In this paper we demonstrate the effectiveness of data flow analysis for verifying requirements of communication protocols. Data flow analysis is a static analysis method for increasing confidence in the correctness of software systems by automatically verifying that a given software artifact (e.g., design or code) must behave consistently with a specified requirement. In this case study, we apply the FLAVERS data flow analysis tool to pseudocode designs of the three way handshake connection establishment protocol and of the alternating bit protocol and prove that the behavior of the pseudocode is consistent with protocol behavioral requirement specifications. We show how FLAVERS is a particularly effective because it is computationally inexpensive, requires minimal human interaction, and is a general approach that can be applied incrementally until the desired accuracy is achieved. In addition, we show how assumptions about the environment in which a software system is executed can be incorporated into the analysis, using message losses as an example. We present experimental results and derive some guidelines about the classes of protocol requirement specifications that may be amenable to verification using FLAVERS.
Recombinant measles virus requiring an exogenous protease for activation of infectivity (2000)

Proteolytic cleavage of the fusion protein (F) is an important control mechanism of the biological activity of paramyxoviruses. The sequence R-R-H-K-R(112) at the cleavage site of the F protein of measles virus (MV) was altered by site-directed mutagenesis to R-N-H-N-R(112), which is not recognized by the ubiquitous cellular protease furin. When transiently expressed in cell cultures standard F protein was cleaved, whereas the mutant remained in the uncleaved form. Syncytium formation by the mutant that was analysed after coexpression with haemagglutinin protein depended on the presence of trypsin. Recombinant MV containing the mutation required trypsin activation for fusion and infectivity in cell culture. Intranasal infection of transgenic mice susceptible to MV infection (Ifnar(tm)-CD46Ge) resulted in a moderately productive infection and inflammation of the lung. In contrast to parental virus, intracerebral inoculation did not induce neural disease. The possible effects of the change in cleavage activation on tissue tropism and pathogenicity are discussed.
A vital role of tubulin-tyrosine-ligase for neuronal organization (2005)

Tubulin is subject to a special cycle of detyrosination/tyrosination in which the C-terminal tyrosine of alpha-tubulin is cyclically removed by a carboxypeptidase and readded by a tubulin-tyrosine-ligase (TTL). This tyrosination cycle is conserved in evolution, yet its physiological importance is unknown. Here, we find that TTL suppression in mice causes perinatal death. A minor pool of tyrosinated (Tyr-)tubulin persists in TTL null tissues, being present mainly in dividing TTL null cells where it originates from tubulin synthesis, but it is lacking in postmitotic TTL null cells such as neurons, which is apparently deleterious because early death in TTL null mice is, at least in part, accounted for by a disorganization of neuronal networks, including a disruption of the cortico-thalamic loop. Correlatively, cultured TTL null neurons display morphogenetic anomalies including an accelerated and erratic time course of neurite outgrowth and a premature axonal differentiation. These anomalies may involve a mislocalization of CLIP170, which we find lacking in neurite extensions and growth cones of TTL null neurons. Our results demonstrate a vital role of TTL for neuronal organization and suggest a requirement of Tyr-tubulin for proper control of neurite extensions.
<title>New fast implementation of cellular array for morphological filters, stack filters, and median filters</title> (1993)

Cellular Array are very important and very suitable in image processing. The local neighborhood operations can be implemented in the cellular array to increase their speed. Recently, the morphological filters and stack filters received very much attention. They are very appropriate to be implemented in the cellular array. In this paper, we use a very powerful method called threshold decomposition to implement these filters in the cellular array. Threshold decomposition provides a very powerful method to transform gray filtering into binary filtering. The filters includes median, order-statistic(OS) and morphological filters. Filtering of a M— level image by threshold decomposition, requires three stages: (1) thresholding (2) binary filtering (3) reconstruction. To increase the performance of the processing element in the array, a fast reconstructor with (2M-2-Log 2M) half adders was developed.
Supplementary Figure 9 from FANCJ Localization by Mismatch Repair Is Vital to Maintain Genomic Integrity after UV Irradiation (2023)

&lt;p&gt;PDF file - 88K, Supplemental Figure 9. FANCJ expression promotes UV induced GFP-polh foci formation in U2OS cells.&lt;/p&gt;
The role of mitochondrial ROS in antibacterial immunity (2017)

Reactive oxygen species (ROS) are essential participants of various innate immune cell responses against microorganisms and are also involved in many cellular regulatory pathways. It was believed that the main pool of ROS in the innate immune cells is generated by the NADPH oxidase enzymatic complex. However, it was discovered recently that mitochondrial ROS (mtROS) are equally important for the functioning of the immune system. mtROS play an important role in the development of the antimicrobial innate immune responses. The present mini-review summarizes the most recent data on the role of mtROS in the antibacterial immunity. The principles of mtROS formation and possible mechanisms of their generation under the activation of innate immunity are highlighted in this review. We also speculate on the possibilities of using activators of mtROS production in clinical practice.
Algal biosensors for aquatic ecosystems monitoring (2006)

The harmful effect of toxic chemicals on natural ecosystems has led to an increasing demand for early-warning systems to detect those toxicants at very low concentrations levels. Whole-cell biosensors based either on chlorophyll fluorescence or enzyme (phosphatase and esterase) inhibition are constructed for real-time detection and on-line monitoring. Results show that these devices are sensitive to heavy metals and pesticides. The system allows the cells to operate in their natural environment which favours long term stability and reflects the toxic action mechanism providing therefore an ecological interest.
Neonatal NET-inhibitory factor and related peptides inhibit neutrophil extracellular trap formation (2016)

Neutrophil granulocytes, also called polymorphonuclear leukocytes (PMNs), extrude molecular lattices of decondensed chromatin studded with histones, granule enzymes, and antimicrobial peptides that are referred to as neutrophil extracellular traps (NETs). NETs capture and contain bacteria, viruses, and other pathogens. Nevertheless, experimental evidence indicates that NETs also cause inflammatory vascular and tissue damage, suggesting that identifying pathways that inhibit NET formation may have therapeutic implications. Here, we determined that neonatal NET-inhibitory factor (nNIF) is an inhibitor of NET formation in umbilical cord blood. In human neonatal and adult neutrophils, nNIF inhibits key terminal events in NET formation, including peptidyl arginine deiminase 4 (PAD4) activity, neutrophil nuclear histone citrullination, and nuclear decondensation. We also identified additional nNIF-related peptides (NRPs) that inhibit NET formation. nNIFs and NRPs blocked NET formation induced by pathogens, microbial toxins, and pharmacologic agonists in vitro and in mouse models of infection and systemic inflammation, and they improved mortality in murine models of systemic inflammation, which are associated with NET-induced collateral tissue injury. The identification of NRPs as neutrophil modulators that selectively interrupt NET generation at critical steps suggests their potential as therapeutic agents. Furthermore, our results indicate that nNIF may be an important regulator of NET formation in fetal and neonatal inflammation.
Intrinsic Differences between Oral and Skin Keratinocytes (2014)

Keratinocytes cover both the skin and some oral mucosa, but the morphology of each tissue and the behavior of the keratinocytes from these two sites are different. One significant dissimilarity between the two sites is the response to injury. Oral mucosal wounds heal faster and with less inflammation than equivalent cutaneous wounds. We hypothesized that oral and skin keratinocytes might have intrinsic differences at baseline as well as in the response to injury, and that such differences would be reflected in gene expression profiles.
DNA photocleavage by an osmium(ii) complex in the PDT window (2010)

The extended pi-delocalization of dppn (benzo[i]dipyrido[3,2-a:2,3-c]phenazine) results in a (3)pipi* state as the lowest triplet excited state in [Os(bpy)(2)(dppn)](2+) (bpy = 2,2'-bipyridine), which generates a (1)O(2) quantum yield of 0.42. Together with its (3)MLCT absorption, this new osmium complex shows efficient DNA cleavage under irradiation of lambda(irr) > or = 645 nm.
Structural studies at elevated pressure and reduced temperatures using synchrotron radiation: application tocerium)/sub 8/lanthanum)/sub 1/thorium)/sub 1/ (1983)

A facility is described which has been developed at the Stanford Synchrotron Radiation Laboratory for the rapid acquisition of structural information from a sample pressurized in a diamond-anvil cell and cooled to cryogenic temperatures. The system employs a closed-cycle He-refrigerator which can be continuously operated, independent of any liquid cryogens, from a remote control station; the sample temperature can be maintained constant to better than 0.05 K. The compressive contact force between the diamond anvils, and hence the sample pressure, is also externally controlled, thereby providing remote control capabilities for both the pressure and the temperature. Preliminary data on the critical points and volume changes associated with the pressure/temperature induced isomorphic phase transition in Ce/sub 8/La/sub 1/Th/sub 1/ are presented.
The contrast between clear and plain speaking style for Mandarin tones (2021)

We examine the acoustic characteristics of clear and plain conversational productions of Mandarin tones. Twenty-one native Mandarin speakers were asked to produce a selection of Mandarin words in both plain and clear speaking styles. Several tokens were gathered for each of the four tones giving a total of 2045 productions. Six critical tonal cues were computed for each production: fundamental frequency (F0) mean, slope, and second derivative, duration, mean intensity, and a binary variable coding whether the production involved creaky voice. A linear mixed-effects regression model was used to explore how these cues changed with respect to the clear versus plain distinction for each tone, with speaking style as the fixed effect and speaker being a random effect. The strongest effects detected were that duration and mean intensity increased in clear speech across speakers and tones. Tones 2 and 3 increased in mean F0 and Tone 4 increased its slope. An additional finding was that, for contour tones, speakers accomplished the increase in duration by stretching out the tone contours in time while largely not changing the F0 range. These results are discussed in terms of signal-based (affecting all tones) and code-based (enhancing contrast between tones) change.
Human chorionic gonadotropin and growth factors at the embryonic–endometrial interface control leukemia inhibitory factor (LIF) and interleukin 6 (IL-6) secretion by human endometrial epithelium (2004)

Through hCG, the blastocyst may be involved in the control of its implantation (via an increase of proimplantatory LIF) and tolerance (via an inhibition of proinflammatory IL-6). Other growth factors present at the embryonic-endometrial interface are also involved in the control of LIF and IL-6 endometrial secretion.
Binary role of an ylide in formation of a terminal methylidene complex of niobium (2014)

The first structurally characterized niobium(v) complex possessing a terminal methylidene ligand is reported in high yield from the reaction of [(Ar'O)2Nb(CH3)2Cl] (Ar' = (2,6-CHPh2)2-4-tBu-C6H2) and two equivalents of H2CPPh3.