gebhart/patrepeval huggingface dataset:
Antiperovskite Nitrides CuNCo3–xVx: Highly Efficient and Durable Electrocatalysts for the Oxygen-Evolution Reaction (2019)

Perovskite oxides have attracted much attention for enabling the oxygen-evolution reaction (OER) over the past decades. Nevertheless, their poor conductivity is still a barrier hindering their use. Herein, we report a catalyst prototype of Co-based antiperovskite nitrides CuNCo<sub>3-<i>x</i></sub>V<sub><i>x</i></sub> (0 ≤ <i>x</i> ≤ 1) to be a highly effective OER electrocatalyst. The synthesized CuNCo<sub>3-<i>x</i></sub>V<sub><i>x</i></sub> exhibits greatly enhanced activity and stability toward the OER in alkaline medium. The CuNCo<sub>2.4</sub>V<sub>0.6</sub> shows a mere 235 mV of overpotential to reach 10 mA cm<sup>-2</sup>, which is comparable to that of Ir/C (232 mV). More importantly, the CuNCo<sub>2.4</sub>V<sub>0.6</sub> is more durable than the conventional Ir/C catalyst. The CuNCo<sub>2.4</sub>V<sub>0.6</sub> catalyst enabled a Zn-air battery to exhibit a cycle life of 143 h with a much higher cell efficiency. The V-substituted CuNCo<sub>2.4</sub>V<sub>0.6</sub> provides a higher content of the desirable Co<sup>3+</sup> species in the post-OER catalyst, which ensures a high activity over a long-term operation. With these enhanced effects enabled by the compositional flexibility of CuNCo<sub>3-<i>x</i></sub>V<sub><i>x</i></sub> antiperovskite nitride, a feasible strategy for optimizing an electrocatalyst with tunable properties is provided.
Genome sequence, phylogenetic analysis, and structure-based annotation reveal metabolic potential of Chlorella sp. SLA-04 (2023)

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Draft Genome Sequences of Two ATCC Staphylococcus aureus subsp. aureus Strains (2017)

Draft genome sequences for <i>Staphylococcus aureus</i> subsp. <i>aureus</i> Rosenbach ATCC 14458 and ATCC 27217 strains were investigated. The genome sizes were 2,880,761 bp and 2,759,100 bp, respectively. Strain ATCC 14458 was assembled into 39 contigs, including 3 plasmids, and strain ATCC 27217 was assembled into 25 contigs, including 2 plasmids.
Transformation of the Multivariate Generalized Gaussian Distribution for Image Editing (2017)

Multivariate generalized Gaussian distributions (MGGDs) have aroused a great interest in the image processing community thanks to their ability to describe accurately various image features, such as image gradient fields. However, so far their applicability has been limited by the lack of a transformation between two of these parametric distributions. In this paper, we propose a novel transformation between MGGDs, consisting of an optimal transportation of the second-order statistics and a stochastic-based shape parameter transformation. We employ the proposed transformation between MGGDs for a color transfer and a gradient transfer between images. We also propose a new simultaneous transfer of color and gradient, which we apply for image color correction.
The knowledge complexity of interactive proof-systems (1985)

How much knowledge should be communicated fir proving a theorem T?
Klebsiella pneumoniae Carbapenemase-2 (KPC-2), Substitutions at Ambler Position Asp179, and Resistance to Ceftazidime-Avibactam: Unique Antibiotic-Resistant Phenotypes Emerge from β-Lactamase Protein Engineering (2017)

The emergence of <i>Klebsiella pneumoniae</i> carbapenemases (KPCs), β-lactamases that inactivate "last-line" antibiotics such as imipenem, represents a major challenge to contemporary antibiotic therapies. The combination of ceftazidime (CAZ) and avibactam (AVI), a potent β-lactamase inhibitor, represents an attempt to overcome this formidable threat and to restore the efficacy of the antibiotic against Gram-negative bacteria bearing KPCs. CAZ-AVI-resistant clinical strains expressing KPC variants with substitutions in the Ω-loop are emerging. We engineered 19 KPC-2 variants bearing targeted mutations at amino acid residue Ambler position 179 in <i>Escherichia coli</i> and identified a unique antibiotic resistance phenotype. We focus particularly on the CAZ-AVI resistance of the clinically relevant Asp179Asn variant. Although this variant demonstrated less hydrolytic activity, we demonstrated that there was a prolonged period during which an acyl-enzyme intermediate was present. Using mass spectrometry and transient kinetic analysis, we demonstrated that Asp179Asn "traps" β-lactams, preferentially binding β-lactams longer than AVI owing to a decreased rate of deacylation. Molecular dynamics simulations predict that (i) the Asp179Asn variant confers more flexibility to the Ω-loop and expands the active site significantly; (ii) the catalytic nucleophile, S70, is shifted more than 1.5 Å and rotated more than 90°, altering the hydrogen bond networks; and (iii) E166 is displaced by 2 Å when complexed with ceftazidime. These analyses explain the increased hydrolytic profile of KPC-2 and suggest that the Asp179Asn substitution results in an alternative complex mechanism leading to CAZ-AVI resistance. The future design of novel β-lactams and β-lactamase inhibitors must consider the mechanistic basis of resistance of this and other threatening carbapenemases.<b>IMPORTANCE</b> Antibiotic resistance is emerging at unprecedented rates and threatens to reach crisis levels. One key mechanism of resistance is the breakdown of β-lactam antibiotics by β-lactamase enzymes. KPC-2 is a β-lactamase that inactivates carbapenems and β-lactamase inhibitors (e.g., clavulanate) and is prevalent around the world, including in the United States. Resistance to the new antibiotic ceftazidime-avibactam, which was designed to overcome KPC resistance, had already emerged within a year. Using protein engineering, we uncovered a mechanism by which resistance to this new drug emerges, which could arm scientists with the ability to forestall such resistance to future drugs.
Statin—A Novel Marker of Nonproliferation:Expression in Nonneoplastic Lymphoid Tissues and Follicular Lymphomas (1994)

Statin is a 57 kDa nuclear protein exclusively found in noncycling cells. Its expression in hematolymphoid cells had not been examined previously. The authors studied statin immunoreactivity in nonneoplastic lymphoid tissues from 26 lymph nodes, 3 tonsils, and 2 spleens. Statin was detected primarily in small lymphoid cells and histiocytes, along with such accessory elements as fibroblasts and endothelial cells. The distribution of positive cells showed an inverse correlation with the proliferative activity of the various lymphoid compartments. Statin labeling was also quantified in 15 follicular lymphomas and compared with that in hyperplastic follicles. Although reactivity in benign germinal centers was less than that in neoplastic follicles, this difference did not prove statistically significant. Statin provides an alternative to proliferation-associated parameters, such as Ki-67 and proliferating cell nuclear antigen, in the analysis of hematolymphoid processes and may be helpful in the dissection of their kinetic heterogeneity.
Uranium(VI) Diffusion in Sodium-Montmorillonite at Alkaline pH (2016)

International audience
Synthesis of tetranuclear rhenium(i) tricarbonyl metallacycles (2021)

Re(I) tricarbonyl complexes have received much attention due to their attractive photochemical, electrochemical, and biological properties. Beyond simple mononuclear complexes, multinuclear assemblies offer greater structural diversity and properties. Despite previous reports on the preparation of di-, tri-, or tetranuclear Re(I) tricarbonyl assemblies, the synthesis of these supramolecular structures remains challenging due to overall low yields or tedious purification protocols. Herein, the facile preparation and characterization of tetranuclear Re(I) tricarbonyl metallacycles with a square geometry is reported using a tetrazole-based ligand. The synthesis of the metallacycle was optimized using different metal precursors, solvents, temperatures, and reagent concentrations. Finally, the scope of suitable tetrazole-based ligands was explored to produce several tetranuclear Re(I) tricarbonyl-based metallacycles.
Rapid likelihood calculation of subspace clustered Gaussian components (2002)

In speech recognition systems, computing the likelihoods of the acoustic models is an intensive task. One approach to reduce this cost is to use subspace distributed clustering HMM. Here individual Gaussian components are stored as indices to, and their likelihoods computed from, a set of subspace Gaussian components. This paper examines a scheme for reducing the computational cost of the likelihood calculation when such an HMM system is used. The proposed method identifies and stores frequently occurring partial sums called meta-atom elements and thus avoids computing them repeatedly. The resultant savings in the number of additions is 50% when all Gaussian components are computed or 20% when a Gaussian selection scheme is used.
Correlation of Gleason Scores with Diffusion-Weighted Imaging Findings of Prostate Cancer (2011)

The purpose of our study was to compare the apparent diffusion coefficient (ADC) derived from diffusion-weighted imaging (DWI) of prostate cancer (PCa) patients with three classes of pathological Gleason scores (GS). Patients whose GS met these criteria (GS 3 + 3, GS 3 + 4, and GS 4 + 3) were included in this study. The DWI was performed using b values of 0, 50, and 400 s/mm(2) in 44 patients using an endorectal coil on a 1.5T MRI scanner. The apparent diffusion coefficient (ADC) values were calculated from the DWI data of patients with three different Gleason scores. In patients with a high-grade Gleason score (4 + 3), the ADC values were lower in the peripheral gland tissue, pathologically determined as tumor compared to low grade (3 + 3 and 3 + 4). The mean and standard deviation of the ADC values for patients with GS 3 + 3, GS 3 + 4, and GS 4 + 3 were 1.135 ± 0.119, 0.976 ± 0.103 and 0.831 ± 0.087 mm(2)/sec. The ADC values were statistically significant (P < 0.05) between the three different scores with a trend of decreasing ADC values with increasing Gleason scores by one-way ANOVA method. This study shows that the DWI-derived ADC values may help differentiate aggressive from low-grade PCa.
A Mutation Causing Reduced BK Channel Activity Leads to Cognitive Inpairment and Progressive Cerebellar Ataxia (P5.394) (2016)

Objective: Determine the functional consequences of a BK potassium channel mutation associated with cerebellar degeneration. Background: We described a 16 yo female with delayed milestones and ataxic gait since 18 months. She had cognitive delay, dysarthria, perioral dyskinesias, and nystagmus. MRI scan showed severe cerebellar atrophy. Exome sequencing revealed a de novo variant in one KCNMA1 gene predicting a G354S mutation in the BK channel α subunit. The only other reported BK channel mutation causes enhanced channel activity, epilepsy, and dyskinesias. Methods: Wild type and G354S mutant BK channel α subunits were expressed in cultured HEK293 cells using eukaryotic expression vectors and immuno-localized using anti-α subunit antibodies. Also, mRNAs encoding the WT and G354S mutant were injected into Xenopus oocytes for macroscopic voltage-activated K+ currrent recordings under voltage-clamp during standard step depolarization protocols. Results: There was no difference in cellular distribution between the WT and G354S mutant. In oocytes expressing the G354S mutant alone, macroscopic K+ currents were 11[percnt] of those detected in WT-expressing oocytes, and the kinetics of activation were signficantly slowed compared to WT. Co-injection of the WT and G354S mutant in equal amounts (imitating heterozygous condition) led to currents less than 35[percnt] of WT. K+ currents recorded from dual-injected oocytes showed slower activation than WT. Unitary single channels recordings showed circa 90[percnt] decrease in the G354S mutant channel conductance relative to WT Thus, co-injection of G354S mutant together with WT α subunit reduced the conductance and slowed activation of BK channels out of proportion to abundance of subunits. Conclusions: The BK channel mutant G354S has a dominant negative effect on channel function. Reduced BK channel activity and delayed activation lead to progressive cerebellar atrophy and ataxia, possibly through damaging delays in repolarization. Drugs that increase BK channel activity may be a rational approach for treating this disease.
Advances in Fuzzy Logic Control for Lateral Vehicle Guidance (1994)

A candidate for intelligent control for lateral guidance of a vehicle is a fuzzy logic controller (FLC). The details of the most recent FLC with a rule base derived from heuristics and designer insight to the problem at hand, as well as a method for estimating a projected lateral displacement are presented along with simulation results. The structure of this FLC is suited to incorporate human knowledge about the steering operation by its choice of inputs and outputs of the FLC which are natural to human steering operation. In addition, a method that makes use of preview information regarding upcoming road curvature is developed and simulated based on human steering operation. This method projects an estimate of the lateral error relative to the reference track at a specified look - ahead time. Simulations imply that there exists an optimal look - ahead time. Too short a time does not make full use of the preview information, while too long a time results in inaccurate estimates of future lateral error, degrading the performance. Successof the FLC strongly depends on the set of rules provided by the designer. It is extremely important to have methodologies for rule development. Therefore, a methodology is considered for automatically generating a fuzzy rule base controller, specifically, a Neural - Network Driven Fuzzy Logic Controller (NNDFLC). This process automates the design of control parameters and uses a clustering technique to cluster the space of inputs to the controller in order to take advantage of local characteristics in the reasoning of the control outputs. Given enough input/output data to train the neural networks involved, simulations show its success. However, this method requires the generation of a complete set of training data, covering the entire space of inputs to the controller. This is an important factor in the design of the NNDFLC with regard to the convergence of control parameters in the learning process and for taking advantage of the clustering features of the controller.
Ultra sensitive and compact VCSEL-based biosensor for detection of protein interactions and dengue antibodies (2004)

We report a label-free biosensor system that consists of a tunable VCSEL, a plastic guided mode resonant filter and two pin detectors. The biosensor has'demonstrated the sensitivity of detecting antigen proteins concentration as low as Ipg/ml (6.7fM) and antibodies to dengue virus.
Array BP-XOR Codes for Parallel Matrix Multiplication using Hierarchical Computing. (2019)

This study presents a novel coded computation technique for parallel matrix-matrix product computation using hierarchical compute architectures that outperforms well known previous strategies in terms of total end-to-end execution time.The proposed method uses array codes to achieve this performance by distributing the encoding operation over the cluster(slave) nodes at the expense of increased master-slave communication. The matrix multiplication is performed using MDS array Belief Propagation (BP)-decodable codes based on pure XOR operations. The proposed scheme is shown to be configurable and suited for modern hierarchical compute architectures equipped with multiple nodes, each having multiple, independent and less capable processing units. In addition, to address scaling number of stragglers, asymptotic versions of the code is used and latency analysis is conducted. We shall demonstrate that the proposed scheme achieves order-optimal computation in both the sublinear as well as the linear regime in the size of the computed product from an end-to-end delay perspective while ensuring acceptable communication requirements that can be addressed by today's high speed network link infrastructures.
Design Optimization of Turbo-Machinery Components With Independent FEA and CFD Tools in an Optimization Software Environment: A Mid-Span Shroud Ring Study Case (2011)

Shrouds are important for damping vibrations in gas turbine blades. In modern industrial high-output, high-efficiency engines, long turbine blades can require the use of a mid-span or partial-span damping ring. However, the inclusion of a mid-span damping shroud, or “snubber,” can have negative effects on the aerodynamic performance of the gas turbine stage and engine. Therefore, a method of iterative study and optimization was applied to minimize the drag force caused by the snubber, while maximizing the structural life of the blade. The approach used integrated design environment software to perform parametric studies of the design space in preparation for optimization of the blade snubber geometry. The drivers employed in Isight 4.0/4.5 [9] optimization software carried out the parametric study and reported the results to the designer. Considering these results, the designer chose the initial seeding geometry of the optimization driver which greatly reduced analysis time and the time required to reach the design objectives. This approach provides an integrated design workflow and facilitates parametric studies of advanced gas turbine blade component geometry, and the optimization of the component to meet targets of minimized aerodynamic drag force and maximized low-cycle fatigue life, goals crucial to the development of an advanced and efficient power generation gas turbine.
Impedance spectrum for the PEP-II RF cavity (2002)

The impedance spectrum presented by the PEP-II RF cavity to the beam is calculated using a 3D MAFIA model which includes the damping waveguides and the input coupler. The simulation assumes that all the ports leading out of the cavity, including the beam pipes, are terminated in matched loads. The effect of the external loading on the longitudinal impedances will be examined. This study takes into account the input coupler damping which has not been considered in previous calculations.
Supplementary Figure S3 from Blocking Angiopoietin-2 Promotes Vascular Damage and Growth Inhibition in Mouse Tumors Treated with Small Doses of Radiation (2023)

&lt;p&gt;Supplementary Figure S3&lt;/p&gt;
The Antiviral Activity of the CXCR4 Antagonist AMD3100 Is Independent of the Cytokine-Induced CXCR4/HIV Coreceptor Expression Level (2003)

The chemokine receptor CXCR4 is the main coreceptor used by T-tropic X4 HIV-1 strains to infect its target T cells. It has been proven that the CXCR4 expression level in T cells is strongly up-regulated by interleukin (IL)-4, a Th2-type cytokine that is secreted preferentially in HIV-infected patients in a later stage of disease. This results in an enhancement of HIV-1 replication in CD4+ T-lymphocytes. We have now evaluated the potency of the CXCR4 antagonist AMD3100 in phytohemagglutinin (PHA)/IL-2- versus PHA/IL-4-activated T cells in order to determine whether the compound has comparable CXCR4-antagonistic and anti-HIV-1 effects under these different cytokine treatments. We analyzed the CXCR4 expression level and the dose-dependent inhibition of CXCR4 expression by AMD3100, by monitoring the binding of an anti-CXCR4 monoclonal antibody (clone 12G5). We also determined stromal cell-derived factor (SDF)-1-induced intracellular calcium signaling and HIV-1 replication in these cells in the absence and presence of AMD3100. The CXCR4 expression level in PHA/IL-4-stimulated cells was much higher than in PHA/IL-2-stimulated cells. However, the potency of the bicyclam AMD3100 to block anti-CXCR4 mAb binding, SDF-1-induced intracellular calcium signaling, and HIV-1 replication of the X4 NL4.3 strain and three primary isolates remained unchanged. Our data indicate that CXCR4 antagonists such as AMD3100 act independently of the HIV-1 coreceptor expression level. These compounds should therefore be useful in suppressing HIV-1 infection in all stages of the disease.
Peyronie’s Disease: Pathophysiology and Medical Therapy (2004)

Peyronie's disease is an acquired benign condition with potential significant impact on quality of life that can include pain, penile deformity, and erectile dysfunction (ED). Modern studies have shown the disease to be prevalent. Once thought to resolve spontaneously, it is now known that the disease consists of an active phase and a mature phase, with resolution of pain and rarely resolution of penile deformity. The disease is now known to be caused by a "trapped" inflammatory response resulting from minor trauma, hematoma formation with fibrin deposition, and resultant cytokine activity. The cytokine transforming growth factor-β1 (TGF-(β1) has demonstrated particular importance and is used in creating animal models to study the disease. This abnormal immune response may have a genetic predisposition. Modern molecular techniques, genomics, and proteomics are being applied to better understand the pathways that lead to Peyronie's disease.
ASP-2/Trans-sialidase chimeric protein induces robust protective immunity in experimental models of Chagas’ disease (2023)

Immunization with the Amastigote Surface Protein-2 (ASP-2) and Trans-sialidase (TS) antigens either in the form of recombinant protein, encoded in plasmids or human adenovirus 5 (hAd5) confers robust protection against various lineages of Trypanosoma cruzi. Herein we generated a chimeric protein containing the most immunogenic regions for T and B cells from TS and ASP-2 (TRASP) and evaluated its immunogenicity in comparison with our standard protocol of heterologous prime-boost using plasmids and hAd5. Mice immunized with TRASP protein associated to Poly-ICLC (Hiltonol) were highly resistant to challenge with T. cruzi, showing a large decrease in tissue parasitism, parasitemia and no lethality. This protection lasted for at least 3 months after the last boost of immunization, being equivalent to the protection induced by DNA/hAd5 protocol. TRASP induced high levels of T. cruzi-specific antibodies and IFNγ-producing T cells and protection was primarily mediated by CD8<sup>+</sup> T cells and IFN-γ. We also evaluated the toxicity, immunogenicity, and efficacy of TRASP and DNA/hAd5 formulations in dogs. Mild collateral effects were detected at the site of vaccine inoculation. While the chimeric protein associated with Poly-ICLC induced high levels of antibodies and CD4<sup>+</sup> T cell responses, the DNA/hAd5 induced no antibodies, but a strong CD8<sup>+</sup> T cell response. Immunization with either vaccine protected dogs against challenge with T. cruzi. Despite the similar efficacy, we conclude that moving ahead with TRASP together with Hiltonol is advantageous over the DNA/hAd5 vaccine due to pre-existing immunity to the adenovirus vector, as well as the cost-benefit for development and large-scale production.