gebhart/patrepeval huggingface dataset:
Host functions used by hepatitis B virus to complete its life cycle: Implications for developing host-targeting agents to treat chronic hepatitis B (2018)

Similar to other mammalian viruses, the life cycle of hepatitis B virus (HBV) is heavily dependent upon and regulated by cellular (host) functions. These cellular functions can be generally placed in to two categories: (a) intrinsic host restriction factors and innate defenses, which must be evaded or repressed by the virus; and (b) gene products that provide functions necessary for the virus to complete its life cycle. Some of these functions may apply to all viruses, but some may be specific to HBV. In certain cases, the virus may depend upon the host function much more than does the host itself. Knowing which host functions regulate the different steps of a virus' life cycle, can lead to new antiviral targets and help in developing novel treatment strategies, in addition to improving a fundamental understanding of viral pathogenesis. Therefore, in this review we will discuss known host factors which influence key steps of HBV life cycle, and further elucidate therapeutic interventions targeting host-HBV interactions.
Effects of vitamin D-induced chronic hypercalcemia on rat renal cortical plasma membranes and mitochondria (1987)

Increases in intracellular and mitochondrial calcium content that accompany ischemic and toxic acute renal failure have been suggested to mediate renal tubular cell injury and dysfunction, but the mechanism(s) are unknown. We studied the effects of in vivo vitamin D-induced chronic hypercalcemia on rat renal cortical brush-border and basolateral membranes and mitochondria. In the brush-border membrane, hypercalcemia caused significant decreases in alkaline phosphatase-specific activity, total phospholipid molar content, and phosphatidylserine percent molar composition and increases in the cholesterol-to-total phospholipid molar ratio and phosphatidylinositol percent molar composition. In the basolateral membrane, hypercalcemia caused significant decreases in Na+-K+-ATPase-specific activity and total phospholipid molar content and increases in the cholesterol-to-total phospholipid molar ratio and phosphatidylinositol 4,5-bisphosphate percent molar composition. In the mitochondria, hypercalcemia caused a mild increase in the mitochondrial calcium content, but no alterations in succinic dehydrogenase-specific activity, succinate-, ADP-, or uncoupler-induced respiration. Thus hypercalcemia caused alterations in brush-border and basolateral membrane enzyme activity and lipid composition, but no functional changes were detected in mitochondria. These hypercalcemia-induced plasma membrane biochemical alterations may be markers of early cell injury and suggest a role for calcium in causing or predisposing to renal tubular cell injury.
Manganese-Enhanced MRI in Patients with Multiple Sclerosis (2020)

This work demonstrates the first use of a manganese-based contrast agent to enhance MS lesions on MR imaging. Multiple sclerosis lesions were enhanced with a temporal and spatial profile distinct from that of gadolinium. Further experiments are necessary to uncover the mechanism of manganese contrast enhancement as well as cell-specific uptake.
Electronic configuration and nucleophilicity of carbon free radicals. α-Alkoxyalkyl, α-alkoxycarbonyl, and cycloalkyl radicals (1974)

The nucleophilicity of carbon free radicals is strongly affected by the hybridization of the orbital occupied by the odd electron. An α-alkoxy-group increases the nucleophilicity of π-type alkyl radicals and decreases that of σ-type acyl radicals. The cyclopropyl radical, which has the highest s character, is the least nucleophilic of the cycloalkyl radicals. The general behaviour is discussed in terms of a transition state similar to a charge-transfer complex.
Electronic and Ionic Transport in Polymers (1988)

Abstract : We have prepared and studied a variety of electroactive polymers including self-doped conducting polypyrroles, high molecular weight poly(3- alkylthiophenes), new polymers containing both various aryl groups along the main chain and solublizing substituents, electroactive polymers containing main chain transition metal complexes, fluoropolymers for high permittivity materials, liquid crystalline polymers and polymers containing PN linkages in the main chain. We have also prepared films and/or fibers of these materials both pure and as blends and molecular composites (using polyelectrolytes). We have used spectroscopy, electrochemistry and microgravimetry to study ion transport and redox switching in these systems and have developed in situ techniques to monitor and quantify this ion transport. We have used theoretical calculations (PRDDO and ab initio) to study HOMOLUMO gaps, spin densities, structures and conformations in monomers and oligomers and have used these methods and Extended Huekel calculations to estimate band gaps and to help understand substituent effects in these polymers. Keywords: Electroactive polymers; Polythiophenes; Polypyrroles; Ion transport; Molecular composites; Molecular orbital calculations; Organometallic polymers; Liquid crystalline polymers.
p-Phosphonic acid calix[8]arene assisted dispersion and stabilisation of pea-pod C60@multi-walled carbon nanotubes in water (2014)

A facile approach has been developed for non-covalently stabilising pristine C60 and multi-walled carbon nanotubes (MWCNTs) in water in the presence of p-phosphonic acid calix[8]arene, along with the formation of a 'pea-pod' encapsulation of the fullerene inside the MWCNTs. Aqueous dispersions of the different carbon nano-materials are readily decorated with palladium nanoparticles.
Bacterial chemotaxis towards aromatic hydrocarbons in Pseudomonas (2011)

Bacterial chemotaxis is an adaptive behaviour, which requires sophisticated information-processing capabilities that cause motile bacteria to either move towards or flee from chemicals. Pseudomonas putida DOT-T1E exhibits the capability to move towards different aromatic hydrocarbons present at a wide range of concentrations. The chemotactic response is mediated by the McpT chemoreceptor encoded by the pGRT1 megaplasmid. Two alleles of mcpT are borne on this plasmid and inactivation of either one led to loss of this chemotactic phenotype. Cloning of mcpT into a plasmid complemented not only the mcpT mutants but also its transfer to other Pseudomonas conferred chemotactic response to high concentrations of toluene and other chemicals. Therefore, the phenomenon of chemotaxis towards toxic compounds at high concentrations is gene-dose dependent. In vitro experiments show that McpT is methylated by CheR and McpT net methylation was diminished in the presence of hydrocarbons, what influences chemotactic movement towards these chemicals.
Synthesis, Characterization, and Physical Properties of Cyclometalated Iridium(III) Complexes with 2-Phenylthiophene or 2-Phenylfuran Ligands (2009)

Tris-cyclometalated Ir(III) complexes bearing C∧S or C∧O ligands have been synthesized and characterized, and their redox behavior, absorption spectra, and luminescence properties are reported. The four Ir(C∧S)- and Ir(C∧O)-type complexes studied here are mer-Ir(dfppz)2(ptp), mer-Ir(ppy)2(ptp), mer-Ir(dfppz)2(pf), and mer-Ir(ppy)2(pf) [dfppz = 1-(2,4-difluorophenyl)pyrazole; ppy = 2-phenylpyridine; ptp = 2-phenylthiophene; pf = 2-phenylfuran]. While no C∧S or C∧O cyclometalation took place using conventional synthetic methods, transmetalation of the chloro-bridged dimeric iridium complexes [(dfppz)2Ir(μ-Cl)2(dfppz)2] and [(ppy)2Ir(μ-Cl)2(ppy)2] with the organozincs of 2-phenylthiophene or 2-phenylfuran afforded the four anticipated complexes in good yields. X-ray structural analyses on complexes Ir(dfppz)2(ptp) and Ir(dfppz)2(pf) were established to confirm their molecular structures. The Ir−C (ptp) (2.121(13) Å) and Ir−C (pf) (2.08(3) Å) bonds are much longer than the other two Ir−C (dfppz) bonds in their respective structures and are also markedly longer than the value of 2.051(2) Å reported for the Ir−C bond trans to a phenyl group in mer-Ir(ppz)3, implying weaker binding of 2-phenylthiophene and 2-phenylfuran to Ir(III) compared to typical C∧N ligands. All of the complexes show reversible oxidation between 0.21 and 0.70 V, measured relative to an internal ferrocene reference. While no room-temperature emission was observed, the four Ir(III) complexes gave emissions upon lowering the temperature to 77 K. The broad, single-band emissions observed from the two ptp-based complexes are assigned to a metal-centered excited state, in accordance with the DFT calculations. The two pf-based complexes showed emissions with the shape of the emission profiles dependent upon the excitation wavelength. Spectral resolution was partially achieved by direct excitation into the lower energy state. The multiple emissions are discussed as originating mainly from two thermally nonequilibrated excited states: one metal-centered state and one π−π state localized on 2-phenylfuran.
Quantitative phase measurement for the damage detection in piezoelectric crystal using angularly placed multiple inter digital transducers (2016)

In the paper, an algorithm has been proposed to detect anomaly/damage in anisotropic piezoelectric crystals. Lithium Niobate piezoelectric single crystal is our test model to demonstrate the damage quantification algorithm. Surface acoustic waves (SAW) sensors are highly sensitive to surface perturbation and abrasions which reduce the performance of piezoelectric sensors. A macro-scale surface flaw has been inserted in between the SIMO IDTs. The sensor response in pristine and damage state is acquired, and changes in time-off-light and phase rotation where its principal components have been evaluated. The received multiple signals were analyzed using a phase retrieval algorithm, which provides quantitative information with high accuracy. Principle component analysis has been employed to detect anomalies. Our proposed method introduces a new approach that could potentially lead to extract lower scale flaws using SIMO methodology.
Supplementary Figure S2 from MFF Regulation of Mitochondrial Cell Death Is a Therapeutic Target in Cancer (2023)

&lt;p&gt;MFF-VDAC1 complex in cancer&lt;/p&gt;
Search for pair production of vector-like quarks in leptonic final states in proton-proton collisions at $$ \sqrt{s} $$ = 13 TeV (2023)

A bstract A search is presented for vector-like T and B quark-antiquark pairs produced in proton-proton collisions at a center-of-mass energy of 13 TeV. Data were collected by the CMS experiment at the CERN LHC in 2016–2018, with an integrated luminosity of 138 fb − 1 . Events are separated into single-lepton, same-sign charge dilepton, and multi-lepton channels. In the analysis of the single-lepton channel a multilayer neural network and jet identification techniques are employed to select signal events, while the same-sign dilepton and multilepton channels rely on the high-energy signature of the signal to distinguish it from standard model backgrounds. The data are consistent with standard model background predictions, and the production of vector-like quark pairs is excluded at 95% confidence level for T quark masses up to 1.54 TeV and B quark masses up to 1.56 TeV, depending on the branching fractions assumed, with maximal sensitivity to decay modes that include multiple top quarks. The limits obtained in this search are the strongest limits to date for $$ \textrm{T}\overline{\textrm{T}} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>T</mml:mi> <mml:mover> <mml:mi>T</mml:mi> <mml:mo>¯</mml:mo> </mml:mover> </mml:math> production, excluding masses below 1.48 TeV for all decays to third generation quarks, and are the strongest limits to date for $$ \textrm{B}\overline{\textrm{B}} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>B</mml:mi> <mml:mover> <mml:mi>B</mml:mi> <mml:mo>¯</mml:mo> </mml:mover> </mml:math> production with B quark decays to tW.
Supplementary Figure 1 from Nitric Oxide Boosts Chemoimmunotherapy via Inhibition of Acid Sphingomyelinase in a Mouse Model of Melanoma (2023)

Supplementary Figure 1 from Nitric Oxide Boosts Chemoimmunotherapy via Inhibition of Acid Sphingomyelinase in a Mouse Model of Melanoma
In-situ etched buried heterostructures for uncooled and extended reach modulated lasers (2003)

We report on in-situ etched and regrown buried heterostructure devices. Excellent surface morphology and reduction in surface damage lead to a 20% decrease in threshold current and 50% reduced burn-in degradation rates compared with standard processed devices.
Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration (2018)

The availability of multiple datasets comprising genome-scale RNAi viability screens in hundreds of diverse cancer cell lines presents new opportunities for understanding cancer vulnerabilities. Integrated analyses of these data to assess differential dependency across genes and cell lines are challenging due to confounding factors such as batch effects and variable screen quality, as well as difficulty assessing gene dependency on an absolute scale. To address these issues, we incorporated cell line screen-quality parameters and hierarchical Bayesian inference into DEMETER2, an analytical framework for analyzing RNAi screens ( https://depmap.org/R2-D2 ). This model substantially improves estimates of gene dependency across a range of performance measures, including identification of gold-standard essential genes and agreement with CRISPR/Cas9-based viability screens. It also allows us to integrate information across three large RNAi screening datasets, providing a unified resource representing the most extensive compilation of cancer cell line genetic dependencies to date.
Control Mechanism for cis Double‐Bond Formation by Polyunsaturated Fatty‐Acid Synthases (2019)

Abstract Polyunsaturated fatty acids (PUFAs) such as docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and arachidonic acid (ARA) are essential fatty acids for humans. Some microorganisms biosynthesize these PUFAs through PUFA synthases composed of four subunits with multiple catalytic domains. These PUFA synthases each create a specific PUFA without undesirable byproducts, even though the multiple catalytic domains in each large subunit are very similar. However, the detailed biosynthetic pathways and mechanisms for controlling final‐product profiles are still obscure. In this study, the FabA‐type dehydratase domain (DH FabA ) in the C‐subunit and the polyketide synthase‐type dehydratase domain (DH PKS ) in the B‐subunit of ARA synthase were revealed to be essential for ARA biosynthesis by in vivo gene exchange assays. Furthermore, in vitro analysis with truncated recombinant enzymes and C 4 ‐ to C 8 ‐acyl ACP substrates showed that ARA and EPA synthases utilized two types of DH domains, DH PKS and DH FabA , depending on the carbon‐chain length, to introduce either saturation or cis double bonds to growing acyl chains.
Enhanced Bone Marrow Homing of Natural Killer Cells Following mRNA Transfection With Gain-of-Function Variant CXCR4R334X (2019)

Adoptive transfer of natural killer (NK) cells can induce remission in patients with relapsed/refractory leukemia and myeloma. However, to date, clinical efficacy of NK cell immunotherapy has been limited to a sub-fraction of patients. Here we show that steps incorporated in the <i>ex vivo</i> manipulation/production of NK cell products used for adoptive infusion, such as over-night IL-2 activation or cryopreservation followed by <i>ex vivo</i> expansion, drastically decreases NK cell surface expression of the bone marrow (BM) homing chemokine receptor CXCR4. Reduced CXCR4 expression was associated with dampened <i>in vitro</i> NK cell migration toward its cognate ligand stromal-derived factor-1α (SDF-1α). NK cells isolated from patients with WHIM syndrome carry gain-of-function (GOF) mutations in CXCR4 (CXCR4<sup>R334X</sup>). Compared to healthy donors, we observed that NK cells expanded from WHIM patients have similar surface levels of CXCR4 but have a much stronger propensity to home to BM compartments when adoptively infused into NOD-<i>scid</i> IL2Rgamma<sup>null</sup> (NSG) mice. Therefore, in order to augment the capacity of adoptively infused NK cells to home to the BM, we genetically engineered <i>ex vivo</i> expanded NK cells to express the naturally occurring GOF CXCR4<sup>R334X</sup> receptor variant. Transfection of CXCR4<sup>R334X</sup>-coding mRNA into <i>ex vivo</i> expanded NK cells using a clinically applicable method consistently led to an increase in cell surface CXCR4 without altering NK cell phenotype, cytotoxic function, or compromising NK cell viability. Compared to non-transfected and wild type CXCR4-coding mRNA transfected counterparts, CXCR4<sup>R334X</sup>-engineered NK cells had significantly greater chemotaxis toward SDF-1α <i>in vitro</i>. Importantly, expression of CXCR4<sup>R334X</sup> on expanded NK cells resulted in significantly greater BM homing following adoptive transfer into NSG mice compared to non-transfected NK cell controls. Collectively, these data suggest up-regulation of cell surface CXCR4<sup>R334X</sup> on <i>ex vivo</i> expanded NK cells via mRNA transfection represents a novel approach to improve homing and target NK cell-based immunotherapies to BM where hematological malignancies reside.
ChemInform Abstract: Pinacol Coupling of 2,2′‐Biaryldiketone: An Application for the Synthesis of Enantiopure 3,4‐Dihydrodibenzo[c,g]phenanthrene‐3,4‐diol Derivatives. (2010)

Abstract The required products are exclusively obtained from substrates (I) bearing alkyl substitutents.
Multi-contrast deep nuclei segmentation using a probabilistic atlas (2010)

In this paper we propose a new hybrid segmentation approach of the deep brain structures based on a multi-contrast deformable model of regions in competition, with deformations preserving the topology of the structures, as well as their shape and position, using a probabilistic atlas and some prior morphological information. The accuracy of our method was evaluated by comparing the results obtained on a base of T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -weighted data contrast with those of FREESURFER and FSL-FIRST. Besides giving very good results from only one contrast, we show that the multi-contrast aspect of our method allows exploiting the complementary contributions of different contrasts, like T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> and diffusion tensor (DT) contrasts, in order to provide a more robust segmentation.
Network Scheduling and Compute Resource Aware Task Placement in Datacenters (2020)

To improve the performance of data-intensive applications, existing datacenter schedulers optimize either the placement of tasks or the scheduling of network flows. The task scheduler strives to place tasks close to their input data (i.e., maximize data locality) to minimize network traffic, while assuming fair sharing of the network. The network scheduler strives to finish flows as quickly as possible based on their sources and destinations determined by the task scheduler, while the scheduling is based on flow properties (e.g., size, deadline, and correlation) and not bound to fair sharing. Inconsistent assumptions of the two schedulers can compromise the overall application performance. In this paper, we propose NEAT+, a task scheduling framework that leverages information from the underlying network scheduler and available compute resources to make task placement decisions. The core of NEAT+ is a task completion time predictor that estimates the completion time of a task under given network condition and a given network scheduling policy. NEAT+ leverages the predicted task completion times to minimize the average completion time of active tasks. Evaluation using ns2 simulations and real-testbed shows that NEAT+ improves application performance by up to 3.7x for the suboptimal network scheduling policies and up to 33% for the optimal network scheduling policy.
The human vaccines project: into the immunome (2022)

The Human Genome Project revolutionized biomedical research. Could mapping the immune system be the next frontier for human health? We caught up with the founder and CEO of the Human Vaccines Project, Wayne Koff, to find out how the initiative aims to decode the immune system and speed up vaccine development.Charlotte Barker, Editor, Vaccine Insights speaks to Wayne Koff, Human Vaccines Project &amp; Harvard TH Chan School of Public HealthWayne Koff, PhD, is the founding president and CEO of the Human Vaccines Project and adjunct professor of epidemiology at the Harvard T.H. Chan School of Public Health. Prior to joining the Human Vaccines Project, Koff was chief scientific officer and senior vice president of research and development at the International AIDS Vaccine Initiative (IAVI) in New York City for 17 years. Earlier in his career, Koff held leadership roles including vice president of vaccine research and development at United Biomedical Inc. (UBI) and chief of the Vaccine Research and Development Branch, Division of AIDS, at the National Institute of Allergy and Infectious Diseases. An internationally recognized viral immunologist in the field of AIDS vaccine research and development, he has been twice honored by the US Department of Health and Human Services with the Special Act of Service Award for developing innovative strategies for accelerating global efforts in AIDS vaccine development.
Regulation of fatty acid transport in Escherichia coli: analysis by operon fusion (1983)

The regulation of the fadL gene, which encodes a long-chain fatty acid (LCFA) transport component, was examined by constructing a strain of Escherichia coli K-12 that bears a phi (fadL-lacZ+) operon fusion plus a wild-type fadL gene. This merodiploid strain expressed LCFA transport and beta-galactosidase activity coordinately under noninducing, inducing, and catabolite-repressing conditions. Merodiploid strains which carried a defective fadR gene expressed LCFA transport and beta-galactosidase activity constitutively. These results suggest that expression of the fadL gene is regulated by the fadR gene and is inducible at the level of transcription by LCFA.
An Analysis of a Wire-Wrapped Mechanical Crack Arrester for Pressurized Pipelines (1979)

Because of the difficulties which have been encountered in efforts to establish fracture toughness standards for arrest of running shear fractures in pressurized pipelines, the possibility of introducing mechanical crack arresters on such pipelines is currently being explored. The purpose here is to discuss the mechanics of the crack arrest process for a mechanical arrester which is fabricated by loosely thread wrapping ductile steel wire rod around a segment of the pipe. The net effect of the wire rod arrester as the crack approaches is to substantially increase the axial in-plane strain in the pipe wall adjacent to the fracture path from the value it would have in the absence of the arrester. The result is that, in the presence of the arrester, the growth of a circumferential tensile fracture can become more favorable than continued growth of the axial tensile fracture, and a criterion for arrest of the axial fracture based on this result is proposed. Through an analysis of rapid crack propagation in a pressurized pipeline, the arrest criterion leads to an expression for the minimum ductility of the wire rod necessary for crack arrest. The required minimum ductility for the wire rod is estimated for system parameters corresponding to available full-scale test data, and the results compare favorably with the independently measured actual ductility of the arrester material.