gebhart/patrepeval huggingface dataset:
Structurally Distinct Complexes of Ubiquitin and Sumo-Modified PCNA Lead to Distinct DNA Damage Response Pathways (2014)

3498-Pos Board B226 Atomistic Studies Support a Detailed Model of RecA Mediated Homology Recognition and Strand Exchange Darren Yang1, Chantal Prevost2, Mara Prentiss3. School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA, Laboratoire de Biochimie Theorique, Institut de Biologie Physico-Chimique, Paris, France, Department of Physics, Harvard University, Cambridge, MA, USA. The bacterial recombinase RecA mediates homologous recombination and recombinational DNA repair through homology search and strand exchange. During homologous recombination, RecA binds an incoming single-stranded DNA (ssDNA) in its primary binding site, site I, to form a nucleoprotein filament whose crystal structure is known. The structure of the final post-stand exchange structure with double stranded DNA (dsDNA) bound in site I is also known; however, despite enormous effort, the details of homology testing have remained uncertain, partly because of the dearth of information about the structure of DNA during homology testing. Recent work has suggested that homology testing begins with the dsDNA binding to the secondary RecA binding site, site II. With detailed examination of the crystal structure, we found that an intermediate structure must exist such that homology recognition does not simply proceed from the searching state to the final post-strand exchange state, suggesting that homology recognition is governed by transitions to and from the intermediate structure that differs significantly from its final position. In this work, we present evidence that ~ 9-15 dsDNA base pairs can bind to site II in a metastable conformation where single complementary strand bases can flip and stably pair with corresponding sequence matched incoming strand bases. That stable pairing deepens the dsDNA binding, allowing time for base flipping and strand exchange which in turn allows more dsDNA bases to bind to site II. In the absence of pairing between the complementary and incoming strands, a series of transitions drives dsDNA unbinding, with little opportunity for additional base flipping. Such a system offers very extremely rapid rejection of almost all mismatched pairings, which allows bacterial genomes to be searched on biologically relevant timescales.
Improved Energy Storage Properties Accompanied by Enhanced Interface Polarization in Annealed Microwave‐Sintered BST (2015)

Microwave‐sintering (MWS) technique was employed to fabricate dense (Ba 0.4 Sr 0.6 )TiO 3 (BST) ceramics. With respect to the high dielectric loss at room temperature, induced by the formation of oxygen defects during the MWS under vacuum atmosphere (−60 kPa), the as‐sintered samples were thermally annealed in air to reduce tanδ and recover the insulating performance. Accompanied by the decreased tanδ, the energy storage properties for annealed MWS BST were optimized, with increasing energy density (γ) from 0.77 to 1.15 J/cm 3 and energy efficiency (η) from 60% to 82%. The lower oxygen vacancy concentrations were believed to account for the enhanced insulating characteristics of grain boundaries and contribute to the improved properties after annealing. Electrical characterization of grain and grain boundary by impedance spectroscopy demonstrated that the annealing preferentially modified the grain boundary. In addition, resistances extracted from the high temperature impedance analysis were found to be inadequate for evaluating the electrical characteristics of materials affected by extrinsic mechanisms, such as the interfacial polarization. For comparison, annealing effect on energy storage properties were also discussed for conventionally sintered BST.
Analysis and Optical Processing of Sea Photographs for Energy Spectra (1972)

An optical Fourier transform analysis of a sea photograph taken under a particular skylight irradiance has been proposed by Stilwell [1] as a means of providing a quantitative description of the sea-vector wave-number spectrum. The process requires an explicit knowledge of the skylight irradiance reflected from the sea surface to the aerial camera. A first-order analysis shows that the photographic density of the transform recording is functionally related to the sea-slope spectrum, provided that the average optical density measured in the sea photographic negative is approximately linear. The analysis of the process and some experimental results are discussed.
Real Time Drivable Surface Determination Based on Stereo Vision (2016)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;For any autonomous vehicle, understanding which area around the vehicle is free or drivable is a key component. It is important to find road boundaries such as ditches, curbs or guard rails. Finding small objects on the road, that might be blocking the vehicle path, is also critical. Most prototypes for autonomous vehicles feature laser scanners for this purpose. We propose a stereo vision based system as redundancy or as a cost efficient replacement for laser scanners in the application of drivable surface determination. The system generates a detailed map that indicates which area in front of the vehicle that is considered to be drivable and non-drivable.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;The base for this map is a dense 3D point cloud generated from the stereo vision system. The left and right images are used to create a disparity image which is then translated into a 3D point cloud. The 3D points are used to generate a detailed elevation grid of the observed area. The gradient of this grid is then used for the judgement of drivable/non-drivable. The 3D point cloud and the drivability map is generated in real time at 22 Hz on production intent hardware.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;We demonstrate the performance on a variety of use cases. We show that stereo vision is a strong candidate to replace the laser scanners used in many autonomous driving applications. At the same time our stereo vision system features many other applications, such as EuroNCAP AEB, lane tracking and traffic sign recognition.&lt;/div&gt;&lt;/div&gt;
Inhibition of class I histone deacetylase with an apicidin derivative prevents cardiac hypertrophy and failure (2008)

The apicidin derivative, API-D, is capable of reducing hypertrophy and, consequently, the transition to heart failure in mice subjected to TAC. Treatment with this substance, therefore, holds promise as an important therapeutic option for heart failure.
ChemInform Abstract: Parallel Synthesis of 3‐Aminoimidazo[1,2‐a]pyridines and ‐pyrazines by a New Three‐Component Condensation. (1998)

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.
Controlled InAs quantum dot nucleation on faceted nanopatterned pyramids (2007)

The selective quantum dot (QD) nucleation on nanofaceted GaAs pyramidal facets is explored. The GaAs pyramids, formed on a SiO2 masked (001) GaAs substrate, are characterized by well-defined equilibrium crystal shapes (ECSs) defined by three crystal plane families including {11n}, {10n}, and (001). Subsequent patterned QD (PQD) nucleation on the GaAs pyramidal facets is highly preferential towards the (11n) planes due to superior energy minimization. The GaAs pyramid ECS and PQDs are examined using high-resolution scanning electron microscopy and room temperature photoluminescence.
Purification, crystallization and preliminary X-ray diffraction analysis of a novel keto-deoxy-D-galactarate (KDG) dehydratase fromAgrobacterium tumefaciens (2013)

D-galacturonic acid is the main component of pectin. It could be used to produce affordable renewable fuels, chemicals and materials through biotechnical conversion. Keto-deoxy-D-galactarate (KDG) dehydratase is an enzyme in the oxidative pathway of D-galacturonic acid in Agrobacterium tumefaciens (At). It converts 3-deoxy-2-keto-L-threo-hexarate to α-ketoglutaric semialdehyde. At KDG dehydratase was crystallized by the hanging-drop vapour-diffusion method. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 169.1, b = 117.8, c = 74.3 Å, β = 112.4° and an asymmetric unit of four monomers. X-ray diffraction data were collected to 1.9 Å resolution using synchrotron radiation. The three-dimensional structure of At KDG dehydratase will provide valuable information on the function of the enzyme and will allow it to be engineered for biorefinery-based applications.
Multilingual Content Moderation: A Case Study on Reddit (2023)

Content moderation is the process of flagging content based on pre-defined platform rules. There has been a growing need for AI moderators to safeguard users as well as protect the mental health of human moderators from traumatic content. While prior works have focused on identifying hateful/offensive language, they are not adequate for meeting the challenges of content moderation since 1) moderation decisions are based on violation of rules, which subsumes detection of offensive speech, and 2) such rules often differ across communities which entails an adaptive solution. We propose to study the challenges of content moderation by introducing a multilingual dataset of 1.8 Million Reddit comments spanning 56 subreddits in English, German, Spanish and French. We perform extensive experimental analysis to highlight the underlying challenges and suggest related research problems such as cross-lingual transfer, learning under label noise (human biases), transfer of moderation models, and predicting the violated rule. Our dataset and analysis can help better prepare for the challenges and opportunities of auto moderation.
Accurate characterization of fiber Bragg grating index modulation by side-diffraction technique (2003)

The performance of fiber Bragg grating (FBG) devices is determined by spatial distribution of FBG parameters. For many applications, like chirped FBG used for dispersion compensation, it is sufficient to control these parameters with spatial resolution of around 1 mm. We improve the sensitivity and accuracy of the side-diffraction FBG characterization at the cost of reducing the spatial resolution and demonstrate simultaneous measurement of fiber grating refractive index modulation with accuracy of 2/spl middot/10/sup -6/, grating period variation with accuracy of 5 pm, and spatial resolution of /spl sim/1 mm. The group delay ripple of a chirped FBG calculated from our side-diffraction characterization is in a good agreement with spectroscopic measurements.
Allosteric inhibition of the SARS-CoV-2 main protease – insights from mass spectrometry-based assays (2020)

Abstract Following translation of the SARS-CoV-2 RNA genome into two viral polypeptides, the main protease M pro cleaves at eleven sites to release non-structural proteins required for viral replication. M Pro is an attractive target for antiviral therapies to combat the coronavirus-2019 disease (COVID-19). Here, we have used native mass spectrometry (MS) to characterize the functional unit of M pro . Analysis of the monomer-dimer equilibria reveals a dissociation constant of K d = 0.14 ± 0.03 μM, revealing M Pro has a strong preference to dimerize in solution. Developing an MS-based kinetic assay we then characterized substrate turnover rates by following temporal changes in the enzyme-substrate complexes, which are effectively “flash-frozen” as they transition from solution to the gas phase. We screened small molecules, that bind distant from the active site, for their ability to modulate activity. These compounds, including one proposed to disrupt the catalytically active dimer, slow the rate of substrate processing by ~35%. This information was readily obtained and, together with analysis of the x-ray crystal structures of these enzyme-small molecule complexes, provides a starting point for the development of more potent molecules that allosterically regulate M Pro activity.
Avian Influenza and Newcastle Disease in Three Risk Areas for H5N1 Highly Pathogenic Avian Influenza in Mali, 2007–2008 (2011)

Our survey aimed to investigate avian influenza (AI) and Newcastle disease (ND) prevalence and risk factors in three areas of Mali at risk for occurrence of H5N1 highly pathogenic avian influenza. Blood samples and cloacal and oropharyngeal swabs were collected from 1470 birds between February 2007 and May 2008 and were tested by commercial enzyme-linked immunosorbent assay to detect antibodies and real-time reverse-transcription (rRT)-PCR to detect virus. Risk factors associated with seropositivity or positive rRT-PCR were identified by random effect logistic regression. AI seroprevalence was significantly lower in birds from commercial farms (0%) than in village backyard birds (3.1%). For backyard birds, no individual risk factors (species, age, sex) were identified, but birds in the Mopti area in the Sahelian zone, where millions of wild birds migrate, were more seropositive than in the Sikasso area in the Sudano-Guinean zone (odds ratio [OR] = 2.0, P = 0.051). Among backyard birds nonvaccinated against ND, ND seroprevalence was 58.4%, and the odds of seropositivity was 2.0 higher in chickens than in ducks, 1.7 higher in females than in males, 3.1 higher in adults than in young birds, and 3.0 higher in poultry from the Sikasso area than from the Mopti area (P < 0.01 in all cases). Prevalence established by rRT-PCR was low for both AI virus (1.1%) and ND virus (2.6%) and was associated with no risk factors for AI but was higher in chickens than in ducks (OR = 5.3, P = 0.05) and in the Sikasso area than in the Mopti area (OR = 3.4, P = 0.027) for ND. For AI and ND, prevalence assessed by serology or rRT-PCR varied over time, although seasonal and interannual variation could not be clearly distinguished. The intracluster correlation coefficient for serologic data was low for AI (0.014) and higher for ND (0.222). These results are useful to optimize surveillance and control strategy for notifiable avian diseases in African countries with similar agroecological and resource-limited contexts.
Applications of Ionic Liquids in Organic Electronic Devices (2017)

We review applications of ionic liquids (ILs) in organic electronic devices. ILs are a new type of materials and have outstanding features unlike conventional compounds, giving novel functions to organic electronic devices. First, we give a general explanation of ILs. Next, we review applications of ILs in some organic electronic devices such as organic light emitting devices, photovoltaics, and organic field effect transistors. Finally, we remark on the outlook for future IL applications in organic electronic devices.
Osteostat/Tumor Necrosis Factor Superfamily 18 Inhibits Osteoclastogenesis and Is Selectively Expressed by Vascular Endothelial Cells (2005)

Vascular endothelial cells (EC) participate in the process of bone formation through the production of factors regulating osteoclast differentiation and function. In this study, we report the selective expression in primary human microvascular EC of Osteostat/TNF superfamily 18, a ligand of the TNF superfamily. Osteostat protein is detectable in human microvascular EC and is highly up-regulated by IFN-alpha and IFN-beta. Moreover, an anti-Osteostat antibody strongly binds to the vascular endothelium in human tissues, demonstrating that the protein is present in the EC layers surrounding blood vessels. Functional in vitro assays were used to define Osteostat involvement in osteoclastogenesis. Both recombinant and membrane-bound Osteostat inhibit differentiation of osteoclasts from monocytic precursor cells. Osteostat suppresses the early stage of osteoclastogenesis via inhibition of macrophage colony-stimulating factor-induced receptor activator of NF-kappaB (RANK) expression in the osteoclast precursor cells. This effect appears to be specific for the differentiation pathway of the osteoclast lineage, because Osteostat does not inhibit lipopolysaccharide-induced RANK expression in monocytes and dendritic cells, or activation-induced RANK expression in T cells. These findings demonstrate that Osteostat is a novel regulator of osteoclast generation and substantiate the major role played by the endothelium in bone physiology.
Superior Temporal Sulcus—It's My Area: Or Is It? (2008)

The superior temporal sulcus (STS) is the chameleon of the human brain. Several research areas claim the STS as the host brain region for their particular behavior of interest. Some see it as one of the core structures for theory of mind. For others, it is the main region for audiovisual integration. It plays an important role in biological motion perception, but is also claimed to be essential for speech processing and processing of faces. We review the foci of activations in the STS from multiple functional magnetic resonance imaging studies, focusing on theory of mind, audiovisual integration, motion processing, speech processing, and face processing. The results indicate a differentiation of the STS region in an anterior portion, mainly involved in speech processing, and a posterior portion recruited by cognitive demands of all these different research areas. The latter finding argues against a strict functional subdivision of the STS. In line with anatomical evidence from tracer studies, we propose that the function of the STS varies depending on the nature of network coactivations with different regions in the frontal cortex and medial-temporal lobe. This view is more in keeping with the notion that the same brain region can support different cognitive operations depending on task-dependent network connections, emphasizing the role of network connectivity analysis in neuroimaging.
Structural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A (2001)

Outer membrane phospholipase A (OMPLA) from Escherichia coli is an integral-membrane enzyme with a unique His-Ser-Asn catalytic triad. In serine proteases and serine esterases usually an Asp occurs in the catalytic triad; its role has been the subject of much debate. Here the role of the uncharged asparagine in the active site of OMPLA is investigated by structural characterization of the Asnl56Ala mutant. Asparagine 156 is not involved in maintaining the overall active-site configuration and does not contribute significantly to the thermal stability of OMPLA. The active-site histidine retains an active conformation in the mutant notwithstanding the loss of the hydrogen bond to the asparagine side chain. Instead, stabilization of the correct tautomeric form of the histidine can account for the observed decrease in activity of the Asnl56Ala mutant.
Syntheses and Structures of the Five-Coordinate Complexes [M(N-N)([9]aneS3)](PF6)2 (M = Pd, (N-N) = 2,2'-Bipyridine; M = Pt, (N-N) = 1,10-Phenanthroline; ([9]aneS3) = 1,4,7-Trithiacyclononane) (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSyntheses and Structures of the Five-Coordinate Complexes [M(N-N)([9]aneS3)](PF6)2 (M = Pd, (N-N) = 2,2'-Bipyridine; M = Pt, (N-N) = 1,10-Phenanthroline; ([9]aneS3) = 1,4,7-Trithiacyclononane)Hans Nikol, Hans-Beat Buergi, Kenneth I. Hardcastle, and Harry B. GrayCite this: Inorg. Chem. 1995, 34, 25, 6319–6322Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/ic00129a017https://doi.org/10.1021/ic00129a017research-articleACS PublicationsRequest reuse permissionsArticle Views215Altmetric-Citations39LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Phosphatidylserine Exposed Lipid Bilayer Models for Understanding Cancer Cell Selectivity of Natural Compounds: A Molecular Dynamics Simulation Study (2022)

Development of drugs that are selectively toxic to cancer cells and safe to normal cells is crucial in cancer treatment. Evaluation of membrane permeability is a key metric for successful drug development. In this study, we have used in silico molecular models of lipid bilayers to explore the effect of phosphatidylserine (PS) exposure in cancer cells on membrane permeation of natural compounds Withaferin A (Wi-A), Withanone (Wi-N), Caffeic Acid Phenethyl Ester (CAPE) and Artepillin C (ARC). Molecular dynamics simulations were performed to compute permeability coefficients. The results indicated that the exposure of PS in cancer cell membranes facilitated the permeation of Wi-A, Wi-N and CAPE through a cancer cell membrane when compared to a normal cell membrane. In the case of ARC, PS exposure did not have a notable influence on its permeability coefficient. The presented data demonstrated the potential of PS exposure-based models for studying cancer cell selectivity of drugs.
Silicon nanowire polarizers for far ultraviolet (sub-200 nm) applications: Modeling and fabrication (2010)

We have previously demonstrated a fabrication technique for the creation of silicon wire grid polarizers (WGPs) for far (deep) ultraviolet applications utilizing a shear-aligned cylinder-forming polystyrene-b-poly(n-hexyl methacrylate) diblock copolymer as a mask for reactive ion etching of an amorphous silicon substrate. In our current work, a numerical model is refined and applied to our experimental systems to describe the impact of wire height and periodicity, and tradeoffs between the two, on polarization efficiency. We focus our attention at a wavelength of 193 nm, the emission wavelength of the ArF excimer laser currently in use in advanced photolithographic processes. Through application of the model’s predictions we have achieved marked improvement in the polarization efficiency of our WGPs by increasing the block copolymer molecular weight, thereby increasing the thickness of the Si wires, which compensates for a simultaneous increase in wire periodicity; the resulting arrays of parallel Si nanowires exhibit polarization efficiencies approaching 64% at 193 nm, a 68% relative increase over our previous Si WGPs.