gebhart/patrepeval huggingface dataset:
A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding (2004)

Extracting knowledge-based statistical potential from known structures of proteins is proved to be a simple, effective method to obtain an approximate free-energy function. However, the different compositions of amino acid residues at the core, the surface, and the binding interface of proteins prohibited the establishment of a unified statistical potential for folding and binding despite the fact that the physical basis of the interaction (water-mediated interaction between amino acids) is the same. Recently, a physical state of ideal gas, rather than a statistically averaged state, has been used as the reference state for extracting the net interaction energy between amino acid residues of monomeric proteins. Here, we find that this monomer-based potential is more accurate than an existing all-atom knowledge-based potential trained with interfacial structures of dimers in distinguishing native complex structures from docking decoys (100% success rate vs. 52% in 21 dimer/trimer decoy sets). It is also more accurate than a recently developed semiphysical empirical free-energy functional enhanced by an orientation-dependent hydrogen-bonding potential in distinguishing native state from Rosetta docking decoys (94% success rate vs. 74% in 31 antibody-antigen and other complexes based on Z score). In addition, the monomer potential achieved a 93% success rate in distinguishing true dimeric interfaces from artificial crystal interfaces. More importantly, without additional parameters, the potential provides an accurate prediction of binding free energy of protein-peptide and protein-protein complexes (a correlation coefficient of 0.87 and a root-mean-square deviation of 1.76 kcal/mol with 69 experimental data points). This work marks a significant step toward a unified knowledge-based potential that quantitatively captures the common physical principle underlying folding and binding. A Web server for academic users, established for the prediction of binding free energy and the energy evaluation of the protein-protein complexes, may be found at http://theory.med.buffalo.edu.
Modulating the thermomechanical properties and self-healing efficiency of siloxane-based soft polymers through metal–ligand coordination (2020)

An efficient strategy to modulate the thermomechanical properties and self-healing of soft polymers has been developed by rationally selecting the metal used for supramolecular crosslinking.
Cross-linking of bromodeoxyuridine-substituted oligonucleotides to the EcoRI and EcoRV restriction endonucleases (1986)

We have synthesized several self-complementary oligodeoxynucleotides which contain bromodeoxyuridine in various positions within and outside of the recognition sequence for the EcoRI and EcoRV restriction endonucleases. These oligodeoxynucleotides are cleaved in the presence of Mg2+ by their respective enzyme. Upon irradiation by long-wavelength ultraviolet light and in the absence of Mg2+ they are cross-linked in low yield to their enzymes, forming 1:1 and 1:2 (oligodeoxynucleotide:enzyme subunit) adducts. Cross-linking occurs with both specific and non-specific complexes. With EcoRI the site of cross-linking was determined to be at or close to Met-137, i.e. in a region of the molecule implicated by other studies from our laboratory [Scholtissek et al. (1986) J. Biol. Chem. 261, 2228-2234] in the binding and cleavage of the substrate.
Safety and efficacy of minimalist approach in transfemoral transcatheter aortic valve replacement: insights from the Optimized transCathEter vAlvular interventioN–Transcatheter Aortic Valve Implantation (OCEAN-TAVI) registry† (2017)

MA-TAVR has similar results to NMA-TAVR in terms of mortality and stroke in this Japanese multicentre registry. Shorter procedure time and hospital stays were seen in the MA-TAVR group. MA-TAVR is as safe and effective as NMA-TAVR.
The transcriptomic signature of developing soybean seeds reveals the genetic basis of seed trait adaptation during domestication (2016)

Summary Cultivated soybean has undergone many transformations during domestication. In this paper we report a comprehensive assessment of the evolution of gene co‐expression networks based on the analysis of 40 transcriptomes from developing soybean seeds in cultivated and wild soybean accessions. We identified 2680 genes that are differentially expressed during seed maturation and established two cultivar‐specific gene co‐expression networks. Through analysis of the two networks and integration with quantitative trait locus data we identified two potential key drivers for seed trait formation, GA 20 OX and NFYA . GA 20 OX encodes an enzyme in a rate‐limiting step of gibberellin biosynthesis, and NFYA encodes a transcription factor. Overexpression of GA 20 OX and NFYA enhanced seed size/weight and oil content, respectively, in seeds of transgenic plants. The two genes showed significantly higher expression in cultivated than in wild soybean, and the increases in expression were associated with genetic variations in the promoter region of each gene. Moreover, the expression of GA 20 OX and NFYA in seeds of soybean accessions correlated with seed weight and oil content, respectively. Our study reveals transcriptional adaptation during soybean domestication and may identify a mechanism of selection by expression for seed trait formation, providing strategies for future breeding practice.
How organizations should manage discrimination and harassment complaints (1999)

Outlines the definitions of harassment and discrimination and then details ways in which any case should be treated. Advocates the need for clear and specific company policies as a preventative measure and the need for claims to be dealt with in a professional manner.
Modelling the optical response of gold nanoparticles (2008)

This tutorial review presents an overview of theoretical methods for predicting and understanding the optical response of gold nanoparticles. A critical comparison is provided, assisting the reader in making a rational choice for each particular problem, while analytical models provide insights into the effects of retardation in large particles and non-locality in small particles. Far- and near-field spectra are discussed, and the relevance of the latter in surface-enhanced Raman spectroscopy and electron energy-loss spectroscopy is emphasized.
VLSI circuit synthesis using a parallel genetic algorithm (2002)

A parallel implementation of a genetic algorithm used to evolve simple analog VLSI circuits is described. The parallel computer system consisted of twenty distributed SPARC workstations whose computational activity is controlled by the parallel environment coordination language Linda. Work-in-progress on using the parallel GA to realize optimized circuits and to discover new types of equivalent-function circuits is presented. The use of biologically inspired development rules to limit the scope of circuits generated by recombination operators to circuits that have an increased chance of surviving is briefly discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fusion of 2D CNN and 3D DenseNet for Dynamic Gesture Recognition (2019)

Gesture recognition has been applied in many fields as it is a natural human–computer communication method. However, recognition of dynamic gesture is still a challenging topic because of complex disturbance information and motion information. In this paper, we propose an effective dynamic gesture recognition method by fusing the prediction results of a two-dimensional (2D) motion representation convolution neural network (CNN) model and three-dimensional (3D) dense convolutional network (DenseNet) model. Firstly, to obtain a compact and discriminative gesture motion representation, the motion history image (MHI) and pseudo-coloring technique were employed to integrate the spatiotemporal motion sequences into a frame image, before being fed into a 2D CNN model for gesture classification. Next, the proposed 3D DenseNet model was used to extract spatiotemporal features directly from Red, Green, Blue (RGB) gesture videos. Finally, the prediction results of the proposed 2D and 3D deep models were blended together to boost recognition performance. The experimental results on two public datasets demonstrate the effectiveness of our proposed method.
<title>Moving Target Identification (MTI) Algorithm For Passive Sensors</title> (1980)

A critical problem in target detection is to develop algorithms for autonomous target acquisition at long ranges. When the angular extent of a target is so small that identification is impossible, then detection of object motion can be an important method for acquiring and tracking military targets. Moving target identification (MTI) may be difficult however for down-looking airborne sensors where the apparent motion of back-ground clutter can mask the movement of any objects in the scene. To get around this problem, an algorithm has been developed which compares successive frames from a passive imaging sensor and estimates the apparent background motion. The velocity model is applied to an earlier image to predict the appearance of the most recent image. The predicted and measured images are compared and the portions of the background which did not move in the expected manner are identified as moving objects. Several sequences of FLIR images are included where the algorithm has successfully extracted targets from cluttered moving backgrounds.
Improved temporal correspondences in stereo-vision by RANSAC (2004)

Determining the image correspondences of scene points in two or more views remain elusive especially for large baselines and (or) rotations. Assuming a calibrated stereo rig, we propose two novel RANSAC-based algorithms to establish temporal correspondences of triplet and quadruplet matches in two stereo pairs robustly. We devise an efficient technique for the absolute orientation problem with minimum three matches [B. Horn et al., 1987]. This drastically reduces the number of random samplings, for a given probability of selecting no outlier in at least one set, compared to the application of the 7-/8-point algorithms [Z. Zhang et al., 1995, P. Torr and D. Murray, 1997]. Within the general RANSAC paradigm, a low-cost selective random sampling scheme is incorporated to further enhance the robustness of the algorithm that utilizes quadruplet matches.
Tunable Workfunction for Fully Silicied Gates (FUSI) and Proposed Mechanisms (2006)

We present fully silicided gate (FUSI) work function modulation and mechanisms using different NiSi alloys as well as different phases (Ni <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">31</sub> Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sub> and Ni <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rich</sub> -Pt-Si). It is shown that the interface layer between gate silicide and dielectric is the key to modulate the work function due to Fermi level pining on HfSiO and HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> . Ge, Yb, Pt, and Al were fully explored to identify good candidates for N and PFET. A ~400meV work function shift was achieved toward the conduction band edge using NiAlSi demonstrating a mobility of 300 cm <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /Vs at peak, matching NiSi control devices on Hf <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> . Ni <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rich</sub> PtSi has shown 4.85eV work function and good mobility. Different gate materials were fully explored to understand the mechanism of work function modulation depending on the dielectrics. It was found that the work function of metal rich silicides are strongly dependent on the pure metal work function and it can be changed by controlling the number of metal atoms which are available at the interface
Speech input in multimodal environments: effects of perceptual structure on speed, accuracy, and acceptance (1997)

A framework of complementary behavior has been identified which maintains that direct manipulation and speech interface modalities have reciprocal strengths and weaknesses. This suggests that user interface performance and acceptance may increase by adopting a multimodal approach that combines speech and direct manipulation. Based on this concept and the theory of perceptual structures, this work examined the hypothesis that the speed, accuracy, and acceptance of a multimodal speech and direct manipulation interface would increase when the modalities match the perceptual structure of the input attributes.
A software prototype to collect histopathology data was developed with two interfaces to test this hypothesis. The first interface used speech and direct manipulation in a way that did not match the perceptual structure of the attributes, while the second interface used speech and direct manipulation in a way that best matched the perceptual structure. A group of 20 clinical and veterinary pathologists evaluated the prototype in an experimental setting using repeating measures. The independent variables were interface order and task order, and the dependent variables were task completion time, speech errors, mouse errors, diagnosis errors, and user acceptance.
The results of this experiment support the hypothesis that the perceptual structure of an input task is an important consideration when designing multimodal computer interfaces. Task completion time improved by 22.5%. speech errors were reduced by 36%, and user acceptance increased 6.7% with the computer interface that best matched the perceptual structure of the input attributes. Mouse errors increased slightly and diagnosis errors decreased slightly. but these were not statistically significant. There was no relationship between user acceptance and time, suggesting that speed is not the predominate factor in determining approval. User acceptance was related to speech recognition errors, suggesting that recognition accuracy is critical to user satisfaction. User acceptance was also shown to be related to domain errors, suggesting that the more domain expertise a person has, the more he or she will embrace the computer interface.
Enhanced Performance of ZnO Nanowire Field Effect Transistors by H<sub>2</sub> Annealing (2007)

The electrical properties of ZnO nanowires are significantly dependent on their surface states. The surface trap charges degrade the device performance of field effect transistors. These trap charges are reduced by H2 annealing. In this work, a back-gate ZnO nanowire field effect transistor (FET) was fabricated by a photolithographic process, and its electrical properties were characterized. This back-gate FET was subsequently annealed under a flow of H2/Ar gas for 20 min. The back-gate FET annealed for 20 min exhibited remarkably enhanced electrical characteristics, as compared with the as-fabricated back-gate FET; the peak transconductance was increased from 40 to 448 nS, the field effect mobility from 27 to 302 cm2 V-1 s-1, and the Imax/Imin ratio from 1.5 to 105.
Identification of Dunaliella Viridis Using its Markers (2013)

The phylogenetic position and taxonomic status of the green alga Dunaliella viridis was investigated based on internal transcribed spacer (ITS) markers. The alga was isolated from saltern in Vinh Hao, Binh Thuan province, Vietnam. Independent phylogenetic trees of ITS1 and ITS2 sequences revealed that the alga belongs to the clade of Dunaliella viridis. The salinity for optimal growth of the alga was 2M NaCl, which was much lower than the original sampling site (4M NaCl). This tolerance to a wide range of salinity may provide distinct advantages to Dunaliella viridis over its competitors in natural environments. Further physiological and biochemical characteristics of this strain will need to be investigated in order to assess its potential for algal biomass production and other applications such as beta-carotene, carbohydrate, lipid and protein for feed, food, aquaculture and biofuels, including opening new search for other Dunaliella species.
ChemInform Abstract: Design, Synthesis and Discovery of 5‐Hydroxyaurone Derivatives as Growth Inhibitors Against HUVEC and Some Cancer Cell Lines. (2011)

Abstract 5‐Hydroxy‐,5‐methoxy‐, and 5‐acetoxyaurones are synthesized by means of Friedel‐Crafts acylation, cyclization, and aldol condensation.
Amino acid sequence of a putative sodium channel expressed in the giant axon of the squid Loligo opalescens. (1993)

A full-length cDNA encoding a putative Na+ channel (GFLN1) has been cloned from a library prepared from the stellate ganglion of Loligo opalescens. The cDNA encodes a predicted protein of 1784 amino acids. Regions of the GFLN1 protein with defined functional importance (membrane span S4, the SS1 and SS2 segments, and interdomain III-IV) are highly conserved among all vertebrate Na+ channel alpha-subunit structures. Northern blot hybridization and RNase protection assays verify that mRNA corresponding to GFLN1 is expressed in neurons of the giant fiber lobe that form the giant axon. We propose that GFLN1 encodes the Na+ channel that has been extensively studied in the squid axon.
Preparation of Thin Films by Coevaporation and Phase Identification in Bi-Sr-Ca-Cu-O System (1988)

Thin films of a Bi-Sr-Ca-Cu-O system were prepared on MgO substrate by coevaporation of Bi 2 O 3 , Sr 0.5 Ca 0.5 alloy and Cu. The films were characterized by X-ray diffraction, dc resistivity and EPMA. By post-deposition annealing the film at 850°C for 12 hours, the film showed a superconducting transition with onset T c of 91 K and zero resistance T c of 82 K. The tetragonal phase Bi 2 Sr 2 CaCu 2 O x with a c -axis of 30.7 Å was responsible for this superconducting transition. The film annealed at 890°C for 5 hours showed a superconduting transition with onset T c of 115 K and zero resistance T c of 103 K. The tetragonal phase Bi 2 Sr 2 Ca 2 Cu 3 O x with a c -axis of ∼37 Å was responsible for this superconducting transition.
Formylpeptide Receptor FPR and the Rapid Growth of Malignant Human Gliomas (2005)

FPR is expressed by highly malignant human glioma cells and appears to mediate motility, growth, and angiogenesis of human glioblastoma by interacting with host-derived agonists. Thus, FPR may represent a molecular target for the development of novel antiglioma therapeutics.
Detecting and Debugging Insecure Information Flows (2005)

A new approach to dynamic information flow analysis is presented that can be used to detect and debug insecure flows in programs. It can be applied offline to validate and debug a program against an information flow policy, or, when fast response is not critical, it can be applied online to prevent illegal flows in deployed programs. Since dynamic analysis alone is inherently unable to detect implicit information flows, our approach incorporates a static preprocessing phase that permits detection of most implicit flows at runtime, in addition to explicit ones. To support interactive debugging of insecure flows, it also incorporates a new forward computing algorithm for dynamic slicing, which is more precise than previous forward computing algorithms and is not restricted to programs with structured control flow. A prototype tool implementing the proposed approach has been developed for Java byte code programs. Case studies in which this tool was applied to several subject programs are described.
Temporal Variance Analysis for Action Recognition (2015)

Slow feature analysis (SFA) extracts slowly varying signals from input data and has been used to model complex cells in the primary visual cortex (V1). It transmits information to both ventral and dorsal pathways to process appearance and motion information, respectively. However, SFA only uses slowly varying features for local feature extraction, because they represent appearance information more effectively than motion information. To better utilize temporal information, we propose temporal variance analysis (TVA) as a generalization of SFA. TVA learns a linear transformation matrix that projects multidimensional temporal data to temporal components with temporal variance. Inspired by the function of V1, we learn receptive fields by TVA and apply convolution and pooling to extract local features. Embedded in the improved dense trajectory framework, TVA for action recognition is proposed to: 1) extract appearance and motion features from gray using slow and fast filters, respectively; 2) extract additional motion features using slow filters from horizontal and vertical optical flows; and 3) separately encode extracted local features with different temporal variances and concatenate all the encoded features as final features. We evaluate the proposed TVA features on several challenging data sets and show that both slow and fast features are useful in the low-level feature extraction. Experimental results show that the proposed TVA features outperform the conventional histogram-based features, and excellent results can be achieved by combining all TVA features.
p107 is a suppressor of retinoblastoma development in pRb-deficient mice (1998)

Hemizygosity for the retinoblastoma gene RB in man strongly predisposes to retinoblastoma. In the mouse, however, Rb hemizygosity leaves the retina normal, whereas in Rb −/− chimeras pRb-deficient retinoblasts undergo apoptosis. To test whether concomitant inactivation of the Rb -related gene p107 is required to unleash the oncogenic potential of pRb deficiency in the mouse retina, we inactivated both Rb and p107 by homologous recombination in embryonic stem cells and generated chimeric mice. Retinoblastomas were found in five out of seven adult pRb/p107-deficient chimeras. The retinal tumors showed amacrine cell differentiation, and therefore originated from cells committed to the inner but not the outer nuclear layer. Retinal lesions were already observed at embryonic day 17.5. At this stage, the primitive nuclear layer exhibited severe dysplasia, including rosette-like arrangements, and apoptosis. These findings provide formal proof for the role of loss of Rb in retinoblastoma development in the mouse and the first in vivo evidence that p107 can exert a tumor suppressor function.
FMNL2 Drives Actin-Based Protrusion and Migration Downstream of Cdc42 (2012)

Cell migration entails protrusion of lamellipodia, densely packed networks of actin filaments at the cell front. Filaments are generated by nucleation, likely mediated by Arp2/3 complex and its activator Scar/WAVE. It is unclear whether formins contribute to lamellipodial actin filament nucleation or serve as elongators of filaments nucleated by Arp2/3 complex. Here we show that the Diaphanous-related formin FMNL2, also known as FRL3 or FHOD2, accumulates at lamellipodia and filopodia tips. FMNL2 is cotranslationally modified by myristoylation and regulated by interaction with the Rho-guanosine triphosphatase Cdc42. Abolition of myristoylation or Cdc42 binding interferes with proper FMNL2 activation, constituting an essential prerequisite for subcellular targeting. In vitro, C-terminal FMNL2 drives elongation rather than nucleation of actin filaments in the presence of profilin. In addition, filament ends generated by Arp2/3-mediated branching are captured and efficiently elongated by the formin. Consistent with these biochemical properties, RNAi-mediated silencing of FMNL2 expression decreases the rate of lamellipodia protrusion and, accordingly, the efficiency of cell migration. Our data establish that the FMNL subfamily member FMNL2 is a novel elongation factor of actin filaments that constitutes the first Cdc42 effector promoting cell migration and actin polymerization at the tips of lamellipodia.