gebhart/patrepeval huggingface dataset:
Template‐based protein structure modeling using TASSER<sup>VMT</sup> (2011)

Template-based protein structure modeling is commonly used for protein structure prediction. Based on the observation that multiple template-based methods often perform better than single template-based methods, we further explore the use of a variable number of multiple templates for a given target in the latest variant of TASSER, TASSER(VMT) . We first develop an algorithm that improves the target-template alignment for a given template. The improved alignment, called the SP(3) alternative alignment, is generated by a parametric alignment method coupled with short TASSER refinement on models selected using knowledge-based scores. The refined top model is then structurally aligned to the template to produce the SP(3) alternative alignment. Templates identified using SP(3) threading are combined with the SP(3) alternative and HHEARCH alignments to provide target alignments to each template. These template models are then grouped into sets containing a variable number of template/alignment combinations. For each set, we run short TASSER simulations to build full-length models. Then, the models from all sets of templates are pooled, and the top 20-50 models selected using FTCOM ranking method. These models are then subjected to a single longer TASSER refinement run for final prediction. We benchmarked our method by comparison with our previously developed approach, pro-sp(3) -TASSER, on a set with 874 easy and 318 hard targets. The average GDT-TS score improvements for the first model are 3.5 and 4.3% for easy and hard targets, respectively. When tested on the 112 CASP9 targets, our method improves the average GDT-TS scores as compared to pro-sp3-TASSER by 8.2 and 9.3% for the 80 easy and 32 hard targets, respectively. It also shows slightly better results than the top ranked CASP9 Zhang-Server, QUARK and HHpredA methods. The program is available for download at http://cssb.biology.gatech.edu/.
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data (2013)

The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online.
Retardation and reaction mechanisms of magnesium phosphate cement mixed with glacial acetic acid (2017)

This study aims to investigate the effect of admixture glacial acetic acid on the setting time, compressive strength, and hydration temperature of magnesium phosphate cement.
Short Answer Grading Using String Similarity And Corpus-Based Similarity (2012)

Most automatic scoring systems use pattern based that requires a lot of hard and tedious work. These systems work in a supervised manner where predefined patterns and scoring rules are generated. This paper presents a different unsupervised approach which deals with students’ answers holistically using text to text similarity. Different String-based and Corpus-based similarity measures were tested separately and then combined to achieve a maximum correlation value of 0.504. The achieved correlation is the best value achieved for unsupervised approach Bag of Words (BOW) when compared to previous work.
New macrosegregation criteria for quality problems in continuous casting of steel (2013)

To estimate the quality condition in continuously cast steel slabs, simple but accurate macrosegregation criteria have been proposed. The formation of macrosegregation phenomena in continuous casting of peritectic carbon steels has been investigated by metallographic study of collected slab samples. The metallographic study involved plant trails to collect the slab samples and to prepare them for chemical macrosegregation analysis. The experimental results show a fluctuation of carbon between positive and negative segregation with distance from slab surface based on the cooling conditions experienced by the slab. Via mathematical analysis, formulae of average macrosegregation level ASL, its fluctuation level FSL and its segregation quality number SQN have been developed. The results calculated by these formulae show good agreement with the description of the formation mechanisms of different continuous casting defects and their locations. Therefore, these calculations illustrated that macrosegregation criteria and their distributions can be considered by experimental, simple and vital tools to evaluate the conditions of surface and inner qualities in continuously cast steel slabs. The mechanisms of these criteria with some mechanisms of continuous casting defects have been explained and discussed.
Instruction-driven wake-up mechanisms for Snoopy TAP controller (2003)

The issue of handling multiple embedded 1149.1-compliant TAP controllers (as part of embedded cores) in a 1149.1-compliant IC, has received significant attention, in recent times. The Hierarchical TAP (HTAP) architecture, previously developed by this author, provides a systematic solution to this problem, by allowing multiple embedded TAPs to share one set of 1149.1-specified test pins on the IC. The HTAP architecture requires an augmented version of the 1149.1-specified TAP-designated the Snoopy TAP (SNTAP)-in the top-level of the design hierarchy, that handles 1149.1-specified TAP functions for the non-TAP'ed parts of the IC, and performs arbitration of the shared IC pins between multiple embedded TAPs. Previously, a mechanism was developed to wake up the SNTAP using a simple string of constant values (0 or 1) on the TMS input. Two new mechanisms to wake up SNTAP by means of an instruction scanned in, are described in this report. Both mechanisms allow embedded 1149.1-compliant TAP's to be used in a hierarchical design, as is, without any hardware modification. Moreover, both mechanisms enable reuse of the test program from the embedded TAP'ed cores, without any modification. The instructions to wake up the SNTAP-to switch access to different TAP-ed cores-can be simply inserted in-between the test programs for the embedded cores.
Direct Determination of the Energy Required to Operate a Single Molecule Switch (2003)

Using a noncontact atomic-force and scanning-tunneling microscope in ultrahigh vacuum, we have measured the switching energy of a single molecule switch based on the rotation of a di-butyl-phenyl leg in a Cu-tetra-3,5 di-tertiary-butyl-phenyl porphyrin. The mechanics and intramolecular conformation of the switched leg is controlled by the tip apex of the noncontact atomic-force microscope. The comparison between experimental and calculated force curves shows that the rotation of the leg requires an energy less than 100 x 10(-21) J, which is 4 orders of magnitude lower than state-of-the-art transistors.
Host-Directed Antimicrobial Drugs with Broad-Spectrum Efficacy against Intracellular Bacterial Pathogens (2014)

We sought a new approach to treating infections by intracellular bacteria, namely, by altering host cell functions that support their growth. We screened a library of 640 Food and Drug Administration (FDA)-approved compounds for agents that render THP-1 cells resistant to infection by four intracellular pathogens. We identified numerous drugs that are not antibiotics but were highly effective in inhibiting intracellular bacterial growth with limited toxicity to host cells. These compounds are likely to target three kinds of host functions: (i) G protein-coupled receptors, (ii) intracellular calcium signals, and (iii) membrane cholesterol distribution. The compounds that targeted G protein receptor signaling and calcium fluxes broadly inhibited Coxiella burnetii, Legionella pneumophila, Brucella abortus, and Rickettsia conorii, while those directed against cholesterol traffic strongly attenuated the intracellular growth of C. burnetii and L. pneumophila. These pathways probably support intracellular pathogen growth so that drugs that perturb them may be therapeutic candidates. Combining host- and pathogen-directed treatments is a strategy to decrease the emergence of drug-resistant intracellular bacterial pathogens. Importance: Although antibiotic treatment is often successful, it is becoming clear that alternatives to conventional pathogen-directed therapy must be developed in the face of increasing antibiotic resistance. Moreover, the costs and timing associated with the development of novel antimicrobials make repurposed FDA-approved drugs attractive host-targeted therapeutics. This paper describes a novel approach of identifying such host-targeted therapeutics against intracellular bacterial pathogens. We identified several FDA-approved drugs that inhibit the growth of intracellular bacteria, thereby implicating host intracellular pathways presumably utilized by bacteria during infection.
[WT1-targeting cancer vaccine]. (2012)

Wilms' tumor gene WT1 encodes a transcription factor and functions as an oncogene. WT1 gene product WT1 protein is a promising par-tumor-associated antigen. WT1 peptide-based immunotherapy has been performing for more than six hundred patients with leukemias and various types of solid tumors. This immunotherapy is safe and has clinical benefit especially for leukemia, glioblastoma multiforme, advanced pancreatic cancer, and ovarian cancer. As a new strategy for cancer treatment, it should be recommended to initiate immunotherapy that had a potential of eradication of cancer stem cells before surgery, chemo- and radio-therapy.
Ambient Technology to Assist Elderly People in Indoor Risks (2016)

While elderly people perform their daily indoor activities, they are subjected to several risks. To improve the quality of life of elderly people and promote healthy aging and independent living, elderly people need to be provided with an assistive technology platform to rely on during their activities. We reviewed the literature and identified the major indoor risks addressed by assistive technology that elderly people face during their indoor activities. In this paper, we identify these risks as: fall, wrong self-medication management, fire, burns, intoxication by gas/smoke, and the risk of inactivity. In addition, we discuss the existing assistive technology systems and classify the risk detection algorithms, techniques and the basic system principles and interventions to enhance safety of elderly people.
Specific Emitter Identification for Cognitive Radio with Application to IEEE 802.11 (2008)

Cognitive radio (CR) is believed to be an enabling technology for increasing spectrum efficiency. A CR collects spectrum usage information from not only its own spectrum sensing module, but also from peer CRs. The heavy dependence on spectrum knowledge from other CRs requires identification of malicious CR devices that could generate spoofed information. In addition, it also needs to track the users associated with problematic CR devices which unintentionally violate spectrum usage etiquette. The specific emitter identification (SEI) concept is applied to identification of such non-cooperative CR devices. In this paper, second-order cyclic features of OFDM signals are proposed as a means of increasing CR network security and stability through SEI. For this exploratory work, IEEE 802.11a/g signals from different WLAN cards are measured and classified using hidden Markov Models (HMMs).
Optical wireless multispot diffusing: a MIMO configuration (2004)

Optical (infrared) wireless communications links offer an attractive solution for indoor applications. To enable terminal mobility and reduce temporal dispersion, a configuration known as multispot-diffusing (MSD) is used, which is a multiinput, multioutput (MIMO) architecture. In this configuration, a transmitter generates multiple narrow beams that get uniformly spread over a reflection surface accessible to a service area. A multibranch receiver with each branch having access to a diffusing spot (generated by transmitter) combines signals on its branches. This scheme creates multiple virtually ideal communications channels between a base station and terminals. This paper considers issues involved in the design of a transmitter-based holographic spot array generator. The generator produces equally-spaced diffusing spots on the room ceiling and/or walls. To overcome power limitation set by eye safety requirements, a receiver optical concentrator is proposed. Furthermore, to improve receiver signal-to-noise ratio, an optical filter that rejects optical noise is needed. Thus, functionally receiver branch optical front-end consists of an optical concentrator and an optical band-pass filter. A single holographic optical element, capable of performing both functions is proposed. Link performance is investigated by providing equivalent link model and comparing probability of error for a bare and a holographic receiver. From performance evaluations, our results show that it is possible to achieve an increase of 11 dB in the SNR and improve power budget by reducing the path loss by over 6 dB.
Hardware for Computing Modular Multiplication Algorithm (1998)

This paper examines the characteristics of an alternative architecture for computing a modular multiplication based on Montgomery&apos;s algorithm, useful in performing the RSA Public Key Cryptosystems. An experimental 12x12 bits modular multiplier prototype has been designed with this architecture. Is fabricated by AMS using 0.6 µm-CMOS technology. The architecture, its operation and some simulation results are presented. The evaluation is provided according to the functionality. The active area size is 1.33 x 0.93 mm 2 containing a number of transistors about 4100. 1. Introduction VLSI circuits that accelerate the encryption and decryption of messages using the RSA encryption technique [1] and circuits capable of performing long wordlength modulo multiplication at very high speed attract much interest for cryptography applications. Modular exponentiation operation is the main and more frequently function to process hidden information, for that reason, modular exponentiation plays impor...
A magnetoelastic force transducer based on bending a circumferentially magnetized tube (2010)

A new type of magnetoelastic device for sensing force is described. It consists of two elements: a circumferentially magnetized tube of magnetoelastically active material, mounted as a beam and loaded by the force to be sensed, and a magnetic field sensor mounted at or near the tube’s surface, at or near a longitudinal location where the bending moment is maximum and at a circumferential location where the stress is zero. The flexural loading is shown to cause a variation in the circumferential magnetization with angular position. This variation is the source of free poles, the field from which is a measure of the applied force. Analysis predicts, and experiments demonstrate that the field intensity is a linear analog of the force over a significant range of push and pull forces.
Comprehensive gene expression analysis of the response to straight-chain alcohols in Saccharomyces cerevisiae using cDNA microarray (2004)

The study of comprehensive gene expression profiles by cDNA microarrays elucidates the straight-chain alcohol adaptation mechanisms.
Interactive Scan Control for Kinematic Study in Open MRI (2007)

The ISC shortens total time for kinematic joint imaging, and because a support tool is not needed, imaging can be done more freely in an open MR imaging apparatus.
Sequenced subset operators: definition and implementation (2003)

Difference, intersection, semi join and anti-semi-join may be considered binary subset operators, in that they all return a subset of their left-hand argument. These operators are useful for implementing SQL's EXCEPT, INTERSECT, NOT IN and NOT EXISTS, distributed queries and referential integrity. Difference-all and intersection-all operate on multi-sets and track the number of duplicates in both argument relations; they are used to implement SQL's EXCEPT ALL and INTERSECT ALL. Their temporally sequenced analogues, which effectively apply the subset operator at each point in time, are needed for implementing these constructs in temporal databases. These SQL expressions are complex; most necessitate at least a three-way join, with nested NOT EXISTS clauses. We consider how to implement these operators directly in a DBMS. These operators are interesting in that they can fragment the left-hand validity periods (sequenced difference-all also fragments the right-hand periods) and thus introduce memory complications found neither in their non-temporal counterparts nor in temporal joins and semijoins. We introduce novel algorithms for implementing these operators by ordering the computation so that fragments need not be retained in main memory. We evaluate these algorithms and demonstrate that they are no more expensive than a single conventional join.
Routes of Synthesis of Carbapenems for Optimizing Both the Inactivation of <scp>l</scp>,<scp>d</scp>-Transpeptidase Ldt<sub>Mt1</sub> of <i>Mycobacterium tuberculosis</i> and the Stability toward Hydrolysis by β-Lactamase BlaC (2016)

Combinations of β-lactams of the carbapenem class, such as meropenem, with clavulanate, a β-lactamase inhibitor, are being evaluated for the treatment of drug-resistant tuberculosis. However, carbapenems approved for human use have never been optimized for inactivation of the unusual β-lactam targets of Mycobacterium tuberculosis or for escaping to hydrolysis by broad-spectrum β-lactamase BlaC. Here, we report three routes of synthesis for modification of the two side chains carried by the β-lactam and the five-membered rings of the carbapenem core. In particular, we show that the azide-alkyne Huisgen cycloaddition reaction catalyzed by copper(I) is fully compatible with the highly unstable β-lactam ring of carbapenems and that the triazole ring generated by this reaction is well tolerated for inactivation of the L,D-transpeptidase LdtMt1 target. Several of our new carbapenems are superior to meropenem both with respect to the efficiency of in vitro inactivation of LdtMt1 and reduced hydrolysis by BlaC.
Molecular Mechanisms of T Cells Activation by Dendritic Cells in Autoimmune Diseases (2018)

The interaction between T cell and dendritic cells (DCs) that leads to T cell activation affects the progression of the immune response including autoimmune diseases. Antigen presentation on immune cell surface, formation of an immunological synapse (IS), and specific identification of complex by T cells including two activating signals are necessary steps that lead to T cell activation. The formation of stimulatory IS involves the inclusion of costimulatory molecules, such as ICAM-1/LFA-1 and CD28/B7-1, and so on. Some fusion proteins and monoclonal antibodies targeting costimulatory molecules have been developed and approved to treat autoimmune diseases, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), multiple sclerosis (MS), type I diabetes (T1D), inflammatory bowel disease (IBD), and psoriasis. These biological agents, including CTLA-4- and LFA-3-Ig, anti-CD3 monoclonal antibody, could prevent the successful engagement of DCs by T cell with significant efficacy and safety profile. In this article, we reviewed the molecular mechanisms of T cell activation during the interaction between T cells and DCs, and summarized some biological agents that target costimulatory molecules involved in the regulation of T cell activation.
Benefits of Chip Scale Atomic Clocks in GNSS Applications (2015)

Due to the limited frequency stability and poor accuracy of GNSS receiver's internal quartz oscillators, a receiver clock error has to be estimated in addition to the coordinates. This leads to two major drawbacks especially in kinematic applications: (i) the up-coordinate is determined two to three times less precise than the horizontal coordinates, (ii) high correlations between the clock estimates and the up-coordinates. This situation can be improved distinctly when connecting an atomic clock to a GNSS receiver, and modeling its behavior in a physically meaningful way. This approach is called receiver clock modeling.
Recent developments in miniaturizing atomic clocks resulted in so called chip scale atomic clocks, and open up the possibility of using a stable atomic clock in GNSS applications. We present a deterministic method of receiver clock modeling in a sequential least-squares adjustment for the application of an atomic clock in code-based GNSS navigation.
The benefits of clock modeling in such a case are assessed as follows: decrease of the noise of the up-coordinates by up to 58%, and enhancement of internal and external reliability. Hence, a more robust position is obtained. Additionally, artificial partial satellite outages are generated to show our method's capability of computing position solutions with only three satellites in view.
Finally, we investigate the benefits of an atomic clock in spoofing detection, and show preliminary results. Especially in the early stages of a spoofing attack, such a stable clock helps to identify the same and warn the user.
Biological Chemistry of<i>o</i>‐Quinones (2011)

This chapter contains sections titled: General Biological Significance of o-Quinones o-Quinone Reactivity Role of o-Quinones in Melanogenesis References
A TRIPLE WIRE MEDIUM AS AN ISOTROPIC NEGATIVE PERMITTIVITY METAMATERIAL (2006)

This paper presents an effective medium approach to calculate the attenuation and phase constants of modes in a 3D connected wire medium both below and above the plasma frequency. Physical and nonphysical modes in the structure are identified for all the important lattice directions. According to this, the medium behaves as an isotropic material in the vicinity of the plasma frequency. These results were compared with the numerical simulation and it was observed that the wave spreads below the plasma frequency along all the important lattice directions with the same attenuation constant. This implies isotropic behavior of the 3D wire lattice below the plasma frequency, and thus this medium can be considered as an isotropic negative permittivity medium.