gebhart/patrepeval huggingface dataset:
A deductive database system PACADE for the three dimensional structure of protein (2002)

Describes a deductive database system PACADE (Protein Atomic Coordinate Analyzer with Deductive Engine) which facilitates a search of three dimensional data kept at the Brookhaven's Protein Data Bank. This system has the following features. Recursive relations can be handled. Long range connectivities between amino acids in proteins can be searched from short range connectivities. The system involves deduction from the approach of bottom up evaluation. Unlike Prolog, it always computes all answers without a description of the control by users and always terminates. This system makes use of query processing techniques proposed for computer science, hence queries are processed efficiently.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Validity, reliability and responsiveness of the Work Productivity and Activity Impairment Questionnaire in ankylosing spondylitis (2010)

ClinicalTrials.gov, http://clinicaltrials.gov/ct2/home, NCT00085644.
Discussion of the Physicochemical Effects of Modifiers on the Extraction Properties of Hydroxyoximes. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Chlorophyll Biosynthesis in Bacteria: The Origins of Structural and Functional Diversity (2007)

The use of photochemical reaction centers to convert light energy into chemical energy, chlorophototrophy, occurs in organisms belonging to only five eubacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, and Firmicutes. All chlorophototrophs synthesize two types of pigments: (a) chlorophylls and bacteriochlorophylls, which function in both light harvesting and uniquely in photochemistry; and (b) carotenoids, which function primarily as photoprotective pigments but can also participate in light harvesting. Although hundreds of carotenoids have been identified, only 12 types of chlorophylls (Chl a, b, d; divinyl-Chl a and b; and 8(1)-hydroxy-Chl a) and bacteriochlorophylls (BChl a, b, c, d, e, and g) are currently known to occur in bacteria. This review summarizes recent progress in the identification of genes and enzymes in the biosynthetic pathways leading to Chls and BChls, the essential tetrapyrrole cofactors of photosynthesis, and addresses the mechanisms for generating functional diversity for solar energy capture and conversion in chlorophototrophs.
Synthesis, high-field NMR, X-ray structure, and conformational analysis of a 10-membered diamide disulfide ring (1997)

N,N′-[Dimethyl-(2,2′-dithiobisacetyl)]ethylenediamine (1) has been synthesized in 30% overall yield from N,N′-dimethylethylenediamine and thioacetic acid by an improved procedure involving simultaneous deprotection and oxidative cyclization with iodine. This cyclic diamide disulfide exists in solution as a mixture of two Z,Z and one Z,E disulfide, and amide ring conformers and has been characterized by nuclear Overhauser effect (NOE), 1 H– 1 H, 1 H– 13 C shift-correlated 2D-NMR and molecular modelling studies. Among the Z,Z ring conformers Z,Z 1 and Z,Z 2 , the former predominates and interconverts with the latter isomer by rotation about the S—S bond with an activation energy of 14.5 ± 1.3 kcal/mol. Coalescence of N-CH 3 signals occurred at ca. 127 °C (500 MHz), which corresponded to an approximate barrier to amide rotation of 19.3 kcal/mol. Aromatic solvent-induced shifts in C 6 D 6 corroborated molecular mechanics and NOE predictions of amide stereochemistry. The structure of the Z,E stereoisomer of 1 has been determined by single-crystal X-ray diffraction at 296 K. A large geminal N-CH 2 inequivalence (>2 ppm in CDCl 3 ) was observed for the Z,Z conformers. Proton chemical shifts have been calculated for the conformers of 1 and related molecular fragments with DFT/GIAO theory. Absolute chemical shifts are modelled within 0.2 ppm of experiment. The unusual nonequivalence of geminal N-CH 2 and S-CH 2 protons can be understood as a combination of shielding mechanisms derived from short N-methyl contacts, amide group orientation, and sulfur lone-pair disposition. An implication of these results is the possibility of using α-CH (and eventually α-CH) shifts to probe the local conformational space in cyclic peptides and other conformationally constrained rings. Keywords: amide/disulfide rotamers, conformational analysis, density functional theory, DFT/GIAO NMR shift calculations, methylene nonequivalence, molecular modelling.
Surface‐Bound Microenclosures for Biomolecules (2010)

It's a trap! A simple process based on reverse-phase layer-by-layer encapsulation can be used to produce surface-bound semipermeable microenclosures that can trap biomolecules. Biomolecules such as nucleic acids and proteins can be encapsulated whilst preserving their functionality. Electrophoresis can be used to create sharp concentration gradients, and enzymatic reactions such as DNA digestion can be controlled by diffusion of ions into the microenclosures (see picture). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Web-based GIS System for Prompted Recall of GPS-Assisted Personal Travel Surveys: System Development and Experimental Study (2008)

The advancement of the Global Positioning System (GPS) and web-based Geographic Information System (GIS) technologies over the past decade has offered an opportunity to develop interactive prompted recall personal travel/activity surveys over the Internet. This thesis project has resulted in the development of a new web-based software system to support emerging GPS-assisted personal travel surveys. The system, called TRIPS, enables data processing and data display, and it provides editing tools for prompted recall and post validation of GPS-based survey data. An experimental study was conducted using TRIPS to investigate various issues related to prompted recall surveys. This study showed the importance of providing human assistance to survey participants, particularly in tasks of activity/link editing. It also addressed other challenges associated with implementing TRIPS, including online data processing performance, multi-task handling, and browser variability.
The tangled web of self-tying knots (2007)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Synthesis of nicotinamide adenine dinucleotide (NAD) from adenosine monophosphate (AMP) (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of nicotinamide adenine dinucleotide (NAD) from adenosine monophosphate (AMP)David R. Walt, Victor M. Rios-Mercadillo, Jacques Auge, and George M. WhitesidesCite this: J. Am. Chem. Soc. 1980, 102, 26, 7805–7806Publication Date (Print):December 1, 1980Publication History Published online1 May 2002Published inissue 1 December 1980https://pubs.acs.org/doi/10.1021/ja00546a041https://doi.org/10.1021/ja00546a041research-articleACS PublicationsRequest reuse permissionsArticle Views626Altmetric-Citations19LEARN 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-Alertsclose Get e-Alerts
Universal loop assembly: open, efficient and cross-kingdom DNA fabrication (2020)

Standardized type IIS DNA assembly methods are becoming essential for biological engineering and research. These methods are becoming widespread and more accessible due to the proposition of a 'common syntax' that enables higher interoperability between DNA libraries. Currently, Golden Gate (GG)-based assembly systems, originally implemented in host-specific vectors, are being made compatible with multiple organisms. We have recently developed the GG-based Loop assembly system for plants, which uses a small library and an intuitive strategy for hierarchical fabrication of large DNA constructs (>30 kb). Here, we describe 'universal Loop' (uLoop) assembly, a system based on Loop assembly for use in potentially any organism of choice. This design permits the use of a compact number of plasmids (two sets of four odd and even vectors), which are utilized repeatedly in alternating steps. The elements required for transformation/maintenance in target organisms are also assembled as standardized parts, enabling customization of host-specific plasmids. Decoupling of the Loop assembly logic from the host-specific propagation elements enables universal DNA assembly that retains high efficiency regardless of the final host. As a proof-of-concept, we show the engineering of multigene expression vectors in diatoms<i>,</i> yeast, plants and bacteria. These resources are available through the OpenMTA for unrestricted sharing and open access.
ChemInform Abstract: Studies on a New Phosphonate Carbanion. (1987)

Abstract Treatment of the phosphonate (I) with NaH/THF produces a pinkish‐red colored solution of the carbanion (II) which reacts with the aldehydes (III) to give the derivatives (IV).
Zinc-finger transcription factor Gfi-1: versatile regulator of lymphocytes, neutrophils and hematopoietic stem cells (2005)

Considerable progress has been made in understanding Gfi-1's context-sensitive roles at defined stages of hematopoietic differentiation.
Coating and photochemical properties of calcia-doped ceria with amorphous silica by a seeded polymerization technique (2005)

Calcia doped ceria is of potential interest as an ultraviolet (UV) radiation blocking material in personal care products because of its excellent UV light absorption properties and its low catalytic ability for the oxidation of organic materials is superior to undoped ceria. In order to reduce the oxidation catalytic activity further, calcia doped ceria was coated with amorphous silica by means of a seeded polymerization technique. The silica shell was confirmed using scanning electron microscopy, TEM, XPS and FT-IR. Silica coating by seeded polymerization was much more efficient in the reduction of the oxidation catalytic activity without loss of the UV-shielding ability, than coating by acid hydrolysis of a sodium silicate solution.
RF and mm-wave SOP module platform using LCP and RF MEMS technologies (2004)

In this paper, we present a Liquid Crystal Polymer (LCP) based multilayer packaging technology combined with RF-MEMS technology and its emergence as an ideal platform for low cost, multi-band and reconfigurable RF front-end module integration. LCP's very low water absorption (0.04%), low cost and high electrical performance makes it very appealing for RF applications. Here, we describe the characterization of LCP material up to W band, design of single input single output (SISO) dual band filters with insertion loss as low as 2.4 dB in L band and 1.8 dB in C band respectively. MEMS-SOP switch fabrication and finally integration of C band wireless LAN (WLAN) module demonstrates the potential for compact, multiband and reconfigurable systems. This is the first complete report on the combination of LCP with RF-MEMS technology as a new approach towards the System-On-Package (SOP) solutions for wireless communication applications.
Bit-level pipelined digit serial GF(2/sup m/) multiplier (2002)

A low latency digit serial multiplier for GF(2/sup m/) that can be pipelined to the bit-level is presented in this paper. Unlike existing structures, the new multiplier does not put any restriction on the type of generator polynomial used or the digit size. Furthermore, the latency of the new multiplier is significantly less than the latency of the existing bit-level pipelined digit-serial multiplier.
Cache aware optimization of stream programs (2005)

Effective use of the memory hierarchy is critical for achieving high performance on embedded systems. We focus on the class of streaming applications, which is increasingly prevalent in the embedded domain. We exploit the widespread parallelism and regular communication patterns in stream programs to formulate a set of cache aware optimizations that automatically improve instruction and data locality. Our work is in the context of the Synchronous Dataflow model, in which a program is described as a graph of independent actors that communicate over channels. The communication rates between actors are known at compile time, allowing the compiler to statically model the caching behavior.We present three cache aware optimizations: 1) execution scaling, which judiciously repeats actor executions to improve instruction locality, 2) cache aware fusion, which combines adjacent actors while respecting instruction cache constraints, and 3) scalar replacement, which converts certain data buffers into a sequence of scalar variables that can be register allocated. The optimizations are founded upon a simple and intuitive model that quantifies the temporal locality for a sequence of actor executions. Our implementation of cache aware optimizations in the StreamIt compiler yields a 249% average speedup (over unoptimized code) for our streaming benchmark suite on a StrongARM 1110 processor. The optimizations also yield a 154% speedup on a Pentium 3 and a 152% speedup on an Itanium 2.
Mislocalized Rhodopsin Does Not Require Activation to Cause Retinal Degeneration and Neurite Outgrowth in<i>Xenopus laevis</i> (2006)

Mutations in the C terminus of rhodopsin disrupt a rod outer segment localization signal, causing rhodopsin mislocalization and aggressive forms of retinitis pigmentosa (RP). Studies of cultured photoreceptors suggest that activated mislocalized rhodopsin can cause cell death via inappropriate G-protein-coupled signaling. To determine whether this pathway occurs in vivo, we developed a transgenic Xenopus laevis model of RP based on the class I rhodopsin mutation Q344Ter (Q350Ter in X. laevis). We used a second mutation, K296R, to block the ability of rhodopsin to bind chromophore and activate transducin. We compared the effects of expression of both mutants on X. laevis retinas alone and in combination. K296R did not significantly alter the cellular distribution of rhodopsin and did not induce retinal degeneration. Q350Ter caused rhodopsin mislocalization and induced an RP-like degeneration, including loss of rods and development of sprouts or neurites in some remaining rods, but did not affect the distribution of endogenous rhodopsin. The double mutant K296R/Q350Ter caused a similar degeneration and neurite outgrowth. In addition, we found no protective effects of dark rearing in these animals. Our results demonstrate that the degenerative effects of mislocalized rhodopsin are not mediated by the activated form of rhodopsin and therefore do not proceed via conventional G-protein-coupled signaling.
<i>In Vivo</i><sup>1</sup>H‐NMR microimaging with respiratory triggering for monitoring adoptive immunotherapy of metastatic mouse lymphoma (1997)

The metastatic ESb-MP murine lymphoma in DBA/2 mice has been used as a model for investigating metastatic disease and its cure by adoptive immunotherapy (ADI) as monitored by in vivo multislice spin-echo 1H NMR microimaging at 7 T. isoflurane inhalation anesthesia facilitated long measurement sessions, and respiratory gating with a fiber-optic sensor greatly reduced motional artifacts. With T2 weighting (TR = 2 s, TE = 30 ms) mean signal-to-noise ratios of 30 and 15 for kidney and liver, respectively, were achieved in 20 min (100-micron pixels, 1-mm slices, 25-mm field of view). Without the use of contrast agents, metastases with diameters > or = 0.3 mm in the imaged plane could be detected as hyperintense lesions in kidney (contrast ratio ca. 1.4) and liver (contrast ratio ca. 2) with a confidence level of > 98%. For the first time the complete eradication of late-stage macroscopic metastases by ADI could be demonstrated noninvasively by MRI.
A Fast and Accurate Method for Approximate String Search (2011)

This paper proposes a new method for approximate string search, specifically candidate generation in spelling error correction, which is a task as follows. Given a misspelled word, the system finds words in a dictionary, which are most “similar ” to the misspelled word. The paper proposes a probabilistic approach to the task, which is both accurate and efficient. The approach includes the use of a log linear model, a method for training the model, and an algorithm for finding the top k candidates. The log linear model is defined as a conditional probability distribution of a corrected word and a rule set for the correction conditioned on the misspelled word. The learning method employs the criterion in candidate generation as loss function. The retrieval algorithm is efficient and is guaranteed to find the optimal k candidates. Experimental results on large scale data show that the proposed approach improves upon existing methods in terms of accuracy in different settings. 1
The influence of 1 alpha-hydroxycholecalciferol on left ventricular function in end-stage renal failure. (1981)

This study was designed to assess the influence of 1 alpha-hydroxycholecalciferol on left ventricular function in end-stage renal failure. Twelve patients, all of whom were on regular haemodialysis, were investigated. M-mode echocardiography and systolic time intervals were used to derive indices of left ventricular function. Measurements were performed before and six weeks after treatment with one microgram daily of 1 alpha-hydroxycholecalciferol. Fractional fibre shortening increased from 34.6 to 37.6% (p less than 0.025) and mean velocity of fibre shortening increased from 1.21 to 1.32 circ/sec (p less than 0.01). These changes were associated with a fall in the mean plasma parathyroid hormone concentration from 1883 to 1123ng/L (p less than 0.0025) and a rise in magnesium concentration from 0.89 to 1.06 mmol/L (p less than 0.0025); plasma calcium increased from 2.59 to 2.70mmol/L but this change was not significant. Our results indicate that 1 alpha-hydroxycholecalciferol improves left ventricular function in end-stage renal failure by influencing both the turnover or secretion of parathyroid hormone and the metabolism of calcium and magnesium ions.
Effects of Glyphosate Combinations by 2,4-D or Dicamba on Field Bindweed (<i>Convolvulus arvensis</i>) (1989)

Applications of isopropylamine glyphosate at 0.28, 0.56, 0.84, and 1.12 kg ae/ha in combination with the dimethylamine salts of 2,4-D or dicamba at 0.14, 0.28, 0.42, and 0.56 kg ae/ha produced additive or synergistic field bindweed control compared to the herbicides applied alone. Leaf and root growth was inhibited more from herbicide combinations than would be predicted from the effects of the chemicals applied alone at the same rate. The uptake of 14 C from glyphosate into the treated leaf and its accumulation in roots increased when 2,4-D or dicamba was combined with the 0.28 kg/ha rate of 14 C-glyphosate. The combination of 2,4-D or dicamba with a higher (0.84 kg/ha) 14 C-glyphosate rate did not change total absorption of 14 C from glyphosate. However, compared to 0.84 kg/ha of 14 C-glyphosate applied alone, less 14 C accumulated above the treated leaf and more accumulated in the roots when 2,4-D was added to the glyphosate. The combination of glyphosate with 2,4-D or dicamba generally resulted in both increased uptake of 14 C from 2,4-D or dicamba and greater accumulation in the roots. The additive or synergistic field bindweed control observed from mixtures of glyphosate with 2,4-D or dicamba appeared to be due to greater accumulation of the herbicides in the roots.
Evaluation of various substances to prevent adsorption of tuberculin purified protein derivative (PPD) to glass surfaces. (1970)

It is well known that a dilute tuberculin PPD solution (1 IU or 5 IU per dose) very rapidly loses its potency owing to adsorption of tuberculoprotein to the wall of the container into which it is dispensed. The amount of tuberculoprotein adsorbed per cm(2) of glass surface has been measured for phosphate-buffered saline over a wide pH range (pH 1 to pH 10). The maximum adsorption was found at pH 4 (0.31 mug/cm(2)) and the least at between pH 6 and pH 10 (0.15 mug/cm(2)). The rate of adsorption of tuberculoprotein to glass was not changed when the phosphate-buffered saline was replaced by borate-buffered saline. Tuberculin PPD prepared by the ammonium sulfate precipitation method, by the trichloroacetic acid precipitation method and by a combination of both methods adsorbed equally well to glass and no difference in the rate of adsorption for these tuberculoproteins was found.Forty-two substances in addition to Tween 80 were tested for their property to prevent adsorption of tuberculoprotein to glass in dilute tuberculin PPD solutions (50 IU/ml of (14)C-labelled PPD). The most efficient anti-adsorption agents were found to be nonionic surfactants, some ionic surfactants and some colloidal substances; polypeptides and non-surface-active substances of low molecular weight showed little or no anti-adsorption property.The labelling of PPD with (14)C has proved to be a valuable tool, particularly for long-term adsorption studies and for screening substances to be used as efficient anti-adsorption agents. These studies have permitted the selection of agents which could be added to dilute solutions of tuberculin PPD (10 IU/ml to 500 IU/ml or 0.2 mug/ml to 10 mug/ml respectively) in order to avoid loss of potency due to adsorption.
“Early” Class III Drugs for the Treatment of Atrial Fibrillation (2004)

AVE0118 markedly prolongs the AERP during AF without affecting QT duration. Cardioversion of AF was due to an approximately 2-fold increase in fibrillation wavelength. Atrium-selective class III drugs like AVE0118 may be a promising new option for safe and effective cardioversion of AF.