gebhart/patrepeval huggingface dataset:
Skipping steps in deformable simulation with online model reduction (2009)

Finite element simulations of nonlinear deformable models are computationally costly, routinely taking hours or days to compute the motion of detailed meshes. Dimensional model reduction can make simulations orders of magnitude faster, but is unsuitable for general deformable body simulations because it requires expensive precomputations, and it can suppress motion that lies outside the span of a pre-specified low-rank basis. We present an online model reduction method that does not have these limitations. In lieu of precomputation, we analyze the motion of the full model as the simulation progresses, incrementally building a reduced-order nonlinear model, and detecting when our reduced model is capable of performing the next timestep. For these subspace steps, full-model computation is "skipped" and replaced with a very fast (on the order of milliseconds) reduced order step. We present algorithms for both dynamic and quasistatic simulations, and a "throttle" parameter that allows a user to trade off between faster, approximate previews and slower, more conservative results. For detailed meshes undergoing low-rank motion, we have observed speedups of over an order of magnitude with our method.
Volatile Leaf Oil ofTagetes lemmoniiGray (1996)

ABSTRACT The essential oil of flowering Tagetes lemmonii Gray, which was examined by GC/MS, was dominated by dihydrotagetone (42.52±11.27%), (E)-tagetone (16.10±18.21%) and (E)-ocimenone (14.18±3.37).
Evidence that the plant cannabinoid Δ9‐tetrahydrocannabivarin is a cannabinoid CB1and CB2receptor antagonist (2005)

Delta9-tetrahydrocannabivarin (THCV) displaced [(3)H]CP55940 from specific binding sites on mouse brain and CHO-hCB(2) cell membranes (K(i)=75.4 and 62.8 nM, respectively).THCV (1 microM) also antagonized CP55940-induced stimulation of [(35)S]GTPgammaS binding to these membranes (apparent K(B)=93.1 and 10.1 nM, respectively). In the mouse vas deferens, the ability of Delta9-tetrahydrocannabinol (THC) to inhibit electrically evoked contractions was antagonized by THCV, its apparent K(B)-value (96.7 nM) approximating the apparent K(B)-values for its antagonism of CP55940- and R-(+)-WIN55212-induced stimulation of [(35)S]GTPgammaS binding to mouse brain membranes. THCV also antagonized R-(+)-WIN55212, anandamide, methanandamide and CP55940 in the vas deferens, but with lower apparent K(B)-values (1.5, 1.2, 4.6 and 10.3 nM, respectively).THCV (100 nM) did not oppose clonidine, capsaicin or (-)-7-hydroxy-cannabidiol-dimethylheptyl-induced inhibition of electrically evoked contractions of the vas deferens. Contractile responses of the vas deferens to phenylephrine hydrochloride or beta,gamma-methylene-ATP were not reduced by 1microM THCV or R-(+)-WIN55212, suggesting that THCV interacts with R-(+)-WIN55212 at prejunctional sites. At 32 microM, THCV did reduce contractile responses to phenylephrine hydrochloride and beta,gamma-methylene-ATP, and above 3 microM it inhibited electrically evoked contractions of the vas deferens in an SR141716A-independent manner. In conclusion, THCV behaves as a competitive CB(1) and CB(2) receptor antagonist. In the vas deferens, it antagonized several cannabinoids more potently than THC and was also more potent against CP55940 and R-(+)-WIN55212 in this tissue than in brain membranes. The bases of these agonist- and tissue-dependent effects remain to be established.
BACE1, a Major Determinant of Selective Vulnerability of the Brain to Amyloid-β Amyloidogenesis, is Essential for Cognitive, Emotional, and Synaptic Functions (2005)

A transmembrane aspartyl protease termed beta-site APP cleavage enzyme 1 (BACE1) that cleaves the amyloid-beta precursor protein (APP), which is abundant in neurons, is required for the generation of amyloid-beta (Abeta) peptides implicated in the pathogenesis of Alzheimer's disease (AD). We now demonstrate that BACE1, enriched in neurons of the CNS, is a major determinant that predisposes the brain to Abeta amyloidogenesis. The physiologically high levels of BACE1 activity coupled with low levels of BACE2 and alpha-secretase anti-amyloidogenic activities in neurons is a major contributor to the accumulation of Abeta in the CNS, whereas other organs are spared. Significantly, deletion of BACE1 in APPswe;PS1DeltaE9 mice prevents both Abeta deposition and age-associated cognitive abnormalities that occur in this model of Abeta amyloidosis. Moreover, Abeta deposits are sensitive to BACE1 dosage and can be efficiently cleared from the CNS when BACE1 is silenced. However, BACE1 null mice manifest alterations in hippocampal synaptic plasticity as well as in performance on tests of cognition and emotion. Importantly, memory deficits but not emotional alterations in BACE1(-/-) mice are prevented by coexpressing APPswe;PS1DeltaE9 transgenes, indicating that other potential substrates of BACE1 may affect neural circuits related to emotion. Our results establish BACE1 and APP processing pathways as critical for cognitive, emotional, and synaptic functions, and future studies should be alert to potential mechanism-based side effects that may occur with BACE1 inhibitors designed to ameliorate Abeta amyloidosis in AD.
An engineered VEGF‐activating zinc finger protein transcription factor improves blood flow and limb salvage in advanced‐age mice (2006)

Advances in understanding the relationship between protein structure and DNA binding specificity have made it possible to engineer zinc finger protein (ZFP) transcription factors to specifically activate or repress virtually any gene. To evaluate the potential clinical utility of this approach for peripheral vascular disease, we investigated the ability of an engineered vascular endothelial growth factor (VEGFa)-activating ZFP (MVZ+426b) to induce angiogenesis and rescue hindlimb ischemia in a murine model. Hindlimb ischemia was surgically induced in advanced-age C57/BL6 mice. Adenovirus (Ad) encoding either MVZ+426b or the fluorescent marker dsRed was delivered to the adducter muscle of the ischemic hindlimb, and the effects on blood flow, limb salvage, and vascularization were assessed. Ad-MVZ+426b induced expression of VEGFa at the mRNA and protein levels and stimulated a significant increase in vessel counts in the ischemic limb. This was accompanied by significantly increased blood flow and limb salvage as measured serially for 4 wk. These data demonstrate that activation of the endogenous VEGFa gene by an engineered ZFP can induce angiogenesis in a clinically relevant model and further document the feasibility of designing ZFPs to therapeutically regulate gene expression in vivo.
Nucleation of misfit dislocations in strained-layer epitaxy in the GexSi1−x/Si system (1989)

We describe theoretical and experimental investigations of the nucleation of lattice mismatch-accommodating dislocations in the strained GexSi1−x /Si(100) system. Experimentally it is found that at lower mismatches nucleation appears to be associated with growth defects, while at higher x, surface loop nucleation is favored. Theoretical predictions of the magnitude of activation barriers for homogeneous nucleation of dislocation half-loops at the growth surface decline dramatically with increasing lattice mismatch (higher x), with nucleation of mixed climb and glide (90°) loops favored to pure glide (60°) loops. These activation barriers for surface half-loops are shown to be lower than previously calculated due to consideration of the random alloy nature of the GexSi1−x epilayer.
Optical performance at the thermodynamic limit with tailored imaging designs (2005)

Ultracompact concentrators and illuminators that approach the thermodynamic limit to optical performance can be realized with purely imaging strategies. We explore two-stage reflector systems where each optical surface is tailored to eliminate one order of aberration--the so-called aplanatic designs. The contours are monotonic functions that can be expressed analytically, which are important for the facilitation of optimization studies and practical fabrication. The radiative performance of the devices presented is competitive with, and even superior to, that of high-flux nonimaging systems. Sample results of practical value in solar concentration and light collimation are presented for systems that cover a wide range of numerical aperture.
Isolation, characterization, and distribution of denitrifying toluene degraders from a variety of habitats (1994)

Enrichments capable of toluene degradation under O2-free denitrifying conditions were established with diverse inocula including agricultural soils, compost, aquifer material, and contaminated soil samples from different geographic regions of the world. Successful enrichment was strongly dependent on the initial use of relatively low toluene concentrations, typically 5 ppm. From the enrichments showing positive activity for toluene degradation, 10 bacterial isolates were obtained. Fingerprints generated by PCR-amplified DNA, with repetitive extragenic palindromic sequence primers, showed that eight of these isolates were different. Under aerobic conditions, all eight isolates degraded toluene, five degraded ethylbenzene, three consumed benzene, and one degraded chlorobenzene, meta-Xylene was the only other substrate used anaerobically and was used by only one isolate. All isolates were motile gram-negative rods, produced N2 from denitrification, and did not hydrolyze starch. All strains but one fixed nitrogen as judged by ethylene production from acetylene, but only four strains hybridized to the nifHDK genes. All strains appeared to have heme nitrite reductase since their DNA hybridized to the heme (nirS) but not to the Cu (nirU) genes. Five strains hybridized to a toluene ortho-hydroxylase catabolic probe, and two of those also hybridized to a toluene meta-hydroxylase probe. Partial sequences of the 16S rRNA genes of all isolates showed substantial similarity to 16S rRNA sequences of Azoarcus sp. Physiological, morphological, fatty acid, and 16S rRNA analyses indicated that these strains were closely related to each other and that they belong to the genus Azoarcus.(ABSTRACT TRUNCATED AT 250 WORDS)
Wild-Type Gyrase A Genotype of Neisseria gonorrhoeae Predicts In Vitro Susceptibility to Ciprofloxacin: A Systematic Review of the Literature and Meta-Analysis (2017)

Multidrug-resistant Neisseria gonorrhoeae infections have been declared 1 of the top 3 urgent threats to public health. Approaches to combat resistance include targeted therapy with antibiotics previously thought to be ineffective, made possible by rapid molecular assays to predict susceptibility. Previous studies have associated the gyrase A (gyrA) gene of N. gonorrhoeae with in vitro resistance to ciprofloxacin. We conducted a systematic review of studies comparing N. gonorrhoeae gyrA genotype results with conventional antimicrobial susceptibility testing results. We identified 31 studies meeting inclusion criteria, among which 7 different loci for mutations in the gyrA gene were identified, from 16 countries between the years of 1996 and 2016. We then performed a meta-analysis among those studies stratifying by use of real-time polymerase chain reaction (PCR) or non-real-time PCR technique, and compared the summary receiver operating characteristic curves between the 2 PCR methods. Among studies using real-time PCR, the pooled estimate of sensitivity and specificity of gyrA genotype results for the prediction of N. gonorrhoeae susceptibility to ciprofloxacin were 98.2% (95% confidence interval [CI], 96.5-99.1%) and 98.6% (95% CI, 97.0-99.3%), respectively. The summary operating characteristic curves for studies using real-time PCR techniques were well separated from those using non-real-time PCR techniques, with only slight overlap in the CIs, suggesting that real-time PCR techniques were a more accurate approach. GyrA genotype testing is a novel approach to combating the emergence of multidrug-resistant N. gonorrhoeae and is a sensitive and specific method to predict in vitro ciprofloxacin susceptibility.
Image Super-Resolution Via Sparse Representation (2010)

This paper presents a new approach to single-image super-resolution, based on sparse signal representation. Research on image statistics suggests that image patches can be well-represented as a sparse linear combination of elements from an appropriately chosen over-complete dictionary. Inspired by this observation, we seek a sparse representation for each patch of the low-resolution input, and then use the coefficients of this representation to generate the high-resolution output. Theoretical results from compressed sensing suggest that under mild conditions, the sparse representation can be correctly recovered from the downsampled signals. By jointly training two dictionaries for the low- and high-resolution image patches, we can enforce the similarity of sparse representations between the low resolution and high resolution image patch pair with respect to their own dictionaries. Therefore, the sparse representation of a low resolution image patch can be applied with the high resolution image patch dictionary to generate a high resolution image patch. The learned dictionary pair is a more compact representation of the patch pairs, compared to previous approaches, which simply sample a large amount of image patch pairs, reducing the computational cost substantially. The effectiveness of such a sparsity prior is demonstrated for both general image super-resolution and the special case of face hallucination. In both cases, our algorithm generates high-resolution images that are competitive or even superior in quality to images produced by other similar SR methods. In addition, the local sparse modeling of our approach is naturally robust to noise, and therefore the proposed algorithm can handle super-resolution with noisy inputs in a more unified framework.
Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians (2004)

For many years algorithms were taught exclusively to computer scientists, with relatively few students from other disciplines attending algorithms courses. A biology student in an algorithms class would be a surprising and unlikely (though not entirely unwelcome) guest in the 1990s. Things change; some biology students now take some sort of Algorithms 101. At the same time, curious computer science students often take Genetics 101. Here comes an important question of how to teach bioinformatics in the 21st century. Will we teach bioinformatics to future biology students as a collection of cookbook style recipes or as a computational science that first explain ideas and builds on applications afterwards? This is particularly important at the time when bioinformatics courses may soon become required for all graduate biology students in leading universities. Not to mention that some universities have already started undergraduate bioinformatics programs and the discussions are underway about adding new computational courses to the standard undergraduate biology curriculum a dramatic paradigm shift in biology education. Since bioinformatics is a computational science, a bioinformatics course should strive to present the principles and ideas that drive an algorithm’s design or explain a crux of a statistical approach, rather than to be a stamp-collection of the algorithms and statistical techniques themselves. Many existing bioinformatics books and courses reduce bioinformatics to a compendium of computational protocols without even trying to explain the computational ideas that drove the development of bioinformatics in the last 30 years. Other books (written by computer scientists for computer scientists) try to explain bioinformatics ideas at the level that is well above the computational level of most biologists. These books often fail to connect the computational ideas and applications thus reducing a biologist’s motivation to invest time and effort into such a book. We feel that focusing on ideas has more intellectual value and represents a long-term investment: protocols change quickly, but the computational ideas don’t seem to. However, the question of how to deliver these ideas
Metabolic adaptations through the PGC‐1α and SIRT1 pathways (2007)

Energy homeostasis in mammals is achieved through tight regulation of tissue-specific metabolic pathways that become dysregulated in metabolic diseases including diabetes and obesity. At the molecular level, main nutrient and hormonal signaling pathways impinge on expression of genes encoding for metabolic enzymes. Among the major components of this transcriptional circuitry are the PGC-1 alpha transcriptional complexes. An important regulatory mechanism of this complex is through acetylation and SIRT1-mediated lysine de-acetylation under low nutrient conditions. Activation of SIRT1 can mimic several metabolic aspects of calorie restriction that target selective nutrient utilization and mitochondrial oxidative function to regulate energy balance. Thus, understanding the PGC-1 alpha and SIRT1 pathways might have important implications for comprehending metabolic and age-associated diseases.
A General Strategy for Epitope Mapping by Direct MALDI-TOF Mass Spectrometry Using Secondary Antibodies and Cross-Linking (2001)

The combination of limited proteolysis and MALDI-TOF mass spectrometry has become an important tool for the determination of epitopes but works best with highly purified antibodies. Here we report the use of capture antibodies to reduce the need for purification of the antibody in the mass spectrometric determination of the epitope. In this new method, a secondary Fc-specific antibody, covalently bound to Sepharose beads, is used to capture the primary antibody (the antibody of interest). After capture, the two antibodies are cross-linked. The antigen is then bound to the immobilized antibodies and subjected to proteolysis using several successive proteinases. In this study, this strategy is demonstrated with a crude mouse anti-ACTH IgG solution and adrenocorticotropin (ACTH). Comparing this strategy with previous methods where the antibody is bound directly to activated beads, the new method (1) results in a higher binding capacity of the bound antibody to ACTH, (2) does not require purification of the antibody of interest, and (3) dramatically reduces the chemical background in the MALDI mass spectra.
Distributed collaborative writing (1994)

Previous research indicates that voice annotation helps reviewers to express the more complex and social aspects of a collaborative writing task. Little direct evidence exists, however, about the effect of voice annotations on the writers who must use such annotations.
Dual-labeled oligonucleotide probe for sensing adenosine via FRET: A novel alternative to SNPs genotyping (2007)

A novel FRET based strategy for DNA sequence analysis utilising base-discriminating fluorescence (BDF) nucleoside, (Py)U/(2-Ant)U, as donor in the dual-labelled oligonucleotide probe is reported; a selective/specific emission from acceptor, was observed upon excitation at the donor, only when the opposite base of the "smart" fluorescently labeled BDF nucleoside, (Py)U/(2-Ant)U, is adenine on the complementary target sequence.
Contents (2009)

The SA Journal of Radiology is the official journal of the Radiological Society of South Africa and the Professional Association of Radiologists in South Africa and Namibia. The SA Journal of Radiology is a general diagnostic radiological journal which carries original research and review articles, pictorial essays, case reports, letters, editorials, radiological practice and other radiological articles.
NEW HIGH STRENGTH AND FASTER DRILLING TSP DIAMOND CUTTERS (2006)

The manufacture of thermally stable diamond (TSP) cutters for drill bits used in petroleum drilling requires the brazing of two dissimilar materials--TSP diamond and tungsten carbide. The ENDURUS{trademark} thermally stable diamond cutter developed by Technology International, Inc. exhibits (1) high attachment (shear) strength, exceeding 345 MPa (50,000 psi), (2) TSP diamond impact strength increased by 36%, (3) prevents TSP fracture when drilling hard rock, and (4) maintains a sharp edge when drilling hard and abrasive rock. A novel microwave brazing (MWB) method for joining dissimilar materials has been developed. A conventional braze filler metal is combined with microwave heating which minimizes thermal residual stress between materials with dissimilar coefficients of thermal expansion. The process results in preferential heating of the lower thermal expansion diamond material, thus providing the ability to match the thermal expansion of the dissimilar material pair. Methods for brazing with both conventional and exothermic braze filler metals have been developed. Finite element modeling (FEM) assisted in the fabrication of TSP cutters controllable thermal residual stress and high shear attachment strength. Further, a unique cutter design for absorbing shock, the densification of otherwise porous TSP diamond for increased mechanical strength, and diamond ion implantation for increased diamond fracture resistance resulted in successful drill bit tests.
Relevance of Transgenic Mouse Models to Human Alzheimer Disease (2008)

During the past 2 decades, the elucidation of susceptibility and causative genes for Alzheimer disease as well as proteins involved in the pathogenic process has greatly facilitated the development of genetically altered mouse models. These models have played a major role in defining critical disease-related mechanisms and in evaluating novel therapeutic approaches, with many treatments currently in clinical trial owing their origins to studies initially performed in mice. This review discusses the utility of transgenic mice as a research tool and their contributions to our understanding of Alzheimer disease.
Aminozucker‐Synthesen, III. Synthese der 2.6‐Didesoxy‐2.6‐diamino‐D‐glucose (1961)

Abstract Durch katalytische Hydrierung der Nitrilgruppe im Benzyl‐ N ‐carbobenzoxy‐3.4‐diacetyl‐α‐ D ‐glucosaminuronsäurenitril (I), mit PtO 2 in Acetanhydrid, Abhydrierung der Carbobenzoxygruppe mit Pd in Methanol und anschließende durchgreifende Hydrolyse kann die 2.6‐Didesoxy‐2.6‐diamino‐ D ‐glucose in 60‐proz. Ausbeute gewonnen werden. Bei Abkürzung der Hydrolysezeiten erhält man wechselnde Mengen des entsprechenden α‐Benzylglykosids. Es wird über die Synthese einer Reihe von D ‐Glucosaminuronsäure‐Derivaten aus bereits früher beschriebenen Verbindungen berichtet.