gebhart/patrepeval huggingface dataset:
Simultaneous localization and mapping with active stereo vision (2005)

We present an algorithm for creating globally consistent three-dimensional maps from depth fields produced by camera-based range measurement systems. Our approach is specifically suited to dealing with the high noise levels and the large number of outliers often produced by such systems. Range data is filtered to reject outliers within each scan. The point-to-plane variant of ICP is used for local alignment, including weightings that favor nearby points and a novel outlier rejection strategy that increases the robustness for this class of data while eliminating the burden of user-specified thresholds. Global consistency is imposed on cycles by optimally distributing the cyclic discrepancy according to the local fit correlation matrices. The algorithm is demonstrated on a dataset collected by an active unstructured-light space-time stereo vision system.
Grounded Cognition (2007)

Grounded cognition rejects traditional views that cognition is computation on amodal symbols in a modular system, independent of the brain's modal systems for perception, action, and introspection. Instead, grounded cognition proposes that modal simulations, bodily states, and situated action underlie cognition. Accumulating behavioral and neural evidence supporting this view is reviewed from research on perception, memory, knowledge, language, thought, social cognition, and development. Theories of grounded cognition are also reviewed, as are origins of the area and common misperceptions of it. Theoretical, empirical, and methodological issues are raised whose future treatment is likely to affect the growth and impact of grounded cognition.
Chemical Transformations of Buddleja davidii Lignin during Ethanol Organosolv Pretreatment (2010)

Detailed chemical structural elucidation of ethanol organosolv lignin (EOL) of Buddleja davidii was performed to determine the fundamental structure released from an ethanol organosolv pretreatment (EOP). Several nuclear magnetic resonance (NMR) techniques were used to analyze the structure of EOL, including quantitative 13C, 31P NMR, and qualitative DEPT-135 13C, 2D 1H−13C correlation NMR. As revealed by NMR, the aryl-O-ether linkage (β-O-4′) of lignin was extensively cleaved via homolysis during pretreatment and led to the formation of stilbene structures. Other linkages, such as resinol (β-β′) and phenylcoumaran (β-5′), were resistant to degradation. The high degree of condensation of EOL indicated that condensation reactions occurred but did not impede the delignification efficiency of EOP. Both guaiacyl and syringyl lignin were found to be reactive toward condensation during pretreatment. The results from gel-permeation chromatography showed that the degree of polymerization (DP) of lignin significantly decreased by ∼85%, facilitating lignin solubilization in ethanol.
What is the Best Surface EMG Measure of Lumbar Flexion-Relaxation for Distinguishing Chronic Low Back Pain Patients From Pain-free Controls? (2013)

Because all SEMG measures of FR performed acceptably, the determination of which SEMG measure of FR is "best" is largely dependent on one's specific purpose. In addition, ROM measures were found to be important components of the FR assessment.
Use of the Rhodopseudomonas palustris genome sequence to identify a single amino acid that contributes to the activity of a coenzyme A ligase with chlorinated substrates (2005)

Rhodopseudomonas palustris strain RCB100 degrades 3-chlorobenzoate (3-CBA) anaerobically. We purified from this strain a coenzyme A ligase that is active with 3-CBA and determined its N-terminal amino acid sequence to be identical to that of a cyclohexanecarboxylate-CoA ligase encoded by aliA from the R. palustris strain (CGA009) that has been sequenced. Strain CGA009 differs from strain RCB100 in that it does not use 3-CBA as a sole carbon source. The aliA gene from the 3-CBA degrading strain differed by a single nucleotide from the aliA gene from strain CGA009, causing the substitution of a serine for a threonine at position 208. Both AliA enzymes, purified as His-tagged fusion proteins, had comparable activities with cyclohexanecarboxylate. However, AliA from the 3-CBA degrading strain was 10-fold more active with 3-CBA (kcat/Km of 4.3 x 10(4) M(-1) s(-1)) than the enzyme from the sequenced strain (kcat/Km 0.32 x 10(4) M(-1) s(-1)). The CGA009 enzyme was not sufficiently active with 3-CBA to complement an RCB100 aliA mutant for growth on this compound. Here, whole genome sequence information enabled us to identify a single nucleotide among 5.4 million nucleotides that contributes to the substrate preference of a coenzyme A ligase.
Mutations in the Escherichia coli fnr and tgt genes: control of molybdate reductase activity and the cytochrome d complex by fnr (1989)

In eubacteria, the tRNA transglycosylase (Tgt) in specific tRNAs exchanges a guanine in the anticodon for 7-aminomethyl-7-deazaguanine, which is finally converted to queuosine. The tgt gene of Escherichia coli has been mapped at 9 min on the genome, and mutant pairs containing an intact or mutated tgt allele were obtained after transduction of the tgt locus by P1 bacteriophages into a genetically defined E. coli strain (S. Noguchi, Y. Nishimura, Y. Hirota, and S. Nishimura, J. Biol. Chem. 257:6544-6550, 1982). These tgt mutants grew anerobically with fumarate as an electron acceptor, while nitrate or trimethylamine N-oxide could not be reduced. Furthermore, molybdate reductase activity was almost lacking and the characteristic absorption maxima, corresponding to cytochrome a1 and the cytochrome d complex, were not detectable in low-temperature reduced-minus-oxidized difference spectra in anaerobically grown cells. Transduction of the mutated tgt locus into another E. coli recipient resulted in tgt mutants without anaerobic defects. Transformation of the original tgt mutants with an fnr gene-containing plasmid reversed the anaerobic defects. Clearly, the original tgt mutants harbor a second mutation, affecting the anaerobic regulator protein Fnr. The results suggest that fnr is involved in anaerobic control of components of the cytochrome d complex and of the redox system that transfers electrons to molybdate. F' plasmids containing a fused lacI-lacZ gene with the nonsense codon UAG at different positions in the lacI part were transferred to E. coli strains with a mutated or nonmutated tgt locus but intact in fnr. A twofold increase in the frequency of incorrect readthrough of the UAG codon, dependent on the codon context, was observed in the tgt mutant and is suggested to be caused by a tRNA(Tyr) with G in place of queuosine.
Estrogen Receptor Mutations in Human Disease (2004)

As early as the 1800s, the actions of estrogen have been implicated in the development and progression of breast cancer. The estrogen receptor (ER) was identified in the late 1950s and purified a few years later. However, it was not until the 1980s that the first ER was molecularly cloned, and in the mid 1990s, a second ER was cloned. These two related receptors are now called ERalpha and ERbeta, respectively. Since their discovery, much research has focused on identifying alterations within the coding sequence of these receptors in clinical samples. As a result, a large number of naturally occurring splice variants of both ERalpha and ERbeta have been identified in normal epithelium and diseased or cancerous tissues. In contrast, only a few point mutations have been identified in human patient samples from a variety of disease states, including breast cancer, endometrial cancer, and psychiatric diseases. To elucidate the mechanism of action for these variant isoforms or mutant receptors, experimental mutagenesis has been used to analyze the function of distinct amino acid residues in the ERs. This review will focus on ERalpha and ERbeta alterations in breast cancer.
Structure and Mechanism of the Glycerol-3-Phosphate Transporter from Escherichia coli (2003)

The major facilitator superfamily represents the largest group of secondary membrane transporters in the cell. Here we report the 3.3 angstrom resolution structure of a member of this superfamily, GlpT, which transports glycerol-3-phosphate into the cytoplasm and inorganic phosphate into the periplasm. The amino- and carboxyl-terminal halves of the protein exhibit a pseudo two-fold symmetry. Closed off to the periplasm, a centrally located substrate-translocation pore contains two arginines at its closed end, which comprise the substrate-binding site. Upon substrate binding, the protein adopts a more compact conformation. We propose that GlpT operates by a single-binding site, alternating-access mechanism through a rocker-switch type of movement.
Artificial lateral line-based localization of a dipole source with unknown vibration amplitude and direction (2011)

The lateral line system is an important sensory organ for fish and many aquatic amphibians, allowing them to detect predators/prey, perform rheotaxis, and coordinate schooling. There is an increasing interest in developing artificial lateral line systems, consisting of arrays of flow sensors, for underwater vehicles and robots. In this paper we consider the problem of localizing a vibrating sphere, also known as a dipole source, using an artificial lateral line system. Dipole sources emulate the movement of fish fins and are often used in the study of biological lateral lines. We assume that the location, vibration amplitude, and vibration direction of the dipole sources are all unknown. A nonlinear estimation problem is formulated based on the analytical model for dipole-generated flow field. We present two recursive algorithms for source localization, the first obtained by linearizing the original nonlinear estimation problem, and the other by solving the equations corresponding to the first-order optimality condition. Simulation results are presented to illustrate the effectiveness of the proposed approaches.
Molecular cloning and expression in Escherichia coli of a cyanobacterial gene coding for phytoene synthase, a carotenoid biosynthesis enzyme (1992)

The first committed step in the biosynthetic pathway of carotenoids in plants and algae is the conversion of geranylgeranyl pyrophosphate (GGPP) to prephytoene pyrophosphate (PPPP), which is converted to phytoene. We have cloned the gene pys that encodes the enzyme phytoene synthase in the cyanobacterium Synechococcus PCC7942. The co-expression of pys in cells of Escherichia coli together with the gene crtE from Erwinia uredovora, which encodes geranylgeranyl pyrophosphate synthase, resulted in accumulation of phytoene. This result indicates that phytoene synthase is a single polypeptide enzyme that catalyzes the 2-step reaction from GGPP to phytoene. The deduced amino acid sequence of pys is highly conserved with that of pTOM5, a tomato cDNA that is differentially expressed during fruit ripening. These findings suggest that pTOM5 encodes phytoene synthase in tomato.
Heterobifunctional Ligands:  Practical Chemoenzymatic Synthesis of a Cell Adhesive Glycopeptide That Interacts with Both Selectins and Integrins (2001)

An efficient and practical synthesis of cell adhesive glycopeptides exhibiting unique properties as a novel type of modulator of cellular recognition is described. A nonnatural glycopeptide 1 composed of sialyl Lewis x and Lys-Gly-Arg-Gly-Asp-Ser that interacts with both selectins and integrins has been systematically synthesized by combined chemical and enzymatic strategy. It is suggested that glycopeptide 1 showed much higher affinity with P-selectin (K(a) = 6.6 x 10(7) M(-1)) and E-selectin (K(a) = 4.5 x 10(5) M(-1)) than sialyl Lewis x. This compound also inhibited a specific interaction between human integrin beta(1) and its monoclonal antibody more effectively than the tetrapeptide Arg-Gly-Asp-Ser. Interestingly, it was demonstrated by surface plasmon resonance analysis that this heterobifunctional glycopeptide exhibited a capacity to form stable complexes with P-selectin and integrin beta(1) concurrently. It is also suggested that this activity can be used for the inhibition of integrin-mediated adhesion of activated helper T cells onto collagen-coated plates as a cell migration model. These results indicate that the chemoenzymatic hybridization strategy of different biological functions of carbohydrates and peptides is a new concept for designing potent glycoconjugates as antiinflammatory and anticancer metastasis reagents.
Release Pattern of Liposomal Bupivacaine in Artificial Cerebrospinal Fluid (2016)

Demonstration of controlled slow-release profile for mutilamellar liposomal bupivacaine in artificial CSF in vitro might support intrathecal use of liposomal bupivacaine in vivo in animal studies.
Artificial distributed-index media fabricated by zero-order gratings (1991)

Zero-order gratings are grating structures with a period that is small compared with the wavelength of light. Only the directly transmitted or reflected light, the zero diffraction order, is nonevanescent and propagates in a distance from the grating. Thus the grating behaves like a slab of ordinary homogeneous material with an effective refractive index. By varying the material composition, i.e., by variation of the duty cycle of the grating, the effective refractive index can be changed. A grating with variable duty cycle therefore behaves like a material with distributed index. Based on such artificial materials, distributed-index elements are proposed. The physical principle is demonstrated with water waves.
Naphthalenesulphonic Acid Derivatives as Potential anti-HIV-1 Agents. Chemistry, Biology and Molecular Modelling of Their Inhibition of Reverse Transcriptase (1991)

Activity against human immunodeficiency virus (HIV) in the naphthalenesulphonic acid series is most pronounced in the disulphonic acid series. In this class of compounds, N-acyl derivatives of 4-amino-5-hydroxy-2,7-naphthalenedisulphonic acid demonstrate significant anti-HIV activity at non-toxic doses. The most potent compounds in this group of agents are bis naphthalenedisulphonic acids. A bis derivative containing a decamethylene spacer demonstrated activity against HIV-1, HIV-2 giant cell formation and reverse transcriptase (RT). This compound also demonstrated an in vitro therapeutic index (ratio of 50% cytotoxic concentration to 50% inhibitory antiviral concentration) of 10.6. Molecular modelling analyses of this agent, suramin, and several suramin analogues were undertaken to explain the potent anti-HIV-1 RT activity. These studies were carried out using the molecular decomposition/recomposition strategy, conformational searching, energy minimization and molecular dynamics (MD) simulation. The bis naphthalenedisulphonic acid derivative compound 1, having a flexible decamethylene spacer, was shown to be able to mimic the helical twist of the B-DNA backbone as a low energy conformer state.
A prospective study of the causes of notably raised aspartate aminotransferase of liver origin (1999)

The commonest cause of a hepatitis like biochemical picture was hepatic hypoxia (50%) followed by pancreatobiliary disease (24%). Drug induced hepatic necrosis (8.8%) was uncommon and viral hepatitis was rare (3.6%). AST concentrations returned towards normal most rapidly in patients with hepatic hypoxia and calculous biliary obstruction. Hepatitis, viral or otherwise, is an uncommon cause of a typical hepatitic biochemical result in this community.
Hypoxia-Inducible Factor-1-Independent Regulation of Vascular Endothelial Growth Factor by Hypoxia in Colon Cancer (2004)

The induction of vascular endothelial growth factor (VEGF) is an essential feature of tumor angiogenesis, and the hypoxia-inducible factor-1 (HIF-1) transcription factor is known to be a key mediator of this process. In colon cancer, the frequently mutated K-ras oncogene also can regulate VEGF expression, but the role that K-ras may play in hypoxia is unknown. Hypoxia induced VEGF promoter activity, mRNA, and protein levels in colon cancer cells. Although HIF-1alpha was induced by hypoxia, VEGF reporter constructs with selectively mutated hypoxia-response elements remained responsive to hypoxia. In addition, "knockdown" of HIF-1alpha by RNA interference only minimally inhibited the hypoxic induction of VEGF. A region of the VEGF promoter between -420 and -90 bp mediated this HIF-independent induction by hypoxia. The introduction of K-ras(Val12) augmented the hypoxic induction of VEGF, and this was observed in wild-type and HIF-1alpha knockdown colon cancer cells. Thus, VEGF may be induced by hypoxia through HIF-dependent and HIF-independent pathways, and K-ras also can induce VEGF in hypoxia independent of HIF-1. These findings suggest the existence of multiple mechanisms regulating the hypoxic induction of VEGF in colon cancer.
Efficient, broadband and compact metal grating couplers for silicon-on-insulator waveguides (2007)

Compact metal grating couplers for efficient and broadband coupling between optical fibers and silicon-on-insulator waveguides are proposed and demonstrated. Simulation results for silver, gold, aluminum and copper grating couplers are presented. Using a uniform silver grating, coupling efficiencies are calculated as high as 60 % at a wavelength of 1.55 mum. Metal grating couplers require only one single etching or lift-off step and are therefore very easy to fabricate. As a proof of principle, a gold grating coupler for near-vertical fiber-to-waveguide coupling was fabricated using e-beam writing and lift-off, demonstrating 34 % coupling efficiency and a 1 dB-bandwidth of 40 nm. Measurement data and simulation results are in good agreement.
Emission spectra of bioluminescent reporters and interaction with mammalian tissue determine the sensitivity of detection in vivo (2005)

In vivo bioluminescence imaging depends on light emitted by luciferases in the body overcoming the effect of tissue attenuation. Understanding this relationship is essential for detection and quantification of signal. We have studied four codon optimized luciferases with different emission spectra, including enzymes from firefly (FLuc), click beetle (CBGr68, CBRed) and Renilla reniformins (hRLuc). At 25 degrees C, the in vitro lambda(max) of these reporters are 578, 543, 615, and 480 nm, respectively; at body temperature, 37 degrees C, the brightness increases and the firefly enzyme demonstrates a 34-nm spectral red shift. Spectral shifts and attenuation due to tissue effects were evaluated using a series of 20-nm bandpass filters and a cooled charge-coupled device (CCD) camera. Attenuation increased and the spectra of emitted light was red shifted for signals originating from deeper within the body relative to superficial origins. The tissue attenuation of signals from CBGr68 and hRLuc was greater than from those of Fluc and CBRed. To further probe tissue effects, broad spectral emitters were created through gene fusions between CBGr68 and CBRed. These resulted in enzymes with broader emission spectra, featuring two peaks whose intensities are differentially affected by temperature and tissue depth. These spectral measurement data allow for improved understanding of how these reporters can be used in vivo and what they can reveal about biological processes in living subjects.
Rationale for prescription omega-3-acid ethyl ester therapy forhypertriglyceridemia: A primer for clinicians (2008)

Very high triglyceride (TG) levels may cause pancreatitis. Elevated TG levels are also often, but not always, a risk factor for atherosclerotic coronary heart disease. Omega-3 fatty acids are polyunsaturated fatty acids found in the oil of fish and other seafood that, when consumed, lower TG levels and reduce the risk of cardiovascular events. Prescription omega-3-acid (P-OM3) ethyl ester is a fish oil formulation that has undergone the rigorous regulatory steps required to obtain US Food and Drug Administration approval as a prescription drug. P-OM3 is derived from marine fish, which are high in omega-3 fatty acids. While omega-3 fatty acids may sometimes increase low- density lipoprotein cholesterol (LDL-C) levels in hypertriglyceridemic patients, non-high-density lipoprotein cholesterol (non-HDL-C) levels are often decreased. This has clinical significance because: 1) non-HDL-C sums the cholesterol carried by atherogenic lipoproteins beyond that of LDL-C alone; 2) non-HDL-C is a better predictor of atherogenic risk compared to LDL-C alone; and 3) after LDL-C treatment goals have been reached, non-HDL-C is a recommended secondary lipid treatment target in patients with persistent TG > or = 200 mg/dl. This paper reviews the U.S. treatment indications for P-OM3, clinical evaluation of hypertriglyceridemic patients, importance of elevated TG levels, relevant TG biochemistry and metabolism, illustrative genetic dyslipidemias, lipid treatment recommendations, fat and fatty acid biochemistry, omega-3 fatty acid biochemistry, and the basis behind recommending omega-3 fatty acids to reduce cardiovascular risk. Finally, this review examines P-OM3's lipid and cardiovascular effects, safety, and tolerability, as well as its practical role in patient management.
Time-integrated measurement of corticosteroids in saliva by oral diffusion sink technology. (1991)

Saliva, as a medium for assessing adrenocortical function in humans, has many advantages and a few distinct disadvantages. Interpretation of measurements of saliva cortisol is complicated by the contamination of saliva by steroid-binding proteins from blood plasma, enzyme activity in the salivary gland that converts cortisol to cortisone, and the amplification in saliva of the episodic fluctuations in systemic cortisol concentrations. We describe a new measurement technology that rejects artifacts from contamination of saliva by plasma protein, provides for measurement of both cortisol and cortisone, and integrates episodic fluctuations in concentration over a period of hours. This oral diffusion sink technology may greatly enhance the reliable interpretation of corticosteroid concentrations measured in saliva.
[Classification of plasmids--approaches and problems]. (1991)

An important part in human and veterinary infections is played by plasmids resistant to antibiotics. During basis investigations of plasmids and their epidemiology it was necessary to introduce typical classification groups of plasmids. Different approaches can be used when creating such groups. In the submitted work the author discusses some experimental approaches to the problem. Part of the work is devoted to phenotype fi, to the morphological, serological and phagotyping conjugation of pili. The author discusses in detail the classification of plasmids into incompatible groups, their technical and methodological problems. Special attention was focused on new approaches of classification of plasmids based on typing of replicons.
Locking a Leukocyte Integrin with Statins (2001)

The first of the hydroxymethylglutaryl coenzyme A (HMG-CoA) reductase inhibitors (collectively referred to as “statins”) was identified in 1976.1 This enzyme was an ideal target for treating hypercholesterolemia, since it catalyzes the conversion of HMG-CoA to mevalonate, a limiting step in cholesterol synthesis. Today, statins are the most powerful hypolipidemic drugs available and are widely prescribed throughout the world.Because lipid intermediates of cholesterol synthesis (isoprenoids) allow the attachment to the cell membrane of signaling proteins involved in various functions, statins have other biologic effects.2 They can stimulate bone formation, alter the function of endothelial cells, induce apoptosis of smooth-muscle . . .