gebhart/patrepeval huggingface dataset:
Assignment of an Usher syndrome type III (USH3) gene to chromosome 3q (1995)

Usher syndrome (USH) refers to genetically and clinically heterogeneous autosomal recessive disorders with combined visual and hearing loss. Type I (USH1) is characterized by a congenital, severe to profound hearing loss and absent vestibular function; in type II (USH2) the hearing loss is congenital and moderate to severe, and the vestibular function is normal. Progressive pigmentary retinopathy (PPR) is present in both types. A third type (USH3) differing from USH2 by the progressive nature of its hearing loss has been suggested. USH3 has previously been estimated to comprise 2% of all USH. However, based on clinical criteria, in Finland 42% of USH patients have progressive hearing loss suggesting enrichment of an USH3 gene. We excluded the four previously mapped USH regions as the site of the USH3 disease locus. Systematic search for USH3 by genetic linkage analyses in 10 multiple affected families using polymorphic microsatellite markers revealed significant linkage with markers mapping to chromosome 3q. Pairwise lod scores at zero recombination distance were 7.87 for D3S1308, and 11.29 for D3S1299, incorporating the observed linkage disequilibrium. Conventional multipoint linkage analysis gave a maximum lod score of 9.88 at D3S1299 assigning USH3 to the 5 cM interval between markers D3S1555 and D3S1279 in 3q21-25.(ABSTRACT TRUNCATED AT 250 WORDS)
ReNoC: A Network-on-Chip Architecture with Reconfigurable Topology (2008)

This paper presents a Network-on-Chip (NoC) architecture that enables the network topology to be reconfigured. The architecture thus enables a generalized System-on-Chip (SoC) platform in which the topology can be customized for the application that is currently running on the chip, including long links and direct links between IP-blocks. The configurability is inserted as a layer between routers and links, and the architecture can therefore be used in combination with existing NoC routers, making it a general architecture. The topology is configured using energy-efficient topology switches based on physical circuit-switching as found in FPGAs. The paper presents the ReNoC (ReconfigurableNoC) architecture and evaluates its potential. The evaluation design shows a 56% decrease in power consumption compared to a static 2D mesh topology
Chondrocytes Cultured in Stirred Suspension with Serum-Free Medium Containing Pluronic-68 Aggregate and Proliferate While Maintaining Their Differentiated Phenotype (2009)

The study of chondrocyte biology requires culture conditions that maintain cell phenotype. Phenotype is rapidly lost in monolayer but is maintained in 3-dimensional scaffolds, which however, experience limited cell proliferation and limited mass transport. In this study, we cultured chondrocytes in aggregates in stirred spinner flask suspension cultures to control aggregate size and promote mass transport. A previously optimized serum-free medium, containing the following growth factors (GFs), epidermal growth factor, platelet-derived growth factor-BB, and basic fibroblast growth factor, all at 2 ng/mL, was used as a control medium. In addition, two modified media were tested: one containing Pluronic F-68 (PF-68) and the other containing PF-68 with 10 times greater GF concentration (20 ng/mL, medium PF-68/10 x GF). Chondrocytes formed limited-size aggregates within 24 h and exhibited high viability (>95%), and cell concentration doubled in 7 days in the presence of PF-68. Low or no collagen I expression was found for any of the three media, whereas collagen II accumulated between cells, as revealed by a dense immunostaining. Integrin alpha10, a marker of differentiated chondrocytes and chondrogenic cells, was also found to be highly expressed. Aggregates resulting from spinner culture were found to be relevant in vitro models and their use for cartilage repair to be also conceivable.
[Caudal anesthesia and its determinant factors]. (2011)

In 130 surgical patients with diseases and injuries in the area of the perineum and lower extremities the clinical effects of three modern local anesthetics: 2% solution of lidocaine, 0.5% solution of bupivacaine, 0.75% solution of ropivacaine and their combinations (2% lidocaine and 0.25% bupivacaine solution 2% lidocaine and ropivacaine 0.375% solution) were followed with regard to the influence of increasing volumes of local anesthetics and different rates of drug administration. It is established that an effective caudal anesthesia is provided with all modern local anesthetics, with increasing use of local anesthetic solution to 40 ml provides duration and the prevalence of sensory and motor blocks, the use of mixture of local anesthetics optimizes the development and maintenance of the caudal blockade.
Sex lethal and U2 small nuclear ribonucleoprotein auxiliary factor (U2AF<sup>65</sup>) recognize polypyrimidine tracts using multiple modes of binding (2003)

The molecular basis for specific recognition of simple homopolymeric sequences like the polypyrimidine tract (Py tract) by multiple RNA recognition motifs (RRMs) is not well understood. The Drosophila splicing repressor Sex lethal (SXL), which has two RRMs, can directly compete with the essential splicing factor U2AF(65), which has three RRMs, for binding to specific Py tracts. We have combined site-specific photocross-linking and chemical cleavage of the proteins to biochemically map cross-linking of each of the uracils within the Py tract to specific RRMs. For both proteins, RRM1 and RRM2 together constitute the minimal Py-tract recognition domain. The RRM3 of U2AF(65) shows no cross-linking to the Py tract. Both RRM1 and RRM2 of U2AF(65) and SXL can be cross-linked to certain residues, with RRM2 showing a surprisingly high number of residues cross-linked. The cross-linking data eliminate the possibility that shorter Py tracts are bound by fewer RRMs. We present a model to explain how the binding affinity can nonetheless change as a function of the length of the Py tract. The results indicate that multiple modes of binding result in an ensemble of RNA-protein complexes, which could allow tuning of the binding affinity without changing sequence specificity.
Systematic study of the genus Acetobacter with descriptions of Acetobacter indonesiensis sp. nov., Acetobacter tropicalis sp. nov., Acetobacter orleanensis(Henneberg 1906) comb. nov., Acetobacter lovaniensis(Frateur 1950) comb. nov., and Acetobacter estunensis(Carr 1958) comb. nov. (2000)

Thirty-one Acetobacter strains obtained from culture collections and 45 Acetobacter strains isolated from Indonesian sources were investigated for their phenotypic characteristics, ubiquinone systems, DNA base compositions, and levels of DNA-DNA relatedness. Of 31 reference strains, six showed the presence of ubiquinone 10 (Q-10). These strains were eliminated from the genus Acetobacter. The other 25 reference strains and 45 Indonesian isolates were subjected to a systematic study and separated into 8 distinct groups on the basis of DNA-DNA relatedness. The known species, Acetobacter aceti, A. pasteurianus, and A. peroxydans are retained for three of these groups. New combinations, A. orleanensis (Henneberg 1906) comb. nov., A. lovaniensis (Frateur 1950) comb. nov., and A. estunensis (Carr 1958) comb. nov. are proposed for three other groups. Two new species, A. indonesiensis sp. nov. and A. tropicalis sp. nov. are proposed for the remaining two. No Indonesian isolates were identified as A. aceti, A. estunensis, and A. peroxydans. Phylogenetic analysis on the basis of 16S rDNA sequences was carried out for representative strains from each of the groups. This supported that the eight species belonged to the genus Acetobacter. Several strains previously assigned to the species of A. aceti and A. pasteurianus were scattered over the different species. It is evident that the value of DNA-DNA relatedness between strains comprising a new species should be determined for the establishment of the species. Thus current bacterial species without data of DNA-DNA relatedness should be reexamined for the stability of bacterial nomenclature.
The significance of active Na<sup>+</sup>,K<sup>+</sup> transport in the maintenance of contractility in rat skeletal muscle (1996)

The effects of reduced Na+,K+ pump capacity on contractile endurance and excitation-induced changes in intracellular Na+ content were investigated in isolated rat soleus and extensor digitorum longus muscles. Pre-incubation with 10(-5) M ouabain increased the rate of force decline measured over the first 5-20 s of tetanic contraction from 0.32 to 0.94% s-1 and 1.4 to 4.6% s-1 in soleus and extensor digitorum longus muscles, respectively. Soleus muscles from K(+)- deficient rats exhibited 54% reduction in the concentration of Na+,K+ pumps and the force decline during 30 s of 60 Hz stimulation was increased from 0.53 to 1.15% s-1. A similar change was induced in control muscles when a comparable reduction in the concentration of functional Na+,K+ pumps was elicited by pre-incubation with ouabain (10(-6)-2 x 10(-6) M). In soleus, the force decline during 60 s of 60 Hz stimulation showed linear correlation to the increase in intracellular Na+ content. In extensor digitorum longus, force decline and increase in Na+ content during 60 Hz stimulation were both four times faster than in soleus as measured over 15 s of excitation. These results indicate that during maximal contractions the Na+,K+ pump capacity is one of the determinants for the contractile endurance in skeletal muscle. Furthermore, the maintenance of contractile force seems to be a function of the rate of Na(+)-influx and this relationship may account for the difference in endurance between slow-twitch and fast-twitch muscles.
A user interface for computer-based message translation (1989)

A generic message translator is described that enables a computer user without programming knowledge to specify a program for translating between two different computer-based message systems. Thus messages formatted for use in one system can be automatically translated by the computer into the proper format for use in the other system. The computer user works interactively with the computer to specify the translating program, making use of the appropriate visual paradigms for the message structure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Structure-Guided Design of Cell Wall Biosynthesis Inhibitors That Overcome β-Lactam Resistance in <i>Staphylococcus aureus</i> (MRSA) (2011)

β-Lactam antibiotics have long been a treatment of choice for bacterial infections since they bind irreversibly to Penicillin-Binding Proteins (PBPs), enzymes that are vital for cell wall biosynthesis. Many pathogens express drug-insensitive PBPs rendering β-lactams ineffective, revealing a need for new types of PBP inhibitors active against resistant strains. We have identified alkyl boronic acids that are active against pathogens including methicillin-resistant S. aureus (MRSA). The crystal structures of PBP1b complexed to 11 different alkyl boronates demonstrate that in vivo efficacy correlates with the mode of inhibitor side chain binding. Staphylococcal membrane analyses reveal that the most potent alkyl boronate targets PBP1, an autolysis system regulator, and PBP2a, a low β-lactam affinity enzyme. This work demonstrates the potential of boronate-based PBP inhibitors for circumventing β-lactam resistance and opens avenues for the development of novel antibiotics that target Gram-positive pathogens.
Stellarator approach to toroidal plasma confinement (1981)

An overview is presented of the development and current status of the stellarator approach to controlled thermonuclear confinement. Recent experimental, theoretical, and systems developments have made this concept a viable option for the evolution of the toroidal confinement program. Some experimental study of specific problems associated with departure from two-dimensional symmetry must be undertaken before the full advantages and opportunities of steady-state, net-current-free operation can be realized.
Carboxymethoximes(I) Carboxymethoximes and Their Methyl Esters of Ketosteroids (1968)

The carboxymethoximes and their methyl esters of several ketosteroids were synthesized. It is suggested that the molecular weights of the ketosteroids could be determined through measuring the neutralization equivalents of their carboxymethoximes. The methyl ester of these carboxymethoximes could be utilized as useful derivatives for the identification of the ketosteriods.
Correction of PET Data for Partial Volume Effects in Human Cerebral Cortex by MR Imaging (1990)

Due to the limited spatial resolution of positron emission tomography (PET), the accuracy of quantitative measurements of regional metabolism or neuroreceptor concentration is influenced by partial volume averaging of brain with CSF, bone, and scalp. This effect is increased in the presence of cortical atrophy, as in patients with Alzheimer disease (AD). Correction for this underestimation in PET measurements is necessary for the comparison of AD patients and normal controls. We have developed a method for three-dimensional correction of human PET data using magnetic resonance (MR) imaging. A composite brain tissue image is created by summing the binary representation of nine MR images, weighted to the PET z-axis line-spread function. This composite tissue image is convolved to the resolution of the PET image. The original PET image is divided by the convolved tissue image on a pixel-by-pixel basis, resulting in an atrophy-corrected PET image in which count density represents activity per volume of brain tissue rather than spatial volume. This has been performed in [11C]carfentanil mu-opiate receptor PET studies of the temporal cortex in two AD patients and one normal volunteer. After correction, average regional increases in count density were 11% (range = 4-21%) in the normal and 46% (range = 28-99%) and 48% (range = 14-109%) in the patient studies. The accuracy of this method of partial volume correction was estimated using a spherical phantom.
Real-Time PCR Assay for Detection and Enumeration of<i>Dekkera bruxellensis</i>in Wine (2003)

Traditional methods to detect the spoilage yeast Dekkera bruxellensis from wine involve lengthy enrichments. To overcome this difficulty, we developed a quantitative real-time PCR method to directly detect and enumerate D. bruxellensis in wine. Specific PCR primers to D. bruxellensis were designed to the 26S rRNA gene, and nontarget yeast and bacteria common to the winery environment were not amplified. The assay was linear over a range of cell concentrations (6 log units) and could detect as little as 1 cell per ml in wine. The addition of large amounts of nontarget yeasts did not impact the efficiency of the assay. This method will be helpful to identify possible routes of D. bruxellensis infection in winery environments. Moreover, the time involved in performing the assay (3 h) should enable winemakers to more quickly make wine processing decisions in order to reduce the threat of spoilage by D. bruxellensis.
Synthesis and antimicrobial activity of 1,2,4-triazoles (2002)

Department of Chemistry, B. K. M. Science College, Valsad-396·001, India <em>Manuscript received 11 September 2001. revised 3 June 2002, accepted 8 August 2002</em> 3-(2<em>'</em> ,4<em>'</em>,6<em>'-</em>Trichlorophenoxymethyl)-4·(4<em>"</em> -methoxyphenyl)-5-aryl-1,2,4-triazoles (4a-j) and 3-(2<em>'</em> ,4<em>'</em>,6<em>' </em>-trichlorophenoxymethyi)-4-(Nbenzylidenylamino)-5-mercapto-1,2,4-triazoles (7a-j) have been synthesized, and their antimicrobial activities studied.
Seismic imaging of the Naga thrust using multiscale waveform inversion (2009)

Abstract This case study images the structural features related to the Naga thrust fault (northeast India) using a combination of multiscale waveform inversion and prestack depth migration (PSDM). The waveform model and the PSDM image complement each other: the former provides a physical-property map (P-wave velocity model) and the latter provides a structural image. The velocity model encompassing the starting model for waveform inversion is constructed using joint inversion of first and reflected traveltimes. The 4–8-Hz data are inverted consecutively in 1-Hz bandwidths to yield the final waveform model, which in turn is used for PSDM. The PSDM image and the waveform model are consistent with the lithological interpretation of an inline exploratory well. When interpreted jointly, the PSDM image and the waveform model reveal the presence of a conjugate fault system in the Naga thrust and fold belt.
Contrasting effects of afferent and efferent vagal nerve stimulation on insulin secretion and blood glucose regulation (2016)

Parasympathetic activation reduces hepatic glucose release and increases pancreatic insulin secretion in hyperglycemic conditions. Thus, vagal nerve stimulation (VNS) may potentially be effective in treating type II diabetes. To investigate this possibility, we hypothesized that VNS reduces blood glucose concentration [Glu] via insulin secretion. [Glu] together with insulin and glucagon serum concentrations were determined in anesthetized rats during baseline conditions and 120 min of cervical VNS with the nerve left intact for combined afferent and efferent VNS (n = 9) or the nerve sectioned proximal or distal from the stimulation electrode for selective efferent (n = 8) or afferent (n = 7) VNS, respectively. Afferent VNS caused a strong and sustained increase in [Glu] (+108.9 ± 20.9% or +77.6 ± 15.4%, after 120 min of combined afferent and efferent VNS or selective afferent VNS) that was not accompanied by an increase in serum insulin concentration. However, serum insulin levels increased significantly with selective efferent VNS (+71.2 ± 27.0% after 120 min of VNS) that increased [Glu] only temporarily (+28.8 ± 11.7% at 30 min of VNS). Efferent VNS initially increased serum glucagon concentration which remained elevated for 120 min when efferent VNS was combined with afferent VNS, but returned to baseline with selective efferent VNS. These findings demonstrate that afferent VNS causes a marked and sustained increase in [Glu] that is partly mediated by suppression of pancreatic insulin secretion. In contrast, efferent VNS stimulates pancreatic glucagon secretion that appears to be antagonized by insulin secretion in the case of selective efferent VNS. Selective efferent VNS may potentially be effective in treating type II diabetes.
[Role of Helicobacter pylori eradication in the prevention of peptic ulcer in NSAID users]. (2007)

Helicobacter pylori (H. pylori) and non-steroidal anti-inflammatory drug (NSAID) are independent risk factors for peptic ulcers and ulcer complications and they have additive or synergistic effects. A meta-analysis showed that the OR for the incidence of peptic ulcer was 61.1 in patients infected with H. pylori and also taking NSAID when compared to patients uninfected with H. pylori and not taking NSAID. H. pylori eradication may prevent NSAID-induced ulcers in NSAID naive patients. In patients receiving long-term NSAID, proton pump inhibitor(PPI) is more effective in the prevention of ulcer recurrence and bleeding. However, H. pylori eradication should be considered in patients receiving long -term PPI maintenance treatment to prevent the development of corpus gastritis and gastric atrophy.
Improvements in Reactivity of Hexakis- (methoxymethyl) -melamine with Selfcondensation and Ethylene-Glycol Bridging (1968)

ヘキサキスメトキシメチルメラミン (HMM) を樹脂状化合物の硬化剤として無触媒下で使用した場合, その反応性があまりよくないため橋カケ速度がおそいという欠陥がある。HMMの反応性を向上させるには, 1分子当たりの官能基数を増加させてやれば効果的であろう。この推論に基づいて, 市販されているHMMを加熱縮合, およびエチレングリコールで加熱橋かけさせて, これらの橋カケ剤効果を調べた。塗膜は熱硬化性アクリル樹脂と硬化剤と顔料の系で作成し, その鉛筆硬度および振かん硬度測定の結果から, 橋カケ剤としては, HMMよりHMM加熱縮合体, さらにはエチレングリコールを用いたHMM加熱縮重合体の方が表面硬度も大になり橋かけ密度も高くなっていることが明らかになった。
Notice of Violation of IEEE Publication Principles: Image inpainting with group based sparse representation using self adaptive dictionary learning (2015)

Notice of Violation of IEEE Publication Principles<br><br> "Image Inpainting with Group Based Sparse Representation using Self Adaptive Dictionary Learning,"<br> by T J V Subrahmanyeswara Rao, M Venu Gopala Rao, T V N L Aswini,<br> in the Proceedings of the International Conference on Signal Processing And Communication Engineering Systems (SPACES), January 2015, pp.301-305<br><br> After careful and considered review of the content and authorship of this paper by a duly constituted expert committee, this paper has been found to be in violation of IEEE's Publication Principles.<br><br> This paper copied large portions of text and figures from the paper cited below. The original content was copied without attribution (including appropriate references to the original author(s) and/or paper title) and without permission.<br><br> Due to the nature of this violation, reasonable effort should be made to remove all past references to this paper, and future references should be made to the following article:<br><br> "Group-Based Sparse Representation for Image Restoration,"<br> by Jian Zhang, Debin Zhao, and Wen Gao, <br> in the IEEE Transactions on Image Processing, Vol. 23, No. 8, May 2014, pp. 3336 – 3351<br><br> <br/> Inpainting is an imaging technique that modifying an image in an undetectable form, is as ancient as art itself. The goals and applications of inpainting are numerous, from the restoration of damaged paintings and photographs to the removal / replacement of selected objects. The popularity of sparse representation and compressed sensing makes the sparse priors to be considered for solving inpainting problems. In earlier works, the patch of an image is taken to be sparse in a particular basis, which is called Patch based sparse representation. The patch based modelling suffers from two severe problems. In our work we exploit the concept of Group based sparse representation (GSR), which takes group (composed of nonlocal patches with similar structures) as the basic unit instead of patch. The GSR sparsely represents natural images in the domain of group, which results intrinsic local sparsity and nonlocal self-similarity of images simultaneously in a unified framework Under the same roof, an efficient self-adaptive dictionary learning method is designed for each group with low complexity, rather than learning the dictionary from natural images.
The Cellular Fatty Acids of the Sulphate-reducing Bacteria, Desulfobacter sp., Desulfobulbus sp. and Desulfovibrio desulfuricans (1983)

The fatty acid profiles of Desulfobacter sp. grown on acetate and Desulfobulbus sp. grown on propionate, lactate and H2/CO2 were analysed. Desulfobacter sp. grown on acetate and Desulfobulbus sp. grown on H2/CO2 gave mainly even numbered straight chain acids but odd numbered acids predominated in Desulfobulbus sp. grown on propionate, reflecting the use of the growth substrates provided as chain initiators for fatty acid biosynthesis. The cellular fatty acids of Desulfobulbus sp. grown on lactate were distributed approximately evenly between even and odd straight chain acids. In contrast those of Desulfovibrio desulfuricans, were dominated by branched chain iso and anteiso fatty acids, when grown on either lactate or H2/CO2. On the basis of the fatty acid biosynthetic pathways these sulphate-reducing bacteria could be separated into two groups, one comprising Desulfobacter sp. and Desulfobulbus sp. and the other more primitive Desulfovibrio desulfuricans.