gebhart/patrepeval huggingface dataset:
The Neurospora Peptide:N-Glycanase Ortholog PNG1 Is Essential for Cell Polarity despite Its Lack of Enzymatic Activity (2009)

Secretory proteins are subjected to a stringent endoplasmic reticulum-based quality control system that distinguishes aberrant from correctly folded proteins. The cytoplasmic peptide:N-glycanase cleaves oligosaccharides from misfolded glycoproteins and prepares them for degradation by the 26 S proteasome. In contrast to abundant in vitro data on its enzymatic function, the in vivo relevance of peptide:N-glycanase activity remains unclear. Here we show that the PNG1 ortholog from the filamentous ascomycete Neurospora crassa is an essential protein, and its deletion results in strong polarity defects. PNG1 and its predicted binding partner RAD23 have distinct functions in N. crassa and are involved in cell wall integrity and DNA repair, respectively. Moreover, wild type PNG1 has substitutions in essential catalytic amino acids, and its deglycosylation activity is lost. These substitutions are conserved in many PNG1 orthologs of the fungal kingdom, implying a so far unrecognized enzyme-independent function of PNG1 that may only become apparent in highly polar cells such as fungal hyphae.
Laparoscopic Bladder Neck Suspension Using Hernia Mesh and Surgical Staples (1993)

A laparoscopic colposuspension technique for the correction of urinary stress incontinence has been described in the recent literature. Herein we describe a laparoscopic adaptation of the Burch procedure, used in the treatment of urinary stress incontinence since 1958. The use of titanium hernia staples and Prolene mesh in place of traditional suture material eliminates the need for laparoscopic suturing in the confined pelvic space, a practice that often poses difficulty for inexperienced surgeons. Of 40 female patients treated, with a mean 6-month follow-up, there has been no relapse of stress incontinence. Complications in this modest population have been minor and self-limiting. As with any laparoscopic procedure, the results obtained here may be influenced by the extensive experience of the laparoscopist.
Signaling of Remotely Controlled Railway Trains (1968)

A train control system has been evaluated in which a remote digital computer is used as the feedback element of a servomechanism. Telemetry signals are required between the train and computer and in the reverse direction, and engineering constraints are placed on the implementation. Signaling requirements are described, and experimental measurements of the electrical noise and ensuing analyses are presented. Equipment using phase and frequency modulation was built and tested, and a serial coding system was tested at typical railway properties. Measurements were made at diminishing power levels in order to determine margins of communication security; error rates approaching 1 in 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> are anticipated for an operating train control system.
Non-invasive pneumococcal disease and antimicrobial resistance: vaccine implications (2002)

We reviewed laboratory data on non-invasive pneumococcal isolates reported from all diagnostic laboratories in Scotland during the period 1988-99. Of 4491 isolates from hospitalized patients, 654 (64.7%) were from sputum, 79 (7.8%) from the nasopharynx and 278 (27.5%) from other superficial sites. The serogroups included in the 23-valent polysaccharide vaccine caused 96.9% of all non-invasive disease in all age groups. The 7-, 9-, and 11-valent conjugated vaccine serogroups were responsible for 87-94%, 85-93%, 74-81% and 75-84% of non-invasive disease respectively in age groups < 2 years, < or = 5 years, > or = 65 years and all ages. The coverage of non-susceptible penicillin and erythromycin non-invasive isolates was > 99% and > 95% with the 23-valent polysaccharide and 7-11-valent conjugate vaccines respectively. The eight most common serogroups were 23, 9, 6, 19, 14, 3, 15 and 11 (in descending order). The serogroups associated with antimicrobial resistance in non-invasive disease were similar to those found in invasive disease. The finding of a similar serogroup distribution in both invasive and non-invasive disease (regardless of the site of clinical isolate), is consistent with serogroups colonizing non-sterile sites and having the potential to invade. The availability of conjugated vaccines reinforces the importance of systematic surveillance to determine accurately and regularly the coverage of pneumococcal serogroups and types causing both invasive and non-invasive disease.
Concomitant<i>MYC</i>and microRNA cluster miR-17-92 (<i>C13orf25</i>) amplification in human mantle cell lymphoma (2007)

Chromosome 13q31 amplification frequently occurs in solid tumours and in lymphomas and it targets miR-17-92 cluster [1],[2]. The mir-17-92 cluster is amplified and over-expressed in lymphomas [2],[...
Cascaded feedforward architectures for parallel Viterbi decoding (2002)

The Viterbi algorithm (VA) is a common application of dynamic programming. Since it contains a nonlinear ACS (add-compare-select) feedback loop, this loop is the bottleneck in high-data-rate implementations. It is shown that, asymptotically, the ACS feedback no longer has to be processed recursively, i.e. there is no feedback, resulting in negligible performance loss. This can be exploited to derive purely feedforward architectures for Viterbi decoding, so that a modular cascadable implementation results. By designing one cascadable module, any speedup can be achieved simply by adding modules to the implementation. It is shown that optimization criteria, e.g. minimum latency or maximum hardware efficiency, are met by very different architectures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Origin of Magnetic Field Dependent Recombination in Alkylcobalamin Radical Pairs (1996)

Magnetic field effect studies of alkylcobalamin photolysis provide evidence for the formation of a reactive radical pair that is born in the singlet spin state. The radical pair recombination process that is responsible for the magnetic field dependence of the continuous-wave (CW) quantum yield is limited to the diffusive radical pair. Although the geminate radical pair of adenosylcob(III)alamin also undergoes magnetic field dependent recombination (A.M. Chagovetz and C. B. Grissom, J. Am. Chem. soc. 115, 12152-12157, 1993), this process does not account for the magnetic field dependence of the CW quantum yield that is only observed in viscous solvents. Glycerol and ethylene glycol increase the microviscosity of the solution and thereby increase the lifetime of the spin-correlated diffusive radical pair. This enables magnetic field dependent recombination among spin-correlated diffusive radical pairs in the solvent cage. Magnetic field dependent recombination is not observed in the presence of nonviscosigenic alcohols such as isopropanol, thereby indicating the importance of the increased microviscosity of the medium. Paramagnetic radical scavengers that trap alkyl radicals that escape the solvent cage do not diminish the magnetic field effect on the CW quantum yield, thereby ruling out radical pair recombination among randomly diffusing radical pairs, as well as excluding the involvement of solvent-derived radicals. Magnetic field dependent recombination among alkylcobalamin radical pairs has been simulated by a semi-classical model of radical pair dynamics and recombination. These calculations support the existence of a singlet radical pair precursor.
Wnt Signaling and Breast Cancer (2004)

Secreted signaling factors of the Wnt protein family regulate many cellular processes, including cell fate decisions and cell proliferation, and aberrant Wnt signaling is associated with tumorigenesis. Many Wnt proteins act via a signaling pathway that results in stabilization of beta-catenin and consequent transcriptional activation of specific target genes. Mutations in beta-catenin or other Wnt pathway components, which result in beta-catenin accumulation, are found in a wide range of human cancers. In contrast, such mutations have been found only rarely in breast cancer. Nevertheless there is strong evidence of stabilization of beta-catenin protein in a majority of human breast tumors. Moreover, studies in mouse model systems clearly demonstrate that activated Wnt signaling leads to mammary tumorigenesis. This review summarizes the current evidence implicating Wnt/beta-catenin signaling in breast cancer and discusses several possible mechanisms by which the pathway may become activated.
Enhanced Optical Activity by Achiral Rod-Like Molecules Nanosegregated in the B<sub>4</sub> Structure of Achiral Bent-Core Molecules (2009)

Chirality in a mixture system consisting of bent-core 1,3-phenylene bis[4-(4-8-alkoxyphenyliminomethyl)benzoates] (P8-O-PIMB) and rod-like n-pentyl-cyanobiphenyl (5CB) molecules has been studied. Precise circular dichroism (CD) spectra using thin sample cells indicate mainly two characteristics: (1) the origin of CD signals is due to chiral-segregated bent-core molecules in the B(4) phase, where 5CB is in the isotropic phase; (2) the enhanced CD signal is detected in the B(X) phase, where 5CB is in the nematic phase. These results suggest that 5CB molecules are embedded in the network of helical nanofilaments formed by P8-O-PIMB and form helical superstructure with the same handedness as the helical nanofilaments in the B(X) phase, resulting in the giant CD signals.
Mitochondrial dysfunction and mitophagy: the beginning and end to diabetic nephropathy? (2013)

Diabetic nephropathy (DN) is a progressive microvascular complication arising from diabetes. Within the kidney, the glomeruli, tubules, vessels and interstitium are disrupted, ultimately impairing renal function and leading to end-stage renal disease (ESRD). Current pharmacological therapies used in individuals with DN do not prevent the inevitable progression to ESRD; therefore, new targets of therapy are urgently required. Studies from animal models indicate that disturbances in mitochondrial homeostasis are central to the pathogenesis of DN. Since renal proximal tubule cells rely on oxidative phosphorylation to provide adequate ATP for tubular reabsorption, an impairment of mitochondrial bioenergetics can result in renal functional decline. Defects at the level of the electron transport chain have long been established in DN, promoting electron leakage and formation of superoxide radicals, mediating microinflammation and contributing to the renal lesion. More recent studies suggest that mitochondrial-associated proteins may be directly involved in the pathogenesis of tubulointerstitial fibrosis and glomerulosclerosis. An accumulation of fragmented mitochondria are found in the renal cortex in both humans and animals with DN, suggesting that in tandem with a shift in dynamics, mitochondrial clearance mechanisms may be impaired. The process of mitophagy is the selective targeting of damaged or dysfunctional mitochondria to autophagosomes for degradation through the autophagy pathway. The current review explores the concept that an impairment in the mitophagy system leads to the accelerated progression of renal pathology. A better understanding of the cellular and molecular events that govern mitophagy and dynamics in DN may lead to improved therapeutic strategies.
Ray tracing for earthquake location in laterally heterogeneous media (1988)

We propose a technique for the fast solution of ray tracing in three‐dimensional laterally heterogeneous media. Analytical solutions for both ray tracing and paraxial ray tracing for a medium with an arbitrary gradient of the square of slowness are used to develop a systematic procedure to construct exact solutions. Complex heterogeneous media are divided into tetrahedral finite elements inside which the square of the slowness has a simple linear distribution. Arbitrarily complex media may be studied by judicious choice of the elements. We develop appropriate boundary conditions for interfaces with zeroth or first‐order velocity discontinuities. Two‐point ray tracing is performed by a Newton method based on paraxial ray theory. With a few iterations the ray trajectories through the source and the observer are calculated with the same overall speed as with ray bending. The paraxial method has the additional advantage that it can be used to identify caustics and to separate travel time branches. We used the previously described method to replace the ray tracing algorithm of the HYPO71 program, probably the most commonly used earthquake location program. The ray tracing routine may be easily modified to adapt it to other earthquake location environments. With the modified HYPO71 program, we relocated the aftershock sequence of the November 23, 1980, Irpinia (Italy) earthquake. The introduction of a low‐velocity zone proposed by different authors shifts aftershock locations to the NE. This horizontal displacement of hypocenters is not very sensitive to the thickness of the low‐velocity zone.
Community Resources and Strategies for Association Mapping in Sorghum (2008)

Association mapping is a powerful strategy for identifying genes underlying quantitative traits in plants. We have assembled and characterized genetic and phenotypic diversity of a sorghum [ Sorghum bicolor (L.) Moench] panel suitable for association mapping, comprised of 377 accessions representing all major cultivated races (tropical lines from diverse geographic and climatic regions), and important U.S. breeding lines and their progenitors. Accessions were phenotyped for eight traits, and levels of population structure and familial relatedness were assessed with 47 simple sequence repeat (SSR) loci. The panel exhibited substantial morphological variation and little genotypic differentiation was observed between the converted tropical and breeding lines. The phenotypic and genotypic data were used to evaluate the performance of several association models in controlling for spurious associations. Our analysis indicated that association models that accounted for both population structure and kinship performed better than those that did not. In addition, we found that the optimal number of subpopulations used to correct for population structure was trait dependent. Although augmentation of the genotypic data with additional SSR loci may be necessary, the association models, genotypic data, and germplasm panel described here provide a starting point for sorghum researchers to begin association studies of traits and markers or candidate genes of interest.
Expression of mRNA and functional alpha <sub>1</sub> ‐adrenoceptors that suppress the GIRK conductance in adult rat locus coeruleus neurons (2002)

1. Locus coeruleus neurons in adult rats express binding sites and mRNA for alpha(1)-adrenoceptors even though the depolarizing effect of alpha(1)-adrenoceptor agonists on neonatal neurons disappears during development. 2. In this study intracellular microelectrodes were used to record from locus coeruleus neurons in brain slices of adult rats and reverse transcription-polymerase chain reaction (RT - PCR) was used to investigate the mRNA expression of alpha(1)- and alpha(2)-adrenoceptors in juvenile and adult rats. 3. The alpha(1)-adrenoceptor agonist phenylephrine had no effect on the membrane conductance of locus coeruleus neurons (V(hold) -60 mV) but decreased the G protein coupled, inward rectifier potassium (GIRK) conductance induced by alpha(2)-adrenoceptor or mu-opioid agonists. The GIRK conductance induced by noradrenaline was increased in amplitude when alpha(1)-adrenoceptors were blocked with prazosin. 4. RT - PCR of total cellular RNA isolated from microdissected locus coeruleus tissue demonstrated strong mRNA expression of alpha(1a)-, alpha(1b)- and alpha(1d)-adrenoceptors in both juvenile and adult rats. However, only mRNA transcripts for the alpha(1b)-adrenoceptors were consistently detected in cytoplasmic samples taken from single locus coeruleus neurons of juvenile rats, suggesting that this subtype may be responsible for the physiological effects seen in juvenile rats. 5. Juvenile and adult locus coeruleus tissue expressed mRNA for the alpha(2a)- and alpha(2c)-adrenoceptors while the alpha(2b)-adrenoceptor was only weakly expressed in juveniles and was not detected in adults. 6. The results of this study show that alpha(1)-adrenoceptors expressed in adult locus coeruleus neurons function to suppress the GIRK conductance that is activated by mu-opioid and alpha(2)-adrenoceptors.
Compiler support for lightweight context switching (2013)

We propose a new language-neutral primitive for the LLVM compiler, which provides efficient context switching and message passing between lightweight threads of control. The primitive, called S wapstack , can be used by any language implementation based on LLVM to build higher-level language structures such as continuations, coroutines, and lightweight threads. As part of adding the primitives to LLVM, we have also added compiler support for passing parameters across context switches. Our modified LLVM compiler produces highly efficient code through a combination of exposing the context switching code to existing compiler optimizations, and adding novel compiler optimizations to further reduce the cost of context switches. To demonstrate the generality and efficiency of our primitives, we add one-shot continuations to C++, and provide a simple fiber library that allows millions of fibers to run on multiple cores, with a work-stealing scheduler and fast inter-fiber sychronization. We argue that compiler-supported lightweight context switching can be significantly faster than using a library to switch between contexts, and provide experimental evidence to support the position.
Classifying mammographic mass shapes using the wavelet transform modulus-maxima method (1999)

In this article, multiresolution analysis, specifically the discrete wavelet transform modulus-maxima (mod-max) method, is utilized for the extraction of mammographic mass shape features. These shape features are used in a classification system to classify masses as round, nodular, or stellate. The multiresolution shape features are compared with traditional uniresolution shape features for their class discriminating abilities. The study involved 60 digitized mammographic images. The masses were segmented manually by radiologists, prior to introduction to the classification system. The uniresolution and multiresolution shape features were calculated using the radial distance measure of the mass boundaries. The discriminating power of the shape features were analyzed via linear discriminant analysis (LDA). The classification system utilized a simple Euclidean metric to determine class membership. The system was tested using the apparent and leave-one-out test methods. The classification system when using the multiresolution and uniresolution shape features resulted in classification rates of 83% and 80% for the apparent and leave-one-out test methods, respectively. In comparison, when only the uniresolution shape features were used, the classification rates were 72 and 68% for the apparent and leave-one-out test methods, respectively.
Distribution and sequence analysis of the centromere‐associated repetitive element CEN38 of <i>Sorghum bicolor</i> (Poaceae) (2000)

Fluorescence in situ hybridization (FISH) of a large-insert genomic clone, BAC 22B2, previously suggested that Sorghum bicolor (2n = 20) has the tetraploid architecture A(b)A(b)B(b)B(b). Here, we report on BAC 22B2 subclone pCEN38 (1047-bp insert) as related to sorghum and sugarcane. Mitotic FISH of six different subclones of BAC 22B2 showed that pCEN38 produced the strongest specificity to the A(b) subgenome and signal occurred primarily near centromeres. Southern blots of pCEN38 to 21 crop plants revealed a narrow taxonomic distribution. Meiotic metaphase I FISH positioned pCEN38 sequences near active centromeres. Pachytene FISH revealed that the distributions are trimodal in several B(b) and possibly all sorghum chromosomes. DNA sequencing revealed that the pCEN38 fragment contains three tandemly repeated dimers (<280 bp) of the same sequence family found in sorghum clone pSau3A10, and that each dimer consists of two divergent monomers (<140 bp). Sequence comparisons revealed homology between the pCEN38 monomers and the SCEN 140 bp tandem repeat family of sugarcane. FISH of pCEN38 yielded signal in centromere regions of most but not all sugarcane chromosomes. Results suggest that sugarcane and sorghum share at least one ancestor harboring elements similar to pCEN38 and SCEN and that each species had an ancestor in which the repetitive element was weakly present or lacking.
THE ISOMERS OF 4-PHENYL- AND 4-CYCLOHEXYL-CYCLOHEXANOL (1948)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE ISOMERS OF 4-PHENYL- AND 4-CYCLOHEXYL-CYCLOHEXANOLHERBERT E. UNGNADECite this: J. Org. Chem. 1948, 13, 3, 361–370Publication Date (Print):May 1, 1948Publication History Published online1 May 2002Published inissue 1 May 1948https://pubs.acs.org/doi/10.1021/jo01161a007https://doi.org/10.1021/jo01161a007research-articleACS PublicationsRequest reuse permissionsArticle Views190Altmetric-Citations26LEARN 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
3D Simulation for Robot Arm Control with Deep Q-Learning (2016)

Recent trends in robot arm control have seen a shift towards end-to-end solutions, using deep reinforcement learning to learn a controller directly from raw sensor data, rather than relying on a hand-crafted, modular pipeline. However, the high dimensionality of the state space often means that it is impractical to generate sufficient training data with real-world experiments. As an alternative solution, we propose to learn a robot controller in simulation, with the potential of then transferring this to a real robot. Building upon the recent success of deep Q-networks, we present an approach which uses 3D simulations to train a 7-DOF robotic arm in a control task without any prior knowledge. The controller accepts images of the environment as its only input, and outputs motor actions for the task of locating and grasping a cube, over a range of initial configurations. To encourage efficient learning, a structured reward function is designed with intermediate rewards. We also present preliminary results in direct transfer of policies over to a real robot, without any further training.