gebhart/patrepeval huggingface dataset:
Afadin: A Novel Actin Filament–binding Protein with One PDZ Domain Localized at Cadherin-based Cell-to-Cell Adherens Junction (1997)

A novel actin filament (F-actin)-binding protein with a molecular mass of approximately 205 kD (p205), which was concentrated at cadherin-based cell-to-cell adherens junction (AJ), was isolated and characterized. p205 was purified from rat brain and its cDNA was cloned from a rat brain cDNA library. p205 was a protein of 1,829 amino acids (aa) with a calculated molecular mass of 207,667 kD. p205 had one F-actin-binding domain at 1,631-1,829 aa residues and one PDZ domain at 1,016- 1,100 aa residues, a domain known to interact with transmembrane proteins. p205 was copurified from rat brain with another protein with a molecular mass of 190 kD (p190). p190 was a protein of 1,663 aa with a calculated molecular mass of 188,971 kD. p190 was a splicing variant of p205 having one PDZ domain at 1,009-1,093 aa residues but lacking the F-actin-binding domain. Homology search analysis revealed that the aa sequence of p190 showed 90% identity over the entire sequence with the product of the AF-6 gene, which was found to be fused to the ALL-1 gene, known to be involved in acute leukemia. p190 is likely to be a rat counterpart of human AF-6 protein. p205 bound along the sides of F-actin but hardly showed the F-actin-cross-linking activity. Northern and Western blot analyses showed that p205 was ubiquitously expressed in all the rat tissues examined, whereas p190 was specifically expressed in brain. Immunofluorescence and immunoelectron microscopic studies revealed that p205 was concentrated at cadherin-based cell-to-cell AJ of various tissues. We named p205 l-afadin (a large splicing variant of AF-6 protein localized at adherens junction) and p190 s-afadin (a small splicing variant of l-afadin). These results suggest that l-afadin serves as a linker of the actin cytoskeleton to the plasma membrane at cell-to-cell AJ.
Broodstock rearing and spawning of Black Sea turbot, Psetta maxima (2002)

Broodstock development and induction of spawning of Black Sea turbot, Psetta maxima has been conducted between 1998 and 2001 in the Central Fisheries Research Institute, Trabzon, Turkey. One of the environmental and feeding conditions evident in broodstock management is the optimum water temperature below 17°C which is the present culture condition at the Institute. Likewise, frozen whiting is considered to be a good broodstock diet from the viewpoint of nu-tritional and ecological aspects. Growth of hatchery-bred broodstock fed this diet is shown as the relationship of body weight to age (month) represented as an equation of: y = 0.072 x + 0.164 (R² = 0.998). Natural spawning was observed for 2-year-old hatchery-bred stock at water temperature of 14°C, however, no spawning was observed by the same broodstock at 3-years of age. On the other hand, induction of spawning for wild-caught broodstock were established through hormonal treatment. A total of 78 artificial inseminations for 61 wild-caught females were carried out between 1998 and 2001spawning season (April and May). An average yearly production of 1.96 million newly hatched larvae was recorded with an average fertilization rate of 39.5% and a mean hatching rate of 32.5%.
Synthesis of High-Density Nickel Cobalt Aluminum Hydroxide by Continuous Coprecipitation Method (2012)

Spherical nickel cobalt aluminum hydroxide (Ni(0.80)Co(0.15)Al(0.05)-hydroxide, NCA) was prepared by a continuous coprecipitation method. A new design of the Al solution and the feeding method was applied, which enabled to prevent rapid precipitation of Al(OH)(3) and to obtain spherical NCA with large enough particle size and high density. The active material (LiNi(0.80)Co(0.15)Al(0.05)O(2) or LNCA) prepared from it showed higher tap-density than that made from NCA prepared by general processes, and homogeneity of Al-distribution was also improved. It is expected that the electrode density of lithium ion batteries adopting LNCA could be improved with the new process proposed in this study.
Modulation of Endothelium by Heparin and Related Polyelectrolytes (1996)

The vascular endothelium is an important me diator of the hemostatic balance. In addition to shielding subendothelial tissue factor from flowing blood, endothe lial cells produce a number of substances which favor an antithrombotic state including TFPI and tPA. The ability of polyelectrolytes such as heparin and defibrotide to modulate endothelial function is examined using animal models and human studies. Like heparin, defibrotide is observed to increase plasma TFPI antigen levels. Addi tionally, defibrotide administration is observed to in crease plasma tPa antigen levels and to decrease PAI, TF and endothelin levels. Modulation of endothelial function by defibrotide may account for its beneficial effect in PAOD.
Throughput analysis of ARQ selective-repeat protocol with time diversity in Markov channels (2002)

An ARQ selective repeat protocol with time-out mechanism is studied. Transmissions on both the forward and the reverse channels are assumed to experience Markovian errors and therefore the feedback is unreliable. Using renewal theory, exact results for the throughput of the protocol are evaluated. Simulation results, that confirm the analysis, are presented; an application to mobile radio is also discussed.
Identification of an alternatively spliced isoform of carbonic anhydrase XII in diffusely infiltrating astrocytic gliomas (2008)

Carbonic anhydrase XII (CA XII) is a transmembrane enzyme that is associated with neoplastic growth. CA XII has been proposed to be involved in acidification of the extracellular milieu, creating an appropriate microenvironment for rapid tumor growth. Because RNA sequence databases have indicated that two isoforms of CA XII might exist in human tissues, and because alternatively spliced protein forms have been linked to aggressive behavior of cancer cells, we designed a study to evaluate the presence of the two forms of CA XII in diffuse astrocytomas, a tumor type known for its aggressive and often noncurable behavior. Reverse transcription PCR of tumor samples surprisingly revealed that CA XII present in diffuse astrocytomas is mainly encoded by a shorter mRNA variant. We further showed by Western blotting that anti-CA XII antibody recognized both isoforms in the glioblastoma cell lines, and we then evaluated the expression of CA XII in astrocytomas using immunohistochemistry and correlated the results with various clinicopathological and molecular factors. Of 370 diffusely infiltrating astrocytomas, 363 cases (98%) showed immunoreactions for CA XII. Importantly, CA XII expression correlated with poorer patient prognosis in univariate (p = 0.010, log-rank test) and multivariate survival analyses (p = 0.039, Cox analysis). From these results, we conclude that CA XII is commonly expressed in diffuse astrocytomas and that it might be used as a biomarker of poor prognosis. The absence of 11 amino acids in the shorter isoform, which seems to be common in astrocytomas, may affect the normal quaternary structure and biological function of CA XII.
Frequency and Precision of Body Condition Scoring in Dairy Cattle (1994)

The objectives of this project were 1) to determine whether mean body condition scores for 30-d lactation and dry period intervals can be utilized to appraise body condition changes in a herd and 2) to determine the precision of the mean body condition score for 30-d lactation and dry period intervals. Cows in a commercial dairy herd were visually scored for body condition on a five-point scale in increments of .25. Dry period intervals were based on expected calving date; lactation intervals were calculated from the calving date for each cow. The first objective was accomplished by comparison of mean body condition scores for the 30-d lactation and dry period intervals. A Student's t test was used to test for differences between adjacent means for body condition score. Mean body condition scores for each 30-d lactation and dry period interval can be used to detect changes in body condition across stages of lactation and the dry period. The precision of the mean body condition score for each 30-d lactation and dry period interval was determined. Precision (or significance) was 95, 90, and 80%. Significance was 95% for all but one of the lactation and dry period intervals, indicating that mean body condition scores for a given interval are significant and precise. Body condition scoring may provide useful management information with the procedures developed in this study.
FPGA Implementation of Temperature Controller for PCR Based on Microfluidic Chip (2014)

In order to meet the requirements such as high precision, small overshoot, fast response in Polymerase Chain Reaction(PCR) when control temperature, this paper designs a PCR microfluidic chip based on temperature control using genetic algorithm PID. The chip adopts genetic algorithm PID to control AT89C51 chip to generate PWM waves which have different duty ratio in order to realize the adjustment and control of temperature. The design of genetic algorithm PID controller is realized by FPGA. And in the MATLAB environment, the simulation is conducted using genetic algorithm PID control. The simulation results show that genetic algorithm PID controller which is realized by FPGA can well track the input signal, and the control effect is better
Dense interest points (2010)

Local features or image patches have become a standard tool in computer vision, with numerous application domains. Roughly speaking, two different types of patch-based image representations can be distinguished: interest points, such as corners or blobs, whose position, scale and shape are computed by a feature detector algorithm, and dense sampling, where patches of fixed size and shape are placed on a regular grid (possibly repeated over multiple scales). Interest points focus on `interesting' locations in the image and include various degrees of viewpoint and illumination invariance, resulting in better repeatability scores. Dense sampling, on the other hand, gives a better coverage of the image, a constant amount of features per image area, and simple spatial relations between features. In this paper, we propose a hybrid scheme, which we call dense interest points, where we start from densely sampled patches yet optimize their position and scale parameters locally. We investigate whether doing so it is possible to get the best of both worlds.
Antibiotics and antiseptics for venous leg ulcers (2013)

At present, no evidence is available to support the routine use of systemic antibiotics in promoting healing of venous leg ulcers. However, the lack of reliable evidence means that it is not possible to recommend the discontinuation of any of the agents reviewed. In terms of topical preparations, some evidence supports the use of cadexomer iodine. Current evidence does not support the routine use of honey- or silver-based products. Further good quality research is required before definitive conclusions can be drawn about the effectiveness of povidone-iodine, peroxide-based preparations, ethacridine lactate, chloramphenicol, framycetin, mupirocin, ethacridine or chlorhexidine in healing venous leg ulceration. In light of the increasing problem of bacterial resistance to antibiotics, current prescribing guidelines recommend that antibacterial preparations should be used only in cases of clinical infection, not for bacterial colonisation.
A novel algorithm for notch detection (2013)

It is common knowledge that DFM guidelines require revisions to design data. These guidelines impose the need for corrections inserted into areas within the design data flow. At times, this requires rather drastic modifications to the data, both during the layer derivation or DRC phase, and especially within the RET phase. For example, OPC. During such data transformations, several polygon geometry changes are introduced, which can substantially increase shot count, geometry complexity, and eventually conversion to mask writer machine formats. In this resulting complex data, it may happen that notches are found that do not significantly contribute to the final manufacturing results, but do in fact contribute to the complexity of the surrounding geometry, and are therefore undesirable. Additionally, there are cases in which the overall figure count can be reduced with minimum impact in the quality of the corrected data, if notches are detected and corrected. Case in point, there are other cases where data quality could be improved if specific valley notches are filled in, or peak notches are cut out. Such cases generally satisfy specific geometrical restrictions in order to be valid candidates for notch correction. Traditional notch detection has been done for rectilinear data (Manhattan-style) and only in axis-parallel directions. The traditional approaches employ dimensional measurement algorithms that measure edge distances along the outside of polygons. These approaches are in general adaptations, and therefore ill-fitted for generalized detection of notches with strange shapes and in strange rotations. This paper covers a novel algorithm developed for the CATS MRCC tool that finds both valley and/or peak notches that are candidates for removal. The algorithm is generalized and invariant to data rotation, so that it can find notches in data rotated in any angle. It includes parameters to control the dimensions of detected notches, as well as algorithm tolerances and data reach.
Comparative effectiveness of the tumour diagnostics, CA 19-9, CA 125 and carcinoembryonic antigen in patients with diseases of the digestive system. (1987)

Serum concentrations of CA 19-9, CA 125 and carcinoembryonic antigen (CEA) in 145 patients with gastrointestinal carcinomas and 89 with non-neoplastic diseases were determined to compare the clinical usefulness of these tumour markers. Significantly fewer positive cases were obtained with serum CA 19-9 (9%) and CA 125 (8%) tests than the CEA test (22%) (both p less than 0.05) in patients with benign diseases, while comparable sensitivities were achieved with the CA 19-9 (44%) test, the CA 125 (41%) test and the CEA test (47%) in those with a carcinoma. High incidences of raised concentrations of serum CA 19-9 and CA 125 were observed in case of cancer of the pancreas (CA 19-9: 87%, CA 125: 67%) and biliary tract (CA 19-9: 63%, CA 125: 48%). Combined tests of CA 19-9 and CA 125 revealed increments in the sensitivity (61%) and provided a higher specificity (87%) than that of the single CEA test (78%). These combined tests were most useful for a differential diagnosis of pancreatic carcinoma (97% positive) and biliary tract carcinoma (74%) from chronic pancreatitis (4%) and cholelithiasis (0%), respectively. Studies on the relations of clinical staging and serum concentrations of CA 19-9 and CA 125 revealed significant rises in cases of disseminated carcinoma. These results clearly show that serum CA 19-9 and CA 125 tests are most pertinent for diagnosing advanced carcinomas of organs in the digestive system.
The 90-kDa heat shock protein is essential for Ah receptor signaling in a yeast expression system. (1994)

In an effort to provide a more powerful system to study the Ah receptor (AHR) signaling pathway, we expressed the AHR, its dimerization partner ARNT, and a beta-galactosidase (lacZ) reporter gene, driven by two dioxin-responsive enhancers, in the yeast Saccharomyces cerevisiae. In this system, the agonists beta-naphthoflavone and alpha-naphthoflavone induced transcription of the lacZ gene, with EC50 values of 7.9 x 10(-8) and 3.0 x 10(-7) M, respectively, while the nonagonist dexamethasone was without effect. As a first application of this system, we examined the relationship between the 90-kDa heat shock protein (hsp90) and AHR function. To accomplish this in a manner that was independent of the ARNT protein, we constructed a chimeric receptor in which the DNA binding and primary dimerization domains of the AHR were swapped with analogous domains from the LexA protein. Coexpression of this AHR-LexA chimera and a lacZ reporter gene driven by eight LexA operator sites in a yeast strain with regulatable levels of hsp90, yielded pharmacology that closely mirrored that of the AHR/ARNT/dioxin-responsive enhancer system described above, but only when hsp90 levels were held near their wild type levels. When hsp90 levels were reduced to approximately 5% of normal, AHR signaling in response to agonist was completely blocked despite normal cell growth. These results provide the first genetic evidence for the role of hsp90 in AHR signaling and provide the basis for a powerful new system in which to study this pathway.
Zinc and copper status of severely burned children during TPN. (1991)

Alterations in zinc (Zn) and copper (Cu) homeostasis have been reported during the acute recovery period following thermal injury in both children and adults. Increased urinary losses of Zn and Cu and decreased plasma concentrations of Zn, Cu, and ceruloplasmin (CP), the major copper transport protein, occur despite adequate provision of these elements in enteral feedings. We now report data for moderately to severely burned children receiving total parenteral nutrition (TPN) supplemented to provide Zn and Cu. Hyperzincuria occurred consistently when 50 micrograms/kg Zn was delivered daily to older children. Similarly, when younger children received 100 micrograms/kg Zn daily, profound hyperzincuria ensued despite a reduction in total plasma Zn. Hypozincemia was accompanied by low levels of Zn in the plasma subfraction normally associated with albumin-bound Zn. The delivery of Cu via TPN was 4-12 micrograms/kg daily, and urinary Cu losses were not elevated. Plasma total Cu and plasma CP were invariably reduced. These findings are discussed in relation to guidelines published for pediatric trace element supplementation during TPN.
The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks (2008)

Reconstructing cellular signaling networks and understanding how they work are major endeavors in cell biology. The scale and complexity of these networks, however, render their analysis using experimental biology approaches alone very challenging. As a result, computational methods have been developed and combined with experimental biology approaches, producing powerful tools for the analysis of these networks. These computational methods mostly fall on either end of a spectrum of model parameterization. On one end is a class of structural network analysis methods; these typically use the network connectivity alone to generate hypotheses about global properties. On the other end is a class of dynamic network analysis methods; these use, in addition to the connectivity, kinetic parameters of the biochemical reactions to predict the network's dynamic behavior. These predictions provide detailed insights into the properties that determine aspects of the network's structure and behavior. However, the difficulty of obtaining numerical values of kinetic parameters is widely recognized to limit the applicability of this latter class of methods. Several researchers have observed that the connectivity of a network alone can provide significant insights into its dynamics. Motivated by this fundamental observation, we present the signaling Petri net, a non-parametric model of cellular signaling networks, and the signaling Petri net-based simulator, a Petri net execution strategy for characterizing the dynamics of signal flow through a signaling network using token distribution and sampling. The result is a very fast method, which can analyze large-scale networks, and provide insights into the trends of molecules' activity-levels in response to an external stimulus, based solely on the network's connectivity. We have implemented the signaling Petri net-based simulator in the PathwayOracle toolkit, which is publicly available at http://bioinfo.cs.rice.edu/pathwayoracle. Using this method, we studied a MAPK1,2 and AKT signaling network downstream from EGFR in two breast tumor cell lines. We analyzed, both experimentally and computationally, the activity level of several molecules in response to a targeted manipulation of TSC2 and mTOR-Raptor. The results from our method agreed with experimental results in greater than 90% of the cases considered, and in those where they did not agree, our approach provided valuable insights into discrepancies between known network connectivities and experimental observations.
A patch memory system for image processing and computer vision (2016)

From self-driving cars to high dynamic range (HDR) imaging, the demand for image-based applications is growing quickly. In mobile systems, these applications place particular strain on performance and energy efficiency. As traditional memory systems are optimized for 1D memory access, they are unable to efficiently exploit the multi-dimensional locality characteristics of image-based applications which often operate on sub-regions of 2D and 3D image data. We have developed a new Patch Memory System (PMEM) tailored to application domains that process 2D and 3D data streams. PMEM supports efficient multidimensional addressing, automatic handling of image boundaries, and efficient caching and prefetching of image data. In addition to an optimized cache, PMEM includes hardware for offloading structured address calculations from processing units. We improve average energy-delay by 26% compared to EVA, a memory system for computer vision applications. Compared to a traditional cache, our results show that PMEM can reduce processor energy by 34% for a selection of CV and IP applications, leading to system performance improvement of up to 32% and energy-delay product improvement of 48--86% on the applications in this study.
A High Performance and Energy Efficient Microprocessor with a Novel Restricted Dynamically Reconfigurable Accelerator (2017)

In the era of Internet of Things, the battery life of edge devices must be extended for sensing connection to the Internet. We aim to reduce the power consumption of the microprocessor embedded in such devices by using a novel dynamically reconfigurable accelerator. Conventional microprocessors consume a large amount of power for memory access, in registers, and for the control of the processor itself rather than computation; this decreases the energy efficiency. Dynamically reconfigurable accelerators reduce such redundant power by computing in parallel on reconfigurable switches and processing element arrays (often consisting of an arithmetic logic unit (ALU) and registers). We propose a novel dynamically reconfigurable accelerator “DYNaSTA” composed of a dynamically reconfigurable data path and static ALU arrays. The static ALU arrays process instructions in parallel without registers and improve energy efficiency. The dynamically reconfigurable data path includes registers and many switches dynamically reconfigured to resolve operand dependencies between instructions mapped on the static ALU array, and forwards appropriate operands to the static ALU array. Therefore, the DYNaSTA accelerator has more flexibility while improving the energy efficiency compared with the conventional dynamically reconfigurable accelerators. We simulated the power consumption of the proposed DYNaSTA accelerator and measured the fabricated chip. As a result, the power consumption was reduced by 69% to 86%, and the energy efficiency improved 4.5 to 13 times compared to a general RISC microprocessor.
Internet-based hearing screening using speech-in-noise: validation and comparisons of self-reported hearing problems, quality of life and phonological representation (2013)

Almost one in five participants was in need of contacting their local hearing clinic. This group had more complaints regarding tinnitus and hyperacusis, rated their own hearing as worse than those who passed, and had a poorer capability of generating accurate phonological representations. This study suggests that it is feasible to screen for hearing status online, and obtain valid data.