gebhart/patrepeval huggingface dataset:
Evolution of Aminoacyl-tRNA Synthetases—Analysis of Unique Domain Architectures and Phylogenetic Trees Reveals a Complex History of Horizontal Gene Transfer Events (1999)

Phylogenetic analysis of aminoacyl-tRNA synthetases (aaRSs) of all 20 specificities from completely sequenced bacterial, archaeal, and eukaryotic genomes reveals a complex evolutionary picture. Detailed examination of the domain architecture of aaRSs using sequence profile searches delineated a network of partially conserved domains that is even more elaborate than previously suspected. Several unexpected evolutionary connections were identified, including the apparent origin of the beta-subunit of bacterial GlyRS from the HD superfamily of hydrolases, a domain shared by bacterial AspRS and the B subunit of archaeal glutamyl-tRNA amidotransferases, and another previously undetected domain that is conserved in a subset of ThrRS, guanosine polyphosphate hydrolases and synthetases, and a family of GTPases. Comparison of domain architectures and multiple alignments resulted in the delineation of synapomorphies-shared derived characters, such as extra domains or inserts-for most of the aaRSs specificities. These synapomorphies partition sets of aaRSs with the same specificity into two or more distinct and apparently monophyletic groups. In conjunction with cluster analysis and a modification of the midpoint-rooting procedure, this partitioning was used to infer the likely root position in phylogenetic trees. The topologies of the resulting rooted trees for most of the aaRSs specificities are compatible with the evolutionary "standard model" whereby the earliest radiation event separated bacteria from the common ancestor of archaea and eukaryotes as opposed to the two other possible evolutionary scenarios for the three major divisions of life. For almost all aaRSs specificities, however, this simple scheme is confounded by displacement of some of the bacterial aaRSs by their eukaryotic or, less frequently, archaeal counterparts. Displacement of ancestral eukaryotic aaRS genes by bacterial ones, presumably of mitochondrial origin, was observed for three aaRSs. In contrast, there was no convincing evidence of displacement of archaeal aaRSs by bacterial ones. Displacement of aaRS genes by eukaryotic counterparts is most common among parasitic and symbiotic bacteria, particularly the spirochaetes, in which 10 of the 19 aaRSs seem to have been displaced by the respective eukaryotic genes and two by the archaeal counterpart. Unlike the primary radiation events between the three main divisions of life, that were readily traceable through the phylogenetic analysis of aaRSs, no consistent large-scale bacterial phylogeny could be established. In part, this may be due to additional gene displacement events among bacterial lineages. Argument is presented that, although lineage-specific gene loss might have contributed to the evolution of some of the aaRSs, this is not a viable alternative to horizontal gene transfer as the principal evolutionary phenomenon in this gene class.
ChemInform Abstract: CATHODIC REDUCTION OF DERIVATIVES OF DIBENZYLIDENESUCCINIC ACID, ATTEMPTED ELECTROHYDROCYCLIZATION OF CONJUGATED SYSTEMS (1978)

Abstract Die Dibenzylidenbernsteinsäuren (I) und (II) und das N‐Methylimid (III) werden an der Quecksilberkathode reduziert.
Database migration: a new architecture for transaction processing in broadband networks (1998)

Due to recent developments in network technologies, broader channel bandwidth is becoming prevalent in worldwide networks. As one of the new technologies making good use of such broadband channels, dynamic relocation of databases through networks, database migration, will soon be used in practice as a powerful and basic database operation. We propose two transaction processing methods to take advantage of database migration in broadband networks. These methods choose the most efficient transaction processing method between the conventional method, based on the two-phase commit protocol, and our method, using database migration. We also propose a concurrency control mechanism and a recovery mechanism for our proposed methods. Simulation results are presented comparing the performance of our proposed methods and the conventional transaction processing method based on the two-phase commit protocol. The results demonstrate that the effective use of database migration produces better performance than the conventional method.
An Image-based Brain-Computer Interface Using the P3 Response (2007)

We present a new image-based interface for using electroencephalographic signals (EEG) to control a humanoid robot. In order to make maximal use of a low-bandwidth brain computer interface (BCI), we use a humanoid robot that has sophisticated capabilities such as navigating to different locations in its environment and interacting with objects. The robot communicates with the BCI by sending images of discovered locations and objects as candidates for interaction. The BCI uses these candidates and exploits the P300 response for detecting the user's selection. We describe the design of the interface, and present results from a 9-user study that characterizes the performance, generalization and training needs of the BCI. Our results indicate that a 4-class selection can be performed in 5 seconds with as low as 5% error. Further, a short training period of 3-4min provides near-optimal accuracy.
Perfect image segmentation using pulse coupled neural networks (1999)

This paper describes a method for segmenting digital images using pulse coupled neural networks (PCNN's). The pulse coupled neuron (PCN) model used in PCNN is a modification of Eckhorn's cortical neuron model. A single layered laterally connected PCNN is capable of perfectly segmenting digital images even when there is a considerable overlap in the intensity ranges of adjacent regions. Conditions for perfect image segmentation are derived. It is also shown that addition of an inhibition receptive field to the neuron model increases the possibility of perfect segmentation. The inhibition input reduces the overlap of intensity ranges of adjacent regions by effectively compressing the intensity range of each region.
A Study of Price and Quality in Service Operations (1994)

Studies the relationship between perceived price and perceived quality for the three types of services, namely, pure, mixed, and quasi‐manufacturing classified by Chase and Tansik, and the relative importance of five dimensions of service quality identified by Parasuraman et al. Finds that the relationship between perceived price and the five dimensions of service quality appears to be very weak for pure and quasi‐manufacturing services, but is statistically significant for mixed service. Reliability dimension is statistically significant for all three types of service. Tangible dimension is a critical variable for mixed service while the empathy dimension is important for quasi‐manufacturing service. On the other hand, the relationship between perceived price and overall service‐quality is significant for quasi‐manufacturing service, but is weak for pure and mixed services.
Synthesis and Antibacterial Activity of Dendritic Architectures (2006)

Synthesis of dendrimers with pentanone as core unit and m-terphenyl as surface end group has been achieved. The inhibitory activity of pentanone and its dendrimers against human pathogenic bacteria is well-documented.
Human carbon catabolite repressor protein (CCR4)-associative factor 1: cloning, expression and characterization of its interaction with the B-cell translocation protein BTG1 (1998)

The human BTG1 protein is thought to be a potential tumour suppressor because its overexpression inhibits NIH 3T3 cell proliferation. However, little is known about how BTG1 exerts its anti-proliferative activity. In this study, we used the yeast 'two-hybrid' system to screen for interacting protein partners and identified human carbon catabolite repressor protein (CCR4)-associative factor 1 (hCAF-1), a homologue of mouse CAF-1 (mCAF-1) and Saccharomyces cerevisiae yCAF-1/POP2. In vitro the hCAF-1/BTG1 complex formation was dependent on the phosphorylation of a putative p34cdc2 kinase site on BTG1 (Ser-159). In yeast, the Ala-159 mutant did not interact with hCAF-1. In addition, phosphorylation of Ser-159 in vitro showed specificity for the cell cycle kinases p34CDK2/cyclin E and p34CDK2/cyclin A, but not for p34CDK4/cyclin D1 or p34cdc2/cyclin B. Cell synchrony experiments with primary cultures of rat aortic smooth-muscle cells (RSMCs) demonstrated that message and protein levels of rat CAF-1 (rCAF-1) were up-regulated under conditions of cell contact, as previously reported for BTG1 [Wilcox, Scott, Subramanian, Ross, Adams-Burton, Stoltenborg and Corjay (1995) Circulation 92, I34-I35]. Western blot and immunohistochemical analysis showed that rCAF-1 localizes to the nucleus of contact-inhibited RSMCs, where it was physically associated with BTG1, as determined by co-immunoprecipitation with anti-hCAF-1 antisera. Overexpression of hCAF-1 in NIH 3T3 and osteosarcoma (U-2-OS) cells was itself anti-proliferative with colony formation reduced by 67% and 90% respectively. Taken together, these results indicate that formation of the hCAF-1/BTG1 complex is driven by phosphorylation at BTG1 (Ser-159) and implicates this complex in the signalling events of cell division that lead to changes in cellular proliferation associated with cell-cell contact.
Phosphate Is a Specific Signal for ATDC5 Chondrocyte Maturation and Apoptosis-Associated Mineralization: Possible Implication of Apoptosis in the Regulation of Endochondral Ossification (2003)

These findings suggest that Pi regulates chondrocyte maturation and apoptosis-associated mineralization, highlighting a possible role for Pi in the control of skeletal development.
Tactile Velocity Estimation for Controlled In-Grasp Sliding (2021)

This letter studies the problem of controlling the sliding motion of an object held by a robot manipulator. We show how a parallel-jaw gripper can reliably control the motion of a rigid, prism-like object by 1) estimating the object's sliding velocity using measurements from tactile sensors at the gripper's fingertips and 2) controlling the grip strength to regulate the sliding velocity. We first train a neural network to estimate the sliding velocity from only tactile signals with data of tactile sensor measurements associated with various sliding velocities determined by an external motion capture system from repeated sliding trials of 28 different objects varying in size, shape, and surface texture. The velocity estimates from the neural network are then used as feedback for a closed-loop grip controller that maintains the desired sliding velocity. Experimental results show that our neural network estimates the object's sliding velocity with mean squared error under 0.5 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$(\text{cm/s})^2$</tex-math></inline-formula> , generalizes well to objects of new shapes and surface textures, and enables our closed loop grip controller to reliably slide objects at different target velocities.
Preparation of next-generation DNA sequencing libraries from ultra-low amounts of input DNA: Application to single-molecule, real-time (SMRT) sequencing on the Pacific Biosciences RS II (2014)

Abstract We have developed and validated an amplification-free method for generating DNA sequencing libraries from very low amounts of input DNA (500 picograms – 20 nanograms) for singlemolecule sequencing on the Pacific Biosciences (PacBio) RS II sequencer. The common challenge of high input requirements for single-molecule sequencing is overcome by using a carrier DNA in conjunction with optimized sequencing preparation conditions and re-use of the MagBead-bound complex. Here we describe how this method can be used to produce sequencing yields comparable to those generated from standard input amounts, but by using 1000-fold less starting material.
Frequent loss of heterozygosity on chromosome 14q in neuroblastoma. (1989)

Using 29 polymorphic DNA markers which detect allelic deletion of genes at specific loci on 19 different chromosomes, we analyzed 14 neuroblastomas for possible loss of chromosomal heterozygosity. The incidence of loss of heterozygosity was high at the D14S1 locus on chromosome 14q, being detected in six of 12 patients (50%). In spite of the cytogenetic finding suggesting high frequency of chromosome 1p deletion, loss of heterozygosity at the MYCL locus on 1p32 was detected only in two of nine patients (22%). It was also found in two of 11 patients (18%) on 13q, but not on chromosomes 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, and 20. The present results indicate that recessive genetic changes involving sequences on chromosome 14q may play an important role in the development of neuroblastoma.
Test case prioritization for regression testing based on fault dependency (2011)

Test case prioritization techniques involve scheduling test cases for regression testing in an order that increases their effectiveness at meeting some performance goal. This is inefficient to re execute all the test cases in regression testing following the software modifications. Using information obtained from previous test case execution, prioritization techniques order the test cases for regression testing so that most beneficial are executed first thus allows an improved effectiveness of testing. One performance goal, rate of dependency detected among faults, measures how quickly dependency among faults are detected within the regression testing process. An improved rate of fault dependency can provide faster feedback on software and let developers start debugging on the severe faults that cause other faults to appear later. This paper presents the new metric for assessing rate of fault dependency detection and an algorithm to prioritize test cases. Using the new metric the effectiveness of this prioritization is shown comparing it with non-prioritized test case. Analysis proves that prioritized test cases are more effective in detecting dependency among faults.
Bond behaviour of reinforcing bars in cracked concrete (2015)

Due to the relatively low tensile strength of concrete, cracks are inherent in reinforced concrete structures. A common cause of cracking is the corrosion of internal steel reinforcement, a deterioration process that can affect the bond behaviour and anchorage capacity of reinforcing bars. Corrosion leads to a reduction of the reinforcing bar diameter, the formation of a weak layer of corrosion products around the bar and expansive forces on the surrounding concrete (that can lead to cracking). In the past, the impact of corrosion on bond has been investigated by means of accelerated corrosion tests. However, the more fundamental impact of cracking as distinct from corrosion products on the bond reduction is still not fully understood. This study applies a novel test method to investigate the bond behaviour of reinforcing bars in cylindrical cracked reinforced concrete specimens. The influence of the number of cracks, crack orientation, confinement and concrete cover are investigated. The results indicate a significant loss of bond strength for single cracked specimens. This reduction becomes as high as 65% for double cracked specimens in the absence of confinement. It is shown that the crack orientation with respect to the rib pattern is of minor influence, but the concrete cover and confinement play a significant role in the obtained bond characteristics.
Sequence analysis and membrane partitioning energies of α-helical antimicrobial peptides (2004)

Sequences of 221 alpha-helical antimicrobial peptides (alphaAMPs) were compared and 63-166 of them were selected and analyzed using Perl programs. The results showed that aliphatic amino acids Gly, Leu, Ala, Ile and two positively charged amino acids Lys and Arg were composed of more than 63% of the first 20 residues of alphaAMPs. The weighed mean membrane partitioning energies at positions from 1 to 25 of alphaAMPs were calculated. Profile of the partitioning energies suggests oblique membrane insertion and an amphipathic alpha-helical structure of the N-terminus of alphaAMP (residues from 1 to 13), a bend structure at positions 13 and 14, and a less structured C-terminus that parallels the surface of the membrane. These structural features are in good agreement with the experimentally determined membrane structure of hemagglutinin fusion peptide from influenza virus. We hypothesize that this (N-terminal oblique alpha-helix)-central bend-(C-terminus) could be a common structural motif of membrane-disruptive peptides.
Case based reasoning approach to automatic comparison of models (2005)

In recent years much work has been done to find regularities in data streams. Normally streams are complete and well ordered. Major defects, such as incomplete or misleading events, occur in practice at least after some finite time. In this paper we describe a method developed for recognizing previously known patterns from a data stream. The solution is based on case based reasoning (CBR) with an extension to handle imperfect information. We also introduce a new idea to use two different case-bases instead of only one. The performance has been evaluated using simulated data and the obtained results are considered encouraging.
Proteins of rat serum, urine, and cerebrospinal fluid: VI. Further protein identifications and interstrain comparison (2001)

We have investigated the biological fluids--serum, cerebrospinal fluid, and urine--of three strains of rats; the present data extend our database (also available on-line) and may be of interest for pharmacological and toxicological investigation. Specifically, we have defined reference maps of the major protein components in cerebrospinal fluid and urine. Compartment-specific isoforms were recognized for transferrin and transthyretin. Mass spectrometric data established the cleavage site of the signal peptide and identified the N-terminal blocking group of prostaglandin D synthase from rat cerebrospinal fluid. A previously undescribed member of the family of low molecular mass rat urinary proteins was characterized as containing a sequence similar, but not identical, to the N-terminal region of rat urinary protein-2 (RUP-2), and divergent from RUP-1.
Control of Wavelength Dispersion of Birefringence by Miscible Polymer Blends (2007)

Abstract Wavelength dispersion of birefringence in a miscible polymer blend of a polynorbornene and poly(styrene‐ co ‐maleic anhydride) was investigated. By adjusting the blend composition, the drawing ratio and the drawing temperature, the wavelength dispersion was controlled and the wide band quarter‐wave film was obtained. From the results, the necessary conditions to control the dispersion for the wide‐band quarter‐wave film and wide‐band birefringence‐free material are discussed.
Early detection of successful decoding for dual-diagonal block-based LDPC codes (2008)

A fast, successful decoding detection mechanism is proposed for dual-diagonal block-based low-density parity-check (LDPC) codes. The algorithm eliminates unnecessary parity check computation by exploiting the structure of dual-diagonal LDPC codes. The average number of decoding iterations can be reduced for both two-phase decoders and layered decoders with no performance degradation on the AWGN channel. Simulation results show that the proposed mechanism reduces average iterations by 10–15% at 10−5 bit error rate compared with standard parity-check equations.
Intelligent sensor-scheduling for multi-kinect-tracking (2012)

This paper describes a method to intelligently schedule a network of multiple RGBD sensors in a Bayesian object tracking scenario, with special focus on Microsoft KinectTM devices. These setups have issues such as the large amount of raw data generated by the sensors and interference caused by overlapping fields of view. The proposed algorithm addresses these issues by selecting and exclusively activating the sensor that yields the best measurement, as defined by a novel stochastic model that also considers hardware constraints and intrinsic parameters. In addition, as existing solutions to toggle the sensors were found to be insufficient, the development of a hardware module, especially designed for quick toggling and synchronization with the depth stream, is also discussed. The algorithm then is evaluated within the scope of a multi-Kinect object tracking scenario and compared to other scheduling strategies.
Hydroxyapatite Microparticles as Feedback-Active Reservoirs of Corrosion Inhibitors (2010)

This work contributes to the development of new feedback-active anticorrosion systems. Inhibitor-doped hydroxyapatite microparticles (HAP) are used as reservoirs, storing corrosion inhibitor to be released on demand. Release of the entrapped inhibitor is triggered by redox reactions associated with the corrosion process. HAP were used as reservoirs for several inhibiting species: cerium(III), lanthanum(III), salicylaldoxime, and 8-hydroxyquinoline. These species are effective corrosion inhibitors for a 2024 aluminum alloy (AA2024), used here as a model metallic substrate. Dissolution of the microparticles and release of the inhibitor are triggered by local acidification resulting from the anodic half-reaction during corrosion of AA2024. Calculated values and experimentally measured local acidification over the aluminum anode (down to pH = 3.65) are presented. The anticorrosion properties of inhibitor-doped HAP were assessed using electrochemical impedance spectroscopy. The microparticles impregnated with the corrosion inhibitors were introduced into a hybrid silica-zirconia sol-gel film, acting as a thin protective coating for AA2024, an alloy used for aeronautical applications. The protective properties of the sol-gel films were improved by the addition of HAP, proving their applicability as submicrometer-sized reservoirs of corrosion inhibitors for active anticorrosion coatings.
Genetic engineering of the yeast Saccharomyces cerevisiae to ferment cellobiose (2007)

107 INTRODUCTION 107 MATERIALS AND METHODS 108 Strains and Media 108 DNA manipulations and vector construction 109 PCR amplification 109 Construction of vectors expressing different β-glucosidase genes 110 DNA sequencing 111 Yeast transformation 111 Enzyme assay 111 Medium and inoculum 111 Cultivations 111 Analytical methods 112 Substrate consumption and product formation 112 Calculations 112 RESULTS 112 Cloning of the β-glucosidase genes 112 Construction of recombinant yeast strains producing β-glucosidase 112 Recombinant β-glucosidase production 112 Growth kinetics of recombinant β-glucosidase-producing strains grown on cellobiose and glucose 113 Biomass and by-product yields during growth on cellobiose and glucose 114 DISCUSSION 115 ACKNOWLEDGEMENTS 117 REFERENCES 117
Nonpalpable In Situ Ductal Carcinoma of the Breast (1989)

Fifty breasts with nonpalpable ductal carcinoma in situ (DCIS) were examined for the presence of microinvasion, multicentricity, and number of involved ducts to see if the biopsy specimen could have predicted the findings in the remainder of the breast. When DCIS was an incidental finding, fewer ducts were involved and no evidence of either microinvasion or multicentricity was found. Solid and cribriform DCIS were rarely multicentric or microinvasive; micropapillary DCIS was often multicentric, rarely microinvasive; comedocarcinoma was more likely to be both microinvasive and multicentric. Ductal carcinoma in situ as an incidental finding may be treated by excision alone; papillary and micropapillary DCIS are best treated by therapy aimed at the entire breast, although axillary dissection may not be required. Therapy for comedocarcinomas should include the entire breast and the axillary nodes.