gebhart/patrepeval huggingface dataset:
Segment reencoding of buffer constrained variable bit rate video streams (2002)

A scheme is presented to reencode segments of buffer constrained video stream. This scheme provides a flexible and effective means to reencode only the part of the stream necessary for quality improvement or bit rate change instead of reencoding the entire stream so that great savings in production cost, storage space, and transmission bandwidth can be achieved. The scheme includes the algorithms for target rate allocation and buffer level adjustment. The rate allocation algorithm incorporates the picture quality measurement to achieve better and smoother video quality. The buffer adjustment algorithm ensures that after the reencoded segment is merged with the other portions of the original stream, the resulting new stream will still conform to all buffer constraints. The scheme has been implemented for a DVD (digital versatile disc) authoring system and the test results have shown that it is very effective and flexible.
X-ray Crystallographic Structures of Oligomers of Peptides Derived from β<sub>2</sub>-Microglobulin (2015)

Amyloid diseases such as Alzheimer's disease, Parkinson's disease, and type II diabetes share common features of toxic soluble protein oligomers. There are no structures at atomic resolution of oligomers formed by full-length amyloidogenic peptides and proteins, and only a few structures of oligomers formed by peptide fragments. The paucity of structural information provides a fundamental roadblock to understanding the pathology of amyloid diseases and developing preventions or therapies. Here, we present the X-ray crystallographic structures of three families of oligomers formed by macrocyclic peptides containing a heptapeptide sequence derived from the amyloidogenic E chain of β2-microglobulin (β2m). Each macrocyclic peptide contains the heptapeptide sequence β2m63-69 and a second heptapeptide sequence containing an N-methyl amino acid. These peptides form β-sheets that further associate into hexamers, octamers, and dodecamers: the hexamers are trimers of dimers; the octamers are tetramers of dimers; and the dodecamers contain two trimer subunits surrounded by three pairs of β-sheets. These structures illustrate a common theme in which dimer and trimer subunits further associate to form a hydrophobic core. The seven X-ray crystallographic structures not only illustrate a range of oligomers that a single amyloidogenic peptide sequence can form, but also how mutation can alter the size and topology of the oligomers. A cocrystallization experiment in which a dodecamer-forming peptide recruits a hexamer-forming peptide to form mixed dodecamers demonstrates that one species can dictate the oligomerization of another. These findings should also be relevant to the formation of oligomers of full-length peptides and proteins in amyloid diseases.
Control of Salmonella enteritidis infections in poultry by polymyxin B and trimethoprim (1991)

Antimicrobial compounds were screened in vitro in Trypticase soy broth for antimicrobial activity against a virulent strain of Salmonella enteritidis. Of the several compounds tested, polymyxin B showed the strongest inhibition in vitro, preventing growth at a concentration of less than or equal to 10 micrograms/ml. Polymyxin B administered in the drinking water was effective in vivo for preventing infections in 1-day-old chickens but did not remove established infections in 1-week-old chickens. It was found that trimethoprim, which was not active in vitro, prevented colonization and removed existing infections in 1-day-old chickens when it was administered together with polymyxin B sulfate. Enrichment cultures in which selenite-cystine and tetrathionate broth media were used showed that chickens given a combination of 100 micrograms of polymyxin B sulfate per ml and 250 micrograms of trimethoprim per ml 24 h prior to oral inoculation with 10(8) to 10(9) CFU were negative for S. enteritidis after 7 days. Established infections (10(5) to 10(6) CFU/g of feces) in 1-week-old chickens were eliminated by treatment with the polymyxin-trimethoprim system. This antimicrobial agent treatment may be useful for preventing colonization in poultry and for eliminating S. enteritidis from infected flocks.
A method for testing performance of tag in high speed motion state (2011)

The radiofrequency identification (RFID) technology is used widely in variety of applications, in most applications standard radiofrequency and communication HW are used and only system SW should be matched to the particular requirements. But in the case of a very high speed of the tracked object, the Doppler frequency shift may lead to serious problems in communication between readers and tags. In this paper, we provide an approach to test the performance of tag at high speed state; especially it can be accomplished in most of RFID test laboratories. The main idea of the test method is to adopt circular motion to simulate linear motion, during which two correction factors are adopted to modify the test result, by doing it the tag performance in high speed state can be tested.
Trilayered tissue structure with leaflet-like orientations developed through <i>in vivo</i> tissue engineering (2019)

A tissue-engineered heart valve can be an alternative to current mechanical or bioprosthetic valves that face limitations, especially in pediatric patients. However, it remains challenging to produce a functional tissue-engineered heart valve with three leaflets mimicking the trilayered, oriented structure of a native valve leaflet. In our previous study, a flat, trilayered nanofibrous substrate mimicking the orientations of three layers in a native leaflet-circumferential, random and radial orientations in fibrosa, spongiosa and ventricularis layers, respectively, was developed through electrospinning. In this study, we sought to develop a trilayered tissue structure mimicking the orientations of a native valve leaflet through in vivo tissue engineering, a practical regenerative medicine technology that can be used to develop an autologous heart valve. Thus, the nanofibrous substrate was placed inside the closed trileaflet-shaped cavity of a mold and implanted subcutaneously in a rat model for in vivo tissue engineering. After two months, the explanted tissue construct had a trilayered structure mimicking the orientations of a native valve leaflet. The infiltrated cells and their deposited collagen fibrils were oriented along the nanofibers in each layer of the substrate. Besides collagen, presence of glycosaminoglycans and elastin in the construct was observed.
Simultaneous Saccharification and Fermentation with substrate, enzyme and yeast feed facilitate bioethanol production at high solids loadings (2012)

Simultaneous saccharification and fermentation (SSF) is an interesting process option for lignocellulosic bioethanol production. The economical viability and commercialization of cellulose-to-ethanol demands the process to work under high-solid loadings to result in high sugar yield and final ethanol titer in S. cerevisiae based SSF process. In a conventional batch SSF process practical limitations to high-solid loadings include, poor mixing and accessibility of enzymes to substrates and high inhibitors concentration that reduces the yeast viability and metabolism. In order to overcome these limitations, we propose an improved SSF process configuration involving feeding of substrate, enzyme and yeast. It is possible to achieve maximum dilution effect with substrate, enzyme and yeast feed thereby overcoming the mixing issues associated with a batch SSF at high-solid loadings. The feed of freshly cultivated yeast throughout the fermentation process ensures active metabolic state of yeast. In addition, the substrate feed ensures low inhibitors concentration at any given time point increasing the survival ability of yeast in contrast to a batch SSF. The enzyme feed ensures slow release of glucose providing an opportunity to xylose consuming yeast strain to co-consume xylose together with glucose. With a feed of enzyme, cells and substrate, a SSF process with 20% WIS of spruce biomass yielded 40 g/l of ethanol compared to the conventional batch SSF that yielded only 13 g/l of ethanol with severe yeast and enzyme inhibition. This novel process was able to work even at 25% WIS of spruce biomass without any difficulties in mixing and therefore reducing the total power consumption due to stirring. These features make this novel configuration of SSF an extremely viable commercial approach to lignocellulosic bioethanol production at high solids loadings.
Pose detection and control of multiple Unmanned Underwater Vehicles (UUVs) using optical feedback (2014)

This paper proposes pose detection and control algorithms in order to control the relative pose between two Unmanned Underwater Vehicles (UUVs) using optical feedback. The leader UUV is configured to have a light source at its crest which acts as a guiding beacon for the follower UUV which has a detector array at its bow. Pose detection algorithms are developed based on a classifier, such as the Spectral Angle Mapper (SAM), and chosen image parameters. An archive look-up table is constructed for varying combinations of 5-degree-of-freedom (DOF) motion (i.e., translation along all three coordinate axes as well as pitch and yaw rotations). Leader and follower vehicles are simulated for a case in which the leader is directed to specific waypoints in horizontal plane and the follower is required to maintain a fixed distance from the leader UUV. Proportional-Derivative (PD) control (without loss of generality) is applied to maintain stability of the UUVs to show proof of concept. Preliminary results indicate that the follower UUV is able to maintain its fixed distance relative to the leader UUV to within a reasonable accuracy.
Cloning and expression of a divergent integrin subunit beta 8. (1991)

Rabbit and human cDNA clones have been identified that encode a novel integrin beta subunit. The sequences that encode this subunit, which has been designated as beta 8, were isolated initially from rabbit placental cDNA libraries using an oligonucleotide probe derived from a highly conserved region of integrin beta subunit sequences. The rabbit clone was used to isolate human beta 8 cDNA clones from human placental and MG-63 osteosarcoma cell libraries. The putative beta 8 polypeptides, which comprise 769 and 768 residues in human and rabbit, respectively, show a high degree of inter-species conservation (approximately 90% identity). In contrast, beta 8 is distinct from the other integrin beta subunits. At the amino acid level human beta 8 ranges from 31 to 37% identity with human beta 1-7. The domain structure of beta 8 is typical of the integrin beta subunits. Human beta 8 has a 42-residue N-terminal signal peptide, a large extracellular domain (approximately 639 residues) that contains four cysteine-rich repeats, a transmembrane domain (approximately 30 residues), and a C-terminal cytoplasmic domain (approximately 58 residues). There are several structural features that are unique to the beta 8 polypeptide, as compared with the other integrin beta subunits. Six of the 56 cysteine residues that are conserved within the extracellular domains of beta 1, beta 2, beta 3, beta 5, beta 6, and the beta subunit from Drosophila are absent in the beta 8 polypeptide. Also, the cytoplasmic domain of the beta 8 subunit shares no homology with the cytoplasmic regions of any of the other integrin beta subunits. Northern analysis demonstrated an approximately 8-kilobase beta 8 mRNA in rabbit placenta, kidney, brain, ovary, and uterus. PCR analysis revealed that beta 8 mRNA is also present in several transformed human cell lines. The beta 8 polypeptide has been transiently expressed in 293 human embryonic kidney cells. A polyclonal antipeptide antibody specific for beta 8 and a polyclonal antibody that recognizes alpha v epitopes were used to show that beta 8 can complex with the endogenous alpha v subunit in 293 cells and that the resulting integrin is expressed as a cell surface complex.
Robust estimation of quantitative perfusion from multi‐phase pseudo‐continuous arterial spin labeling (2019)

Using a retrospective algorithmic approach, it was possible to exploit common information found in multiple voxels within a whole region of the brain, offering superior SNR and thus overcoming the bias in perfusion quantification from multi-phase PCASL.
Recorded Well Data Enriches the Testing of Automation Systems by Using a Deep Neural Network Approach (2018)

Abstract One technique useful in the testing and development of drilling automation system is to use synthetic data. A good drilling time series simulator can enrich a dataset for testing, and enable the inference of the states of drilling in real time. However, conventional simulators do not generate the "warts" of real data (noise, gaps, etc.). The proposed solution is a model that learns from real data, characterizes the different drilling responses and conditions the data with a deep neural network (DNN) approach, and generate realistic drilling time series dataset. To simulate a drilling-time series dataset, a DNN can model physical properties of the formation, rig, and sensors, and generates data with realistic curve patterns when it is trained on actual measurements, e.g. block position, hook load, standpipe pressure, and surface torque. The neural network has multiple convolutional, recurrent, and fully-connected layers. The model, trained with wellsite recorded data, captures the spatio-temporal distributions among data channels, and then uses a windowed input to predict the next data points, which are then fed back into the network to generate the simulated data sequence recursively. An actual sensor drilling-time series dataset containing various channels are input into the DNN. The networks contain eight convolutional layers with three max-pooling layers, three recurrent layers, and four fully-connected layers. The time window used in the input contains 512 samples for each channel, while the output is 1 sample for each channel. After training the network for 200 epochs, the network can successfully simulate time series data recursively. The simulated time series preserve the features of the original training data, while maintaining the data distribution of multiple channels. For example, the network shows a consistent "inslips" pattern in the hook load channel when the block position moves quickly from bottom to top. Currently the simulation is autonomous based on the training data, and does not take input as controls, which is our future steps. The proposed DNN model is a low-cost, robust model that simulate drilling-time series datasets containing complex spatio-temporal patterns. Our proposed algorithm is the first known simulator of drilling time series datasets that models the nontrivial physics laws and properties, including formation, rig, and sensors, and generates data containing realistic curve patterns with a deep neural network approach. The simulator greatly helps the inference component of automation systems with the enrichment of datasets that are available for testing.
Current-induced spin-orbit torque switching of perpendicularly magnetized Hf|CoFeB|MgO and Hf|CoFeB|TaOx structures (2015)

We study the effect of the oxide layer on current-induced perpendicular magnetization switching properties in Hf|CoFeB|MgO and Hf|CoFeB|TaOx tri-layers. The studied structures exhibit broken in-plane inversion symmetry due to a wedged CoFeB layer, resulting in a field-like spin-orbit torque (SOT), which can be quantified by a perpendicular (out-of-plane) effective magnetic field. A clear difference in the magnitude of this effective magnetic field (HzFL) was observed between these two structures. In particular, while the current-driven deterministic perpendicular magnetic switching was observed at zero magnetic bias field in Hf|CoFeB|MgO, an external magnetic field is necessary to switch the CoFeB layer deterministically in Hf|CoFeB|TaOx. Based on the experimental results, the SOT magnitude (HzFL per current density) in Hf|CoFeB|MgO (−14.12 Oe/107 A cm−2) was found to be almost 13× larger than that in Hf|CoFeB|TaOx (−1.05 Oe/107 A cm−2). The CoFeB thickness dependence of the magnetic switching behavior, and the resulting HzFL generated by in-plane currents are also investigated in this work.
A High‐Throughput Process for the Solid‐Phase Purification of Synthetic DNA Sequences (2017)

An efficient process for the purification of synthetic phosphorothioate and native DNA sequences is presented. The process is based on the use of an aminopropylated silica gel support functionalized with aminooxyalkyl functions to enable capture of DNA sequences through an oximation reaction with the keto function of a linker conjugated to the 5'-terminus of DNA sequences. Deoxyribonucleoside phosphoramidites carrying this linker, as a 5'-hydroxyl protecting group, have been synthesized for incorporation into DNA sequences during the last coupling step of a standard solid-phase synthesis protocol executed on a controlled pore glass (CPG) support. Solid-phase capture of the nucleobase- and phosphate-deprotected DNA sequences released from the CPG support is demonstrated to proceed near quantitatively. Shorter than full-length DNA sequences are first washed away from the capture support; the solid-phase purified DNA sequences are then released from this support upon reaction with tetra-n-butylammonium fluoride in dry dimethylsulfoxide (DMSO) and precipitated in tetrahydrofuran (THF). The purity of solid-phase-purified DNA sequences exceeds 98%. The simulated high-throughput and scalability features of the solid-phase purification process are demonstrated without sacrificing purity of the DNA sequences. © 2017 by John Wiley & Sons, Inc.
Emergence of a R-Type Ca <sup>2+</sup> Channel (Ca <sub>V</sub> 2.3) Contributes to Cerebral Artery Constriction After Subarachnoid Hemorrhage (2005)

Cerebral aneurysm rupture and subarachnoid hemorrhage (SAH) inflict disability and death on thousands of individuals each year. In addition to vasospasm in large diameter arteries, enhanced constriction of resistance arteries within the cerebral vasculature may contribute to decreased cerebral blood flow and the development of delayed neurological deficits after SAH. In this study, we provide novel evidence that SAH leads to enhanced Ca2+ entry in myocytes of small diameter cerebral arteries through the emergence of R-type voltage-dependent Ca2+ channels (VDCCs) encoded by the gene CaV 2.3. Using in vitro diameter measurements and patch clamp electrophysiology, we have found that L-type VDCC antagonists abolish cerebral artery constriction and block VDCC currents in cerebral artery myocytes from healthy animals. However, 5 days after the intracisternal injection of blood into rabbits to mimic SAH, cerebral artery constriction and VDCC currents were enhanced and partially resistant to L-type VDCC blockers. Further, SNX-482, a blocker of R-type Ca2+ channels, reduced constriction and membrane currents in cerebral arteries from SAH animals, but was without effect on cerebral arteries of healthy animals. Consistent with our biophysical and functional data, cerebral arteries from healthy animals were found to express only L-type VDCCs (CaV 1.2), whereas after SAH, cerebral arteries were found to express both CaV 1.2 and CaV 2.3. We propose that R-type VDCCs may contribute to enhanced cerebral artery constriction after SAH and may represent a novel therapeutic target in the treatment of neurological deficits after SAH.
ChemInform Abstract: ANTIHYPERTENSIVE (2‐AMINOETHYL)THIOUREA DERIVATIVES. 1 (1981)

Abstract Dargestellt werden die Verbindungen (III) und (IV), von denen der Vertreter (III) (R1, R4=Cl, R2, R3=H) sedative und antihypertensive Wirkung besitzt.
Protective human immunity as a vaccine discovery tool for falciparum malaria (2005)

RAMA-pr is a rationally identified vaccine candidate preferentially recognized by antibodies produced by humans with a high level of naturally acquired resistance to P. falciparum infection. Our results demonstrate that naturally acquired protective antibody responses are useful tools to identify vaccine candidates for falciparum malaria.
Epigenetic Predictor of Age (2011)

From the moment of conception, we begin to age. A decay of cellular structures, gene regulation, and DNA sequence ages cells and organisms. DNA methylation patterns change with increasing age and contribute to age related disease. Here we identify 88 sites in or near 80 genes for which the degree of cytosine methylation is significantly correlated with age in saliva of 34 male identical twin pairs between 21 and 55 years of age. Furthermore, we validated sites in the promoters of three genes and replicated our results in a general population sample of 31 males and 29 females between 18 and 70 years of age. The methylation of three sites--in the promoters of the EDARADD, TOM1L1, and NPTX2 genes--is linear with age over a range of five decades. Using just two cytosines from these loci, we built a regression model that explained 73% of the variance in age, and is able to predict the age of an individual with an average accuracy of 5.2 years. In forensic science, such a model could estimate the age of a person, based on a biological sample alone. Furthermore, a measurement of relevant sites in the genome could be a tool in routine medical screening to predict the risk of age-related diseases and to tailor interventions based on the epigenetic bio-age instead of the chronological age.
Optimizing Data Warehousing Applications for GPUs Using Kernel Fusion/Fission (2012)

Data warehousing applications represent an emergent application arena that requires the processing of relational queries and computations over massive amounts of data. Modern general purpose GPUs are high core count architectures that potentially offer substantial improvements in throughput for these applications. However, there are significant challenges that arise due to the overheads of data movement through the memory hierarchy and between the GPU and host CPU. This paper proposes a set of compiler optimizations to address these challenges. Inspired in part by loop fusion/fission optimizations in the scientific computing community, we propose kernel fusion and kernel fission. Kernel fusion fuses the code bodies of two GPU kernels to i) eliminate redundant operations across dependent kernels, ii) reduce data movement between GPU registers and GPU memory, iii) reduce data movement between GPU memory and CPU memory, and iv) improve spatial and temporal locality of memory references. Kernel fission partitions a kernel into segments such that segment computations and data transfers between the GPU and host CPU can be overlapped. Fusion and fission can also be applied concurrently to a set of kernels. We empirically evaluate the benefits of fusion/fission on relational algebra operators drawn from the TPC-H benchmark suite. All kernels are implemented in CUDA and the experiments are performed with NVIDIA Fermi GPUs. In general, we observed data throughput improvements ranging from 13.1% to 41.4% for the SELECT operator and queries Q1 and Q21 in the TPC-H benchmark suite. We present key insights, lessons learned, and opportunities for further improvements.