gebhart/patrepeval huggingface dataset:
Microbial enzyme systems for biomass conversion: emerging paradigms (2010)

The contemporary relevance of biofuels as an attractive replacement for liquid fossil fuels has rekindled global interest in the conversion of cellulosic biomass – the most abundant renewable source of carbon and energy on our planet. In order to achieve efficient systems for such a formidable substrate, we take guidance from the native enzyme systems of the microbes that have evolved to rid the natural environment of plant-derived wastes. These cellulolytic bacteria and fungi employ a diversity of contrasting but complementary mechanisms for the hydrolysis of cellulose and other related complex plant cell wall polysaccharides. This review covers various known microbial approaches for attacking the recalcitrance problem in the conversion of cellulosic biomass to soluble sugars en route to a biofuels-based society.
Behçet's disease patients present high levels of deglycosylated anti-lipoteichoic acid IgG and high IL-8 production after lipoteichoic acid stimulation. (2006)

These results suggest a mechanism involving LTA from streptococci in the pathogenesis of BD.
Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problems in computational biology (2009)

For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great complexity. Indeed, even to simulate the fastest folding protein would require decades on the fastest modern CPUs. Here, we review novel methods to fundamentally speed such previously intractable problems using a new computational paradigm: distributed computing. By efficiently harnessing tens of thousands of computers throughout the world, we have been able to break previous computational barriers. However, distributed computing brings new challenges, such as how to efficiently divide a complex calculation of many PCs that are connected by relatively slow networking. Moreover, even if the challenge of accurately reproducing reality can be conquered, a new challenge emerges: how can we take the results of these simulations (typically tens to hundreds of gigabytes of raw data) and gain some insight into the questions at hand. This challenge of the analysis of the sea of data resulting from large-scale simulation will likely remain for decades to come.
Cephalometric and demographic characteristics of obstructive sleep apnea: an evaluation with partial least squares analysis. (1997)

Obstructive sleep apnea (OSA) is caused by repeated obstruction of the upper airway during sleep. The purpose of this study was to test the relative contributions of specific demographic and cephalometric measurements to OSA severity. Demographic, cephalometric, and overnight polysomnographic records of 291 male OSA patients and 49 male nonapneic snorers were evaluated. A partial least squares (PLS) analysis was used for statistical evaluation. The results revealed that the predictive powers of obesity and neck size variables for OSA severity were higher than the cephalometric variables used in this study. Compared with other cephalometric characteristics, an extended and forward natural head posture, lower hyoid bone position, increased soft palate and tongue dimensions, and decreased nasopharyngeal and velopharyngeal airway dimensions had relatively higher associations with OSA severity. The respiratory disturbance index (RDI) was the OSA outcome variable that was best explained by the demographic and cephalometric predictor variables. We conclude that the PLS analysis can successfully summarize the correlations between a large number of variables, and that obesity, neck size, and certain cephalometric measurements may be used together to evaluate OSA severity.
STUDIES ON THE ANTI-OVULATORY AND OVULATORY ACTION OF CLOMIPHENE CITRATE IN THE RAT (1971)

Summary. To study the site and mechanism of its ovulation-inhibiting effect, clomiphene citrate was implanted bilaterally into the hypothalamus and hypophysis of adult di-oestrous rats and of prepuberal females which were also treated with oestradiol benzoate. The results suggest that this effect is primarily due to the action of clomiphene on the anterior pituitary. The anti-oestrogenic activity of clomiphene may prevent the action of oestrogen on the hypophysis, thus suppressing the increased gonadotrophin secretion leading to ovulation. The ovulation-inducing effect of clomiphene was investigated in adult female rats which had been made anovulatory by destruction of the suprachiasmatic nuclei. Bilateral implantation of a small quantity of clomiphene citrate into the ventromedial-arcuate region resulted in corpus luteum formation and ovulation in these animals. A direct stimulation of the central hypothalamus is thought to be responsible for the ovulatory action of clomiphene in rats with cerebral lesions.
Root‐flipped multiband refocusing pulses (2015)

The proposed root-flipped multiband radiofrequency pulse design method produces low peak power pulses for simultaneous multislice spin echo MRI.
A Novel Gene Family NBPF: Intricate Structure Generated by Gene Duplications During Primate Evolution (2005)

Partial and complete genome duplications occurred during evolution and resulted in the creation of new genes and gene families. We identified a novel and intricate human gene family located primarily in regions of segmental duplications on human chromosome 1. We named it NBPF, for neuroblastoma breakpoint family, because one of its members is disrupted by a chromosomal translocation in a neuroblastoma patient. The NBPF genes have a repetitive structure with high intragenic and intergenic sequence similarity in both coding and noncoding regions. These similarities might expose these genomic regions to illegitimate recombination, resulting in structural variation in the NBPF genes. The encoded proteins contain a highly conserved domain of unknown function, which we have named the NBPF repeat. In silico analysis combined with the isolation of multiple full-length cDNA clones showed that several members of this gene family are abundantly expressed in a large variety of tissues and cell lines. Strikingly, no discernable orthologues could be identified in the completed genomes of fruit fly, nematode, mouse, or rat, but sequences with low homology could be isolated from the draft canine and bovine genomes. Interestingly, this gene family shows primate-specific duplications that result in species-specific arrays of NBPF homologous sequences. Overall, this novel NBPF family reflects the continuous evolution of primate genomes that resulted in large physiological differences, and its potential role in this process is discussed.
Dynapack: space-time compression of the 3D animations of triangle meshes with fixed connectivity (2003)

Dynapack exploits space-time coherence to compress the consecutive frames of the 3D animations of triangle meshes of constant connectivity. Instead of compressing each frame independently (space-only compression) or compressing the trajectory of each vertex independently (time-only compression), we predict the position of each vertex v of frame f from three of its neighbors in frame f and from the positions of v and of these neighbors in the previous frame (space-time compression). We introduce here two extrapolating spacetime predictors: the ELP extension of the Lorenzo predictor, developed originally for compressing regularly sampled 4D data sets, and the Replica predictor. ELP may be computed using only additions and subtractions of points and is a perfect predictor for portions of the animation undergoing pure translations. The Replica predictor is slightly more expensive to compute, but is a perfect predictor for arbitrary combinations of translations, rotations, and uniform scaling. For the typical 3D animations that we have compressed, the corrections between the actual and predicted value of the vertex coordinates may be compressed using entropy coding down to an average ranging between 1.37 and 2.91 bits, when the quantization used ranges between 7 and 13 bits. In comparison, space-only compression yields a range of 1.90 to 7.19 bits per coordinate and time-only compressions yields a range of 1.77 to 6.91 bits per coordinate. The implementation of the Dynapack compression and decompression is trivial and extremely fast. It perform a sweep through the animation, only accessing two consecutive frames at a time. Therefore, it is particularly well suited for realtime and out-of-core compression, and for streaming decompression.
Induction of autophagy contributes to crizotinib resistance in ALK-positive lung cancer (2014)

Use of the inhibitor of ALK fusion onco-protein, crizotinib (PF02341066), has achieved impressive clinical efficacy in patients with ALK-positive non-small cell lung cancer. Nevertheless, acquired resistance to this drug occurs inevitably in approximately a year, limiting the therapeutic benefits of this novel targeted therapy. In this study, we found that autophagy was induced in crizonitib-resistant lung cancer cells and contributed to drug resistance. We observed that ALK was downregulated in the crizotinib-resistant lung cancer cell line, H3122CR-1, and this was causally associated with autophagy induction. The degree of crizotinib resistance correlated with autophagic activity. Activation of autophagy in crizotinib-resistant H3122CR-1 cells involved alteration of the Akt/mTOR signaling pathway. Furthermore, we demonstrated that chloroquine, an inhibitor of autophagy, could restore sensitivity of H3122CR-1 to crizotinib and enhance its efficacy against drug-resistant lung cancer. Thus, modulating autophagy may be worth exploring as a new strategy to overcome acquired crizonitib resistance in ALK-positive lung cancer.
Performance of polar codes for channel and source coding (2009)

Polar codes, introduced recently by Arikan, are the first family of codes known to achieve capacity of symmetric channels using a low complexity successive cancellation decoder. Although these codes, combined with successive cancellation, are optimal in this respect, their finite-length performance is not record breaking. We discuss several techniques through which their finite-length performance can be improved. We also study the performance of these codes in the context of source coding, both lossless and lossy, in the single-user context as well as for distributed applications.
Amination of <i>N</i>-Aryl Prolinol via Ring Expansion and Contraction:  Application to the Chiral Ligand for the Catalytic Asymmetric Reaction (2005)

Chiral diaminophosphines 4 were prepared from (S)-prolinol-derived aminophosphine oxide 5 by bromination with ring expansion followed by amination with ring contraction and reduction, using trichlorosilane. In the presence of 4 as a ligand, palladium-catalyzed asymmetric allylic alkylation of 1,3-diphenyl-2-propenyl acetate (11) with a dialkyl malonate-BSA-LiOAc system was successfully carried out with good enantioselectivities (up to 98% ee).
Suppression of substrate injection by RESURF LDMOS devices in a smart power technology for 20-30 V applications (2002)

Suppression of substrate injection has been achieved by integration of a RESURF LDMOS device in a 20-30 V smart power technology. A successful use of the single n-implant for both depletion mode NMOS and RESURF LDMOS results in a dramatic increase in performance and functionality of this technology with virtually no extra process complexity.
A RADIOIMMUNOASSAY FOR PLASMA ARGININE-VASOPRESSIN IN MAN AND DOG: APPLICATION TO PHYSIOLOGICAL AND PATHOLOGICAL STATES (1975)

A radioimmunoassay has been developed for plasma arginine-vasopressin in man and dog. The mean recovery of added arginine-vasopressin (AVP) was 60 +/-6.9 (S.D.)% and the lower threshold of detection 2.0 pmol/1. A close correlation was found between concurrent radioimmunoassay and bioassay values. The mean concentration found in peripheral venous blood in healthy men after overnight fasting was 5.3 pmol/1 (range 4.6-6.2 pmol/1.) In man, significant increases in plasma AVP occurred after dehydration (5-9-9-5 pmol/1) and significant decreases after oral water-loading (5.9-9.5 pmol/1). During i.v. infusion of graded doses of synthetic AVP in normal men, plasma levels were closely correlated with infusion rate. On stopping the infusion, plasma vasopressin fell exponentially with a half-life of between 7 and 8 min. In man, plasma AVP was unaffected by tilting head-up for 2 h, or by a non-hypotensive bleeding of 500 ml in 10 min. In the dog, haemorrhage of 5 ml/kg and over caused proportionate increases in AVP in the circulation. In normal men, plasma vasopressin was significantly correlated with concurrent urinary osmolality. Five patients with oat-cell bronchial carcinoma and hyponatraemia showed a marked increase of plasma vasopressin. Five patients with diabetes insipidus had significantly reduced, but detectable, levels of plasma AVP. The plasma concentration in these patients did not increase after water restriction.
The Electrodeposition of Magnesium (1933)

Magnesium could not be electrodeposited from solutions of simple magnesium salts in non‐aqueous solutions. Magnesium was successfully electrodeposited from solutions of complex magnesium compounds similar to Grignard compounds dissolved in various non‐aqueous solvents. The best non‐aqueous liquid for addition to the Grignard reagent was dimethylaniline. The anodes of magnesium would not dissolve, but deposits of magnesium could be obtained easily on the cathodes.
Multiple server WWW-based synthesis of VLSI circuits (2002)

A three-tier client/server system for the synthesis of VLSI circuits has been developed. The design system uses the World Wide Web as a backbone communications medium, whilst the sub-components of the synthesis applications are organised as servers, accessed through client/server communications between a tool server and thin client applets. This paper describes the architecture of the system, and in particular examines the use of multi-threading and multiple servers for improving system performance.
Mass spectrometry for the analysis of organic compounds. A review (1971)

A. E. Williams and H. E. Stagg, Analyst, 1971, 96, 1 DOI: 10.1039/AN9719600001
Deep Learning Based Attribute Classification Insider Threat Detection for Data Security (2018)

With the evolution of network threat, identifying threat from internal is getting more and more difficult. To detect malicious insiders, we move forward a step and propose a novel attribute classification insider threat detection method based on long short term memory recurrent neural networks (LSTM-RNNs). To achieve high detection rate, event aggregator, feature extractor, several attribute classifiers and anomaly calculator are seamlessly integrated into an end-to-end detection framework. Using the CERT insider threat dataset v6.2 and threat detection recall as our performance metric, experimental results validate that the proposed threat detection method greatly outperforms k-Nearest Neighbor, Isolation Forest, Support Vector Machine and Principal Component Analysis based threat detection methods.
Three-terminal charge-injection device (1976)

A new configuration of the charge-injection device (CID) image sensor is described in this paper. Readout is performed by means of buried stripes (e.g., p stripes in an n-type substrate) acting as collectors of the injected minority carriers previously stored under the gates. This scheme provides separate paths for the displacement and diffusion currents and consequently improves the signal-to-noise (S/N) ratio. Furthermore, the new configuration yields simple X-Y selection without the need for extra crosspoint switches. In the present device, a word organized readout is achieved by means of polysilicon stripes perpendicular to the buried p stripes. The silicon area therefore can be used very efficiently.
Nodits: Position Triggered Information and Messages (2006)

Location based services (LBS) were one of the new emerging technologies that appeared and fell with the WAP non-revolution. The concept of providing information and facilities based on a user's physical location was simple and intuitive, but over-hyped. These services were imprecise and one-way. No feedback could be given for the quality of the presented company, and no community could be created. Nodits is a piece of software that runs on GPS-enabled mobile devices, and provides location based information and data. The software is intended to run on next generation mobile phones and current PDAs. This paper presents an overview of the Nodits software system, its uses and potential markets
Major histocompatibility complex class I-specific and -restricted killing of beta 2-microglobulin-deficient cells by CD8+ cytotoxic T lymphocytes. (1992)

Cytotoxic T lymphocytes (CTLs) recognize major histocompatibility complex (MHC) class I molecules, normally composed of a heavy chain, a beta 2-microglobulin (beta 2m), and peptide antigens. beta 2m is considered essential for the assembly and intracellular transport of MHC class I molecules as well as their peptide presentation to CTLs. Contrary to this dogma, we now report the generation of allospecific and restricted CD8+ and TCR alpha beta+ CTLs (where TCR is T-cell receptor) capable of killing beta 2m-deficient cells. Such CTLs were obtained by priming mice with live allogeneic beta 2m- spleen cells or mutant lymphoma cells producing MHC class I protein but no detectable beta 2m. Although both beta 2m- and beta 2m-expressing lymphoma cells were rejected in allogeneic mice, only the former were efficient inducers of CTLs recognizing beta 2m- cells. These CTLs were MHC class I (H-2Kb or Db)-specific and CD8-dependent and did not require serum as a source of external beta 2m in the culture. They could be induced across major and minor histocompatibility barriers. The H-2-restricted CTLs generated in the latter case failed to kill the antigen-processing-deficient target RMA-S cells. The results show that MHC class I heavy chains in beta 2m- cells can be transported to the cell surface and act as antigens or antigen-presenting molecules to allospecific and MHC-restricted CTLs.
Growth of Y-Shaped Nanorods through Physical Vapor Deposition (2005)

This work presents a proposed mechanism for fabricating Y-shaped nanorods, demonstrates the feasibility of the proposal through classical molecular dynamics simulations, and validates the simulations through magnetron sputter deposition experiments. The proposed mechanism relies primarily on the formation of stacking faults during deposition and to a lesser degree on diffusion kinetics and geometrical shadowing. Applications of the proposed mechanism may enable the design of nanorod arrays with controlled branching.
Measurement and analysis of static magnetic fields that block action potentials in cultured neurons (1995)

To characterize the properties of static magnetic fields on firing of action potentials (AP) by sensory neurons in cell culture, we developed a mathematical formalism based on the expression for the magnetic field of a single circular current loop. The calculated fields fit closely the field measurements taken with a Hall effect gaussmeter. The biological effect induced by different arrays of permanent magnets depended principally on the spatial variation of the fields, quantified by the value of the gradient of the field magnitude. Magnetic arrays of different sizes (macroarray: four center-charged neodymium magnets of approximately 14 mm diameter; microarray; four micromagnets of the same material but of approximately 0.4 mm diameter) allowed comparison of fields with similar gradients but different intensities at the cell position. These two arrays had a common gradient value of approximately 1 mT/mm and blocked > 70% of AP. Alternatively, cells placed in a field strength of approximately 0.2 mT and a gradient of approximately 0.02 mT/mm produced by the macroarray resulted in no significant reduction of firing; a microarray field of the same strength but with a higher gradient of approximately 1.5 mT/mm caused approximately 80% AP blockade. The experimental threshold gradient and the calculated threshold field intensity for blockade of action potentials by these arrays were estimated to be approximately 0.02 mT/mm and approximately 0.02 mT, respectively, In conclusion, these findings suggest that spatial variation of the magnetic field is the principal cause of AP blockade in dorsal root ganglia in vitro.
THE pH STABILITY OF PROTYROSINASE AND TYROSINASE (1942)

1. pH stability diagrams for protyrosinase and for tyrosinase were constructed. 2. Above pH 7.30 protyrosinase is unstable. Between pH 7.30 and pH 9.30 there is a partial destruction. Beyond pH 9.30 it changes irreversibly into tyrosinase which in turn is destroyed beyond pH 10.12. 3. Through the lower ranges of pH protyrosinase is less stable than tyrosinase The former is destroyed below pH 4.80, while the latter is unaffected until the pH drops below 4.10. 4. The tyrosinase produced at high pH values resembles that produced by other methods.
Efficient Wavelength Tuning Techniques for Integrated Silicon Photonics (2014)

The past decade has seen a significant amount of academic and industrial research into interconnect topologies that employ optical channels for next generation high speed communication systems. Integrated optical interconnects have taken center stage in tackling channel loss limitations of traditional electrical links and bandwidth requirements for inter-chip and intra-chip signal processing for multi-core processors. Wavelength-division multiplexing (WDM) optical interconnect architectures based on microring resonator devices offer a low-area and energy-efficient approach to realize both high-speed modulation and WDM with high-speed transmit-side ring modulators and high-Q receive-side drop filters.\n\nAt the heart of silicon photonics is the silicon microring resonator. These high-Q refractive devices can achieve high contrast ratios with their small footprint and enable distance independent communication. A major challenge to the use of microring resonators is the sensitivity of their resonance wavelength to process and fabrication imperfections and temperature perturbations. To curtail the effects of resonance wavelength drifts, stabilization schemes are implemented to properly align the resonance wavelength of the microring device with the input laser wavelength. \n\nThis thesis work focuses on three main issues. Firstly, the sources and effects of mismatch in silicon microring resonators are identified. Secondly, a review of literature is done to examine existing resonance wavelength stabilization techniques. Based on the reference search tuning algorithm, a new dual-loop tuning method which combines the benefits of bias-based and thermal-based tuning schemes is proposed. Furthermore, we evaluate the tuning efficiency of some existing and the proposed tuning schemes using a statistical model to determine optimal power and speed efficiency. Modeling results of carrier injection ring resonator devices with common thermal tuning and the new dual-bias/thermal scheme reveals that the latter scheme offers ~ 50% improvement in power with small variations and close to 16X speed improvement.\n\nFinally, the tuning control loop is fabricated in GP 65nm CMOS process. Transmit-side and receive-side are independently implemented for a 5-channel WDM system. Measurement results are presented in both cases. The transmitter IC achieved both static and dynamic tuning, stabilizing ring resonance wavelength in the midst of temperature fluctuations from an adjacent ring. The total power consumed was 5.17mW while covering a wavelength tuning range of ~ 0:8nm. Static tuning was successfully demonstrated for the receiver IC. A tuning range of 0:7nm was achieved over a 2mA dynamic range of current.