gebhart/patrepeval huggingface dataset:
Manipulation of prenyl chain length determination mechanism of <i>cis</i>‐prenyltransferases (2006)

The carbon backbones of Z,E-mixed isoprenoids are synthesized by sequential cis-condensation of isopentenyl diphosphate (IPP) and an allylic diphosphate through actions of a series of enzymes called cis-prenyltransferases. Recent molecular analyses of Micrococcus luteus B-P 26 undecaprenyl diphosphate (UPP, C55) synthase [Fujihashi M, Zhang Y-W, Higuchi Y, Li X-Y, Koyama T & Miki K (2001) Proc Natl Acad Sci USA98, 4337-4342.] showed that not only the primary structure but also the crystal structure of cis-prenyltransferases were totally different from those of trans-prenyltransferases. Although many studies on structure-function relationships of cis-prenyltransferases have been reported, regulation mechanisms for the ultimate prenyl chain length have not yet been elucidated. We report here that the ultimate chain length of prenyl products can be controlled through structural manipulation of UPP synthase of M. luteus B-P 26, based on comparisons between structures of various cis-prenyltransferases. Replacements of Ala72, Phe73, and Trp78, which are located in the proximity of the substrate binding site, with Leu--as in Z,E-farnesyl diphosphate (C15) synthase--resulted in shorter ultimate products with C(20-35). Additional mutation of F223H resulted in even shorter products. On the other hand, insertion of charged residues originating from long-chain cis-prenyltransferases into helix-3, which participates in constitution of the large hydrophobic cleft, resulted in lengthening of the ultimate product chain length, leading to C(60-75). These results helped us understand reaction mechanisms of cis-prenyltransferase including regulation of the ultimate prenyl chain-length.
Signal processing for high-density digital magnetic recording (2003)

The signal-processing techniques most often used in digital magnetic recording systems are run-length limited (RLL) coding and peak detection (PD). The application of more advanced methods, such as partial-response (PR) signaling and maximum-likelihood sequence detection (MLSD), allows a further increase in the recording densities and reliability presently achieved. After reviewing RLL coding an PD schemes, recording systems using PR signaling and MLSD (PRML) are described. Viterbi decoding and decision-directed algorithms for automatic gain control and timing recovery are discussed for the two types of PR scheme best suited for magnetic recording, class-IV (PR-IV) and extended class-IV (EPR-IV). Results of a performance study on PD and PRML systems which demonstrate the superiority of the PRML approach are presented. For the two PRML systems considered, sensitivity to various parameters and performance in an off-track situation were investigated. The results shown indicate that the two schemes are equally robust and that PR-IV signaling is superior to EPR-IV in off-track situations. A PRML system based on PR-IV signaling is also simpler to realize.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fan-Out Wafer-Level Packaging for Heterogeneous Integration (2018)

The design, materials, process, fabrication, and reliability of a heterogeneous integration of four chips and four capacitors by a fan-out wafer-level packaging (FOWLP) method are investigated in this paper. Emphasis is placed on the application of a new assembly process for fabricating the redistribution layers of the FOWLP. Reliability assessments, such as the thermal cycling and drop test, are also performed.
Cisapride May Improve Feeding Tolerance of Preterm Infants: A Randomized Placebo-Controlled Trial (2005)

To evaluate the efficacy of cisapride in improving tolerance of enteral feeding, 59 premature infants were randomized into a blinded placebo-controlled study. Treatment was initiated with the introduction of enteral feeding and continued until 150 ml/kg/day of milk were tolerated. Only in extremely low birth weight (ELBW) infants, was the time to tolerate full enteral feeding shorter in the treatment group, whereas ECG recordings showed a significantly prolonged QTc interval during treatment. Two children developed cardiac rhythm disturbances. In conclusion premature infants may not benefit from routine use of the drug to improve enteral feeding, and seem to be more vulnerable to its side effects.
Automatic Liver Segmentation Method based on Maximum A Posterior Probability Estimation and Level Set Method (2007)

Abstract. This paper describes an automatic liver segmentation method from three dimensional abdominal X-ray CT images. Our method ex-tracts liver regions based on the following two steps: (1) rough extraction based on maximum a posterior probability (MAP) estimation, and (2) precise segmentation using level set method. In the former process, the segmentation can be performed more accurately by using a combination of the probability density function approximated by the extended gaus-sian mixture distribution and a prior probability derived from a prob-abilistic atlas of liver. In the latter process, we introduce a novel term to prevent the level set method from extracting muscles as a part of the liver incorrectly. From the experimental results using ten test datasets distributed for the competition, it was confirmed that our method seg-mented the liver regions with volumetric overlap of about 88%. 1
Electrical properties of heavily doped polycrystalline silicon-germanium films (1994)

The electrical properties of polycrystalline silicon-germanium (poly-Si/sub 1/spl minus/x/Ge/sub x/) films with germanium mole fractions up to 0.56 doped by high-dose ion implantation are presented. The resistivity of heavily doped p-type (P/sup +/) poly-Si/sub 1/spl minus/x/Ge/sub x/ is much lower than that of comparably doped poly-Si, because higher levels of boron activation and higher hole mobilities are achieved in poly-Si/sub 1/spl minus/x/Ge/sub x/. The resistivity of heavily doped n-type (N/sup +/) poly-S/sub 1/spl minus/x/Ge/sub x/ is similar to that of comparably doped poly-Si for x<0.45; however, it is considerably higher for larger Ge mole fractions due to significant reductions in phosphorus activation. Lower temperatures (/spl sim/500/spl deg/C), as well as lower implant doses, are sufficient to achieve low resistivities in boron-implanted poly-Si/sub 1/spl minus/x/Ge/sub x/ films, compared to poly-Si films. The work function of P/sup +/ poly-Si/sub 1/spl minus/x/Ge/sub x/ decreases significantly (by up to /spl sim/0.4 Volts), whereas the work function of N/sup +/ poly-Si/sub 1/spl minus/x/Ge/sub x/ decreases only slightly, as Ge content is increased. Estimates of the energy bandgap of poly-Si/sub 1/spl minus/x/Ge/sub x/ show a reduction (relative to the bandgap of poly-Si) similar to that observed for unstrained single-crystalline Si/sub 1/spl minus/x/Ge/sub x/ for a 26% Ge film, and a reduction closer to that observed for strained single-crystalline Si/sub 1/spl minus/x/Ge/sub x/ for a 56% Ge film. The electrical properties of poly-Si/sub 1/spl minus/x/Ge/sub x/ make it a potentially favorable alternative to poly-Si for P/sup +/ gate-material applications in metal-oxide-semiconductor technologies and also for p-channel thin-film transistor applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Water and Ion Pairing in Polyelectrolyte Multilayers (1999)

The water content in multilayers made from poly(styrenesulfonate) and poly(diallyldimethylammonium chloride) was determined using infrared spectroscopy and thermal gravimetric analysis. Under ambient conditions the polyelectrolyte multilayer contains 10−20 wt % water, which is removed by heating under dry conditions to 100 °C. FTIR comparison of multilayers with solution-precipitated polyelectrolyte complexes of the same polymers revealed that both the composition and sulfonate group environment were identical.
Green Light Photoplethysmography Monitoring of Free Flaps (2000)

Green light photoplethysmography with AC/DC ratio analysis provides a rapid, precise method with which to determine flap ischemia and can differentiate venous compromised and arterial compromised flaps almost immediately after the onset of an ischemic insult. It may provide a clinically useful tool for postoperative free flap monitoring.
Finding Domain-Generation Algorithms by Looking at Length Distribution (2014)

In order to detect malware that uses domain fluxing to circumvent blacklisting, it is useful to be able to discover new domain-generation algorithms (DGAs) that are being used to generate algorithmically-generated domains (AGDs). This paper presents a procedure for discovering DGAs from Domain Name Service (DNS) query data. It works by identifying client IP addresses with an unusual distribution of second-level string lengths in the domain names that they query. Running this fairly simple procedure on 5 days' data from a large enterprise network uncovered 19 different DGAs, nine of which have not been identified as previously-known. Samples and statistical information about the DGA domains are given.
A high-speed FFT processor for OFDM systems (2003)

This paper proposes a high-speed FFT processor for orthogonal frequency-division multiplexing (OFDM) systems. The proposed architecture uses a single-memory for a small hardware size and uses a radix-4 algorithm for high speed. Its memory is partitioned into four banks for high-speed computation. It uses an in-place memory strategy that stores butterfly outputs in the same memory location used by butterfly inputs. The architecture has been modeled by VHDL and logic synthesis has been performed using the Samsung/sup /spl trade// 0.5/spl mu/m SOG cell library (KG80). The implemented FFT processor consists of 98,326 gates excluding RAM. The processor can operate at 42MHz and calculate a 256-point complex FFT in 6/spl mu/s.
Investigating the Role of Virtual Reality in Planning for Sustainable Smart Cities (2017)

With rapid population growth, urban designers face tremendous challenges to accommodate the increasing size of the population in urban areas while simultaneously considering future environmental, social, and economic impacts. A “smart city” is an urban development vision that integrates multiple information and communication technologies to manage the assets of a city, including its information systems, transportation systems, power plants, water supply networks, waste management systems, and other community services provided by a local department. The goal of creating a smart city is to improve the quality of life of citizens by using technology and by addressing the environmental, social, cultural, and physical needs of a society. Data modeling and data visualization are integral parts of planning a smart city, and planning professionals currently seek new methods for real-time simulations. The impact analysis of “what-if scenarios” frequently takes a significant amount of time and resources, and virtual reality (VR) is a potential tool for addressing these challenges. VR is a computer technology that replicates an environment, whether real or imagined, and simulates the physical presence and environment of a user to allow for user interaction. This paper presents a review of the capacity of VR to address current challenges in creating, modeling, and visualizing smart cities through material modeling and light simulation in a VR environment. This study can assist urban planners, stakeholders, and communities to further understand the roles of planning policies in creating a smart city, particularly in the early design stages. The significant roles of technologies, such as VR, in targeting real-time simulations and visualization requirements for smart cities are emphasized.
Problems (2001)

Michael Golomb, Costas Efthimiou, Mihaly Bencze, Donald Knuth, Gotz Trenkler, Joaquin Gomez Rey, Murray S. Klamkin, Kent Holing, Herb Bailey, Wu Wei Chao, Walter Stromquist, L. R. King, Constantin P. Niculescu, Li Zhou, Daniele Donini, Hoe-Teck Wee, Marty Getz, Dixon Jones, Problems, Mathematics Magazine, Vol. 74, No. 2 (Apr., 2001), pp. 154-161
A Genome Scan for Positive Selection in Thoroughbred Horses (2009)

Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed a genome scan using 394 autosomal and X chromosome microsatellite loci and identified positively selected loci in the extreme tail-ends of the empirical distributions for (1) deviations from expected heterozygosity (Ewens-Watterson test) in Thoroughbred (n = 112) and (2) global differentiation among four geographically diverse horse populations (F(ST)). We found positively selected genomic regions in Thoroughbred enriched for phosphoinositide-mediated signalling (3.2-fold enrichment; P<0.01), insulin receptor signalling (5.0-fold enrichment; P<0.01) and lipid transport (2.2-fold enrichment; P<0.05) genes. We found a significant overrepresentation of sarcoglycan complex (11.1-fold enrichment; P<0.05) and focal adhesion pathway (1.9-fold enrichment; P<0.01) genes highlighting the role for muscle strength and integrity in the Thoroughbred athletic phenotype. We report for the first time candidate athletic-performance genes within regions targeted by selection in Thoroughbred horses that are principally responsible for fatty acid oxidation, increased insulin sensitivity and muscle strength: ACSS1 (acyl-CoA synthetase short-chain family member 1), ACTA1 (actin, alpha 1, skeletal muscle), ACTN2 (actinin, alpha 2), ADHFE1 (alcohol dehydrogenase, iron containing, 1), MTFR1 (mitochondrial fission regulator 1), PDK4 (pyruvate dehydrogenase kinase, isozyme 4) and TNC (tenascin C). Understanding the genetic basis for exercise adaptation will be crucial for the identification of genes within the complex molecular networks underlying obesity and its consequential pathologies, such as type 2 diabetes. Therefore, we propose Thoroughbred as a novel in vivo large animal model for understanding molecular protection against metabolic disease.
Digital breast tomosynthesis using an amorphous selenium flat panel detector (2005)

A prototype breast tomosynthesis system has been developed, allowing a total angular view of ±25°. The detector used in this system is an amorphous selenium direct-conversion digital flat-panel detector suitable for digital tomosynthesis. The system is equipped with various readout sequences to allow the investigation of different tomosynthetic data acquisition modes. In this paper, we will present basic physical properties -- such as MTF, NPS, and DQE -- measured for the full resolution mode and a binned readout mode of the detector. From the measured projections, slices are reconstructed employing a special version of filtered backprojection algorithm. In a phantom study, we compare binned and full resolution acquisition modes with respect to image quality. Under the condition of same dose, we investigate the impact of the number of views on artifacts. Finally, we show tomosynthesis images reconstructed from first clinical data.
Light-Driven Molecular Hinge:  A New Molecular Machine Showing a Light-Intensity-Dependent Photoresponse that Utilizes the Trans−Cis Isomerization of Azobenzene (2004)

[reaction: see text] A new class of molecular machine exhibits a hingelike motion upon photoirradiation. The motion (close and open) can be operated by alternate irradiation with UV and visible light. The trans/trans and cis/cis isomers are thermally stable at 40 degrees C, and the photochemical closure reaction (from trans/trans to cis/cis isomer) is dependent on the intensity of the light used because of the short-lived intermediate (trans/cis isomer).
Low-Temperature Preparation of Oxygen- and Carbon-Free Silicon and Silicon-Germanium Surfaces for Silicon and Silicon-Germanium Epitaxial Growth by Rapid Thermal Chemical Vapor Deposition (2000)

Photoluminescence (PL) from commensurately strained SiGe layers grown directly on silicon substrates and secondary ion mass spectroscopy (SIMS) of buried Si/SiGe interfaces are used to evaluate different low‐temperature cleaning methods of substrate surfaces for silicon and SiGe epitaxy in a nonultrahigh vacuum system. Both the sources of contamination as well as effective cleaning methods were investigated. The dominant source of contamination came from the wafer being outside the reactor, not in the load lock or deposition chamber itself. The optimum surface preparation depends on the ratios of HF, , and deionized water of solutions that were used to remove the wet chemical oxide on the substrate surface. In situ bakes between 300 and 800°C in 0.25–250 Torr of hydrogen were examined after the ex situ clean using PL and SIMS measurements. An optimized ex situ clean [1:1000 HF(49%):deionized water (DI)] and in situ hydrogen bake (2 min at 800°C in 10 Torr) produces an oxygen‐ and carbon‐free surface for silicon and SiGe epitaxy. © 2000 The Electrochemical Society. All rights reserved.
Ironing out a therapy for Friedreich ataxia (2007)

Boddaert and colleagues show the positive effects of selective iron chelation in young patients with Friedreich ataxia, a devastating inborn error of mitochondrial iron metabolism.
Control of the Bacillus subtilis Antiterminator Protein GlcT by Phosphorylation (2003)

Bacillus subtilis transports glucose by the phosphotransferase system (PTS). The genes for this system are encoded in the ptsGHI operon, which is induced by glucose and depends on a termination/antitermination mechanism involving a riboswitch and the RNA-binding antitermination protein GlcT. In the absence of glucose, GlcT is inactive, and a terminator is formed in the leader region of the ptsG mRNA. If glucose is present, GlcT can bind to its RNA target and prevent transcription termination. The GlcT protein is composed of three domains, an N-terminal RNA binding domain and two PTS regulation domains, PTS regulation domain (PRD) I and PRD-II. In this work, we demonstrate that GlcT can be phosphorylated by two PTS proteins, HPr and the glucose-specific enzyme II (EIIGlc). HPr-dependent phosphorylation occurs on PRD-II and has a slight stimulatory effect on GlcT activity. In contrast, EIIGlc phosphorylates the PRD-I of GlcT, and this phosphorylation inactivates GlcT. This latter phosphorylation event links the availability of glucose to the expression of the ptsGHI operon via the phosphorylation state of EIIGlc and GlcT. This is the first in vitro demonstration of a direct phosphorylation of an antiterminator of the BglG family by the corresponding PTS permease.
An investigation of light transport through scattering bodies with non-scattering regions (1996)

Near-infra-red (NIR) spectroscopy is increasingly being used for monitoring cerebral oxygenation and haemodynamics. One current concern is the effect of the clear cerebrospinal fluid upon the distribution of light in the head. There are difficulties in modelling clear layers in scattering systems. The Monte Carlo model should handle clear regions accurately, but is too slow to be used for realistic geometries. The diffusion equation can be solved quickly for realistic geometries, but is only valid in scattering regions. In this paper we describe experiments carried out on a solid slab phantom to investigate the effect of clear regions. The experimental results were compared with the different models of light propagation. We found that the presence of a clear layer had a significant effect upon the light distribution, which was modelled correctly by Monte Carlo techniques, but not by diffusion theory. A novel approach to calculating the light transport was developed, using diffusion theory to analyze the scattering regions combined with a radiosity approach to analyze the propagation through the clear region. Results from this approach were found to agree with both the Monte Carlo and experimental data.
Asymmetric Synthesis of the Highly Methylated Tryptophan Portion of the Hemiasterlin Tripeptides (2002)

[reaction: see text] The asymmetric synthesis of the methylated tryptophan portion of hemiasterlin peptides is described. The key reactions are a SnCl4-mediated ring opening of epoxynitriles or epoxysulfones by N-methylindole followed by an asymmetric Strecker reaction. A second approach involving opening of glycidic esters by indoles is also described.
Creating micro-scale surface topology to achieve anisotropic wettability on an aluminum surface (2006)

A technique for fabricating micropatterned aluminum surfaces with parallel grooves 30 µm wide and tens of microns in depth is described. Standard photolithographic techniques are used to obtain this precise surface-feature patterning. Positive photoresists, S1813 and AZ4620, are selected to mask the surface, and a mixture of BCl3 and Cl2 gases is used to perform the etching. Experimental data show that a droplet placed on the micro-grooved aluminum surface using a micro-syringe exhibits an increased apparent contact angle, and for droplets condensed on these etched surfaces, more than a 50% reduction in the volume needed for the onset of droplet sliding is manifest. No chemical surface treatment is necessary to achieve this water repellency; it is accomplished solely by an anisotropic surface morphology that manipulates droplet geometry and creates and exploits discontinuities in the three-phase contact line. These micro-structured surfaces are proposed for use in a broad range of air-cooling applications, where the management of condensate and defrost liquid on the heat transfer surface is essential to the energy-efficient operation of the machine.
Neurotoxicity and Physicochemical Properties of Aβ Mutant Peptides from Cerebral Amyloid Angiopathy (2003)

Cerebral amyloid angiopathy (CAA) due to beta-amyloid (Abeta) is one of the specific pathological features of familial Alzheimer's disease. Abeta mainly consisting of 40- and 42-mer peptides (Abeta40 and Abeta42) exhibits neurotoxicity and aggregative abilities. All of the variants of Abeta40 and Abeta42 found in CAA were synthesized in a highly pure form and examined for neurotoxicity in PC12 cells and aggregative ability. All of the Abeta40 mutants at positions 22 and 23 showed stronger neurotoxicity than wild-type Abeta40. Similar tendency was observed for Abeta42 mutants at positions 22 and 23 whose neurotoxicity was 50-200 times stronger than that of the corresponding Abeta40 mutants, suggesting that these Abeta42 mutants are mainly involved in the pathogenesis of CAA. Although the aggregation of E22G-Abeta42 and D23N-Abeta42 was similar to that of wild-type Abeta42, E22Q-Abeta42 and E22K-Abeta42 aggregated extensively, supporting the clinical evidence that Dutch and Italian patients are diagnosed as hereditary cerebral hemorrhage with amyloidosis. In contrast, A21G mutation needs alternative explanation with the exception of physicochemical properties of Abeta mutants. Attenuated total reflection-Fourier transform infrared spectroscopy spectra suggested that beta-sheet content of the Abeta mutants correlates with their aggregation. However, beta-turn is also a critical secondary structure because residues at positions 22 and 23 that preferably form two-residue beta-turn significantly enhanced the aggregative ability.