gebhart/patrepeval huggingface dataset:
Towards predicting Ca<sup>2+</sup>‐binding sites with different coordination numbers in proteins with atomic resolution (2008)

Ca(2+)-binding sites in proteins exhibit a wide range of polygonal geometries that directly relate to an equally-diverse set of biological functions. Although the highly-conserved EF-Hand motif has been studied extensively, non-EF-Hand sites exhibit much more structural diversity which has inhibited efforts to determine the precise location of Ca(2+)-binding sites, especially for sites with few coordinating ligands. Previously, we established an algorithm capable of predicting Ca(2+)-binding sites using graph theory to identify oxygen clusters comprised of four atoms lying on a sphere of specified radius, the center of which was the predicted calcium position. Here we describe a new algorithm, MUG (MUltiple Geometries), which predicts Ca(2+)-binding sites in proteins with atomic resolution. After first identifying all the possible oxygen clusters by finding maximal cliques, a calcium center (CC) for each cluster, corresponding to the potential Ca(2+) position, is located to maximally regularize the structure of the (cluster, CC) pair. The structure is then inspected by geometric filters. An unqualified (cluster, CC) pair is further handled by recursively removing oxygen atoms and relocating the CC until its structure is either qualified or contains fewer than four ligand atoms. Ligand coordination is then determined for qualified structures. This algorithm, which predicts both Ca(2+) positions and ligand groups, has been shown to successfully predict over 90% of the documented Ca(2+)-binding sites in three datasets of highly-diversified protein structures with 0.22 to 0.49 A accuracy. All multiple-binding sites (i.e. sites with a single ligand atom associated with multiple calcium ions) were predicted, as were half of the low-coordination sites (i.e. sites with less than four protein ligand atoms) and 14/16 cofactor-coordinating sites. Additionally, this algorithm has the flexibility to incorporate surface water molecules and protein cofactors to further improve the prediction for low-coordination and cofactor-coordinating Ca(2+)-binding sites.
Salt Tolerance in Wild Rices (1987)

This article 'Salt Tolerance in Wild Rices' appeared in the International Rice Research Newsletter series, created by the International Rice Research Institute (IRRI). The primary objective of this publication was to expedite communication among scientists concerned with the development of improved technology for rice and for rice based cropping systems. This publication will report what scientists are doing to increase the production of rice in as much as this crop feeds the most densely populated and land scarce nations in the world.
A Comparison of Torque Required to Fracture Three Different Nickel-Titanium Rotary Instruments Around Curves of the Same Angle but of Different Radius When Bound at the Tip (2003)

Instrument fracture is an unfortunate but possible sequela of instrumentation of canals, especially when the instrument is bound at the tip. The purpose of this study was to compare the torque required to fracture three file sizes of three different rotary file types around two simulated canal curvatures, gradual or acute, when the tip of the working end of the file was bound. Profile Series 29 0.04 and 0.06 taper and Profile 0.06 ISO rotary files were placed passively into simulated canal curvatures of the same angle but of different radii. The file tips were bound 2 mm from the working end and a measurable torque was applied until fracture. ANOVA with Tamhane post-hoc comparison showed that the 0.06 Series 29 did not differ from the ISO 0.06 taper or the 0.04 Series 29 but there was statistical difference (p < 0.01) showing that the 0.04 Series 29 broke with less force than did the 0.06 ISO files. Statistical tests (p < 0.01) also showed smaller files failed with less torque, as did files in more acute canal curvatures.
Function Extraction Technology: Computing the Behavior of Malware (2011)

Current methods of malware analysis are increasingly challenged by the scope and sophistication of attacks. Recent advances in software behavior computation illuminate an opportunity to compute the behavior of malware at machine speeds, to aid in understanding intruder methods and developing countermeasures. The behavior computation process helps eliminate certain forms of malware obfuscation and computes the net effects of the remaining functional code. This paper describes behavior computation technology and provides an example of its use in malware analysis.
Optical properties of multicomponent oxide glasses and glass fibers (2003)

Abstract We experimentally studied the optical properties of multicomponent oxide glasses that contain metallic components, such as potassium and sodium, and their glass fibers. The Rayleigh scattering coefficients of glasses such as Na 2 O‐B 2 O 3 ‐SiO 2 (NBS), K 2 O‐MgO‐SiO 2 (KMS), K 2 O‐Na 2 O‐MgO‐SiO 2 (KNMS) are smaller than that of pure quartz glass. In particular, the Rayleigh scattering coefficient of KNMS glass was significantly lower at 38% of the value for pure quartz glass. This is believed to be the result of suppressing the composition fluctuations of KNMS glass by the mixed alkali effect. Furthermore, we studied the absorption properties of OH group impurities included in multicomponent oxide glasses. In particular, we fabricated NAS glass fibers that substituted the OH group impurity with an OD group (deuterium) by the double crucible method and verified a loss reduction of about 800 dB/km at the 1.55‐µm wavelength. Through these studies, we clearly showed that the absorption losses of the OH group that hydrogen bonds to nonbridging oxygen clearly affected the increase in the 1.55‐µm band loss in multicomponent oxide glass fibers. © 2003 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 86(12): 21–35, 2003; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/ecja.10128
A high frequency solution for hybrid renewable energy systems (2015)

With the growth of telecommunication systems in remote areas, demand of wind solar hybrid systems is demanding in this industry. In this paper a 3 MHz DC-DC converter for standalone wind/solar application is proposed. The proposed converter is able to operate at a high frequency and to function in a wide range of input voltage. These specs make the system ideal for wind/solar energy systems. All MOSFETs and diodes in this converter are switched under soft switching condition. In addition, using finite inductors in the input of the converter makes it suitable for bang-bang control to keep the high efficiency at low loads. Experimental results are in agreement with simulations and analysis.
Longitudinal functional and NMR assessment of upper limbs in Duchenne muscular dystrophy (2016)

Our results underscore complementarity of functional and NMR assessments in patients with DMD. Sensitivity to change of various indices may differ according to disease stage.
<i>Artemisia asiatica</i> extracts protect against ethanol‐induced injury in gastric mucosa of rats (2008)

The data suggest that the ethanol extracts of Artemisia asiatica exerted significant protection from alcohol-induced gastric mucosal injury through bio-regulation, which is essential for cytoprotection and anti-inflammation.
Energy management for motors, systems, and electrical equipment (2002)

Energy management embodies engineering, design, applications, operation, and maintenance of electrical power systems to provide optimal use of the electrical energy. The key element of the energy management process is the identification and analysis of energy conservation opportunities (ECOs). This paper presents a brief summary of Chapter 5 of the IEEE Std 739-1995, where the standard discusses the energy management and energy conservation for motors, systems, and electrical equipment.
Fracture Behaviour of Thermoplastic Modified Epoxy Resins (1992)

Abstract This work has shown that the addition of polyetherimide (PEI) can significantly increase the toughness of highly cross-linked epoxy resins, whilst retaining a high Tg and modulus. These combined properties indicate the potential of PEI modified epoxy resins for use as matrices for advanced composite materials. In terms of GIC, addition of 20wt% PEI raised the toughness by a factor of eight. Evidence from SEM fracture surfaces suggests that the toughening mechanism operating in bulk PEI modified epoxy resin is ductile drawing of the PEI. Carbon fibre composites based on 30wt% PEI modified epoxy resin matrices show considerable improvement in toughness at low and high strain rates when compared with CFRP possessing unmodified or 20wt% modified PEI content epoxy resins.
The Mutagenicity of Electrocautery Smoke (1992)

Careful analysis of electrocautery smoke produced during breast surgery has found organic compounds that are unidentifiable with current analytical techniques. The purpose of this study was to determine the potential mutagenicity of the smoke produced by the electrocautery knife during reduction mammaplasty. Multiple air samples were collected in the operating room during two reduction mammaplasty procedures. Airborne smoke particles were tested for mutagenic potential in both tester strains of Salmonella typhimurium (TA98 and TA100) using the standard Salmonella microsomal test (Ames test). All testing was performed by the Hazard Evaluations and Technical Assistance Branch of the National Institute of Occupational Safety and Health. The smoke produced with the electrocautery knife during reduction mammaplasty was found to be mutagenic to the TA98 strain. The Ames test, an established technique for evaluating the mutagenicity of a substance, was convincingly positive for the smoke collected during the breast surgery. Whether the smoke represents a serious health risk to operating room personnel is not known. Development of techniques to limit electrocautery smoke exposure in the operating room appears to be needed, and surgeons should attempt to minimize their exposure.
Bioavailability of Magnesium Diglycinate vs Magnesium Oxide in Patients with Ileal Resection (1994)

Data from this study support the suggestion that some portion of magnesium diglycinate is absorbed intact, probably via a dipeptide transport pathway. Magnesium diglycinate may be a good alternative to commonly used magnesium supplements in patients with intestinal resection.
Synthesis of a [<sup>18</sup>F]fluorobenzothiazole as potential amyloid imaging agent (2008)

Abstract This study describes the synthesis of a fluoroethylated derivative of [ N ‐methyl‐ 11 C]2‐(4′‐methylaminophenyl)‐6‐hydroxybenzothiazole ([ 11 C]6‐OH‐BTA‐1; Pittsburgh Compound B (PIB)), an already established amyloid imaging agent. The [ 11 C]methylamino group of [ 11 C]6‐OH‐BTA‐1 was formally replaced by a fluoroethyl group in a cold synthesis via N‐alkylation of N ‐Boc‐2‐(4′‐aminophenyl)‐6‐(methoxyethoxymethoxy)benzothiazole with fluoroethyl tosylate. Subsequent deprotection gave the target compound 2‐[4′‐(2‐fluoroethyl)aminophenyl]‐6‐hydroxybenzothiazole (FBTA). In a radioligand competition assay on aggregated synthetic amyloid fibrils using N ‐[ 3 H‐methyl]6‐OH‐BTA‐1, 100 nM FBTA inhibited binding with 93 ± 1 and 83 ± 1% efficiency for A β 1–40 and A β 1–42 , respectively. For the radiosynthesis a precursor carrying a tosylethyl moiety was prepared allowing the introduction of [ 18 F]fluoride via nucleophilic substitution with [ 18 F]tetra‐ n ‐butyl‐ammonium fluoride (TBAF). Subsequent removal of all protecting groups was performed in a one‐pot procedure followed by semi‐preparative HPLC, delivering the target compound [ 18 F]FBTA in good radiochemical yield of 21% on average and radiochemical purity of ⩾98% at EOS. In vitro autoradiography on human postmortem AD brain tissue slices showed intense cortical binding of [ 18 F]FBTA (1 nM), which was displaced in presence of 6‐OH‐BTA‐1 (1 µM). Brain up‐take was evaluated in wild‐type (wt) mice with microPET imaging. Based on these results, [ 18 F]FBTA appears to be a suitable candidate tracer for amyloid imaging in humans. Copyright © 2008 John Wiley & Sons, Ltd.
A behavioural programme for the modification of encopresis (1976)

This paper describes a behaviour modification programme for the treatment of encopresis. The programme, which is carried out by the parents over a relatively short period of time in the home setting, aims to make the child aware of internal cues prior to elimination and to rearrange the contingencies for appropriate use of the toilet. To date, seven of eleven children, both continuous and discontinuous encopretics, have been treated successfully and have remained clean for up to 7 months regardless of other problems in the child and his family. From a relatively detailed analysis of those treated it can be concluded that a behavioural approach is effective with chronic encopretic children, many of whom had been previously treated unsuccessfully by both physical and psychotherapeutic procedures. The failures suggest, firstly that careful assessment of each child and the motivation of the parents is required, so that the standard programme can be modified to suit each individual case. Secondly a maintenance programme must follow the intensive treatment procedure to ensure that parents continue to handle the child consistently.
Multishell Microspheres with Integrated Chromatographic and Detection Layers for Use in Array Sensors (2003)

The development of miniaturized chromatographic systems localized within individual polymer microspheres and their incorporation into a bead-based cross-reactive sensor array platform is reported. The integrated chromatographic and detection concept is based on the creation of distinct functional layers within the microspheres. In this first example of the new methodology, complexing ligands have been selectively immobilized to create "separation" layers harboring an affinity for various metal cations. Additionally, a broadly responsive compleximetric dye is used to yield the "detection" layers that exhibit optical responses in the presence of a wide range of metal cations. Information concerning the identities and concentrations of solution-dissolved metal cations can be drawn from the temporal properties of the beads' optical responses. Varying the nature of the ligand in the separation shell yields a collection of cross-reactive sensing elements well-suited for use in array-based micrototal analysis systems. Accordingly, such beads have been incorporated into the "Electronic Taste Chip" platform and used for discriminating among aqueous metal cation solutions.
Drift-free attitude estimation for accelerated rigid bodies (2002)

We study the attitude estimation problem for an accelerated rigid body using gyros and accelerometers. The application in mind is that of a walking robot and particular attention is paid to the large and abrupt changes in accelerations that can be expected in such an environment. We propose a state estimation algorithm that fuses data from rate gyros and accelerometers to give long-term drift free attitude estimates. The algorithm does not use any local parameterization of the rigid body kinematics and can thus be used for a rigid body performing any kind of rotations. The algorithm is a combination of two non-standard, but in a sense linear, Kalman filters between which a trigger based switching takes place. The kinematics representation used makes it possible to construct a linear algorithm that can be shown to give convergent estimates for this nonlinear problem. The state estimator is evaluated in simulations demonstrating how the estimates are long term stable even in the presence of gyrodrift.
Microstrip-fed cylindrical slot antennas for GPS avionics applications (2002)

The printed cylindrical slot antenna presented is useful in the application where low-profile installation is required on a high dynamic aircraft. This new printed GPS antenna provides compact size, low cost, ease of mass production, near-hemispherical radiation coverage and circular polarization properties. Experimental results show that the cylindrical slot antennas have a 3 dB beamwidth of more than 1200 and a front-back ratio of more than 15 dB.
A multi-scale morphologic runway detector (2010)

In order to enhance the environmental awareness of pilots to some extent, runway detectors play a very important role in Synthetic Vision System. Based on the characters of infrared image, which has bad contrast and heavy noises, an improved multi-scale morphologic edge detector is proposed in this paper. It uses different size of structuring elements to extract the edge points of infrared runway image at first, integrating the superiority of small size detecting fine edges and large size removing more noise. By setting the edge information detected at each different size with different weight just according to their abilities of removing noise, and then combine them together, we can obtain the actual and explicit runway edge. Comparative study reveals its superiority over other traditional edge detectors and morphologic edge detectors. It can detect the runways effectively and precisely which is very beneficial in the aviation areas.
Polyunsaturated fatty acids, membrane function and metabolic diseases such as diabetes and obesity (1998)

Lipids play an extraordinary range of roles in normal and deranged metabolism. In diabetes and obesity, lipids have often been seen just as impacting on the energy balance equation. New data are extending our understanding of how lipid subclasses influence carbohydrate and lipid metabolism at multiple control points: from the modulation of membrane proteins to the regulation of gene transcription.
Time for a redefinition of type 2m von willebrand disease (2002)

The recent paper by Riddell et al (2002) was interesting and timely. However, the results were entirely predictable without any experimentation because of preselection of patients and the currently used definition of type 2M von Willebrand disease (VWD). Both the ristoctin cofactor (VWF:RCo) assay and the collagen-binding (VWF:CB) assay will be sensitive to loss of von Willebrand factor (VWF) protein and especially to the loss of the higher-molecular-weight (HMW) multimers. The current definition of type 2M VWD is ‘decreased platelet-dependent function that is not caused by the absence of HMW-VWF multimers’. Defects in the VWF glycoprotein Ib binding site will lead to loss of platelet-dependent function, cause type 2M VWD by this definition, and be detected by the VWF:RCo (but not the VWF:CB). Defects in the VWF collagen binding site will lead to loss of collagen-dependent function, cause a currently unclassified form of VWD, and be detected by the VWF:CB (but not the VWF:RCo). I suggest that ‘platelet-dependent’ is removed from the definition of type 2M VWD. Type 2M can then be subtyped as type 2Mp – decreased platelet-dependent function (the old 2M), or as type 2Mc – decreased collagen-dependent function. The VWF:RCo detects only the former and the VWF:CB only the latter. That type 2Mc exists is clear (Ribba et al, 2001). We will only know the relative importance of type 2Mp and type 2Mc when the VWF:CB is used as widely as the VWF:RCo.
A NEW BUPLEURUM (UMBELLIFERAE) FROM CENTRAL CHINA (1992)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Formation of Chiral Nematic Films from Cellulose Nanocrystal Suspensions Is a Two-Stage Process (2014)

The evaporation of aqueous suspensions of cellulose nanocrystals (CNCs) gives iridescent chiral nematic films with reflection colors at visible wavelengths. A key problem is controlling the chiral nematic pitch, P, and hence the reflection colors of CNC films. By adding D-(+)-glucose to the suspension, we show that the change in P during evaporation occurs in two distinct stages. The first stage is the decrease in P as the concentration of CNC in the chiral nematic suspension increases due to evaporation; the addition of glucose causes a decrease in P at this stage. In a second stage, a concentration of CNC is reached where the formation of ordered gels and glasses prevents further major changes in P. The addition of glucose lowers the CNC concentration at which this occurs, leading to an increase in P and hence an overall shift to the red end of the spectrum in the final film.
Both α2,3- and α2,6-Linked Sialic Acids on O-Linked Glycoproteins Act as Functional Receptors for Porcine Sapovirus (2014)

Sapovirus, a member of the Caliciviridae family, is an important cause of acute gastroenteritis in humans and pigs. Currently, the porcine sapovirus (PSaV) Cowden strain remains the only cultivable member of the Sapovirus genus. While some caliciviruses are known to utilize carbohydrate receptors for entry and infection, a functional receptor for sapovirus is unknown. To characterize the functional receptor of the Cowden strain of PSaV, we undertook a comprehensive series of protein-ligand biochemical assays in mock and PSaV-infected cell culture and/or piglet intestinal tissue sections. PSaV revealed neither hemagglutination activity with red blood cells from any species nor binding activity to synthetic histo-blood group antigens, indicating that PSaV does not use histo-blood group antigens as receptors. Attachment and infection of PSaV were markedly blocked by sialic acid and Vibrio cholerae neuraminidase (NA), suggesting a role for α2,3-linked, α2,6-linked or α2,8-linked sialic acid in virus attachment. However, viral attachment and infection were only partially inhibited by treatment of cells with sialidase S (SS) or Maackia amurensis lectin (MAL), both specific for α2,3-linked sialic acid, or Sambucus nigra lectin (SNL), specific for α2,6-linked sialic acid. These results indicated that PSaV recognizes both α2,3- and α2,6-linked sialic acids for viral attachment and infection. Treatment of cells with proteases or with benzyl 4-O-β-D-galactopyranosyl-β-D-glucopyranoside (benzylGalNAc), which inhibits O-linked glycosylation, also reduced virus binding and infection, whereas inhibition of glycolipd synthesis or N-linked glycosylation had no such effect on virus binding or infection. These data suggest PSaV binds to cellular receptors that consist of α2,3- and α2,6-linked sialic acids on glycoproteins attached via O-linked glycosylation.
Superconducting Quantum Interferometers for Nondestructive Evaluation (2017)

We review stationary and mobile systems that are used for the nondestructive evaluation of room temperature objects and are based on superconducting quantum interference devices (SQUIDs). The systems are optimized for samples whose dimensions are between 10 micrometers and several meters. Stray magnetic fields from small samples (10 µm-10 cm) are studied using a SQUID microscope equipped with a magnetic flux antenna, which is fed through the walls of liquid nitrogen cryostat and a hole in the SQUID's pick-up loop and returned sidewards from the SQUID back to the sample. The SQUID microscope does not disturb the magnetization of the sample during image recording due to the decoupling of the magnetic flux antenna from the modulation and feedback coil. For larger samples, we use a hand-held mobile liquid nitrogen minicryostat with a first order planar gradiometric SQUID sensor. Low-T<sub>c</sub> DC SQUID systems that are designed for NDE measurements of bio-objects are able to operate with sufficient resolution in a magnetically unshielded environment. High-T<sub>c</sub> DC SQUID magnetometers that are operated in a magnetic shield demonstrate a magnetic field resolution of ~4 fT/√Hz at 77 K. This sensitivity is improved to ~2 fT/√Hz at 77 K by using a soft magnetic flux antenna.