cssi/SciSciGPT-SciSciNet huggingface dataset:
Compression of protein sequence databases

We have created an algorithm for compressing a PIR database to assist individual researchers and software developers who utilize sequence database information but may not have huge storage space. The resulting compact databank contains compressed PIR information and an interface written in C which allows fast direct access to the stored information without extensive decompression of corresponding files. The databank files as well as the interface C-file can be used on both PC-compatibles and UNIX-based computers without any modifications. The interface supports all standard PIR Request Network queries (i.e. gets databank SEQ number by entry; for a defined databank SEQ number, gets specified information like: name, organism(s), keyword(s), sequence, sequence features with coordinates, etc.). In contrast with PIR Request Network, our package allows us to call PIR-contained information directly from the C programs, even on a personal computer not on a network. Our PIR-derived databank, SAGITTARIUS PIR, was implemented in the form of separate file sets. Each file set contains database information of independent types (i.e. sequences, entry indexes, organisms, etc.). On a particular computer, the available configuration of the PIR information (and storage space) can be easily changed as needed by the user without affecting retrievals of other types of stored information. Due to an original alignment-based algorithm, in the compression of protein sequences themselves, our package out-performs the well-known ZIP file compressor. For PC-compatibles, a dialogue shell is available which supports all standard PIR Request Network queries plus homology searches, alignments, etc.
The Near Infrared Absorption Spectrum of Methane

The infrared absorption spectrum of methane between 1.4\ensuremath{\mu} and 2.6\ensuremath{\mu} was obtained with an infrared spectrometer having a grating of 5000 lines to the inch. Strong bands were found in the 1.6\ensuremath{\mu} and 2.3\ensuremath{\mu} regions. The fine structure of the 2.3\ensuremath{\mu} band was resolved in the first order spectrum. The fine structure of the 1.6\ensuremath{\mu} band was resolved in the second order but not in the first order spectrum. Only at the 2.20\ensuremath{\mu} and the 1.66\ensuremath{\mu} bands could the fine structure be measured. The 2.20\ensuremath{\mu} band has spacing of 10.7 ${\mathrm{cm}}^{\ensuremath{-}1}$, giving for the value of the moment of inertia 5.17\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}40}$ c.g.s. units. The corresponding values for the 1.66\ensuremath{\mu} band are 10.4 ${\mathrm{cm}}^{\ensuremath{-}1}$ and 5.32\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}40}$ c.g.s. units. These results are quite close to the values of 9.77 ${\mathrm{cm}}^{\ensuremath{-}1}$ and 5.66\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}40}$ c.g.s. units found for the 3.31\ensuremath{\mu} band by Cooley.
The role of management and representation in improving performance of disadvantaged students: An application of Bum Phillips's "Don Shula Rule"

Scholars and practitioners within the U.S. education system have focused considerable attention on developing new programs aimed at raising educational achievement for disadvantaged students. New programs are only one way to improve student performance, however; recent work in public administration suggests that public management and implementation practices might also have a large impact on student performance. Existing research shows that managerial networking, managerial quality, and effective personnel management can significantly improve the quality of the education received by disadvantaged students. Additional work highlights the contribution of representative bureaucracy. Because these research agendas have targeted the public administration literature rather than the education policy literature, this article seeks to bring this research back to education policy. Using data from several hundred Texas public school districts, spanning 1995 to 2002, and focusing on disadvantaged student performance (Latinos, blacks, and low-income students), this article illustrates how both management and processes to enhance the representativeness of teaching faculty produce benefits for disadvantaged students.
Cohesive Zone Property Measurement by a Hybrid Experimental and Numerical Method Using Ball Indentations

Although there are several techniques available for the evaluation of various interfacial cohesive zone properties of coatings, each has difficulties and limitations. For instance, the four-point bend method is often plagued by excessive deformation and plasticity without any coating delamination, and the button test is limited by the constant stress distribution assumption. Given such issues, a new hybrid numerical/experimental technique has been developed that is based on ball indentations, which can usually induce delamination regardless of the materials used. Using this method, indentations were first made on coated samples (nickel-on-steel and aluminum-on-aluminum for the current study) to intentionally create localized, circular delaminations, the initiation and dimensions of which were functions of the applied loads. Numerical models using finite element analysis were then used with the known indentation loads to inversely evaluate the cohesive zone properties, which reproduced the experimental results. The technique was validated based on the successful prediction of the indentation results evaluated using properties from four-point bend results.
Strain-dependence of the structure and ferroic properties of epitaxial Ni1 − xTi1 − yO3 thin films grown on sapphire substrates

Abstract Polarization-induced weak ferromagnetism has been predicted a few years back in compounds MTiO 3 (M = Fe, Mn, Ni) (Fennie, 2008). We set out to stabilize this metastable, distorted perovskite structure by growing NiTiO 3 epitaxially on sapphire Al 2 O 3 (001) substrate, and to control the polar and magnetic properties via strain. Epitaxial Ni 1 − x Ti 1 − y O 3 films of different Ni/Ti ratios and thicknesses were deposited on Al 2 O 3 substrates by pulsed laser deposition at different temperatures, and characterized using several techniques. The effect of film thickness, deposition temperature, and film stoichiometry on lattice strain, film structure, and physical properties was investigated. Our structural data from x-ray diffraction, electron microscopy, and x-ray absorption spectroscopy shows that substrate-induced strain has a marked effect on the structure and crystalline quality of the films. Physical property measurements reveal a dependence of the Neel transition and lattice polarization on strain, and highlight our ability to control the ferroic properties in NiTiO 3 thin films by film stoichiometry and thickness.
Named entity recognition through classifier combination

This paper presents a classifier-combination experimental framework for named entity recognition in which four diverse classifiers (robust linear classifier, maximum entropy, transformation-based learning, and hidden Markov model) are combined under different conditions. When no gazetteer or other additional training resources are used, the combined system attains a performance of 91.6F on the English development data; integrating name, location and person gazetteers, and named entity systems trained on additional, more general, data reduces the F-measure error by a factor of 15 to 21% on the English data.
Using pedigree reconstruction to estimate population size: genotypes are more than individually unique marks

Estimates of population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Noninvasive genetic methods are increasingly used to estimate population size, particularly in elusive species such as large carnivores, which are difficult to count by most other methods. In most such studies, genotypes are treated simply as unique individual identifiers. Here, we develop a new estimator of population size based on pedigree reconstruction. The estimator accounts for individuals that were directly sampled, individuals that were not sampled but whose genotype could be inferred by pedigree reconstruction, and individuals that were not detected by either of these methods. Monte Carlo simulations show that the population estimate is unbiased and precise if sampling is of sufficient intensity and duration. Simulations also identified sampling conditions that can cause the method to overestimate or underestimate true population size; we present and discuss methods to correct these potential biases. The method detected 2–21% more individuals than were directly sampled across a broad range of simulated sampling schemes. Genotypes are more than unique identifiers, and the information about relationships in a set of genotypes can improve estimates of population size.
Nuclear localization of testosterone, dihydrotestosterone and estradiol-17β in basal rat brain

Abstract (1) One-half hour after the intravenous injection of [3H]testosterone, basal brain cell nuclei isolated from castrated male rats contained more radioactivity with the thin layer chromatography mobility of estradiol-17β and dihydrotestosterone (DHT) than nuclei from female rats. (2) The sex differences in the subcellular localization of [3H]DHT and [3H]estradiol-17β were not reflected in the ratio of the nuclear to whole homogenate radioactivity. (3) In the basal brain, estradiol-17β was the only metabolite examined that showed more DPM/mg protein in the nuclear fraction than in the whole homogenate. (4) In the basal brain and pituitary, unlabeled DHT was more effective than testosterone in blocking the nuclear localization of [3H]testosterone and [3H]DHT. (5) Unlabeled estradiol-17β only blocked the nuclear concentration of [3H]estradiol-17β and not [3H]testosterone or [3H]DHT.
Transdermal nitroglycerin as a step 3 antihypertensive drug.

The antihypertensive effect of transdermal nitroglycerin was tested in 11 men with hypertension (mean age 60 years) whose diastolic blood pressure exceeded 90 mm Hg while receiving a diuretic and a β-adrenergic blocker. In a double-blind, randomized crossover trial the subjects received weekly increments of placebo or nitroglycerin (5, 10, 20, and 30 cm2) for 4 weeks each. The final dose of nitroglycerin was 22.5 cm2(mean). During week 4 of nitroglycerin dosing, sitting and standing systolic blood pressures were reduced (P < 0.05). Diastolic blood pressures and heart rates did not change during the study. In the five subjects with systolic hypertension (≥150 mm Hg), the mean reduction in systolic blood pressure was 24 mm Hg (P < 0.01). Further studies are needed to determine if transdermal nitroglycerin has a role in the treatment of systolic hypertension. Clinical Pharmacology and Therapeutics (1986) 40, 42–45; doi:10.1038/clpt.1986.137
Optimal integration of renewable energy resources in data centers with behind-the-meter renewable generator

Because of their intermittency and inter-temporal variations, the integration of renewable energy resources is usually very challenging. Some of the previously proposed solutions, such as the use of energy storage units and fast-responding generators, are costly and may not be desirable in practice. Instead, in this paper, we argue that due to the workload flexibility in the Internet and Cloud Computing data centers they can offer a unique opportunity to tackle the challenges in integrating renewable energy resources. Moreover, by running data centers with behind-the-meter renewable generators, we can significantly reduce not only data centers' energy cost but also their Carbon Footprint. To achieve these objectives, we propose to optimally distribute the workload among geographically dispersed data centers such that we can benefit from the location diversity of different types of available renewable energy resources. The quality-of-service is guaranteed by real-time monitoring of the queue lengths and effectively stabilizing short queue lengths in each data center. Simulation results, based on various experimental data, show that the proposed design can significantly reduce data centers' cost of electricity while maintaining quality-of-service.
Intramolecular Diels-Alder reactions with furan: the gem-dialkyl effect revisited

Abstract Remote substituents that influence ground state state rotamer populations were found to be important controlling factors in the intramolecular Diels-Alder reaction with furan.
Correlation of Bone Ba/Ca and Sr/Ca due to Biological Purification of Calcium

Analyses of more than 1000 samples of soils, plants and bones of many species from a temperate woodland environment confirm the ubiquity of biopurification processes in which Ba/Ca and Sr/Ca decrease with increasing trophic position. This study reveals that differences among Ba/Ca and Sr/Ca ratios in soils and plants themselves are comparable to or greater than differences due to biopurification and preclude the use of these ratios for the quantitative assessment of dietary plant/meat ratios. The data also reveal that much of this variation at the base of the food web is removed at higher trophic positions through the extraordinary effectiveness of bone in providing a long-term statistical average of diet composition. This reduction in variation effects a pronounced correlation between Ba/Ca and Sr/Ca at higher levels of biopurification such that, given either Ba/Ca or Sr/Ca, a strong constraint can be placed upon the other ratio. This provides a tool for directly assessing whether measured Ba/Ca and Sr/Ca ratios are biological or reflect substantial post-mortem alteration.
Approximations for the capacity of binary input discrete memoryless channels

In this paper, we present our results on lower and upper bounds for the capacity of binary input discrete memoryless channels. These bounds also serve as good approximations for the capacity of these channels. Our results generalize previous analysis of bounds for binary input, binary output discrete memoryless channels and also constitute an extension of the new field of algebraic information theory.
Effect of prior body experience on adaptation to visual displacement

The effect of proprioceptive adaptation to visual displacement is to produce a violation of the normal constraints on the relative position of body parts. In order to investigate the effect of this violation of constraints on the adaptation, the relative position of body parts for a group of dancers and a group of nondancers was determined after 5 and 15 min of adaptation. Empirical and theoretical support were provided for the propositions that (1) there is a tendency to resist the violation of constraints, and (2) the nature of the adaptation process is such as to minimize the amount of violation of constraints.
Hunting Issues in Contemporary Society: Perspectives of Resident Hunters in Montana (USA)

Hunting is a popular recreational activity in many rural regions of the United States. There is a need for information about individuals who hunt, including their attitudes and perceptions of the activity. The objective of this research was to identify issues affecting hunters in modern society. This study took a qualitative approach to data collection and examined hunting issues in Montana. Data were gathered from a mail survey that used open-ended questions. The survey was sent to a random sample of resident elk hunters. Responses revealed five central concerns of hunters in Montana. These included the presence of wolves on the landscape, the commercialization of wildlife, nonresident hunters, high license prices, and motorized vehicles and the hunting experience. The findings of this study enhance our understanding of hunting issues in contemporary society.
Video compression by coefficient compensation

This paper discusses a new video compression algorithm called Coefficient Compensation that achieves high performance by optimizing the DCT encoding loop structure, and demonstrates its improvement characteristic as compared with the conventional JPEG or MPEG I/P picture encoding under the condition that movement compensation is not available. The first part of the paper analyzes the performance of the DCT encoding loop structure, the method of optimization and the concept of soft-decision. The second part reports on the simulation results. Encoding performance is tested by various MPEG test sequences compressed in 20 Mbits/sec. The difference between JPEG and MPEG I is in the quantization table. For JPEG, the quantization table widely accepted as one producing a good compression quality is used. All the encoded binary outputs are fully compatible to the MPEG2 syntax but additional 2 bits/block information is coded as the user data for the Coefficient Compensation.
Observations of sodium in the coma of Comet C/2012 S1 (ISON) during outburst

Abstract Prior to disintegration near its 2.7 R ⊙ perihelion, the dynamically new Comet C/2012 S1(ISON) briefly exhibited resonantly scattered sodium emission at the 5890 A and 5896 A D lines. In this work, we report a rapid increase in sodium production of >3× between observations made only one day apart and the first observations of cometary sodium during an outburst. Mean Na production is estimated at 1.6 ± 0.3 × 10 23 atoms s −1 on UT 19.5 Nov 2013 and 5.8 ± 1 × 10 23 atoms s −1 on UT 20.5. At a heliocentric distance of 0.44 AU, the anti-sunward Na tail was detected >10 6 km from the nucleus. Surprisingly, these production rates are well below those of any previously determined when Na is seen from a comet. Accurately reproducing the emission in the Na tail on UT 20.5 Nov 2013 requires a source near the nucleus that varies with time due to the outburst. Data prior to outburst one day earlier can be reproduced if nearly half of total sodium production is attributed to an extended source such as dust grains. This suggests sources of sodium vapor in cometary coma are sensitive to the dust to gas ratio.
Studies of the many-body approximations using the pairing-plus-quadrupole model

Abstract Reduced transition probabilities B (E2) for spherical doubly even nuclei are calculated in the quasiboson approximation (QBA), the random-phase approximation (RPA) and the improved random-phase approximation (IRPA). A comparison is made with experiments for each approximation, and the effect of the Pauli principle is demonstrated. The effect of these approximations on the systematics is studied by comparing the average of the absolute deviations from the experimental values for each approximation. The problem is formulated by using double-time Green function techniques.
SLEEP, SLEEP DISORDERED BREATHING, AND NOCTURNAL HYPOVENTILATION IN CHILDREN WITH NEUROMUSCULAR DISEASES

Sleep disordered breathing (SDB) is now well recognized in children with neuromuscular diseases (NMD) and may lead to significant morbidity and increased mortality. Predisposing factors to SDB in children with NMD include reduced ventilatory responses, reduced activity of respiratory muscles during sleep and poor lung mechanics due to the underlying neuro-muscular disorder. SDB may present long before signs of respiratory failure emerge. When untreated, SDB may contribute to significant cardiovascular morbidities, neuro-cognitive deficits and premature death. One of the problems in detecting SDB in patients with NMD is the lack of correlation between lung function testing and daytime gas exchange. Polysomnography is the preferred method to evaluate for SDB in children with NMD. When the diagnosis of SDB is confirmed, treatment by non-invasive ventilation (NIV) is usually recommended. However, other modalities of mechanical ventilation do exist and may be indicated in combination with or without other supportive measures.
Peptic ulcer disease and the tar and nicotine yield of currently smoked cigarettes.

Abstract In order to examine the association of smoking cigarettes with a lower tar and nicotine yield to peptic ulcer disease, a common disease associated in past studies with cigarette smoking, we used questionnaire information provided by 9009 current regular cigarette smokers. The percentages who ever had peptic ulcer disease in smokers whose current cigarette yielded 0.00–0.81, 0.81–0.99, 1.00–1.27 and 1.28+ milligrams of nicotine per cigarette were 8.5, 9.2, 9.2 and 9.5, respectively. The percentages who ever had peptic ulcer in smokers whose current cigarette yielded 0.0–11.9, 12.0–15.9, 16.0–18.9 and 19.0+ milligrams of tar per cigarette were 8.6, 9.1, 8.9 and 10.8 per 100, respectively. In contrast, the percentages who ever had peptic ulcer disease increased with the smoking of a greater number of cigarettes, being 5.9, 8.8, 9.0, 11.8 and 10.5 in smokers of p = 0.002) associated with number of cigarettes (RR = 1.12 per 10 cigarettes; 95% CI 1.08. 1.16), age and sex. There was no significant association (both p ' s ? 0.10) either with the current cigarette's tar yield (RR = 1.09 per 10 milligrams; 95% CI 0.96, 1.25) or with its nicotine yield (RR = 1.15 per milligram; 95% CI 0.94, 1.42).
Testing the accuracy of microstructure reconstruction in three dimensions using phantoms

Three-dimensional (3D) multi-region explicit geometric modeling of implicit images of polycrystalline materials microstructure is tested for accuracy and fitness using 3D Phantom geometries. Implicit data sets are generated from the explicit phantoms by sampling the phantoms over a range of resolutions, from which explicit representations are then reconstructed. The reconstructed models are tested for error against the phantoms to characterize the accuracy of the reconstruction techniques as a function of resolution. The error of the reconstructed geometries decreases with increasing resolution. However, the mean width of the reconstructed regions are consistently lower than the phantoms.
Sbe2p and Sbe22p, Two Homologous Golgi Proteins Involved in Yeast Cell Wall Formation

The cell wall of fungal cells is important for cell integrity and cell morphogenesis and protects against harmful environmental conditions. The yeast cell wall is a complex structure consisting mainly of mannoproteins, glucan, and chitin. The molecular mechanisms by which the cell wall components are synthesized and transported to the cell surface are poorly understood. We have identified and characterized two homologous yeast proteins, Sbe2p and Sbe22p, through their suppression of a chs5 spa2 mutant strain defective in chitin synthesis and cell morphogenesis. Although sbe2 and sbe22 null mutants are viable, sbe2 sbe22 cells display several phenotypes indicative of defects in cell integrity and cell wall structure. First, sbe2 sbe22 cells display a sorbitol-remediable lysis defect at 37°C and are hypersensitive to SDS and calcofluor. Second, electron microscopic analysis reveals that sbe2 sbe22 cells have an aberrant cell wall structure with a reduced mannoprotein layer. Finally, immunofluorescence experiments reveal that in small-budded cells, sbe2 sbe22 mutants mislocalize Chs3p, a protein involved in chitin synthesis. In addition, sbe2 sbe22 diploids have a bud-site selection defect, displaying a random budding pattern. A Sbe2p–GFP fusion protein localizes to cytoplasmic patches, and Sbe2p cofractionates with Golgi proteins. Deletion of CHS5, which encodes a Golgi protein involved in the transport of Chs3p to the cell periphery, is lethal in combination with disruption of SBE2 and SBE22. Thus, we suggest a model in which Sbe2p and Sbe22p are involved in the transport of cell wall components from the Golgi apparatus to the cell surface periphery in a pathway independent of Chs5p.
Wavelet Codes: Detection and Correction Using Kalman Estimation

Wavelet codes encoded by uniform oversampled filter banks where the wavelet coefficients represent code symbols are decoded employing Kalman fixed-lag estimation procedures. The code symbol error estimates are based on the mean-squared error (MSE) criterion and are first used to detect the presence of large numerical errors. Then the correction of symbols uses these Kalman estimators directly. The wavelet code symbols are corrupted by low levels of processing noise continuously and occasionally by large disruptive errors, e.g., impulsive noise. The modeling variables have time-varying statistics allowing both types of errors to be handled naturally. Kalman time-varying tracking filters, which use wavelet syndromes as their measurement inputs, develop the fixed-lag smoothed estimates for the larger errors. The syndromes are also modeled as corrupted by processing noise modeling computational failure errors, large and small. Hypothesis detection methods are used to locate large errors and their statistics must include Kalman mismatch characteristics to be valid. Estimators from several adjacent lag positions assist in the detection procedures. Simulation results show correction accuracy in the time domain as well as on a MSE basis. Large classes of wavelet codes are designed using binary convolutional codes as starting points from which the proper filter weights for encoding and syndrome evaluating are determined.
p‐i‐n Heterojunction Solar Cells with a Colloidal Quantum‐Dot Absorber Layer

A quantum-dot (QD) p-i-n heterojunction solar cell with an increased depletion region is demonstrated by depleting the QD layer from both the front and back junctions. Due to a combination of improved charged extraction and increased light absorption, a 120% increase in the short-circuit current is achieved compared with that of conventional ZnO/QD devices.
Specific health-related quality of life concerns in children with intermittent exotropia.

Purpose: To assess the frequency of specific health-related quality of life (HRQOL) concerns in children with intermittent exotropia (XT) using the Intermittent Exotropia Questionnaire (IXTQ).Methods: Eighty children with intermittent XT (aged 5 to <17 years), plus one parent for each child, completed the Child and Proxy IXTQ respectively. Each item was scored from 0 to 100 (worst to best HRQOL). Mean scores were calculated for each item and items were ranked from lowest to highest impact (worst HRQOL). Analysis was repeated for sub-groups of 5- to <8-year-olds (n = 46) and 8- to <17-year-olds (n = 34).Results: Highest impact Child IXTQ items were: “It bothers me that I have to shut one eye when it is sunny,” “I worry about my eyes,” and “It bothers me because I have to wait for my eyes to clear up.” Highest impact Proxy IXTQ items were: “It bothers my child because he/she has to shut one eye when it is sunny” and “My child worries about his/her eyes.” Lowest impact Child and Proxy items were “My eyes mak...
Eimeria (protozoa: eimeriidae) from white-tailed deer odocoileus virginianus in Pennsylvania, Texas, and Wisconsin, with descriptions of two new species.

Fecal samples were collected from white-tailed deer, Odocoileus virginianus, in Pennsylvania, Texas, and Wisconsin. Four species of Eimeria which have not been reported previously from white-tailed deer were found. Two new species, E. virginianus and E. madisonensis are described, while E. mccordocki and E. odociolei are compared with their original descriptions from mule deer, Odocoileus hemionus. Oocysts of E. virginianus are elongate ovoid to ellipsoidal with micropyle. They have a rough outer wall and measure 42.3 to 55.0 by 26.2 to 42.0μ, mean 49.2 by 32.6. Oocysts of E. madisonensis are nearly round with a smooth outer wall and measure 14.0 to 19.1 by 12.8 to 16.3μ, means 16.1 by 15.5. Eimeria mccordocki and E. odocoilei were found in deer from all three states, E. virginianus, in deer from Pennsylvania and Wisconsin, and E. madisonensis, only from Wisconsin deer.
Driver activity monitoring through supervised and unsupervised learning

This paper presents two different learning methods applied to the task of driver activity monitoring. The goal of the methods is to detect periods of driver activity that are not safe, such as talking on a cellular telephone, eating, or adjusting the dashboard radio system. The system presented here uses a side-mounted camera looking at a driver's profile and utilizes the silhouette appearance obtained from skin-color segmentation for detecting the activities. The unsupervised method uses agglomerative clustering to succinctly represent driver activities throughout a sequence, while the supervised learning method uses a Bayesian eigen-image classifier to distinguish between activities. The results of the two learning methods applied to driving sequences on three different subjects are presented and extensively discussed.
An expression index for Affymetrix GeneChips based on the generalized logarithm

Motivation: Affymetrix GeneChip high-density oligonucleotide arrays interrogate a single transcript using multiple short 25mer probes. Usually, a necessary step in the analysis of experiments using these GeneChips is to summarize each of these probe sets into a single expression index that can then be used for determining differential expression, for classification, for clustering, and for other analyses. In this paper, we propose a new expression index that is competitive with the best existing methods, and superior in many cases. We call this expression index method GLA, for GLog Average, since after normalization at the probe level, we take the mean generalized logarithm of perfect match probes. Results: In this paper, we use Affycomp as the primary tool to assess the weaknesses and strengths of GLA. Comparisons are made between GLA and most widely used summary methods (RMA, MAS5.0 and MBEI) in great detail. The substantial reduction in variability and increased ability to detect differential expression, together with the simplicity of implementation, make GLA a plausible candidate for analysis of Affymetrix GeneChip data. Contact: dmrocke@ucdavis.edu
Experimental evaluation of a sacrificial seismic fuse device for masonry infill walls

Presented herein are the details and results of an experimental study conducted to evaluate the performance of a proposed infill wall fuse system. The purpose of this system, referred to as the sei...
Mutational Analysis of Adeno-Associated Virus Type 2 Rep68 Protein Endonuclease Activity on Partially Single-Stranded Substrates

The endonuclease activity of the Rep68 and Rep78 proteins (Rep68/78) of adeno-associated virus type 2 (AAV) cuts at the terminal resolution site (trs) within the hairpin structure formed by the AAV inverted terminal repeats. Recent studies suggest that a DNA unwinding function of Rep68/78 may be required for endonuclease activity. We demonstrate that several mutant proteins which are endonuclease negative on a fully duplex hairpin substrate are endonuclease positive on a partially single-stranded hairpin substrate. Truncation analysis revealed that the endonuclease function is contained within the first 200 amino acids of Rep68/78. This endonucleolytic cleavage is believed to involve the covalent attachment of Rep68/78 to the trs via a phosphate-tyrosine linkage. A previous report (S. L. Walker, R. S. Wonderling, and R. A. Owens, J. Virol. 71:2722–2730, 1997) suggested that tyrosine 152 was part of the active site. We individually mutated each tyrosine within the first 200 amino acids of the Rep68 moiety of a maltose binding protein-Rep68/78 fusion protein to phenylalanine. Only mutation of tyrosine 156 resulted in a protein incapable of covalent attachment to a partially single-stranded hairpin substrate, suggesting that tyrosine 156 is part of the endonuclease active site.
The inaccuracy of surface-measured model-derived tibiofemoral kinematics

This study assessed the accuracy of surface-measured OpenSim-derived tibiofemoral kinematics in functional activities. Ten subjects with unilateral, isolated grade II PCL deficiency performed level running and stair ascent. A dynamic stereo radiography (DSX) system and a Vicon motion capture system simultaneously measured their knee or lower extremity movement. Surface marker motion data from the Vicon system were used to create subject-specific models in OpenSim and derive the tibiofemoral kinematics. The surface-measured model-derived tibiofemoral kinematics in all six degrees of freedom (DOFs) were then compared with those measured by the DSX as the benchmarks. The differences between surface- and DSX-measured tibiofemoral kinematics were found to be substantial: the overall mean (7SD) RMS differences during running were 9.17 3.21, 2.071.21, and 6.47 4.51 for the flexion–extension, abduction–adduction, and internal–external rotations, respectively, and 7.17 3.2 mm, 8.87 3.7 mm, and 1.97 1.2 mm for anterior–posterior, proximal–distal, and medial– lateral translations, respectively. The differences were more pronounced in relatively higher speed running than in stair ascent. It was also found that surface-based measures significantly underestimated the mean as well as inter-subject variability of the differences between PCL-injured and intact knees in abduction–adduction, internal–external rotations, and anterior–posterior translation.
Processing of ZrC–Mo Cermets for High Temperature Applications, Part II: Pressureless Sintering and Mechanical Properties

Pressureless sintering of ZrC-Mo cermets was investigated in a He/H 2 atmosphere and under vacuum. A large density increase was observed for specimens with > 20 vol% Mo after heating at 2150°C for 60 min in a He/H 2 atmosphere. The increase in density was attributed to the formation of Mo 2 C during heating and its subsequent eutectic reaction with Mo, which produced rounded ZrC grains in a Mo-Mo 2 C matrix. Sintering in vacuum did not produce the same increase in density, due to the lack of Mo 2 C formation and subsequent lack of liquid formation, which resulted in a microstructure with irregular ZrC grains with isolated areas of Mo. Mechanical properties testing showed a decrease in Young's modulus with increasing Mo content that was consistent with the models presented. Flexure strength of ZrC-Mo cermets sintered in He/H 2 atmosphere materials increased with increasing Mo content from 320 MPa at 20 vol% Mo to 410 MPa at 40 vol% Mo. Strength was predicted by adapting theories developed previously for WC-Co cermets.
A floating communication processor architecture in a distributed real-time system

The issues involved in providing hardware communication support at each mode in a distributed real-time system are studied. First, a general architecture for each node of the system is described. An algorithm for message handling by dedicated hardware called a communication processor (CP) is proposed, to maximize the number of requests handled over the various constraints. A floating CP architecture is proposed, to maximize the number of requests handled under the various constraints. A floating CP architecture is proposed to maximize the utilization of the processors at a node and provide greater fault-tolerance in the system. >
Ordinal Regression by Extended Binary Classification

We present a reduction framework from ordinal regression to binary classification based on extended examples. The framework consists of three steps: extracting extended examples from the original examples, learning a binary classifier on the extended examples with any binary classification algorithm, and constructing a ranking rule from the binary classifier. A weighted 0/1 loss of the binary classifier would then bound the mislabeling cost of the ranking rule. Our framework allows not only to design good ordinal regression algorithms based on well-tuned binary classification approaches, but also to derive new generalization bounds for ordinal regression from known bounds for binary classification. In addition, our framework unifies many existing ordinal regression algorithms, such as perceptron ranking and support vector ordinal regression. When compared empirically on benchmark data sets, some of our newly designed algorithms enjoy advantages in terms of both training speed and generalization performance over existing algorithms, which demonstrates the usefulness of our framework.
Poly(arylate‐phosphonate) copolymers with deoxybenzoin in the backbone: Synthesis, characterization, and thermal properties

Deoxybenzoin-based copolymers containing various relative ratios of arylate and phosphonate units in the backbone were synthesized by solution polycondensation. These copolymers were characterized by gel permeation chromatography, Fourier Transform infrared spectrometry, and proton, carbon, and phosphorous nuclear magnetic resonance spectroscopy (1H, 13C, and 31P NMR). Pyrolysis combustion flow calorimetry (PCFC) performed on these copolymers revealed their very low heat release capacity, making them attractive for applications in which halogen-free, low flammability materials are desired. Integration of phosphonate units into the polymer backbone is advantageous for achieving high molecular weight polymers with solution processbility while retaining the low flammability inherent to deoxybenzoin-based polymers. Char yields greater than 50% and heat release capacities of 40–60 J/g K, were observed for these copolymers by PCFC. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4573–4580, 2007
Factors associated with outcome after interventional treatment of symptomatic iliac vein compression syndrome.

Background Iliac vein compression syndrome (IVCS) results from compression of the left iliac vein by the overlying right iliac artery against the pelvic brim. In many cases, patients are symptomatic. In symptomatic cases, management consists of angioplasty and stenting. Although therapy is often initially successful, factors associated with long-term outcome have been poorly defined. The purpose of this study was to identify factors associated with stent patency. Methods The medical records of all patients who underwent iliac vein percutaneous transluminal angioplasty and stenting from January 1996 to December 2006 for symptomatic IVCS were reviewed retrospectively. There were 50 women and 8 men, with a mean age of 42 years (median, 39 years; range, 17-71 years). Primary, assisted primary, and secondary patency rates were determined. Patient characteristics and clinical variables were evaluated by univariate and multivariate analysis to determine association with vein patency. Results Symptoms consisted of lower extremity swelling (81%) and lower extremity pain (67%). Iliac vein obstruction was treated with pharmacologic thrombolysis (31% of patients) and mechanical thrombus fragmentation (17% of patients). The primary, assisted primary, and secondary patency rates of angioplasty/stenting were 74.1%, 79.7%, and 85.8% at 1 year and 38.1%, 62.8%, and 73.8% at 5 years, respectively. Using a Cox proportional risk model, male sex (hazard ratio, 6.5; P = .001), recent trauma (hazard ratio, 5.3; P = .001), and age younger than 40 years (hazard ratio, 3.8; P = .015) were associated with decreased primary patency. In the absence of any risk factors, primary patency was 94.4% at 1 year and 63.0% at 5 years, decreasing to 28.6% and 0% for two or more risk factors. Conclusions Patency rates for iliac vein percutaneous transluminal angioplasty and stenting in patients with IVCS can potentially be predicted on the basis of a multivariate model. Assessing risk factors allows for patient stratification and appropriate clinical decision making. Prospective validation of these variables is necessary.
MAP kinase pathways: The first twenty years

The MAP kinases, discovered approximately 20 years ago, together with their immediate upstream regulators, are among the most highly studied signal transduction molecules. This body of work has shaped many aspects of our present views of signal transduction by protein kinases. The effort expended in this area reflects the extensive participation of these regulatory modules in the control of cell fate decisions, i.e., proliferation, differentiation and death, across all eukaryotic phylla and in all tissues of metazoans. The discovery of these kinases is reviewed, followed by a discussion of some of the features of this signaling module that account for its broad impact on cell function and its enormous interest to many investigators.
State-dependent memory effects using caffeine and placebo do not extend to metamemory.

Abstract The authors examined the impact of caffeine on human memory and predictions of memory (i.e., metamemory). On Day 1, 83 college students drank a sweetened beverage containing either caffeine (4 mg/kg body weight) or a placebo before they studied 40 pairs of words. While the participants studied, they predicted their future memory performance for each word pair. On Day 2, the participants again received caffeine or a placebo before the memory test. The participants who drank the same beverage on both days (either caffeine or a placebo) recalled more word pairs than did those who drank different beverages (caffeine on 1 day and a placebo on the other day). In contrast, memory predictions were more accurate when the beverages did not match on both days. These data provide evidence for state-dependent memory when caffeine is used, but not for state-dependent metamemory. People's memory and their predictions of memory can be influenced in different ways if they drink caffeine before they study or take ...
Interleukin-11 attenuates human vascular smooth muscle cell proliferation

Interleukin (IL)-11 is a growth factor for megakaryocytes, osteoclasts, and intestinal mucosa. IL-11 is also an anti-inflammatory agent, mediating many of its effects by inhibition of the transcrip...
A women and technology program for freshman engineering students

In the Fall of 1999, Texas A&M University (TAMU) was selected as a participating university in the Virtual Development Center (VDC) program sponsored by the Institute for Women and Technology (IWT). The intent is that the ideas generated by women and for women through these centers can be realized by a cooperative effort between students and industries. A special section of the Foundations of Engineering (Engr 111/112) course at TAMU has been created in support of the VDC program. The student teams will collaborate with students from other courses, both technical and nontechnical, and at all levels. The result of this multilevel, interdisciplinary interaction is intended to be the design and implementation of idea(s). The classroom environment, interdisciplinary work, and industry interaction will give the students a very positive experience and open their eyes to many and varied engineering issues in ways that are not typically addressed by the curriculum.
RBFN restoration of nonlinearly degraded images

We investigate a technique for image restoration using nonlinear networks based on radial basis functions. The technique is also based on the concept of training or learning by examples. When trained properly, these networks are used as spatially invariant feedforward nonlinear filters that can perform restoration of images degraded by nonlinear degradation mechanisms. We examine a number of network structures including the Gaussian radial basis function network (RBFN) and some extensions of it, as well as a number of training algorithms including the stochastic gradient (SG) algorithm that we have proposed earlier. We also propose a modified structure based on the Gaussian-mixture model and a learning algorithm for the modified network. Experimental results indicate that the radial basis function network and its extensions can be very useful in restoring images degraded by nonlinear distortion and noise.
Grammar and technical writing

Harris argues that linguistic theory is useful for solving certain problems encountered in technical writing theory and pedagogy [1]. However, he undermines his purpose by introducing irrelevant distinctions between competing syntactic theories (Generalized Phrase Structure Grammar and Transformational Grammar) and by failing to exploit the full potential of the few applications he mentions. The passive rule is a case in point. It not only constitutes an operational test for identifying passive sentences, it also contributes to the flow of discourse by rearranging both thematic roles (e.g. agent and patient) and given/new information. The passive rule is only one of a class of noun phrase-moving operations that technical writing specialists may find useful
Investigating parent of origin effects in studies of Type 2 Diabetes and Obesity

The role of parent-of-origin effects (POE) in the etiology of complex diseases such as type 2 diabetes (T2DM) and obesity is currently of intense interest, but still largely unclear. POE are transmittable genetic effects whereby the expression of the phenotype in the offspring depends upon whether the transmission originated from the mother or father. In mammals, POE can be caused by genetic imprinting, intrauterine effects, or maternally inherited mitochondrial genes. In this paper, we describe the different mechanisms underlying POE, characterize known examples of POE in rare forms of diabetes, and review the evidence from linkage and association studies for POE in T2DM and obesity. Finally, we summarize some of the new and established statistical and experimental approaches commonly used to detect POE. Through this paper, we hope emphasizes the potentially significant importance of POE in the etiology of T2DM and obesity.
Product quality and the direction of trade

Abstract A substantial amount of theoretical work predicts that quality plays an important role as a determinant of the global patterns of bilateral trade. This paper develops an empirical framework to estimate the empirical relevance of this prediction. In particular, it identifies the effect of quality operating on the demand side through the relationship between per capita income and aggregate demand for quality. The model yields predictions for bilateral flows at the sectoral level and is estimated using cross-sectional data for bilateral trade among 60 countries in 1995. The empirical results confirm the theoretical prediction: rich countries tend to import relatively more from countries that produce high-quality goods.
Epidemiological analysis of respiratory viral etiology for influenza-like illness during 2010 in Zhuhai, China

Background Influenza-like illnesses (ILI), a subset of acute respiratory infections (ARI), are a significant source of morbidity and mortality worldwide. ILI can be caused by numerous pathogens, however; there is limited information on the etiology and epidemiology of ILI in China.
A nonradioactive assay of bacterial productivity optimized for oligotrophic pelagic environments

The measurement of bacterial production is a cornerstone of research in aquatic biogeochemistry and microbial ecology, yet the standard radioisotope-based techniques are threatened by increasing logistical obstacles. The two primary goals of this study were (1) the development of a reliable nonradioactive assay of bacterial productivity interpretable in the context of previous 3 H-thymidine ( 3 H-TdR)‐based metrics, and (2) maximizing the sensitivity of the assay to allow routine measurement of bacterial productivity in open-ocean and lowproductivity environments. We optimize existing methods for immunochemical detection of the incorporation of the thymidine analog 5-bromo-2′-deoxyuridine (BrdU) to present a functional assay of community bacterial productivity comparable to radioisotope-based assays in economy and field implementation and capable of consistently detecting bacterial production rates within the range of 0.1 to 10 pmol BrdU L ‐1 h ‐1 . A standardization procedure provides complete separation of radioisotopes from the working methodology and gives statistically consistent results between calibrations with no degradation of the labeled DNA standards. Immunoassayed BrdU incorporation rates were highly correlated with parallel measurements of 3 H-TdR incor