cssi/SciSciGPT-SciSciNet huggingface dataset:
Functional genomics—bioinformatics is ready for the challenge

I thank X. Zhang for the analysis used to construct Fig. 1Fig. 1. This work was supported by Grant P41 LM05205 from the National Library of Medicine and DE-FG02-98ER62558 from the US Department of Energy. Its contents are solely the responsibility of the author and do not necessarily represent the official views of the granting agencies.
AC susceptibility measurements with a biomedical SQUID system

Abstract A technique is described whereby a set of small copper coils can be temporarily attached to the dewar of a standard biomedical SQUID system for ac measurements of the magnetic susceptibility of large or awkwardly shaped objects.
Simulation of electron ionization mass spectra of cycloalkyl fluorophosphonates

The mass spectra of highly toxic cycloalkyl alkylfluorophosphonates can be divided into two components: organophosphorus and hydrocarbon. The organophosphorus component is a generalized spectral image of a taxonomic group among those forming a homologous series of cycloalkyl alkylfluorophosphonates. The hydrocarbon component is interpreted as a spectrum of the cycloolefin which is the main product of cycloalkyl alkylfluorophosphonate fragmentation. A method for simulation of the electron ionization mass spectra of these compounds is proposed.
Philanthropic Mobility and the Influence of Duration of Donor Residency on Donation Choices

Scholars have long been interested in what influences philanthropic behavior. However, little is known about the effects of length of residency on charitable gifts to local and non-local organizations. Using 2010 survey data from 470 older individuals, we examine whether donors’ geographic relocations influence philanthropic behavior and whether these moves are a bigger challenge for some types of nonprofits than others. We find variations in giving to specific types of nonprofits based on residency duration. The giving patterns we uncover add depth to our understanding of philanthropic behavior and inform nonprofit managers seeking to better understand older adults’ giving to local and non-local religious, human services, arts, and education nonprofits.
Fluorescence dynamics studies of troponin C

The time decay of fluorescence anisotropy for a dansylaziridine (DANZ) conjugate with Met-25, which lies within the N-terminal lobe of troponin C (TnC), shows at 10 and 25°C a longer correlation time characteristic of the entire molecule and a shorter correlation time arising from a more localized motion of the probe. In the absence of Ca2+, the amplitude of the shorter correlation time increases, suggesting an increased mobility of the probe. At 40°C, in both the absence and presence of Ca2+, a significant increase in probe mobility occurs. A 2,6-toluidinyl naphthalene sulfonate (2,6-TNS) complex with Ca2+-liganded TnC shows only the longer correlation time at 12 and 25°C. An N-(iodoacetylaminoethyl-5-naphthylamine-1-sulfonate) conjugate with Cys-98 shows both a long and a short correlation time; the amplitude of the shorter correlation time is greater than for the DANZ conjugate. At 9, 25, and 40°C in the presence of Ca2+, and at 9°C in its absence, the magnitude of the long correlation time is consistent with motion of the entire molecule; at higher temperatures in the absence of Ca2+ it is substantially smaller, suggesting the presence of internal rotation. For Ca2+-liganded TnC at temperatures of 25°C or lower, the results with all three labels are interpretable in terms of the crystallographic structure of TnC.
Thermal fatigue of a SiC/Ti-15Mo-2.7Nb-3Al-0.2Si composite

The influence of thermal cycling and isothermal exposures in air on the residual ambient temperature strength of SCS-6/Ti-15Mo-2.7Nb-3Al-0.2Si (weight percent) metal-matrix composites comprised of [0]4 and [0/90]s laminates has been determined. A maximum temperature of 815 °C was used in thermal cycling and isothermal exposure. Temperature range, cycle count, maximum/minimum temperature, environment, and hold time at temperature were systematically varied. Postexposure ambient-temperature tension testing, scanning electron and optical microscopy, and fractography were performed on selected specimens to determine the degree of damage. A reduced residual strength was noted in thermal fatigue with increasing cycle count, maximum temperature, and hold time for all specimens tested in air. Isothermal exposures at 815 °C also substantially reduced residual ambient-temperature strength. Considerably less reduction in strength occurred in inert environment than in air. Damage processes included matrix cracking, fiber/matrix interface damage, matrix embrittlement by interstitials, and oxide scale formation at specimen surfaces and, in some cases, at matrix/fiber interfaces. Fiber orientations which allowed rapid ingress of oxygen lead to greater matrix embrittlement and resulted in more pronounced reductions in strength.
Methods in Elastic Tissue Biology: Elastin Isolation and Purification

Elastin provides recoil to tissues subjected to repeated stretch, such as blood vessels and the lung. It is encoded by a single gene in mammals and is secreted as a 60-70 kDa monomer called tropoelastin. The functional form of the protein is that of a large, highly crosslinked polymer that organizes as sheets or fibers in the extracellular matrix. Purification of mature, crosslinked elastin is problematic because its insolubility precludes its isolation using standard wet-chemistry techniques. Instead, relatively harsh experimental approaches designed to remove non-elastin 'contaminates' are employed to generate an insoluble product that has the amino acid composition expected of elastin. Although soluble, tropoelastin also presents problems for isolation and purification. The protein's extreme stickiness and susceptibility to proteolysis requires careful attention during purification and in tropoelastin-based assays. This article describes the most common approaches for purification of insoluble elastin and tropoelastin. It also addresses key aspects of studying tropoelastin production in cultured cells, where elastin expression is highly dependent upon cell type, culture conditions, and passage number.
Bin packing problems on one dimension: heuristic solutions and confidence intervals

Abstract The one-dimensional bin packing problem has many applications to problems of data management, scheduling and resource allocation. Very large examples of this problem are likely to exceed the limits of computational tractability, and in such circumstances the use of approximate (heuristic) methods is suggested. We adapt a variety of heuristic methods for generating feasible solutions, and the results are then used to generate confidence intervals for the (in practice unknown) value of the optimal solution. A large-scale computational study for randomly generated problems with prespecified optimal values suggests that these intervals are extremely narrow and are also highly likely to contain the optimal solution value. The interval estimation procedure seems to generate much better results for the bin packing problem than for other problems tested in the literature.
Arabidopsis defense response against Pseudomonas syringae - Effects of major regulatory genes and the impact of coronatine

Arabidopsis defense response against the bacterial pathogen, Pseudomonas syringae, is a complex and highly regulated process. Previous studies have identified many critical genes encoding regulators that govern innate immunity, but comprehensive transcriptome analysis of corresponding mutants is lacking. Using a custom microarray, we profiled the transcriptome of many mutants with mutations in critical regulatory genes affecting Arabidopsis disease resistance. We show that previously identified mutants affecting the salicylic acid (SA) sector of the defense network have similar transcriptional profiles. Surprisingly, jin1, jar1 and dde2 that are involved in jasmonates (JA) sector did not show major transcriptome changes, while coi1 did. Further analysis revealed that the phytotoxin, coronatine, secreted by P. syringae, is responsible for nearly all COI1-mediated responses.
Adrenergic effects on pineal cell membrane potential.

Abstract Pineal bodies from female rats were studied in vitro , using microelectrodes to monitor cell membrane potentials. Norepinephrine and isoproterenol caused dose-dependent hyperpolarization of pinealocyte membrane potential, while phenylephrine was incative. The changes produced by norepinephrine were inhibited by propranolol but not by phentolamine. Estradiol also inhibited norepinephrine effects; the effects of estradiol were not readily reversible by washing. It is concluded that a β-adrenergic receptor mechanism in pinealocytes regulates membrane potential and that estradiol inhibits the effect of norepinephrine in this system.
The simultaneous analysis of discrete and continuous outcomes in a dose–response study: Using desirability functions☆

Multiple types of outcomes are sometimes measured on each animal in toxicology dose-response experiments. The potential false-positive rate from statistical tests on each endpoint may be inflated. We introduce a method of deriving a composite score that combines information from discrete and continuous outcomes through the use of desirability functions. These functions transform observed responses of any type to a 0-to-1 unitless scale. The geometric mean is used to combine the scores and then a statistical model is fit to the dose-response curve of the overall score. The overall desirability score is more sensitive to toxicity evident in only a few endpoints than other composite scores that are based on sums of components. We analyze the overall score using a nonlinear exponential model with a threshold parameter. In this example, the threshold parameter was statistically significant and its estimate was less than the lowest dose. Compared to the vehicle control, the lower overall scores at this dose group were due to lower levels of brain and blood cholinesterase (90% and 82% of control, respectively) whereas other endpoints were not altered, thus demonstrating the sensitivity of the desirability function to detect low levels of toxicity in a small number of outcomes.
An Inequality from Moment Theory

We show how certain simple lp–inequalities may be proved by “ignoring the p.” An application to moment sequences is considered.
Using legal rules in an indeterminate world: Overcoming the limitations of jurisprudence

Face a l'indetermination du sens et de l'application des lois dans le domaine des procedures juridiques, l'A. souligne le danger d'une manipulation de ces lois par les juges sous couvert de leur pretendue protection. Tirant les consequences politiques, sociales et normatives de la dependance contextuelle des lois en jurisprudence, l'A. etudie l'utilisation des lois dans le comportement des individus dans un monde indetermine. S'inspirant de Husserl et du pragmatisme americain, l'A. adopte une approche ethnomethodologique (H. Garfinkel) du comportement juridique fonde sur la competence, le connu et l'inconnu, l'autonomie par rapport a la loi, le non conformisme creatif, les methodes pratiques, l'application des situations a la loi, d'une part, et la compare a l'approche de la jurisprudence conventionnelle fondee sur l'auto-ordonnancement, l'utilisation pragmatique, locale et non-normative de la loi, d'autre part
Crack cocaine and schizophrenia as risk factors for PPD reactivity in the dually diagnosed.

Abstract We studied factors contributing to an increased risk of PPD positive status among 147 inpatients dually diagnosed for mental illness and substance abuse in a large urban hospital. Ninety-three percent (N = 137) were tested for PPD on admission. The rate of positive PPDs was 30.7%. Significant correlates of PPD positive status were the diagnosis of schizophrenia/psychosis NOS (p < .05), and crack cocaine use in the 30 days prior to admission (p <.01). A multiple logistic regression revealed a relative risk of 3.53 (p < .005) for PPD positive status for the crack using group and a relative risk of 2.16 (p < .06) for PPD positive status for the schizophrenic group. Reasons for why patients whose primary drug of abuse is crack cocaine and those whose diagnosis is schizophrenia/psychosis NOS may be at an increased risk for exposure to tuberculosis are discussed as are the implications for public health.
Modeling the Determinants of a Professional Golfer's Tournament Earnings: A Multiequation Approach

Studies examining the determinants of success in professional golf constitute a relatively new and growing literature. Based on the consistency of empirical findings, there is little debate that certain shot-making skills influence a golfer's score and hence tournament earnings. However, the theoretical development of a player's production function in support of empirical specifications is lacking in the literature. Moreover, virtually all studies specify single-equation models that assume a direct relationship between performance and skill, an approach recently questioned in the literature. In response, this research develops a structural model of a professional golfer's tournament success and uses a multiequation framework to estimate the determinants of a player's season-ending earnings. Using this framework, estimates of the value of the marginal product for each shot-making skill are determined and found to be markedly different from those derived from single-equation models.
From Siècles Obscurs to revolutionary centuries on the Middle Niger

Abstract In a period of little over a decade, excavations have transformed our characterization of Middle Niger prehistory from hidden and humble to one of the world's most original theatres of change. After situating the Middle Niger evidence for geomorphology, domestication, organization of society and production, and belief systems against a backdrop of current concerns in West African prehistory, we suggest future research directions of particular potential. The Middle Niger lends a new perspective on current thinking about the prehistorian's enterprise, most notably about the symbolic component of the world as socially constructed, cross‐cultural studies, and the integrity of our traditional analytical categories.
Metabolism of 1-131 by Human Thyroid Tissue in Organ Culture.∗

SummaryThe incubation of human thyroid tissue in tissue culture medium containsing I-131 by an organ culture technique is described. The histology of the gland was preserved up to 7 days. Labeled MIT, DIT, and T4 were present following papain hydrolysis of the tissue. Addition of TSH to the culture medium apparently accelerated the conversion of MIT to DIT as well as the rate of coupling of DIT to form T4 and released T4 from the thyroid tissue into the medium. No labeled amino acids were detected in the culture medium when TSH was not added.
Slowing of dexterous manipulation in old age: force and kinematic findings from the ‘nut-and-rod’ task

The task of sliding a nut from a rod has been used to study manual slowing in old age (Smith et al. in Neurology 53:1458-1461, 1999; Neurobiol Aging 26:883-890, 2005). In this experiment, we sought to determine if the age-related slowing in this task occurs with losses of motor precision, as indicated by the forces exerted on the rod. The forces exerted by the nut on the rod were monitored along with the kinematics of the hand in old and young adults while they attempted to lift a nut from three vertically oriented rods of different shape (straight, single curve, double curve). Old adults performed the task 64% slower than young adults for the straight rod, 100% slower for the single-curve rod, and 80% slower for the double-curve rod. Old adults did not differ from the young adults in the amount of force exerted against the rods in the horizontal plane, or in the steadiness of these forces, but exerted greater force impulses in the vertical direction over the course of a trial (359% straight, 236% single curve, 214% double curve) and much more force in the vertical direction (255% straight, 267% single curve, 159% double curve). Old adults also performed the task with 35% greater average roll of the hand into pronation. We suspect that old adults tilted the nut, even for the straight rod, dragging it against the rod to create the elevated vertical forces. These observations support previous speculation that old adults do not control the external moments applied to grasped objects as well as young adults.
Contamination of the Air Sac Areas of Chicken Carcasses and Its Relationship to Scalding and Method of Killing

Abstract THE shelf life of market poultry has been shown to be a function of the growth of spoilage organisms present on the surface of the carcass. The growth of organisms in deeper tissues has been considered a less important source of spoilage because the numbers found in intramuscular tissue were small compared with numbers found on the surface of spoiled chicken (Lochhead and Landerkin, 1935; Ayres et al., 1950). It has been suggested that the air sac structures, which connect the exterior of the carcass with the deeper tissues, magnify the hazard of contamination when several carcasses are stored in the same receptacle (Gunderson et al., 1954). Sturkie (1954), referring to work by Locy and Larsell (1916), described the anatomy of the air sac structures as follows: “The air sacs are connected to the lungs by way of the mesobronchi and secondary bronchi. Other connections to the lungs are provided …
Small molecule versus DNA repair nanomachine

The MRN protein megacomplex mediates repair of double-stranded DNA breaks (DSBs) by tethering together broken ends of chromosomes and signaling a cascade of events required for DNA repair. The first small-molecule inhibitor that disrupts MRN function provides a valuable new tool for functional studies of DSB repair in cells.
Leveraging Gene Ontology Annotations to Improve a Memory-Based Language Understanding System

This work evaluates how detailed knowledge about proteins can be leveraged for language understanding and disambiguation by OpenDMAP. OpenDMAP is a memory-based language understanding system that uses patterns to identify concepts in text. These patterns match not only lexical elements, such as words, but also semantic elements, such as references to proteins. This work started with an existing pattern set used to extract biological activation events from a corpus of GeneRIFs (sentences or phrases that each describe one of many of the functions of a gene). This is a challenging task because many distinct activation concepts, in addition to being semantically similar, are described using very similar language. We augment the previous approach with additional semantic knowledge about proteins, in the form of associated Gene Ontology annotations, and a small corresponding modification to the ontology used by OpenDMAP. By incorporating additional background knowledge we demonstrate that performance can be significantly improved without modifying the pattern set being used. Specifically precision is improved by 20%, at a modest 6% cost to recall. The additional semantic knowledge allows for more specificity in the ontology used by OpenDMAP, which in turn automatically improves the specificity of the patterns being used to extract knowledge from text reducing false positives by 75%.
Laser spectroscopy of the transitional nucleus 151Sm.

The isotope shift, magnetic moment, and quadrupole moment of the radioactive transitional nucleus $^{151}\mathrm{Sm}$ has been measured using the atomic-beam resonance-fluorescence technique. The hyperfine structure of the 591.6 nm transition was observed with an energy resolution of 20 MHz. The isotope shift of this line is found to be \ensuremath{\delta}${\ensuremath{\nu}}_{i}^{151}$,152=-1472.2\ifmmode\pm\else\textpm\fi{} 2.9 MHz. We have constructed a King plot of muonic atom \ensuremath{\delta}〈${r}^{2}$〉 versus optical isotope shifts to determine electronic parameters, and obtain \ensuremath{\delta}〈${r}^{2}$${〉}^{151}$,152=0.279\ifmmode\pm\else\textpm\fi{}0.012 ${\mathrm{fm}}^{2}$.
Expression, purification, and characterization of rat interferon-β, and preparation of an N-terminally PEGylated form with improved pharmacokinetic parameters

To identify potential new clinical uses and routes of administration for human interferon-beta-1a (IFN-beta-1a), we have developed an expression and purification procedure for the preparation of highly purified rat interferon-beta (IFN-beta) suitable for testing in rat models of human disease. An expression vector containing the rat IFN-beta signal sequence and structural gene was constructed and transfected into Chinese hamster ovary (CHO) cells. The protein was purified from CHO cell conditioned medium and purified to > 99.5% purity using standard chromatographic techniques. Analytical characterization indicated that the protein was a heavily glycosylated monomeric protein, with two of the four predicted N-glycosylation sites occupied. Analysis of the attached oligosaccharides showed them to be a complex mixture of bi-antennary, tri-antennary, and tetra-antennary structures with a predominance of sialylated tri-antennary and tetra-antennary structures. Peptide mapping, N-terminal sequencing, and mass spectrometry confirmed the identity and integrity of the purified protein. The purified protein had a specific activity of 2.1x10(8)U/mg when assayed on rat RATEC cells, which is similar in magnitude to the potencies observed for murine IFN-beta and human IFN-beta-1a assayed on murine and human cells, respectively. We also prepared an N-terminally PEGylated form of rat IFN-beta in which a 20 kDa methoxy polyethylene glycol (PEG)-propionaldehyde was attached to the N-terminal alpha-amino group of Ile-1. The PEGylated protein, which retained essentially full in vitro antiviral activity, had improved pharmacokinetic parameters in rats as compared to the unmodified protein. Both the unmodified and PEGylated forms of rat IFN-beta will be useful for testing in rat models of human disease.
Variation in resource consumption across a gradient of increasing intra‐ and interspecific richness

Based on the premise that ecosystems with more species will function at more efficient rates, declining biodiversity is expected to alter important ecosystem functions, goods, and services across the globe. However, applicability of this general hypothesis to genetic or clonal richness in assemblages composed of few species is understudied. This illustrates the need to expand the focus of biodiversity-ecosystem-function experiments across all levels of biological diversity (including genetic). To explore this generality, we manipulated intraspecific (clonal) and interspecific (species) richness of a primary consumer, Daphnia, and measured assemblage feeding rate and total resource consumption. Our results showed that greater clonal richness had no effect on Daphnia feeding, and greater species richness decreased feeding-related effects of Daphnia. This suggests that multiclonal Daphnia assemblages may be no more efficient at consuming resources than monocultures, and that monocultures of Daphnia may consume resources more efficiently than more species-rich assemblages. The inhibitory effect of increasing richness observed in this study resulted from chemical and mechanical interference among some of the Daphnia taxa. This suggests that consumer-mediated ecosystem functions could be reduced when assemblages include taxa equipped with adaptations for interference competition.
GEOTEXTILES TO MITIGATE FROST EFFECTS IN SOILS: A CRITICAL REVIEW

The use of geotextiles to mitigate frost effects in soils has been studied, but few techniques have been developed. Guidelines developed for the placement of granular capillary barriers are presented to serve as preliminary guidelines for geotextile capillary barriers. Laboratory research shows that pore size distribution, wettability, and, for some geotextiles, thickness influence capillary barrier performance in a given soil. Geotextiles that easily wet do not reduce frost heave and may even exacerbate it. On the basis of the literature reviewed, guidance for selection of geotextile capillary barriers in field trials is given. If geotextiles function as capillary barriers during freezing and reinforce or separate and filter the subgrade at the base course interface during thaw, then the potential exists for their use in a combination of functions to reduce frost-related damage in geotechnical structures. It was found that properly designed geotextiles have the potential to reduce frost heave by functioning as capillary barriers, they can be filters for capillary barriers, and they can provide reinforcement or separation or filtration (or all of these) of the subgrade soil to reduce thaw-related damage.
CHILDHOOD SEXUAL ABUSE AND COUPLES' RELATIONSHIPS: FEMALE SURVIVORS' REPORTS IN THERAPY GROUPS

Therapy videotapes from five therapy groups for female child sexual abuse (CSA) survivors were analyzed for emerging themes of couples' difficulties reported by clients. Subsequently, the thematic categories were applied to sessions selected from an additional four groups and then correlated with CSA-specific variables. The two most frequent relationship themes were difficulties with emotional communication or intimacy, and polarized positions on control. Whereas these two themes were correlated with survivors' CSA characteristics, sexual difficulties were correlated with survivors' level of current traumatic symptomatology. Results are discussed in terms of implications for the treatment of CSA survivors and their partners.
Laser Studies of Vibrational Energy Exchange in Gas-Solid Collisions

Recent measurements on the probability of vibrational deactivation in gas-solid collisions are summarized. The experiments were performed by using a tunable infrared laser source to excite gas-phase molecules vibrationally before their collision with the surface and by measuring the population of vibrationally excited molecules through their time-resolved infrared fluorescence. On polycrystalline silver surfaces, the deactivation probability for CO(v=2) was found to decrease from 0.33 at 300 K to 0.20 at 440 K, while the deactivation probability for CO2(001) was found to decrease from 0.72 at 300 K to 0.37 at 440 K. In contrast, the probability for dectivation of CO2(001) was found to be 0.16 and to vary only slightly with temperature. These observations are consistent with a mechanism involving trapping followed by electron-hole pair formation. In separate experiments, state-resolved scattering of rotationally cold NO from an Ir(111) surface held at 80K has demonstrated the exchange between translational and rotational energy. A similar technique employing vibrational excitation of the in-coming molecular beam should provide a very detailed picture of vibrational deactivation at surfaces.
Optimization of mechanical and thermo-mechanical properties of epoxy and E-glass/epoxy composites using NH2-MWCNTs, acetone solvent and combined dispersion methods

Abstract We have used a combination of ultrasound processor and 3-roll shear mixer to disperse 0.2–0.4 wt.% functionalized multi-walled carbon nanotubes (MWCNTs-NH 2 ) in SC-15 epoxy with and without acetone media. Epoxy and e-glass/epoxy composites were prepared with this modified resin. In addition, control composites without MWCNT were also prepared for baseline comparison. Fourier transform infrared spectroscopy (FTIR), rheology, dynamic mechanical thermal analysis (DMTA) and flexure tests were conducted. Effective dispersion of MWCNTs achieved through solvent media, and the enhanced interfacial interaction between epoxy and amine functional groups of MWCNTs lead to optimum increase in DMTA and flexural properties of composites. Micrographic analyses revealed bridging of MWCNTs with epoxy and rougher fracture surfaces in epoxy composites. Also, a better interfacial bonding was observed in MWCNT incorporated e-glass/epoxy samples over control samples.
Whitened rainbows: how white college students protect whiteness through diversity discourses

This qualitative study investigates white students’ attitudes toward campus diversity at a large, multiracial public university. Drawing upon focus group data gathered from a larger campus climate study, we identified four themes: participants voiced that: (1) racial diversity fosters campus tolerance; (2) diversity fragments into de facto racial segregation; (3) institutional support of diversity undermines and excludes whites; and (4) the university should avoid acknowledging white identity. Employing critical multiculturalism as a theoretical lens, we argue that these discourses maintain white dominance within a framework that promotes inclusion. These findings suggest that without more direct institutional guidance, white students will protect white supremacy even as they celebrate diversity in multiracial spaces.
A Bayesian segmentation methodology for parametric image models

Region-based image segmentation methods require some criterion for determining when to merge regions. This paper presents a novel approach by introducing a Bayesian probability of homogeneity in a general statistical context. The authors' approach does not require parameter estimation and is therefore particularly beneficial for cases in which estimation-based methods are most prone to error: when little information is contained in some of the regions and, therefore, parameter estimates are unreliable. The authors apply this formulation to three distinct parametric model families that have been used in past segmentation schemes: implicit polynomial surfaces, parametric polynomial surfaces, and Gaussian Markov random fields. The authors present results on a variety of real range and intensity images. >
Binarized Forest to String Translation

Tree-to-string translation is syntax-aware and efficient but sensitive to parsing errors. Forest-to-string translation approaches mitigate the risk of propagating parser errors into translation errors by considering a forest of alternative trees, as generated by a source language parser. We propose an alternative approach to generating forests that is based on combining sub-trees within the first best parse through binarization. Provably, our binarization forest can cover any non-consitituent phrases in a sentence but maintains the desirable property that for each span there is at most one nonterminal so that the grammar constant for decoding is relatively small. For the purpose of reducing search errors, we apply the synchronous binarization technique to forest-to-string decoding. Combining the two techniques, we show that using a fast shift-reduce parser we can achieve significant quality gains in NIST 2008 English-to-Chinese track (1.3 BLEU points over a phrase-based system, 0.8 BLEU points over a hierarchical phrase-based system). Consistent and significant gains are also shown in WMT 2010 in the English to German, French, Spanish and Czech tracks.
Applications of Photoacoustic Spectroscopy to Problems in Dermatology Research

The technique of photoacoustic spectroscopy (PAS) was applied in two areas of dermatology research: 1) drug detection and drug diffusion rates in skin, and 2) thermal properties and water content of skin. The drug studies involved detection of the drug tetracycline in the skin and determination of the diffusion rate of the drug through the skin. The water content studies involved determining the thermal properties of the epidermis as a function of water content and the effect of the water concentration gradient across the epidermis. A multilayer model for the photoacoustic effect was developed to account for the nonuniform thermal properties of the intact skin arising from the water concentration gradient. This model was used to determine the width of the region comprising the diffusional barrier in skin. The width of the barrier region was found to correspond to that of the outermost layer of the epidermis, the stratum corneum. This finding coincides with previous research indicating that the stratum corneum comprises the primary barrier to the diffusion of water through the epidermis.
Biophysical and Microscopic Analysis of Homologous Dermal and Fascial Materials for Facial Aesthetic and Reconstructive Uses

Objectives: To evaluate the microscopic structure and physical properties of homologous tissue grafts commonly used in aesthetic and reconstructive facial plastic surgery in order to determine specific properties of these materials that may affect their performance in vivo. Methods: Two decellularized dermal materials (AlloDerm and DuraDerm) and 2 fascia lata tissue grafts (Tutoplast and cadaveric fascia lata) were examined by light microscopy (hematoxylin-eosin and Movat staining) and scanning electron microscopy. The physical properties of these materials were also examined for thickness, maximum sustainable load, strain, conformability, and elasticity. Results: Significant differences in microscopic appearance existed between the 2 dermal materials and the 2 fascial materials. AlloDerm and Tutoplast fascia lata retained architecture closer to that of untreated tissue than did DuraDerm and cadaveric fascia lata, respectively. Tutoplast fascia lata and AlloDerm were also stronger than cadaveric fascia lata and DuraDerm, respectively. AlloDerm retained significantly more elasticity than DuraDerm. Conclusions: AlloDerm and Tutoplast fascia lata retain more natural architecture and physical properties than do DuraDerm and cadaveric fascia lata, respectively. These differences clearly show the effect of the specific processing of these materials. The alteration in architecture and the degradation of the physical properties of DuraDerm and cadaveric fascia lata may hinder the performance of these grafts in vivo. Further studies on these materials in humans are currently under way. Arch Facial Plast Surg. 2002;4:164-171
Distribution of submersed aquatic macrophytes in the tidal Potomac River

Abstract Results of a 3-year survey (1978–1980) and review of historic trends have shown a major decline in the number of species and the distribution of submersed aquatic macrophytes in the tidal Potomac River since the early 1900's. The freshwater tidal river is essentially devoid of plants and only very sparse populations remain in the mesohaline section of the estuary. Present plant populations are largely confined to the transition-zone region where salinity instability at the fresh-to-brackish water interface is believed to reduce biotic stress on submersed vegetation. Many factors may be implicated in the loss of vegetation over major regions of the tidal Potomac River; however, long-term conditions of excessive nutrients appear to be primarily responsible for the present distribution.
Caregiving demand and difficulty in older adult spousal caregivers after coronary artery bypass surgery

The purpose of this study was to describe the caregiving demands and difficulties for older adult spousal caregivers of coronary artery bypass (CAB) surgery patients. Caregiving demands and difficulties were measured by the Caregiving Burden Scale. The sample size was 35 caregivers of CAB surgery patients who were, on average, 60 years old and 19 days since hospital discharge. Descriptive analysis revealed that the top four most demanding caregiving activities perceived by spousal caregivers were providing transportation, additional household tasks, providing emotional support, and two tied for fourth: monitoring symptoms and additional tasks outside the home. The top four most difficult caregiving tasks were additional household tasks, providing transportation, and two tied for third: additional tasks outside home and managing behavior problems. Also, caregivers reported experiencing more demands than difficulties. Examining the demanding and difficult caregiving tasks provides information from which to develop and test tailored interventions for caregivers of this population.
An EPIC Processor with Pending Functional Units

The Itanium processor, an implementation of an Explicitly Parallel Instruction Computing (EPIC) architecture, is an in-order processor that fetches, executes, and forwards results to functional units in-order. The architecture relies heavily on the compiler to expose Instruction Level Parallelism (ILP) to avoid stalls created by in-order processing. The goal of this paper is to examine, in small steps, changing the in-order Itanium processor model to allow execution to be performed out-of-order. The purpose is to overcome memory and functional unit latencies. To accomplish this, we consider an architecture with Pending Functional Units (PFU). The PFU architecture assigns/schedules instructions to functional units in-order. Instructions sit at the pending functional units until their operands become ready and then execute out-of-order. While an instruction is pending at a functional unit, no other instruction can be scheduled to that functional unit. We examine several PFU architecture designs. The minimal design does not perform renaming, and only supports bypassing of non-speculative result values. We then examine making PFU more aggressive by supporting speculative register state, and then finally by adding in register renaming. We show that the minimal PFU architecture provides on average an 18% speedup over an in-order EPIC processor and produces up to half of the speedup that would be gained using a full out-of-order architecture.
Widely-linear recursive least-squares algorithm for adaptive beamforming

Adaptive beamforming algorithms typically rely on a complex linear model between the sensor measurements and the desired signal output that does not enable the best performance from the data in some situations. In this paper, we present an extension of the well-known recursive least-squares algorithm for adaptive filters to widely-linear complex-valued signal and system modeling. The widely-linear RLS algorithm exploits a structured covariance matrix update that maintains information about the non-circularity of the input data to solve the widely-linear least-squares task at each snapshot. In addition, the WL-RLS algorithm can easily be switched between conventional and widely-linear complex modeling as needed. Application of the method to adaptive beamforming of mixed BPSK and QPSK signal transmissions shows that the system can extract all of the transmitted signal outputs in certain overloaded scenarios, and it performs up to 3dB better than the conventional RLS beamformer when the array is not overloaded.
Mechanisms of Vaccine-Induced Protective Immunity against Coxiella burnetii Infection in BALB/c Mice

To elucidate the mechanisms of vaccine-induced protective immunity against Coxiella burnetii infection, we compared the protective efficacy and immunogenicity between formalin-inactivated phase I vaccine (PI-V) and phase II vaccine (PII-V) in BALB/c mice. PI-V generated significant protection while PII-V did not confer measurable protection. Analysis of cytokine and subclass Ab responses indicated that both PI-V and PII-V were able to induce a Th1-dominant immune response but did not identify the component of host response that distinguished their ability to induce protective immunity. Interestingly, immunoblot analysis identified a difference between PI-V and PII-V vaccinates in antigenic recognition by specific Ab isotypes. The observation that PI-LPS elicited significant protection but PII-LPS did not confer measurable protection suggests PI-LPS may play a key role in PI-V-induced protection. Adoptive transfer of either immune sera or splenocytes mediated significant protection in naive BALB/c mice, supporting the notion that both humoral and cellular immunity are important for development of protective immunity. However, the evidence that immune sera and B cells were unable to control infection while T cells conferred significant protection in SCID mice supports the hypothesis that T cell-mediated immunity is critical for host defense against C. burnetii infection. This report presents novel evidence to highlight the importance of PI-LPS and Abs in protective immunity and has important implications for the design of new generation vaccines against Q fever.
Man/machine communications in the biological medical research environment

The key source of raw data in most biomedical research is the patient's medical record. The hospital patient medical record is most commonly thought of as the repository for all pertinent facts relating to laboratory test results, diagnostic conclusions, treatment procedures, and observations. Depending on the nature of the patient's complaint, there are varying amounts of medical history information incorporated into the record. In many instances, the compilation of the record has become so routine that little thought is given to its potential value as a medical research tool. Ideally, the medical record would serve the clinician during treatment of the patient and when no longer needed by him would pass to the researcher to be associated with other similar records for statistical analysis. Obviously, the method presently used would satisfy both of these needs to only a limited extent.
Transgenic zebrafish that express tyrosine hydroxylase promoter in inner retinal cells

We have generated a transgenic zebrafish line [Tg(Th:GFP)] that expresses green fluorescence proteins (GFP) driven by rat tyrosine hydroxylase (TH) promoter. In zebrafish, the transgene was expressed as early as 16 hr postfertilization (hpf). The first transgene expression was detected in the midbrain. Within a few hours of development, the expression spread to the forebrain and hindbrain. In the retina, the first transgene expression was detected at approximately 40 hpf, at which time a single GFP-positive cell was seen in the ventral-nasal patch of the retina. In late development, GFP spread across the inner retina. GFP was found in retinal cells that expressed TH or phenylethanolamine N-methyl-transferase (PNMT), the first and last enzymes for synthesis of catecholamine, respectively. This suggests that the transgene is expressed in catecholaminergic neurons. Of interest, GFP was also detected in some retinal cells that release gamma-aminobutyric acid. These latter data suggest that the transgene may also be expressed in noncatecholaminergic cells.
Regionally heterogeneous tissue mechanics in cardiac amyloidosis.

Objective. The goal of this study was to examine in vitro tissue stiffness and contractile performance in myocardial amyloidosis.Background. Primary systemic amyloidosis involves the deposition of amyloid protein in mesodermal tissues including the heart. Functional assessment of cardiac amyloidosis is usually performed using echocardiography. However, this technique does not involve assessment of preload-dependent contractile reserve (the Frank-Starling mechanism).Methods. At the time of heart transplantation, isolated myocardial trabeculae were dissected from the right ventricle of a patient with primary systemic amyloidosis. In vitro length-tension experiments were performed and trabeculae were subsequently fixed, sectioned and stained with crystal violet to determine amyloid deposition.Results. Among the nine trabeculae capable of generating force transients, various combinations of myocardial stiffness and contractile performance were observed including normal stiffness and contractility, severely in...
Organizational and Environmental Correlates to Preventive Quality of Care in US Rural Health Clinics

Purpose: To identify organizational and environmental correlates to rural health clinics’ preventive quality of care in the United States. Design: A retrospective observational cohort study design was applied under Donabedian’s Structure-Process-Outcome framework. Three structure measures of care (proportion of nonphysicians, absence of physicians, and provider affiliation) and three measures of process (total clinical visits, prevention use for congestive heart failure and diabetes) were used as explanatory variables. Five environmental correlates were included. The Centers for Medicare and Medicaid Services National Medicare Chronic Care Condition Data Warehouse for 2007 was used to obtain clinical data. Preventive quality of care outcomes were measured through Agency for Healthcare Research and Quality prevention quality indicators. The indicators were risk adjusted for age, sex, race, severity, and comorbidity of patients. Methods: Structural equation modeling with maximum likelihood estimation was us...
The Carina spiral feature: Strömgren-β photometry approach II. Distances and space distribution of the O and B stars

Aims. In recent years a significant development has become evident in the study of the stellar structure of the Galactic disk. This is especially true for the 3rd Galactic quadrant, where the stellar population was extensively investigated beyond 10 kpc, revealing details about the warped geometry of the thin and thick disks and outer arm. The 4th Galactic quadrant offers even better opportunity to follow the distribution of the young stellar populace to a large distance, since the line of sight is parallel to the largest single segment of a spiral arm seen from our position in the Galaxy: the Carina spiral feature. This paper further contributes to the study of the structure of the Galactic disk in the direction of Carina field utilizing homogeneous photometric distances of a sample of about 600 bright early-type stars seen in this direction up to 6 kpc. Methods. The derived stellar distances are based on uvbyβ photometry. All O and B type stars with uvbyβ data presently available are included in the study. Results. The photometry-derived parameters allow us to study the structure and characteristics of this segment of the Carina arm. We find that the stellar distribution is consistent with a location of the apparent edge of the arm at l = 287 ◦ . Toward the edge of the arm the warp of the Galactic plane can be traced up to 6 kpc where it reaches negative 200 pc. The field toward the edge seems to be much more complex than harboring just one OB association, and it is likely that some of the apparent concentrations in this field represent parts of long segments of the edge. In the 284 ◦ ‐289 ◦ longitude range an interarm space about 1 kpc wide is found beyond 850 pc from the Sun. The giant molecular clouds and open clusters do not follow the edge of the arm as defined by the OB stars and indicate a possible presence of an age gradient in a direction perpendicular to the formal Galactic plane.
An Application of the Impact Evaluation Process for Designing a Performance Measurement and Evaluation Framework in K-12 Environments.

This article illustrates the application of the Impact Evaluation Process for the design of a performance measurement and evaluation framework for an urban high school. One of the key aims of this framework is to enhance decision-making by providing timely feedback about the effectiveness of various performance improvement interventions. The framework design process is guided by the Impact Evaluation Process, and included the participation of key stakeholders including administrative and teaching staff who all contributed to the performance measurement and evaluation framework design process. Key performance indicators at the strategic, tactical, and operational levels were derived from the school vision, and linked to specific interventions to facilitate the continuous evaluation and improvement process.