cssi/SciSciGPT-SciSciNet huggingface dataset:
Regulation of androgen receptor levels: implications for prostate cancer progression and therapy.

Androgen deprivation has been the standard therapy for advanced and metastatic prostate cancer for over half a century, as prostate tumors are initially dependent on androgens for growth and survival. Unfortunately, in most patients undergoing androgen ablation, relapse (recurrent tumor growth) eventually occurs. The actions of the principal androgens, testosterone and dihydrotestosterone (DHT), are mediated via androgen receptors (ARs), ligand-activated transcription factors that belong to the nuclear receptor superfamily. Because of the presence of transcriptionally active ARs in tumors from recurrent or androgen-independent disease, there is a heightened interest in new therapeutic paradigms that target the AR and its regulatory pathways. The regulation of AR levels is highly complex with control exerted by several pathways and in a cell-, tissue-, and developmental-stage specific manner. Androgens are important regulators of AR mRNA and protein through transcriptional and post-transcriptional mechanisms. This article reviews the evidence implicating the AR in recurrent prostate cancer and discusses the multiple mechanisms that regulate AR levels in normal and neoplastic cells. The complexity of AR regulation suggests that there will be an ample array of potential new drug targets for modulating levels of this receptor, a key signal ing molecule in prostate cancer.
Criteria for Design and Requalification of Platforms in the Bay of Campeche, Mexico

Risk assessment and management based hurricane and earthquake criteria have been developed for design and requalification of Petroleos Mexicano platforms in the Bay of Campeche. Results from recent field tests were used to verify the loading and capacity analytical models and to characterize the biases and uncertainties in these models. American Petroleum Institute wind and wave loading and earthquake response spectra-based procedures were used to determine the loadings associated with extreme condition hurricanes and earthquakes. Assessment of the platform capacities included recognition of the time-dependent loading and nonlinear platform capacity characteristics. The platform element capacities were based on current American Petroleum Institute working stress design and load and resistance factor design procedures. Design and requalification criteria to evaluate the platform system reserve strength ratios that resulted from the application of the risk assessment and management are summarized in this paper. Working stress design and LRFD parameters are not detailed in this paper due to paper length limitations.
Invasive breast carcinoma: Analysis of dynamic magnetic resonance imaging enhancement features and cell proliferative activity determined by DNA S‐phase percentage

BACKGROUND: There is little information regarding associations between magnetic resonance imaging (MRI) enhancement and biologic parameters of breast carcinoma. A prospective study was undertaken to correlate MRI dynamic contrast enhancement features with cell proliferative activity, as determined by DNA S-phase percentage. METHODS: Seventeen patients with invasive breast cancer underwent MRI at 1.5 tesla using a dynamic gadolinium-enhanced spoiled gradient recall echo technique. DNA analysis of samples of the excised lesions was then performed using flow cytometry. RESULTS: Invasive carcinomas with high DNA S-phase percentages (> or = 6.9%, the median value in this study), a measure of increased cell proliferation, were associated with a peripheral MRI enhancement pattern in 4 of 6 (67%) lesions compared with 0 of 11 carcinomas with lower DNA S-phase percentages (< or = 6.9%) (P = 0.006). There was no significant association between a high DNA S-phase percentage and greater MRI enhancement amplitude, rate, or washout. There was no significant association between aneuploid DNA content and any MRI enhancement feature. CONCLUSIONS: Increased cell proliferation in invasive breast carcinoma, as determined by high DNA S-phase percentage, is significantly associated with a peripheral MRI enhancement pattern but unrelated to greater MRI enhancement amplitude, rate, or washout.
Global statistical tests for comparing multiple outcomes in rheumatoid arthritis trials

Objective To evaluate global statistical tests (GSTs) of treatment effectiveness for rheumatoid arthritis (RA) trials measuring multiple outcomes. Methods Using outcome measures from American College of Rheumatology (ACR) core set variables available in 3 RA trials, GSTs were calculated using the O'Brien ranking procedure and a procedure for binary data. GSTs take correlations among outcomes into account. Power calculations using 1 trial data set provide comparisons of GSTs and ACR criteria for improvement. Results Spearman correlations among outcomes ranged from 0.21 to 0.73. Erythrocyte sedimentation rate had the lowest correlation with other outcomes in all 3 trials. Within a trial, joint swelling and joint tenderness or patient and physician assessment had the highest correlations, depending on the trial. Results were consistent with results using the ACR criteria, although the GST was more powerful. Conclusion GSTs are a useful tool for comparing treatment effects across multiple clinically meaningful outcome measures. The GST allows easy inclusion of validated, reliable new measures that are not a part of ACR criteria, such as quality of life, and can be computed with or without selecting a cutoff point defining patient improvement. GSTs should be considered for rheumatic disease treatment trials.
Synthesis of bi-fluorescence-labeled lactoside: A substrate for continual assay of ceramide glycanase

Abstract A bi-fluorescence labeled derivative suitable for analysis of ceramide glycanase activity was constructed from 4-pentenyl lactoside. Selective modification of the galactosyl residue was attained by formation of 4′,6′-naphthylmethylidene derivative, which was followed by regioselective reductive ring opening. The aglycon was extended by Michael addition of 2-aminoethanetiol, and dansylated at the terminal amino group. Excitation of the naphthyl group results in emission from the dansyl group, while the emission from the naphthyl group is quenched by the dansyl group. Upon digestion with ceramide glycanase, the energy transfer is severed and a decrease in the dansyl emission concommitant with an increase in the naphthyl emission was observed. This substrate was successfully used to analyze ceramide glycanase activity.
Model of peripheral and amblyopic hyperacuity.

Vernier thresholds rise much more rapidly in the periphery than do grating thresholds. A similar dissociation between acuity and hyperacuity has been shown to be present in strabismic but not in anisometropic amblyopia, thus leading to the suggestion that the strabismic fovea is similar to the normal periphery. Here it is shown that a quantitative model for spatial pattern discrimination, which accounts for foveal hyperacuity data, can be extended to encompass both the periphery and amblyopia if appropriate alterations are made. For the periphery it is necessary to increase the size of model receptive fields and to introduce both spatial undersampling and position irregularity (i.e. irregularity in the location of cortical filters). The strabismic fovea also requires spatial undersampling and position irregularity but no change in receptive field size. Defects in the good eye of strabismics can be explained by spatial irregularity. Finally, the anisometropic fovea requires a reduction in mechanism sensitivity but neither spatial undersampling nor position irregularity.
The Association Between Overparenting, Parent-Child Communication, and Entitlement and Adaptive Traits in Adult Children

What is colloquially referred to as “helicopter parenting” is a form of overparenting in which parents apply overly involved and developmentally inappropriate tactics to their children who are otherwise able to assume adult responsibilities and autonomy. Overparenting is hypothesized to be associated with dysfunctional family processes and negative child outcomes. Predictions were tested on 538 parent-young adult child dyads from locations throughout most of the United States. Parents completed a newly developed measure of overparenting as well as family enmenshment, parenting styles, and parent-child communication scales. Young adult children completed measures of parent-child communication, family satisfaction, entitlement, and several adaptive traits. Results showed that overparenting is associated with lower quality parent-child communication and has an indirect effect on lower family satisfaction. Overparenting was also a significant predictor of young adult child entitlement, although it was not related to any of the adaptive traits measured in young adult children.
Institutional Legitimacy, Policy Legitimacy, and the Supreme Court

As they relate to the Supreme Court, institutional legitimacy and policy legitimacy have most frequently been studied in isolation. In this article, a holistic framework is proposed and examined. The political capital hypothesis holds that the Supreme Court can introduce institutional support in its efforts to generate legitimacy for particular policies, but that the Court risks its institutional backing by advancing controversial edicts. Therefore, institutional legitimacy functions as an expendable political capital with which the Supreme Court can confer some increment of policy legitimacy. Two experiments are conducted to test this dynamic, with results providing strong support for the hypothesized process of legitimation.
Influence of Sodium Chloride and Potassium Bicarbonate on Udder Edema and Selected Blood Parameters

Abstract Forty-four first lactation heifers were fed NaCl (23 and 136 g/d) or KHCO 3 (0 and 272g/d) beginning 42 d prepartum and continuing to 10 d postpartum to study the influence of these salts on udder edema and selected blood parameters. Addition of NaCl or KHCO 3 singly to the diet significantly increased the severity of udder edema, but the addition of both salts did not increase edema. Blood samples were collected from the jugular vein at 42 d prepartum and at 1, 3, and 10 d postpartum. Hematocrit and pH were measured on whole blood and osmolarity on serum samples. Concentrations of protein, Ca, Na, K, and Cl in serum were also determined. Serum total proteins were reduced and serum osmolarity was increased in the cows fed NaCl. Blood pH was elevated in the group receiving KHCO 3 . Serum K was higher in groups receiving supplemental KHCO 3 . No differences across dietary treatments were observed in the other parameters. Although addition of NaCl or KHCO 3 to the diet increased the severity of udder edema, the exact mechanism causing edema could not be determined.
Syntactic Maturity of Spontaneous Speech and Elicited Imitations of Hearing-Impaired Children

Two language measures, designed for normal-hearing children, were applied to a sample of 52 severely and profoundly hearing-impaired children between four and 15 years of age. The Developmental Sentence Analysis (Lee, 1974) was used to assess their spontaneous language and the Carrow Elicited Language Inventory (Car-row, 1974a) to assess imitated language. The correlation between scores on the two measures was similar to that found by Carrow (1974b) for normal children (r = .75). However, there was little relation between either measure and reading achievement in hearing-impaired children. A subsample of children retested one year later showed those who remained in a school for the deaf showed greater improvement in their ability to imitate while those who had been integrated into schools with normal-hearing children improved most in spontaneous language. Over half of the hearing-impaired subjects scored below normal hearing three-year-olds on both measures. Caution is advised, however, in applying these ...
Inhibition of the mitochondrial Ca2+ uniporter by pure and impure ruthenium red.

Commercial ruthenium red is often purified by a single recrystallization as described by Luft, J.H. (1971) Anat Rec 171, 347–368, which yields small amounts of material having an apparent molar extinction coefficient of ∼67,400 at 533 nm. A simple modification to the procedure dramatically improves the yield, allowing crystallization to be repeated. Three times recrystallized ruthenium red has an apparent extinction coefficient of ∼ 85,900, the highest value reported to date. Both crude and highly purified ruthenium red can be shown to inhibit reverse activity of the mitochondrial Ca2+ uniporter (uncoupled mitochondria), provided that care is taken to minimize and account for Ca2+ release through the permeability transition pore. Crude ruthenium red is 7–10 fold more potent than the highly purified material in this regard, on an actual ruthenium red concentration basis. The same relative potency is seen against forward uniport (coupled mitochondria), however, the I50 values are 10 fold lower for both the crude and purified preparations. These data demonstrate unambiguously that the energy state of mitochondria affects the sensitivity of the Ca2+ uniporter to ruthenium red preparations, and that both the forward and reverse reactions are subject to complete inhibition. The data suggest, however, that the active inhibitor may not be ruthenium redper se, but one or more of the other ruthenium complexes which are present in ruthenium red preparations.
An Improved Stream Bottom Fauna Sampler

(1961). An Improved Stream Bottom Fauna Sampler. Transactions of the American Fisheries Society: Vol. 90, No. 2, pp. 225-226.
Empirical evaluation of OS endsystem support for real-time CORBA object request brokers

ABSTRACT There is increasing demand to extend Object Request Broker (ORB) middleware to support applications with stringent qualityof service (QoS) requirements. In particular, distributed multimedia applications require efficient and predictable performancefrom the middleware layer and below to deliver necessary end-to-end QoS. Although ORB middleware, such as CORBA,COM+, and Java RMI, offers transparent distribution, the QoS that it can provide depends largely on the support from theunderlying endsystems and networks.This paper provides two contributions to the study of OS endsystem support for real-time ORB middleware. First, weempirically compare and evaluate the suitability of real-time operating systems, VxWorks and LynxOS, and general-purposeoperating systems with real-time scheduling classes, Windows NT, Solaris, and Linux, for real-time ORB middleware. Whileholding the hardware and ORB constant, we systematically vary the OS and measure key platform-specific variations in latency,jitter, operation throughput, and CPU processing overhead. Second, we describe specific areas where these operating systemsmust improve so that ORB middleware will be predictable, efficient, and scalable enough to support the QoS requirements ofmultimedia applications.Our findings illustrate that general-purpose operating systems are not yet suited to meet multimedia applications withstringent QoS requirements. Our results underscore the need for a measurement-driven methodology to (1) provide an empiricalbasis for metrics that are crucial to multimedia computing and (2) to use these metrics to pinpoint and alleviate sources ofpriority inversion and non-determinism in real-time ORB endsystems.Keywords: Real-time Operating System Services, QoS-enabled 00 Middleware
Enantioselective Syntheses of Both Enantiomers of Noranabasamine

Both the R and S enantiomers of the amphibian alkaloid noranabasamine were prepared in >30% overall yield with 80% ee and 86% ee, respectively. An enantioselective iridium-catalyzed N-heterocyclization reaction with either (R)- or (S)-1-phenylethylamine and 1-(5-methoxypyridin-3-yl)-1,5-pentanediol was employed to generate the 2-(pyridin-3-yl)-piperidine ring system in 69−72% yield.
Patterns of failure and toxicity after intensity-modulated radiotherapy for head and neck cancer.

Purpose To determine the outcome of patients treated with intensity-modulated radiotherapy (IMRT) for head and neck cancer. Methods and Materials We reviewed the charts of 100 consecutive patients treated with IMRT for squamous cell carcinoma of the oropharynx (64%), nasopharynx (16%), hypopharynx (14%), and larynx (6%). Most patients were treated with a concomitant boost schedule to 72 Gy. Of the 100 patients, 54 (54%) received adjuvant chemotherapy, mostly concurrent cisplatin. The dosimetry plans for patients with either locoregional failure or Grade 4-5 complications were reviewed and fused over the computed tomography images corresponding with the location of the event. Marginal failures were defined as those that occurred at a region of high-dose falloff, where conventional fields would have provided better coverage. Results The median follow-up of living patients was 3.1 years (range, 1–5.2 years). The 3-year rate of local control, locoregional control, freedom from relapse, cause-specific survival, and overall survival for all patients was 89%, 87%, 72%, 78%, and 71%, respectively. The 3-year rate of freedom from relapse, cause-specific survival, and overall survival for the 64 oropharynx patients was 86%, 92%, and 84%, respectively. Of the 10 local failures, 2 occurred at the margin of the high-dose planning target volume. Both regional failures occurred within the planning target volume. No locoregional failures occurred outside the planning target volume. Of the 100 patients, 8 and 5 had Grade 4 and 5 complications from treatment, respectively. All patients with Grade 5 complications had received adjuvant chemotherapy. No attempt was made to discriminate between the complications from IMRT and other aspects of the patients' treatment. Conclusion Intensity-modulated radiotherapy did not compromise the outcome compared with what we have achieved with conventional techniques. The 2 cases of recurrence in the high-dose gradient region highlight the potential hazard of approaches that involve highly conformal dose distributions.
Notes on Temperature-Dependent Lidar Equations

The temperature dependence of molecular backscatter coefficients must be taken into account when narrowband interference filters are used in lidar measurements. Thus, the spectral backscatter differential cross section of the molecules involved in the backscattering of the radiation has to be calculated or measured and the interference filter transmission efficiency must be known. The present paper is intendedto describe in an easily reproducible manner the procedure involved in calculating the temperature-dependent functions introduced in the lidar equations, including the computation of the differential cross sections for air, nitrogen, and water vapor. The temperature-dependent functions are computed for the Howard University Raman lidar (HURL). The interference filter efficiencies are given by the manufacturer. Error estimates in water vapor mixing ratio and aerosol backscatter ratio involved when temperature-dependent functions are omitted are given for measurements taken with HURL. For the data analyzed, it is found that errors in estimating the water vapor mixing ratio are up to ;6% while in estimating the aerosol backscattering ratio the errors are up to ;1.3% in the planetary boundary layer and ;2.2% in cirrus clouds. Theoretical computations are performed to determine temperature-dependent functions for nitrogen, water vapor, and their ratio, using simulated Gaussian-shaped filters. The goal is to find the optimum combination of different filters that will determine the ratio profiles of the temperature-dependent functions that are either the closest to unity or the least variable. The analyses reveal that quite constant profiles can be obtained for several combinations of the filters.
Tobacco Use and Control in the United States

Tobacco use remains the leading cause of preventable death in the United States despite numerous advances in tobacco prevention and control within the past two decades. Although smoking prevalence rates are declining as a result of these efforts, the Centers for Disease Control and Prevention (CDC) estimates 46 million, or 20.6%, adults in the United States smoke cigarettes. The CDC also estimates 1 in 5 deaths in the United States is attributable to cigarette smoking and that, on average, adult cigarette smokers will die 14 years earlier than nonsmokers. Researchers have unequivocally linked smoking with multiple forms of cancer, cardiovascular diseases, pulmonary diseases, fertility issues, and damaging developmental effects. Additionally, secondhand smoke (SHS), which includes smoke from the end of a burning cigarette, cigar, or pipe, combined with smoke exhaled by the smoker, is also indisputably related to increased risk of lung cancer and heart disease in adults, and ear infections, asthma attacks, respiratory infections, and sudden infant death syndrome in infants and children. The economic costs related to smoking are staggering as well. Smokers spend approximately $83.6 billion on cigarettes and $2.6 billion on smokeless tobacco products annually in the United States. Smoking-related diseases result in more than $96 billion in direct health care costs, while it is estimated that $97 billion is lost in productivity annually. As cigarette smoking has become less socially acceptable in the United States, the tobacco industry has changed their advertising focus to other markets, including developing countries, alternative tobacco products, and targeting younger smokers. Today tobacco can be consumed by methods other than cigarette smoking, including chewing tobacco, moist snuff, snus, pellets, electronic cigarette devices, cigar and pipe smoking, and hookah use. Many of these alternative products are being targeted at younger smokers who are the most susceptible to marketing and advertising strategies.
A Food Systems Approach To Healthy Food And Agriculture Policy

Food has become a prominent focus of US public health policy. The emphasis has been almost exclusively on what Americans eat, not what is grown or how it is grown. A field of research, policy, and practice activities addresses the food-health-agriculture nexus, yet the work is still often considered "alternative" to the mainstream. This article outlines the diverse ways in which agriculture affects public health. It then describes three policy issues: farm-to-school programming, sustainability recommendations in the Dietary Guidelines for Americans, and antibiotic use in animal agriculture. These issues illustrate the progress, challenges, and public health benefits of taking a food systems approach that brings together the food, agriculture, and public health fields.
Social Science and School Desegregation: Did We Mislead the Supreme Court?

During the deliberations prior to its school desegregation decision in 1954 the Supreme Court had before it a Social Science Statement on the effects of segregation and desegregation. This article reassesses the quality of that Statement 25 years later. Key points in the Statement are compared to the results of subsequent research. Some points, e.g., no negative effect on the school achievement of white students, have been supported. Others, e.g., improvement in black self-esteem, are difficult to evaluate due to inconsistent and uninterpretable research findings. Still others, e.g., more favorable racial attitudes, cannot be compared to the research findings because desegregation was not carried out in accord with conditions that were specified as conducive to the outcomes predicted in the Statement. Much research effort has been wasted in the study of school desegregation conducted under conditions unknown to the investigator. In order to avoid such waste in the future it is suggested that investigators...
Comparing Adherence to Two Different HIV Antiretroviral Regimens: An Instrumental Variable Analysis

The objective of this observational cohort study was to compare adherence to protease inhibitor (PI)-based regimens or non-nucleoside reverse transcriptase inhibitor (NNRTI)-based regimens. HIV-seropositive, antiretroviral-naive patients initiating therapy between 1998 and 2006 were identified using Veterans Health Administration databases. First-year adherence ratios were calculated as proportion of days covered (PDC). Multivariable regressions were run with an indicator for PDC >95, 90, 85, and 80 % as the dependent variable and an indicator for a PI-based regimen as the key independent variable. We controlled for residual unmeasured confounding by indication using an instrumental variable technique, using the physician's prescribing preference as the instrument. Out of 929 veterans on PI-based and 747 on NNRTI-based regimens, only 19.7 % of PI patients had PDC >80 %, compared to 35.1 % of NNRTI patients. In multivariable analysis, starting a PI regimen was significantly associated with poor adherence for all 4 adherence thresholds using conventional regressions and instrumental variable methods.
The Surprising Power of Neighborly Advice

Two experiments revealed that (i) people can more accurately predict their affective reactions to a future event when they know how a neighbor in their social network reacted to the event than when they know about the event itself and (ii) people do not believe this. Undergraduates made more accurate predictions about their affective reactions to a 5-minute speed date (n = 25) and to a peer evaluation (n = 88) when they knew only how another undergraduate had reacted to these events than when they had information about the events themselves. Both participants and independent judges mistakenly believed that predictions based on information about the event would be more accurate than predictions based on information about how another person had reacted to it.
Enhancing malware detection in an IM environment

As Instant Messaging (IM) becomes the favorite means of personal and work-related communications, the attacks exploiting vulnerabilities in IM will increase in frequency. Although some attacks employ well known strategies used in attacks on other communication systems, many are newly developed to exploit the properties unique to IM. In this paper, we present a new enhancement in controlling virus infections in IM systems. The new method is effective and easy to implement.
The Liberal Future of Relational Feminism: RobinWest's Caring for Justice

Robin West. Caring for Justice. New York: New York University Press, 1997. Pp. 356. Robin West is one of the most prolific1 and creative members of the legal academy. Her distinctive voice, as expressed in several books and numerous scholarly articles, informs and shapes debates within such diverse areas as constitutional theory (West 1990b; West 1994), feminist jurisprudence (West 1987; West 1988), and law and literature (West 1993). Indeed, some of her early articles concerning feminist jurisprudence (West 1987, West 1988) are now "classics" in a relatively new field of inquiry and appear in virtually every anthology or textbook in the field (Bartlett and Kennedy 1991, 201; Becker, Bowman, and Torrey 1994, 90; Fineman and Thomadsen 1991, 115; Frug 1992, 807; Smith 1993, 493; Weisberg 1993, 75; Weisberg 1996, 162). Such articles continue to inspire a rich body of both sympathetic and critical work by feminists and other scholars.
Challenges for the Collective Defense of Democracy on the Tenth Anniversary of the Inter‐American Democratic Charter

This article examines contemporary sources of democratic crisis and the international responses to these crises from 1990 to 2011. The analysis is based on an original dataset of five domestic sources of democratic crisis: classic military coup or coup attempt, incumbent leaders, intragovernmental clashes between branches of government, armed nonstate actors, and unarmed nonstate actors including societal mass protests and blockades. Several trends are identified. The newest sources of democratic crises include nonstate actors and intragovernmental disputes resulting in constitutional crises; threats from incumbents are persistent over the entire time period; despite a decline in classic military coups since 1990, the Inter-American Democratic Charter does not appear to have made a difference in preventing coups; the participation of rebellious military or police units in challenging civilian leaders presents a continued challenge from the armed forces in new guises; and many contemporary democratic crises include multiple actors and behaviors. This article offers explanations for the weak capacity of the international community to prevent democratic tensions from erupting into full-blown crises or the undermining of democratic obligations by government, despite strong commitments in the form of international charters and protocols, and offers policy suggestions to strengthen that capacity. Este articulo examina los origenes contemporaneos de las crisis democraticas y sus respuestas internacionales entre 1990 y 2011. El analisis se basa en un conjunto de datos originales sobre cinco fuentes internas de crisis democratica: golpe militar clasico o intentona golpista, lideres involucrados, choques intra-gubernamentales entre ramas de gobierno, actores armados no estatales y actores no armados incluyendo protestas sociales masivas y bloqueos. Se identifican varias tendencias. Las nuevas razones de las crisis democraticas incluyen actores no estatales y disputas intra-gubernamentales que resultan en crisis constitucionales; las amenazas provenientes de lideres en disputa son persistentes durante todo el periodo; a pesar de una declinacion en los clasicos golpes militares desde 1990, la Carta Democratica Inter-Americana no parece haber hecho la diferencia en prevenir golpes; la participacion de unidades rebeldes de militares o policias desafiando a los lideres presenta un desafio persistente de las fuerzas de seguridad bajo una nueva forma; muchas de las crisis contemporaneas incluyen multiples actores y comportamientos. El articulo ofrece explicaciones de la debil capacidad de la comunidad internacional para prevenir tensiones democraticas que se convierten en crisis de gran escala o la erosion en
Haplotype phasing using semidefinite programming

Diploid organisms, such as humans, inherit one copy of each chromosome (haplotype) from each parent. The conflation of inherited haplotypes is called the genotype of the organism. In many disease association studies, the haplotype data is more informative than the genotype data. Unfortunately, getting haplotype data experimentally is both expensive and difficult. The haplotype inference with pure parsimony (HPP) problem is the problem of finding a minimal set of haplotypes that resolve a given set of genotypes. We provide a quadratic integer program (QIP) formulation for the HPP problem, and describe an algorithm for the HPP problem based on a semi-definite programming (SDP) relaxation of that QIP program. We compare our approach with existing approaches. Further, we show that the proposed approach is capable of incorporating a variety of additional constraints, such as missing or erroneous genotype data, outliers etc.
Therapeutic developments in matrix metalloproteinase inhibition

A family of zinc-dependent endopeptidases called matrix metalloproteinases (MMPs) have the capacity to degrade all elements of the extracellular matrix (ECM) and are required for homeostatic maintenance of the ECM. However, interest in MMPs predominantly arises from the accumulating evidence implicating that dysregulated MMP expression plays a role in mediating or accompanying a diverse array of pathologies. These include tumour invasion and metastasis and inflammatory diseases characterised by excessive tissue destruction, such as arthritis, periodontal disease, atherosclerosis, plaque rupture, arterial aneurysms, postmyocardial infarction, ventricular remodelling and cardiac rupture. Several patents representing therapeutic drugs and strategies to treat the associated conditions have been claimed, some resulting in clinical drug trials. This review will: i) summarise the current status of our understanding of MMPs and how they participate in normal and functional ECM degradation; ii) review therapeutic ...
Evolution and phylogeny of gonad morphology in bony fishes.

SYNOPSIS. Gonad morphology at the gross anatomical or histological levels has long been studied by fisheries biologists to identify annual reproductive cycles and length of breeding season, among other goals. Comparative surveys across vertebrate taxa have not been detailed enough, however, to describe fully the differences and similarities among gonads of bony fishes and other vertebrates, and to use gonad morphology in phylogenetic systematic analyses. An emerging constant among vertebrates is the presence of a germinal epithelium composed of somatic and germ cells in both males and females. In females, the germinal epithelium lines the ovarian lamellae. In males, arrangement of the germinal epithelium into compartments varies among osteichthyans: basal taxa have an anastomosing tubular testis, whereas derived taxa have a lobular testis. The lobular testis is proposed as a synapomorphy of the Neoteleostei. The annual reproductive cycle is hypothesized to be the source of morphological variation among testis types. Elongation of germinal compartments during early maturation may result in a transition from anastomosing tubular to lobular testes. In all male atherinomorphs surveyed, spermatogonia are restricted to the distal termini of lobules rather than being distributed along the lobule; there is an epithelioid arrangement of Sertoli and germ cells rather than a germinal epithelium. Arrest of the maturation-regression phases is hypothesized to lead to formation of the atherinomorph testis. Atherinomorphs also have a distinctive egg with fluid, rather than granular, yolk. Variation among germinal epithelia is interpreted in a developing phylogenetic framework to understand evolution of gonad morphology and to propose gonad characters for phylogenetic analyses.
Perspectives on reproductive and developmental toxicity.

Human reproduction and development is a cycle of interdependent events. Virtually all of its phases have been shown to be the primary target of one or more non-mutagenic exogenous agents (Table 1). Such agents interfere with certain of the countless epigenetic or ontogenic events essential for normal completion of the cycle. Mutagens disrupt this cycle at some points, but the overwhelming majority of reproduc tive and developmental toxins are not mutagenic.As in all aspects of toxicology, the reproductive and developmental effects of chemicals are determined by the intrinsic nature of the chemical, the quantity of the chemical exposure, the duration of exposure and the stage of the cycle at which it occurs. Signs of repro ductive toxicity range from reduced fertility to spontaneous abortion. Adverse effects on the conceptus are categorized as functional deficits, developmental retardation, structural abnormality and death. One or more of these is anticipated to occur as a result of excess exposure to most...
Laparoscopic ultrasonographic appearance of the common bile duct mucosa: a predictor of choledocholithiasis.

Previously we reported on the use of laparoscopic ultrasonography in detecting common bile duct stones during laparoscopic cholecystectomy. The aim of this study is to describe the laparoscopic ultrasonographic appearance of the common bile duct mucosa in patients with choledocholithiasis. Medical records of 44 patients with an increased risk for common bile duct stones undergoing laparoscopic cholecystectomy between 1993 and 1998 were reviewed. In the operating room, the laparoscopic ultrasonographic appearance of the common bile duct mucosa was scored in real time as normal, mild changes (hyperechoic mucosa), or severe changes (hyperechoic with mucosal thickening). Of the 31 patients (70%) with stones or sludge in the biliary tree, 29 (94%) had either severe (58%) or mild (36%) hyperechoic and 2 (6%) had normal-appearing common bile duct mucosa on laparoscopic ultrasonography. Of the 13 patients (30%) with no documented stones or sludge, 11 (85%) had normal and 2 (15%) had mild hyperechoic common bile duct mucosa on laparoscopic ultrasonography. Both of these patients had laboratory values indicating recent passage of common bile duct stones. The association between common bile duct stones and the presence of hyperechoic common bile duct mucosa was statistically significant (P < .0001, Fisher's exact test). This is the first report of hyperechoic common bile duct mucosa demonstrated by laparoscopic ultrasonography as a predictor of common bile duct stones. This finding is evident in the majority of patients with common bile duct stones and also may be associated with recent passage of a stone into the duodenum.
Measurement of Earth Medium Electrical Characteristics: Techniques, Results, and Applications

An overview of measurement techniques, measurement results, and factors influencing the conductivity and dielectric constant of earth medium is given. Application of these measurement techniques to geophysical investigations is also discussed.
In Situ Electrochemical Transmission Electron Microscopy for Battery Research

The recent development of in-situ liquid stages for (scanning) transmission electron microscopes now makes it possible for us to study the details of electrochemical processes under operando conditions. As electrochemical processes are complex, care must be taken to calibrate the system before any in-situ/operando observations. In addition, as the electron beam can cause effects that look similar to electrochemical processes at the electrolyte/electrode interface, an understanding of the role of the electron beam in modifying the operando observations must also be understood. In this paper we describe the design, assembly, and operation of an in-situ electrochemical cell, paying particular attention to the method for controlling and quantifying the experimental parameters. The use of this system is then demonstrated for the lithiation/delithiation of silicon nanowires.
Particle export and the biological pump in the Southern Ocean

The organic carbon particle export to the interior layers in the Southern Ocean in the New Zealand–Tasmania Sector was approximately 170 mmolC m−2 yr−1. The export of particulate inorganic carbon in CaCO3 was 110 mmolC m−2 yr−1 and was contributed mostly by pteropods shells in the Antarctic Zones. The Si flux from biogenic opal at the sub-Antarctic Zone was 67 mmolSi m−2 yr−1 and rapidly increased to the south up to nearly 1 molSi m−2 yr−1 in the Antarctic Zone. The Antarctic Polar Front clearly demarcated the area where the biological pump was driven by CaCO3 to the north and biogenic SiO2 particle export to the south. Summer stratification caused by the sub-zero winter water layer in the Seasonal Ice Zone (SIZ) curtails the zooplankton community and hinders the replenishment of Fe. This hypothesis explains the large organic carbon export with large f- and export ratios at the SIZ and extremely large opal production at the Antarctic Circumpolar Zone. Estimated regeneration rate of CO2 from the export production and settling particulate fluxes of organic carbon in the water column between 100 m to 1 km was about 13 mmolC m−2 d−1 in the Antarctic Zone and Polar Frontal Zone.
Retrieving reflections by source-receiver wavefield interferometry

Source-receiver wavefield interferometry has been proposed recently as an extension of classical correlation-based interferometry. Under idealized assumptions, it allows the Green's function between a source and a receiver to be reconstructed from boundary data that are collected using two closed contours of sources and receivers, respectively. An intuitive geometric description of this method, based on ray theory, can be used to design a method for reconstructing virtual-gather events that typically are lost when conventional interferometry is employed. In classical interferometry, events in the Green's function between two receiver locations are reconstructed by automatically finding a ray that emanates from a stationary source, passes through the virtual source, reflects off the structure, and finally is recorded by the second receiver. The common path to both receivers is then canceled by a suitable crosscorrelation. If illumination of the structure is not ideal, such a ray may not exist and the reflection is not reconstructed. Source-receiver wave interferometry can be given a similar geometric description. The reflection off the structure can be constructed using not one but multiple rays produced simultaneously by two stationary sources. This new redatuming technique proves successful in geometries in which classical interferometry fails. Extensive numerical simulations support these theoretical conclusions.
Derivative analysis of hyperspectral data for detecting spectral features

A derivative algorithm was adapted to deal with spectral data acquired in narrow, continuous bands as truly spectrally continuous data. An investigation on intelligently detecting spectral features from a synthetic spectrum and a laboratory vegetation spectrum demonstrated the use of derivative algorithm in extraction of subtle information at different spectral scales of interest.
Intersexual spatial relationships in a lekking species: blue-crowned manakins and female hot spots

Leks offer an intriguing evolutionary problem: why do males aggregate when this apparently leads to fitness costs? Aggregation costs can be balanced if males settle on patches where they are more likely to encounter females (hot-spot hypothesis). We evaluated whether female hot spots can account for patterns of lek structure in the blue-crowned manakin (Lepidothrix coronata) by modeling female distribution patterns relative to lek locations in two 100-ha plots. Individual females were mapped based on nest locations and capture points and had their home ranges (HRs) modeled based on radiotelemetry data. The number of females that lekking males can be expected to encounter was estimated as the number of individual female HRs overlapping each male territory; hot spots were defined as patches where more females are found than average. We investigated how changes in female HR size and devaluation effects (decrease in female availability due to the presence of neighboring males) influence male access to females. Both factors strongly influenced the expected rates of female encounter, but the hot-spot hypothesis was not supported: most male territories consistently overlapped fewer or just as many female HRs as expected by chance. Leks were not closer to hot spots than similar-sized nonlek sites. A proportion of males were, indeed, settled at hot spots, but, contrary to predictions of the hot-spot hypothesis, they belonged to smaller leks than males located outside hot spots. Our results indicate that this lack of spatial correlation between males and females results partly from differences in sex-specific habitat preferences.
Software product line engineering for Web services and UML

Summary form only given. A software product line consists of a family of software systems that have some common functionality and some variable functionality. A better understanding of the product line can be obtained by considering the different perspectives, such as requirements modeling, static modeling, and dynamic modeling. This paper describes a multiple view UML based product line modeling approach for modeling software product lines based on Web services.
Cell-type-specific proteome and interactome: using HIV-1 Tat as a test case

HIV-1 is a small retrovirus that wreaks havoc on the human immune system. It is a puzzle to the scientific community how a virus that encodes only nine proteins can take complete control of its host and redirect the cell to complete replication or maintain latency when necessary. One way to explain the control elicited by HIV-1 is through numerous protein partners that exist between viral and host proteins, allowing HIV-1 to be intimately involved in virtually every aspect of cellular biology. In addition, we postulate that the complexity exerted by HIV-1 can not merely be explained by the large number of protein-protein interactions documented in the literature but, rather, cell-type-specific interactions and post-translational modifications of viral proteins must be taken into account. We use HIV-1 Tat and its influence on viral transcription as an example of cell-type-specific complexity. The influence of post-translational modifications (acetylation and methylation), as well as subcellular localization on Tat binding partners, is also discussed.
The second axillary in Hymenoptera

The wing base of basal hymenopterans (Insecta) have never been properly described perhaps due to the difficulties of its visualization and understanding the 3D relationships between wing base components. Novel 3D visualization techniques such as microCT and Confocal Laser Scanning Microscopy (CLSM) allow us to provide easily digestible morphological data. The wing base of four basal Hymenoptera and 10 apocritan species have been imaged with CLSM and dissected under a stereomicroscope. The second axillary is composed of two sclerites (on the dorsal wing membrane and one on the ventral in Macroxyela, Xyela and Athalia whereas it is represented by a single sclerite traversing the wing in other Hymenoptera. Consequences related to this observation as well are drawn and future directions in Hymenoptera wing base studies are provided.
Intuitionism versus degrees of truth

L'avantage de la logique intuitionniste sur la logique classique et la theorie des degres de verite comme logique du vague, reside dans le fait qu'elle n'a pas besoin d'imposer des criteres de demarcation des termes vagues. Discussion de G. Rea, " Degrees of Truth versus Intuitionism " (ibid, 1989, vol. 49, pp. 31-32)
Illumination by translates of convex sets

Let S be a compact set in the plane. If every three points of S are illuminated clearly by some translate of the compact convex set T, then there is a translate of T which illumines every point of S. Various analogues hold for translates of flats in Rdas well.
Exercise: Great for Heart Health, Just as Great for Cardiac Preconditioning Research

Ischemic heart disease remains a leading cause of morbidity and mortality in the United States and other industrialized countries [1]. Ongoing research efforts within the biomedical science community seek to discover counter therapies that will mitigate ischemic damage in those with coronary artery disease. Candidate therapies are intended to invoke cardioprotection by pharmacologic activation of endogenous mechanisms of cellular protection [2]. In concept the process of pharmacologic development is fundamentally simple: a cardioprotective pathway against ischemic injury is discovered, animal-based experiments provide proof of concept for pharmacologic induction of cardioprotection, and then clinical trials are undertaken. The reality, however, is somewhat more complicated. Within the context of discovery at different organizational levels (isolated cells, isolated organs, whole animal), numerous cellular pathways that elicit robust cardioprotection against ischemic injury are now well characterized [3]. Translation of this knowledge into clinical practice has proven far more difficult than expected. The point is famously articulated in a 2004 position paper by preeminent physicians and scientists is Circulation Research, “over the past 30 years, hundreds of experimental interventions (both pharmacologic and nonpharmacologic) have been reported to protect the ischemic myocardium in experimental animals; however, with the exception of early reperfusion, none has been translated into clinical practice” [4]. Given the collective effort to date, this is the central question: What scientific breakthrough is needed to translate our understanding of cardiac preconditioning into clinical practice? The underlying premise of this editorial is that the major limitation of cardiac preconditioning research is the nature of the stimulus, which traditionally has been derived from ischemia-induced adaptations.