cssi/SciSciGPT-SciSciNet huggingface dataset:
We need a geriatric assessment for oncologists.

Older patients are less likely to receive standard treatments for cancer than similar younger patients. Arti Hurria proposes a specific oncology geriatric assessment, including functional status, comorbid medical conditions, nutritional status, cognitive function, psychological state and social support, and medication review, to pinpoint an individual's functional age and facilitate appropriate care.
Electric Field Controlled, Pulsed Autoionization in Two Electron Wave Packets

In this paper, control of the evolution of a two electron wave packet through the application of a static electric field is demonstrated. Specifically, application of a small electric field is used to produce pulsed autoionization events, the timing of which can be controlled on a picosecond time scale. The technique is demonstrated by exciting calcium atoms using a short-pulsed laser to the 4p(3/2)19d doubly excited state, which is energy degenerate with the 4p(1/2)nk stark states. Evolution of the resultant wave packet is monitored through the application of a second short laser pulse, which stimulates the atoms to emit a photon producing singly excited Rydberg states which are detected using field ionization.
New features for duplicate bug detection

Issue tracking software of large software projects receive a large volume of issue reports each day. Each of these issues is typically triaged by hand, a time consuming and error prone task. Additionally, issue reporters lack the necessary understanding to know whether their issue has previously been reported. This leads to issue trackers containing a lot of duplicate reports, adding complexity to the triaging task. Duplicate bug report detection is designed to aid developers by automatically grouping bug reports concerning identical issues. Previous work by Alipour et al. has shown that the textual, categorical, and contextual information of an issue report are effective measures in duplicate bug report detection. In our work, we extend previous work by introducing a range of metrics based on the topic distribution of the issue reports, relying only on data taken directly from bug reports. In particular, we introduce a novel metric that measures the first shared topic between two topic-document distributions. This paper details the evaluation of this group of pair-based metrics with a range of machine learning classifiers, using the same issues used by Alipour et al. We demonstrate that the proposed metrics show a significant improvement over previous work, and conclude that the simple metrics we propose should be considered in future studies on bug report deduplication, as well as for more general natural language processing applications.
On the CD helix band for long helical polymers.

The CD helix bands for infinitely long helical polymers are shown tobe composed of two parts: a derivative-shaped band plus an ordinary Gaussian-like band. The derivative-shaped band results from the zero-order term of an expansion while the Gaussian-like band results from the first-order expansion term. However, the intensities of the two bands are shown to be of the same order of magnitude. They are both linear in the coulombic coupling of transition charge densities for polymer transitions. The sum yields a skewed derivative-shaped band. The shapes of net CD helix bands are shown to not depend on the approximations used for averaging over orientations if the usual systems, such as polypeptides and polynucleotides, are considered in their long-wave-length spectral regions.
Disulfide Bond Formation of Cysteine-37 and Cysteine-66 of BetaB2 Crystallin During Cataractogenesis of the Human Lens

Abstract BetaB2 crystallin has been prepared from total protein of normal (transparent) and cataractous human lenses. After digestion with endoprotease lys-C, the crude digests were resolved on a C 18 reverse phase column. The lys-C digests of betaB2 crystallin from cataractous lenses consistently showed the presence of a major peptide that was not present in the lys-C digests from normal lenses. Treatment of this peptide with dithiothreitol resulted in the production of two peptides, corresponding to betaB2 crystallin sequences 18–41 and 48–67, containing cysteine-37 and cysteine-66, respectively. The results demonstrated that intramolecular disulfide bonding of these two residues had occurred in vivo. Based upon previous knowledge of the three dimensional structure of betaB2 crystallin, formation of this disulfide bond suggests that significant denaturation of the betaB2 crystallin molecule has occurred during the process of human lens opacification.
The space between the steps: reckoning in an era of reconciliation

For over 100 years the government of Canada operated residential schools for Aboriginal children that required children be taken out of their homes and educated away from their families. These schools became sites of widespread abuse, the legacy of which continues to influence the lives of those who attended and the generations that followed. As Canada moves through a reconciliation process that includes reparation payments, official apologies, and Truth Commissions, this article considers other modalities that happen in the space between the expected flow from apology to reconciliation and resolution. Based on ethnographic fieldwork with the Royal Canadian Mounted Police, this article considers the ways in which a community crime prevention workshop is transformed into a different type of work space as participants engage in problem solving by discussing the role of residential schools in daily life. They do so in meetings with police officers who represent one of the branches of government associated to...
High-affinity binding sites in detergent-solubilized gonadotropin receptors.

Solubilization and characterization of particulate high-affinity gonadotropin receptors derived from the interstitial cell fraction of the rat testis [l-3] , and homogenates of the pseudopregnant rat ovary [4,5], has been performed by extraction with the non-ionic detergents Triton X-l 00, Lubrol PX and Lubrol WX. Binding studies with 1 25 I-labeled hCG have shown that such soluble preparations contain a single class of gonadotropin binding sites, with Ka = 0.6 X 10” M-’ and binding capacity of 0.02 0.13 X 1 O-l2 mol/mg protein [l-4] . The mean affinity constant of the solubilized receptors is significantly lower than that observed in the original particulate receptors (Ka = 2-4 X 10” M-‘) from which the Tritonextracted fraction was prepared. During incubation at 4°C and 34”C, the free or uncharged soluble receptors were found to be relatively unstable, probably due to enzymatic degradation of the gonadotropin binding site. By contrast the formed hormone-receptor complex was much less susceptible to degradation after solubilization, suggesting that the binding sites were stabilized by association with the trophic hormone [2,3,6]. More recently, serial measurement of the binding capacity of solubiked free receptors during storage have revealed the presence of a small proportion of high-affinity receptors with association constant similar to that of the parent preparation. The demonstration and possible significance of these high-affinity sites are described in the present report.
A new species of Satureja (Lamiaceae) from the Chihuahuan Desert region

Satureja maderensis of sect.Gardoquia from the pine-fir forests of the Sierra de la Madera in central Coahuila is described.
The geometrical location of information centers

Abstract The use of geometrical factors to locate information centers for a spatially distributed user population will be shown. The total amount of information for the community of users is considered to be predetermined. A proportion of that information is to be allocated to each information center created. An optimal user versus distance and contents of the center compromise will be obtained using standard mathematical programming techniques. An interesting theoretical situation results for those cases where the “satisfaction benefit” due to quantity of information increases more slowly than the quantity of information. For such cases, the optimal decentralization (or pluralization) is no decentralization at all—a single location results. A case study locating the Mathematics information of a University concludes the work.
Surface engineering with poly(ethylene glycol) photolithography to create high-density cell arrays on glass

This manuscript presents a microfabrication-derived approach for controlling mammalian cell−surface interactions. Poly(ethylene glycol)-diacrylate (PEG-DA) was patterned, in a process analogous to photolithography, to manufacture high-density arrays of micrometer-scale PEG hydrogel wells on glass. Individual wells consisted of PEG walls and glass attachment pads; thus, as a result of the biological inertness of PEG, microwell patterning created a highly ordered biointerface with modulating-cell or protein-repellent properties. Fabricated hydrogel microstrucures proved very effective in guiding and confining adhesion of transformed 3T3 fibroblasts and primary rat hepatocytes to defined regions on the glass substrate. PEG-patterned glass surfaces were selectively modified with collagen (type I) to induce hepatocyte attachment. Localization of the fluorescein-conjugated collagen within the glass attachment pads of PEG hydrogel microwells was visualized by fluorescence microscopy. Further surface analysis was...
A standardized evaluation of psychosocial factors in chronic pain

A number of psychosocial factors are generally considered to be important in exacerbating and maintaining chronic pain problems. However, standardized and reliable methods of evaluating these factors are needed. We have developed such an evaluation system, called the Psychosocial Pain Inventory (PSPI), and have obtained normative data from a large sample of chronic pain patients. Scores on the PSPI were approximately normally distributed and had good inter-rater reliability. Patients with high PSPI scores were more likely to be considered exaggerating their symptoms during their physical examinations, but they did not show less evidence of an organic basis for pain. Significant correlations were obtained between PSPI scores and some measures from the McGill Pain Questionnaire, but scores on the PSPI were essentially unrelated to personality disturbance as measured by the Minnesota Multiphasic Personality Inventory (MMPI). The PSPI and MMPI appear to provide different types of information that can be used in a complementary way in evaluating pain patients. Results of a small pilot study suggest that high scores on the PSPI predict poor response to medical treatment for pain.
Scientific uncertainty and the International Whaling Commission: an alternative perspective on the use of science in policy making

Abstract Prior to the decline of the whaling industry in the 1960s, scientific uncertainty issues often were raised in the International Whaling Commission to argue against lower Antarctic quotas. But by the1970s, many of the same uncertainty issues were being reinterpreted by former whaling nations (and others) as good reasons for adopting a moratorium on all commercial whaling. This article argues that because science is unable to provide certainty, due to fundamental problems in its epistemology, the treatment of scientific advice by policy makers in the commission and elsewhere should be understood in relation to the utility it is believed to provide rather than simple claims of science's ability to provide truth or accuracy about the “real” world.
POSTSCHOOL LEARNING AND HUMAN RESOURCE ACCOUNTING

The central concern of this paper is with the treatment of human resources in dynamic applications of capital and growth accounting. Despite many advances, national accounting conventions still give biased profiles of the economy, but the time is ripe for experimentation with measures that can correct those biases and provide a more adequate base for assessment of long-term economic performance and prospects. In the first section, the logic and feasibility of forward and backward measures of formation of human capital in the simplest case (of full-time schooling) is examined in parallel with physical capital. In a dynamic economy, which is rarely if ever in equilibrium, these approaches complement each other; they are poor substitutes. In section two a number of conceptual and measurement issues are considered with particular reference to human-capital investment periods and the treatment of appreciation, depreciation and obsolescence of human versus physical capital. Here special attention is given to the extended periods of investments in human resources, which overlap with realization of returns, and to the processes and agencies through which postschool investments are made. The last section presents a brief statement concerning asymmetries in disequilibrium biases with respect to the formation of human relative to physical capital. Drawing upon section 1 with regard to forward and backward measures and section 2 with regard to the critical importance of postschool learning, new possibilities in contributions of national accounting to a dynamic analysis of economic development are suggested.
Health of Children 3 to 17 Years of Age With Down Syndrome in the 1997–2005 National Health Interview Survey

OBJECTIVE. This study provides population-based estimates of recent medical conditions, concurrent developmental disorders, and health impact and utilization indicators for US children with and without Down syndrome. METHODS. The sample included children 3 to 17 years of age in the 1997–2005 National Health Interview Survey Child Sample Core and specifically included 146 children with Down syndrome, 604 children with mental retardation but without Down syndrome, and 95 454 children without either condition reported. Developmental and medical conditions, health status, and service use were reported by parents or other knowledgeable caregivers. RESULTS. After adjustment for demographic factors, children with Down syndrome had higher odds, compared with children without mental retardation, of recent food/digestive allergy, frequent diarrhea/colitis, 3 ear infections in the previous year, very recent head/chest cold, and developmental disabilities other than mental retardation. They had increased odds that approached significance for recent seizures, very recent stomach/ intestinal illness, and asthma. They had substantially higher rates (threefold or higher, compared with children without mental retardation) for nearly all health impact and health and special education service use measures. Of note, 25% of children with Down syndrome needed help with personal care, regularly took prescription medications, had recently seen a medical specialist, and received physical therapy or related therapy. The comparison group with mental retardation without Down syndrome represented many children with multiple serious disabilities who also had high rates of medical conditions and high levels of health impact and service use. CONCLUSION. These findings provide empirical, population-based data to inform guidelines for frequent monitoring and support for children with Down syndrome. Pediatrics 2009;123:e253–e260
Case Report: Chlamydia Pneumoniae Pneumonia in an HIV-Infected Man

We report a case of an HIV-infected adult with Chlamydia pneumoniae. Our patient presented with a clinical picture suggestive of Pneumocystis carinii pneumonia (PCP), but did not respond to empiric anti-PCP therapy. The diagnosis was eventually confirmed by bronchoscopy and serology. C. pneumoniae pneumonia should be considered in the differential of pathogens that cause interstitial infiltrates in HIV-infected persons.
Zero-inflated Poisson and binomial regression with random effects: a case study.

Summary. In a 1992 Technometrics paper, Lambert (1992, 34, 1–14) described zero-inflated Poisson (ZIP) regression, a class of models for count data with excess zeros. In a ZIP model, a count response variable is assumed to be distributed as a mixture of a Poisson(λ) distribution and a distribution with point mass of one at zero, with mixing probability p. Both p and λ are allowed to depend on covariates through canonical link generalized linear models. In this paper, we adapt Lambert's methodology to an upper bounded count situation, thereby obtaining a zero-inflated binomial (ZIP) model. In addition, we add to the flexibility of these fixed effects models by incorporating random effects so that, e.g., the within-subject correlation and between-subject heterogeneity typical of repeated measures data can be accommodated. We motivate, develop, and illustrate the methods described here with an example from horticulture, where both upper bounded count (binomial-type) and unbounded count (Poisson-type) data with excess zeros were collected in a repeated measures designed experiment.
Two Closely Related but Distinct Retroviruses Are Associated with Walleye Discrete Epidermal Hyperplasia

Walleye discrete epidermal hyperplasia (WEH) is a hyperproliferative skin disease that is prevalent on adult walleye fish throughout North America. We have identified two retroviruses associated with WEH, designated here as walleye epidermal hyperplasia virus type 1 and type 2 (WEHV1 and WEHV2), that are closely related to one another (77% identity) and to walleye dermal sarcoma virus (64% identity) within the polymerase region. WEHV1 and/or WEHV2 viral DNA was readily detected by PCR in hyperplastic tissue samples, but only low levels of viral DNA were detected in uninvolved skin. Southern blot analysis showed one to three copies of integrated WEHV2 viral DNA in lesions but did not detect WEHV2 viral DNA in uninvolved skin from the same fish. Northern blots detected abundant levels of WEHV1 and/or WEHV2 virion RNA transcripts of approximately 13 kb in hyperplastic tissue, but virion RNA was not observed in uninvolved skin and muscle. These results suggest that WEHV1 and WEHV2 are the causative agents of discrete epidermal hyperplasia.
Object selection by oscillatory correlation

One of the classical topics in neural networks is winner-take-all (WTA), which has been widely used in unsupervised (competitive) learning, cortical processing, and attentional control. With global connectivity WTA networks, however, do not encode spatial relations in the input, and thus cannot support sensory and perceptual processing where spatial relationships are important. We propose a new architecture that maintains spatial relations. This selection network builds on oscillatory dynamics and slow inhibition In an input scene with many objects, the network selects the largest object. The system can be easily adjusted to select several largest objects, which then alternate in time. The network is applied successfully to select the most salient objects in real images.
Environmental literacy, ecological literacy, ecoliteracy: What do we mean and how did we get here?

Numerous scholars have argued that the terms environmental literacy, ecological literacy, and ecoliteracy have been used in so many different ways and/or are so all-encompassing that they have very little useful meaning. However, despite the seemingly arbitrary and, at times, indiscriminate use of these terms, tremendous efforts have in fact been made to explicitly define and delineate the essential components of environmental literacy, ecological literacy, and ecoliteracy, and to firmly anchor their characterizations in deep theoretical and philosophical foundations. A driving purpose behind these ongoing conversations has been to advance complete, pedagogy-guiding, and broadly applicable frameworks for these ideals, allowing for standards and assessments of educational achievement to be set. In this manuscript, we review a diversity of perspectives related to the often nuanced differences and similarities of these terms. A classification of the numerous proposed frameworks for environmental literacy, ec...
On the Modeling of Honest Players in Reputation Systems

The effectiveness of reputation-based trust management fundamentally relies on the assumption that an entitypsilas future behavior may be predicted based on its past behavior. Though many reputation-based trust schemes have been proposed, they can often be easily exploited, as an attacker may adapt its behavior and make the above assumption invalid. In this paper, we build a statistic model for honest entities in decentralized systems, which serves as a profiling tool to identify suspicious entities. It can be combined with existing trust schemes to ensure that they are applied to entities whose transaction records are consistent with the statistic model. This approach limits the manipulation capability of adversaries, and thus can greatly improve the quality of reputation-based trust assessment.
Evolutionary Patterns of Flexible Automation and Performance: A Longitudinal Study

This study presents a longitudinal analysis of patterns of investment in advanced manufacturing technologies AMT and financial performance. Investments in AMT from 112 manufacturing plants in the metal-working industries are examined. Data were collected via a mail survey administered to 202 plants in 1994, and readministered to 112 of the same plants in 1996. This study seeks to fill a void in the area of technology management, which is comprised primarily of cross-sectional studies that do not address the dynamic nature of investments in technology. Four major conclusions are drawn from the data. First, several individual technologies have higher investments in 1996 than in 1994. In particular, electronic mail has the largest increase in investment, a finding that suggests that manufacturing firms are finding ways to take advantage of the exploding potential of electronic communication. Our second conclusion is that plants invest in technology in an incremental fashion over time rather than using an all-or-nothing approach. Plants with low investments follow one of three technology strategies as their investments in AMTs evolve: 1 continued low investment, 2 investment primarily in design-based technologies, or 3 equalized investment in design, manufacturing, and administrative AMTs. Third, analysis of the degree of manufacturing involvement in developing business strategy indicates that plants that have a more proactive role for manufacturing invest greater resources in AMTs. Finally, while AMT investment was not positively associated with performance in a cross-sectional analysis, longitudinal analysis of data collected two years later does reveal a relationship. In short, the analysis supports the proposition that there is a lag between initial investment and resulting performance improvements.
Stigmaphyllon lanceolatum (Malpighiaceae), a New Species from Espírito Santo, Brazil

Abstract. Stigmaphyllon lanceolatum, a new species of Malpighiaceae, is described from Espirito Santo, Brazil. It is distinctive in its abaxially sericeous, lanceolate laminas borne on relatively short petioles. The limb of the posterior petal bears a pair of basal, stout, gland-tipped fimbriae. The stamens are heteromorphic. All styles bear apical folioles. A brief discussion of Stigmaphyllon in Espirito Santo accompanies a key to the thirteen species recorded (and one expected) from that state.
Entropy Coding via Parametric Source Model with Applications in Fast and Efficient Compression of Image and Video Data

In this paper a framework is proposed for efficient entropy coding of data which can be represented by a parametric distribution model. Based on the proposed framework, an entropy coder achieves coding efficiency by estimating the parameters of the statistical model (for the coded data), either via Maximum A Posteriori (MAP) or Maximum Likelihood (ML) parameter estimation techniques.
Meaningfulness and trigram recognition

Recognition, after 1, 3, 6, 15, and 30 intervening events, for CCC and CVC trigrams of low, medium, and high meaningfulness (M) was studied in the Shepard-Teghtsoonian paradigm. Correct recognition varied directly with M and inversely with number of intervening events. False recognition varied inversely with M and increased with total number of presentations. Confidence in correct recognitions varied directly with M and inversely with number of intervening events, but remained stable over the experimental session. Confidence in"new'judgments of new trigrams declined sharply over the experimental session. Evidence is presented to the effect that false recognition is largely item specific and not a matter of general decision criterion. Shepard (1963) has argued that a characteristic of verbal units low in meaningfulness (M) is that they are sequentially unintegrated. Of the two trigrams RZQ and MOP, the former may be viewed as more fractionable than the latter from the point of view of Ss who are faced either with reproducing it in recall or with using it as a stimulus in paired-associate learning. Melton's (1963) intra-unit interference interpretation of forgetting in the short-term memory situation is consistent with Shepard's interpretation of M. A low-M unit is seen to be received in memory as a set of more or less independent elements that in recall must be assembled in the presence of interelement interference. A high-M unit, however, is seen to be received as approximately a single element without internal interference. This interpretation is supported by Murdock's (1961) finding that short-term recall of word
A DExH/D-box protein coordinates the two steps of splicing in a group I intron

Proteins of the DExH/D family are ATPases that can unwind duplex RNA in vitro. Individual members of this family coordinate many steps in ribonucleoprotein enzyme assembly and catalysis in vivo, but it is largely unknown how the action of these co-factors is specified and precisely timed. As a first step to address this question biochemically, we describe the development of a new protein-dependent group I intron splicing system that requires such an ATPase for coordinating successive steps in splicing. While genetic analysis in yeast has shown that at least five nuclear-encoded proteins are required for splicing of the mitochondrial aI5beta group I intron, we show that efficient in vitro splicing of aI5beta occurs with only two of these co-factors and, furthermore, they fulfill distinct functions in vitro. The Mrs1p protein stabilizes RNA structure and promotes the first step in splicing. In contrast, a DExH/D protein, Mss116p, acts after the first step and, utilizing ATP hydrolysis, specifically enhances the efficiency of exon ligation. An analysis of Mss116p variants with mutations that impair its RNA-stimulated ATP hydrolysis activity or reduce its ability to unwind duplexes show that the efficiency of ATP hydrolysis is a major determinant in promoting exon ligation. These observations suggest that Mss116p acts in aI5beta splicing by catalyzing changes in the structure of the RNA/protein splicing intermediate that promote the second step. More broadly, these observations are consistent with a model in which the "functional-timing" of DExH/D-box protein action can be specified by a specific conformation of its substrate due to the "upstream" activity of other co-factors.
Aspects of Quantitative Research in Economic History

If we are successfully to relate our work with the main body of Economic History, we must be able to show the fundamental relationship between quantitative analysis and more conventional methods of economic historians. The historian reconstructs events of the past, and with them attempts to understand the institutions and modes of behavior associated with those events. He seeks to construct a consistent story revealing the fundamental nature and meaning to us of the past, thus creating insight into the past and understanding of it—something considerably beyond a mere account of what probably happened. However, this story must be based upon, and be consistent with, the reconstructed events of the past, “what probably happened.”
Medicaid managed care and the emergency department: The first one hundred days

Spurred by concerns over increasing costs and variable quality, public and private third-party payors are moving their subscribers into managed care plans. A central feature of many of these plans is coordination of patient care through a primary care provider (PCP). In exchange for easy access to the PCP, patients are expected to limit their use of emergency services for episodic, primary, and urgent care problems. The State of Connecticut has begun a transition from a fee-for-service Medicaid plan into a managed care product. Because many Medicaid patients had freely used emergency services under the fee-for-service arrangement, urban teaching hospital emergency departments rapidly became a focus of efforts to control cost and change care-seeking behavior. The Hartford Hospital Emergency Department (ED) began screening, education, and referral of managed Medicaid patients in the fall of 1995 and recorded experiences with patients, administrators, and health care providers involved in the implementation of the managed care program. The first 3 mo following plan implementation were chaotic and frustrating for all parties, with many difficulties due to an unprepared infrastructure. Changes in ED operations and maturation of the payor and health care provider network eventually resulted in a reasonably smooth system accompanied by reductions in ED visit volumes of at least 15%. Continual evolution of role and goals will be necessary if EDs are to maintain an active presence in a health care system dominated by managed care plans.
Multiple-valued CCD circuits

The benefits and current state of the art of charge-coupled-device logic are examined. The fundamentals of CCD logic operations and basic CCD configurations are presented. Programmable logic arrays are considered. The logic design of CCD multivalued logic and its applications are discussed. >
Don't fuel the fire: decreasing intravenous haloperidol use in high risk patients via a customized electronic alert.

Delivering useful clinical decision support to providers who are ordering high risk drugs for high risk patients is imperative for safe pharmacotherapy. This paper presents a focused electronic clinical decision support intervention designed to decrease the risk of corrected QT interval (QTc) related adverse drug events in a high risk patient population. Results showed that a customized alert can both decrease the number of alerts sent to providers while still improving the safety of prescribing practices for intravenous haloperidol. The alert leveraged components of the electronic health record to significantly decrease the rate of inappropriate prescription of intravenous haloperidol in patients with QTc >500 ms from 50% to 14%. The results also suggest providers may abandon the appropriate prescription of a medication in response to an alert. The findings support the necessity of careful targeting of electronic alerts and monitoring for unintended consequences when implementing these types of electronic alerts.
Thyroid stimulating hormone and prolactin responses to thyrotropin releasing hormone in nondepressed alcoholic inpatients.

Abstract Thyroid stimulating hormone (TSH) and prolactin (PRL) responses to thyrotropin releasing hormone (TRH) stimulation are sometimes blunted in alcoholic subjects; however, the mechanisms involved in these phenomena have not been established. We hypothesized that elevations in free thyroid concentrations might be related to these abnormal responses and then tested that hypothesis in a sample of nondepressed alcoholic inpatients ( n = 21). Four alcoholic patients had Δ max TSH responses that were 4 ) and baseline TSH both were significant predictors of peak PRL. The average baseline FT 4 concentration in alcoholic patients was significantly higher than that in healthy control subjects ( n = 10). Our data, thus, suggest that small elevations of FT 4 play a role in the inhibition of TSH and PRL responses to TRH among nondepressed, abstinent alcoholic patients.
Efficient alignment of RNA secondary structures using sparse dynamic programming

Current advances of the next-generation sequencing technology have revealed a large number of un-annotated RNA transcripts. Comparative study of the RNA structurome is an important approach to assess their biological functionalities. Due to the large sizes and abundance of the RNA transcripts, an efficient and accurate RNA structure-structure alignment algorithm is in urgent need to facilitate the comparative study. Despite the importance of the RNA secondary structure alignment problem, there are no computational tools available that provide high computational efficiency and accuracy. In this case, designing and implementing such an efficient and accurate RNA secondary structure alignment algorithm is highly desirable. In this work, through incorporating the sparse dynamic programming technique, we implemented an algorithm that has an O(n3) expected time complexity, where n is the average number of base pairs in the RNA structures. This complexity, which can be shown assuming the polymer-zeta property, is confirmed by our experiments. The resulting new RNA secondary structure alignment tool is called ERA. Benchmark results indicate that ERA can significantly speedup RNA structure-structure alignments compared to other state-of-the-art RNA alignment tools, while maintaining high alignment accuracy. Using the sparse dynamic programming technique, we are able to develop a new RNA secondary structure alignment tool that is both efficient and accurate. We anticipate that the new alignment algorithm ERA will significantly promote comparative RNA structure studies. The program, ERA, is freely available at http://genome.ucf.edu/ERA .
"Do You Want to Be in My Story?": Collaborative Writing in an Urban Elementary Classroom

Based on a year-long interpretive research project, this article describes the arrangements for collaborative writing in an urban elementary classroom. In contrast to typical descriptions of collaboration, this study suggests a more complex view, one that includes a range of ways for students to participate in writing together. This study begins to answer the following questions: What happens when teachers allow students to talk as they write? What does a classroom look like when collaboration is conceptualized as more than a technique, but as a way to understand students as members of a writing community? In this classroom, collaborative writing included the following arrangements: Students wrote alone and shared their work with others; they wrote in pairs or small, consistent groups called networks; and they worked together to author a single text. Brief case studies are used to illustrate each of these types of collaboration. This study describes the ways students responded to opportunities for collabo...
Double C(sp3) dehydrogenation as a route to coordinated Arduengo carbenes: experiment and computation on comparative π-acidity

Reaction of [RuHClL2]2 (L=PiPr3) with the C/C unsaturated cyclic carbene:C(NMeCH)2 produces the 16-electron square-pyramidal RuHCl[CNMeCHCHNMe]L2 by a chloride bridge-splitting reaction. Double H2C(sp3) dehydrogenation of cyclic H2C(NMeCH2)2 is successful for producing the C/C saturated carbene (bound to Ru); the two hydrogens removed are found as RuHCl(H2)L2. In this case, the free carbene is unstable with respect to dimerization to the olefin. The 13C chemical shifts of the carbene carbons of these two complexes, the Ru/C distance, the N–C(carbene) distance, and a variety of reaction energies (from DFT calculations) and calculated atomic charges are generally consistent with these two carbenes, aromatic and non-aromatic, both binding similarly, and with little back donation from this electron-rich center. The 13C chemical shifts are perhaps the most sensitive parameter. Collectively, these results suggest that, if the C/C unsaturated and the C/C saturated Arduengo carbenes differ in their binding to this electron-rich metal center, the difference is at or below detection limits.
Reactive Ion Etching of the fluorinated polyimide film

The etch conditions affecting the etching of the fluorinated polyimide films in RF plasma using oxygen or fluorine-containing oxygen has been investigated. The effect of power, oxygen gas flow rate, and gas composition on the etch rate of fluorinated polyimide have been determined. The etch rate of the fluorinated polyimide increases linearly with the power and oxygen gas flow. The saturation at high oxygen flow rate indicates a saturation or steady state achieved at the polyimide-oxygen reaction interface. However, the etch rate increases when CF4 is added to oxygen, up to about 10% CF4 in O2, and then decreases to a smaller and CF4 concentration independent value. The etch selectivity of hard mask against fluorinated polyimide has been determined. The PECVD silicon nitride and PETEOS are found to be excellent hard mask for pattering these polyimides. The trench profile of the polyimide film also has been examined by patterning and etching the different trench sizes in fluorinated polyimide. It is concluded that this fluorinated polyimide can be etched with oxygen or fluorine containing oxygen plasma.
Chaos and order in exchange rates

This paper asks what accounts for differing levels of exchange rate variance among countries over time. It suggests that the type of political system (i.e., number of policy veto players) is a determinant of policy outcomes in foreign exchange markets. If exchange rate decisions are made by larger groups of actors, we are more likely to witness greater chaos and thus variability in exchange rate outcomes. When we recognise that chaos is part of the background reality of exchange rates, we are more likely to be able to see the order organising it all.
A Novel KCNQ2 Mutation in a Child with Benign Familial Neonatal Seizures and Rolandic Epilepsy

Voltage-gated potassium channel gene mutations in KCNQ2 and KCNQ3 α subunits may result in benign familial neonatal seizure (BFNS). Previous reports have implicated KCNQ2 mutations in patients with BFNS who later developed rolandic epilepsy (RE). We describe an 8-year-old boy with BFNS who developed RE. A three-generation pedigree showed multiple individuals presenting with seizures within the first days of life. Whole exome sequencing in this patient revealed a novel mutation in the KCNQ2 pore region. To our knowledge, this is the first report of BFNS with RE described with a KCNQ2 mutation localizing to the pore domain.
Prostate cancer detection with magnetic resonance-ultrasound fusion biopsy: The role of systematic and targeted biopsies

BACKGROUND The current study was conducted to evaluate the performance of magnetic resonance (MR)-ultrasound-guided fusion biopsy in diagnosing clinically significant prostate cancer (csCaP). METHODS A total of 1042 men underwent multiparametric MR imaging (mpMRI) and fusion biopsy consecutively in a prospective trial (2009-2014). An expert reader graded mpMRI regions of interest (ROIs) as 1 to 5 using published protocols. The fusion biopsy device was used to obtain targeted cores from ROIs (when present) followed by a fusion image-guided, 12-core systematic biopsy in all men, even if no suspicious ROI was noted. The primary endpoint of the study was the detection of csCaP (ie, Gleason score ≥ 7). RESULTS Among 825 men with ≥ 1 suspicious ROI of ≥ grade 3, 289 (35%) were found to have csCaP. Powerful predictors of csCaP were ROI grade (grade 5 vs grade 3: odds ratio, 6.5 [P<.01]) and prostate-specific antigen density (each increase of 0.05 ng/mL/cc: odds ratio, 1.4 [P<.01]). Combining systematic and targeted biopsies resulted in the detection of more patients with csCaP (289 patients) than targeting (229 patients) or systematic (199 patients) biopsy alone. Among patients with no suspicious ROI, 35 (16%) were found to have csCaP on systematic biopsy. CONCLUSIONS In this prospective trial, MR-ultrasound fusion biopsy allowed for the detection of csCaP, with a direct relationship noted with ROI grade and prostate-specific antigen density. The combination of targeted and systematic biopsy detected more csCaP than either modality alone; systematic biopsies revealed csCaP in 16% of men with no suspicious MRI target. The advantages of this new biopsy method are apparent, but issues of cost, training, and reliability await resolution before its widespread adoption. Cancer 2016;122:884–92. © 2016 American Cancer Society.
Anti-TNF-α therapies for the treatment of Crohn's disease: the past, present and future.

ABSTRACTIntroduction: Anti-TNF-α therapy is a novel approach that has transformed the way moderate-to-severe Crohn’s disease (CD) is treated and has significantly improved clinical outcomes of patients with enhanced remission induction and maintenance efficacies. As a result, anti-TNF-α agents have become the primary cost driver in the treatment of CD, as the frequency of hospitalizations and surgical interventions have been drastically reduced.Areas Covered: In the review, the authors cover current anti-TNF-α treatments for CD including efficacy, mechanisms of action, pharmacokinetics and safety. In addition, the authors discuss future anti-TNF-α agents currently in the development pipeline including biosimilars, golimumab, oral AVX-470, TNF-α-kinoid vaccine, and non-biologic HMPL-004.Expert opinion: While new therapeutics are in the pipeline like anti-integrin and anti-interleukin therapeutics, anti-TNF-α therapy remains at the forefront of CD treatment due to its long-term efficacy and safety profiles....
Research and Development of Small Business and Entrepreneurship is the Small Business Advancement National Center

This article' s purpose is to acquaint the reader with the services available at the Small Business Advancement National Center listed in this article you will find information on the SBIDA National Center , Small Business Advancement Network , and long range goals and objectives of the Small Business Advancement National Center , all housed at the University of Central Arkansas in Conway, Arkansas. There is also a brief summary of some of the data collected on a national Small Business Institute survey.
2-D Phase Unwrapping of Noise Contaminated Interferograms

Phase unwrapping of interference patterns is important in many applications such as surface profiling, SAR interferometry and optical interferometry, wavefront compensation in imaging through aberrating media, homomorphic processing and in inverse scattering when using the Rytov approximation. It is usually impossible to impose conditions of continuity on the wavefront to unwrap the interference pattern since wavefront dislocations cannot be avoided. It is necessary to localize these dislocations to the maximum extent possible. In this paper, we identify the use of so-called effective and ineffective zero locations to determine the phase unambiguously in neighborhoods near wavefront dislocations. We also propose a technique to help smooth and reconnect noisy and broken interference fringes, prior to unwrapping.
Growth and casting of horns by pronghorns and exfoliation of horns by bovids.

Growth of horns by mature male pronghorns (Antilocapra ameri- cana) in Montana ceased during August when the stratum germinativum became inactive under mature sheaths. During October after the rut, growth of new horns resumed under the old horns and the stratum germinativum proliferated soft, hairy integument. Annular swellings of this integument at the tops of the bony cores produced hard-keratin tips, which aided in loosening old sheaths that were cast in November. The stratum comeum of the new horn formed a tissue layer that permitted abscission to occur. Histologically, horn formation resembled that of skin. New horns consisted of bony cores approximately 134 millimeters (mm) long covered by gray hairy skin and topped by cones of hard horn 20-25 mm long. During December, rapid differential growth from the thickened integument at the tops of the cores extruded curved horn tips, and frontal prongs began forming approximately 50 mm above horn bases. By February, prongs and hooks were nearly developed. From March through July, hard keratin formed around the cores while skin around the bases of the cores thickened and extruded horny material distally, lengthening the horns. During keratinization, some hair was incorporated into the horn sheaths but the results are no more "hair horns" than those of bovids. Observations of four species of bovids, plus a search of the literature, revealed that at least one species from each of the five subfamilies of Bovidae exfoliate old horns, or outer layers of horns, once or twice during their lives. In those species, new horny material must de- velop under old in a manner similar to early horn growth by pronghorns. Further research is needed on exfoliation by Bovidae. At least six species of bovids possess lacrimal vacuities similar to those of antilocaprids. The diagnostic familial characteristics of Antilocapridae and Bovidae are similar, with the ex- ception of horn formation and casting which are shown here to be more alike than generally thought. Skeletal and dental characters of the earliest known fossils from each family are similar. We feel that reclassification of Antilocapridae to Antilocaprinae, the sixth subfamily of Bovidae, and the present subfamilies Merycodontinae and Antilocaprinae to tribes Merycodontini and Antilocaprini would more accurately reflect the true relationship of antilocaprids to other artiodactyls than does the present system.
Examination of the 3x2 Achievement Goal Model in Collegiate Recreation: Comparison Across Sport Programs

Sport is a central achievement context through which participants’ direct competence-related behavior to achieve desired outcomes. Achievement goal theory provides a framework for understanding self-directed behavior in achievement contexts. Theorists postulate that achievement goals reflect one’s purpose and anticipated outcomes which guide behavior. To assess this psychological construct, several achievement goal measures have been developed, from a dichotomous model (Nicholls, 1989) to the most recent 3x2 model (Elliot, Murayama, & Pekrun, 2011). In the present research, the 3x2 achievement goal model (i.e., task-approach, task-avoidance, self-approach, self-avoidance, other-approach, other-avoidance) was translated for the collegiate recreational sport domain and tested against alternative theoretical models. A questionnaire was developed and administered to recreational sport participants ( N = 614) at a large, post-secondary institution in the United States. Using confirmatory factor analysis (CFA), the researchers found the 3x2 model to provide a better fit than the alternative theoretical models. These findings support the most recent theoretical advancement of the achievement goal construct. Through use of multivariate analysis of variance, significant differences across the six achievement goals were found between intramural and sport club participants. These results have implications for researchers and recreational sport practitioners seeking to measure and understand the motivational differences across sport participants.
THE INFLUENCE OF ACCULTURATION ON CONSUMER BEHAVIOR

Culture is recognized as the most profound influence on consumer behavior.Containing four measures of acculturation dimensions and examining a multi-cultural sample of four ethnic minority consumers in US,this study sets up the Logit model and examines the influence of cultural adaptation on purchase traditional ethnic vegetable.The results indicate significant effects of acculturation on the behaviors of minority consumers.Language,ethnic identity and culture identity,the three measures of acculturation,have highest correlation with the behaviors of minority consumers.Specifically,there is a positive correlation between ethnic identity and consumer behavior;Language and culture identity have negative correlation with consumer behavior.Rather,the relationship between the length of residence and consumption behaviors proves to be irrelevant in this paper.Hence,implications of multi-nationality country's consumer behavior are suggested.