cssi/SciSciGPT-SciSciNet huggingface dataset:
Identification of a Nonsense Mutation in CWC15 Associated with Decreased Reproductive Efficiency in Jersey Cattle

With the recent advent of genomic tools for cattle, several recessive conditions affecting fertility have been identified and selected against, such as deficiency of uridine monophosphate synthase, complex vertebral malformation, and brachyspina. The current report refines the location of a recessive haplotype affecting fertility in Jersey cattle using crossover haplotypes, discovers the causative mutation using whole genome sequencing, and examines the gene’s role in embryo loss. In an attempt to identify unknown recessive lethal alleles in the current dairy population, a search using deep Mendelian sampling of 5,288 Jersey cattle was conducted for high-frequency haplotypes that have a deficit of homozygotes at the population level. This search led to the discovery of a putative recessive lethal in Jersey cattle on Bos taurus autosome 15. The haplotype, denoted JH1, was associated with reduced fertility, and further investigation identified one highly-influential Jersey bull as the putative source ancestor. By combining SNP analysis of whole-genome sequences aligned to the JH1 interval and subsequent SNP validation a nonsense mutation in CWC15 was identified as the likely causative mutation underlying the fertility phenotype. No homozygous recessive individuals were found in 749 genotyped animals, whereas all known carriers and carrier haplotypes possessed one copy of the mutant allele. This newly identified lethal has been responsible for a substantial number of spontaneous abortions in Jersey dairy cattle throughout the past half-century. With the mutation identified, selection against the deleterious allele in breeding schemes will aid in reducing the incidence of this defect in the population. These results also show that carrier status can be imputed with high accuracy. Whole-genome resequencing proved to be a powerful strategy to rapidly identify a previously mapped deleterious mutation in a known carrier of a recessive lethal allele.
Too cool for school?: The effects of gamification in an advanced interdisciplinary course

Gamification is a subject of a great deal of conversations and advocates believe that the familiarity of gaming to the current student population gives it considerable potential to transform teaching and learning. The research literature presents a more ambiguous view and it remains to be seen whether or not gamifying instruction can significantly strengthen student learning outcomes. This question forms the basis of the current study, which focuses on an extensive gamification exercise applied in an upper-division interdisciplinary course. To phrase it colloquially, this research asks whether or not gamification is too cool for school.
An Early Stage of Membrane Fusion Mediated by the Low pH Conformation of Influenza Hemagglutinin Depends upon Membrane Lipids

While the specificity and timing of membrane fusion in diverse physiological reactions, including virus–cell fusion, is determined by proteins, fusion always involves the merger of membrane lipid bilayers. We have isolated a lipid-dependent stage of cell–cell fusion mediated by influenza hemagglutinin and triggered by cell exposure to mildly acidic pH. This stage preceded actual membrane merger and fusion pore formation but was subsequent to a low pH–induced change in hemagglutinin conformation that is required for fusion. A low pH conformation of hemagglutinin was required to achieve this lipid-dependent stage and also, downstream of it, to drive fusion to completion. The lower the pH of the medium applied to trigger fusion and, thus, the more hemagglutinin molecules activated, the less profound was the dependence of fusion on lipids. Membrane-incorporated lipids affected fusion in a manner that correlated with their dynamic molecular shape, a characteristic that determines a lipid monolayer's propensity to bend in different directions. The lipid sensitivity of this stage, i.e., inhibition of fusion by inverted cone–shaped lysophosphatidylcholine and promotion by cone-shaped oleic acid, was consistent with the stalk hypothesis of fusion, suggesting that fusion proteins begin membrane merger by promoting the formation of a bent, lipid-involving, stalk intermediate.
Composite Primary Neuronal High-Content Screening Assay for Huntington's Disease Incorporating Non-Cell-Autonomous Interactions

Huntington's disease (HD) is a fatal neurodegenerative disease characterized by progressive cognitive, behavioral, and motor deficits and caused by expansion of a polyglutamine repeat in the Huntingtin protein (Htt). Despite its monogenic nature, HD pathogenesis includes obligatory non-cell-autonomous pathways involving both the cortex and the striatum, and therefore effective recapitulation of relevant HD disease pathways in cell lines and primary neuronal monocultures is intrinsically limited. To address this, the authors developed an automated high-content imaging screen in high-density primary cultures of cortical and striatal neurons together with supporting glial cells. Cortical and striatal neurons are transfected separately with different fluorescent protein markers such that image-based high-content analysis can be used to assay these neuronal populations separately but still supporting their intercellular interactions, including abundant synaptic interconnectivity. This assay was reduced to practice using transfection of a mutant N-terminal Htt domain and validated via a screen of ~400 selected small molecules. Both expected as well as novel candidate targets for HD emerged from this screen; of particular interest were target classes with close relative proximity to clinical testing. These findings suggest that composite primary cultures incorporating increased levels of biological complexity can be used for high-content imaging and "high-context" screening to represent molecular targets that otherwise may be operant only in the complex tissue environment found in vivo during disease pathogenesis.
Chronic and intermittent hypoxia differentially regulate left ventricular inflammatory and extracellular matrix responses.

We evaluated the left ventricle (LV) response to hypoxia by comparing male Sprague Dawley rats exposed for 7 days to normoxia (control; n=18), chronic sustained hypoxia (CSH; n=12) and chronic intermittent hypoxia (CIH; n=12). Out of the 168 inflammatory, extracellular matrix and adhesion molecule genes evaluated, Ltb, Cdh4, Col5a1, Ecm1, MMP-11 and TIMP-2 increased in the LV (range: 87–138%), whereas Tnfrsf1a decreased 27%, indicating an increase in inflammatory status with CSH (all P<0.05). CIH decreased Ltb, Spp1 and Ccl5 levels, indicating reduced inflammatory status. While Laminin β2 gene levels increased 123%, MMP-9 and fibronectin gene levels both decreased 74% in CIH (all P<0.05). Right ventricle/body weight ratios increased in CSH (1.1±0.1 g g−1) compared with control (0.7±0.1 g g−1) and CIH (0.8±0.1 g g−1; both P<0.05). Lung to body weight increased in CSH, while LV/body weight ratios were similar among all three groups. With CIH, myocyte cross sectional areas increased 25% and perivascular fibrosis increased 100% (both P<0.05). Gene changes were independent of global changes and were validated by protein levels. MMP-9 protein levels decreased 94% and fibronectin protein levels decreased 42% in CIH (both P<0.05). Consistent with a decreased inflammatory status, HIF-2α and eNOS protein levels were 36% and 44% decreased, respectively, in CIH (both P<0.05). In conclusion, our results indicate that following 7 days of hypoxia, inflammation increases in response to CSH and decreases in response to CIH. This report is the first to demonstrate specific and differential changes seen in the LV during chronic sustained and CIH.
Effects of Forage Quality Restrictions on Optimal Production Systems Determined by Linear Programming

consideration of intake restrictions will change the optimal LP forage production system, livestock grazaData presented indicate the upper limits of dry matter ing system or supplemental feeding strategies when consumption possible where cattle are receiving a balanced diet. Dry matter intake will be considerably less than forages are an important nutrient source. indicated limits where nutrients such as protein, phosphorous As forage quality declines, cow intake restricor vitamin A are deficient [2, 4]. tions become more critical. Just how critical depends on weaning weights of calves, timing of the calving FIGURE 1. RELATIONSHIP BETWEEN PERCENT period within the year, and quality and quantity DIGESTIBLE DRY MATTER AND characteristics of alternative forages and supplemental DAILY DRY MATTER INTAKEa
Detection of physiologically active compounds using cell-based biosensors

Cell-based biosensors are portable devices that contain living biological cells that monitor physiological changes induced by exposure to environmental perturbations such as toxicants, pathogens or other agents. Methods of detecting physiological changes include extracellular electrical recordings, optical measurements, and, in the future, functional genomics and proteomics. Several technical developments are occurring that will increase the feasibility of cell-based biosensors for field applications; these developments include stem cell and 3D culture technologies. Possible scenarios for the use of cell-based biosensors include broad-range detectors of unknown threat agents and functional assessment of identified agents.
Ferromagnetic exchange, spin-orbit coupling and spiral magnetism at the LaAlO3/SrTiO3 interface

The interface between two non-magnetic band insulators, LaAlO3 and SrTiO3, can exhibit conductivity, superconductivity and magnetism. These interfacial phenomena can be reconciled by a theory that predicts a spiral magnetic ground state.
The Deflection and Division of an Oceanic Baroclinic Jet by a Coastal Boundary: A Case Study in the Alboran Sea

Abstract An oceanic baroclinic jet impinging on a coastal boundary represents a particular type of ocean–coast interaction. This specific oceanographic phenomenon is an example of the stagnation in line flows occurring in fluid dynamics with three additional features: rotation, stratification, and a sloping boundary. In this study the authors describe the density, vorticity, and deformation characteristics of an oceanic jet impinging on a sloping boundary. The case study corresponds to the impinging process of the Atlantic jet at the African coast (Alboran Sea). In the impinging region, the acceleration field is divergent related to the fact that the magnitude of the deformation is larger than the magnitude of the rotation. It is also found that the stagnation streamsurface does not lie in a vertical plane but tilts in the opposite direction to the tilt of the isopycnals. The flow upstream of the stagnation point is characterized by backing, speed convergence, diffluence, and negative streamwise vorticity...
A Survey of Vietnamese Opinion on the Ethics of Tax Evasion

Although much has been written about tax evasion from the perspective of public finance, not many studies have focused on the ethical aspects of tax evasion. One of the most comprehensive early studies on the ethics of tax evasion was done by Martin Crowe (1944), a Catholic priest who surveyed the philosophical and religious (mostly Catholic) literature that had been written over the previous five centuries. Crowe found that three basic positions had emerged over the centuries. Tax evasion was considered to be: never ethical, always ethical or ethical under certain facts and circumstances. More recent studies were done by Torgler (2003) and McGee (1994, 1998a). The Torgler study was mostly empirical but did not examine the philosophical and ethical literature in depth. The McGee studies examined the philosophical and ethical literature but did not conduct empirical investigations. Although very few philosophical studies on the ethics of tax evasion have been made, the ones that have been done span all three viewpoints. Block (1989, 1993) surveyed the public finance literature but failed to find any adequate explanations or arguments to justify taxation. McGee (1994) applied Lysander Spooner’s (1870) philosophy to the issue of tax evasion, which challenged the social contract theories of Hobbes (1651), Locke (1689) and Rousseau (1762). At the other end of the spectrum, a few philosophical studies concluded that tax evasion is never justified. The literature of the Baha’i religion strictly prohibits tax evasion, the main argument being that individuals have a duty to obey the laws of the country in which they live (DeMoville 1998). A study of the Mormon religious literature reached the same conclusion and for the same reason (Smith and Kimball 1998). Two philosophical studies of the ethics of tax evasion from a Jewish perspective (Cohn 1998; Tamari 1998) both concluded that tax evasion is
A Neural Model of Auditory Space Compatible with Human Perception under Simulated Echoic Conditions.

In a typical auditory scene, sounds from different sources and reflective surfaces summate in the ears, causing spatial cues to fluctuate. Prevailing hypotheses of how spatial locations may be encoded and represented across auditory neurons generally disregard these fluctuations and must therefore invoke additional mechanisms for detecting and representing them. Here, we consider a different hypothesis in which spatial perception corresponds to an intermediate or sub-maximal firing probability across spatially selective neurons within each hemisphere. The precedence or Haas effect presents an ideal opportunity for examining this hypothesis, since the temporal superposition of an acoustical reflection with sounds arriving directly from a source can cause otherwise stable cues to fluctuate. Our findings suggest that subjects’ experiences may simply reflect the spatial cues that momentarily arise under various acoustical conditions and how these cues are represented. We further suggest that auditory objects may acquire “edges” under conditions when interaural time differences are broadly distributed.
Extensive Dark Biological Production of Reactive Oxygen Species in Brackish and Freshwater Ponds

Within natural waters, photodependent processes are generally considered the predominant source of reactive oxygen species (ROS), a suite of biogeochemically important molecules. However, recent discoveries of dark particle-associated ROS production in aquatic environments and extracellular ROS production by various microorganisms point to biological activity as a significant source of ROS in the absence of light. Thus, the objective of this study was to explore the occurrence of dark biological production of the ROS superoxide (O2–) and hydrogen peroxide (H2O2) in brackish and freshwater ponds. Here we show that the ROS superoxide and hydrogen peroxide were present in dark waters at comparable concentrations as in sunlit waters. This suggests that, at least for the short-lived superoxide species, light-independent processes were an important control on ROS levels in these natural waters. Indeed, we demonstrated that dark biological production of ROS extensively occurred in brackish and freshwater environ...
Positioning Students as Teacher Educators: Preparing Learners to Transform Schools

This chapter considers the potential role teacher education programs—specifically those that draw on student input and insight—can play in school transformation. Three distinct areas are considered: (1) developing the capacity among new teachers entering schools to learn with students to consistently improve practice; (2) supporting the empowerment of high school students who, positioned as teacher educators, develop confidence and take ownership over their own learning and (3) fostering strong student-teacher relationships among those participating in the project. Each of these areas has the potential to improve and transform schools. The multiple barriers that exist to fostering student empowered change—and the collaboration between school and university this kind of program entails—are also considered.
The complex gaussian scale mixtures of complex wavelet coefficients and applications

In this thesis, the complex Gaussian scale mixture (CGSM), which is an extension of the Gaussian scale mixture (GSM) for real-valued random variables to the complex case, is presented to model the complex wavelet coefficients. Along with some related propositions and miscellaneous results, the probability density functions (pdf) of the magnitude and phase of the complex random variable are presented. Specifically, the closed forms of the magnitude pdf for the case of complex generalized Gaussian distribution (CGGD) and the phase pdf for the general case are presented. Subsequently, the pdf of the relative phase is derived. Moreover, parameter estimation methods in the presence of noise for several magnitude pdf’s which are special cases of the magnitude pdf related to the CGSM, and for the relative phase pdf (RP pdf) are proposed. In addition, the parameter estimation of the RP pdf is investigated, and a non-iterative estimator for the relative phase pdf’s parameters is also proposed. To show the usefulness of the proposed model, the CGSM is then applied to image denoising using Bayes least square estimator. The experimental results show that using the CGSM of complex wavelet coefficients visually improves the quality of denoised images from the real case. Moreover, the derived magnitude pdf of the CGGD is then utilized in texture image retrieval that uses complex coefficient magnitude to improve the accuracy rate from using the real or imaginary parts. Finally, the problem of noisy texture retrieval, where the query image is contaminated by noise, is studied. This texture retrieval scheme is based on the proposed parameter estimation methods in the presence of noise. The retrieval results show that using both magnitude and phase information of complex coefficients improves the accuracy rate from solely using the magnitude or phase information, and also from using the real or the imaginary parts. These simulation results are also consistent in several complex transform domains.
CAN UNIFORM SELECTION RETARD RANDOM GENETIC DIVERGENCE BETWEEN ISOLATED CONSPECIFIC POPULATIONS

It has long been understood that different species cannot evolve in exactly identical ways, even in response to identical selection pressures (Simpson, 1950). Each species will respond by changes made possible by its own unique store of genetic variation (Simpson, 1967 p. 165). Thus, parallel evolution among different species has not been construed as an allele-for-allele identity of genetic change, but rather as a similarity in trends of phenotypic change. However, it has not been so widely accepted that even conspecific populations will diverge genetically when subjected to similar selection regimes. It has been argued, for example, that random genetic divergence between conspecific populations is not prevented so much by gene flow as by uniformity of selection pressures acting on isolated populations (Ehrlich and Raven, 1969; Levin, 1979). Implicit in this argument is the assumption that conspecific populations will respond to uniform selection in genetically identical manners. But conspecific populations of many species of animals and plants have diverged under similar selection pressures for a great variety of physiological, biochemical, and morphological characters (Table 1). For instance, different populations of the spider mite Tetranychus urticae have responded to selection for organophosphate (OP) resistance by alternative mechanisms: a New York population has responded by detoxifying the poison, while a European population has altered its neural sensitivity to OP's (Matsumura and Voss, 1964). A model is presented here which suggests that weak, uniform selection im-
Characterizing the spatial variation of air pollutants and the contributions of high emitting vehicles in Pittsburgh, PA.

We used a mobile measurement platform to characterize a suite of air pollutants (black carbon (BC), particle-bound polycyclic aromatic hydrocarbons (PB–PAH), benzene, and toluene) in the city of Pittsburgh and surrounding areas. More than 270 h of data were collected from forty-two sites which were selected based on analysis in the geographic information system (GIS). Mobile measurements were performed during three different times of day (mornings, afternoons/evenings, and overnight) in both winter (November 2011 to February 2012) and summer (June 2012 to August 2012). Pollutant concentrations were elevated in river valleys by 9% (benzene) to 30% (PB–PAH) relative to upland areas. Traffic had strong impacts on measured pollutants. PB–PAH and BC concentrations at high traffic sites were a factor of 2 and 30% higher than at low traffic sites, respectively. Pollutant concentrations were highest in the morning sessions due to a combination of traffic and meteorological conditions. The highly time-resolved dat...
Joint inversion of gravity and gravity gradient data using a binary formulation

Gravity and gravity gradient data inherently have different frequency contents based on the differing decay rates with distance from the source and differing signal to noise ratios. Gravity contains more low frequency content while more sensitive to deeper structures, and gravity gradient contains relatively more high frequency content while more sensitive to near surface features. We apply techniques for jointly inverting the two data sets using a 3D binary formulation to the SEG/EAGE salt body model. The inversion algorithm is able to recover a meaningful model of the salt body because the density contrast profile is known a priori. The recovered models also help to highlight the interaction between the two data sets and the information they contain.
Abstract 1426: Identification of secretory stromal gene signature of the ovarian tumor microenvironment and implications for ovarian cancer progression

Ovarian cancer the deadliest gynecologic disease and despite the significant role of the tumor-associated stroma in cancer progression, little research has been done on the specific role of the tumor-associated stromal microenvironment on ovarian cancer progression. Our objective was to identify genes that are differentially regulated in the stromal component of high-grade late-stage serous ovarian cancer and illustrate direct and specific effects of their differential expression on ovarian cancer progression. Microarray analysis performed on RNA isolated from 10 microdissected normal ovarian fibroblasts, and the epithelial and stromal component of 16 high-grade late stage serous ovarian cancers revealed more than 40 secreted proteins that are overexpressed more than 5 fold by cancer-associated fibroblasts (CAFs) exclusively. Quantitative RT-PCR validated the overexpression of several genes, including sFRP2, by the CAFs. Clinical data correlated stromal sFRP2 overexpression with poorer overall survival and chemoresistance in patients with high-grade late stage serous ovarian cancer, suggesting that sFRP2 promotes ovarian cancer progression. In vitro functional studies illustrate increased ovarian cancer cell proliferation rates in response to recombinant sFRP2 as well as CAF-conditioned medium and pathway analysis via transcription-reporter assays revealed that recombinant sFRP2 signals through the NFκB and Wnt pathways in ovarian cancer cells, both of which affect cell growth. While not affecting cell proliferation, recombinant sFRP2 increased endothelial signaling to the NFAT pathway, which affects endothelial tubal branching. These results were corroborated in vivo such that microenvironments expressing higher levels of sFRP2 exhibited significantly higher microvessel density compared with microenvironments with lower sFRP2 expression. Our results illustrate a direct and specific signaling linkage from the tumor microenvironment to tumor cells and endothelial cells that contributes to tumor progression. In this case, sFRP2 exhibited significant influence on characteristics of tumor progression (i.e. tumor proliferation, microvessel morphology) suggesting that other differentially expressed genes identified by the microarray in CAFs may also play significant roles in this process. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1426.
Study on the Application of Self-Organization Neural Network in Document Classification in This Paper

To address documents classification in data mining,a classification method is presented in this paper.The self-organization network is constituted of input layer and competition layer.The nodes of input layer and the nodes of competition layer link with each other totally.Input layer performs import of samples while competition layer extracts the implicit pattern characters of input samples and takes self-organization to them,then represents the classification result at competition layer.The network training includes two phases: non-supervision and supervision.The information of its locality in the document is considered while the keywords are extracted.The classification results of this method are more precise than that of general method because fuzzy eigenvectors are applied.Finally the availability of model and algorithms is proved by classification of some documents in china periodical document database.
EBV-associated aggressive natural killer cell leukemia

![Figure][1] A 78-year-old white American man presented with fever, jaundice, and respiratory distress. Laboratory tests showed the following: white blood cells 4.2 (4-11) × 109/L, hemoglobin 11.7 (13.1-17.2) g/dL, platelets 21 (140-440) × 109/L, bilirubin 9.2 (0.2-1.2) mg/dL, aspartate
Tumor Suppressor Gene Allelic Loss in Human Renal Cancers

It is now apparent that multiple genetic alterations, including oncogene activation and tumor suppressor gene inactivation, are necessary steps in carcinogenesis. We have studied this concept in renal cancers by looking at specific tumor suppressor genes implicated in several allelotyping studies. Primary, predominantly low stage renal tumors of varying grades and histologic subtypes were investigated for allelic loss of 3p, 17p and the p53 gene, the DCC gene and the Rb gene and its product. 3p loss occurred in 47% of tumors studied and was much more common in clear cell cancers (85%). 17p and p53 gene loss were relatively uncommon events with only 6 of 42 tumors demonstrating loss. None of the tumors with typical histologies had allelic loss of the DCC gene, though loss did occur in leiomyosarcoma and a collecting duct tumor. Allelic loss of the Rb gene occurred in one clear cell tumor, the leiomyosarcoma, and, interestingly, in both collecting duct tumors in this series. Allelic loss of the Rb gene was correlated with little or no RB protein expression as judged by immunohistochemistry. At all loci studied, allelic loss did not appear to correlate with tumor grade or stage. These results suggest that inactivation of the p53, Rb, and DCC genes by allelic loss are uncommon events in the early stages of renal carcinogenesis.
Introduction: Fear of Uncertainty—Enter at Your Own Risk

Beginnings are some of the most confused, exciting, overwhelming, daunting times you will encounter when starting your research program. But the beginning is set even further back than most realize. This process necessarily starts from an idea, the zygote of a project nestled in your brain.
Abstract A62: Alcohol consumption, genetic variation in alcohol dehydrogenase genes, and risk of clear cell renal cell carcinoma

Introduction: An inverse association between alcohol consumption and risk of renal cell carcinoma (RCC) is well reported in the literature. Despite this, no investigators have explored the potential for effect modification of this association by genetic variations in enzymes that metabolize alcohol. Motivated by this, we conducted a pilot investigation of the role of genetic variation in the alcohol dehydrogenase genes (ADH) as an effect modifier of the association of alcohol and RCC risk. Methods: We analyzed data on 121 RCC cases and 121 controls. Cases were prospectively collected as part of our Renal Registry in the Department of Urology. Controls were recruited through the Family Medicine and frequency matched to cases on age, gender and state of residence. We collected detailed risk factor data (self-report questionnaire) as well as a DNA sample on cases and controls. We utilized Sequenome analysis to determine presence of published SNPs in the ADH gene cluster (ADH1-7). We employed logistic regression with interaction terms as well as stratified analyses to evaluate effect modification by genetic variants in the ADH gene cluster on the association of alcohol consumption and RCC risk. Results: Compared to non-drinkers, those that consumed alcohol above the median experienced a lowering in RCC risk (OR=0.80; 95% CI 0.5 to 1.43). We observed evidence of interactions with 6 SNPs in the ADH gene (p-values from 0.05-0.2). As an example, in stratified analysis, the inverse association strengthened in those without the minor allele present at rs1154454 in ADH7 (OR=0.56; 95% CI 0.3 to 1.0; p=0.08) while evidence of an increased in RCC risk was noted among those with the minor allele (OR=2.14; 95CI 0.8 – 5.7; p=0.1). Adjustment for age and gender did not alter our results. Conclusion: Our pilot data suggest that specific variants in the ADH gene cluster may modify the reported protective effect of alcohol consumption on RCC risk. Given the possible implications for improving our understanding of the biology of this association and informing prevention, future investigations that analyze a larger sample size and examine additional variants are warranted. Citation Format: Alexander Scott Parker, Nancy Diehl, Michelle L. Arnold, Shauna Rivera, Ashley Cannon, Kaitlynn Custer, Bradley Leibovich. Alcohol consumption, genetic variation in alcohol dehydrogenase genes, and risk of clear cell renal cell carcinoma. [abstract]. In: Proceedings of the Twelfth Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2013 Oct 27-30; National Harbor, MD. Philadelphia (PA): AACR; Can Prev Res 2013;6(11 Suppl): Abstract nr A62.
Decision Theory Meets Linear Optimization Beyond Computation

The paper is concerned with decision making under complex uncertainty. We consider the Hodges and Lehmann-criterion relying on uncertain classical probabilities and Walley’s maximality relying on imprecise probabilities. We present linear programming based approaches for computing optimal acts as well as for determining least favorable prior distributions in finite decision settings. Further, we apply results from duality theory of linear programming in order to provide theoretical insights into certain characteristics of these optimal solutions. Particularly, we characterize conditions under which randomization pays out when defining optimality in terms of the Gamma-Maximin criterion and investigate how these conditions relate to least favorable priors.
1.3 The development of high-speed DNA sequencing: Jurassic Park, Neanderthal, Moore, and you

Since Watson and Crick's 1953 landmark discovery that biological information was encoded in DNA as a sequence of chemical building-block “letters”, developing technology for reading (or “sequencing”) this chemical code has been fundamental to advances in biology and medicine. Techniques that first enabled this were invented by Sanger in 1978, and were taken to massively parallel form by 454 Life Sciences in 2003 [1]. This ushered in the current or “next-gen” era of genome sequencing technologies for research, medicine, and the emerging field of Genomic-Personalized Medicine, in which healthcare is more fully informed by the individuals' personal genetic makeup.
High-content behavioral profiling reveals neuronal genetic network modulating Drosophila larval locomotor program

Two key questions in understanding the genetic control of behaviors are: what genes are involved and how these genes interact. To answer these questions at a systems level, we conducted high-content profiling of Drosophila larval locomotor behaviors for over 100 genotypes. We studied 69 genes whose C. elegans orthologs were neuronal signalling genes with significant locomotor phenotypes, and conducted RNAi with ubiquitous, pan-neuronal, or motor-neuronal Gal4 drivers. Inactivation of 42 genes, including the nicotinic acetylcholine receptors nAChRα1 and nAChRα3, in the neurons caused significant movement defects. Bioinformatic analysis suggested 81 interactions among these genes based on phenotypic pattern similarities. Comparing the worm and fly data sets, we found that these genes were highly conserved in having neuronal expressions and locomotor phenotypes. However, the genetic interactions were not conserved for ubiquitous profiles, and may be mildly conserved for the neuronal profiles. Unexpectedly, our data also revealed a possible motor-neuronal control of body size, because inactivation of Rdl and Gαo in the motor neurons reduced the larval body size. Overall, these data established a framework for further exploring the genetic control of Drosophila larval locomotion. High content, quantitative phenotyping of larval locomotor behaviours provides a framework for system-level understanding of the gene networks underlying such behaviours.
Psychosocial Risk Factors for Perinatal Depression among Female Adolescents: A Systematic Review

Perinatal depression is a health concern among pregnant and postpartum adolescents as it may negatively impact fetal development and result in complications such as preterm delivery, low infant birth weight, and poor maternal-infant attachment. The purpose of this systematic review is to examine psychosocial risk factors for depression among adolescents during pregnancy and postpartum. A literature search was conducted from five databases from 1995 to 2016. A total of 17 studies matched the inclusion criteria. Lack of social support, perceived stress, prior history of depression, and a history of sexual or physical violence were most frequently identified as potential risk factors for perinatal depression. Additional risk factors include the adolescent's perception of her pregnancy, family criticism, self-efficacy, self-esteem, substance use, parental stress, community violence, anxiety, and African-American ethnicity. Research and clinical implications are indicated for adolescents at risk for perinatal depression.
Post-operative stereotactic radiosurgery versus observation for completely resected brain metastases: a single-centre, randomised, controlled, phase 3 trial

Summary Background After brain metastasis resection, whole brain radiotherapy decreases local recurrence, but might cause cognitive decline. We did this study to determine if stereotactic radiosurgery (SRS) to the surgical cavity improved time to local recurrence compared with that for surgical resection alone. Methods In this randomised, controlled, phase 3 trial, we recruited patients at a single tertiary cancer centre in the USA. Eligible patients were older than 3 years, had a Karnofsky Performance Score of 70 or higher, were able to have an MRI scan, and had a complete resection of one to three brain metastases (with a maximum diameter of the resection cavity ≤4 cm). Patients were randomly assigned (1:1) with a block size of four to either SRS of the resection cavity (within 30 days of surgery) or observation. Patients were stratified by histology of the primary tumour, metastatic tumour size, and number of metastases. The primary endpoint was time to local recurrence in the resection cavity, assessed by blinded central review of brain MRI scans by the study neuroradiologist in the modified intention-to-treat population that analysed patients by randomised allocation but excluded patients found ineligible after randomisation. Participants and other members of the treatment team (excluding the neuroradiologist) were not masked to treatment allocation. The trial is registered with ClinicalTrials.gov, number NCT00950001, and is closed to new participants. Findings Between Aug 13, 2009, and Feb 16, 2016, 132 patients were randomly assigned to the observation group (n=68) or SRS group (n=64), with 128 patients available for analysis; four patients were ineligible (three from the SRS group and one from the observation group). Median follow-up was 11·1 months (IQR 4·8–20·4). 12-month freedom from local recurrence was 43% (95% CI 31–59) in the observation group and 72% (60–87) in the SRS group (hazard ratio 0·46 [95% CI 0·24–0·88]; p=0·015). There were no adverse events or treatment-related deaths in either group. Interpretation SRS of the surgical cavity in patients who have had complete resection of one, two, or three brain metastases significantly lowers local recurrence compared with that noted for observation alone. Thus, the use of SRS after brain metastasis resection could be an alternative to whole-brain radiotherapy. Funding National Institutes of Health.
Interfacial self-healing of nanocomposite hydrogels: Theory and experiment

Abstract Polymers with dynamic bonds are able to self-heal their fractured interfaces and restore the mechanical strengths. It is largely elusive how to analytically model this self-healing behavior to construct the mechanistic relationship between the self-healing properties (e.g., healed interfacial strength and equilibrium healing time) and the material compositions and healing conditions. Here, we take a self-healable nanocomposite hydrogel as an example to illustrate an interfacial self-healing theory for hydrogels with dynamic bonds. In the theory, we consider the free polymer chains diffuse across the interface and reform crosslinks to bridge the interface. We analytically reveal that the healed strengths of nanocomposite hydrogels increase with the healing time in an error-function-like form. The equilibrium self-healing time of the full-strength recovery decreases with the temperature and increases with the nanoparticle concentration. We further analytically reveal that the healed interfacial strength decreases with increasing delaying time before the healing process. The theoretical results quantitatively match with our experiments on nanosilica hydrogels, and also agree well with other researchers’ experiments on nanoclay hydrogels. We expect that this theory would open promising avenues for quantitative understanding of the self-healing mechanics of various polymers with dynamic bonds, and offer insights for designing high-performance self-healing polymers.
Systematic Optimization of Battery Materials: Key Parameter Optimization for the Scalable Synthesis of Uniform, High-Energy, and High Stability LiNi0.6Mn0.2Co0.2O2 Cathode Material for Lithium-Ion Batteries.

Ni-rich LiNixMnyCo1-x-yO2 (x > 0.5) (NMC) materials have attracted a great deal of interest as promising cathode candidates for Li-ion batteries due to their low cost and high energy density. However, several issues, including sensitivity to moisture, difficulty in reproducibly preparing well-controlled morphology particles and, poor cyclability, have hindered their large scale deployment; especially for electric vehicle (EV) applications. In this work, we have developed a uniform, highly stable, high-energy density, Ni-rich LiNi0.6Mn0.2Co0.2O2 cathode material by systematically optimizing synthesis parameters, including pH, stirring rate, and calcination temperature. The particles exhibit a spherical morphology and uniform size distribution, with a well-defined structure and homogeneous transition-metal distribution, owing to the well-controlled synthesis parameters. The material exhibited superior electrochemical properties, when compared to a commercial sample, with an initial discharge capacity of 205...
Semantic Interference Test: Evidence for Culture and Education Fairness from an Ethnically Diverse Sample in the USA.

OBJECTIVE Tests of cognitive abilities are particularly susceptible to culture-based bias because these abilities are culturally bound. The specific purpose of this study was to examine the Semantic Interference Test, a clinical neuropsychological test, for culture bias. METHOD The sample included 415 community-dwelling participants (mean age 74, SD = 8.32; 308 were females) living in South Florida (USA). The sample included 72 African Americans, 93 Afro-Caribbeans, 77 Hispanic Americans, and 173 European Americans. An Item Response Theory analysis of bias was employed using the Differential Item Functioning (DIF) procedure. RESULTS Overall, the items appear to be invariant across gender, ethnicity, and education levels. Although the DIF identified several items that appear to differ across the two latter groupings, the multiple group confirmatory factor analysis (MG-CFA) suggests that these items have low impact on the overall measure. There were however, meaningful differences across age groups in the MG-CFA, suggesting that an age adjustment might be required. CONCLUSION The SIT can be considered a cognitive test that is not significantly affected by the participants' cultural background, at least within the culture range included in this study.
Antibacterial Aqueous Emulsions

Researchers at the Center for Biologic Nanotechnology, University of Michigan, Ann Arbor Michigan published and patented results of project MDA 972-1-007 of the Unconventional Pathogen Countermeasures Program, Defense Advanced Research Project Agency. The introduction of biological agents to our working and living environment has forced an examination of preventative and decontamination methods (Mobley 1995). The project involved antibacterial aqueous nanoemulsions to treat bacteria-infected people and disinfect contaminated surfaces such as vehicles and medical equipment exposed to anthrax spores. Literature and patents were reviewed, materials and equipment were procured, and emulsions were prepared and evaluated for antibacterial activity. The antibacterial emulsion technology could possibly be useful if it is reproducible. Regarding emulsion technology, the term “emulsion” is the industry standard, and “nanoemulsion” pertains to emulsified particle less than a micron in diameter (e.g., typical of paint latex particle size), but greater than a nanometer. Actually, particle diameters for industrial emulsions are usually in the nanometer range.
Complex Hyperspherical Equations, Nodal-Partitioning, and First-Excited-State Theorems in ℝ n

Three problems related to the spherical quantum billiard in $$\mathbb{R}^n$$ are considered. In the first, a compact form of the hyperspherical equations leads to their complex contracted representation. Employing these contracted equations, a proof is given of Courant's nodal-symmetry intersection theorem for “diagonal eigenstates” of “spherical-like” quantum billiards in $$\mathbb{R}^n $$ . The second topic addresses the “first-excited-state theorem” for the spherical quantum billiard in $$\mathbb{R}^n $$ . Wavefunctions for this system are given by the product form, ( $${1 \mathord{\left/ {\vphantom {1 {\rho ^q }}} \right. \kern-\nulldelimiterspace} {\rho ^q }}$$ )Z q+l(ρ)Y l (n) , where ρ is dimensionless displacement, $$\ell $$ is angular-momentum number, qis an integer function of dimension, Z(ρ) is either a spherical Bessel function (nodd) or a Bessel function of the first kind (neven) and θrepresents (n− 1) independent angular components. Generalized spherical harmonics are written $$Y_\ell ^{(n)}(\theta )$$ . It is found that the first excited state (i.e., the second eigenstate of the Laplacian) for the spherical quantum billiard in $$\mathbb{R}^n $$ is n-fold degenerate and a first excited state for this quantum billiard exists which contains a nodal bisecting hypersurface of mirror symmetry. These findings establish the first-excited-state theorem for the spherical quantum billiard in $$\mathbb{R}^n $$ . In a third study, an expression is derived for the dimension of the lth irreducible representation (“irrep”) of the rotation group O(n) in $$\mathbb{R}^n $$ by enumerating independent degenerate product eigenstates of the Laplacian.
Effect of diet on activity of enzymes involved in fatty acid and cholesterol synthesis.

Publisher Summary This chapter discusses the effect of diet on activity of enzymes involved in fatty acid and cholesterol synthesis. Adipose tissue is the major organ contributing to de novo fatty acid synthesis in the nonlactating pig and ruminant, while the liver is more important in birds and man. In rats and mice, both organs contribute significantly to de novo fatty acid synthesis. In species such as the rat, where both liver and adipose tissue contribute to de novo fatty acid synthesis, dietary manipulations generally affect both tissues in a similar fashion; however, there are exceptions. The quantity of hepatic fatty acid synthetase can regulate the rate of fatty acid synthesis in rats fed high-carbohydrate diets. Unlike enzymes involved in fatty acid synthesis, a change in β -Hydroxy- β -methylglutaryl-CoA reductase activity precedes changes in hepatic acetate conversion to cholesterol. Allosteric control of enzyme activity plays a major role in the rapid regulation of metabolic flux. Adaptive changes in enzyme content reflect sustained changes in metabolic flux and such adaptations are involved in the longer term regulation of metabolism.
The role of mitochondrial oxidative stress in retinal dysfunction

In the eye, the retina and surrounding tissues are exposed to one of the most highly oxidizing microenvironments in the entire human body. This is due, in part, to constant visible light exposure, elevated oxygen partial pressure and phagocytosis of the polyunsaturated fatty acid-loaded photoreceptor outer segments. Accordingly, numerous retinal degenerations including age-related macular degeneration (AMD), diabetic retinopathy, and glaucoma are associated with oxidative stress. Oxidative damage and mitochondrial dysfunction are considered to be significant factors underlying the initiation and progression of cellular changes during aging and disease. This chapter discusses the high vulnerability of mitochondria and outlines current evidence implicating this organelle as a weak link in the retina. In particular, mitochondrial DNA (mtDNA) damage and defects in the mtDNA repair system may be particularly important to the pathogenesis retinal degenerations. We also consider the importance of mitochondrial biogenesis as well as removal of damaged mitochondria via autophagy as cellular strategies to minimize the effect of mitochondrial damage on cellular function. The specific targeting of mitochondria (e.g., biogenesis, removal, antioxidants, and DNA repair) with pharmacological agents able to protect against retinal damage may offer novel alternatives for the treatment of retinal degenerations.
Recommendations and Cautions

During the design of a data system, indirect estimators rarely, if ever, are considered for Federal statistical programs when resources to produce direct estimates of adequate precision are available. However, given an existing system, if direct estimation is judged to be inadequate for a domain not specified in the design, indirect estimation may, in some cases, prove to be a valuable alternative. There are a number of reasons that direct estimators are preferable to indirect ones and, if federal statistical agencies are to improve the usefulness of indirect estimates, a number of important issues, including those that follow, should receive additional attention. The following points are developed further in the sections of this chapter.
Optimizing a video preprocessor for OCR

This paper describes how optimal video preprocessor performance can be achieved using a software recognition system and a set of controlled experiments. It basically involves optimizing on a constant threshold and then using recognition logic designed from that threshold to optimize an adaptive threshold function or threshold operator. By using this technique, the video preprocessor can be optimized early In the development of an OCR (Optical Character Recognition) machine. The software recognition system is described and experimental data is presented to illustrate the procedures.