cssi/SciSciGPT-SciSciNet huggingface dataset:
Synesthesia, at and near its borders.

In synesthesia, experiences in one domain evoke additional experiences in another, as when musical notes or letters of the alphabet evoke colors. Both the domains and their pairings are diverse. Indeed, Day's (2013) recently tabulated 60 types of synesthesia, each referring to a different combination of inducing and induced domains. The domains conjoined through synesthesia may belong to different sense modalities, as in music-color synesthesia, but may also belong to the same modality: In grapheme-color synesthesia, seeing printed letters or numbers evokes color experiences. In music-color and grapheme-color synesthesia, the inducing stimuli are perceptual, reflecting culture-specific categories (notes of the Western musical scale, letters of the alphabet) learned by synesthetes and non-synesthetes alike. Synesthesia may be triggered not only by sounds, tastes, smells, and pains, but also by more complex signals: words(e.g., Simner, 2007), emotional states (e.g., Ward, 2004), and even personalities (e.g., Novich et al., 2011). Analogously, the domains of synesthetic responses too can range widely. The composer Rimsky-Korsakoff “saw” the key of D-major as golden (Myers, 1914), while a grapheme-personification synesthete reported, “Ts are generally crabbed, ungenerous creatures” (Calkins, 1893; p. 454). Other phenomena, however, such as cross-modally evoked images or memories, are not typically considered examples of synesthesia. In this article, we briefly describe half a dozen illustrative cases that border on traditional forms of synesthesia: cross-modal correspondence, cross-modal imagery, sensory (cross-modal) autobiographical memory, empathic perception, hallucination, and the Doppler illusion. Do any or all of the six constitute forms of synesthesia? The answer depends, we suggest, on the framework for characterizing synesthesia. Consequently, after describing the six phenomena, we sketch three frameworks that differ in how they characterize these phenomena relative to prototypical forms of synesthesia. Several investigators, taking different perspectives and coming to different conclusions, have already considered possible relations to synesthesia in three of the six: cross-modal correspondence (Martino and Marks, 2001; Deroy and Spence, 2013); cross-modal imagery (Craver-Lemley and Reeves, 2013; Spence and Deroy, 2013); and empathic perception (Fitzgibbon et al., 2010; Rothen and Meier, 2013).
Adrenal venous sampling and adrenal biopsy.

The current status of adrenal vein sampling and the role of adrenal gland percutaneous biopsy will be reviewed.
Some symmetries in nuclear physics

Abstract Some nuclear symmetries that have received recent attention are discussed. They include nuclear shapes, Wigner and Serber Symmetries, and dynamical symmetries, including supersymmetry.
A method for approximating missing data in spatial patterns

Abstract Spatial patterns such as historical landscape records or digital photographs are often plagued by large numbers of missing or otherwise corrupted data points or pixels that cannot be easily reproduced. A method is described in which a simple stochastic cellular automaton is used to produce fictitious fractal data at arbitrarily many spatial points such that the resulting pattern mimics the morphological features of the actual pattern. The method is simple to implement, preserves all the existing data, has no adjustable parameters, and can be used to fill in regions of arbitrary size and shape, even outside the region for which data are available. Furthermore, it reduces to more conventional interpolation methods when only a few isolated data points are missing.
Courbure scalaire prescrite sur une variété C∞ compacte de dimension 2

Resume Soient ( V 2 , g ) une variete riemannienne C ∞ compacte de dimension 2 a courbure scalaire negative et f une fonction C ∞ definie sur V 2 . On met en evidence une condition simple sur f pour que cette fonction soit la courbure scalaire d'une metrique conforme a la metrique initiale g.
Characterization of integrin β6 and thrombospondin‐1 double‐null mice

To identify overlapping and non-overlapping functions for TSP-1 and αvβ6, we crossed TSP-1-null and β6-null mice and compared the phenotype of the double-null mice with those of wild-type and single-null mice. The double-null mice exhibited focal acute and organizing pneumonia that was more severe than the wild-type and single-null mice as well as a significantly higher incidence of inflammation in tissues other than the lung. The TSP-1-null and β6-null mice exhibited a five to eight-fold increase in granulocyte recruitment to the lung three days after exposure to lipopolysaacharide. They also had abnormalities that were infrequently observed in the wild-type and single-null mice, including heart degeneration (8.35% in wild-type and 28.1% in double-null mice), hyperplasia of the glandular epithelium of the stomach (2.8% in wild-type and 21.1% in double-null mice) and endometrial hyperplasia (0% in wild-type and 38.5% in double-null females). Furthermore, the β6-null and double-null mice displayed a significant elevation in benign and malignant cancers. Stomach papillomas, squamous cell carcinomas of the ear and stomach, and adenocarcinomas of the lungs, vagina/cervix and colon were observed with the highest frequency. These data demonstrate that TSP-1 and αvβ6 are involved in regulation of the immune system and epithelial homeostasis. They also indicate that αvβ6 functions as a tumor suppressor gene and that activation of TGFβ by TSP-1 and αvβ6 contributes to normal tissue architecture and function.
PSYCHOLOGICAL AND BEHAVIORAL EFFECTS OF MOOD-INDUCTION PROCEDURES WITH CHILDREN

The experimental manipulation of mood in the laboratory is a viable approach for studying mood in children. The present paper describes the use with children of direct mood inductions and the behavioral and cognitive effects. The procedure produces effects similar to those produced by naturally occurring depressed mood. It is concluded that direct induction procedures may enhance current methodological, theoretical, and clinical understanding about depression in children. Recommendations for research are suggested.
Synthesis of the CETP Inhibitor Torcetrapib: The Resolution Route and Origin of Stereoselectivity in the Iminium Ion Cyclization

A practical, efficient synthesis of (−)-(2R,4S)-4-[(3,5-bis-trifluoromethyl-benzyl)methoxycarbonylamino]-2-ethyl-6-trifluoromethyl-3,4-dihydro-2H-quinoline-1-carboxylic acid ethyl ester (1), a cholesteryl ester transfer protein (CETP) inhibitor, is described. The key reaction in the synthesis, addition of an N-vinylcarbamate to an iminium ion rapidly followed by an iminium ion cyclization onto the aryl ring, sets up the cis relationship of the two subsituents of the tetrahydoquinoline ring of 6. The origin of the high cis stereoselectivity in the cyclization was explored using high-level quantum chemistry calculations.
The Chubby lock service for loosely-coupled distributed systems

We describe our experiences with the Chubby lock service, which is intended to provide coarse-grained locking as well as reliable (though low-volume) storage for a loosely-coupled distributed system. Chubby provides an interface much like a distributed file system with advisory locks, but the design emphasis is on availability and reliability, as opposed to high performance. Many instances of the service have been used for over a year, with several of them each handling a few tens of thousands of clients concurrently. The paper describes the initial design and expected use, compares it with actual use, and explains how the design had to be modified to accommodate the differences.
The Natural Imperative for Biological Conservation

To contribute significantly to environmnentalpolicy of the next century, conservationists wi.ll need to reach a consensus on their fundamental values and goals and to persuade society to adopt tbem. Resolu- tion of the debate over the continued role of naturalness as a guiding concept bas imnportant implications for how conservation is practiced and the future of the discipline. I examine five aspects of naturalness in the context of biological conservation: (1) its utility, (2) its assessment, (3) its relation to values and ethics, (4) al- ternative imperatives,, and (5) implications of adopting it as a guiding concept. Naturalness can be viewed as a continuous gradient with comnpletely natural and completely artificial extremes. Human actions are unnat- ural to the extent that they rely on technology to transform natural ecosystems. The ecological consequences of technological transformnation often overwhelm the capacity of other biota to adapt and are a root cause of biodiversity loss. The naturalness of most ecosystems or ecosystem alterations can be assessed objectively de- spite imperfect knowledge if evolutionary limits and natural ranges of variability are carefaully considered. Most conservationists value naturally evolved biotic elements such as genomes and communities over artifi- cial elements. This judgment, which is not shared by society at large, is based on intrinsic and instrumental
Urmylation controls Nil1p and Gln3p-dependent expression of nitrogen-catabolite repressed genes in Saccharomyces cerevisiae

Urm1 is a modifier protein that is conjugated to substrate proteins through thioester formation with the E1-like enzyme, Uba4. Here is shown that the lack of urmylation causes derepression of the GAP1 gene (encoding a nitrogen-regulated broad-spectrum amino acid-scavenging permease) in the presence of rich nitrogen sources, and simultaneous inhibition of the expression of CIT2, a TCA-cycle gene involved in the production of glutamate and glutamine. This effect is dependent on the TORC1- and nutrient-regulated transcriptional factors, Nil1p and Gln3p. Evidence is provided that, in the absence of urmylation, nuclear/cytosolic shuffling of both transcriptional factors is altered, ultimately leading to inability to repress GAP1 gene in the presence of a rich nitrogen source. Altogether, the data presented here indicate an important role of the urmylation pathway in regulating the expression of genes involved in sensing and controlling amino acids levels.
Postoperative pneumonia in the intensive care unit

Postoperative pneumonia in the surgical patient may occur from atelectasis and inadequate postoperative TV, from ventilator-associated pathophysiology and from aspiration. Each process ultimately elicits the proinflammatory responses from the lung in the effort to eradicate the infectious pathogens. Postoperative pneumonia is best prevented by maintaining a clear understanding of the biologic basis for infection in the lung. Therapy requires aggressive tracheobronchial drainage strategies and antibiotic therapy directed toward the pathogens that are producing the pulmonary inflammatory response.
A former continuation of the Alps

There is strong evidence that microplates have played an important role in the tectonic evolution of the Western Mediterranean. A reconstruction of the Oligocene positions of these microplates leads to recognition of the Hercynian “Protoligurian Massif” (new term) and suggests that the Alpine belt (Late Cretaceous and early Tertiary deformation) formerly continued southwest from Alpine Corsica to Calabria and perhaps as far as the Betic Cordilleras of southern Spain. Fragments of this orogenic belt were dispersed during the Miocene-Pliocene episode of microplate movement that also produced the Apennine-Atlas orogenic belt. This hypothesis provides a new solution to the old question of why the Alps presently terminate in Corsica. A comparison of geological data from the Alps, northeastern Corsica, and Calabria supports the hypothesis that they were formerly continuous segments of the Alpine orogenic belt.
The Participatory Consequences of Internal and External Political Efficacy: a Research Note:

GOOD DEAL of scholarly attention has been paid in recent years to the increasing disaffection of the American electorate. Much of this concern has centered on the sources and meaning of political discontent, such as the erosion of political trust. Some have interpreted this trend as transient dissatisfaction (Citrin 1974); others have been considerably less sanguine (Miller 1974a, 1974b). In any case, political trust, taken by itself, is not a strong predictor of levels of political participation (Muller 1977; Milbrath and Goel 1977: 68-74). Better behavioral explanations are obtained when political efficacy also is taken into account (Aberbach 1969; Miller and Miller 1975: 406-7). It appears that, when low levels of trust are combined with high levels of efficacy, the potential for unconventional or "nonallegiant" action is optimal. Presumably, efficacy affects the level of initiative required by the act, and trust structures its allegiant or nonallegiant nature. This is the familiar "mistrust-sense of political efficacy" hypothesis, and it has been widely investigated (Abravenal and Busch 1975; Craig 1979; Craig and Maggiotto 1981; Finifter 1970; Fraser 1970; Hart 1978: chap. 2; Hawkins, Marando, and Taylor 1971; Paige 1971; Watts 1973; Zurcher and Monts 1972). Of course, in his original formulation of the hypothesis, Gamson (1968) connected this cynical combination of beliefs to all forms of activism conventional and unconventional. Even so, most studies have shown low trust and high efficacy to be related to nonallegiant action, but not to conventional participation. However, the development of cumulative research in this area has proven difficult for several reasons. One problem was mentioned above. We know that political trust is declining, but there is still some question whether we are witnessing a fundamental rejection of political institutions or a less durable disapproval of government officials and policies (Abramson and Finifter 1981). Clearly, our behavioral predictions depend on this distinction: Conditions of low diffuse support will foster different participatory consequences than conditions of low specific support for the system (Craig 1980). Additionally, most studies have not been sensitive to the emergent dimensional properties of political efficacy. All evidence now strongly indicates that political efficacy itself measures an "external," system-regarding attitude, as well as an "internal," personal dimension of belief (Converse 1972; Balch 1974; Craig 1979). Finally, we lack evidence for the connections between these political attitudes and a wider range of conventional or "within-system" behaviors, other than voting (Verba and Nie 1972).
Hardware accelerators for biocomputing: A survey

Computing research has become a vital cog in the machinery required to drive biological discovery. Computing has made possible significant achievements over the last decade, especially in the genomics sector. An emerging area is the investigation of hardware accelerators for speeding up the massive scale of computation needed in large-scale biocomputing applications. Various hardware platforms, such as FPGA, Graphics Processing Unit (GPU), the Cell Broadband Engine (CBE) and multi-core processors are being explored. In this paper, we present a survey of hardware accelerators for biocomputing by choosing a representative set of each.
Anharmonicity of the hydrogen-carbon stretch mode on diamond (111)-1×1

The structural and vibrational properties of the hydrogen-capped diamond (111)-1\ifmmode\times\else\texttimes\fi{}1 surface are calculated using a first-principles total-energy approach. The stretching vibration of the hydrogen-carbon bond on the surface and, in particular, its anharmonicity are investigated. The calculated stretch-mode frequency is in agreement with experimental results from sum-frequency generation measurements to within 2.5%. The frequency shift arising from the anharmonicity, i.e., the difference between the overtone frequency and twice the fundamental frequency, is predicted to be 0.014 eV or 113 ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$. This rather large anharmonicity should make it possible to measure directly the overtone frequency by near-infrared absorption.
Abstract 1073: A systematic approach to identify the Ras-dependent C-RAF(Ser338)-phosphorylating kinase

Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL Phosphorylation of c-RAF at Ser338 is an absolute requirement for c-RAF activation and Ras-mediated signaling; however, definitive identification of the c-RAF(Ser338)-phosphorylating kinase has remained elusive. As a first step towards this end, we screened a collection of ∼600 expressible kinase open reading frames to determine which are sufficient to induce phosphorylation of c-RAF on Ser338. In total, 12 kinases induced c-RAF(Ser338) phosphorylation, including 9 Ser/Thr kinases, 1 kinase with unknown site specificity, 1 adapter factor and 1 scaffolding protein. Notably, two proteins previously shown to regulate c-RAF(Ser338) phosphorylation (PAK3 and KSR) also scored in this assay, highlighting the utility of this approach to uncover plausible effectors. We have initiated follow-up studies, including recombinant protein-based kinase assays and loss of function experiments, to characterize the kinase(s) responsible for Ras-mediated c-RAF(Ser338) phosphorylation in vivo. Given the inherent difficulty of targeting Ras-dependent cancers, a more detailed understanding of c-RAF phosphorylation and Ras-dependent activation may inform new therapeutic inroads to targeting these lesions. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1073. doi:10.1158/1538-7445.AM2011-1073
Primary cosmic ray flux

Abstract We discuss the primary cosmic ray flux from the point of view of particle interactions and production of atmospheric neutrinos. The overall normalization of the cosmic ray flux and its time variations and site dependence are major ingredients of the atmospheric neutrino predictions and the basis for the derivation of the neutrino oscillation parameters.
Strategies to prevent weight gain in workplace and college settings: a systematic review.

Abstract Objective To compare the effectiveness of self-management, dietary, physical activity, and/or environmental strategies for the prevention of weight gain among adults in work and college settings. Method We conducted a systematic review of work/college-based studies that intervened on adults using one or more of the above strategies with follow up over at least a 12-month period. We excluded studies with a weight loss component. Our weight outcomes included body mass index (BMI), weight, and waist circumference. Results We included 7 work- and 2 college-based interventional studies, which all used combinations of different strategies. There was moderate strength of evidence that work/college-based combination interventions prevented weight gain of ≥ 0.5 kg over 12 months as compared to control; however, we were unable to perform meta-analysis due to substantial heterogeneity in the intervention strategies and study populations. These programs did not prevent BMI gain or waist circumference increase. Conclusion While we found limited evidence that work/college-based interventions employing a combination of strategies prevent adult weight gain, the combination of personalized diet and physical activity counseling for the individual along with the promotion of healthy lifestyle changes in the environment may be a promising strategy to explore in future research.
Technical English and the Future

“Technical English and the Future” begins by discussing two methods of teaching technical English: the practical and the imaginative. It then argues that these methods need not be mutually exclusiv...
The effects of religious contextual norms, structural constraints, and personal religiosity on abortion decisions.

Abstract Researchers have established that individual religiosity influences abortion attitudes, and that abortion attitudes, in turn, shape abortion restrictions and access. Less clear is whether religion and abortion structural constraints influence abortion decisions. This study examines the several individual, contextual, and structural factors that could shape the abortion decisions of women who conceive before marriage. Special attention is given to the importance of academic aspirations and structural constraints, in contrast to religious beliefs and county religious context, for making an abortion decision. Hierarchical modeling techniques and two waves of data from the National Longitudinal Study of Adolescent Health (Add Health) are employed. Neither generic religiosity nor conservative Protestant religious context appear to influence women’s abortion decisions. Conversely, young women’s abortion decisions are shaped by academic ambition, identification with a conservative Protestant denomination, proximity to an abortion clinic and the level of public abortion funding in their county of residence.
An efficient physics-based preconditioner for the fully implicit solution of small-scale thermally driven atmospheric flows

In atmospheric flow situations typical of a small-scale atmospheric thermal, a separation of time scales exists between the fast sound wave time scale and the advective time scale. Atmospheric models have been designed to take advantage of this disparity of time scales with numerical approaches such as the semi-implicit or split-explicit approach being used to efficiently step over the fast sound waves. Some of these numerical approaches are first order in time. To improve accuracy over these methods, a fully implicit and nonlinearly consistent (INC) flow solver has been developed for the Navier-Stokes equation set. In our INC method, the equation set is solved by use of the Jacobian-free Newton-Krylov (JFNK) method. An efficient preconditioner has been developed which uses the semi-implicit method to solve the governing equations. Being that this preconditioner was designed to attack the fastest waves in the system and not other features in the implicit system such as advection or turbulent diffusion, the preconditioning technique is labeled as a physics-based preconditioner. A variety of linear solvers including SSOR, Krylov methods and/or multigrid approaches are used to approximately invert the pressure matrix in the semi-implicit algorithm. A suite of simulations will be conducted utilizing different linear solvers for the simple problem of the bouyant rise of a warm bubble. The problem will also document the ability of the INC approach to achieve second order in time accuracy.
Regional Variation in the Incidence of Symptomatic Pesticide Exposures: Applications of Geographic Information Systems

Objective: To evaluate the epidemiology of symptomatic human pesticide exposures using poison control center data and geographic information systems. Methods: All symptomatic human pesticide exposures reported to the poison center during the period from January 1 to December 31, 2000 were included for analysis using geographic information systems. A space–time scan statistic was utilized to evaluate for clustering of symptomatic human exposures. Results: Of 322 symptomatic pesticide exposures, 297 (92%) contained spatial identifiers that could be further analyzed using geographic information systems. A spatial and temporal cluster of symptomatic pesticide exposures was identified during the period from April 1 to August 31, 2000, covering a large geographic area of eastern and predominantly rural regions of the state. The relative risk of reporting a symptomatic pesticide exposure among individuals living within this geographic area was 1.8 (log likelihood ratio=18.5, P=0.0005). Conclusions: Geographic in...
Polyunsaturated fatty acids stimulate superoxide formation in tumor cells: A mechanism for specific cytotoxicity and a model for tumor necrosis factor?

Some neoplastic cell lines are readily killed when incubated in the presence of polyunsaturated fatty acids (PUFA). In an attempt to elucidate this phenomenon, we studied PUFA-driven superoxide (O2 − ) production by cultured NS-1 cells (murine lymphoid tumor cells). We find: (1) Even in the absence of added PUFA, NS-1 cells generate O2 − (i.e., reduce nitroblue tetrazolium). (2) addition of PUFA increases O2 − by >50%. (3) Artificial loading of NS-1 cells with liposome encapsulated superoxide dismutase prevents the majority of spontaneous and PUFA-driven NBT reduction. We conclude that PUFA drives O2 − generation by tumor cells, that this generation is largely intracellular, and that this phenomenon may help explain toxicity of PUFA for tumor cells.
Variations of the local electronic surface properties of TiO 2 ( 110 ) induced by intrinsic and extrinsic defects

Variation of the local electronic structure at rutile ${\mathrm{TiO}}_{2}(110)$ surfaces was studied by scanning tunneling spectroscopy (STS). Structural surface features such as step edges, $(1\ifmmode\times\else\texttimes\fi{}2)$ reconstructed strands, and their terminations were correlated to changes in tunneling spectra. In particular, band-gap states, associated with a reduced surface, showed characteristic variations. In addition, electronic variations due to extrinsic defects are discussed. Nanometer wide protrusions in constant current scanning tunneling microscopy images were identified in STS as local electronic alterations. These features are interpreted to be due to local band bending induced by individual, charged impurity atoms.
The experience of disability and quality of life in social anxiety disorder.

Although disability is a concept most often associated with role dysfunction, and quality of life is most often associated with life satisfaction, these terms are frequently used interchangeably in the literature. In contrast, this study proposes that disability and quality of life are independent but related constructs. Additionally, we propose that disability partially mediates the relationship between symptoms and quality of life. That is, greater symptoms are associated with more impairment, which is, in turn, associated with less satisfaction with one's life. Ninety-six individuals with social anxiety disorder were given measures of social anxiety symptoms, disability, and quality of life. The results of the study suggest that disability and quality of life are, in fact, distinct concepts, and the experience of disability partially mediates the relationship between a patient's experience of symptoms and his or her perceived life satisfaction.
Reflective teaching: theory within classroom practices

The core of the Senate Bill 2042 (1998) was designed to provide the guidelines needed to prepare teachers who can meet the needs of a diverse K-12 student population in California. Following the guidelines marked by this bill, faculty working in Teacher Credential Programs across California are designing activities to prepare candidates with a deep understanding of effective pedagogies applicable to a full range of students. A key component in this preparation is to provide teacher candidates with opportunities to critically read and reflect on theory and research. Understanding the importance of this component, I designed an assignment, Quadruple Entry Journals (QEJ), which asks teacher candidates to first, critically read texts on theory; secondly, to reflect and analyze those texts; thirdly, to reflect on the reflections of their classmates; and, finally, to connect these theoretical reflections with practice. In this article, I explain the pedagogy followed when implementing QEJ with teacher candidate...
Domestic violence and the trauma surgeon.

Abstract Background: Domestic violence has become increasingly recognized as a public health problem, and was declared a national epidemic by C. Everett Koop in 1992. In the United States, 1 to 2 million women yearly suffer injuries due to domestic violence, and 30% to 50% of female homicides are committed by a present or former partner. The majority of these murder victims had either been seen in emergency rooms for prior domestic violence-related injuries, or had reported these injuries to the police. It is estimated that 50% of all acute injuries and 21% of all injuries in women requiring urgent surgery are the result of partner abuse. Data source: Medline and current literature review. Conclusions: Health care professionals in the emergency room are an important contact with the victims of domestic violence, and timely identification and intervention can save lives. Overall, upwards of 35% of all emergency room visits by women are the result of domestic violence, whether due to acute injury, problems during pregnancy, or stress-related complaints. Unfortunately, domestic abuse is infrequently disclosed voluntarily by the patient, and often overlooked by the treating physician. Thus, the purpose of this review is to familiarize surgeons with the presentation and management of victims of this hidden epidemic.
Evidence of microbial consortia metabolizing within a low-latitude mountain glacier

Carbon dioxide (CO 2 ), nitrous oxide (N 2 O), and methane (CH 4 ) concentrations of ice samples from a South American mountain glacier are larger than those in coeval polar ice cores. Of the six possible mechanisms that may cause the composition of air measured in ice cores to depart from that of the overlying troposphere (gravitational fractionation, thermal fractionation, gases trapped in refrozen meltwater, atmospheric heterogeneity, abiotic chemical reactions, and biologically mediated chemical reactions), only metabolism of a consortium of microorganisms within the ice can explain our data.
Detection of oxidative DNA damage in oesophageal biopsies of patients with reflux symptoms and normal pH monitoring

Summary Background : Gastro-oesophageal reflux has been shown to induce oxidative DNA damage. Aim : To determine whether oxidative DNA damage, detected in oesophageal biopsies by simple immunohistochemical staining, correlates with gastro-oesophageal reflux disease as determined by pH monitoring. Methods : The study included 47 patients with reflux symptoms who had oesophageal biopsy and 24-h pH monitoring studies performed within 3 months of each other with no variation in treatment in the time between the two procedures. Sections of formalin-fixed and paraffin-embedded oesophageal biopsies were stained for 8-hydroxy-2′-deoxyguanosine using the standard immunoperoxidase method. Positive nuclear immunoreactivity was considered to indicate oxidative DNA damage. Results : Seven (33%) of the 21 cases with normal 24-h pH monitoring results were negative for oxidative DNA damage, compared with only two (8%) of the 26 cases with abnormal 24-h pH results (P = 0.058, two-sided Fisher's exact test). Five of the patients with normal 24-h pH results had oesophageal biopsies performed within 24 h of the monitoring procedure and, of these, four (80%) were positive for oxidative DNA damage, including a case in which both biopsy and 24-h pH monitoring were performed on the same day whilst the patient was on proton pump inhibitor therapy. All cases with normal 24-h pH results and positive oxidative DNA damage showed features of reflux on routine morphological evaluation. Conclusions : Oxidative DNA damage can occur in the absence of acid reflux and despite adequate antisecretory therapy. This may indicate that other agents, such as bile, can induce oxidative DNA damage in an acid-suppressed environment. The significant discordance between oxidative DNA damage and 24-h pH results makes the determination of oxidative DNA damage a poor surrogate marker for 24-h pH monitoring.
Paying Attention to Pronunciation: The Role of Self‐monitoring in Perception

U It is widely recognized that a crucial component in developing effective second language pronunciation is, in fact, the development of particular listening skills. In many textbooks ostensibly dedicated to improving ESL pronunciation, a substantial number of exercises are devoted to making sure that the student, as listener, can first recognize the types of sound distinctions that are phonemic in English. As Prator and Robinett (1985) claim in the introduction to their pronunciation manual, the first step in learning to pronounce in a second language is "learning to hear and identify a sound or sound contrast when a native speaker produces it" (p. xvi). To develop this perceptual ability, most pronunciation texts offer various types of phoneme discriminaton exercises. The assumption is that the more often ESL learners can accurately identify the English sound contrasts presented, the more sensitive they will become to the basic elements in the English sound system. It should prove particularly disturbing, then, to ESL pronunciation teachers if, after a period of instruction employing such materials, a major proportion of their learners actually get worse, in terms of test scores, on a phoneme discrimination task.
Reconstructive expert system explanation

Existing explanation facilities are typically far more appropriate for knowledge engineers engaged in system maintenance than for end-users of the system. This is because the explanation is little more than a trace of the detailed problem-solving steps. An alternative approach recognizes that an effective explanation often needs to substantially reorganize the actual line of reasoning and bring to bear additional information to support the result. Explanation itself becomes a complex problem-solving process that depends not only on the actual line of reasoning, but also on additional knowledge of the domain. This paper presents a new computational model of explanation and argues that it results in significant improvements over traditional approaches. — Authors' Abstract
Abstract 3911: Functional copy number alterations (CNAS) in oral cancer

Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL Background: Alterations in DNA copy number can functionally affect genes and produce a transformed cancer phenotype. Discoevery of novel cancer genes can be facilitated by identifying genomic regions undergoing frequent, significant alteration. Array comparative genomic hybridization techniques have generated vast amounts of raw copy number data requiring computational analysis to identify aberrations likely to be functional. In this analysis, we present data from a comprehensive computational approach designed to robustly map chromosomal aberrations in oral cavity squamous cell carcinoma (OCSCC). Methods: DNA was extracted from 31 microdissected OCSCC frozen tumors and hybridized with reference DNA on the Agilent 1M copy number array, containing nearly 1 million probes across the genome at high resolution. The RAE computational framework was used to identify CNAs. In this analysis, segmentation of probe data is first performed using paired reference HapMap data and individual-tumor thresholds to account for stromal admixture and tumor heterogeneity. Scores (single-copy gain, amplification, hemizygous loss, homozygous deletion) are then assigned, followed by soft discrimination thresholding and significance testing with false discovery rate correction. Regions of interest (ROIs) are then agnostically identified as regions of significant (FDR<0.01) alteration, expanded to adjacent loci to account for spatial and amplitude uncertainty. Finally, described copy number polymorphisms were excluded. Results: 49 ROIs were identified, 27 amplification regions (chromosomes 3,4,5,7,8,9,11,16,18,20,21) and 22 deletion regions (chromosomes 2,3,4,5,7,8,9,10,13,15,16,18,19). ROIs ranged in prevalence from 6.5-77.4% of samples, and encompassed 0-483 genes (total=2799, median=4), and 0-13 microRNAs (total=77, median=0). Eleven ROIs were focal intragenic CNAs. Four ROIs contained no named genes or microRNAs. Hierarchical clustering identified 3 clusters, based on escalating levels of CNA. Complete gene details of the 49 ROIs will be presented. Conclusions: We report significant regions of CNA in oral cancer, by applying a robust computational framework to identify recurrent chromosomal aberrations in OCSCC, which represent highly significant candidate functional events. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3911. doi:10.1158/1538-7445.AM2011-3911
Attrition prevention with individuals awaiting publicly funded drug treatment

Aims. To evaluate the effectiveness of a motivational intervention to reduce attrition from a waiting list for substance abusers seeking publicly funded treatment. Design. Randomized clinical trial comparing an "attrition prevention" condition to standard care while awaiting treatment admission. Setting. A centralized substance abuse assessment and referral center in Seattle, Washington. Participants. Substance abusers (n = 654) eligible for publicly funded drug abuse treatment. Measurements. Alcohol and drug use, substance-related negative consequences, areas in need of help, perceived need for help, emotional status, readiness to change, reasons for seeking and perceived barriers to entering treatment. Findings. Overall, approximately 70% of clients entered treatment, and of these approximately 70% completed their assigned treatment. Those who entered treatment showed significant reductions in substance use and improved psychosocial function at a short-term 3-month follow-up. However, the attrition prevention intervention had no differential effect on treatment entry, completion or outcome compared to the standard waiting list. Further, there were no differences across therapists on these outcome measures. Conclusions. A motivational attrition prevention intervention did not enhance treatment entry, completion or outcome among treatment-seeking substance abusers. It is suggested that alternative strategies, such as contingency management and case management, may help facilitate treatment entry for individuals seeking publicly funded treatment.
Tachyons, broken Lorentz invariance, and a penetrable light barrier

We present a class of theories differing from special relativity in the existence of a preferred reference frame and deviations from the Lorentz transformations. Finally, the theories can be made to agree with existing experiments, but predict, for v close enough to c, departures from the special-relativistic dependence of masses and lifetimes on velocity, and allow the possibility, at least in principle, of accelerating ordinary particles to speeds greater than c.
Production of vitamers of biotin by Corynebacterium xerose.

Abstract Corynebacterium xerose ATCC No. 9016 appears to produce four vitamers of biotin as measured by S. cerevisiae assay when grown in a chemically defined medium containing pimelic acid. That one of these vitamers is probably dethiobiotin has been concluded on the basis of bioautographic analysis in three solvent systems, avidin combinability, and destruction by acid hydrolysis. From the chromatographic results, none of the vitamers appears to be oxybiotin. Nor do the biotin sulfoxides or biocytin appear to be among these vitamers. C. xerose ATCC No. 9016 produces biotin-like activity when grown in the presence of suberic and azelaic acids but not in the presence of adipic or α-aminoadipic acids. Two other strains of C. xerose give evidence of biotin-like activity in the culture fluids after growth in the presence of pimelic acid.
Matching simulation and experiment (extended abstract): a new simplified model for simulating protein folding

Simulations of simplified protein folding models have provided much insight into solving the protein folding problem. We propose here a new off-lattice bead model, capable of simulating several different fold classes of small proteins. We present the sequence for an a/b protein resembling the IgG-binding proteins L and G. The thermodynamics of the folding process for this model are characterized using the multiple multi-histogram method combined with constant-temperature Langevin simulations. The folding is shown to be highly cooperative, with chain collapse nearly accompanying folding. Two parallel folding pathways are shown to exist on the folding free energy landscape. One pathway contains an intermediate—similar to experiments on protein G, and one pathway contains no intermediates—similar to experiments on protein L. The folding kinetics are characterized by tabulating mean-first passage times, and we show that the onset of glasslike kinetics occurs at much lower temperatures than the folding temperature. This model is expected to be useful in many future contexts; investigating questions of the role of local versus non-local interactions in various fold classes, addressing the effect of sequence mutations affecting secondary structure propensities, and providing a computationally feasible model for studying the role of solvation forces in protein folding.
Transfusion-Related Acute Gut Injury: Necrotizing Enterocolitis in Very Low Birth Weight Neonates after Packed Red Blood Cell Transfusion

Objective This is a repeat cohort study in which we sought to determine whether an association of necrotizing enterocolitis (NEC) Study design All very low birth weight neonates with NEC Stage ≥IIB admitted over an 18-month period were categorized for NEC: (1) Results Eight hundred eighty-three admissions over 18 months were reviewed; 256 were very low birth weight that resulted in 36 NEC cases and 25% were associated with PRBC (n = 9). PRBC-associated cases had lower birth weight, hematocrit, and rapid onset of signs ( 2 = 170.7, df=40; P Conclusions We conclude that PRBC-related NEC exists. Transfusion-related acute gut injury is an acronym we propose to characterize a severe neonatal gastrointestinal reaction proximal to a transfusion of PRBCs for anemia. The convergence at 31 weeks postconceptual age approximates the age of presentation of other O 2 delivery and neovascularization syndromes, suggesting a link to a generalized systemic maturational mechanism.
Pathologic features of bladder tumors after nephroureterectomy or segmental ureterectomy for upper urinary tract transitional cell carcinoma.

OBJECTIVES To determine the pathologic features of bladder tumors after nephroureterectomy or segmental ureterectomy for upper urinary tract transitional cell carcinoma (UUT-TCC). METHODS From 1993 to 2003, 82 patients without a history of bladder cancer underwent nephroureterectomy or segmental distal ureterectomy for UUT-TCC. We reviewed the pathologic features of the subsequent bladder tumors, including stage, grade, and progression to cystectomy in these patients at a median follow-up of 44.1 months. RESULTS A total of 36 (44%) of 82 patients developed bladder tumors after definitive therapy for UUT-TCC at a mean interval of 13.9 months. The mean number of bladder tumors diagnosed per patient in the follow-up interval was 2.1 (range 1 to 6), for a total of 74 bladder tumors. Of the 74 bladder tumors, 71 (96%) were superficial (Stage Ta, Tis, T1), 49 of these superficial tumors (69%) being low grade (grade 1 and 2) and 22 (31%) high grade (grade 3). Three patients had high-grade, muscle-invasive disease, and all progressed to cystectomy during follow-up. A greater than 75% concordance was found in pathologic grade between the UUT lesion and subsequent bladder tumors. The stage of the UUT malignancy, however, did not correlate with subsequent bladder tumor pathologic findings. CONCLUSIONS Bladder tumors developed in 44% of patients after treatment of UUT-TCC. Of these bladder tumors, over 60% were superficial, low-grade lesions, yielding a similar pathologic distribution to that of bladder cancer de novo. The grade, but not the stage, of the UUT tumors correlated with the pathologic findings of subsequent bladder tumor recurrence. Aggressive surveillance with cystoscopy and urinary cytology after surgical management of UUT-TCC is imperative.
Suppression of Listeria monocytogenes Scott A in Fluid Milk by Free and Liposome-Entrapped Nisin

Nisin is an antimicrobial polypeptide inhibitory toward Gram-positive bacterial pathogens, including Listeria monocytogenes. Encapsulating nisin in lipid nanocapsules (i.e., liposomes) has been shown to protect antimicrobial functionality in complex food matrices. The capacity of liposomes to encapsulate a fluorescent reporter was determined via spectroscopy. Survival and growth of L. monocytogenes incubated in fluid milk containing 50 IU/ml free or liposome-entrapped nisin was assayed via periodic enumeration of survivors. Liposomes were formulated from phosphatidylcholine (PC) and phosphatidyl-DL-glycerol (PG) and prepared as PC, PC/PG 7/3 or PC/PG 6/4 (mol. fraction). Antilisterial activity of nisin-loaded liposomes was determined in ultra-high temperature processed fluid milk containing approximately 4.0 log10 CFU/ml L. monocytogenes Scott A plus liposomal or free nisin at 50 IU/mL. Samples were aerobically held at 5 or 20°C; L. monocytogenes were enumerated via plating after 0, 1, 3, 6, 12, 24, 48, and 72 incubation hours. Liposome entrapment did not enhance pathogen inhibition when compared to free nisin as a function of storage temperature or incubation duration.
Hyperoxaluria and Genitourinary Disorders in Children Ingesting Almond Milk Products

We describe 3 children presenting with hematuria, dysuria or kidney stones, and hyperoxaluria believed to be related to ingestion of excessive amounts of almond milk products. Our investigation of the oxalate content of several popular plant-based milk substitutes indicates that almond milk products are a particularly rich source of dietary oxalate. All genitourinary and urinary metabolic disturbances resolved after discontinuation of almond milk ingestion. Therefore, pediatricians should be aware of this potential link.
Image-Based Modeling of Flow in Natural Partially Cemented Fractures

Natural fractures in unconventional reservoirs are characteristically filled or lined with mineral cement. Despite the significance of natural fractures for stimulation and production, the effect of cement linings on fracture fluid flow is poorly understood. In this work, we focus on correlating permeability with geometric tortuosity of both pore (fracture) space and individual fluid phases for fractured Torridonian Sandstone, an outcrop analog for tight sandstone reservoirs. The input geometries for simulation are binarized, high-resolution microtomography images at two different resolutions. We use a combination of lattice-Boltzmann simulation and the level-set-method-based progressive-quasistatic (LSMPQS) algorithm to characterize the capillary dominated displacement properties (capillary pressure-saturation and relative permeability-saturation relationships) of the natural, partially cemented fractures within. We also use image analysis to characterize the connectivity and tortuosity of the pore space, as well as individual fluid phases at different saturations. The partially cemented fractures of the Torridonian Sandstone are found to be very constricted, with many crystals bridging across the fracture but keeping large portions open to flow. The adjacent matrix, however, is almost completely cemented. We compare the tortuosity distribution in the Torridonian Sandstone with those in other porous media. We find that the fractures have considerably narrower tortuosity distribution when compared to other porous materials. Despite their cement lining, these fractures provide the most direct path across the material. In addition, we find that tortuosity in both consolidated porous media and partially cemented fractures increases with an increase in the amount of carbonate or quartz overgrowth cement. When analyzing tortuosity of different fluid phases, we find very weak correlation between fluid phase tortuosity and relative permeability. Relative permeability correlations and capillary pressure curves found here can be used in reservoir simulators to model recovery of hydrocarbons in fractured tight reservoirs.