cssi/SciSciGPT-SciSciNet huggingface dataset:
Speeding up the detection of tandem repeats over the edit distance

A tandem repeat in a string is a sequence of two or more contiguous, approximate copies of a pattern. Finding an efficient, deterministic algorithm to perform an exhaustive search for tandem repeats in a string is an important and practical problem, due to the relevance of tandem repeats in several areas, including human identity testing, disease diagnosis, sequence homology, and population studies. In this paper, we present an O(nklog^2k+Occ) algorithm to find all approximate tandem repeats within a sequence of length n, allowing at most k insertions, deletions and mismatches in each repeat. Our algorithm utilizes the Lempel-Ziv factorization which was previously used in algorithms that locate exact tandem repeats, and algorithms that locate tandem repeats with only mismatches. The LZ framework is combined with speedups for calculating the edit distance, achieving a new and efficient exhaustive search for finding tandem repeats in a string.
Long-term outcome of a third anti-TNF monoclonal antibody after the failure of two prior anti-TNFs in inflammatory bowel disease.

Summary Background A significant proportion of patients with IBD lose response to anti-TNF therapies. There is limited knowledge of the long-term outcomes of those who have failed two anti-TNF agents and commenced a third. Aim To examine the safety and efficacy of third anti-TNF treatment after failure of two prior anti-TNF agents in patients with inflammatory bowel disease. Methods This was a retrospective study of all IBD patients [Crohn's disease (CD), ulcerative colitis (UC)] treated with a third anti-TNF agent after loss of response or intolerance to two prior anti-TNF agents at a single tertiary North American centre. Disease activity, drug therapy and Montreal phenotypes were noted at disease onset and commencement of the third anti-TNF agent. Kaplan–Meier estimates were used to calculate the probability of remaining on the third anti-TNF agent and to identify predictors of long-term clinical response. Results A total of 63 patients (64% women, 57 CD and 6 UC) were included in the analysis. The mean disease duration at initiation of third anti-TNF was 12 years. Thirty-five (55.6%) patients discontinued the third anti-TNF after a mean of 13.2 months. Probability of remaining on the third anti-TNF was 0.69, 0.55, 0.37 and 0.25 at 6, 12, 24 and 36 months respectively. Prior primary nonresponders to the first anti-TNF agent [hazard ratio (HR) 6.4, 95% CI 2.5–16.1] and persistent disease activity at 3 months after commencement of a third anti-TNF (HR 3.2, 95% CI 1.3–7.8) predicted poorer response. Conclusions Over half of patients with inflammatory bowel disease, initiated on a third anti-TNF agent after failure of two prior anti-TNF drugs, are able to remain on the third anti-TNF at 1 year.
Rhinoplasty in the graft-depleted patient

As more surgeons become familiar with varying autogenous donor sites, a group of secondary rhinoplasty patients is emerging with donor-site depletion, having already had septoplasty or harvesting of one or more auricular, calvarial, iliac, or rib grafts. Even the primary patient may be donor-site depleted if the septum is bony and yields minimal usable cartilage. This article outlines some principles for achieving acceptable functional and aesthetic results with suboptimal or minimal graft material.
Efficient spin squeezing with optimized pulse sequences

Spin squeezed states are a class of entangled states of spins that have practical applications to precision measurements. In recent years spin squeezing with one-axis twisting (OAT) has been demonstrated experimentally with spinor Bose-Einstein condensates (BECs) with more than ${10}^{3}$ atoms. Although the noise is below the standard quantum limit, the OAT scheme cannot reduce the noise down to the ultimate Heisenberg limit. Here we propose an experimentally feasible scheme based on optimized quantum control to greatly enhance the performance of OAT to approach the Heisenberg limit, requiring only an OAT Hamiltonian and the use of several coherent driving pulses. The scheme is robust against technical noise and can be readily implemented for spinor BECs or trapped ions with current technology.
Photoautotrophic potato cells: Transition from heterotrophic to autotrophic growth

Cells of potato (Solanum tuberosum L.) were obtained which were capable of photoautotrophic growth in liquid suspension culture under a photon flux density of 90–110 μmol m−2 s−1 PAR and in an atmosphere enriched with 2% CO2. These photoautotrophic cells contained between 100 to 200 μg Chl (g fresh weight)−1 and fixed CO2 at a maximum rate of 16 μmol CO2 (g fresh weight)−1h−1. In order to obtain cells capable of photoautotrophic growth it was necessary to adapt highly chlorophyllous heterotrophic cells (>50 μg Chl (g fresh weight)−1) for growth in medium with 2.5 g sucrose 1−1 (photomixotrophic cells). The photomixotropic cells had a Chl content of ca 100 μg Chl (g fresh weight)−1 and were capable of photosynthetic activity which allowed them to survive after sugars had been depleted from the medium. It was from the photomixotrophic cells that cells capable of photoautotrophic growth were obtained. Heterotrophic cells initially established in liquid medium with 25 g sucrose I−1 from chlorophyllous callus contained about 50 to 150 μg Chl (g fresh weight)−1. However, after 5 to 10 passages the Chl content decreased to a maximum of 15 μg Chl (g fresh weight)−1. These cells could not be adapted to photomixotrophic or photoautotrophic growth. These cells also were not able to regain Chl or initiate high rates of CO2 fixation during the stationary phase of growth as did photomixotrophic cells or chlorophyllous heterotrophic cells. The loss of Chl exhibited by the cells during adaption to heterotrophic growth could be attributed at least in part to unbalanced growth (when cell division and growth exceeds Chl accumulation). Sucrose appeared to have an inhibitory effect directly on photosynthesis independent of Chl accumulation.
Metabolism of taurine in the growing chicken.

Abstract 1. 1. When taurine-S 35 was injected into young chickens fed a diet slightly deficient in the sulfur-containing amino acids, only 16% of the S 35 was excreted after 1 day and a total of 39% 9 days after the injection. 2. 2. The incorporation of S 35 into tissues 1 day after injection of taurine-S 35 varied considerably. The heart, tissues of the gastrointestinal tract, and the spleen contained the highest concentration of radioactivity. 3. 3. Only a trace of S 35 could be recovered in the protein fraction of these tissues; small amounts occurred in the bile acid fraction with the major portion in the protein-free extracts. The radioactivity in these extracts was largely accounted for as taurine-S 35 . In the liver and kidney, however, a taurine-containing conjugate accounted for a large portion of the S 35 . 4. 4. When taurine-S 35 was administered orally, 80% of the S 35 recovered in the excreta was accounted for as taurine, 4% as bile acids, 2% as sulfate, 7% as unidentified compounds, and 7% as a compound apparently identical to the taurine conjugate found in tissues. This compound yielded taurine-S 35 , ornithine, and several other ninhydrin-reactive compounds after acid hydrolysis. 5. 5. When arginine was administered concomitantly with taurine-S 35 , excretion of S 35 was greatly diminished.
The “other” COPD

Chronic obstructive pulmonary disease (COPD) is currently a leading cause of death worldwide, but the burden of disease shared by females is particularly heavy. In the USA alone, the number of deaths among females has quadrupled since 1980 and now exceeds male deaths from COPD; hospitalisation of females due to the disease also now surpasses that of males [1]. Concerns have also been raised that females may be more susceptible to the effects of tobacco smoke with respect to development of impaired lung function [2]. Other differences in symptom presentation and greater exacerbation frequency among females have also been noted [3, 4]. However, when viewed globally, the impact of this disease in females is influenced not only by the burden of tobacco use but also the less discussed and less well studied COPD related to biomass smoke exposure. Biomass fuel in particular can be dangerous, as the fine particles derived from solid-fuel combustion can be breathed more deeply into the lungs [5]. It has been demonstrated that the indoor particulate concentrations resulting from biomass fuel combustion can be even higher than the outdoor particulate concentrations seen in even the most polluted cities [5]. Furthermore, the frequency and duration of contact with the polluted air also increases the risk of respiratory impairment. The widespread practice of using …
Light-neutrino masses and the strong CP problem

A minimal extension of the standard model is proposed to incor- porate the light-neutrino masses and the resolution of the strong CP problem. A unique light pseudo-Goldstone boson, whose coupling to the electron is 1 or 2 orders of magnitude greater than that of the conventional hadronic axion, arises from the model. The scale of Peccei-Quinn symmetry breaking is shown to be greater than 10/sup 10/ GeV through its connection to the light-neutrino masses, and is further constrained if the (hypothetical) fourth family of quarks and leptons exist.
Moving at Mid-Career

. Discernment about when to make career moves is often clouded by a host of competing desires and motivations. In this essay the author peels back layers of vocational choices in order to begin to reveal motivations behind those choices. Questions pertaining to notions of prestige, imaginative projection into a new position, clarity about what one values in theological education, and shifts in thinking about pedagogy in a new context are explored.
Information processing-related infrastructural antecedents of manufacturing flexibility – a real options perspective

The relationship between manufacturing flexibility and environmental uncertainty has been widely studied; however, research involving manufacturing flexibility and associated infrastructural antecedents is sparse. In this paper, using the real options perspective, we develop a research model to explicate management support’s influence on an organisation’s manufacturing flexibility. We use a second-order, multi-dimensional construct and survey data collected from US manufacturers to test our hypotheses. The study provides evidence to suggest that management support through teamwork, information systems effectiveness, and integrated supply chain effectiveness enhances an organisation’s manufacturing flexibility.
Volatile Profiles of Young Leaves of Rutaceae spp. Varying In Susceptibility to the Asian Citrus Psyllid (Hemiptera: Psyllidae)

require the newly expand-ing terminal leaves (flush) of citrus and related species in order to complete their development (Shavankar et al. 2000; Michaud 2004). The study presented here examined host plant vola-tiles from uninfested flush and young leaves of citrus genotypes that were reported to vary in susceptibility as measured by colonization by
Hormone induction of luteinization and prostaglandin endoperoxide synthase-2 involves multiple cellular signaling pathways.

To determine the cellular signaling pathways involved in granulosa cell luteinization, known activators of protein kinase-A (LH and FSH) and protein kinase-C [GnRH and phorbol 12-myristate 13-acetate (PMA)] as well as inhibitors of tyrosine kinases (AG18 and genistein) were tested in an in vitro system using specific markers of luteinization (cell hypertrophy, side-chain cleavage cytochrome P450, and progesterone) and ovulation [prostaglandin endoperoxide synthase-2 (PGS-2)]. When preovulatory follicles were incubated in the presence of an ovulatory (500 ng/ml) dose of LH or high GnRH (1 microM), the granulosa cells harvested from these follicles assumed and maintained a stable luteal cell phenotype in vitro. Granulosa cells harvested from follicles incubated in subovulatory doses of LH (5 and 50 ng/ml), lower doses of GnRH (5, 50, and 500 nM), or PMA alone were unable to form a stable luteal cell phenotype. When PMA was combined with subovulatory doses of LH, granulosa cells luteinized, and PGS-2 protein...
Adaptive mechanisms of left ventricular diastolic function to the physiologic load of pregnancy.

Background: Pregnancy is associated with marked alteration in cardiovascular hemodynamics. Recent reports have characterized the effects on cardiac systolic function. Little has been written on the influences of loading conditions on Doppler measures of diastolic function during pregnancy. Hypothesis: Stage of pregnancy has an impact on Doppler indices of diastolic function independent of loading conditions, systolic function, and heart rate. Method: Thirty healthy women were prospectively evaluated by serial echocardiography and Doppler examinations at six time periods: 10-12, 18-20, 28-30, 36-38 weeks gestation, 2-4 and 12-14 weeks postpartum. The related effects on indices of diastolic function and its interaction with load, heart rate, mass, and systolic function were determined. Results: Compared with the nonpregnant state, early (E) velocity increased (0.7 ± 0.1-0.9 ± 0.1 m/s, p = 0.0001), peaking at 18 weeks and returning to normal levels during late pregnancy. Atrial phase (A) velocity peaked at 18 weeks (0.48 ± 0.12-0.60 ± 0.13 m/s, p = 0.0001), remaining high throughout the rest of pregnancy. Consequently, the E/A ratio fell significantly during late pregnancy, from 1.9 ± 0.4 to 1.4 ± 0.3 (p = 0.02). In addition, mean acceleration was significantly increased in early pregnancy with a peak at 18 weeks (7.4 ± 1.3 m/s2), returning to nonpregnant level at term (5.7 ± 1.4 m/s2, p = 0.0001). Generalized estimating equation using multivariate regression analysis demonstrated that rising heart rate and stroke volume index had an independent effect on A velocity, and that contractility and preload had an independent effect on E velocity. Pregnancy itself had an independent influence on early filling, not explained by the other parameters. Conclusions: During normal pregnancy, there is a reversible shift in transmitral flow velocities from early to late filling with a decrease in acceleration, consistent with an increase in ventricular compliance. Changes in heart rate, preload, and contractility, as well as stage of pregnancy influence this alteration.
Immediate-early Genes and Synaptic Function

Classical studies have demonstrated a role for protein synthesis in long-term memory. The focus of our research is to identify the proteins that are essential for memory and to discover how they contribute to activity-dependent neuronal plasticity. We have developed whole-animal models that maximize the induction of activity-dependent genes and have used differential cloning techniques to identify a set of novel, neuronal immediate-early genes (IEGs). Neuronal IEGs encode transcription factors, cytoskeletal proteins, growth factors, metabolic enzymes, and proteins involved in signal transduction. The biochemical and cell biological properties of these molecules provide important insights into mechanisms that contribute to neuronal plasticity. Recently, we identified a subset of IEGs that appear to function at the synapse. These molecules extend the functional repertoire of IEGs and may provide insight into how IEGs can contribute to synapse-specific plasticity.
Life, death, and lawfulness on the electronic frontier

To facilitate users’ ability to make sense of large collections of hypertext we present two new techniques for inducing clusters of related documents on the World Wide Web. Users’ ability to find relevant information might also be enhanced by finding lawful properties of document behavior and use. We present models and analyses of document use and change for the World Wide Web.
PRINCIPAL COMPONENTS, B-SPLINES, AND FUZZY SYSTEM REDUCTION

This paper proposes to use the method of principal components to reduce the dimensionality of input space and the B-splines to represent the membership functions of input variables. A model reduction strategy, which is based on Johansen’s optimality theorem, also suggested. The utility of this approach is illustrated using a fuzzy system modeling example.
Synthesis, structures and preliminary biological screening of bis(diphenyl)chlorotin complexes and adducts : Ph2ClSn-CH2-R-CH2-SnClPh2, R = p-C6H4, CH2CH2

The reaction between ClCH 2 –R–CH 2 Cl, R = p -C 6 H 4 , and [Ph 3 Sn] − Li + yields Ph 3 Sn–CH 2 –R–CH 2 –SnPh 3 ( 1 ) in high yield. The related known compound R = CH 2 CH 2 ( 1a ) is synthesized by the reaction of the di-Grignard reagent BrMg(CH 2 ) 4 MgBr with two equivalents of Ph 3 SnCl. Cleavage of a single Sn–Ph group at each tin centre of both compounds using HCl/Et 2 O yields the corresponding bis-chlorostannanes Ph 2 ClSn–CH 2 –R–CH 2 –SnClPh 2 , R = (CH 2 ) 4 ( 2 ) and R = C 6 H 4 ( 3 ), respectively. Compounds 1 , 2 and 3 are crystalline solid materials and their single crystal X-ray structures are reported. In the solid state both 2 and 3 form self-assembled ladder structures involving alternating intermolecular Cl–Sn⋯Cl and Cl⋯Sn–Cl bonded chains at both ends of the distannanes with 5-coordinate tin atoms. Recrystallization of 3 from CH 2 Cl 2 in the presence of DMF yields the bis-DMF adduct ( 4 ) in which no self-assembled structures were noted. Evaluation of the chlorostannanes 2 and 3 against a suite of bacteria, Staphylococcus aureus , Escherichia coli and Photobacterium phosphoreum is reported and compared to the related mono-chlorostannanes Ph 2 (CH 3 )SnCl and Ph 2 (PhCH 2 )SnCl.
What can you teach about cardiopulmonary resuscitation (CPR) in 30 seconds? Evaluation of a television campaign.

This study evaluated an 8-month media campaign, implemented in western Washington, to educate people on the basic steps of cardio-pulmonary resuscitation (CPR) for cardiac arrest. A telephone survey was conducted with a total of 384 adults randomly selected from two towns, one that had been exposed to the campaign (intervention town) and one that had not been exposed to the campaign (comparison town). Results showed that respondents in the intervention town were more likely than respondents in the comparison town to report (a) having heard messages on CPR in the past month, (b) having seen the CPR media campaign, and (c) knowing the three basic steps of CPR. Respondents who had seen the campaign evaluated it very favorably. There were no differences between respondent groups in self-reported CPR training or intentions to perform CPR, suggesting that the campaign had a greater impact on knowledge and awareness than on intentions and behavior.
When Supervising Physicians See Patients Strategies Used in Difficult Situations

As part of training in an internal medicine ambulatory clinic, a supervising physician may see a patient who has already been seen by a trainee. The authors conducted qualitative analyses of videotapes of medical interactions and of the participants commentaries regarding the interactions. They found that physicians and trainees showed concerns regarding the emerging definitions of their relationship to each other and to the patient in opening the interaction and in taking history from the patient. The concerns experienced by supervising physicians and by trainees are described arid the strategies used in opening the interaction and in interviewing the patient are analyzed. The article concludes with an evaluation of the strategies used to manage interactional difficulties.
Protection of arc furnace supply systems from switching surges

An arc furnace supply system consists of one or several furnace transformers connected to a larger supply transformer through cables and overhead lines. In a conventional arc furnace, controlled arc between three phase electrodes heats a scrap material to the melting temperature. Due to the nature of the metallurgical processes involved, arc furnace transformers are very frequently energized and de-energized at their higher voltage side. Several transformer failures related to switching transients have been experienced in different arc furnace supply systems. The paper presents a practical approach to study switching transients in actual arc furnace systems. Both field tests and computer simulations have shown that current chopping and repetitive reignitions in circuit-breakers result in severe overvoltages at transformer terminals. An RC filter can reduce the risk of failure due to switching surges and improve the transformer protection. A practical approach is presented for selection of the optimum filter parameters.
On the performance of peaky capacity-achieving signaling on multipath fading channels

We analyze the error probability of peaky signaling on bandlimited multipath fading channels, the signaling strategy that achieves the capacity of such channels in the limit of infinite bandwidth under an average power constraint. We first derive an upper bound for general fading, then specialize to the case of Rayleigh fading, where we obtain upper and lower bounds that are exponentially tight and, therefore, yield the reliability function. These bounds constitute a strong coding theorem for the channel, as they not only delimit the range of achievable rates, but also give us a relationship among the error probability, data rate, bandwidth, peakiness, and fading parameters, such as the coherence time. They can be used to compare peaky signaling systems to other large bandwidth systems over fading channels, such as ultra-wideband radio and wideband code-division multiple access. We find that the error probability decreases slowly with the bandwidth W; under Rayleigh fading, the error probability varies roughly as W/sup -/spl alpha//, where /spl alpha/>0. With parameters typical of indoor wireless situations, we study the behavior of the upper and lower bounds on the error probability and the reliability function numerically.
The Challenge Of Recruiting And Retaining Teachers In The United States: Is This A Compensation Or Demand Issue?

School districts and educational leaders as well as administrators across the nation believe they are facing teacher shortages. There is a widely-held belief that they are facing a critical shortage of teachers, primarily due to recent increases in teacher retirements and student enrollments. However, others believe that this is a superficial conclusion drawn from growing student enrollments, smaller class sizes, and retirements. The assumption incorrectly surmised is that there is not enough supply, in this case, of new teachers entering the profession, to meet demand. Studies looking at both supply and demand for new teachers entering the profession have found that the demand for teachers has indeed grown over the last decade. However, many researchers contend that there is an ample supply of teachers to not only meet, but exceed the demand. This paper explores the two sides of this topic and provides recommendations for administrators and educational leaders.
SCALE SELECTION FOR GEOMETRIC FITTING IN NOISY POINT CLOUDS

In recent years, there has been a resurgence in the use of raw point cloud data as the geometric primitive of choice for several modeling tasks such as rendering, editing and compression. Algorithms using this representation often require reliable additional information such as the curve tangent or surface normal at each point. Estimation of these quantities requires the selection of an appropriate scale of analysis to accommodate sensor noise, density variation and sparsity in the data. To this goal, we present a new class of locally semi-parametric estimators that allows analysis of accuracy with finite samples, as well as explicitly addresses the problem of selecting optimal support volume for local fitting. Experiments on synthetic and real data validate the behavior predicted by the model, and show competitive performance and improved stability over leading alternatives that require a preset scale.
UPTAKE, LOCALIZATION, AND NONCARBOXYLASE ROLES OF BIOTIN*

▪ Abstract Evidence is emerging that biotin participates in processes other than classical carboxylation reactions. Specifically, novel roles for biotin in cell signaling, gene expression, and chromatin structure have been identified in recent years. Human cells accumulate biotin by using both the sodium-dependent multivitamin transporter and monocarboxylate transporter 1. These transporters and other biotin-binding proteins partition biotin to compartments involved in biotin signaling: cytoplasm, mitochondria, and nuclei. The activity of cell signals such as biotinyl-AMP, Sp1 and Sp3, nuclear factor (NF)-κB, and receptor tyrosine kinases depends on biotin supply. Consistent with a role for biotin and its catabolites in modulating these cell signals, greater than 2000 biotin-dependent genes have been identified in various human tissues. Many biotin-dependent gene products play roles in signal transduction and localize to the cell nucleus, consistent with a role for biotin in cell signaling. Posttranscript...
Chronic non-invasive corticosterone administration abolishes the diurnal pattern of tph2 expression.

HPA axis; Stress; ACTH; Adrenocorticotropin; Depression; Anxiety; Raphe; tph2; Tryptophan hydroxylase; Serotonin; 5-HT; Glucose Summary Both hypothalamic—pituitary—adrenal (HPA) axis activity and serotonergic systems are commonly dysregulated in stress-related psychiatric disorders. We describe here a non-invasive rat model for hypercortisolism, as observed in major depression, and its effects on physiology, behavior, and the expression of tph2, the gene encoding tryptophan hydroxylase 2, the rate-limiting enzyme for brain serotonin (5-hydroxytryptamine; 5-HT) synthesis. We delivered corticosterone (40 mg/ml, 100 mg/ml or 400 mg/ml) or vehicle to adrenal-intact adult, male rats via the drinking water for 3 weeks. On days 15, 16, 17 and 18, respectively, the rats’ emotionality was assessed in the open-field (OF), social interaction (SI), elevated plus-maze (EPM), and forced swim tests (FST). On day 21, half of the rats in each group were killed 2 h into the dark phase of a 12/12 h reversed light/ dark cycle; the other half were killed 2 h into the light phase. We then measured indices of HPA axis activity, plasma glucose and interleukin-6 (IL-6) availability, and neuronal tph2 expression at each time point. Chronic corticosterone intake was sufficient to cause increased anxiety- and depressivelike behavior in a dose-dependent manner. It also disrupted the diurnal pattern of plasma adrenocorticotropin (ACTH), corticosterone, and glucose concentrations, caused adrenal atrophy, and prevented regular weight gain. No diurnal or treatment-dependent changes were found for plasma concentrations of IL-6. Remarkably, all doses of corticosterone treatment abolished the diurnal variation of tph2 mRNA expression in the brainstem dorsal raphe nucleus (DR) by elevating the gene’s expression during the animals’ inactive (light) phase. Our data demonstrate that chronic elevation of corticosterone creates a vulnerability to a depression-like syndrome that is associated with increased tph2 expression, similar to that observed in depressed patients.
Relational Vulnerabilities of Incarcerated and Reentry Mothers: Therapeutic Implications

A qualitative study involving a follow-up interview with 10 incarcerated and reentry mothers in rural southwest and central Virginia was conducted to explore the influence that women's close relationships have on their reentry experiences with their families. The Vulnerability Conceptual Model (VCM) was used to sensitize an examination of how incarcerated and reentry mothers negotiate relational vulnerabilities in the context of varying situational vulnerability. Grounded theory analysis revealed three themes that characterized relational vulnerabilities. Given our focus on close relationships and the potential of the VCM to identify opportunities for resilience and vulnerability, we highlighted the influence of ambiguous and ambivalent relationships and unresolved loss and grief due to relationship dissolution or the death of a parent, sibling, child, or intimate partner in the reentry process. The data revealed two types of reentry mothers with divergent trajectories for social reintegration. Implications of these types for therapeutic treatment approaches for reentry women are discussed.
Nitrogen oxides in the boundary layer and free troposphere at the Mt. Bachelor Observatory

Abstract. Nitrogen oxide (NOx=NO+NO2) observations were made at the Mt. Bachelor Observatory in central Oregon, USA (MBO; 2.73 km above sea level) during one autumn and three springtime (15 April–20 May) periods. This is the first study to discuss interannual variability in NOx for this region. NOx concentrations (mean±1σ) for spring 2007, 2008 and 2009 were 119±65, 117±65, and 91±54 pptv, respectively. The difference in mean mixing ratios between 2007 and 2008 is not statistically significant, whereas the difference between these years and 2009 is significant (p We developed a novel means of segregating boundary layer (BL)-influenced vs. free tropospheric (FT) air. During spring 2008 we collected "chairlift soundings" of temperature, relative humidity and pressure in an effort to better understand the diurnal pattern of a BL influence at our summit station. Results from this experiment revealed that, on average, a BL influence begins around 10:00 PDT (UTC – 07:00 h) in spring. Using this information to isolate FT air, we characterize probable pollution sources and synoptic conditions for the top 20 FT NOx events over three spring campaigns. Half (n=10) of these 20 events were determined to be "Imported" events characterized by anomalously: (1) high geopotential heights off the west coast of North America, (2) warm temperatures stretching from the Aleutian Islands to Baja California, and (3) strong southwesterly winds in the Asian outflow region. Five events exhibited an influence from the North American continent. These events are characterized by very strong cyclonic behavior off the northwestern USA coast.
Toward an optimal "antiplatelet" dose of aspirin: Preliminary observations.

It remains unclear which dose of aspirin (ASA) confers the optimal antiplatelet effect. This study focuses on long-term responses to different ASA doses by selected normal subjects. Their baseline platelet aggregabilities exemplified both the average values and the extremes of hyper-and hypoaggregability. Only 41 mg ASA daily stopped all arachidonic acid aggregations and maximally spared endogenous nucleotides. When 2.8 and 9 μM adenosine diphosphate were used as the aggregants, it became evident that higher ASA doses yielded still further grades of change both in aggregation and disaggregation. Disaggregations proved of special interest: distinctive for each subject, they clearly improved more on 325 mg ASA daily than on 41 mg or 81 mg. "Low-dose" ASA, at longer dose intervals of 48 or 72 h, may not be optimal to sustain an adequate antiplatelet effect. More individualized ASA doses, based on selected in vitro measurements of platelet function, might prove useful both in reducing the size and number of cerebral ischemic infarcts and in avoiding hemorrhagic complications in certain patients.
Comparative high speed optical interconnections using thin film photodetectors embedded in polymer waveguides

As data rates increase, optical interconnections at the boards and substrate levels become interesting alternatives for high performance interconnections according to Miller (2000) and Horowitz et al. (1998). Optical interconnection using embedded thin film photodetectors (PDs) in polymer waveguides is a chip to chip optical interconnection implementation that offers high speed interconnections with the potential for high integration density. This paper reports upon the integration of independently optimized waveguides and embedded PDs onto a Si substrate that utilizes a different material for each of these three components in the integrated interconnection. For the first time, reported herein are comparative measurements of the impulse responses and coupling efficiencies for two different directly coupled waveguide structures with embedded thin film InGaAs-based photodetectors. The difference between these two structures is the position of the thin film photodetector in the waveguide core. This information enables the designer to optimize embedded active photodetector/passive waveguide interconnections, particularly for high speed or multi-drop applications.
A change-point model for identifying 3′UTR switching by next-generation RNA sequencing

Motivation: Next-generation RNA sequencing offers an opportunity to investigate transcriptome in an unprecedented scale. Recent studies have revealed widespread alternative polyadenylation (polyA) in eukaryotes, leading to various mRNA isoforms differing in their 3′ untranslated regions (3′UTR), through which, the stability, localization and translation of mRNA can be regulated. However, very few, if any, methods and tools are available for directly analyzing this special alternative RNA processing event. Conventional methods rely on annotation of polyA sites; yet, such knowledge remains incomplete, and identification of polyA sites is still challenging. The goal of this article is to develop methods for detecting 3′UTR switching without any prior knowledge of polyA annotations. Results: We propose a change-point model based on a likelihood ratio test for detecting 3′UTR switching. We develop a directional testing procedure for identifying dramatic shortening or lengthening events in 3′UTR, while controlling mixed directional false discovery rate at a nominal level. To our knowledge, this is the first approach to analyze 3′UTR switching directly without relying on any polyA annotations. Simulation studies and applications to two real datasets reveal that our proposed method is powerful, accurate and feasible for the analysis of next-generation RNA sequencing data. Conclusions: The proposed method will fill a void among alternative RNA processing analysis tools for transcriptome studies. It can help to obtain additional insights from RNA sequencing data by understanding gene regulation mechanisms through the analysis of 3′UTR switching. Availability and implementation: The software is implemented in Java and can be freely downloaded from http://utr.sourceforge.net/. Contact: ude.tijn@iewihz or ude.nnepu.dem.liam@ehzgnoh Supplementary information: Supplementary data are available at Bioinformatics online.
Current issues pertaining to the Nocardia species

Because the number of recognized Nocardia species is continuing to increase, members of the genus Nocardia are becoming increasingly difficult to identify using phenotypic criteria. Molecular techniques, such as restriction endonuclease analysis and 16S rRNA gene sequencing, have become increasingly useful methodologies for the definitive identification of clinical isolates in this genus. While molecular methods have been useful for rapid and accurate identification, their use has complicated nocardial taxonomy by revealing new, clinically relevant species that are genetically distinct from known species but which may have few distinguishing phenotypic characteristics. We present here an overview of some taxonomic issues concerning Nocardia species and describe molecular techniques that are useful in the identification of the majority of clinically relevant species.
CD4+ TCR Repertoire Heterogeneity in Schistosoma mansoni-Induced Granulomas

The hallmark of Schistosoma mansoni infection is the formation of liver granulomas around deposited ova. The initiation of granuloma formation is T cell-dependent since granulomas are not formed in their absence. We investigated whether a few T cells arrive to initiate the inflammatory lesion and subsequently expand locally, or whether a large repertoire of systemically activated T cells home to the delayed type hypersensitivity reaction induced by the ova. The TCR repertoire of single granulomas from the same liver were analyzed by PCR using Vβ-specific primers and CDR3 analysis. Each granuloma has a very diverse TCR repertoire indicating that most of the T cells recruited to these lesions are activated systemically. At the same time, sequence analysis of individually sized CDR3 products from single granuloma indicate that a fraction of T cells expand locally at the lesion site. Using TCR transgenic mice containing a pigeon cytochrome c -specific T cell population or lymphocytic choriomeningitis virus infection tracked with lymphocytic choriomeningitis virus-specific tetramers, we demonstrated that nonspecific T cells home to the granuloma if they are activated. However, recombinase-activating gene 2 −/− pigeon cytochrome c -specific TCR transgenic mice fail to form granulomas in response to S. mansoni ova even after T cell activation, suggesting a requirement for egg-specific T cells in the initiation of these inflammatory lesions. Understanding the mechanism of T cell recruitment into granulomas has important implications for the rational design of immunotherapies for granulomatous diseases.
When Family Means More (or Less) Than Genetics: The Intersection of Culture, Family, and Genomics

There is renewed interest in the use of family history to predict individual disease susceptibility, and as a result, standardized online family history tools are being developed and marketed as a “new genetic test.” It is not known how cultural variations in definitions of family influence collection of these data or what is the best format to use. This is significant given that the populations who carry the greatest burden of the target diseases have not been considered in efforts to test these tools. A qualitative study with a convenience sample of 19 Japanese Americans and Samoan Americans, two groups at high risk for type 2 diabetes, was conducted to explore the process of collecting family history. A particularly strong finding was the high degree of acceptance experienced by the participants with the process and their pride in visualizing their family graphically displayed in pedigrees. It was also found that Samoans included those linked by nonbiological ties in their families, which reflects their cultural practices. Further research is needed to assess the most effective and efficient way to gather family history given the complexities surrounding the deceptively simple concept of family.
Towards a Theor etical Fr amework for Studying the Effect of Mobile- ICT on Coor dination

The use of mobile information and communications technologies is increasing rapidly in modern organizations. We present a theory based framework for studying the effect of these technologies on coordination in organizations. Four temporal workstyles that embed the key contingencies of dependence and uncertainty from organizational theory, and a set of fundamental question about coordination and mobility, provide the basis for the framework. We apply the framework to four mini-cases of coordination that include some element of mobility to gain initial insight into the effects of m-ICTs. The next steps include a more extensive meta-study of the literature to bolster these initial findings and to provide a foundation for the creation of a design theory
Economic Scarcity and Political Philosophy Ancient and Modern Views

The history of political philosophy exhibits two fundamentally opposed responses to economic scarcity. The classical view, exemplified by Aristotle's Politics, accepts scarcity as an inevitable feature of human existence, but endeavors to direct at least some individuals toward a life of virtue that transcends the concern with economic acquisition. Aristotle rhetorically exaggerates nature's beneficence to humans in order to facilitate this goal. A concomitant of his approach is the acceptance of slavery, despite its acknowledged injustice, as the precondition of the leisure essential to the practice of virtue by the city's governing class. In contrast, the modern doctrine, as expounded in Montaigne's Essays, emphasizes the natural neediness of humans and their consequent need to ameliorate their condition by the technological mastery of nature. The modern view aims to liberate human acquisitiveness from the moral and political restraints that both classical and medieval thinkers had endeavored to impose ...
Fatigue characteristics of McKibben artificial muscle actuators

The McKibben artificial muscle is a pneumatic actuator whose properties include a very high force to weight ratio. This characteristic makes it very attractive for a wide range of applications such as mobile robots and prosthetic appliances for the disabled. Typical applications often require a significant number of repeated contractions and extensions or cycles of the actuator. This repeated action leads to fatigue and failure of the actuator, yielding a life span that is often shorter than its more common robotic counterparts such as electric motors or pneumatic cylinders. In this paper, we develop a model that predicts the maximum number of life cycles of the actuator based on available uniaxial tensile properties of the actuator's inner bladder. Experimental results, which validate the model, reveal McKibben actuators fabricated with natural latex rubber bladders have a fatigue limit 24 times greater than actuators fabricated with synthetic silicone rubber at large contraction ratios.
Harvesting and conservation: are both possible for the palm, Iriartea deltoidea?

Abstract We consider the mechanism of certification to encourage sustainable harvesting and best management practices of Iriartea deltoidea Ruiz and Pavon, in the context of current land use and agricultural management in Amazonian Ecuador. Interviews and observations with harvesters, storeowners, and furniture-makers provided information about current and potential markets for goods made from the palm. To understand the demographic variables that are critical for population stability, data from five plots in each of three different forest types (mature, secondary, and dissected) were collected. Matrix models were used to develop harvesting simulations through which biological constraints on sustainable harvesting were explored. These simulations suggest that sparing individuals 5–15 m tall when pastures are cleared and adding this palm to current agroforestry polycultures can improve the likelihood of sustainable harvesting for this species. Results showed that harvesting Iriartea could fit within current land use. Some forest colonists clear pastures to graze cattle, while others devote land to agriculture, including polycultures of annuals and perennials. In either case, palms can be left standing when forests are cleared. Swidden agriculture (slash and burn or slash and mulch) depends on a fallow period during which secondary forest may begin to regenerate. These secondary forests are ideal locations for extraction of forest products that fit within the cycle of fallow regeneration in areas near human settlements. Sparing Iriartea individuals 5–15 m tall could benefit agriculture, encourage the sustainability of future harvests, and help ensure the future of this palm as a part of the Amazonian landscape. Interviews with staff of governmental and non-governmental conservation organizations investigated the policy context for certification as a mechanism for conservation. Establishing guidelines for harvesting requires input from all stakeholders in the decision, not simply an ecological analysis. Such guidelines for certifying good management practices, if they are developed, should include provisions for monitoring unanticipated consequences of harvesting or changes in future environmental conditions. Transportation issues and stem drying processes need to be addressed if efforts to expand markets are to succeed. More generally, guidelines for management of forest resources can be improved by combining ecological and social research perspectives; the potential for carrying out such guidelines can be improved by incorporating the knowledge of local forest dwellers and NGOs.
Combination and structure, not gradedness, is the issue.

We agree that connectionist networks are not always analogy mechanisms. Our point (based on explications by McClelland and other connectionists) is that pattern associators (the most common connectionist model of the past tense) tend towards analogy when learning competing patterns under standard training regimes. This is what gives such models their predictive power with irregular forms. The claim that some connectionist model can, given a specific architecture, training schedule and input features, approximate any linguistic phenomenon might be true, but it is in danger of reducing connectionism to a universal statistical approximation technique rather than a source of empirical predictions. Language cannot be treated as just a collection of ‘regularities in the input’ that can be approximated by some mechanism; those regularities are themselves the products of human minds and need to be explained.
SEPIC converter to perform power factor correction in a ballast for fluorescent lamps

Due to their inherent advantages, electronic ballasts for gas discharge lamps have found widespread application in recent years. But, up to now, each ballast had to be tailored to fit a given lamp, resulting in a multitude of ballasts, that differ only by their operating parameters. One important requirement in order to operate different lamps with the same ballast was the availability of cost-effective microcontrollers which allow a great amount of flexibility. The second barrier to overcome was the restriction of a fixed bulk voltage given by a standard boost converter. This paper will point out how a SEPIC converter used as a power factor correction circuit will introduce a new degree of freedom to the ballast, resulting in multi-lamp ability. An introduction to the operating principles of the SEPIC will be given and the extra features, which are inherent to the SEPIC, will be discussed.
An update on tumors of the anal canal.

Abstract Context.—The anal canal possesses complex anatomy and histology and gives rise to a variety of tumor types. Challenging issues remain with regard to both the pathologic diagnosis and the clinical management of these tumors. Objectives.—To provide an updated overview of the histogenesis, clinical and pathologic characteristics, diagnostic terminology, and relevant clinical management of the various types of anal canal tumors. Data Sources.—Recent literature on clinical and pathologic characteristics of anal canal tumors. Conclusions.—Although most anal canal tumors are of squamous lineage, a complex variety of other tumors also occurs. Recognition of such diverse tumor entities will allow accurate pathologic diagnosis and most optimal clinical management.