cssi/SciSciGPT-SciSciNet huggingface dataset:
A Network Model for Dispersion of Communicable Diseases

The spread of communicable diseases through a population is an intrinsic spatial and temporal process. This paper presents an individual-based analytical framework for modeling the spatial and temporal heterogeneity in the disease transmission. The framework specifies a network model structure and six associated parameters. These parameters describe the properties of nodes, the properties of links, and the topology of the network. Through this model structure and associated parameters, this framework allows the representation of discrete individuals, individualized interactions, and interaction patterns in a network of human contact. The explicit representation of the spatial distribution and mobility of individuals in particular facilitates the modeling of spatial heterogeneity in the disease transmission.
Extracellular purines are biomarkers of neutrophilic airway inflammation

Purinergic signalling regulates airway defence mechanisms, suggesting that extracellular purines could serve as airway inflammation biomarkers in cystic fibrosis (CF). The purines adenosine triphosphate (ATP), adenosine diphosphate (ADP), adenosine monophosphate (AMP) and adenosine were measured in sputum from 21 adults (spontaneously expectorated from seven CF patients, induced from 14 healthy controls) to assess normal values and CF-associated changes. Subsequently, purine levels were measured in bronchoalveolar lavage fluid (BALF) from 37 children (25 CF patients, 12 disease controls) and compared with neutrophil counts, presence of airway infection and lung function. To noninvasively assess airway purines, ATP levels were measured using luminometry in exhaled breath condensate (EBC) from 14 children with CF and 14 healthy controls, then 14 CF children during a pulmonary exacerbation. Both ATP and AMP were elevated in sputum and BALF from CF subjects compared with controls. In BALF, ATP and AMP levels were inversely related to lung function and strongly correlated with neutrophil counts. In EBC, ATP levels were increased in CF relative to controls and decreased after treatment of CF pulmonary exacerbation. The purines adenosine triphosphate and adenosine monophosphate are candidate biomarkers of neutrophilic airways inflammation. Measurement of purines in sputum or exhaled breath condensate may provide a relatively simple and noninvasive method to track this inflammation.
Prostaglandin E1 Treatment of Congenital Heart Disease: Use Prior to Neonatal Transport

Prostaglandin E1 (PGE1) is used to maintain the patency of the ductus arteriosus in neonates when it is necessary to circumvent a defect in the heart or aorta in order to provide adequate peripheral perfusion. It has recently been recommended that medical stabilization with PGE1 be done as soon as a ductus-dependent cardiac defect is suspected, preferably prior to transport of the infant to a tertiary care center for surgical repair of the defect. To accomplish this, hospitals providing obstetric services will need to maintain a supply of PGE1. This commentary provides guidelines for determining the need to stock PGE1 and presents a brief review of the physiology of the ductus arteriosus and the pharmacology and adverse effects of PGE1 therapy.
Assembly Planning Effectiveness Using Virtual Reality

Planning the sequence of components (or parts) to be assembled during manufacturing is an important application problem for virtual environments for three main reasons. First, it is a difficult combinatorial optimization but a highly visual problem. Second, a majority of assembly operations in factories (with the exception of simple pick-and-place operations) are still performed manually, because they are difficult to automate. Hence, it is an important problem involving human-machine interface. Third, there are a number of assembly operations which require dextrous operator training. Hence, it is also an important training problem. Recent research suggests a promising approach for assembly determination based on using heuristic rules to generate soft constraints in addition to the regular hard quantitative constraints due to part geometry and topology. We believe that the emergence of virtual environments can enable us to systematically use these soft constraints, which previously has not been possible. In this paper, we report results of experiments involving fifteen voluntary participants using a nonvirtual reality (VR) environment involving blueprints, a nonimmersive desktop VR environment, and an immersive projection-based VR environment to first teach participants skills in handling soft and hard constraints for assembly planning through examples, and then to measure the effectiveness of their learnt skills in solving a different example problem. We have classified soft constraints as infeasibility constraints, reorientation constraints, difficulty constraints, instability constraints, and dissimilarity constraints. A significant observation is that the participants could, on average, perform the assembly operations in approximately half the time in the immersive and nonimmersive VR environments than in the traditional environment using blueprints.
Laparoscopic Management of Adnexal Masses

: Suspected ovarian neoplasm is a common clinical problem affecting women of all ages. Although the majority of adnexal masses are benign, the primary goal of diagnostic evaluation is the exclusion of malignancy. It has been estimated that approximately 5–10% of women in the United States will undergo a surgical procedure for a suspected ovarian neoplasm during their lifetime. Despite the magnitude of the problem, there is still considerable disagreement regarding the optimal surgical management of these lesions. Traditional management has relied on laparotomy to avoid undertreatment of a potentially malignant process. Advances in detection, diagnosis, and minimally invasive surgical techniques make it necessary now to review this practice in an effort to avoid unnecessary morbidity among patients. Here, we review the literature on the laparosopic approach to the treatment of the adnexal mass without sacrificing the principles of oncologic surgery. We highlight potentials of minimally invasive surgery and address the risks associated with the laparoscopic approach.
The role thermal physiology plays in species invasion

The characterization of physiological phenotypes that may play a part in the establishment of non-native species can broaden our understanding about the ecology of species invasion. Here, an assessment was carried out by comparing the responses of invasive and native species to thermal stress. The goal was to identify physiological patterns that facilitate invasion success and to investigate whether these traits are widespread among invasive ectotherms. Four hypotheses were generated and tested using a review of the literature to determine whether they could be supported across taxonomically diverse invasive organisms. The four hypotheses are as follows: (i) broad geographical temperature tolerances (thermal width) confer a higher upper thermal tolerance threshold for invasive rather than native species; (ii) the upper thermal extreme experienced in nature is more highly correlated with upper thermal tolerance threshold for invasive vs. native animals; (iii) protein chaperone expression-a cellular mechanism that underlies an organism's thermal tolerance threshold-is greater in invasive organisms than in native ones; and (iv) acclimation to higher temperatures can promote a greater range of thermal tolerance for invasive compared with native species. Each hypothesis was supported by a meta-analysis of the invasive/thermal physiology literature, providing further evidence that physiology plays a substantial role in the establishment of invasive ectotherms.
BIOSYNTHESIS OF PHENYLALANINE AND TYROSINE IN YOUNG WHEAT AND BUCKWHEAT PLANTS

Several C14-labelled compounds were fed to shoots excised from young plants of Triticum vulgare Vill. or Fagopyrum tataricum (L.) Gaertn. The free and bound phenylalanine and tyrosine were isolated after a metabolic period of 6 hours and their C14 content measured. Shikimic acid was superior to glucose and acetate as a precursor of both phenylalanine and tyrosine. Phenyllactic acid and phenylpyruvic acid were easily converted to free phenylalanine and were incorporated into bound phenylalanine as readily as was free phenylalanine itself. Similarly, p-hydroxyphenyllactic acid and p-hydroxyphenylpyruvic acid were converted preferentially to tyrosine. There was some conversion of phenyl compounds to p-hydroxyphenyl compounds but little evidence of the reverse reaction. Radioactive carbon fed as cinnamic, dihydrocinnamic, or p-coumaric acids was not incorporated into either phenylalanine or tyrosine.
Treatment of pediatric pulmonary hypertension with simvastatin: an observational study.

Background Animal studies and an adult human case series suggest that statins may have a role in the treatment of pulmonary hypertension. We reviewed the results of empirical therapy for children at Primary Children's Medical Center to determine whether simvastatin had a favorable effect on non-invasive estimates of pulmonary arterial pressure. Materials and Methods The medical records of children with pulmonary hypertension who were treated with simvastatin were reviewed. Mean measurements of the gradient of tricuspid valve regurgitation before and after treatment were compared by a paired t-test. A favorable response to simvastatin was defined as a 20% decrease in the average measurement of the gradient of tricuspid valve regurgitation or a 20% decrease in right ventricular anterior wall thickness when tricuspid valve regurgitation resolved during treatment. Potential factors associated with a favorable response to simvastatin were identified with a Fisher exact test. Results Twelve children, 4–15 years of age, had adequate Doppler velocity waveforms to reliably measure gradients of tricuspid valve regurgitation during a period of 1 year before treatment. Eleven patients had gradients of tricuspid valve regurgitation that could be measured during a period of 1 year after treatment. Patients were treated with simvastatin 0.09–0.28 mg/kg/day. Collectively, there was no difference between the average measurements of the gradient of tricuspid valve regurgitation before and after treatment (66 ± 21 mmHg vs. 63 ± 28 mmHg). Three of the five patients with clinical findings consistent with alveolar hypoxia and none of the seven patients without clinical findings consistent with alveolar hypoxia had a favorable response to treatment with simvastatin (P = 0.05). Conclusion Simvastatin may decrease pulmonary arterial pressure in a subset of patients with pulmonary hypertension. Pediatr Pulmonol. 2011; 46:261–265. © 2011 Wiley-Liss, Inc.
Through the 10-mm Looking Glass: Advances in Minimally Invasive Surgery in Trauma

Background: Minimally invasive surgery is increasingly being used in trauma surgery as both a diagnostic and a therapeutic tool. however, significant debate regarding the accuracy, safety, and indications for minimally invasive surgery in trauma continues to impede widespread acceptance of these techniques among trauma surgeons. Method: herein, we report a contemporary review of the current role of both laparoscopy and thoracoscopy in modern trauma surgery. Literature search was performed using PubMed database and the following keywords: “Trauma,” “Minimally invasive surgery,” “Laparoscopy,” and “Thoracoscopy.” Results: current recommendations advocate for the use of laparoscopy as a diagnostic tool in penetrating trauma for the diagnosis of diaphragm injuries and peritoneal violation. a significant body of research demonstrates that laparoscopy in select hemodynamically normal patients can significantly decrease nontherapeutic laparotomy rates and hospital costs and is highly sensitive and specific with very low missed injury rates, including small bowel injuries. Laparoscopic repairs to a wide breadth of abdominal and thoracic injuries have been reported with impressive results. adherence to a standardized laparoscopic examination system and routine use of laparoscopy in elective or acute care practice strongly influence positive results with minimally invasive surgery in trauma. video-assisted thoracoscopic surgery is most commonly used for evaluation of diaphragm, evacuation of retained hemothorax, and management of ongoing bleeding post-trauma. Conclusion: Minimally invasive surgery does offer several advantages compared to traditional open surgery and should be considered as an additional tool in the trauma surgeon’s armamentarium in the care of select injured patients.
Elastic and Mechanical Properties of the MAX Phases

The more than 60 ternary carbides and nitrides, with the general formula Mn+1AXn—where n = 1, 2, or 3; M is an early transition metal; A is an A-group element (a subset of groups 13–16); and X is C and/or N—represent a new class of layered solids, where Mn+1Xn layers are interleaved with pure A-group element layers. The growing interest in the Mn+1AXn phases lies in their unusual, and sometimes unique, set of properties that can be traced back to their layered nature and the fact that basal dislocations multiply and are mobile at room temperature. Because of their chemical and structural similarities, the MAX phases and their corresponding MX phases share many physical and chemical properties. In this paper we review our current understanding of the elastic and mechanical properties of bulk MAX phases where they differ significantly from their MX counterparts. Elastically the MAX phases are in general quite stiff and elastically isotropic. The MAX phases are relatively soft (2–8 GPa), are most readily machinable, and are damage tolerant. Some of them are also lightweight and resistant to thermal shock, oxidation, fatigue, and creep. In addition, they behave as nonlinear elastic solids, dissipating 25% of the mechanical energy during compressive cycling loading of up to 1 GPa at room temperature. At higher temperatures, they undergo a brittle-to-plastic transition, and their mechanical behavior is a strong function of deformation rate.
Evaluation of the Missouri River shallow water habitat using a 2D-hydrodynamic model

Many of the Upper Missouri River dikes have been notched to create additional shallow water habitat (SWH, operationally defined as areas in the stream with depth 5225 m2 dike−1 during the same period. Analysis of the Missouri River annual discharge records at the study site showed that the dikes can provide the minimum required SWH for mean annual discharges 667 m3 s−1, new alternative structures or restoration facilities were needed, in addition to the existing dikes, to sustain the minimum required SWH. The dikes were not effective in providing any SWH for mean annual discharges > 2000 m3 s−1. Copyright © 2010 John Wiley & Sons, Ltd.
Prevalence and correlates of leisure-time physical activity among Nigerians

Background: Physical inactivity levels are rising in many countries with major implications for the prevalence of non-communicable diseases and the general health of the population worldwide. We conducted this study to examine leisure-time physical activity levels among African adults in an urban setting. Methods: We conducted a cross-sectional study among a random sample of 1,058 adults at a government worksite, in Abuja, an urban Nigerian city. We used log-binomial regression models to estimate the multivariable-adjusted associations of correlates of physical activity. Results: The mean age of the study population was 42 ± 9.3 years, 60% were men and 40% were women. The mean metabolic equivalent hours per week for all the participants was 6.8 ± 7.2. In univariate analysis comparing the lowest to highest tertiles of physical activity, the prevalence ratio (PR) and (95% confidence interval, CI) was 0.95 (0.81-1.11) p = 0.49, comparing women to men; compared to those aged <30 years the PR (95% CI) was 0.70 (0.57-0.86), 0.70 (0.58-0.85) and 0.78 (0.63-0.96) for age 30–39, 40–49 and ≥50 years respectively, p for trend = 0.03; compared to those who were normal weight, the PR was 0.93 (0.79-1.10) and 0.90 (0.74-1.09) for overweight and obese persons respectively, p = 0.26. The PR for age was attenuated to non-significant levels in multivariable analyses. Being married was a statistically significant correlate of higher physical activity levels, the PR comparing unmarried to married persons in multivariate analysis was 0.81 (0.67-0.97), p = 0.03. Conclusions: More than 80% of urban, professional Nigerian adults do not meet the WHO recommendations of physical activity. Urbanized Africans in this study population had low levels of leisure-time physical activity, independent of age, sex and body-mass index. This has major implications for the prevalence of non-communicable diseases in this population.
Parasol cells of the hemiellipsoid body in the crayfish Procambarus clarkii: dendritic branching patterns and functional implications.

Multimodal, higher-order sensory integration in decapod crustaceans occurs in local interneurons (parasol cells) within a structure in the lateral protocerebrum, the hemiellipsoid body, which is located dorsal to the terminal medulla. The hemiellipsoid body is targeted by projection neuron inputs by means of the olfactory globular tract from bilateral deutocerebral neuropils, the accessory lobes, which receive secondary visual, mechanosensory, and olfactory inputs. Parasol cell dendrites arborize extensively within the two neuropils of the hemiellipsoid body and possibly have some neurites within another neuropil at its base. The two neuropils of the hemiellipsoid body, neuropils I and II, are known to receive asymmetrical inputs from the contralateral and ipsilateral accessory lobes, and our current study addresses the question of the distribution of parasol cells within these two neuropils. Three anatomic methods were used to analyze this distribution: intracellular filling of cells with neurobiotin and visualization of the cells by using either a fluorescent or a peroxidase avidin conjugate, or placement of a fluorescent lipophilic tracer within a lobe of the hemiellipsoid body. All of these methods demonstrated that single parasol cells exclusively arborize within one of the two lobes of the hemiellipsoid body, but not in both lobes. Electrophysiological recordings from pairs of parasol cells with dendrites in the same or different lobes confirm a functional separation between neuropils I and II. Comparisons are made between insect and crustacean systems, emphasizing the inputs to the hemiellipsoid body and the mushroom body and similarities between extrinsic cells in insects and parasol cells in decapod crustaceans.
Elder mistreatment predicts later physical and psychological health: Results from a national longitudinal study

Stress process theory predicts that elder mistreatment leads to declines in health, and that social support buffers its ill effects. We test this theory using nationally representative, longitudinal data from 2,261 older adults in the National Social Life Health and Aging Project. We regress psychological and physical health in 2010/2011 on verbal and financial mistreatment experience in 2005/2006 and find that the mistreated have more anxiety symptoms, greater feelings of loneliness, and worse physical and functional health 5 years later than those who did not report mistreatment. In particular, we show a novel association between financial mistreatment and functional health. Contrary to the stress buffering hypothesis, we find little evidence that social support moderates the relationship between mistreatment and health. Our findings point to the lasting impact of mistreatment on health but show little evidence of a buffering role of social support in this process.
PP02.6 – 2349: Unilateral ventricular dilatation. Follow up during the first 2 years of life

Objective To investigate if the unilateral ventricular dilatation detected by fetal and neonatal ultrasound is associated with neurological abnormalities during the first 2 years of life. Methods A number of 1319 neonates were examined by head ultrasound on day of life 1 and 3. Prenatal histories and ultrasound were collected in all the cases. Theere were selected the cases with unilateral ventricular dilation that were examined by head ultrasound at 1, 2, 4, 6 months and by clinical and neurologic examination and, if needed, specific imaging and neurologic investigations at 1, 2, 4 6, 12 months and 2 years. Results There were detected the dilatation of the left ventricle (18cases); posterior horn of the left ventricle (88cases), posterior horn of the right ventricle (12cases). All these cases were asymptomatic during the neonatal period and only 6/88 cases with left posterior horn dilatation and 1/12 of the cases with right posterior horn dilatation developed neurologic abnormalities. All these cases were identified before delivery by fetal ultrasound. The abnormalities identified were: tonus abnormalities – hypotonic at 4 and 6 months with normalization at 12 months in 3/88cases with left posterior horn dilatation and 1/12cases with dilatation of the posterior horn of the right ventricle. There were delays in the fine motor skills in all the 6 symptomatic cases with left ventricular dilation and 1/12 cases with right ventricular dilation. The cases of ventricular dilatation that manifested with neurologic abnormalities, were all detected as ventricular dilatation by fetal ultrasound. Conclusion The antenatal ultrasound predicted the appearance of the abnormalities. No case with abnormal development would have been missed without head ultrasound in the neonatal period.
Gremlin Induces Ocular Hypertension in Mice Through Smad3-Dependent Signaling

Elevated IOP is a well-known causative risk factor for both the development and progression of glaucoma. Intraocular pressure is regulated by aqueous humor (AH) production in the ciliary body and drainage from the eye via the trabecular meshwork (TM) and uveoscleral pathway. The role of the TM and the surrounding extracellular matrix (ECM) in IOP regulation has been extensively studied. Primary open-angle glaucoma (POAG) is associated with changes in the ECM composition within the TM, increased AH outflow resistance, and elevated IOP.1,2 Transforming growth factor–β2 signaling pathway has been shown to be an important regulator of ECM proteins in the TM,3–9 and TGFβ2 has been found to be elevated in the AH and TM of POAG patients.7,10–13 Transforming growth factor–β2 has also been shown to cause ocular hypertension in both ex vivo anterior segment perfusion organ culture models,14,15 and by overexpression of a bioactivated form of TGFβ2 in mouse eyes.4,16 Transforming growth factor–β2 is known to regulate the expression of ECM proteins through the canonical Smad pathway as well as noncanonical signaling pathways.17–20 We have previously demonstrated that TGFβ2 signals through the canonical Smad and non-Smad pathways and alters the ECM in human TM cells.5,7 We have also determined that TGFβ2 signaling through the canonical Smad pathway is essential for TGFβ2-induced ocular hypertension in mice.21 Transforming growth factor–β2 signaling is regulated by bone morphogenetic proteins (BMPs) that control a variety of functions in different cell types, and are present in the TM.9,22 Bone morphogenetic proteins are regulated by BMP antagonists, such as gremlin, which bind BMP ligands and block BMP binding to their receptors.23,24 We have previously shown higher expression of gremlin in glaucomatous TM cells and tissues.9 In addition, we have shown that gremlin antagonizes BMP4 inhibition of TGFβ2-induced ECM proteins in TM cells. Gremlin and TGFβ2 are involved in a “feed-forward” pathogenic fibrotic pathway in the TM, where gremlin increases TGFβ2 expression and TGFβ2 increases gremlin expression. Gremlin also elevates IOP in perfusion-cultured human anterior segments.5,9 Here, we demonstrate that gremlin induces ocular hypertension and alters the ECM composition in the TM of mice. We also show that gremlin signaling through the canonical Smad pathway is essential for this gremlin-induced ocular hypertension.
Radiation dose reduction through re-imaging patients with suspected artifact related abnormalities studied with a stress first SPECT/CT myocardial perfusion protocol

1833 Objectives The objective of this study was to determine the potential clinical benefits on diagnostic normalcy and radiation dose reduction of re-imaging the stress distribution in a population of patients scanned with a stress first myocardial perfusion protocol found to have unexpected abnormalities possibly related to motion or normalization artifacts. Methods All patients referred for a clinically indicated stress myocardial perfusion study in 2011 (n=2,341) imaged with a stress first, stress only if normal, protocol were reviewed. Patients were injected with Tc-99m sestamibi during symptom-limited maximal exercise stress or regadenoson vasodilator stress. If abnormal, the patient were injected at rest and imaged using the same standard gated SPECT/CT protocol used for stress. Of this population, 231 patients (9.9%) had the stress images repeated because of suspected artifacts, generally due to motion or normalization errors. Retrospective analyses to determine the number patients that did not require high dose rest injection studies because of quality improvement with re-imaging and the associated clinical outcomes were performed. Results Studies reported as normal after re-imaging that did not require a rest scan was 109 (47.2%) while 122 (52.8%) required a rest scan despite re-imaging. Of the cases that required rest imaging, 40 (17.3%) were reported as normal while 82 (35.5%) were abnormal. Among cases without previously documented disease (n=160), 68.1% were normal after repeat imaging and did not require high dose rest imaging. Hard cardiac events (death or MI) did not occur in any normal case. Of abnormal studies with angiographic correlates, 65% had confirmation of disease (n=24). Conclusions Patients with abnormal findings suspected to be artifact on a stress first protocol can frequently be studied without rest injection by re-imaging. This approach results in significantly reduced radiation dose and improved diagnostic accuracy, especially in cases without prior documented disease
Hessian Fly Larval Strain Responses to Simulated Weather Conditions in the Greenhouse and Laboratory

Hessian fly, Mayetiola destructor (Say), larval responses to simulated weather under laboratory conditions indicated that the migratory stage of the larvae is extremely sensitive to adverse environmental situations. Low temperature, low relative humidity, high rainfall, and wind caused high mortality in the newly hatched larvae. Freezing temperatures caused mortality in all larval stages. The 2 populations of Hessian fly tested differed in their respouse to wind and low temperatures.
Pair breaking caused by magnetic impurities in the high-temperature superconductor Bi 2.1 Sr 1.9 Ca(Cu 1 − x Fe x ) 2 O y

Conventional superconductivity is robust against the addition of impurities unless the impurities are magnetic in which case superconductivity is quickly suppressed. Here we present a study of the cuprate superconductor Bi${}_{2}$Sr${}_{2}$Ca${}_{1}$Cu${}_{2}$O${}_{8+\ensuremath{\delta}}$ that is intentionally doped with the magnetic impurity, Fe. Through the use of our tomographic density of states technique, we find that while the superconducting gap magnitude is essentially unaffected by the inclusion of iron, the onset of superconductivity, ${T}_{\mathrm{C}}$, and the pair-breaking rate are strongly dependent and correlated. These findings suggest that, in the cuprates, the pair-breaking rate is critical to the determination of ${T}_{\mathrm{C}}$ and that magnetic impurities do not disrupt the strength of pairing but rather the lifetime of the pairs.
Learning and Generalizing Cross-Category Relations Using Hierarchical Distributed Representations.

Recent work has begun to investigate how structured relations can be learned from non-relational and distributed input representations. A difficult challenge is to capture the human ability to evaluate relations between items drawn from distinct categories (e.g., deciding whether a truck is larger than a horse), given that different features may be relevant to assessing the relation for different categories. We describe an extension of Bayesian Analogy with Relational Transformations (BART; Lu, Chen & Holyoak, 2012) that can learn cross-category comparative relations from autonomously-generated and distributed input representations. BART first learns separate representations of a relation for different categories and creates second-order features based on these category-specific representations. BART then learns weights on these second-order features, resulting in a category-general representation of the relation. This hierarchical learning model successfully generalizes the relation to novel pairs of items (including items from different categories), outperforming a flat version of the learning model.
Adenocarcinoma of the Prostate Discovered in 2 Young Patients Following Total Prostatovesiculectomy for Refractory Prostatitis

Adenocarcinoma of the prostate gland is the most common cancer in men in the United States but it occurs rarely in men younger than 40 years. Incidental prostate cancer has been shown to exist in a significant number of patients older than 50 years, found either at autopsy or after cystoprostatectomy for a pathological condition of the bladder. We report 2 cases of unsuspected adenocarcinoma of the prostate gland discovered after total prostatovesiculectomy for refractory prostatitis in men 25 and 36 years old, respectively.
Inferring metabolic pathway activity levels from RNA-Seq data.

Assessing pathway activity levels is a plausible way to quantify metabolic differences between various conditions. This is usually inferred from microarray expression data. Wide availability of NGS technology has triggered a demand for bioinformatics tools capable of analyzing pathway activity directly from RNA-Seq data. In this paper we introduce XPathway, a set of tools that compares pathway activity analyzing mapping of contigs assembled from RNA-Seq reads to KEGG pathways. The XPathway analysis of pathway activity is based on expectation maximization and topological properties of pathway graphs. XPathway tools have been applied to RNA-Seq data from the marine bryozoan Bugula neritina with and without its symbiotic bacterium “Candidatus Endobugula sertula”. We successfully identified several metabolic pathways with differential activity levels. The expression of enzymes from the identified pathways has been further validated through quantitative PCR (qPCR). Our results show that XPathway is able to detect and quantify the metabolic difference in two samples. The software is implemented in C, Python and shell scripting and is capable of running on Linux/Unix platforms. The source code and installation instructions are available at http://alan.cs.gsu.edu/NGS/?q=content/xpathway .
One-Step Generation of Cell-Encapsulating Compartments via Polyelectrolyte Complexation in an Aqueous Two Phase System.

Diverse fields including drug and gene delivery and live cell encapsulation require biologically compatible encapsulation systems. One widely adopted means of forming capsules exploits cargo-filled microdroplets in an external, immiscible liquid phase that are encapsulated by a membrane that forms by trapping of molecules or particles at the drop surface, facilitated by the interfacial tension. To eliminate the potentially deleterious oil phase often present in such processes, we exploit the aqueous two phase system of poly(ethylene glycol) (PEG) and dextran. We form capsules by placing dextran-rich microdroplets in an external PEG-rich phase. Strong polyelectrolytes present in either phase form complexes at the drop interface, thereby forming a membrane encapsulating the fluid interior. This process requires considerable finesse as both polyelectrolytes are soluble in either the drop or external phase, and the extremely low interfacial tension is too weak to provide a strong adsorption site for these mol...
Surface Energy as a Descriptor of Catalytic Activity

Computational searches for catalysts of the hydrogen evolution reaction commonly use the hydrogen binding energy (HBE) as a predictor of catalytic activity. Accurate evaluation of the HBE, however, can involve large periodic supercell slab models that render high-throughput screening relatively expensive. In contrast, calculations of other relevant surface properties, such as the surface energy, work function, and potential of zero charge (PZC), require only small surface unit cells and are hence less expensive to compute. Correlations between catalytic activity and these surface properties warrant exploration because of this reduced computational cost. Here, we use density functional theory in conjunction with three different exchange-correlation functionals—the local density approximation (LDA), the Perdew–Burke–Ernzerhof (PBE) generalized gradient approximation, and the PBEsol functional (a reparameterization of the PBE functional)—to calculate the lattice constants, surface energy, cohesive energy, an...
Examples of Scalable Performance

We define scaled performance of an application as performance on a scalable system when the work per processor is held fixed and the problem size is varied. In this paper, we show some examples of good scalable performance. We also discuss how scalable performance compliments a neatly proposed model for general purpose parallel computing.
A Historical Perspective of Death in the Western World

Humans appear to have had awareness from their early consciousness that death was inevitable for all living things. Religions and spiritual practices throughout history have provided belief structures that support the religious and social needs of practitioners regarding death and an existence after life. Death beliefs and practices throughout history have been influenced by environmental, social, and religious and spiritual factors that guide societies’ approach to the dying, the dead, and the bereaved.
A tabu search heuristic for a generalized quadratic assignment problem

The generalized quadratic assignment problem (GQAP) is the task of assigning a set of facilities to a set of locations such that the sum of the assignment and transportation costs is minimized. The facilities may have different space requirements, and the locations may have varying space capacities. Also, multiple facilities may be assigned to each location such that space capacity is not exceeded. In this paper, an application of the GQAP is presented for assigning a set of machines to a set of locations on the plant floor. Construction algorithms and a simple tabu search heuristic are developed for the GQAP. A set of test problems available in the literature was used to evaluate the performances of the TS heuristic using different construction algorithms. The results show that the simple TS heuristic is effective for solving the GQAP.
Anisotropic Magnetic Fibers Produced via a Magnetic Drawing Process

This work aims to develop magnetic fibers whose magnetic properties improve upon fibers produced using existing techniques. The goal of this work is to develop magnetic fibers that are magnetically anisotropic, with high squareness ratios when the fibers are oriented parallel to the applied magnetic field, and lower square ratios when the fibers are oriented perpendicular to the field. In this work, barium hexaferrite particles were embedded in a Sylgard elastomer matrix. The magnetic material was placed on a sheet of acrylic with spacers on opposite ends. A top sheet of acrylic was placed on the spacers. A 0.5 T permanent magnet was placed on top of the upper piece of acrylic. Magnetic fibers were drawn as the material aligned itself with the magnetic field lines of the magnet. After the fibers cured they were tested on a vibrating sample magnetometer at angles parallel and perpendicular to the field. The results showed that the fibers were highly anisotropic, with an average squareness ratio of 0.82 in the easy axis and an average squareness ratio of 0.34 in the hard axis. Although, the fibers were anisotropic, there was a high variability in the magnetization when normalized by the total volume of the fiber. This indicates that the magnetic content varies within each fiber, likely due to the variation in the strength of the magnetic field lines of the external magnet. This research demonstrated that magnetic fibers with high anisotropy can be fabricated, but the amount of magnetic material in each fiber from the same batch needs to be tuned to decrease variability. Fitting this experimentally found squareness ratio to a von Mises distribution, the concentration parameter was calculated to be 0.14. This indicates the magnetic domains within each fiber are highly aligned with the externally applied field.
Theories of Moral Responsibility and the Responsibility Barter Game

In Responsibility Matters, Peter French embraces a deflationary view of moral responsibility’s nature: It amounts to nothing more than a collection of practices. We might be able to offer some general and illuminating insights about it, but we will not find out anything metaphysically distinctive about the world. Nor will we discover anything about moral responsibility required by our nature as practical reasoners. Hence, no substantive theory will be true to the metaphysical facts or the norms of living as practical agents. Moreover, when we tend to these practices, we will find some basic strategies for negotiating the Responsibility Barter Game, a game whose aim is for accountable agents to avoid bearing the burdens of being held to account for various outcomes. In this essay, I will assess French’s view and resist him while advancing my own conversational theory of moral responsibility.
Imaging Appearance and Clinical Impact of Preoperative Breast MRI in Pregnancy-Associated Breast Cancer.

OBJECTIVE. The purpose of this study is to describe the imaging features of pregnancy-associated breast cancer (PABC) on breast MRI and to consider the impact of preoperative MRI on patient management. MATERIALS AND METHODS. A retrospective review of medical records from January 1994 to May 2014 identified 183 women who presented with a new diagnosis of breast cancer during pregnancy or within 1 year postpartum. MR images were available for 53 of these patients, all of whom were included in the study. Clinical history and available breast images were reviewed. The clinical impact of preoperative breast MRI was also recorded. RESULTS. Of the 53 women, nine (17%) presented during pregnancy and 44 (83%) presented during the first year postpartum. The sensitivity of MRI was 98% (52/53). Among the 53 patients, the most common findings of PABC on MRI included a solitary mass (29 patients [55%]), nonmass enhancement (12 patients [23%]), and multiple masses (eight patients [15%]). For 12 patients (23%), MRI showe...
The Linkages Between Insecurity, Health, and Well-Being in Latin America: An Initial Exploration Based on Happiness Surveys

This chapter explores the effects of crime and insecurity on well-being – both happiness and health – in Latin America and the Caribbean. We posited that crime victimization would have negative effects on both and, at the same time, tested the extent to which those effects were mitigated by people’s ability to adapt to those phenomena. The effects of victimization also varied across cohorts, with being mugged – which is typically a more threatening experience than having something stolen – having stronger effects for more vulnerable groups, such as the elderly, and/or for groups for whom they are rare – e.g., the wealthy – and likely produce more stigma. The effects were typically greater for happiness than for health, although the general direction of the findings is similar. At the same time, we also found significant evidence of adaptation. (An “adaptation” is defined herein as the unconscious adjustments in one’s perception of the issues in question.) Using the unexplained possibility of being victimized as a proxy for adaptation, we were able to mitigate the negative effects of victimization on life satisfaction, but not on health satisfaction. We also found that victimization had negative effects on both friendships and confidence in public institutions, suggesting that it has aggregate, society-wide costs in addition to individual welfare costs. Our results are an initial exploration into a new area of research and should be treated as such.
Location-aware, Trust-based Detection and Isolation of Compromised Nodes in Wireless Sensor Networks

The detection and isolation of compromised nodes in wireless sensor networks is a difficult task. However, failure to identify and isolate compromised nodes results in significant security breaches which lowers the integrity of gathered data. Using a reputation-based trust framework for wireless sensor networks we introduce a location-aware, trust-based protocol that detects and isolates compromised nodes. We employ a secure cluster formation algorithm to facilitate the establishment of trusted clusters via pre-distributed keys. Reputation and trust is built over time through the monitoring of neighboring nodes. Our scheme provides a mechanism for developing reputation and trust so that a device can determine whether other devices have been compromised, and take corrective action, through negative information sharing and independent trust-based decision making. We also present a simple location verification algorithm that utilizes the received signal strength information in the process of verifying reported location information. The effectiveness of our approach in the detection and isolation of compromise nodes is validated through simulation. The results indicate that our scheme provides an effective mechanism for detecting and isolating compromised colluding nodes.
Heat Flow in Glasses on a Picosecond Timescale

The transient thermal properties of amorphous materials have been the subject of several recent investigations [1–4]. These experiments have mainly been designed to study the time-dependence of the specific heat at low temperature (T≤2K) on time scales ≥0.1µsec. In this paper we describe a new technique which enables measurements of thermal properties to be made on a time scale into the picosecond range, and we present preliminary results of measurements of this type.
Polymorphisms in Protein Tyrosine Phosphatase Non-receptor Type 2 and 22 (PTPN2/22) Are Linked to Hyper-Proliferative T-Cells and Susceptibility to Mycobacteria in Rheumatoid Arthritis.

A shared genetic pre-disposition, chronic inflammation and treatment with similar biologics between Rheumatoid arthritis (RA) and Crohn’s disease (CD) have intrigued us to investigate whether the two disorders share trigger association or possible causation. We hypothesized earlier that Single Nucleotide Polymorphisms (SNPs) in the negative regulators Protein Tyrosine Phosphatase Non-receptor type 2 and 22 (PTPN2/22) lead to a dysregulated immune response, susceptibility to environmental triggers, and continued apoptosis as seen in chronic inflammation in RA and CD. To test the hypothesis, peripheral leukocytes samples from 131 consented subjects were genotyped for 9 SNPs in PTPN2/22 using TaqMan™ genotyping. The effect of the SNPs on PTPN2/22 and IFN-γ expression was determined using real time PCR. T-cell proliferation and response to phytohematoagglutonin (PHA) mitogen and mycobacterial antigens were determined by BrdU proliferation assay. Blood samples were also analyzed for the Mycobacterium avium subspecies paratuberculosis (MAP) IS900 gene by nPCR. Out of 9 SNPs examined, heterozygous (TC) or minor (CC) alleles of PTPN2:rs478582 occurred in 79% RA compared to 60% healthy controls (p-values ≤ 0.05; OR= 2.28). Similarly, heterozygous (GA) or minor (AA) alleles of PTPN22:rs2476601 occurred in 29% RA compared to 6% healthy controls (p-values ≤ 0.05; OR= 5.90). PTPN2/22 expression in RA was decreased by 1.2 fold compared to healthy controls. PTPN2:rs478582 upregulated IFN-γ in RA by 1.5 fold. Combined PTPN2:rs478582 and PTPN22:rs2476601 increased T-cell proliferation by 2.7 fold when treated with PHA. Surprisingly, MAP DNA was detected in 34% of RA samples compared to 8% healthy controls, (p-values ≤ 0.05, OR= 5.74). RA samples with PTPN2:rs478582 and/or PTPN22:rs2476601 were more positive for MAP than samples without polymorphisms. Combined occurrence of PTPN2:rs478582 and PTPN22:rs2476601 in association with the presence of MAP has significantly increased T-cell response and elevated IFN-γ expression in RA samples. The data suggest that genetic polymorphisms may play vital role in T-cell regulation, susceptibility to mycobacteria and ultimately response to treatment. This is the first study to report the detection of MAP DNA in the blood of RA patients; further studies are needed using larger number of samples.
Synthesis and Properties of Bulk Amorphous and Nanocrystalline Alloys

High-strength Al-based amorphous alloys have been produced in sub-millimeter thick ribbons (sheets) by single-roller melt-spinning. The excellent glass formability of Al-alloys has been studied by thermal and structural experiments. Amorphous Al-alloy powders can be consolidated to form bulk amorphous or nanocrystalline Al-alloys as high-strength, low-density engineering materials. Submillimeter Mg-(Cu,Ni)-Sn amorphous ribbons with good mechanical properties can also be produced. Recently, refractory metal based rod-shaped samples containing mixtures of amorphous and nanocrystalline phases have been produced by mold casting, and their properties have been studied. Based on these results as well as those from the variety of bulk-glass forming systems reported recently, several key factors for easy vitrification are suggested.
Managing Issues of IT Service Offshore Outsourcing Projects

Western countries’ information technology and software intensive firms are increasingly producing software and IT services in developing countries. Regardless of the swift advancement in offshore outsourcing, there are arrays of issues that must be investigated in order for companies to benefit from the offshore outsourcing. Numerous significant benefits can be accomplished through the successful management of offshore outsourcing. Critical issues are the challenges that can happen throughout the lifecycle of offshore outsourcing IT service projects. This research will investigate these critical issues throughout the whole lifecycle of executed offshore outsourcing projects in the IT service industry from the client managerial perspective.
DOES 'MEANINGFUL USE' OF EMR IMPROVE THE QUALITY AND EFFICIENCY OF HEALTH CARE? AN EXPLORATORY ANALYSIS OF AMBULATORY EMR USAGE

The US government has initiated incentive programs to encourage the adoption of Electronic Medical Records (EMR). To qualify for the incentive payment, healthcare providers need to demonstrate 'meaningful use' of EMR systems, which requires the use of certified EMRs and the implementation of a set of standard functionalities. In this research-in-progress paper, we examine how the meaningful use of EMRs will affect health care outcomes in outpatient settings. Our preliminary results show that the use of core functionalities required by 'meaningful use' criteria has positive impact on the quality and efficiency of health care. We also find the relationship between the meaningful use and quality of care is moderated by the length of use. In addition, using certified EMR could improve quality and efficiency of health care. Our future research plan is also presented.