cssi/SciSciGPT-SciSciNet huggingface dataset:
A machine learning perspective on the development of clinical decision support systems utilizing mass spectra of blood samples

Currently, the best way to reduce the mortality of cancer is to detect and treat it in the earliest stages. Technological advances in genomics and proteomics have opened a new realm of methods for early detection that show potential to overcome the drawbacks of current strategies. In particular, pattern analysis of mass spectra of blood samples has attracted attention as an approach to early detection of cancer. Mass spectrometry provides rapid and precise measurements of the sizes and relative abundances of the proteins present in a complex biological/chemical mixture. This article presents a review of the development of clinical decision support systems using mass spectrometry from a machine learning perspective. The literature is reviewed in an explicit machine learning framework, the components of which are preprocessing, feature extraction, feature selection, classifier training, and evaluation.
Multipath exploitation for radar target classification

Inclusion of multipath ghost target images, alongside direct target images, is shown to improve performance in radar target classification. When ultra wideband waveforms are employed there is sufficient range resolution that the components of the received signal relating to indirect paths appear as unique peaks. The additional returns result in a point spread function with peaks at locations other than that of the target — the ghosts. A method for localizing the ghosts is provided, and is then used to include the ghosts in target classification testing. A gain of up to 17% in classification performance is shown when the ghost targets are included. This study makes use of real radar data.
Plasma pancreatic polypeptide levels are associated with differences in body fat distribution in human subjects.

Pancreatic polypeptide (PP) is produced by the F-cells of the pancreas, and its plasma concentration has been used as a marker of parasympathetic activity. Recent work in rodents suggests that there is both sympathetic and parasympathetic innervation of white adipose tissue and that parasympathetic activity is anabolic resulting in lipid accumulation. We have examined whether in humans increased PP levels are associated with increased intra-abdominal fat (IAF), and thereby insulin resistance. We measured PP levels in 177 non-diabetic subjects (75 male/102 female; age 32–75 years) 3 min after an i.v. glucose bolus during a frequently sampled intravenous glucose tolerance test. IAF and s.c. fat (SCF) areas were measured by CT scan. The insulin sensitivity index (S I) was quantified using Bergman’s minimal model. PP levels were higher in men than in women (96.2 ± 72.2 vs 76.1 ± 55.0 pg/ml, mean ± SD, p = 0.037), as was IAF area (124.7 ± 67.4 vs 83.0 ± 57.7 cm2, p < 0.001). While PP levels were significantly associated with IAF (r = 0.16, p = 0.031), WHR (r = 0.30, p < 0.001) and age (r = 0.37, p < 0.01), they were not associated with SCF (r = 0.02, p = 0.829). The association between PP and IAF was not independent of age and/or sex. S I was negatively associated with PP levels (r = −0.17, p = 0.026) and IAF area (r = −0.65, p < 0.001). The association between S I and PP disappeared after adjusting for IAF area, indicating that S I was not a major determinant of PP levels. In humans, age and sex may modulate the association between plasma PP level and IAF area, suggesting that they may be determinants of parasympathetic activity and thus IAF accumulation.
Time course of vulnerability to fibrillation after experimental coronary occlusion.

Abstract The early time course of vulnerability of the ventricles to fibrillation after coronary artery occlusion was measured in 6 dogs. The duration of a train of 60 Hz stimuli with currents of 2 to 3 times the diastolic threshold was used as the measure of vulnerability to fibrillation. Within 2 minutes of coronary occlusion the duration of the train of 60 Hz stimuli inducing fibrillation fell by an average of 25 percent of control values. Five minutes after coronary occlusion the duration of the train was an average of 34 percent shorter than control values. In all animals, the duration of the train required to produce fibrillation began to increase 30 minutes after coronary occlusion and approached control values. The relation of these findings to the time course of arrhythmias in experimental infarction and the early high mortality rate in cases of infarction in man is discussed.
Intentionality and Economics

In his recent book, Economics – Mathematical Politics or Science of Diminishing Returns, Alexander Rosenberg has offered a forceful critique of the scientific pretensions of economics. I am encouraged to note that in his JEL review, Wade Hands (1993) singles out Rosenberg's ‘important discussion of intentionality’ as one of the most significant aspects of the book. Encouraged, because this was exactly my impression, and Hands's judgment confirmed my intention to respond to Rosenberg's argument. I hope, however, to be able to disappoint Hands's expectation that this aspect of Rosenberg's work ‘will be least challenged by economists’!
Communication Disorders in Ethiopia: Emerging Needs and New Models of Development

In this article, the author considers the state of communication disorders in Ethiopia today by first discussing the health status of adults and children, particularly as it relates to the prevalen...
Reactivity of oxidized nickel(II) PnAO quasi-aromatic complexes

Abstract The chemical and physical properties of a neutral nickel(II) complex ion containing a Ni, 2N, 3C quasi-aromatic ring are presented. Electrophilic substitution at the C12 position of the ring readily occurs producing highly stable compounds whose identity has been determined by single crystal X-ray diffraction. The ring is capable of conjugation with aromatic molecules giving substances with very high visible light absorption. The platinum(II) analogue has been prepared and shows similar reactivity.
First-order thermal model of commercial EDLCs

Abstract This study presents a first-order thermal analysis for electric double layer capacitors (EDLCs). It is based on the lumped-capacitance approximation and accounts for both irreversible and reversible internal heat generation. A simple analytical expression for the overall temperature rise during galvanostatic cycling was derived. A scaling analysis was performed and demonstrated with experimental data collected from commercial EDLCs. This thermal model enables rapid estimation of reversible heat generation and prediction of the temperature evolution in EDLCs without performing computationally intensive numerical simulations.
Nursing Students’ Feedback to a Spiritual Health Reflection

It is common for young students to enter nursing school with untested or immature spiritual belief systems. This exploratory study elicited feedback from nursing students in response to a guided reflection about spiritual health. As a precursor to classroom teaching, participants wrote a short, nongraded anonymous response to a series of 10 broad questions, with no single answer considered right or wrong. At the conclusion of this classroom activity, students completed a survey indicating the extent to which they believed it was beneficial. The majority of the participants (97%) considered it important to identify their own beliefs about spiritual matters prior to entering the clinical setting. As a result of the classroom reflection activity, most of the participants agreed or strongly agreed that the exercise (a) heightened their awareness about spiritual issues, (b) encouraged them to consider spiritual matters they had never thought about before, (c) caused them to feel more confident discussing spiri...
The impact of aquatic genomics on fish immunology

The study of fish immunology presents unique challenges, for several reasons. Fish are not a true monophyletic taxon: rather, the term “fish” includes members of at least five separate lineages that diverged early in vertebrate evolution. The fishes are extremely diverse both in numbers of species and in their physiological adaptations to different environments. This diversity is manifest just as much in the immune responses of fishes as in their other physiological systems. Studies at the genomic level are predicted to provide unifying themes and approaches to the understanding of fish immunology. However, parallel advances in the cell biology of fishes, involving for example effective cell culture techniques and the further development of clonal in vitro grown cell lines, will be necessary if the promise of genomic approaches is to achieve its full impact on our understanding of fish immunology.
Less-than-standard treatment in rectal cancer patients: which patients are at risk?

Abstract Objective Guidelines recommend that patients with non-metastatic rectal cancer receive surgery and adjuvant chemotherapy and/or radiation therapy (XRT) after surgery (especially if stage II and III). Studies reported that 90% of stage II and III patients received surgery, and 70% received adjuvant treatment. In states where socioeconomics and limited medical resources may hinder treatment, cancer care is understudied. The objective is to describe initiation and completion of rectal cancer treatment in Alabama. Methods Medicare claims were obtained for 675 stage I to III rectal cancer patients diagnosed in 1999–2003, enrolled in fee-for-service Medicare, and with at least 9 months of follow-up. Logistic regressions were used to identify significant differences by sex, age, and race in the likelihood of initiating treatment and receiving an incomplete course of chemotherapy or XRT ( Results Overall, 90% received surgery, of which 43% received some adjuvant treatment. Among stage II to III patients, 58.8% received adjuvant treatment. Except for patients aged 75 years and greater being less likely to start chemotherapy, there were no significant differences in initiation by age, sex, and race. Depending on concurrent administration of chemotherapy and XRT, 29% to 35% received incomplete chemotherapy, and 16% to 23% incomplete XRT. Women were more likely to have incomplete chemotherapy than men. Conclusions Adjuvant treatment was less than reported in previous studies. Treatment initiation and completion did not differ across demographic factors. Future studies should explore reasons why older rectal cancer patients in Alabama are less likely to receive recommended treatment.
An LPV path-following controller for small fixed-wing UAS

Multiple path-following controllers for a small fixed-wing unmanned aircraft system (UAS) are presented, including a linear parameter-varying (LPV) controller scheduled over path curvature. The controllers were synthesized based on a lumped path-following and UAS dynamic system, effectively combining the six degree-of-freedom aircraft dynamics with established parallel transport frame virtual vehicle dynamics. The robustness and performance of these controllers were tested in a rigorous MATLAB simulation environment that included steady winds, turbulence, measurement noise, and delays. The controllers presented within were found to be robust to the disturbances and uncertainties in the simulation environment, and allowed the aircraft to follow prescribed geometrically defined paths bounded by a maximum curvature.
NGOs, Turnout, and the Left: A Sub-national Analysis of Brazil

This article is designed to examine the role non-governmental organizations (NGOs) play in politics. Previous evidence suggests that NGOs mobilize communities to challenge existing patterns of authority or that they serve hand in glove with existing elites. We reconcile these two contradictory findings by identifying an important contextual feature that helps determine the extent NGOs mobilize or anesthetize. We argue that a community’s level of education influences not only whether people vote but how they vote. We employ a cross-sectional data set from Brazilian municipalities that allows us to estimate the relationship between NGOs, voting turnout, and electoral results. We find that although there is a significant statistical interaction between literacy and NGOs when explaining voting turnout, the effect is not substantively important. The interaction between literacy and NGOs is, however, an important consideration in determining how people vote: in communities with relatively low literacy rates, a ...
Generalized Functions on the Unit Circle

(1975). Generalized Functions on the Unit Circle. The American Mathematical Monthly: Vol. 82, No. 3, pp. 256-261.
Dielectronic recombination of Zn-like W 44 + from Cu-like W 45 +

Energy levels, radiative transition probabilities, and autoionization rates for $\text{[Ar]}3{d}^{10}4{l}^{\ensuremath{'}}nl (n=4--12, l\ensuremath{\le}n\ensuremath{-}1), \text{[Ar]}3{d}^{10}5{l}^{\ensuremath{'}}nl (n=5--8, l\ensuremath{\le}n\ensuremath{-}1)$, and $\text{[Ar]}3{d}^{9}4{l}^{\ensuremath{'}}4{l}^{\ensuremath{'}\ensuremath{'}}nl (n=4--5, l\ensuremath{\le}n\ensuremath{-}1$) states in Zn-like tungsten (${\mathrm{W}}^{44+}$) are calculated using the relativistic Hartree-Fock method (cowan code), the multiconfiiguration relativistic Hebrew University Lawrence Livermore Atomic Code (hullac code), and the relativistic many-body perturbation theory method (rmbpt code). Autoionizing levels above the thresholds $\text{[Ar]}3{d}^{10}4s$ are considered. It is found that configuration mixing $[4sns+4pnp+4dnd+4fnf], [4snp+4pns+4pnd+4dnp+4fns+4fnd]$ plays an important role for all atomic characteristics. Branching ratios relative to the first threshold and intensity factors are calculated for satellite lines, and dielectronic recombination (DR) rate coefficients are determined for the first excited odd- and even-parity states. It is shown that the contribution of the highly excited states is very important for the calculation of total DR rates. Contributions to DR rate coefficients from the excited $\text{[Ar]}3{d}^{10}4{l}^{\ensuremath{'}}nl$ states with $ng12$ and $\text{[Ar]}3{d}^{10}5{l}^{\ensuremath{'}}nl$ states with $ng8$, and additionally from core-excited $\text{[Ar]}3{d}^{9}4{l}^{\ensuremath{'}}4{l}^{\ensuremath{'}\ensuremath{'}}nl$ states with $ng5$, are estimated by extrapolation of all atomic parameters. The orbital angular momentum quantum number $l$ distribution of the rate coefficients shows two peaks at $l=2$ and $l=5$. The total DR rate coefficient is derived as a function of electron temperature. The dielectronic satellite spectra of ${\mathrm{W}}^{44+}$ are important for $M$-shell diagnostic of very high-temperature laboratory plasmas such as those found in future tokamaks.
A dual-process Qualia Modeling Framework (QMF)

Abstract We present the software implementation of our Qualia Modeling Framework (QMF), a computational cognitive model based on the dual-process theory, which theorizes that reasoning and decision making rely on integrated experiences from two interactive minds: the autonomous mind, without the agent’s conscious awareness, and the reflective mind, of which the agent is consciously aware. In the QMF, artificial qualia are the vocabulary of the conscious mind, required to reason over conceptual memory, and generate cognitive inferences. The autonomous mind employs pattern-matching, for fast reasoning over episodic memories. An ACT-R model with conventional declarative memory represents the autonomous mind. A second ACT-R model, with an unconventional implementation of declarative memory utilizing a hypernetwork theory based model of qualia space, represents the reflective mind. Using real-world, non-trivial, data sets, our cognitive model achieved classification accuracy comparable to, or greater than, analogous machine learning classifiers kNN and DT, while providing improvements in flexibility by allowing the Target Attribute to be identified or changed any time during training and testing. We advance the BICA challenge by providing a generalizable, efficient, algorithm which models the phenomenal structure of consciousness as proposed by a contemporary theory, and provides an effective decision aid in complex environments where data are too broad or diverse for a human to evaluate without computational assistance.
Abstract 1709: STRAP mediates the stemness of human colorectal cancer cells by epigenetic regulation of Notch pathway

Human colon cancer-initiating cells (CCICs) are responsible for the unrestrained cell proliferation and chemoresistance of colorectal tumors. Notch signaling is critical for the maintenance and self-renewal of cancer-initiating cells in colon cancer. We have shown that the serine-threonine kinase receptor-associated protein (STRAP), a ubiquitous WD40 protein, is involved in promoting tumorigenesis through activated MAPK/ERK pathway and pRb phosphorylation. In addition, our previous studies uncovered that STRAP is up-regulated in 60% colon carcinomas and behaves as an oncogene in a TGF-β-dependent or -independent manner. Based on our new finding that STRAP stabilizes intracellular fragment of Notch3 (ICN3) via post-translational modification, we sought to explore the cross-talk between STRAP and Notch pathway in regulating stemness of CCICs. Here, we have generated STRAP knock down (KD) colorectal cancer cell lines (RKO, DLD1, HCT116, HT29, WiDr, SW480, SW620, and LOVO) to show how STRAP abrogates apoptosis by up-regulating CD44+/CD133+ subpopulations of CCICs. Heterozygous Strap KO inhibits tumorigenesis accompanied by the reduction of stemness phenotype (CD44+, Lgr5+) in a colitis-associated mouse model. Western blot assays and immunofluorescene staining demonstrated that the expression of stemness biomarkers (Nanog, Oct4 and Sox2) is decreased in STRAP KD cells. Furthermore, the transcriptional activation of Notch pathway related genes is downregulated in the STRAP KD cells. EpiTect Chip qPCR Arrays profiled that 17 out of 84 genes key to Notch signal transduction had higher activating (H3K4me3) and lower repressive (H3K27me3) histone modifications in WT cells compared to STRAP KD cells. Among these genes, we identified two transcription factors, Hes1 and Hes5, that are transcriptionally regulated by STRAP as demonstrated by luciferase assays and qPCR. We further demonstrated that Hes1 and Hes5 were transcriptionally activated by STRAP through Polycomb Repressive Complex 2 (PRC2)-dependent mechanism. Immunoprecipitation experiments showed that STRAP interacts with the key components, EZH2 and SUZ12 of PRC2 complex in vivo, which antagonizes the histone methyltransferase activity in H3K27 on the promoters of Hes1 and Hes5, resulting in activating these two genes. Of interest, ectopic expression of either Hes1 or Hes5 can rescue the stemness phenotype in STRAP KD cells. Together, our findings provide a novel mechanistic insight into the regulation of CCICs via STRAP-PRC2-Hes1/5 regulatory axis, which represents a potential target for CCICs, thus overcoming cancer chemoresistance and relapse. Citation Format: Lin Jin, Trung Tam Vu, Pran K. Datta. STRAP mediates the stemness of human colorectal cancer cells by epigenetic regulation of Notch pathway. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1709.
COULOMB EXCITATION OF THE FIRST 2$sup +$ STATE OF $sup 24$Mg.

Coulomb excitation of the first excited state of $^{24}\mathrm{Mg}$ has been investigated by means of a coincidence experiment using a position-sensitive detector. Interpreting the data according to the semiclassical theory and correcting for quantal effects, we obtained a reduced transition probability of $B(E2; {0}^{+}\ensuremath{\rightarrow}{2}^{+})=0.042\ifmmode\pm\else\textpm\fi{}0.002 {e}^{2}{\mathrm{b}}^{2}$ and a static quadrupole moment of ${Q}_{{2}^{+}}=\ensuremath{-}0.305\ifmmode\pm\else\textpm\fi{}0.064 e\mathrm{b}$.
Bacterial membrane vesicles: biogenesis, immune regulation and pathogenesis.

Summary: Outer membrane vesicles (OMV) were first described approximately 50 years ago, and for many years were considered to be an artefact of bacterial growth. Since that initial discovery, it has become evident that OMVs are produced by almost all Gram-negative bacteria as part of their normal growth in addition to driving pathogenesis within the host. More recently, the identification of membrane vesicle (MV) production by some Gram-positive bacteria, parasites, fungi, mycobacteria and infected host cells has significantly broadened the field of MV production and emphasised their importance to pathogenesis. In this review we will focus on discussing recent advances in the field of bacterial membrane vesicle biogenesis and the mechanisms whereby they modulate immunity and contribute to pathogenesis. We will highlight findings identifying the contribution of extracellular vesicles produced by Gram-positive bacteria, fungi, parasites and infected host cells in mediating pathogenesis in addition to the functions of MVs produced by commensal bacteria. Finally, we discuss recent progress in the development of bacterial MVs as novel vaccines capable of mediating cellular and humoral immune responses.
Are U.S. national parks in the Upper Midwest acting as refugia? Inside vs. outside park disturbance regimes

Landscape disturbances such as forest harvest, blowdowns, fire, and development activities create patches on the landscape that modify the structure and integrity of ecosystems. Understanding the agents of change, where they occur, and how much of the landscape they are affecting will assist resource managers in making difficult decisions. To fulfill this goal, the National Park Service implemented a long-term monitoring program to quantify landscape dynamics across 1.5 million ha within and adjacent to eight national parks in the Upper Midwest United States using an automated satellite-based change detection program called LandTrendr (Landsat-based detection of trends in disturbance and recovery). The disturbance agents detected inside parks included beaver, blowdown, development, fire, flooding, insect/disease, and forest harvest. Pictured Rocks National Lakeshore had the largest percentage of area affected inside a park (11.83%, 1.96% per yr), and Isle Royal National Park had the lowest percentage of land affected (0.03%, 0.05% per yr). Tree defoliation due to insect/disease affected the largest percentage of land inside parks (1.56%, or 0.26% per yr) but did not result in tree mortality. Adjacent to parks, disturbance agents detected included agriculture, beaver, blowdown, development, insect/disease, fire, flooding, and forest harvest. Lands adjacent to Pictured Rocks National Lakeshore experienced the highest rate of disturbance (8.75%, 1.45% per yr), largely due to forest harvests. The lands adjacent to the Mississippi National River and Recreation Area experienced the lowest percentage of change (0.62%, 0.10% per yr), with development activities being responsible for most of the change. Forest harvesting was the major change agent outside six of the eight parks, an indication of how important the wood products industry is in the region and the level to which this region is forested. These national parks are acting as integral buffers from adjacent lands that either do not have the ability or lack the capacity to allow the ecosystem to function without intensive management efforts.
Introduction to Tourism Design and Design Science in Tourism

This chapter introduces design science in tourism (DST) as a framework which can guide both the theoretical foundations and applications in tourism design. It is argued that since 1972 when Clare Gunn first published Vacationsape huge progress has been made which now provides the theory and tools needed to support DST. This chapter discusses the concept of DST and the tools available to support tourism design. Finally, it introduces the chapters comprising this book which set the stage for the development of tourism design within today’s cultural and technological contexts.
Effect of Hemorrhagic Hypotension on Hydroxyl Radicals in Cat Brain

This study investigated the relationships between blood pressure, cortical oxygen pressure and hydroxyl radicals in the brain of adult cats during hemorrhagic hypotension and retransfusion. Oxygen pressure in the blood of the cortex was measured optically by the oxygen dependent quenching of phosphorescence and hydroxyl radicals by in vivo microdialysis. Following a 2 h stabilization period after implantation of the microdialysis probe in the striatum, the mean arterial blood pressure (MAP) was decreased in a stepwise manner from 132±2 Torr (control) to 90±1 Torr, 70±3 Torr and 50±3 Torr, holding the pressure at each level for 15 min. The whole blood was then retransfused and measurements were continued for 90 min. Cortical oxygen pressure progressively decreased with decrease in MAP, decreasing from 50±2 Torr (control) to 42±1 Torr, 31 ±2 Torr and 22±2 Torr, respectively. The level of hydroxyl radical increased by 20–25% following first 15 min of bleeding and stay on this level during the remaining period of hypotension. Maximal increase (by 78%) in level of hydroxyl radicals was observed after 15 min of retransfusion. The present study demonstrated that during hypotension and retransfusion there was an increase in the level of hydroxyl radicals in striatum. These can be important mediators of postischemic injury to the striatum.
Culture and Subjective Well-Being

(2002). Culture and Subjective Well-Being. Journal of Economic Issues: Vol. 36, No. 3, pp. 830-833.
Optimal monitoring and control under state uncertainty: Application to lionfish management☆

Abstract State variables in many renewable resource management problems, such as the abundance of a fish stock, are imperfectly observed over time. In systems characterized by state uncertainty, decision makers often invest in monitoring to learn about the level of a stock. We develop a stochastic bioeconomic model of marine invasive species management under state uncertainty. The decision maker in our model simultaneously evaluates optimal investment in monitoring and population control. Using a recently-devised method for solving continuous-state Partially Observable Markov Decision Processes (POMDPs), we find that the ability to learn through monitoring can alter the role of population control in the optimal policy function, for example by reducing control intensity in favor of monitoring. Optimal monitoring depends on the management context, including in our application lionfish population structure. The rich transient dynamics of our model depend critically on the relationship between the initial conditions for information and invader abundance.
Combining SIMD and Many/Multi-core Parallelism for Finite State Machines with Enumerative Speculation

Finite State Machine (FSM) is the key kernel behind many popular applications, including regular expression matching, text tokenization, and Huffman decoding. Parallelizing FSMs is extremely difficult because of the strong dependencies and unpredictable memory accesses. Previous efforts have largely focused on multi-core parallelization, and used different approaches, including {\em speculative} and {\em enumerative} execution, both of which have been effective but also have limitations. With increasing width and improving flexibility in SIMD instruction sets, this paper focuses on combining SIMD and multi/many-core parallelism for FSMs. We have developed a novel strategy, called {\em enumerative speculation}. Instead of speculating on a single state as in speculative execution or enumerating all possible states as in enumerative execution, our strategy speculates transitions from several possible states, reducing the prediction overheads of speculation approach and the large amount of redundant work in the enumerative approach. A simple lookback approach produces a set of guessed states to achieve high speculation success rates in our enumerative speculation. We evaluate our method with four popular FSM applications: Huffman decoding, regular expression matching, HTML tokenization, and Div7. We obtain up to 2.5x speedup using SIMD on one core and up to 95x combining SIMD with 60 cores of an Intel Xeon Phi. On a single core, we outperform the best single-state speculative execution version by an average of 1.6x, and in combining SIMD and many-core parallelism, outperform enumerative execution by an average of 2x.
Feature Illustration: Hyperechoic Foci and Calcifications

The specific imaging characteristics of echogenic foci within thyroid nodules can determine if the nodule’s appearance is suspicious or non-suspicious for malignancy. In this chapter, we describe five different types of echogenic foci seen in thyroid nodules: those with no posterior artifact, those with large comet-tail artifact (>1.0 mm), those with small comet-tail artifact (≤1.0 mm), internal foci (calcifications) with posterior shadowing, and peripheral rim-like foci (calcifications) with posterior shadowing. In general, independent of the additional nodule parenchymal features, all categories of echogenic foci, except those with large comet-tail artifacts, are associated with an increased risk of thyroid cancer.
Performance Analysis and Optimization of SAMtools Sorting

SAMtools is a suite of tools that is widely-used in genomics workflows for post-processing sequence alignment data from large high-throughput sequencing data sets. A common use of SAMtools is to sort the standard Binary Alignment/Map (BAM) format emitted by many sequence aligners. This can be computationally- and I/O-intensive: BAM files can be many gigabytes in size, and may need to be decompressed before sorting and compressed afterwards. As a result, BAM-file sorting can be a bottleneck in genomics workflows. This paper presents a case study on the performance characterization and optimization of BAM sorting with SAMtools. OpenMP task parallelism to enhance concurrency and memory optimization techniques were employed in both SAMtools and the underlying library HTSlib. Utilizing all 32 processor cores on the benchmark system, the optimizations resulted in a speedup of 3.92X for an in-memory sort of 24.6 GiB of BAM data (102.6 GiB uncompressed), while a 1.55X speedup was achieved for an out-of-core sort.
Hatching Success and Other Reproductive Attributes of Gopher Tortoises in Southwest Georgia

Abstract Broad variation in egg hatching success observed in gopher tortoise (Gopherus polyphemus) populations led us to investigate hatching success and other reproductive attributes within a unique, high-quality site in the eastern portion of the species' range. We documented use of a juvenile tortoise burrow as a nest site, a mean clutch size of 5.9 eggs, long oviposition-to-hatchling emergence times (96–128 d), and 73% hatching success for predator-protected eggs. Although consistent with previous reports of greater hatching success in eastern gopher tortoise populations than in western ones, hatching success at our eastern site was on the low end of values from other eastern populations, possibly reflecting above average rainfall during this study.
Prospective computerized monitoring of cognitive functioning before and after blood and marrow transplantation.

Prospective computerized monitoring of cognitive functioning before and after blood and marrow transplantation
Influence of paternal age on perinatal outcomes

Background There is an increasing trend to delay childbearing to advanced parental age. Increased risks of advanced maternal age and assisted reproductive technologies are widely accepted. There are limited data regarding advanced paternal age. To adequately counsel patients on risk, more research regarding advanced paternal age is necessary. Objective We sought to determine the influence of paternal age on perinatal outcomes, and to assess whether this influence differs between pregnancies achieved spontaneously and those achieved with assisted reproductive technology. Study design A population-based retrospective cohort study of all live births in Ohio from 2006 through 2012 was completed. Data were evaluated to determine if advanced paternal age is associated with an increased risk of adverse outcomes in pregnancies. The analysis was stratified by status of utilization of assisted reproductive technology. Generalized linear regression models assessed the association of paternal age on pregnancy complications in assisted reproductive technology and spontaneously conceived pregnancies, after adjusting for maternal age, race, multifetal gestation, and Medicaid status, using Stata software (Stata, Release 12; StataCorp, College Station, TX). Results Paternal age was documented in 82.2% of 1,034,552 live births in Ohio during the 7-year study period. Paternal age ranged from 12-87 years, with a median of 30 (interquartile range, 26-35) years. Maternal age ranged from 11-62 years, with a median of 27 (interquartile range, 22-31) years. The use of assisted reproductive technology in live births increased as paternal age increased: 0.1% 60 years, P Conclusion Older paternal age does not appear to pose an independent risk of adverse perinatal outcomes, in pregnancies achieved either with or without assisted reproductive technology. However, small effect sizes such as very small risk increases or decreases may not be detectable despite the large sample size in this study of >830,000 births.
Musculoskeletal Involvement in Non-Hodgkin Lymphoma

Lymphoreticular neoplasm of the reticulo-endothelial system is a well-known entity in which the tumor arises from lymphoid precursor cells. The disorders included in this group are NHL and HD, with a changing terminology. The old classification of primary NHL included lymphosarcoma and reticulum cell sarcoma. The cells of malignant lymphomas may exhibit various degrees of differentiation, which may be shown with immunohistochemistry (Resnick and Haghighi 1996; National Cancer Institute 1982).
Weight resilience and fruit and vegetable intake among African-American women in an obesogenic environment.

Objective To investigate relationships between weight resilience (maintaining a normal weight in a food desert environment) and fruit and vegetable (FV weight and height were measured. Multivariable regression models estimated prevalence ratios (95 % CI). Setting Two low-income, predominantly African-American food deserts in Pittsburgh, Pennsylvania, USA. Subjects Women aged 18-49 years (n 279) who were the primary food shopper in a household randomly selected for a parent study. Results Fifteen per cent were weight resilient, 30 % were overweight and 55 % were obese. Overall, 25 % reported eating ≥5 FV 1·10, 3·43). Across BMI groups, self-efficacy regarding FV 0·09, 0·94). In a model predicting consuming ≥5 FV 1·00, 2·24). Conclusions In this population, weight resilience may be encouraged by improving access to affordable and convenient F&V options and providing education on ways to make them palatable to the entire household, rather than by shifting women's F&V perceptions, which are already positive.
Evaluation of MUC1-Aptamer Functionalized Hybrid Nanoparticles for Targeted Delivery of miRNA-29b to Nonsmall Cell Lung Cancer

The objective of this study was to evaluate the therapeutic efficacy and pharmacokinetic study of mucin1-aptamer functionalized miRNA-29b-loaded hybrid nanoparticles (MAFMILHNs) in lung tumor-bearing SCID mice. MAFMILHNs were manufactured using an isoelectric point based nanotechnology. They were then fully characterized for particle size, loading capacity, zeta potential, and encapsulation efficiency. The ability of MAFMILHNs to downregulate oncoprotein DNMT3B both at the cellular level and in vivo was monitored using Western blot, while the effect of the downregulation of DNMT3B on tumor growth was assessed using bioluminescence. Results indicate that the presence of MUC1-aptamer conjugated to the surface of the nanoparticles enhanced the selective delivery of miRNA-29b to tumor cells and tissues. Further, the downregulation of DNMT3B by MAFMILHNs resulted in the inhibition of tumor growth in mouse models.
pyNBS: a Python implementation for network-based stratification of tumor mutations.

Summary We present pyNBS: a modularized Python 2.7 implementation of the network-based stratification (NBS) algorithm for stratifying tumor somatic mutation profiles into molecularly and clinically relevant subtypes. In addition to release of the software, we benchmark its key parameters and provide a compact cancer reference network that increases the significance of tumor stratification using the NBS algorithm. The structure of the code exposes key steps of the algorithm to foster further collaborative development. Availability and implementation The package, along with examples and data, can be downloaded and installed from the URL https://github.com/idekerlab/pyNBS.
In Vivo Intrinsic Optical Signal Imaging of Neocortical Epilepsy

Intrinsic optical signal (IOS) imaging is a technique for measuring changes in blood flow, metabolism, and cellular swelling associated with neuronal activity. The combined spatial and temporal resolution, in addition to the ability to sample large areas of cortex simultaneously, make it a powerful technique for brain mapping. IOS has only recently been applied systematically to the study of epilepsy. This chapter will explore the utility and feasibility of mapping interictal spikes, ictal onsets, offsets, and horizontal propagation using IOS imaging in acute and chronic animal models of epilepsy. The implementation of IOS imaging in the operating room during neurosurgical procedures will be discussed as well as technical challenges that currently restrict this translational work to a very few centers.
Feminists Reshaping Gender

The gender order is incredibly durable, and persists relatively unchanged despite major cultural and structural changes. Feminists, however, have collectively mobilized to change some aspects of the gender structure. Over hundreds of years, participants in the U.S. feminist movement have advanced women’s position in the workplace, home, and economy. Feminists have challenged social institutions such as the nuclear family, interpersonal relationships privileging men, and the gender binary. Over the years, feminists helped win woman suffrage, they shaped social policy during the New Deal, they helped win the right to birth control and safe and accessible abortion, they raised awareness about the harms of sexual harassment and gendered violence, and helped draft and pass laws around equal pay and access to work, among other wins. Using a range of tactics, from community-based groups, to protest and Internet organizing, feminists have unquestionably improved women’s position in society. Scholarship about feminist movements has also pushed social movement scholarship in new directions, emphasizing a diversity of targets and tactics, focusing on movement continuity over time, and foregrounding the importance of community-building and other extra-political activities in the maintenance and growth of social movements. Areas for additional research include a deeper empirical and theoretical analysis of the intersectional nature of feminism and more attention to the heterogeneity of women’s experiences. Greater methodological diversity in the study of feminist movements would offer a more robust understanding of the movement, including a better grasp of the cultural and discursive outcomes of feminist movements and those like them.
Nonequilibrium Surface and Interface Thermodynamics

Thermodynamics strictly is the science which tells one what is not possible. It is quite powerful for equilibrium for then all changes have become impossible. It is less useful far away from equilibrium. While it still forbids many changes, many remain possible and thermodynamics provides no information about which of those will actually occur. Thermodynamics provides us with inequalities based on the second law which all possible processes must comply with.
EOQ-Type Models with Demand Selection

This chapter discusses a generalized version of the economic order quantity (EOQ). In particular, we consider a situation in which a single inventory stage must select from among a set of demand streams, those which it will satisfy. Each demand stream carries with it a constant demand rate as well as a constant revenue rate. We consider several problem variants within this class, including problems with lot size and demand rate constraints.
Celiac disease: adenovirus and alpha gliadin

Celiac disease (gluten-sensitive enteropathy, celiac sprue, nontropical sprue) is characterized by damage to the small intestinal mucosa and malabsorption of most nutrients (reviewed in Cole and Kagnoff 1985; Kagnoff 1989). The disease is activated by dietary exposure to wheat gluten and similar proteins in several other grains. Wheat gluten is a mixture of gliadin and glutenin (Kasarda 1981). It is the gliadin fraction that is responsible for activating this disease (Kasarda 1981). The symptoms commonly appear during the first 3 years of life after the introduction of cereals into the diet, with a second peak incidence occurring during the 3rd and 4th decades. Clinical manifestations predominantly reflect the consequences of malabsorption. Treatment consists of a gluten-free diet (i.e., a diet free of gluten and related, disease-associated grains) (Cole and Kagnoff 1985).
Investigation into the Mechanism and Kinetic of bod Reduction due to Pressurization

Abstract Investigations concerning the application of pressure to domestic sewage and simulated sewage samples have demonstrated a decrease in the rate of biochemical assimilation of the organic matter. Also, BOD and COD values after pressurization were approximately 75% of the unpressurized samples. This suggested a change in the biochemical composition of the wastes being pressurized. A pilot plant pressure chamber was constructed where presures to 40 psi could be maintained by compressed air. Raw wastes were pressurized, aerated, and left quiescent and the BOD, COD, and microorganisms were monitored. The waste content of the pressurized samples showed greater reductions whereas the aerated and quiescent samples displayed similar changes. An investigation was made to show that the reductions which occured were due to an increased rate of hydrolysis of the large molecular weight organic fractions to their smaller counterparts. Polysaccharides, fats, and proteins were pressurized, hydrolyzed, and analyzed to their monosacchatides, fatty acids, and amino acids. In all cases the larger compounds showed an increased rate of hydrolysis due to pressure. As has been shown in the literature the decomposition constant, k 1 , is proportional to the organic matter present. This is reasonable if the rate constant is assumed to be kinetically first order. As the time of exposure to pressure is increased the BOD and COD values also decrease as does the BOD rate constant which supports the argument that pressurization increased the rate of hydrolysis.
On Some Questions Concerning Price Reform in the People’s Republic of China

The purpose of this paper is to examine some conceptual issues involved in price reform in a system of central administrative command planning such as China’s, and the way these issues were addressed in the People’s Republic of China in the wake of the Cultural Revolution.
Does It Take a School? Revisiting the Influence of First Arrest on Subsequent Delinquency and Educational Attainment in a Tolerant Educational Background:

Objectives:By drawing on cumulative influences of labeling in Western samples, this study examined the relationship between first-time arrest and delinquency and educational attainment in South Kor...
On Informational Nudging for Boundedly Rational Decision Makers

We consider the problem of informational nudge design (i.e., the strategic revelation of possibly altered information) for a boundedly rational decision-maker facing choices at every time instant. Bounded rationality manifests itself through the presence of a belief vector, which influences how provided information is used and which itself varies dynamically (possibly in a self-reinforcing, yet unwarranted way), depending on the decision maker's best response. We show that an arbitrary mixed-strategy equilibrium point can be created and stabilized given if the belief's update is slow enough and demonstrates adequate level of non-compliance to revealed information.
Small, non-peptide C5a receptor antagonists: Part 1

The optimisation of a series of amides for C5a receptor binding and functional activity, and physicochemical properties is described. The initial hit, 1 (IC(50) 1 microM), was discovered during high throughput screening, from which highly potent C5a receptor antagonists (e.g.14, IC(50) 5 nM) were developed.
Milton and the Art of Rhetoric

Challenging the conventional view of John Milton as an iconoclast who spoke only to a 'fit audience though few', Daniel Shore argues that Milton was a far more pragmatic writer than previous scholarship has recognized. Summoning evidence from nearly all of his works - poetry and prose alike - Shore asserts that Milton distanced himself from the prescriptions of classical rhetoric to develop new means of persuasion suited to an age distrustful of traditional eloquence. Shore demonstrates that Milton's renunciation of agency, audience, purpose and effect in the prose tracts leads not to quietism or withdrawal, but rather to a reasserted investment in public debate. Shore reveals a writer who is committed to persuasion and yet profoundly critical of his own persuasive strategies. An innovative contribution to the field, this text will appeal to scholars of Milton, seventeenth-century literature, Renaissance literature and the history and theory of rhetoric.
One-Year Mortality of Patients After Emergency Department Treatment for Nonfatal Opioid Overdose.

Study objective Despite the increased availability of naloxone, death rates from opioid overdose continue to increase. The goal of this study is to determine the 1-year mortality of patients who were treated for a nonfatal opioid overdose in Massachusetts emergency departments (EDs). Methods This was a retrospective observational study of patients from 3 linked statewide Massachusetts data sets: a master demographics list, an acute care hospital case-mix database, and death records. Patients discharged from the ED with a final diagnosis of opioid overdose were included. The primary outcome measure was death from any cause within 1 year of overdose treatment. Results During the study period, 17,241 patients were treated for opioid overdose. Of the 11,557 patients who met study criteria, 635 (5.5%) died within 1 year, 130 (1.1%) died within 1 month, and 29 (0.25%) died within 2 days. Of the 635 deaths at 1 year, 130 (20.5%) occurred within 1 month and 29 (4.6%) occurred within 2 days. Conclusion The short-term and 1-year mortality of patients treated in the ED for nonfatal opioid overdose is high. The first month, and particularly the first 2 days after overdose, is the highest-risk period. Patients who survive opioid overdose should be considered high risk and receive interventions such as being offered buprenorphine, counseling, and referral to treatment before ED discharge.