cssi/SciSciGPT-SciSciNet huggingface dataset:
Environment analysis of higher-order languages

Any analysis of higher-order languages must grapple with the tri-facetted nature of λ. In one construct, the fundamental control, environment and data structures of a language meet and intertwine. With the control facet tamed nearly two decades ago, this work brings the environment facet to heel, defining the environment problem and developing its solution: environment analysis. Environment analysis allows a compiler to reason about the equivalence of environments, i.e., name-to-value mappings, that arise during a program's execution. In this dissertation, two different techniques—abstract counting and abstract frame strings—make this possible. A third technique, abstract garbage collection, makes both of these techniques more precise and, counter to intuition, often faster as well. An array of optimizations and even deeper analyses which depend upon environment analysis provide motivation for this work. In an abstract interpretation, a single abstract entity represents a set of concrete entities. When the entities under scrutiny are bindings—single name-to-value mappings, the atoms of environment—then determining when the equality of two abstract bindings infers the equality of their concrete counterparts is the crux of environment analysis. Abstract counting does this by tracking the size of represented sets, looking for singletons, in order to apply the following principle:If {x} = { y}, then x = y. Abstract frame strings enable environmental reasoning by statically tracking the possible stack change between the births of two environments; when this change is effectively empty, the environments are equivalent. Abstract garbage collection improves precision by intermittently removing unreachable environment structure during abstract interpretation.
Correlations for the pressure drop for flow through metal foam

Steady-state unidirectional pressure-drop measurements for incompressible airflow through nine open-cell aluminum foam samples, having different porosities and pore densities, were undertaken. The pressure drop increased with increasing Darcian velocity following the quadratic Forchheimer equation. The lower-porosity foam produced significantly higher pressure drop. Both the permeability and the form drag coefficient correlated well with the porosity. The correlations predicted the results of some previous studies reasonably well, especially for the low-pore-density foam.
Increasing incidence of testicular germ cell tumors among black men in the United States.

Purpose There has been marked disparity in the incidence of testicular germ cell tumors (TGCT) among white and black men for a number of decades in the United States. Since at least the beginning of the Surveillance, Epidemiology, and End Results (SEER) Program in 1973, incidence rates among white men have been five times higher than rates among black men. In addition, rates among white men have been increasing, whereas rates among black men have remained stable. However, a recent examination of ethnic-specific rates suggested that the incidence among black men may have begun to change in the 1990s. Patients and Methods TGCT incidence data from nine registries of the SEER Program were analyzed for the years 1973 to 2001. Trends were examined separately for seminoma and nonseminoma. Results Analyses found that the incidence of TGCT began to increase among black men between the 1988 to 1992 and 1993 to 1997 periods. Before that time, incidence among black men had decreased by 14.8%. Between 1988 to 1992 and...
Effect of Loop-Unrolling in Hardware Reconfigurable Implementations of RC5-192 Encryption Algorithm

The objective of this paper is to determine the effects of 'loop-unrolling' design concept, on the performance of hardware based implementations of the RC5 encryption algorithm. An effort has been done to determine the best value of the number of unrolled loops to implement the RC5 algorithm using 192-bit encryption key. The various models tested were based on single-custom processor with: no-loop-unrolling; loop unrolled implementations with different unrolling sizes. In this research, various performance measures are considered, such as the maximum frequency of operation, circuit size, throughput, and energy consumption. To achieve proper comparison results, all models were developed and mapped to the same hardware reconfigurable chip, a Field Programmable Gate Array (FPGA). The performance parameters of each model were evaluated to determine the best hardware model. Verilog hardware description language was used to model and test all implementations. While no-loop-unrolling provided the least circuit size, the 3-loop-unrolled approach provided the highest throughput, amongst all tested implementations. A throughput speed up of 24% was achieved compared to a reference system implemented in a different target device using a Xilinx FPGA family. Comparing our implementations on the same Altera FPGA family, a maximum throughput speed up of 50% was achieved.
Comparison of single-echelon vs. multi-echelon inventory systems using multi-objective stochastic modelling

Recent advancements in inventory management have identified need for investigating benefits of single-echelon and multi-echelon systems. Single-echelon inventory control problems focus on determining the appropriate level of inventory for an individual unit within the supply chain network, while multi-echelon inventory optimisation takes a holistic approach by focusing on the correct levels of inventory across the entire network. This paper presents a stochastic modelling approach for multi-tier supply chains with multiple inventory items. The approach will be used to compare behaviour of single-echelon vs. multi-echelon inventory systems. A multi-objective optimisation method is used to optimise model's behaviour with two conflicting objectives: minimising average inventory across the supply chain and maximising overall fill rate. The results show that single-echelon systems result in higher inventory levels and lower fill rates, while multi-echelon systems result in lower inventory levels while maintaining higher fill rates for the entire supply chain network. The methods are demonstrated on a sample network database.
A Chord Distribution Description of Porous Glass

Small angle neutron scattering data of Vycor is analyzed using a chord distribution model describing the microporous structure. In addition, the same model is applied in interpreting the data taken when capillary condensation takes place in the porous medium. In both cases, the results are in good agreement with other measurements, and shows a promising potential in describing such a bicontinuous system.
Statewide surveillance of halogenated flame retardants in fish in Illinois, USA.

Abstract In order to better understand the exposure of aquatic systems to halogenated flame retardant contaminants, the present study investigated a variety of legacy and emerging flame retardants in common carp and largemouth bass collected from 58 stations across Illinois (United States). The data revealed that polybrominated diphenyl ethers (PBDEs) generally dominated the flame retardant residues in Illinois fish. Concentrations of ΣPBDEs (including all detectable PBDE congeners) ranged from 24.7 to 8270 ng/g lipid weight (median: 135 ng/g lw) in common carp and 15–3870 ng/g lw (median: 360 ng/g lw) in largemouth bass. In addition to PBDEs, Dechlorane analogues (i.e. Dec-603, Dec-604, and Chlordane Plus) were also frequently detected. Median concentrations of ΣDechloranes (including all detected Dechlorane analogues) were 34.4 and 23.3 ng/g lw in common carp and largemouth bass, respectively. Other emerging flame retardants, including tetrabromo- o -chlorotoluene (TBCT), hexabromobenzene (HBBZ), 2-ethylhexyltetrabromobenzoate (EH-TBB), and bis(2-ethylhexyl)-3,4,5,6-tetrabromo-phthalate (BEH-TEBP), were also detected in 40–78% of the fish at the monitored stations. Spatial analysis revealed significantly greater PBDE concentrations in fish living in impaired urban streams and lakes compared to those from the impaired agricultural and unimpaired agricultural/urban waters, demonstrating a significant urban influence on PBDE contamination. Future studies and environmental monitoring are recommended to focus on temporal trends of PBDEs and alternative flame retardants, as well as human exposure risks via edible fishes, in the identified Areas of Concern within Illinois.
Analysis on adverse events following immunization surveillance in Weifang City from 2010 to 2012

Objective To analyze the occurrence features of adverse events following immunization(AEFI) in Weifang City from 2010 to 2012.And to evaluate the implementation of AEFI surveillance system and the immunization safety related to the National Immunization Program(NIP) Vaccines.Methods AEFI data was collected through the AEFI Information System,which reported from January 1,2010 to December 31,2012.The descriptive methodology was used.Results The city received a total of 1893 cases of AEFI monitoring system from 2010 to 2012,among them,targets aged ≤1 year accounted for 56.31%,the sex ratio of male and female was 1.34:1.NIP vaccine has high incidence of AEFIs.96.62% AEFIs were common,minor reactions,with 83.15% occurred ≤1 after vaccination;abnormal reaction rate of 2.54%,allergy and BCG lymphadenitis mainly,the vast majority of cases had been recovered.The vaccine reaction estimated reporting rate of NIP vaccines were 5.05-76.00 per one hundred thousand.12 counties reported to the AEFI surveillance system from 2010 to 2012.The coverage rate of reporting counties,the reported rate within within 48 th and the investigated rate within 48 th were 100%.Conclusion The sensitivity of AEFI surveillance is still low and uneven between reporting units.AEFIs are often occurred in young children and NIP vaccines,and they are the focus of the AEFI surveillance.The estimate reporting rate of vaccine reactions of NIP vaccines are not over the expected,the vaccines safety is well.
The Urgent Question of the Research and Development of Marxist Philosophy at Present

During the latest two decades,all of the big disputes about philosophy is actually a kind of introspection and doubt about the traditional explaination of marxist philosophy.So,how to evaluate the traditional system is actually the urgent question of the research and development of philosophy. The traditional system doesn't stipulate correctly the object of philosophy,fundamental concept,fundamental question and the nature of philosophy. Its method doesn't embody the principle of development either.It even can't stipulate exactly the relations between philosophy and economy and between philosophy and politics.So,it is not "roughly appropriate",but "roughly not appropriate".Thus we should take scientific critical attitude towards the traditional system and put it into a wider system.
Analysis of immunoglobulin and T-cell receptor gene rearrangements in human fetal bone marrow B lineage cells.

Fetal bone marrow B lineage cells representing multiple stages of B cell development were isolated by two-color cell sorting and analyzed for immunoglobulin H and T-cell receptor (TCR) gamma and delta gene rearrangements. Analysis of CD10+/surface mu- cells using a JH probe revealed a high frequency of rearrangements; some of these rearrangements used the 3′ D region gene DQ52. Analysis of CD10+/surface mu- cells revealed no detectable TCR-gamma or -delta rearrangements, nor were TCR-delta rearrangements detected in CD10+/surface mu+ cells, despite the limited repertoire of these genes. These observations are surprising given the high frequency of TCR delta/gamma rearrangements in B cell precursor acute lymphoblastic leukemia, and identify a potential difference in patterns of gene rearrangement that distinguish normal and leukemic B cell precursors.
The spectrum of anomalies of aortopulmonary septation

Embryologically related defects resulting from abnormal septation of the aortopulmonary trunk in 13 patients were reviewed and grouped according to a new classification system. Seven patients (54 percent) had typical aortopulmonary septal defects or windows (Type I), three (23 percent) had a more cephalad defect between the ascending aorta and the origin of the right pulmonary artery (Type II), and three (23 percent) had anomalous origin of the right pulmonary artery from the ascending aorta (Type III). Type I defects are caused by incomplete septation of the aortopulmonary trunk; Type II and III defects result from unequal partitioning of the aortopulmonary trunk by the conotruncal ridges. Three of six patients survived correction of Type I defects; both patients having correlation of Type II defects and all three patients with Type III defects survived and remain well 2 to 216 months (mean 61 months) postoperatively. The recommended technique for Type I and II defects is transaortic closure of the defect by prosthetic patch with the aid of cardiopulmonary bypass, supplemented by profound hypothermia (20° C.), and circulatory arrest for improved exposure in selected cases. For Type III defects, division of the anomalous connection plus direct implantation of the right pulmonary artery into the main pulmonary artery is the preferred approach.
Ramanujan’s Elementary Method in Partition Congruences

Page 182 in Ramanujan’s lost notebook corresponds to page 5 of an otherwise lost manuscript of Ramanujan closely related to his paper providing elementary proofs of his partition congruences \(p(5_n+4) \equiv 0\) (mod 5) and \(p(7_n+5) \equiv 0\). The claims on page 182 are proved and discussed, and further results depending on Ramanujan’s ideas are established.
Finite Element Analysis of Patient-Specific Mitral Valve with Mitral Regurgitation

Functional mitral regurgitation (FMR) is a significant complication of left ventricular dysfunction and strongly associated with a poor prognosis. In this study, we developed a patient-specific finite element (FE) model of the mitral apparatus in a FMR patient which included: both leaflets with thickness, annulus, chordae tendineae, and chordae insertions on the leaflets and origins on the papillary muscles. The FE model incorporated human age- and gender-matched anisotropic hyperelastic material properties, and MV closure at systole was simulated. The model was validated by comparing the FE results from valve closure simulation with the in vivo geometry of the MV at systole. It was found that the FE model could not replicate the in vivo MV geometry without the application of tethering pre-tension force in the chordae at diastole. Upon applying the pre-tension force and performing model optimization by adjusting the chordal length, position, and leaflet length, a good agreement between the FE model and the in vivo model was established. Not only were the chordal forces high at both diastole and systole, but the tethering force on the anterior papillary muscle was higher than that of the posterior papillary muscle, which resulted in an asymmetrical gap with a larger orifice area at the anterolateral commissure resulting in MR. The analyses further show that high peak stress and strain were found at the chordal insertions where large chordal tethering forces were found. This study shows that the pre-tension tethering force plays an important role in accurately simulating the MV dynamics in this FMR patient, particularly in quantifying the degree of leaflet coaptation and stress distribution. Due to the complexity of the disease, the patient-specific computational modeling procedure of FMR patients presented should be further evaluated using a large patient cohort. However, this study provides useful insights into the MV biomechanics of a FMR patient, and could serve as a tool to assist in pre-operative planning for MV repair or replacement surgical or interventional procedures.
Nek2 Stabilization By Usp7 Leads to Activation of NF-Kb in Multiple Myeloma

Abstract NIMA (Never In Mitosis Gene A)-Related Kinase 2 (Nek2), a centrosomal Serine/Threonine kinase, is a key player in numerous malignancies. Overexpression of Nek2 has been related to many cancers including Multiple Myeloma (MM). In MM, Nek2 is one of the chromosomal instability genes associated with drug resistance and disease relapse. However, very little is known about the mechanisms that lead to these Nek2-driven disparities. Here, we show that the Ubiquitin Specific Peptidase 7 (USP7) stabilizes Nek2 leading to activation of NF-kb pathway. Using gene expression profile (GEP) data from patients and cell lines we discovered that Nek2 overexpression leads to increases of several targets of the NF-kb pathway. We, thus, hypothesize that Nek2 is activating NF-kb. To address this, we overexpressed Nek2 and tested the classic canonical NF-kb hallmarks proteins by western blotting. Nek2 overexpression led to an increase in phosphorylation of IKK, activator of NF-kb, and to decrease levels of IKb-alpha, a negative regulator of the pathway. Nek2 overexpression also increased nuclear and phosphorylated p65 on residue S536, known as active transcriptional site. To further confirm that Nek2 is activating canonical NF-kb luciferase assay was performed. The luciferase reporter is driven by a p65 promoter and in cells overexpressing Nek2 luciferase levels were increased. To characterize Nek2 interacting partners a tandem affinity purification/mass spectrometry (TAP/MS) approach was performed. We found that Nek2 binds to Usp7, a deubiquitinase overexpressed in numerous cancers. This led to hypothesize that that Nek2, a known target of the ubiquitin proteasome system, is being stabilized by the Usp7 contributing to its overexpression and the increased activation of the NF-kb pathway. To test our hypothesis, we treated different cancer cell lines with the commercially available Usp7 inhibitor, P5091, or silenced the protein using shRNA. In both case, we found a reduction in Nek2 protein level. Additionally, we overexpressed Usp7 and Nek2 increased confirming that Usp7 stabilizes Nek2. To further show that Usp7 stabilizes Nek2 by de-ubiquitination, we overexpressed Usp7 and analyzed Nek2 ubiquitination after immunoprecipitation. When Usp7 was overexpressed no ubiquitination of Nek2 was detected. Finally, by using GEP data from MM patients, we found that individuals who overexpressed Nek2 along with an active NF-kb signature have worst event free survival as well as overall survival, indicating Nek2 overexpression leading to increased NF-kb signature has clinical significance. Disclosures No relevant conflicts of interest to declare.
Time stamping of single optical photons with 10 ns resolution

High spatial and temporal resolution are key features for many modern applications, e.g. mass spectrometry, probing the structure of materials via neutron scattering, studying molecular structure, etc.1-5 Fast imaging also provides the capability of coincidence detection, and the further addition of sensitivity to single optical photons with the capability of timestamping them further broadens the field of potential applications. Photon counting is already widely used in X-ray imaging,6 where the high energy of the photons makes their detection easier. TimepixCam is a novel optical imager,7 which achieves high spatial resolution using an array of 256×256 55 μm × 55μm pixels which have individually controlled functionality. It is based on a thin-entrance-window silicon sensor, bump-bonded to a Timepix ASIC.8 TimepixCam provides high quantum efficiency in the optical wavelength range (400-1000 nm). We perform the timestamping of single photons with a time resolution of 20 ns, by coupling TimepixCam to a fast image-intensifier with a P47 phosphor screen. The fast emission time of the P479 allows us to preserve good time resolution while maintaining the capability to focus the optical output of the intensifier onto the 256×256 pixel Timepix sensor area. We demonstrate the capability of the (TimepixCam + image intensifier) setup to provide high-resolution single-photon timestamping, with an effective frame rate of 50 MHz.
Viewing the future in the past: historical ecology applications to environmental issues

In recent decades, scientists’ concern over climate change has increasingly pushed archaeologists to demonstrate the applicability of the historical sciences and long-term ecological research to mo...
Wanted Alive: Finding Bacteria in Your Food.

In this issue of Cell Chemical Biology, Pezacki and co-workers (Sherratt et al., 2017) report a simple method to metabolically label viable bacteria, which can be used to detect and capture foodborne pathogens. The method may also find many other applications because it can be used to recover live cells, pathogens and non-pathogens, from various biomedical and environmental samples.
Insect Tissue Culture

Publisher Summary This chapter defines tissue culture as the study of organs, tissues, and cells removed from the body of the animal and grown or maintained in vitro for more than 24 hours. It discusses the equipment and supplies of insect tissue culture. Insect cells and tissues are usually cultured at 26–30°C. The tissue culture media are sterilized by filtration. Excised insect organs and tissues are usually quite small, and therefore special culture vessels are often used. Insect tissue culture originated with the work of Goldschmidt in 1915, when he observed spermatogenesis in testes of the moth, Sumiu cecropia—in vitro. Insects possess an open circulatory system, and organs are directly bathed in the hemolymph. The tissues employed for primary cultures must be sterile or have a low microbial population. The inclusion of antibiotics, usually penicillin and streptomycin, reduce contamination problems in culture media. Antibiotics, however, should be used only when it is absolutely necessary.
Men and masculinities in global English language teaching

Appleby begins the book by addressing the peculiar absence of discussion on white Western men and their lived experience in the international English Language Teaching (ELT) contexts, despite the d...
The impact of instrumentation errors on dynamic state estimation-based protection

Protective relays work with low level voltage and current signals that are produced by instrumentation transformers. These non-ideal devices introduce errors and secondary signals are not always an exact scaled replica of primary quantities. The errors degrade the performance of relays and consequently the reliability of the protective system. This paper investigates the impact of instrumentation transformers on dynamic state estimation-based protection algorithm. It is shown that while the potential transformers do not introduce large errors, current transformers do if the primary current results in CT saturation. As a result, the true state of the protected device cannot be accurately estimated if the detailed CT model is not integrated with the device. Simulation results are also provided to highlight the possibility of insecure operation from instrumentation errors and also to verify the performance of the non-ideal modeling.
Spinal Muscular Atrophy: Entering the Treatment Age

Spinal muscular atrophy is a devastating neurodegenerative disorder. With the recent approval of the first treatment, nusinersen (Spinraza), the natural course of the disease will change. It poses new challenges in administration and highlights the importance of early diagnosis. Nusinersen, an antisense oligonucleotide, helps to ameliorate disease severity in patients with spinal muscular atrophy (SMA)1 and SMA2 early in their disease course, helping to decrease the risk of death and respiratory support, as well as enhance motor outcomes in all patients with SMA. Treatment earlier in the course of disease is associated with better outcomes. Overall, treatment is well tolerated, but repeated intrathecal administration can be both technically difficult as well as expensive. Nusinersen is an important step forward in the treatment of spinal muscular atrophy. With the availability of a treatment, we have to change our approach to diagnosis, focusing on carrier testing and/or newborn screening as well as a low threshold for clinical testing.
Late-Life Depression

This chapter reviews the literature on late-life depression. Support for a neuroanatomical substrate underlying depression in late life will be articulated using findings from the neuropsychological, neuroimaging, and medical literature. This chapter does not cover treatment issues for depression in late life, but the reader is referred to Chapter 3, Mood Disorders, in this text. The purpose of this chapter is to integrate findings from diverse literature and to review evidence suggesting that depression in late life is a unique disorder, different from depression in young adulthood, and related to dysfunction of particular regions of the brain.
SYNTHESIS OF A SPECIFIC SEQUENCE OF DNA USING RESTRICTION ENZYMES

Publisher Summary This chapter discusses the method for the synthesis of a specific sequence of DNA using restriction enzymes. The restriction enzyme MboII recognizes the DNA sequence GAAGA and cleaves the DNA eight bases downstream from this site, leaving a single 3' protruding base. There are no apparent sequence requirements in the stretch of DNA between the recognition sequence and the point of cleavage. Using this property, a segment of DNA from one fragment can be transferred to another fragment. The scheme can be demonstrated by the formation of a restriction enzyme recognition site from two MboII cleavage products. The extension of the basic scheme would allow the production of more generalized fragments useful in constructing gene sequences.
Evaluation of Enrichment for Reptiles in Zoos

Studies on environmental enrichment for reptiles are lacking in the scientific literature. Although the literature reflects a limited take on reptile enrichment in the zoological community, it may not be the case in reality as enrichment is generally considered an important aspect of the care of nonhuman animals in captivity. This project investigated the current state of reptile enrichment as it is being used in zoos. Although respondents were disproportionately accredited by the Association of Zoos and Aquariums, the results showed many forms of enrichment being used for reptiles in zoos and happening at much greater levels than what has been suggested in the scientific literature. There were significant differences between a) reptile groups for each form of enrichment, and b) enrichment forms within each reptile group, except with the use of natural enrichment devices and structural/habitat design, which did not differ across all reptile groups. Enrichment goals, assessment methods, and sources of information for reptile enrichment used by zoos suggest the need for more scientific publications for facilities to make evidence-based decisions to improve the welfare of reptiles in captivity.
Wilderness and Civilization

This chapter examines early twentieth century constructions of “wildness” and common Euroamerican beliefs about what it means to be civilized. In her explanation of the significance of the “Wild Indian” and the “Indian Devil” to Yurok culture, Thompson challenges racist assumptions about indigenous people. She also presents a critique of how Euroamericans both denigrate and romanticize Native culture, eventually highlighting thought-provoking similarities between the so-called “Wild Indian” and the white man.
Diagnostic method by using vibration analysis for pump fault detection

Abstract Pump cavitation is a common problem affecting pumping systems. It occurs when the pressure of the liquid in the pump drops below a threshold and causes the liquid to vaporize creating tiny bubbles that, when they implode or collapse, trigger intense shockwaves inside the pump determining destructive damage. Excessive vibration on the pump casing could indicate cavitation. Consequently, vibration monitoring can help the detection and prevention of this harmful and undesired phenomenon. The purpose of this research is to analyze the capability of vibration-based techniques to detect, monitor and prevent pump cavitation. Experimental tests were performed on a gear pump used in the lubrication circuit of internal combustion engines. The pump, installed on a dedicated test bench, was forced to cavitate by placing a calibrated orifice on the suction side. Main working parameters, like oil flow rate, suction and delivery pressure, shaft speed, were accurately measured. Different pump operating conditions with and without cavitation occurrence were investigated through the use of a non-intrusive accelerometer, installed in proximity of the suction port so as to monitor the phenomenon in terms of vibration amplitude. A preliminary spectral analysis, based on the Fast Fourier Transform (FFT) of the vibrational signal, was performed in order to easily identify cavitation fundamental frequencies. A time-domain analysis technique was then implemented, aiming to realize an on line pump cavitation detection. Specifically, a NonLinear AutoRegressive (NLAR) approach based on the use of Artificial Neural Networks (ANN) was applied for modeling system behavior. In the paper, the results of the vibration-based method are discussed in depth, highlighting the pros and cons of the methodology. The presented outcomes demonstrate the ability of the proposed algorithm in accurately detect the presence of cavitation phenomena and to determine its intensity in pump real time operation. Hence, it may turn out to be a powerful tool for early detection of pumps incipient faults.
Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species.

Background The usual analysis of RNA sequencing (RNA-seq) reads is based on an existing reference genome and annotated gene models. However, when a reference for the sequenced species is not available, alternatives include using a reference genome from a related species or reconstructing transcript sequences with de novo assembly. In addition, researchers are faced with many options for RNA-seq data processing and limited information on how their decisions will impact the final outcome. Using both a diploid and polyploid species with a distant reference genome, we have tested the influence of different tools at various steps of a typical RNA-seq analysis workflow on the recovery of useful processed data available for downstream analysis. Findings At the preprocessing step, we found error correction has a strong influence on de novo assembly but not on mapping results. After trimming, a greater percentage of reads could be used in downstream analysis by selecting gentle quality trimming performed with Skewer instead of strict quality trimming with Trimmomatic. This availability of reads correlated with size, quality, and completeness of de novo assemblies and with number of mapped reads. When selecting a reference genome from a related species to map reads, outcome was significantly improved when using mapping software tolerant of greater sequence divergence, such as Stampy or GSNAP. Conclusions The selection of bioinformatic software tools for RNA-seq data analysis can maximize quality parameters on de novo assemblies and availability of reads in downstream analysis.
Design of a Gateway for Open Source Software Development in a Traditional CS Curriculum

Many computer science students are eager to learn about how to contribute to Free and Open Source Software (FOSS) projects, but like most computer science departments, ours has no courses to help them achieve that goal. Creating such courses requires buy-in by deans, department chairs, and other faculty, who, because of lack of knowledge, can have little interest in supporting such efforts. Our poster shows how we solved this problem and created a means for students to simultaneously learn how to be contributors to FOSS projects and earn credit toward their major. It shows how we sought and found interested students and engaged them through repeated, informal meetings, which we used to gain the support of the chair and dean, and how we simulated a prototype course by having the students sign up for independent study credit. The group then met at regular intervals, communicated and shared work using discussion forums, source code repositories, and IRC chat. All course content is based on open source materials, including free textbooks, an abundance of on-line tutorials and reference materials, lecture notes and assignments that we wrote, with open source licenses, and other materials borrowed from http://foss2serve.org. The success of this simulated course led to the creation of a pilot course for the Spring 2019 semester, endorsed by the college. The poster presents several assignments, discusses preliminary findings, and provides links to materials that we created for this course. It also shows how we encouraged students to work on humanitarian FOSS (HFOSS) projects.
Enhanced recovery pathways in orthopedic surgery

The enhanced recovery after surgery (ERAS) concept, sometimes referred to as "fast track", "accelerated," or "Rapid Recovery" surgery, was first introduced in 1997. The concept of ERAS targets factors that delay postoperative recovery such as surgical stress and organ dysfunction. ERAS protocols or programs are a care package of evidence-based interventions used in a multimodal and coordinated clinical care pathway. They represent a multidisciplinary approach directed to reducing postoperative complications, shortening length of hospital stay, improving patient satisfaction, and accelerating recovery. ERAS was initially centered on abdominal and colorectal surgery patients; however, ERAS protocols have been widely extended to include other specialties. Orthopedic surgery, particularly elective hip and knee arthroplasty is one of such areas where ERAS principles have been adopted. It has been associated with reduced length of hospital stay, readmission rate, and improved functional recovery. The common interventions used in orthopedic ERAS programs have been divided into those performed in the preoperative, intraoperative, and postoperative phases of care. A PubMed literature search was performed for articles that included the terms enhanced recovery and orthopedic surgery. In this article, we summarized the clinical application of ERAS and highlighted the key elements that characterize an enhanced recovery program.
Essentially normal composition operators on H2

Abstract We prove a simple criterion for essential normality of composition operators on the Hardy space induced by maps in a reasonably large class S of analytic self-maps of the unit disk. By combining this criterion with boundary Caratheodory–Fejer interpolation theory, we exhibit a parametrization for all rational self-maps of the unit disk which induce essentially normal composition operators.
A new OPIATE (Optimizing Positive Ibuprofen and Acetaminophen Treatment Expectations) model: A brief comment on "Concurrent and lagged associations of prescription opioid use with pain and negative affect in the daily lives of chronic pain patients" (Carpenter, Lane, Bruehl, & Trull, 2019).

Objective This commentary expands upon the clinical implications arising from the Carpenter et al. (2019) negative reinforcement model of opioid use. A new model called OPIATE-which stands for Optimizing Positive Ibuprofen and Acetaminophen Treatment Expectations-is introduced. This commentary highlights possible strategies for reducing the supply and demand of opioids through enhancing expectations for alternative pain medications. Method This commentary features an integration of concepts from social psychology, cognitive psychology, and consumer psychology with empirical findings from observational studies and randomized trials of opioid and nonopioid medications. Results Four behavioral strategies are offered for potential enhancing expectations for ibuprofen and acetaminophen. These strategies are (a) altering defaults in electronic medical record systems; (b) highlighting appropriate descriptive social norms to patients; (c) improving the quality of interactions during discharges between patients and their physicians, nurses, and pharmacists; and (d) priming patients to have positive expectations regarding ibuprofen and acetaminophen involving careful selection of language to describe these medications. Conclusions Instead of creating alternative pharmaceuticals, efforts to prevent opioid misuse may be more fruitful by focusing on behavioral change of prescribers and patients because viable medication options-namely ibuprofen and acetaminophen-already exist. Psychologists have an opportunity to play a leading role in evaluating behavioral strategies for increasing expectations for and use of nonopioid pain medications. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Secure precision time protocol in packet switched networks

IEEE 1588-2008 protocol is used to provide time and frequency synchronization in network. As time and frequency distribution protocols are becoming increasingly common and widely deployed across the networks, concern about their exposure to security threats and vulnerabilities are increasing. One can use external security mechanisms like IPSEC or MACSEC to safe-guard network from various attacks and not specific to timing protocols. To address security related threats IEEE 1588-2019 draft standard D1.5 defines a “PTP integrated security(PTPIS)” mechanism which is complex and not completely integrated because key management mechanism is left open. A simple and “ Fully PTP Integrated Security(FPTPIS)” mechanism which includes key management is proposed by introducing a new general message and TLV. This paper describes how new general message and TLV enables “fully PTPIS” and thus solving the security requirements of the RFC7384.
Neighborhood Physical Disorder and Adverse Pregnancy Outcomes among Women in Chicago: a Cross-Sectional Analysis of Electronic Health Record Data

Adverse pregnancy outcomes increase infants' risk for mortality and future health problems. Neighborhood physical disorder may contribute to adverse pregnancy outcomes by increasing maternal chronic stress. Google Street View technology presents a novel method for assessing neighborhood physical disorder but has not been previously examined in the context of birth outcomes. In this cross-sectional study, trained raters used Google's Street View imagery to virtually audit a randomly sampled block within each Chicago census tract (n = 809) for nine indicators of physical disorder. We used an item-response theory model and spatial interpolation to calculate tract-level neighborhood physical disorder scores across Chicago. We linked these data with geocoded electronic health record data from a large, academic women's hospital in Chicago (2015-2017, n = 14,309 births). We used three-level hierarchical Poisson regression to estimate prevalence ratios for the associations of neighborhood physical disorder with preterm birth (overall and spontaneous), small for gestational age (SGA), and hypertensive disorder of pregnancy (HDP). After adjustment for maternal sociodemographics, multiparity, and season of birth, living in a neighborhood with high physical disorder was associated with higher prevalence of PTB, SGA, and HDP (prevalence ratios and 95% confidence intervals 1.21 (1.06, 1.39) for PTB, 1.13 (1.01, 1.37) for SGA, and 1.23 (1.07, 1.42) for HDP). Adjustment for neighborhood poverty and maternal health conditions (e.g., hypertension, diabetes, asthma, substance use) attenuated associations. Results suggest that an adverse neighborhood physical environment may contribute to adverse pregnancy outcomes. However, future work is needed to disentangle the unique contribution of physical disorder from other characteristics of disadvantaged neighborhoods.
From nursery rhymes to childlore: orality and ideology

When approaching nursery rhymes, they appear as a concrete, limited and cohesive collection shared by all English-speaking countries packaged in colorful books or fun, animated Youtube channels. Yet they have truly been something that was alive: a group of productions that changed and increased throughout time, drawn from and shared with different languages and cultures, accommodated or purged, considered to hide secret meanings and, subsequently, fossilized in print. They pre-date literary culture although, since society has become literary, nursery rhymes have been generally approached either from the folkloric ethnography field through a collection and analysis of rhymes, their variations and their influences; or as a means to an end, taking into account their possible usage in phonological awareness, literacy and first and second language acquisition. Few have intended to answer what exactly nursery rhymes are, how they work and why it is that they have existed for so long. Understanding nursery rhymes offers essential knowledge of their position in children’s literature, children’s agency and the shared discourse between adults and children. It also illustrates how the relationship between adults, infants, communication and connection has preserved its essential features.
Survey of Books and Guides on Academic Presentations

The chapter provides a survey of a number of books and guides on academic presentations, published between 2000 and 2017. The main objectives of the survey are to determine how the Anglophone academic culture views the genre of academic presentations, what the notion of effectiveness entails, what specific language features the sources promote in relation to audience accommodation, and the extent to which these language recommendations are data-based. Overall, the survey revealed a remarkable degree of consistency with regard to the general principles underlying the genre of academic presentations in oral English academic discourse. However, most of the surveyed sources diverged (and lacked) in the depth and breadth of their treatment of specific aspects of the language of academic presentations that make it audience-friendly.
Effects of Sucrose on Phase Transitions of Organic/Inorganic Aerosols

Aerosol morphology influences the interactions of particles with light, water uptake, and heterogeneous chemistry. Through these mechanisms, morphology may be important to the role of aerosol parti...
Reliability, standard error of measurement, and minimal detectable change of the star excursion balance test in children with cerebral palsy.

OBJECTIVE The present study aimed to estimate the reliability, standard error of measurement (SEM), and minimum detectable change (MDC) of the star excursion balance test (SEBT) in children with cerebral palsy (CP). METHODS Eight children with CP (five boys and three girls, sixteen legs) participated in this study. Each child carried out the SEBT and was assessed by two examiners. To determine intra-rater reliability, the intra-class correlation coefficient (ICC) model (3, 3) was calculated. To determine the inter-rater reliability, the ICC model (2, 3) was computed. RESULTS In terms of the intra-rater reliability of the SEBT, the ICC varied from 0.98 to 0.99 and the total ICC score was 0.99 (p< 0.001). For the inter-rater reliability, the ICC varied from 0.98 to 1.00 and the total ICC score was 0.99 (p< 0.001). The SEBT had an SEM of 2.63 and an MDC of 7.31. CONCLUSION The SEBT is not only reliable with a small SEM, but is also a simple and cheap assessment of dynamic balance in children with CP.
School-Based 4-H Programming: Getting Started

School-based programs provide an opportunity to youth who would not be able to participate in traditional 4-H club offerings otherwise. If you want to expand your 4-H program in diversity, subject matter, and/or number of youth reached, school-based programming may be the solution for you. This 6-page document discusses school-based programs, differences between school-based programming and traditional club programming, reasons to start school-based programs, ways to work with school sites, and enrollment for school-based program youth. It is part of the 4-H 101 Fact Sheet series. Written by Vanessa Spero-Swingle and Susan Munyan, and published by the UF/IFAS 4-H Youth Development Department, April 2018. http://edis.ifas.ufl.edu/4h389
UvrC Coordinates an O2-Sensitive [4Fe4S] Cofactor

Recent advances have led to numerous landmark discoveries of [4Fe4S] clusters coordinated by essential enzymes in repair, replication, and transcription across all domains of life. The cofactor has notably been challenging to observe for many nucleic acid processing enzymes due to several factors, including a weak bioinformatic signature of the coordinating cysteines and lability of the metal cofactor. To overcome these challenges, we have used sequence alignments, an anaerobic purification method, iron quantification, and UV-visible and electron paramagnetic resonance spectroscopies to investigate UvrC, the dual-incision endonuclease in the bacterial nucleotide excision repair (NER) pathway. The characteristics of UvrC are consistent with [4Fe4S] coordination with 60-70% cofactor incorporation, and additionally, we show that, bound to UvrC, the [4Fe4S] cofactor is susceptible to oxidative degradation with aggregation of apo species. Importantly, in its holo form with the cofactor bound, UvrC forms high affinity complexes with duplexed DNA substrates; the apparent dissociation constants to well-matched and damaged duplex substrates are 100 ± 20 nM and 80 ± 30 nM, respectively. This high affinity DNA binding contrasts reports made for isolated protein lacking the cofactor. Moreover, using DNA electrochemistry, we find that the cluster coordinated by UvrC is redox-active and participates in DNA-mediated charge transport chemistry with a DNA-bound midpoint potential of 90 mV vs NHE. This work highlights that the [4Fe4S] center is critical to UvrC.
Psychometric Scales Measuring Hypersomnolence

Hypersomnolence is a common complaint in clinical practice. Subjective measurement of hypersomnolence is complicated by evolving definitions across diagnostic nomenclatures and limited by psychometric scales which focus exclusively on single facets of hypersomnolence. The present article reviews existing and emerging measures to assess subjective hypersomnolence and discusses psychometric validation, clinical utility, and use considerations of various scales. The majority of scales in adult and pediatric populations focus exclusively on excessive sleepiness. Two instruments have recently been developed which assess hypersomnolence across multiple domains (long sleep, excessive daytime sleepiness, sleep inertia) together with functional impairment and are intended for use in specific populations. A variety of validated scales may be used to assess hypersomnolence depending on clinical or research considerations. Future research is needed to examine the temporal stability and clinical sensitivity of various measures, their relationship to objective measures of sleep/sleepiness, and greater inclusion of scale items specific to long total sleep time.
Cancer-secreted miRNAs regulate amino-acid-induced mTORC1 signaling and fibroblast protein synthesis

Metabolic reprogramming of non-cancer cells residing in a tumor microenvironment, as a result of the adaptations to cancer-derived metabolic and non-metabolic factors, is an emerging aspect of cancer-host interaction. We show that in normal and cancer-associated fibroblasts, breast cancer-secreted extracellular vesicles suppress mTOR signaling upon amino acid stimulation to globally reduce mRNA translation. This is through delivery of cancer-derived miR-105 and miR-204, which target RAGC, a component of Rag GTPases that regulate mTORC1 signaling. Following amino acid starvation and subsequent re-feeding, 13 C-arginine labeling of de novo synthesized proteins shows selective translation of proteins that cluster to specific cellular functional pathways. The repertoire of these newly synthesized proteins is altered in fibroblasts treated with cancer-derived extracellular vesicles, in addition to the overall suppressed protein synthesis. In human breast tumors, RAGC protein levels are inversely correlated with miR-105 in the stroma. Our results suggest that through educating fibroblasts to reduce and re-prioritize mRNA translation, cancer cells rewire the metabolic fluxes of amino acid pool and dynamically regulate stroma-produced proteins during periodic nutrient fluctuations.