cssi/SciSciGPT-SciSciNet huggingface dataset:
Acid stress damage of DNA is prevented by Dps binding in Escherichia coli O157:H7

Acid tolerance in Escherichia coli O157:H7 contributes to persistence in its bovine host and is thought to promote passage through the gastric barrier of humans. Dps (DNA-binding protein in starved cells) mutants of E. coli have reduced acid tolerance when compared to the parent strain although the role of Dps in acid tolerance is unclear. This study investigated the mechanism by which Dps contributes to acid tolerance in E. coli O157:H7. The results from this study showed that acid stress lead to damage of chromosomal DNA, which was accentuated in dps and recA mutants. The use of Bal31, which cleaves DNA at nicks and single-stranded regions, to analyze chromosomal DNA extracted from cells challenged at pH 2.0 provided in vivo evidence of acid damage to DNA. The DNA damage in a recA mutant further corroborated the hypothesis that acid stress leads to DNA strand breaks. Under in vitro assay conditions, Dps was shown to bind plasmid DNA directly and protect it from acid-induced strand breaks. Furthermore, the extraction of DNA from Dps-DNA complexes required a denaturing agent at low pH (2.2 and 3.6) but not at higher pH (>pH4.6). Low pH also restored the DNA-binding activity of heat-denatured Dps. Circular dichroism spectra revealed that at pH 3.6 and pH 2.2 Dps maintains or forms α-helices that are important for Dps-DNA complex formation. Results from the present work showed that acid stress results in DNA damage that is more pronounced in dps and recA mutants. The contribution of RecA to acid tolerance indicated that DNA repair was important even when Dps was present. Dps protected DNA from acid damage by binding to DNA. Low pH appeared to strengthen the Dps-DNA association and the secondary structure of Dps retained or formed α-helices at low pH. Further investigation into the precise interplay between DNA protection and damage repair pathways during acid stress are underway to gain additional insight.
State of the Science: Women and the Nonpharmacological Treatment of Substance Abuse:

BACKGROUND:Substance abuse affects men and women differently, and as a result, treatment programs should be designed specific to their unique needs. The nonpharmacological treatment of substance abuse among women has been largely neglected in the literature.OBJECTIVE:The purpose of this review was to analyze critically the existing literature related to the nonpharmacological treatment of substance abuse among women. The methodological rigor of existing research was critiqued and gaps in knowledge identified.DESIGN: The databases Cumulative Index to Nursing and Allied Health Literature (CINAHL), PsycINFO, Sociological Abstracts, and MEDLINE were searched using the key words women and substance abuse treatment. Studies included in the review were those that were published between 1975 and 2003 and were related to the nonpharmacological treatment of substance abuse for women.RESULTS:Forty-three articles were reviewed. Evidence suggests that there are gender and cultural differences related to substance abus...
Discontinuous perturbation analysis of discrete-event dynamic systems

The discontinuous perturbation analysis (DPA) method is presented to deal with discontinuous sample performance functions. This method is applicable to derivative estimation with respect to most threshold-type problems in discrete-event dynamic systems (DEDS). Through modeling of discontinuities by step function, we are able to provide a unified framework for constructing the derivative estimation of a DEDS. As a result, we offer an alternate approach to derive derivative estimation in DEDS's. Finally, some relationships with other PA techniques are discussed, and a numerical example is presented.
Technical challenges of computing available transfer capability (ATC) in electric power systems

A key concept in the restructuring of the electric power industry is the ability to accurately and rapidly quantify the capabilities of the transmission system. Transmission transfer capability is limited by a number of different mechanisms, including thermal, voltage, and stability constraints. This paper discusses the ATC definitions and determination guidelines approved by the North American Electric Reliability Council (NERC) and presents several concepts for dealing with the technical challenges of computation.
Effects of Diet and/or Low-Intensity Resistance Exercise Training on Arterial Stiffness, Adiposity, and Lean Mass in Obese Postmenopausal Women

BACKGROUND Obesity and aging are associated with increased arterial stiffness as indicated by an increased pulse-wave velocity (PWV). We evaluated the independent and combined effects on PWV and body composition of a hypocaloric diet and low-intensity resistance exercise training (LIRET) with slow movement. METHODS Forty-one postmenopausal women (mean age, 54±6 years; body mass index (BMI), 33.8±0.5kg/m(2)) were randomly assigned to LIRET (n = 14), diet (n = 13), or diet + LIRET (n = 14) for 12 weeks. The women's PWV, mean arterial pressure (MAP), body composition by dual-en ergy x-ray absorptiometry (DXA), and plasma adipokine and insulin levels were measured before and after the interventions. RESULTS Body weight (P = 0.0001), trunk-fat mass (FM, P = 0.0001), and the serum concentration of leptin (P = 0.02 and P = 0.004) decreased similarly with diet and diet + LIRET, but not with LIRET alone. Leg lean mass (LM) decreased (P = 0.02) with diet, but did not change with diet + LIRET or with LIRET alone. Leg muscle strength increased similarly with LIRET (P = 0.001) and diet + LIRET (P = 0.0001), but did not change with diet alone. Brachial-ankle PWV (baPWV) decreased with diet (P = 0.04) and diet + LIRET (P = 0.01), whereas femoral-ankle PWV (legPWV) decreased only with diet (P = 0.01). Mean arterial pressure (MAP) decreased after LIRET (P = 0.03), diet (P = 0.04), and diet + LIRET (P = 0.004). Carotid-femoral PWV, serum adiponectin concentration, and insulin were not significantly affected by the interventions examined in the study. The reductions in baPWV and legPWV were correlated with one another (r = 0.73, P = 0.0001), and the reductions in legPWV and trunk FM were also correlated with one another (r = 0.36, P = 0.03). CONCLUSIONS A hypocaloric diet decreases baPWV mainly by reducing legPWV, and this reduction is related to the loss of truncal fat. Although LIRET alone does not affect PWV or body composition, LIRET combined with diet improves baPWV and muscle strength while preventing loss of lean body mass in obese postmenopausal women.
Pertussis Toxin Inhibits Migration of B and T Lymphocytes into Splenic White Pulp Cords

The normal migration route of B cells into follicular areas of spleen and lymph nodes is altered in the case of autoreactive cells that have bound self-antigen. To begin characterizing the molecular requirements for B cell migration into follicles, cells were treated with pertussis toxin (PTX), an inhibitor of signaling by many G protein-coupled chemokine receptors. Lymphocyte accumulation in the spleen is not inhibited by PTX and, therefore, the distribution of transferred cells was examined in this tissue. In contrast to untreated cells that localized predominantly in follicular areas within white pulp cords, PTX-treated B cells failed to enter white pulp areas altogether and accumulated in the splenic red pulp. T cells were also excluded from white pulp cords and in the case of both cell types, the adenosine diphosphate-ribosylating subunit of the toxin was required to block white pulp entry. These findings implicate a G protein-coupled receptor in lymphocyte migration into splenic white pulp cords. Exclusion of PTX-treated cells from all organized areas of secondary lymphoid tissues raises the possibility that the association observed between PTX treatment and predisposition to autoimmune disease results from inhibition of tolerance mechanisms that normally operate within secondary lymphoid tissues.
A new theoretic framework for cross-layer optimization

Cross-layer optimization aims at improving the performance of network users operating in a time-varying, error-prone wireless environment. However, current solutions often rely on ad-hoc optimization approaches, which ignore the different environmental dynamics experienced at various layers by a user and violate the layered network architecture of the protocol stack. This paper presents a new theoretic framework in which the cross-layer optimization problem is formulated as a layered Markov decision process (MDP). In this framework, each layer adapts its own protocol parameters and exchanges information (messages) with other layers in order to cooperatively maximize the performance of the wireless user. Hence, this layered cross-layer framework does not change the current layered architecture and is suitable for the delay-sensitive applications over wireless networks.
Automatic geometric rectification for patient registration in image-guided spinal surgery

Accurate and efficient patient registration is crucial for the success of image-guidance in open spinal surgery. Recently, we have established the feasibility of using intraoperative stereovision (iSV) to perform patient registration with respect to preoperative CT (pCT) in human subjects undergoing spinal surgery. Although a desired accuracy was achieved, the method required manual segmentation and placement of feature points on reconstructed iSV and pCT surfaces. In this study, we present an improved registration pipeline to eliminate these manual operations. Specifically, automatic geometric rectification was performed on spines extracted from pCT and iSV into pose-invariant shapes using a nonlinear principal component analysis (NLPCA). Rectified spines were obtained by projecting the reconstructed 3D surfaces into an anatomically determined orientation. Two-dimensional projection images were then created with image intensity values encoding feature "height" in the dorsal-ventral direction. Registration between the 2D depth maps yielded an initial point-wise correspondence between the 3D surfaces. A refined registration was achieved using an iterative closest point (ICP) algorithm. The technique was successfully applied to two explanted and one live porcine spines. The computational cost of the registration pipeline was less than 1 min, with an average target registration error (TRE) less than 2.2 mm in the laminae area. These results suggest the potential for the pose-invariant, rectification-based registration technique for clinical application in human subjects in the future.
Solvent-Driven Reductive Activation of Carbon Dioxide by Gold Anions

Catalytic activation and electrochemical reduction of CO2 for the formation of chemically usable feedstock and fuel are central goals for establishing a carbon neutral fuel cycle. The role of solvent molecules in catalytic processes is little understood, although solvent–solute interactions can strongly influence activated intermediate species. We use vibrational spectroscopy of mass-selected Au(CO2)n– cluster ions to probe the solvation of AuCO2– as a model for a reactive intermediate in the reductive activation of a CO2 ligand by a single-atom catalyst. For the first few solvent molecules, solvation of the complex preferentially occurs at the CO2 moiety, enhancing reductive activation through polarization of the excess charge onto the partially reduced ligand. At higher levels of solvation, direct interaction of additional solvent molecules with the Au atom diminishes reduction. The results show how the solvation environment can enhance or diminish the effects of a catalyst, offering design criteria for...
Ideas and Interests: Businessmen and the Interstate Commerce Act

H ISTORIANS have generally seen the Interstate Commerce Act of 1887 as the first major step on the road to federal regulation of business. While much of the rhetoric of American politics painted the issue in terms of "the people" or "the farmers" against "business," scholars have long been aware of the inadequacy of that view. Rather than opposing all government regulation, businessmen were often involved in sponsoring and supporting such legislation. Within the last two decades historians have published several important studies concerning the origin and purpose of the Interstate Commerce Act of 1887. Lee Benson, studying the New York State movement toward regulation of the roads, was able to delineate the impact of railroad development on various economic interest groups in the state and explain the conflict generated among them. He focused mainly on merchants, especially those in New York City, and their fight for more favorable freight rates. "New York merchants," he concluded, "constituted the single most important group behind the passage of the Interstate Commerce Act."' More recently, Gabriel Kolko finished an examination of federal regulation from 1877 to 1916, which concentrated on the machinations and motives of railroad leaders. The railroads were ruining themselves by cutthroat competition, Kolko argued; and hence they actually sought government regulation to stabilize their industry and to make it more profitable. He amply demonstrated that many railroad men both accepted the premise of federal regulation and strongly supported certain proposed laws. Although railroad managers were obviously not alone in urging federal action and often disagreed among themselves, Kolko maintained that "the rail-
Phototriggered DNA complexation and compaction using poly(vinyl alcohol) carrying a malachite green moiety.

Photoinduced DNA compaction was performed using the interaction of DNA with a photoresponsive random copolymer of poly(vinyl alcohol) carrying a malachite green moiety (PVAMG). Although PVAMG does not have any affinity for DNA under dark conditions, it undergoes photoionization upon exposure to UV light, consequently resulting in a cationic binding site for DNA. Electrophoresis results demonstrated that irradiation of PVAMG retarded the DNA bands due to their complexation, whereas the bands remained unchanged under dark conditions. The binding of PVAMG to DNA occurs at a cationic site/DNA phosphate ratio of approximately 0.036. Single-molecule observations of DNA by fluorescence microscopy revealed that irradiation of PVAMG induced a coil–globule transition in the DNA molecule. Complete compaction of DNA has been accomplished at a cationic site/DNA phosphate ratio >8.0, indicating that PVAMG offers an effective system to photochemically trigger DNA compaction.
Education: Perceptions of Medical Technology Deans and Faculty Regarding Tenure Criteria

Our research was designed to ascertain the perceptions of deans and faculty in the health science center/medicalschool setting and in the college/university setting regarding criteria for tenure. Questionnaires were sent to deans and faculty in 124 institutions located throughout the United States and Puerto Rico. Responses were received from 80 deans and 269 faculty. Participants were asked to respond to each of the 49 tenure criteria using a five-point scale. Comparisons between medical technology dean and faculty responses were performed utilizing the independent test. The results indicated that differences in perception exist between medical technology deans and faculty regarding the importance of tenure criteria, especially in the teaching and education categories.
Establishment of co-culture model in vitro to induce bone marrow mesenchymal stem cells differentiate into lung epithelial cells

Objective To establish the co-culture model in vitro and induce bone marrow mesenchymal stem cells(MSCs) to differentiate into lung alveolar epithelial cells.Methods Each group had 6 samples,control group was MSCs alone;Group A was the MSCs cultured with the cells from normal lung;and Group B was the MSCs with the cells from injuried lung.Each group was cultured for 8 days and the two markers of lung alveolar epithelial cells including AQP5 and SP-C were tested by laser confocal microscopy and RT-PCR.Results Only AQP5 was detected in the control group and Group A,both AQP5 and SP-C were detected in Group B,the AQP5 mRNA expression in Group B was significantly increased compared with that in the control group(P0.01).The AQP5 mRNA expression in Group B was also significantly increased compared with that in Group A(P0.01).But there was no significant difference in AQP5 mRNA expression between Group A and control group.Conclusion We have successfully established the co-culture model in vitro to induce bone marrow mesenchymal stem cells to differentiate into lung epithelial cells.
The Collaborative Improvement Model: An Interpretive Study of Revising a Curriculum

Curriculum revisions in nursing programs are necessary to maintain currency and ensure that nursing students are prepared to competently practice nursing. Yet, the research for curriculum revisions in nursing education is sparse, leaving nursing educators with a thin evidence base upon which to revise curricula. The purpose of this phenomenological and hermeneutical study was to understand the experiences of faculty members and students who used the Collaborative Improvement Model (CIM) at a midwestern nursing department as an approach to revise their curriculum. The findings of this study demonstrate how the CIM (a) promoted student involvement in revising a curriculum, (b) facilitated faculty collaboration across two campuses with different campus cultures, (c) encouraged the Scholarship of Teaching and Learning, and (d) emphasized the need to use external facilitators when revising a curriculum. Faculty members in nursing programs can use this study when considering the CIM as a framework for revising their curricula.
Voice in Student Essays

Voice in written language — a metaphorical concept capturing the sense of author identity that comes through when readers interact with texts — has intrigued many writing teachers and researchers. While some teachers regard voice to be an essential feature of good writing, others consider it to be unnecessary, if not distracting, especially in the context of academic and professional writing. One of the most obvious reasons for this discrepancy is the varied conception of voice. In the early years, voice was conceptualized in individualistic terms, focusing on the expression of authentic self (Elbow, 1968; Stewart, 1969, 1972). This perspective has often been at odds with social-constructionist views of voice that emphasize the normative aspects of language use (Cope and Kalantzis, 1993; Hyland, 2008). There are more recent, social-constructivist conceptions of voice that see individual and social voice to be mutually constitutive and inevitable (Ivanic, 1998; Ivanic and Camps, 2001; Matsuda, 2001; Prior, 2001). Studies using a social-constructivist definition of voice (Matsuda, 2001) have shown that voice plays an important role in advanced academic literacy (Matsuda and Tardy, 2007; Tardy and Matsuda, 2009). Yet, as Tardy (this volume) has pointed out, the debate over the notion of voice has tended to be caught in a simplistic individual—social dichotomy.
The Swan-Ganz catheter: its clinical versatility.

Insertion techniques, findings, and complications of cardiac catheterization are reviewed in the contexts of critical medical care and perioperative management.
Ultrasonic Velocimetry in Resection of Renal Arteriovenous Fistulas and Other Intrarenal Surgical Procedures

Abstract The Doppler velocimetry is considered to be useful frequently and indispensable occasionally for intrarenal surgery. Current equipment is relatively inexpensive, the operation is technically simple and maintenance is minimal. The instrument provides an instantaneous appraisal of the precise location of a blood vessel and some characteristics of blood flow with a facility unlikely to be achieved with any other technique. It is important that the limitations of current instruments be appreciated since the concepts of the procedure and current instrumentation are deceptively conducive to expectations beyond their capability.
Hard measures of subjective outcomes : validating symptom indexes in urology

Scientifically validated (accurate), and reproducible (precise) methods of assessing the frequency and severity of patient symptoms are becoming more widely used in medicine. Such a symptom index has been developed for patients with benign prostatic hyperplasia, and may find use in clinical practice and research. The criteria for developing and validating such indexes are presented, using the new benign prostatic hyperplasia symptom index as an example. The same approach can be applied to many other disease entities in urology that demand a quantitation of the illness experience from the perspective of the patients.
In‐Season Nitrogen Status Sensing in Irrigated Cotton: II. Leaf Nitrogen and Biomass

Pre-plant soil NO - 3-N tests and petiole NO - 3-N analysis are bases for Upland cotton (Gossypium hirsutum L.) N management in the western USA. Alternative approaches include proximal multispectral reflectance sensing and chlorophyll meter readings. Our objective was to determine if spectral reflectance and chlorophyll meter measurements correlate with cotton leaf N and biomass. Urea ammonium nitrate was applied after emergence and with low energy precision (LEPA) center-pivot, surface or subsurface drip irrigation water up to peak bloom. Multispectral reflectance readings 0.5 m above the canopy, chlorophyll meter readings, and biomass samplings were taken at early squaring, early bloom, and peak bloom for 3 site-years in Lubbock, TX and Ropesville, TX. Green vegetative indices (GVI) and green normalized difference vegetative indices (GNDVI) calculated from reflectance data generally correlated better with leaf N and leaf N accumulation than did red vegetative indices (RVI) and red normalized difference vegetative indices (RNDVI). Biomass and lint yield correlated more often with red-based indices than green-based indices. Chlorophyll meter readings correlated with leaf N as often as GVI and GNDVI did. Biomass, however was poorly related to chlorophyll meter readings. These results demonstrate the effectiveness of GVI, GNDVI, and chlorophyll meter readings in assessing leaf N, and RVI and RNDVI in assessing cotton biomass. However, we recommend converting vegetative indices or chlorophyll meter readings to sufficiency indices, which are calculated from indices or readings relative to well-fertilized plots. Sufficiency indices were able to successfully predict little or no need for in-season N fertilizer in the low-yielding 2000 crops (sufficiency index > 0.95), and predicted greater need of N fertilizer in the high-yielding 2001 crop (sufficiency index < 0.95).
Embedded non-volatile memory system as an enabler of smarter world

As an enabler of sustainable and innovative progress in wide range of applications from automotive to IoT, embedded non-volatile memory (eNVM) including embedded Flash (eFlash) has been and will be playing key roles. To meet more stringent and/or diversified requirements while overcoming many challenges along with memory cell scaling, hierarchical optimization in eNVM design from memory cell to hard macro and system level has greater significance. By taking MONOS based eFlash design as a preferred example, this paper will survey the latest eNVM design in hierarchical manner as well as future directions of eNVMs including emerging memories.
Multi-Time Step Service Restoration for Advanced Distribution Systems and Microgrids

Modern power systems are facing increased risk of disasters that can cause extended outages. The presence of remote control switches, distributed generators (DGs), and energy storage systems (ESS) provides both challenges and opportunities for developing post-fault service restoration methodologies. Inter-temporal constraints of DGs, ESS, and loads under cold load pickup conditions impose extra complexity on problem formulation and solution. In this paper, a multi-time step service restoration methodology is proposed to optimally generate a sequence of control actions for controllable switches, ESSs, and dispatchable DGs to assist the system operator with decision making. The restoration sequence is determined to minimize the unserved customers by energizing the system step by step without violating operational constraints at each time step. The proposed methodology is formulated as a mixed-integer linear programming model and can adapt to various operation conditions. The proposed method is validated through several case studies that are performed on modified IEEE 13-node and IEEE 123-node test feeders.
Clinicopathologic significance of in vivo antinuclear autoantibodies in oral mucosal biopsies.

Objective Although antinuclear autoantibody (ANA) staining of oral biopsy specimens is indicative of chronic ulcerative stomatitis, it is not known whether this staining is characteristic of other autoimmune diseases. Our study was undertaken to characterize the various in vivo ANA patterns detected in the oral mucosa by direct immunofluorescence to describe the associated hematoxylin and eosin findings, and determine whether patients with these findings had a coexisting systemic connective tissue disease. Study Design This was a retrospective analysis of oral biopsy specimens submitted from 2013 to 2016. Results In vivo ANA staining was present in 72 of the 2019 cases examined. Immunoglobulin G was the most common immunoreactant (71 of 72 cases), and speckled nuclear staining was the most frequent in vivo ANA pattern (52 of 72). In most cases, hematoxylin and eosin staining of biopsy specimens showed mucositis (24 of 34). Detailed clinical information was available for 10 patients, and all of them had an autoimmune disease. Conclusions We found similar prevalence of ANA staining with direct immunofluorescence in oral epithelial biopsy specimens as reported for those of skin. In vivo ANA in the oral epithelium may indicate the presence of an immune-mediated disease. Patients who show ANA deposits in oral mucosal biopsy specimens should be investigated for systemic connective tissue disease as well as for chronic ulcerative stomatitis.
Elucidating Factors Controlling Long-Term Stability of Radical Anions for Negative Charge Storage in Nonaqueous Redox Flow Batteries

Radical anions of electrochemically reduced compounds (anolytes) have been suggested for storage of negative charge in nonaqueous redox flow batteries. The lower the redox potential of the anolyte molecule, the higher is the stored energy density. However, the stability of the radical ions frequently suffers as their redox potentials become extreme, and there is a compromise between the energy density and the chemical stability in the active form. In this study, we scrutinize this trade-off using one such “extreme,” the heterocyclic anolyte 2,1,3-benzothiadiazole, BzNSN, by adjusting the redox potential of BzNSN via installed electron-donating and electron-withdrawing groups. We show that the stability of the radical anion strongly depends on the degree of ion pairing in solution, with the worst being for the contact lithium ion pairs. For BzNSN derivatives, there is a strong correlation between the lifetime of the radical anion and the redox potential. The root cause appears to be the proton transfer fro...
Designing economic impact assessments for USFS wildfire programs

As often happens in the wake of a series of extreme fire seasons, such as those in 2000, 2002 and 2003, federal wildfire policy is being scrutinized and recommendations regarding changes both large and small are prevalent (Stephens and Ruth 2005, Busenberg 2004, Dellasalla et al. 2004, Dombeck et al. 2004). It is common practice for increases in acres burned and in suppression costs to be cited as evidence that existing policy is a failure and that changes must be made. For example, Busenberg (2004) argues that "the wildfire crisis in America was created by a longstanding policy failure" which "greatly increased the risk of wildfire damages."(p. 145). However, there is scant empirical evidence regarding the magnitude of total economic damages (much less, the benefits) resulting from wildfire, and empirical evidence that would permit an overall evaluation of wildfire programs is limited. Stephens and Ruth (2005) mru. suggestions for reducing the trend in wildfire acres burned, which begs the question of whether the objective of federal wildfire policy is to minimize acres burned, economic impacts, or some other measure. Although the 2001 Federal Fire Policy has as its primary tenets the protection of life, property and resources, it does this through 9 guiding principles, 28 findings, 17 policy statements and 19 implementation actions (United States Interagency Federal Wildland Fire Policy Review Working Group 200 1). Thus, despite a clear statement about protecting life, property and resources, the firefighting agencies are often faced with determining priorities in the face of multiple guiding statements that may imply contradictory objectives. One interpretation of this policy could be an objective of minimizing acres burned, although this results in treating all acres as equal in value, whether they are endangered species habitat, wildland-urban interface, or some other designation. In the past, prior to the current epoch of increasing fuel loads and the expansion of the wildland urban interface into fire-prone areas, and with easier success in suppression, a goal of minimizing acres burned may have been synonymous with minimizing damages. Over the last 100 years, however, changes in suppression
Examination of the Statistical Effects Associated with Tracking Propulsive Particles

Particle tracking of active colloidal particles can be used to compute mean-squared displacements that are fit to extract properties of the particles including the propulsive speed. Statistical errors in the mean-squared displacement leads to errors in the extracted properties especially for more weakly propelling particles. Brownian dynamics simulations in which the particle parameters are prescribed were used to examine the statistics of tracking self-propelling objects. It was found that the manner in which tracking data is analyzed has a profound impact on the precision and accuracy of measurements. To properly extract particle parameters, it was necessary to apply a nonlinear fit of the mean-squared displacement over a time region that includes transition behavior from ballistic to diffusive. The dependence of the statistics on the number of particles tracked and the length of movies was examined, showing how and why weakly propelling particles are difficult to analyze.
From Short Reads to Chromosome-Scale Genome Assemblies

A high-quality, annotated genome assembly is the foundation for many downstream studies. However, obtaining such an assembly is a complex, reiterative process that requires the assimilation of high-quality data and combines different approaches and data types. While some software packages incorporating multiple steps of genome assembly are commercially available, they may not be flexible enough to be routinely applied to all organisms, particularly to nonmodel species such as pathogenic oomycetes and fungi. If researchers understand and apply the most appropriate, currently available tools for each step, it is possible to customize parameters and optimize results for their organism of study. Based on our experience of de novo assembly and annotation of several oomycete species, this chapter provides a modular workflow from processing of raw reads, to initial assembly generation, through optimization, chromosome-scale scaffolding and annotation, outlining input and output data as well as examples and alternative software used for each step. The accompanying Notes provide background information for each step as well as alternative options. The final result of this workflow could be an annotated, high-quality, validated, chromosome-scale assembly or a draft assembly of sufficient quality to meet specific needs of a project.
The Atlantic Sugar Trade at the End of the Seventeenth Century

In their efforts to undermine Dutch hegemony in the Atlantic sugar trade, the British were only partially successful in channeling colonial trade from the West Indian and American colonies to England. In the last chapter, Schreuder documents and concludes that merchants and commodity brokers of Amsterdam and London (including Sephardic merchants) helped to sustain the Anglo-Dutch sugar reexport trade and Amsterdam’s sugar refining industry for most of the second half of the seventeenth century but, as direct supplies of sugar from the Caribbean diminished, the Sephardic merchant network lost part of its function. As Sephardic merchants had sojourned from port to port and island to island to sustain their network of trade, and had shown great flexibility and business acumen, they justifiably deserve the designation of Port Jew.
Positive life events and social support and the relationship between life stress and psychological disorder

This study investigated the relationship between negative life events and psychological disorder and the roles of positive life events and received and perceived social support in moderating this relationship. A prospective design was used and statistical analyses were based on a hierarchical regression model. College undergraduates served as subjects. Negative events were significantly related to psychological disorder at each of two measurement periods. This relationship was found even when initial disorder was statistically controlled. The cross-sectional analyses, but not the prospective analyses, provided some support for the stress-buffering (interaction) effects of positive events. There was no support for the stress-buffering effects of received social support, but the cross-sectional and prospective regression analyses provided strong support for the stress-buffering effects of perceived social support.
Barriers and Facilitators to Food Security among Adult Burundian and Congolese Refugee Females Resettled in the US

Sub-Saharan African refugees in the US have reported food security rates seven times below the national average. Dietary acculturation issues may be a contributing factor. Criterion-specific sample (n = 18) was recruited using network then snowball sampling methods. Semi-structured interviews were facilitated with the aid of a culturally and linguistically appropriate interpreter. An iterative, two cycle coding analytic process was completed within NVivo 11 by two coders who sought inter-rater reliability. Codes were organized into hierarchical maps and coding matrices for direct content analysis, and pattern and theme detection. Saturation was achieved and validated with an additional two interviews. Participants were primarily Burundian (67% vs. 33% Congolese), married (72%), held no high school degree (72%), unemployed (56%) and reported limited English proficiency (72%). Barriers and facilitators to food security across all levels of the Socio-Ecological Model (SEM) were noted. Emerging themes included difficulty with language, cooking, and shopping; transportation; social network support; orientation services; reliance on nutrition assistance programs; limited culturally relevant food and land access; and program policy miscomprehension. The complex relationship between dietary acculturation barriers and facilitators at various SEM levels demonstrates the need for a multi-level intervention to improve food security among refugees.
A consistent Timoshenko hysteretic beam finite element model

Abstract A parametrized Timoshenko hysteretic beam finite element model is developed, using consistent two-node elements, to efficiently simulate the nonlinear behavior of structures. New displacement interpolation functions are derived that satisfy both the exact equilibrium and kinematic conditions. Therefore, nodal strain field continuity is achieved, resulting in a consistent formulation without shear locking effects. Multiaxial interactions are considered through yield/capacity functions and distributed plasticity is accounted for by appropriate hysteretic interpolation functions. The suggested interpolation functions yield constant element matrices that do not require updating throughout the analysis, and the nonlinearities are captured in terms of hysteretic curvatures, axial and shear deformations, which are set to evolve through ordinary differential equations. A computationally efficient solution scheme is also suggested, without requiring any linearization, to straightforwardly solve the resulting system of equations for quasi-static problems. The consistency, efficiency, versatility and validity of the suggested model is explained in detail and demonstrated through several numerical examples and comparisons with experimental data from available tests.
NamedKeys: Unsupervised Keyphrase Extraction for Biomedical Documents

A vast amount of biomedical literature is generated and digitized every year. As a result is a growing need to develop methods for discovering, accessing, and sharing knowledge from medical literature. Keyphrase extraction is the task of summarizing a text by identifying the key concepts. The keyphrases can be single-word or multi-word linguistic units which can concisely represent a document. Although a variety of models have been proposed for automated keyphrase extraction, the performance is poor in comparison with other natural language processing tasks. The problem is even more daunting for biomedical domain where the text is filled with highly domain-specific terminologies. We propose a new method, NamedKeys, to automatically identify meaningful and informative keyphrases from biomedical text. NamedKeys integrates named entity recognition, phrase embedding, phrase quality scoring, ranking, and clustering to extract author-assigned keywords from biomedical documents. Performance evaluation on PubMed abstracts demonstrates that NamedKeys achieves significant improvements over existing state-of-the-art keyphrase extraction models. Furthermore, we propose the first benchmark dataset for keyphrase extraction from biomedical text.
Pair distribution function analysis of neutron-irradiated silicon carbide

Abstract We have employed x-ray total scattering to investigate the structure of polycrystalline 3C-silicon carbide following neutron irradiation. The structure as a function of irradiation temperature and dose was quantified by analyzing pair distribution functions. Although the SiC matrix retains its crystal structure after irradiation, a significant increase in the diffuse scattering component is observable indicating that neutron irradiation leads to changes in both the short- and medium-range order. These changes include both an irradiation dose- and temperature-dependent increase in the vacancy concentration leading to an increase in the Si and C atomic displacement parameters. A dose-dependent decrease in the size of defect free material is also quantified from the structural refinements due to an increase in the number of defects and defect clusters. Evidence of additional correlations in the short-range order (up to ∼4 A) from differential pair distribution function analysis indicate that combinations of atomistic defects including anti-site defects, vacancies and defect clusters are present after these irradiation conditions. Such structural information will be valuable for direct comparison of experimental and simulated atomic structures of irradiated silicon carbide.
Pastoralists’ use of income diversification as a strategy for adapting to social-ecological change in Samburu, Kenya

Pastoralists in the Samburu region of Kenya, like many pastoralists around the world, have endured significant effects of social-ecological change. Improvements in infrastructure, access to education, roads, and cellular networks, combined with changing land tenure systems and impacts from more frequent extreme weather events place Samburu herders squarely in the middle of substantial change. In our study, we interviewed 100 pastoralists to determine how income sources changed over the past 20 years, following an extreme drought in 1998, as a measure of adapting to change. Questions about livestock holdings, income sources, and household demographics were used to conduct a cluster analysis and group comparisons that indicated Samburu pastoralists have chosen one of three primary paths in the past 20 years: increased herd size and retained pastoralism as a primary income source; reduced herd size but retained livestock herding as the primary income source, while adding other modest sources of income; and substantially reduced herd size and pursued non-herding options as a primary income source. Our results show a number of differences among Samburu pastoralists, and the extent to which paths were chosen primarily to alleviate adverse impacts from social-ecological change is unclear, as community members provided numerous explanations for changing herd size.
Phase-Control-Enabled Enhancement in Hydrophilicity and Mechanical Toughness in Nanocrystalline Tungsten Oxide Films for Energy-Related Applications

We report on the phase-control-enabled enhancement in the hydrophilicity and mechanical properties of nanostructured WO3 films for energy-related applications. Nanostructured WO3 films were fabrica...
Prediction of Oblique Saccade Trajectories Using Learned Velocity Profile Parameter Mappings

This manuscript proposes and validates two techniques for predicting the trajectory of oblique saccades using a Gaussian velocity profile model. Profile parameters and event duration are estimated at the onset of each saccade using support vector machine regression models. The proposed techniques are evaluated using a set of 47,652 saccades with a mean amplitude of 12.25 degrees of the visual angle gathered from 322 subjects during a random saccade task. Numerous performance metrics are evaluated for predictions made at various fractions of the saccade duration. An average landing point estimation error of less than three degrees of the visual angle is obtained for predictions formed at 30% of the saccade duration.
Electrochemotherapy for a cutaneous squamous cell carcinoma in a Vietnamese pot-bellied Pig (Susscrofa)

ABSTRACT Background: With increasing numbers of Vietnamese pot-bellied pigs (Susscrofa) being cared for as pets and increased survival times due to improved husbandry and veterinary care, the possibility of naturally occurring cancer is likely to increase in this species. Case description: A 9-year old, female spayed, Vietnamese pot-bellied pig was presented for evaluation of raised, hemorrhagic crusts, and ulcerated lesions of both flanks, dorsum, ventral abdomen, hind limbs, and caudal ears. The pig's skin was biopsied and histopathology confirmed diffuse squamous cell carcinoma. The pig was treated with eight sessions of electrochemotherapy over the course of one year: 15 IU/m2 of bleomycin intravenously 5 minutes prior to electroporation (series of electrical pulses (1200–1300 V) delivered to the lesions in a grid pattern). The pig tolerated electrochemotherapy without evidence of myelosuppression or substantial gastrointestinal upset and had mild local inflammation/irritation following treatments. At the time of submission, the pig was 18 months post diagnosis and in a sustained partial remission. A new lesion in an untreated location has slowly grown over 2 months. Conclusions and clinical relevance: This is the first report of successful treatment of squamous cell neoplasia in a pot-bellied pig. Cognizance of family pet vs. an animal entering the food chain is important when considering chemotherapy in food producing animals. We received written confirmation from the owner that this pig would not enter the human food supply. Electrochemotherapy is a viable option for cutaneous squamous cell carcinoma in pigs.
CHAOPT: A Testbed for Evaluating Human-Autonomy Team Collaboration Using the Video Game Overcooked!2

This paper introduces a new testbed called Cooking with Humans and Autonomy in Overcooked!2 for studying Performance and Teaming (CHAOPT). A validation study was conducted to examine the viability of Overcooked!2 as a research platform to explore teamwork and communication in humanautonomy teams. Unique measures derived from this platform such as productive chef actions (PCA), team expertise score and chef role contribution (CRC) distinguished performance between levels and players. Our findings demonstrate that we can derive meaningful team process, performance and communication measures and that the interactions within Overcooked!2 meet the requirements of psychological fidelity of teaming research.
Design and evaluation of a wearable assistive technology for hemianopic stroke patients

More than one million people in the US suffer from hemianopia, which blinds the vision in one half of the peripheral vision in both eyes. Patients with hemianopia are often not aware of what they cannot see and frequently bump into walls, trip over objects, or walk into people on the side where the peripheral vision is diminished. In this study, we present an augmented reality based assistive technology that expands the peripheral vision of hemianopic patients at all distances. In a pilot trial, we evaluate the utility of this assistive technology for ten hemianopic patients. We measure and compare outcomes related to target identification and visual search in the participants. Improvements in target identification are noted in all participants ranging from 18% to 72%. Similarly, all the participants benefit from the assistive technology in performing a visual search task with an average increase of 24% in the number of successful searches compared to unaided trials. The proposed technology is the first instance of an electronic vision enhancement tool for patients with hemianopia and is expected to maximize the residual vision and quality of life in this growing, yet largely overlooked population.
Can machine learning improve the model representation of turbulent kinetic energy dissipation rate in the boundary layer for complex terrain

Abstract. Current turbulence parameterizations in numerical weather prediction models at the mesoscale assume a local equilibrium between production and dissipation of turbulence. As this assumption does not hold at fine horizontal resolutions, improved ways to represent turbulent kinetic energy (TKE) dissipation rate ( ϵ ) are needed. Here, we use a 6-week data set of turbulence measurements from 184 sonic anemometers in complex terrain at the Perdigao field campaign to suggest improved representations of dissipation rate. First, we demonstrate that the widely used Mellor, Yamada, Nakanishi, and Niino (MYNN) parameterization of TKE dissipation rate leads to a large inaccuracy and bias in the representation of ϵ . Next, we assess the potential of machine-learning techniques to predict TKE dissipation rate from a set of atmospheric and terrain-related features. We train and test several machine-learning algorithms using the data at Perdigao, and we find that the models eliminate the bias MYNN currently shows in representing ϵ , while also reducing the average error by up to almost 40 %. Of all the variables included in the algorithms, TKE is the variable responsible for most of the variability of ϵ , and a strong positive correlation exists between the two. These results suggest further consideration of machine-learning techniques to enhance parameterizations of turbulence in numerical weather prediction models.