cssi/SciSciGPT-SciSciNet huggingface dataset:
Impact of grazing dairy steers on winter rye (Secale cereale) versus winter wheat (Triticum aestivum) and effects on meat quality, fatty acid and amino acid profiles, and consumer acceptability of organic beef.

Meat from Holstein and crossbred organic dairy steers finished on winter rye and winter wheat pastures was evaluated and compared for meat quality, fatty acid and amino acid profiles, and consumer acceptability. Two adjacent 4-ha plots were established with winter rye or winter wheat cover crops in September 2015 at the University of Minnesota West Central Research and Outreach Center (Morris, MN). During spring of 2015, 30 steers were assigned to one of three replicate breed groups at birth. Breed groups were comprised of: Holstein (HOL; n = 10), crossbreds comprised of Montbeliarde, Viking Red, and HOL (MVH; n = 10), and crossbreds comprised of Normande, Jersey, and Viking Red (NJV; n = 10). Dairy steers were maintained in their respective replicate breed group from three days of age until harvest. After weaning, steers were fed an organic total mixed ration of organic corn silage, alfalfa silage, corn, soybean meal, and minerals until spring 2016. Breed groups were randomly assigned to winter rye or winter wheat and rotationally grazed from spring until early summer of 2016. For statistical analysis, independent variables were fixed effects of breed, forage, and the interaction of breed and forage, with replicated group as a random effect. Specific contrast statements were used to compare HOL versus crossbred steers. Fat from crossbreds had 13% greater omega-3 fatty acids than HOL steers. Furthermore, the omega-6/3 ratio was 14% lower in fat from crossbreds than HOL steers. For consumer acceptability, steaks from steers grazed on winter wheat had greater overall liking than steers grazed on winter rye. Steak from crossbreeds had greater overall liking than HOL steers. The results suggest improvement in fatty acids and sensory attributes of beef from crossbred dairy steers compared to HOL steers, as well as those finished on winter wheat compared to winter rye.
Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women

We measured the microbial community structure of genital ulcers in women. Swabs from clinically detected ulcers were tested for HSV-2 and Treponema pallidum by polymerase chain reaction (PCR). HSV-2 and T. pallidum were detected by serum antibody testing. Microbial community structure was characterized by high-throughput 16 s rRNA gene amplicon sequencing. Multiple group testing and Elastic net and Lasso regressions identified taxa associated with differences in factors of interest. Among 49 ulcer specimens from 49 HSV-2 seropositive women, by PCR HSV-2 was recovered from 28 (57%) specimens and T. pallidum from none; one woman showed serologic evidence of syphilis. Overall, 63% of women were HIV-positive and 49% had an uncircumcised male sex partner. By both multiple group testing and regression, Porphyromonas (FDR p-value = 0.02), Prevotella (FDR p-value = 0.03), Anaerococcus (FDR p-value = 0.07), and Dialister (FDR p-value = 0.09) were detected at higher relative abundance in HSV-2 PCR-positive than negative ulcers. The presence of HSV-2 in a lesion was associated with presumed bacterial agents of Bacterial vaginosis. Differences in bacterial communities may contribute to HSV-2 ulcer pathogenesis, severity, or prolonged healing. If these results are confirmed, future studies may consider the influence of BV treatment on women’s GUD and HSV-2 incidence and recurrence.
Blockade of Treg Cell Differentiation and Function by the Interleukin-21-Mechanistic Target of Rapamycin Axis Via Suppression of Autophagy in Patients With Systemic Lupus Erythematosus.

Objective The mechanistic target of rapamycin (mTOR) has become a therapeutic target in systemic lupus erythematosus (SLE). In T cells, mTOR plays a central role in lineage specification, including development of regulatory cells (Treg cells). This study sought to investigate whether mTOR is activated within Treg cells and whether this contributes to the depletion and dysfunction of Treg cells in patients with SLE. Methods Activities of mTOR complexes 1 (mTORC1) and 2 (mTORC2) were examined by quantifying phosphorylation of translation initiation factor 4E-binding protein 1, S6 kinase, and Akt in SLE patients relative to age- and sex-matched female healthy control subjects. Polarization of Treg cells from naive CD4+ T cells was assessed in the presence of interleukin-6 (IL-6), IL-17, and IL-21. The suppressor function of sorted CD4+CD25+ Treg cells was measured by determining their impact on the proliferation of autologous CD4+CD25- responder T cells. Treg cell expression of FoxP3, GATA-3, and CTLA-4 was monitored by flow cytometry. Autophagy was assessed using immunoblotting of light chain 3 lipidation. The effect of mTOR blockade was evaluated by testing the impact of rapamycin treatment on Treg cell function. Results SLE Treg cells exhibited increased activities of mTORC1 and mTORC2, whereas autophagy, the expression of GATA-3 and CTLA-4, and the suppressor function of Treg cells were diminished. IL-21, but not IL-6 or IL-17, blocked the development of Treg cells. IL-21 stimulated mTORC1 and mTORC2, and it abrogated the autophagy, differentiation, and function of Treg cells. Moreover, IL-21 constrained the expression of GATA-3 and CTLA-4 selectively in Treg cells. In turn, blockade of mTORC1 by 3-day rapamycin treatment enhanced transforming growth factor β production, while dual blockade of mTORC1 and mTORC2 by 4-week rapamycin treatment induced autophagy, restored the expression of GATA-3 and CTLA-4, and corrected Treg cell function. Conclusion IL-21-driven mTOR activation is a pharmacologically targetable checkpoint of the deficient autophagy that underlies Treg cell dysfunction in SLE.
José Martí, the United States, and Race by Anne Fountain

“Brevity is the source of wit,” claimed the Bard, and Argentine-American scholar Anne Fountain’s latest contribution to Marti studies, Jose Marti, the United States, and Race (UP of Florida, 2014), one of many, clearly exemplifies this adage. Almost any presentation or manual on how to turn a dissertation into a book conveys the same message: outside the most elite circles, academic books longer than 90,000 words are things of the past. The polysyllabic gobbledygook in which so many cultural studies scholars peddle simply does not sell. With an ever-smaller canvas on which to paint, one must choose her colors carefully. Fountain found a way to add many shades of Marti into her work, encapsulating the author’s entire twenty-seven volume oeuvre and adding perspective to a limpid, compelling argument: Jose Marti’s notions of race were, while sometimes inconsistent and contradictory, highly progressive and profoundly influenced by his exile in the United States, which lasted one third of his life. Overcoming racism was central to his vision for an independent Cuba and an autonomous Latin America. These arguments make the book relevant to scholars on Cuba, race, the African diaspora, Native Americans, and Latino studies.
Ethics in Pediatric Endocrinology: Curriculum for Fellows and Faculty

Introduction In clinical practice, ethical dilemmas are frequently faced by pediatric endocrinologists. This initiative's objectives were to (a) determine if endocrine fellows and faculty perceived...
Mini-incision versus hand-assisted laparoscopic donor nephrectomy in living-donor kidney transplantation: A retrospective cohort study

Abstract Background Increasing use of Living Donor Kidney Transplantation (LDKT) would decrease the discrepancy between patients awaiting transplantation and organ availability. Minimally invasive surgical approaches attempt to improve outcomes and foster living donation. This report compares outcomes of open minimal incision nephrectomy (Mini N) and a hand assisted laparoscopic nephrectomy (HALN). Methods This is a retrospective analysis of a prospectively maintained clinical database of LDKT using HALN or Mini N at a single institution between July 2007 and December 2015. Donor and recipient demographics, relevant pre-, intra- and post-operative factors, outcomes such as patient and graft survival rates, and complications were evaluated. Results Four hundred and fifty-four adult LDKT (243 Mini N, 211 HALN) were performed during the study period. Recipient and donor demographics were comparable except for higher BMI (p = 0.027) in HALN donors. One-, 3- and 5-year patient and graft survival rates were comparable. Six HALN donors experienced infectious wound complications or superficial skin dehiscence; none did in the Mini N group (p = 0.009). Eight HALN donors and one Mini N donor required an incisional hernia repair (p = 0.014). Recipients had similar warm ischemia times (33 v. 35 min, p = 0.491), but recipient surgeons of HALN nephrectomies subjectively noted higher anastomotic difficulty (10.4% v. 4.5%, p = 0.0183). Other parameters were similar between groups. Conclusion Both Mini N and HALN provide similar long term recipient and donor outcomes. Offering techniques such as Mini N and HALN for living donor kidney procurement facilitates the opportunity to provide living donors safer and better tolerated nephrectomy procedures.
Two-Dimensional Problems

There is a class of problems in elasticity which, due to geometry and boundary conditions, have solution stress, strain, and displacement fields that are independent of one of the coordinate variables. The equations of elasticity for this class of problem reduce to a simplified form of the general equations. Recognizing that a body with given boundary conditions is a member of this class, in advance of solving the attendant boundary value problem, enables one to take advantage of these simplified equations. Members of this class of problem are subdivided into three types known as antiplane strain, plane strain, and plane stress, as discussed below. It will be seen that the reduced form of the equations of elasticity for the later two are functionally equivalent.
Extraposition and Parasitic Gaps

Since Taraldsen (1981), Engdahl (1983), and Chomsky (1982), the “parasitic gap construction” has been discussed extensively in the literature. A typical example of this “construction” is shown in (1).
Concluding Remarks and Suggestions for Further Research

IF ONLY THE ANALYSES in this book could provide definitive replies to the problems that I posed in the Introduction! The case studies analyzed here suggest that there is good reason to agree with Poincare and Einstein, among others, that this shall not come to pass. But, like them, we are not deterred from exploring a phenomenon through which “we may hope to arrive at what is most essential in the human mind” (Poincare, 1908b; see epigraph above). The methods of analysis in this book offer a step toward that goal because they indicate that when the problem of the “mystery” of creative thinking is properly defined, it can shed light on several other problems hitherto unrelated: the process of thinking itself, the changing views of physical reality required by progress in science, and the process by which theories supplant one another. It is mainly to these associations that I address the concluding remarks.
Computational Experience in Nonlinear Mixed Integer Programming

An interior-point algorithm within a branch-and-bound framework for solving nonlinear mixed integer programs is described. In contrast to solving the relaxation to optimality at each tree node, the relaxation is only solved to near-optimality. Analogous to using advanced bases for warmstart solutions in the case of linear MIP, a “dynamic” collection of warmstart vectors are kept. Computational results on various classes of nonlinear mixed integer programs are presented.
Databases for Bioenergy-Related Enzymes

As one of the many clean and renewable energy forms, bioenergy, especially the liquid biofuels, has received great attention in the past 5 years, as biofuels have a great potential to be used for replacing the fossil-based gasoline as transportation fuels. However, the lignocellulosic biofuels are currently too expensive because plant cell walls, the major component of plant biomass, are recalcitrant to microbial/enzymatic deconstruction. In order to achieve the practical goals, reduce plant cell wall recalcitrance to enzymatic degradation and develop low-cost microbial or engineering approaches to releasing sugars, plant and microbial biologists as well as engineers have been working together to study the molecular mechanisms underlying plant biomass formation and microbial degradation. The past decades have seen a lot of genes experimentally characterized to be involved in plant cell wall synthesis or deconstruction. As a result, many bioenergy-related databases have been developed to collect and classify these genes, which are further used for annotating newly sequenced genomes. Here we summarize these bioenergy-related databases, with a special focus on plant resources. We also discuss the limitation of existing resources and suggest that there is still a strong need for new databases. The newly developed database should include not only enzymes, but also other important genes such as transcription factors, micro ribonucleic acid and transporters by extensive literature curation. The integration of various high-throughput omics data, e.g. comparative genomics data and precomputed bioinformatics data, is also highly recommended for developing new bioenergy-related databases.
Process maps for plasma spray. Part II: Deposition and properties

This is the second paper of a two part series based on an integrated study carried out at the State University of New York at Stony Brook and Sandia National Laboratories. The goal of the study is the fundamental understanding of the plasma-particle interaction, droplet/substrate interaction, deposit formation dynamics and microstructure development as well as the deposit property. The outcome is science-based relationships, which can be used to link processing to performance. Molybdenum splats and coatings produced at 3 plasma conditions and three substrate temperatures were characterized. It was found that there is a strong mechanical/thermal interaction between droplet and substrate, which builds up the coatings/substrate adhesion. Hardness, thermal conductivity, and modulus increase, while oxygen content and porosity decrease with increasing particle velocity. Increasing deposition temperature resulted in dramatic improvement in coating thermal conductivity and hardness as well as increase in coating oxygen content. Indentation reveals improved fracture resistance for the coatings prepared at higher deposition temperature. Residual stress was significantly affected by deposition temperature, although not significant by particle energy within the investigated parameter range. Coatings prepared at high deposition temperature with high-energy particles suffered considerably less damage in wear tests. Possible mechanisms behind these changes are discussed within the context of relational maps which are under development.
Regular Reporting and Talking to Stakeholders

This chapter focuses on using web analytics to communicate with stakeholders. A UX team can continually monitor the state of the user experience on the website and report on this status to business stakeholders as part of a regular communication plan. You must select a handful of metrics that provide the best summary of how well the website is serving users. Reports using analytics data should be concise and include enough context to make the numbers meaningful. Web analytics data can help you make the case for doing usability activities by showing stakeholders how many users will be affected by your work, and perhaps even allowing you to estimate how many additional users will benefit from this work.
Transoral endoscopic radical resection for a recurrent pyriform sinus fistula

Abstract In revision surgery for a recurrent pyriform sinus fistula (PSF), complete resection of the fistula via a transcervical approach is difficult because of the surrounding scar tissue that results from previous surgery and infections. We successfully performed transoral endoscopic radical resection of the fistula for a recurrent PSF in two patients. Approaching the fistula from the orifice is reasonable and radical resection of the fistula is a reliable procedure in revision surgery. Transoral endoscopic resection is a feasible surgical option for a recurrent PSF.
Experimental investigation of aerial–ground network communication towards geospatially large-scale structural health monitoring

Recognizing the importance of realizing integrated remote sensing and structural monitoring for civil structures at a geospatially large scale, this paper first proposes a concept design toward developing an aerial–ground wireless sensing network (AG-WSN) system for improving the efficiency of systems-level structural health monitoring. Upon this design, this paper further investigates the communication interference within such sensing network, which if not understood would diminish the practical value of such a system. This interference arises because of the UAV’s and the WSN’s communication protocols, for which most UAVs use 2.4 GHz radio for flight control and Wi-Fi (802.11 b/g/n) for imagery data streaming, and the WSNs often use the low-power ZigBee 802.15.4 protocol at 2.4 GHz as well. With the development of the proposed AG-WSN prototype using commercially available products, this paper experimentally achieves two important findings: (1) the key parameters that affect the short-range Wi-Fi and ZigBee interference and the experimental relations; and (2) the ‘comfort zone’ and the sensitive parameters for the long-range optimal ZigBee transmission between the aerial UAV and the ground sensors.
Probing the coupling of a dipole-bound electron with a molecular core

A dipolar molecule can weakly bind an electron in a diffuse orbital. However, the spin–orbit coupling between this weakly bound electron and the electrons in the molecular core is not known. Here we probe this coupling using the linear C2P− anion with the 3Σ+ ground state, which possesses dipole-bound excited states because neutral C2P (2Π) has a sufficiently large dipole moment. Photodetachment spectroscopy and resonant photoelectron spectroscopy are used to probe the nature of the dipole-bound states. Two dipole-bound excited states are observed with a binding energy of 37 cm−1, corresponding to the two spin–orbit states of neutral C2P (2Π1/2 and 2Π3/2). The current study demonstrates that the weakly bound electron in the dipole-bound excited states of C2P− is not spin-coupled to the electrons in the C2P core and can be considered as a quasi-free electron.
High-Efficiency Nose-to-Lung Aerosol Delivery in an Infant: Development of a Validated Computational Fluid Dynamics Method

Abstract Background: Computational fluid dynamics (CFD) provides a powerful tool for developing new high-efficiency aerosol delivery strategies, such as nose-to-lung (N2L) aerosol administration to...
Visualizing politics: A feminist political ecology and participatory GIS approach to understanding smallholder farming, climate change vulnerability, and seed bank failures in Northern Ghana

Abstract Over the past three decades, seeds banks have emerged as a major strategy for building seed systems resilience to climate change. Often initiated and funded by non-governmental organizations, seeds banks have grown prolifically, but questions remain concerning their long-term sustainability. Despite their precipitous rise, and effectives during initial years, many seed banks cut back on activities or stop altogether once external NGO funding is withdrawn. This rise and fall of seed banks raise three questions worthy of examination: (1) What factors shape the sustainability of community seed banks? (2) Do community seed banks function as they are designed to be? (3) How well do seed banks target farmers based upon true underlying need? Drawing upon insights from feminist political ecology (FPE) and Participatory Geographic Information Systems (PGIS), this paper examines these questions with data collected from drought-prone northern Ghana. The empirical research includes participant-observations; 144 in-depth interviews; participatory geospatial data analysis; gender-disaggregated data validation workshops; and analyses of seed bank inventory, lending, and payment records. Contrary to previous work emphasizing the role of climate variability and crop failure, this paper highlights the centrality of rural politics in the sustainability of seed banks. Specifically, the findings show that the lack of respect for indigenous knowledge, pseudo seed borrowing, and local elite capture, all work together to undermine the sustainability of seed banks. When seed banks do not meet farmers’ needs, the paper also demonstrates how farmers covertly resist such projects. Finally, the paper shows how through a repertoire of gender politics, village men undermine seed banks’ vision of ensuring equitable and democratic access to seeds. Overall, the paper contributes to existing research by demonstrating how FPE and PGIS could be used in parallel to permit a more rigorous testing of claims of village and gender politics on the ground.
EUS-guided biliary drainage: A systematic review and meta-analysis

ERCP is the current procedure of choice for patients with jaundice caused by biliary obstruction. EUS-guided biliary drainage (EUS-BD) has emerged as an alternative to ERCP in patients requiring biliary drainage. The aim of the study was to conduct a systematic review and meta-analysis to report the overall efficacy and safety of EUS-BD. We conducted a comprehensive search of several databases including PubMed, EMBASE, Web of Science, Google Scholar, and LILACS databases (earliest inception to June 2018) to identify studies that reported EUS-BD in patients. The primary outcome was to look at the technical and clinical success of the procedure. The secondary analysis focused on calculating the pooled rate of re-interventions and all adverse-events, along with the commonly reported adverse-event subtypes. Twenty-three studies reporting on 1437 patients were identified undergoing 1444 procedures. Majority of the patient population were male (53.86%), with an average age of 67.22 years. The pooled technical success rates and clinical success rates were 91.5% (95% confidence interval [CI]: 87.7-94.2, I[2] = 76.5) and 87% (95% CI: 82.3-90.6, I[2] = 72.4), respectively. The total adverse event rates were 17.9% (95% CI: 14.3-22.2, I[2] = 69.1). Subgroup analysis of three major individual adverse events was bile leak: 4.1% (2.7-6.2, I[2] = 46.7), stent migration: 3.9% (2.5-6.2, I[2] = 43.5), and infection: 3.8% (2.8-5.1, I[2] = 0) Substantial heterogeneity was noted in the analysis. EUS-BD has high technical and clinical success rate and hence a very effective procedure. Concerns about publication bias exist. Careful consideration should be given to the adverse events and weighing the risks and benefits of the alternative nonsurgical/surgical approaches.
Programming animal physiology and behaviors through engineered bacteria

Abstract A central goal of synthetic biology is to predictably and efficiently reprogram living systems to perform computations and carry out specific biological tasks. Although there have been many advances in the bio-computational design of living systems, these advances have mainly been applied to microorganisms or cell lines; programming animal behavior and altering animal physiology remain challenges for synthetic biology because of the system complexity. Here, we present a bacteria-animal symbiont system in which engineered bacteria recognize external signals and modulate animal gene expression, twitching behavior, and fat metabolism through RNA interference. By using genetic circuits in bacteria to control RNA expression, we programmed the physiology and behavior of the model animal Caenorhabditis elegans with logic gates. We anticipate that engineered bacteria can be used more extensively to program animal metabolism and behaviors for agricultural, therapeutic, and basic science applications. One Sentence Summary Animal physiology and behaviors are programmed via engineered bacteria.
Adhesins in Opportunistic Fungal Pathogens

This chapter deals with cell surface proteins in two Candida species, C. albicans and C. glabrata, and in their nonpathogenic relative Saccharomyces cerevisiae, specifically focusing on the diversity and function of proteins implicated in adherence of the yeasts to each other or to other surfaces, including host cells. The most extensively studied family of adhesins in any Candida species is the one corresponding to the C. albicans ALS gene family, which includes eight family members. Two adhesins in family IV have similarity to the protein corresponding to DAN1 in S. cerevisiae, another subtelomeric adhesin whose expression is regulated by oxygen availability in the environment. Mass spectrometry was identify covalently linked cell wall proteins (CWPs), including adhesins, on the surface of C. glabrata. In total, five adhesins were detected: Epa6 and four uncharacterized proteins that were subsequently named Awp1 to -4 (adhesin-like wall protein). The FLO genes play essential roles during flocculation, a process by which yeast cells bind to the mannose residues on the surface of neighboring cells, forming clusters of cells called flocs, and sediment. CWPs are key to the interaction of fungi with the environment, and not surprisingly, changes within the CWP repertoire accompany the evolutionary adaptation to a particular niche. The relatively limited repertoire of FLO genes in S. cerevisiae primarily serves to mediate yeast-yeast interactions that adapt it to growth in communities/biofilms as well as to respond to nutritional cues.
13. Uncommon rash and neurological symptoms related to Shingrix

Background Shingrix is a non-live recombinant vaccine approved by the Food and Drug Administration (FDA) in 2017 to prevent shingles and postherpetic neuralgia in immunocompetent adults age 50 years and older. A myriads of local and systemic reactions due to the vaccine have been reported, but diffuse erythematous maculopapular rash and neurological symptoms have not yet been reported in English literature.
Region-wide characterization of structural diversity of the U.S. Outer Coastal Plain Mixed Forests Province

Abstract Forest structural diversity is related to stability, biodiversity, adaptability and resilience, as well as productivity of forest ecosystems. In this study, we characterized structural diversity of the diverse forest type groups in the southeastern Outer Coastal Plains Mixed Forest Province of the United States. We utilized data from 13,658 Forest Inventory and Analysis (FIA) plots across the region and classified them on the basis of forest type group (i.e., longleaf-slash pine, loblolly-shortleaf pine, oak-pine, oak-hickory, oak-gum-cypress, or other), disturbance type (disturbed by animal, fire, insect and disease, weather, other disturbances, or no disturbance), ownership (public or private and Native American), site condition (xeric, mesic, or hydric), stand origin (natural or planted), and age structure (one or two age classes). The structural diversity was estimated as Shannon index of tree size diversity. Our findings indicate a range of 0.00 to 2.40 for Shannon index values across the forest type groups and the ecoregion. All forest attributes (i.e., forest type groups, disturbance type, ownership, site condition, stand origin, and age structure) significantly affected structural diversity at α = 0.05. Oak-gum-cypress was structurally the most diverse forest type group. Overall, plots that were publicly owned, naturally regenerated, two-aged, and affected by weather disturbances exhibited higher structural diversity. We also created region-wide structural diversity distribution and hot spot maps. The maps identified southern Mississippi, northern and eastern Virginia, northern North Carolina, eastern South Carolina, and the border between the states of Texas and Louisiana as the structural diversity hot spots. The middle part of Outer Coastal Plain consisting of southcentral Georgia, northcentral Florida, and southwest Alabama exhibited the lowest structural diversity.
Accounting for exotic matter and the extreme radial tension in Morris–Thorne wormholes of embedding class one

The embedding of a curved spacetime in a higher-dimensional flat spacetime has continued to be a topic of interest in the general theory of relativity, as exemplified by the induced-matter theory. This paper deals with spacetimes of embedding class one, i.e., spacetimes that can be embedded in a five-dimensional flat spacetime. Einstein’s theory allows the fifth dimension to be either spacelike or timelike. By assuming the latter, this paper addresses two fundamental issues concerning Morris–Thorne wormholes, the origin of exotic matter and the frequently inexplicable enormous radial tension at the throat.
Illumina But With Nanopore: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2

High-throughput short-read sequencing has taken on a central role in research and diagnostics. Literally hundreds of different assays exist today to take advantage of Illumina short-read sequencers, the predominant short-read sequencing technology available today. Although other short read sequencing technologies exist, the ubiquity of Illumina sequencers in sequencing core facilities, and the inertia associated with the research enterprise as a whole have limited their adoption. Among a new generation of sequencing technologies, Oxford Nanopore Technologies (ONT) holds a unique position because the ONT MinION, an error-prone long-read sequencer, is associated with little to no capital cost. Here we show that we can make short-read Illumina libraries compatible with the long-read ONT MinION by circularizing and rolling circle amplifying the short library molecules using the R2C2 method. This results in longer DNA molecules containing tandem repeats of the original short library molecules. This longer DNA is ideally suited for the ONT MinION, and after sequencing, the tandem repeats in the resulting raw reads can be converted into millions of high-accuracy consensus reads with similar error rates to that of the Illumina MiSeq. We highlight this capability by producing and benchmarking RNA-seq, ChIP-seq, as well as regular and target-enriched Tn5 libraries. We also explore the use of this approach for rapid evaluation of sequencing library metrics by implementing a real-time analysis workflow.
Management of Liver Metastases from Testicular Cancer

Testicular cancer is a disease of young males. Histologically, these tumors are divided into pure seminomatous and non-seminomatous germ cell types. Typically spreading to axial (i.e., iliac, para-aortic) nodal chains and systemically to distant organ sites, they can express variable aggressiveness. Visceral metastases are common with the lungs predominating. Metastatic disease patients are typically treated with systemic chemotherapy, with surgery at local-regional and metastatic sites reserved for staging and consolidation of therapy. With modern systemic therapy as many as 95 % of patients will be cured. Given the rarity of these tumors, their mode and distribution of spread, and the efficacy of systemic therapies, there is a very narrow indication for liver-directed therapies. This chapter will review the international literature on the topic, including multimodality therapies, indications for liver surgery, and outcomes following liver-directed therapy in patients with metastases from testicular cancer.
General and Specific Strategies Used to Facilitate Locomotor Maneuvers.

People make anticipatory changes in gait patterns prior to initiating a rapid change of direction. How they prepare will change based on their knowledge of the maneuver. To investigate specific and general strategies used to facilitate locomotor maneuvers, we manipulated subjects’ ability to anticipate the direction of an upcoming lateral “lane-change” maneuver. To examine specific anticipatory adjustments, we observed the four steps immediately preceding a maneuver that subjects were instructed to perform at a known time in a known direction. We hypothesized that to facilitate a specific change of direction, subjects would proactively decrease margin of stability in the future direction of travel. Our results support this hypothesis: subjects significantly decreased lateral margin of stability by 69% on the side ipsilateral to the maneuver during only the step immediately preceding the maneuver. This gait adaptation may have improved energetic efficiency and simplified the control of the maneuver. To examine general anticipatory adjustments, we observed the two steps immediately preceding the instant when subjects received information about the direction of the maneuver. When the maneuver direction was unknown, we hypothesized that subjects would make general anticipatory adjustments that would improve their ability to actively initiate a maneuver in multiple directions. This second hypothesis was partially supported as subjects increased step width and stance phase hip flexion during these anticipatory steps. These modifications may have improved subjects’ ability to generate forces in multiple directions and maintain equilibrium during the onset and execution of the rapid maneuver. However, adapting these general anticipatory strategies likely incurred an additional energetic cost.
2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum [APDCM Introduction]

The main goal of this workshop is to provide a timely forum for the exchange and dissemination of new ideas, techniques and research in the field of the parallel and distributed computational models. The workshop is meant to bring together researchers and practitioners interested in all aspects of parallel and distributed computing taken in an inclusive, rather than exclusive, sense. We are convinced that the workshop atmosphere will be conducive to open and mutually beneficial exchanges of ideas between the participants.
Strategic Decision Making in Federal District Courts: Evidence from Securities Fraud Actions

Scholars employing the tools of public choice theory hypothesize that judges are strategic actors whose decisions, while goal oriented, are influenced by the anticipated reactions of other political actors and by their institutional settings. Critics argue, however, that attempts to find empirical evidence of strategic decision making at the U.S. Supreme Court or Courts of Appeals have been spectacularly unsuccessful. This paper expands the search for strategic decision making by looking at federal district court decisions, specifically interpretations of the higher pleading standard contained in the Private Securities Litigation Reform Act of 1995. Initial interpretations of the Act articulated polar liberal and conservative positions. The evidence compiled here supports the hypothesis that the later emergence of an intermediate approach was the result of strategic decision making, rather than simply judges acting consistently with their strict ideological preferences. Using a much more nuanced measure of judicial ideology than previously employed in the legal literature, the article finds that liberal and conservative judges sitting in ideologically dissimilar circuits were significantly more likely to adopt the intermediate standard than other judges. There is also evidence that the likelihood of strategic decision making is a function of the likelihood of appeal and reversal and that changes in reversal rates had the largest influence on moderate judges. While there is some evidence that horizontal precedents also influenced the decision, those correlations are generally weaker than for strategic variables and are not consistently significant across model specifications.
The Drosophila Protein Mustard Tailors the Innate Immune Response Activated by the Immune Deficiency Pathway

In this study, we describe a Drosophila melanogaster transposon insertion mutant with tolerance to Vibrio cholerae infection and markedly decreased transcription of diptericin as well as other genes regulated by the immune deficiency innate immunity signaling pathway. We present genetic evidence that this insertion affects a locus previously implicated in pupal eclosion. This genetic locus, which we have named mustard (mtd), contains a LysM domain, often involved in carbohydrate recognition, and a TLDc domain of unknown function. More than 20 Mtd isoforms containing one or both of these conserved domains are predicted. We establish that the mutant phenotype represents a gain of function and can be replicated by increased expression of a short, nuclearly localized Mtd isoform comprised almost entirely of the TLDc domain. We show that this Mtd isoform does not block Relish cleavage or translocation into the nucleus. Lastly, we present evidence suggesting that the eclosion defect previously attributed to the Mtd locus may be the result of the unopposed action of the NF-κB homolog, Relish. Mtd homologs have been implicated in resistance to oxidative stress. However, to our knowledge this is the first evidence that Mtd or its homologs alter the output of an innate immunity signaling cascade from within the nucleus.
Using omnidirectional structure from motion for registration of range images of minimal overlap

We propose a novel method of merging a series of range images with a minimal overlap between any two consecutive range images. We rigidly mount a parabolic catadioptric camera to the range scanner. Using two omniviews we are able to accurately estimate the relative displacement between two range views. The resultant motion is used for the registration of all range data to the same coordinate system. An additional perspective camera calibrated with respect to the scanner is used for texture mapping.
The use of continuous flow bioreactors to explore gene expression and physiology of suspended and adherent populations of oral streptococci

Most pathogenic bacteria elicit diseases as populations colonizing surfaces of a susceptible host. In the biofilms that form on host tissues, pathogenic bacteria can encounter huge variations in environmental conditions that can critically affect persistence and expression of virulence. Gaining a comprehensive understanding of molecular aspects of pathogenesis by streptococci and enterococci will require a detailed dissection of the phenotypic capacities of these organisms under conditions that may be experienced in vivo. Described herein are technologies that i) merge the study of bacterial gene expression with continuous chemostat culture, allowing for the strict modulation of key physiologic parameters, and ii) for the cultivation of oral streptococci as adherent populations which are suitable for analysis using reporter gene fusions and advanced microscopic techniques. These techniques extend the capabilities of investigators to control key physiologic parameters and to cultivate the organisms in environments that may more closely mimic conditions in vivo. Thus, these approaches should be useful in enhancing our understanding of bacterial pathogenesis.
Growth and development of larval Taenia crassiceps (cestoda). I. Aneuploidy in the anomalous ORF strain.

Abstract The diploid chromosome number for the KBS strain of larval Taenia crassiceps was found to be 16; for the ORF strain, the diploid number is 14. The chromosomes are morphologically identical in the two strains, except that one homologous pair is missing in ORF larvae. It is concluded that the morphologic, antigenic and reproductive abnormalities described for the ORF strain are a result of aneuploidy.
Three-Dimensional Flow and Pressure Patterns in a Hydrostatic Journal Bearing Pocket.

The laminar flow in a hydrostatic pocket is described by a mathematical model that uses the three-dimensional Navier-Stokes equations written in terms of the primary variables, u, v, w, and p. Using a conservative formulation, a finite volume multiblock method is applied through a collocated, body fitted grid. The flow is simulated in a shallow pocket with a depth/length ratio of 0.02. The flow structures obtained and described by the authors in their previous two dimensional models are made visible in their three dimensional aspect for both the Couette, and the jet dominated flows. It has been found that both flow regimes formed central and secondary vortical cells with three dimensional corkscrew-like structures that lead the fluid on an outward bound path in the axial direction of the pocket. In the Couette dominated flow the position of the central vortical cell center is at the exit region of the capillary restrictor feedline, while in the jet dominated flow a flattened central vortical cell is formed in the downstream part of the pocket. It has also been determined that a fluid turn around zone occupies all the upstream space between the floor of the pocket and the runner, thus preventing any flow exit through the upstream exit of the pocket. The corresponding pressure distribution under the shaft for both flow regimes is presented as well. It was clearly established that both for the Couette, and the jet dominated cases the pressure varies significantly in the pocket in the circumferential direction, while its variation is less pronounced axially.
Movement-evoked hyperalgesia induced by lipopolysaccharides is not suppressed by glucocorticoids.

Systemic exposure to lipopolysaccharides (LPS) produces a variety of effects, including movement-evoked hyperalgesia that can be measured using the grip force assay in mice. Because both lethality and enhanced sensitivity to cutaneous pain following exposure to endotoxins have each been attributed to inflammatory mediators, we explored the possibility that LPS-induced movement-evoked hyperalgesia is also sensitive to manipulations of glucocorticoids that regulate these other LPS responses. We found that the hyperalgesic effect of LPS (5 mg/kg s.c.) in mice that were adrenalectomized did not differ from that in control mice that were sham operated, even though mortality after LPS was potentiated by adrenalectomy. The development of tolerance to the movement-evoked hyperalgesic effect of LPS also did not differ between adrenalectomized and sham-operated control mice. In addition, mifepristone (25 mg/kg s.c.), a glucocorticoid antagonist, did not attenuate the hyperalgesic effect of LPS (2 mg/kg s.c.), yet this dose of mifepristone was sufficient to enhance the incidence of lethality induced by LPS. Enhancement of glucocorticoid activity by two injections of dexamethasone (1 mg/kg s.c.) had no effect on the degree of hyperalgesia in mice injected with LPS (5 mg/kg s.c.), yet this dose of dexamethasone was sufficient to attenuate the incidence of mortality induced by LPS in adrenalectomized mice. Finally, morphine (10 mg/kg i.p.) reversed the decrease in grip force caused by LPS (5 mg/kg i.p.), supporting the interpretation that decreases in grip force produced by LPS reflect muscle hyperalgesia that is not sensitive to glucocorticoids.
TRANSCRIPTION OF SATELLITE 2 DNA FROM THE NEWT IS DRIVEN BY A SNRNA TYPE OF PROMOTER

The transcriptional promoter of satellite 2 from the eastern newt, Notophthalmus viridescens, was analyzed by assaying the activity of deleted or mutated satellite 2 clones in Xenopus laevis oocytes. Two elements in the promoter were found to be important for transcription. These elements have sequences that are similar to the sequences of the octamer and the proximal sequence element of vertebrate snRNA genes transcribed by RNA polymerase II. Furthermore, the organization of these elements and their respective roles in transcription are the same as their organization and roles in the snRNA genes. To further investigate the relationship between the satellite 2 and snRNA gene promoters, the ability of the satellite 2 promoter to drive transcription of a true snRNA gene was tested. The satellite 2 promoter initiated transcription of the Xenopus U1b2 snRNA gene as efficiently as the native U1b2 promoter, and the 3' ends of the resulting U1b2 transcripts were accurately formed. This latter result confirms that the satellite 2 promoter is a functional analog of the snRNA promoter, since 3'-end formation of snRNA genes transcribed by RNA polymerase II requires that transcription be initiated from a compatible promoter. The structural and functional similarities between the satellite 2 and the snRNA gene promoters suggest that these elements are evolutionarily related. These findings were used to extend a previously proposed model concerning the nature and derivation of satellite 2.
Investigations of Stability & Dynamic Performances of a Current-Injected Regulator

The stability and dynamic performances of a buck/boost regulator employing a current-injected control are examined. Small-signal models for the power state, the multiloop error processor, and the duty-cycle pulse modulator are developed. The error-processor model which incorporates the current-injected loop, the dc loop, and the compensation network permits evaluation of the effects of each individual control loop and their combined efforts toward shaping the performance characteristics of the closed-loop system. Comparisons are made between this modeling approach and earlier approaches. Some important yet subtle dissimilarities are discussed. This model predicts the constant-frequency 50-percent duty-cycle instability which is inherent to the current-injected control.
Pathways for alanine transport in intestinal basal lateral membrane vesicles.

Membrane vesicles obtained from the basal lateral membranes of the rat intestinal epithelium were used to study the pathways for neutral amino acid transport. In the absence of sodium there was a stereospecific uptake ofl-alanine which exhibited saturation kinetics (K m 0.73mm andV max 5.3 nmol/mg min at 22°C). The activation energy for this process was 8.1 kcal/mole between 5 and 25°C. Preloading the vesicles with alanine increased the unidirectional influx of alanine into the vesicle. Competition experiments indicated that the affinity of the sodium-independent transport system was glutamine > threonine > alanine > phenylalanine > valine > methionine > glycine > histidine > proline, N-MeAIB. These are the characteristics of the classical “L” transport system. External sodium increased the rate of the stereospecificl-alanine uptake. The Na-dependent flux had aK m of 0.04mm and aV max of 0.26 nmol/mg min at 22°, and an activation energy of 9.1 kcal/mole between 5 and 25°C. Competition experiments suggest the existence of three separate pathways for alanine transport in the presence of sodium. A major pathway is shared by all other amino acids tested (i.e., threonine, glutamine, methionine, phenylalanine, valine, proline and N-MeAIB). This resembles the classical “A” system. A second pathway is unavailable to either phenylalanine or N-MeAIB; this is reminiscent of the classical “ASC” system; and the third is a novel pathway which is shared by N-MeAIB but not phenylalanine. The sodium-independent and the sodium-dependent transport ofl-alanine was blocked by PCMBS and significantly inhibited by DTP and NEM. It is concluded that the sodium-independent system (the “L”-like system) accounts for the efflux of neutral amino acids from the epithelium to the blood during the absorption of amino acids from the gut, and that the sodium-dependent transport processes may play an important role in the supply of amino acids to the epithelium in the absence of amino acids from the gut lumen.