cssi/SciSciGPT-SciSciNet huggingface dataset:
GenOO: A Modern Perl Framework for High Throughput Sequencing analysis

Background: High throughput sequencing (HTS) has become one of the primary experimental tools used to extract genomic information from biological samples. Bioinformatics tools are continuously being developed for the analysis of HTS data. Beyond some well-defined core analyses, such as quality control or genomic alignment, the consistent development of custom tools and the representation of sequencing data in organized computational structures and entities remains a challenging effort for bioinformaticians. Results: In this work, we present GenOO [jee-noo], an open-source; object-oriented (OO) Perl framework specifically developed for the design and implementation of HTS analysis tools. GenOO models biological entities such as genes and transcripts as Perl objects, and includes relevant modules, attributes and methods that allow for the manipulation of high throughput sequencing data. GenOO integrates these elements in a simple and transparent way which allows for the creation of complex analysis pipelines minimizing the overhead for the researcher. GenOO has been designed with flexibility in mind, and has an easily extendable modular structure with minimal requirements for external tools and libraries. As an example of the framework’s capabilities and usability, we present a short and simple walkthrough of a custom use case in HTS analysis. Conclusions: GenOO is a tool of high software quality which can be efficiently used for advanced HTS analyses. It has been used to develop several custom analysis tools, leading to a number of published works. Using GenOO as a core development module can greatly benefit users, by reducing the overhead and complexity of managing HTS data and biological entities at hand.
NOAA’s Historical Tsunami Event Database, Raw and Processed Water Level Data, and Model Output Relevant to the 11 March 2011 Tohoku, Japan Earthquake and Tsunami

On 11 March 2011, a magnitude 9.0 Mw earthquake occurred near the east coast of Honshu Island, Japan. The earthquake generated a tsunami with wave heights up to 40 m triggering a response from the National Oceanic and Atmospheric Administration (NOAA). NOAA is the lead federal agency responsible for tsunami warnings issuance, technology innovation, research, and mitigation for the United States. These activities are matrixed across several closely integrated bureaus, including the National Weather Service National Data Buoy Center, Tsunami Warning Centers, and UNESCO/IOC – NOAA International Tsunami Information Center; the National Ocean Service Center for Operational Oceanographic Products and Services, the Pacific Marine Environmental Laboratory; and the National Environmental Satellite, Data, and Information Service National Geophysical Data Center (NGDC). Each of these bureaus work together to improve tsunami forecasting and thereby protect lives. Immediately following the March 2011 Japan earthquake and tsunami, all NOAA offices were involved in complimentary tsunami activities. In this paper, we describe the status of data associated with this tsunami event, review the processing and availability of tide gauge and tsunameter data, including Deep-ocean Assessment and Reporting of Tsunamis (DART®) and discuss the uses of these data in tsunami models. The basic data in the NGDC historical event databases include: date, time, event location, magnitude of the phenomenon, and socio-economic information such as the total number of fatalities and dollar damage estimates. The tsunami database includes additional information on runups (locations where tsunami waves were observed by eyewitnesses, post-tsunami field surveys, tide gauges, or deep ocean sensors). Therefore, an introduction and summary of the effects of the earthquake and tsunami is also included.
Recovery and Range Expansion of Parasitoids (Hymenoptera: Aphelinidae and Braconidae) Released for Biological Control of Diuraphis noxia (Homoptera: Aphididae) in Wyoming

Abstract Aphelinus albipodus Hayat & Fatima, A. asychis Walker (Hymenoptera: Aphelinidae), Diaeretiella rapae (M’Intosh), Aphidius matricariae Haliday, Aphidius colemani (Viereck), Aphidius picipes (Nees), Aphidius rhopalosiphi DeStefani-Perez, Ephedrus plagiator (Ness), and Praon gallicum Stary (Hymenoptera: Braconidae) were released in southeastern Wyoming for biological control of Diuraphis noxia (Mordvilko), Russian wheat aphid (Homoptera: Aphididae). A total of 407,028 parasitoids in the form of mummified aphids was released from 1989 to 1996. Three species, A. albipodus, A. asychis, and D. rapae, were first detected in winter wheat fields 3 yr after first release and spread throughout the wheat production region within 5 yr of release. Other primary aphid parasitoids were recovered sporadically and in very small quantities, and hyperparasitoids consisted of up to 20% of the specimens recovered. There were significant differences in abundance of A. albipodus, A. asychis, and D. rapae. In 1992, D. rap...
The Role of Chronology in Analyzing Introductory Programming Assignments (Abstract Only)

Entry-level college programming courses have high failure rates, which lead to high dropout rates for associated majors. These courses typically cover fundamental programming concepts for students to master in order to succeed in their majors. When attempting to perceive a student's competency, instructors often utilize Automated Assessment Tools, but most tools do not fully record student progress in assignments. Access to the student's problem solving steps can provide educators a more complete understanding of the student's thought process. Our tool tracks the student's steps and sequencing while attempting to complete assignments. With this resource, teaching methodologies can be modified to more effectively foster successful problem-solving strategies within early programming courses.
Photon Management for Near-Total Solar Absorption in Hematite Photoanodes

Using first-principles full-field electromagnetic simulations, we demonstrate that near-perfect above-band-gap solar absorption can be achieved in nanostructured, ultra-thin-film iron oxide photoanodes for photoelectrochemical (PEC) water splitting. In our designed core-shell nanocone structures, all regions of hematite (α-iron oxide) are away from the interface between hematite and water by a minimum distance of less than the hole diffusion length in hematite, which is assumed to be no greater than 20nm. The optical absorption in our structure corresponds to a photocurrent density of 12.5mA/cm2 if one assumes an air mass 1.5 solar spectrum and a unity absorbed photon-to-current efficiency (APCE) for all wavelengths in that spectrum. Our photon management strategy eliminates the trade-off between optical absorption and carrier collection as commonly found in conventional designs of PEC cells, and variants of the strategy are generally applicable to other material systems.
Allostery and substrate channeling in the tryptophan synthase bienzyme complex: evidence for two subunit conformations and four quaternary states.

The allosteric regulation of substrate channeling in tryptophan synthase involves ligand-mediated allosteric signaling that switches the α- and β-subunits between open (low activity) and closed (high activity) conformations. This switching prevents the escape of the common intermediate, indole, and synchronizes the α- and β-catalytic cycles. 19F NMR studies of bound α-site substrate analogues, N-(4′-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F6) and N-(4′-trifluoromethoxybenzenesulfonyl)-2-aminoethyl phosphate (F9), were found to be sensitive NMR probes of β-subunit conformation. Both the internal and external aldimine F6 complexes gave a single bound peak at the same chemical shift, while α-aminoacrylate and quinonoid F6 complexes all gave a different bound peak shifted by +1.07 ppm. The F9 complexes exhibited similar behavior, but with a corresponding shift of −0.12 ppm. X-ray crystal structures show the F6 and F9 CF3 groups located at the α–β subunit interface and report changes in both the ligan...
New sources of γ‐linolenic acid

γ-Linolenic acid (18:3Δ6,9,12) occurs in significant amounts in various species of plants surveyed. Of the species analyzed in this study, Nonnea macrospernia, with 5.1% 7-linolenic acid in the seed, is the richest source of this fatty acid. Other species in the same family (Boraginaceae) are also good sources: Adelocaryum coelestinum, Alkanna froedinii, Alkanna orientalis and Brunnera orientalis. Scrophularia marilandica (family Scrophulariaceae) seeds contain 37.9% oil, of which 9.6% is γ-linolenic acid. All species mentioned above are better sources, when the total amount of γ-linolenic acid in the seed is considered, than that used traditionally, Evening Primrose (Oenothera biennis, family Onagraceae). None of the other Onagraceae nor any of the Ribes (family Saxifragaceae) species analyzed are as rich in γ-linolenic acid as Evening Primrose. Octadecatetraenoic acid (18:4Δ,6,9,12,15) was found in significant amounts in most of the Boraginaceae and Ribes surveyed. The Onagraceae and Scrophulariaceae lack detectable amounts of this fatty acid.
Evaluation of Bacterial Pathogen and Indicator Densities After Dewatering of Anaerobically Digested Biosolids Phase II and III

The sudden increase in indicator bacteria, including fecal coliforms (FCs) and E. coli , was evaluated at several full-scale facilities, in addition to the increase measured during cake storage. The results showed that the sudden increase was a statistically verifiable occurrence at some facilities, but not all, as was the additional increases measured during cake storage. The sudden increase and growth were much more prevalent in processes that utilized centrifuge dewatering compared to belt filter press dewatering. The sudden increase appears to be a result of the reactivation of indicator bacteria that become reversibly non-culturable (RNC) during digestion. Although other hypotheses, such as contamination and presence of inhibitors, cannot be ruled out in all cases. Only one plant that was sampled with high solids centrifugation did not show reactivation and/or regrowth and this plant was different from others in that it utilized thermophilic reactors in series. The results showed a good correlation between the digestion temperature and the reactivation potential and amount of reactivation measured after dewatering. As temperature of digestion increased, the amount of reactivation increased (for plants with reactivation). Similarly, this was generally true, on average for the extent of regrowth. The digestion SRT and VS reduction did not correlate well with reactivation or regrowth. This title belongs to WERF Research Report Series ISBN: 9781780403731 (eBook) ISBN: 9781843397847 (Print)
Bacterial food poisoning in Xuchang City from 2006-2010

[Objective]To understand the prevalence of bacterial food poisoning in Xuchang City in recent years,especially the epidemiological characteristics and laboratory testing results,and provide evidence for judgment,treatment,prevention and control of food poisoning.[Methods]The detection on samples of suspected food poisoning was based on GB / T 4789 standard and conventional food poisoning testing procedures.[Results] A total of 59 incidents of food poisoning occurred in 5 years,with 574 detected samples,38 incidents were detected with pathogens(69 strains).Thirty-five incidents caused by single pathogen,while 3 caused by mixed strains.Six kinds of pathogens were detected,the major was Salmonella(25.42%),followed by Vibrio parahaemolyticus(13.56%),Proteus(10.17%).The pollution characteristics were Salmonella contamination of meat,Vibrio parahaemolyticus contamination of aquatic products,Proteus contamination of meat,rice and vegetables.Most incidents occurred in catering industry followed by school canteen.[Conclusion]Most of the bacterial food poisoning incidents caused bySalmonella and Vibrio parahaemolyticus in this city,the peak incidence appears in 2nd and 3rd quarter.The health inspection on catering industry and school canteen should be strengthened to prevent and reduce the incidence of bacterial food poisoning.
A General Approach for Efficiently Accelerating Software-based Dynamic Data Flow Tracking on Commodity Hardware.

Despite the demonstrated usefulness of dynamic data flow tracking (DDFT) techniques in a variety of security applications, the poor performance achieved by available prototypes prevents their widespread adoption and use in production systems. We present and evaluate a novel methodology for improving the performance overhead of DDFT frameworks, by combining static and dynamic analysis. Our intuition is to separate the program logic from the corresponding tracking logic, extracting the semantics of the latter and abstracting them using a Taint Flow Algebra. We then apply optimization techniques to eliminate redundant tracking logic and minimize interference with the target program. Our optimizations are directly applicable to binary-only software and do not require any high level semantics. Furthermore, they do not require additional resources to improve performance, neither do they restrict or remove functionality. Most importantly, our approach is orthogonal to optimizations devised in the past, and can deliver additive performance benefits. We extensively evaluate the correctness and impact of our optimizations, by augmenting a freely available high-performance DDFT framework, and applying it to multiple applications, including command line utilities, server applications, language runtimes, and web browsers. Our results show a speedup of DDFT by as much as 2.23×, with an average of 1.72× across all tested applications.
Expression of opioid receptors in mammalian cell lines.

17 From: Methods in Molecular Medicine, Vol. 84: Opioid Research: Methods and Protocols Edited by: Z. Z. Pan © Humana Press Inc., Totowa, NJ
Health (care) and human rights: a fundamental conditions approach

Many international declarations state that human beings have a human right to health care. However, is there a human right to health care? What grounds this right, and who has the corresponding duties to promote this right? Elsewhere, I have argued that human beings have human rights to the fundamental conditions for pursuing a good life. Drawing on this fundamental conditions approach of human rights, I offer a novel way of grounding a human right to health care.
Art and the Museum

Between approximately 1509 and 1511, as Michelangelo completed the Sistine ceiling nearby, Raphael set to work on his first major commission in Rome, a set of frescoes for the Stanza della Segnatura at the Vatican. On one wall of the room he painted the fresco that would become famous as The School of Athens (Figure 1.1); on the facing wall a theological subject that has come to be called the Disputation of the Sacrament (Figure 1.2); and on a third, a vision of poetry, Parnassus (Figure 1.3), presided over by Apollo and the Muses and inhabited by the great poets of antiquity and the modern era. Raphael’s program presents a beautifully realized illustration of the various realms of achievement — divine, intellectual, and creative — given weight not only by the painter’s mastery of technique and originality of conception, but also by the location of his works in the heart of Christendom.
Comrades of Color: East Germany in the Cold War World

The past decade has witnessed the growth of literature exploring the dynamic relations between Germany and the world, especially during the Cold War. Whether involving international affairs, cultur...
Arithmetic properties for hyper -ary partition functions.

Numerous functions which enumerate partitions into powers of a fixed number m have been studied ever since Churchhouse’s original work in the late 1960’s on the unrestricted binary partition function. In particular, Calkin and Wilf recently considered the hyperbinary partition function (as they “recounted the rationals”). In this paper, we first prove an unexpected partition congruence satisfied by the hyperbinary partition function. We then consider a natural generalization of hyperbinary partitions, which we call hyper m–ary partitions, and prove surprising arithmetic properties for these via elementary means.
Surface-Modified Porous Carbon Nitride Composites as Highly Efficient Electrocatalyst for Zn-Air Batteries

Porous carbon nitride (PCN) composites are fabricated using a top-down strategy, followed by additions of graphene and CoSx nanoparticles. This subsequently enhances conductivity and catalytic activity of PCN (abbreviated as CoSx@PCN/rGO) and is achieved by one-step sulfuration of PCN/graphene oxides (GO) composite materials. As a result, the as-prepared CoSx@PCN/rGO catalysts display excellent activity and stability toward both oxygen evolution and reduction reactions, surpassing electrocatalytic performance shown by state-of-the-art Pt, RuO2 and other carbon nitrides. Remarkably, the CoSx@PCN/rGO bifunctional activity allows for applications in zinc-air batteries, which show better rechargeability than Pt/C. The enhanced catalytic performance of CoSx@PCN/rGO can primarily be attributed to the highly porous morphology and sufficiently exposed active sites that are favorable for electrocatalytic reactions.
“Migrants With Attitude”: Shailja Patel and the Phenomenology of South Asian African Diasporas

AbstractIn her performance piece and book Migritude, Shailja Patel traces South-Asian diasporas in East Africa and her own migrations from Africa to England and the United States. This tracing stages the fraught and historical intimacies of Africa, Asia, Europe, and the Americas. East African Asian writers like M.G. Vassanji, Yasmin Alibhai-Brown, and others are similarly global and diasporic in scope. Yet, Patel's project Migritude refashions Negritude-era identity politics and engages the material histories of migration and Empire to challenge systemic violence against immigrants under neoliberal globalization. In this essay I analyze Shailja Patel's relationship to Negritude, migration in Patel's work, and conclude with remarks on the critique of gendering in migration and the promise of Patel's “migrant attitude.”
Proposed unified discrete event simulation content roadmap for M&S curricula

This paper presents a new educational roadmap for teaching discrete event system (DES) simulation software design. This roadmap represents the hierarchical structure and inter-relationships characterizing the worldviews of DES simulation, namely, event scheduling and process interaction. The roadmap was developed from the authors' experience while teaching DES simulation to both undergraduate and graduate students, spanning several years. The roadmap's development was motivated by the need to strive for greater completeness as well as fewer inconsistencies in the material curriculum. The commonality between the worldviews is highlighted in striving for a uniform approach. The intent of this paper is to provide other educators a foundation for their own DES simulation course development. A simple example is used to illustrate the worldviews within the roadmap.
Complement levels as predictors of survival in pancreatic adenocarcinoma.

315Background: Novel biomarkers to predict outcomes in pancreatic adenocarcinoma (PDA) are urgently needed. Complement activation, an important mediator of inflammatory processes, has been reported...
3D IC With Embedded Microfluidic Cooling: Technology, Thermal Performance, and Electrical Implications

In this paper, a novel thermal testbed with an embedded micropin-fin heat sink is designed and fabricated. The micropin-fin array has a nominal height of 200 μm and a diameter of 90 μm. Single phase and two phase thermal testing of the micropin-fin array heat sink are performed using deionized (D.I.) water as the coolant below atmospheric pressure. The measured pressure drop is as high as 100 kPa with a mass flux of 1637 kg/m2s at a heat flux of 400 W/cm2 in a two-phase regime. The heat transfer coefficient and the vapor quality are calculated and reported. The impact of microfluidic cooling on the electrical performance of the 3D interconnects is also analyzed. The high aspect ratio through silicon vias (TSVs) used in the electrical analysis have a nominal diameter of 10 μm.© 2015 ASME
Evaluation of an Algorithm To Identify Women with Carcinoma of the Breast

Although claims data are increasingly being used to measure and manage the cost and quality of health care, few studies have evaluated algorithms developed for such analyses. Therefore, the present study was performed to evaluate prospectively a previously published algorithm used to identify women with the new diagnosis of carcinoma of the breast. This algorithm had been developed from the patterns of claims that suggested common clinical presentations of carcinoma of the breast. In the present study, this algorithm was used to identify 177 potential cases of women with newly diagnosed carcinoma of the breast from the claims database of a large health maintenance organization (HMO). The algorithm's positive predictive value for cases identified in the present study was 83% (147/177). To attempt to improve upon the positive predictive value, multiple modifications of the algorithm were performed. The previously defined best modification of the initial algorithm yielded a positive predictive value of 84% (147/174) in the present study with the loss of none of the true positive cases. These results demonstrate that logic-based algorithms can be used as a valid and efficient method of identifying large numbers of new breast cancer cases from claims data. This algorithm provides a powerful tool to perform health care analysis and research for women with newly diagnosed carcinoma of the breast.
Fungal, plant and animal retrotransposon elements

Publisher Summary This chapter discusses the structural chemistry and the biological aspects of fungal, plant and animal retrotransposon. Retrotransposons infest the genomes of all eukaryotes, in which they have replicated for eons using retrotransposon-encoded reverse transcriptases to make new copies of themselves. These elements easily make up the majority by weight of most plant genomes and even the human genome is ∼35% retrotransposon sequence by weight. However, the major types of retrotransposons found in plants and animals differ in a very significant way. Whereas, the major human retrotransposon, LI (or LINE-1), does not encode any recognizable protease and the typical plant (and fungal) transposon encodes an aspartyl protease, PR. These two classes of retrotransposons differ in several other important aspects; most notably, the protease-containing class contains LTRs and generally resembles, in both structure and replication mechanism, the retroviruses, which encode aspartyl proteases of family A2. The life cycle of the yeast LTR retrotransposon Tyl, which can be extrapolated in outline to most LTR retrotransposons, is summarized in the chapter.
The use of improvisational theater training to reduce social anxiety in adolescents

Abstract Adolescents who have Social Anxiety Disorder do not receive the support they need. Improvisational theater involves regular exposure to social performance situations, and is recognized as a potential psycho-social support to enhance well-being and symptom reduction. The current study examines whether participating in a school-based improvisational theater program predicts reductions in symptoms of social anxiety. A total of 268 middle and high school students who participated in a ten-week school-based improvisational theater program completed surveys in a single group pre/post design. Adolescents who screened positive for social phobia at the beginning of class reported reduced symptoms of social anxiety at post-test. This change predicts increases in social skills, hope, creative self-efficacy, comfort performing for others, and willingness to make mistakes, along with marginal decreases in symptoms of depression. Given that no prior study has examined school-based improvisational theater training and its relationship to social anxiety, this work offers an important early contribution to the empirical literature on improvisation and mental health. School-based improvisational theater training offers an accessible, non-clinical alternative for addressing social anxiety problems among adolescents.
Hilar Biliary Strictures

Hilar biliary strictures present a unique challenge to endoscopists because of the difficulty in securing a diagnosis for the stricture and providing adequate therapeutic drainage. Hilar strictures can be secondary to underlying liver disease, such as primary sclerosing cholangitis (PSC), or postsurgical complications. However, the majority of hilar strictures are concerning for underlying malignancy such as cholangiocarcinoma. The challenge in diagnosing cholangiocarcinoma lies in part due to its desmoplastic character and tropism for bile such that it extends along the duct rather than grow intraluminally. Endoscopic retrograde cholangiopancreatography (ERCP) plays a critical role in the diagnosis of hilar strictures through the use of cytology brushings, biopsy forceps, and cholangioscopy and may require several procedures to secure a diagnosis. Therapeutic management of these strictures is also complex since endoscopists have to decide between unilateral versus bilateral biliary drainage, plastic or self-expandable metal stent (SEMS) placement, and, if bilateral SEMS is pursued, the ideal configuration for the SEMS. The goal of this chapter is to help present current data and our own personal approach to the diagnosis and therapeutic management of hilar strictures.
A framework for classroom assessment, learning, and self-regulation

We present a conceptual framework that leverages synergies between classroom assessment (CA) practices and self-regulated learning (SRL) theory to support academic growth and instruction. We articu...
Relation of Magnetic Resonance Elastography to Fontan Failure and Portal Hypertension.

Fontan associated liver disease is associated with morbidity and mortality in palliated single-ventricle congenital heart disease patients. Magnetic resonance elastography (MRE) provides a quantitative assessment of liver stiffness in Fontan patients. We hypothesized that MRE liver stiffness correlates with liver enzymes, hemodynamics, portal hypertension, and Fontan failure (FF). All adult Fontan patients who had MRE between 2011 and 2018 were included. Radiologic portal hypertension was defined as splenomegaly, ascites, and/or varices. FF was defined as death, transplantation, or heart failure symptoms requiring escalation of diuretics. Seventy patients with a median age of 24.7 years and a median follow-up from MRE of 3.9 years were included. The median liver stiffness was 4.3 kPa (interquartile range [IQR]: 3.8 to 5.0 kPa). There was a weak, positive correlation between liver stiffness and Fontan pathway pressure (r = 0.34, p = 0.03). There was a moderate negative correlation of liver stiffness with ventricular ejection fraction (r = −0.52, p = 0.03). Liver stiffness was weakly positively correlated with liver transaminases and gamma glutamyl transferase. Patients with portal hypertension had higher liver stiffness compared to patients without (5.2 ± 1.3 vs 4.2 ± 0.8 kPa, p = 0.03). At MRE or during follow-up, 13 patients (19%) met definition of FF and had significantly higher liver stiffness compared to patients without FF (5.1 [IQR: 4.3 to 6.3] vs 4.2 [IQR: 3.7 to 4.7] kPa, p = 0.01). Liver stiffness above 4.5 kPa differentiated FF with a sensitivity of 77% and specificity of 77%. In conclusion, elevated MRE-derived liver stiffness is associated with worse hemodynamics, liver enzymes and clinical outcomes in Fontan patients. This measure may serve as a global imaging biomarker of Fontan health.
The STEM Gender Gap: An Evaluation of the Efficacy of Women in Engineering Camps: This article is about outreach programs and summer engagement opportunities designed to expose high school women to engineering. Malle Schilling and Dr. Margaret Pinnellâ€™s findings on the impact of these programs is found in their article, â€œThe STEM Gender Gap: An Evaluation of the Efficacy of Women in Engineering Camps.â€

In the present day, it is not uncommon for there to be a class full of engineering students with very few women among them. To combat this lack of gender diversity, colleges and universities have employed outreach programs and developed summer engagement opportunities that allow women to explore engineering before they graduate high school. The present research conducted at a university evaluates the effects of a single-sex camp and a co-ed residential engineering camp on female participantsâ€™ interest in and self-efficacy related to engineering. Surveys were used to collect quantitative and qualitative data, and observation provided additional context. Data was collected at a total of four engineering camps during the summers of 2017 and 2018. Analysis of the survey responses indicated that these engineering camps have a significant impact on female participantsâ€™ self-efficacy in engineering, indicating the importance of scheduling camp activities that engage participantsâ€™ creativity while building their confidence in engineering. Furthermore, the way engineering camp activities are presented may affect participantsâ€™ perceptions of their own abilities in engineering. These findings add to the existing body of research exploring engineering self-efficacy and the participation of women in engineering, in addition to the effects of K-12 engineering outreach and camp programming.
Autobidding with Constraints

Autobidding is becoming increasingly important in the domain of online advertising, and has become a critical tool used by many advertisers for optimizing their ad campaigns. We formulate fundamental questions around the problem of bidding for performance under very general affine cost constraints. We design optimal single-agent bidding strategies for the general bidding problem, in multi-slot truthful auctions. The novel contribution is to show a strong connection between bidding and auction design, in that the bidding formula is optimal if and only if the underlying auction is truthful.
Exercise Training Induced Changes In Nuclear Magnetic Resonance-Measured Lipid Particles In Mild Cognitively Impaired Elderly African American Volunteers: A Pilot Study

Purpose Poor cardiorespiratory fitness (CRF) is linked to cognitive deterioration, but its effects on lipid heterogeneity and functional properties in older African American (AA) subjects with mild cognitive impairment (MCI) need elucidation. This study determined whether exercise training-induced changes in blood lipid particle sizes (LPS) were associated with CRF determined by VO2Max in elderly AAs with MCI. Given the pivotal role of brain-derived neurotrophic factor (BDNF) on glucose metabolism, and therefore, "diabetic dyslipidemia", we also determined whether changes in LPS were associated with the levels of serum BDNF. Methods This analysis included 17 of the 29 randomized elderly AAs with MCI who had NMR data at baseline and after a 6-month training. We used Generalized Linear Regression (GLM) models to examine cardiorespiratory fitness (VO2Max) effects on training-induced change in LPS in the stretch and aerobic groups. Additionally, we determined whether the level of BDNF influenced change in LPS. Results Collectively, mean VO2Max (23.81±6.17) did not differ significantly between aerobic and stretch groups (difference=3.17±3.56, P=0.495). Training-related changes in very low-density lipoprotein, chylomicrons, and total low-density lipoprotein (LDL) particle sizes correlated significantly with VO2Max, but not after adjustment for age and gender. However, increased VO2Max significantly associated with reduced total LDL particle size after similar adjustments (P = 0.046). While stretch exercise associated with increased protective large high-density lipoprotein particle size, the overall effect was not sustained following adjustments for gender and age. However, changes in serum BDNF were associated with changes in triglyceride and cholesterol transport particle sizes (P < 0.051). Conclusion Promotion of stretch and aerobic exercise to increase CRF in elderly AA volunteers with MCI may also promote beneficial changes in lipoprotein particle profile. Because high BDNF concentration may reduce CVD risk, training-related improvements in BDNF levels are likely advantageous. Large randomized studies are needed to confirm our observations and to further elucidate the role for exercise therapy in reducing CVD risk in elderly AAs with MCI.
Engaging Students in Global Citizen Science: A U.S.-Japan collaborative watershed project

Innovative education approaches include citizen science projects that allow students to participate in locally relevant scientific work, connecting content to the real world. Global collaboration p...
PRIMARY ADRENAL INSUFFICIENCY SECONDARY TO CHRONIC POSACONAZOLE USE.

ABSTRACT Objective: Posaconazole (PSO) is commonly used in the treatment of invasive fungal infections. PSO-induced primary adrenal insufficiency (PAI) is rare, and we present what we think to be t...
Valuation of uncertain and delayed rewards in primate prefrontal cortex

Humans and animals often must choose between rewards that differ in their qualities, magnitudes, immediacy, and likelihood, and must estimate these multiple reward parameters from their experience. However, the neural basis for such complex decision making is not well understood. To understand the role of the primate prefrontal cortex in determining the subjective value of delayed or uncertain reward, we examined the activity of individual prefrontal neurons during an inter-temporal choice task and a computer-simulated competitive game. Consistent with the findings from previous studies in humans and other animals, the monkey's behaviors during inter-temporal choice were well accounted for by a hyperbolic discount function. In addition, the activity of many neurons in the lateral prefrontal cortex reflected the signals related to the magnitude and delay of the reward expected from a particular action, and often encoded the difference in temporally discounted values that predicted the animal's choice. During a computerized matching pennies game, the animals approximated the optimal strategy, known as Nash equilibrium, using a reinforcement learning algorithm. We also found that many neurons in the lateral prefrontal cortex conveyed the signals related to the animal's previous choices and their outcomes, suggesting that this cortical area might play an important role in forming associations between actions and their outcomes. These results show that the primate lateral prefrontal cortex plays a central role in estimating the values of alternative actions based on multiple sources of information.
Gender and Selection During the Holocaust: Transports of Western European Jews to the East

This paper examines the impact of gender on decisions that military, police, and bureaucrats made in selection of western European Jews for deportation venues, on initial treatment at Auschwitz and...
Polysubstance Involvement in Opioid Overdose Deaths in Adolescents and Young Adults, 1999-2018

This cross-sectional study examines US trends in polysubstance-involved opioid overdose deaths among adolescents and young adults aged 13 to 25 years.
Evolution of a melanoma in situ to a sarcomatoid dedifferentiated melanoma.

Sarcomatoid dedifferentiated melanoma (SDDM) is a recently recognized subtype of melanoma that stains diffusely for CD10 and lacks the expression of the usual melanocytic markers including S100, SOX10, MITF, and Melan A. Advances in next-generation DNA sequencing technology have facilitated the increased recognition of this rare, aggressive spindle cell melanoma. Herein, a case of relatively early lesion of SDDM arising in association with melanoma in situ is highlighted. A 72-year-old man with a history of previously treated melanoma in situ on the face five years prior presented with a new rapidly growing lesion within the scar of the treated site. A shave biopsy of the lesion revealed a centrally located 1.8-mm deep, poorly differentiated spindle cell neoplasm in association with an adjacent recurrent melanoma in situ. The spindle cell component stained diffusely for CD10, but failed to stain for S100, SOX10, and Melan-A while the melanoma in situ expressed all three melanocytic markers. Next-generation DNA sequencing assay revealed mutations in NF1, CDKN2A, TP53, and TSC1. A diagnosis of stage 2B SDDM arising in association with melanoma in situ was established based on the clinical context and genomic assay results.
Host versus cell-dependent effects of β-arrestin 1 expression in prostate tumorigenesis

Prostate cancer constitutes a serious health challenge and remains one of the main causes of cancer-related death among men. The more aggressive form of the disease has been attributed to androgen independence; resulting in lack of response to androgen deprivation therapy and sustained activation of other growth pathways. The scaffold proteins β-arrestin 1 and 2 (βarr1 and βarr2) which are known to mediate G protein-coupled receptor desensitization and internalization, were also shown to modulate prostate tumorigenesis. βarr1 is significantly overexpressed (>4 fold) in prostate cancer cells relative to βarr2. In this study, we investigated the effect of βarr1 overexpression in prostate cancer development and progression using the mouse and human PCa cell xenografts, and autochthonous transgenic adenocarcinoma mouse prostate (TRAMP) models deficient in β-arrestins Depletion of βarr1 in TRAMP mice (TRAMP/βarr1 -/-) increased PCa growth and decreased overall survival relative to control TRAMP or TRAMP/βarr2 -/- animals. Prostate tissues from TRAMP/βarr1 -/- tumors displayed an increase in androgen receptor expression whereas overexpression of βarr1 in TRAMP-C1 (TRAMP-C1-βarr1-GFP) which derived from TRAMP decreased AR expression, cell proliferation and tumor growth in nude mice xenografts, relative to control TRAMP-C1-GFP. Knockdown of βarr1 expression in human MDA PCa 2b cells (MDA PCa 2b-βarr1 -/-) also decreased AR expression cell proliferation and tumor growth relative to control (MDA PCa 2b-Sham) cells. Interestingly, both TRAMP-C1-βarr1-GFP and MDA PCa 2b-βarr1 -/- xenografts showed a decrease in AKT phosphorylation, but an increase MAPK activation. Altogether, the data indicate that the effect of βarr1 in modulating AR signaling to regulate prostate cancer aggressiveness is cell and host autonomous.
Enhanced Recovery After Surgery Nutrition Protocol for Major Head and Neck Cancer Surgery.

Objective To determine whether an enhanced recovery after surgery (ERAS) nutrition protocol is reasonably possible among our head and neck cancer (HNC) population with respect to system feasibility and patient compliance. Second, we aim to identify improvements in patient outcomes as a result. Methods Preexperimental research design among patients undergoing major HNC surgery after implementation of the ERAS nutrition protocol from July 2018 to July 2019 as quality improvement (QI). Preoperative clinical nutritional assessment and laboratory values were completed the same day as informed surgical consent in the clinic. Protocol focus was patient consumption of nutritional supplements perioperatively, monitored by our outpatient dietitian. Early postoperative enteral nutrition was initiated with monitoring of nutritional laboratory values. To support our model, we provide preliminary analysis of HNC patient outcomes after implementation of the ERAS nutritional protocol. Results Twenty-five patients were enrolled. Preoperatively, 40% of patients were malnourished, and 100% complied with perioperative nutrition supplementation. Health care provider compliance obtaining preoperative laboratory values was 56%. There was a strong negative correlation between modified Nutrition-Related Index (mNRI) and number of complications (P = .01), specifically, fistula rate (P = .04) and unplanned reoperation (P = .04). Enrolled patient average length of stay was 7 ± 4.4 days. Discussion Our patients demonstrated compliance with implementation of an ERAS nutrition protocol likely facilitated by dietitian engagement. mNRI potentially reflects risk for head and neck surgery complications. Implications for practice QI processes demand reassessment and modification to ensure efficient and targeted approaches to improving patient care.
Evidence-Based Pragmatic Approach to the Management of Borderline or High-Risk Breast Lesions.

The management of borderline or high-risk breast lesions (HRLs) remains controversial. We propose a pragmatic evidence-based approach based on lesion type. For lobular carcinoma in situ with pleomo...
Epstein Barr Virus: Development of Vaccines and Immune Cell Therapy for EBV-Associated Diseases

Epstein-Barr virus (EBV) is the first human tumor virus discovered and is strongly implicated in the etiology of multiple lymphoid and epithelial cancers. Each year EBV associated cancers account for over 200,000 new cases of cancer and cause 150,000 deaths world-wide. EBV is also the primary cause of infectious mononucleosis, and up to 70% of adolescents and young adults in developed countries suffer from infectious mononucleosis. In addition, EBV has been shown to play a critical role in the pathogenesis of multiple sclerosis. An EBV prophylactic vaccine that induces neutralizing antibodies holds great promise for prevention of EBV associated diseases. EBV envelope proteins including gH/gL, gB and gp350 play key roles in EBV entry and infection of target cells, and neutralizing antibodies elicited by each of these proteins have shown to prevent EBV infection of target cells and markedly decrease EBV titers in the peripheral blood of humanized mice challenged with lethal dose EBV. Recent studies demonstrated that immunization with the combination of gH/gL, gB and/or gp350 induced markedly increased synergistic EBV neutralizing activity compared to immunization with individual proteins. As previous clinical trials focused on gp350 alone were partially successful, the inclusion of gH/gL and gB in a vaccine formulation with gp350 represents a promising approach of EBV prophylactic vaccine development. Therapeutic EBV vaccines have also been tested clinically with encouraging results. Immunization with various vaccine platforms expressing the EBV latent proteins EBNA1, LMP1, and/or LMP2 promoted specific CD4+ and CD8+ cytotoxic responses with anti-tumor activity. The addition of EBV envelope proteins gH/gL, gB and gp350 has the potential to increase the efficacy of a therapeutic EBV vaccine. The immune system plays a critical role in the control of tumors, and immune cell therapy has emerged as a promising treatment of cancers. Adoptive T-cell therapy has been successfully used in the prevention and treatment of post-transplant lymphoproliferative disorder. Chimeric antigen receptor T cell therapy and T cell receptor engineered T cell therapy targeting EBV latent proteins LMP1, LMP2 and/or EBNA1 have been in development, with the goal to increase the specificity and efficacy of treatment of EBV associated cancers.
Modeling of tungsten filament in gas discharge in H- ion source.

Sources of negative ions such as H− are essential elements of proton accelerators and tokamaks. They have limited lifetime. The replacement of an ion source is a costly process causing delays in the operation of the entire machine. The hot tungsten filament is the key element that limits the lifetime of the H− ion source at the Los Alamos Neutron Science Center (LANSCE) facility. An accurate model, which describes the filament physics and provides a reliable estimate on its lifetime, may significantly improve the operation of the facility. Here, we describe such a model, including a comprehensive list of relevant physical processes from first principles. The model can be used to describe different regimes of operation using diagnostics data as input parameters. It has been benchmarked against the data collected during the production cycle at LANSCE and shows good agreement with experimental data.
Preparation of Metal Surfaces

The importance of a clean surface for investigations of the interaction of atom, molecule, and ion beams with surfaces is evident from the foregoing. The methods for preparation of surfaces with a minimum degree of physical, chemical, and induced heterogeneity (see Sections 1.1.1, 1.1.2, and 1.1.3) can be divided into those in which surface layers are removed (e.g., through thermal desorption, electrolysis, or ion bom bardment) and those in which metal films are deposited (as, for example, by an evaporation process or electroplating*).
Tort Reform as Carrot-and-Stick

The most persuasive of tort reforms are limits on damages that a plaintiff can recover in a medical malpractice lawsuit. More than half of states have passed some brand of liability limit under the guise of tort reform. Hospitals, physicians, and defense lawyers praise these reforms and regard them as a panacea, a good way to stanch increased medical costs from medical malpractice lawsuits and young physicians from high-risk medical practices. On the other side of the debate, trial lawyers and patient advocates argue that these so-called reforms are a scourge that creates a second harm to those who need compensation the most, the injured, and gives a protection to those who deserve it the least, the injurer. Is there a way out of this simple binary in which the players are either for tort reform or against it? Previous reform-minded commentators have failed to offer a solution that both creates better incentives to behave well and recognizes the political appeal of limits on damages. This Article breaks new ground in the tort reform debate by proposing to link the debate about tort reform explicitly to the debate about hospital and physician performance. Specifically, this Article proposes that states consider treating tort reforms as a carrot or incentive for positive behavior. That is, state legislatures bent on passing liability-restricting tort reforms should only use these measures to reward healthcare providers, like hospitals and physicians, who routinely follow best practices. For instance, as the Article will show, state legislatures might approve a liability limit only for hospitals that are compliant with the recommended best treatments. These top-performing hospitals, but only these hospitals, would be protected from the specter of virtually unlimited damages in the event of suit. In this way, hospitals will have new incentives to avoid medical error, police misconduct, and strictly adhere to best practices. To demonstrate application, the Article draws on a database of 21 quality measures of performance for four defined conditions, heart attack, heart failure, adult surgery, and pneumonia. The data is collected by most hospitals in the United States and maintained by the Centers for Medicare and Medicaid Services. The Article proposes tying eligibility for tort reform to healthcare performance based, initially, on these 21 measures.
Experimental characterization of volume-mode waves in near-field anisotropic metamaterials with application to wireless power transfer

In this work we characterize the magnetoquasistatic waves in an anisotropic, indefinite metamaterial used in wireless power applications. We show that the magnetic resonances in the metamaterial are volume mode waves and calculate the expected complex wave number, which represents the wavelength and attenuation, versus frequency from the complex permeability of the metamaterial. We then compare the calculated wavenumber to an experimentally extracted number. Our results show that the loss of the metamaterial increases with frequency due to the shortening of the wavelength even though the imaginary part of μ is lower at these frequencies.