cssi/SciSciGPT-SciSciNet huggingface dataset:
BlackOPs: increasing confidence in variant detection through mappability filtering

Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin (‘mismapping’) and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, for a given sample, are expected to be almost completely false positives. We show that these blacklist positions are specific to the alignment algorithm and read length used, and BlackOPs allows users to generate a blacklist specific to their experimental setup. We queried the dbSNP and COSMIC variant databases and found numerous variants indistinguishable from mapping errors. We demonstrate how filtering against blacklist positions reduces the number of potential false variants using an RNA-seq glioblastoma cell line data set. In summary, accounting for mapping-caused variants tuned to experimental setups reduces false positives and, therefore, improves genome characterization by high-throughput sequencing.
Characteristics and Sources of Phase Noise in Stable Oscillators

The frequency stability of an oscillator is a very important characteristic for many applications. Yet the causes and sources of some basic types of noise are poorly understood, particularly for close-to-carrier noise. A review is presented in this paper of the present state of knowledge about the sources and characteristics of frequency fluctuations in stable oscillators using quartz acoustic resonators (BAW and SAW) or dielectric resonators as the high Q frequency stabilizing element. A brief discussion of the various parameters used to quantify random frequency fluctuations is presented along with the relative merits of open- and closed-loop phase noise measurements. Phase noise in stable oscillators usually arises from additive voltage fluctuations and direct parameter modulation processes. Additive
KSHV regulation of fibulins in Kaposi's sarcoma: implications for tumorigenesis

Kaposi’s sarcoma (KS) is an angioproliferative tumor of vascular endothelial cells and produces rare B cell lymphoproliferative diseases in the form of primary effusion lymphomas (PELs) and some forms of Multicentric Castleman’s Disease (MCD). Kaposi’s sarcoma-associated herpesvirus, also known as KSHV or human herpesvirus type 8 (HHV8), is the etiological agent of KS. Fibulins are extra-cellular matrix (ECM) proteins involved in cell adhesion, proliferation, migration, invasion, and angiogenesis, and have been linked to progression of several cancer types. However, to our knowledge, they have not been studied in KS. We examined fibulin-2 because we found it to be significantly downregulated by microarray analysis in KSHV-infected DMVEC cells. Here we demonstrate that fibulin-2 protein expression is downregulated 50-fold in 10 day KSHV-infected dermal microvascular endothelial cells (DMVEC) with a 26-fold reduction in fibulin-2 message. By time-course transcriptional analysis there was consistent reduction of fibulin-2 message accompanied by an increase in KSHV latency associated nuclear antigen (LANA) transcription. Of the fibulins assayed, fibulins -2, -5, and -3 were downregulated over time in KSHV infected DMVEC, while fibulins 1C and 1D were upregulated, with no change in fibulins 4, 6, and 7. In pleural effusion lymphoma cell lines that express different levels of KSHV lytic replication, we observed no detectable fibulin-2 expression. Tissue microarrays representing patch/plaque and nodular forms of KS from 86 different patients were shown to be statistically significant for downregulation of fibulin-2 in virus-infected LANA positive cells by dual labeled immunohistochemical staining. This represents the first study that examines fibulin-2 expression in KSHV-infected DMVEC and KS to determine whether suppression of this ECM protein plays a role in KS tumor progression. Understanding the interactions between KSHV and the fibulin family of extra-cellular matrix proteins that modulate angiogenesis cancer cell proliferation, migration and invasion could lead to development of novel therapies for treatment of KS.
Neurovascular and Neurometabolic Couplings in Dynamic Calibrated fMRI: Transient Oxidative Neuroenergetics for Block-Design and Event-Related Paradigms.

Functional magnetic resonance imaging (fMRI) with blood-oxygenation level dependent (BOLD) contrast is an important tool for mapping brain activity. Interest in quantitative fMRI has renewed awareness in importance of oxidative neuroenergetics, as reflected by cerebral metabolic rate of oxygen consumption (CMRO2), for supporting brain function. Relationships between BOLD signal and the underlying neurophysiological parameters have been elucidated to allow determination of dynamic changes in CMRO2 by “calibrated fMRI”, which require multi-modal measurements of BOLD signal along with cerebral blood flow (CBF) and volume (CBV). But how do CMRO2 changes, steady-state or transient, derived from calibrated fMRI compare with neural activity recordings of local field potential (LFP) and/or multi-unit activity (MUA)? Here we discuss recent findings primarily from animal studies which allow high magnetic fields studies for superior BOLD sensitivity as well as multi-modal CBV and CBF measurements in conjunction with LFP and MUA recordings from activated sites. A key observation is that while relationships between neural activity and sensory stimulus features range from linear to non-linear, associations between hyperemic components (BOLD, CBF, CBV) and neural activity (LFP, MUA) are almost always linear. More importantly, the results demonstrate good agreement between the changes in CMRO2 and independent measures of LFP or MUA. The tight neurovascular and neurometabolic couplings, observed from steady-state conditions to events separated by <200 ms, suggest rapid oxygen equilibration between blood and tissue pools and thus calibrated fMRI at high magnetic fields can provide high spatiotemporal mapping of CMRO2 changes.
A comparison of semi-active control strategies for the MR damper

Because the behavior of semi-active devices is often highly nonlinear, one of the main challenges in the application of this technology is the development of appropriate control algorithms. In this paper, a number of recently proposed semi-active control algorithms are evaluated for use with the magnetorheological (MR) damper, an innovative semi-active control device that appears to be particularly promising for civil engineering applications. The performance of the resulting control systems are compared through simulation, and the advantages of each algorithm are discussed. The results demonstrate that the performance of the control system is highly dependent on the choice of algorithm employed.
Cooperative Control of Vehicle Swarms for Acoustic Target Localization by Energy Flows

A control algorithm has been developed and experimentally validated for guiding swarms of robotic vehicles to acoustic targets. This novel algorithm uses pressure measurements from a set of sensors, each attached to a vehicle of the swarm, to deduce energy flows from the environment, and to move in the direction of maximum reflected intensity while controlling constraints between vehicles. The algorithm was validated using a collective of eight hand-placed microphones in an open-space area with a 50-m separation between an emitter and scatterer.
Epidemiology and Public Health Policy of Tobacco Use and Cardiovascular Disorders in Low- and Middle-Income Countries

All forms of tobacco lead to an increased risk of cardiovascular disorders. During the past few decades, the number of people who consume tobacco has increased worldwide because of an overall increase in the global population. It is estimated that close to 80% of the >1.3 billion people who smoke tobacco in the world are in low- and middle-income countries. Smokeless forms of tobacco are also widely consumed in low- and middle-income countries, including chewable and snuffed forms. Lack of targeted and effective strategies to control tobacco consumption contributes to a large burden of cardiovascular disorders in low- and middle-income countries, where cardiovascular disorders have become the leading cause of morbidity and mortality. In this review, we evaluate the epidemiology of tobacco use in low- and middle-income countries and assess the public health policies needed to control tobacco use in such regions for the prevention of cardiovascular disorders and other tobacco-related morbidities and mortality.
A Variance for k‐Free Numbers in Arithmetic Progressions

The second moment for the the distribution of $k$-free numbers into arithmetic progression is studied and the asymptotic formula of Hooley-Montgomery type is obtained for a wider range of values for the modulus than hitherto. In the special case of squarefree numbers this improves on the theorem of Warlimont from 1980.
Spontaneous Septic Arthritis Complicating Rheumatoid Arthritis

Thirteen cases (in twelve patients) of septic arthritis complicating rheumatoid arthritis are reported. One ankle, one metacarpophalangeal joint, one shoulder, and ten knees were involved. Staphylococcus aureus was cultured from twelve joints and Escherichia coli , from one. Treatment consisted of repeated needle aspirations in two patients, arthrotomy with Penrose drainage in six, and arthrotomy with through-and-through irrigation in four. Needle aspiration was the least effective therapy. The authors recommend as the treatment of choice: systemic antibiotic therapy and immediate arthrotomy followed by through-and-through irrigation with fluid containing the appropriate antibiotics.
A comparison of thermocouples and temperature paints to monitor spatial and temporal characteristics of landscape-scale prescribed fires

A method to better monitor landscape-level fire characteristics is presented. Three study areas in southern Ohio oak-hickory (Quercus-Carya) forests were established with four treatment areas of ~20 ha each: control (C), burn only (B), thin only (T) or thin plus burn (TB). Two independent measures useful for qualitatively characterising fire intensity were established on a 50-m grid, resulting in over 120 sampling locations at each site, in the burned areas: aluminum tags painted with temperature-sensitive paints, and logger-probe units that logged probe temperature every 2 s during burns. Fires were conducted in spring 2001. The logger-probe units allowed five measures qualitatively related to fire intensity or timing to be calculated at each grid point: maximum probe temperature; duration of probe temperature above 30°C; a heat index, defined as the summed temperatures above 30°C; time of maximum temperature; and estimated rate of spread. Maximum temperatures recorded by the two measuring systems were highly correlated (r2 = 0.83). Relative to painted tags, logger-probe units provide information useful for assessing some other components of fire behaviour. The temporal recording of temperatures allowed us to prepare a web-based simulation of the fires. Heat index and rate of spread estimates provided additional fire information. The TB units consistently burned cooler than the B units, perhaps because of uncured slash and a disrupted fuel bed in those units.
Central Arctic: Battleground of natural and man‐made climate forcing

Alarming observations have been reported on recent climate changes in the Arctic. Sea ice is thinning and shrinking, and its area was the lowest since 1979 when systematic microwave satellite observations began. Will the summertime ice completely disappear due to man-made greenhouse gases as predicted by climate models? Twenty-three experts from the United States and abroad gathered in January to address this question. Additional scientists participated in the discussion sessions or contributed by mail.
The myth of goiter in pregnancy

A common belief is that pregnancy causes goiter. Forty-nine matched pairs each consisting of a pregnant and a nonpregnant woman were examined by means of a blind, multiple-observer design. In 22 pairs the pregnant woman had the larger thyroid, whereas in 20 pairs the opposite was true. In six pairs the thyroid glands were not palpable, and in one pair the thyroid glands were of equal size. Five pregnant and three nonpregnant women had clinically significant goiters. None of the differences was statistically significant. No significance appeared when the data were controlled for race, age, body weight, or family history of thyroid disease. Therefore, goiter in pregnancy should be considered to be a pathologic condition in an iodine-replete population. (Am. J. Obstet. Gynecol. 137:701, 1980.)
Efficient, End-Pumped, 1053-nm Nd:YLF Laser

A fiber-coupled, 100-W QCW diode laser arrays were used to efficiently end-pump a Nd:YLF laser operated at 1053 nm. A single-pass, small-signal gain of 4.2 was demonstrated. Output TEM00 energies of 20 mJ in the free-running mode and 13.6 mJ in the Q-switching mode at 1053 nm were measured.
Interactions between multiple rhythm generators produce complex patterns of oscillation in the developing rat spinal cord.

Neural networks capable of generating coordinated rhythmic activity form at early stages of development in the spinal cord. In this study, voltage-imaging techniques were used to examine the spatio...
Electrical/thermal co-design and co-simulation, from chip, package, board to system

It has been well known for years that as the critical feature size within a chip keeps shrinking, design and optimization among power, heat and performance would become even challenging. On one hand, the electrical functionalities of the devices are closely coupled with temperature and power distributions. On the other hand, the devices within the chip are not totally isolated and confined — the connection and interaction with the environments such as the package, board, and enclosure cannot be ignored especially from the heat transport perspective. Simulation tools in electronic design automation have to satisfy the requirement of electrical/thermal co-simulation for advanced electronic systems having a wide range of critical sizes, and provide efficient approaches with accurate data for design optimization. This is the main purpose of this paper, and we introduce a portfolio of tools to facilitate electrical/thermal co-simulation from chip, package, board to system.
Diversity and Status of Bryophytes in Panch Pokhari Region of the Northern Sindhupalchok District of Central Nepal

This is the first exploration of bryophytes in Panch Pokhari of Sindhupalchok district of central Nepal vertically ranged from 850 to 4300 m asl. Of the total record of 151 species, 60 species were categorized as rare in status and two species Jamesoniella automnalis (D.C.) Steph. and Campylopus rechardii Brid were recorded as threatened species. J. Nat. Hist. Mus. Vol. 27, 2013: 45-58
Dental Impacts on Health-related Quality of Life of Children with Orofacial Clefts.

PURPOSE Children with orofacial clefts experience risks for psychosocial and behavioral problems, making it important to evaluate for negative impacts on health-related quality of life. The purpose of this study was to evaluate health-related quality of life (HRQOL) and surgical history to determine if these measures correlated with caries and/or behavior during dental treatment. METHODS Data for this retrospective study were obtained for children encountered between March 2011 and August 2013. Inclusion criteria were four- to 10-year-olds with a non-syndromic orofacial cleft diagnosis. Parent-reported HRQOL data were obtained for 79 children and child-reported data for a subgroup of 23. Pediatric Quality Of Life Inventory (PedsQL) scores, surgeries, and demographics were collected from craniofacial team medical charts. Decayed, missing, and filled teeth (dmft) and behavior (Frankl) scores were collected from dental records. RESULTS Significant correlations were found between total parent-reported sample PedsQL scores and dmft scores, and between the subgroup's PedsQL scores and Frankl scores. CONCLUSIONS For children with orofacial clefts, higher caries was associated with lower health-related quality of life in the total parent-reported sample. Negative behavior was associated with lower HRQOL in eight- to 10-year-olds, who also more accurately reported psychosocial risks for negative behavior than parents by proxy. Surgeries were not associated with caries or behavior.
Ideological and Historical Background

The Soviet Union proclaims itself a socialist society and professes Marxism as its official ideology. Unfortunately, this does not tell us much about the kind of economic system the Russians have constructed or the kind of economic policy choices Soviet leaders have made. Marx’s analysis was mainly concerned with the future development of nineteenth-century industrial capitalist countries — not with the task of propelling a peasant society into the twentieth century. It is true that the Soviet leaders take great pains to interpret and justify their acts by appeal to Marx but, as I hope to demonstrate further on, this is mostly rationalization after the fact. The vague Marxist goal of achieving communism is something they can make ritual obeisance to, but their motivations and preoccupations grow out of more immediate problems. Thus, it is useful to reject the Marxian label as a point of departure and to formulate a new definition. The definition I propose is that the Soviet economy is totalitarianism harnessed to the task of rapid industrialization and economic growth.
2008: The Adam Smith Address Adam Smith and the Political Economy of Modern Financial Crisis

The United States is now in the midst of a major financial crisis that has spread to affect credit and equity markets and financial institutions all around the world. Many have characterized the present crisis as the worst since the Great Depression—a description that is becoming more apt with each passing day. Whatever the ultimate scale of the present crisis, it is not the only important financial crisis to beset the United States in the past 50 years; by my count there have been at least seven: 1971, 1974–1975, 1980–1982, 1987, 1991, 2000–2002, and 2007-?. Looking further back through the 19th and 20th centuries, the average frequency of crises has been roughly constant at about one per decade. Most other countries, both economically advanced and developing, also have histories of not infrequent financial crises.1
Treatment of multiple myeloma with monoclonal antibodies and the dilemma of false positive M-spikes in peripheral blood.

Objectives To characterize the effect of three humanized IgG κ monoclonal antibodies (daratumumab, isatuximab, and elotuzumab) on the interpretation of results generated by protein electrophoresis, immunofixation, free light chain, and heavy/light chain assays performed on human serum. Methods Healthy volunteer serum and serum from multiple myeloma patients were supplemented with clinically relevant concentrations of each of the three monoclonal antibodies. These specimens then underwent analysis via serum protein electrophoresis, immunofixation, serum free light chain quantification, heavy/light chain quantification, total IgG, and total protein. In addition, serum specimens from patients who had undergone treatment with elotuzumab for multiple myeloma underwent similar analysis. Results Addition of the study drugs to serum from both the healthy donor as well as multiple myeloma patients resulted in a visible and quantifiable M-protein on SPEP and a visible IgGκ band by IFE. Increases were also noted in total IgG, IgGκ, and IgGκ/IgGλ-ratios. Analysis of serum from multiple myeloma patients receiving study drug showed similar findings with an additional IgGκ band and quantifiable M-protein with similar migration patterns in specimens drawn after administration. Conclusion The treatment of multiple myeloma patients with monoclonal antibodies results in a visible and quantifiable M-protein that has the potential to falsely indicate poor response to therapy.
Positron Emission Tomography-Computed Tomography (PET-CT and PET) in Well-Differentiated Thyroid Cancer

The objective of this chapter is to present an overview of the following topics: PET physics and scanners, radiopharmaceutical for PET and indications, imaging technique, normal findings and variations, interpretation of PET-CT scans, false-positive findings, 18F-FDG PET-CT and PET scanning in differentiated thyroid cancer (DTC), role in thyroglobulin (Tg)-positive and iodine-negative patients, prognostic value of 18F-FDG PET scans, and the role of TSH in 18F-FDG PET scanning. The chapter concludes with a brief introduction to 124I PET scanning and other PET-CT radiopharmaceuticals.
The Role of Prevention in Deterring Teachers Bullied by Students

Few past studies discuss the subject of bullying by students with their teachers as targets. Examining preventative measures to gain a more thorough understanding of the complex, behavioral issue needs to be addressed. As a starting point the purpose of this study is to examine the scope of the problem as well as the various preventative initiatives with an added focus on clear rules, classroom management and consequences along with application while proposing that higher education be the educational sector that takes the leadership role in a community approach to diminish the problematic behavioral issue of teacher’s being bullied by students.
Immune Reconstitution After Cord Blood Transplantation in Adults Depends on Activity of Thymic Epithelial Cells and Vascular Endothelial Elements

Abstract Abstract 4075 Umbilical cord blood (UCB) grafts are increasingly used as sources of hematopoietic stem cells. UCBT in adults results in delayed and insufficient immune reconstitution leading to high infection-related morbidity and mortality. We recently determined that thymic regeneration as identified by T-cell receptor rearrangement excision circles (TREC) is a strong predictive factor for clearance of CMV viremia and for overall survival in adult UCBT recipients. We were able to detect TRECs by 100 days that was faster than in other adult UCBT studies reported previously, in which TRECs remained undetectable during the first year. A significant difference between our study and previous reports was the use of 2 UCB units in all our patients whereas only a single unit was used in the previous trials. Human UCB is enriched in endothelial precursors that sustain thymopoiesis in SCID mice transplanted with human thymic grafts where they engraft and promote neovascularization and wound healing. The loss of thymopoietic capacity after allogeneic stem cell transplantation results from injury of the thymic microenvironment, particularly of thymic epithelial cells (TEC). We hypothesized that thymic neovascularization induced by UCB-derived endothelial progenitors might be a critical factor promoting early recovery of TEC, which support T cell development and expansion via production of interelukin-7 (IL-7) and stem cell factor (SCF; a kit ligand). In the present study we examined whether thymic regeneration and immune reconstitution in adult recipients of double UCBT was associated with IL-7 and SCF levels and with activity of endothelial progenitors. Thirty-two patients with a median age of 50 years with hematopoietic malignancies were treated with reduced intensity conditioning (Flu/Mel/rATG) followed by infusion with two sequential UCB units. GvHD prophylaxis was with tacrolimus and sirolimus. Results are based on 27 evaluable patients. Assessments were done prior to and at 1, 2, 3, 6 and 12 months after UCBT. Serum levels of IL-7 displayed a 3-fold increase at 1 month after UCBT and gradually declined to the pre-transplant levels at 12 months. SCF peaked at 2 months after UCBT and gradually decreased to the pre-transplant levels by 12 months. Strikingly, IL-7 and SCF levels displayed a strong inverse correlation (p Disclosures: No relevant conflicts of interest to declare.
Photoactivated Structurally Tailored and Engineered Macromolecular (STEM) gels as precursors for materials with spatially differentiated mechanical properties

Abstract The concept of a Structurally Tailored and Engineered Macromolecular gel (STEM gel) is presented. A STEM gel is comprised of a network with latent initiating sites allowing for the post-synthesis, spatially specific modification of the matrix. A direct synthetic method was employed and photo-active STEM gels based on (meth)acrylates were synthesized by free radical copolymerization of different monomers, a crosslinker, and a photo-active dormant initiator/monomer (inimer) based on the radical photoinitiator 2-hydroxy-4′-(2-hydroxyethoxy)-2-methylpropiophenone (Irgacure 2959). Infiltration by a solution of a crosslinker was followed by the UV triggered polymerization of secondary polymeric chains. Irradiation through masks with different transmittance resulted in materials with spatially differentiated mechanical properties.
20 Years of Learning About Vision: Questions Answered, Questions Unanswered, and Questions Not Yet Asked

I have been asked to review the progress that computational neuroscience has made over the past 20 years in understanding how vision works. In reflecting on this question, I come to the conclusion that perhaps the most important advance we have made is in gaining a deeper appreciation of the magnitude of the problem before us. While there has been steady progress in our understanding—and I will review some highlights here—we are still confronted with profound mysteries about how visual systems work. These are not just mysteries about biology, but also about the general principles that enable vision in any system whether it be biological or machine. I devote much of this chapter to examining these open questions, as they are crucial in guiding and motivating current efforts. Finally, I shall argue that the biggest mysteries are likely to be ones we are not currently aware of, and that bearing this in mind is important as it encourages a more exploratory, as opposed to strictly hypothesis-driven, approach.
Vascular Erectile Dysfunction and Subclinical Cardiovascular Disease

We review the recent literature on the hypothesized temporal relationship between subclinical cardiovascular disease (CVD), vascular erectile dysfunction (ED), and clinical CVD. In addition, we combine emerging research with expert consensus guidelines such as The Princeton Consensus III to provide a preventive cardiologist’s perspective toward an ideal approach to evaluating and managing CVD and ED risk in patients. Development of ED was found to occur during the progression from subclinical CVD to clinical CVD. A strong association was observed between subclinical CVD as assessed by coronary artery calcium (CAC) and carotid plaque and subsequent ED, providing evidence for the role of subclinical CVD in predicting ED. ED is also identified as a substantial independent risk factor for overt clinical CVD, and ED symptoms may precede CVD symptoms by 2–3 years. Given the body of evidence on the relationship between subclinical CVD, ED, and clinical CVD, we recommend that all men with vascular ED should undergo cardiovascular risk assessment. We further recommend using CAC scores for advanced risk assessment in patients at low–intermediate to intermediate risk (5–20% CVD risk), with risk driving subsequent lifestyle and pharmacologic treatment decisions.
Improving the cardiac cath-lab interventional imaging eco-system.

Minimally invasive, transcatheter therapeutic interventions for structural heart disease have evolved over the past several decades as appealing alternatives to open-chest surgery. Smaller incisions, shorter hospital stays and quicker recovery are outcomes that are ubiquitous to all approved transcatheter procedures, in comparison to traditional surgery. X-ray fluoroscopy (XRF) is the most commonly used imaging modality to guide transcatheter procedures. XRF offers certain advantages. Interventionalists have close familiarity with XRF systems. These systems are also widely available in centers with cardiac catheterization laboratories. XRF can visualize high X-ray attenuating devices such as radio-opaque catheters and metallic stents. However, XRF has certain disadvantages. For example, soft tissues such as myocardium, and valves are visualized poorly. Chambers and vessels are only transiently visible when filled with boluses of iodinated contrast, which can be nephrotoxic in susceptible individuals. Conventional X-ray also images using the principle of “projection” imaging, making it difficult to judge three dimensional (3D) perspective. Finally, over-reliance on XRF as the sole imaging modality exposes the patient and in-room personnel to the harmful effects of ionizing radiation. Wholly magnetic resonance imaging (MRI) (1-4) and ultrasound guided (US) (5,6) cardiovascular interventions have been tested in animal models and clinical studies as ionizing radiation-free alternatives to XRF. However, wide adoption of these methods has been prevented in large part by the lack of visually conspicuous devices that still maintain high mechanical performance.
Genomic Resistance Patterns to Second-Generation Androgen Blockade in Paired Tumor Biopsies of Metastatic Castration-Resistant Prostate Cancer.

PurposePatients with castration-resistant prostate cancer (CRPC) receive second-generation androgen-deprivation therapy, but frequently experience relapse or do not respond. Understanding the genetic mechanisms of resistance will help to identify strategies and biomarkers that are essential for the next line of therapy.Patients and MethodsWe analyzed whole exomes of patient-matched pre- and post-treatment tumors from patients with CRPC. These patients had received the secondary androgen-deprivation therapy agent, abiraterone, which suppresses androgens to below castration levels, or enzalutamide, which competitively inhibits the key androgen signaling effector, androgen receptor.ResultsWe observed that abiraterone-resistant tumors harbored alterations in AR and MYC, whereas enzalutamide-resistant tumors gained alterations in cell-cycle pathway genes, such as mutation in cyclin-dependent kinase N2A (CDKN2A) or amplification of CDK6. Experimentally, overexpressing cell-cycle kinases promoted enzalutamide re...
Development of a method to study real-time engineering writing processes

Engineering writing and communication is increasingly required of engineering undergraduate and graduate students; yet this call is rarely met through research-based methods. This research posits that deep investigation of the cognitive processes within engineering writing requires a novel method for data time-dependent analysis. However, no such method exists. This paper details our decision-making processes as we examine the available methods to analyze screen-capture video data of real time writing in an authentic engineering writing context. We detail the process of selecting the most appropriate approach and then provide a proof of concept for this method though analysis of screen capture video data of authentic engineering writing spanning several weeks. Complex issues in engineering education require creative interpretations of what can be used as “data,” and similarly, creative and rigorous solutions for analysis. The results of this paper directly affect researchers doing real-time analysis of video data in all respects, and will also help other engineering education researchers to analyze non-traditional data.
Altered skeletal muscle mitochondrial phenotype in COPD: Disease vs. disuse

Chronic obstructive pulmonary disease (COPD) is associated with debilitating alterations in the function of skeletal muscle mitochondria. By comparing the mitochondrial phenotype of patients with C...
First-Principles Calculations of Stacking Fault Energies in Quinary High-Entropy Alloy Systems

High entropy alloys (HEAs) are composed of equal or nearly equal quantities of five or more metals that solidify into a single, or sometimes dual, solid solution phase. Due to improved properties in high-temperature and high-stress applications, HEAs have the potential to replace traditional alloy systems in future engineering applications, such as turbine blades and thermal spray coatings. In the present work, first-principle calculations based on density functional theory are used to calculate and rank the stacking fault energies of several quinary HEA systems in order to better understand the slip and deformation behavior of HEA systems. Special quasirandom structures are used to represent the single solid solution with a finite number of atoms and calculations are performed in the Vienna ab initio simulation package within the generalized gradient approximation as implemented by Perdew, Burke, and Ernzerhof. Stacking fault energy calculations are based on the difference between the ground state energy of the perfect HEA structure and the ground state energy of a faulted HEA structure. To validate the calculations, results are compared to experimental data, such as lattice parameter and formation energy, for well-studied HEA system.
Contribution of Adipose-Derived Factor D/Adipsin to Complement Alternative Pathway Activation: Lessons from Lipodystrophy

Factor D (FD) is an essential component of the complement alternative pathway (AP). It is an attractive pharmaceutical target because it is an AP-specific protease circulating in blood. Most components of the complement activation pathways are produced by the liver, but FD is highly expressed by adipose tissue. Two critical questions are: 1) to what degree does adipose tissue contribute to circulating FD levels and 2) what quantity of FD is sufficient to maintain a functional AP? To address these issues, we studied a novel mouse strain with complete lipodystrophy (LD), the fld mouse with partial LD, an FD-deficient mouse, and samples from lipodystrophic patients. FD was undetectable in the serum of LD mice, which also showed minimal AP function. Reconstitution with purified FD, serum mixing experiments, and studies of partial LD mice all demonstrated that a low level of serum FD is sufficient for normal AP activity in the mouse system. This conclusion was further supported by experiments in which wild-type adipose precursors were transplanted into LD mice. Our results indicate that almost all FD in mouse serum is derived from adipose tissue. In contrast, FD levels were reduced ∼50% in the sera of patients with congenital generalized LD. Our studies further demonstrate that a relatively small amount of serum FD is sufficient to facilitate significant time-dependent AP activity in humans and in mice. Furthermore, this observation highlights the potential importance of obtaining nearly complete inhibition of FD in treating alternative complement activation in various autoimmune and inflammatory human diseases.
Computationally Efficient and Flexible Magnetic-Field-Analysis-Based Scaling Strategy for Permanent-Magnet Machines

Electric machine performance (peak torque versus speed) and efficiency characteristics are frequently estimated using magnetic finite element analysis (FEA). In this paper, it is shown that the governing mathematical relationships that are solved in such an analysis allow for the implementation of straightforward scaling laws. Instead of rerunning the FEA code for a variety of electric machine lengths, diameters, excitation frequencies, and number of winding turns, only one FEA simulation or experimental characterization is required. The results from that single FEA or experimental result can then be incorporated into the scaling laws derived here to determine the performance and efficiency of permanent-magnet machines with a variety of lengths, diameters, excitation frequencies, and number of winding turns. The utility is a significant speedup in the computation of a variety of design choices as a result of not having to re-execute the FEA for each design iteration or option. Following a mathematical development, scaling-law-based performance/efficiency estimates and those from FEA are directly compared and shown to be exactly the same.
The genetics of murine leukemia viruses

The murine leukemia viruses are prototypical replication-competent retroviruses. These viruses were among the first known oncogenic agents in mammals and have been the subjects of intensive study for more than 3 decades (Gross 1970). We now have a detailed understanding of the life cycle of these viruses and of some of the genetic effects they can have on the host cell; we are even beginning to discover how these viruses cause leukemia. Today, these viruses remain popular systems for the study of gene transfer and expression, site-specific recombination in mammalian cells, mutagenesis, and the processes of induction and progression of tumors. Most recently, their similarity to the human T-cell leukemia viruses (HTLVs) (Poiesz et al. 1982) and to sequences endogenous to the human genome (Repaske et al. 1983) has stimulated interest in a still larger scientific community.
Hybrid Dynamical Systems, Dynamical Intelligence, and Meta-Intelligence in Embodied Agents

By employing hybrid dynamical systems-oriented techniques for reasoning about dynamical systems, it is possible to formalize some typically informal meta-intelligence about realtime intelligence of embodied agents. Furthermore, this meta-reasoning could be straightforwardly implemented in an embodied agent, forming a basis for meta-intelligent planning or deeper logical reflection. This paper concretely illustrates the underlying concepts, discussing a specific dynamical system for navigation intelligence, a specific system for meta-level reasoning, and a hypothetical case of their integration in an embodied agent. The paper also suggests that the fundamental ideas generalize to other, similarly expressed intelligence models, and that some high-level meta-reasoning over dynamical intelligence could thus be straightforwardly reduced to meta-reasoning over logical representations.
Cytokine abnormalities in schizophrenia: a review of their pathogenic significance, with particular reference to the autoimmune hypothesis

Over the past 65 years, a variety of immunologic abnormalities have been reported in association with schizophrenia. These abnormalities have included alterations in lymphocyte subpopulations, alterations in immunoglobulin production both quantitatively and qualitatively, and altered cytokine physiology (for a review see Ganguli etal., 1994). Of these immunologic findings reported in association with schizophrenia, changes in cytokine physiology appear to be the most consistent and uncontroversial. This chapter will focus primarily on the evidence of cytokine abnormalities in a subgroup of patients, and will place these findings in the framework of the hypothesis that, for this subgroup of patients, an autoimmune process may play a pathogenetic role in their disorder. First, however, since this area of research remains mired in controversy and skepticism (DeLisi, 1996), some methodologic issues will be addressed, which pertain to the theoretical and practical aspects of study design and interpretation of results.
Wellness Advantage: An Experiential Learning Opportunity for Community Dietetic Students and University Faculty and Staff

Abstract In order to gain counseling experience, community nutrition students participated in an extensive nutrition counseling program. Wellness Advantage, the university sponsored worksite wellness program, and twenty senior dietetic students enrolled in community nutrition offered a nutrition counseling program. The nutrition counseling service was designed for healthy individuals who wanted to improve their dietary intake and overall level of health. Each senior student was randomly assigned to a university faculty or staff member. Participants were solicited from a one time announcement in the monthly Wellness Advantage newsletter. Participant requests far outnumbered dietetic students available to provide the service. To participate the university member agreed to meet with the student five times and to evaluate the student's effort. Initially, each student conducted a variety of anthropometric, historical, and dietary assessments and upon determining the client's goals designed a series of five nutrition education sessions. Each student worked independently with his or her client but was in frequent contact with the community nutrition professor. The students were required to provide written evidence of counseling objectives, follow up, and evaluation of each session. Following the last counseling session, clients completed an evaluation of their counselor and returned it to the professor. The evaluation utilized a likert-type scale to rate the dietetic student's efforts. Additionally, the students completed an evaluation and review at the end of the activity. Quantitative and qualitative data supported the value of the program for clients and dietetic students. Students who were initially tentative gained confidence and realistic counseling experience. Students learned to think outside their usual nutrition paradigm; they were required to seek out information to meet client requests and to present the information in a manner which their client could utilize. None of the clients had ever consulted with a dietitian prior to this counseling experience yet all expressed a keen interest in nutrition. Dietetic students positively influenced university faculty and staff both as nutrition educators and as ambassadors for the field of dietetics.
Tinea faciei starting at day two of life.

Dermatophyte infections are exceedingly rare in neonates, possibly due to the thin stratum corneum and high sebum content of neonatal skin. Only a handful of cases of tinea faciei have been reported in neonates, with the majority of reports occuring in India. Here, we report what to our knowledge is the earliest reported presentation of tinea faciei in the United States. We also provide a brief literature review of other reported cases of tinea faciei in neonates less than 30 days of age.
Risk of emergent carotid endarterectomy varies by type of presenting symptoms.

Abstract Background The timing of carotid revascularization in symptomatic patients is a matter of ongoing debate. Current evidence indicates that carotid endarterectomy (CEA) within 2 weeks of symptoms is superior to delayed treatment. However, there is little evidence on the outcomes of emergent CEA (eCEA). The purpose of this study was to compare outcomes of emergency eCEA vs nonemergent CEA (non-eCEA), stratified by type of presenting symptoms. Methods We analyzed the Vascular Targeted-National Surgical Quality Improvement Program dataset from 2011 to 2016. Symptomatic patients were divided into two groups: eCEA and non-eCEA. Univariable and multivariable methods were used to compare patient characteristics and to evaluate stroke, death, myocardial infarction (MI), stroke/death, and stroke/death/MI within 30 days of surgery adjusting for all potential confounders. A further subgroup analysis was done to compare the outcomes of eCEA vs non-eCEA stratified by the type of presenting symptoms (amaurosis, transient ischemic attack [TIA], and stroke). Results A total of 9271 patients were identified, of which 10.7% were eCEA vs 89.3% non-eCEA. Comparing eCEA vs non-eCEA, the two groups were similar in age (70.8 vs 70.5), female gender (36.3% vs 36.9%), diabetes (26.2% vs 28.9%), and smoking status (31.9% vs 28.7%; all P > .05). Patients undergoing eCEA were less likely to be hypertensive (76.2% vs 80.2%; P = .025), but more likely to belong to non-white race (51.5% vs 20.5%; P Conclusions In patients presenting with stroke, eCEA does not seem to add significant risk compared with non-eCEA. However, patients presenting with TIA might be better served with non-emergent surgery as their risk of stroke is tripled when CEA is performed emergently.
Challenges in diagnosis and treatment of comorbid eating disorders and mood disorders.

PURPOSE This paper explores complex challenges in diagnosis and treatment of patients with comorbid eating disorders and mood disorders. An integrative review of the literature examines overlapping symptoms, phenotypes, neural circuits, and genetic factors for these disorders. A case study illustrates how the integration of knowledge from research and practice can inform a diagnostic formulation and multifaceted treatment plan. CONCLUSIONS Patients with complex clinical presentations inspire a search for research and clinical literature that helps build the neuroscience foundations of advanced practice. PRACTICE IMPLICATIONS Sharing clinical challenges and processes of discovery is a form of scholarship that promotes the evolution of advanced psychiatric nursing practice.
Risk Factors Associated with Lead Migration Requiring Revision in Dorsal Root Ganglion Stimulation

Background Neuromodulation is an evolving therapy for chronic pain. Aiming to meet the limitations of traditional spinal cord stimulation, dorsal root ganglion (DRG) stimulation targets pain in a dermatomal distribution at the site of pain transmission. Despite these advantages, lead migration is a significant complication that hinders the long-term efficacy of DRG stimulation. This study aims to identify risk factors for lead migration requiring revision in DRG stimulation. Methods We performed a retrospective review of all subjects who had DRG stimulators implanted at T10-S2 by a single physician over a 2-year period. Their history was reviewed for the following: age, sex, diagnosis, lead placement, reported symptom relief, complications, and postoperative activity. Results In total, 19 cases of DRG stimulator implantation were identified. All patients reported pain relief, with 84.2% (16/19) describing >50% relief. In total, 31.6% of patients (6/19) developed lead migration and 15.8% of total implanted leads (9/57) migrated. Of the migrated leads, 4% (4/9) occurred at S1 and 33.3% (3/9) occurred at L4. The underlying etiology of lead migration was clear and preventable in 66.7% of patients (4/6). All patients who developed lead migration were women. Conclusions Premature activity, hardware manipulation, and female sex appear to be associated with an increased risk for lead migration. Leads on the S1 and L4 locations may be more likely to migrate. Large trials are necessary to gain a more conclusive understanding of these risk factors for lead migration.