cssi/SciSciGPT-SciSciNet huggingface dataset:
Ethical Issues in Trauma Research Involving 'Vulnerable' Subjects with 'Diminished' Autonomy: A View from the Survivor's Perspective

The current paradigm for ethical research with subjects who are survivors of violence or trauma presumes that these individuals are vulnerable and have diminished autonomy and so require additional protections from research risks, including the risk of coercion. These additional protections purportedly arise from the requirements of the ethical principle of respect for persons. Using the case of research focused on and involving survivors of sexual assault, I argue that conceiving of survivors of violence and trauma in this way - as necessarily altered by the experience of violence such that they are vulnerable, diminished, and less able to choose freely - is a mistake that not only fails to protect these subjects, but disrespects them in ways that may be reminiscent of some of the harms related to the trauma or violence they have experienced. Conceiving of these survivors as vulnerable and diminished in virtue of their victimization suggests not only that they are less free than they may actually be, but that the violence or trauma has had the effect of necessarily, intrinsically, and permanently reducing them as people. In contrast to the assumptions implicit in this paradigm, recent research suggests that treating survivors of sexual assault as if they are "different" or "less worthy" persons - as though the assault permanently transformed them somehow - may exacerbate post traumatic stress disorder symptoms among this population. Moreover, this research suggests that talking about the trauma more extensively with others may be beneficial and therapeutic for survivors of sexual assault, not risky and harmful as many IRBs assert. While researchers need to be cognizant of and diligent in anticipating and recognizing the real, lasting, and at times unpredictable consequences of traumatic experiences, the way to respectfully engage survivors in research is through frank open discussions of research goals and design at all stages of the research process. Rather than respecting survivors' autonomy and maximizing their empowerment, the current paradigm is disrespectful in its presumptive reduction of survivors' ability to choose freely and possibilities for recovery from trauma.
Row Rank and Column Rank of a Matrix

(1960). Row Rank and Column Rank of a Matrix. Mathematics Magazine: Vol. 34, No. 1, pp. 33-34.
Geometric Characterization of Electromigration Voids

The areas, perimeters, lengths, and widths of 998 electromigration induced voids on 38 test stripes have been measured by SEM and digital image analysis. Virtually all of the voids occurred along the passivation-conductor interface on the side of the stripe. Plots of number of voids or total void area versus time to failure do not extrapolate to zero voids at zero time to failure which suggests there is a certain number of active nucleation sites predisposed to voiding.
Development of the Large Range CCD Coordinate to Use in the Vacuum Laser Collimation Monitoring System

The effect on the measurement precision is analyzed when the image acquisition appear distortion in the vacuum laser collimation monitoring system.The large range CCD coordinate instrument for the system is designed and the coordinate instrument structure,measuring principle,measuring circuit and image analysis method is introduced.Through the practical application of the structure show the instrument has high accuracy and good stability.This instrument has the advantages of simple structure,easy to realize,is suitable for the vacuum laser collimation system monitoring.
Guidelines for using five new prenatal laboratory tests.

PreviewHealthcare professionals have recognized for years that prenatal care is one of the most powerful factors in ensuring the health of the newborn and the well-being of the mother. Dr Weiss describes new prenatal evaluations that have been endorsed by national health policy organizations: tests for gestational diabetes mellitus, hepatitis B, Chlamydia trachomatis, human immunodeficiency virus, and neural tube defects.
The Gastrointestinal System

Both aerobic (with oxygen) and anaerobic (without oxygen) cellular metabolisms require simple hydrocarbons. Although the tissues of both plants and animals are composed of hydrocarbons, these organic compounds are too complex chemically for use in cellular metabolism. The two basic functions of the gastrointestinal (GI) system are to chemically break down the complex hydrocarbons contained in food into simple hydrocarbons and to expel chemical wastes such as fiber that cannot be digested.
Micro-Machining of Glass Using Electrochemical Discharge Assisted Cutting

Glass is a hard-to-machine material with vast industrial application. Electrochemical discharge machining (ECDM) is a non-traditional machining technology that has shown potential for effective glass machining. However, ECDM has not been widely used in industry despite being studied for over a decade. Major challenges of ECDM include limited machinable depth and low material removal rate. In this paper, an innovative hybrid machining process combining ECDM and traditional cutting is presented, namely electrochemical discharge assisted cutting. The material removal rate of the hybrid ECDM process is significantly higher than conventional processes. Experimental results are presented to prove the feasibility and capability of the process. Discussion concentrates on the improvement of geometric accuracy and surface integrity through experimentation.Copyright © 2016 by ASME
Herpesvirus Sylvilagus: Lymphoproliferative Agent of Cottontail Rabbits

Herpesvirus sylvilagus is an indigenous virus of cottontail rabbits. Infection of rabbits results in a lymphoproliferative disorder characterized by spleen and lymph node hyperplasia, the appearance of atypical lymphocytes in the peripheral blood, and an intense T-cell proliferation. In vivo, the virus is present latently in B and T lymphocytes in both a covalently closed circular form and a linear duplex form. In vitro, the virus is able to bind to lymphocytes but a productive infection is not detected. In productively infected cultured rabbit kidney cells, the virus induces the synthesis of at least 45 virus-induced polypeptides of which at least 14 are glycosylated.
Defining the topography of a planetary body

Rivers develop on planetary bodies from the interplay of climate and topography. In planetary contexts, rivers and their effects are used to constrain short- and long-term climate models. However, rivers are also controlled by the short- and long-wavelength topography of the planetary surface. Rivers thus provide a means to constrain the generation of topography. On page 727 of this issue, Black et al. ( 1 ) compare topography at a range of scales with mapped river drainages to provide new insights into the topography-generating mechanisms on Earth, Mars, and Titan.
Role of Hepatectomy for Hepatocellular Carcinoma in the Era of Transplantation and Locoregional Therapy

Hepatocellular carcinoma (HCC) remains the most common primary liver neoplasm and is a leading cause of cancer-related mortality worldwide. Therapeutic options are increasing in HCC and now include surgical resection, transplantation, local ablation, directed transarterial therapies, and systemic therapies. Efficacy for each modality varies widely with the chance for cure dictated predominantly by disease biology. Surgical extirpation remains the mainstay of therapy in a curative paradigm. The role of hepatectomy and transplantation, however, has evolved as multidisciplinary management and now integrates other locoregional and systemic therapies. Herein, we review the modern approach to HCC within the context of historical trials. Studies informing a current practice that combine surgery with locoregional therapies are highlighted. A variety of transarterial options are critically examined and selection criteria for use are suggested. Finally, current best-practice guidelines are discussed with updates and practical advice where warranted.
Who should receive the subcutaneous implanted defibrillator?: Timing is not right to replace the transvenous implantable cardioverter defibrillator.

On September 28, 2012, the US Food and Drug Administration approved the totally subcutaneous implantable cardioverter defibrillator (S-ICD) for the treatment of life-threatening ventricular tachyarrhythmias in patients who do not have symptomatic bradycardia, incessant ventricular tachycardia (VT), or spontaneous, frequently recurring VT that is reliably terminated with antitachycardia pacing (ATP). These devices hold the promise of life-saving defibrillation without some of the known problems of transvenous defibrillator systems (TV-ICD), including limited vascular access, transvenous lead durability, hazardous lead extractions, and risks of bloodstream infections. There are trade-offs with the S-ICD devices including reports of increased infections and the inability to deliver ATP. The subcutaneous position of the electrodes requires higher energy delivery with longer charge times. In addition, sophisticated signal processing is required for accurate arrhythmia detection and diagnosis. As we consider the appropriate patient population for S-ICD therapy, it is important to review the trade-offs of this system compared with traditional TV-ICD systems. Response by Poole and Gold on p 1251 Unlike transvenous ICDs that sense the local ventricular myocardial depolarization with an endocardial bipolar electrode, the S-ICD records a signal from 2 of its 3 subcutaneous electrodes. These are the distal sensing electrode located at the lead tip, a proximal sensing electrode located 14 cm proximal to the distal electrode, and the pulse generator itself. By their nature, the S-ICD signals are more susceptible to external and myopotential noise, as well as T-wave oversensing. Thus, sophisticated algorithms have been developed to filter noise from the true cardiac signals.1 Nevertheless, oversensing is responsible for the majority of inappropriate shocks in these systems as reported in a recent multicenter case–control study.2 The competing concern is that of undersensing true arrhythmias that can lead to delays in therapies. The best data available on S-ICD time to therapy come from …
Probabilistic demand forecasting at scale

We present a platform built on large-scale, data-centric machine learning (ML) approaches, whose particular focus is demand forecasting in retail. At its core, this platform enables the training and application of probabilistic demand forecasting models, and provides convenient abstractions and support functionality for forecasting problems. The platform comprises of a complex end-to-end machine learning system built on Apache Spark, which includes data preprocessing, feature engineering, distributed learning, as well as evaluation, experimentation and ensembling. Furthermore, it meets the demands of a production system and scales to large catalogues containing millions of items.We describe the challenges of building such a platform and discuss our design decisions. We detail aspects on several levels of the system, such as a set of general distributed learning schemes, our machinery for ensembling predictions, and a high-level dataflow abstraction for modeling complex ML pipelines. To the best of our knowledge, we are not aware of prior work on real-world demand forecasting systems which rivals our approach in terms of scalability.
In the Footsteps of John Marshall: European Courts and the Expansion of Protection of Forced Migrants

The Court of Justice of the European Union and the European Court of Human Rights share with the Marshall Court the reputation (and reality) of being activist institutions. Well aware of the long-term structural implications of many of the disputes before them, they are important drivers of the European project. They have already left their mark on the development of the Common European Asylum System (CEAS) through recent decisions, such as Hirsi Jamaa and Others v. Italy, Germany v. B and D, and Elgafaji v. State Secretary of Justice. These judicial opinions demonstrate that the supra-national European courts are not shy about issuing broad rulings. In stark contrast to the limitations on U.S. judicial power that we are accustomed to in the plenary power doctrine, the European courts do not exhibit substantial deference to executive control of forced migration. Nor do these European judicial opinions resonate with the complex preemption analyses adopted by U.S. courts in their review of state and local challenges to federal immigration power. The Court of Justice of the European Union and the European Court of Human Rights are actively expanding the scope of EU law and, along with it, the right to asylum in Europe.
Outcaste Politics and Organized Crime in Japan: The Effect of Terminating Ethnic Subsidies

In 1969, Japan launched a massive subsidy program for the "burakumin" outcastes. The subsidies attracted the mob, and the higher incomes now available through organized crime compensated those burakumin who abandoned the legal sector for criminal careers. In the process, the subsidies gave new support to the tendency many Japanese already had to equate the burakumin with the mob. The government ended the subsidies in 2002. We explore the effect of the termination by merging 30 years of municipality data with a long-suppressed 1936 census of burakumin neighborhoods. First, we find that outmigration from municipalities with more burakumin increased after the end of the program. Apparently, the higher illegal income generated by the subsidies had restrained young burakumin from joining mainstream society. Second, we find that once the mob-tied corruption and extortion associated with the subsidies neared its end, real estate prices rose in municipalities with burakumin neighborhoods. With the subsidies gone and the mob in retreat, other Japanese found the formerly burakumin communities increasingly attractive places to live.
RAB27B requirement for stretch-induced exocytosis in bladder umbrella cells

Umbrella cells, which must maintain a tight barrier, modulate their apical surface area during bladder filling by exocytosis of an abundant, subapical pool of discoidal- and/or fusiform-shaped vesi...
Recent advances in liquid chromatographic methods for the determination of selective serotonin reuptake inhibitors and serotonin norepinephrine reuptake inhibitors

Depression is now the second largest public health burden throughout the world. Selective serotonin reuptake inhibitors (SSRIs) and serotonin norepinephrine reuptake inhibitors (SNRIs) have replaced older antidepressants to become first-line medications to treat this disease with increased remission rates and markedly decreased incidence of severe adverse events. Traditional and modern bioanalytical strategies for SSRI and SNRI determination are being continuously improved. There has also been a recent increase in the use of unconventional sample preparation methods. This review critically evaluates the development of SSRI and SNRI liquid chromatographic analytical methods published between 2014 and mid-2019, with special attention to novel sample preparation methods.
When do looks matter? Effects of mate quality and environmental variability on lifetime reproduction

Inter-individual variation in lifetime reproduction is the key target for natural selection, and it is influenced by many factors. Yet, we lack an understanding of how abiotic and biotic factors interact to influence lifetime reproductive output (number of offspring) and reproductive effort (total biomass invested into reproduction). Thus, we used a factorial design to manipulate variability in food availability and temperature while also accounting for mate quality. We tested hypotheses related to estimates of lifetime reproductive output and effort in females of the wing-dimorphic sand field cricket (Gryllus firmus). Environmental variability influenced a temporal tradeoff of reproduction because females experiencing fluctuating temperatures had a particular bias toward reproductive output during early adulthood. Also, complex environmental variability (i.e., multiple and co-varying environmental factors) influenced differential allocation, which is when individuals adjust their reproductive efforts according to mate quality. Females mated to higher quality males laid more eggs only in environments that were highly stable (constant temperature and ad libitum food access). Reproductive effort was affected by a food–temperature interaction—fluctuating temperatures promoted egg production when food was limited, while constant temperature promoted egg production when food was abundant. Although a wing dimorphism mediates a well-established flight–fecundity tradeoff during early adulthood in G. firmus, short- and long-winged morphs exhibited similar lifetime reproduction and responded similarly to complex environmental variability. Given the natural co-variation of many environmental factors (e.g., water limitation often accompanies heat waves), we encourage continued work examining the role of complex environmental variability in tradeoffs related to reproductive decision-making and allocation. It is unclear how abiotic and biotic factors interact to influence lifetime reproductive output (number of offspring) and reproductive effort (total biomass invested into reproduction). Thus, we examined the effects of mate quality and complex environmental variability (variable food and temperature) on several metrics of lifetime reproduction. Female crickets mated to high-quality males had greater reproductive output, but only in highly stable or environmental conditions. Fluctuating temperatures biased reproductive output toward early adulthood, particularly in short-winged females. Reproductive effort was affected by a food–temperature interaction—fluctuating temperatures promoted egg production when food was limited, while constant temperature promoted egg production when food was abundant. Females can also retain unfertilized eggs, and egg retention (i.e., unrealized fitness potential) was influenced by a combination of mate quality and complex environments. Thus, it is important to carefully consider the interplay between biotic and abiotic factors in aspects of lifetime reproduction and reproductive decision-making.
The Rise and Fall of Transcendent Constitutionalism in the Civil War Era

In the aftermath of the Civil War, American intellectuals saw the war itself as a force of transcendent lawmaking. They viewed it as a historical catalyst that had forged the United States into a nation. In writing the Fourteenth Amendment, Congress sought to translate the war’s nationalistic spirit into text. But in the eyes of many contemporary thinkers, the war’s centripetal energy was a double-edged sword. It could create a nation out of disparate parts, but it was also potentially uncontainable, divorced from the regular lawmaking process and beyond the control of human actors. As a result, many American jurists feared that the war could result in the complete destruction of American federalism and the erection of a system based on unitary sovereignty. After the Civil War, the Supreme Court significantly narrowed the revolutionary potential of the Fourteenth Amendment, as generations of legal scholars have noted. What scholars have failed to appreciate, however, is exactly what the Court meant to do in its controversial opinion in the Slaughterhouse Cases. In Slaughterhouse and other post-war cases, the Court sought to provide a counterforce against the forces of transcendent lawmaking, intending to preserve the fundamental distinction between state and federal authority in the United States, which the justices feared might be entirely elided otherwise. To many Americans living in the aftermath of the Civil War, the Supreme Court’s decision to quash the radical potential of transcendent constitutionalism represented a welcome return to the ordinary operation of law in the United States.
Alert! Automated Vehicle (AV) System Failure - Drivers' Reactions to a Sudden, Total Automation Disengagement.

Despite the “driverless” term, drivers of automated vehicles still constitute an integral part of the human-machine team that will be driving the future. This study emphasized drivers by evaluating the attentiveness, stress levels, and reactions of 67 participants, ages 18–65+ years, during a sudden, total disengagement of automation in a driving simulator-based rural freeway setting. Attentiveness was characterized by a significant increase in gaze fixation and a significant decrease in fatigue, yet stress levels did not appear to significantly change. Regardless of age, gender, or level of non-driving related task involvement, participants reacted to the failure first by steering, requiring 12.30 s (50th percentile) to 29.26 s (90th percentile), followed by speed control after 18.26 s (50th percentile) to 40.86 s (90th percentile). These findings highlight the need for addressing the potentially dangerous implications of automation failure.
Fentanyl Quality Assurance Project Prompted Change in Clinical Workflow and Test Configurations.

BACKGROUND Deaths attributable to fentanyl (FEN, a synthetic opioid) are high in Appalachia and highest in West Virginia. The goal of the study was to determine FEN prevalence among specimens submitted for definitive opioid testing and monitor responses to provider notifications of unexpected FEN findings during Q1 2020. METHODS All definitive opioid test data were reviewed daily for FEN signatures in Q1 2020. Unexpected FEN results were communicated to providers and monitored for 10 days to record actions taken. Prevalence data were categorized. Behavioral Medicine (BMED) leaders analyzed January data and implemented FEN screening in the clinic. BMED Q1 clinic visits and order volumes for drug screens were reviewed after Q1. RESULTS FEN positivity was 11% in Q1; >60% of findings were unexpected. Actions were taken for 54% of notifications in January but only 18% in March. Notifications required 70 hours of combined laboratory effort each month. BMED providers ordered 44% of definitive opioid tests and 69% of definitive FEN tests. Data prompted the addition of FEN to routine drug screen panels in the laboratory, and a 10% random FEN screening rate in the BMED opioid use disorder clinics (COAT). CONCLUSIONS Prevalence of FEN positivity was higher than initially expected, even for this region in Appalachia. Expanded presence of FEN screening should assist BMED providers with clinical efforts and help identify patients in need of intervention/therapy.
Bayesian Hierarchical Model for Characterizing Electric Vehicle Charging Flexibility

The proliferation of electric vehicle (EV) adoption introduces a suite of opportunities and risks to power system operation which have the potential to significantly increase loading, reduce equipment lifespan, impact rate design and offer energy flexibility. The uncertainty in space, time, power and energy presented by EV charging demand creates a unique challenge to the development of utility best practices. Specifically, this work seeks to predict the aggregate number of EVs initiating charging sessions per hour within a region’s EV charger fleet. Therefore, we propose a Bayesian hierarchical model to learn the EV arrival as a stochastic process. The model is trained and tested by a 20/80 data split. Sampling convergence is confirmed by observation of the Gelman-Rubin statistic and predictions are made against the test data. Results indicate a prediction error of less than 3% over the testing data set.
Field Density Investigation of Asphalt Mixtures in Minnesota

In a current research effort, University of Minnesota and Minnesota Department of Transportation have been working on designing asphalt mixtures that can be constructed at 5% air voids, similar to ...
Global Minimum Variance Portfolio: A Horse Race of Volatilities

We conduct a horse race using three asset return volatility estimates: the sample variance, the exponential smoother used by RiskMetrics, and the generalized autoregressive conditional heteroskedasticity (GARCH). Our results are performed in both univariate and multivariate analysis. Our goal is to test whether using econometric tools achieves better economic performance. Economic performance is captured by portfolio performance as in DeMiguel et al (2009), who use three metrics to evaluate portfolios: risk-return, Sharpe-ratio, and turnover. Our portfolio of interest is the global minimum variance (GMV) portfolio since its inputs are determined solely by the variances and covariances of the asset returns. Computing the three portfolio performances for the three volatility candidate, we provide an evidence in support of the GARCH approach; however, this edge is undermined by greater portfolio turnover and larger estimation error, when the number assets in the portfolio is large.
Surgical Principles for Management of Major Vessel Injury during Laparoscopic Gynecologic Surgery

Study Objective Vascular injury of the major pelvic vessels is one of the most dreaded complications in gynecologic laparoscopy. Risk factors include distorted anatomy, fibrosis secondary to pathology or previous surgery, and procedures involving retroperitoneal dissection. We aim to outline fundamental principles for management of major vessel injury during gynecologic laparoscopy. Design Case report. Setting Tertiary academic medical center. Patients or Participants We present the case of 32-year-old patient who sustained an injury to the left external iliac artery during surgical excision of deeply infiltrating endometriosis. Interventions Critical steps demonstrated in this video include rapid identification, application of direct pressure, and communication with the operating room team regarding the need for additional resources. Once bleeding has slowed, mobilization of surrounding structures including the ureter and bowel can be performed to improve visualization and minimize risk of secondary injury. Atraumatic self-retaining vascular clamps such as laparoscopic Satinsky clamps can be used to occlude without traumatizing vessel walls. If bleeding is unable to be controlled with laparoscopic pressure or additional visualization is required for primary repair, laparotomy must be performed expeditiously. Measurements and Main Results This patient received definitive primary repair of a 5mm external iliac artery defect with Vascular Surgery and was discharged home in stable condition on postoperative day two. Conclusion This case demonstrates fundamental principles for initial management of acute major vessel injury during gynecologic laparoscopy, including application of direct pressure, communication, identification and mobilization of surrounding anatomy, and application of vascular clamps to temporize bleeding when definitive repair is not possible through a minimally invasive approach.
FPGA Implementation of Pipelined On-Line Scheme for 3-D Vector Normalization

A three-dimensional vector normalizer based on pipelined on-line arithmetic is presented. The clock period is kept small by the use of redundant adders and low-precision estimates. The throughput is greatly improved by unfolding and pipelining on-line units and the area is reduced due to left-to-right processing. Assuming the same area/delay metric, the proposed scheme can improve throughput by 89% compared with PROVEN scheme, an ASIC normalizer, and by 10.2× compared with VU, a vector-processing unit for 3-D graphics computing. When implemented as an FPGA-based hardware accelerator, our scheme allows 85% more throughput than VU, and 2.3× more throughput than Pentium III SSE.
Determinants of Perceptions of Cheating: Ethical Orientation, Personality and Demographics

A sample of 227 business students from the United States and Australia was used to evaluate factors that impact business students' ethical orientation and factors that impact students' perceptions of ethical classroom behaviors. Perceptions of classroom behaviors was considered a surrogate for future perceptions of business behaviors. Independent factors included age, gender, religious orientation, country of origin, personality, and ethical orientation. A number of factors were related to ethical orientation, but only age and religious orientation exhibited much impact upon perceptions of ethical classroom behaviors.
Proceedings of the 47th Design Automation Conference

It is a great pleasure to welcome you to the 47th edition of the Design Automation Conference in Anaheim. As the central "meeting place" for electronic design and design automation where the industry puts on its grand annual show, there are many facets to DAC. It's the place where new contacts are made, where deals are sealed, where theory meets practice, where colleagues across the industry network, where the seeds of great new ideas are sown --- and much more. DAC is our annual signpost that points the way to the future.
Proteomics comes to the surface.

Microarrays of purified proteins, representing most of the yeast genome, prove useful for studying protein function on a genome-wide scale.
Getting kids from the Big Easy hospitals to our place (not easy): preparing, improvising, and caring for children during mass transport after a disaster

The incapacitating blows dealt to the New Orleans, Louisiana, health care infrastructure by Hurricane Katrina and its aftermath are unprecedented in the United States. Much can be learned about disaster preparedness from the events that unfolded in New Orleans after Katrina swept the Gulf shoreline. Problem areas in the management of this disaster such as internal and external communication failures, transportation, triage, personnel allocation, and resource allocation have long been identified in the literature as core disaster-response issues.1–3 In addition, damage to the physical plant, water and power system failures, and hazardous-materials exposure are encountered commonly in the face of disaster.1 Between 1950 and 2005, 286 hospital evacuations have been described, including horizontal evacuation (within the same floor), vertical evacuation (between floors), evacuation of a ward or wing, and complete hospital evacuation.4–10 Of the 286 between 1971 and 1999, 275 were reviewed by Sternberg et al.8 There are 22 reported cases of complete hospital evacuation since 1950; of these, 1 occurred in Canada and 8 resulted from the 1994 Northridge, California, earthquake.4,5,7–18 Of 43 reported incidents for which duration is known, only 12 evacuations lasted longer than 24 hours.8 Eleven percent of evacuations in the series reviewed by Sternberg et al listed at least 1 casualty, and the deadliest reported hospital disaster occurred in 1971, when partial collapse of a California Veteran's Administration hospital claimed 49 lives.8 Hurricanes are the third most common cause for hospital evacuation, accounting for 38 of 286 reported evacuations; only internal fire and internal hazardous-material events are more common. It is notable that only 3 evacuations since 1950 involved 1000 or more patients.8 Over a 5-day span in June 2001, Tropical Storm Allison brought nearly 39 inches … Address correspondence to Susan M. Distefano, MSN, RN, CNAA, BC. E-mail: smdistef{at}texaschildrenshospital.org
Genetic architecture of inter-individual variability in apolipoprotein, lipoprotein and lipid phenotypes.

Phenotypes that predict coronary heart disease (CHD) are the consequence of interactions between many genetic and environmental factors. Quantitative measures of plasma apolipoproteins, lipoproteins and lipids are examples of phenotypes that link genetic and environmental factors to the CHD end-point. Population studies in Hawaii, Michigan and elsewhere have established that a significant fraction of variability in these phenotypes is attributable to genetic differences among individuals. Recent advances in molecular biology provide measures of the gene loci that code for the apolipoproteins, the cellular receptors for lipoprotein particles and the catalysts and cofactors in lipoprotein metabolism. By measuring polymorphic protein variability and restriction site variability in small regions of DNA known to contain genes that code for the proteins involved in these functions, it is possible to assign polygenetic effects to specific alleles or haplotypes. This 'measured genotype' approach may be used to study the genetic architecture (number of loci involved, the frequencies and effects of their alleles, and the type of loci, i.e., structural or regulatory) of quantitative variation in the plasma apolipoproteins, lipoproteins and lipids. This paper reviews statistical models, sampling designs and results of studies designed to estimate the genetic architecture of selected apolipoproteins, lipoproteins and lipids. The usefulness of these studies for answering questions about the prediction of CHD in the population, the family and the individual are discussed and the directions that human quantitative genetic studies will take in the future are considered.
A Goodness‐Of‐Fit Test for Time Series with Long Range Dependence

We propose a test statistic for goodness of fit in time series with slowly decaying serial correlations. The asymptotic distribution of the test statistic, originally proposed by Milhoj for time series with smooth spectra, turns out to be the same, under the null hypothesis, even if the spectrum has a pole at 0. In particular, the test is suitable to detect lack of independence in the observations, or estimated residuals, if the first few correlations are small but the decay of the correlations is slow
Interfacial interaction in carbon fiber/thermoplastic composites

This work was undertaken in order to increase the understanding of the mechanism responsible for fiber/matrix interaction in carbon fiber/thermoplastic composite. From results of previous study on carbon fiber/PEEK composite, which suggested that the formation of the fiber/ matrix interaction was primarily related to a chemisorption mechanism, a study was done of the conditions required to obtain efficient fiber/matrix interaction in PA-12 and PP/carbon fiber composites. The interest in studying carbon fiber composite based on PP and PA-12 was that these two matrices are very different in terms of reactivity, polyamide having many more reactive groups than polypropylene. As expected, due to the non-reactive chemical structure of the polypropylene, fiber/matrix interaction in carbon fiber/PP composite occurred only when the matrix was thermally degraded, i.e. when the composite was molded at high temperature or under long residence time at the melt temperature. For the carbon fiber/PA-12 composite, strong ...
Survival of Cyclical Particle Systems

We consider here a continuous time interacting particle system on Z with possible states 0,1,…,N-1 at each site. We denote by ξt(i) the state taken at site i and time t. Our models, which we call cyclical particle systems, are specified by the following transition rates: $${\xi _{\rm{t}}}{\rm{(i)}} \to {\xi _{\rm{t}}}({\rm{i}}) + {\rm{l (mod}}{\mkern 1mu} {\rm{N) at rate }}{\mkern 1mu} \lambda ,$$ where $$\lambda = \left| {\,\left\{ {\,{\rm{j}} = \pm 1:\,{\xi _{\rm{t}}}({\rm{i + j) = }}{\xi _{\rm{t}}}({\rm{i) + 1}}\,{\mkern 1mu} {\rm{(mod}}\;{\rm{N)}}} \right\}\,} \right|.$$ . Note in particular that i cannot change state until at least one of its immediate neighbors has state ξt(i) + 1. For convenience, one may equip ξ with a space-time percolation substructure. Arrows from i to i+1 and i-1 are each put dow in a Poisson manner with rate 1. A state change is induced at (t, i) by an arrow at time t which enters i from i+1 or i-1, where the state is ξt(i) + 1. In diagram 1 below, numbers at the points of arrows indicate state change in the realization (N=5). Here, we will always assume that ξ0 has product measure with $${\rm{P(}}{\xi _0}{\rm{(i) = k) = 1/N}}\;{\rm{for}}\;{\rm{k = 0,}}{\mkern 1mu} 1,...,{\mkern 1mu} {\rm{N - 1}}{\rm{.}}$$
Interaction of Fe-protoporphyrin IX and heme analogues with purified recombinant heme oxygenase-2, the constitutive isozyme of the brain and testes.

Heme oxygenase-2 (HO-2) is the predominant form of heme oxygenase in the brain and testes. The enzyme is not readily amenable to isolation from mammalian tissues and has not been characterized for its kinetic properties and interaction with metalloporphyrins. Presently a rat HO-2 cDNA (Rotenberg, M.O., and Maines, M. D. (1990) J. Biol. Chem. 265, 7501-7506) was used to generate a construct with a neutral hydrophobicity profile at its COOH terminus for expression of nearly full-length HO-2 protein in Escherichia coli. The procedures used for HO-1 were of no utility in purification of HO-2. A multistep protocol developed for isolation of HO-2 resulted in a homogeneous protein with a specific activity up to 6,500 nmol of bilirubin/mg/h. Based on SDS-polyacrylamide gel electrophoresis and Western blot analyses, the protein had an apparent molecular mass of approximately 34 kDa. HO-2 binds Fe-protoporphyrin (heme) at near molar unity to give a complex with the absorption maximum at 403 nm. The Soret band has a blue shift to 430 nm when heme iron is reduced, with distinct alpha and beta bands at 485 and 550 nm, respectively. The Soret band of the CO complex of ferrous heme.HO-2 is at 420 nm, and alpha and beta bands are at 540 and 572 nm, respectively. The apparent Km for Fe-protoporphyrin is 0.33 microM, with a Vmax of 0.45 nmol of bilirubin/mg/h. Zn-protoporphyrin is a strong mixed inhibitor of enzyme activity, whereas Co-protoporphyrin is a poor competitive inhibitor of activity. When HO-2 was preincubated (10 min at 4 degrees C) with Fe-protoporphyrin, the cobalt complex did not inhibit enzyme activity, whereas the Zn-protoporphyrin effectively inhibited activity. Calorimetric measurements suggest that HO-2/heme interaction involves one type of association producing a single heat absorption peak upon melting of the complex and that the unfolding is not reversible. The association increases the enthalpy of HO-2 (130 kcal/mol versus 184 kcal/mol) and increases the stability to heat denaturation by 9 degrees C. Heat duration of zinc complex involves at least two stages of unfolding.
Low-temperature specific heat of C60.

We have measured a large specific heat of polycrystalline ${\mathrm{C}}_{60}$ from T=1.4 to 20 K. The data were adequately fitted by a model containing Debye terms, Einstein oscillators, and a linear contribution. An analysis incorporating both vibrational and strongly coupled rotational degrees of freedom expected for the simple-cubic structure at low temperatures is proposed. We also discuss a possible interpretation based on a fairly narrow feature in the excitation spectrum. The large linear term may be a consequence of disorder resulting in a distribution of two-level tunneling centers.
Identification of Spinal Cord MicroRNA and Gene Signatures in a Model of Chronic Stress-Induced Visceral Hyperalgesia in Rat

Author(s): Bradesi, Sylvie; Karagiannides, Iordanes; Bakirtzi, Kyriaki; Joshi, Swapna Mahurkar; Koukos, Georgios; Iliopoulos, Dimitrios; Pothoulakis, Charalabos; Mayer, Emeran A | Abstract: IntroductionAnimal studies have shown that stress could induce epigenetic and transcriptomic alterations essential in determining the balance between adaptive or maladaptive responses to stress. We tested the hypothesis that chronic stress in rats deregulates coding and non-coding gene expression in the spinal cord, which may underline neuroinflammation and nociceptive changes previously observed in this model.MethodsMale Wistar rats were exposed to daily stress or handled, for 10 days. At day 11, lumbar spinal segments were collected and processed for mRNA/miRNA isolation followed by expression profiling using Agilent SurePrint Rat Exon and Rat miRNA Microarray platforms. Differentially expressed gene lists were generated using the dChip program. Microarrays were analyzed using the Ingenuity Pathways Analysis (IPA) tool from Ingenuity Systems. Multiple methods were used for the analysis of miRNA-mRNA functional modules. Quantitative real time RT-PCR for Interleukin 6 signal transducer (gp130), the Signal Transducer And Activator Of Transcription 3 (STAT3), glial fibrillary acidic protein and mir-17-5p were performed to confirm levels of expression.ResultsGene network analysis revealed that stress deregulated different inflammatory (IL-6, JAK/STAT, TNF) and metabolic (PI3K/AKT) signaling pathways. MicroRNA array analysis revealed a signature of 39 deregulated microRNAs in stressed rats. MicroRNA-gene network analysis showed that microRNAs are regulators of two gene networks relevant to inflammatory processes. Specifically, our analysis of miRNA-mRNA functional modules identified miR-17-5p as an important regulator in our model. We verified miR-17-5p increased expression in stress using qPCR and in situ hybridization. In addition, we observed changes in the expression of gp130 and STAT3 (involved in intracellular signaling cascades in response to gp130 activation), both predicted targets for miR-17-5p. A modulatory role of spinal mir17-5p in the modulation of visceral sensitivity was confirmed in vivo.ConclusionUsing an integrative high throughput approach, our findings suggest a link between miR-17-5p increased expression and gp130/STAT3 activation providing new insight into the possible mechanisms mediating the effect of chronic stress on neuroinflammation in the spinal cord.
Abstract 2764: High-resolution HLA typing by next-generation sequencing and risk of follicular lymphoma

Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL The molecular basis of follicular lymphoma (FL) has been fairly well characterized, although its root causes remain less clear. Recently, in two genome-wide association studies of European-Americans, we identified novel genetic susceptibility loci for FL, narrowed down to two independent regions on chromosome 6p21.3 in the major histocompatibility complex (MHC) (Skibola et al., Nat Gen 41(8):873-5., 2009; Conde et al., Nat Gen 42(8):661-4, 2010). The first susceptibility locus, rs6457327 (combined allelic p-value=4.7 × 10-11 in 645 patients and 3,377 controls), is part of a 26-kb region of high linkage disequilibrium (LD) in the MHC Class 1 region at 6p21.33 in close proximity to the psoriasis susceptibility region 1 (PSORS1). A second locus at 6p21.32, in the MHC Class II region upstream of HLA-DQB1, two SNPs in high LD, rs10484561 and rs7755224, were associated with 2-fold increased risks for FL in 1,465 patients and 6,958 controls (combined p-values=1.12×10-29, 2.00×10-19). Using tag SNPs as surrogates for HLA allelotypes, the latter loci were found to be part of an extended haplotype that includes HLA-DRB1\*0101-HLA-DQA1\*0101-HLA-DQB1*0501 and that was associated with increased FL risk [odds ratio (OR) = 2.07, 95% confidence interval (CI) = 1.40-3.06]. These findings were further validated by direct typing of HLA-DQB1 alleles in a subset of 265 FL cases and 757 controls using multiplexed, ligation-dependent probe amplification. We verified the positive association between FL and the HLA-DQB1*05 allele group (OR=1.56, 95% CI 1.22-1.99; adjusted p-value=7.7×10-3), and found an inverse association between the HLA-DQB1*06 allele group and FL risk (OR=0.53, 95% CI 0.40-0.69; adjusted p-value=1.98×10-5). To gain further insight into the role of HLA alleles in FL susceptibility, high-resolution HLA typing by next-generation sequencing of the HLA class I (A, B, C) and class II (DRB1/3/4/5, DQA1, DQB1, DPB1) genes was conducted in 222 FL patients and 220 sex- and age-matched controls. HLA typing was performed by sequencing exon 2 for the class II genes and exons 2-4 for the class I genes, as described previously (Bentley, G et al. Tissue Antigens. 74:393-403, 2009), and data analysis is underway. To our knowledge, this study will present the highest resolution (up to 8-digit) HLA typing reported in a sample of European-Americans, and is an important next step to determine the role of MHC genetic variation in the pathogenesis of FL. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2764. doi:10.1158/1538-7445.AM2011-2764
Comparison of insertion/deletion calling algorithms on human next-generation sequencing data

Insertions/deletions (indels) are the second most common type of genomic variant and the most common type of structural variant. Identification of indels in next generation sequencing data is a challenge, and algorithms commonly used for indel detection have not been compared on a research cohort of human subject genomic data. Guidelines for the optimal detection of biologically significant indels are limited. We analyzed three sets of human next generation sequencing data (48 samples of a 200 gene target exon sequencing, 45 samples of whole exome sequencing, and 2 samples of whole genome sequencing) using three algorithms for indel detection (Pindel, Genome Analysis Tool Kit's UnifiedGenotyper and HaplotypeCaller). We observed variation in indel calls across the three algorithms. The intersection of the three tools comprised only 5.70% of targeted exon, 19.52% of whole exome, and 14.25% of whole genome indel calls. The majority of the discordant indels were of lower read depth and likely to be false positives. When software parameters were kept consistent across the three targets, HaplotypeCaller produced the most reliable results. Pindel results did not validate well without adjustments to parameters to account for varied read depth and number of samples per run. Adjustments to Pindel's M (minimum support for event) parameter improved both concordance and validation rates. Pindel was able to identify large deletions that surpassed the length capabilities of the GATK algorithms. Despite the observed variability in indel identification, we discerned strengths among the individual algorithms on specific data sets. This allowed us to suggest best practices for indel calling. Pindel's low validation rate of indel calls made in targeted exon sequencing suggests that HaplotypeCaller is better suited for short indels and multi-sample runs in targets with very high read depth. Pindel allows for optimization of minimum support for events and is best used for detection of larger indels at lower read depths.
The psychosocial effects of cleft lip and palate in non-Anglo populations: a cross-cultural meta-analysis.

Objective: A meta-analytic study was conducted to examine the cross-cultural psychosocial impact of cleft lip and/or palate in non-Anglo populations. Design: A total of 333 citations were initially identified for review using electronic and hand-search strategies. Of the six studies that met inclusion criteria, two were later excluded due to insufficient data. The four remaining studies represented a combined sample size of 2276 adolescents and adults with cleft lip and/or palate from China, Hong Kong, Taiwan, and Norway. Main Outcome Measures: Effect size using Cohen's d and confidence intervals were estimated using data from four studies of empirical, controlled study designs. Results: The magnitude of effect sizes indicated that men (d = −0.75) with cleft lip and/or palate in non-Anglo cultures are more prone to psychosocial issues than women (d = −0.33). Adults (d = −0.50) are more impacted than adolescents (d = −0.04). Overall, regardless of age, gender, or culture, individuals with cleft lip...
Book Review of Rethinking Ecomomic Recovery: A Global Green New Deal

Mona M. Lyne reviews Rethinking Economic Recovery: A Global Green New Deal by Edward B. Barbier. The author examines the power of an extraordinary economic crisis to politically engage the winds of change in the realm of global energy dependence.