cssi/SciSciGPT-SciSciNet huggingface dataset:
Peptide Methionine Sulfoxide Reductase (MsrA) Is a Virulence Determinant in Mycoplasma genitalium

Mycoplasma genitalium is the smallest self-replicating microorganism and is implicated in human diseases, including urogenital and respiratory infections and arthritides. M. genitalium colonizes host cells primarily through adherence mechanisms mediated by a network of surface-associated membrane proteins, including adhesins and cytadherence-related proteins. In this paper, we show that cytadherence in M. genitalium is affected by an unrelated protein known as peptide methionine sulfoxide reductase (MsrA), an antioxidant repair enzyme that catalyzes the reduction of methionine sulfoxide [Met(O)] residues in proteins to methionine. An msrA disruption mutant of M. genitalium, constructed through homologous recombination, displayed markedly reduced adherence to sheep erythrocytes. In addition, the msrA mutant was incapable of growing in hamsters and exhibited hypersensitivity to hydrogen peroxide when compared to wild-type virulent M. genitalium. These results indicate that MsrA plays an important role in M. genitalium pathogenicity, possibly by protecting mycoplasma protein structures from oxidative damage or through alternate virulence-related pathways.
The devil is in the details: in America, can you really say “God” in school?

This article examines conflicts that have unfolded over the past 75 years regarding the separation of church and state in American public education. Through discussion of the Establishment and Free Exercise Clauses as articulated in the First Amendment to the US Constitution, as well as influential court cases that have set legal precedent and driven educational policy, it examines what is typically referred to as the “separation” mandate. This mandate, codified in the Constitution and interpreted and upheld by the courts, concerns the inclusion of religion in public schools, including discussion of religious history and ideology in the classroom setting as well as tolerance for religious exercise through such venues as school prayer and/or the celebration of religious holidays. It advances the argument that the controversy and litigation that have surrounded issues regarding separation of church and state in the realm of public education have prompted schools to remove most study and discussion of religi...
Mother-to-infant HIV transmission: timing, risk factors and prevention

Summary. Identifying when - during pregnancy, delivery or the postnatal period - transmission of human immunodeficiency virus (HIV) from mother to infant usually takes place is critical to the development of methods to prevent maternal-infant transmission. Evidence is reviewed in this paper as to whether transmission occurs prepartum (early or late in gestation), intrapartum, or postpartum with breast feeding. Evidence in support of the notion of prepartum transmission has come from isolation of HIV from aborted fetal organs, comparison of maternal-child viral genotypes and study of neonatal cell-mediated immune responses. Evidence against prepartum transmission is that fewer than half of the children later known to be HIV-infected can be identified by virological tests carried out close to birth. A reduced rate of transmission in infants delivered by Caesarean section, and a reduced risk of transmission to second-born twins delivered vaginally, offers support to the view that intrapartum factors influence the risk of HIV transmission. Transmission through breast feeding can occur if a mother is infected postpartum and seems to pose some additional risk if she is already infected at parturition. The risk of infection increases with the stage of maternal HIV disease, but specific immunological, clinical and viral characteristics need to be investigated further. A clinical trial of zidovudine, used during late pregnancy and delivery and given to the infant at birth, has reported a significant reduction in transmission. Primary prevention of HIV infection in women remains a principal priority.
Invited commentary on “Decorative sentinel lymph node – a new entity?” by Vandeweyer and Van De Casseye

In an age of super-specialization we are all most comfortable in our own areas of expertise. To the operating surgeon an unexpected black-hued lymph node is a surprising and disturbing finding that appropriately raises concern that the node may harbor melanoma, even in the absence of a history of prior melanoma. To pathologists pigments in tissues are relatively commonplace, but can be challenging. A dark-colored node may contain melanin pigment, in melanoma cells or in macrophages, hemosiderin or, as in the case reported in this issue, particulate carbon. Rarer possibilities include lipofuscin or homogentisic acid in patients with alkaptonuria. In interpreting the nature and significance of tissue pigmentation pathologists follow wellestablished algorithms. Iron-based pigments, such as hemosiderin react precisely in the Prussian blue histochemical reaction and turn a striking blue color. Melanins turn darker with silver stains and are removed by bleaching agents such as potassium permanganate (iron and carbon are not bleachable). The cytology and histology of a melanized lymph node are remarkably easier to interpret in a hematoxylin and eosin-stained section after removal of the masking melanin by bleaching. Nodal carbon is relatively common: deriving from the tattoo artist in the case of peripheral nodes and cigarette smoke, the coal mine and the polluted urban environment in the case of pulmonary and mediastinal nodes. Carbon pigment is now used to confirm the ‘‘sentinel’’ status of a lymph node [1]. Thus, the intriguing clinical dilemma presented by Vandeweyer et al. in this issue is readily resolved by careful pathologic evaluation of the tissues. Note that this requires fixed tissues and special stains and is thus not a matter that can readily or certainly be resolved by intraoperative frozen-section analysis. A node that is dark-colored on clinical inspection may be the site of metastatic melanoma, but it would seem inappropriate to undertake further and substantial surgery purely on the basis of gross inspection, without detailed and thoughtful histological analysis. Close consultation between the operating room and the surgical pathology laboratory provides a solid basis for optimal clinical management.
Relating the progeny production curve to the speed of an epidemic.

Ferrandino, F. J. 2013. Relating the progeny production curve to the speed of an epidemic. Phytopathology 103:204-215. The dependence of the initial infection rate, r, on the basic reproductive number, R0, and the temporal moments of the progeny production curve are examined. A solution to the linearized Kermack-McKendrick equation is presented and used to analyze a variety of theoretical models of pathogen reproduction. The solution yields a relation between r and the basic reproductive number, R0; the mean time between pathogen generations, µ; and the standard deviation about this mean, σ. A transformation using the dimensionless variables rµ and rσ is introduced, which maps the solution onto a one-dimensional curve. An approximation for the value of r in terms of R0 and the first four temporal moments of the reproductive curve is derived. This allows direct comparison of epidemics resulting from theoretical models with those generated using experimentally obtained reproduction curves. For epidemics characterized by a value of rµ < 5, the value of r is well determined (<2%) by this fourth-order expansion regardless of the functional form of the reproduction curve.
In vivo pharmacokinetics and in vitro production of cocaethylene in pregnant guinea pigs

Abstract Simultaneous exposure to cocaine and ethanol results in the formation of cocaethylene, an active metabolite of cocaine. The concurrent abuse of both cocaine and ethanol is common during human pregnancy, but the kinetics of elimination and formation of this ethyl ester of cocaine have not been studied during pregnancy in any species. In the late gestation guinea pig (61 to 63 days), cocaethylene, at doses of 2 to 4 mg · kg −1 , is rapidly eliminated with a half-life of 29 min and a total body clearance of 77 ml · min −1 · kg −1 . It is formed enzymatically by hepatic microsomal preparations from fetal, neonatal and maternal guinea pigs. The maximum rate of cocaethylene production (apparent V max ) when either ethanol or cocaine are varied while the other substrate is held constant, increases with age, from the late fetal period (65 days gestation, term 70 days) to adulthood. However, the Michaelis-Menten constant (apparent K M ) does not change with age. The rapid elimination of cocaethylene, coupled with the slow rate of formation (apparent V max of 140 pmol · min −1 · mg microsomal protein −1 ) and the small amount of plasma analyzed most likely explains the inability to detect cocaethylene in vivo after concomitant cocaine and ethanol administration.
Computational modeling of carbon nanostructures for energy storage applications

We present a theoretical model for electrical double layers formed by ion adsorption in nanoscale carbon pores. In this work a combination of computational methods, including first-principles and classical modeling, are used to explain the onset of an anomalous increase in capacitance for small pores. The study highlights the key role played by pore curvature and nanoconfinement on the capacitance performance. We emphasize the role of modeling in providing a precise understanding of the processes responsible for capacitive energy storage, and how simulations can be used to enhance desired properties and suppress unwanted ones.
Should individual PI3 kinase isoforms be targeted in cancer

Activation of the phosphoinositide-3-kinase (PI3K) signaling pathway is frequently found in common human cancers, brought about by oncogenic receptor tyrosine kinases (RTKs) acting upstream, PTEN loss, or activating mutations of PI3K itself. Recent studies have delineated distinct but overlapping functions in cell signaling and tumorigenesis for p110α and p110β, the two major catalytic subunits of PI3K expressed in the tissues of origin for the common tumor types. In most cell types studied, p110α carries the majority of the PI3K signal in classic RTK signal transduction, while p110β responds to GPCRs. Both p110α and p110β function in cellular transformation induced by alterations in components of PI3K pathway. Specifically, p110α is essential for the signaling and growth of tumors driven by PIK3CA mutations and/or oncogenic RTKs/Ras, whereas p110β is the major isoform in mediating PTEN-deficient tumorigenesis. While pan-PI3K inhibitors are currently being tested in the clinic, p110 isoform-specific inhibition holds promise as a therapeutic strategy.
Obstructive lower urinary tract symptoms correlate with erectile dysfunction.

Abstract Objectives To examine whether the severity of lower urinary tract symptoms (LUTS), when controlled for other factors, is related to erectile dysfunction (ED) in the male veteran population. Early evidence suggests that LUTS may be associated with ED in men. Methods A total of 181 male veterans were prospectively entered into the study. They completed the Sexual Health Inventory for Men (SHIM) and International Prostate Symptom Score (IPSS) questionnaires. Of the 181 men, 144 also underwent uroflowmetry, including determination of the postvoid residual urine volume. Demographic and medical history data were recorded. Pearson correlation coefficients and multiple linear regression analysis were used to examine the relationship between LUTS and ED, as well as the effects of age and comorbidities. Results The correlation coefficient (r) for the SHIM score with the total IPSS was −0.17 ( P = 0.023); with the obstructive IPSS, it was −0.20 ( P = 0.006); and with the irritative IPSS, −0.05 ( P = 0.492). Age was the only other factor with a statistically significant correlation with the SHIM score ( r = −0.23, P = 0.002). Multiple linear regression modeling showed obstructive IPSS ( P = 0.001) and depression ( P = 0.017) to be the only statistically significant predictors of the SHIM score. A consistent negative correlation was found between obstructive IPSS and the SHIM score across age groups, with the strongest effect for men aged 60 to 70 years ( r = −0.412, P = 0.003). Conclusions Obstructive LUTS correlated with, and were predictive of, ED, even after controlling for age and comorbidities. Although age correlated with ED, it did not add to the power of the multiple linear regression model composed of obstructive IPSS and depression.
V(D)J recombination: on the cutting edge

The vertebrate immune system has evolved an elegant mechanism for generating an enormous diversity in antigen receptor binding specificity from a limited amount of genetic information. Recent advances are rapidly increasing our understanding of this unusual site-specific DNA rearrangement that assembles the antigen receptor genes during lymphoid development.
Ventricular Structure and Function in Aged Dogs With Renal Hypertension. A Model of Experimental Diastolic Heart Failure

Background— Heart failure (HF) with normal ejection fraction (diastolic HF [DHF]) usually occurs in elderly patients with hypertension. The presence and significance of altered systolic and diastolic ventricular function in DHF is increasingly controversial. Our objective was to develop a clinically relevant large-animal model to better understand the pathophysiology of DHF. Methods and Results— Ventricular structure and function were characterized in young control (YC group; n=6), old control (OC group; n=7), and old dogs made hypertensive by renal wrapping (experimental DHF [ExDHF] group; n=8). The ExDHF group was associated with normal left ventricular (LV) volume, increased LV mass, and myocardial fibrosis. LV relaxation was impaired in ExDHF (τ=53±6 ms) compared with OC (τ=35±3 ms; P<0.05) and YC (τ=33±6 ms; P<0.05) dogs. The percent diastole at which relaxation is complete was increased in ExDHF (116±30%) compared with OC (69±8%; P<0.05) and YC (35±5%; P<0.05) dogs. The coefficient of LV diastolic s...
Developmental shifts in functional morphology of the retina in Atlantic tarpon, Megalops atlanticus (Elopomorpha: Teleostei) between four ecologically distinct life-history stages

The Atlantic tarpon, Megalops atlanticus, is a large piscivorous fish that supports economically important recreational fisheries in the Gulf of Mexico, Caribbean, and Florida Atlantic coast. Megalops atlanticus undergoes ontogenetic shifts in morphology, hatching in the open ocean as larvae (less than 1 cm in length), moving into hypoxic turbid mangrove marshes as juveniles (around 10 cm in length), and then moving into coastal oceanic waters as adults (over 100 cm in length). In this study, photoreceptor distributions, opsin distributions, and photoreceptor absorbance characteristics were studied with light microscopy, transmission electron microscopy, antiopsin immunofluorescence, and microspectrophotometry, respectively, at four ecologically distinct life-history stages—premetamorphic larva, settlement stage, juvenile, and adult. The purposes of this study were 1) to determine the extent to which the retina of M. atlanticus changes over the course of development and 2) to relate these retinal changes with ecological shifts between developmental stages. The new data presented here indicate that the M. atlanticus retina changes substantially in rod and cone distributions and absorbance characteristics over the course of development and that these changes correlate closely with those in habitat and behavior. We show that M. atlanticus has a rod-dominated retina at the larval stage (which is unusual for teleost larvae) and that the scotopic visual system becomes far better developed with maturity, adding a substantial tapetum and high densities of small, bundled, and stacked rod cells. We also show that there are shifts in cone and rod spectral sensitivities and an increase in the diversity of spectrally distinct cone classes, including the addition of ultraviolet cones as fish mature into adults.
Epigenetic activation of tumor suppressor microRNAs in human cancer cells.

MicroRNAs (miRNAs) are small non-coding RNAs that function as endogenous post-transcriptional silencers of target genes. miRNAs are expressed in a tissue specific manner and play important roles in cell proliferation, apoptosis, and differentiation during animal development. Recent studies have shown a distinct connection between aberrant expression of miRNAs and the development of cancer, suggesting that miRNAs can be potential therapeutic targets. Our recent study has shown that some miRNAs are controlled by epigenetic alterations such as DNA methylation and histone modification in human cancer cells. Activation of tumor suppressor miRNAs by chromatin modifying drugs may cause downregulation of target oncogenes and could be a novel strategy for the prevention and treatment of human cancer.
Developmental toxicity of 1,1,1-trichloroethane in CD rats.

1,1,1-Trichloroethane (TCEN), a major industrial and household solvent, was evaluated for pre- and postnatal developmental effects in Sprague-Dawley rats. This study was designed to assess the repeatability of a report (S.C. Dapson, D.E. Hutcheon, and D. Lehr, Teratology 29, 25A, 1984) that indicated that 10 ppm TCEN in drinking water caused cardiac malformations in developing rats. In the present study, TCEN (97% pure) was administered in the drinking water at target concentrations of 3, 10, and 30 ppm, using 0.05% Tween 80 as an emulsifying agent. Two control groups, one receiving deionized/filtered water and the other receiving a vehicle control solution containing 0.05% Tween 80 and 0.9 ppm 1,4-dioxane, a stabilizing agent found in the bulk chemical, were also included. Male and female breeders (more than 30 per group) were exposed to the control solutions or test compound for 14 consecutive days prior to cohabitation and for up to 13 days during the cohabitation phase. Sperm-positive females (24-29 per group) continued to be exposed to these formulations during pregnancy and lactation to Postnatal Day (PND) 21. Parental animals exhibited a slight aversion to the 30-ppm drinking water during the premating exposure. No significant effect on reproductive competence of the parental animals or postnatal growth and development of the offspring to PND 21 was noted. A slight increase in mortality from implantation to PND 1, possibly due to high mortality in one litter, was observed in the 30-ppm dose group. There was no indication of an increase in the incidence of cardiac or other malformations in PND 21 pups. In summary, TCEN administered at 3, 10, and 30 ppm in the drinking water had no significant effect on the morphological development of CD rats.
Templatic transfer in Arabic broken plurals

In summary, we have shown how transfer can account for some cases of templatic morphology, beyond the reduplication examples discussed by Clements. John McCarthy observes that Modern Hebrew Pi'el and Hitpa'el could also be analyzed along these lines. See McCarthy (1984) and Bat-El (1986) for alternative analyses. We are not proposing that transfer should replace normal direct melodic linking. Rather, we are proposing that direct melodic linking cannot insightfully account for all cases of templatic morphology and must be supplemented by transfer. It should be noted that our use of transfer differs from that of reduplicative transfer. First, while a reduplicative affix undergoes linearization with respect to the stem, templatic transfer does not entail linearization. A second difference between templatic transfer and reduplicative transfer is that, in templatic transfer, association between skeleta is one-to-one, left-to-right. In reduplicative transfer, Clements proposes a different procedure where vowels associate before consonants. This latter method simply would not work in the case of broken plurals. A third potential differences between them is OVERRIDING. In templatic association, a directly associated melodic element overrides a transferred melodic element. In reduplication, it is unclear whether prespecificaion precludes association or overrides it as here. To maintain this analysis in light of these differences, it must be supposed that these differences correspond to parameters along which languages can vary. The strongest claim we could make is that these differences are not independent, but correspond to a single parameter. Another explanation for these differences might be that transfer simply does not occur in reduplication, and that its apparent effects there are due to other mechanisms, perhaps along the lines of those suggested in note 8 above. However, whatever the merits of reduplicative transfer, some sort of transfer must be available for templatic morphology.
Exemplary Models of Firm Innovation: Strategy and Leadership for the Twenty-First Century Competitive Environment

The author begins the article by outlining factors that influence the innovation success of firms. Second, he presents the resource-based view and the contingency perspective as the theoretical underpinnings. Third, he presents the literature review, methodology, and three approaches employed by exemplary innovators in stimulating creative and innovative ideas within their organizations. Fourth, the author discusses how exemplary innovators manage creativity and innovation. Fifth, he draws implications for would-be innovators seeking to make innovation an integral part of their strategic thrust. The author concludes by emphasizing a similarity between innovations of the previous two centuries and those of the twenty-first century. He then draws a lesson from the above centuries that can be applied today: adept, well-managed companies that commit the right resources to innovation and leverage their external environment will shape the markets and build the new industries of the twenty-first century (Chesbrough & Teece, 2002).
Transformed pseudo-random patterns for BIST

This paper presents a new approach for on-chip test pattern generation. The set of test patterns generated by a pseudo-random pattern generator (e.g., an LFSR) is transformed into a new set of patterns that provides the desired fault coverage. The transformation is performed by a small amount of mapping logic that decodes sets of patterns that don't detect any new faults and maps them into patterns that detect the hard-to-detect faults. The mapping logic is purely combinational and is placed between the pseudo-random pattern generator and the circuit under test (CUT). A procedure for designing the mapping logic so that it satisfies test length and fault coverage requirements is described. Results are shown for benchmark circuits which indicate that an LFSR plus a small amount of mapping logic reduces the test length required for a particular fault coverage by orders of magnitude compared with using an LFSR alone. These results are compared with previously published results for other methods, and it is shown that the proposed method requires much less overhead to achieve the same fault coverage for the same test length.
The elephantine shape of addiction

By summarizing, in a single piece, various current perspectives on addiction, Redish et al. have performed a useful service to the field. Their central message is that addiction comprises many vulnerabilities rather than a single vulnerability. Such a message may not be new, but it is worth repeating.
Cardiac Alternans Do Not Rely on Diastolic Sarcoplasmic Reticulum Calcium Content Fluctuations

Cardiac alternans are thought to be a precursor to life-threatening arrhythmias. Previous studies suggested that alterations in sarcoplasmic reticulum (SR) Ca 2+ content are either causative or not associated with myocyte Ca 2+ alternans. However, those studies used indirect measures of SR Ca 2+ . Here we used direct continuous measurement of intra-SR free [Ca 2+ ] ([Ca 2+ ] SR ) (using Fluo5N) during frequency-dependent Ca 2+ alternans in rabbit ventricular myocytes. We tested the hypothesis that alternating [Ca 2+ ] SR is required for Ca 2+ alternans. Amplitudes of [Ca 2+ ] SR depletions alternated in phase with cytosolic Ca 2+ transients and contractions. Some cells showed clear alternation in diastolic [Ca 2+ ] SR during alternans, with higher [Ca 2+ ] SR before the larger SR Ca 2+ releases. However, the extent of SR Ca 2+ release during the small beats was smaller than expected for the modest decrease in [Ca 2+ ] SR . In other cells, clear Ca 2+ alternans was observed without alternations in diastolic [Ca 2+ ] SR . Additionally, alternating cells were observed, in which diastolic [Ca 2+ ] SR fluctuations occurred interspersed by depletions in which the amplitude was unrelated to the preceding diastolic [Ca 2+ ] SR . In all forms of alternans, the SR Ca 2+ release rate was higher during large depletions than during small depletions. Although [Ca 2+ ] SR exerts major influence on SR Ca 2+ release, alternations in [Ca 2+ ] SR are not required for Ca 2+ alternans to occur. Rather, it seems likely that some other factor, such as ryanodine receptor availability after a prior beat (eg, recovery from inactivation), is of greater importance in initiating frequency-induced Ca 2+ alternans. However, once such a weak SR Ca 2+ release occurs, it can result in increased [Ca 2+ ] SR and further enhance SR Ca 2+ release at the next beat. In this way, diastolic [Ca 2+ ] SR alternans can enhance frequency-induced Ca 2+ alternans, even if they initiate by other means.
PIV flow measurements for heat transfer characterization in two-pass square channels with smooth and 90° ribbed walls

Abstract Particle image velocimetry (PIV) experiments have been carried out to study the correlation between the high-Reynolds number turbulent flow and wall heat transfer characteristics in a two-pass square channel with a smooth wall and a 90° rib-roughened wall. Detailed averaged velocity distributions and turbulent kinetic energy for both the main and the secondary flows are given for a representative Reynolds number (Re) of 30,000. The PIV measurement results were compared with the heat transfer experimental data of Ekkad and Han [International Journal of Heat Mass Transfer 40 (11) (1997) 2525–2537]. The result shows that the flow impingement is the primary factor for the two-pass square channel heat transfer enhancement rather than the flow turbulence level itself. The characteristics of the secondary flow, for example, vortex's shape, strength, rotating-direction and positions, are closely correlated with the wall heat transfer enhancements for both smooth and ribbed wall two-pass square channels. The rib-induced flow turbulence increases the heat transfer mainly because of the enhanced local flow impingement near the rib.
On the nature and evolution of the neural bases of human language

The traditional theory equating the brain bases of language with Broca's and Wernicke's neocortical areas is wrong. Neural circuits linking activity in anatomically segregated populations of neurons in subcortical structures and the neocortex throughout the human brain regulate complex behaviors such as walking, talking, and comprehending the meaning of sentences. When we hear or read a word, neural structures involved in the perception or real-world associations of the word are activated as well as posterior cortical regions adjacent to Wernicke's area. Many areas of the neocortex and subcortical structures support the cortical-striatal-cortical circuits that confer complex syntactic ability, speech production, and a large vocabulary. However, many of these structures also form part of the neural circuits regulating other aspects of behavior. For example, the basal ganglia, which regulate motor control, are also crucial elements in the circuits that confer human linguistic ability and abstract reasoning. The cerebellum, traditionally associated with motor control, is active in motor learning. The basal ganglia are also key elements in reward-based learning. Data from studies of Broca's aphasia, Parkinson's disease, hypoxia, focal brain damage, and a genetically transmitted brain anomaly (the putative "language gene," family KE), and from comparative studies of the brains and behavior of other species, demonstrate that the basal ganglia sequence the discrete elements that constitute a complete motor act, syntactic process, or thought process. Imaging studies of intact human subjects and electrophysiologic and tracer studies of the brains and behavior of other species confirm these findings. As Dobzansky put it, "Nothing in biology makes sense except in the light of evolution" (cited in Mayr, 1982). That applies with as much force to the human brain and the neural bases of language as it does to the human foot or jaw. The converse follows: the mark of evolution on the brains of human beings and other species provides insight into the evolution of the brain bases of human language. The neural substrate that regulated motor control in the common ancestor of apes and humans most likely was modified to enhance cognitive and linguistic ability. Speech communication played a central role in this process. However, the process that ultimately resulted in the human brain may have started when our earliest hominid ancestors began to walk.
Use of Vacuum for Counter Gravity Casting of Metals

The use of vacuum to fill molds to form investment castings in a countergravity casting fashion was started in the early 1970s. This paper describes how the processes work and the reasons for their advantages in cost, quality, and process control. Countergravity casting is being done in sand, permanent, and investment (lost wax) ceramic molds and alloys are cast in air and inert atmospheres. The process started with common steels, was extended to heat resistant superalloys, and recently even titanium alloys are being cast routinely using ceramic crucibles. The use of a unique mold design enables a great reduction in metal cast to yield a given part, thereby greatly reducing the energy use in making such castings. Computerized control of the rate of vacuum application enables complete control of filling rates, permitting casting of very high quality castings in very viscuous metals, such as metal matrix composites of aluminum. These processes are used to produce more than $200 million worth of castings annually and this will greatly increase in the next few years due to the production of automotive exhaust manifolds in stainless steel.
WHAM: a high-throughput sequence alignment method

Over the last decade the cost of producing genomic sequences has dropped dramatically due to the current so called "next-gen" sequencing methods. However, these next-gen sequencing methods are critically dependent on fast and sophisticated data processing methods for aligning a set of query sequences to a reference genome using rich string matching models. The focus of this work is on the design, development and evaluation of a data processing system for this crucial "short read alignment" problem. Our system, called WHAM, employs novel hash-based indexing methods and bitwise operations for sequence alignments. It allows richer match models than existing methods and it is significantly faster than the existing state-of-the-art method. In addition, its relative speedup over the existing method is poised to increase in the future in which read sequence lengths will increase. The WHAM code is available at http://www.cs.wisc.edu/wham/.
Mobile node rostering in intermittently connected passive RFID networks

This paper focuses on the problem of rostering in intermittently connected passive RFID networks. It aims to report a list of tagged mobile nodes that appear in given interested area(s) and time interval(s). Such rostering faces several unique challenges. First, the network consists of two dramatically different types of nodes: powerful static readers and extremely resource-constrained mobile tags. Communication can be established from a reader to a tag only, but not tags to tags or readers to readers. Therefore the connectivity is very low and intermittent. Besides connectivity, the tag's computation power is also intermittent. It is available only for a short interval when the tag is powered up by a nearby reader, rendering any continuous functions impossible. Moreover, the capacity of tags is so limited that it becomes the critical network resource and communication bottleneck. To address the above challenges, we propose a rostering algorithm that employs a dynamic space-efficient coding scheme to construct hypothetic packet candidates, appraises their values according to information redundancy and tag mobility, and establishes a 0–1 Knapsack model to choose the best set of packets, which together maximize their total (redundancy-excluded) value but do not exceed the capacity of a tag. We carry out experiments that involve 38 volunteers for 9 days and perform large-scale simulations to evaluate the proposed rostering scheme.
Real-Time Dynamic Power Management through Device Forbidden Regions

Dynamic power management (DPM) techniques are crucial in minimizing the overall energy consumption in real-time embedded systems. The timing constraints of real-time applications and non-trivial time/energy transition overheads introduce significant challenges, as the device sleep intervals should be longer than a minimum threshold (called the break-even time) to ensure energy-efficiency. In this paper, we present a novel approach to the real-time DPM problem by explicitly enforcing long device sleep intervals for different devices, called device forbidden regions. We focus on the application of our technique to task systems with rate-monotonic priorities, and develop our algorithm DFR-RMS. Our solution includes a static component where the duration and frequency of forbidden regions are determined through the extended time-demand analysis to preserve the temporal correctness of all the tasks, while enhancing the energy savings. Then, we present a sophisticated on-line component which interacts with existing prediction-based DPM schemes to realize the full potential of device forbidden regions. Further, our scheme can be used with or without dynamic voltage scaling (DVS). Our experimental evaluation hints that significant energy gains can be obtained, when compared to the existing prediction-based techniques. Another contribution of this research effort is to show that the general problem of generating feasible schedules for preemptive periodic real-time tasks where all device sleep intervals are longer than the device break-even times is NP-hard in the strong sense.
Retrofitting the IBM POWER Hypervisor to Support Mandatory Access Control

Server virtualization more readily enables the collocation of disparate workloads on a shared physical platform. When employed on systems across a data center, the result can be a dramatic increase in server utilization and a decrease in overall power, cooling and floor space requirements. However, in an environment where workloads share the underlying platforms, achieving other desirable workload goals, such as availability and security, becomes a challenge. In particular, enforcing isolation between workloads in a large, dynamic, and virtualized data center requires strong yet easily configurable controls on the sharing of resources at the virtualization layer. Commercial hypervisors usually offer reasonable isolation of individual virtual machines (VMs). However, on hypervisor-based platforms, one cannot currently define a single policy that automatically enforces restrictions on the sharing of resources between multiple VMs or request an air gap between workloads. In this paper, we describe the design and implementation of a Hypervisor-based Mandatory Access Control (MAC) that achieves policy-driven distributed workload isolation for the IBM Power Hypervisor (PHYP). We discuss our experiences and lessons learned and examine the implications and trade-offs involved in providing MAC on a production- level, commercially-available hypervisor. Our goal is to simplify the security management of data centers through centralized security management and policy- driven distributed access control and data protection.
Parallel Particle-In-Cell Simulation of Colliding Beams in High Energy Accelerators

In this paper we present a self-consistent simulation model of colliding beams in high energy accelerators. The model, which is based on a particle-in-cell method, uses a new developed shifted-Green function algorithm for the efficient calculation of the beam-beam interaction. The model uses transfer maps to treat the external focusing elements and a stochastic map to treat radiation damping and quantum excitation of the beams. In the parallel implementation we studied various strategies to deal with the particular nature of the colliding beam system - a system in which there can be significant particle movement between beam-beam collisions. We chose a particle-field decomposition approach instead of the conventional domain decomposition or particle decomposition approach. The particle-field approach leads to good load balance, reduced communication cost, and shows the best scalability on an IBM SP3 among the three parallel implementations we studied. A performance test of the beam-beam model on a Cray T3E, IBM SP3, and a PC cluster is presented. As an application, we studied the effect of long-range collisions on antiproton lifetime in the Fermilab Tevatron.
Omega-3 Supplementation Lowers Inflammation and Anxiety in Medical Students: A Randomized Controlled Trial

Observational studies have linked lower omega-3 (n-3) polyunsaturated fatty acids (PUFAs) and higher omega-6 (n-6) PUFAs with inflammation and depression, but randomized controlled trial (RCT) data have been mixed. To determine whether n-3 decreases proinflammatory cytokine production and depressive and anxiety symptoms in healthy young adults, this parallel group, placebo-controlled, double-blind 12-week RCT compared n-3 supplementation with placebo. The participants, 68 medical students, provided serial blood samples during lower-stress periods as well as on days before an exam. The students received either n-3 (2.5 g/d, 2085 mg eicosapentaenoic acid and 348 mg docosahexanoic acid) or placebo capsules that mirrored the proportions of fatty acids in the typical American diet. Compared to controls, those students who received n-3 showed a 14% decrease in lipopolysaccharide (LPS) stimulated interleukin 6 (IL-6) production and a 20% reduction in anxiety symptoms, without significant change in depressive symptoms. Individuals differ in absorption and metabolism of n-3 PUFA supplements, as well as in adherence; accordingly, planned secondary analyses that used the plasma n-6:n-3 ratio in place of treatment group showed that decreasing n-6:n-3 ratios led to lower anxiety and reductions in stimulated IL-6 and tumor necrosis factor alpha (TNF-α) production, as well as marginal differences in serum TNF-α. These data suggest that n-3 supplementation can reduce inflammation and anxiety even among healthy young adults. The reduction in anxiety symptoms associated with n-3 supplementation provides the first evidence that n-3 may have potential anxiolytic benefits for individuals without an anxiety disorder diagnosis. ClinicalTrials.gov identifier: NCT00519779.
Alcohol outlet density and violence: a geospatial analysis.

Aims: To examine the relationship between alcohol outlet density and violent crime controlling for neighbourhood sociostructural characteristics and the effects of spatially autocorrelated error. Design: The sample for this ecologic study comprised 188 census tracts from the City of Austin, Texas and 263 tracts from the City of San Antonio, Texas. Data pertaining to neighbo urhood social structure, alcohol density and violent crime were collected from archival sources, and analysed using bivariate, multiva riate and geospatial analyses. Results: Using ordinary least squares analysis, the neighbourhood sociostructural covariates explained close to 59% of the variability in violent crime rates in Austin and close to 39% in San Antonio. Adding alcohol outlet density in the target and adjacent census tracts improved the explanatory power of both models. Alcohol outlet density in the target census tract remaine d a significant predictor of violent crime rates in both cities when the effects of autocorrelated error were controlled for. In Austin, the effects of alcohol outlet density in the adjacent census tracts also remained significant. The final model explains 71% of the variance in violent crime in Austin and 56% in San Antonio. Conclusions: The findings show a clear association between alcohol outlet density and violence, and suggest that the issues of alcohol availability and access are fundamental to the prevention of alcohol-relat ed problems within communities.
Magnetic resonance angiography detection of abnormal carotid artery plaque in patients with cryptogenic stroke.

Background Magnetic resonance imaging of carotid plaque can aid in stroke risk stratification in patients with carotid stenosis. However, the prevalence of complicated carotid plaque in patients with cryptogenic stroke is uncertain, especially as assessed by plaque imaging techniques routinely included in acute stroke magnetic resonance imaging protocols. We assessed whether the magnetic resonance angiography–defined presence of intraplaque high‐intensity signal (IHIS), a marker of intraplaque hemorrhage, is associated with ipsilateral cryptogenic stroke. Methods and Results Cryptogenic stroke patients with magnetic resonance imaging evidence of unilateral anterior circulation infarction and without hemodynamically significant (≥50%) stenosis of the cervical carotid artery were identified from a prospective stroke registry at a tertiary‐care hospital. High‐risk plaque was assessed by evaluating for IHIS on routine magnetic resonance angiography source images using a validated technique. To compare the presence of IHIS on the ipsilateral versus contralateral side within individual patients, we used McNemar's test for correlated proportions. A total of 54 carotid arteries in 27 unique patients were included. A total of 6 patients (22.2%) had IHIS‐positive nonstenosing carotid plaque ipsilateral to the side of ischemic stroke compared to 0 patients who had IHIS‐positive carotid plaques contralateral to the side of stroke ( P =0.01). Stroke severity measures, diagnostic evaluations, and prevalence of vascular risk factors were not different between the IHIS‐positive and IHIS‐negative groups. Conclusions Our findings suggest that a proportion of strokes classified as cryptogenic may be mechanistically related to complicated, nonhemodynamically significant cervical carotid artery plaque that can easily be detected by routine magnetic resonance imaging/magnetic resonance angiography acute stroke protocols.
Deterrence, Compellence, and Prospect Theory

Deterrence and compellence couple demands for inaction and action, respectively, to a threat of sanctions. Conventional wisdom holds that deterrence requires less coercive effort than compellence, yet expected utility theory contradicts this claim. Only if exogenous factors affect these situations in a systematic and asymmetrical manner will the claim hold within expected utility theory. Prospect theory provides a systematic and endogenous account for this claim. Experimental findings suggest the degree of effort required to obtain compliance in comparable deterrence and compellence situations. Deterrence is “easier” than compellence, but this relationship is variable. Deterrence requires less effort than expected, and the relative effort it requires decreases substantially as the stakes demanded and costs threatened grow. Compellence requires more effort than expected, and the relative effort it requires decreases slightly as the stakes demanded and costs threatened grow.
Parallel real-time systems: formal specification

For many real time applications, parallel computers offer a natural computing platform. However, very little attention has been paid to software support for real time embedded systems on parallel machines. The paper addresses the problem of formal software specification for parallel real time systems, and presents some features of a formal specification language-PRETSEL (Parallel REal Time SpEcification Language). The syntax of PRETSEL is presented and the formal semantic rules are defined. The effectiveness of PRETSEL is demonstrated through the specification of the functionality and timing requirements of a Sonar system.
Jean Giono’s Le Chant du Monde : The Harmony of the Elements

It was Giono’s ambition to write a novel in which man is one with nature. Every elemental force would have a particular value and a particular voice stronger than that of the human characters. These voices join in an harmonious song in Le Chant du Monde.
Intra-arterial cisplatin and concomitant radiation therapy followed by surgery for advanced paranasal sinus cancer.

Objective: To report the long-term efficacy of a combined regimen of intra-arterial high-dose cisplatin chemotherapy and concomitant radiation therapy followed by organ-sparing surgery when possible in the treatment of advanced paranasal sinus cancer. Design: Review of prospectively collected data. Setting: Academic referral center. Patients:Nineteenpatientswithadvancedparanasalsinus malignancies with a minimum follow-up of 2 years. Malignancies included 14 squamous cell carcinomas (74%), 2 adenocarcinomas (10%), 2 adenoid cystic carcinomas (10%), and 1 undifferentiated carcinoma (5%). Sixteen patients (84%) had T4 disease. Intervention: Treatment consisted of preoperative radiation therapy (2.0 Gy/fraction per day; total dose, 50 Gy in 5 weeks) given concomitantly with 3 to 4 weekly infusionsofintra-arterialcisplatin(150mg/m 2 perweek) andsystemicsodiumthiosulfateneutralization.Theregimen included planned surgery performed approximately8weeksaftercompletionofradiationtherapy.Ten patients underwent a transcranial anterior craniofacial resection; 1, a medial maxillectomy; and 1, an endoscopic restaging only. Results: After a median follow-up of 53 months, actuarial overall survival at 2 and 5 years was 68% and 53%, respectively. One patient died of myocardial infarction duringtreatment.Noothertreatment-limitingtoxiceffect was noted. Although 3 patients had persistence of disease, delayed local failure occurred only in 2 and distant metastasis in 3. Except for cataract in 2 patients, no visual loss developed. Conclusion: Despite the advanced stage and unfavorable nature of cancer in this cohort, our results indicate thatthisregimenholdspromiseandmeritsfurtherstudy. Arch Otolaryngol Head Neck Surg. 2004;130:948-955
Increasing off-chip bandwidth in multi-core processors with switchable pins

Off-chip memory bandwidth has been considered as one of the major limiting factors to processor performance, especially for multi-cores and many-cores. Conventional processor design allocates a large portion of off-chip pins to deliver power, leaving a small number of pins for processor signal communication. We observed that the processor requires much less power than that can be supplied during memory intensive stages. This is due to the fact that the frequencies of processor cores waiting for data to be fetched from off-chip memories can be scaled down in order to save power without degrading performance. In this work, motivated by this observation, we propose a dynamic pin switch technique to alleviate the bandwidth limitation issue. The technique is introduced to dynamically exploit the surplus pins for power delivery in the memory intensive phases and uses them to provide extra bandwidth for the program executions, thus significantly boosting the performance