cssi/SciSciGPT-SciSciNet huggingface dataset:
Engineered human dicentric chromosomes show centromere plasticity

The centromere is essential for the faithful distribution of a cell's genetic material to subsequent generations. Despite intense scrutiny, the precise genetic and epigenetic basis for centromere function is still unknown. Here, we have used engineered dicentric human chromosomes to investigate mammalian centromere structure and function. We describe three classes of dicentric chromosomes isolated in different cell lines: functionally monocentric chromosomes, in which one of the two genetically identical centromeres is consistently inactivated; functionally dicentric chromosomes, in which both centromeres are consistently active; and dicentric chromosomes heterogeneous with respect to centromere activity. A study of serial single cell clones from heterogeneous cell lines revealed that while centromere activity is usually clonal, the centromere state (i.e. functionally monocentric or dicentric) in some lines can switch within a growing population of cells. Because pulsed field gel analysis indicated that the DNA at the centromeres of these chromosomes did not change detectably, this switching of the centromere state is most likely due to epigenetic changes. Inactivation of one of the two active centromeres in a functionally dicentric chromosome was observed in a percentage of cells after treatment with Trichostatin A, an inhibitor of histone deacetylation. This study provides evidence that the activity of human centromeres, while largely stable, can be subject to dynamic change, most likely due to epigenetic modification.
The effects of labeled and unlabeled praise upon lower and middle class children

Abstract This study investigated the relative effectiveness of two types of content of praise, labeled and unlabeled, with lower and middle class children. Following two brief observation periods designed to assess differences in the frequency with which lower and middle class mothers employed labeled and unlabeled praise, each mother played the marble-in-the-hole game with her child. Half of the mothers in each group were given labeled and half were given unlabeled praise statements to make contingent upon their child dropping marbles in a particuler hole. The results indicated that the children were more responsive to labeled than to unlabeled praise. The mothers from the two socioeconomic groups did not differ in the frequency with which they employed labeled and unlabeled praise in the initial observation periods.
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

By utilizing Graphics Processing Units, we show that constant pH molecular dynamics simulations (CpHMD) run in Generalized Born (GB) implicit solvent for long time scales can yield poor pKa predictions as a result of sampling unrealistic conformations. To address this shortcoming, we present a method for performing constant pH molecular dynamics simulations (CpHMD) in explicit solvent using a discrete protonation state model. The method involves standard molecular dynamics (MD) being propagated in explicit solvent followed by protonation state changes being attempted in GB implicit solvent at fixed intervals. Replica exchange along the pH-dimension (pH-REMD) helps to obtain acceptable titration behavior with the proposed method. We analyzed the effects of various parameters and settings on the titration behavior of CpHMD and pH-REMD in explicit solvent, including the size of the simulation unit cell and the length of the relaxation dynamics following protonation state changes. We tested the method with th...
Pentoxifylline restores the depressed cardiac performance after trauma-hemorrhage and resuscitation.

Although studies have shown that pentoxifylline (PTX) improves tissue perfusion and hepatocellular function after trauma-hemorrhage and resuscitation, it is not known whether this agent has any beneficial effects on left ventricular performance under such conditions. To study this, rats underwent laparotomy (i.e., trauma induced) and were bled to and maintained at a blood pressure of 40 mm Hg until 40% of the maximum shed blood volume was returned in the form of Ringer's lactate. The animals were then resuscitated with four times the volume of shed blood with Ringer's lactate over 60 min, following which PTX (50 mg/kg body wt) or an equivalent volume of normal saline was infused intravenously over 100 min. Maximum dP/dtduring contraction (+dP/dtmax) and relaxation (−dP/dtmax), maximum rate of a “pressure-normalized” change in ventricular pressure during ventricular contraction (dP/dtmax/P), and ventricular peak systemic pressure (VPSP) were determined at 15 min before the completion of resuscitation and every 30 min up to 4 hr after resuscitation. The results indicated that both +dP/dtmaxand −dP/dtmaxdecreased significantly beginning at 0.5 h after resuscitation and remained depressed throughout the study period in saline-treated animals. In addition, VPSP was significantly depressed at 2.5 to 4 hr after resuscitation. Treatment with PTX, however, significantly improved the above parameters as well as dP/dtmax/Pand heart rate. Since PTX restores various left ventricular performance parameters, this agent appears to be a useful adjunct for improving cardiac function after trauma and hemorrhagic shock, even in the absence of blood resuscitation.
Infantile Hemangioma Research: Looking Backward and Forward

This is a remarkable time to be a student of infantile hemangiomas (IHs). IH is a common tumor, estimated to occur in approximately 4% of infants. Studied for many decades, the acquisition of knowledge and pace of IH research are accelerating. The article by Greenberger et al. in this issue is a welcome addition to the literature. It examines rapamycin as a possible treatment for IH that could potentially be curative because suppression of self-renewal of stem cells might deplete hemangiomas of the stem cells from which they originate. However, before we get too enthusiastic about using rapamycin for IHs, it is important to reflect on lessons learned from previous hemangioma therapies.
Unusual triplet state relaxation in C60 oxide

Abstract The photophysics of C 60 O has been investigated. The calibrated UV–visible absorption spectrum, fluorescence quantum yield, and triplet–triplet absorption spectrum are compared to those of C 60 . Intrinsic triplet decay is anomalous, with typically weak temperature dependence below 180 K but unusual strong activation ( E A =20 kJ mol −1 ) above. At 295 K, the triplet lifetime is only 4.2 μs, or 34 times shorter than that of C 60 . It is proposed that the activated decay channel involves reversible cleavage of the C–C epoxide bond. C 60 O efficiently quenches triplet C 60 with a rate constant of 3.6×10 9 M −1 s −1 .
Circadian periodicity of tissue glutathione and its relationship with lipid peroxidation in rats.

Abstract Circadian fluctuations in tissue glutathione (GSH) concentrations and lipid peroxidation in male Sprague-Dawley rats were investigated. Blood and all the organs studied exhibited distinct circadian variation both in GSH concentrations and peroxidation of polyunsaturated fatty acids. There was a great variation among organs in the periodicity and amplitude of the fluctuations in GSH concentrations. Liver displayed the highest variation (∼50%) followed by stomach (≈37%), heart (∼25%) and kidney (∼19%). The changes in other organs were significant but less magnitude. Implications of such variations and caution in interpretation of experimental results in response to the exposure of animals to xenobiotics are discussed.
Rearrangements of Ylides Generated from Reactions of Diazo Compounds with Allyl Acetals and Thioketals by Catalytic Methods. Heteroatom Acceleration of the [2,3]-Sigmatropic Rearrangement

Les acetals allyliques se transforment en ylures par reactions avec des diazoesters catalysees par l'acetate de rhodium(II) puis donnent des dialcoxy-2,5 alcene-4oates par transposition sigmatrope. Une cyclopropanation et une transposition Stevens concurrencent la transposition sigmatrope dans certains cas; l'influence de la structure du reactif et des conditions de reaction sur cette competition est rapportee
Design and implementation issues in an integrated database management system for engineering design environment

Abstract The need for a unified database management system for various engineering applications has long been felt. Due to the conflicting requirements, so far, most of the attempts in this field are at best partially successful. This paper presents broad perspectives of design and implementation issues of an integrated database management system. A unique feature of the system is its ability to define a unifying data model for matrices and relations. The system also provides for a unified language interface for different user groups. System architecture and a few distinguishing features are described. An evaluation of the system is presented.
Order of the QCD transition and QCD sum rules.

We propose using the finite-temperature {rho}-meson mass as an order parameter to monitor the QCD transition. This is suggested by the {rho}-meson mass formula that emerges from finite-temperature QCD sum rules in the vector channel, and which encompasses the effects of both quark and gluon condensates. We find that a second-order chiral-restoring transition implies a second-order behavior for the {rho} mass even if the value of the gluon condensate is unaffected by the transition.
Illumination-free gaze estimation method for first-person vision wearable device

Gaze estimation is a key technology to understand a person's interests and intents, and it is becoming more popular in daily situations such as driving scenarios. Wearable gaze estimation devices are use for long periods of time, therefore non-active sources are not desirable from a safety point of view. Gaze estimation that does not rely on active source, is performed by locating iris position. To estimate the iris position accurately, most studies use ellipse fitting in which the ellipse is defined by 5 parameters(position (x,y), rotation angle, semi-major axis and semi-minor axis). We claim that, for iris position estimation, 5 parameters are redundant because they might be influenced by non-iris edges. Therefore, we propose to use 2 parameters(position) introducing a 3D eye model(the transformation between eye and camera coordinate and eyeball/iris size). Given 3D eye model, projected ellipse that represents iris shape can be specified only by position under weak-perspective approximation. We quantitatively evaluate our method on both iris position and gaze estimation. Our results show that our method outperforms other state-of-the-art's iris estimation and is competitive to commercial product that use infrared ray with respect to both accuracy and robustness.
Spawning-Site Selection by Kokanee along the Shoreline of Flaming Gorge Reservoir, Wyoming-Utah

Abstract We assessed spawning-site selection by kokanee Oncorhynchus nerka (lacustrine sockeye salmon) in three shoreline areas of Flaming Gorge Reservoir, Wyoming–Utah, where they were known to spawn, Kokanee selected shale particles 10 cm in length or less on slopes of 21–40° for spawning; there was no apparent selection for water depth, The three spawning areas were unique among 26 potential spawning sites in the reservoir due to their steep slopes and the abundance of small, loose shale particles present. Protecting these three spawning areas from alteration and minimizing water level drawdown during winter are suggested as management alternatives to maintain recruitment of kokanee from shoreline spawning areas in Flaming Gorge Reservoir.
A 3D Motion Phantom for Assessing the Accuracy and Precision of Dynamic Magnetic Resonance Measurement of In Vivo Knee Kinematics

Measurement of in vivo knee kinematics can provide useful insight into disease, injury, and clinical treatment. Cartilage loading patterns are of particular interest while studying the progression of osteoarthritis [1]. However, inferring cartilage contact from skeletal kinematics requires high resolution volumetric models of cartilage surfaces and accurate skeletal positions and orientations. This is a challenging requirement at the knee, which exhibits substantial translation and non-sagittal rotation during normal activities such as gait [2]. We have recently introduced a novel 3D cine magnetic resonance (MR) imaging technique to measure in vivo tibiofemoral kinematics [3]. The purpose of this study was to develop a MR-compatible motion phantom that can generate repeatable 3D skeletal motion suitable for quantifying the accuracy and precision of kinematics derived from dynamic MRI.Copyright © 2013 by ASME
Chemical Modification of Crystalline Porous Silicon Surfaces

Abstract A large number of mild chemical reactions have recently been developed to modify porous silicon surfaces for optical or sensor applications. The modification reactions generally fall into two classes: those which link a reagent to the Si surface through Si-O linkages, and those which use Si-C linkages. Examples of these reactions and the relative advantages of each approach are presented.
A Handy Script to Implement Genetic Models in R

Genome-wide associations between genotypic and phenotypic data often assume certain genetic models. A handy script in R was written to implement three commonly used genetic models: additive, dominant and recessive models. This script can be easily inserted into more complicated programs to facilitate high-throughput association studies.
In Defense of Pharmacoepidemiology — Embracing the Yin and Yang of Drug Research

The past decade has not been kind to observational studies of medications. Dr. Jerry Avorn writes that, when done correctly, epidemiologic studies of drug effects can be more powerful than the average randomized, controlled trial, especially in assessing drug safety.
Discriminative stimulus and subjective effects of theobromine and caffeine in humans

Theobromine versus placebo discrimination and caffeine versus placebo discrimination were studied in two consecutive experiments in seven volunteers who abstained from methylxanthines. Daily sessions involved PO double-blind ingestion of two sets of capsules sequentially, one of which contained drug and the other placebo. Subjects attempted to identify, and were later informed, which set of capsules contained the drug. In each experiment subjects were exposed to progressively lower doses. Five subjects acquired the theobromine discrimination; the lowest dose discriminated ranged from 100 to 560 mg. All seven subjects acquired the caffeine discrimination; the lowest dose discriminated ranged from 1.8 to 178 mg. A final experiment evaluated subjective effect ratings following 560 mg theobromine, 178 mg caffeine and placebo, which were administered double-blind in capsules once daily, five times each in mixed sequence. Caffeine produced changes in both group and individual ratings (e.g. increased well-being, energy, social disposition and alert). Theobromine did not produce changes in group ratings but changed ratings in some subjects. Across subjects, sensitivity to caffeine discriminative effects in the discrimination experiment correlated significantly with the number and magnitude of caffeine subjective effects in the final experiment. This study documents modest discriminative effects of theobromine in humans, but the basis of the discrimination is unclear. This study suggests that commonly consumed cocoa products contain behaviorally active doses of caffeine and possibly theobromine.
Contemporary approaches for the laboratory diagnosis of Clostridium difficile infections

Since its recognition 35 years ago as a major cause of diarrheal disease in the industrialized world, the laboratory diagnosis of Clostridium difficile infections (CDI) has been in constant evolution. Currently, two approaches are recommended: a multi-step algorithm using glutamate dehydrogenase (GDH) detection as a screening test and a method to detect either C. difficile toxins or toxigenic C. difficile organisms as a confirmatory test for GDH-positive specimens. One potential algorithm uses the detection of both toxin and organisms in a stepwise manner. The second approach is the use of a nucleic acid amplification test to detect toxigenic organisms. Both methods have been proven to be sensitive and to have acceptable turnaround times. Questions still remain about which of these two approaches are optimal for establishing the diagnosis of CDI.
A Least-Squares Galerkin Split Finite Element Method for Compressible Navier-Stokes Equations

A novel finite element method is proposed that employs a least-squares method for first-order derivatives and a Galerkin method for second order derivatives, thereby avoiding the need for additional unknowns required by a pure LSFEM approach. When the unsteady form of the governing equations is used, a streamline upwinding term is introduced naturally by the least-squares method. Resulting system matrix is always symmetric and positive definite and can be solved by iterative solvers like pre-conditioned conjugate gradient method. The method is stable for convection-dominated flows and allows for equal-order basis functions for both pressure and velocity. The stability and accuracy of the method are demonstrated in the context of compressible flows by results of few compressible benchmark problems solved using low-order C0 continuous elements.Copyright © 2009 by ASME
The effect of donor body mass index on primary graft nonfunction, retransplantation rate, and early graft and patient survival after liver transplantation

Previous studies have suggested that moderate donor liver steatosis is associated with an increased incidence of primary graft nonfunction (PGNF), delayed graft function, early graft loss, and retransplantation rates. The objective of our study was to determine the effect of donor body mass index (dBMI), after adjusting for other known confounding variables, on PGNF, early graft failure, retransplantation rate, and patient survival. The United Network for Organ Sharing (UNOS) database (1987 to 2001) of 22,303 adult patients, excluding patients of pediatric age (age less than 18 years) and those with multiple organ transplantations, living donors, and retransplantations, was used for this study. Based on the BMI (kg/m(2)) of the organ donor, transplant recipients were divided into four groups as follows: BMI or = 35 (group 4, n = 924). Information on donor liver histology was available for 1603 patients who underwent transplantation after 1999, and this subgroup was divided into three groups based on severity of steatosis (group A, 35%). Incidence of PGNF and early retransplantation rates were similar in groups 1 to 4 and in groups A, B, and C. Logistic regression analysis showed that dBMI or severity of steatosis was not a predictor of PGNF and early retransplantation. Cox regression analysis, after adjusting for confounding variables, showed similar patient and graft survival at 1 month and 1, 2, and 5 years for groups 1 to 4, and at 1 month and 6 months for groups A, B, and C. Severe donor obesity or moderate steatosis did not influence short-term and long-term outcome of liver transplantation.
Effect of chemical sympathectomy on pressor responses to norepinephrine, angiotensin and tyramine.

L'action de la dopamine 6-OH (6-OH DA) sur les reponses de la tension arterielle a la norepinephrine, la tyramine, et l'angiotensin II a ete etudiee chez le rat. 24 h apres l'injection i.v. de 6-OH DA (100 mg/kg), la difference de tension due a la norepinephrine fut nettement plus marquee alors que celle a la tyramine avait presque disparu. L'ablation chimique du systeme sympathique n'a aucun effet sur la reponse de la tension a l'angiotensine II.
Hepatic perfusion before and after the transjugular intrahepatic portosystemic shunt procedure: Impact on survival

PURPOSE This study correlates transjugular intrahepatic portosystemic shunt (TIPS) mortality with flow patterns in the cirrhotic liver. MATERIALS AND METHODS Twenty-seven TIPS patients and 10 control subjects were used for this study. The authors evaluated hepatic perfusion with venous injections of Tc-99m pertechnetate before and after TIPS. Hepatic time-activity curves were analyzed for type and amount of liver perfusion. These parameters were correlated with survival for a mean follow-up of 18 months. RESULTS The mean arterial contribution to liver blood flow was 25.4% in the normal control patients, 39.9% in patients prior to TIPS, and increased to 48.3% after TIPS. Although the proportion of arterial supply to the cirrhotic liver varied widely, TIPS mortality did not correlate with the preprocedure hepatic artery/portal venous perfusion ratio. However, patients with both an "arterialized" flow pattern and low total hepatic perfusion had higher mortality, with a mean survival of 2 months compared to patients with a more favorable perfusion profile (mean survival, 28.4 months). CONCLUSION The proportion of arterial perfusion to the liver before TIPS did not affect survival. However, patients with a combination of reduced total hepatic perfusion and an arterial flow pattern had poorer survival, suggesting that both the quantity and quality of hepatic perfusion predicts TIPS outcome.
A Point Mutation in the LIM Domain of Lhx3 Reduces Activation of the Glycoprotein Hormone α-Subunit Promoter

Lhx3, a member of the LIM homeodomain family of transcription factors, is required for development of the pituitary in mice. A recent report has described a point mutation in the humanLHX3 gene that is associated with a combined pituitary hormone disorder. The mutation is predicted to lead to the replacement of a tyrosine residue with a cysteine in the second LIM domain of LHX3. We have characterized the effects of this point mutation (Y114C) when analyzed in the context of the mouse Lhx3 coding sequence. Mobility shift assays demonstrated that the Lhx3 Y114C mutant is capable of binding DNA, although a decrease in the formation of a specific complex was observed. Transfection assays using an expression vector for either full-length Lhx3 or a GAL4-Lhx3 LIM domain fusion provided evidence that the Lhx3 Y114C mutant has a decreased ability to stimulate transcription. In particular, a GAL4-Lhx3 Y114C LIM mutant was unable to support Ras responsiveness of a modified glycoprotein hormone α-subunit reporter gene. Protein interaction studies suggest that the Y114C mutation may modestly reduce binding to the POU transcription factor, Pit-1. Interestingly, the Y114C mutation essentially abrogated binding to the putative co-activator/adapter, selective LIM-binding protein. The findings provide insights into the mechanisms mediating transcriptional activation by Lhx3 and suggest that the observed phenotype of the human mutation probably involves reduced transcriptional activity of the mutant LHX3.
Error minimizing jammer localization through smart estimation of ambient noise

Jammer can jeopardize the dependability of wireless networks, and jammer's position information allows the network to cope with jamming leveraging varieties of defense strategies. Thus, in this paper, we address the problem of localizing jammer. Prior work relies on indirect measurements derived from jamming effects, which makes it difficult to accurately localize jammer. We localize jammer by directly using the strength of jamming signals (JSS). Estimating JSS is challenging as they may be embedded in other signals. As such, we devise an estimation scheme based on ambient noise floor and validate it with real world experiments. To improve localization accuracy, we define an evaluation feedback metric to quantify the estimation errors and formulate jammer localization as a nonlinear optimization problem, whose optimal solution approaches jammer's true position. We exploit a heuristic search based algorithm for approximating the global optimal solution, and our extensive simulation shows that our error-minimizing-based algorithm outperforms existing algorithms.
An ICEBs1-like element may be associated with the extreme radiation and desiccation resistance of Bacillus pumilus SAFR-032 spores.

Comparisons of the genomes of Bacillus pumilus SAFR-032 and the closely related type strain, B. pumilus ATCC7061T, exposed an extended region of non-homologous genes. A detailed examination of this region revealed the presence of an ICEBs1-like integrative conjugative element in SAFR-032. A similar element was subsequently located elsewhere in the ATCC7061T genome. A detailed comparison of these elements and the ICEBs1 of B. subtilis revealed extremely rapid flux in gene content, genome organization and sequence similarity. It is not clear if the B. pumilus elements as they are currently structured are functional. However, it is clear that the past involvement of these elements has brought multiple genes of unknown function to the SAFR-032 genome and these genes may be responsible for the rapid evolution that led to the extreme radiation and desiccation resistance of this organism’s spores.
FUNCTIONAL NEAR-INFRARED SPECTROSCOPY–BASED ASSESSMENT OF ATTENTION IMPAIRMENTS AFTER TRAUMATIC BRAIN INJURY

A frequent consequence of traumatic brain injury (TBI) is cognitive impairment, which results in significant disruption of an individual's everyday living. To date, most clinical rehabilitation interventions still rely on behavioral observation, with little or no quantitative information about physiological changes produced at the brain level. Functional brain imaging has been extensively used in the study of cognitive impairments following TBI. However, its applications to rehabilitation have been limited. This is due in part to the expensive or invasive nature of these modalities. The objective of this study is to apply functional near-infrared spectroscopy (fNIR) to the assessment of attention impairments following TBI. fNIR provides a localized measure of prefrontal hemodynamic activation, which is susceptible to TBI, and it does so in a noninvasive, affordable and wearable way, thus partially overcoming the limitations of other modalities. Participants included 5 TBI subjects and 11 healthy controls....
Autophagy gone awry in neurodegenerative diseases

Autophagy is essential for neuronal homeostasis, and its dysfunction has been directly linked to a growing number of neurodegenerative disorders. The reasons behind autophagic failure in degenerating neurons can be very diverse because of the different steps required for autophagy and the characterization of the molecular players involved in each of them. Understanding the step(s) affected in the autophagic process in each disorder could explain differences in the course of these pathologies and will be essential to developing targeted therapeutic approaches for each disease based on modulation of autophagy. Here we present examples of different types of autophagic dysfunction described in common neurodegenerative disorders and discuss the prospect of exploring some of the recently identified autophagic variants and the interactions among autophagic and non-autophagic proteolytic systems as possible future therapeutic targets.
Effects of nitrogen on leaf physiology and growth of different families of loblolly and slash pine

Leaf physiology and fractional dry weight allocation were examined in four open-pollinated families of loblolly pine (Pinus taeda L.) and slash pine (Pinus elliottii Englm. var. elliottii) in response to growth under low and high N supply for six months. Nitrogen greatly influenced dry weight allocation, total mass, leaf net photosynthesis and leaf conductance in seedlings of both species. Family variation in fine root allocation was observed under low but not high N treatment, but for the majority of physiological and growth traits, family variation was stable under varying N treatment. Family rankings based on juvenile height, diameter and biomass accretion were similar to rankings based on field performance at 22 years in slash pine but not loblolly pine. Lower leaf maintenance respiration rates were associated with families exhibiting the most rapid juvenile growth.
The Effect of Anterior Cruciate Ligament Graft Elongation at the Time of Implantation on the Biomechanical Behavior of the Graft and Knee

This investigation determined the effect that anterior cruciate ligament graft elongation at the time of surgical reconstruction has on the long-term biomechanical behavior of the graft and knee joint. We chose the canine model for anterior cruciate ligament reconstruction, using the medial third of the patellar tendon with attached proximal bone block. Elongation of the graft was measured immediately after graft fixation during passive knee flexion using the Hall effect transducer. The dogs were divided into either Group 1 (graft elongation behavior within the 95% confidence limits of the normal anterior cruciate ligament) or Group 2 (graft elongation behavior more than the 95% confidence limits of the normal anterior cruciate ligament). All of the dogs were sacrificed 18 months postoperatively, and we evaluated anteroposterior load displacement (i.e., anteroposterior laxity) of the knee and the structural properties of the graft. The anteroposterior laxity behavior of the reconstructed knees in Group 2 was significantly more than that of Group 1. Group 2 had significantly less linear stiffness of the graft than Group 1. There was no difference in the ultimate failure load and absorbed energy at failure values of the grafts between Groups 1 and 2. The findings from this investigation indicate that the graft elongation behavior at the time of reconstruction is a critical factor that influences the long-term success of anterior cruciate ligament reconstruction.
Prevalence of obesity in the United States

Obesity is a major public health problem in the United States. Data on measured heights and weights indicates that the prevalence of obesity has significantly increased among the US population over the past 30 years. Data collected from 1999 to 2002 estimates that nearly 1/3 of adults are obese (27.6% of men and 33.2% of women) and one in six children and adolescents is overweight. Increased prevalence of excessive weight is noted among all age, gender and racial/ethnic groups; however, disparities exist. There is a need for further research to better understand why these increases have occurred, why the observed disparities exist and how to reverse these trends.
coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data

Motivation: ChIP-seq data are enriched in binding sites for the protein immunoprecipitated. Some sequences may also contain binding sites for a coregulator. Biologists are interested in knowing which coregulatory factor motifs may be present in the sequences bound by the protein ChIP'ed. Results: We present a finite mixture framework with an expectation–maximization algorithm that considers two motifs jointly and simultaneously determines which sequences contain both motifs, either one or neither of them. Tested on 10 simulated ChIP-seq datasets, our method performed better than repeated application of MEME in predicting sequences containing both motifs. When applied to a mouse liver Foxa2 ChIP-seq dataset involving ~ 12 000 400-bp sequences, coMOTIF identified co-occurrence of Foxa2 with Hnf4a, Cebpa, E-box, Ap1/Maf or Sp1 motifs in ~6–33% of these sequences. These motifs are either known as liver-specific transcription factors or have an important role in liver function. Availability: Freely available at http://www.niehs.nih.gov/research/resources/software/comotif/. Contact: vog.hin.shein@3il Supplementary Information: Supplementary data are available at Bioinformatics online.
A NEW CONCEPT OF PLANNED INSPECTIONS.

Abstract : The issue of preventive maintenance is examined in conceptual terms, with special attention to the planned inspection portion of the problem, in the belief that the quantitative methods and the engineering aspects will be more readily worked out if a consensus is reached first on fundamental concepts. The problem is an extremely important one for Air Force logistics, because a very large fraction of the Air Force resources in the using commands are expended directly in planned inspections, and also indirectly as a consequence of possible inadequacies in these inspections.
Micellar charge effects as mechanistic criteria in spontaneous hydrolyses of acid chlorides

Reaction rates in aqueous micelles, treated in terms of a pseudophase model, depend on transfer equilibria between water and micelles and rate constants in each pseudophase. Rate constants of spontaneous reactions of fully micellar-bound substrates are independent of transfer and are those in the micellar pseudophase. They depend on its properties as a reaction region and the sensitivity of the reaction to medium effects. For a wide range of spontaneous reactions there are simple relationships between rate constants and properties of the micellar interfacial region, e.g. apparent polarity and head-group charge, which depend on the reaction mechanism. Aqueous micelles inhibit nucleophilic substitutions at alkyl centers, but rate constants, k+, in cationic micelles are higher than those, k−, in anionic micelles for SN2 reactions and lower for SN1 reactions. Except for nitro derivatives, hydrolyses of substituted benzoyl chlorides are micellar inhibited and k+/k−≈18 for nitro derivative and ca 0.04 for 4-OMe and Me derivatives, indicating different extents of bond making and breaking in the transition state, but there is no evidence of rate-limiting dissociation in hydrolyses of the latter. For hydrolyses of substituted benzenesulfonyl chlorides, values of k+/k− decrease from 21 for the 4-NO2 derivative to 1.1 for the 4-OMe derivative, indicating dominant bond making. These mechanism-related charge effects are ascribed to charge asymmetries at micelle–water interfaces and zwitterionic sulfobetaine micelles behave very similarly to cationic micelles in these hydrolyses. Copyright © 2004 John Wiley & Sons, Ltd.
Treating coagulopathy in trauma patients

Coagulopathy in patients with severe trauma is related to platelet and coagulation factor loss, consumption, and dysfunction. It is exacerbated by dilution, acidosis, and hypothermia. Hemorrhage control, warming, and appropriate blood product support are lifesaving. Further improvements in hemorrhage control will save additional lives and resources.
A simple, template-free route for the synthesis of mesoporous titanium dioxide materials

Mesoporous titanium dioxide (TiO2) materials have been synthesized by a novel simple, template-free synthetic approach, which was carried out via nitric acid-catalyzed hydrolysis and polycondensation reactions of titanium(IV) n-butoxide. The as-prepared and calcinated mesoporous TiO2 materials are characterized by X-ray diffraction (XRD), transmission electron microscope (TEM), and N2 adsorption/desorption measurements. The as-prepared amorphous TiO2 possesses a high BET surface area of 470 m2 g−1 and a pore volume of 0.28 cm3 g−1. After calcinations at 450 °C, anatase mesoporous TiO2 is formed with a BET surface area of 106 m2 g−1 and an average pore size of 4.8 nm. Avoidance of the structure-directing template during the synthesis of mesoporous TiO2 is of significant importance for application from both environmental and industrial points of view.
Sleep Duration, Sleep Regularity, Body Weight, and Metabolic Homeostasis in School-aged Children

OBJECTIVE: The goal was to explore the effects of duration and regularity of sleep schedules on BMI and the impact on metabolic regulation in children. METHODS: Sleep patterns of 308 community-recruited children 4 to 10 years of age were assessed with wrist actigraphs for 1 week in a cross-sectional study, along with BMI assessment. Fasting morning plasma levels of glucose, insulin, lipids, and high-sensitivity C-reactive protein also were measured for a subsample. RESULTS: Children slept 8 hours per night, on average, regardless of their weight categorization. A nonlinear trend between sleep and weight emerged. For obese children, sleep duration was shorter and showed more variability on weekends, compared with school days. For overweight children, a mixed sleep pattern emerged. The presence of high variance in sleep duration or short sleep duration was more likely associated with altered insulin, low-density lipoprotein, and high-sensitivity C-reactive protein plasma levels. Children whose sleep patterns were at the lower end of sleep duration, particularly in the presence of irregular sleep schedules, exhibited the greatest health risk. CONCLUSIONS: Obese children were less likely to experience “catch-up” sleep on weekends, and the combination of shorter sleep duration and more-variable sleep patterns was associated with adverse metabolic outcomes. Educational campaigns, aimed at families, regarding longer and more-regular sleep may promote decreases in obesity rates and may improve metabolic dysfunction trends in school-aged children.
Listeria: A foodborne pathogen that knows how to survive

The foodborne pathogen Listeria is the causative agent of listeriosis, a severe disease with high hospitalization and case fatality rates. Listeria monocytogenes can survive and grow over a wide range of environmental conditions such as refrigeration temperatures, low pH and high salt concentration. This allows the pathogen to overcome food preservation and safety barriers, and pose a potential risk to human health. This review focuses on the key issues such as survival of the pathogen in adverse environments, and the important adaptation and survival mechanisms such as biofilm formation, quorum sensing and antimicrobial resistance. Studies on the development of technologies to prevent and control L. monocytogenes contamination in foods and food processing facilities are also discussed.
Wildfire risk in the wildland―urban interface: A simulation study in northwestern Wisconsin

The rapid growth of housing in and near the wildland–urban interface (WUI) increases wildfire risk to lives and structures. To reduce fire risk, it is necessary to identify WUI housing areas that are more susceptible to wildfire. This is challenging, because wildfire patterns depend on fire behavior and spread, which in turn depend on ignition locations, weather conditions, the spatial arrangement of fuels, and topography. The goal of our study was to assess wildfire risk to a 60,000 ha WUI area in northwestern Wisconsin while accounting for all of these factors. We conducted 6000 simulations with two dynamic fire models: Fire Area Simulator (FARSITE) and Minimum Travel Time (MTT) in order to map the spatial pattern of burn probabilities. Simulations were run under normal and extreme weather conditions to assess the effect of weather on fire spread, burn probability, and risk to structures. The resulting burn probability maps were intersected with maps of structure locations and land cover types. The simulations revealed clear hotspots of wildfire activity and a large range of wildfire risk to structures in the study area. As expected, the extreme weather conditions yielded higher burn probabilities over the entire landscape, as well as to different land cover classes and individual structures. Moreover, the spatial pattern of risk was significantly different between extreme and normal weather conditions. The results highlight the fact that extreme weather conditions not only produce higher fire risk than normal weather conditions, but also change the fine-scale locations of high risk areas in the landscape, which is of great importance for fire management in WUI areas. In addition, the choice of weather data may limit the potential for comparisons of risk maps for different areas and for extrapolating risk maps to future scenarios where weather conditions are unknown. Our approach to modeling wildfire risk to structures can aid fire risk reduction management activities by identifying areas with elevated wildfire risk and those most vulnerable under extreme weather conditions.
Conservation Status of Etheostoma luteovinctum and Notes on Observations of a Burying Behavior

Etheostoma luteovinctum (Redband Darter) is a benthic headwater fish of the Caney Fork and Stones rivers (Cumberland River drainage) and the Duck and Elk rivers (Tennessee River drainage) of central Tennessee. The Redband Darter was regarded as a species of special concern due to its small native range, but was recently designated as stable. The current status of the species was assessed by sampling 65 historical localities and collecting other nearby habitat-appropriate sites to document presence or absence. Redband Darter was not found at 63% of the 65 sampled historical localities, indicating the stable status of the species is not valid. Additionally, comments on observations of a unique burying behavior are provided.
Feeding and reproductive biology of eleotrid fishes in a tropical estuary

Five species of eleotrid fishes (Gobiomorus dormitor, Dormitator maculatus, Eleotris amblyopsis, Eleotris pisonis and Leptophilypnus fluviatilis) are known from the Tortuguero estuary of Costa Rica. One, E. amblyopsis, appears tightly linked to the presence of mats of macrophytes and two others, E. pisonis and D. maculatus, are largely limited to this habitat in the lower estuary. All three of these species feed on hyacinth roots. Despite certain food and habitat specializations among the forms, there is evidence of competition and predation among four species. Individuals of breeding size have never been found in the system for D. maculatus and L. fluviatilis. Alternative means of establishing and maintaining eleotrid populations are suggested.
Normal Tissue Anatomy for Oropharyngeal Cancer: Contouring Variability and Its Impact on Optimization

Purpose To evaluate the variability of organ at risk (OAR) delineation and the resulting impact on intensity modulated radiation therapy (IMRT) treatment plan optimization in head-and-neck cancer. Methods and Materials An expert panel of 3 radiation oncologists jointly delineated OARs, including the parotid and submandibular glands (SM), pharyngeal constrictors (PC), larynx, and glottis (GL), in 10 patients with advanced oropharynx cancer in 3 contouring sessions, spaced at least 1 week apart. Contour variability and uncertainty, as well as their dosimetric impact on IMRT planning for each case, were assessed. Results The mean difference in total volume for each OAR was 1 cm 3 (σ 0.5 cm 3 ). Mean fractional overlap was 0.7 (σ 0.1) and was highest (0.8) for the larynx and bilateral SMs and parotids and lowest (0.5) for PC. There were considerable spatial differences in contours, with the ipsilateral parotid and PC displaying the most variability (0.9 cm), which was most prominent in cases in which tumors obliterated fat planes. Both SMs and GL had the smallest differences (0.5 cm). The mean difference in OAR dose was 0.9 Gy (range 0.6-1.1 Gy, σ 0.1 Gy), with the smallest difference for GL and largest for both SMs and the larynx. Conclusions Despite substantial difference in OAR contours, optimization was barely affected, with a 0.9-Gy mean difference between optimizations, suggesting relative insensitivity of dose distributions for IMRT of oropharynx cancer to the extent of OARs.
A comparison of some radiation boundary conditions for differential equation calculations of scattering

An approximate boundary condition is necessary to close the computational grid for a differential-equation-based solution (either in the frequency or time domain) of an electromagnetic scattering problem. While the asymptotic form for r to infinity is well-known, it is not sufficient for large problems. For efficiency, one needs to find higher-order boundary conditions that allow the computational grid to be terminated as close to the scatterer as possible. The author discusses the two-dimensional, frequency-domain case in detail. However, the results for three dimensions and/or the time domain are quite similar. >
“European Copyright Code” – Back to First Principles (with Some Additional Detail)

The "Wittem Group" of copyright scholars has proposed a "European Copyright Code," to "serve as an important reference tool for future legislatures at the European and national levels." Because, notwithstanding twenty years of Directives and a growing ECJ caselaw, copyright law in EU Member States continues to lack uniformity, the Wittem Group’s endeavor should be welcomed, at least as a starting point for reflection on the desirable design of an EU copyright regime. Whether or not the proposed Code succeeds in influencing national or Community legislation, it does offer an occasion to consider the nature of the rights that copyright secures, and of the goals that a copyright system should serve.The following commentary will reproduce the provisions of the proposed Code, together with annotations of particular articles. The proposed Code contains five chapters: (1) Works; (2) Authorship and Ownership; (3) Moral Rights; (4) Economic Rights; (5) Limitations. The text provides neither for remedies, nor for voluntary formalities. It also does not address neighboring rights. The five chapters vary in ambition, from cautious synthesis to radical prescription. If some timidity characterizes the chapters addressing authors’ rights, the hallmark of the chapter on limitations is its temerity, displaying an impetus to break through the rigidity of the current EU and national systems of copyright exceptions in order to favor EU-wide uses of copyrighted works in which, in the drafters’ perception, the interests of third parties, including the public, outweigh those of the authors or copyright owners. Reaction to the Wittem endeavor may turn at least in part on one’s assessment of whether the drafters have correctly stated and/or weighted the third party interests
General theory of virtual heavy-particle effects in renormalizable field theories (I)

We develop a systematic method of isolating the effects of virtual heavy particles in renormalizable field theories. With a q54-type field-theory model involving two real scalar fields (one with a heavy mass M, and the other light), we show in detail that, up to order 1/M 2 (but to all orders in renormalized couplings), effects of ~irtual heavy particles can be completely incorporated into pure light-particle theory via effective local vertices which involve operators of canonical dimension at most six. All the coupling strengths for such effective local interactions are of order 1/M 2 (the decoupling theorem) and are systematically calculable in renormalized perturbation theory. We also derive a closed set of Callan-Symanzik equations which are satisfied by these coupling strengths. Using these equations, we explicitly sum all the leading logarithms (i.e., g log M ~ O(1)) which appear in the perturbative calculations of the effective coupling strengths. In field-theoretic studies of strong interaction physics, there has been much interest recently in isolating genuine large-momentum processes from complicated longdistance dynamics like confinement - so called factorization. This has been studied in terms of the operator product expansion [1 ] or from the viewpoint of mass singularity cancellation [2]. In the language of the former, genuine large-momentum processes are described by the so-called coefficient functions, and long-distance dynamics by the matrix elements of various local operators. In an asymptotically free field theory like QCD, the coefficient functions may be reliably calculated through perturbation theory and further improved by using the renormalization group [3]. In this paper, we discuss another kind of factorization: heavy particles versus light particles. Specifically, we wish to calculate systematically effects of virtual heavy particles on light-particle Green functions in renormalizable field theories, when all the external momenta are much smaller than the masses of heavy particles. In renormalizable field theories without spontaneous symmetry breaking, Appel