cssi/SciSciGPT-SciSciNet huggingface dataset:
Classification of genetic profiles of Crohn’s disease: a focus on the ATG16L1 gene

Inflammatory bowel disease constitutes two related clinical entities, Crohn’s disease (CD) and ulcerative colitis (UC), both of which have increased in prevalence over the last decade. Family and twin studies have strongly indicated that genetic factors play a large role in an individual’s risk of developing inflammatory bowel disease. Despite this, it has proven difficult to isolate disease genes that confer susceptibility to this disease using classical candidate gene and linkage approaches, with the notable exception of the isolation of the caspase recruitment domain family, member 15 (CARD15) gene. However, over the last 2 years, genome-wide association (GWA) studies have become feasible, where modern high-throughput single nucleotide polymorphism (SNP) genotyping technologies can be applied to large and comprehensively phenotyped patient cohorts. Such approaches have enabled scientists to robustly associate specific variants with many complex diseases, including age-related macular degeneration, Type...
Influence of Urine pH and Citrate Concentration on the Upper Limit of Metastability for Calcium Phosphate

ABSTRACTPurpose: We determined the effects on the urine upper limit of metastability for calcium phosphate of citrate concentration and pH, and achievement of the upper limit of metastability by adding calcium or phosphate.Materials and Methods: The citrate concentration in aliquots of 24-hour urine samples from normal males without a history of kidney stones was increased. The upper limit of metastability was determined by the point of visible crystal formation, as confirmed by increased optical density at 620 nm. when calcium or pH was increased. In additional experiments the upper limit of metastability was determined by adding calcium or phosphate at pH 5.9 and 6.4.Results: Regardless of how the upper limit of metastability was achieved increasing the citrate concentration increased the former value by about 0.4 units per mM. citrate per l. The upper limit of metastability achieved in a given urine sample by adding phosphate or calcium did not differ. Increasing urine pH increased the upper limit of m...
Calculations of molecular octopole moments for water and methane

Abstract Molecular octopole moments are rigorously calculated using two different semi-empirical wavefunctions. The results are compared with ab initio calculations and experimental data where available. IEHT wavefunctions are found to give a reasonable of multipole moments up to octopole.
Chronic LSD alters gene expression profiles in the mPFC relevant to schizophrenia

Chronic administration of lysergic acid diethylamide (LSD) every other day to rats results in a variety of abnormal behaviors. These build over the 90 day course of treatment and can persist at full strength for at least several months after cessation of treatment. The behaviors are consistent with those observed in animal models of schizophrenia and include hyperactivity, reduced sucrose-preference, and decreased social interaction. In order to elucidate molecular changes that underlie these aberrant behaviors, we chronically treated rats with LSD and performed RNA-sequencing on the medial prefrontal cortex (mPFC), an area highly associated with both the actions of LSD and the pathophysiology of schizophrenia and other psychiatric illnesses. We observed widespread changes in the neurogenetic state of treated animals four weeks after cessation of LSD treatment. QPCR was used to validate a subset of gene expression changes observed with RNA-Seq, and confirmed a significant correlation between the two methods. Functional clustering analysis indicates differentially expressed genes are enriched in pathways involving neurotransmission (Drd2, Gabrb1), synaptic plasticity (Nr2a, Krox20), energy metabolism (Atp5d, Ndufa1) and neuropeptide signaling (Npy, Bdnf), among others. Many processes identified as altered by chronic LSD are also implicated in the pathogenesis of schizophrenia, and genes affected by LSD are enriched with putative schizophrenia genes. Our results provide a relatively comprehensive analysis of mPFC transcriptional regulation in response to chronic LSD, and indicate that the long-term effects of LSD may bear relevance to psychiatric illnesses, including schizophrenia.
In situ high-temperature scanning tunneling microscopy study of bilayer graphene growth on 6H-SiC(0001)

Abstract Using in situ high-temperature (1395 K), ultra-high vacuum, scanning tunneling microscopy (STM), we investigated the growth of bilayer graphene on 6H-SiC(0001). From the STM images, we measured areal coverages of SiC and graphene as a function of annealing time and found that graphene grows at the expense of SiC. Graphene domains were observed to grow, at comparable rates, at (I) graphene-free SiC step edges, (II) graphene–SiC interfaces, and (III) the existing graphene domain edges. Based upon our results, we suggest that the rate-limiting step controlling bilayer graphene growth is the desorption of Si from the substrate.
The Effect of Price Promotions on Repeat Purchase Behavior

Abstract While there is general agreement that price promotions generally have an immediate positive impact on the sales of consumer nondurables, there is little agreement about their repeat-purchasing effects. Promotion usage effects may exist in which brand repurchase rates are negatively affected by the fact that a promotion was used to make a purchase. Using scanner data, this study examines the effect of price promotions on brand repurchase rates in four product categories. Findings indicate that repurchase rates are generally higher after non-deal purchases, however, this seems largely attributable to differences in household pre-purchase probabilities.
Importance of allergic rhinitis management in achieving asthma control: ARIA update

Asthma continues to be a major burden for the health and healthcare of people worldwide. The recent updates of the Global Initiative for Asthma and the National Heart, Lung and Blood Institute asthma guidelines stress the need for achieving and monitoring asthma ‘control’, emphasizing the importance of identifying, assessing and treating comorbid conditions. Allergic rhinitis (AR) is a major comorbid condition in people with asthma and is related to inflammation of the upper portions of the airway. Recognizing and treating AR has been shown to improve asthma control, specifically by decreasing rates of asthma attacks or asthma exacerbations. In 2008, updated Allergic Rhinitis in Asthma (ARIA) guidelines were published. The updated version of the guidelines has a familiar look, with classification systems and care algorithms that are similar to those presented in other asthma guidelines. The new ARIA guidelines make one major change that should affect the care of adults and children with asthma: everyone w...
Defining the Computer: Herbert Simon and the Bureaucratic Mind--Part 1

Herbert Simon understood the computer, the organization, and the individual mind as being "species of the genus information processor." By defining the computer in this way - in a new understanding of mind and machine - Simon hoped to provide answers to the problems of choice and control in complex systems. Part 1 discusses Simon's work before he came to computing. Part 2 covers Simon's early work in computer science.
Mechanisms underlying production of double-strand breaks in plasmid DNA after decay of 125I-Hoechst.

Abstract Balagurumoorthy, P., Chen, K., Bash, R. C., Adelstein, S. J. and Kassis, A. I. Mechanisms Underlying Production of Double-Strand Breaks in Plasmid DNA after Decay of 125I-Hoechst. Radiat. Res. 166, 333–344 (2006). Previously, the kinetics of strand break production by 125I-labeled m-iodo-p-ethoxyHoechst 33342 (125IEH) in supercoiled (SC) plasmid DNA had demonstrated that ∼1 DSB is produced per 125I decay both in the presence and absence of the hydroxyl radical scavenger DMSO. In these experiments, an 125IEH:DNA molar ratio of 42:1 was used. We now hypothesize that this DSB yield (but not the SSB yield) may be an overestimate due to subsequent decays occurring in any of the 41 125IEH molecules still bound to nicked (N) DNA. To test our hypothesis, 125IEH was incubated with SC pUC19 plasmids (125IEH:DNA ratio of ∼3:1) and the SSB and DSB yields were quantified after the decay of 125I. As predicted, the number of DSBs produced per 125I decay is one-half that reported previously (∼0.5 compared to ∼1,...
Atomic transport at liquid metal/Al2O3 interfaces

Author(s): Saiz, Eduardo; Cannon, Rowland M.; Tomsia, Antoni P. | Abstract: In this work, atomic force microscopy (AFM) has been used to identify the controlling transport mechanisms at metal/oxide interfaces and measure the corresponding diffusivities. Interfacial transport rates in our experiments are two to four orders of magnitude faster than any previously reported rates for the oxide surface. The interfacial diffusivities and the degree of interfacial anisotropy depend on the oxygen activity of the system. Atomic transport at metal/oxide interfaces plays a defining role in many technological processes, and these experiments provide fundamental data for the formulation of the atomic theory needed to explain many of the observed phenomena.
Effect of Interparticle Interaction on Particle Deposition in a Crossflow Microfilter

Recent studies show that inter-particle interaction can affect particle trajectories and particle deposition causing fouling in the microfilters used for metal working fluids (MWFs). Inter-particle interaction depends on various factors: particle geometry and surface properties, membrane pore geometry and surface properties, MWF’s properties and system operating conditions, etc. A mathematical model with a Langevin equation for particle trajectory and a hard sphere model for particle deposition has been used to study the effect of particle’s size, particle’s surface zeta potential, inter-particle distance, and shape of membrane pore wall surface on particle trajectory and its deposition on membrane pore wall. The study reveals that bigger particles have a lesser tendency to be deposited on membrane pore walls than smaller particles. The shape of the membrane pore wall surface can also affect the particle deposition behavior.Copyright © 2013 by ASME
Pharmacokinetics of Cefodizime in Volunteers with Normal or Impaired Renal Function

The pharmacokinetics of single, 1- or 2-g intravenous doses of cefodizime were studied in subjects with normal, impaired renal function or requiring chronic hemodialysis. Drug concentrations were measured using high-performance liquid chromatography. Forty-five subjects (20 with creatinine clearance of > or = 90 mL/min, 15 with creatine clearances between 5 and 89 mL/min, and 10 requiring chronic hemodialysis) were studied. The concentration-time curve of cefodizime was best represented by an open two-compartment model. The elimination half-lives in subjects with normal (Group 1) and impaired renal function (Group 2) or requiring chronic hemodialysis (Group 3) were 4.14 +/- 1.55, 5.10 +/- 2.24, and 10.1 +/- 6.01 hours, respectively (Group 3 versus 1 or 2, P .05). The total body (serum) clearances in the same groups were 3 +/- 0.52, 2.22 +/- 0.61, and 0.99 +/- 0.33 L/hour, respectively (Group 1 versus 2 or 3, P < .05; Group 2 versus 3, P < .05). Although renal function has an effect on the pharmacokinetics of cefodizime, its effect on the elimination half life is marginal in subjects with creatinine clearance of more than 25 mL/min. In individuals with more severe renal impairment or those requiring chronic hemodialysis, dosage adjustment would be required.
Some Effects of Cavities on the Fracture of Ceramics: I, Cylindrical Cavities

Fracture probabilities associated with spherical cavities were analyzed by combining principles of fracture mechanics and fracture statistics. The analysis is based on the theory that fracture occurs from a distribution of cracks located at the cavity surfaces. It predicts effects on strength of cavity size and cavity volume content (porosity) that depend sensitively on the flaw population in relation to the cavity size distribution. The theory has limit solutions that coincide with several models of fracture derived for porous ceramics. The predicted effects of pore size on strength are compared with some available data.
Recent results on polyphase sequences

A polyphase sequence of length n+1, A={a/sub j/}/sub j=0//sup n/, is a sequence of complex numbers, each of unit magnitude. The (unnormalized) aperiodic autocorrelation function of a sequence is denoted by C(/spl tau/). Associated with the sequence A, the sequence polynomial f/sub A/(z) of degree n and the correlation polynomial g/sub A/(z) of degree 2n are defined. For each root /spl alpha/ of f/sub A/(z), 1//spl alpha/* is a corresponding root of f*/sub A/(z/sup -1/). Transformations on the sequence A which leave |C(/spl tau/)| invariant are exhibited, and the effects of these transformations on the roots of f/sub A/(z) are described. An investigation of the set of roots A of the polynomial f/sub A/(z) has been undertaken, in an attempt to relate these roots to the behavior of C(/spl tau/). Generalized Barker (1952, 1953) sequences are considered as a special case of polyphase sequences, and examples are given to illustrate the relationship described above.
Studies of the effect of orientation on the elastic constants of stretched and hydrostatically extruded polychlorotriflouroethylene: A reorientational model in semicrystalline polymers

A reorientational model of polymer solids is given. The solid is described as a collection of small, orientable units. The elastic constants of the oriented polymer are given as a combination of the elastic constants of the orientable units and of the orientation parameters 〈P2(cosθ)〉 and 〈P4(cosθ)〉. The elastic constants of stretched and hydrostatically extruded samples of polychlorotriflouroethylene are obtained with Brillouin light scattering. These are fitted to the model and the orientation parameters are calculated. The elastic constants from the extruded samples are fit well by the model but the fit to the stretched film is less satisfactory. Hydrostatic extrusion in polymers is thus assumed to be a reorientation process in the amorphous phase, but the stretching process is not completely reorientational.
AGE-DEPENDENT CHANGES IN PLASMA AND BRAIN CHOLINESTERASE ACTIVITIES OF HOUSE WRENS AND EUROPEAN STARLINGS

We determined age-dependent changes in plasma and brain cholinesterase (ChE) activity for two species of passerines: house wren (Troglodytes aedon) and European starling (Sturnus vulgaris, starling). In plasma from nestlings of both species, total ChE activity increased with age, acetylcholinesterase (AChE, EC 3.1.1.7) activity declined rapidly immediately after hatching, and butyrylcholinesterase (BChE, EC 3.1.1.8) activity increased steadily. For both species, total ChE and BChE activities and the BChE:AChE ratio in plasma were significantly greater in adults than nestlings suggesting trends observed in nestlings continue post fledging. In older nestlings and adults, AChE activity in plasma was significantly greater and BChE:AChE ratio less in house wrens than starlings. For house wrens as compared with starlings, ChE activity in brain increased at a significantly greater rate with age in nestlings and was significantly greater in adults. However, ChE activity in brain was similar at fledging for both s...
Enterostatin inhibition of dietary fat intake is dependent on CCK-A receptors.

Enterostatin, a pentapeptide released from the exocrine pancreas and gastrointestinal tract, selectively inhibits fat intake through activation of an afferent vagal signaling pathway. This study in...
Balancing copy number in ribosomal DNA

Ecologists recognize the balance of nature as a complex system that arises from interacting and connected parts; disturbing the balance can affect other species in nonlinear and dynamic ways. Like ecosystems, the cell and genome are extensively connected by an abundance of molecular interactions. Upsetting the molecular balance, through changes in gene regulation, abnormal copy number variants, and changes in cell size can create consequences for genome and organismal function (1, 2). In PNAS, Gibbons et al. (3) advance the idea of genome balance further by identifying a new source of genetic variation that results in balancing transcriptional subunits of the ribosome. Using data from human and mouse, the authors characterized copy number variation (CNV) in tandemly repeated ribosomal DNA (rDNA) arrays and found that subunits of the array vary together in what they define as concerted copy number variation (cCNV). cCNV raises new questions about how CNV can function to restore balance in eukaryotic genomes, especially on the assembly and function of the ribosome.
Integrating Behavioral and Physical Health Care in the Real World: Early Lessons from Advancing Care Together

Background: More than 20 years ago the Institute of Medicine advocated for integration of physical and behavioral health care. Today, practices are integrating care in response to recent policy initiatives. However, few studies describe how integration is accomplished in real-world practices without the financial or research support available for most randomized controlled trials. Methods: To study how practices integrate care, we are conducting a cross-case comparative, mixed-methods study of 11 practices participating in Advancing Care Together (ACT). Using a grounded theory approach, we analyzed multiple sources of data (eg, documents, practice surveys, field notes from observation visits, semistructured interviews, online diaries) collected from each ACT innovator. Results: Integration requires making changes in organization and interpersonal relationships. During early integration efforts, challenges related to workflow and access, leadership and culture change, and tracking and using data to evaluate patient- and practice-level improvement emerged for ACT innovators. We describe the strategies innovators are developing to address these challenges. Conclusion: Integrating care is a fundamental and difficult change for practices and health care professionals. Research identifying common challenges that manifest in early efforts can help others attempting integration and inform state, local, and federal policies aimed at achieving wide-spread implementation.
Treatment of groundwater contaminated with PAHs, gasoline hydrocarbons, and methyl tert-butyl ether in a laboratory biomass-retaining bioreactor.

In this study, we investigated the treatability of co-mingled groundwater contaminated with polycyclic aromatic hydrocarbons (PAHs), gasoline hydrocarbons, and methyl tert-butyl ether (MtBE) using an ex-situ aerobic biotreatment system. The PAHs of interest were naphthalene, methyl-naphthalene, acenaphthene, acenaphthylene, and carbazole. The gasoline hydrocarbons included benzene, toluene, ethyl benzene, and p-xylene (BTEX). Two porous pot reactors were operated for a period of 10 months under the same influent contaminant concentrations. The contaminated groundwater was introduced into the reactors at a flow rate of 4 and 9 l/day, resulting in a hydraulic retention time (HRT) of 32 and 15 h, respectively. In both reactors, high removal efficiencies were achieved for the PAHs (>99%), BTEX and MtBE (>99.7%). All the PAHs of interest and the four BTEX compounds were detected at concentrations less than 1 μg/l throughout the study duration. Effluent MtBE from both reactors was observed at higher levels; nevertheless, its concentration was lower than the 5 μg/l Drinking Water Advisory for MtBE implemented in California.
Studies in the System (Ba, Ca, Pb)TiO3

The weight loss, dye absorption, crystalline phase or phases, dielectric constant, dissipation factor, and temperature variation of dielectric constant were determined for various bodies in the system (Ba, Ca, Pb)TiO3 fired in an air atmosphere at temperatures from 800?° to 1400°C. The per cent of PbO loss is proportional to e−B/T, where B is a constant and T is the absolute temperature. It is possible to fire most bodies in this system to zero (visual) dye absorption, but the sensitivity of the dissipation factor to moisture shows that some bodies are not well fired in the electrical sense. The electrical properties correlate well with the crystalline constitution. The two-phase region of the barium-calcium titanate binary extends into the ternary to about 35 mole %, lead titanate.
Identification of a conjunctivitis-associated gene locus from the virulence plasmid of Yersinia enterocolitica.

Abstract The virulence plasmid (pYV) of Yersinia enterocolitica is necessary for production of conjunctivitis in guinea pigs and for mouse lethality. To identify the genes responsible for production of conjunctivitis in guinea pigs, we subcloned the BamHI and SalI restriction fragments of the virulence plasmid of Y. enterocolitica A2635 (serotype O:8) into derivatives of the broad-host-range plasmid pRK290 and introduced the constructions into plasmid-negative Y. enterocolitica strains. A mild, transient conjunctivitis was evident 24 h after inoculation with strains containing a 2.8-kilobase (kb) BamHI fragment of pYV. These strains were cytotoxic to HEp-2 cells but did not cause death in iron-loaded adult mice. When the 2.8- and adjacent 0.5-kb BamHI fragments were deleted from the virulence plasmid of a fully virulent Y. enterocolitica isolate, the resultant strain did not cause conjunctivitis in guinea pigs and was not cytotoxic to HEp-2 cells. However, the strain with the deletion appeared to be more virulent for mice, with more rapid dissemination after orogastric inoculation, compared with that of the parent strain. When the deletion was complemented by introduction of a plasmid containing the 2.8-kb BamHI fragment, the strain again caused conjunctivitis but had decreased virulence for mice.
Modeling, design, and control of flexible manipulator arms: a tutorial review

High performance manipulators with dynamic behavior in which the flexibility is an essential aspect are addressed. The mathematical representations commonly used in modeling flexible arms and arms with flexible drives are first examined. Then design considerations directly arising from the flexible nature of the arm are discussed. Finally, controls of joints for general and tip motion are discussed. >
Jets in effective theory: Summing phase space logs

We demonstrate how to resum phase space logarithms in the Sterman-Weinberg (SW) dijet decay rate within the context of soft collinear effective theory (SCET). An operator basis corresponding to two and three jet events is defined in SCET and renormalized. We obtain the renormalization group equation of the two and three jet operators and run the operators from the scale {mu}{sup 2}=Q{sup 2} to the phase space scale {mu}{sub {delta}}{sup 2}={delta}{sup 2}Q{sup 2}. This phase space scale, where {delta} is the cone half angle of the jet, defines the angular region of the jet. At {mu}{sub {delta}}{sup 2} we determine the mixing of the three and two jet operators. We combine these results with the running of the two jet shape function, which we run down to an energy cut scale {mu}{sub {beta}}{sup 2}. This defines the resummed SW dijet decay rate in the context of SCET. The approach outlined here demonstrates how to establish a jet definition in the context of SCET. This allows a program of systematically improving the theoretical precision of jet phenomenology to be carried out.
Baclofen alters gustatory discrimination capabilities and induces a conditioned taste aversion (CTA).

Background: Studies intending to measure drug-induced changes in learning and memory are challenged to parse out the effects of drugs on sensory, motor, and associative systems in the brain. In the context of conditioned taste aversion (CTA), drugs that alter the sensorium of subjects and affect their ability to taste and/or feel malaise may limit the ability of investigators to make conclusions about associative effects of these substances. Since the GABAergic system is implicated in inhibition, the authors were hopeful to use the GABA agonist, baclofen (BAC), to enhance extinction of a CTA, but first a preliminary evaluation of BAC’s peripheral effects on animals’ sensorium had to be completed due to a lack of published literature in this area. Findings: Our first experiment aimed to evaluate the extent to which the GABAB agonist, BAC, altered the ability of rats to differentiate between 0.3% and 0.6% saccharin (SAC) in a two bottle preference test. Here we report that 2 or 3 mg/kg (i.p.) BAC, but not 1 mg/kg BAC, impaired animals’ gustatory discrimination abilities in this task. Furthermore, when SAC consumption was preceded by 2 or 3 mg/kg (i.p.) BAC, rats depressed their subsequent SAC drinking. A second experiment evaluated if the suppression of SAC and water drinking (revealed in Experiment 1) was mediated by amnesiac effects of BAC or whether BAC possessed US properties in the context of the CTA paradigm. The time necessary to reach an asymptotic level of CTA extinction was not significantly different in those animals that received the 3 mg/kg dose of BAC compared to more conventionally SAC + lithium chloride (LiCl, 81 mg/kg) conditioned animals. Conclusions: Our findings were not consistent with a simple amnesia-of-neophobia explanation. Instead, results indicated that 2 and 3 mg/kg (i.p.) BAC were capable of inducing a CTA, which was extinguishable via repeated presentations of SAC only. Our data indicate that, depending on the dose, BAC can alter SAC taste discrimination and act as a potent US in the context of a CTA paradigm.
Stage progression in Ta papillary urothelial tumors: relationship to grade, immunohistochemical expression of tumor markers, mitotic frequency and DNA ploidy.

Purpose: We studied 363 patients with stage Ta bladder tumors during long-term followup who were classified according to the 1998 WHO and International Society of Urological Pathology consensus classifications. We determine whether various immunohistochemical and molecular markers could predict tumor progression.Materials and Methods: A total of 680 patients in western Sweden with a first diagnosis of bladder carcinoma in 1987 and 1988 were registered and followed for at least 5 years. There were 363 (53%) tumors that were papillary stage pTa. The tumors were classified as papillary urothelial neoplasm of low malignant potential in 95 patients, low grade papillary urothelial carcinoma in 160 and high grade carcinoma in 108. Of the patients in the latter group 95 were subdivided into WHO grade 2 and 13 into WHO grade 3. Tissue from the primary tumors that progressed in stage during followup was further analyzed with immunohistochemical methods (p21, p53, Ki67 and pRb), DNA ploidy and mitotic frequency. The...
Robustness of an Odds-ratio Test in a Stratified Group Sequential Trial with a Binary Outcome Measure

Many clinical trials compare two or more treatment groups by using a binary outcome measure. For example, the goal could be to determine whether the frequency of pain episodes is significantly reduced in the treatment group (arm A) as compared to the control group (arm B). However, for ethical or regulatory reasons, group sequential designs are commonly employed. Then, based on a binomial distribution, the stopping boundaries for the interim analyses are constructed for assessing the difference in the response probabilities between the two groups. This is easily accomplished by using any of the standard procedures, e.g., those discussed by Jennison and Turnbull (2000), and using one of the most commonly used software packages, East (2000). Several factors are known to often affect the primary outcome of interest, but their true distributions are not known in advance. In addition, these factors may cause heterogeneous treatment responses among individuals in a group, and their exact effect size may be unknown. To limit the effect of such factors on the comparison of the two arms, stratified randomization is used in the actual conduct of the trial. Then, a stratified analysis based on the odds ratio proposed in Jennison and Turnbull (2000, pages 251-252) and consistent with the stratified design is undertaken. However, the stopping rules used for the interim analyses are those obtained for determining the differences in response rates in a design that was not stratified. The purpose of this paper is to assess the robustness of such an approach on the performance of the odds ratio test when the underlying distribution and effect size of the factors that influence the outcome may vary. The simulation studies indicate that, in general, the stratified approach offers consistently better results than does the unstratified approach, as long as the difference in the weighted average of the response probabilities across strata between the two groups remains closer to the hypothesized values, irrespective of the differences in the (allocation) distributions and heterogeneous response rate. However, if the response probabilities deviate significantly from the hypothesized values so that the difference in the weighted average is less than the hypothesized value, then the proposed study could be significantly underpowered.
Towards self‐caring MapReduce: a study of performance penalties under faults

Summary Self-caring IT systems are those that can proactively avoid system failures rather than reactively handle failures after they have occurred. In this paper, we focus on failures in which a MapReduce job is unable to execute within an service-level agreement based completion time. The existing fault-tolerance capability provided by MapReduce frameworks such as Hadoop, is simple and the penalty associated with handling faults could potentially lead to excessive job execution times. Our goal in this paper is to bring out the severity of this penalty for different job and framework parameters. We quantitatively evaluate the penalty in execution time associated with node faults using the MRPerf simulator. We then perform an empirical study of penalties on a virtualized testbed consisting of Xen domains, by varying system characteristics along four dimensions: hardware, application, dataset, and fault types. Through simulation and empirical results, we show that job-completion-time service-level agreement violations can be reduced using dynamic resource scaling. Scaling leverages, the elastic properties of a virtualized environment, to mitigate execution time penalties and hence proactively avoids a potential job failure. We show that using resource scaling, performance penalties can be decreased to less than 5% of the no-fault execution time, at minimal additional cost. Copyright © 2013 John Wiley & Sons, Ltd.
Electronic and nuclear structural snapshots in ligand dissociation and recombination processes of iron porphyrin in solution: a combined optical/X-ray approach.

The photodissociation and recombination of CO and 1-methylimidazole (Im) from iron protoporphyrin IX (FePP–ImCO) dissolved in a 30% v/v aqueous solution of Im was studied using ultrafast optical transient absorption (TA) and X-ray transient absorption (XTA) spectroscopies. FePP–ImCO was shown to lose the CO ligand upon excitation at the Q bands, with 3.8 ps vibrational cooling and 21.6 ps intersystem crossing time constants derived from optical TA experiments, followed by ligation of a second Im on the nanosecond time scale. The penta-coordinate FePP–Im intermediate which forms following CO dissociation adopts a square pyramidal geometry with a “domed” iron center that is reminiscent of that formed upon loss of CO from carbonmonoxymyoglobin (MbCO). Unlike MbCO, which typically retains its newly generated penta-coordinated geometry until CO recombination, FePP can adopt a hexa-coordinate geometry by binding an additional Im ligand (FePP–(Im)2), allowing the porphyrin to exist in the low-spin electronic sta...
On Subgroups of the Nottingham Group of Positive Hausdorff Dimension

By a Theorem of Camina, the Nottingham group &#x1d4a9;(&#x1d53d;p) contains an isomorphic copy of every finitely generated pro-p group. In this article we obtain several restrictions on the structure of subgroups of &#x1d4a9;(&#x1d53d;p) which have positive Hausdorff dimension and show that such groups, if finitely generated, cannot be linear over a local field. This implies that just-infinite subgroups of &#x1d4a9;(&#x1d53d;p) studied in Fesenko (1999) and Barnea and Klopsch (2003) are not linear over any profinite ring.
REGULATION OF RABBIT ERYTHROCYTE CA2+-PUMP SENSITIVITY TO CALMODULIN IN EXPERIMENTAL HYPERLIPIDEMIA

Intracellular free calcium activity is in part determined by a calmodulin-regulated plasma membrane Ca(2+)-pump. Since changes in Ca2+ permeability have been implicated in atherosclerotic plaque formation, we initiated a lipid hyperalimentation protocol during which we measured various erythrocyte calcium flux parameters and early atheroma development. Adolescent New Zealand White rabbits were fed a diet with 0.5% cholesterol and 2.5% lard over a 3-month period. Plasma cholesterol and triacylglycerols increased on average 18.7- and 13.9-fold respectively, while erythrocyte membrane cholesterol content decreased 18% and total phospholipids by 54%. After 3 months of lipid hyperalimentation, 22% of the aortic arch was covered with large, early-stage, raised atheroma. Basal and calmodulin-activated (Ca2+ + Mg2+)-ATPase activities in erythrocyte membranes increased by 31% and 123%, respectively at 2 months, with a concomitant increase in calmodulin affinity (Km) from 15.6 to 4.2 nM. These differences were transient on account of changes in the control animals which exhibited a slowly developing sensitivity to calmodulin during maturation. Basal Ca2+ transport and passive Ca2+ permeability increased about 7-fold during the hyperlipidemic phase. This suggests that overt hyperlipidemia, leading to atherosclerotic plaque development, alters plasma membrane Ca2+ regulatory mechanisms including passive Ca2+ permeability. The changes in enzymatic function, membrane composition, and Ca2+ permeability seen in this red cell model system may be a reflection of early changes in cells that are directly involved in the development of atherosclerotic plaques.
The Nature and Classification of Lichens.—I. Views and Arguments of Botanists Concerning Classification

Early in November, I909, circular letters were sent to 75 American botanists and an equal number of foreign botanists asking for their views regarding the classification of lichens. Gathering data of this kind is an unusual method of approaching a scientific problem; but it was thought that the views of botanists might aid in the final solution of the problem. No man is able to express himself very certainly on the classification of all plants; consequently it is not surprising that certain men who write regarding the classification of many or all of the large groups of plants expressed themselves very doubtfully when asked for a statement. As was to be expected a rather small proportion of those who replied made statements which are of great value. The form of the circular letter is given below.
ISOCT study of collagen crosslinking of collagen in cancer models(Conference Presentation)

The role of extracellular matrix modification and signaling in cancer progression is an increasingly recognized avenue for the progression of the disease. Previous study of field effect carcinogenesis with Inverse Spectroscopic Optical Coherence Tomography (ISOCT) has revealed pronounced changes in the nanoscale-sensitive mass fractal dimension D measured from field effect tissue when compared to healthy tissue. However, the origin of this difference in tissue ultrastructure in field effect carcinogenesis has remained poorly understood. Here, we present findings supporting the idea that enzymatic crosslinking of the extracellular matrix is an effect that presents at the earliest stages of carcinogenesis. We use a model of collagen gel with crosslinking induced by lysyl oxidase (LOXL4) to recapitulate the difference in D previously reported from healthy and cancerous tissue biopsies. Furthermore, STORM imaging of this collagen gel model verifies the morphologic effects of enzymatic crosslinking at length scales as small as 40 nm, close to the previously reported lower length scale sensitivity threshold of 35 nm for ISOCT. Analysis of the autocorrelation function from STORM images of collagen gels and subsequent fitting to the Whittle-Matern correlation function shows a similar effect of LOXL4 on D from collagen measured with ISOCT and STORM. We extend this to mass spectrometric study of tissue to directly measure concentrations of collagen crosslink residues. The validation of ISOCT as a viable tool for non-invasive rapid quantification of collagen ultrastructure lends it to study other physiological phenomena involving ECM restructuring such as atherosclerotic plaque screening or cervical ripening during pregnancy.
The Planar Lipid Bilayer System Serves as a Reductionist Approach for Studying NK Cell Immunological Synapses and Their Functions

The immunological synapse (IS) is the junction between an immune cell (e.g., a T or NK cell) and another cell (e.g., an antigen-presenting cell (APC), or a tumor cell). The formation of the IS is crucial for cell-mediated immunity, and as such, an understanding of both the composition of the IS and the factors that drive its formation are essential for understanding how and when NK cells eliminate susceptible target cells. The supported lipid bilayer (SLB) system is a highly effective tool for directly studying the IS. SLBs confer three main advantages: (1) they allow for synapse formation on a level horizontal surface, allowing for direct visualization of the IS under high resolution imaging systems, (2) they mimic the surface of a target cell by providing a fluid mosaic into which surface proteins can be embedded while permitting free motion in two dimensions, which is important for studying the dynamics of synapse formation, and (3) they allow investigators to determine the exact composition of the bilayer, thus in turn allowing them to answer very specific questions about the IS. It is our hope that this chapter will furnish readers with an awareness of the applications of the SLB system for studying the IS in NK cells, and also of a basic knowledge of how to use this system for themselves.
Plastic Debris in 29 Great Lakes Tributaries: Relations to Watershed Attributes and Hydrology

Plastic debris is a growing contaminant of concern in freshwater environments, yet sources, transport, and fate remain unclear. This study characterized the quantity and morphology of floating micro- and macroplastics in 29 Great Lakes tributaries in six states under different land covers, wastewater effluent contributions, population densities, and hydrologic conditions. Tributaries were sampled three or four times each using a 333 μm mesh neuston net. Plastic particles were sorted by size, counted, and categorized as fibers/lines, pellets/beads, foams, films, and fragments. Plastics were found in all 107 samples, with a maximum concentration of 32 particles/m3 and a median of 1.9 particles/m3. Ninety-eight percent of sampled plastic particles were less than 4.75 mm in diameter and therefore considered microplastics. Fragments, films, foams, and pellets/beads were positively correlated with urban-related watershed attributes and were found at greater concentrations during runoff-event conditions. Fibers,...
Retrovirus-mediated delivery of short hairpin RNA targeting human papillomavirus (HPV) 16 E6 and E7 oncogenes and induction of apoptosis in oropharyngeal squamous cell cancer (OSCC) cell line

6002 Background: Human papillomavirus type 16 is identified in almost 50% of the cases of OSCC. The E6 and E7 genes of HPVs encode oncoproteins that bind and degrade the tumor suppressor proteins p...
Introduction to Special Issue 16(1)

The symposium attracted well over a hundred participants. Attendees included many veterinarians, animal welfare workers and attorneys, as well as academics and students representing a wide variety of disciplines. The papers included here are merely a selection. Even so the range is wide. There are three by legal scholars (Taimie Bryant, David Favre and Iris Goodwin), four by philosophers (Jon Garthoff, Joel MacClellan, Clare Palmer and me), one by a philosopher/cognitive scientist (Colin Allen), and one by a psychologist/ethologist (Gordon Burghardt).
A Phase I Study of Temozolomide (Temodar®) in Pediatric Patients with Relapsed or Refractory Leukemia—A Children’s Oncology Group Study.

A phase I study of oral temozolomide, administered daily for 5 days every 28 days, was performed in children with relapsed or primary refractory leukemias. The starting dose was 200 mg/m 2 /day with subsequent dose escalation to 260 mg/m 2 /day. Ten patients (5 male, 5 female), median age 9 years (range: 1–18 years), with leukemia (6 with acute lymphocytic leukemia [ALL], 4 with acute myelogenous leukemia [AML]) received a total of 14 cycles of temozolomide. Serum pharmacokinetic (PK) samples were obtained in 6 patients using a limited pharmacokinetic sampling strategy. Samples were also obtained from 8 patients for correlative biology studies, including analysis of methyl-guanine methyl transferase (MGMT) activity and microsatellite instability (MSI). MGMT activity was measured in 7 patients; all 3 patients with ALL tested for MGMT had elevated MGMT activity, with a median MGMT activity of 1240 fmol/mg protein (range: 356–1756). In contrast, 3 out of 4 patients with AML had MGMT activity below the limits of detection. Eight patients were tested for microsatellite instability by multiplex PCR using a panel of 13 MSI loci. Two patients (one with ALL and one with AML) demonstrated probable MSI instability. Temozolomide has been well tolerated, with no patients developing dose-limiting toxicity to date. One patient with AML, undetectable MGMT activity and no microsatellite instability had a partial response (PR) lasting 4 cycles (
Emerging Applications to Signal Processing

In this chapter we discuss some new applications of algebra to signal processing. The first way in which this arises is via the transfer function of a filter. This leads to questions about polynomials and rational functions, which can sometimes be solved by ideas from algebraic geometry, often with better results than through numerical methods. The second application of algebra is to image processing. We already saw how three-dimensional rotations can be simply described by quaternions – now we look at an application in face recognition.
Autophagy Inhibition and Chemosensitization in Cancer Therapy

Abstract Autophagy is a cellular degradation mechanism involving protein turnover as well as the recycling of excessive and dysfunctional organelles. Autophagy is generally considered to occur at basal levels in cells, but may be induced to higher levels under conditions of stress, such as starvation, hypoxia, ionizing radiation treatment, or chemotherapy. Aberrations in the autophagic machinery may represent either cause or effect in various diseases. In cancer, autophagy has been shown to be one of the mechanisms affecting the response to chemotherapy and/or radiation treatment. In this chapter, the different types and functional forms of autophagy, the autophagy signaling pathway, as well as the role of autophagy in transformation and tumor suppression are discussed. Modulation of autophagy for improving tumor cell chemosensitivity and radiosensitivity is currently being explored in clinical trials; the potential impact and limitations of these studies are discussed. We also briefly review the intersection between autophagy and the immune system with regard to the effectiveness of chemotherapy. The chapter concludes with future directions in cancer treatment in relation to novel therapies and potential drug targets for autophagy modulation.
Modelling Regulatory Distortions with Real Options: An Extension

The introduction of uncertainty can make a significant difference in the valuation of a project. In a regulatory environment, this manifests itself, inter alia, in situations where regulatory constraints can affect the valuations of a firm’s investment which, in turn, has an adverse impact on consumers’ welfare. In particular, the inability of a regulated firm to exercise any or all of the delay, abandon, start/stop, and time-to-build options has an economic and social cost. With this view in mind, we specify a model using real options methodology where regulatory delay constraints impact the firm’s cash flow and its investment valuation.
Grey-Lethal, Grizzled, Mocha, Pallid, Muted, Misty, and Pearl

In considering the influence of grey-lethal on pigmentation, one is faced with the dilemma of whether to limit the discussion to those observations which bear directly on this subject or to include the considerably greater number of efforts which have been directed toward investigating the other effects of this osteopetrotic mutant. The decision to include a brief resume of all of the effects of the mutation is based on the belief that they are germane and that such treatment may help focus attention on the mutation’s primary effect.
Normal Histology of Female Genital Organs

The anatomy of vulva covers mons pubis, ­prepuce, frenulum, clitoris, labia minora, labia major, vulvar vestibule, urethral meatus, Bartholin’s and Skene’s glands, hymen, and introitus. Squamous epithelium covers surfaces of all vulvar ­structures. Mons pubis and labia major are covered by keratinizing squamous epithelium (skin) ­associated with all types of cutaneous adnexa, including hair follicles, sebaceous glands, apocrine glands, and sweat glands. Labia minor and inward to vaginal introitus and hymen are mainly covered by nonkeratinizing squamous epithelium ­associated with no or rare sweat and sebaceous glands. Bilateral Bartholin’s glands are located ­posterolaterally in the vulvar vestibule and have ­tubuloalveolar structures, including acini of mucin-secreting columnar cells and ducts lined by transitional to squamous epithelium. There are also minor vestibular glands that are tubular and lined by mucin-secreting columnar cells. Skene’s glands are also paired glandular structures covered by ­pseudostratified mucin-secreting columnar epithelium, located closely and posterolateral to the urethra. The clitoris is covered by nonkeratinizing squamous epithelium and contains stroma that is rich in erectile vascular structures similar to corpora cavernosa of the penis.
Perturbation Method: Strained Coordinates

This chapter describes the yield and procedure of strained coordinates. It is applicable to differential equations that have a small parameter present. It yields an approximation to the solution, valid on a long time scale. A regular perturbation expansion may give the correct answer, but at the wrong location. It is found that by scaling the dependent variable, and one, or more of the independent variables by the small parameter, the solution may be approximated at the correct location. It is observed that if the regular perturbation solution to a differential equation has secular terms, but the original equation has bounded solutions, then the regular perturbation approximation is not valid for large values of the independent variables. One way to obtain a solution that is valid for longer scales is by straining the coordinates, and that is, expanding the dependent variable, and one, or more of the independent variables in terms of the small parameter.
Economic, Situational, and Psychological Correlates of the Decision-Making Process of Battered Women:

The author presents the findings of a descriptive, exploratory study designed to measure the correlates of battered women's decisions to return home to the abuser after termination by a shelter. Da...