cssi/SciSciGPT-SciSciNet huggingface dataset:
Calculation of ground-state and optical properties of boron nitrides in the hexagonal, cubic, and wurtzite structures

The electronic structures, the charge-density distribution, and the total energies of boron nitrides (BN) in the hexagonal, cubic, and wurtzite structures are studied by first-principles self-consistent local-density calculations. For the ground-state properties, the band structures, the equilibrium lattice constants, the bulk modulus and their derivatives, and the cohesive energy are in good agreement with other recent calculations and with experimental data. The relative stabilities and possible phase transitions among these three phases are discussed. The linear optical properties of these three crystals are also calculated and compared with the available measurements. For hexagonal BN, all the structures in the electron-energy-loss function as measured by inelastic electron scattering have been reproduced by the calculation. For cubic BN, the calculated dielectric functions is also in good agreement with the reflectance data. For wurtzite-structure BN, no optical data are available for comparison. These results are discussed in the context of crystal structure and bonding in these three crystals. Based on the analysis of the calculated and measured optical data on cubic and hexagonal BN, it is argued that the assessment of the accuracy of the conduction-band states should rely mainly on the reproduction of major structures in the optical-absorption curves rather than on the size of the band gap. The accuracy of the higher conduction-band states as calculated by the local-density theory is strongly energy and momentum dependent. Furthermore, a determination of the optical gap is complicated by the different roles of the direct and indirect transitions, and by the difficult task of extrapolating data to the low-frequency region.
Bone curvature: sacrificing strength for load predictability?

Nearly all long bones of terrestrial mammals that have been studied are loaded in bending. Yet bending requires greater bone mass than axial compression for effective support of equivalent static loads. Most long bones, in fact, are curved along their length; their curvature augmenting rather than diminishing stresses developed due to bending. The most “efficient” design of a bone (maximal strength per unit mass) should be a form which is straight and resists axial compression. Bone curvature and the bending developed in the long bones of most species studied, therefore, poses a paradox in design. However, under natural conditions an animal's skeleton must support a range of dynamic loads that vary in both direction and magnitude. Thus, improved predictability of dynamic loading should represent an important feature in the design of the bone, in addition to its absolute strength. We present an explanation of long bone curvature, based on the conditions of stability for bending vs. axial compression in a column, that describes this apparent design paradox as a mechanism for improving the predictability of loading direction (and, consequently, the pattern of stresses within the bone). Our hypothesis argues that in order to understand the design “effectiveness” of long bone shape the role of the bone as a structural unit must be redefined to one in which bone strength is optimized concurrently with loading predictability. In agreement with our hypothesis, bone curvature appears to meet this requirement.
Exhaled breath condensate isoprostanes are elevated in patients with acute lung injury or ARDS.

Background Oxidant stress is a purported mechanism of tissue damage in patients with ARDS and acute lung injury (ALI). Isoprostanes, prostanoid compounds primarily formed nonenzymatically via lipid peroxidation, are precise markers of in vivo oxidant stress. Plasma levels of metabolites of 8-iso-prostaglandin-F 2α (8-iso-PGF 2α ) correlate with outcome in patients with ARDS. Objective To examine exhaled breath condensate levels of 8-iso-PGF 2α as a noninvasive quantification of pulmonary oxidant stress in patients with, or at risk for, ARDS/ALI. Methods Breath condensate was collected from 22 patients with, or at risk for, ARDS/ALI by placing Tygon tubing submerged in an ice bath in line with the expiratory limb of the ventilator circuit. Ten patients without lung disease, who were intubated while undergoing minor surgical procedures, served as control subjects. Between 1 and 3 mL of condensate was collected over a 30- to 60-min period, then immediately frozen and stored at −70°C until analysis. The 8-iso-PGF 2α was purified and derivatized, then quantified by stable isotope dilution in conjunction with gas chromatography/mass spectrometry. Results The mean level of exhaled 8-iso-PGF 2α in the patients with ALI/ARDS, 87 ± 28 pg/mL, was significantly higher than the mean in the normal group, 7 ± 4 pg/mL (p = 0.007). The 8-iso-PGF 2α levels were greater than two standard deviations above the mean of the normal group in 12 of 22 patients with or at risk for ARDS/ALI. Conclusions These results provide further evidence that lipid peroxidation does occur in patients with ARDS/ALI. The measurement of exhaled isoprostanes provides a novel, noninvasive method to quantify oxidant stress in such patients.
The Origins of Pandemic Influenza — Lessons from the 1918 Virus

The 1918 virus spread rapidly around the world and was associated with mortality measured in the thousands per 100,000 population. Dr. Robert Belshe describes what the 1918 virus teaches us about avian H5N1 influenza.
What if utility functions do not exist

Often the preferences of decision-makers are sufficiently inconsistent so as to preclude the existence of a utility function in the classical sense. Several alternatives for dealing with this situation are discussed. One alternative, that of modifying classical demands on utility functions, is emphasized and described in the context of the theory of measurement developed in recent years by behavioral scientists. The measurement theory approach is illustrated by discussing the concept of the dimension of a partial order. Even if we cannot assign numerical utility or worth values which reflect preferences in the classical utility function sense, from the measurement theory point of view we can still learn a lot about the preferences by finding several measures of worth so that a given alternative x is preferred to an alternative y if and only if x is ranked higher than y on each of the worth scales. If such measures can be found, it follows that the preferences define a partial order, and the smallest number of such scales needed is called the dimension of the partial order. If one-dimensional preferences (those amenable to classical utility assignments) cannot be found, then the next best thing is to search for partially ordered preferences with as small a dimension as possible. Several conditions under which a partial order is two-dimensional are described.
Measuring the Level, Pattern, and Sequence of Government Respect for Physical Integrity Rights

We employ a polychotomous version of Mokken Scaling Analysis to create an improved measure of government respect for a subset of human rights known as physical integrity rights. The scale we produce is shown to be unidimensional, and it contains information about the level, pattern, and sequence of government respect for these rights. No previous measure has explicitly addressed the issue of sequence of government respect for human rights. The sequence, or ordering, of respect for physical integrity rights that we find tells us which rights are more commonly respected (the rights not to be killed or disappeared) and which ones are more commonly violated (the rights not to be imprisoned arbitrarily or tortured). Our findings improve upon previous studies that have assumed unidimensionality and that have made a priori assertions of patterns of respect. They also stand in contrast to McCormick and Mitchell's (1997) claim that government respect for physical integrity rights is necessarily a multidimensional phenomenon.
Reliability of oxide VCSELs in non-hermetic environments

We have identified three failure mechanisms in oxide VCSELs under bias in high humidity and developed environmentally robust oxide VCSELs. Following the discussion of the failure mechanisms, we report on our environmental reliability test results. We have identified three failure modes in the biased 85/85 testing. The most common moisture-related failure mode is dislocation growth in the active layers. The other two failure modes, semiconductor cracking and aperture surface degradation are accelerated by the bias current.
Smoking in Video Games: A Systematic Review

Author(s): Forsyth, Susan R; Malone, Ruth E | Abstract: IntroductionVideo games are played by a majority of adolescents, yet little is known about whether and how video games are associated with smoking behavior and attitudes. This systematic review examines research on the relationship between video games and smoking.MethodsWe searched MEDLINE, psycINFO, and Web of Science through August 20, 2014. Twenty-four studies met inclusion criteria. Studies were synthesized qualitatively in four domains: the prevalence and incidence of smoking imagery in video games (n = 6), video game playing and smoking behavior (n = 11), video game addiction and tobacco addiction (n = 5) and genre-specific game playing and smoking behavior (n = 3).ResultsTobacco content was present in a subset of video games. The literature is inconclusive as to whether exposure to video games as a single construct is associated with smoking behavior. Four of five studies found an association between video game addiction and smoking. For genre-specific game playing, studies suggest that the type of game played affected association with smoking behavior.ConclusionsResearch on how playing video games influences adolescents' perceptions of smoking and smoking behaviors is still in its nascence. Further research is needed to understand how adolescents respond to viewing and manipulating tobacco imagery, and whether engaging in game smoking translates into changes in real-world attitudes or behavior. Smoking imagery in video games may contribute to normalizing adolescent smoking.ImplicationsA large body of research has shown that smoking imagery in a variety of media types contributes to adolescent smoking uptake and the normalization of smoking behavior, and almost 90% of adolescents play video games, yet there has never been a published systematic review of the literature on this important topic. This is the first systematic review to examine the research on tobacco and video games.We found that tobacco imagery is indeed present in video games, the relationship between video game playing and smoking remains unclear, there appears to be a correlation between problem gaming and smoking and the genre of games may play a role in adolescent smoking behavior.
Framework for interpretation of genetic variations in pancreatitis patients

Chronic pancreatitis (CP) is defined by irreversible damage to the pancreas as a result of inflammation-driven pancreatic tissue destruction and fibrosis occurring over many years. The disorder is complex, with multiple etiologies leading to the same tissue pathology, and unpredictable clinical courses with variable pain, exocrine and endocrine organ dysfunction and cancer. Underlying genetic variants are central CP susceptibility and progression. Three genes, with Mendelian genetic biology (PRSS1, CFTR, SPINK1) have been recognized for over a decade, and little progress has been made since then.. Furthermore, application of high-throughput genetic techniques, including genome-wide association studies (GWAS) and next generation sequencing (NGS) will provide a large volume of new genetic variants that are associated with CP, but with small independent effect that are impossible to apply in the clinic. The problem of interpretation is using the old framework of the germ theory of disease to understand complex genetic disorders. To understand these variants and translate them into clinically useful information requires a new framework based on modeling and simulation of physiological processes with or without genetic, metabolic and environmental variables considered at the cellular and organ levels, with integration of the immune system, nervous system, tissue injury and repair system and DNA repair system. The North American Pancreatitis Study II (NAPS2) study was designed to capture this type of date and construct a time line to understand and later predict rates of disease progression from the initial symptom to end-stage disease. This effort is needed to target the etiology of pancreatic dysfunction beginning at the first signs of disease and thereby prevent the development of irreversible damage and the complications of CP. The need for a new framework and the rational for implementing it into clinical practice are described.
Vertebral osteology and swimming style in living and fossil whales (Order: Cetacea)

Morphological modification of the cetacean vertebral column for axial locomotion was one of many changes that occurred during and after the invasion of aquatic habitats by the ancestors of living whales. These modifications resulted in a column that can be divided into neck, chest, torso, and fluke structural and functional units. Variations in these units allow subdivision of living whales into three morphological groups that reflect differences in regional flexibility of the column and of locomotor style. Both odontocete and mysticete cetaceans exhibit trends toward reduction of relative centrum length in the neck and torso, restricting the flexibility of the column with increasing adaptation to aquatic lifestyles. Mysticetes and physeterid odontocetes retain the archaeocete pattern of constant vertebral shape along the torso, which acts as an undulatory unit. The location of secondary sites of reduced centrum length in non-physeterid odontocetes subdivides them into subgroups, one with reduced posterior, and the other with reduced anterior, torso flexibility. The relationships between particular osteological patterns and swimming styles in living taxa are used to support predictions of swimming style in fossil species after adoption of a fluke in the late Eocene.
A Monotonicity Property for Weighted Delaunay Triangulations

Given a triangulation of points in the plane and a function on the points, one may consider the Dirichlet energy, which is related to the Dirichlet energy of a smooth function. In fact, the Dirichlet energy can be derived from a finite element approximation. S. Rippa showed that the Dirichlet energy (which he refers to as the “roughness”) is minimized by the Delaunay triangulation by showing that each edge flip which makes an edge Delaunay decreases the energy. In this paper, we introduce a Dirichlet energy on a weighted triangulation which is a generalization of the energy on unweighted triangulations and an analogue of the smooth Dirichlet energy on a domain. We show that this Dirichlet energy has the property that each edge flip which makes an edge weighted Delaunay decreases the energy. The proof is done by a direct calculation, and so gives an alternate proof of Rippa’s result.
A pilot study of heart rate variability biofeedback therapy in the treatment of perinatal depression on a specialized perinatal psychiatry inpatient unit

Heart rate variability biofeedback (HRVB) therapy may be useful in treating the prominent anxiety features of perinatal depression. We investigated the use of this non-pharmacologic therapy among women hospitalized with severe perinatal depression. Three questionnaires, the State Trait Anxiety Inventory (STAI), Warwick–Edinburgh Mental Well-Being Scale, and Linear Analog Self Assessment, were administered to 15 women in a specialized inpatient perinatal psychiatry unit. Participants were also contacted by telephone after discharge to assess continued use of HRVB techniques. The use of HRVB was associated with an improvement in all three scales. The greatest improvement (−13.867, p < 0.001 and −11.533, p < 0.001) was among STAI scores. A majority (81.9 %, n = 9) of women surveyed by telephone also reported continued frequent use at least once per week, and over half (54.6 %, n = 6) described the use of HRVB techniques as very or extremely beneficial. The use of HRVB was associated with statistically significant improvement on all instrument scores, the greatest of which was STAI scores, and most women reported frequent continued use of HRVB techniques after discharge. These results suggest that HRVB may be particularly beneficial in the treatment of the prominent anxiety features of perinatal depression, both in inpatient and outpatient settings.
Cultural beliefs about rape and victims' response in three ethnic groups

Cultural definitions of rape were assessed among 101 African-American, Hispanic, and non-Hispanic white female rape victims and 89 nonvictims matched for ethnicity, age, marital status, and socioeconomic status. Hispanics scored highest and whites lowest both in perceived community victim-blaming and in victims' psychological distress. Social and treatment implications are discussed.
Efficient Embedded Runtime Systems through Port Communication Optimization

Traditionally shared data areas have been used to efficiently communicate between embedded system tasks, such as periodically executing control system tasks. Such implementations are highly sensitive to the execution order of tasks, i.e., they depend on a static timeline. SAE AADL supports a port communication model that ensures deterministic processing of signal streams. In this paper we discuss an analytical framework that allows us to optimize such port-based communication by generating a runtime executive that utilizes shared data areas where appropriate, while ensuring the timing semantic assumed by the control application.
Green Fluorescent Protein-Dal80p Illuminates up to 16 Distinct Foci That Colocalize with and Exhibit the Same Behavior as Chromosomal DNA Proceeding through the Cell Cycle of Saccharomyces cerevisiae

Four GATA family DNA binding proteins mediate nitrogen catabolite repression-sensitive transcription in Saccharomyces cerevisiae. Gln3p and Gat1p are transcriptional activators, while Dal80p and Deh1p repress Gln3p- and Gat1p-mediated transcription by competing with these activators for binding to DNA. Strong Dal80p binding to DNA is thought to result from C-terminal leucine zipper-mediated dimerization. Many Dal80p binding site-homologous sequences are relatively evenly distributed across the S. cerevisiae genome, raising the possibility that Dal80p might be able to “stain” DNA. We demonstrate that cells containing enhanced green fluorescent protein-Dal80p (EGFP-Dal80p) exhibit up to 16 fluorescent foci that colocalize with DAPI (4′,6′-diamidino-2-phenylindole)-positive material and follow DNA movement through the cell cycle, suggesting that EGFP-Dal80p may indeed be useful for monitoring yeast chromosomes in live cells and in real time.
Behavioral phenotypes of genetic mouse models of autism

More than a hundred de novo single gene mutations and copy-number variants have been implicated in autism, each occurring in a small subset of cases. Mutant mouse models with syntenic mutations offer research tools to gain an understanding of the role of each gene in modulating biological and behavioral phenotypes relevant to autism. Knockout, knockin and transgenic mice incorporating risk gene mutations detected in autism spectrum disorder and comorbid neurodevelopmental disorders are now widely available. At present, autism spectrum disorder is diagnosed solely by behavioral criteria. We developed a constellation of mouse behavioral assays designed to maximize face validity to the types of social deficits and repetitive behaviors that are central to an autism diagnosis. Mouse behavioral assays for associated symptoms of autism, which include cognitive inflexibility, anxiety, hyperactivity, and unusual reactivity to sensory stimuli, are frequently included in the phenotypic analyses. Over the past 10 years, we and many other laboratories around the world have employed these and additional behavioral tests to phenotype a large number of mutant mouse models of autism. In this review, we highlight mouse models with mutations in genes that have been identified as risk genes for autism, which work through synaptic mechanisms and through the mTOR signaling pathway. Robust, replicated autism-relevant behavioral outcomes in a genetic mouse model lend credence to a causal role for specific gene contributions and downstream biological mechanisms in the etiology of autism.
Dietary patterns, gastrointestinal complaints, and nutrition knowledge of recreational triathletes.

Dietary habits, nutrition knowledge, and gas- trointestinal complaints were evaluated in 2 1 female and 50 male triathletes; 30 completed hemoccult slides to determine the frequency of gastrointestinal bleeding. Triathbetes trained 1 1 h/wk with weekly distances of 5.3, 1 16.5, and 40.9 km for swimming, biking, and running, respectively. Mean daily en- ergy intake averaged 9058 and 1 1 59 1 U for women and men, respectively; 53.8% of the energy was from carbohydrates. Mean intakes ofvitamins and most minerals exceeded the Rec- ommended Dietary Allowances (RDAs), but many had intakes below RDAs for some nutrients; > 60% had low zinc and cop- per intakes. Because 39% took a daily multivitamin-mineral supplement, some had intakes 200-600% above the RDA. Al- though there were notable misconceptions about nutrition, nu- trition knowledge was high. Upper-gastrointestinal com- plaints, reported by 50%, included bloating and abdominal gas; the incidence of positive hemoccult slides was 27%. The rela- tion among performance, dietary patterns, nutrition knowl- edge, and gastrointestinal function remains to be estab- lished. AmfClinNutr l990;51:690-7.
Analysis of post-buckling and delamination in laminated composite St. Venant–Kirchhoff beams using CZM and layer-wise TSNDT

A layer-wise third order shear and normal deformable plate/shell theory (TSNDT) incorporating a cohesive zone model (CZM) is used to study the initiation and growth of delamination in straight and curved laminated beams. Upon satisfaction of the delamination criteria at a point on the interface between two layers, displacements there of two abutting points on the interface between the two layers are made discontinuous. Delaminations under mode-I, mode-II and mixed-mode static and transient loadings have been studied. All geometric nonlinearities, including the von Karman nonlinearity, are considered. The material of each layer is assumed to be St. Venant–Kirchhoff for which the second Piola–Kirchhoff stress tensor is a linear function of the Green-St. Venant strain tensor. Example problems studied also include delamination growth during axial buckling of a three-layer beam. It is found that the consideration of inertia forces noticeably delays the buckling load and significantly affects the deformed shape of an axially compressed laminated beam.
Multipath channel identification based on partial system information

Due to the wide spread application of digital broadcast and mobile communication systems, blind channel identification has become a popular research subject. By relying on known information such as the pulse shaping filter and the anti-aliasing filter responses, the performance of channel identification and equalization can be significantly enhanced for digital communication systems. We present simple methods designed for time-domain and frequency domain implementations. Our simulation results demonstrate the performance of these approaches.
Sequential Path Delay Fault Identification Using Encoded Delay Propagation Signatures

A complete function-based scheme is presented to identify at-speed sequentially untestable path delay faults. We introduce signature variables to implicitly track error propagation through combinational and sequential circuits. The path sensitization test functions are encoded with the signature variables. These encoded test functions allow implicit identification of all propagating transitions corresponding to each individual test function minterm. We then utilize the signature variables during the fault propagation in a way such that the latched error propagates robustly to an observable point irrespective of other latched errors. Results presented on the ISCAS'89 benchmarks show a large number of sequentially untestable path delay faults are identified.
Prediction of Douglas-fir fertilizer response using biogeoclimatic properties in the coastal Pacific Northwest

Fertilizer response of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) has been related to site and soil properties in the past, but the models have explained only about half of the variation in these investigations. Fertilizer response and percent response after two years were examined, according to mapped and measured biogeoclimatic variables, for 71 Douglas-fir installations in the coastal Pacific Northwest. Paired-tree installations consisted of 12-20 pairs of Douglas-fir trees with one tree fertilized with urea at 224 kg N·ha−1. Pearson correlation coefficients and boosted regression tree (BRT) models were used to determine the best predictor variables and models of Douglas-fir fertilizer response. The BRT models, using the combination of mapped and measured variables, performed the best for predicting fertilizer response. Basal area and volume responses were most related to high forest floor and surface soil carbon to nitrogen ratios. Basal area mean annual increment (MAI) and site index were both negatively correlated with fertilizer response. Also, low basal area MAI was the most important tree measure- ment for predicting fertilizer response in the BRT models. Installations with many of the predictors from the BRT models (>66% of the model criteria) were found to have a significantly greater fertilizer response than installations with only a few predictors (<33% of the model criteria). These findings support the use of these models for predicting fertilizer response of similar Douglas-fir stands in the coastal Pacific Northwest.
Child emotional aggression and abuse: Definitions and prevalence

Research on and intervention for child emotional abuse and emotional aggression toward children have been severely hampered because there have been no agreed-upon, clinically usable definitions.
622 Mbit/s CMOS limiting amplifier with 40 dB dynamic range

A monolithic, fully differential limiting amplifier has been successfully demonstrated in 1 /spl mu/m CMOS technology. The amplifier exhibits high input dynamic range of 40 dB (from 15 mV/sub p-p/ to 1.5 V/sub p-p/) at constant output voltage swing of 800 mV/sub p-p/ into 50 /spl Omega/, operating at 622 Mbit/s. This CMOS limiting amplifier is characterised by high speed, with sensitivity, and wide dynamic range.
Incidence and Prognostic Importance of Acute Renal Failure After Percutaneous Coronary Intervention

Background— In patients undergoing percutaneous coronary intervention (PCI) in the modern era, the incidence and prognostic implications of acute renal failure (ARF) are unknown. Methods and Results— With a retrospective analysis of the Mayo Clinic PCI registry, we determined the incidence of, risk factors for, and prognostic implications of ARF (defined as an increase in serum creatinine [Cr] >0.5 mg/dL from baseline) after PCI. Of 7586 patients, 254 (3.3%) experienced ARF. Among patients with baseline Cr 2.0, all had a significant risk of ARF. In multivariate analysis, ARF was associated with baseline serum Cr, acute myocardial infarction, shock, and volume of contrast medium administered. Twenty-two percent of patients with ARF died during the index hospitalization compared with only 1.4% of patients without ARF (P<0.0001). After adjustment, ARF remained strongly associated with death. Amo...
Sigma-1 Receptors Regulate Bcl-2 Expression by Reactive Oxygen Species-Dependent Transcriptional Regulation of Nuclear Factor κB

The expression of Bcl-2, the major antiapoptotic member of the Bcl-2 family, is under complex controls of several factors, including reactive oxygen species (ROS). The σ-1 receptor (Sig-1R), which was recently identified as a novel molecular chaperone at the mitochondria-associated endoplasmic reticulum membrane (MAM), has been shown to exert robust cellular protective actions. However, mechanisms underlying the antiapoptotic action of the Sig-1R remain to be clarified. Here, we found that the Sig-1R promotes cellular survival by regulating the Bcl-2 expression in Chinese hamster ovary cells. Although both Sig-1Rs and Bcl-2 are highly enriched at the MAM, Sig-1Rs neither associate physically with Bcl-2 nor regulate stability of Bcl-2 proteins. However, Sig-1Rs tonically regulate the expression of Bcl-2 proteins. Knockdown of Sig-1Rs down-regulates whereas overexpression of Sig-1Rs up-regulates bcl-2 mRNA, indicating that the Sig-1R transcriptionally regulates the expression of Bcl-2. The effect of Sig-1R small interfering RNA down-regulating Bcl-2 was blocked by ROS scavengers and by the inhibitor of the ROS-inducible transcription factor nuclear factor κB (NF-κB). Knockdown of Sig-1Rs up-regulates p105, the precursor of NF-κB, while concomitantly decreasing inhibitor of nuclear factor-κBα. Sig-1R knockdown also accelerates the conversion of p105 to the active form p50. Lastly, we showed that knockdown of Sig-1Rs potentiates H2O2-induced apoptosis; the action is blocked by either the NF-κB inhibitor oridonin or overexpression of Bcl-2. Thus, these findings suggest that Sig-1Rs promote cell survival, at least in part, by transcriptionally regulating Bcl-2 expression via the ROS/NF-κB pathway.
HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch.

Motivation: Recently developed profile–profile methods rival structural comparisons in their ability to detect homology between distantly related proteins. Despite this tremendous progress, many genuine relationships between protein families cannot be recognized as comparisons of their profiles result in scores that are statistically insignificant. Results: Using known evolutionary relationships among protein superfamilies in SCOP database, support vector machines were trained on four sets of discriminatory features derived from the output of HHsearch. Upon validation, it was shown that the automatic classification of all profile–profile matches was superior to fixed threshold-based annotation in terms of sensitivity and specificity. The effectiveness of this approach was demonstrated by annotating several domains of unknown function from the Pfam database. Availability: Programs and scripts implementing the methods described in this manuscript are freely available from http://hhsvm.dlakiclab.org/. Contact: ude.anatnom@cikaldm Supplementary information: Supplementary data are available at Bioinformatics online.
Continuous photodetection of resonance fluorescence

The concept of photodetection as a continuous quantum measurement introduced by Srinivas and Davies is extended to the detection of resonance fluorescence. This is a new approach to an old subject. This is also a new development in continuous photodetection in the sense that a fermion rather than the traditional boson field is the subject of monitoring. The superoperators for the no-count and the one-count processes are postulated, following the examples of Srinivas and Davies. The probability for the m-count process is then derived on the basis of these postulates. The first two factorial moments of the photon-number distribution are calculated, which are then used to evaluate the non-classical effects in resonance fluorescence. A parameter slightly different from Mandel's is found to be more suitable indicator of photon antibunching in the transient state.
SATB1 Cleavage by Caspase 6 Disrupts PDZ Domain-Mediated Dimerization, Causing Detachment from Chromatin Early in T-Cell Apoptosis

SATB1 is expressed primarily in thymocytes and orchestrates temporal and spatial expression of a large number of genes in the T-cell lineage. SATB1 binds to the bases of chromatin loop domains in vivo, recognizing a special DNA context with strong base-unpairing propensity. The majority of thymocytes are eliminated by apoptosis due to selection processes in the thymus. We investigated the fate of SATB1 during thymocyte and T-cell apoptosis. Here we show that SATB1 is specifically cleaved by a caspase 6-like protease at amino acid position 254 to produce a 65-kDa major fragment containing both a base-unpairing region (BUR)-binding domain and a homeodomain. We found that this cleavage separates the DNA-binding domains from amino acids 90 to 204, a region which we show to be a dimerization domain. The resulting SATB1 monomer loses its BUR-binding activity, despite containing both its DNA-binding domains, and rapidly dissociates from chromatin in vivo. We found this dimerization region to have sequence similarity to PDZ domains, which have been previously shown to be involved in signaling by conferring protein-protein interactions. SATB1 cleavage during Jurkat T-cell apoptosis induced by an anti-Fas antibody occurs concomitantly with the high-molecular-weight fragmentation of chromatin of ~50-kb fragments. Our results suggest that mechanisms of nuclear degradation early in apoptotic T cells involve efficient removal of SATB1 by disrupting its dimerization and cleavage of genomic DNA into loop domains to ensure rapid and efficient disassembly of higher-order chromatin structure.
In Spaces of Marginalization: Dispossession, Incorporation, and Resistance in Bolivia

Recent scholarship conceptualizing primitive accumulation as an ongoing process in global capitalism has noted the difficulties faced in bringing struggles against exploitation and dispossession together. While some scholars suggest that an 'organic link" exists between these conflicts. they have yet to clearly specify the conditions and mechanisms through which such a link can form. Examining cases in Bolivia at the turn of the twenty-first century. I argue that struggles against exploitation and dispossession do not merely converge when facing a common oppressor. but also as the changing forms and geographies of exploitation and dispossession bring people together in more proximate locations. I illustrate that the changing means through which Bolivia was incorporated into the global economy enhanced levels of marginalization and subsequently resulted in patterns of migration that led to a convergence of peasant and proletarian struggles. As both segments of Bolivian society were excluded from the country's major economic sectors. they migrated to the places where they thought they could best satisfy their livelihood needs. But as people continually struggled to meet these needs, these places became spaces of marginalization, and eventually, spaces of resistance.
Terrain classification of LADAR data over Haitian urban environments using a lower envelope follower and adaptive gradient operator

In response to the 2010 Haiti earthquake, the ALIRT ladar system was tasked with collecting surveys to support disaster relief efforts. Standard methodologies to classify the ladar data as ground, vegetation, or man-made features failed to produce an accurate representation of the underlying terrain surface. The majority of these methods rely primarily on gradient- based operations that often perform well for areas with low topographic relief, but often fail in areas of high topographic relief or dense urban environments. An alternative approach based on a adaptive lower envelope follower (ALEF) with an adaptive gradient operation for accommodating local slope and roughness was investigated for recovering the ground surface from the ladar data. This technique was successful for classifying terrain in the urban and rural areas of Haiti over which the ALIRT data had been acquired.
Effects of ride motion on reaction times for reaching tasks

In future operational environments, the ability of Soldiers to quickly and accurately reach controls and displays, while they are in enclosed moving vehicles, is critical to the design of U.S. Army crew stations. This study examines degradations in the timing and accuracy of reaches associated with such enclosed and moving environments. Twenty participants completed several series of reaches to touch-screens. The results supported that the motion environment, touch-screen location, target size and appearance, and the number of target choices influenced reach timing and accuracy. These results illustrate the need to develop mitigation strategies for effective Soldier performance in future vehicle crew stations.
Functional cardiac depression caused by defibrillator shocks. Quantitation of the safety factor for electrical defibrillation.

The overdose shock strengths required to depress ventricular contraction were determined for damped sinusoidal current in 7 metabolically supported, isolated contracting canine hearts. Each heart was suspended in an isoresistive and isotonic solution-through which the defibrillating shocks were delivered. Defibrillation thresholds were determined with standard damped sine wave shocks of 4.4-5.5msec duration. Then overdose shocks were delivered and the depressant effect on systolic left ventricular pressure was measured for shocks of 3-12 times threshold current. The minimum (threshold) current and energy densities required to defibrillate were 59.5±4.6mA/cm2 (average) and 3.12±0.2mJ/cm3. Increasing the shock strength above threshold produced a concomitant reduction of postshock left ventricular systolic pressure. The current and energy densities required to produce 50% depression (TD50) of left ventricular systolic pressure were 5.0 and 24.1 times the threshold current and energy densities respectively, indicating a wide safety margin using this criterion.
The Organizational Impacts of Managing Social Marketing Interventions

Since social marketing’s formal introduction in 1971, the field has advanced through employing innovations in marketing thought. Despite debates over whether or not marketing principles should be u...
Organic-Inorganic Network Assembles of Nanoparticles as Chemically Sensitive Interfacial Materials

This paper reports the result of a study of organic-inorganic network assembles as chemically sensitive interfacial materials. Core-shell gold nanoparticles of a 5 nm size and organic linkers such as 1,9-nonanedithiol and 1,5-pentadithiol are utilized as building blocks for constructing network assembles on planar substrates. To explore the responsive properties of such materials to volatile organic compounds, we utilized interdigitated microelectrodes as transducer. The responses at these nanostructured interfaces are demonstrated to be dependent on the chain length of the linking molecules. The difference of molecular interactions at the nanostructured interface has a significant impact to the response profile and sensitivity. The implications of the findings to the delineation of design parameters for constructing organic-inorganic network assemblies as chemically-sensitive interfacial materials are also discussed.
DISJUNCTORS IN MONILINIA (DISCOMYCETIDAE: SCLEROTINIACEAE) AND THEIR SIGNIFICANCE IN CLASSIFICATION

A disjunctor is a spindle- or needle-like crystalline organelle unique to the majority of Monilinia spp. It develops through the pores ofseptal lamellae of adjacent maturing conidia. At each end of a disjunctor one or two telomeric knobs are observed. The disjunctors are variable in size (3-10 x 0.25-2.5 Am) and ornamentation, depending upon the species. In many taxa ornamentation consists of more or less concentric ridges which represent coalesced individual warts, some of which remain attached to the corresponding discrete warts on the septal lamellae. The development of the disjunctor in Monilinia vaccinii-corymbosi, a pathogen of blueberries, is described in detail and compared with that of several other Monilinia spp. A list of the species with or without disjunctors is provided. In Monilinia Honey (anamorph: Monilia Bonorden), an economically significant fungal group, conidiogenesis is holoblastic and acroauxic; conidia are catenate, with maturation and secession or disarticulation from the base upward; and conidiophores and conidial chains are branched. Adjacent fully formed conidia of most species are separated by a spindle-shaped, crystalline organelle called a disjunctor. The disjunctor is formed while the conidia are still enclosed by host epidermis or cuticle; apparently it facilitates dispersal of conidia. This organelle is unique among the fungi to Monilinia. Disjunctors were first described by Woronin
Angioscopy in vascular reconstructions

Early attempts to perform endoscopy of the cardiovascular system were limited to the heart. Rigid endoscopes were used to visualize intracardiac pathology. While successful, these systems were too large to be used in peripheral vessels. In addition, displacement of the blood for clear visualization was difficult and was based on a transparent balloon. Using rigid choledochoscopes, Greenstone was able to visualize the lumens of large vessels in dogs and human cadavers in a blood-free field1. In 1974 Vollmar and Storz reported clinical success using a flexible choledochoscope2. Crispin (1973)3 and, later, Towne (1977)4 concurred that angioscopy was a safe technique which minimally prolonged the operative procedure, and was a potential alternative to completion arteriography. Modern technology has produced high-resolution, small-diameter angioscopes which provide high-quality images of even small-calibre vessels. Coupled with efficient irrigating systems, the lumens of many arteries and veins can now be inspected.
Multiphoton excitation spectroscopy of the B 1 ∑ + and C 1 ∑ + Ryberg states of CO

Early measurements1 of the CO B1Σ+←←X1Σ+ (v′, v″) = (0,0) band found a strong Q branch, an absence of other rotational structures, and a (linear/circular) polarization ratio which was incompatible with the theory of two-photon absorption.2-4 In contrast, the present measurements show the expected O and S branches and reveal that the polarization ratio exceeds 80:1.
“Just This Breath…” How Mindfulness Meditation Can Shift Everything, Including Neural Connectivity

In this issue of EBioMedicine, Shao et al. (2016-in this issue) make a significant and interesting contribution to a growing literature of changes seen in participants who receive formal programmatic instruction in mindfulness meditation. Since Kabat-Zinn's (1982) paper reporting on what would become the mindfulness-based stress reduction (MBSR) program, the literature and application of mindfulness meditation instruction within the Western biomedical approach has expanded greatly. The initial MBSR program was developed for patients at an academic medical center who had on-going chronic pain despite maximized allopathic treatment. These participants reported significant reductions in pain, improvements in mood, and fewer medical symptoms (Kabat-Zinn, 1982). Since that time, mindfulness meditation instruction has been applied and, especially MBSR, studied in broadening clinical scenarios, as well as for general health and wellness.
A Field Inventory and Collections Summary of Herpetofauna from the Sutter Buttes, an “Inland Island” within California's Great Central Valley

Abstract. The Sutter Buttes (Buttes) are a small, isolated mountain range in the Great Central Valley of California. Systematic study of the fauna and flora of this unique habitat has been limited by the private ownership of the entire mountain range. As a result, much of our knowledge about the herpetofauna of the Buttes is based on isolated observations and scattered museum records, most over 4 decades old. In this study, we present an updated inventory of the herpetofauna of the Buttes, based on a 2-year field survey within the boundaries of the first publicly protected property within the Buttes (Sutter Buttes State Park) and a comprehensive survey of museum specimens. The objective of this study was to develop a current herpetofaunal species list for the Buttes as a whole and the park specifically. We verify the occurrence of 16 previously identified herpetofaunal species within the park and provide evidence for 3 additional species. We also provide the first record of the widely invasive Pond Slider...
Analyses of polycyclic aromatic hydrocarbon (PAH) and chiral-PAH analogues-methyl-β-cyclodextrin guest-host inclusion complexes by fluorescence spectrophotometry and multivariate regression analysis

The negative health impact of polycyclic aromatic hydrocarbons (PAHs) and differences in pharmacological activity of enantiomers of chiral molecules in humans highlights the need for analysis of PAHs and their chiral analogue molecules in humans. Herein, the first use of cyclodextrin guest-host inclusion complexation, fluorescence spectrophotometry, and chemometric approach to PAH (anthracene) and chiral-PAH analogue derivatives (1-(9-anthryl)-2,2,2-triflouroethanol (TFE)) analyses are reported. The binding constants (Kb), stoichiometry (n), and thermodynamic properties (Gibbs free energy (ΔG), enthalpy (ΔH), and entropy (ΔS)) of anthracene and enantiomers of TFE-methyl-β-cyclodextrin (Me-β-CD) guest-host complexes were also determined. Chemometric partial-least-square (PLS) regression analysis of emission spectra data of Me-β-CD-guest-host inclusion complexes was used for the determination of anthracene and TFE enantiomer concentrations in Me-β-CD-guest-host inclusion complex samples. The values of calculated Kb and negative ΔG suggest the thermodynamic favorability of anthracene-Me-β-CD and enantiomeric of TFE-Me-β-CD inclusion complexation reactions. However, anthracene-Me-β-CD and enantiomer TFE-Me-β-CD inclusion complexations showed notable differences in the binding affinity behaviors and thermodynamic properties. The PLS regression analysis resulted in square-correlation-coefficients of 0.997530 or better and a low LOD of 3.81×10-7M for anthracene and 3.48×10-8M for TFE enantiomers at physiological conditions. Most importantly, PLS regression accurately determined the anthracene and TFE enantiomer concentrations with an average low error of 2.31% for anthracene, 4.44% for R-TFE and 3.60% for S-TFE. The results of the study are highly significant because of its high sensitivity and accuracy for analysis of PAH and chiral PAH analogue derivatives without the need of an expensive chiral column, enantiomeric resolution, or use of a polarized light.
Nutritional Genomics and Biological Sex

Abstract Sex influences the risk of most common diseases that affect both men and women. The goal of this work has been to present the existing evidence in humans about the interplay between genes, sex, and disease susceptibility, in the context of the complexity of environmental factors (i.e., dietary habits, smoking, alcohol consumption) in the modulation of the balance between health and disease. Some of the most compelling evidence was generated more than a decade ago and the data support the concept that gender-specific differences in morbidity and mortality may be mediated in part by genetic factors and by their differential response to the environment. Despite this evidence and the renewed interest and call for action to account for biological sex in the experimental design and the analyses, many of the most recent studies in the area of genetic associations and gene–diet interactions do not present results stratified by sex. Knowledge generated by a more careful and complete elucidation of the complex interactions predisposing to common diseases will result in an increased ability to provide successful personalized behavioral recommendations to prevent chronic disorders.
Implantable insulin pump improved quality of life in NIDDM

Source Citation Saudek CD, Duckworth WC, Giobbie-Hurder A, et al., for the Department of Veterans Affairs Implantable Insulin Pump Study Group. Implantable insulin pump vs multiple-dose insulin for...