cssi/SciSciGPT-SciSciNet huggingface dataset:
Confocal analysis of the dystrophin protein complex in muscular dystrophy.

The dystrophin protein complex (DPC), composed of at least 10 proteins that associate with dystrophin, is critical for the maintenance of normal muscle fiber structure and physiology. In this study, we used immunohistochemistry and confocal microscopy to examine the relative abundance and distribution of several of these proteins in muscle biopsies taken from patients with various muscular dystrophies. The optical sectioning capability of confocal microscopy allowed us to comprehensively analyze the semiquantitative expression of components of the DPC. Alpha-sarcoglycan–deficient patients displayed a marked reduction in membrane immunostaining of the sarcoglycan complex. Gamma-sarcoglycan–deficient patients showed variable decreased immunostaining of the sarcoglycan complex proteins. When β-sarcoglycan was expressed appropriately at the sarcolemma of γ-sarcoglycan–deficient patients, intracellular labeling of β-sarcoglycan was also present. Beta-sarcoglycan–deficient patients showed poor localization of extracellular matrix proteins in addition to a complete absence of the sarcoglycans. Merosin-deficient patients showed relatively normal immunostaining levels of all other members of the DPC. Finally, dystrophin-deficient patients showed little or no change in the expression of extracellular matrix proteins; however, some sarcoglycans were significantly decreased. These data allowed us to suggest unique fundamental interactions between the members of the DPC. © 2001 John Wiley & Sons, Inc. Muscle Nerve 24: 262–272, 2001
Mechanical and Environmental Factors in the Cyclic and Static Fatigue of Silicon Nitride

The effects of environment on cyclic and static fatigue behavior were investigated with hot-pressed silicon nitride materials. Tests were conducted at ambient temperature on standard compact tension specimens, and a dc electric potential technique was used to monitor crack lengths in situ. The results indicate that the environmental sensitivity of our materials under both cyclic and static loading mirrors that of durable glasses in static fatigue. The materials were most sensitive to water in the environment, while changes in pH had no significant effect in the range tested. In addition, NH3 was much less reactive with our materials than with vitreous SiO2. In some cases, the intergranular glass appears to be the site of environmental interaction. Evidence was also found that cyclic fatigue is not simply a manifestation of static fatigue. Cyclic fatigue was seen to occur in the absence of measurable static fatigue, and the data indicate that the mechanism of cyclic fatigue involves damage to the crack wake shielding zone.
Agogic Contrast in French and English Themes: Further Support for Patel and Daniele (2003)

A. D. Patel and J. R. Daniele (2003) compared the rhythms of musical themes written by French and English composers. They found a significant difference that mirrors known prosodic differences in French and English speech. Specifically, Patel and Daniele found the note-to-note durational contrast to be higher in English music than in French music. Their study was based on 137 English themes and 181 French themes that were selected according to stringent criteria. Here we report a replication of Patel and Daniele with a greatly expanded sample of nearly 2000 themes.
Epidemiology in multiple sclerosis: a pilgrim's progress.

There was more neurology taught under Harold G. Wolff at Cornell University Medical College in New York than perhaps anywhere else in the country when I attended from 1948 to 1952. I took my residency at the Veterans Administration Hospital in the Bronx, New York, a teaching hospital of Cornell, with Wolff as my Director of Training. While a resident, we thought we had found a treatment for multiple sclerosis. To test our conclusion, the first Class 1 treatment trial ever conducted for multiple sclerosis was performed. This showed no effect, but the participants began investigating multiple sclerosis among the 16 million persons at prime age for symptom onset who had served in the military in World War II. This led me to study its epidemiology worldwide, beginning with a detailed review of all published population-based estimates of frequency. Among these were nationwide surveys from Sweden, Denmark, Switzerland and later Norway and Finland, which showed in each country a concentration of the significantly high regions into contiguous areas forming a single ‘focus’ in each land, maximal in Denmark under the age of 15 years. The primary locus of high frequency multiple sclerosis seemed to be in the south-central inland lake region of Sweden, with spread to its contiguous neighbours. These concentrations in time and space indicated that multiple sclerosis was a disease probably acquired in early adolescence. Migration studies supported this: moves from high to low showed retention of birthplace risk only for those aged >15 years, whereas opposite moves indicated susceptibility limited to some 11–45 year olds. Epidemics of multiple sclerosis would suggest the disease is not only acquired but also infectious. If an infectious origin were true, transmission would have to occur before clinical onset, and would have to involve a much greater number of subjects than clinically involved. I believe there have been epidemics in Iceland, Shetland-Orkney and the Faroe Islands. On the Faroes there were no cases of multiple sclerosis among native-born resident Faroese from 1900 until 1943, when the first of 21 cases had clinical onset, heralding a type 1 epidemic with peak incidence rates >10 per 100 000 for 1945–46. British troops who occupied the islands from April 1940 to September 1945 we believe brought a widespread (because of the scatter of Faroese cases), asymptomatic (because they were healthy troops), persistent infection we called the primary multiple sclerosis affection that involved a large proportion of Faroese, with clinical multiple sclerosis ensuing in a very small proportion. Primary multiple sclerosis affection itself may have been manifest there as a newly introduced cause of acute infectious gastroenteritis and is possibly the underlying cause of multiple sclerosis in general.
Regional blood flow and neurohormonal responses to milrinone in congestive heart failure

We measured systemic hemodynamics, regional blood flow, and neurohormonal parameters in 13 patients with severe chronic congestive heart failure before and after 1 month of therapy with oral milrinone, a bipyridine cardiotonic agent. After milrinone there were significant reductions in pulmonary wedge pressure (27 ± 2 to 19 ± 3 mm Hg; P < 0.02) and systemic vascular resistance (1866 ± 152 to 1393 ± 93 dyne · sec/cm5; P < 0.05) that were associated with increases in cardiac index (1.85 ± 0.15 to 2.47 ± 0.20 L/min/m2; P < 0.02). There was a marked improvement in forearm blood flow (1.98 ± 0.14 to 3.02 ± 0.16 ml/min/dl; P < 0.01) and a reduction in forearm vascular resistance (45 ± 3 to 30 ± 3 U; P<0.01). Overall there was no significant change in renal blow flow, renal vascular resistance, or glomerular filtration rate. However, there was a heterogeneous response of renal blood flow and glomerular filtration rate, such that both were directly correlated with the magnitude of increase of cardiac index (r = 0.587 [P < 0.05] and r = 0.721 [P < 0.01], respectively). After milrinone there were no significant overall or subgroup changes in urinary sodium excretion, blood volume, plasma renin activity, urinary aldosterone levels, plasma or platelet vasopressin levels, or plasma norepinephrine levels. Thus 1 month of therapy with milrinone improves systemic and forearm hemodynamics, but its effects on renal blood flow and function were heterogeneous. These heterogeneous effects on regional blood flow may depend on the relative vasodilator and inotropic effects of milrinone. Clinical Pharmacology and Therapeutics (1986) 39, 128–135; doi:10.1038/clpt.1986.23
Quantization noise improvement of Time to Digital converter (TDC) for ADPLL

A number of communication applications are moving to digitally motivated architectures for their radio frequency module. This includes GSM-EDGE, WLAN, Bluetooth, GSM-GPRS, WiMAX. The All Digital PLL(ADPLL) forms the core of this architecture. The objective of the ADPLL is to generate a clean carrier frequency ƒ c , based on a input reference frequency ƒ ref . As part of the phase error measurement of the PLL, a Time to Digital converter(TDC) is used to measure the delay between ƒ ref clock edge and carrier clocking edge. An inverter chain is used to measure this delay as a integer number of basic inverter delay. This measurement error is termed TDC quantization error and effects the phase noise present in the final carrier. Due to the coarse delay of the basic inverter available, TDC introduces large quantization noise at the output of the PLL. This is too high for systems operating at high carrier frequencies or systems which have a tight phase noise requirement. This paper presents techniques to improve TDC quantization noise.
Studies of alkali adsorption on Rh(111) using optical second-harmonic generation

Dramatic changes were observed in the optical second-harmonic generation from the Rh(111) crystal surface as the surface was covered with alkali atoms. For low alkali coverage, these changes are explained qualitatively in terms of optical transitions between alkali atomic-derived electronic states and, for high coverage, in terms of the plasmon resonance of the alkali layer. The results establish the surface specificity of second-harmonic generation to the topmost 1 or 2 atomic layers of alkali metals.
Supplier Selection Decisions: A Fuzzy Logic Model Based on Quality Aspects of Delivery

This paper presents a decision making model to address uncertainty in requirement planning. The model proposes a DSS to evaluate the quality of suppliers where quality is categorized into three primary areas dealing with delivery specifics, front office quality, and support specific quality. The application of the model is restricted to delivery specifics with two quality criteria illustrated of on-time delivery and accuracy of shipping. Results of the model provide ranking of suppliers based on belief that each supplier can provide average or greater performance. Extension of the model will determine overall fuzzy-set based rankings based upon all considered quality parameters.
Invasion of the Body Snatchers: Prescription Privileges, Professional Schools, and the Drive to Create a New Behavioral Health Profession

The effect and perhaps the purpose of the prescription privilege movement in psychology will be to create a new behavioral health profession under the name “psychology,” initially controlled by practice interests and by professional schools of psychology. It is a logical extension not of psychology per se but of certain trends within professional practice. A new behavioral health profession might be worthwhile, considered on its own terms, but ironically the very forces giving rise to it within psychology are pushing the movement down a path that could create a public health hazard and problems both for empirical clinical psychology and for the existing practice base.
Tattooing the Body, Marking Culture:

This article examines the complex relationship between power and the physical and social practices of tattooing in contemporary United States. Briefly tracing the history of tattooing from ancient Greece to contemporary America, I highlight the temporal and geographical changes in the practices and perceptions of tattooing. In addition to creating a historical narrative, I situate the sociocultural practice of tattooing the body for the tattooist and the `tattooee'. This investigation into body inscription serves as a means to elucidate the contemporary practice of tattooing as one that is simultaneously physical and social, with multiple levels of constructed meaning. Finally, I will explore how tattooing, as a form of body modification, can be analyzed as a form of resistance to or a symptom of a culture that has commodified the body.
Design of a Cryogenic Calorimeter for Synchrotron Light Source Beam-Based Heating

Superconducting insertion devices using Nb3Sn conductors offer the potential of higher brightness photon beams and enhanced spectral range over existing permanent magnet technology. However, Nb3Sn is a low temperature superconductor that must be operated at temperatures near 4.2 K. At these temperatures, any small heat dissipation can potentially be sufficient to lose the superconducting state of a section of a superconducting electromagnet. To quantify the amount of power deposited on the winding emanating from beam-induced heating on a storage ring, we propose a diagnostic calorimeter that will be temporarily integrated into the synchrotron ring. The design of the calorimeter is discussed and the various heat input sources, expected to disturb the operation of a superconducting electromagnet, are reviewed.
Subject preference and ergativity

Abstract This paper presents the first-ever processing experiment on relativization in Avar, an ergative language with prenominal relatives. The results show no processing difference between the ergative subject gap and the absolutive object gap. The absolutive subject gap, however, is processed much faster. We propose a principled explanation for this result. On the one hand, Avar has a subject preference (cf. the Accessibility Hierarchy, Keenan and Comrie, 1977 ), which would make the processing of the ergative and the absolutive subject gap easier than the processing of the absolutive object gap. On the other hand, the ergative DP in a relative clause serves as a strong cue that allows the parser to project the remainder of the clause, including the absolutive object DP (cf. Marantz, 1991 , Marantz, 2000 ); such morphological cueing favors the absolutive object gap. Thus, two processing preferences, the one for subject relatives and the other for morphologically cued clauses, cancel each other out in terms of processing difficulty. As a result, reading time results for the ergative subject and absolutive object relative clauses are very similar. The overall processing results are significantly different from what is found in accusative languages, where subject preference and morphological cueing reinforce each other, leading to a strong transitive subject advantage.
Depolymerization of poly(ethylene terephthalate) recycled from post‐consumer soft‐drink bottles

Poly(ethylene terephthalate), recycled from post-consumer soft-drink bottles, is depolymerized by glycolysis in excess ethylene glycol at 190°C in the presence of a metal acetate catalyst. The glycolyzed products consist mostly of the PET monomer, bis(hydroxyethyl) terephthalate, and the dimer, and after long reaction time (up to and longer than 8 h), an equilibrium is attained between these two species. No other higher PET oligomers were detected in the study. Of the four metal acetates (lead, zinc, cobalt, and manganese) tested, zinc acetate is the best in terms of the extent of depolymerization, that is, the relative amount of monomer formed. The presence of green pigment in one type of recycled PET apparently has no effects on the glycolysis reaction.
Errorless Learning for Training Individuals With Schizophrenia at a Community Mental Health Setting Providing Work Experience

The effects of errorless learning (EL) on work performance, tenure, and personal well-being were compared with conventional job training in a community mental health fellowship club offering 12-week time-limited work experience. Participants were 40 clinically stable schizophrenia and schizoaffective disorder outpatients randomly assigned to EL vs conventional instruction (CI) at a thrift-type clothing store. EL participants received training on how to perform their assigned job tasks based on principles of EL, such as error reduction and automation of task performance. CI participants received training common to other community-based entry-level jobs that included verbal instruction, a visual demonstration, independent practice, and corrective feedback. Participants were scheduled to work 2 hours per week for 12 weeks. For both groups, job training occurred during the first 2 weeks at the worksite. Work performance (assessed using the Work Behavior Inventory, WBI) and personal well-being (self-esteem, job satisfaction, and work stress) were assessed at weeks 2, 4, and 12. Job tenure was defined as the number of weeks on the job or total number of hours worked prior to quitting or study end. The EL group performed better than the CI group on the Work Quality Scale from the WBI, and the group differences were relatively consistent over time. Results from the survival analyses of job tenure revealed a non-significant trend favoring EL. There were no group differences on self-esteem, job satisfaction, or work stress. The findings provide modest support for the extensions of EL to community settings for enhancing work performance.
Inoculation of Astragalus racemosus and Astragalus convallarius with selenium-hyperaccumulator rhizosphere fungi affects growth and selenium accumulation

Little is known about how fungi affect plant selenium (Se) accumulation. Here we investigate the effects of two fungi on Se accumulation, translocation, and chemical speciation in the hyperaccumulator Astragalus racemosus and the non-accumulator Astragalus convallarius. The fungi, Alternaria astragali (A3) and Fusarium acuminatum (F30), were previously isolated from Astragalus hyperaccumulator rhizosphere. A3-inoculation enhanced growth of A. racemosus yet inhibited growth of A. convallarius. Selenium treatment negated these effects. F30 reduced shoot-to-root Se translocation in A. racemosus. X-ray microprobe analysis showed no differences in Se speciation between inoculation groups. The Astragalus species differed in Se localization and speciation. A. racemosus root-Se was distributed throughout the taproot and lateral root and was 90 % organic in the lateral root. The related element sulfur (S) was present as a mixture of organic and inorganic forms in the hyperaccumulator. Astragalus convallarius root-Se was concentrated in the extreme periphery of the taproot. In the lateral root, Se was exclusively in the vascular core and was only 49 % organic. These findings indicate differences in Se assimilation between the two species and differences between Se and S speciation in the hyperaccumulator. The finding that fungi can affect translocation may have applications in phytoremediation and biofortification.
Prevalence of Staphylococcus aureus Nasal Colonization in the United States, 2001–2002

confidence interval [CI], 30.7%–34.1%) and 0.8% (95% CI, 0.4%–1.4%), respectively, and population estimates were 89.4 million persons (95% CI, 84.8–94.1 million persons) and 2.3 million persons (95% CI, 1.2–3.8 million persons), respectively. S. aureus colonization prevalence was highest in participants 6–11 years old. MRSA colonization was associated with age60 years and being female but not with recent health-care exposure. In unweighted analyses, the SCCmec type IV gene was more frequent in isolates from participants of younger age and of nonHispanic black race/ethnicity; the PVL gene was present in 9 (2.4%) of 372 of isolates tested. Conclusions. Many persons in the United States are colonized with S. aureus; prevalence rates differ demographically. MRSA colonization prevalence, although low nationally in 2001–2002, may vary with demographic and organism characteristics.
Suppression of mitochondria-dependent neutrophil apoptosis with thermal injury

Neutrophil apoptosis is delayed under trauma and/or sepsis conditions. The mechanism for the delay has remained unclear. We hypothesize that modulation of the mitochondrial pathway of apoptosis con...
Medical Management of Patients Undergoing Dentoalveolar Surgery

The oral and maxillofacial surgeon (OMS) should have an understanding of common medical comorbidities. This understanding allows for risk stratification and thus prevention of potential problems. Remaining knowledgeable regarding diseases, diagnosis, treatment strategies, and pharmacology ultimately improves patient care. This article provides an update on some of the most common medical diseases for the patient undergoing dentoalveolar surgery.
Reproduction beyond menopause: how old is too old for assisted reproductive technology?

Background Due to the recent media attention on postmenopausal women giving birth, there has been an increased scrutiny on the utility and safety of assisted reproductive technology in postmenopausal women.
Glial cell regulation of neuronal activity and blood flow in the retina by release of gliotransmitters.

Astrocytes in the brain release transmitters that actively modulate neuronal excitability and synaptic efficacy. Astrocytes also release vasoactive agents that contribute to neurovascular coupling. As reviewed in this article, Muller cells, the principal retinal glial cells, modulate neuronal activity and blood flow in the retina. Stimulated Muller cells release ATP which, following its conversion to adenosine by ectoenzymes, hyperpolarizes retinal ganglion cells by activation of A1 adenosine receptors. This results in the opening of G protein-coupled inwardly rectifying potassium (GIRK) channels and small conductance Ca2+-activated K+ (SK) channels. Tonic release of ATP also contributes to the generation of tone in the retinal vasculature by activation of P2X receptors on vascular smooth muscle cells. Vascular tone is lost when glial cells are poisoned with the gliotoxin fluorocitrate. The glial release of vasoactive metabolites of arachidonic acid, including prostaglandin E2 (PGE2) and epoxyeicosatrienoic acids (EETs), contributes to neurovascular coupling in the retina. Neurovascular coupling is reduced when neuronal stimulation of glial cells is interrupted and when the synthesis of arachidonic acid metabolites is blocked. Neurovascular coupling is compromised in diabetic retinopathy owing to the loss of glial-mediated vasodilation. This loss can be reversed by inhibiting inducible nitric oxide synthase. It is likely that future research will reveal additional important functions of the release of transmitters from glial cells.
A new framework for analyzing organizational workplace religion and spirituality

This paper proposes the Faith and Work Organizational Framework as a new organizational framework that builds on and addresses shortcomings of existing rubrics by giving needed attention to human, religious, legal, and organizational dynamics. This framework describes corporate actions and attitudes toward workplace spirituality and religion. It draws on symbolic management theory, and earlier conceptions of faith-friendly workplaces. The Faith and Work Organizational Framework identifies four distinct organizational approaches to addressing religion and spirituality at work (i.e. faith-avoiding, faith-based, faith-safe, and faith-friendly). Part one of this paper contextualizes the need for such a framework in light of the faith-at-work movement, Title VII, and human rights theory. Part two of the paper addresses shortcomings of existing models and offers a new language and framework (with four modalities). The paper concludes with theoretical, research, and practical implications of this framework.
EGFR Is Regulated by TFAP2C in Luminal Breast Cancer and Is a Target for Vandetanib

Expression of TFAP2C in luminal breast cancer is associated with reduced survival and hormone resistance, partially explained through regulation of RET. TFAP2C also regulates EGFR in HER2 breast cancer. We sought to elucidate the regulation and functional role of EGFR in luminal breast cancer. We used gene knockdown (KD) and treatment with a tyrosine kinase inhibitor (TKI) in cell lines and primary cancer isolates to determine the role of RET and EGFR in regulation of p-ERK and tumorigenesis. KD of TFAP2C decreased expression of EGFR in a panel of luminal breast cancers, and chromatin immunoprecipitation sequencing (ChIP-seq) confirmed that TFAP2C targets the EGFR gene. Stable KD of TFAP2C significantly decreased cell proliferation and tumor growth, mediated in part through EGFR. While KD of RET or EGFR reduced proliferation (31% and 34%, P < 0.01), combined KD reduced proliferation greater than either alone (52% reduction, P < 0.01). The effect of the TKI vandetanib on proliferation and tumor growth response of MCF-7 cells was dependent upon expression of TFAP2C, and dual KD of RET and EGFR eliminated the effects of vandetanib. The response of primary luminal breast cancers to TKIs assessed by ERK activation established a correlation with expression of RET and EGFR. We conclude that TFAP2C regulates EGFR in luminal breast cancer. Response to vandetanib was mediated through the TFAP2C target genes EGFR and RET. Vandetanib may provide a therapeutic effect in luminal breast cancer, and RET and EGFR can serve as molecular markers for response.
Pigment Reënforcement of Reclaimed Rubber

Abstract COMPOUNDING ingredients of many types are in use in rubber compounds and, although their effect on rubber has been extensively investigated, there has been very little work published to show their effect on reclaim alone. The behavior of reclaimed rubber in compounds which also contain crude rubber, accelerators, and pigments is well known. The presence of these variables makes it impossible to determine the effect of the pigment on the reclaim itself. In this study we propose to show (1) the effect of varying volume loadings of different pigments on a whole-tire reclaim cured with sulfur, (2) the effect of accelerators and activators, and (3) the effect of curing at lower temperatures. With crude rubber the desired physical properties may often be obtained by cure or, by the combined effect of cure and the reeˆnforcing action of compounding ingredients. Owing to the degree of disaggregation of the reclaimed rubber the effect of cure is greatly decreased and the action of reeˆnforcing pigments is...
Application of Stress Measurement to the Study of Thermally Activated Processes in Thin-Film Materials

Changes in mechanical stress occurring in unpatterned thin films on substrates at elevated temperatures can yield information about the kinetics of the controlling processes. In this study, a specialized furnace allowed stress at elevated temperatures to be measured by the optical-lever method. The furnace was designed for good temperature control, short thermal transient periods, accurate stress measurement with low scatter, and control of the gas ambient. Stress changes in phosphosilicate glass films measured during exposure to steam at 110–150°C allowed water diffusion coefficients to be calculated. Diffusivity decreased with increasing phosphorus content and with pre-annealing treatments. The effective activation energy for water sorption was about 0.43 eV. Analysis of stress changes associated with crystallization of amorphous silicon at temperatures near 600°C yielded an effective activation energy of 3.1 eV and a density change of about 1% for the transformation.
New Dirac Fermions in Periodically Modulated Bilayer Graphene

We investigate the effect of periodic potentials on the electronic structure of bilayer graphene and show that there is a critical value of the external potential below which new Dirac fermions are generated in the low-energy band structure, and above which a band gap is opened in the system. Our results, obtained from a self-consistent tight-binding calculation, can be simply explained by a two-band continuum model as a consequence of the pseudospin physics in graphene. The findings are robust against changes in the form of the potential, as well as bias voltages between the layers.
Magnesium pemoline: stimulant effects on performance of fatigued subjects.

Magnesium pemoline, 100 mg., as compared to placebo, facilitated performance of fatigued subjects required to do repetitious arithmetic problems for 5 hours. It acted like methylphenidate hydrochloride, 20 mg., and d-amphetamine, 15 mg., by maintaining speed and accuracy near a predrug base line. Smaller doses of magnesium pemoline, 25 and 50 mg., were not significantly different from placebo.
Tip-enhanced Raman spectroscopy: From concepts to practical applications

Abstract Tip-enhanced Raman spectroscopy (TERS) is a powerful technique that integrates the vibrational fingerprinting of Raman spectroscopy and the sub-nanometer resolution of scanning probe microscopy (SPM). As a result, TERS is capable of obtaining chemical maps of analyzed specimens with exceptional lateral resolution. This is extremely valuable for the study of interactions between molecules and substrates, in addition to structural characterization of biological objects, such as viruses and amyloid fibrils, 2D polymeric materials, and monitoring electrochemical and photo-catalytic processes. In this mini-review, we discuss the most significant advances of TERS, including: super high resolution chemical imaging, monitoring of catalytic processes, incorporation of pulsed-excitation techniques, single-site electrochemistry, biosensing, and art conservation. We begin with a short overview of TERS, comparing it with other surface analytical techniques, followed by an overview of recent developments and future applications in TERS.
The Radiative Characteristics of Cirrus and Marine Stratus from High Altitude Aircraft Observations

Experimental observations of cirrus and marine stratus clouds have been obtained with remote sensing instrumentation on board a high altitude research aircraft. The principal instruments have been an active cloud top lidar system and a cross track scanning radiometer with selected spectral channels in the visible and infrared. The relative thermal emittance and visible albedo of cirrus have been derived from the lidar and radiometer observations. The distribution of height structure for marine stratus has been measured and related to the distribution of visible reflectivity.
Relative benefits of amino-acid, codon, degeneracy, DNA, and purine-pyrimidine character coding for phylogenetic analyses of exons

Both traditional as well as 10 more recent methods of coding characters from exons of protein-coding genes are reviewed. The more recent methods collectively blur the distinction between nucleotide and amino-acid coding and enable investigators to carefully quantify the effects of different sources of phylogenetic signal as well as their potential biases. Codon models, which explicitly model silent and replacement substitutions, are a major advance and are expected to be broadly useful for simultaneously inferring recent and ancient divergences, unlike amino-acid coding. Degeneracy coding, wherein ambiguity codes are used to eliminate silent substitutions at the individual-nucleotide level, has clear advantages over scoring amino-acid characters. Nucleotide, codon, and amino-acid models are now directly comparable with easy-to-use programs, and widely used phylogenetics programs can analyze partitioned supermatrices that incorporate all three types of model. Therefore, it should become standard practice to test among these alternative model types before conducting parametric phylogenetic analyses. An earlier study of 78 protein-coding genes from 360 green-plant plastid genomes is used as an empirical example with which to quantify the relative performance of alternative character-coding methods using five quantification measures. Codon models were selected as having the best fit to the data, yet were outperformed by nucleotide models for all five quantification measures. Third-codon positions were found to be an important source of phylogenetic signal and even outperformed analyses of first and second positions for some measures. Degeneracy coding generally performed at least as well as amino-acid coding and is an arguably more effective alternative.
Sedimentary Characteristics of Offshore Sediments in Maggona to Induruwa, South-Western Region of Sri Lanka

Particle size is a fundamental property of any sediment which can provide important clues on its provenance and the mode of transport. During depositional process the particle size is characterizing with the energy conditions of the environment. A study on grain size distribution, textural and statistical parameters of the south western region: Maggona to Induruwa was carried out to interpret the sediment deposition and energy dispersion status of the area to understand the relationship between them. Twenty eight surface sediment samples were collected using Van-veen grab .Sieve analysis was done using mechanical sieve shaker at 1/2 phi intervals and statistical parameters were obtained using “GRADISAT” software following Folk and Ward (1957) method for classifications. The visual observations revealed that majority of the sediments are typically light yellow to olive green in color and contain 5-20% biogenic carbonates with exception of six samples which composed of totally shell fragments. Sediments grabbed around Bentota Ganga inlet are sub rounded to rounded in shape while the majority of other locations are of rounded to sub angular grains. Larger and angular sediments close to rocky islands show that they are younger sediments and perhaps derived from nearby rocks. The mean grain size of the sediments range between 1.55-4.36phi with an average of 3.52 phi, indicative of very coarse silt to medium grained sand. The sediments fall under fine sand to very fine sand (50% of total samples) are localized near areas where the bottom is rough and rocky. Among the analyzed samples, 45.5% are well, 22.72% moderately, 18.18% moderately well and 9.09% poorly sorted. The ~68% of samples are exhibited unimodal distribution and all samples of bimodal distribution are poorly or moderately sorted and it probably due to debris of organic origin mixed with the normal bottom sediments. Majority of the sediments (~54%) are negatively coarse skewed and are localized opposite headlands. It indicates the selective removal of fine grains by the action of high energy waves which dissipate on headlands. The Kurtosis varies from 0.56 to 2.95 phi. Kurtosis of the inlet face of Bentota Ganga shows mesokurtic to platykurtic nature indicating high energy and wide distribution of sediments. Moreover, the sediments in north-south (towards south) direction shows leptokurtic nature except near headlands, which indicates the moderate energy conditions toward south. Keywords: Statistical parameters, Sediment distribution, Skewness, Kurtosis
Zebrafish sin3b mutants are viable but have size, skeletal, and locomotor defects.

Background The transcriptional co-repressor Sin3 is highly conserved from yeast to vertebrates and has multiple roles controlling cell fate, cell cycle progression, and senescence programming. Sin3 proteins recruit histone deacetylases and other chromatin modifying factors to specific loci through interactions with transcription factors including Myc, Rest, p53 and E2F. Most vertebrates have two Sin3 family members (sin3a and sin3b), but zebrafish have a second sin3a paralogue. In mice, sin3a and sin3b are essential for embryonic development. Sin3b knockout mice show defects in growth as well as bone and blood differentiation. Results To study the requirement for Sin3b during development, we disrupted zebrafish sin3b using CRISPR-Cas9, and studied the effects on early development and locomotor behavior. Conclusions Surprisingly, Sin3b is not essential in zebrafish. sin3b mutants show a decrease in fitness, small size, changes to locomotor behavior, and delayed bone development. We did not detect a role for Sin3b in cell proliferation. Our analysis of the sin3b mutant revealed a more nuanced requirement for zebrafish Sin3b than would be predicted from analysis of mutants in other species. Developmental Dynamics 246:946-955, 2017. © 2017 Wiley Periodicals, Inc.
Implications of Climate Change on Water Budgets and Reservoir Water Harvesting of Nuuanu Area Watersheds, Oahu, Hawaii

AbstractAssessing freshwater availability under changing climate and land-use conditions is critical for tropical islands, where small watershed sizes and unique hydrological features mean that fre...
Sard’s Theorem

This chapter introduces a powerful tool in smooth manifold theory, Sard’s theorem, which says that the set of critical values of a smooth function has measure zero. After proving the theorem, we use it to prove three important results about smooth manifolds. The first result is the Whitney embedding theorem, which says that every smooth manifold can be smoothly embedded in some Euclidean space. (This justifies our habit of visualizing manifolds as subsets of ℝ n .) The second result is the Whitney approximation theorem, which comes in two versions: every continuous real-valued or vector-valued function can be uniformly approximated by smooth ones, and every continuous map between smooth manifolds is homotopic to a smooth map. The third result is the transversality homotopy theorem, which says, among other things, that embedded submanifolds can always be deformed slightly so that they intersect “nicely” in a certain sense that we will make precise.
Response of eastern white pine and associated foliar, blister rust, canker and root rot pathogens to climate change

Abstract Climate model predictions for the northeastern U.S. forecast a warmer and wetter climate, which favors the survival, reproduction and dispersal of foliar diseases of eastern white pine, collectively called White Pine Needle Damage (WPND). Foliar diseases cause defoliation of white pine, leading to growth reductions, canopy dieback and predisposing trees to other pathogens and insects. This situation is very similar to other conifer foliar diseases, such as Dothistroma needle blight (DNB) in British Columbia and Swiss needle cast (SNC) in Oregon, where the climate is also becoming warmer and wetter. The purpose of this review is to summarize recent WPND findings of the impact climate change, particularly increased spring precipitation and annual warming has on the emergence of this disease complex. These findings will then be related to what is currently known about climatic factors affecting DNB and SNC and their role as native foliar pathogens affecting their natural forest ecosystems. We also discuss other eastern white pine diseases such as blister rust, cankers, and root rots in relation to climate change.
Acrylonitrile–Butadiene–Styrene Polymers

Acrylonitrile–butadiene–styrene (ABS) polymers are composed of elastomer dispersed as a grafted particulate phase in a thermoplastic matrix of styrene and acrylonitrile copolymer (SAN). The presence of SAN grafted onto the elastomeric component, usually polybutadiene or a butadiene copolymer, compatabilizes the rubber with the SAN component. Property advantages provided by this graft terpolymer include excellent toughness, good dimensional stability, good processibility, and good chemical resistance. The system is structurally complex. This allows considerable versatility in the tailoring of properties to meet specific product requirements. Numerous grades of ABS are available, including alloys and specialty grades for high heat, flaming-retardant, or static dissipative product requirements. Good chemical resistance combined with the relatively low water absorptivity (<1%) results in high resistance to staining agents. The three commercial processes for manufacturing ABS are emulsion, mass, and mass-suspension. ABS can be processed by compression and injection molding, extrusion, calendering, and blow molding. Post-processing operations include cold forming, painting, and adhesive bonding. As a “bridge” polymer between commodity plastics and higher performance engineering thermoplastics, ABS has become the largest selling engineering thermoplastic. Keywords: ABS; acrylonitrile–butadiene–styrene; acrylonitrile; poly(SAN); impact; thermoplastic; styrenic
IS PHYLOGENY RECAPITULATING ONTOGENY

There are three things I would like to accomplish in these comments. First, I would like to mention some of the larger issues addressed by Stuart Kauffnan’s work. They are related to important questions in other fields; pointing out the relationships could be useful for finding the kinds of interdisciplinary connections to which this conference is devoted. Second, I will describe my own perspective on Kauffman’s work; my interests are basically conceptual, not technical. Finally, I want to draw some parallels between arguments about phylogenetic and ontogenetic origins; these parallels cast additional light of Kauffman’s endeavors.
Using file relationships in malware classification

Typical malware classification methods analyze unknown files in isolation. However, this ignores valuable relationships between malware files, such as containment in a zip archive, dropping, or downloading. We present a new malware classification system based on a graph induced by file relationships, and, as a proof of concept, analyze containment relationships, for which we have much available data. However our methodology is general, relying only on an initial estimate for some of the files in our data and on propagating information along the edges of the graph. It can thus be applied to other types of file relationships. We show that since malicious files are often included in multiple malware containers, the system's detection accuracy can be significantly improved, particularly at low false positive rates which are the main operating points for automated malware classifiers. For example at a false positive rate of 0.2%, the false negative rate decreases from 42.1% to 15.2%. Finally, the new system is highly scalable; our basic implementation can learn good classifiers from a large, bipartite graph including over 719 thousand containers and 3.4 million files in a total of 16 minutes.
Implications of modeling approaches on seismic performance of low- and mid-rise office and hospital shear wall buildings

Abstract This paper investigates implications of using three conceptually different modeling approaches for reinforced concrete (RC) shear walls on seismic performance of several building designs including low-rise and mid-rise office and hospital buildings. Selected archetype buildings are designed to meet current code provisions for a site in downtown Los Angeles and are analyzed considering hazard levels characterized with 50%, 10%, and 2% probabilities of exceedance in 50 years. The study considers different models for structural walls, with either coupled or uncoupled shear and flexural behavior, and either linear or constant curvature distribution along the element height. FEMA P-58 methodology is used to assess damage and associated building repair cost. Performance assessment study illuminates the importance of utilizing high-fidelity models that consider coupled shear and flexural responses when conducting performance assessments for low- and mid-rise RC shear wall buildings; variations in median loss estimates obtained using uncoupled models range from 70% to 130% of the coupled model. In addition, the study reveals that the repair cost for hospitals are approximately 2 to 4 times larger than for office buildings due to significant damage to hospital equipment, warranting the use of RC structural walls for hospital builidngs in the regions of high seismicity. Finally, the study shows that the curtain walls generate significant loss in the case of low-rise RC wall buildings, reaching up to 50% of the total loss and highlighting the need for improved provisions for curtain walls for this type of construction.
Acute Pain Management in Children

Children’s pain may be difficult to recognize and to measure reliably. Pain assessment tools must be age and developmentally appropriate because children’s understanding and ability to describe pain changes as they grow. The options available to manage pain also vary with age. Non-pharmacological strategies supplement analgesic drugs and are especially useful for procedural pain. The metabolism of analgesic drugs matures during growth, affecting doses in neonates and infants. Some drugs that are useful analgesics in adults cannot be used in children because they are not available in liquid form for oral dosing. Morphine is the most widely studied and used opioid in children. Morphine metabolism is reduced in neonates and infants, and the incidence of respiratory depression from opioids is almost ten times more in neonates than adults. Intravenous opioids are the preferred route for the management of severe pain. Intravenous infusions for children are made up differently to those for adults—the concentration in the syringe varies with the weight of the child, but the volume administered is similar regardless of age. This standardizes volume independent of age and weight, and staff can see the infusion rate and are able to place the dose into context of the dose range usually given to children. Children aged 6 years and older are usually able to use patient controlled analgesia, but unlike adults, background infusions improve analgesia, promote sleep and do not increase adverse effects in children with severe and constant pain.
The Justice Project: Protecting the Guilty in the Era of Innocence

In the modern “Era of Innocence,” concerns about factual innocence dominate the conversation about criminal justice. Alongside the growth of law clinics and policy reforms centered on innocence, innocence-focused media has exploded in popularity over the last thirty years. Concurrent with this narrative shift, courts have curtailed appellate review of criminal convictions, except in cases of apparent or actual innocence. The focus on innocence has led to important criminal justice reforms, but too little attention has been paid to the costs of such a focus. In this paper, I outline the Era of Innocence, highlighting the ways in which factual innocence has begun to dominate the legal and cultural landscape. Then, I explain several potential downsides of innocentrism, paying particular attention to effects on the way in which people approach the criminal justice system. Using experimental psychology methods, I next present some initial data in support of these theorized downsides; I find that focusing on innocence may erode public support for criminal defense. Finally, I discuss some ways in which courts and reformers may be able to mitigate the risks of focusing on innocence.
Historical changes in hydrology, geomorphology, and floodplain vegetation of the Willamette River, Oregon

Historical trends in hydrology, geomorphology, and floodplain vegetation provide fundamental contexts for designing future management of large rivers, an area of fluvial research extensively informed by studies of historical channel dynamics. Changes in hydrology, channel structure, floodplain forests, and large wood were documented for the 273‐km main stem of the Willamette River from 1850 to present. Reduced sediment supply and frequency and magnitude of floods have decreased channel mobility and incised channels, leading to fewer gravel bars, islands, and side channels. Human alteration of channel morphology, vegetation, and bank hardening has exacerbated channel simplification caused by reductions in floods, sediment supply, and inputs of wood. A substantial number of floodplain channels reoccupied remnants of previous active channels inundated during recent floods, demonstrating functional but often forgotten role of historical geomorphic structure in modern floodplains and flood processes. In most reaches, area of floodplain forests in 1990 was only 10% to 25% of the area of forests in 1850. Abundance of wood in the wetted channel was generally greater in reaches with higher abundances of floodplain forests. Future trajectories will be influenced by legacies of the historical river but increasingly will reflect evolution of a new river shaped by human development, changing climate, and emerging hydrogeomorphic and vegetation processes. Understanding historical characteristics and anticipating future rates and patterns of ecosystem change provide fundamental contexts for restoring biophysical processes and structure in a large floodplain river.