cssi/SciSciGPT-SciSciNet huggingface dataset:
Parameter reduction and context selection for compression of gray-scale images

In the compression of multilevel (color or gray) image data, effective compression is obtained economically by judicial selection of the predictor and the conditioning states or contexts which determine what probability distribution to use for the prediction error. We provide a cost-effective approach to the following two problems: (1) to reduce the number of coding parameters to describe a distribution when several contexts are involved, and (2) to choose contexts for which variations in prediction error distributions are expected. We solve Problem 1 (distribution description) by a partition of the range of values of the outcomes into equivalence classes, called buckets. The result is a special decomposition of the error range. Cost-effectiveness is achieved by using the many contexts only to predict the bucket (equivalence class) probabilities. The probabilities of the value within the bucket are assumed to be independent of the context, thus enormously reducing the number of coding parameters involved. We solve Problem 2 (economical contexts) by using the buckets of the surrounding pixels as components of the conditioning class. The bucket values have the desirable properties needed for the error distributions.
Changes in the definition of ADHD in DSM-5: subtle but important

While there were earlier descriptions of children with high levels of activity and impulsivity , what is now called ADHD first appeared in the American Psychiatric Association’s DSMâÂÂII in 1968. In DSMâÂÂII, the disorder was termed hyperkinetic reaction of childhood, which as the name implies focused primarily on symptoms of excessive motor activity. With the publication of DSMâÂÂIII in 1980, the disorder was markedly reconceptualized with a focus on problems with attention, impulsivity and hyperactivity, and was renamed attention deficit disorder (with and without hyperactivity).
The Inverse Relationship between Productivity and Farm Size: A Test Using Regional Data from India

The farm size-productivity debate for India needs little introduction; it has occupied a prominent position in the agricultural economics literature since 1962, when Sen observed that Indian farm management data revealed an inverse relationship between farm size and yields per acre. Since then, no fewer than twenty journal papers have appeared on this subject (Sen 1975). The objective of this paper is to test two hypotheses that were either not given enough attention or left unresolved in the debate. The first is that the inverse relationship is valid for all of Indian agriculture; it is not merely a phenomenon observed in a few sample villages. This means a test of the hypothesis that the small farm sector as a whole is more productive than the large farm sector in Indian agriculture. The second hypothesis is that the inverse relationship is true only of a traditional agriculture, and that it breaks down with technical progress. A methodology is developed below which uses cross-sectional regional data to test the two hypotheses simultaneously. On applying this methodology to Indian district-level data (272 districts) for 1970-71, it is found that the hypothesis of the small farm sector being more productive than the large farm sector cannot be rejected at low levels of agricultural technology, but can be rejected at higher levels. This suggests that the inverse relationship between yields and farm size, although valid for a traditional agriculture, cannot be assumed to exist in an agriculture experiencing technical change.
Paradise Lost and the Rhetoric of Literary Forms

The Experience of Defeat: Milton and Some Contemporaries Milton and Scriptural Tradition
Lumbar Sagittal Plane Mobility and Lordosis in the Well Elderly as Related to Gender and Activity Level

Diminished spinal mobility and altered posture with ageing may be normal or due to decreasing activity levels or gender differences. We investigated the effect of gender and physical activity on lumbar mobility and lordosis in well elderly men and women. Additionally we examined the data by ethnicity. Forty-one subjects (70.5 years ± 5.3) from two senior centers all exhibited a low physical activity score. Caucasians exhibited 6.45° more lumbar flexion than African Americans. Males averaged 6.45° less lordosis than females. African American women demonstrated a moderate inverse relationship between lordosis and lumbar flexion. Women had more lumbar flexion than men did and Caucasians had more lumbar flexion than African Americans. In the elderly, ethnic and gender-related differences may exist in lumbar spine mobility and spinal posture.
Relativistic density-functional theory with the optimized effective potential and self-interaction correction: Application to atomic structure calculations (Z=2–106)

We present a self-interaction-free relativistic density-functional theory ~DFT!. The theory is based on the extension of our recent nonrelativistic DFT treatment with optimized effective potential ~OEP! and selfinteraction correction ~SIC !@ Phys. Rev. A 55, 3406 ~1997!# to the relativistic domain. Such a relativistic OEP-SIC procedure yields an orbital-independent single-particle local potential with proper long-range Coulombic (21/r) behavior. The method is applied to the ground-state energy calculations for atoms with Z52 ‐106. A comparison with the corresponding nonrelativistic OEP-SIC calculations and other relativistic calculations is made. It is shown that the ionization potentials ~obtained from the highest occupied orbital energies! and individual orbital binding energies determined by the present relativistic OEP-SIC method agree well with the experimental data across the Periodic Table. @S1050-2947~98!06201-5#
Balanced cross-rate model for saturated molecular fluorescence in flames using a nanosecond pulse length laser

The balanced cross-rate model is proposed to analyze laser-induced molecular fluorescence signals when the laser pulse length is of the order of nanoseconds. Nanosecond pulse length lasers, specifically Q-switched Nd:YAG-pumped dye lasers, are attractive for saturated molecular fluorescence spectroscopy because of their high peak power and because their short pulse length minimizes the risk of laser-induced chemistry. In the balanced cross-rate model, single upper and lower rotational levels are assumed to be directly coupled by the laser radiation. Because the laser-induced processes which couple these levels are so fast at saturation intensities, a steady state is established between the two levels within picoseconds. Provided that the total population of the two laser-coupled rotational levels is constant during the laser pulse, the total molecular population can be calculated from the observed upper rotational level population using a two-level saturation model and Boltzmann statistics. Numerical simulation of the laser excitation dynamics of OH in an atmospheric pressure H2/O2/N2 flame indicates that the balanced cross-rate model will give accurate results provided that the rotational relaxation rates in the upper and lower sets of rotational levels are approximately equal.
Heat Shock Inhibits Radiation-induced Activation of NF-κB via Inhibition of I-κB Kinase

Radiation stimulates signaling cascades that result in the activation of several transcription factors that are believed to play a central role in protective response(s) to ionizing radiation (IR). It is also well established that heat shock alters the regulation of signaling cascades and transcription factors and is a potent radiosensitizing agent. To explore the hypothesis that heat disrupts or alters the regulation of signaling factors activated by IR, the effect of heat shock on IR-induced activation of NF-kappaB was determined. Irradiated HeLa cells demonstrated transient increases in NF-kappaB DNA binding activity and NF-kappaB protein nuclear localization. In addition, irradiated cells demonstrated increased I-kappaB phosphorylation and decreased I-kappaBalpha cytoplasmic protein levels, corresponding temporally with the increase of NF-kappaB DNA binding. Heat shock prior to IR inhibited the increase in NF-kappaB DNA binding activity, nuclear localization of NF-kappaB, and the phosphorylation and subsequent degradation of I-kappaB. I-kappaB kinase (IKK) immunoprecipitation assays demonstrated an increase in IKK catalytic activity in response to IR that was inhibited by pretreatment with heat. Kinetic experiments determined that heat-induced inhibition of NF-kappaB activation in response to IR decayed within 5 h after heating. Furthermore, pretreatment with cycloheximide, to block de novo protein synthesis, did not alter heat shock inhibition of IR induction of NF-kappaB. These experiments demonstrate that heat shock transiently inhibits IR induction of NF-kappaB DNA binding activity by preventing IKK activation and suggests a mechanism independent of protein synthesis.
Comparison between some digestive processes after eating and gastric loading in rats

Physiological and biochemical differences were found between normal and intragastric feeding in the rat. Milk ingested orally remained in the stomach significantly longer than milk ingested via a chronic intragastric fistula. Milk samples were removed from the stomach at intervals of 5, 20 and 45 min after ingestion and it was found that milk which had been ingested via intragastric fistula underwent substantially less lipolysis than did milk which had been ingested orally. These results are discussed in relation to the aversive and rewarding effects obtained by injections of edible nutrients into the stomachs of rats.
Impact on pre-and post-sarbanes oxley users’ perceptions by incorporating the auditor’s fraud detection responsibility into the auditor’s internal control report

Abstract The Department of the Treasury’s Advisory Committee on the Auditing Profession ( Advisory Committee, 2008 ) has recommended that the Public Company Accounting Oversight Board (PCAOB) clarify the auditor’s role in detecting fraud in the auditor’s report. The PCAOB replaced Auditing Standard No. 2 (AS2) with Auditing Standard No. 5 (AS5) but did not clarify the auditor’s fraud detection responsibility in the auditor’s report covering internal control and/or the financial statements. The focus of this study is to evaluate (i) whether the PCAOB mandated auditor’s internal control report (ICR) format with a ‘limitations’ paragraph meets users’ expectations, (ii) whether users’ prefer an ICR incorporating auditor’s fraud detection responsibility, and (iii) whether users’ expectations have changed over time. Results based on analyses of data from prior studies indicate that in pre-and post-SOX time frames, an ICR format without a limitations paragraph and clarifying the auditor’s role for fraud detection best met users’ expectations from an audit, consistent with the Advisory Committee’s recommendation. Users’ perceptions of potential auditor liability associated with ICR formats have changed significantly over time. Pre-SOX users perceived reduced auditor liability associated with an ICR that contained a limitations paragraph, but post-SOX users perceive similar potential auditor liability with all ICR formats.
Treatment of sinusitis in the next millennium.

Abstract Sinusitis is an increasingly more important disease due to its increasing prevalence, costs, and recognition. Most acute sinusitis episodes follow colds or acute allergic rhinitis. Chronic sinusitis is most commonly due to allergic and nonallergic rhinitis or anatomical defects in the nose. Several common immunologic abnormalities usually present as sinusitis and may be recognized first by the allergist-immunologist. Treatment involves a carefully selected antibiotic prescribed for an adequate period of time, nasal hygiene using nasal saline washes, topical nasal corticosteroids, and decongestants. Medical management of sinusitis tends to be effective, even in patients with long-standing sinus disease.
An improved chiral stationary phase for the facile separation of enantiomers

Abstract A chiral stationary phase (CSP) derived from cis- 3-(1, 1-dimethylethyl)-4-phenyl-2-azetidinone is quite effective for the chromatographic separation of the enantiomers of a variety of compounds. This CSP (CSP 2) is conceptually related to the N-(3,5-dinitrobenzoyl) amino acid derived phases ( e. g CSP 1), but has two stereo-genic centers. For many enantiomers, CSP 2 exhibits superior performance to that of the widely used analogue, phenylglycine-derived CSP 1.
Alterations in brain structures underlying language function in young adults at high familial risk for schizophrenia

Introduction Neuroanatomical and cognitive alterations typical of schizophrenia (SZ) patients are observed to a lesser extent in their adolescent and adult first-degree relatives, likely reflecting neurodevelopmental abnormalities associated with genetic risk for the illness. The anatomical pathways for language are hypothesized to be abnormal and to underlie the positive symptoms of schizophrenia. Examining non-psychotic relatives at high familial risk (FHR) for schizophrenia may clarify if these deficits represent trait markers associated with genetic vulnerability, rather than specific markers resulting from the pathological process underlying schizophrenia.
Study of the sintering of nanosized titania agglomerates in flames using in situ light scattering measurements

A premixed flame aerosol reactor was used to produce titania particles by oxidation of titanium isopropoxide vapor. The growth, aggregation of particles, and the agglomerate structure were determined as a function of height in the flame using in situ light scattering and transmission electron microscopy (TEM) measurements. A methodology to determine the sintering characteristic time using light scattering data was established. The light scattering data provided the evolution of the fractal dimension which was then related to the normalized surface area change using a computer simulation. The sintering equation was redeveloped in terms of the normalized surface area, thus not having to account for coagulation effects. Experimental results indicate that isolated titania particles were observed at the high temperatures due to fast sintering. An agglomerate was obtained at downstream locations with an associated change in fractal dimension due to sintering.
Cheshire at GeoCLEF 2008: text and fusion approaches for GIR

In this paper we will briefly describe the approaches taken by the Berkeley Cheshire group for the main GeoCLEF 2008 tasks (Mono and Bilingual retrieval), and present some analyses of the fusion approach used. This year our submissions used probabilistic text retrieval based on logistic regression and incorporating blind relevance feedback for all of the runs and in addition we ran a number of tests combining this type of search with OKAPI BM25 searches using a fusion approach. We did not, however, use any explicit geographic processing. All translation for bilingual tasks was performed using the LEC Power Translator PC-based MT system.
Clinical Presentation of Patients with Tears of the Acetabular Labrum

Background: The clinical presentation of a labral tear of the acetabulum may be variable, and the diagnosis is often delayed. We sought to define the clinical characteristics associated with symptomatic acetabular labral tears by reviewing a group of patients who had an arthroscopically confirmed diagnosis. Methods: We retrospectively reviewed the records for sixty-six consecutive patients (sixty-six hips) who had a documented labral tear that had been confirmed with hip arthroscopy. We had prospectively recorded demographic factors, symptoms, physical examination findings, previous treatments, functional limitations, the manner of onset, the duration of symptoms until the diagnosis of the labral tear, other diagnoses offered by health-care providers, and other surgical procedures that these patients had undergone. Radiographic abnormalities and magnetic resonance arthrography findings were also recorded. Results: The study group included forty-seven female patients (71%) and nineteen male patients (29%) with a mean age of thirty-eight years. The initial presentation was insidious in forty patients, was associated with a low-energy acute injury in twenty, and was associated with major trauma in six. Moderate to severe pain was reported by fifty-seven patients (86%), with groin pain predominating (sixty-one patients; 92%). Sixty patients (91%) had activity-related pain (p < 0.0001), and forty-seven patients (71%) had night pain (p = 0.0006). On examination, twenty-six patients (39%) had a limp, twenty-five (38%) had a positive Trendelenburg sign, and sixty-three (95%) had a positive impingement sign. The mean time from the onset of symptoms to the diagnosis of a labral tear was twenty-one months. A mean of 3.3 health-care providers had been seen by the patients prior to the definitive diagnosis. Surgery on another anatomic site had been recommended for eleven patients (17%), and four had undergone an unsuccessful operative procedure prior to the diagnosis of the labral tear. At an average of 16.4 months after hip arthroscopy, fifty-nine patients (89%) reported clinical improvement in comparison with the preoperative status. Conclusions: The clinical presentation of a patient who has a labral tear may vary, and the correct diagnosis may not be considered initially. In young, active patients with a predominant complaint of groin pain with or without a history of trauma, the diagnosis of a labral tear should be suspected and investigated as radiographs and the history may be nonspecific for this diagnosis. Level of Evidence: Diagnostic Level IV. See Instructions to Authors for a complete description of levels of evidence.
Gas Chromatographic-Mass Spectrometric Analysis of Sulfur Mustard-Plasma Protein Adducts: Validation and Use in a Rat Inhalation Model

Sulfur mustard (HD) is an alkylating agent that reacts rapidly with macromolecular targets resulting in the formation of stable adducts providing depots for markers of exposure. The purpose of this study was to validate an analytical procedure for detection of HD-plasma protein adducts and to establish the utility of the method in an HD rat inhalation study. Calibration curves were prepared in human and rat plasma at six levels of HD (12.5 to 400nM). Correlation coefficients for the mean data were 0.9987 for human and 0.9992 for rat plasma. The percent coefficient of variation (%CV) derived from the mean concentration data ranged from 0.53 to 14.1% in human (n = 5) and 0.57 to 10.63% in rat (n -- 6) plasma. Intraday and interday precision and accuracy studies were conducted at three concentration levels (25, 150, 300nM) to represent low, medium, and high concentrations of HD relative to those employed in the calibration curve. Precision and accuracy were assessed by determining %CV and % error, respectively. For intra- and interday studies, the %CVs and absolute % errors were less than 15%. The limits of quantitation were 20.88nM for human and 16.73nM for rat plasma. In animal studies, rats received nebulized HD at six doses. The data indicate a dose-dependent relationship between maximal plasma concentrations and dose administered (R 2 -- 0.9728). Results from this study indicate an accurate, precise, and sensitive method. The method was useful in determining plasma protein adduct formation in a rat inhalation model.
Power Penalty of High-Data-Rate Transmission Delay through a Silicon Photonic Crystal Slow-Light Waveguide

The power penalty of a silicon photonic crystal slow-light waveguide, which can be used for optical buffering, is characterized experimentally and with simulations. The distortion, caused by dispersion near the mode onset, imposes a design performance trade-off between the obtainable delay and the tolerable degradation.
Subtractive immunization: a tool for the generation of discriminatory antibodies to proteins of similar sequence

Antibodies specific for a protein of interest are invaluable tools for monitoring the protein's structure, location and activity. Due to the tendency of an immune system to mount a response toward the abundant, immunodominant epitopes in a protein mixture, difficulties are inherent in the isolation of antibodies specific for proteins that are rare or poorly immunogenic. Likewise, isolation of antibodies specific for a protein with significant sequence similarity to other proteins, such as those derived from protein engineering, may be challenging. Subtractive immunization is a technique proven to facilitate efforts to produce monoclonal antibodies specific for antigens that are present in low abundance in a protein mixture, poorly immunogenic and/or similar in sequence or structure to other proteins. This protocol provides a detailed, stepwise procedure for the isolation of antibodies specific for a protein with sequence similarity to other proteins. As an example, we describe methods established to isolate antibodies specific to a methionine-enriched variant of soybean vegetative storage protein beta (VSPbeta-Met) that shares 91.8% amino acid sequence identity to the wild-type protein (VSPbeta-WT). These methods include cyclophosphamide-induced immunosuppression of mice for the wild-type protein followed by immunization with VSPbeta-Met. As a result of this procedure, mouse polyclonal antibodies that exhibited 10-fold greater reactivity with VSPbeta-Met than VSPbeta-WT in an ELISA were generated. It is anticipated that this strategy will have utility for generating antibodies specific to protein variants derived from protein engineering.
Acoustic beacon navigation

Navigation schemes in deep and shallow water using a crystal controlled acoustic beacon are presented together with a discussion of errors related to crystal accuracies and platform and environmental factors.
Characterization of Pulsed-Laser Deposited Amorphous Diamond Films by Spectroscopic Ellipsometry

Spectroscopic ellipsometry is used to characterize amorphous diamond, also known as tetrahedral amorphous carbon, (ta-C) films grown by pulsed laser ablation. The ellipsometry data is collected with the two-modulator generalized ellipsometer, which measures all three parameters required to characterize isotropic samples, as well as additional parameters used to characterize strain-induced birefringence of the focusing optics. Lenses are used to focus the light spot to an ellipse 0.7 × 2.0 mm 2 , allowing us to perform several ellipsometric measurements across the profile of ta-C films grown on 7.5 cm diameter Si wafers. The spectroscopic ellipsometry data are fit using a model of the ta-C dielectric function based on the Tauc band edge and the Lorentz expression of the dielectric function for an ensemble of atoms. These fits are used to determine the thicknesses of the rough surface layer, the ta-C film, and the interface layer, as well as the energy gap of the film. Comparisons are made with fits to an earlier formulation due to Forouhi and Bloomer [Phys. Rev. B 34, 7018 (1986).]. In addition to being Kramers-Kronig consistent, the Tauc-Lorentz formulation fits the ta-C data better.
Practices and principles of clinical neuropsychology: "Focusing on the hole rather than the doughnut".

(1979). Practices and Principles of Clinical Neuropsychology: “Focusing on the Hole rather than the Doughnut”. International Journal of Neuroscience: Vol. 9, No. 4, pp. 233-238.
Measuring the Concentration of Power in Political Systems

The unequal distribution of power among the members of a political system is one of the most pervasive facts of political life. Yet, while many studies have confirmed the fact that a few members exercise disproportionate control over many others in most systems, the configurations of power relations that occur among the few have generally not been subjected to systematic comparative analysis. In a few notable empirical studies, attempts have been made to compare the exercise of power in different issue-areas and across different decisions. Comparative analyses have suffered, however, from the lack of any means to make tractable and compare, except in a qualitative way, schematic representations of power relations either in different political systems or over different issue-areas in the same system. When diagrams of power structures become complex and unwieldy, it is easiest to forget about making precise comparisons about the way power is distributed among decision-makers somehow identified as being influential in the political process.
Combinatorial synthesis of oxide powders

Combinatorial libraries of the mixed oxide system Cu1−xCexO3 (0 ≤ x ≤ 1) have been generated using a modified Pechini powder synthesis process in conjunction with inkjet deposition. Mixed oxide crystalline powders were formed at temperatures below 500 °C. These powders have particle sizes in the range of 20.0 to 85.5 nm, and the powder surface area increases with cerium content. In addition, each of the mixed oxides (0 < x < 1) displayed catalytic activity in the CO oxidation reaction at temperatures between 150 and 350 °C. This novel protocol has also been used to generate a library of oxide powders of the perovskite-like La1−xSrxCoO3?δ system. The La–Sr–Co–O system from this protocol exhibits lower average surface areas than the Cu–Ce–O system (approximately 11.2 m2/g) due to higher decomposition temperatures but still acts as an active catalyst for the CO oxidation reaction.
Associations between dietary factors and pancreatitis in dogs.

Objective—To estimate associations between dietary factors and pancreatitis in dogs. Design—Retrospective case-control study. Animals—198 dogs with a clinical diagnosis of pancreatitis and 187 control dogs with a diagnosis of renal failure without clinical evidence of pancreatitis. Procedures—Information on signalment, weight, body condition, dietary intake, medical history, diagnostic tests performed, concurrent diseases, treatments, duration of hospitalization, and discharge status was extracted from medical records. Information on dietary intake, signalment, weight, and medical, surgical, and environmental history was collected through a telephone questionnaire. Logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals. Results—On the basis of information extracted from the medical record, ingesting unusual food items (OR, 4.3) increased the odds of pancreatitis. On the basis of information gathered through the telephone questionnaire, ingesting unusual food items (OR, 6.1)...
Development of Advanced All-SiC Power Modules

A thermally integrated packaging structure for an all silicon carbide (SiC) power module was used to realize highly efficient cooling of power semiconductor devices through direct bonding of the power stage and a cold baseplate. The prototype power modules composed of SiC metal-oxide-semiconductor field-effect transistors and Schottky barrier diodes demonstrate significant improvements such as low-power losses and low-thermal resistance. Direct comparisons to their silicon counterparts, which are composed of insulated gate bipolar transistors and PiN diodes, as well as conventional thermal packaging, were experimentally performed. The advantages of this SiC module in efficiency and power density for power electronics systems have also been identified, with clarification of the SiC attributes and packaging advancements.
Fully-integrated CMOS RF transceivers

The market for cellular wireless handsets demands very high levels of sophistication and also low component cost and power. In addition to wide-area network interfaces such as GPRS, EDGE, and WCDMA, wireless connectivity features such as GPS, Bluetooth, WLAN, and mobile digital TV are now becoming commonplace. This has driven the demand for many air interfaces to be supported in a single handset design. Conventional silicon integration, employing separate digital baseband, analog, and RF components for each air interface would result in far too many components for an efficient integration. As a result, CMOS SOC devices that integrate all of these functions into single-chip components have become increasingly popular. This paper explains the motivation and challenges of SOC integration in deep submicron CMOS. Examples of SOC devices are provided along with experimental results.
Epitaxial growth of C60 thin films on mica

Single crystal films of C60 of different thickness values have been deposited on mica substrates by resistance evaporation. Electron diffraction and high resolution microscopy have been used to assess the orientational ordering and the nature of the defects present in these face-centered cubic films which exhibit a 〈111〉 direction normal to the film surface.
A Pilot Study of Vitamins to Lower Plasma Homocysteine Levels in Alzheimer Disease

OBJECTIVE Authors determined the impact of high-dose vitamin supplements on plasma homocysteine levels in patients with Alzheimer disease (AD). METHODS Authors used an open-label trial of folic acid, vitamin B 12 , and vitamin B 6 , in combination for 8 weeks, with measurement of plasma homocysteine levels in the fasting state and after methionine-loading. A total of 69 subjects with AD were enrolled, including 33 who were taking standard multivitamin supplements; 66 were available at 8-week follow-up. RESULTS The high-dose vitamin regimen was associated with a significant reduction in fasting and post–methionine-loading homocysteine. Reductions were greater in the subgroup not using multivitamins, but were also significant in the multivitamin users. CONCLUSION High-dose vitamin supplementation reduces homocysteine levels in patients with AD. The effect of supplementation on rate of cognitive decline will be assessed later in a randomized, double-blind study.
Unequal error protection for transmission of JPEG2000 codestreams over noisy channels

A method for joint source/channel rate allocation for transmission of JPEG2000 (J2K) codestreams over noisy channels is proposed. The rate allocation method uses the BER statistics of different channel codes and the rate-distortion characteristics of the source generated by the J2K encoder. The features of the J2K codestream are utilized to form a multilayer codestream and an unequal amount of protection is applied to each layer. The proposed method is capable of accommodating different channel coding strategies. Experimental results indicate that the presented method compares favorably with methods existing in the literature.
Improved side‐chain torsion potentials for the Amber ff99SB protein force field

Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. Finally, we used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side-chain conformations. The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data. Proteins 2010. © 2010 Wiley-Liss, Inc.
Prediction of sample size effects on the measured temporal and geographic distribution patterns of species

Few paleontological studies of species distribution in time and space have adequately considered the effects of sample size. Most species occur very infrequently, and therefore sample size effects may be large relative to the faunal patterns reported. Examination of 10 carefully compiled large data sets (each more than 1,000 occurrences) reveals that the species-occurrence frequency distribution of each fits the log series distribution well and therefore sample size effects can be predicted. Results show that, if the materials used in assembling a large data set are resampled, as many as 25% of the species will not be found a second time even if both samples are of the same size. If the two samples are of unequal size, then the larger sample may have as many as 70% unique species and the smaller sample no unique species. The implications of these values are important to studies of species richness, origination, and extinction patterns, and biogeographic phenomena such as endemism or province boundaries. I provide graphs showing the predicted sample size effects for a range of data set size, species richness, and relative data size. For data sets that do not fit the log series distribution well, I provide example calculations and equations which are usable without a large computer. If these graphs or equations are not used, then I suggest that species which occur infrequently be eliminated from consideration. Studies in which sample size effects are not considered should include sample size information in sufficient detail that other workers might make their own evaluation of observed faunal patterns.
Importance of Radiation Oncologist Experience Among Patients With Head-and-Neck Cancer Treated With Intensity-Modulated Radiation Therapy

PurposeOver the past decade, intensity-modulated radiation therapy (IMRT) has replaced conventional radiation techniques in the management of head-and-neck cancers (HNCs). We conducted this population-based study to evaluate the influence of radiation oncologist experience on outcomes in patients with HNC treated with IMRT compared with patients with HNC treated with conventional radiation therapy.MethodsWe identified radiation providers from Medicare claims of 6,212 Medicare beneficiaries with HNC treated between 2000 and 2009. We analyzed the impact of provider volume on all-cause mortality, HNC mortality, and toxicity end points after treatment with either conventional radiation therapy or IMRT. All analyses were performed by using either multivariable Cox proportional hazards or Fine-Gray regression models controlling for potential confounding variables.ResultsAmong patients treated with conventional radiation, we found no significant relationship between provider volume and patient survival or any to...
The discovery of IgE 50 years later.

In 1906, Von Pirquet1 used the term supersensitivity without immunity to describe (1) symptoms of inhalant allergy, (2) positive immediate skin test results, and (3) the fact that the results of other tests of immunity were not positive in these patients. The other tests he referred to were precipitin tests and complement fixation. Thus, he opened up the question of serum tests for supersensitivity. In 1919, Ramirez2 reported that a patient who had received a blood transfusion from a horse allergic donor became allergic to horse dander. At this point, Prausnitz and Kustner3 set out to investigate whether the serum of allergic individuals contained a factor or factors that could sensitize the skin. In 1921, they reported that the local injection of serum from a fish allergic individual, Kustner, to an individual who was only allergic to pollen, Prausnitz, would transfer specific sensitivity.3 This transfer of sensitivity came to be known as the P-K test and was used widely to study sensitivity not only to common allergens but also to extracts as diverse as those obtained from schistosomes.4,5 Furthermore, in New York, Cooke et al6 identified that there were other antibodies in the serum that increased during desensitization treatment and could block the skin-sensitizing activity. By the 1950s, it was clear that the transferred sensitivity was specific, that it could be diluted extensively, and that the skin remained locally sensitive for days if not weeks after the injection of serum.7,8 It was also already clear that the ability to sensitize the skin was lost after moderate heating of the serum.7 Several studies had also been reported on the physical properties of P-K activity. Indeed, Heimlich et al9 at Cal Tech reported on the sedimentation properties of skin-sensitizing antibodies in 1960. However, the studies before 1964 had not succeeded in defining the nature of these antibodies.
“The Stippling Shows Statistically Significant Grid Points”: How Research Results are Routinely Overstated and Overinterpreted, and What to Do about It

AbstractSpecial care must be exercised in the interpretation of multiple statistical hypothesis tests—for example, when each of many tests corresponds to a different location. Correctly interpreting results of multiple simultaneous tests requires a higher standard of evidence than is the case when evaluating results of a single test, and this has been known in the atmospheric sciences literature for more than a century. Even so, the issue continues to be widely ignored, leading routinely to overstatement and overinterpretation of scientific results, to the detriment of the discipline. This paper reviews the history of the multiple-testing issue within the atmospheric sciences literature and illustrates a statistically principled and computationally easy approach to dealing with it—namely, control of the false discovery rate.
A Proposed Antigenic Schemia for the Identification of Strains of Pseudomonas Aeruginosa

Since Pseudomonas aeruginosa has become more important as a potential etiologic agent of sporadic and epidemic illness in man, the need for more satisfactory methods of identification has increased. For epidemiologic studies and for tracing the spread of infection in institutions, the typing of strains is essential. A schema for the systematic classification of the types would be valuable. The widespread dissemination of organisms of this genus in man and lower animals, as well as in their respective environments, provides an infinite variety of possible sources for infecting strains. Virulent strains can inflict a multiplicity of ills ranging from inapparent infection to rapidly fulminating septicemias (Asay et al, 1959; Eggers and Wockel, 1958; Epstein and Grossman, 1933 Forkner et al, 1958; Fraenkel, 1917 Geppert et al, 1952; Kietzmann, 1955 Stanley, 1947). Through a study of some of the antigenic components of strains of P. aeruginosa isolated from both infected and healthy individuals in 3 widely separated geographic areas, we have developed a serological schema of types with antigenic formulas based on the heatstable O and heat-labile H factors
Reductive-Oxidation Electrogenerated Chemiluminescence (ECL) Generation at a Transparent Silver Nanowire Electrode

We present the fabrication of a conductive, transparent electrode composed of Ag nanowires (NW) for spectroelectrochemical studies. Reductive-oxidation electrogenerated chemiluminescence (ECL) of Ru(bpy)32+ is generated at the Ag NW electrode in the presence of hydrogen peroxide and collected through the new transparent electrode. The ECL performance at the new nanostructured electrode is compared with several other electrodes, including bulk silver wire, glassy carbon disk, and thermally reduced transparent graphene oxide (tr-GO) electrodes. The Ag NW electrode is found to be the best electrode for the reductive-oxidation ECL generation because of its catalytic properties with respect to the reduction of hydrogen peroxide and its high surface area.
The influence of sex on the pathologic aspects of cirrhosis of the liver.

A review of 100 consecutive cases of cirrhosis of the liver in each sex showed that cirrhosis is largely postnecrotic in women and of the Laennec or so-called alcoholic type in men.The high incidence of postnecrotic cirrhosis in women is probably due to the fact that women are more susceptible to severe damage from viral hepatitis than are men. The greater frequency of Laennec's cirrhosis in men undoubtedly is due to the higher incidence of alcoholism among men than among women.Carcinoma of the liver is found more frequently in men who have cirrhosis than in women.
Large-Area, Transfer-Free, Oxide-Assisted Synthesis of Hexagonal Boron Nitride Films and Their Heterostructures with MoS2 and WS2.

Ultrasmooth hexagonal boron nitride (h-BN) can dramatically enhance the carrier/phonon transport in interfaced transition metal dichalcogenides (TMDs), and amplify the effect of quantum capacitance in field-effect gating. All of the current processes to realize h-BN-based heterostructures involve transfer or exfoliation. Rational chemistries and process techniques are still required to produce large-area, transfer-free, directly grown TMDs/BN heterostructures. Here, we demonstrate a novel boron–oxygen chemistry route for oxide-assisted nucleation and growth of large-area, uniform, and ultrathin h-BN directly on oxidized substrates (B/N atomic ratio = 1:1.16 ± 0.03 and optical band gap = 5.51 eV). These intimately interfaced, van der Waals heterostructures of MoS2/h-BN and WS2/h-BN benefit from 6.27-fold reduced roughness of h-BN in comparison to SiO2. This leads to reduction in scattering from roughness and charged impurities, and enhanced carrier mobility verified by an increase in electrical conductivit...
Hydraulic Circuit Analysis

The previous chapters introduce the governing equations for fluid flow and provide solutions for simple unidirectional flows. Although we can only rarely use these simple solutions to exactly describe real flows, these unidirectional flows provide a framework for generating engineering estimates for many flows, and these estimation techniques reduce complex systems with large numbers of components into a relatively simple, approximate, linear description. This is relevant for flow in microdevices both (1) because microdevices can straightforwardly be made with large numbers of microchannels and (2) because those microchannels often have long, thin geometries that lead to largely unidirectional flows that are well approximated by the solutions presented in Chapter 2. Our approach, called hydraulic circuit analysis , involves assuming that the Poiseuille flow derived in Chapter 2 provides a sound engineering estimate of the pressure drops and flow rates through long, straight channels, even if the cross section is not exactly circular and the channels are neither perfectly straight nor infinite in extent. We thus write an approximate linear relation between pressure drops and flow rates through these channels – the Hagen – Poiseuille law . This law, combined with conservation of mass, approximately prescribes fluid flow through complex rigid networks by solution of sets of algebraic equations. By adding a hydraulic capacitance or compliance , this linearized analysis also allows prediction of unsteady flow through channels with a finite flexibility.
Simultaneous detection of multiple charged particles using a borosilicate nanopore-based sensor

Nanopore sensing has been widely researched owing to its single molecule sensitivity. In this work, we have demonstrated the potential application of a relatively low-cost single borosilicate nanopore-based sensor for simultaneous detection of multiple charged particles with various diameters.
Contemporary Outcomes of Endovascular Intervention for Critical Limb Ischemia

Critical limb ischemia (CLI) remains a significant cause of morbidity and mortality in patients with peripheral arterial disease. Optimal treatment strategies for CLI remain controversial. The only randomized trial comparing surgical with endovascular revascularization suggests no significant difference in limb salvage between open surgical bypass and angioplasty. Although novel endovascular strategies are now available, their efficacies remain largely untested in a randomized fashion. This review provides an overview of the data surrounding contemporary outcomes of endovascular therapy with an emphasis on current knowledge gaps.
Methanesulfonic acid (MSA) migration in polar ice: data synthesis and theory

Abstract. Methanesulfonic acid (MSA; CH3SO3H) in polar ice is a unique proxy of marine primary productivity, synoptic atmospheric transport, and regional sea-ice behavior. However, MSA can be mobile within the firn and ice matrix, a post-depositional process that is well known but poorly understood and documented, leading to uncertainties in the integrity of the MSA paleoclimatic signal. Here, we use a compilation of 22 ice core MSA records from Greenland and Antarctica and a model of soluble impurity transport in order to comprehensively investigate the vertical migration of MSA from summer layers, where MSA is originally deposited, to adjacent winter layers in polar ice. We find that the shallowest depth of MSA migration in our compilation varies over a wide range (∼ 2 to 400 m) and is positively correlated with snow accumulation rate and negatively correlated with ice concentration of Na+ (typically the most abundant marine cation). Although the considered soluble impurity transport model provides a useful mechanistic framework for studying MSA migration, it remains limited by inadequate constraints on key physico-chemical parameters – most notably, the diffusion coefficient of MSA in cold ice (DMS). We derive a simplified version of the model, which includes DMS as the sole parameter, in order to illuminate aspects of the migration process. Using this model, we show that the progressive phase alignment of MSA and Na+ concentration peaks observed along a high-resolution West Antarctic core is most consistent with 10−12 m2 s−1
Improving Learning Performance by Applying Economic Knowledge

Digital information economies require information goods producers to learn how to position themselves within a potentially vast product space. Further, the topography of this space is often nonstationary, due to the interactive dynamics of multiple producers changing their positions as they try to learn the distribution of consumer preferences and other features of the problem’s economic structure. This presents a producer or its agent with a difficult learning problem: how to locate profitable niches in a very large space.
Excellence and Durability: A Normally Functioning Björk-Shiley Flat-Disc Prosthesis 42 Years Post Implantation.

Mechanical heart valves have been used worldwide for more than 60 years. While the composition and design of the valves, and the surgical techniques employed to implant them, have changed and advanced over that time, some of the earlier mechanical heart valves showed such great durability that they are still functioning in patients today. One of the most often-used and long-lasting mechanical prostheses was the Bjork-Shiley heart valve. While many versions of this valve were used during its 25 years of production, the most durable was the Bjork-Shiley flat-disc valve. This valve was first implanted in 1971 and was the first successful tilting-disc valve. Here, the complex medical history is reported of an elderly patient with a well-functioning Bjork-Shiley flat-disc valve in the aortic position that was placed over 42 years ago. The history of mechanical heart valves - in particular the Bjork-Shiley heart valve, including the flat-disc mechanical valve - is also briefly reviewed.
Thermal and Structural Issues of Target Injection into a Laser-Driven Inertial Fusion Energy Chamber

Inertial fusion energy (IFE) targets injected into fusion chambers must withstand the demanding acceleration forces and the intense thermal environment of the fusion chamber. For indirect targets, ...
Expression of immune genes and a signature of PD-1 inhibition resistance in basal-like pancreatic adenocarcinoma (PDAC) subtypes.

277Background: PDAC is a lethal disease with poor survival even when detected at an early stage. Recurrence rates after surgical resection remain high. Recently, two distinct molecular subtypes of ...