bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graph construction and random graph generation for modeling protein structures
Authors: Wagaman Amy 
Published: August 2013

AbstractResearchers often model folded protein structures as graphs with amino acids as the vertices and edges representing contacts between amino acids. The vertices in these graphs are naturally ordered in the amino acid sequence order. There are many different graph construction methods and there is no consensus about what construction to use or what the major issues are with each construction in the literature. We investigate different constructions and examine their effect on various graph measures. We also consider the small‐world network model for proteins, discuss its validity under the different constructions, and discuss random protein graph generation. We propose a new graph property for graphs with ordered vertices, the contact distribution, and propose a method of reciprocal attachment to merge neighborhoods for protein graphs. Statistical Analysis and Data Mining Statistical Analysis and Data Mining 2013 DOI: 10.1002/sam.11203
Concentration driven phase transitions in multiphase porous media with application to methane oxidation in landfill cover layers
Authors: Ricken T. , Sindern A. , Bluhm J. , Widmann R. , Denecke M. , Gehrke T. , Schmidt T.C. 
Published: August 2013

AbstractThis study focuses on a formulation within the theory of porus media for continuum multicomponent modeling of bacterial driven methane oxidation in a porous landfill cover layer which consists of a porous solid matrix (soil and bacteria) saturated by a liquid (water) and gas phase. The solid, liquid, and gas phases are considered as immiscible constituents occupying spatially their individual volume fraction. However, the gas phase is composed of three components, namely methane (CH4), oxygen (O2), and carbon dioxide (CO2). A thermodynamically consistent constitutive framework is derived by evaluating the entropy inequality on the basis of Coleman and Noll [8], which results in constitutive relations for the constituent stress and pressure states, interaction forces, and mass exchanges. For the final set of process variables of the derived finite element calculation concept we consider the displacement of the solid matrix, the partial hydrostatic gas pressure and osmotic concentration pressures. For simplicity, we assume a constant water pressure and isothermal conditions. The theoretical formulations are implemented in the finite element code FEAP by Taylor [29]. A new set of experimental batch tests has been created that considers the model parameter dependencies on the process variables; these tests are used to evaluate the nonlinear model parameter set. After presenting the framework developed for the finite element calculation concept, including the representation of the governing weak formulations, we examine representative numerical examples.
A Proposal for Physicochemical Standards and Antioxidant Activity of Portuguese Propolis
Authors: Falcão Soraia I. , Freire Cristina , Vilas‐Boas Miguel 
Published: August 2013

AbstractPropolis is a complex resinous product gathered by honeybees whose chemical composition is highly variable, depending strongly on the plant sources available to the bees at the site of collection. Propolis from several locations in Portugal, including islands, was fully characterized in terms of physicochemical properties, phenolic composition and antioxidant activity, enabling the establishment of quality standards. Color, frequently used as a commercial parameter, was accessed by the first time in propolis with the CIELAB system, and proposed as a quick and reliable method for quality recognition. The results attested the existence of two different types of propolis within the six regions under study. One, the poplar propolis most common in temperate regions, revealed a high content in phenolics and show high bioactivity. The other, with darker green color is less rich in phenolics and generally less bioactive.
Regeneration of Used Frying Oil
Authors: Turan Semra , Yalcuk Arda 
Published: August 2013

AbstractUsed frying oils were purified in a packed column using different amounts of silica gel (SG), aluminum oxide (AO), activated charcoal (AC), bentonite (B), magnesol XL (M), calcium carbonate (CC), zeolite (Z), bleaching earth (BE) and/or their binary, triple, and quaternary combinations. SG (15 g) improved total polar material (TPM) by 100 %, conjugated diene (CD) content by 84 %, and p‐anisidine value (AV) by 104 %, while AO and M improved free fatty acid (FFA) contents by 103 and 105 %, respectively. On the other hand, AC and M bleached the color by 100 and 90 %, respectively. As the amount of adsorbent in the column increased, FFA, CD, AV, and color improved. When the amount of used sunflower oil (UO1) loaded in the column containing SL was increased, FFA, CD, AV and color values increased, while no change was observed in TPM up to 60 g of UO1. Loading UO1 at 150 °C in the column caused the absorbance values at 460 nm to decrease from 0.740 to 0.240, while the amount of adsorbed tocopherol increased compared to UO1 at 25 °C. The increasing number of adsorbents within the column further improved the physicochemical properties of UO1 when it was used 30 g. However, as the amount of different type of used oils (UO2, UO3 and UO4) was increased to 300 g, improvement ratios of all parameters decreased.
Self-harm induced somatic admission after discharge from psychiatric hospital – a prospective cohort study
Authors: Mellesdal L. , Kroken R.A. , Lutro O. , Wentzel-Larsen T. , Kjelby E. , Oedegaard K.J. , Jørgensen H.A. , Mehlum L. 
Published: August 2013

AbstractBackground:Few studies have examined rate and predictors of self-harm in discharged psychiatric patients.Aims:To investigate the rate, coding, timing, predictors and characteristics of self-harm induced somatic admission after discharge from psychiatric acute admission.Method:Cohort study of 2827 unselected patients consecutively admitted to a psychiatric acute ward during three years. Mean observation period was 2.3 years. Combined register linkage and manual data examination. Cox regression was used to investigate covariates for time to somatic admission due to self-harm, with covariates changing during follow-up entered time dependently.Results:During the observation period, 10.5% of the patients had 792 somatic self-harm admissions. Strongest risk factors were psychiatric admission due to non-suicidal self-harm, suicide attempt and suicide ideation. The risk was increased throughout the first year of follow-up, during readmission, with increasing outpatient consultations and in patients diagnosed with recurrent depression, personality disorders, substance use disorders and anxiety/stress-related disorders. Only 49% of the somatic self-harm admissions were given hospital self-harm diagnosis.Conclusions:Self-harm induced somatic admissions were highly prevalent during the first year after discharge from acute psychiatric admission. Underdiagnosing of self-harm in relation to somatic self-harm admissions may cause incorrect follow-up treatments and unreliable register data.
Devonian volcanism in the Minusa basin in the Altai–Sayan area: geological, geochemical, and Sr–Nd isotopic characteristics of rocks
Authors: Vorontsov A.A. , Fedoseev G.S. , Andryushchenko S.V. 
Published: August 2013

Abstract
Based on geological data and the geochemical and isotopic (Sr, Nd) parameters of the Devonian volcanic associations of the Minusa basin, the main regularities of volcanism development are considered, the composition of magmatic sources is studied, and the geodynamic mechanisms of their involvement in rifting are reconstructed. The early stage of formation of the Minusa basin was characterized by intense volcanism, which resulted in differentiated and, more seldom, bimodal volcanic complexes composed of pyroclastic rocks and dolerite sills. At the late stage, only terrigenous deposits accumulated in the basin. It has been established that the basites are similar in composition and are intermediate in geochemical characteristics between intraplate rocks (OIB) and continent-marginal ones (IAB). The basites, like OIB, have high contents of all lithophile elements, which is typical of enriched mantle sources, and, like IAB, show negative anomalies of Nb, Ta, Ti, and, to a smaller extent, Rb, Th, Zr, and Hf, selective enrichment in Pb and Ba (and, sometimes, Sr), and a weak REE differentiation (7 &lt; (La/Yb)N &lt; 17). In contrast to the basins in other segments of the Devonian Altai–Sayan rift area, the igneous associations in the Minusa basin are characterized by a worse expressed geochemical inhomogeneity of rocks and lack of high-Ti (&gt;2 wt.% TiO2) basites. The Sr and Nd isotope compositions of the Minusa basites deviate from the mantle rock series toward the compositions with high radiogenic-strontium and low REE contents. This points to the melting of a mantle substratum (PREMA-type) and carbonate-rich sedimentary rocks, which were probably assimilated by basaltic magma. The correlations between the contents of trace incompatible elements in rocks with SiO2 = 53–77 wt.% testify to the assimilation of crustal substrata by parental basaltic melts and the subsequent differentiation of contaminated magmas (AFC model). We propose a model for the formation of primary melts with the simultaneous participation of magmatic sources of two types: plume and fluid-saturated suprasubductional, localized beneath the active continental margin.
Biostratigraphy and ammonites of the Middle Oxfordian to lowermost Upper Kimmeridgian in northern Central Siberia
Authors: Wierzbowski A. , Rogov M.A. 
Published: August 2013

Abstract
The Middle Oxfordian to lowermost Upper Kimmeridgian ammonite faunas from northern Central Siberia (Nordvik, Chernokhrebetnaya, and Levaya Boyarka sections) are discussed, giving the basis for distinguishing the ammonite zones based on cardioceratid ammonites of the genus Amoeboceras (Boreal zonation), and, within the Kimmeridgian Stage, faunas–for distinguishing zones based on the aulacostephanid ammonites (Subboreal zonation). The succession of Boreal ammonites is essentially the same as in other areas of the Arctic and NW Europe, but the Subboreal ammonites differ somewhat from those known from NW Europe and Greenland. The Siberian aulacostephanid zones—the Involuta Zone and the Evoluta Zone—are correlated with the Baylei Zone (without its lowermost portion), and the Cymodoce Zone/lowermost part of the Mutabilis Zone (the Askepta Subzone) from NW Europe. The uniform character of the Boreal ammonite faunas in the Arctic makes possible a discussion on their phylogeny during the Late Oxfordian and Kimmeridgian: the succession of particular groups of Amoeboceras species referred to successive subgenera is revealed by the occurrence of well differentiated assemblages of typical normal-sized macro and microconchs, intermittently marked by the occurrence of assemblages of paedomorphic “small-sized microconchs” appearing at some levels preceeding marked evolutionary modifications. Some comments on the paleontology of separate groups of ammonites are also given. These include a discussion on the occurrence of Middle Oxfordian ammonites of the genus Cardioceras in the Nordvik section in relation to the critical review of the paper of Rogov and Wierzbowski (2009) by Nikitenko et al. (2011). The discussion shows that the oldest deposits in the section belong to the Middle Oxfordian, which results in the necessity for some changes in the foraminiferal zonal scheme of Nikitenko et al. (2011). The ammonites of the Pictonia involuta group are distinguished as the new subgenus Mesezhnikovia Wierzbowski and Rogov.
A geosteering tool for horizontal well logging
Authors: Epov M.I. , Mironov V.L. , Muzalevskiy K.V. , Eltsov I.N. , Salomatov U.P. 
Published: August 2013

Abstract
A theoretical study has been performed to check the possibility of using ultrabroadband nanosecond electromagnetic pulses as a geosteering tool for horizontal drilling to estimate the distance to the oil-water contact (OWC) in a floating oil accumulation. The voltage of a microwave-bandwidth pulse at the dipole receiver of a downhole radar was modeled for the case of a horizontal borehole near OWC in a formation saturated with oil and water. Numerical solutions to the boundary problem formulated on the basis of the Maxwell equations were obtained with the Microwave Studio software (www.cst.com). The frequency-dependent dielectric constants of the layered saturated formation and the drilling fluid were assumed according to experimentally tested models. The modeling has demonstrated that nanosecond electromagnetic pulses arriving from a layered oil-water contact can in principle be acquired and the distance from the wellbore to the OWC median can be inferred from the respective time delays recorded by a downhole radar. Additionally, the possible dynamic range and accuracy of sensing have been estimated.
Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus
Authors: Ebina Hirotaka , Misawa Naoko , Kanemura Yuka , Koyanagi Yoshio 
Published: August 2013

AbstractEven though highly active anti-retroviral therapy is able to keep HIV-1 replication under control, the virus can lie in a dormant state within the host genome, known as a latent reservoir and poses a threat to re-emerge at any time. However, novel technologies aimed at disrupting HIV-1 provirus may be capable of eradicating viral genomes from infected individuals. In this study, we showed the potential of the CRISPR/Cas9 system to edit the HIV-1 genome and block its expression. When LTR-targeting CRISPR/Cas9 components were transfected into HIV-1 LTR expression-dormant and -inducible T cells, a significant loss of LTR-driven expression was observed after stimulation. Sequence analysis confirmed that this CRISPR/Cas9 system efficiently cleaved and mutated LTR target sites. More importantly, this system was also able to remove internal viral genes from the host cell chromosome. Our results suggest that the CRISPR/Cas9 system may be a useful tool for curing HIV-1 infection.
The Role of Caffeine in the Alcohol Consumption Behaviors of College Students
Authors: Cobb Caroline O. , Nasim Aashir , Jentink Kade , Blank Melissa D. 
Published: August 2013

Background Evidence suggests that alcohol mixed with caffeine in any form may spur risky drinking behavior among young adults; however, most studies have only examined drinking behavior related to alcohol mixed with energy drinks (AmEDs) compared with alcohol alone. This survey assessed the consumption patterns and reasons for use of alcohol mixed with any caffeinated beverages (alcohol-caffeine) versus alcohol-only beverages among current users. Methods Students ( N = 1174) at a large, urban university completed a Web-based survey in October–December of 2010. Predictors of alcohol-caffeine use versus alcohol-only use were examined, as were drinking characteristics and reasons for alcohol-caffeine consumption as a function of type of alcohol-caffeine beverage usually consumed. Results Past-30-day prevalence was 34% for any alcohol-caffeine beverages and 36% for alcohol-only. The most frequent alcohol-caffeine beverages usually consumed were manufactured ready-to-drink AmED products (no longer sold in the United States; 50.3%), followed by self-mixed alcoholic beverages containing caffeinated sodas (26.4%) and energy drinks (18.5%). Users of alcohol-caffeine displayed a riskier drinking profile than alcohol-only users; however, there were few differences in overall alcohol drinking behaviors between consumers of AmEDs (manufactured or self-mixed) versus other caffeinated alcoholic beverages (e.g., alcohol mixed with caffeinated sodas). Conclusions Although alcohol-caffeine consumption was associated with heavier drinking characteristics compared with alcohol-only consumption, overall alcohol consumption patterns were similar between users of various alcohol-caffeine combinations. Future examinations should assess alcohol in combination with a variety of caffeine sources to determine whether energy drinks present a unique risk.
Intimate Partner Violence among Individuals in Methadone Maintenance Treatment
Authors: de Dios Marcel A. , Anderson Bradley J. , Caviness Celeste M. , Stein Michael 
Published: August 2013

Background Intimate partner violence (IPV) is a highly prevalent and concerning problem among methadone maintenance populations, and previous studies have shown a relationship between a history of IPV and increased substance use and affective disturbances. Methods The current study examined (1) the association between recent IPV victimization and alcohol and cocaine use and (2) the relationship between recent IPV victimization and depression in a sample of smokers ( N = 203) in methadone maintenance treatment (MMT). Participants in this study completed a battery of assessments that included standard questionnaires of trauma, alcohol and substance use, and depression. Parallel logistic and linear regression models were used to estimate the adjusted association of IPV victimization and depressive symptoms and evaluate the adjusted association of victimization with recent substance use. Results Participants recently victimized by partners were shown to have significantly higher mean Center for Epidemiologic Studies Depression Scale (CES-D) scores ( b = 0.54, 95% confidence interval [CI]: [0.07; 1.02], P <.05) and were found to have a 6 times greater likelihood of cocaine use (odds ratio [OR] = 6.65, 95% CI: [1.61; 27.46], P <.01) after controlling for age, gender, education, opiate use, and ethnicity. Conclusions These findings support the notion that IPV victimization can potentially increase depression and other substance use among MMT patients, which can have a deleterious impact on treatment.
Ineffectiveness of nectar scent in generating bumblebee visits to flowers of Impatiens textori
Authors: Raihan Jahir , Kawakubo Nobumitsu 
Published: August 2013

AbstractTo clarify if bumblebees can recognize nectar through its scent in Impatiens textori flowers, we examined the behavior of Bombus diversus on nectarless flowers in which the spurs had been artificially removed. Bumblebee visits to both natural flowers and spur‐cut flowers were captured using a long‐term video recording system. Visiting behavior and frequency were compared between the two flower types. Many bumblebees visited both types of flower, and their visit frequencies were not significantly different. However, the length of stay on each flower type did differ, with the bumblebees remaining on the spur‐cut flowers for a significantly shorter time than on the natural flowers. Our results suggest that bumblebees cannot detect the absence of nectar in I. textori flowers before probing them. Therefore, the nectar scent of I. textori does not serve to attract bumblebees although the presence of nectar will detain bumblebees on flowers for longer periods.
Treatment of refractory irritable bowel syndrome with visceral osteopathy: Short‐term and long‐term results of a randomized trial
Authors: Attali Thu‐Van , Bouchoucha Michel , Benamouzig Robert 
Published: August 2013

ObjectiveIn light of the low efficiency of available drugs in treating irritable bowel syndrome (IBS), there has been a growing interest in its alternative therapies. The aim of this study was to evaluate the effectiveness of visceral osteopathy for IBS.MethodsIn total, 31 consecutive refractory IBS patients were prospectively included in a randomized, crossover placebo‐controlled study. Qualitative evaluation of depression and four symptoms including constipation, diarrhea, abdominal distension and abdominal pain before and after each phase of the study were conducted using visual analog scales, measures of rectal sensitivity and colonic transit time. One year after the study, the assessment of symptoms was performed again in all patients.ResultsVisceral osteopathy was associated with a significant amelioration of self‐reported diarrhea, abdominal distension and abdominal pain, while constipation did not change significantly after this therapy. It was also associated with decreased rectal sensitivity, presenting as an increase in threshold volume, constant sensation volume and maximum tolerable volume (P < 0.001). However, no significant evolution of rectal sensitivity was observed when patients underwent placebo manipulations. Modifications of depression and total or segmental colonic transit time were not observed. One year after the end of this trial, symptom scores of diarrhea, abdominal distension and abdominal pain were significantly lower than those at enrollment (P < 0.05).ConclusionThis study suggests that visceral osteopathy improves short‐term and long‐term abdominal distension and pain, and also decreases rectal sensitivity in IBS patients.
Histology of Palate and Soft Palate Tonsil of Collared Peccary (Tayassu tajacu)
Authors: Teófilo T. S. , Morais M. R. P. T. , Dias G. F. , Diniz A. N. , Chaves H. S. A. , Fontenele‐Neto J. D. 
Published: August 2013

SummaryPeccaries are characterized by a prominent skin gland, known as scent gland, which is located in the middle of the rump. These animals are able to survive in a great variety of habitats, from humid tropical forests to semi‐arid areas. They are omnivorous animals, and their diet includes fibrous material, vegetables, fruits, small vertebrates and insects. Collared peccary hard palate and soft palate tonsils were studied, macroscopic morphometric data were collected and tissue samples were paraffin‐embedded. Sections were stained with HE, Gomori′s trichrome and von Kossa; the first two were used to study general organization and the latter to detect calcium deposits. The hard palate showed one incisive papilla followed by several rugae united by a distinct raphe. The hard palate is lined by a keratinised squamous epithelium resting on a dense connective, whereas in the soft palate, the epithelium is parakeratinised and showed lymphocyte infiltration. The palate showed several pacinian corpuscles in the propria‐submucosa. Two ovoid‐shaped tonsils were found in the soft palate, and several crypts were observed on its surface. The epithelium was highly infiltrated by lymphocytes, and within the crypts, tonsilloliths were frequently observed. The study showed that the general organization of collared peccary palate is similar to other species, but in its oropharynx, only the soft palate tonsil was present and the pacinian corpuscles formed small aggregates.