bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancement of Penicillium echinulatum glycoside hydrolase enzyme complex
Authors: dos Santos Costa Patrícia , Büchli Fernanda , Robl Diogo , da Silva Delabona Priscila , Rabelo Sarita Candida , da Cruz Pradella José Geraldo 
Published: February 2016

Abstract
The enhancement of enzyme complex produced by Penicillium echinulatum grown in several culture media components (bagasse sugarcane pretreated by various methods, soybean meal, wheat bran, sucrose, and yeast extract) was studied to increment FPase, xylanase, pectinase, and β-glucosidase enzyme activities. The present results indicated that culture media composed with 10 g/L of the various bagasse pretreatment methods did not have any substantial influence with respect to the FPase, xylanase, and β-glucosidase attained maximum values of, respectively, 2.68 FPU/mL, 2.04, and 115.4 IU/mL. On the other hand, proposed culture media to enhance β-glucosidase production composed of 10 g/L steam-exploded bagasse supplemented with soybean flour 5.0 g/L, yeast extract 1.0 g/L, and sucrose 10.0 g/L attained, respectively, 3.19 FPU/mL and 3.06 IU/mL while xylanase was maintained at the same level. The proteomes obtained from the optimized culture media for enhanced FPase, xylanase, pectinase, and β-glucosidase production were analyzed using mass spectrometry and a panel of GH enzyme activities against 16 different substrates. Culture medium designed to enhance β-glucosidase activity achieved higher enzymatic activities values (13 measured activities), compared to the culture media for FPase/pectinase (9 measured activities) and xylanase (7 measured activities), when tested against the 16 substrates. Mass spectrometry analyses of secretome showed a consistent result and the greatest number of spectral counts of Cazy family enzymes was found in designed β-glucosidase culture medium, followed by FPase/pectinase and xylanase. Most of the Cazy identified protein was cellobiohydrolase (GH6 and GH7), endoglucanase (GH5), and endo-1,4-β-xylanase (GH10). Enzymatic hydrolysis of hydrothermally pretreated sugarcane bagasse performed with β-glucosidase enhanced cocktail achieved 51.4 % glucose yield with 10 % w/v insoluble solids at enzyme load of 15 FPU/g material. Collectively the results demonstrated that it was possible to rationally modulate the GH activity of the enzymatic complex secreted by P. echinulatum using adjustment of the culture medium composition. The proposed strategy may contribute to increase enzymatic hydrolysis of lignocellulosic materials.
Dynamic Analysis of the Removal of Fatty Acid from a Pet Surface Using a Quartz Crystal Microbalance
Authors: Kanasaki Yu , Kobayashi Yasuyuki , Gotoh Keiko 
Published: February 2016

AbstractA quartz crystal microbalance (QCM) was used to study the removal of stearic acid from poly(ethylene terephthalate) (PET) substrate in aqueous alkali and surfactant solutions. The PET substrate was prepared on a QCM gold electrode by spin‐coating; its properties were examined by scanning electron microscopy, X‐ray photoelectron spectroscopy, and water contact angle measurements. As a result, the QCM electrode was found to be completely covered with a smooth PET film. To investigate the effect of soil deposition state on its removal, stearic acid (an oily soil model) was deposited onto the PET substrate with the Langmuir–Blodgett (LB) technique or by spraying. The QCM frequency was recorded during the removal of stearic acid from the PET substrate in aqueous solutions. In NaOH solution, stearic acid deposited by the LB method was more rapidly removed than when deposited by the spraying method. However, the LB films of stearic acid were difficult to be removed in surfactant solutions. With respect to removal behavior of spray‐deposited stearic acid in surfactant solutions, the results determined by the QCM method were compared with those from microscopic image analysis. The removal efficiencies in the sodium dodecyl sulfate solution were in good agreement between the two methods. However, in the alkyl ethoxylate solution, the removal efficiencies obtained by the QCM method were larger than those from microscopic image analysis. These experimental results were explained by the removal mechanism of stearic acid by the alkali and surfactant solutions.
Benchmarking the Self‐Assembly of Surfactin Biosurfactant at the Liquid–Air Interface to those of Synthetic Surfactants
Authors: Onaizi Sagheer A. , Nasser M. S. , Al‐Lagtah Nasir M. A. 
Published: February 2016

AbstractThe adsorption of surfactin, a lipopeptide biosurfactant, at the liquid–air interface has been investigated in this work. The maximum adsorption density and the nature and the extent of lateral interaction between the adsorbed surfactin molecules at the interface were estimated from surface tension data using the Frumkin model. The quantitative information obtained using the Frumkin model was also compared to those obtained using the Gibbs equation and the Langmuir–Szyszkowski model. Error analysis showed a better agreement between the experimental and the calculated values using the Frumkin model relative to the other two models. The adsorption of surfactin at the liquid–air interface was also compared to those of synthetic anionic, sodium dodecylbenzenesulphonate (SDBS), and nonionic, octaethylene glycol monotetradecyl ether (C14E8), surfactants. It has been estimated that the area occupied by a surfactin molecule at the interface is about 3‐ and 2.5‐fold higher than those occupied by SDBS and C14E8 molecules, respectively. The interaction between the adsorbed molecules of the anionic biosurfactant (surfactin) was estimated to be attractive, unlike the mild repulsive interaction between the adsorbed SDBS molecules.
Ventricular Septal Defect with Overriding Great Artery, Differential Diagnosis, Case Presentation, and Review of Literature
Authors: Choudhary Sandeep Bajaj , Choudhary Rajeev 
Published: February 2016

Abstract Embryologically, conotruncal abnormalities result from abnormal development of the conotruncal septum expressing variably as double outlet right ventricle, tetralogy of Fallot, absent pulmonary valve syndrome, complete transposition, corrected transposition, and pulmonary atresia with ventricular septal defect (PA-VSD). It is not very uncommon to see a VSD with one single large artery overriding the defect, along with nonvisualization of the right ventricular outflow tract and ventricular origin of the Pulmonary artery. In situations with above findings and a near normal four chamber heart view the differential diagnosis include common arterial trunk (CAT), and pulmonary atresia with VSD and rare disorders like aortic atresia. CAT is characterized by a single great artery supplying the coronary, cranial and pulmonary circulation. Similar findings in PA-VSD may create confusion in prenatal diagnosis of these two conditions, more so in CAT type II/III. The diagnosis of CAT type I is comparatively easy as the pulmonary artery arises immediately beyond the origin of the trunk. This article discusses a case, the approach to and differential diagnosis of a single great artery overriding a VSD with a near normal four chamber view. The role of cardiac screening during the early morphology scan and the role of 4D imaging with color and power Doppler angiography are also highlighted for the correct diagnosis and description of spatial relationships of the vessels and chambers. Correct prenatal diagnosis of these conditions is important for patient counseling and prognostication.
Physical health comorbidities in women with personality disorder: Data from the Geelong Osteoporosis Study
Authors: Quirk SE , Stuart AL , Brennan-Olsen SL , Pasco JA , Berk M , Chanen AM , Koivumaa-Honkanen H , Kotowicz MA , Lukkala PS , Williams LJ 
Published: February 2016

AbstractBackgroundAssociations between common psychiatric disorders, psychotic disorders and physical health comorbidities are frequently investigated. The complex relationship between personality disorders (PDs) and physical health is less understood, and findings to date are varied. This study aims to investigate associations between PDs with a number of prevalent physical health conditions.MethodsThis study examined data collected from women (n = 765; ≥ 25 years) participating in a population-based study located in south-eastern Australia. Lifetime history of psychiatric disorders was assessed using the semi-structured clinical interviews (SCID-I/NP and SCID-II). The presence of physical health conditions (lifetime) were identified via a combination of self-report, medical records, medication use and clinical data. Socioeconomic status, and information regarding medication use, lifestyle behaviors, and sociodemographic information was collected via questionnaires. Logistic regression models were used to investigate associations.ResultsAfter adjustment for sociodemographic variables (age, socioeconomic status) and health-related factors (body mass index, physical activity, smoking, psychotropic medication use), PDs were consistently associated with a range of physical health conditions. Novel associations were observed between Cluster A PDs and gastro-oesophageal reflux disease (GORD); Cluster B PDs with syncope and seizures, as well as arthritis; and Cluster C PDs with GORD and recurrent headaches.ConclusionsPDs were associated with physical comorbidity. The current data contribute to a growing evidence base demonstrating associations between PDs and a number of physical health conditions independent of psychiatric comorbidity, sociodemographic and lifestyle factors. Longitudinal studies are now required to investigate causal pathways, as are studies determining pathological mechanisms.
The relevance of professionals’ attachment style, expectations and job attitudes for therapeutic relationships with young people who experience psychosis
Authors: Berry C. , Greenwood K. 
Published: February 2016

AbstractBackgroundTherapeutic relationships are a central component of community treatment for psychosis and thought to influence clinical and social outcomes, yet there is limited research regarding the potential influence of professional characteristics on positive therapeutic relationships in community care. It was hypothesised that professionals’ relating style and attitudes toward their work might be important, and thus this exploratory study modelled associations between these characteristics and therapeutic relationships developed in community psychosis treatment.MethodsDyads of professionals and young patients with psychosis rated their therapeutic relationships with each other. Professionals also completed measures of attachment style, therapeutic optimism, outcome expectancy, and job attitudes regarding working with psychosis.ResultsProfessionals’ anxious attachment predicted less positive professional therapeutic relationship ratings. In exploratory directed path analysis, data also supported indirect effects, whereby anxious professional attachment predicts less positive therapeutic relationships through reduced professional therapeutic optimism and less positive job attitudes.ConclusionsProfessional anxious attachment style is directly associated with the therapeutic relationship in psychosis, and indirectly associated through therapeutic optimism and job attitudes. Thus, intervening in professional characteristics could offer an opportunity to limit the impact of insecure attachment on therapeutic relationships in psychosis.
Non-pharmacological interventions for reducing aggression and violence in serious mental illness: A systematic review and narrative synthesis
Authors: Rampling J , Furtado V , Winsper C , Marwaha S , Lucca G , Livanou M , Singh SP 
Published: February 2016

AbstractBackgroundFor people with mental illness that are violent, a range of interventions have been adopted with the aim of reducing violence outcomes. Many of these interventions have been borrowed from other (offender) populations and their evidence base in a Serious Mental Illness (SMI) population is uncertain.AimsTo aggregate the evidence base for non-pharmacological interventions in reducing violence amongst adults with SMI and PD (Personality Disorder), and to assess the efficacy of these interventions. We chose to focus on distinct interventions rather than on holistic service models where any element responsible for therapeutic change would be difficult to isolate.MethodsWe performed a systematic review and narrative synthesis of non-pharmacological interventions intended to reduce violence in a SMI population and in patients with a primary diagnosis of PD. Five online databases were searched alongside a manual search of seven relevant journals, and expert opinion was sourced. Eligibility of all returned articles was independently assessed by two authors, and quality of studies was appraised via the Cochrane Collaboration Tool for Assessing Risk of Bias.ResultsWe included 23 studies of diverse psychological and practical interventions, with a range of experimental and quasi-experimental study designs that included 7 Randomised Controlled Trials (RCTs). The majority were studies of Mentally Disordered Offenders. The stronger evidence existed for patients with a SMI diagnosis receiving Cognitive Behavioural Therapy or modified Reasoning & Rehabilitation (R&R). For patients with a primary diagnosis of PD, a modified version of R&R appeared tolerable and Enhanced Thinking Skills showed some promise in improving attitudes over the short-term, but studies of Dialectical Behaviour Therapy in this population were compromised by high risk of experimental bias. Little evidence could be found for non-pharmacological, non-psychological interventions.ConclusionsThe evidence for non-pharmacological interventions for reducing violence in this population is not conclusive. Long-term outcomes are lacking and good quality RCTs are required to develop a stronger evidence base.
Transsexual Attractions and Sexual Reassignment Surgery: Risks and Potential Risks
Authors: Fitzgibbons Richard P. 
Published: February 2016

Transsexual issues and sexual reassignment surgery (SRS) are receiving a great deal of attention and support in the media, schools, and government. Given the early age at which youth seek treatment for transsexual attractions (TSA) and gender dysphoria and given the serious risks associated with such treatment, it is essential that family and youth be advised about these risks and alternative treatment options. Physicians and mental-health professionals have a professional responsibility to know and communicate the serious risks, in particular risk of suicide, that are associated with SRS; the spontaneous resolution of TSA in youth; the psychological conflicts that have been identified in such patients and in their parents; the successful treatment of conflicts associated TSA and the regrets of those who have been through SRS. SRS and gender theory are also viewed from the faith perspective of Pope Francis and Pope Emeritus Benedict XVI. Lay summary Transsexuals and sex-change operations are receiving a great deal of attention. Young people may seek treatment for transsexual attractions at an early age even though these attractions may go away on their own. Psychological conflicts have been identified in these patients and their parents and may be successfully treated. There are serious risks associated with sex change. They include the risk of depressive illness and suicide. Physicians and mental-health professionals should know these risks and the regrets of those who have been through sex-change operations. These patients and their families also should be informed of other treatment options.
Phylogeography of a widespread species: pre-glacial vicariance, refugia,
occasional blocking straits and long-distance migrations
Authors: Santiso Xabier , Lopez Lúa , Retuerto Rubén , Barreiro Rodolfo 
Published: February 2016

Abstract
Phylogeographic studies give us the opportunity to reconstruct the historical migrations of species and link them with climatic and geographic variation. They are, therefore, a key tool to understanding the relationships among biology, geology and history. One of the most interesting biogeographical areas of the world is the Mediterranean region. However, in this area, the description of concordant phylogeographic patterns is quite scarce, which limits the understanding of evolutionary patterns related to climate. Species with one-dimensional distribution ranges, such as the strawberry tree ( Arbutus unedo ), are particularly useful to unravel these patterns. Here, we describe its phylogeographic structure and check for concordance with patterns seen in other Mediterranean plants: longitudinal/latitudinal clines of diversity, evidence for glacial refugia and the role of sea straits in dispersal. We also identify the most likely source for the disjunct Irish population. With this aim, we sequenced four chloroplast non-coding fragments of A. unedo from 23 populations covering its whole distribution. We determined the genetic diversity, population structure, haplotype genealogy and time to the most recent common ancestor. The genealogy revealed two clades that separated during the last 700 ky but before the last glacial maximum. One clade occupies Atlantic Iberia and North Africa, while the other occurs in the Western Mediterranean. The Eastern Mediterranean is inhabited by newer haplotypes derived from both clades, while the Irish population is closely related to Iberian demes. The straits of Sicily and Gibraltar partially restricted the gene flow. We concluded that a vicariance event during the Late Quaternary in the western end of the species' range followed by eastward migration seems a likely explanation for the observed phylogeographic pattern. The role of straits indicates an occasional communication between Europe and North Africa, suggesting that the latter was a novel refugia. The East–West genetic split in Iberia is consistent with the refugia-within-refugia model. Finally, the strawberry tree possibly reached Ireland from Iberia instead of throughout the maritime fringe of France as previously thought.
Trait responses of invasive aquatic macrophyte congeners: colonizing diploid outperforms polyploid
Authors: Grewell Brenda J. , Skaer Thomason Meghan J. , Futrell Caryn J. , Iannucci Maria , Drenovsky Rebecca E. 
Published: February 2016

AbstractUnderstanding traits underlying colonization and niche breadth of invasive plants is key to developing sustainable management solutions to curtail invasions at the establishment phase, when efforts are often most effective. The aim of this study was to evaluate how two invasive congeners differing in ploidy respond to high and lowresource availability following establishment from asexual fragments. Because polyploids are expected to have wider niche breadths than diploid ancestors, we predicted that a decaploid species would have superior ability to maximize resource uptake and use, and outperform a diploid congener when colonizing environments with contrasting light and nutrient availability. A mesocosm experiment was designed to test the main and interactive effects of ploidy (diploid and decaploid) and soil nutrient availability (low and high) nested within light environments (shade and sun) of two invasive aquatic plant congeners. Counter to our predictions, the diploid congener outperformed the decaploid in the early stage of growth. Although growth was similar and low in the cytotypes at low nutrient availability, the diploid species had much higher growth rate and biomass accumulation than the polyploid with nutrient enrichment, irrespective of light environment. Our results also revealed extreme differences in time to anthesis between the cytotypes. The rapid growth and earlier flowering of the diploid congener relative to the decaploid congener represent alternate strategies for establishment and success.
PhamDB: a web-based application for building Phamerator databases
Authors: Lamine James G. , DeJong Randall J. , Nelesen Serita M. 
Published: February 2016

Abstract
Summary: PhamDB is a web application which creates databases of bacteriophage genes, grouped by gene similarity. It is backwards compatible with the existing Phamerator desktop software while providing an improved database creation workflow. Key features include a graphical user interface, validation of uploaded GenBank files, and abilities to import phages from existing databases, modify existing databases and queue multiple jobs.
Availability and implementation: Source code and installation instructions for Linux, Windows and Mac OSX are freely available at https://github.com/jglamine/phage. PhamDB is also distributed as a docker image which can be managed via Kitematic. This docker image contains the application and all third party software dependencies as a pre-configured system, and is freely available via the installation instructions provided.
Contact: snelesen@calvin.edu
An algorithm for designing minimal microbial communities with desired metabolic capacities
Authors: Eng Alexander , Borenstein Elhanan 
Published: February 2016

Abstract
Motivation: Recent efforts to manipulate various microbial communities, such as fecal microbiota transplant and bioreactor systems’ optimization, suggest a promising route for microbial community engineering with numerous medical, environmental and industrial applications. However, such applications are currently restricted in scale and often rely on mimicking or enhancing natural communities, calling for the development of tools for designing synthetic communities with specific, tailored, desired metabolic capacities.
Results: Here, we present a first step toward this goal, introducing a novel algorithm for identifying minimal sets of microbial species that collectively provide the enzymatic capacity required to synthesize a set of desired target product metabolites from a predefined set of available substrates. Our method integrates a graph theoretic representation of network flow with the set cover problem in an integer linear programming (ILP) framework to simultaneously identify possible metabolic paths from substrates to products while minimizing the number of species required to catalyze these metabolic reactions. We apply our algorithm to successfully identify minimal communities both in a set of simple toy problems and in more complex, realistic settings, and to investigate metabolic capacities in the gut microbiome. Our framework adds to the growing toolset for supporting informed microbial community engineering and for ultimately realizing the full potential of such engineering efforts.
Availability and implementation: The algorithm source code, compilation, usage instructions and examples are available under a non-commercial research use only license at https://github.com/borenstein-lab/CoMiDA.
Contact: elbo@uw.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
FRED 2: an immunoinformatics framework for Python
Authors: Schubert Benjamin , Walzer Mathias , Brachvogel Hans-Philipp , Szolek András , Mohr Christopher , Kohlbacher Oliver 
Published: February 2016

Abstract
Summary: Immunoinformatics approaches are widely used in a variety of applications from basic immunological to applied biomedical research. Complex data integration is inevitable in immunological research and usually requires comprehensive pipelines including multiple tools and data sources. Non-standard input and output formats of immunoinformatics tools make the development of such applications difficult. Here we present FRED 2, an open-source immunoinformatics framework offering easy and unified access to methods for epitope prediction and other immunoinformatics applications. FRED 2 is implemented in Python and designed to be extendable and flexible to allow rapid prototyping of complex applications.
Availability and implementation: FRED 2 is available at http://fred-2.github.io
Contact: schubert@informatik.uni-tuebingen.de
Supplementary information: Supplementary data are available at Bioinformatics online.