bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding the Need to Exist Here
Authors: McPhatter Marlon R.
Published: August 2015

There are unwritten rules for Black males in the American society in regards to expected behaviors that are contradictory to how other males in the majority of American society are expected to interact with others. These unwritten rules are a carry over from the days of slavery, Jim Crow, and the Civil Rights movement. Today, many are quick to point to the state of black progress in many areas of business, government, and education but the vast majority of black males are still not accepted in many of these privileged areas. The existence of a black male is perceived to be still too black and too strong for white America and threatens what white males perceive as benefits entitled to them. Even in today’s American society, black males must remember not to live as if color does not exist and should remember that white society expects them to be appreciative for whatever concessions are granted to them even though their work must equal or surpass the work of their white male counterparts. Black males who demand to be treated as equal can be alienated not just by white society but by black Americans who see them as acting white in order to operate and survive in society. Today’s American society has been pressed by possible economic sanctions to conceal its overt racism in place of a systematic process of racism to limit opportunities for black males to succeed. Every opportunity at each level in this space should not be wasted.
Raman Spectroscopy of Experimental Oral Carcinogenesis
Authors: Kumar Piyush , Bhattacharjee Tanmoy , Ingle Arvind , Maru Girish , Krishna C. Murali
Published: August 2015

Oral cancers suffer from poor 5-year survival rates, owing to late detection of the disease. Current diagnostic/screening tools need to be upgraded in view of disadvantages like invasiveness, tedious sample preparation, long output times, and interobserver variances. Raman spectroscopy has been shown to identify many disease conditions, including oral cancers, from healthy conditions. Further studies in exploring sequential changes in oral carcinogenesis are warranted. In this Raman spectroscopy study, sequential progression in experimental oral carcinogenesis in Hamster buccal pouch model was investigated using 3 approaches— ex vivo, in vivo sequential, and in vivo follow-up. In all these studies, spectral changes show lipid dominance in early stages while later stages and tumors showed increased protein to lipid ratio and nucleic acids. On similar lines, early weeks of 7,12-dimethylbenz(a)anthracene-treated and control groups showed higher overlap and low classification. The classification efficiency increased progressively, reached a plateau phase and subsequently increased up to 100% by 14 weeks. The misclassifications between treated and control spectra suggested some changes in controls as well, which was confirmed by a careful reexamination of histopathological slides. These findings suggests Raman spectroscopy may be able to identify microheterogeneity, which may often go unnoticed in conventional biochemistry wherein tissue extracts are employed, as well as in histopathology. In vivo findings, quite comparable to gold-standard supported ex vivo findings, give further proof of Raman spectroscopy being a promising label-free, noninvasive diagnostic adjunct for future clinical applications.
Clinical Assessments as Predictors of Primary On-Road Outcomes in Parkinson’s Disease
Authors: Classen Sherrilene , Holmes Jeffrey D. , Alvarez Liliana , Loew Katherine , Mulvagh Ashley , Rienas Kayla , Walton Victoria , He Wenqing
Published: August 2015

Parkinson’s disease (PD) is a neurodegenerative disorder that affects fitness to drive. Research that has examined clinical predictors of fitness to drive in PD, using the on-road assessment as the gold standard, has generally used a dichotomous pass/fail decision. However, on-road assessments may also result in one of two additional outcomes (pass with recommendations, or fail-remediable). Individuals within these subgroups may benefit from interventions to improve their fitness to drive abilities. This study investigated clinical predictors that could be indicative of the pass, pass with recommendations, or fail-remediable categories for drivers with PD ( N = 99). Trails B, Left Finger to Nose Test, and contrast sensitivity measures were identified as significant predictors for the pass, and pass with recommendations subgroups. No significant predictors were identified for the fail-remediable subgroup. Results from this study provide a foundation for clinicians to identify drivers who can benefit from recommendations to preserve their driving abilities.
From Stories to Schemas
Authors: Steinbauer Robert , Rhew Nicholas D. , Chen H. Shawna
Published: August 2015

Today’s leaders face unprecedented complexity and dynamism in the external environment. Sensemaking provides a useful framework for understanding how leaders extract meaning from that environment; however, its focus on purely conscious processes limits its applicability. We revisit and overcome major epistemological and ontological arguments against reconciling sensemaking with other decision-making models. This allows us to propose a dual systems model of sensemaking by introducing unconscious sensemaking as a complementary process that supports conscious sensemaking. We propose that the plausible stories that result from conscious sensemaking lead to schemas over time through which leaders can unconsciously make sense of their environment. This dual systems model holds important implications for leadership scholarship, in both describing leaders’ cognitive processes and how those leaders can utilize this improved model to better effect change.
Patient Decision Making Prior to Radical Prostatectomy
Authors: Doğan Çağatay , Gültekin Hamza M. , Erdoğan Sarper M. , Özkara Hamdi , Talat Zübeyr , Erözenci Ahmet N. , Öbek Can
Published: August 2015

The current study assessed the decision-making process before surgery in prostate cancer patients. A structured telephone interview was conducted by an independent third party in 162 consecutive patients who underwent surgery for prostate cancer. Responders revealed that details regarding diagnosis and treatment alternatives were withheld from a significant number of patients. Radiation and active surveillance were presented as alternative options to surgery in 57 (39%) and 20 (14%) of responders, respectively. Twenty-six (18%) patients reported not being informed regarding potential surgical side effects. Patients were not active participants in critical aspects of decision making in 61 (42%) of the cases. Being inadequately informed and more frequent visits to the urologist appeared to make decisions more difficult. Treatment regret was reported by 23 (16%) of the patients who underwent surgery and was more common when the patient was not involved in the decision or was inadequately informed. As such, shared decision making should replace paternalism when managing patients with localized prostate cancer in urologic practice.
Factor Structure of the Gotland Scale of Male Depression in Two Samples of Men With Prostate Cancer
Authors: Sharpley Christopher F. , Bitsika Vicki , Christie David R. H. , Hunter Myra S.
Published: August 2015

Up to a quarter of all prostate cancer (PCa) patients suffer from clinically significant depression but treatments are inconsistent and short-lived in their efficacy. One possible reason could be that “male depression” is not adequately diagnosed by the criteria for major depressive disorder (MDD) used in many clinical settings. In response to this limitation, the Gotland Scale of Male Depression (GSMD) was developed to identify the extra symptoms of MDD in men. Although the factor structure of the GSMD has been reported in non-PCa samples, it has not been determined for this group of men. Two samples of PCa patients were recruited, 191 from Australia and 138 from the United Kingdom and all patients received the GSMD individually, plus a background questionnaire. Two-factor solutions were identified for each of the two samples. The Australian sample was characterized by changes in emotional and somatic function, followed by depressed mood. The U.K. sample exhibited the same two-factor solution but in reverse order of weighting. Targeted treatments for depression in PCa patients may benefit from identification of the loadings that individual patients have on these two GSMD factors so that specific clinical profiles and treatment needs may be based on this information about their depression.
Integrating Multidisciplinary Results to Produce New Knowledge About the Physician–Patient Relationship
Authors: Schieber Anne-Cécile , Kelly-Irving Michelle , Génolini Jean-Paul , Membrado Monique , Tanguy Ludovic , Fabre Cécile , Marchand Pascal , Lang Thierry ,   for the INTERMEDE Group
Published: August 2015

The INTERMEDE Project brought together a number of research teams to study the interaction between a patient and their general practitioner, and how this can produce social inequalities in health. The ultimate objective of the project was to formalize a core of common findings by integrating qualitative and quantitative results. The methodology chosen for the integration was inspired by the Delphi participatory method. It involves several rounds of questions and feedback in writing between all members of project teams, in order to compare contradictory opinions and identify key concepts arising from the project. This interdisciplinary research has provided a more nuanced understanding of the mechanisms underlying physician–patient interaction by revealing the convergences of the various disciplinary approaches.
Defect analysis in drilling needle-punched carbon–carbon composites perpendicular to nonwoven fabrics
Authors: Shan Chenwei , Lin Xiaojun , Wang Xiao , Yan Jiaqiang , Cui Dongpeng
Published: August 2015

Carbon–carbon composites are unique materials consisting of carbon fibers embedded in a carbonaceous matrix. Drilling of carbon–carbon composites is difficult to carry out due to the anisotropic, high specific stiffness and brittleness, nonhomogeneous inner structure of composites, and high abrasiveness of their reinforcing constituents. These typically result in defects being introduced into the workpiece and in very rapid wear development in the drilling tool. Defects are the undesired effects of machining using nonappropriate drilling parameters or worn drill. Aimed at this issue, first, the major defects caused in drilling needle-punched carbon–carbon composites are analyzed in detail. Second, the fiber fuzz factor and the ripping factor of fibers are defined to depict the drilling defects. Experiments are carried out using a conventional twist drill, and the results indicate that material structures, federates, and cutting speeds are reckoned to be the most significant factors contributing to defects.
Perceptions of British Columbia residents and their willingness to pay for medication management services provided by pharmacists
Authors: Tsao Nicole W. , Khakban Amir , Gastonguay Louise , Li Kathy , Lynd Larry D. , Marra Carlo A.
Published: August 2015

Background:

Across Canada, pharmacists have expanded their scope of practice by performing medication management (MM) services. However, little is currently known about the opinions and attitudes of patients and the general population toward MM services.

Methods:

A cross-sectional online survey, including a best-worst scaling task, was designed to understand the general public’s opinions, preferences and willingness-to-pay with respect to MM services in British Columbia.

Results:

Of 977 individuals contacted, 819 responded to the questionnaire (84% response rate). The mean age was 45 years (standard deviation [SD] 16 years), and 37% were male. Overall, 93% of respondents felt that the medication advice from their pharmacist resulted in improvement in patient outcomes and/or medication use. This was also selected as the “best” attribute of MM, while other preferred attributes of MM included being able to obtain an appointment with the pharmacist on the same day or via walk-in, improved patient-physician relationships and MM sessions able to be completed in 15 minutes with the pharmacist. The average willingness to pay for MM was $24.55 (SD $21.44). Younger males with higher household income and those who had had MM in the past were willing to pay more for MM services out of pocket.

Discussion and Conclusion:

The accessibility of pharmacists was valued highly by respondents who, overall, were supportive of MM services and recognized the potential of pharmacists’ involvement in drug therapy management to improve patient outcomes and medication use. Alternative models of funding are worth considering for the sustainability of MM service provision.
The hidden challenges of pharmaceutical serialisation by Domino Printing Sciences
Authors: Stobie Craig
Published: August 2015

In the almost 40 years since counterfeiting of pharmaceutical products was recognised as a problem by the World Health Organization (WHO), the industry has waged a constant battle against increasingly sophisticated and organised counterfeiters, with drug packaging serving as one of its foremost defences. The true extent of the counterfeiting is unknown, since no global study has ever been carried out, but according to WHO estimates, up to 15% of all medicines are counterfeit and there was a recorded rise of 92% in seizures of falsified medicines between 2005 and 2011.
Combining detached watchdog journalism with development ideals: An exploration of Fijian journalism culture
Authors: Hanusch Folker , Uppal Charu
Published: August 2015

Development journalism has been a key focus of discussion among journalism scholars for around half a decade, but most of the attention has been firmly on African and Asian countries. This article examines the situation on the little-researched island nation of Fiji, which has experienced considerable political instability since independence in 1970. Based on interviews with 77 of the country's small population of just over 100 journalists, we find that journalism in Fiji exhibits similarities to Western journalism ideals, but also a significant development journalism orientation. A comparison with six other countries from the global South shows that this mix is not unique, and we argue that Western journalism approaches and development ideals are not by necessity mutually exclusive, as has often been argued. In this way, the article aims to contribute to a reassessment of our understanding of development journalism and how journalists in developing societies view their work.
The impact of victim advocacy on the prosecution of domestic violence offences: Lessons from a Realistic Evaluation
Authors: Taylor-Dunn Holly
Published: August 2015

This article explores the impact of a court-based advocacy service on the prosecution of domestic violence offences. The research, conducted as part of a PhD thesis, evaluated a team of Independent Domestic Violence Advisers (IDVAs) based within a Specialist Domestic Violence Court (SDVC). The author adopted the methodology of Realistic Evaluation in order to understand first, any impact of the court-based IDVA service on court outcomes, second, how any such outcomes were achieved and, finally, in what contexts they occurred. As this article explores, effective victim advocacy has the potential to impact positively on the prosecution of domestic violence offences.
Brands and Instagram: Point, tap, swipe, glance
Authors: Carah Nicholas , Shaul Michelle
Published: August 2015

Brands are a critical part of the ongoing experimentation that underpins the development of mobile social media platforms like Instagram. Instagram had no dedicated advertising or analytics tools until 2014 so, in the absence of such devices, brands have developed uses of the platform that engage with the productive ability of cultural intermediaries and consumers to create and circulate images of their bodies, everyday lives, and cultural practices. This article examines the Instagram activities of the global vodka brand Smirnoff and the fashion retailer General Pants. Each brand engages with cultural intermediaries and builds themed activations at cultural events to orchestrate the production of images. Following Wissinger’s (2007a) study of fashion models, we conceptualize Instagram as an image machine that captures and calibrates attention. Instagram expands the terrain upon which brands operate by dispersing the work of creating and engaging with images into consumers’ everyday lives. The efforts made by brands to experiment with mobile media demonstrate the need to critically examine how participatory, discursive, and algorithmic modes of control are interrelated.
Some Manifestations of Japanese Exclusionism
Authors: Morita Liang
Published: August 2015

The Japanese subscribe to ethnic nationalism, which is an ideology with the aim to develop an ethnically exclusive and homogeneous nationhood. One manifestation of ethnic nationalism is the belief that Japan is, or should be, a mono-ethnic society. Ethnic nationalism is manifested in the exclusionary attitude or opinion of the Japanese. In the context of foreigners living in Japan, the exclusionary attitude or opinion of the Japanese often translates into the insistence that foreigners should do things the Japanese way. This is unfriendly to foreigners living in Japan, to say the least. This article illustrates how unwelcoming and inconvenient Japanese exclusionism can be by using two examples that directly affect foreigners: housing and discrimination against foreigners.
Fifteen-Year Prospective Analysis of Television Viewing and Adiposity in African American and Caucasian Men and Women
Authors: Chen Chung-Yu , Pereira Mark A. , Kim Kevin H. , Erickson Darin , Jacobs David R. , Zgibor Janice C. , Chung Tammy , Sidney Stephen , Iribarren Carlos , Fabio Anthony
Published: August 2015

There are limited data from long-term prospective studies on the association between television (TV) viewing and obesity. We investigated this association between TV viewing and body mass index (BMI) and waist circumference (WST) over 15 years on 3,269 participants from the Coronary Artery Risk Development in Young Adults (CARDIA) study. We used cross-lagged panel models at exam Years 5, 10, 15, and 20 over 15 years to assess the association between TV viewing and obesity. The cross-lagged effects of TV viewing on anthropometry were significant from exam Year 5 to Year 10 ( B = 0.034 for BMI and 0.036 for WST). However, the cross-lagged effects of TV viewing at Years 10 and 15 on obesity at Years 15 and 20, respectively, were nonsignificant. The findings indicate that higher levels of TV viewing predicted higher BMI and WC in young adulthood, but this association was not observed as individuals aged over the following decade.
Cross-Border Country Planning Dialogue in Interwar Europe
Authors: Geertse Michel
Published: August 2015

The past years witnessed many publications on the roles of transnational expert networks in defining new professional fields and lobbying for social reform in the first half of the 20th century. The modern spatial planning profession, still in a stage of formation then, featured prominently in this transnational infrastructure. Pierre Yves Saunier has dubbed this international sphere the “Urban Internationale.” The participating planners devoted themselves to town and country planning. Rural historians so far have not discovered the potential of the transnational planning societies in the Urban Internationale as a source to study transnational country planning dialogue. Urban historians who have discovered these societies usually focus on urban planning models and neglect the planning of the countryside. This article uses the international congresses of the International Federation for Housing and Town Planning (IFHTP) to analyze transnational country planning dialogue in interwar Europe. This London-based association sustained one of the largest transnational platforms for transnational planning dialogue between the wars.
Racial/Ethnic Differences in Youth Depression Indicators
Authors: Vaughn-Coaxum Rachel A. , Mair Patrick , Weisz John R.
Published: August 2015

Accurate assessment of dysfunction is central to clinical psychological science, essential for valid conclusions about prevalence, risk, and appropriate intervention. Measures applied without adjustment across diverse racial/ethnic groups may risk errors if measurement equivalence has not been established. We tested this possibility in the domain of youth depression, applying item response theory (IRT) and differential item functioning (DIF) analyses to reports by White, Black, Latino, and Asian youths ( N = 2,335) on the most widely used measure of symptoms, the Children’s Depression Inventory (CDI). Analyses revealed that 77% of CDI items were nonequivalent indicators of symptom severity across groups. CDI sum scores exhibited marked overestimations of group differences and inappropriate classification as “clinically elevated” for 29% of Latino, 23% of Black, and 10% of Asian youths. Applying DIF adjustment corrected these errors. The study demonstrates a useful strategy for ethnically sensitive assessment, applicable to other symptom domains and ethnic groups.
The Lingering Impact of Resolved PTSD on Subsequent Functioning
Authors: Bryant Richard A. , McFarlane Alexander C. , Silove Derrick , O’Donnell Meaghan L. , Forbes David , Creamer Mark
Published: August 2015

This study investigated whether impairment persists after posttraumatic stress disorder (PTSD) has resolved. Traumatically injured patients ( N = 1,035) were assessed during hospital admission and at 3 (85%) and 12 months (73%). Quality of life prior to traumatic injury was measured with the World Health Organization Quality of Life–BREF during hospitalization and at each subsequent assessment. PTSD was assessed using the Clinician-Administered PTSD Scale at 3 and 12 months. After controlling for preinjury functioning, current pain, and comorbid depression, patients whose PTSD symptoms had resolved by 12 months were more likely to have poorer quality of life in psychological (OR = 3.51), physical (OR = 10.17), social (OR = 4.54), and environmental (OR = 8.83) domains than those who never developed PTSD. These data provide initial evidence that PTSD can result in lingering effects on functional capacity even after remission of symptoms.
Gendered Language
Authors: Bigler Rebecca S. , Leaper Campbell
Published: August 2015

The language used to describe concepts influences individuals’ cognition, affect, and behavior. A striking example comes from research on gendered language, or words that denote individuals’ gender (e.g., she, woman, daughter). Gendered language contributes to gender biases by making gender salient, treating gender as a binary category, and causing stereotypic views of gender. In our review, we first summarize some of the major ways that language marks individuals’ gender, focusing on the English language but noting patterns in other languages as well. Second, we describe research on the relation between gendered language, on one hand, and gender-related cognition, affect, and behavior (e.g., gender salience, categorization, stereotyping, and prejudice), on the other hand. Third, we review past and contemporary efforts at changing gendered language, including calls for the use of gender-neutral nouns (e.g., “Good evening, folks” instead of “Good evening, ladies and gentlemen”) and pronouns (e.g., ze instead of he or she). Finally, we highlight the role of values in shaping views of language policies that may mitigate the pervasiveness and consequences of gendered language.
Debiasing Decisions
Authors: Morewedge Carey K. , Yoon Haewon , Scopelliti Irene , Symborski Carl W. , Korris James H. , Kassam Karim S.
Published: August 2015

From failures of intelligence analysis to misguided beliefs about vaccinations, biased judgment and decision making contributes to problems in policy, business, medicine, law, education, and private life. Early attempts to reduce decision biases with training met with little success, leading scientists and policy makers to focus on debiasing by using incentives and changes in the presentation and elicitation of decisions. We report the results of two longitudinal experiments that found medium to large effects of one-shot debiasing training interventions. Participants received a single training intervention, played a computer game or watched an instructional video, which addressed biases critical to intelligence analysis (in Experiment 1: bias blind spot, confirmation bias, and fundamental attribution error; in Experiment 2: anchoring, representativeness, and social projection). Both kinds of interventions produced medium to large debiasing effects immediately (games ≥ −31.94% and videos ≥ −18.60%) that persisted at least 2 months later (games ≥ −23.57% and videos ≥ −19.20%). Games that provided personalized feedback and practice produced larger effects than did videos. Debiasing effects were domain general: bias reduction occurred across problems in different contexts, and problem formats that were taught and not taught in the interventions. The results suggest that a single training intervention can improve decision making. We suggest its use alongside improved incentives, information presentation, and nudges to reduce costly errors associated with biased judgments and decisions.
Composition and optoelectrical properties of sputtering MoSex films
Authors: Li N. , Liu Z.-T. , Feng L.-P. , Jia R.-T.
Published: August 2015

Influence of sputtering pressure on composition, optical and electrical properties of amorphous MoSex films has been systematically investigated. The highest Se concentration and nearly stoichiometric ratio Se/Mo in MoSex films were observed at a sputtering pressure of 0.3 Pa. When the sputtering pressure is increased, the binding energies of Mo 3d and Se 3d peaks of the MoSex films increase, the blue shift of optical transmission edge is observed and the optical band gap decreases from 0.92 to 0.78 eV. Additionally, Hall mobility decreases first and then increases slightly, the resistivity of the films decreases, whereas the carrier concentration of the films increases with an increase in sputtering pressure. The MoSex films deposited at 0.3 Pa have larger Hall mobility (6.45 cm2 V− 1 s− 1) and higher optical band gap (0.92 eV) because of lower Se vacancy defect concentration.
Frailty and Physical Function in Chronic Kidney Disease: The CanFIT Study
Authors: Walker Simon R. , Brar Ranveer , Eng Frederick , Komenda Paul , Rigatto Claudio , Prasad Bhanu , Bohm Clara J. , Storsley Leroy J. , Tangri Navdeep
Published: August 2015

Background:

Frailty, a manifestation of unsuccessful aging, is highly prevalent in people with chronic kidney disease (CKD) and is associated with comorbid conditions in cross-sectional studies. Longitudinal studies investigating the progression of frailty in those with advanced non-dialysis CKD are lacking.

Objectives:

Canadian Frailty Observation and Interventions Trial (CanFIT). To determine the natural history, prevalence of perceived and measured frailty and its association with dialysis treatment choices and adverse outcomes in patients with advanced CKD.

Design:

Longitudinal observational study, designed to collect data from 600 participants over 2 years.

Setting:

Interprofessional non-dialysis CKD clinics at four tertiary health care centres in central Canada.

Patients:

People with CKD stage 4 and 5 (eGFR <30 ml/min/1.73 m2) who are not on dialysis at enrollment.

Measurements:

Multiple Frailty Definitions: Short Physical Performance Battery (SPPB), Fried Frailty Criteria, Frailty Index. Dialysis start: In-Centre Hemodialysis, Home Hemodialysis or Peritoneal Dialysis Outcomes: Death, Opt-out or Lost to follow up.

Methods:

We will perform physical and cognitive assessments annually. We plan to analyze the relationships between frailty, treatment choices and patient centered outcomes.

Results:

We have recruited 217 participants in 2 centres; of these, 56 % had reduced physical function at baseline, as defined by the SPPB. Risk of reduced physical function was 8 fold higher in those with diabetes after adjusting for age, gender, eGFR and comorbidities.

Limitations:

Referred population, use of SPPB as a measure of frailty, inter-operator variability in measurement of hand grip and gait speed, cross-sectional analysis of baseline data in the subset recruited to date.

Conclusions:

People with advanced CKD have a high burden of reduced physical function, especially those with diabetes. We will continue enrollment into the CanFIT study to further understand the clinical history of CKD and frailty in this population.
Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4
Authors: Shetty Ameesha R. , de Gannes Vidya , Obi Chioma C. , Lucas Susan , Lapidus Alla , Cheng Jan-Fang , Goodwin Lynne A. , Pitluck Samuel , Peters Linda , Mikhailova Natalia , Teshima Hazuki , Han Cliff , Tapia Roxanne , Land Miriam , Hauser Loren J. , Kyrpides Nikos , Ivanova Natalia , Pagani Ioanna , Chain Patrick S. G. , Denef Vincent J , Woyke Tanya , Hickey William J.
Published: August 2015

Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of PAH-contaminated soil. Delftia acidovorans Cs1-4 (formerly Delftia sp. Cs1-4) was isolated by using phenanthrene as the sole carbon source from PAH contaminated soil in Wisconsin. Its full genome sequence was determined to gain insights into a mechanisms underlying biodegradation of PAH. Three genomic libraries were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads), a 454 Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size of 8 kb, 508,092 reads). The initial assembly contained 40 contigs in two scaffolds. The 454 Titanium standard data and the 454 paired end data were assembled together and the consensus sequences were computationally shredded into 2 kb overlapping shreds. Illumina sequencing data was assembled, and the consensus sequence was computationally shredded into 1.5 kb overlapping shreds. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks. A total of 182 additional reactions were needed to close gaps and to raise the quality of the finished sequence. The final assembly is based on 253.3 Mb of 454 draft data (averaging 38.4 X coverage) and 590.2 Mb of Illumina draft data (averaging 89.4 X coverage). The genome of strain Cs1-4 consists of a single circular chromosome of 6,685,842 bp (66.7 %G+C) containing 6,028 predicted genes; 5,931 of these genes were protein-encoding and 4,425 gene products were assigned to a putative function. Genes encoding phenanthrene degradation were localized to a 232 kb genomic island (termed the phn island), which contained near its 3’ end a bacteriophage P4-like integrase, an enzyme often associated with chromosomal integration of mobile genetic elements. Other biodegradation pathways reconstructed from the genome sequence included: benzoate (by the acetyl-CoA pathway), styrene, nicotinic acid (by the maleamate pathway) and the pesticides Dicamba and Fenitrothion. Determination of the complete genome sequence of D. acidovorans Cs1-4 has provided new insights the microbial mechanisms of PAH biodegradation that may shape the process in the environment.
Geologic pattern recognition from seismic attributes: Principal component analysis and self-organizing maps
Authors: Roden Rocky , Smith Thomas , Sacrey Deborah
Published: August 2015

Interpretation of seismic reflection data routinely involves powerful multiple-central-processing-unit computers, advanced visualization techniques, and generation of numerous seismic data types and attributes. Even with these technologies at the disposal of interpreters, there are additional techniques to derive even more useful information from our data. Over the last few years, there have been efforts to distill numerous seismic attributes into volumes that are easily evaluated for their geologic significance and improved seismic interpretation. Seismic attributes are any measurable property of seismic data. Commonly used categories of seismic attributes include instantaneous, geometric, amplitude accentuating, amplitude-variation with offset, spectral decomposition, and inversion. Principal component analysis (PCA), a linear quantitative technique, has proven to be an excellent approach for use in understanding which seismic attributes or combination of seismic attributes has interpretive significance. The PCA reduces a large set of seismic attributes to indicate variations in the data, which often relate to geologic features of interest. PCA, as a tool used in an interpretation workflow, can help to determine meaningful seismic attributes. In turn, these attributes are input to self-organizing-map (SOM) training. The SOM, a form of unsupervised neural networks, has proven to take many of these seismic attributes and produce meaningful and easily interpretable results. SOM analysis reveals the natural clustering and patterns in data and has been beneficial in defining stratigraphy, seismic facies, direct hydrocarbon indicator features, and aspects of shale plays, such as fault/fracture trends and sweet spots. With modern visualization capabilities and the application of 2D color maps, SOM routinely identifies meaningful geologic patterns. Recent work using SOM and PCA has revealed geologic features that were not previously identified or easily interpreted from the seismic data. The ultimate goal in this multiattribute analysis is to enable the geoscientist to produce a more accurate interpretation and reduce exploration and development risk.
A comparison of classification techniques for seismic facies recognition
Authors: Zhao Tao , Jayaram Vikram , Roy Atish , Marfurt Kurt J.
Published: August 2015

During the past decade, the size of 3D seismic data volumes and the number of seismic attributes have increased to the extent that it is difficult, if not impossible, for interpreters to examine every seismic line and time slice. To address this problem, several seismic facies classification algorithms including [Formula: see text]-means, self-organizing maps, generative topographic mapping, support vector machines, Gaussian mixture models, and artificial neural networks have been successfully used to extract features of geologic interest from multiple volumes. Although well documented in the literature, the terminology and complexity of these algorithms may bewilder the average seismic interpreter, and few papers have applied these competing methods to the same data volume. We have reviewed six commonly used algorithms and applied them to a single 3D seismic data volume acquired over the Canterbury Basin, offshore New Zealand, where one of the main objectives was to differentiate the architectural elements of a turbidite system. Not surprisingly, the most important parameter in this analysis was the choice of the correct input attributes, which in turn depended on careful pattern recognition by the interpreter. We found that supervised learning methods provided accurate estimates of the desired seismic facies, whereas unsupervised learning methods also highlighted features that might otherwise be overlooked.
Effective medium modeling: How to efficiently infer porosity from seismic data?
Authors: Adelinet Mathilde , Le Ravalec Mickaële
Published: August 2015

Many geophysical studies in reservoir characterization focus on the variations in the elastic properties of rocks. They commonly involve seismic data, which are processed in terms of seismic attributes. These processed data still have to be related to the physical properties of the rock mass and the fluids saturating the pore space. This need motivated the development of research projects based upon the effective medium theory (EMT). We have used the EMT to infer porosity and also fracture data from seismic impedances in part of the Fort Worth Basin, Texas. The main idea was to take advantage of the available impedances to characterize porosity in terms of equant pores and cracks. We then focused on the volume fraction of spherical pores and crack density. Shortly thereafter, we developed an effective medium (EM) model that provided numerical responses for seismic impedances. These responses were then compared to the impedances obtained from stratigraphic inversion. The overall procedure consisted in adjusting the input parameters of the EMT model, which were the spherical porosity and the crack density, to minimize the impedance mismatch. Our case study involved two limestone formations of the Fort Worth Basin (the Marble Falls and Ellenburger Formations) and one shaly formation (the Barnett Shale). The results are promising — The EMT turns out to be a very useful tool to explain reservoir and geophysical data in terms of microstructural properties, in particular, for fractured reservoirs.
One-Hour Postload Hyperglycemia Is a Stronger Predictor of Type 2 Diabetes Than Impaired Fasting Glucose
Authors: Fiorentino Teresa Vanessa , Marini Maria Adelaide , Andreozzi Francesco , Arturi Franco , Succurro Elena , Perticone Maria , Sciacqua Angela , Hribal Marta Letizia , Perticone Francesco , Sesti Giorgio
Published: August 2015

Context:

Subjects with normal glucose tolerance (NGT) but 1-h postload glucose ≥ 155 mg/dL (NGT-1h-high) exhibit an intermediate cardiometabolic risk profile between individuals with NGT and impaired glucose tolerance (IGT).

Objective:

This study aimed to evaluate whether NGT-1h-high subjects have different cardiometabolic characteristics and an increased risk of type 2 diabetes compared with individuals with isolated impaired fasting glucose (IFG).

Setting, Design, and Patients:

A cross-sectional analysis was performed on 595 nondiabetic subjects who underwent an oral glucose tolerance test and an euglycemic hyperinsulinemic clamp in an ambulatory care setting. In addition, a longitudinal analysis was performed on 392 individuals, who were reexamined after a followup of 5.2 ± 0.9 y.

Main Outcome Measures:

Insulin sensitivity, beta-cell function, and risk of developing diabetes were measured.

Results:

Subjects with NGT-1h-high have a significant reduction of peripheral insulin sensitivity and beta-cell function, assessed by the disposition index, compared with either 1-h postload glucose < 155 mg/dL (NGT-1h-low) or IFG individuals, but not compared with IGT. Among the 392 subjects studied in the longitudinal analysis the incidence rate of type 2 diabetes over the follow-up period was 2.9, 16.7, 12.5, and 31.4% for subjects with NGT-1h-low, NGT-1h-high, IFG, and IGT, respectively. In a Cox proportional hazard regression analysis the risk of developing diabetes for NGT-1h-high subjects was 4.02 (95% confidence interval [CI] 1.06–15.26); an even higher risk (6.67; 95% CI, 2.09–21.24) was observed in subjects with IGT, but not in the isolated IFG group (1.91; 95% CI, 0.44–8.29).

Conclusions:

NGT-1h-high subjects exhibit a higher risk of developing diabetes than those with IFG or NGT-1h-low, likely due to decreased insulin sensitivity and beta-cell function.
Ode to the American Century: Ambivalent Americanism and the Founding of the Jobs with Justice Coalition
Authors: Larson Eric
Published: August 2015

This article examines the founding of Jobs with Justice, one of the most influential union-community coalitions of the post–New Deal order. More than two decades before the Occupy movement mobilized scorn against the “1 percent,” Jobs with Justice convened its coalitions by directing popular ire toward the “corporate robber barons.” While its anticorporate vision propelled its efforts to advance union struggle “beyond the ruins” of the Reagan era and early neoliberal reforms, it also overlapped with the populist contours of the ascendant New Right. By marshaling the moral weight of family, community, and Middle America, the coalition's vision of class and nation—through what the article terms its “ambivalent Americanism”—both animated and blurred the antagonism between workers and robber barons that the coalition so energetically developed.
Together We Shall Be Heard: Exploring the 1981 “Solidarity Day” Mass March
Authors: Minchin Timothy J.
Published: August 2015

This article provides the first detailed examination of the “Solidarity Day” march, which was held on September 19, 1981, in Washington, DC. Well funded and well organized, Solidarity Day was a mass protest against President Reagan's policies, particularly his cuts to social programs. Although the march was initiated by the AFL-CIO, participants came from 250 organizations, including 100 unions and a variety of civil rights, religious, and civic groups. Despite an impressive turnout of at least 260,000 people, Solidarity Day has received little scholarly attention. Drawing on unutilized archival records, this article argues that Solidarity Day was a protest that deserves more scholarly—and public—recognition. Solidarity Day showed that the AFL-CIO, which has often been viewed as bureaucratic and conservative, could mobilize mass street protests. It also boosted the morale of many union members, helped to strengthen the leadership of AFL-CIO president Lane Kirkland, and set the precedent for a different kind of AFL-CIO, one that was much more connected to its members. While Kirkland proved unable—or unwilling—to fundamentally reorient the AFL-CIO toward grassroots activism, these ideas were ultimately carried through by John Sweeney, a reformer who won the federation's presidency in 1995.
Cellular functions of Rab GTPases at a glance
Authors: Zhen Yan , Stenmark Harald
Published: August 2015

Rab GTPases control intracellular membrane traffic by recruiting specific effector proteins to restricted membranes in a GTP-dependent manner. In this Cell Science at a Glance and the accompanying poster, we highlight the regulation of Rab GTPases by proteins that control their membrane association and activation state, and provide an overview of the cellular processes that are regulated by Rab GTPases and their effectors, including protein sorting, vesicle motility and vesicle tethering. We also discuss the physiological importance of Rab GTPases and provide examples of diseases caused by their dysfunctions.
Induction of lateral lumens by disruption of a monoleucine-based basolateral sorting motif in betacellulin
Authors: Singh Bhuminder , Bogatcheva Galina , Starchenko Alina , Sinnaeve Justine , Lapierre Lynne A. , Williams Janice A. , Goldenring James R. , Coffey Robert J.
Published: August 2015

Directed delivery of EGF receptor (EGFR) ligands to the apical or basolateral surface is a crucial regulatory step in the initiation of EGFR signaling in polarized epithelial cells. Herein, we show that the EGFR ligand, betacellulin (BTC), is preferentially sorted to the basolateral surface of polarized MDCK cells. By sequential truncations and site-directed mutagenesis within the BTC cytoplasmic domain, combined with selective cell-surface biotinylation and immunofluorescence, we have uncovered a monoleucine-based basolateral sorting motif (EEXXXL:E156EMETL). Disruption of this sorting motif led to equivalent apical and basolateral localization of BTC. Unlike other EGFR ligands, BTC mistrafficking induced formation of lateral lumens in polarized MDCK cells, and this process was significantly attenuated by EGFR inhibition. Additionally, expression of a cancer-associated somatic BTC mutation (E156K) also led to BTC mistrafficking and induced lateral lumens in MDCK cells. Overexpression of BTC, especially mistrafficking forms, increased the growth of MDCK cells. These results uncover a unique role for BTC mistrafficking in promoting epithelial reorganization.
FoxO1 inhibits transcription and membrane trafficking of epithelial sodium channel (ENaC)
Authors: Shen Yachen , Xu Weifeng , You Hui , Su Dongming , Xing Jing , Li Min , Li Lei , Liang Xiubin
Published: August 2015

The epithelial sodium channel (ENaC), regulated by insulin, is of fundamental importance in the control of sodium reabsorption in the distal nephron. The potential role of Forkhead box O1 (FoxO1), one of insulin downstream molecules, in the regulation of ENaC remains to be investigated. Here, we found that the overexpression of ADA-FoxO1 (a constitutively active form of FoxO1) suppressed α-ENaC mRNA level and apical ENaC density in mouse cortical collecting duct (mCCD) cells. Conversely, FoxO1 knockdown increased apical membrane ENaC and Na+ transport under basal conditions. Insulin elevated α-ENaC expression and induced FoxO1 phosphorylation; however, the increase in α-ENaC and phosphorylated-FoxO1 expression observed with insulin treatment was blunted ∼60% in cells expressing ADA-FoxO1. Moreover, insulin induced the interaction between phosphorylated-FoxO1 with 14-3-3ε, which indicate that FoxO1 phosphorylation promotes ENaC membrane trafficking by binding with 14-3-3ε. FoxO1 also suppressed activity of the α-ENaC promoter and the putative FoxO1 target site located in the -500/-200nt region of α-ENaC promoter. These findings indicate that FoxO1 is a key negative regulatory factor in the insulin-dependent control of ENaC expression and forward trafficking in mCCD epithelia.
Polycomb RING1A/RING1B-dependent histone H2A monoubiquitylation at pericentromeric regions promotes S phase progression
Authors: Bravo Mónica , Nicolini Fabio , Starowicz Katarzyna , Barroso Sonia , Calés Carmela , Aguilera Andrés , Vidal Miguel
Published: August 2015

Functions of Polycomb products extend beyond their well known activity as transcriptional regulators to include genome duplication processes. Polycomb activities in DNA replication and DNA damage repair are unclear, particularly without induced replicative stress. We have used a cellular model of conditionally inactive Polycomb E3 ligases (RING1A and RING1B) that monoubiquitylate lysine 119 of histone H2A (H2AK119Ub) to examine DNA replication in unperturbed cells. We identify slow elongation and fork stalling during DNA replication, associated to the accumulation of mid and late S cells. Signs of replicative stress and colocalization of double strand breaks with chromocenters, the sites of coalesced pericentromeric heterocromatic (PCH) domains, were enriched in cells at mid S, the stage at which PCH is replicated. Altered replication was rescued by targeted monoubiquitylation of PCH through methyl-CpG binding domain protein 1. The acute senescence associated to the depletion of RING1 proteins, mediated by CDKN1A/p21 upregulation, could be uncoupled from a response to DNA damage. These findings link cell proliferation and Polycomb RING1A/B to S phase progression through a specific function in PCH replication.