bluuebunny/crossref_metadata_2025 huggingface dataset:
“You Never Know What’s Gonna Happen”
Authors: Romo Lynsey Kluever , Davis Christine , Fea Alyssa
Published: September 2014

Student-athletes are regularly faced with uncertainty, particularly at the highest levels of collegiate sports. Although it can result in both adverse and beneficial outcomes, little is known about the nature of this uncertainty. Thus, framed by Uncertainty Management Theory (UMT), this study relied on in-depth interviews of 17 student-athletes at an athletically-and-academically elite U.S. university to uncover what uncertainty scholar-athletes encountered and how they managed this ambiguity communicatively. The investigation found student-athletes experienced personal (e.g., injury), social (e.g., friends), and future (e.g., career) uncertainty. Participants managed this uncertainty through the use of communication strategies such as seeking social support, not disclosing their athlete status, or relying on prayer. While most participants perceived uncertainty as negative and sought to reduce it, some embraced it and learned to adapt. In addition to uncovering tangible uncertainty management strategies, the study recommends that college athletics departments implement several measures to address uncertainty.
Trends in the Management of Achilles Tendon Ruptures in the United States Medicare Population, 2005-2011
Authors: Erickson Brandon J. , Cvetanovich Gregory L. , Nwachukwu Ben U. , Villarroel Leonardo D. , Lin Johnny L. , Bach Bernard R. , McCormick Frank M.
Published: September 2014

Background:

Achilles tendon ruptures are one of the most commonly treated injuries by orthopaedic surgeons and general practitioners. Achilles tendon ruptures have classically been thought to affect the middle-aged “weekend warrior” participating in basketball, volleyball, soccer, or any other ground sport that requires speed and agility; however, with a more active elderly population, these tears are becoming more common in older patients.

Purpose:

To report trends in nonoperative and operative treatment of Achilles tendon tears in the United States from 2005 to 2011 in patients registered with a large Medicare database.

Study Design:

Descriptive epidemiological study.

Methods:

Patients who underwent nonoperative and operative treatment of Achilles tendon ruptures by either primary repair or primary repair with graft (International Classification of Diseases 9 [ICD-9] diagnosis code 727.67, Current Procedural Terminology [CPT] codes 27650 and 27652) for the years 2005 to 2011 were identified using the PearlDiver Medicare Database. Demographic and utilization data available within the database were extracted for patients who underwent nonoperative as well as operative treatment for Achilles tendon ruptures. Statistical analysis involved Student t tests, chi-square tests, and linear regression analyses, with statistical significance set at P < .05.

Results:

From 2005 to 2011, there were a total of 14,127 Achilles tendon ruptures. Of these, 9814 were managed nonoperatively, 3531 were treated with primary repair, and 782 were treated with primary repair with graft. The incidence of Achilles tendon increased from 0.67 per 10,000 in 2005 to 1.08 per 10,000 in 2011 ( P < .01). There was no significant difference in the number of Achilles ruptures between males (6636) and females (7582) ( P > .05). There was an increase in the overall number of Achilles tendon ruptures over time (1689 in 2005 compared with 2788 in 2011; P < .001) but no difference in the percentage of Achilles ruptures treated operatively ( P > .05). Older patients were more likely to be treated nonoperatively ( P < .05). No differences in operative versus nonoperative treatment were seen between yearly quarter ( P > .05), sex ( P > .05), or region ( P > .05).

Conclusion:

The incidence of Achilles tendon ruptures is increasing with time, but the trend in operative and nonoperative treatment has not changed between 2005 and 2011. Older patients, especially those older than 85 years, are more likely to be treated nonoperatively. No differences in treatment patterns were seen based on sex, region, or yearly quarter.
Baseline Neurocognitive Performance in Professional Lacrosse Athletes
Authors: Plancher Kevin D. , Brooks-James Ariana , Nissen Carl W. , Diduch B. Kent , Petterson Stephanie C.
Published: September 2014

Background:

Concussions have become a major public health concern for both youth and professional athletes. The long-term consequences of concussion can be debilitating or even life threatening. To reduce these concerns, baseline neurocognitive performance can aid decision making in postconcussion recovery and return to play for athletes sustaining concussions. To date, these data are not available for lacrosse athletes.

Purpose:

To present baseline neurocognitive performance for Major League Lacrosse (MLL) players and to determine differences between athletes with and without a history of concussion.

Study Design:

Cross-sectional study; Level of evidence, 3.

Methods:

A retrospective review was conducted of Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) scores from MLL players who completed baseline testing from June 2010 to June 2011. Inclusion required a valid baseline test and no history of concussion in the 3 months prior to testing. Means ± standard deviations were computed for all demographic variables and ImPACT composite scores including visual and verbal memory, reaction time, and visual motor processing speed. Independent-samples t tests were used to determine differences between athletes with and without a history of concussion.

Results:

Valid baseline ImPACT testing was available for 235 MLL athletes (mean age, 25.1 ± 3.0 years). Forty percent of MLL athletes (n = 94) reported a history of concussion, with 14% of those (n = 13) reporting a history of 3 or more previous concussions. There were no differences on any demographic variables between MLL athletes with and without a history of concussion. MLL athletes with a history of concussion had lower ImPACT composite scores than those without a history of concussion, although only the verbal memory composite was found to be statistically significant (MLL with concussion, 83.2 ± 10.8 vs MLL without concussion, 86.9 ± 9.5; P = .007).

Conclusion:

This study establishes baseline ImPACT scores for MLL and demonstrates that athletes with a history of concussion have poorer neurocognitive performance compared with MLL athletes without a history of concussion.

Clinical Relevance:

These data can serve as normative values for subsequent testing following concussion to assess neurocognitive recovery.
The Socialization of Music Teachers
Authors: Isbell Daniel S.
Published: September 2014

Many institutions provide an undergraduate experience that can lead to professional certification to teach music. Each institution provides a unique socialization experience in the music teaching profession. In this literature review, studies are presented that provide information on the decision to become a music teacher, the early socialization of music teachers, the culture within schools of music, and models of music teacher identity.
The Challenges of Imitation for Children with Autism Spectrum Disorders with Implications for General Music Education
Authors: Scott Sheila
Published: September 2014

With emphasis on inclusive education, many music teachers interact with children on the autism spectrum within regular classroom settings. Many of these teachers rely on rote learning to teach a variety of musical skills. This creates difficulties for children on the autism spectrum who respond differently to imitation than their typically developing peers. By understanding this phenomenon, music teachers are better prepared to interact with children on the autism spectrum. To this end, learning through imitation as a foundational strategy for teachers in primary music education is summarized here. This is followed by a review of research findings to build a profile for how children on the autism spectrum respond to imitation. Implications for music teaching explains how strategies currently used by music teachers support interventions suggested in psychological literature and how these strategies may be adapted to better meet the needs of students on the autism spectrum.
Recent developments in myelodysplastic syndromes
Authors: Bejar Rafael , Steensma David P.
Published: September 2014

Once thought to be rare disorders, the myelodysplastic syndromes (MDS) are now recognized as among the most common hematological neoplasms, probably affecting >30 000 patients per year in the United States. US regulatory approval of azacitidine, decitabine, and lenalidomide between 2004 and 2006 seemed to herald a new era in the development of disease-modifying therapies for MDS, but there have been no further drug approvals for MDS indications in the United States in the last 8 years. The available drugs are not curative, and few of the compounds that are currently in development are likely to be approved in the near future. As a result, MDS diagnoses continue to place a heavy burden on both patients and health care systems. Incomplete understanding of disease pathology, the inherent biological complexity of MDS, and the presence of comorbid conditions and poor performance status in the typical older patient with MDS have been major impediments to development of effective novel therapies. Here we discuss new insights from genomic discoveries that are illuminating MDS pathogenesis, increasing diagnostic accuracy, and refining prognostic assessment, and which will one day contribute to more effective treatments and improved patient outcomes.
Marrow failure: a window into ribosome biology
Authors: Ruggero Davide , Shimamura Akiko
Published: September 2014

Diamond-Blackfan anemia, Shwachman-Diamond syndrome, and dyskeratosis congenita are inherited syndromes characterized by marrow failure, congenital anomalies, and cancer predisposition. Genetic and molecular studies have uncovered distinct abnormalities in ribosome biogenesis underlying each of these 3 disorders. How defects in ribosomes, the essential organelles required for protein biosynthesis in all cells, cause tissue-specific abnormalities in human disease remains a question of fundamental scientific and medical importance. Here we review the overlapping and distinct clinical features of these 3 syndromes and discuss current knowledge regarding the ribosomal pathways disrupted in each of these disorders. We also explore the increasing complexity of ribosome biology and how this informs our understanding of developmental biology and human disease.
An autologous leukemia cell vaccine prevents murine acute leukemia relapse after cytarabine treatment
Authors: Gibbins John D. , Ancelet Lindsay R. , Weinkove Robert , Compton Benjamin J. , Painter Gavin F. , Petersen Troels R. , Hermans Ian F.
Published: September 2014

Key Points

A cellular vaccine incorporating the glycolipid α-galactosylceramide prevents relapse of acute leukemia following cytarabine chemotherapy.
Dissecting the genetics of chronic mucus hypersecretion in smokers with and without COPD
Authors: Dijkstra Akkelies E. , Boezen H. Marike , van den Berge Maarten , Vonk Judith M. , Hiemstra Pieter S. , Barr R. Graham , Burkart Kirsten M. , Manichaikul Ani , Pottinger Tess D. , Silverman Edward K. , Cho Michael H. , Crapo James D. , Beaty Terri H. , Bakke Per , Gulsvik Amund , Lomas David A. , Bossé Yohan , Nickle David C. , Paré Peter D. , de Koning Harry J. , Lammers Jan-Willem , Zanen Pieter , Smolonska Joanna , Wijmenga Ciska , Brandsma Corry-Anke , Groen Harry J.M. , Postma Dirkje S. ,   the LifeLines Cohort Study group
Published: September 2014

Smoking is a notorious risk factor for chronic mucus hypersecretion (CMH). CMH frequently occurs in chronic obstructive pulmonary disease (COPD). The question arises whether the same single-nucleotide polymorphisms (SNPs) are related to CMH in smokers with and without COPD.

We performed two genome-wide association studies of CMH under an additive genetic model in male heavy smokers (≥20 pack-years) with COPD (n=849, 39.9% CMH) and without COPD (n=1348, 25.4% CMH), followed by replication and meta-analysis in comparable populations, and assessment of the functional relevance of significantly associated SNPs.

Genome-wide association analysis of CMH in COPD and non-COPD subjects yielded no genome-wide significance after replication. In COPD, our top SNP (rs10461985, p=5.43×10−5) was located in theGDNF-AS1gene that is functionally associated with theGDNFgene. Expression ofGDNFin bronchial biopsies of COPD patients was significantly associated with CMH (p=0.007). In non-COPD subjects, four SNPs had a p-value <10−5in the meta-analysis, including a SNP (rs4863687) in theMAML3gene, the T-allele showing modest association with CMH (p=7.57×10−6, OR 1.48) and with significantly increasedMAML3expression in lung tissue (p=2.59×10−12).

Our data suggest the potential for differential genetic backgrounds of CMH in individuals with and without COPD.
What are the environmental impacts of property rights regimes in forests, fisheries and rangelands? a systematic review protocol
Authors: Ojanen Maria , Miller Daniel C , Zhou Wen , Mshale Baruani , Mwangi Esther , Petrokofsky Gillian
Published: September 2014

Background

Property rights to natural resources comprise a major policy instrument for those seeking to advance sustainable resource use and conservation. Despite decades of policy experimentation and empirical research, however, systematic understanding of the influence of different property rights regimes on resource and environmental outcomes remains elusive. A large, diverse, and rapidly growing body of literature investigates the links between property regimes and environmental outcomes, but has not synthesized theoretical and policy insights within specific resource systems and especially across resource systems. Here we provide a protocol for conducting a systematic review that will gather empirical evidence over the past two decades on this topic. We will ask the following questions: a) What are the environmental impacts of different property regimes in forests, fisheries, and rangelands? b) Which property regimes are associated with positive, negative or neutral environmental outcomes? c) How do those environmental outcomes compare within and across resource systems and regions?

Methods

We will assess current knowledge of the environmental impacts of property rights regimes in three resource systems in developing countries: forests, fisheries and rangelands. These resource systems represent differing levels of resource mobility and variability and capture much of the range of ecosystem types found across the globe. The review will use a bundle of rights approach to assess the impacts of three main property regimes—state, private, and community—as well as mixed property regimes that involve some combination of these three. Assessment of the impacts of property rights regimes across a range of different resource systems and ecosystem types will enable exploration of commonalities and differences across these systems. Our analysis will emphasize major insights while highlighting important gaps in current research.
Digital mammographic density and breast cancer risk: a case–control study of six alternative density assessment methods
Authors: Eng Amanda , Gallant Zoe , Shepherd John , McCormack Valerie , Li Jingmei , Dowsett Mitch , Vinnicombe Sarah , Allen Steve , dos-Santos-Silva Isabel
Published: September 2014

Introduction

Mammographic density is a strong breast cancer risk factor and a major determinant of screening sensitivity. However, there is currently no validated estimation method for full-field digital mammography (FFDM).

Methods

The performance of three area-based approaches (BI-RADS, the semi-automated Cumulus, and the fully-automated ImageJ-based approach) and three fully-automated volumetric methods (Volpara, Quantra and single energy x-ray absorptiometry (SXA)) were assessed in 3168 FFDM images from 414 cases and 685 controls. Linear regression models were used to assess associations between breast cancer risk factors and density among controls, and logistic regression models to assess density-breast cancer risk associations, adjusting for age, body mass index (BMI) and reproductive variables.

Results

Quantra and the ImageJ-based approach failed to produce readings for 4% and 11% of the participants. All six density assessment methods showed that percent density (PD) was inversely associated with age, BMI, being parous and postmenopausal at mammography. PD was positively associated with breast cancer for all methods, but with the increase in risk per standard deviation increment in PD being highest for Volpara (1.83; 95% CI: 1.51 to 2.21) and Cumulus (1.58; 1.33 to 1.88) and lower for the ImageJ-based method (1.45; 1.21 to 1.74), Quantra (1.40; 1.19 to 1.66) and SXA (1.37; 1.16 to 1.63). Women in the top PD quintile (or BI-RADS 4) had 8.26 (4.28 to 15.96), 3.94 (2.26 to 6.86), 3.38 (2.00 to 5.72), 2.99 (1.76 to 5.09), 2.55 (1.46 to 4.43) and 2.96 (0.50 to 17.5) times the risk of those in the bottom one (or BI-RADS 1), respectively, for Volpara, Quantra, Cumulus, SXA, ImageJ-based method, and BI-RADS (P for trend <0.0001 for all). The ImageJ-based method had a slightly higher ability to discriminate between cases and controls (area under the curve (AUC) for PD = 0.68, P = 0.05), and Quantra slightly lower (AUC = 0.63; P = 0.06), than Cumulus (AUC = 0.65).

Conclusions

Fully-automated methods are valid alternatives to the labour-intensive "gold standard" Cumulus for quantifying density in FFDM. The choice of a particular method will depend on the aims and setting but the same approach will be required for longitudinal density assessments.
Erratum to: Cardiovascular medication burden in dementia disorders: a nationwide study of 19, 743 dementia patients in the Swedish Dementia Registry
Authors: Cermakova Pavla , Fereshtehnejad Seyed-Mohammad , Johnell Kristina , Winblad Bengt , Eriksdotter Maria , Religa Dorota
Published: September 2014

No abstract.
Task context-aware e-mail platform for collaborative tasks
Authors: Katsumata Masashi
Published: September 2014

E-mail communication has become an essential part of collaborative tasks in enterprises. However, when conventional e-mail applications are used for collaborative tasks, problems with task-related resources management arise. In this paper, we present a task context-aware e-mail platform that helps users to send e-mails quickly and efficiently. This platform also automatically extracts data from reply e-mail messages. It enables users to automatically classify task-related information and user support services using a task context model. The task context model is built based on ontology as a semantic representation of the associations between task and task-related e-mail processes. This paper describes the design and implementation of this system on the basis of the task context model. To verify the efficacy of the prototype system, we conducted experiments that demonstrate the systems effective task awareness and user support services.
N-Substituted indole carbohydrazide derivatives: synthesis and evaluation of their antiplatelet aggregation activity
Authors: Mirfazli Seyedeh Sara , Kobarfard Farzad , Firoozpour Loghman , Asadipour Ali , Esfahanizadeh Marjan , Tabib Kimia , Shafiee Abbas , Foroumadi Alireza
Published: September 2014

Background

Platelet aggregation is one of the most important factors in the development of thrombotic disorders which plays a central role in thrombosis (clot formation). Prophylaxis and treatment of arterial thrombosis are achieved using anti-platelet drugs. In this study, a series of novel substituted indole carbohydrazide was synthesized and evaluated for anti-platelet aggregation activity induced by adenosine diphosphate (ADP), arachidonic acid (AA) and collagen.

Methods

Our synthetic route started from methyl 1H-indole-3-carboxylate (1) and ethyl 1H-indole-2-carboxylate (4) which were reacted with hydrazine monohydrate 99%. The aldol condensation of the later compound with aromatic aldehydes led to the formation of the title compounds. Sixteen indole acylhydrazone derivatives, 3d-m and 6d-i were tested for anti-platelet aggregation activity induced by adenosine diphosphate (ADP), arachidonic acid (AA) and collagen.

Results

Among the synthesized compounds, 6g and 6h with 100% inhibition, proved to be the most potent derivatives of the 2-substituted indole on platelet aggregation induced by AA and collagen, respectively. In 3-substituted indole 3m with 100% inhibition and 3f and 3i caused 97% inhibition on platelet aggregation induced by collagen and AA, respectively.

Conclusion

In this study, compounds 6g, 6h, 3m, 3f and 3i showed better inhibition on platelet aggregation induced by AA and collagen among the title compounds. Quantitative structure–activity relationship (QSAR) analysis between the structural parameters of the investigated derivatives and their antiplatelet aggregation activity was performed with various molecular descriptors but, analysis of the physicochemical parameters doesn't show a significant correlation between the observed activities and general molecular parameters of the synthesized derivatives. Although, due to the existence of several receptors on the platelets surface which are responsible for controlling the platelet aggregation, the investigated compounds in the present study may exert their activities through binding to more than one of these receptors and therefore no straight forward SAR could be obtained for them.
Can computer simulators accurately represent the pathophysiology of individual COPD patients?
Authors: Wang Wenfei , Das Anup , Ali Tayyba , Cole Oanna , Chikhani Marc , Haque Mainul , Hardman Jonathan G , Bates Declan G
Published: September 2014

Background

Computer simulation models could play a key role in developing novel therapeutic strategies for patients with chronic obstructive pulmonary disease (COPD) if they can be shown to accurately represent the pathophysiological characteristics of individual patients.

Methods

We evaluated the capability of a computational simulator to reproduce the heterogeneous effects of COPD on alveolar mechanics as captured in a number of different patient datasets.

Results

Our results show that accurately representing the pathophysiology of individual COPD patients necessitates the use of simulation models with large numbers (up to 200) of compartments for gas exchange. The tuning of such complex simulation models ‘by hand’ to match patient data is not feasible, and thus we present an automated approach based on the use of global optimization algorithms and high-performance computing. Using this approach, we are able to achieve extremely close matches between the simulator and a range of patient data including PaO2, PaCO2, pulmonary deadspace fraction, pulmonary shunt fraction, and ventilation/perfusion (V̇/Q) curves. Using the simulator, we computed combinations of ventilator settings that optimally manage the trade-off between ensuring adequate gas exchange and minimizing the risk of ventilator-associated lung injury for an individual COPD patient.

Conclusions

Our results significantly strengthen the credibility of computer simulation models as research tools for the development of novel management protocols in COPD and other pulmonary disease states.
Brain function in iNOS knock out or iNOS inhibited (l-NIL) mice under endotoxic shock
Authors: Schweighöfer Hanna , Rummel Christoph , Mayer Konstantin , Rosengarten Bernhard
Published: September 2014

Background

Microcirculatory dysfunction due to excessive nitric oxide production by the inducible nitric oxide synthase (iNOS) is often seen as a motor of sepsis-related organ dysfunction. Thus, blocking iNOS may improve organ function. Here, we investigated neuronal functional integrity in iNOS knock out (−/−) or l-NIL-treated wild-type (wt) animals in an endotoxic shock model.

Methods

Four groups of each 10 male mice (28 to 32 g) were studied: wt, wt + lipopolysaccharide (LPS) (5 mg/kg body weight i.v.), iNOS(−/−) + LPS, wt + LPS + l-NIL (5 mg/kg body weight i.p. 30 min before LPS). Electric forepaw stimulation was performed before LPS/vehicle and then at fixed time points repeatedly up to 4.5 h. N1-P1 potential amplitudes as well as P1 latencies were calculated from EEG recordings. Additionally, cerebral blood flow was registered using laser Doppler. Blood gas parameters, mean arterial blood pressure, and glucose and lactate levels were obtained at the beginning and the end of experiments. Moreover, plasma IL-6, IL-10, CXCL-5, ICAM-1, neuron-specific enolase (NSE), and nitrate/nitrite levels were determined.

Results

Decline in blood pressure, occurrence of cerebral hyperemia, acidosis, and increase in lactate levels were prevented in both iNOS-blocked groups. SEP amplitudes and NSE levels remained in the range of controls. Effects were related to a blocked nitrate/nitrite level increase whereas IL-6, ICAM-1, and IL-10 were similarly induced in all sepsis groups. Only CXCL-5 induction was lower in both iNOS-blocked groups.

Conclusions

Despite similar hyper-inflammatory responses, iNOS inhibition strategies appeared neurofunctionally protective possibly by stabilizing macro- as well as microcirculation. Overall, our data support modern sepsis guidelines recommending early prevention of microcirculatory failure.
The Absence of GH Signaling Affects the Susceptibility to High-Fat Diet-Induced Hypothalamic Inflammation in Male Mice
Authors: Baquedano Eva , Ruiz-Lopez Ana M. , Sustarsic Elahu G. , Herpy James , List Edward O. , Chowen Julie A. , Frago Laura M. , Kopchick John J. , Argente Jesús
Published: September 2014

GH is important in metabolic control, and mice with disruption of the gene encoding the GH receptor (GHR) and GH binding protein (GHR−/− mice) are dwarf with low serum IGF-1 and insulin levels, high GH levels, and increased longevity, despite their obesity and altered lipid and metabolic profiles. Secondary complications of high-fat diet (HFD)-induced obesity are reported to be associated with hypothalamic inflammation and gliosis. Because GH and IGF-1 can modulate inflammatory processes, our objective was to evaluate the effect of HFD on hypothalamic inflammation/gliosis in the absence of GH signaling and determine how this correlates with changes in systemic metabolism. On normal chow, GHR−/− mice had a higher percentage of fat mass and increased circulating nonesterified free fatty acids levels compared with wild type (WT), and this was associated with increased hypothalamic TNF-α and phospho-JNK levels. After 7 weeks on a HFD, both WT and GHR−/− mice had increased weight gain, with GHR−/− mice having a greater rise in their percentage of body fat. In WT mice, HFD-induced weight gain was associated with increased hypothalamic levels of phospho-JNK and the microglial marker Iba-1 (ionized calcium-binding adapter molecule 1) but decreased cytokine production. Moreover, in GHR−/− mice, the HFD decreased hypothalamic inflammatory markers to WT levels with no indication of gliosis. Thus, the GH/IGF-1 axis is important in determining not only adipose tissue accrual but also the inflammatory response to HFD. However, how hypothalamic inflammation/gliosis is defined will determine whether it can be considered a common feature of HFD-induced obesity.
The role of specific PP2A complexes in the dephosphorylation of γ-H2AX
Authors: Chen Liping , Lai Yandong , Zhu Xiaonian , Ma Lu , Bai Qing , Vazquez Iria , Xiao Yongmei , Liu Caixia , Li Daochuan , Gao Chen , He Zhini , Zeng Xiaowen , Xing Xiumei , Zhang Zhengbao , Li Jie , Zhang Bo , Wang Qing , Sablina Anna A. , Hahn William C. , Chen Wen
Published: September 2014

The formation of γ-H2AX in response to DNA double-strand breaks (DSBs) marks damaged regions for recognition and repair. Dephosphorylation of γ-H2AX is required for cells to resume cell cycle. However, the mechanisms of γ-H2AX dephosphorylation remain underexplored. Using a loss of function screen, we identified PP2A specific subunits, B56ε and α4, involved in elimination of γ-H2AX during DSBs repair process. In the early stage of DSBs repair the inhibitory subunit α4 binds and renders PP2Ac inactive. As DNA is repaired, α4 releases PP2Ac and triggers the assembly of an active PP2A B56ε holoenzyme. PP2A B56ε, which translocates from cytoplasm into the nucleus upon DNA damage, is responsible for a direct dephosphorylation of γ-H2AX. Suppression of both B56ε and α4 leads to persistence of γ-H2AX and defects in DNA repair. In contrast, the rapid clearance of γ-H2AX in human hepatocarcinoma is correlated with the over-expression of both B56ε and α4. Functional analysis reveals that PP2A B56ε coordinates with α4 in accelerating HR repair upon DNA damage. Together, these observations gain insight of how γ-H2AX dephosphorylation is kinetically regulated during DNA repair response.
NoFold: RNA structure clustering without folding or alignment
Authors: Middleton Sarah A. , Kim Junhyong
Published: September 2014

Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function—for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures.
circBase: a database for circular RNAs
Authors: Glažar Petar , Papavasileiou Panagiotis , Rajewsky Nikolaus
Published: September 2014

Recently, several laboratories have reported thousands of circular RNAs (circRNAs) in animals. Numerous circRNAs are highly stable and have specific spatiotemporal expression patterns. Even though a function for circRNAs is unknown, these features make circRNAs an interesting class of RNAs as possible biomarkers and for further research. We developed a database and website, “circBase,” where merged and unified data sets of circRNAs and the evidence supporting their expression can be accessed, downloaded, and browsed within the genomic context. circBase also provides scripts to identify known and novel circRNAs in sequencing data. The database is freely accessible through the web server at http://www.circbase.org/.
Information Buried in Information Technology Service Contracts: Extracting Process–Performance Interrelationships
Authors: Deokar Amit V. , Sen Sagnika
Published: September 2014

Service-level agreements (SLAs) for multiservice information technology (IT) outsourcing contracts contain voluminous text that often makes it difficult for the customer organization to appreciate the complex interplay of various process elements (e.g., activities, resources, events) with key performance indicators (KPIs). We employ an ontology-based information extraction approach combined with a rule base in developing a decision support framework that derives analytic insights about hidden process–performance relationships from SLAs. The framework is instantiated in a prototype system, SLA-Miner. The system aids in decision making by encapsulating formal and semiformal domain knowledge through an IT service ontology and associated rule base. Advantages of the system include compact knowledge representation, maintainability, and adaptability to changing business environment. Sets of real life SLAs are analyzed to demonstrate the feasibility of SLA-Miner. Results demonstrate the utility of the decision support framework to empower service analysts/managers in the customer organization in identifying KPI interrelationships as well as deficiencies and potential conflicts in the current contract. This knowledge is useful to both the service provider and customer organizations in contract formulation and process management, and incentive decisions.
Do Consumers Perceive Money-Back Guarantees as Believable? The Effects of Money-Back Guarantee Generosity, Store Name Familiarity, and Perceived Price
Authors: Jeng Shih-Ping , Huang Li-Shia , Chou Yu-Jen , Teng Ching-I
Published: September 2014

A money-back guarantee (MBG) is a service guarantee offered by a retailer. This research examined how MBG generosity, store name familiarity, and consumer perception of price interacted to influence MBG believability (the extent to which a consumer believes the MBG) and consumer store patronage. The results show that MBG generosity positively affected consumer patronage intentions by increasing MBG believability. When the perceived price was low, MBG generosity positively affected MBG believability for both well-known and lesser-known stores. When the perceived price was high, MBG generosity positively affected MBG believability only for well-known stores.
Thromboelastography Is a Suboptimal Test for Determination of the Underlying Cause of Bleeding Associated With Cardiopulmonary Bypass and May Not Predict a Hypercoagulable State
Authors: Welsh Kerry J. , Padilla Angelica , Dasgupta Amitava , Nguyen Andy N. D. , Wahed Amer
Published: September 2014

Objectives:

Patients undergoing cardiac surgery with cardiopulmonary bypass (CPB) are at risk of bleeding. The goal of this investigation was to compare thromboelastography (TEG) with standard coagulation tests (prothrombin time [PT], partial thromboplastin time [PTT], fibrinogen, and D-dimer) in patients with active bleeding.

Methods:

A retrospective study of patients who underwent cardiac surgery with CPB was performed. A second analysis was performed to determine if a shortened TEG R time is associated with thrombosis.

Results:

Paired TEG and standard coagulation tests were available from 21 bleeding patients; of the 15 patients with normal TEG values and three with a shortened R time, all had abnormalities of standard coagulation tests. Eighteen of 67 patients who underwent surgery with CPB had an episode of postoperative bleeding. The TEG R time and coagulation index, PT, and PTT collected after CPB were associated with postoperative bleeding in the univariate analysis, but only PT was independently associated with postoperative bleeding in the multivariate analysis. In the second analysis, three of 38 patients with a normal TEG and four of 43 patients with a shortened R time had a thrombotic event during hospitalization (P = 1.00).

Conclusions:

TEG had limited utility in identifying the underlying cause of bleeding and was not predictive of postoperative bleeding associated with cardiac surgery compared with conventional coagulation tests. A shortened TEG R time may not represent a hypercoagulable state.
Effects of rotation period on biomass production and atmospheric CO2 emissions from broadleaved stands growing on abandoned farmland
Authors: Eriksson Erik , Johansson Tord
Published: September 2014

The growth rates and carbon stocks of unthinned young and mature stands of broadleaved trees growing on abandoned farmland were determined to assess whether their management regimes should involve short (15-year) or long (45-year) rotations to maximize biomass production and reductions of CO emissions. Dry mass production and mean annual increment (MAI) were calculated for 28 young stands and 65 mature stands of European aspen (Populus tremula L.), common alder (Alnus glutinosa (L.) Gaertn.), grey alder (Alnus incana (L.) Moench.), silver birch (Betula pendula Roth) and downy birch (Betula pubescens Ehrh.) ranging in latitude from 57Â° to 63Â° N in Sweden. The potential for using biomass from the stands to replace coal as a fuel and to store carbon was then evaluated both in short and long rotation scenarios. The results indicate that long rotations are beneficial if the objective is to maximize the average carbon stock in biomass. If, on the other hand, the intention is to optimize reductions in atmospheric CO emissions, rotations should be short for aspen, silver birch and grey alder stands. For downy birch and common alder, the MAI was higher for the mature stands than the young stands, indicating that in these species the mature stands are superior for both storing carbon and replacing fossil fuel. Stands of broadleaved trees grown to produce biofuel on abandoned farmland should be established on fertile soils to promote high MAI. If the MAI is low, the rotation period should be long to maximize the average carbon stock.22
Site quality curves for birch stands in north-western Spain
Authors: Diéguez-Aranda Ulises , Grandas-Arias José , Álvarez-González Juan , Gadow Klaus
Published: September 2014

A model for predicting the height growth of even-aged, birch (Betula pubescens Ehrh.) dominated stands in Galicia (north-western Spain) was developed. Data from stem analysis of 214 trees were used for model construction. Two dynamic site equations derived with the generalized algebraic difference approach (GADA) were tested, which combine compatible site index and height models in one common equation. Both equations are base-age invariant and directly estimate height and site index from any height and age. The fittings were done in one stage using the base-age-invariant dummy variables method. A second-order continuous-time autoregressive error structure was used to correct the inherent autocorrelation of the longitudinal data used in this study. Cieszewskiâs model best described the data. This model is therefore recommended for height growth prediction and site classification of birch stands in Galicia.
Bayesian estimation of diameter distribution during harvesting
Authors: Uusitalo Jori , Puustelli Anne , Kivinen Veli-Pekka , Nummi Tapio , Sinha Bikas
Published: September 2014

This research aims to combine two different data sets with Bayesian statistics in order to predict the diameter distribution of trees at harvest. The parameters of prior distribution are derived from the forest management plans supplemented by additional ocular information. We derive the parameters for the sample data from the first trees harvested, and then create the posterior distribution within the Bayesian framework. We apply the standard normal distribution to construct diameter (dbh) distributions, although many other theoretical distributions have been proved better with dbh data available. The methodology developed is then tested on nine mature spruce (Picea abies) dominated stands, on which the normal distribution seems to work well in mature spruce stands. The tests indicate that prediction of diameter distribution for the whole stand based on the first trees harvested is not wise, since it tends to give inaccurate predictions. Combining the first trees harvested with prior information seems to increase the reliability of predictions.
Empirical errors of small area estimates from the multisource National Forest Inventory in Eastern Finland
Authors: Katila Matti
Published: September 2014

The precision of multisource national forest inventory (MS-NFI) estimators and simple synthetic estimators based on NFI field data only was assessed employing an independent inventory data set of several small areas in Eastern Finland. There were seven test units of size 100 km and three test units of size 1 km for which a systematic field sampling was carried out. The âimprovedâ MS-NFI method yielded the most precise estimates for mean volume and mean volume of pine and spruce: relative root mean square errors (RMSE) were 5%, 12% and 15% for 100 km test units and 13%, 27% and 40% for 1 km test units respectively. The stratified MS-NFI method was best for broad-leaved volume estimation. Synthetic estimation based on the NFI9 field plots post-stratified with coarse scale forest variable maps from NFI8 resulted in RMSEs comparable to those of the ordinary MS-NFI in areas of 100 km for mean volume and mean volume of pine and spruce. The amount of variation between the field inventory estimates for the test units explained by the MS-NFI estimators remained the same or increased when the size of the area increased from of 1 km to 100 km and up to 2000 km. The validation of the largest areas was made against the NFI9 field inventory estimates for groups of municipalities in the study area.22*22*2222
One-pot, three-component synthesis of pyranocoumarins containing an aroyl group
Authors: Khodabakhshi Saeed , Jafari Fariba , Marahel Farzaneh , Baghernejad Mojtaba
Published: September 2014

An expeditious method to prepare pyranocoumarins containing an aroyl group by the three-component reaction of 4-hydroxycoumarin with arylglyoxals and malononitrile is described. The reaction is efficiently catalyzed by Mohr’s salt, and the products were obtained in good to excellent yields with high purity. The method is simple, inexpensive, and environmentally friendly.
Exogenous Treatment and Endogenous Factors: Vanishing of Omitted Variable Bias on the Interaction Term
Authors: Nizalova Olena Y. , Murtazashvili Irina
Published: September 2014

Whether interested in the differential impact of a particular factor in various institutional settings or in the heterogeneous effect of policy or random experiment, the empirical researcher confronts a problem if the factor of interest is correlated with an omitted variable. This paper presents the circumstances under which it is possible to arrive at a consistent estimate of the mentioned effect. We find that if the source of heterogeneity and omitted variable are jointly independent of policy or treatment, then the OLS estimate on the interaction term between the treatment and endogenous factor turns out to be consistent.
Fluorescence lifetime imaging with near-infrared dyes
Authors: Becker Wolfgang , Shcheslavskiy Vladislav
Published: September 2014

Near-infrared (NIR) dyes are used as fluorescence markers in small animal imaging and in diffuse optical tomography. In these applications it is important to know whether the dyes bind to proteins or to other tissue constituents, and whether their fluorescence lifetimes depend on the targets they bind to. Unfortunately, neither the optical beam paths nor the detectors of commonly used in confocal and multiphoton laser scanning microscopes (LSMs) directly allow for excitation and detection of NIR fluorescence. This paper presents three ways of adapting existing LSMs with time-correlated single photon counting (TCSPC) fluorescence lifetime imaging (FLIM) systems for NIR FLIM: 1) confocal systems with wideband beamsplitters and diode laser excitation, 2) confocal systems with wideband beamsplitters and one-photon excitation by titanium-sapphire lasers, and 3) two-photon systems with optical parametric oscillator (OPO) excitation and non-descanned detection. A number of NIR dyes are tested in biological tissue. All of them show clear lifetime changes depending on the tissue structures they are bound to. We therefore believe that NIR FLIM can deliver supplementary information about the tissue composition and on local biochemical parameters.
Research on Modeling of Propeller in a Turboprop Engine
Authors: Huang Jiaqin , Huang Xianghua , Zhang Tianhong
Published: September 2014

In the simulation of engine-propeller integrated control system for a turboprop aircraft, a real-time propeller model with high-accuracy is required. A study is conducted to compare the real-time and precision performance of propeller models based on strip theory and lifting surface theory. The emphasis in modeling by strip theory is focused on three points as follows: First, FLUENT is adopted to calculate the lift and drag coefficients of the propeller. Next, a method to calculate the induced velocity which occurs in the ground rig test is presented. Finally, an approximate method is proposed to obtain the downwash angle of the propeller when the conventional algorithm has no solution. An advanced approximation of the velocities induced by helical horseshoe vortices is applied in the model based on lifting surface theory. This approximate method will reduce computing time and remain good accuracy. Comparison between the two modeling techniques shows that the model based on strip theory which owns more advantage on both real-time and high-accuracy can meet the requirement.
Efficient CRISPR/Cas9 Plasmids for Rapid and Versatile Genome Editing inDrosophila
Authors: Gokcezade Joseph , Sienski Grzegorz , Duchek Peter
Published: September 2014

The CRISPR-associated RNA-guided nuclease Cas9 has emerged as a powerful tool for genome engineering in a variety of organisms. To achieve efficient gene targeting rates in Drosophila, current approaches require either injection of in vitro transcribed RNAs or injection into transgenic Cas9-expressing embryos. We report a simple and versatile alternative method for CRISPR-mediated genome editing in Drosophila using bicistronic Cas9/sgRNA expression vectors. Gene targeting with this single-plasmid injection approach is as efficient as in transgenic nanos-Cas9 embryos and allows the isolation of targeted knock-out and knock-in alleles by molecular screening within 2 months. Our strategy is independent of genetic background and does not require prior establishment of transgenic flies.
The Effects of Demography and Long-Term Selection on the Accuracy of Genomic Prediction with Sequence Data
Authors: MacLeod Iona M , Hayes Ben J , Goddard Michael E
Published: September 2014

The use of dense SNPs to predict the genetic value of an individual for a complex trait is often referred to as “genomic selection” in livestock and crops, but is also relevant to human genetics to predict, for example, complex genetic disease risk. The accuracy of prediction depends on the strength of linkage disequilibrium (LD) between SNPs and causal mutations. If sequence data were used instead of dense SNPs, accuracy should increase because causal mutations are present, but demographic history and long-term negative selection also influence accuracy. We therefore evaluated genomic prediction, using simulated sequence in two contrasting populations: one reducing from an ancestrally large effective population size (Ne) to a small one, with high LD common in domestic livestock, while the second had a large constant-sized Ne with low LD similar to that in some human or outbred plant populations. There were two scenarios in each population; causal variants were either neutral or under long-term negative selection. For large Ne, sequence data led to a 22% increase in accuracy relative to ∼600K SNP chip data with a Bayesian analysis and a more modest advantage with a BLUP analysis. This advantage increased when causal variants were influenced by negative selection, and accuracy persisted when 10 generations separated reference and validation populations. However, in the reducing Ne population, there was little advantage for sequence even with negative selection. This study demonstrates the joint influence of demography and selection on accuracy of prediction and improves our understanding of how best to exploit sequence for genomic prediction.