bluuebunny/crossref_metadata_2025 huggingface dataset:
Strength Training and Sport Psychology
Authors: Moore E. Whitney G.
Published: April 2017

Strength training sessions are developed and overseen by strength and conditioning coaches, whose primary responsibilities are to maximize individuals’ athletic performance and minimize their injury risk. As the majority of education and certification for being a strength and conditioning coach focuses on physiology and physiological adaptations, biomechanics, and related scientific areas of study, there has been less emphasis on coaching behaviors, motivational techniques, pedagogical approaches, or psychological skills. These are important areas because to accomplish both long-term and short-term training goals, strength and conditioning coaches should use and train their athletes in the use of these techniques.

Motivation of training session participants is essential to being an effective strength and conditioning coach. Coaches motivate their athletes through their behaviors, design and organization of the training sessions, teaching techniques, role modeling, relationships with the athletes, and the psychological skills they incorporate within and outside of the training sessions. Coaches also often teach athletes about psychological skills not to motivate the athlete but to assist the athlete in their performance, mental health, or general well-being. Some of these psychological skills are so ingrained in the strength and conditioning discipline that coaches do not recognize or categorize them as psychological skills. Because of the relationship built between strength coach and athlete, the strength and conditioning coach often provides informal knowledge of advice on topics regarding general life lessons or skills that can actually be categorized under psychological skills. However, the lack of formal education and training in sport psychology techniques also means that strength and conditioning coaches do not take full advantage of many behaviors, motivational techniques, and other psychological skills. These areas remain an area for further professional development and research within the strength and conditioning field.
Burnout in Sport and Performance
Authors: Eklund Robert C. , Defreese J.D.
Published: April 2017

Athlete burnout is a cognitive-affective syndrome characterized by perceptions of emotional and physical exhaustion, reduced accomplishment, and devaluation of sport. A variety of theoretical conceptualizations are utilized to understand athlete burnout, including stress-based models, theories of identity, control and commitment, and motivational models. Extant research has highlighted myriad antecedents of athlete burnout including higher levels of psychological stress and amotivation and lower levels of social support and psychological need (i.e., autonomy, competence, relatedness) satisfaction. Continued longitudinal research efforts are necessary to confirm the directionality and magnitude of these associations. Moreover, theoretically focused intervention strategies may provide opportunities for prevention and treatment of burnout symptoms via athlete-focused stress-management and cognitive reframing approaches as well as environment-focused strategies targeting training loads and enhancement of athlete psychological need satisfaction. Moving forward, efforts to integrate research and practice to improve burnout recognition, prevention, and intervention in athlete populations likely necessitate collaboration among researchers and clinicians.
Statistical Analysis of White-Collar Crime
Authors: Cliff Gerald , Wall-Parker April
Published: April 2017

As far back as the 19th century, statistics on reported crime have been relied upon as a means to understand and explain the nature and prevalence of crime (Friedrichs, 2007). Measurements of crime help us understand how much of it occurs on a yearly basis, where it occurs, and the costs to our society as a whole. Studying crime statistics also helps us understand the effectiveness of efforts to control it by tracking arrests and convictions. Analysts can tell whether it is increasing or decreasing relative to other possible mitigating factors such as the economy or unemployment rates in a community. Politicians can point to crime statistics to define a problem or indicate a success. Sociologists can study the ups and downs of crime rates and any number of other variables in the society such as education, employment rates, ethnic demographics, and a long list of other factors thought to affect the rate at which crime is committed. Property value is affected by the crime rates in a given neighborhood, and insurance rates are said to fluctuate with the ups and downs of crime.

Analyzing any criminal act’s prevalence, cost to society, impact on victims, potential preventive measures, correction strategies, and even the characteristics of perpetrators and victims has provided valuable insights and a wealth of useful information in society’s efforts to combat violent/index crimes. This information has only been possible because there is little disagreement as to exactly what constitutes a criminal act when discussing violent or property crimes or what has come to be grouped under the catch-all heading of “street crime”; this is decidedly not the case with crimes included under the white-collar crime umbrella.
Defensible Space
Authors: Mawby Robert I.
Published: April 2017

While the term “defensible space” is widely referenced in literature on situational crime pre vention and Crime Prevention Through Environmental Design, it is commonly mentioned in passing, almost as an historical landmark, with its relationship to more recent work assumed rather than rigorously examined. Yet, Oscar Newman’s work bridged the gap between criminological theories and preventive approaches in the pre-1970s era and the more grounded and policy driven approaches that are common today. Consequently, this article looks at the context within which Newman developed his ideas and revisits his core work. It then considers the initial response from the criminology and planning communities, which focused on the methodological and theoretical weaknesses that undermined what were, essentially, a series of imaginative, exploratory propositions about the influence of design on crime patterns. In this sense, it is clear that Newman both provoked and inspired further research into the relationship between urban design and crime, and indeed, between crime, crime targets, and space, looking at the specific influence of design, technology, social engineering, and so on. Terms such as ownership, visibility, occupancy, accessibility, image, and juxtaposition, which Newman used, are now incorporated into more sophistical theories of situational crime prevention. This article thus offers a reanalysis of defensible space in the context of later refinements and the application of Newman’s ideas to current policies.
Religious Pilgrimages in the United States
Authors: Campo Juan E.
Published: April 2017

Pilgrimage, as a type of religious journey, involves embodied movement across geographic, social, political, cultural, and often religious boundaries to a sacred place or landscape. It is arguably a universal phenomenon that can engage individual pilgrims or millions, especially with the onset of modernity, which has facilitated travel over distances great and small. As an aspect of religious life in the United States, pilgrimage is often overlooked. Nevertheless, the country’s landscape encompasses numerous sites of sacred significance associated with organized religions, civil religion, and facets of its cultural religion that attract millions of visitors annually. As a dynamic set of phenomena, pilgrimages to such sites are constantly evolving, affected by factors such as religious and social movements, national politics, immigration, and tourism.
Sea Level Rise and Coastal Management
Authors: London James B.
Published: April 2017

Coastal zone management (CZM) has evolved since the enactment of the U.S. Coastal Zone Management Act of 1972, which was the first comprehensive program of its type. The newer iteration of Integrated Coastal Zone Management (ICZM), as applied to the European Union (2000, 2002), establishes priorities and a comprehensive strategy framework. While coastal management was established in large part to address issues of both development and resource protection in the coastal zone, conditions have changed. Accelerated rates of sea level rise (SLR) as well as continued rapid development along the coasts have increased vulnerability. The article examines changing conditions over time and the role of CZM and ICZM in addressing increased climate related vulnerabilities along the coast.

The article argues that effective adaptation strategies will require a sound information base and an institutional framework that appropriately addresses the risk of development in the coastal zone. The information base has improved through recent advances in technology and geospatial data quality. Critical for decision-makers will be sound information to identify vulnerabilities, formulate options, and assess the viability of a set of adaptation alternatives. The institutional framework must include the political will to act decisively and send the right signals to encourage responsible development patterns. At the same time, as communities are likely to bear higher costs for adaptation, it is important that they are given appropriate tools to effectively weigh alternatives, including the cost avoidance associated with corrective action. Adaptation strategies must be pro-active and anticipatory. Failure to act strategically will be fiscally irresponsible.
Recognizing common parasitic infestations
Authors: Truscott Judy , Abebe Alyssa , Donkers Kelly , Segers Daria
Published: April 2017

Parasitic infestations commonly are seen in patients in primary care, urgent care, and EDs. These infestations are a common cause of pruritus and may lead to secondary infestations. This article reviews the signs and symptoms of pinworms, lice, bedbug, and scabies infestations, as well as diagnosis and appropriate treatment.
Development of an HIV Postexposure Prophylaxis (PEP) Protocol for Trainees Engaging in Academic Global Health Experiences
Authors: Arora Gitanjli , Hoffman Risa M.
Published: April 2017

Problem

Global health (GH) education programs have become increasingly common in U.S. medical schools and graduate medical education programs, with growing numbers of medical students, residents, and fellows participating in clinical experiences in settings with high HIV prevalence and limited resources. However, there are no guidelines for provision of HIV postexposure prophylaxis (PEP) to trainees engaging in these academic GH experiences.

Approach

Faculty of the Global Health Education Programs (GHEP) at the David Geffen School of Medicine at UCLA and GH partner institutions recognized the need for PEP access for trainees engaged in GH experiences. In 2013–2014, key UCLA faculty collaborated in the development of the UCLA GHEP PEP Protocol, which includes provision of PEP medications to trainees prior to departure, an on-call infectious disease/HIV specialist to advise trainees who have exposures, and a system for following up with exposed trainees while on the GH rotation and after their return.

Outcomes

Between February 2014 and September 2016, 112 medical students and 110 residents received education on the PEP protocol during their predeparture orientation. The protocol was used for 28 exposures (27 occupational, 1 nonoccupational), with PEP recommended in 3 occupational cases (all needlesticks) and the single nonoccupational case. There were no reported HIV seroconversions.

Next Steps

The authors plan to formally evaluate the PEP protocol, conduct a qualitative assessment with trainees and both UCLA and GH partner faculty, and discuss best practices with institutions across the United States and with GH partners.
A Study of Pediatricians’ Debt Repayment a Decade After Completing Residency
Authors: Cull William L. , Katakam Shesha K. , Starmer Amy Jost , Gottschlich Elizabeth A. , Miller Ashley A. , Frintner Mary Pat
Published: April 2017

Purpose

Pediatricians’ education debt has been increasing. Less is known about the pace of their debt repayment. The authors examined patterns of debt repayment for pediatricians who completed residency from 2002–2004.

Method

The authors analyzed weighted 2013 survey data from the American Academy of Pediatrics Pediatrician Life and Career Experience Study. They categorized participants based on education debt level at residency completion ($0; $1–$49,999; $50,000–$99,999; $100,000–$149,999; ≥ $150,000) and explored debt repayment and well-being by starting debt group using multivariable logistic regression.

Results

Of 830 pediatricians surveyed, 266 (32%) had no starting debt and 166 (20%) had ≥ $150,000 in starting debt. A decade after residency, the percentage of participants who completely repaid their debt varied from 76% (68/89) of those with $1–$49,999 of starting debt to 15% (25/164) of those with ≥ $150,000 of starting debt. The percentage of participants concerned about their debt increased with starting debt level, with over half of those in the highest group concerned. Starting debt was associated with all examined measures of debt repayment and with recent financial difficulties among those in the two highest debt groups ($100,000–$149,999: adjusted odds ratio = 3.82, confidence interval = 1.17–12.43; ≥ $150,000: adjusted odds ratio = 4.55, confidence interval = 1.47–14.14).

Conclusions

A decade after completing residency, pediatricians had made progress repaying their debt, yet many still expressed concern, especially those with the greatest amount of starting debt. As debt levels continue to increase, these issues could worsen.
Hydrogen Sulfide Confers Lung Protection During Mechanical Ventilation via Cyclooxygenase 2, 15-deoxy Δ12,14-Prostaglandin J2, and Peroxisome Proliferator-Activated Receptor Gamma
Authors: Spassov Sashko G. , Faller Simone , Hummel Matthias , Helo Khaled , Ihle Andreas , Ryter Stefan W. , Strosing Karl M. , Hoetzel Alexander
Published: April 2017

Objectives:

Hydrogen sulfide reduces ventilator-induced lung injury in mice. Here, we have examined the underlying mechanisms of hydrogen sulfide-mediated lung protection and determined the involvement of cyclooxygenase 2, 15-deoxy Δ12,14-prostaglandin J2, and peroxisome proliferator-activated receptor gamma in this response.

Design:

Randomized, experimental study.

Setting:

University medical center research laboratory.

Subjects:

C57BL/6 mice and in vitro cell catheters.

Interventions:

The effects of hydrogen sulfide were analyzed in a mouse ventilator-induced lung injury model in vivo as well as in a cell stretch model in vitro in the absence or presence of hydrogen sulfide. The physiologic relevance of our findings was confirmed using pharmacologic inhibitors of cyclooxygenase 2 and peroxisome proliferator-activated receptor gamma.

Measurements and Main Results:

Mechanical ventilation caused significant lung inflammation and injury that was prevented in the presence of hydrogen sulfide. Hydrogen sulfide-mediated protection was associated with induction of cyclooxygenase 2 and increases of its product 15-deoxy Δ12,14-prostaglandin J2 as well as cyclooxygenase 2/15-deoxy Δ12,14-prostaglandin J2-dependent activation of peroxisome proliferator-activated receptor gamma. Hydrogen sulfide-dependent effects were mainly observed in macrophages. Applied mechanical stretch to RAW 264.7 macrophages resulted in increased expression of interleukin receptor 1 messenger RNA and release of macrophage inflammatory protein-2. In contrast, incubation of stretched macrophages with sodium hydrosulfide prevented the inflammatory response dependent on peroxisome proliferator-activated receptor gamma activity. Finally, application of a specific peroxisome proliferator-activated receptor gamma inhibitor abolished hydrogen sulfide-mediated protection in ventilated animals.

Conclusions:

One hydrogen sulfide-triggered mechanism in the protection against ventilator-induced lung injury involves cyclooxygenase 2/15-deoxy Δ12,14-prostaglandin J2-dependent activation of peroxisome proliferator-activated receptor gamma and macrophage activity.
An Innovative Risk-Reducing Approach to Postmastectomy Radiation Delivery after Autologous Breast Reconstruction
Authors: Piper Merisa L. , Evangelista Maristella , Amara Dominic , Daar David , Foster Robert D. , Fowble Barbara , Sbitany Hani
Published: April 2017

Introduction:

Postmastectomy radiation therapy (PMRT) has known deleterious side effects in immediate autologous breast reconstruction. However, plastic surgeons are rarely involved in PMRT planning. Our institution has adopted a custom bolus approach for all patients receiving PMRT. This offers uniform distribution of standard radiation doses, thereby minimizing radiation-induced changes while maintaining oncologic safety. We present our 8-year experience with the custom bolus approach for PMRT delivery in immediate autologous breast reconstruction.

Methods:

All immediate autologous breast reconstruction patients requiring PMRT after 2006 were treated with the custom bolus approach. Retrospective chart review was performed to compare the postirradiation complications, reconstruction outcomes, and oncologic outcomes of these patients with those of previous patients at our institution who underwent standard bolus, and to historical controls from peer-reviewed literature.

Results:

Over the past 10 years, of the 29 patients who received PMRT, 10 were treated with custom bolus. Custom bolus resulted in fewer radiation-induced skin changes and less skin tethering/fibrosis than standard bolus (0% vs 10% and 20% vs 35%, respectively), and less volume loss and contour deformities compared with historical controls (10% vs 22.8% and 10% vs 30.7%, respectively).

Conclusions:

Custom bolus PMRT minimizes radiation delivery to the internal mammary vessels, anastomoses, and skin; uniformly doses the surgical incision; and provides the necessary radiation dose to prevent recurrence. Because custom bolus PMRT may reduce the deleterious effects of radiation on reconstructive outcomes while maintaining safe oncologic results, we encourage all plastic surgeons to collaborate with radiation oncologists to consider this technique.
Difference in Success Treating Proximal Interphalangeal and Metacarpophalangeal Joints with Collagenase: Results of 208 Treatments
Authors: Hansen Karina Liv , Werlinrud Jens Christian , Larsen Søren , Ipsen Tune , Lauritsen Jens
Published: April 2017

Background:

Dupuytren disease (DD) is a fibroproliferative disorder of the palmar fasciae causing extension deficit and impaired hand function. Treatment with injection of collagenase clostridium histolyticum (CCH) is a nonsurgical treatment method. The aim of this study was to evaluate the difference in efficiency and recurrence at 12-month follow-up when treating metacarpophalangeal (MP) and proximal interphalangeal (PIP) joints with CCH. None of the patients had received previous treatments of their condition.

Methods:

This study is a prospective study of a consecutive series of patients with DD presenting with an extension deficit greater than 20° affecting the MP or PIP joint.

Results:

We found a mean reduction in extension deficit of 47° (91%) for MP joints and 47° (76%) for PIP joints. Full correction (max 5° deficit) was achieved in 76% of MP and 28% of PIP joints. Skin rupture was seen in 34% of treatments. The 1-year relapse rate was 15% for MP and 67% for PIP joints. The reduction in quickDASH score was only statistically significant for MP joints at 1 year. Eighty-one percent of all patients reported being satisfied or very satisfied. No major adverse events were recorded.

Conclusion:

Excellent results can be achieved in the treatment of MP-joint contractures, whereas the success rate is significantly lower and recurrence rate is greater for PIP joints.
Rapid Intraocular Tube Trimming for Glaucoma Drainage Implant Devices
Authors: Baciu Paul , Moster Stephen J. , Lee Richard K.
Published: April 2017

Purpose:

To describe a new approach for shortening silicone tubes of glaucoma drainage devices (GDDs).

Materials and Methods:

A retrospective intervention case series describing 3 patients undergoing the same treatment at a single institutional center

Results:

Three patients underwent successful ab interno trimming of GDD silicone tubes without complication

Conclusions:

This technique allows for rapid and successful shortening of GDD tubes via an ab interno approach avoiding risks of traditional glaucoma tube trimming approaches.
Edwin Smith. 28 July 1931 — 4 July 2010
Authors: Burdekin Frederick Michael , Knott John Frederick
Published: April 2017

Ted Smith is best known for his contributions to the analysis of continuous dislocations in deformed crystals and the application of this to understanding the conditions leading to plastic flow and fracture in metals. He applied his knowledge to a range of practical problems, particularly ones concerned with the structural integrity of key components in the nuclear power generation industry. His career spanned both industry and academia, including 20 years as Professor of Metallurgy at the University of Manchester, during which time he helped oversee the joint operation of the Departments of Metallurgy at both the University and UMIST and served at senior levels in the University administration. His research was frequently motivated by interactions with industry in consultancy work. He published over 500 papers, the great majority of which were of his sole authorship.
Diverse integrin adhesion stoichiometries caused by varied actomyosin activity
Authors: Bulgakova Natalia A. , Wellmann Jutta , Brown Nicholas H.
Published: April 2017

Cells in an organism are subjected to numerous sources of external and internal forces, and are able to sense and respond to these forces. Integrin-mediated adhesion links the extracellular matrix outside cells to the cytoskeleton inside, and participates in sensing, transmitting and responding to forces. While integrin adhesion rapidly adapts to changes in forces in isolated migrating cells, it is not known whether similar or more complex responses occur within intact, developing tissues. Here, we studied changes in integrin adhesion composition upon different contractility conditions inDrosophilaembryonic muscles. We discovered that all integrin adhesion components tested were still present at muscle attachment sites (MASs) when either cytoplasmic or muscle myosin II was genetically removed, suggesting a primary role of a developmental programme in the initial assembly of integrin adhesions. Contractility does, however, increase the levels of integrin adhesion components, suggesting a mechanism to balance the strength of muscle attachment to the force of muscle contraction. Perturbing contractility in distinct ways, by genetic removal of either cytoplasmic or muscle myosin II or eliminating muscle innervation, each caused unique alterations to the stoichiometry at MASs. This suggests that different integrin-associated proteins are added to counteract different kinds of force increase.
Control of mitochondrial biogenesis and function by the ubiquitin–proteasome system
Authors: Bragoszewski Piotr , Turek Michal , Chacinska Agnieszka
Published: April 2017

Mitochondria are pivotal organelles in eukaryotic cells. The complex proteome of mitochondria comprises proteins that are encoded by nuclear and mitochondrial genomes. The biogenesis of mitochondrial proteins requires their transport in an unfolded state with a high risk of misfolding. The mislocalization of mitochondrial proteins is deleterious to the cell. The electron transport chain in mitochondria is a source of reactive oxygen species that damage proteins. Mitochondrial dysfunction is linked to many pathological conditions and, together with the loss of cellular protein homeostasis (proteostasis), are hallmarks of ageing and ageing-related degeneration diseases. The pathogenesis of neurodegenerative disorders, such as Alzheimer's disease and Parkinson's disease, has been associated with mitochondrial and proteostasis failure. Thus, mitochondrial proteins require sophisticated surveillance mechanisms. Although mitochondria form a proteasome-exclusive compartment, multiple lines of evidence indicate a crucial role for the cytosolic ubiquitin–proteasome system (UPS) in the quality control of mitochondrial proteins. The proteasome affects mitochondrial proteins at stages of their biogenesis and maturity. The effects of the UPS go beyond the removal of damaged proteins and include the adjustment of mitochondrial proteome composition, the regulation of organelle dynamics and the protection of cellular homeostasis against mitochondrial failure. In turn, mitochondrial activity and mitochondrial dysfunction adjust the activity of the UPS, with implications at the cellular level.
A sister of
NANOG
regulates genes expressed in pre-implantation human development
Authors: Dunwell Thomas L. , Holland Peter W. H.
Published: April 2017

The
NANOG
homeobox gene plays a pivotal role in self-renewal and maintenance of pluripotency in human, mouse and other vertebrate embryonic stem cells, and in pluripotent cells of the blastocyst inner cell mass. There is a poorly studied and atypical homeobox locus close to the
Nanog
gene in some mammals which could conceivably be a cryptic paralogue of
NANOG,
even though the loci share only 20% homeodomain identity. Here we argue that this gene,
NANOGNB (NANOG Neighbour)
, is an extremely divergent duplicate of
NANOG
that underwent radical sequence change in the mammalian lineage. Like
NANOG
, the
NANOGNB
gene is expressed in pre-implantation embryos of human and cow; unlike
NANOG
,
NANOGNB
expression is restricted to 8-cell and morula stages, preceding blastocyst formation. When expressed ectopically in adult cells, human
NANOGNB
elicits gene expression changes, including downregulation of a set of genes that have an expression pulse at the 8-cell stage of pre-implantation development. We conclude that gene duplication and massive sequence divergence in mammals generated a novel homeobox gene that acquired new developmental roles complementary to those of
Nanog.
Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
Authors: Ryu Ann H. , Eckalbar Walter L. , Kreimer Anat , Yosef Nir , Ahituv Nadav
Published: April 2017

Standard cell culture guidelines often use media supplemented with antibiotics to prevent cell contamination. However, relatively little is known about the effect of antibiotic use in cell culture on gene expression and the extent to which this treatment could confound results. To comprehensively characterize the effect of antibiotic treatment on gene expression, we performed RNA-seq and ChIP-seq for H3K27ac on HepG2 cells, a human liver cell line commonly used for pharmacokinetic, metabolism and genomic studies, cultured in media supplemented with penicillin-streptomycin (PenStrep) or vehicle control. We identified 205 PenStrep-responsive genes, including transcription factors such as ATF3 that are likely to alter the regulation of other genes. Pathway analyses found a significant enrichment for “xenobiotic metabolism signaling” and “PXR/RXR activation” pathways. Our H3K27ac ChIP-seq identified 9,514 peaks that are PenStrep responsive. These peaks were enriched near genes that function in cell differentiation, tRNA modification, nuclease activity and protein dephosphorylation. Our results suggest that PenStrep treatment can significantly alter gene expression and regulation in a common liver cell type such as HepG2, advocating that antibiotic treatment should be taken into account when carrying out genetic, genomic or other biological assays in cultured cells.
Neural Correlates of human cognitive abilities during sleep
Authors: Fang Zhuo , Ray Laura B. , Owen Adrian M. , Fogel Stuart M.
Published: April 2017

Inter-individual differences in sleep spindles are highly correlated with “Reasoning” abilities (problem solving skills; i.e., the ability to employ logic, identify complex patterns), but not Short Term Memory or Verbal abilities. Simultaneous electroencephalography and functional magnetic resonance imaging (EEG-fMRI) have revealed brain activations time-locked to spindles (e.g., thalamic, paralimbic, and motor cortical areas)–yet the functional significance of inter-individual differences in spindle-related brain activation remains to be investigated. Using EEG-fMRI during sleep, we identified, for the first time, the neural activation patterns time-locked to spindles that are correlated with cognitive abilities. Similar to previous studies, activations time-locked to spindles were observed in thalamocortical circuitry and basal ganglia regions. Importantly, spindle-related activation in a subset of these regions were specifically related to inter-individual differences in Reasoning, but not STM or Verbal abilities. These results may help elucidate the physiological mechanisms which support the function of sleep for the capacity for reasoning.
Lacer: accurate base quality score recalibration for improving variant calling from next-generation sequencing data in any organism
Authors: Chung Jade C.S. , Chen Swaine L.
Published: April 2017

Next-generation sequencing data is accompanied by quality scores that quantify sequencing error. Inaccuracies in these quality scores propagate through all subsequent analyses; thus base quality score recalibration is a standard step in many next-generation sequencing workflows, resulting in improved variant calls. Current base quality score recalibration algorithms rely on the assumption that sequencing errors are already known; for human resequencing data, relatively complete variant databases facilitate this. However, because existing databases are still incomplete, recalibration is still inaccurate; and most organisms do not have variant databases, exacerbating inaccuracy for non-human data. To overcome these logical and practical problems, we introduce Lacer, which recalibrates base quality scores without assuming knowledge of correct and incorrect bases and without requiring knowledge of common variants. Lacer is the first logically sound, fully general, and truly accurate base recalibrator. Lacer enhances variant identification accuracy for resequencing data of human as well as other organisms (which are not accessible to current recalibrators), simultaneously improving and extending the benefits of base quality score recalibration to nearly all ongoing sequencing projects. Lacer is available at:https://github.com/swainechen/lacer.
Widespread dysregulation of the circadian clock in human cancer
Authors: Shilts Jarrod , Chen Guanhua , Hughey Jacob J.
Published: April 2017

The mammalian circadian clock is a critical regulator of metabolism and cell division. Although multiple lines of evidence indicate that systemic disruption of the circadian clock can promote cancer, whether the clock is disrupted in primary human tumors is unknown. Here we used transcriptome data from mice to define a signature of the mammalian circadian clock based on the co-expression of 12 genes that form the core clock or are directly controlled by the clock. Our approach can be applied to samples that are not labeled with time of day and were not acquired over the entire circadian (24-h) cycle. We validated the clock signature in transcriptome data from healthy human tissues, then developed a metric we call the delta clock correlation distance (ΔCCD) to describe the extent to which the signature is perturbed in samples from one condition relative to another. We calculated the ΔCCD comparing human tumor and non-tumor samples from The Cancer Genome Atlas and eight independent datasets, discovering widespread dysregulation of clock gene co-expression in tumor samples. Subsequent analysis of data from clock gene knockouts in mice suggested that clock dysregulation in human cancer is not caused solely by loss of activity of clock genes. Furthermore, by analyzing a large set of genes previously inferred to be rhythmic in healthy human lung, we found that dysregulation of the clock in human lung cancer is accompanied by dysregulation of broader patterns of circadian co-expression. Our findings suggest that clock dysregulation is a common means by which human cancers achieve unrestrained growth and division, and that restoring clock function could be a viable therapeutic strategy in multiple cancer types. In addition, our approach opens the door to using publicly available transcriptome data to quantify clock disruption in a multitude of human phenotypes. Our method is available as a web application athttps://hugheylab.shinyapps.io/deltaccd.
Mass univariate testing biases the detection of interaction effects in whole-brain analysis of variance
Authors: Chavez Robert S. , Wagner Dylan D.
Published: April 2017

Whole-brain analysis of variance (ANOVA) is a common analytic approach in cognitive neuroscience. Researchers are often interested in exploring whether brain activity reflects to the interaction of two factors. Disordinal interactions — where there is a reversal of the effect of one independent variable at a level of a second independent variable — are common in the literature. It is well established in power-analyses of factorial ANOVAs that certain patterns of interactions, such as disordinal (e.g., cross-over interactions) require less power than others to detect. This fact, combined with the perils of mass univariate testing suggests that testing for interactions in whole-brain ANOVAs, may be biased towards the detection of disordinal interactions. Here, we report on a series of simulated analysis --including whole-brain fMRI data using realistic multi-source noise parameters-- that demonstrate a bias towards the detection of disordinal interactions in mass-univariate contexts. Moreover, results of these simulations indicated that spurious disordinal interactions are found at common thresholds and cluster sizes at the group level. Moreover, simulations based on implanting true ordinal interaction effects can nevertheless appear like crossover effects at realistic levels of signal-to-noise ratio (SNR) when performing mass univariate testing at the whole-brain level, potentially leading to erroneous conclusions when interpreted as is. Simulations of varying sample sizes and SNR levels show that this bias is driven primarily by SNR and larger sample sizes do little to ameliorate this issue. Together, the results of these simulations argue for caution when searching for ordinal interactions in whole-brain ANOVA.
Two cadmium(II) fluorous coordination compounds tuned by different bipyridines
Authors: Kong Ya-Jie , Li Peng , Han Li-Juan , Fan Lu-Tong , Li Peng-Peng , Yin Shuang
Published: April 2017

Fluorine is the most electronegative element and can be used as an excellent hydrogen-bond acceptor. Fluorous coordination compounds exhibit several advantageous properties, such as enhanced high thermal and oxidative stability, low polarity, weak intermolecular interactions and a small surface tension compared to hydrocarbons. C—H...F—C interactions, although weak, play a significant role in regulating the arrangement of the organic molecules in the crystalline state and stabilizing the secondary structure. Two cadmium(II) fluorous coordination compounds formed from 2,2′-bipyridine, 4,4′-bipyridine and pentafluorobenzoate ligands, namely catena-poly[[aqua(2,2′-bipyridine-κ2
N,N′)(2,3,4,5,6-pentafluorobenzoato-κO)cadmium(II)]-μ-2,3,4,5,6-pentafluorobenzoato-κ2
O:O′], [Cd(C7F5O2)2(C10H8N2)(H2O)]
n
, (1), and catena-poly[[diaquabis(2,3,4,5,6-pentafluorobenzoato-κO)cadmium(II)]-μ-4,4′-bipyridine-κ2
N:N′], [Cd(C7F5O2)2(C10H8N2)(H2O)2]
n
, (2), have been synthesized solvothermally and structurally characterized. Compound (1) shows a one-dimensional chain structure composed of Cd—O coordination bonds and is stabilized by π–π stacking and O—H...O hydrogen-bond interactions. Compound (2) displays a one-dimensional linear chain structure formed by Cd—N coordination interactions involving the 4,4′-bipyridine ligand. Adjacent one-dimensional chains are extended into two-dimensional sheets by O—H...O hydrogen bonds between the coordinated water molecules and adjacent carboxylate groups. Moreover, the chains are further linked by C—H...F—C interactions to afford a three-dimensional network. In both structures, hydrogen bonding involving the coordinated water molecules is a primary driving force in the formation of the supramolecular structures.
Crystal structure of CD27 in complex with a neutralizing noncompeting antibody
Authors: Teplyakov Alexey , Obmolova Galina , Malia Thomas J. , Gilliland Gary L.
Published: April 2017

CD27 is a T-cell and B-cell co-stimulatory glycoprotein of the tumor necrosis factor (TNF) receptor superfamily that is dependent on the availability of the TNF-like ligand CD70. Therapeutic approaches to treating autoimmune diseases and cancers with antagonistic and agonistic anti-CD27 monoclonal antibodies (mAbs), respectively, have recently been developed. Mouse anti-human CD27 mAb 2177 shows potency in neutralizing CD70-induced signaling; however, it does not block the binding of soluble CD70. To provide insight into the mechanism of action of the mAb, the crystal structure of the CD27 extracellular domain in complex with the Fab fragment of mAb 2177 was determined at 1.8 Å resolution. CD27 exhibits the assembly of cysteine-rich domains characteristic of the TNF receptor superfamily. The structure reveals a unique binding site of mAb 2177 at the edge of the receptor molecule, which allows the mAb to sterically block the cell-bound form of CD70 from reaching CD27 while leaving the ligand epitope clear. This mode of action suggests a potential dual use of mAb 2177 either as an antagonist or as an agonist.
The first plant acyl-CoA-binding protein structures: the close homologues OsACBP1 and OsACBP2 from rice
Authors: Guo Ze-Hua , Chan Wallace H. Y. , Kong Geoffrey K. W. , Hao Quan , Chye Mee-Len
Published: April 2017

Acyl-CoA-binding proteins (ACBPs) are a family of proteins that facilitate the binding of long-chain acyl-CoA esters at a conserved acyl-CoA-binding domain. ACBPs act to form intracellular acyl-CoA pools, transport acyl-CoA esters and regulate lipid metabolism. In the model plantArabidopsis thaliana, a family of six ACBPs has been demonstrated to function in stress and development. Six ACBPs (OsACBPs) have also been identified inOryza sativa(rice), but they are not as well characterized as those inArabidopsis thaliana. To understand the need in rice for the two 10 kDa ACBPs, namely OsACBP1 and OsACBP2, which share 79% sequence identity, their crystal structures were elucidated and their affinities toward acyl-CoA esters were compared using isothermal titration calorimetry. OsACBP2 was found to display a higher binding affinity for unsaturated acyl-CoA esters than OsACBP1. A difference between the two proteins is observed at helix 3 and is predicted to lead to different ligand-binding modes in terms of the shape of the binding pocket and the residues that are involved. OsACBP1 thus resembles bovine ACBP, while OsACBP2 is similar to human liver ACBP, in both structure and binding affinity. This is the first time that ACBP structures have been reported from plants, and suggests that OsACBP1 and OsACBP2 are not redundant in function despite their high sequence identity and general structural similarity.
Investigating the friction coefficient in functionally graded rapid prototyping of Al–Al2O3 composite prepared by fused deposition modelling
Authors: Singh Rupinder , Singh Sunpreet
Published: April 2017

Purpose

The present research work aims to study the friction coefficient in functionally graded rapid prototyping of Al–Al2O3 composite prepared via fused deposition modelling (FDM)-assisted investment casting (IC) process. The optimized settings of the process parameters (namely, filament proportion, volume of FDM pattern, density of FDM pattern, barrel finishing (BF) time, BF media weight and number of IC slurry layers) suggested in the present research work will help fabricate parts possessing higher frictional coefficient.

Design/methodology/approach

Initially, melt flow index (MFI) of two different proportions of Nylon6-Al–Al2O3 (to be used as an alternative FDM filament material) was tested on the melt flow indexer and matched with MFI of commercially used acrylonitrile–butadiene–styrene filament. After this, the selected proportions of Nylon6-Al–Al2O3 were prepared in the form of the FDM filament by using a single screw extruder. Further, this FDM filament has been used for developing sacrificial IC patterns in the existing FDM system which was barely finished to improve their surface finish. Castings developed were tested for their wear resistance properties on a pin-on-disc-type tribo-tester under dry conditions at sliding conditions to check their suitability as a frictional device for industrial applications. In the methodology part, Taguchi L18 orthogonal array was used to study the effect of selected process variables on the coefficient of friction (μ).

Findings

It has been found that filament proportion, volume of FDM pattern and density of FDM pattern have significantly affected the μ-values. Further, density of the FDM pattern was found to have 91.62 per cent contribution in obtaining μ-values. Scanning electron micrographs highlighted uniform distribution of Al2O3 particles in the Al-matrix at suggested optimized settings.

Practical implications

The present methodology shows the development of a functional graded material that consisted of surface reinforcement with Al2O3 particles, which could have applications for manufacturing friction surfaces such as clutch plates, brake drum, etc.

Originality/value

This paper describes the effect of process parameters on wear properties of the Al–Al2O3 composite developed as a functionally graded material by the FDM-based pattern in the IC process.
Force control for a rigid dual peg-in-hole assembly
Authors: Zhang Kuangen , Shi MinHui , Xu Jing , Liu Feng , Chen Ken
Published: April 2017

Purpose

This paper aims to realize the automatic assembly process for multiple rigid peg-in-hole components.

Design/methodology/approach

This paper develops fuzzy force control strategies for the rigid dual peg-in-hole assembly. Firstly the fuzzy force control strategies are presented. Secondly the contact states and contact forces are analyzed to prove the availability of the force control strategies.

Findings

The rigid dual peg-in-hole assembly experimental results show the effectiveness of the control strategies.

Originality/value

This paper proposes fuzzy force control strategies for a rigid dual peg-in-hole assembly task.
Linking positive psychological capital with customer value co-creation
Authors: Lee Yi-Hsuan , Hsiao Chan , Chen Yee-Chen
Published: April 2017

Purpose

This study aims to identify the driving forces of customer value co-creation (VCC) that occur through employee positive psychological capital (PPC), employee service-oriented organizational citizenship behavior (SOOCB) and customer brand experience (BE).

Design/methodology/approach

In total, 493 valid samples were retrieved from 30 hotels in Taiwan. Hierarchical linear modeling was used to extensively and accurately examine customer VCC from a cross-level perspective.

Findings

The results showed that employee PPC was not positively related to customer VCC, that employee PPC affected customer VCC indirectly through the mediating effect of employee SOOCB and that the relationship between employee SOOCB and customer VCC was positively moderated by customer BE.

Originality/value

First, this study investigated the customer VCC driving forces through the role of the employee, and thus advances the customer VCC field. Second, it identified employee SOOCB as a key mediating mechanism that links the indirect relationship between employee PPC and customer VCC. Third, it identified customer BE as a key moderating mechanism in the relationship between employee SOOCB and customer VCC. Fourth, regarding methodology, few studies investigate VCC through a cross-level approach. The present study used hierarchical linear modeling to extensively and accurately examine customer VCC and its cross-level relationships, thus providing greater research value compared with single-level analysis. Finally, the result findings suggest that organizational leaders should enhance the PPC of employees in furtherance of encouraging the employees to perform extra-role SOOCB, which makes customer co-creation behavior, and ultimately, contributes to managerial practice.
Preparing business students for workplace reality – using global virtual teams in logistics and SCM education
Authors: Trautrims Alexander , Defee Cliff , Farris Ted
Published: April 2017

Purpose

The purpose of this paper is to present and examine the use and effects of global virtual teams as a tool in the logistics and supply chain management classroom to prepare students in a simulation environment for the demands of their future careers in the profession.

Design/methodology/approach

Literature of logistics and supply chain management education is combined with streams from management learning literature. The way the tool of global virtual teams was applied is explained, followed by an analysis of quantitative and qualitative participant response data. From the data analysis the effects of individual factors in the design and application of the global virtual team are isolated and recommendations are extracted for future use of the tool.

Findings

The paper finds that the application of global virtual teams helped participating students to develop the management skills required for a career in logistics and supply chain management. Although students perceived the international nature and the lose frame provided by the tool as challenges, most learning effects were caused by these challenges. The paper also shows that the set up by the involved educators is crucial for the learning effect in particular toward similar weights of the assessments and the number of group members from each geographical area.

Research limitations/implications

The paper does not examine all potentially amendable factors but focuses on those that were seen as relevant and practically achievable under the available resources to ensure the tool can be easily scaled up by adding further institutions and participants.

Originality/value

The paper is the first application of global virtual teams in logistics and supply chain management education. It provides the theoretical foundations and rationale for its application and is relevant to educators by giving them access to this tool for improvement of their students’ career preparedness.