bluuebunny/crossref_metadata_2025 huggingface dataset:
Therapists’ Metacognitive Monitoring of the Psychotherapeutic Process With Patients With Borderline Personality Disorder
Authors: BOURKE MARIANNE E. , GRENYER BRIN F.S.
Published: July 2017

Background:

Therapy for borderline personality disorder (BPD) is challenging, in part, because of the impact of BPD on the therapeutic relationship. The therapist’s metacognitive capacity within therapy may be perturbed due to the complexity of verbal and nonverbal affect and cognition in the therapeutic interchange; however, research on this issue is lacking.

Methods:

Therapists (N=20 clinical psychologists) were asked to discuss the treatment process when working with their patients with BPD (N=40) and their patients with major depressive disorder (N=40). Verbatim transcripts of the therapists’ verbalizations were then scored using computerized linguistic content analysis.

Results:

When discussing their patients with BPD, clinicians used significantly fewer words associated with cognitive processes (think, understand, realize) or words indicating causation (cause, because, effect), and more first-person singular pronouns, and adverbs. When describing their depressed patients, the therapists used more words associated with negative emotions, anxiety, anger, and sadness than positive words. The results did not seem to be influenced by the therapists’ age, sex, or years of experience.

Conclusions:

Reflection on the psychotherapeutic process with patients with BPD induced in therapists a self-focused, emotionally intense linguistic style dominated by references to themselves and their experience of intense emotional states. These results suggest that, when describing their work with patients with BPD, therapists experience metacognitive challenges and mentalization processes that may parallel the challenges therapists face when thinking and working during the psychotherapy sessions themselves. The results underscore the important role of supervision in assisting therapists to organize their reflective processes when working with patients with BPD.
Abdominoplasty with Lymphatic Microsurgery for Patients with Secondary Lower Extremity Lymphedema
Authors: Akita Shinsuke , Yamaji Yoshihisa , Tokumoto Hideki , Adachi Naoki , Sasahara Yoshitaro , Kubota Yoshitaka , Kuriyama Motone , Mitsukawa Nobuyuki
Published: July 2017

Background:

Patients with secondary lower extremity lymphedema often develop suprapubic lymphedema. The authors developed a novel surgical method of shaping the lower abdomen and debulking suprapubic lymphedema with simultaneous reconstruction of lymphatic flow in case of lower extremity lymphedema.

Methods:

A fleur-de-lis skin incision pattern was performed for horizontal and vertical abdominal skin and fat resection. A caudally based isosceles triangular flap was created on the central suprapubic region to reduce wound tension at the intersection of the horizontal and vertical incisions. After resection and debulking of the suprapubic region, a lymphaticovenular anastomosis between the efferent lymphatic vessel of the groin node and the superficial inferior epigastric vein was created or vascularized lymph node transfer to the groin region was performed to restore lymphatic flow. Lymphaticovenular anastomosis and lymph node transfer were also performed at the lower extremities to improve lower extremity lymphedema. Perioperative change in limb volume was evaluated using the lower extremity lymphedema index, and lymphatic function was evaluated by lymphoscintigraphy.

Results:

Simultaneous abdominoplasty and reconstructive lymphatic microsurgery were performed in 11 patients. The lower extremity lymphedema index improved perioperatively, with a significant difference (p < 0.01). In eight patients who underwent lymphoscintigraphy before and after surgery, the lymphatic function was found to have not deteriorated in any limb.

Conclusions:

When simultaneous lymphatic microsurgical procedures and careful observation for complications were performed, abdominoplasty resulted in good outcomes in patients with lower extremity lymphedema and suprapubic lymphedema without worsening of lymphedema.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, V.
Does the Organization of Plastic Surgery Units into Independent Departments Affect Academic Productivity?
Authors: Loewenstein Scott N. , Duquette Stephen , Valsangkar Nakul , Avula Umakanth , Lad Neha , Socas Juan , Flores Roberto L. , Sood Rajiv , Koniaris Leonidas G.
Published: July 2017

Background:

There is an increased push for plastic surgery units in the United States to become independent departments administered autonomously rather than as divisions of a multispecialty surgery department. The purpose of this research was to determine whether there are any quantifiable differences in the academic performance of departments versus divisions.

Methods:

Using a list of the plastic surgery units affiliated with the American Council of Academic Plastic Surgeons, unit Web sites were queried for departmental status and to obtain a list of affiliated faculty. Academic productivity was then quantified using the SCOPUS database. National Institutes of Health funding was determined through the Research Portfolio Online Reporting Tools database.

Results:

Plastic surgery departments were comparable to divisions in academic productivity, evidenced by a similar number of publications per faculty (38.9 versus 38.7; p = 0.94), number of citations per faculty (692 versus 761; p = 0.64), H-indices (9.9 versus 9.9; p = 0.99), and National Institutes of Health grants (3.25 versus 2.84; p = 0.80), including RO1 grants (1.33 versus 0.84; p = 0.53). There was a trend for departments to have a more equitable male-to-female ratio (2.8 versus 4.1; p = 0.06), and departments trained a greater number of integrated plastic surgery residents (9.0 versus 5.28; p = 0.03).

Conclusion:

This study demonstrates that the academic performance of independent plastic surgery departments is generally similar to divisions, but with nuanced distinctions.
Effect of Immediate Initiation of Antiretroviral Treatment in HIV-Positive Individuals Aged 50 Years or Older
Authors: Lodi Sara , Costagliola Dominique , Sabin Caroline , del Amo Julia , Logan Roger , Abgrall Sophie , Reiss Peter , van Sighem Ard , Jose Sophie , Blanco Jose-Ramon , Hernando Victoria , Bucher Heiner C. , Kovari Helen , Segura Ferran , Ambrosioni Juan , Gogos Charalambos A. , Pantazis Nikos , Dabis Francois , Vandenhende Marie-Anne , Meyer Laurence , Seng Rémonie , Gill M. John , Krentz Hartmut , Phillips Andrew N. , Porter Kholoud , Grinsztejn Beatriz , Pacheco Antonio G. , Muga Roberto , Tate Janet , Justice Amy , Hernán Miguel A.
Published: July 2017

Background:

Clinical guidelines recommend immediate initiation of combined antiretroviral therapy for all HIV-positive individuals. However, those guidelines are based on trials of relatively young participants.

Methods:

We included HIV-positive antiretroviral therapy–naive, AIDS-free individuals aged 50–70 years after 2004 in the HIV-CAUSAL Collaboration. We used the parametric g-formula to estimate the 5-year risk of all-cause and non-AIDS mortality under (1) immediate initiation at baseline and initiation at CD4 count, (2) <500 cells/mm3, and (3) <350 cells/mm3. Results were presented separately for the general HIV population and for a US Veterans cohort with high mortality.

Results:

The study included 9596 individuals (28% US Veterans) with median (interquantile range) age of 55 (52–60) years and CD4 count of 336 (182–513) at baseline. The 5-year risk of all-cause mortality was 0.40% (95% confidence interval (CI): 0.10 to 0.71) lower for the general HIV population and 1.61% (95% CI: 0.79 to 2.67) lower for US Veterans when comparing immediate initiation vs initiation at CD4 <350 cells/mm3. The 5-year risk of non-AIDS mortality was 0.17% (95% CI: −0.07 to 0.43) lower for the general HIV population and 1% (95% CI: 0.31 to 2.00) lower for US Veterans when comparing immediate initiation vs initiation at CD4 <350 cells/mm3.

Conclusions:

Immediate initiation seems to reduce all-cause and non-AIDS mortality in patients aged 50–70 years.
Functional Gastrointestinal Disorders Common Among Nurses With Poor Sleep Quality in Shanghai, China
Authors: Zhou Hui-Qing , Yao Min , Chen Yuan-Wen , Huang Jia-Yi , Chen Guang-Yu
Published: July 2017

This study aimed to determine whether functional gastrointestinal disorders are more common among nurses with self-reported poor sleep. In total, 468 nurses working the day shift or rotating shifts completed two questionnaires: the questionnaire for irritable bowel syndrome (IBS) using Rome III criteria and the Pittsburgh Sleep Quality Index (PSQI). The prevalence of poor sleep was 41.04% (95% confidence interval, CI: [36.23, 45.85]), and poor sleep was significantly more common among rotating-shift nurses than among day-shift nurses (50.70% vs. 29.95%; p < .05). Among nurses with poor sleep, the prevalence of IBS and functional constipation was 35.15% (95% CI: [27.86, 42.44]) and 11.52% (95% CI: [6.65, 16.39]), respectively. After adjusting for age, work schedule, night pain, and psychological factors, IBS (odds ratio, OR: 1.88; 95% CI: [1.03, 2.49]) and functional constipation (OR: 1.77; 95% CI: [0.64, 2.57]) were significantly more common in nurses with poor sleep. We conclude that IBS and functional constipation are prevalent in nurses with poor sleep. Poor sleep was independently associated with IBS and functional constipation among nurses in Shanghai, China.
Aquatic Exercise Among Older Adults
Authors: Mobily Kenneth , Lenartz Andrea
Published: July 2017

The purpose of the study was to determine how older adults understood their exercise with particular attention to enrollment in an aquatic exercise class and subsequent compliance with participation in a 6-week class. Participants were interviewed and their narratives about exercise and the program were recorded. Five main themes emerged after transcripts were independently reviewed by the authors, including affective accounts that surrounded participation, exercise defined through somatic signs, social support associated with better attendance, exercise class as an “organizing structure,” and difficulty in knowing how much exercise was “enough.” Implications for future generations (eg, millennials) are discussed.
Active Aging for L.I.F.E.
Authors: Roberts Emily , Bishop Alex , Ruppert-Stroescu Mary , Clare Gregory , Hermann Janice , Singh Chitra , Balasubramanan Mahendran , Struckmeyer Kristopher M. , Kang Mihyun , Slevitch Lisa
Published: July 2017

Objective:

Active aging involves staying engaged in life in a number of ways, including maintaining independence, physical and mental fitness, and social engagement. This investigation highlights Active Aging for L.I.F.E., an intergenerational pilot health initiative developed and implemented in the state of Oklahoma.

Subject and Methods:

Program participants included college students 18 to 25 years of age (n = 20) and older adults older than 65 years (n = 23) who attended a 4-part speaker series focused on the domains of longevity, independence, fitness, and engagement and participated in a pre-/postsurvey.

Results:

College-aged students reported greater changes in their perception of an individual's role in the aging process than the older adults, and differences between genders were also identified. This pilot determined that attitudes about active aging can be changed through education for both college-aged students and older adults.
Influence of scene structure and content on visual search strategies
Authors: Amor Tatiana A. , Luković Mirko , Herrmann Hans J. , Andrade José S.
Published: July 2017

When searching for a target within an image, our brain can adopt different strategies, but which one does it choose? This question can be answered by tracking the motion of the eye while it executes the task. Following many individuals performing various search tasks, we distinguish between two competing strategies. Motivated by these findings, we introduce a model that captures the interplay of the search strategies and allows us to create artificial eye-tracking trajectories, which could be compared with the experimental ones. Identifying the model parameters allows us to quantify the strategy employed in terms of ensemble averages, characterizing each experimental cohort. In this way, we can discern with high sensitivity the relation between the visual landscape and the average strategy, disclosing how small variations in the image induce changes in the strategy.
Evolutionary online behaviour learning and adaptation in real robots
Authors: Silva Fernando , Correia Luís , Christensen Anders Lyhne
Published: July 2017

Online evolution of behavioural control on real robots is an open-ended approach to autonomous learning and adaptation: robots have the potential to automatically learn new tasks and to adapt to changes in environmental conditions, or to failures in sensors and/or actuators. However, studies have so far almost exclusively been carried out in simulation because evolution in real hardware has required several days or weeks to produce capable robots. In this article, we successfully evolve neural network-based controllers in real robotic hardware to solve two single-robot tasks and one collective robotics task. Controllers are evolved either from random solutions or from solutions pre-evolved in simulation. In all cases, capable solutions are found in a timely manner (1 h or less). Results show that more accurate simulations may lead to higher-performing controllers, and that completing the optimization process in real robots is meaningful, even if solutions found in simulation differ from solutions in reality. We furthermore demonstrate for the first time the adaptive capabilities of online evolution in real robotic hardware, including robots able to overcome faults injected in the motors of multiple units simultaneously, and to modify their behaviour in response to changes in the task requirements. We conclude by assessing the contribution of each algorithmic component on the performance of the underlying evolutionary algorithm.
Do pet dogs (
Canis familiaris
) follow ostensive and non-ostensive human gaze to distant space and to objects?
Authors: Duranton Charlotte , Range Friederike , Virányi Zsófia
Published: July 2017

Dogs are renowned for being skilful at using human-given communicative cues such as pointing. Results are contradictory, however, when it comes to dogs' following human gaze, probably due to methodological discrepancies. Here we investigated whether dogs follow human gaze to one of two food locations better than into distant space even after comparable pre-training. In Experiments 1 and 2, the gazing direction of dogs was recorded in a gaze-following into distant space and in an object-choice task where no choice was allowed, in order to allow a direct comparison between tasks, varying the ostensive nature of the gazes. We found that dogs only followed repeated ostensive human gaze into distant space, whereas they followed all gaze cues in the object-choice task. Dogs followed human gaze better in the object-choice task than when there was no obvious target to look at. In Experiment 3, dogs were tested in another object-choice task and were allowed to approach a container. Ostensive cues facilitated the dogs’ following gaze with gaze as well as their choices: we found that dogs in the ostensive group chose the indicated container at chance level, whereas they avoided this container in the non-ostensive group. We propose that dogs may perceive the object-choice task as a competition over food and may interpret non-ostensive gaze as an intentional cue that indicates the experimenter's interest in the food location she has looked at. Whether ostensive cues simply mitigate the competitive perception of this situation or they alter how dogs interpret communicative gaze needs further investigation. Our findings also show that following gaze with one's gaze and actually choosing one of the two containers in an object-choice task need to be considered as different variables. The present study clarifies a number of questions related to gaze-following in dogs and adds to a growing body of evidence showing that human ostensive cues can strongly modify dog behaviour.
Modulational instability, beak-shaped rogue waves, multi-dark-dark solitons and dynamics in pair-transition-coupled nonlinear Schrödinger equations
Authors: Zhang Guoqiang , Yan Zhenya , Wen Xiao-Yong
Published: July 2017

The integrable coupled nonlinear Schrödinger equations with four-wave mixing are investigated. We first explore the conditions for modulational instability of continuous waves of this system. Secondly, based on the generalized
N
-fold Darboux transformation (DT), beak-shaped higher-order rogue waves (RWs) and beak-shaped higher-order rogue wave pairs are derived for the coupled model with attractive interaction in terms of simple determinants. Moreover, we derive the simple multi-dark-dark and kink-shaped multi-dark-dark solitons for the coupled model with repulsive interaction through the generalizing DT. We explore their dynamics and classifications by different kinds of spatial–temporal distribution structures including triangular, pentagonal, ‘claw-like’ and heptagonal patterns. Finally, we perform the numerical simulations to predict that some dark solitons and RWs are stable enough to develop within a short time. The results would enrich our understanding on nonlinear excitations in many coupled nonlinear wave systems with transition coupling effects.
Ancient DNA and morphometric analysis reveal extinction and replacement of New Zealand's unique black swans
Authors: Rawlence Nicolas J. , Kardamaki Afroditi , Easton Luke J. , Tennyson Alan J. D. , Scofield R. Paul , Waters Jonathan M.
Published: July 2017

Prehistoric human impacts on megafaunal populations have dramatically reshaped ecosystems worldwide. However, the effects of human exploitation on smaller species, such as anatids (ducks, geese, and swans) are less clear. In this study we apply ancient DNA and osteological approaches to reassess the history of Australasia's iconic black swans (
Cygnus atratus
) including the palaeo-behaviour of prehistoric populations. Our study shows that at the time of human colonization, New Zealand housed a genetically, morphologically, and potentially ecologically distinct swan lineage (
C. sumnerensis
, Poūwa), divergent from modern (Australian)
C. atratus
. Morphological analyses indicate
C. sumnerensis
exhibited classic signs of the ‘island rule’ effect, being larger, and likely flight-reduced compared to
C. atratus
. Our research reveals sudden extinction and replacement events within this anatid species complex, coinciding with recent human colonization of New Zealand. This research highlights the role of anthropogenic processes in rapidly reshaping island ecosystems and raises new questions for avian conservation, ecosystem re-wilding, and de-extinction.
Pale and dark morphs of tawny owls show different patterns of telomere dynamics in relation to disease status
Authors: Karell Patrik , Bensch Staffan , Ahola Kari , Asghar Muhammad
Published: July 2017

Parasites are expected to exert long-term costs on host fecundity and longevity. Understanding the consequences of heritable polymorphic variation in disease defence in wild populations is essential in order to predict evolutionary responses to changes in disease risk. Telomeres have been found to shorten faster in malaria-diseased individuals compared with healthy ones with negative effects on longevity and thereby fitness. Here, we study the impact of haemosporidian blood parasites on telomere dynamics in tawny owls, which display a highly heritable plumage colour polymorphism. Previously, it has been shown that blood parasites have morph-specific impact on body mass maintenance. Here, we show that telomeres shortened faster in individuals with shorter breeding lifespan. Telomere length was negatively associated with the degree of pheomelanic brown coloration and shorter in infected than uninfected individuals. The rate of telomere shortening between breeding seasons was faster in darker pheomelanic individuals and suppression of parasite intensity between seasons was associated with faster telomere shortening in the paler individuals but not in darker ones. We propose that morph-specific physiological profiles cause differential telomere shortening and that this is likely to be a mechanism involved in previously documented environment-driven survival selection against the pheomelanic morph in this population.
Bioengineered intestinal muscularis complexes with long-term spontaneous and periodic contractions
Authors: Wang Qianqian , Wang Ke , Solorzano-Vargas R. Sergio , Lin Po-Yu , Walthers Christopher M. , Thomas Anne-Laure , Martín Martín G. , Dunn James C. Y.
Published: July 2017

Although critical for studies of gut motility and intestinal regeneration, thein vitroculture of intestinal muscularis with peristaltic function remains a significant challenge. Periodic contractions of intestinal muscularis result from the coordinated activity of smooth muscle cells (SMC), the enteric nervous system (ENS), and interstitial cells of Cajal (ICC). Reproducing this activity requires the preservation of all these cells in one system. Here we report the first serum-free culture methodology that consistently maintains spontaneous and periodic contractions of murine and human intestinal muscularis cells for months. In this system, SMC expressed the mature marker myosin heavy chain, and multipolar/dipolar ICC, uniaxonal/multipolar neurons and glial cells were present. Furthermore, drugs affecting ENS, ICC or SMC altered the contractions. Combining this method with scaffolds, contracting cell sheets were formed with organized architecture. With the addition of intestinal epithelial cells, this platform enabled at least 9 types of cells from mucosa and muscularis to coexist and function. The method constitutes a powerful tool for mechanistic studies of gut motility disorders and the regeneration of full-thickness engineered intestine.

In the small intestine, the mucosa processes partially digested food and absorbs nutrients while the muscularis actuates the peristaltic flow to transport luminal content aborally. Gut motility is central to its digestive and absorptive function. The intestinal muscularis contains various types of cells: of these, smooth muscle cells, the enteric nervous system (ENS)1,2, and the pacemaker interstitial cells of Cajal (ICC)3are three important players involved in the development of gut motility. Recent studies on intestinal tissue engineering have highlighted the importance of regenerating the functional intestinal muscularis4–9. A variety of systems derived from different cell sources, including pluripotent stem cells (PSC)4–6, embryonic stem cells (ESC)7and primary tissue8,9, have been established to accomplish this goal and different contractile activities were developed in these systems. Notably, spontaneous contractions have been generated in culture systems that contained both ICC and smooth muscle cells4,6,10–13. In addition, electrical-induced neurogenic contractions were also successfully produced4,5,8when ENS was introduced into culture. In one of the most recent studies, both spontaneous contractions and electrical-induced neurogenic contractions were developed in a PSC-based culture system4.
Beyond Homology Transfer: Deep Learning for Automated Annotation of Proteins
Authors: Nauman Mohammad , Rehman Hafeez Ur , Politano Gianfranco , Benso Alfredo
Published: July 2017

Accurate annotation of protein functions is important for a profound understanding of molecular biology. A large number of proteins remain uncharacterized because of the sparsity of available supporting information. For a large set of uncharacterized proteins, the only type of information available is their amino acid sequence. In this paper, we propose DeepSeq – a deep learning architecture – that utilizes only the protein sequence information to predict its associated functions. The prediction process does not require handcrafted features; rather, the architecture automatically extracts representations from the input sequence data. Results of our experiments with DeepSeq indicate significant improvements in terms of prediction accuracy when compared with other sequence-based methods. Our deep learning model achieves an overall validation accuracy of 86.72%, with an F1 score of 71.13%. Moreover, using the automatically learned features and without any changes to DeepSeq, we successfully solved a different problem i.e. protein function localization, with no human intervention. Finally, we discuss how this same architecture can be used to solve even more complicated problems such as prediction of 2D and 3D structure as well as protein-protein interactions.
Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis
Authors: Poetsch Anna R , Boulton Simon J , Luscombe Nicholas M
Published: July 2017

DNA is subject to constant chemical modification and damage, which eventually results in variable mutation rates throughout the genome. Although detailed molecular mechanisms of DNA damage and repair are well-understood, damage impact and execution of repair across a genome remains poorly defined. To bridge the gap between our understanding of DNA repair and mutation distributions we developed a novel method, AP-seq, capable of mapping apurinic sitesand 8-oxo-7,8-dihydroguanine bases at ∼300bp resolution on a genome-wide scale. We directly demonstrate that the accumulation rate of oxidative damage varies widely across the genome, with hot spots acquiring many times more damage than cold spots. Unlike SNVs in cancers, damage burden correlates with marks for open chromatin notably H3K9ac and H3K4me2. Oxidative damage is also highly enriched in transposable elements and other repetitive sequences. In contrast, we observe decreased damage at promoters, exons and termination sites, but not introns, in a seemingly transcription-independent manner. Leveraging cancer genomic data, we also find locally reduced SNV rates in promoters, genes and other functional elements. Taken together, our study reveals that oxidative DNA damage accumulation and repair differ strongly across the genome, but culminate in a previously unappreciated mechanism that safe-guards the regulatory sequences and the coding regions of genes from mutations.
Impaired social contacts with familiar anesthetized conspecific in CA3-restricted BDNF knockout mice
Authors: Ito Wataru , Huang Howard , Brayman Vanessa , Morozov Alexei
Published: July 2017

Familiarity is the vital characteristic conveyed by social cues to determine behaviors towards conspecific. Here we characterize social contacts to familiar vs unfamiliar male conspecific, anesthetized to eliminate inter-male aggression. During initial 10 min (phase-1), subjects contacted demonstrators vigorously regardless of familiarity. During subsequent 80 min (phase-2), however, they contacted more with familiar than unfamiliar conspecifics. Then, this test was applied on highly aggressive mice with hippocampal CA3-restricted BDNF knockout (KO), in which aggression may mask other behaviors. KO showed less preference to contacting familiar conspecific than wild type (WT) during phase-2 but no differences during phase-1. Among non-social behaviors, eating duration was shorter in the presence of familiar than unfamiliar conspecific in WT, but same in KO. Additionally, KO exhibited reduced pain sensitization. Altogether, these findings suggest that KO has deficits in circuits that process social cues from familiar conspecifics and pain and, possibly, underlie empathy-like behaviors.
Computational proteogenomic identification and functional interpretation of translated fusions and micro structural variations in cancer
Authors: Lin Yen Yi , Gawronski Alexander , Hach Faraz , Li Sujun , Numanagić Ibrahim , Sarrafi Iman , Mishra Swati , McPherson Andrew , Collins Colin , Radovich Milan , Tang Haixu , Sahinalp S. Cenk
Published: July 2017

Motivation

Rapid advancement in high throughput genome and transcriptome sequencing (HTS) and mass spectrometry (MS) technologies has enabled the acquisition of the genomic, transcriptomic and proteomic data from the same tissue sample. In this paper we introduce a novel computational framework which can integratively analyze all three types of omics data to obtain a complete molecular profile of a tissue sample, in normal and disease conditions. Our framework includes MiStrVar, an algorithmic method we developed to identify micro structural variants (microSVs) on genomic HTS data. Coupled with deFuse, a popular gene fusion detection method we developed earlier, MiStrVar can provide an accurate profile of structurally aberrant transcripts in cancer samples. Given the breakpoints obtained by MiStrVar and deFuse, our framework can then identify all relevant peptides that span the breakpoint junctions and match them with unique proteomic signatures in the respective proteomics data sets. Our framework's ability to observe structural aberrations at three levels of omics data provides means of validating their presence.

Results

We have applied our framework to all The Cancer Genome Atlas (TCGA) breast cancer Whole Genome Sequencing (WGS) and/or RNA-Seq data sets, spanning all four major subtypes, for which proteomics data from Clinical Proteomic Tumor Analysis Consortium (CPTAC) have been released. A recent study on this dataset focusing on SNVs has reported many that lead to novel peptides [1]. Complementing and significantly broadening this study, we detected 244 novel peptides from 432 candidate genomic or transcriptomic sequence aberrations. Many of the fusions and microSVs we discovered have not been reported in the literature. Interestingly, the vast majority of these translated aberrations (in particular, fusions) were private, demonstrating the extensive inter-genomic heterogeneity present in breast cancer. Many of these aberrations also have matching out-of-frame downstream peptides, potentially indicating novel protein sequence and structure. Moreover, the most significantly enriched genes involved in translated fusions are cancer-related. Furthermore a number of the somatic, translated microSVs are observed in tumor suppressor genes.

Contact

cenksahi@indiana.edu
Rare genetic variants in the endocannabinoid system genesCNR1andDAGLAare associated with neurological phenotypes in humans
Authors: Smith Douglas R. , Stanley Christine M. , Foss Theodore , Boles Richard G. , McKernan Kevin
Published: July 2017

Rare genetic variants in the core endocannabinoid system genesCNR1,CNR2,DAGLA,MGLLandFAAHwere identified in molecular testing data from up to 6.032 patients with a broad spectrum of neurological disorders. The variants were evaluated for association with phenotypes similar to those observed in the orthologous gene knockouts in mice. Heterozygous rare coding variants inCNR1, which encodes the type 1 cannabinoid receptor (CB1), were found to be significantly associated with pain sensitivity (especially migraine), sleep and memory disorders - alone or in combination with anxiety - compared to a set of controls without suchCNR1variants. Similarly, heterozygous rare variants inDAGLA, which encodes diacylglycerol lipase alpha, were found to be significantly associated with seizures and developmental disorders, including abnormalities of brain morphology, compared to controls. Rare variants inMGLL,FAAHandCNR2were not associated with any neurological phenotypes in the patients tested. Diacylglycerol lipase alpha synthesizes the endocannabinoid 2-AG in the brain, which interacts with CB1 receptors. The phenotypes associated with rareCNR1variants are reminiscent of those implicated in the theory of clinical endocannabinoid deficiency syndrome. The severe phenotypes associated with rareDAGLAvariants underscore the critical role of rapid 2-AG synthesis and the endocannabinoid system in regulating neurological function and development. Mapping of the variants to the 3D structure of the type 1 cannabinoid receptor, or primary structure of diacylglycerol lipase alpha, reveals clustering of variants in certain structural regions and is consistent with impacts to function.
Identification of Pathways Associated with Chemosensitivity through Network Embedding
Authors: Wang Sheng , Huang Edward , Cairns Junmei , Peng Jian , Wang Liewei , Sinha Saurabh
Published: July 2017

Basal gene expression levels have been shown to be predictive of cellular response to cytotoxic treatments. However, such analyses do not fully reveal complex genotype-phenotype relationships, which are partly encoded in highly interconnected molecular networks. Biological pathways provide a complementary way of understanding drug response variation among individuals. In this study, we integrate chemosensitivity data from a recent pharmacogenomics study with basal gene expression data from the CCLE project and prior knowledge of molecular networks to identify specific pathways mediating chemical response. We first develop a computational method called PACER, which ranks pathways for enrichment in a given set of genes using a novel network embedding method. It examines known relationships among genes as encoded in a molecular network along with gene memberships of all pathways to determine a vector representation of each gene and pathway in the same low-dimensional vector space. The relevance of a pathway to the given gene set is then captured by the similarity between the pathway vector and gene vectors. To apply this approach to chemosensitivity data, we identify genes with basal expression levels in a panel of cell lines that are correlated with cytotoxic response to a compound, and then rank pathways for relevance to these response-correlated genes using PACER. Extensive evaluation of this approach on benchmarks constructed from databases of compound target genes, compound chemical structure, as well as large collections of drug response signatures demonstrates its advantages in identifying compound-pathway associations, compared to existing statistical methods of pathway enrichment analysis. The associations identified by PACER can serve as testable hypotheses about chemosensitivity pathways and help further study the mechanism of action of specific cytotoxic drugs. More broadly, PACER represents a novel technique of identifying enriched properties of any gene set of interest while also taking into account networks of known gene-gene relationships and interactions.
Ewald: an extended wide-angle Laue diffractometer for the second target station of the Spallation Neutron Source
Authors: Coates Leighton , Robertson Lee
Published: July 2017

Visualizing hydrogen atoms in biological materials is one of the biggest remaining challenges in biophysical analysis. While X-ray techniques have unrivaled capacity for high-throughput structure determination, neutron diffraction is uniquely sensitive to hydrogen atom positions in crystals of biological materials and can provide a more complete picture of the atomic and electronic structures of biological macromolecules. This information can be essential in providing predictive understanding and engineering control of key biological processes, for example, in catalysis, ligand binding and light harvesting, and to guide bioengineering of enzymes and drug design. One very common and large capability gap for all neutron atomic resolution single-crystal diffractometers is the weak flux of available neutron beams, which results in limited signal-to-noise ratios giving a requirement for sample volumes of at least 0.1 mm3. The ability to operate on crystals an order of magnitude smaller (0.01 mm3) will open up new and more complex systems to studies with neutrons which will help in our understanding of enzyme mechanisms and enable us to improve drugs against multi resistant bacteria. With this is mind, an extended wide-angle Laue diffractometer, `Ewald', has been designed, which can collect data using crystal volumes below 0.01 mm3.
Influence of sodium alginate inhibitor addition on the corrosion protection performance of AZ91D magnesium alloy in NaCl solution
Authors: Li Yan , Ba Zhi Xin , Li Yong Liang , Ge Yan , Zhu Xi Chang
Published: July 2017

Purpose

This paper aims to investigate the inhibition effect of sodium silicate (SS), sodium alginate (SA) and sodium tungstate (ST) on the corrosion behavior of AZ91D magnesium alloy in 3.5 per cent NaCl solution through polarization curve test at room temperature, electrochemical impedance spectroscopy and weight loss measurement.

Design/methodology/approach

The influence of SA concentration on the inhibition efficiency of the corrosion inhibitor was mainly analyzed. The corrosion morphology and inhibition mechanism of the samples were also analyzed with scanning electron microscopy and energy-dispersive spectroscopy.

Findings

The results show that with the increase of SA concentration, the corrosion inhibition first increases and then decreases. When SA concentration is 0.03 mol/L, the inhibition efficiency is the highest, reaching 98 per cent. The adsorption film formed by SA and other deposition films produce a synergistic effect on the improvement of corrosion resistance of AZ91D magnesium alloy.

Originality/value

The adsorption film formed by SA with other deposition films produces a synergistic effect on the improvement of corrosion resistance of AZ91D magnesium alloy. With the increase of SA concentration, the corrosion inhibition first increases and then decreases. When the concentrations of SA, SS and ST are 0.03 mol/L, 0.015 mol/L and 0.02 mol/L, respectively, the inhibition efficiency of the inhibitor is the highest, reaching 98 per cent.
Hot corrosion behaviour of Super 304H for marine applications at elevated temperatures
Authors: Khan M. Adam , Sundarrajan S. , Natarajan S.
Published: July 2017

Purpose

The aim of this paper is to study the hot corrosion behaviour of super 304H stainless steel for marine applications.

Design/methodology/approach

The investigation was carried out with three different combinations of salt mixture (Na2SO4, NaCl and V2O5) at two different temperatures (800 and 900°C).

Findings

The spalling and growth of oxide layer was observed more with the presence of V2O5 in the salt mixture at 900°C during experimentation than what was observed in 800°C. The mass change per unit area is calculated to study the corrosion kinetics and also the influence of salt mixture. Further, the samples are analysed through materials characterisation techniques using optical image, scanning electron microscope (SEM), energy dispersive X-ray (EDAX) and X-ray diffraction (XRD) analysis. The presence of V2O5 in the salt mixture was the most important influencing species for accelerating hot corrosion.

Originality/value

SEM, EDAX and XRD analysis confirmed the formation of Fe2O3 and Cr2O3 at 900°C showing contribution in corrosion protection.
Essential oil of “Foeniculum vulgare”: antioxidant and corrosion inhibitor on mild steel immersed in hydrochloric medium
Authors: Bouoidina Asmae , Chaouch Mehdi , Abdellaoui Abdelfattah , Lahkimi Amal , Hammouti Belkheir , El-Hajjaji Fadoua , Taleb Mustapha , Nahle Ayssar
Published: July 2017

Purpose

The inhibition effect ofFoeniculum vulgareseeds’ (FVS) extract on the corrosion of mild steel in acidic medium was studied using weight loss, electrochemical impedance spectroscopy and Tafel polarization, as well as the surface morphology of the mild steel.

Design/methodology/approach

Weight loss measurements, potentiodynamic tests, electrochemical impedance spectroscopy studies and gas chromatography/mass spectrometry and scanning electron microscopy analysis of FVS extract were performed.

Findings

FVS extract acts as a good inhibitor for the corrosion of mild steel in 1.0 M HCl. The inhibition efficiency increases with the increase in inhibitor concentration but decreases with the increase of temperature.

Practical implications

FVS extract was observed to play an important role in the corrosion inhibition of mild steel in acidic solution.

Originality/value

This paper is intended to be added to the family of green inhibitors which are highly efficient inhibitors and can be used in the area of corrosion prevention and control.
Studies on erosion-corrosion behaviour of plasma sprayed Ni3Al coating in a coal-fired thermal power plant environment at 540°C
Authors: Mishra S.B. , Chandra Kamlesh , Prakash Satya
Published: July 2017

Purpose

The purpose of this study is to investigate the application of Ni3Al coating for boilers and other power plant equipment, which suffer severe erosion-corrosion problems resulting in substantial losses. Currently, superalloys are being used to increase the service life of the boilers. Although the superalloys have adequate mechanical strength at elevated temperature, they often lack resistance to erosion-corrosion environments.

Design/methodology/approach

In this paper, the erosion-corrosion performance of plasma-sprayed nickel aluminide (Ni3Al) coating on nickel- and iron-based superalloys have been evaluated by exposing them to the low temperature primary superheater zone of the coal-fired thermal power plant at the temperature zone of 540°C for ten cycles of 100 h duration. The exposed products were analysed along the surface and cross-section using scanning electron microscopy (SEM), X-ray diffraction (XRD) and electron micro probe analysis (EPMA).

Findings

The XRD, SEM and EPMA analyses have shown the formation of mainly NiO, NiAl2O4 and indicated the presence of Ni3Al, Ni and Al2O3. In the boiler environment, Ni3Al coating partially oxidizes and acts as a perfect barrier against erosion-corrosion of superalloys. The partially oxidised Ni3Al coating remains intact even after 1,000 h cycle exposure.

Originality/value

The probable mechanism of attack for the plasma-sprayed Ni3Al coating in the given boiler environment is presented.
Integrating the IR into strategic goals at the University of Toledo: case study
Authors: Sabharwal Arjun , Natal Gerald R.
Published: July 2017

Purpose

The purpose of this case study is to demonstrate a current model, as well as explore future models, for integrating institutional repositories (IRs) in higher education goals at the University of Toledo.

Design/methodology/approach

This is a case study that uses literature review as an exploratory framework for new approaches while reflecting on existing literature to present the current practical framework for using IRs.

Findings

The digital environment has pushed academic institutions toward new strategies for curating their record on scholarship and preserving their heritage collections, using their IRs. Innovative approaches are also vital to curating the IR content digitally to facilitate access to those contents in ways that was not possible a few decades ago. Surveys and existing literature point to increasing uses of IRs despite abstinence from considering open access for scholarly activity among faculty concerned about copyright, plagiarism and sustainability. Staffing and funding IR initiatives are important factors in sustaining the curation of scholarship in the digital environment.

Practical implications

IRs with open access publishing, expert gallery and digital library features place academic libraries in a central role as partners in digital scholarship.

Originality/value

This case study presents an original approach to incorporating the IR into the curation of digital content while also considering potential uses of knowledge management approaches for data and knowledge sharing in an academic environment.
Back to basics
Authors: Fox Robert
Published: July 2017

Purpose

This paper aims to explore several methods for developing an effective content model for library websites.

Design/methodology/approach

This paper is conceptual.

Originality/value

Websites can take a couple of approaches to design. One is “top down” that focuses on the User Interface (UI) and graphic design. Another is “bottom up” that focuses on the organization of content. This paper encourages website designers to take a more “bottom up” approach to web design.
PlumX: a tool to showcase academic profile and distinction
Authors: Wong Elise Y. , Vital Sarah M.
Published: July 2017

Purpose

The Saint Mary’s College of California (SMC) library plays an integral role in supporting one of the goals in the College’s Strategic Plan: “Raise the Academic Profile and Distinction”. This case study aims to assess the effectiveness of PlumX as a tool to showcase the academic profile and distinction of SMC. The library recognizes the importance of capturing impact of non-traditional creativity and engagement in addition to just traditional impact metrics of research.

Design/methodology/approach

This paper describes the collaborative effort of the College and the College’s library to identify faculty scholarship, creativity and engagement and collect data demonstrating the impact of the works. Traditional metrics, like citation counts, do not do SMC faculty justice because faculty scholarship comes beyond just books and articles. To more fully document the real intellectual corpus the College, the library is working with a new system, PlumX, to collect web-based information about both traditionally and non-traditionally published work.

Findings

The collection of metrics across five categories (citations, usage, social media, mentions and captures), and the flexibility of displaying on screen or downloading for use in other analytic reports made possible through PlumX proved to be a start toward demonstrating the academic distinction of College’s unique faculty. SMC will continue to partner with PlumX to assess and improve its usability and effectiveness.

Originality/value

This paper outlines how altmetrics can be used to measure and share impact of faculty research at a liberal arts, teaching-focused college in ways reflective of the unique intellectual contributions.
Restrained by design: the political economy of cybersecurity
Authors: Lindsay Jon Randall
Published: July 2017

Purpose

The empirical record of cyberattacks features much computer crime, espionage and hacktivism, but none of the major damage feared in prevalent threat narratives. The purpose of this article is to explain the absence of serious adverse consequences to date and the durability of this trend.

Design/methodology/approach

This paper combines concepts from international relations theory and new institutional economics to understand cyberspace as a complex global institution with contracts embodied in both software code and human practice. Constitutive inefficiencies (market and regulatory failure) and incomplete contracts (generative features and unintended flaws) create the vulnerabilities that hackers exploit. Cyber conflict is a form of cheating within the rules, rather than an anarchic struggle, more like an intelligence-counterintelligence contest than traditional war.

Findings

Cyber conflict is restrained by the collective sociotechnical constitution of cyberspace, where actors must cooperate to compete. Maintenance of common protocols and open access is a condition for the possibility of attack, and successful deceptive exploitation of these connections becomes more difficult in politically sensitive situations as defense and deterrence become more feasible. The distribution of cyber conflict is, thus, bounded vertically in severity but unbounded horizontally in the potential for creative exploitation.

Originality/value

Cyber conflict can be understood with familiar political economic concepts applied in fresh ways. This application provides counterintuitive insights at odds with prevalent threat narratives about the likelihood and magnitude of cyber conflict. It also highlights the important advantages of strong states over the weaker non-state actors widely thought to be empowered by cyberspace.