bluuebunny/crossref_metadata_2025_split 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.
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.
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

AbstractAlthough 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

ABSTRACTAccurate 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

AbstractDNA 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

AbstractFamiliarity 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

MotivationRapid 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.ResultsWe 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.Contactcenksahi@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

AbstractRare 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

ABSTRACTBasal 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.