bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical impact of clonal and subclonal TP53, SF3B1, BIRC3, NOTCH1, and ATM mutations in chronic lymphocytic leukemia
Authors: Nadeu Ferran , Delgado Julio , Royo Cristina , Baumann Tycho , Stankovic Tatjana , Pinyol Magda , Jares Pedro , Navarro Alba , Martín-García David , Beà Sílvia , Salaverria Itziar , Oldreive Ceri , Aymerich Marta , Suárez-Cisneros Helena , Rozman Maria , Villamor Neus , Colomer Dolors , López-Guillermo Armando , González Marcos , Alcoceba Miguel , Terol Maria José , Colado Enrique , Puente Xose S. , López-Otín Carlos , Enjuanes Anna , Campo Elías 
Published: February 2016

Key Points
Clonal and subclonal mutations of NOTCH1 and TP53, clonal mutations of SF3B1, and ATM mutations in CLL have an impact on clinical outcome. Clonal evolution in longitudinal samples occurs before and after treatment and may have an unfavorable impact on overall survival.
ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research
Authors: Pandey Ram Vinay , Pabinger Stephan , Kriegner Albert , Weinhäusel Andreas 
Published: February 2016

Abstract
Background
Traditional Sanger sequencing has been used as a gold standard method for genetic testing in clinic to perform single gene test, which has been a cumbersome and expensive method to test several genes in heterogeneous disease such as cancer. With the advent of Next Generation Sequencing technologies, which produce data on unprecedented speed in a cost effective manner have overcome the limitation of Sanger sequencing. Therefore, for the efficient and affordable genetic testing, Next Generation Sequencing has been used as a complementary method with Sanger sequencing for disease causing mutation identification and confirmation in clinical research. However, in order to identify the potential disease causing mutations with great sensitivity and specificity it is essential to ensure high quality sequencing data. Therefore, integrated software tools are lacking which can analyze Sanger and NGS data together and eliminate platform specific sequencing errors, low quality reads and support the analysis of several sample/patients data set in a single run.

Results
We have developed ClinQC, a flexible and user-friendly pipeline for format conversion, quality control, trimming and filtering of raw sequencing data generated from Sanger sequencing and three NGS sequencing platforms including Illumina, 454 and Ion Torrent. First, ClinQC convert input read files from their native formats to a common FASTQ format and remove adapters, and PCR primers. Next, it split bar-coded samples, filter duplicates, contamination and low quality sequences and generates a QC report. ClinQC output high quality reads in FASTQ format with Sanger quality encoding, which can be directly used in down-stream analysis. It can analyze hundreds of sample/patients data in a single run and generate unified output files for both Sanger and NGS sequencing data. Our tool is expected to be very useful for quality control and format conversion of Sanger and NGS data to facilitate improved downstream analysis and mutation screening.

Conclusions
ClinQC is a powerful and easy to handle pipeline for quality control and trimming in clinical research. ClinQC is written in Python with multiprocessing capability, run on all major operating systems and is available at https://sourceforge.net/projects/clinqc.
Assessment of central venous catheter colonization using surveillance culture of withdrawn connectors and insertion site skin
Authors: Pérez-Granda María Jesús , Guembe María , Cruces Raquel , Barrio José María , Bouza Emilio 
Published: February 2016

Abstract
Background
Culture of catheter hubs and skin surrounding the catheter entry site has a negative predictive value for catheter tip colonization. However, manipulation of the hub for culture requires the hubs to be swabbed, introducing potential dislodging of biofilm and subsequent migration of microorganisms. Hubs are usually closed with needleless connectors (NCs), which are replaced regularly. Our objective was to evaluate whether culture of flushed withdrawn NCs is an alternative to hub culture when investigating central venous catheter colonization.

Methods
The study population comprised 49 intensive care unit patients whose central venous catheters had been in place for at least 7 days. Cultures of NCs and skin were obtained weekly.

Results
We included 82 catheters with more than 7 days’ indwelling time. The catheter tip colonization rate was 18.3 % (15/82). Analysis of skin and NC cultures revealed a 92.5 % negative predictive value for catheter colonization. Three episodes of catheter-related bloodstream infection (C-RBSI) occurred in patients with colonized catheters.

Conclusion
Surveillance of NC and skin cultures could help to identify patients at risk for C-RBSI.
The use of laser in garment manufacturing: an overview
Authors: Nayak Rajkishore , Padhye Rajiv 
Published: February 2016

AbstractLaser is being used in apparel industry from nineteenth century for various garment manufacturing applications. There are several advantages of using laser over the conventional processes in cutting, engraving, embossing, denim fading and other applications. In addition, product damage potential is reduced, no/less consumables are needed and no problem of toxic by-product disposal as found in some processes. Today’s laser equipment is a result of continuous research and development of earlier products, which has undergone several changes. The initial laser systems were cumbersome, hard to run and difficult to maintain. However, the modern laser systems are simpler in operation and maintenance. Furthermore, the earlier systems were involved with more safety issues and needed the gasses to be constantly replenished. The garment manufactures around the globe should take the advantage of laser application in the post multi-fibre agreement regime to make their products more competitive. This review focuses on the technology of laser including various classifications. In addition it includes the applications of laser in garment manufacturing, their potential hazards and health related concerns.
Cardiovascular Disease Among Survivors of Adult-Onset Cancer: A Community-Based Retrospective Cohort Study
Authors: Armenian Saro H. , Xu Lanfang , Ky Bonnie , Sun Canlan , Farol Leonardo T. , Pal Sumanta Kumar , Douglas Pamela S. , Bhatia Smita , Chao Chun 
Published: February 2016

Purpose Cardiovascular diseases (CVDs), including ischemic heart disease, stroke, and heart failure, are well-established late effects of therapy in survivors of childhood and young adult (< 40 years at diagnosis) cancers; less is known regarding CVD in long-term survivors of adult-onset (≥ 40 years) cancer. Methods A retrospective cohort study design was used to describe the magnitude of CVD risk in 36,232 ≥ 2-year survivors of adult-onset cancer compared with matched (age, sex, and residential ZIP code) noncancer controls (n = 73,545) within a large integrated managed care organization. Multivariable regression was used to examine the impact of cardiovascular risk factors (CVRFs; hypertension, diabetes, dyslipidemia) on long-term CVD risk in cancer survivors. Results Survivors of multiple myeloma (incidence rate ratio [IRR], 1.70; P < .01), carcinoma of the lung/bronchus (IRR, 1.58; P < .01), non-Hodgkin lymphoma (IRR, 1.41; P < .01), and breast cancer (IRR, 1.13; P < .01) had significantly higher CVD risk when compared with noncancer controls. Conversely, prostate cancer survivors had a lower CVD risk (IRR, 0.89; P < .01) compared with controls. Cancer survivors with two or more CVRFs had the highest risk of CVD when compared with noncancer controls with less than two CVRFs (IRR, 1.83 to 2.59; P < .01). Eight-year overall survival was significantly worse among cancer survivors who developed CVD (60%) when compared with cancer survivors without CVD (81%; P < .01). Conclusion The magnitude of subsequent CVD risk varies according to cancer subtype and by the presence of CVRFs. Overall survival in survivors who develop CVD is poor, emphasizing the need for targeted prevention strategies for individuals at highest risk of developing CVD.
Clueless is a conserved ribonucleoprotein that binds the ribosome at the mitochondrial outer membrane
Authors: Sen Aditya , Cox Rachel T. 
Published: February 2016

ABSTRACTMitochondrial function is tied to the nucleus, in that hundreds of proteins encoded by nuclear genes must be imported into mitochondria. While post-translational import is fairly well understood, emerging evidence supports that mitochondrial site-specific import, or co-translational import, also occurs. However, the mechanism and the extent to which it is used are not fully understood. We have previously shown Clueless (Clu), a conserved multi-domain protein, associates with mitochondrial outer membrane proteins, including Translocase of outer membrane 20, and genetically and physically interacts with the PINK1–Parkin pathway. The human ortholog of Clu, Cluh, was shown to bind nuclear-encoded mitochondrially destined mRNAs. Here we identify the conserved tetratricopeptide domain of Clu as predominantly responsible for binding mRNA. In addition, we show Clu interacts with the ribosome at the mitochondrial outer membrane. Taken together, these data support a model whereby Clu binds to and mitochondrially targets mRNAs to facilitate mRNA localization to the outer mitochondrial membrane, potentially for site-specific or co-translational import. This role may link the presence of efficient mitochondrial protein import to mitochondrial quality control through the PINK1–Parkin pathway.
ER stress and basement membrane defects combine to cause glomerular and tubular renal disease resulting from Col4a1 mutations in mice
Authors: Jones Frances E. , Bailey Matthew A. , Murray Lydia S. , Lu Yinhui , McNeilly Sarah , Schlötzer-Schrehardt Ursula , Lennon Rachel , Sado Yoshikazu , Brownstein David G. , Mullins John J. , Kadler Karl E. , Van Agtmael Tom 
Published: February 2016

ABSTRACT
Collagen IV is a major component of basement membranes, and mutations in COL4A1, which encodes collagen IV alpha chain 1, cause a multisystemic disease encompassing cerebrovascular, eye and kidney defects. However, COL4A1 renal disease remains poorly characterized and its pathomolecular mechanisms are unknown. We show that Col4a1 mutations in mice cause hypotension and renal disease, including proteinuria and defects in Bowman's capsule and the glomerular basement membrane, indicating a role for Col4a1 in glomerular filtration. Impaired sodium reabsorption in the loop of Henle and distal nephron despite elevated aldosterone levels indicates that tubular defects contribute to the hypotension, highlighting a novel role for the basement membrane in vascular homeostasis by modulation of the tubular response to aldosterone. Col4a1 mutations also cause diabetes insipidus, whereby the tubular defects lead to polyuria associated with medullary atrophy and a subsequent reduction in the ability to upregulate aquaporin 2 and concentrate urine. Moreover, haematuria, haemorrhage and vascular basement membrane defects confirm an important vascular component. Interestingly, although structural and compositional basement membrane defects occurred in the glomerulus and Bowman's capsule, no tubular basement membrane defects were detected. By contrast, medullary atrophy was associated with chronic ER stress, providing evidence for cell-type-dependent molecular mechanisms of Col4a1 mutations. These data show that both basement membrane defects and ER stress contribute to Col4a1 renal disease, which has important implications for the development of treatment strategies for collagenopathies.
Description of the school environment related to physical education classes, recess, extracurricular activities and physical spaces in the city of Pelotas, RS, Brazil
Authors: Knuth Alan , Silva Inácio , Hallal Pedro 
Published: February 2016

The aim of the present study was to describe the school environment of public and private primary schools from the city of Pelotas, RS, Southern Brazil, according to the availability of Physical Education (PE) classes, breaks, extracurricular activities and physical spaces. A cross-sectional study was conducted, including both public and private schools. In each school, the principal or a PE teacher was interviewed to assess PE classes, recess and extracurricular activities, while a checklist was carried out to evaluate the quality and availability of physical spaces. A total of 71.9% of the 99 schools had PE classes for grades 1 to 4. Extracurricular projects were available in 59.6% of the schools and 71.2% offered free activities to students. The most common activities are dancing and “futsal”. There was a gym in 10.1% of schools (40.0% of private and 4.8% of public schools). Higher availability and quality of outdoor courts, indoor rooms, multimedia rooms and green areas were more consistently found among private schools than public schools. Our findings indicated a low coverage of PE classes in grades 1 to 4, and insufficient availability and quality of physical structures in the public schools, compared to private ones. Many environmental features should be used in order to improve students’ health and well-being.
A Stimulation and rehabilitation program: Oficina da Lembrança
Authors: Krug Rodrigo , Ono Lariane , Quialheiro Anna , D’Orsi Eleonora , Ramos Luiz , Xavier André 
Published: February 2016

This study aimed to present the method of the multi-center program of cognitive stimulation and rehabilitation known as “Oficina da Lembrança” (Memory Workshop), held at the University of Southern Santa Catarina, Federal University of Santa Catarina and Federal University of São Paulo. This project has assisted about 450 people aged 50 or older with memory complaints. Each session consists of one to three meetings/week (approximately 20 meetings/semester), with groups of 10 to 20 participants to carry out activities on computers, physical activity and individual oral reports of the experiences they had at the meetings (approximately 90 minutes). In the first and final six-monthly meeting, socio-demographic, health and behavioral variables, cognitive performance, functional disability and presence of depressive symptoms are collected. The project was implemented in 2006 and it is expected to continue. Programs like this are extremely important in society because they can provide benefits to the population, especially in terms of helping cognitive improvement, thus promoting health and socialization.
Quantifying mercury isotope dynamics in captive Pacific bluefin tuna (Thunnus orientalis)
Authors: Kwon Sae Yun , Blum Joel D. , Madigan Daniel J. , Block Barbara A. , Popp Brian N. 
Published: February 2016

Abstract
Analyses of mercury (Hg) isotope ratios in fish tissues are used increasingly to infer sources and biogeochemical processes of Hg in natural aquatic ecosystems. Controlled experiments that can couple internal Hg isotope behavior with traditional isotope tracers (δ13C, δ15N) can improve the applicability of Hg isotopes as natural ecological tracers. In this study, we investigated changes in Hg isotope ratios (δ202Hg, Δ199Hg) during bioaccumulation of natural diets in the pelagic Pacific bluefin tuna (Thunnus orientalis; PBFT). Juvenile PBFT were fed a mixture of natural prey and a dietary supplement (60% Loligo opalescens, 31% Sardinops sagax, 9% gel supplement) in captivity for 2914 days, and white muscle tissues were analyzed for Hg isotope ratios and compared to time in captivity and internal turnover of δ13C and δ15N. PBFT muscle tissues equilibrated to Hg isotope ratios of the dietary mixture within ∼700 days, after which we observed a cessation in further shifts in Δ199Hg, and small but significant negative δ202Hg shifts from the dietary mixture. The internal behavior of Δ199Hg is consistent with previous fish studies, which showed an absence of Δ199Hg fractionation during Hg bioaccumulation. The negative δ202Hg shifts can be attributed to either preferential excretion of Hg with higher δ202Hg values or individual variability in captive PBFT feeding preferences and/or consumption rates. The overall internal behavior of Hg isotopes is similar to that described for δ13C and δ15N, though observed Hg turnover was slower compared to carbon and nitrogen. This improved understanding of internal dynamics of Hg isotopes in relation to δ13C and δ15N enhances the applicability of Hg isotope ratios in fish tissues for tracing Hg sources in natural ecosystems.
A prospective review of appetite loss and recovery time in primary joint replacement patients
Authors: Prodger S , McAuliffe M , Bopf D , Kingston D 
Published: February 2016

Introduction Appetite loss is commonly reported by patients following major surgery, including total joint arthroplasty (TJA). A number of studies have examined related problems, particularly in relation to physiological responses to surgery. However, no published paper has looked specifically at the duration of appetite loss in total knee arthroplasty (TKA) and total hip arthroplasty (THA) patients. Methods A simple, established appetite screening tool was administered preoperatively and at 2-week intervals postoperatively in 50 TJA patients until appetite levels returned to preoperative levels. The results were examined for various descriptive parameters and compared using the chi-squared test. Results Thirty-three patients underwent TKA and 17 THA. There were 27 female and 23 male patients. No patients were lost to follow-up. The median time for return of appetite in both male and female patients was 4 weeks (interquartile range [IQR]: male, 2–4; female, 4–6). The median time for return of appetite was 4 weeks both in TKA patients (IQR 4–6) and in those undergoing THA (IQR 4–4). The time to return of appetite was not significantly associated with either the gender of the patients (p=0.13) or the type of joint replacement (p=0.49). Conclusions The study provides a clear time frame for return of appetite in uncomplicated primary joint replacements. This is a commonly noted patient problem that has not previously been specifically reviewed.
Chauchesko caught at the centre of Cock Fight
Authors: Shand Ryan 
Published: February 2016

Abstract
Chauchesko is caught at the centre of a conflict that he attempts to defuse. This article demonstrates that he is often visually positioned between the two main characters (Shots 14, 16, 27, 29, 31, 50, 62, 88) as the situation escalates. His character provides an outsider’s perspective, and importantly an accompanying reflective tone, to this short narrative.
Checkpoint identities: The battle of masculinities
Authors: Anishchenkova Valerie 
Published: February 2016

Abstract
The entirety of Cock Fight takes place at a checkpoint – a physical and symbolic space where, by definition, identities are ‘checked’ and thereby established and articulated. The article argues that this cinematic location invites four distinct constructions of masculinity, while commenting on gender discourses in the pre-second intifada Israeli society.
Blocking space: Metaphorical spatial constraints in the cinematography and mise-en-scène of Cock Fight
Authors: Schupp Janina 
Published: February 2016

Abstract
Roadblocks represent great spatial restrictions for the West Bank population. This article explores how the film Cock Fight employs the cinematic tools of cinematography and mise-en-scène in the framing of characters and objects to metaphorically reflect and question the effect of these imposed constraints on human relations and spatial mobility.
Productive failure in a machine-centric universe
Authors: Hesselberth Pepita 
Published: February 2016

Abstract
Drawing on the writings of Borgmann, Virilio and Lazzarato, this article comments on the prevalence of failure in Draft: the failure to communicate, the failure of technology, of perception, and arguably of war. Productive failure, I set out to demonstrate, is the key component of the film’s cultural critique.
The ideological ashtray: Draft’s political allegory of disillusionment
Authors: Utin Pablo 
Published: February 2016

Abstract
Made after the collapse of the Oslo peace process, Draft expresses the sense of failure and disorientation of left-wing Israeli ideologies and their replacement with more nationalistic right-wing views. Through the analysis of mise-en-scène and the film’s use of narrow point of view (PoV), the article will depict Draft’s political allegory of disillusion.
A quadratic model of consciousness
Authors: Wood John 
Published: February 2016

Abstract
This article describes methods and ideas that emerged from a continuing enquiry into ‘metadesign’ that led us to think about the role of ‘consciousness’ in teams, communities and the biosphere. In the West the notion of ‘consciousness’ has been shaped by humanism, industrialization and some strident forms of individualism. These have encouraged us to see it in strongly anthropocentric and solipsistic terms. The global economic system also reflects this individualistic ideology, given that ‘growth’, is driven by personal avarice on a collective scale. On the other hand, capitalism encourages enterprises to scale-up when they become successful. Both tendencies reduce the consciousness of organizations and communities. The article illustrates this idea by describing a ‘quadratic’ model of team consciousness that was developed to enhance practical developments that support personal, interpersonal, transpersonal and environmentally situated modes of awareness.
The spaces of narrative consciousness: Or, what is your event?
Authors: Alsobrook Law 
Published: February 2016

Abstract
Cyberspace, a term popularized in the 1984 novel Neuromancer, was used by William Gibson to describe the ‘consensual hallucination’ and interstitial online world that lies between the reality of our world and that of the surreal terrain of dreamscapes. While many attempts have been made to describe this intangible, yet seemingly perceptible space, the digital domain as a metaphor mirrors in many ways our own inadequate understanding of consciousness. Conversely, the physicist Michio Kaku explains that our reality is bounded by hyperspace – a multi-dimensioned space beyond our quotidian 3D existence that runs parallel, or tangential, to us along with the phenomenon of time. Indeed, if space and time (here considered as space–time) are a consolidated whole in the physical sense, perhaps our consciousness, as a structure manifest within this continuum may itself be thought of as a sensorial projection of this amalgam that attempts to observe and make sense, or meaning, of this condition. In truth, what if our need and delight in storytelling is driven by the evolution of our biology, as well as our impulse to locate our place in the universe? This article will attempt to examine and delimit the narrative confines of space–time as an appeal to, and an endeavour at, uncovering the alterity of storytelling as a function of consciousness. It will visit the realms of the holograph, quantum mechanics, virtual and augmented realities, as well as other scientific and philosophical tracts as a means to investigate and explore the physiology of space and our imperative desire to share stories.
On the distinction between distinction and division
Authors: Straeubig Michael 
Published: February 2016

Abstract
In this article I discuss the use of distinctions as a method for reasoning. First I trace the role of distinctions in three different theories: the formal calculus of George Spencer Brown, the constructivist biology of Humberto Maturana and Francisco Varela, and Niklas Luhmann’s theory of social systems. In the second part, play is used as an example to illustrate the concept. In particular, I contrast walking through a series of distinctions with traditional ways of argumentation based on definitions. Finally, I hint at the role of distinctions in a metaphysical sense.