bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallelizing a finite element solver in computational hemodynamics
Authors: Auricchio F , Ferretti M , Lefieux A , Musci M , Reali A , Trimarchi S , Veneziani A 
Published: May 2016

In the last 20 years, a new approach has emerged to investigate the physiopathology of circulation. By merging medical images with validated numerical models, it is possible to support doctors’ decision-making process. The iCardioCloud project aims at establishing a computational framework to perform a complete patient-specific numerical analysis, specially oriented to aortic diseases (like dissections or aneurysms) and to deliver a compelling synthesis. The project can be considered a pioneering example of a Computer Aided Clinical Trial: i.e., a comprehensive analysis of patients where the level of knowledge extracted by traditional measures and statistics is enhanced through the massive use of numerical modeling. From a computer engineering point of view, iCardioCloud faces multiple challenges. First, the number of problems to solve for each patient is significantly huge – this is typical of computational fluid dynamics (CFD) – and it requires parallel methods. In addition, working in a clinical environment demands efficiency as the timeline requires rapid quantitative answers (as may happen in an emergency scenario). It is therefore mandatory to employ high-end parallel systems, such as large clusters or supercomputers. Here we discuss a parallel implementation of an application within the iCardioCloud project, built with a black-box approach – i.e., by assembling and configuring existing packages and libraries and in particular LifeV, a finite element library developed to solve CFD problems. The goal of this paper is to describe the software architecture underlying LifeV and to assess its performance and the most appropriate parallel paradigm. This paper is an extension of a previous work presented at the PBio 2015 Conference. This revision extends the description of the software architecture and discusses several new serial and parallel optimizations to the application. We discuss the introduction of hybrid parallelism in order to mitigate some performance problems previously experienced.
Exploring Environmental Variation in Residential Care Facilities for Older People
Authors: Nordin Susanna , McKee Kevin , Wijk Helle , Elf Marie 
Published: May 2016

Objective: The aim of this study was to explore variation in environmental quality in Swedish residential care facilities (RCFs) using the Swedish version of the Sheffield Care Environment Assessment Matrix (S-SCEAM). Background: Well-designed physical environments can positively impact on health and well-being among older persons with frail health living in RCFs and are essential for supporting person-centered care. However, the evidence base for informing the design of RCFs is weak, partly due to a lack of valid and reliable instruments that could provide important information on the environmental quality. Methods: Twenty RCFs were purposively sampled from several regions, varying in their building design, year of construction, size, and geographic location. The RCFs were assessed using S-SCEAM and the data were analyzed to examine variation in environmental quality between and within facilities. Results: There was substantial variation in the quality of the physical environment between and within RCFs, reflected in S-SCEAM scores related to specific facility locations and with regard to domains reflecting residents’ needs. In general, private apartments and dining areas had high S-SCEAM scores, while gardens had lower scores. Scores on the safety domain were high in the majority of RCFs, whereas scores for cognitive support and privacy were relatively low. Conclusions: Despite high building standard requirements, the substantial variations regarding environmental quality between and within RCFs indicate the potential for improvements to support the needs of older persons. We conclude that S-SCEAM is a sensitive and unique instrument representing a valuable contribution to evidence-based design that can support person-centered care.
Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?
Authors: Prabh Neel , Rödelsperger Christian 
Published: May 2016

Abstract
Background
Current genome sequencing projects reveal substantial numbers of taxonomically restricted, so called orphan genes that lack homology with genes from other evolutionary lineages. However, it is not clear to what extent orphan genes are real, genomic artifacts, or represent non-coding RNAs.

Results
Here, we use a simple set of assumptions to test the nature of orphan genes. First, a sequence that is transcribed is considered a real biological entity. Second, every sequence that is supported by proteome data or shows a depletion of non-synonymous substitutions is a protein-coding gene. Using genomic, transcriptomic and proteomic data for the nematode Pristionchus pacificus, we show that between 4129–7997 (42–81 %) of predicted orphan genes are expressed and 3818–7545 (39–76 %) of orphan genes are under negative selection. In three cases that exhibited strong evolutionary constraint but lacked expression evidence in 14 RNA-seq samples, we could experimentally validate the predicted gene structures. Comparing different data sets to infer selection on orphan gene clusters, we find that the presence of a closely related genome provides the most powerful resource to robustly identify evidence of negative selection. However, even in the absence of other genomic data, the availability of paralogous sequences was enough to show negative selection in 8–10 % of orphan genes.

Conclusions
Our study shows that the great majority of previously identified orphan genes in P. pacificus are indeed protein-coding genes. Even though this work represents a case study on a single species, our approach can be transferred to genomic data of other non-model organisms in order to ascertain the protein-coding nature of orphan genes.
Herbal formula GAPT prevents beta amyloid deposition induced Ca2+/Calmodulin-dependent protein kinase II and Ca2+/Calmodulin-dependent protein phosphatase 2B imbalance in APPV717I mice
Authors: Shi Jing , Zhang Xuekai , Yin Long , Wei Mingqing , Ni Jingnian , Li Ting , Wang Pengwen , Tian Jinzhou , Wang Yongyan 
Published: May 2016

Abstract
Background
Synaptic dysfunction is one of the pathological characteristics of Alzheimer's disease (AD), which is directly related to the progressive decline of cognitive function. CaMKII and CaN have been found to play important roles in memory processes and synaptic transmission. So present study aimed to elucidate relationships between CaMKII, CaN and cognitive decline in APPV717I mice, and to reveal whether the cognitive improving effects of GAPT is conducted through rebalance CaMKII and CaN.

Methods
Three-month-old-male APPV717I mice were randomly divided into ten groups (n = 12 per group) and received intragastrically administrated vehicle, donepezil or different doses of herbal formula GAPT for 8 or 4 months. Three-month-old male C57BL/6 J mice was set as vehicle control.

Results
Immunohistochemistry analysis showed that there were CaMKII expression decrease in the CA1 region of APPV717I transgenic mice, while the CaMKII expression of donepezil or GAPT treated transgenic mice were all increased. And there were CaN expression increase in the brain cortex of APPV717I transgenic mice, while there were decrease of CaN expression in donepezil or GAPT treated transgenic group. Western blot analysis showed the similar expression pattern without significant difference.

Conclusion
GAPT extract have showed effectiveness in activating the expression of CaMKII and inhibiting the expression of CaN either before or after the formation of amyloid plaques in the brain of APPV717I transgenic mice, which may in certain way alleviated neuron synaptic dysfunction in AD.
Equilibrum and Nonequilibrium Chemical Reactions of Helicene Oligomers in the Noncovalent Bond Formation
Authors: Yamaguchi Masahiko , Arisawa Mieko , Shigeno Masanori , Saito Nozomi 
Published: May 2016

Abstract
Chemical reactions involving noncovalent bond formation are discussed with regard to the equilibrium and nonequilibrium states: An equilibrium-to-equilibirum chemical reaction involves change of equilibrium states by changing the environment; a nonequilibrium-to-equilibrium reaction involves change of metastable state to equilibrium. Complex nature of the chemical reactions, especially in the latter, is shown in terms of the multiple-path nature in the microscopic molecular structure changes and macroscopic concentration changes. Irreversible and reversible nonequilibrium-to-equilibrium chemical reactions are also compared in terms of the multiple-path. Helicene oligomers, which reversibly form double-helix and random-coil by temperature changes, are discussed with regard to the reversible nonequilibrium-to-equilibrium chemical reaction with self-catalysis, where notable chemical phenomena appear under nonequilibrium conditions.
Rare case of a liposarcoma in the brachial plexus
Authors: Kosutic D , Gajanan K 
Published: May 2016

Introduction A liposarcoma is a rare cancer of connective tissues that resemble fat cells under light microscopy. Case History A 73-year old female patient presented to our tertiary cancer centre with an eight-year history of a large, slow-growing painless mass in the right axilla. Magnetic resonance imaging showed a lipomatous, well-circumscribed mass of dimension 30 × 16 × 10cm extending towards the right clavicle and causing deformation to the right chest wall and right breast. Surgery revealed a large tumour that had stretched all three cords of the brachial plexus. Histopathology was consistent with a diagnosis of a low-grade liposarcoma. After a period of neuropraxia, the patient returned to normal activities 4 months after surgery. Conclusions Although extremely rare, low-grade liposarcomas of the brachial plexus should be considered in the differential diagnosis of a slow-growing axillary mass. Referral to a tertiary sarcoma centre is essential for an appropriate diagnosis, adequate treatment, and long-term follow-up.
Recurrence after composite repair of a giant hiatus hernia: ‘the golf club’ deformity is a distinctive clinical and radiological picture
Authors: Furtado RV , Falk GL , Vivian SJ 
Published: May 2016

Background Recurrence of a hiatus hernia after cardiopexy repair can obstruct the lower oesophagus but also provide characteristic radiographic images after a barium meal. Case History Two patients with recurrence of a hiatus hernia underwent repeat surgery. Here, we provide and discuss diagnostic imaging, surgical findings and outcome for these male and female patients. Conclusions Repeat surgery is indicated in patients with recurrence of a hiatus hernia after repair.
An unusual case of lipoma arborescens
Authors: Mohammad HR , Chaturvedi A , Peach C 
Published: May 2016

Introduction Lipoma arborescens is a rare condition of the synovial lining. It is particularly uncommon in the bicipitoradial bursae of the elbow. Case Report A 68-year-old woman presented with a 5-month history of anterior elbow pain and swelling causing discomfort. Radiography demonstrated reactive changes of radial tuberosity and magnetic resonance imaging confirmed lipoma arborescens of the bicipitoradial bursa with distal biceps tendinopathy. A bicipital bursa bursectomy and lipoma excision was performed. Gross pathology and histology was consistent with lipoma arborescens. Three months postoperatively, our patient had full range of motion and good strength. Conclusions To our knowledge, this is the first published case report of lipoma arborescens affecting the elbow. Recognising the differential diagnoses of anterior elbow pain and the characteristic imaging is essential for accurate diagnosis.
Necrotising fasciitis secondary to a colocutaneous fistula
Authors: Husnoo N , Patil S , Jackson A , Khan M 
Published: May 2016

Colocutaneous fistulae secondary to diverticular disease are rare, especially spontaneous fistulae. We report a case of a 74-year-old lady, with no previous history of diverticular disease, presenting with necrotising fasciitis of the anterior abdominal wall in the left iliac fossa, without any other symptoms. Urgent surgery was performed. An initial diagnostic laparoscopy demonstrated a perforated sigmoid diverticulum forming a fistula to the anterior abdominal wall. Following soft tissue debridement, a sigmoid colectomy was performed through a midline laparotomy. Gastrointestinal pathology should be considered as a potential cause of abdominal wall necrotising fasciitis. Our approach of using laparoscopic visualisation to assess for intra-abdominal sources in this context (in the absence of preoperative imaging when imaging could delay treatment) has not been described before. To our knowledge, only two cases of abdominal wall necrotising fasciitis secondary to diverticular disease with a colocutaneous fistula have been reported in the English literature.
The Iraq war in the context of global capitalism
Authors: Aoudé Ibrahim G. 
Published: May 2016

Abstract
The 1991 Gulf War and the 2003 occupation of Iraq were central to US global strategy to dominate global capitalism after the fall of the Soviet Union. The United States dealt with perceived challenges to its domination through conquest. The Middle East has been central to US global strategy to maintain control of Western Europe and in its rivalry with its two main competitors, the Russian Federation and China. Developing crises in global capitalism exposed the United States to instability in its global position, which it countered by invading and destabilizing Middle Eastern states. The following questions present themselves: What is the relationship between the crises of capitalist globalization and US global strategy? In what way is the Middle East central to US global strategy and instrumental in meeting the challenges posed by its rivals and competitors, the Russian Federation, China, the European Union and Iran? What role has Iraq played in this strategy? Attempting to answer these questions would go a significant way in assessing the US role in Iraq and the Middle East.
Iraq’s political economy post 2003: From transition to corruption
Authors: Sassoon Joseph 
Published: May 2016

Abstract
This article focuses on the transition of Iraq after the collapse of Saddam Hussein’s regime in 2003 as a result of the American-led invasion. Although the country’s institutions were shattered, efforts to rebuild them and create a truly open and democratic society failed. Thus, regime change did not lead to changes in the fundamentals of Iraq’s political economy. The article emphasizes how money was not the reason for lack of development; on the contrary, funds flooded the system, creating an all-encompassing corruption that seeped into every facet of life. The article discusses Prime Minister Hadi al-Abadi’s reforms after eight years of new authoritarianism in Iraq under Nuri al-Maliki (2006–2014).
Development of Preverbal Communication Skills Scale for Children with Multiple Disabilities and Visual Impairment
Authors: Ayyıldız Emine , Akçin Nur , Güven Yıldız 
Published: May 2016

Communication is crucial for any human being and the children with disabilities are no exception. Due to the number and combination of their disabilities and/or conditions, children with multiple disabilities and visual impairment (MDVI) have especially limitations of the ability to communicate the meaningful and functional way with their environment. In order to improve the communication skills of children with MDVI, it is very important to identify unique, individual communication behaviors of these children. Thus, the aim of this study was to develop a valid and reliable developmental assessment tool to evaluate preverbal communication skills of Turkish children with MDVI.Sequential explanatory mixed methods were used in the study. In the qualitative phase, semi-structured interviews were conducted with the mothers of 34 children suffering from MDVI to explore the preverbal communication behaviors of the children based on the daily observances of their mothers’ with a descriptive analysis being performed on the data. From the findings of the interviews and the literature review, Preverbal Communication Skills Scale for Children with Multiple Disabilities and Visual Impairment (PCSS-MDVI) and the scoring guide were developed. During the quantitative phase, 65 mothers of children with MDVI were given this scale in order to determine the validity and reliability of the scale. For the reliability analysis, 34 mothers of typically developing (TD) children age between 1 to 24 months old also were given the scale.The findings of the qualitative phase indicated that children with MDVI were communicating mostly with preverbal behaviors and the analysis on data from the quantitative phase with respect to item analysis, reliability and validity revealed that the scale is valid and reliable. The scale has 17 items and three subscales, which are; regulating behaviors, social interaction and joint attention. The majority of children with MDVI cannot communicate verbally and there is lack of studies and assessment tools for the purpose of effectively evaluate these children’s preverbal communicative behaviors in our country. Based on the analysis, the PCSS-MDVI has been demonstrated good preliminary psychometric properties and it can be used as an instrument to evaluate preverbal communication behaviors of children with MDVI. It is the preliminary study of the development of the scale. Thus, validation of the scale should be repeated with more participants and the data of the video observations of preverbal communication behaviors of children with MDVI should be added to the analysis.
Diagnosis is a team sport – partnering with allied health professionals to reduce diagnostic errors
Authors: Thomas Dana B. , Newman-Toker David E. 
Published: May 2016

Abstract

Background: Diagnostic errors are the most common, most costly, and most catastrophic of medical errors. Interdisciplinary teamwork has been shown to reduce harm from therapeutic errors, but sociocultural barriers may impact the engagement of allied health professionals (AHPs) in the diagnostic process.

Methods: A qualitative case study of the experience at a single institution around involvement of an AHP in the diagnostic process for acute dizziness and vertigo. We detail five diagnostic error cases in which the input of a physical therapist was central to correct diagnosis. We further describe evolution of the sociocultural milieu at the institution as relates to AHP engagement in diagnosis.

Results: Five patients with acute vestibular symptoms were initially misdiagnosed by physicians and then correctly diagnosed based on input from a vestibular physical therapist. These included missed labyrinthine concussion and post-traumatic benign paroxysmal positional vertigo (BPPV); BPPV called gastroenteritis; BPPV called stroke; stroke called BPPV; and multiple sclerosis called BPPV. As a consequence of surfacing these diagnostic errors, initial resistance to physical therapy input to aid medical diagnosis has gradually declined, creating a more collaborative environment for ‘team diagnosis’ of patients with dizziness and vertigo at the institution.

Conclusions: Barriers to AHP engagement in ‘team diagnosis’ include sociocultural norms that establish medical diagnosis as something reserved only for physicians. Drawing attention to the valuable diagnostic contributions of AHPs may help facilitate cultural change. Future studies should seek to measure diagnostic safety culture and then implement proven strategies to breakdown sociocultural barriers that inhibit effective teamwork and transdisciplinary diagnosis.
The ACA: Impacts on Health, Access, and Employment
Authors: Serakos Maria , Wolfe Barbara 
Published: May 2016

Abstract
On March 23, 2010, President Barack Obama signed the Patient Protection and Affordable Care Act (ACA) into law. This comprehensive health care reform legislation sought to expand health care coverage to millions of Americans, control health care costs, and improve the overall quality of the health care system. The ACA required that all US citizens and legal residents have qualifying health insurance by 2014. In this paper we give readers a brief overview of the effects of the ACA based on recent research. We then turn our attention to the possibility of using the ACA expansion to answer important underlying questions, such as: To what extent does the holding of insurance lead to improvements in access to care? To what extent does the holding of coverage lead to improvements in health? In mental health? Are there likely general equilibrium effects on labor force participation, hours worked, employment setting, and indeed even the probability of marrying? By necessity, researchers’ ability to answer these questions depends on the availability of data, so we discuss current and potential data sources relevant for answering these questions. We also look to what has been studied about the health reform in Massachusetts and early Medicaid expansions to speculate what we can expect to learn about the effects of the ACA on these outcomes in the future.
Genetic variation in Heteromys nelsoni (Rodentia: Heteromyidae) reveals its possible natural extinction
Authors: Rios Evelyn , Lorenzo Consuelo , Álvarez-Castañeda Sergio Ticul 
Published: May 2016

Abstract

Heteromys nelsoni is restricted to cloud forests in the mountain range of the southern state of Chiapas, Mexico, and western Guatemala. It is considered an endemic species, under special protection, and endangered because its habitat has been modified by excessive logging and extensive cattle grazing. We evaluated the genetic variation of H. nelsoni and the relationship between individuals from two geographic areas surrounding Cerro Mozotal, Chiapas, using three mitochondrial genes [cytochrome b (Cyt b), cytochrome c oxidase subunit 1 (COI), and control region (D-Loop)]. Low genetic diversity (d<0.9, π<0.005) and average divergence (<0.6%) in mtDNA were observed among the specimens examined. The haplotypes are distributed throughout the areas sampled; therefore, no areas where individuals showed genetic identity, with exclusive haplotypes, were found. Heteromys nelsoni populations have undergone a very recent demographic contraction and the low genetic diversity observed indicates an unfavorable future for the species. Changes in the climatic conditions coupled with other anthropogenic pressures have likely reduced the optimal habitat area for the species. It is imperative to develop programs aiming to reduce the probable risk of extinction of this species.
Crystal structure of 3,5,7-tris(morpholinomethyl)tropolone·0.67 hydrate, C22H33N3O5·0.67H2O
Authors: Schutte-Smith Marietjie , Eselem Bungu Paul Severin , Steyl Gideon , Roodt Andreas 
Published: May 2016

Abstract
C22H33N3O5·0.67H2O, monoclinic, P21/c, a = 11.9915(6) Å, b = 18.9934(10) Å, c = 10.5332(5) Å, β = 112.155(2)°, V = 2221.91(19) Å3, Z = 4, R
gt(F) = 0.0417, wR
ref(F
2) = 0.1139, T = 100(2) K.