bluuebunny/crossref_metadata_2025_split huggingface dataset:
A survey of computer game development
Authors: Aktaş AZ , Orçun E 
Published: October 2014

A computer game is special software to run on a computer for enjoyment and education. A computer game interacts with a user interface and generates audio-visual feedback. In this article computer games and the relevant processes and methodologies for their development were surveyed. Basically a computer game consists of design elements and technical components. The players, stories, rules, objectives, procedures, conflicts and challenges are the design elements of a computer game. They all have conflicts and challenges and have effects over gameplay. In addition to design elements, there are technical components that may be grouped into four as ‘the render engine and rendering pipeline’, ‘physics engine and physics-related techniques’, ‘game codes’ and ‘artwork contents’. Fixed-function pipeline and flexible pipeline are the render engine and rendering pipeline. Physics engine and physics-related techniques are collision detection, ray casting, etc. Game codes are for game mechanics, artificial intelligence, scenario creation and management. Artwork contents have game level, three-dimensional models, two-dimensional maps for shaders, skeletal animation and audio assets. The major objective of the study to be reported in this article was to apply all these methodologies, techniques and tools on a case problem after studying design elements and technical components.
The risk factors associated with subluxation of the distal interphalangeal joint in mallet fracture
Authors: Kim J. K. , Kim D. J. 
Published: October 2014

Surgical fixation is recommended when a mallet fracture involves more than one-third of the articular surface of the distal phalanx. This recommendation originates from the idea that involvement of more than one-third of the base of the distal phalanx causes subluxation of the distal interphalangeal (DIP) joint. Eighty-six fingers of 85 patients with a mallet fracture involving more than one-third of the articular surface of the distal phalanx were enrolled in this study. Patients were allocated on the basis of subluxation of the DIP joint into a group with no subluxation or a group with subluxation. These two groups were compared with respect to age, sex, fracture size, fracture displacement, time to finger immobilizer application, and initial extensor lag of the DIP joint. Backward stepwise multiple logistic regression analysis was performed to identify the risk factors of DIP joint subluxation, and receiver operating curve analysis was used to calculate the optimal cut-off point for the risk factors. Half of our patients with a mallet fracture involving > one-third of the articular surface of the distal phalanx showed subluxation of the DIP joint. A significant intergroup difference was found for fracture size and time to application of a finger immobilizer, but no significant difference was observed for other parameters. The risk factors of DIP joint subluxation were fracture size and time to application of finger immobilizer. The optimal cut-off values for the development of DIP joint subluxation were 48% for the fracture size and 12.5 days for time to finger immobilizer application. Level of Evidence: Prognosis, II
Patient preferences for disease-modifying drugs in multiple sclerosis therapy: a choice-based conjoint analysis
Authors: Utz Kathrin S. , Hoog Jana , Wentrup Andreas , Berg Sebastian , Lämmer Alexandra , Jainsch Britta , Waschbisch Anne , Lee De-Hyung , Linker Ralf A. , Schenk Thomas 
Published: October 2014

Objectives: With an increasing number of disease-modifying treatments (DMTs) for multiple sclerosis (MS), patient preferences will gain importance in the decision-making process. We assessed patients’ implicit preferences for oral versus parenteral DMTs and identified factors influencing patients’ treatment preference. Methods: Patients with relapsing–remitting MS ( n = 156) completed a questionnaire assessing treatment preferences, whereby they had to decide between pairs of hypothetical treatment scenarios. Based on this questionnaire a choice-based conjoint analysis was conducted. Results: Treatment frequency and route of administration showed a stronger influence on patient preference compared with frequency of mild side effects. The latter attribute was more important for treatment-naïve patients compared with DMT-experienced patients. The higher the Extended Disability Status Scale score, the more likely pills, and the less likely fewer side effects were preferred. Pills were preferred over injections by 93% of patients, when treatment frequency and frequency of side effects were held constant. However, preference switched to injections when pills had to be taken three times daily and injections only once per week. Injections were also preferred when pills were associated with frequent side effects. Conclusions: Our results suggest that route of administration and treatment frequency play an important role in the patients’ preference for a given DMT.
The electronic and optical properties of quaternary GaAs1-x-yN
x
Bi
y
alloy lattice-matched to GaAs: a first-principles study
Authors: Ma Xiaoyang , Li Dechun , Zhao Shengzhi , Li Guiqiu , Yang Kejian 
Published: October 2014

Abstract
First-principles calculations based on density functional theory have been performed for the quaternary GaAs1-x-y
N
x
Bi
y
alloy lattice-matched to GaAs. Using the state-of-the-art computational method with the Heyd-Scuseria-Ernzerhof (HSE) hybrid functional, electronic, and optical properties were obtained, including band structures, density of states (DOSs), dielectric function, absorption coefficient, refractive index, energy loss function, and reflectivity. It is found that the lattice constant of GaAs1-x-y
N
x
Bi
y
alloy with y/x =1.718 can match to GaAs. With the incorporation of N and Bi into GaAs, the band gap of GaAs1-x-y
N
x
Bi
y
becomes small and remains direct. The calculated optical properties indicate that GaAs1-x-y
N
x
Bi
y
has higher optical efficiency as it has less energy loss than GaAs. In addition, it is also found that the electronic and optical properties of GaAs1-x-y
N
x
Bi
y
alloy can be further controlled by tuning the N and Bi compositions in this alloy. These results suggest promising applications of GaAs1-x-y
N
x
Bi
y
quaternary alloys in optoelectronic devices.
A survey of footwear advice, beliefs and wear habits in people with knee osteoarthritis
Authors: Paterson Kade L , Wrigley Tim V , Bennell Kim L , Hinman Rana S 
Published: October 2014

AbstractBackgroundExpert opinion recommends cushioned and supportive footwear for people with knee osteoarthritis (OA). However, little is known about the footwear advice people receive from healthcare professionals, or the beliefs and footwear habits of people with knee OA. This study aimed to determine i) what types of shoes people are advised to wear for their knee OA and by whom; ii) establish which types of shoes people with knee OA believe are best for managing their knee OA symptoms and (iii) which shoes they wear most often.Methods204 people with symptomatic knee OA completed an online survey. The survey comprised 14 questions asking what footwear advice people had received for their knee OA and who they received it from, individual beliefs about optimal footwear styles for their knee OA symptoms and the types of footwear usually worn.ResultsOnly one third (n = 69, 34%) of participants reported receiving footwear advice for their knee OA, and this was most frequently received from a podiatrist (n = 47, 68%). The most common advice was to wear sturdy/supportive shoes (n = 96, 47%) or shoes with arch supports (n = 84, 41%). These were also amongst the shoe styles that participants believed were best for their knee OA (n = 157 (77%) and n = 138 (68%) respectively). The type of shoes most frequently worn were athletic (n = 131, 64%) and sturdy/supportive shoes (n = 116, 57%).ConclusionsMost people with knee OA who completed our survey had not received advice about footwear for their knee OA symptoms. Our participants typically believed that sturdy/supportive shoes were best for their knee OA and this shoe style was most frequently worn, which is reflective of expert opinion. Future research is needed to confirm whether sturdy/supportive shoes are indeed optimal for managing symptoms of knee OA.
Hospital mortality of adults admitted to Intensive Care Units in hospitals with and without Intermediate Care Units: a multicentre European cohort study
Authors: Capuzzo Maurizia , Volta Carlo Alberto , Tassinati Tania , Moreno Rui Paulo , Valentin Andreas , Guidet Bertrand , Iapichino Gaetano , Martin Claude , Perneger Thomas , Combescure Christophe , Poncet Antoine , Rhodes Andrew 
Published: October 2014

Abstract
Introduction
The aim of the study was to assess whether adults admitted to hospitals with both Intensive Care Units (ICU) and Intermediate Care Units (IMCU) have lower in-hospital mortality than those admitted to ICUs without an IMCU.

Methods
An observational multinational cohort study performed on patients admitted to participating ICUs during a four-week period. IMCU was defined as any physically and administratively independent unit open 24 hours a day, seven days a week providing a level of care lower than an ICU but higher than a ward. Characteristics of hospitals, ICUs and patients admitted to study ICUs were recorded. The main outcome was all-cause in-hospital mortality until hospital discharge (censored at 90 days).

Results
One hundred and sixty-seven ICUs from 17 European countries enrolled 5,834 patients. Overall, 1,113 (19.1%) patients died in the ICU and 1,397 died in hospital, with a total of 1,397 (23.9%) deaths. The illness severity was higher for patients in ICUs with an IMCU (median Simplified Acute Physiology Score (SAPS) II: 37) than for patients in ICUs without an IMCU (median SAPS II: 29, P <0.001). After adjustment for patient characteristics at admission such as illness severity, and ICU and hospital characteristics, the odds ratio of mortality was 0.63 (95% CI 0.45 to 0.88, P = 0.007) in favour of the presence of IMCU. The protective effect of the IMCU was absent in patients who were admitted for basic observation, for example, after surgery (odds ratio 1.15, 95% CI 0.65 to 2.03, P = 0.630) but was strong in patients admitted to an ICU for other reasons (odds ratio 0.54, 95% CI 0.37 to 0.80, P = 0.002).

Conclusions
The presence of an IMCU in the hospital is associated with significantly reduced adjusted hospital mortality for adults admitted to the ICU. This effect is relevant for the patients requiring full intensive treatment.

Trial registration
Clinicaltrials.gov NCT01422070. Registered 19 August 2011.
New concepts in breast cancer genomics and genetics
Authors: Goncalves Rodrigo , Warner Wayne A , Luo Jingqin , Ellis Matthew J 
Published: October 2014

AbstractMassively parallel DNA and RNA sequencing approaches have generated data on thousands of breast cancer genomes. In this review, we consider progress largely from the perspective of new concepts and hypotheses raised so far. These include challenges to the multistep model of breast carcinogenesis and the discovery of new defects in DNA repair through sequence analysis. Issues for functional genomics include the development of strategies to differentiate between mutations that are likely to drive carcinogenesis and bystander background mutations, as well as the importance of mechanistic studies that examine the role of mutations in genes with roles in splicing, histone methylation, and long non-coding RNA function. The application of genome-annotated patient-derived breast cancer xenografts as a potentially more reliable preclinical model is also discussed. Finally, we address the challenge of extracting medical value from genomic data. A weakness of many datasets is inadequate clinical annotation, which hampers the establishment of links between the mutation spectra and the efficacy of drugs or disease phenotypes. Tools such as dGene and the DGIdb are being developed to identify possible druggable mutations, but these programs are a work in progress since extensive molecular pharmacology is required to develop successful ‘genome-forward’ clinical trials. Examples are emerging, however, including targeting HER2 in HER2 mutant breast cancer and mutant ESR1 in ESR1 endocrine refractory luminal-type breast cancer. Finally, the integration of DNA- and RNA-based sequencing studies with mass spectrometry-based peptide sequencing and an unbiased determination of post-translational modifications promises a more complete view of the biochemistry of breast cancer cells and points toward a new discovery horizon in our understanding of the pathophysiology of this complex disease.
Stigmatization and racial selection after September 11, 2001: self-identity among Arab and Islamic Americans
Authors: Mason Patrick L , Matella Andrew 
Published: October 2014

Abstract
During the 2000s Arab and Islamic American racial identity selection was subjected to an exogenous racializing event, viz., public and private reaction to the Al Qaeda attacks of September 11, 2001. The Al Qaeda attacks clearly demarcate a period in which there was a structural increase in the intensity of US stigmatization of persons with Islamic religious affiliation and Arab ethnicity. This stigmatization created an exogenous reduction in the expected payoff to acculturation relative to non-acculturation. This paper uses self-identification as white as its measure of acculturation and the fraction of all hate crimes directed at Muslims as its measure of stigmatization after 9/11. Comparing 2002–2012 to 1996–2001, there is a statistically significant and substantively large decrease in the unconditional and conditional probabilities that Arab and Islamic Americans will self-identify as white. The data are combined cross sections of the Current Population Survey Annual Social and Economic Supplement.

Jel codes: J11, J15, Z13
Nucleotide synthesis is regulated by cytoophidium formation during neurodevelopment and adaptive metabolism
Authors: Aughey Gabriel N. , Grice Stuart J. , Shen Qing-Ji , Xu Yichi , Chang Chia-Chun , Azzam Ghows , Wang Pei-Yu , Freeman-Mills Luke , Pai Li-Mei , Sung Li-Ying , Yan Jun , Liu Ji-Long 
Published: October 2014

ABSTRACT
The essential metabolic enzyme CTP synthase (CTPsyn) can be compartmentalised to form an evolutionarily-conserved intracellular structure termed the cytoophidium. Recently, it has been demonstrated that the enzymatic activity of CTPsyn is attenuated by incorporation into cytoophidia in bacteria and yeast cells. Here we demonstrate that CTPsyn is regulated in a similar manner in Drosophila tissues in vivo. We show that cytoophidium formation occurs during nutrient deprivation in cultured cells, as well as in quiescent and starved neuroblasts of the Drosophila larval central nervous system. We also show that cytoophidia formation is reversible during neurogenesis, indicating that filament formation regulates pyrimidine synthesis in a normal developmental context. Furthermore, our global metabolic profiling demonstrates that CTPsyn overexpression does not significantly alter CTPsyn-related enzymatic activity, suggesting that cytoophidium formation facilitates metabolic stabilisation. In addition, we show that overexpression of CTPsyn only results in moderate increase of CTP pool in human stable cell lines. Together, our study provides experimental evidence, and a mathematical model, for the hypothesis that inactive CTPsyn is incorporated into cytoophidia.
In vitro co-culture systems for studying molecular basis of cellular interaction between Aire-expressing medullary thymic epithelial cells and fresh thymocytes
Authors: Yamaguchi Yoshitaka , Kudoh Jun , Yoshida Tetsuhiko , Shimizu Nobuyoshi 
Published: October 2014

ABSTRACT
We previously established three mouse cell lines (Aire+TEC1, Aire+TEC2 and Aire+DC) from the medullary thymic epithelial cells (mTECs) and dendritic cells (mDCs). These cells constitutively expressed “autoimmune regulator (Aire) gene” and they exhibited various features of self antigen-presenting cells (self-APCs) present in the thymic medullary region.
Here, we confirmed our previous observation that Aire+ thymic epithelial cells adhere to fresh thymocytes and kill them by inducing apoptosis, thus potentially reproducing in vitro some aspects of the negative selection of T cells in vivo. In this system, a single Aire+ cell appeared able to kill ∼30 thymocytes within 24 hrs. Moreover, we observed that ectopic expression of peripheral tissue-specific antigens (TSAs), and expression of several surface markers involved in mTEC development, increased as Aire+ cell density increases toward confluency. Thus, these Aire+ cells appear to behave like differentiating mTECs as if they pass through the developmental stages from intermediate state toward mature state. Surprisingly, an in vitro co-culture system consisting of Aire+ cells and fractionated sub-populations of fresh thymocytes implied the possible existence of two distinct subtypes of thymocytes (named as CD4+ killer and CD4− rescuer) that may determine the fate (dead or alive) of the differentiating Aire+mTECs. Thus, our in vitro co-culture system appears to mimic a part of “in vivo thymic crosstalk”.
Vesicular transport of a ribonucleoprotein to mitochondria
Authors: Mukherjee Joyita , Mahato Biraj , Adhya Samit 
Published: October 2014

ABSTRACT
Intracellular trafficking of viruses and proteins commonly occurs via the early endosome in a process involving Rab5. The RNA Import Complex (RIC)-RNA complex is taken up by mammalian cells and targeted to mitochondria. Through RNA interference, it was shown that mito-targeting of the ribonucleoprotein (RNP) was dependent on caveolin 1 (Cav1), dynamin 2, Filamin A and NSF. Although a minor fraction of the RNP was transported to endosomes in a Rab5-dependent manner, mito-targeting was independent of Rab5 or other endosomal proteins, suggesting that endosomal uptake and mito-targeting occur independently. Sequential immunoprecipitation of the cytosolic vesicles showed the sorting of the RNP away from Cav1 in a process that was independent of the endosomal effector EEA1 but sensitive to nocodazole. However, the RNP was in two types of vesicle with or without Cav1, with membrane-bound, asymmetrically orientated RIC and entrapped RNA, but no endosomal components, suggesting vesicular sorting rather than escape of free RNP from endosomes. In vitro, RNP was directly transferred from the Type 2 vesicles to mitochondria. Live-cell imaging captured spherical Cav1− RNP vesicles emerging from the fission of large Cav+ particles. Thus, RNP appears to traffic by a different route than the classical Rab5-dependent pathway of viral transport.
Projected near-future CO2 levels increase activity and alter defensive behaviours in the tropical squid Idiosepius pygmaeus
Authors: Spady Blake L. , Watson Sue-Ann , Chase Tory J. , Munday Philip L. 
Published: October 2014

ABSTRACT
Carbon dioxide (CO2) levels projected to occur in the oceans by the end of this century cause a range of behavioural effects in fish, but whether other highly active marine organisms, such as cephalopods, are similarly affected is unknown. We tested the effects of projected future CO2 levels (626 and 956 µatm) on the behaviour of male two-toned pygmy squid, Idiosepius pygmaeus. Exposure to elevated CO2 increased the number of active individuals by 19–25% and increased movement (number of line-crosses) by nearly 3 times compared to squid at present-day CO2. Squid vigilance and defensive behaviours were also altered by elevated CO2 with &gt;80% of individuals choosing jet escape responses over defensive arm postures in response to a visual startle stimulus, compared with 50% choosing jet escape responses at control CO2. In addition, more escape responses were chosen over threat behaviours in body pattern displays at elevated CO2 and individuals were more than twice as likely to use ink as a defence strategy at 956 µatm CO2, compared with controls. Increased activity could lead to adverse effects on energy budgets as well as increasing visibility to predators. A tendency to respond to a stimulus with escape behaviours could increase survival, but may also be energetically costly and could potentially lead to more chases by predators compared with individuals that use defensive postures. These results demonstrate that projected future ocean acidification affects the behaviours of a tropical squid species.
Altered synaptic architecture and glycosylated synaptomatrix composition in aDrosophilaclassic galactosemia disease model
Authors: Jumbo-Lucioni Patricia , Parkinson William , Broadie Kendal 
Published: October 2014

AbstractClassic galactosemia (CG) is an autosomal recessive disorder resulting from loss of galactose-1-phosphate uridyltransferase (GALT) that catalyzes conversion of galactose-1-phosphate and uridine diphosphate (UDP)-glucose to glucose-1-phosphate and UDP-galactose, immediately upstream of UDP-N-acetylgalactosamine and UDP-N-acetylglucosamine synthesis. These four UDP-sugars are essential donors driving synthesis of glycoproteins and glycolipids that heavily decorate cell surfaces and extracellular spaces. In addition to acute, potentially lethal neonatal symptoms, maturing CG patients develop striking neurodevelopmental, motor and cognitive impairments. Previous studies suggest association of neurological symptoms with glycosylation defects, with CG recently described as a Congenital Disorder of Glycosylation (CDG) showing defects in both N- and O-linked glycans. Here, we characterize behavioral traits, synaptic development and glycosylated synaptomatrix formation in a GALT-deficient Drosophila disease model. Loss of Drosophila GALT (dGALT) greatly impairs coordinated movement and results in structural overelaboration and architectural abnormalities at the neuromuscular junction (NMJ). Dietary galactose and mutation of galactokinase (dGALK) or UDP-glucose dehydrogenase (sugarless) genes are identified as critical environmental and genetic modifiers, respectively, of behavioral and cellular defects. Assaying the NMJ extracellular synaptomatrix with a broad panel of lectin probes reveals profound alterations in dGALT mutants, including depletion of galactosyl/N-acetylgalactosamine and fucosylated horseradish peroxidase (HRP) moieties, which are differentially corrected by dGALK co-removal and sugarless overexpression. Synaptogenesis relies on trans-synaptic signals modulated by this synaptomatrix carbohydrate environment, and dGALT null NMJs display striking changes in heparan sulfate proteoglycan (HSPG) co-receptor and Wnt ligand levels, which are also corrected by dGALK co-removal and sugarless overexpression. These results reveal synaptomatrix glycosylation losses, altered trans-synaptic signaling pathway components, defective synaptogenesis and impaired coordinated movement in a CG neurological disease model.