Miracle-dz/UniFAR-FTUs huggingface dataset:
Joint Modeling of Transitional Patterns of Alzheimer's Disease

While the experimental Alzheimer's drugs recently developed by pharmaceutical companies failed to stop the progression of Alzheimer's disease, clinicians strive to seek clues on how the patients would be when they visit back next year, based upon the patients' current clinical and neuropathologic diagnosis results. This is related to how to precisely identify the transitional patterns of Alzheimer's disease. Due to the complexities of the diagnosis of Alzheimer's disease, the condition of the disease is usually characterized by multiple clinical and neuropathologic measurements, including Clinical Dementia Rating (CDRGLOB), Mini-Mental State Examination (MMSE), a score derived from the clinician judgement on neuropsychological tests (COGSTAT), and Functional Activities Questionnaire (FAQ). In this research article, we investigate a class of novel joint random-effects transition models that are used to simultaneously analyze the transitional patterns of multiple primary measurements of Alzheimer's disease and, at the same time, account for the association between the measurements. The proposed methodology can avoid the bias introduced by ignoring the correlation between primary measurements and can predict subject-specific transitional patterns.
From Green to Red: Horizontal Gene Transfer of the Phycoerythrin Gene Cluster between Planktothrix Strains

ABSTRACT Horizontal gene transfer is common in cyanobacteria, and transfer of large gene clusters may lead to acquisition of new functions and conceivably niche adaption. In the present study, we demonstrate that horizontal gene transfer between closely related Planktothrix strains can explain the production of the same oligopeptide isoforms by strains of different colors. Comparison of the genomes of eight Planktothrix strains revealed that strains producing the same oligopeptide isoforms are closely related, regardless of color. We have investigated genes involved in the synthesis of the photosynthetic pigments phycocyanin and phycoerythrin, which are responsible for green and red appearance, respectively. Sequence comparisons suggest the transfer of a functional phycoerythrin gene cluster generating a red phenotype in a strain that is otherwise more closely related to green strains. Our data show that the insertion of a DNA fragment containing the 19.7-kb phycoerythrin gene cluster has been facilitated by homologous recombination, also replacing a region of the phycocyanin operon. These findings demonstrate that large DNA fragments spanning entire functional gene clusters can be effectively transferred between closely related cyanobacterial strains and result in a changed phenotype. Further, the results shed new light on the discussion of the role of horizontal gene transfer in the sporadic distribution of large gene clusters in cyanobacteria, as well as the appearance of red and green strains.
Wideband planar folded monopole antenna with tapered resistively loadings

A wideband planar folded monopole antenna with resistively loadings is proposed. This antenna is designed to cover the extremely wide frequency region, 30 MHz to 2000 MHz. By locating loadings at the upper part of the antenna, the loaded monopole antenna operates as a travelling-wave antenna. In addition, to reduce the total length of the monopole, upper part of the antenna is folded. A width of the line, a total length, a folded length, and the distance between the lines are optimized. Moreover, the wideband RF transformer is utilized. Due to the operating range of this transformer, VSWR of the fabricated antenna becomes worse than that of the simulation at the high frequency region. In case of the ideal impedance transformer, a measured VSWR of the proposed antenna agrees well with the simulated values. Therefore, additional research about a low-loss transformer operating in required bands should be performed to obtain the similar measured result close to the simulated one. From these results, the proposed antenna geometry can be applicable for the broadband wireless communication systems, especially in military vehicle antenna systems.
AEF1/MPR25 is implicated in RNA editing of plastid atpF and mitochondrial nad5, and also promotes atpF splicing in Arabidopsis and rice.

RNA editing is an essential mechanism that modifies target cytidines to uridine in both mitochondrial and plastid mRNA. Target sites are recognized by pentatricopeptide repeat (PPR) proteins. Using bioinformatics predictions based on the code describing sequence recognition by PPR proteins, we have identified an Arabidopsis editing factor required for editing of atpF in plastids. A loss-of-function mutation in ATPF EDITING FACTOR 1 (AEF1, AT3G22150) results in severe variegation, presumably due to decreased plastid ATP synthase levels. Loss of editing at the atpF site is coupled with a large decrease in splicing of the atpF transcript, even though the editing site is within an exon and 53 nucleotides distant from the splice site. The rice orthologue of AEF1, MPR25, has been reported to be required for editing of a site in mitochondrial nad5 transcripts, and we confirm that editing of the same site is affected in the Arabidopsis aef1 mutant. We also show that splicing of chloroplast atpF transcripts is affected in the rice mpr25 mutant. AEF1 is thus highly unusual for an RNA editing specificity factor in that it has functions in both organelles.
International Conference on Computational Science , ICCS 2013 PACHA : Low Cost Bare Metal Development for Shared Memory Manycore Accelerators

Today, efficiently implementing an application on shared memory manycore accelerators is a hard task. Linux eases the development, but is not adapted to exploit the maximum of the platform yet. Bare metal programming environments provided with accelerators give a low-overhead access to the platform. However, they increase the complexity of development, mainly due to 4 gaps: each accelerator has its own specific environment; bare metal environments are only supported on the hardware platform or on the proprietary simulator; they have seldom, if ever, execution debugging support; they do not have parallel programming models, and whenever they exist, they are platform-specific. In order to fill the gaps and thus, to lower the barrier to develop on bare metal on shared memory manycore accelerators, we present PACHA. It features two aspects: a low overhead, Platform Agnostic, Close-to-HArdware (PACHA) programming interface, which allows to handle only one version of the application code for all supported accelerators, and an easy-to-use multi-platform development environment, which abstracts the complexity of each accelerator’s development environment. With a x86 support and a Linux compatibility, PACHA offers a functional simulator and all the Linux set of debugging tools. Further, based on the programming interface, three parallel execution models have been ported in order to facilitate the development and comparison of applications. PACHA is currently fully supported for x86 platforms, TILEPro64 and STHORM. A case study on a TILEPro64 is presented: the performance gain using PACHA rather than Linux with OpenMP or Pthread is about 1,8x to 4x, without increasing the development cost.
The Duffy Antigen Receptor for Chemokines

The Duffy blood group antigen is a serpentine protein with seven transmembrane domains that is not coupled to G-proteins or other known intracellular effectors. In addition to erythrocytes, it is also expressed in endothelial cells and neurons. In recent years the Duffy antigen has received much attention because of its diverse roles in health and disease. These include its functions as a docking receptor for the invasion of human erythrocytes by the malaria parasite Plasmodium vivax. In addition, the Duffy antigen is a binding protein for multiple inflammatory chemokines. Its expression allows erythrocytes to regulate intravascular levels of chemokines. It has also been shown recently that the Duffy antigen plays an important role in endothelial cells by facilitating chemokine transcytosis and presentation. Given these diverse functions of the Duffy antigen, this short review presents detailed methods that can be used to investigate each of these potential roles of this multifaceted protein. The Duffy Antigen Receptor for Chemokines
Tibetan word segmentation system based on conditional random fields

Unlike English and other western languages, there are no delimiters to mark word boundaries in both Chinese and Tibetan. Therefore, word segmentation is the first step for Chinese and Tibetan natural language processing such as machine translation and information retrieval. However, Chinese word segmentation has been studied for many years and the technology is relatively mature. In contrast, Tibetan word segmentation is less concerned by researchers. In this paper, we learn from Chinese word segmentation approach and analysis the characteristic of Tibetan language, designs a Tibetan word segmentation system based on conditional random fields. The experiment shows that the algorithm is effective and can be preliminary applied.
Hierarchical parametrisation and classification for musical instrument recognition

The extraction of the timbre for musical identification from the audio signal has been subject of several researches, where various spectro-temporal parameters have been proposed and compared. Classification strategies are generally based on two discrimination approaches: direct classification and hierarchical classification. In both strategies, the feature vector is static and is used during the whole treatment process. In this paper, we propose a hierarchical classification where the feature vector is dynamic and changes depending on each level and each node of the hierarchical tree. The feature vector is optimized and is determined with the sequential backward selection (SBS) algorithm. Using a large database (RWC), the results show a score gain in musical instrument recognition performances with the proposed approach compared to reference systems.
Serological Differences in Folate/Vitamin B12 in Pregnancies Affected by Neural Tube Defects

Background: Laboratory evidence is presented of significant associations between reduced maternal serum folate and vitamin B12 levels and neural tube birth defects (NTD) compared to referents. Methods: This was an incident case-control study. Cases of neural tube defects (including anencephaly and open spina bifida) diagnosed in residents within 100 miles of the US-Mexico border from January 1993 to October 2000 were eligible. Most cases were diagnosed in utero upon visits to clinics, obstetrical or genetic expert offices. Cases identified upon hospital admission or at delivery were also eligible. Cases identified after discharge were not. Controls were matched on geographic region, maternal age, race/ethnicity, gestational age, and type of health insurance (including none). Results: Three hundred eighty-two border area residents (107 cases and 275 individually matched controls) provided biological specimens. Median folate concentrations for case mothers were 36% lower than controls (9.8 ng/mL vs. 15 ng/mL). Maternal serum folate concentrations in quartiles above 9.5 ng/mL indicated significantly reduced risk (OR = 0.4, OR = 0.3, and OR = 0.2). Likewise, the risk for NTD decreased (OR = 0.4, OR = 0.3, and OR = 0.2) in quartiles of sera B12 concentrations above 246 pg/mL. Conclusions: Physician attention is invited to significantly lower concentrations of serum folate and vitamin B12 in women with NTD-affected pregnancies. This study assayed sera samples from women while still pregnant or immediately after delivery. The confounding effect of reduced folate and B12 levels with other biological and chemical exposures will be addressed in subsequent communications.
ABO blood groups and risk of cancer: a systematic review and meta-analysis.

BACKGROUND For decades, studies have been performed to evaluate the association between ABO blood groups and risk of cancer. However, whether ABO blood groups are associated with overall cancer risk remains unclear. We therefore conducted a meta-analysis of observational studies to assess this association. MATERIALS AND METHODS A search of Pubmed, Embase, ScienceDirect, Wiley, and Web of Knowledge databases (to May 2013) was supplemented by manual searches of bibliographies of key retrieved articles and relevant reviews. We included case-control studies and cohort studies with more than 100 cancer cases. RESULTS The search yielded 89 eligible studies that reported 100,554 cases at 30 cancer sites. For overall cancer risk, the pooled OR was 1.12 (95%CI: 1.09-1.16) for A vs. non- A groups, and 0.84 (95%CI: 0.80-0.88) for O vs. non-O groups. For individual cancer sites, blood group A was found to confer increased risk of gastric cancer (OR=1.18; 95%CI: 1.13-1.24), pancreatic cancer (OR=1.23; 95%CI: 1.15-1.32), breast cancer (OR=1.12; 95%CI: 1.01-1.24), ovarian cancer (OR=1.16; 95%CI: 1.04-1.27), and nasopharyngeal cancer (OR=1.17; 95%CI: 1.00-1.33). Blood group O was found to be linked to decreased risk of gastric cancer (OR=0.84; 95%CI: 0.80-0.88), pancreatic cancer (OR=0.75; 95%CI: 0.70-0.80), breast cancer (OR=0.90; 95%CI: 0.85-0.95), colorectal cancer (OR=0.89; 95%CI: 0.81-0.96), ovarian cancer (OR=0.76; 95%CI: 0.53-1.00), esophagus cancer (OR=0.94; 95%CI: 0.89-1.00), and nasopharyngeal cancer (OR=0.81; 95%CI: 0.70-0.91). CONCLUSIONS Blood group A is associated with increased risk of cancer, and blood group O is associated with decreased risk of cancer.
Full-wave analysis of a lossy rectangular waveguide containing rough inner surfaces

The full-wave mode-matching method employing the similarity transformation is used to derive the eigenvalue equation for the periodic bumpy regions that model the surface roughness of a WR-10 (75-110-GHz) waveguide. For the case study reported, attenuation losses increased by approximately 60% (36%) at 75 GHz (110 GHz). <<ETX>>
Hypothyroidism and Major Depression: A Common Executive Dysfunction?

Little is known about the possible link between the cognitive disorders associated with hypothyroidism and those encountered in depression. This study examines attentional and executive functions as well as the intensity of anxiety and depressive symptoms in hypothyroidism and major depression and the possible link between these symptoms and cognitive disturbances. This study confirms the existence of psychomotor slowing associated with attentional and executive disturbance in major depression as well as in hypothyroidism. However, while depressed subjects manifested a conscious bias with material of negative emotional valence, no such bias was found in the hypothyroid subjects. While the hypothyroid state is accompanied by anxiety/depressive symptoms, it seems that the latter are too discrete for an attentional bias to be observed with material with a negative emotional valence.
Welcome to MY Virtual Place

This paper briefly describes our proposal for storytelling in virtual environments from a virtual guide perspective. In our model the guide begins at a particular location and starts to navigate the world telling the user stories related to the places she visits. Our guide tries to emulate a real guide’s behaviour in such a situation. In particular, she behaves as a spontaneous real guide who knows stories about the places in the virtual world but has not prepared an exhaustive tour nor a storyline. In addition the paper exposes the concrete scenario where the guide has been successfully tested, as well as the performance obtained by using two guides with different profiles.
Compiling Stratified Belief Bases

Many coherence-based approaches to inconsistency handling within propositional belief bases have been proposed so far. They consist in selecting one or several preferred consistent subbases of the given (usually inconsistent) stratified belief base (SBB), then using classical inference from some of the selected subbases. Unfortunately, deciding the corresponding inference relations is typically hard from the computational complexity point of view. In this paper, we show how some knowledge compilation techniques for classical inference can be used to circumvent the intractability of such sophisticated inference relations. For several families of compiled SBBs and several selection policies, the complexity of skeptical inference is identified. Interestingly, some tractable restrictions are exhibited.
Inhaled long acting beta agonists for stable chronic asthma.

BACKGROUND Asthma is a common respiratory disease among both adults and children and short acting inhaled beta-2 agonists are used widely for 'reliever' bronchodilator therapy. Long acting beta-2 agonists were introduced as prospective 'symptom controllers' in addition to inhaled corticosteroid 'preventer' therapy (ICS). OBJECTIVES This review aimed to determine the benefit or detriment on the primary outcome of asthma control with the regular use of long acting inhaled beta-2 agonists compared with placebo. SEARCH STRATEGY We carried out searches using the Cochrane Airways Group trial register, most recently in October 2002. We searched bibliographies of identified RCTs for additional relevant RCTs and contacted authors of identified RCTs for other published and unpublished studies. SELECTION CRITERIA All randomised studies of at least two weeks duration, comparing a long acting inhaled beta-agonist given twice daily with a placebo, in chronic asthma. DATA COLLECTION AND ANALYSIS Two reviewers performed data extraction and study quality assessment independently. We contacted authors of studies for missing data. MAIN RESULTS Eighty five studies met the inclusion criteria, 56 parallel group and 29 cross over design. Salmeterol xinafoate was used as long acting agent in 60 studies and formoterol fumarate in 25. The treatment period was two to four weeks in 32 studies, and 12 to 52 weeks in 53 studies. 34 study groups used concurrent inhaled corticosteroid treatment, 21 studies did not permit their use and 35 permitted either inhaled corticosteroid or cromones. There were significant advantages to long acting beta-2 agonist treatment compared to placebo for a variety of measurements of airway calibre including morning peak expiratory flow (PEF) (weighted mean difference (WMD) 26.78 L/min 95%CI 20.36 to 33.20), evening PEF (WMD 19.17 L/min 95%CI 11.63 to 26.73). They were associated with significantly fewer symptoms, less use of rescue medication and higher quality of life scores. The risk of exacerbation was lower in adults using regular inhaled corticosteroids. REVIEWER'S CONCLUSIONS Long acting beta-2 agonists are effective in the control of chronic asthma, and the evidence supports their use in addition to inhaled corticosteroids, as emphasised in current guidelines. Further research is needed on their use in children under 12 and in mild asthmatics not taking ICS.
Using Data Parallelism in Lisp for Implementing a Quantum Simulator

This paper describes two implementations of QLisp (a Lisp extension to simulate quantum computations) in two different dataparallel extensions of Lisp: *Lisp and Paralation Lisp. First, the basic concepts of the languages and the quantum simulator are explained. Then, the porting process is described and a comparative evaluation of the two implementations is made. It is shown that data parallel languages are well suited for parallelizing QLisp. Also, in the porting process, we discovered some non-obvious differences between the different data parallel languages.
Structure and Properties of Biomorphous Al/C/TiO/TiC Composite Materials Reinforced with Charcoals Coated in ALD and the Sol-Gel Process

In this framework, an investigation of biomorphous composite materials was performed. The application of a natural reinforcement allows to obtain biomorphous composite materials. Pine wood samples were subjected to the pyrolysis process in order to obtain carbon char. The samples were subjected to Atomic Layer Deposition and the sol-gel coating process in order to obtain a titanium oxide and titanium carbide coating, respectively. Ti-gel carbon char samples were subjected to ceramisation. Pure carbon char coated with TiO and TiC was infiltrated with an Al alloy. The investigations of the obtained composite materials were performed using light microscopy, transmission and scanning electron microscopy for microstructure determination. Raman spectroscopy and X-ray analysis were performed, along with hardness and tribological tests. Crystallites were detected after infiltration of the porous samples with an Al alloy, which were up to several microns in size, depending on the selected coating. As a result of the investigation on coating samples, a significantly smaller presence of Al carbides was found. An increase of hardness and wear resistance of biomorphous composite materials containing the carbides phase was confirmed. The TiO2 coating prevents the occurrence of a reaction during the infiltration process and the formation of Al carbides.
Diversity driven attention model for query-based abstractive summarization

Abstractive summarization aims to generate a shorter version of the document covering all the salient points in a compact and coherent fashion. On the other hand, query-based summarization highlights those points that are relevant in the context of a given query. The encode-attend-decode paradigm has achieved notable success in machine translation, extractive summarization, dialog systems, etc. But it suffers from the drawback of generation of repeated phrases. In this work we propose a model for the query-based summarization task based on the encode-attend-decode paradigm with two key additions (i) a query attention model (in addition to document attention model) which learns to focus on different portions of the query at different time steps (instead of using a static representation for the query) and (ii) a new diversity based attention model which aims to alleviate the problem of repeating phrases in the summary. In order to enable the testing of this model we introduce a new query-based summarization dataset building on debatepedia. Our experiments show that with these two additions the proposed model clearly outperforms vanilla encode-attend-decode models with a gain of 28% (absolute) in ROUGE-L scores.
Conception date affects litter type and foetal sex ratio in femalemoose in

1. The Trivers–Willard model of optimal sex ratios predicts that in polygynous species mothers in better condition should produce more male than female offspring. However, empirical support for this hypothesis in mammals and especially ungulates has been equivocal. This may be because the fitness of mothers has been defined in different ways, reflecting morphological, physiological or behavioural measures of condition. In addition, factors other than maternal condition can influence a mother’s fitness. Given that recent studies of wild ungulates have demonstrated the importance of the timing of conception and birth on offspring fitness, litters conceived at different stages of the rut might be expected to exhibit differences in types and embryonic sex ratio. 2. Based on a 6-year survey of the reproductive tracts of female moose harvested in Estonia, we investigated the effect of conception date on the types of litters produced and on the foetal sex ratio. 3. There was a clear relationship between conception date and litter characteristics. Overall, earlier conceived litters were more likely than those conceived late to containmultiple embryos and a high proportion of males. However, while foetal sex ratio varied nonlinearly with conception date in yearlings and subadults, no relationship was found in adults. 4. We conclude that female moose adjust foetal sex ratio and litter type ⁄ size depending on their age and the date of conception, and that these adjustments are in accordance with the Trivers– Willard hypothesis if females that conceive earlier are in better condition.