Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide SNP Discovery from Transcriptome of Four Common Carp Strains

Background Single nucleotide polymorphisms (SNPs) have been used as genetic marker for genome-wide association studies in many species. Gene-associated SNPs could offer sufficient coverage in trait related research and further more could themselves be causative SNPs for traits. Common carp (Cyprinus carpio) is one of the most important aquaculture species in the world accounting for nearly 14% of freshwater aquaculture production. There are various strains of common carp with different economic traits, however, the genetic mechanism underlying the different traits have not been elucidated yet. In this project, we identified a large number of gene-associated SNPs from four strains of common carp using next-generation sequencing. Results Transcriptome sequencing of four strains of common carp (mirror carp, purse red carp, Xingguo red carp, Yellow River carp) was performed with Solexa HiSeq2000 platform. De novo assembled transcriptome was used as reference for alignments, and SNP calling was done through BWA and SAMtools. A total of 712,042 Intra-strain SNPs were discovered in four strains, of which 483,276 SNPs for mirror carp, 486,629 SNPs for purse red carp, 478,028 SNPs for Xingguo red carp and 488,281 SNPs for Yellow River carp were discovered, respectively. Besides, 53,893 inter-SNPs were identified. Strain-specific SNPs of four strains were 53,938, 53,866, 48,701, 40,131 in mirror carp, purse red carp, Xingguo red carp and Yellow River carp, respectively. GO and KEGG pathway analysis were done to reveal strain-specific genes affected by strain-specific non-synonymous SNPs. Validation of selected SNPs revealed that 48% percent of SNPs (12 of 25) were tested to be true SNPs. Conclusions Transcriptome analysis of common carp using RNA-Seq is a cost-effective way of generating numerous reads for SNP discovery. After validation of identified SNPs, these data will provide a solid base for SNP array designing and genome-wide association studies.
Benign Paroxysmal Positional Vertigo

Benign paroxysmal positional vertigo (BPPV) has received renewed clinical interest. At the Johns Hopkins Otological Vestibular Laboratory, 781 patients were tested on more than one occasion between September 1976 and November 1992. Of these patients, 187 (24%) were found to have positional nystagmus consistent with a diagnosis of BPPV. A retrospective analysis of these patients' records, including vestibular test and eye movement reports, audiograms, questionnaires, and hospital charts was performed. After this review, the nystagmus, initially diagnosed as due to BPPV, was believed to be a manifestation of another disease process in 36 cases. Of the remaining 151 diseases, 52 (34%) presented with no significant preceding disorder and have been termed primary BPPV. In the remaining 99 patients we found coexisting or associated disorders which included Meniere's disease, head trauma, prior ear surgery, vestibular neuronitis, migraine, and others. Forty‐five of these 151 patients (31%) had an associated diagnosis of Meniere's disease. To our knowledge a significant association between Meniere's disease and BPPV has not been reported. A review of the literature with discussion of BPPV and the associated disorders is offered.
A non-contact ECG sensing system with motion artifact equalization

This paper presents an electrocardiograph (ECG) non-contact sensing system that compensates the high-frequency noises and the distortion due to motion artifact via two-channel interleaved electrodes in concert with proportional design and equalization algorithm. Specifically, the equivalent input capacitances of the sensing electrodes are deliberately designed to achieve a fast, low-cost, and real-time compensation signal processing. This proposed system has been implemented with a worst case of 2% unit capacitance mismatch and 25% motion artifact with a normal distribution, where the equalization can still achieve average 98.6% high accuracy.
Superstabilizing , Fault-containing Multiagent Combinatorial Optimization

Self stabilization in distributed systems is the ability of a system to respond to transient failures by eventually reaching a legal state, and maintaining it afterwards. This makes such systems particularly interesting because they can tolerate faults, and are able to cope with dynamic environments. In this paper we propose the first self stabilizing mechanism for multiagent combinatorial optimization, which stabilizes in a state corresponding to the optimal solution of the optimization problem. Our algorithm is based on dynamic programming, and requires a linear number of messages to find the optimal solution in the absence of faults. We show how our algorithm can be made super-stabilizing, in the sense that while transiting from one stable state to the next, our system preserves the assignments from the previous optimal state (similar to a "last-known-good" state), until the new optimal solution is found (without "random" changes to the variables). We offer equal bounds for the stabilization and the superstabilization time. Furthermore, we describe a general scheme for fault containment and fast response time upon low impact failures. Multiple, isolated failures are handled effectively. To show the merits of our approach we report on experiments with practical sized distributed meeting scheduling problems in a multiagent system.
Infinitely Divisible Matrices

Assembling natural numbers in such nice patterns often has interesting consequences, and so it is in this case. Each of the aforementioned matrices is endowed with positive definiteness of a very high order: for every positive real number r the matrices with entries a\-, b\-, c\-, and d\are positive semidefinite. This special property is called infinite divisibility and is the subject of this paper. Positive semidefinite matrices arise in diverse contexts: calculus (Hessians at minima of functions), statistics (correlation matrices), vibrating systems (stiffness matrices), quantum mechanics (density matrices), harmonic analysis (positive definite functions), to name just a few. Many of the test matrices used by numerical analysts are positive definite. One of the interests of this paper might be the variety of examples that are provided in it. The general theorems and methods presented in the context of these examples are, in fact, powerful techniques that could be used elsewhere. In this introductory section we begin with the basic definitions and notions related to positive semidefinite matrices.
Scheduling and voltage scaling for energy/reliability trade-offs in fault-tolerant time-triggered embedded systems

In this paper we present an approach to the scheduling and voltage scaling of low-power fault-tolerant hard real-time applications mapped on distributed heterogeneous embedded systems. Processes and messages are statically scheduled, and we use process re-execution for recovering from multiple transient faults. Addressing simultaneously energy and reliability is especially challenging because lowering the voltage to reduce the energy consumption has been shown to increase the transient fault rates. In addition, time-redundancy based fault-tolerance techniques such as re-execution and dynamic voltage scaling-based low-power techniques are competing for the slack in the schedules. Our approach decides the voltage levels and start times of processes and the transmission times of messages, such that the transient faults are tolerated, the timing constraints of the application are satisfied and the energy is minimized. We present a constraint logic programming-based approach which is able to find reliable and schedulable implementations within limited energy and hardware resources.
Poster : Effort-based Detection of Comment Spammers

Social media has become ubiquitous and important for content sharing. A typical example of how users contribute content to a social media platform is through comment threads in online articles. Unfortunately, there is an increasing prevalence of malicious activity in these threads by spammers through comment messages. The existing approaches tackling comment spam are comment-level in that they attempt to classify a comment message as spam or not spam. We propose EDOCS, a graph-based userlevel approach that quantifies how much effort a user exerted over his or her comments, to detect if the user is a comment spammer or not. We conjecture that spammers can only exert limited effort in terms of time and money over preparing and disseminating their comments, hence their effort scores are expected to be lower than those of the legitimate users. Our experimental evaluation of EDOCS shows its effectiveness in detecting comment spammers accurately with 95% true positive rate at 3% false positive rate as well as preemptively.
Effects of systematic errors in blood pressure measurements on the diagnosis of hypertension

ObjectiveTo estimate the effects of systematic errors in measurements of blood pressure on the diagnosis of hypertension. MethodsWe fitted regression curves to distributions of diastolic and systolic BP from recent Canadian and UK surveys and calculated the effect of systematic measurement errors on changes in the numbers of patients who would be classified hypertensive at thresholds of 85, 90 and 95 mmHg diastolic and 140 and 160 mmHg systolic pressure respectively. ResultsOverestimation of diastolic BP by 5 mmHg increases the number of patients whose diastolic BP exceeds 85, 90 and 95 mmHg by 102, 132 and 166% respectively. Equivalent underestimation causes 57, 62 and 67% respectively of hypertensive patients to be missed. If systematic error in diastolic pressure is limited to ±1 mmHg the diagnosis errors are between −15 and +23%. Overestimation of systolic BP by 3 and 5 mmHg increases the number classified as hypertensive by 24 and 43% respectively. Equivalent underestimation causes 19 and 30% of patients with systolic hypertension to be missed. ConclusionsSmall systematic errors in BP measurements may cause large variations in the proportion of patients diagnosed as hypertensive. To limit over- or under-diagnosis of diastolic hypertension to approximately 20%, systematic errors in diastolic BP measurements should be limited to 1 mmHg. An uncertainty of 3 mmHg may be adequate for detecting systolic hypertension.
Immunotherapy in renal cell cancer: the more the merrier?

Renal cell carcinoma (RCC) is the most common primary malignancy affecting the kidney and considered a disease refractory to systemic therapy beyond cytokine therapy (the use of interferon alfa and interleukin 2 was limited when targeted therapies became available) (1). Currently, eight drugs are approved in the European Union (EU) for the treatment of advanced RCC, including IL-2, IFN-α, sorafenib, sunitinib, everolimus, temsirolimus, bevacizumab in combination with IFN-α, and pazopanib.
Early microglial colonization of the human forebrain and possible involvement in periventricular white‐matter injury of preterm infants

Amoeboid microglial subpopulations visualized by antibodies against ionized calcium‐binding adapter molecule 1, CD68, and CD45 enter the forebrain starting at 4.5 postovulatory or gestational weeks (gw). They penetrate the telencephalon and diencephalon via the meninges, choroid plexus, and ventricular zone. Early colonization by amoeboid microglia–macrophages is first restricted to the white matter, where these cells migrate and accumulate in patches at the junctions of white‐matter pathways, such as the three junctions that the internal capsule makes with the thalamocortical projection, external capsule and cerebral peduncle, respectively. In the cerebral cortex anlage, migration is mainly radial and tangential towards the immature white matter, subplate layer, and cortical plate, whereas pial cells populate the prospective layer I. A second wave of microglial cells penetrates the brain via the vascular route at about 12–13 gw and remains confined to the white matter. Two main findings deserve emphasis. First, microglia accumulate at 10–12 gw at the cortical plate–subplate junction, where the first synapses are detected. Second, microglia accumulate in restricted laminar bands, most notably around 19–30 gw, at the axonal crossroads in the white matter (semiovale centre) rostrally, extending caudally in the immature white matter to the visual radiations. This accumulation of proliferating microglia is located at the site of white‐matter injury in premature neonates. The spatiotemporal organization of microglia in the immature white and grey matter suggests that these cells may play active roles in developmental processes such as axonal guidance, synaptogenesis, and neurodevelopmental apoptosis as well as in injuries to the developing brain, in particular in the periventricular white‐matter injury of preterm infants.
Species-Dependent Expression of the Hyoscyamine 6[beta]-Hydroxylase Gene in the Pericycle

The tropane alkaloid scopolamine is synthesized in the pericycle of branch roots in certain species of the Solanaceae. The enzyme responsible for the synthesis of scopolamine from hyoscyamine is hyoscyamine 6[beta]-hydroxylase (H6H). The gene for H6H was isolated from Hyoscyamus niger. It has an exon/intron organization very similar to those for ethylene-forming enzymes, suggesting a common evolutionary origin. The 827-bp 5[prime] flanking region of the H6H gene was fused to the [beta]-glucuronidase (GUS) reporter gene and transferred to three solanaceous species by Agrobacterium-mediated transformation systems: H. niger and belladonna (Atropa belladonna), which have high and low levels, respectively, of H6H mRNA in the root, and tobacco (Nicotiana tabacum), which has no endogenous H6H gene. Histochemical analysis showed that GUS expression occurred in the pericycle and at the root meristem of transgenic H. niger hairy roots, but only at the root meristem of hairy roots and plants of transgenic tobacco. In transgenic hairy roots and regenerated plants of belladonna, the root meristem was stained with GUS activity, except for a few transformants in which the vascular cylinder was also stained. These studies indicate that the cell-specific expression of the H6H gene is controlled by some genetic regulation specific to scopolamine-producing plants.
Massive intractable pericardial effusion in a patient with systemic lupus erythematosus treated successfully with pericardial fenestration alone

Systemic lupus erythematosus (SLE) is often complicated by pericarditis with effusion, which generally responds well to glucocorticoid. We report herein a Japanese patient with SLE who showed a sign of cardiac tamponade and severe chest and back pain because of massive intractable pericardial effusion. Pulse glucocorticoid and pulse cyclophosphamide gained marginal effects. Pericardial effusion accumulated again soon after ultrasound-guided pericardiocentesis and drainage. Pericardial fenestration performed surgically as a last resort, for draining pericardial fluid into the pleural space, was very effective, and only a much smaller amount of fluid was observed in the space thereafter in comparison with the volume before the surgery. Pathological examination of the retrieved pericardium unfolded intense hyperplasia of small vessels and capillaries. Levels of IL-6 and TNF-α in pericardial effusion were extremely higher than those in serum. Pericardial effusion with extensive capillary hyperplasia in SLE would be resistant to medical treatment and require surgical fenestration.
Mainland Chinese Tourists to Hawaii: Their Characteristics and Preferences

ABSTRACT Tourism is the most economically important industry to the United States' only island state, Hawaii. With Hawaii's highest spending and largest international tourist segment, Japanese, decreasing significantly (a loss from over 2,000,000 in 1997 to just over 1,000,000 Japanese visitors in 2009), Hawaii needs to prepare to replace the significant decrease of Japanese visitors with a new visitor market. The logical new international visitor target market would be tourists from the fastest growing economy in the world, that being China. The purpose of this study is to explore the differences in attitudinal and behavioral characteristics, and preferences of Chinese tourists in Hawaii according to key sociodemographic variables. The results of this study conclude that sociodemographic variables show significant differences in attitudinal and behavioral characteristics. For example, when comparing the number of times a respondent had visited Hawaii, first-time visitors showed the highest level of preference for a deluxe hotel while second-time visitors showed the highest level of preference for a budget hotel. Those who had visited Hawaii three or more times indicated the highest preference for a first class hotel and also to be more interested in high-end shopping. First-time visitors showed the highest percentage in the lowest category of estimated cost of gifts (US$0–US$300). This indicates that Hawaii tour operators should focus on introducing more discounted shopping to first-time visitors. The results of this study are likely to be beneficial for understanding Chinese tourists and establishing marketing policies to enhance their satisfaction and raise their intention to revisit Hawaii. The findings of this study could be helpful for all stakeholders including local tour operators, the hotels, and Hawaii's tourism officials.
Phospho.ELM: a database of phosphorylation sites—update 2008

Phospho.ELM is a manually curated database of eukaryotic phosphorylation sites. The resource includes data collected from published literature as well as high-throughput data sets. The current release of Phospho.ELM (version 7.0, July 2007) contains 4078 phospho-protein sequences covering 12 025 phospho-serine, 2362 phospho-threonine and 2083 phospho-tyrosine sites. The entries provide information about the phosphorylated proteins and the exact position of known phosphorylated instances, the kinases responsible for the modification (where known) and links to bibliographic references. The database entries have hyperlinks to easily access further information from UniProt, PubMed, SMART, ELM, MSD as well as links to the protein interaction databases MINT and STRING. A new BLAST search tool, complementary to retrieval by keyword and UniProt accession number, allows users to submit a protein query (by sequence or UniProt accession) to search against the curated data set of phosphorylated peptides. Phospho.ELM is available on line at: http://phospho.elm. eu.org
ORIGINAL PAPER: Individualized homeopathic therapy for male infertility

This prospective observational pilot study investigated the effect of individualized homeopathy on male infertility based on sperm count, hormone values and general health. Forty-five subfertile men were treated with single homeopathic remedies for an average of 10.3 months. The drugs were prescribed on the basis of the overall symptomatic situation. The variables ‘sperm density’, ‘percentage of sperm with good progressive motility’ and ‘density of sperm with good propulsive motility’ improved significantly, especially in cases of oligoasthenozoospermia. The general health of patients improved significantly. The following factors emerged as positive predictors of therapy success: alcohol consumption below 30 g/day, non-smoking, the presence of less than five dental amalgam fillings, no exposure to noxious substances at the workplace and no previous inflammatory genital diseases. The factors stress, age above 36, high coffee consumption and long duration of unwanted childlessness did not have a negative impact on therapy outcome in this study. The rate of improvement in sperm count through homeopathic therapy is comparable to the improvement achieved by conventional therapy, so that individualized-homeopathic treatment may be considered a useful alternative to conventional treatment of subfertile men. For further investigation, a randomised, therapy-controlled clinical study with parallel group design would be useful (homeopathic therapy vs conventional andrological therapy). Homeopathy (2002) 91, 133–144.
Wide-band indoor localization effectiveness in presence of moving people

Recently, new standards have emerged in the telecommunication industry. These standards provide an open global specification that enables mobile devices to access and interact with information and services instantly. Paving the way to the emergence of new added-values services, these devices require more and more a localization agent. When deployed, these wireless resources have to operate in non-stationary propagation conditions and from outdoors to indoors. This paper concentrates on the evaluation of UWB radio signals used for localization, in presence of moving people modifying the indoor propagation channel. Different frequencies, bandwidths and densities of moving people are considered. Impacts of these parameters are evaluated on two different ranging methods: time of arrival (TOA) based and received signal strength (RSS) based.
Using Science-Fiction Prototyping as a Means to Motivate Learning of STEM Topics and Foreign Languages

In this paper we report on the operation and results of a pilot trial on the use of Science-Fiction Prototyping (SFP) as a means to motivate students to engage with STEM and language learning courses. In particular we describe two case studies. The first was conducted in Shijiazhuang University, China, and involved approximately 102 students following a course aimed at improving their English language abilities for computer science applications. The second case study concerned the use of micro science-fiction prototypes, in the form of Twitter-fiction, as a means of motivating pre-university students to take up STEM studies and careers. Finally, the paper concludes by describing future directions of this work.
The Changing Role of the University in Contemporary Society

One of the most remarkable paradoxes of our time involves the university. There appears to have been a loss of public confidence in higher education at the very time that the university has been more and more moving away from its ivy walls into the arena of public service. It is this very fact of increased public service which has caused the university to be more and more an object of public knowledge and public inspection. Traditionally, the university has been a place which has operated within its own rules and regulations somewhat separated from the rest of society. While this has not been strictly true for a rather long time, it is only since World War II that the university has become closely associated with social change in the eyes of its publics.
Digital game-based learning (DGBL) model and development methodology for teaching history

History subject plays a vital role in instilling the spirits of patriotism among the students; to nourish and instill love and loyalty to one's country and to be a true citizen. The lack of creativity in history teaching caused process effectively and interestingly especially among young learners. Digital Game Based Learning (DGBL) approach utilizes the game as a medium for conveying learning contents. There are many models for educational games development which combined the Instructional Design (ID) and game development process. However, there is still a conflict on how to merge ID and game development effectively. Therefore, we looked into the pedagogy and game design aspects. We then propose a DGBL model for History educational games design and a development methodology which combined the ID and game development process, named DGBL-ID model. The DGBL-ID model consists of five phases: analysis, design, development, quality assurance as well as implementation and evaluation.