Miracle-dz/UniFAR-FTUs huggingface dataset:
Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation.

We have developed a methodology we call ROMA (representational oligonucleotide microarray analysis), for the detection of the genomic aberrations in cancer and normal humans. By arraying oligonucleotide probes designed from the human genome sequence, and hybridizing with "representations" from cancer and normal cells, we detect regions of the genome with altered "copy number. " We achieve an average resolution of 30 kb throughout the genome, and resolutions as high as a probe every 15 kb are practical. We illustrate the characteristics of probes on the array and accuracy of measurements obtained using ROMA. Using this methodology, we identify variation between cancer and normal genomes, as well as between normal human genomes. In cancer genomes, we readily detect amplifications and large and small homozygous and hemizygous deletions. Between normal human genomes, we frequently detect large (100 kb to 1 Mb) deletions or duplications. Many of these changes encompass known genes. ROMA will assist in the discovery of genes and markers important in cancer, and the discovery of loci that may be important in inherited predispositions to disease.
Incremental Joint Approach to Word Segmentation, POS Tagging, and Dependency Parsing in Chinese

We propose the first joint model for word segmentation, POS tagging, and dependency parsing for Chinese. Based on an extension of the incremental joint model for POS tagging and dependency parsing (Hatori et al., 2011), we propose an efficient character-based decoding method that can combine features from state-of-the-art segmentation, POS tagging, and dependency parsing models. We also describe our method to align comparable states in the beam, and how we can combine features of different characteristics in our incremental framework. In experiments using the Chinese Treebank (CTB), we show that the accuracies of the three tasks can be improved significantly over the baseline models, particularly by 0.6% for POS tagging and 2.4% for dependency parsing. We also perform comparison experiments with the partially joint models.
A Free-living Panagrolaimus sp. from Armenia Can Survive in Anhydrobiosis for 8.7 Years.

Although the ability of plant-parasitic nematodes to survive in a dehydrated or anhydrobiotic state for long periods of time has been well documented, the ability of free-living nematodes has not. Here we report on the survival of a free-living nematode, Panagrolaimus sp. , from Armenia in the anhydrobiotic state for 8.7 years. This Panagrolaimus sp. can be cultured and maintained readily and may provide a good system for studying anhydrobiosis in nematodes.
Blending history and fiction in a pervasive game prototype

Pervasive games represent an exciting development in gaming which leverages the use of sensor, visualization and networking technologies to provide immerse live-action game experiences. The field of pervasive games has been intensively researched in the recent years, as evidenced from the proliferation of available prototypes. Existing pervasive game projects commonly do not enable relocation of the game space while also overlooking several aspects which critically affect user acceptance and game experience such as scenario design, usability of employed technologies, game duration and intensity. This article introduces Barbarossa, an outdoor pervasive role-playing game. Barbarossa addresses the abovementioned issues featuring several portable game modes. It also takes into account concrete technology usage requirements for each game mode according to the game session duration and player effort required. Further, game experience is enhanced through incorporating several contextual parameters. User evaluation trials indicated warm reception of Barbarossa by players and confirmed that the main game design objectives have been largely achieved.
Partners, guests or competitors

Recent policy documents have promoted partnership working between criminal justice agencies and third sector organizations (TSOs) as a means to tackle re-offending. However, the context in which such partnership working takes place has received little attention despite the fact that relationships between frontline criminal justice staff and TSOs are likely to be crucial to successful initiatives. This article draws on qualitative interviews with prison staff and representatives from TSOs in eight prisons to examine relations between the two groups and to consider whether TSOs are treated as partners, guests or competitors in prisons.
Marine Collagen Peptides from the Skin of Nile Tilapia (Oreochromis niloticus): Characterization and Wound Healing Evaluation

Burns can cause tremendous economic problems associated with irreparable harm to patients and their families. To characterize marine collagen peptides (MCPs) from the skin of Nile tilapia (Oreochromis niloticus), molecular weight distribution and amino acid composition of MCPs were determined, and Fourier transform infrared spectroscopy (FTIR) was used to analyze the chemical structure. Meanwhile, to evaluate the wound healing activity, in vitro and in vivo experiments were carried out. The results showed that MCPs prepared from the skin of Nile tilapia by composite enzymatic hydrolysis were composed of polypeptides with different molecular weights and the contents of polypeptides with molecular weights of less than 5 kDa accounted for 99.14%. From the amino acid composition, the majority of residues, accounting for over 58% of the total residues in MCPs, were hydrophilic. FTIR indicated that the main molecular conformations inside MCPs were random coil. In vitro scratch assay showed that there were significant effects on the scratch closure by the treatment of MCPs with the concentration of 50.0 μg/mL. In the experiments of deep partial-thickness scald wound in rabbits, MCPs could enhance the process of wound healing. Therefore, MCPs from the skin of Nile tilapia (O. niloticus) have promising applications in wound care.
Burden of Visceral Leishmaniasis in Villages of Eastern Gedaref State, Sudan: An Exhaustive Cross-Sectional Survey

Background Since December 2009, Médecins Sans Frontières has diagnosed and treated patients with visceral leishmaniasis (VL) in Tabarak Allah Hospital, eastern Gedaref State, one of the main endemic foci of VL in Sudan. A survey was conducted to estimate the VL incidence in villages around Tabarak Allah. Methods Between the 5th of May and the 17th of June 2011, we conducted an exhaustive door-to-door survey in 45 villages of Al-Gureisha locality. Deaths were investigated by verbal autopsies. All individuals with (i) fever of at least two weeks, (ii) VL diagnosed and treated in the previous year, and (iii) clinical suspicion of post-kala-azar dermal leishmaniasis (PKDL) were referred to medical teams for case ascertainment. A new case of VL was a clinical suspect with a positive rk39 rapid test or direct agglutination test (DAT). Results In the 45 villages screened, 17,702 households were interviewed, for a population of 94,369 inhabitants. The crude mortality rate over the mean recall period of 409 days was 0.13/10'000 people per day. VL was a possible or probable cause for 19% of all deaths. The VL-specific mortality rate was estimated at 0.9/1000 per year. The medical teams examined 551 individuals referred for a history of fever of at least two weeks. Out of these, 16 were diagnosed with primary VL. The overall incidence of VL over the past year was 7.0/1000 persons per year, or 7.9/1000 per year when deaths possibly or probably due to VL were included. Overall, 12.5% (11,943/95,609) of the population reported a past VL treatment episode. Discussion and Conclusion VL represents a significant health burden in eastern Gedaref State. Active VL case detection had a very low yield in this specific setting with adequate access to care and may not be the priority intervention to enhance control in similar contexts.
Modeling and Simulation of TCSC with Dynamic Phasors Considering Harmonic Characteristics

A dynamic phasors model for TCSC is proposed in this paper to understand the interactions between TCSC and power system better. The distinguishing feature of the model is that the harmonics characteristics are considered in the derivation of the model. The order of the model is maintained to a second-order state-space equation. Validation of the model is performed and the results show that the proposed model has a good agreement with the waveforms of the simulation results of the time-domain model. This model has an accurate simulation of the dynamic process of the power system which can be more valuable for transient simulation and control design.
Securing Network Input via a Trusted Input Proxy

The increasing popularity of online transactions involving sensitive personal data, such as bank account and social security numbers, has created a huge security problem for today's computer users. Malicious software (malware) that steals passwords and other critical user input has led to countless cases of identity theft and financial fraud. Client computers remain susceptible to key logging attacks due to inadequate defense against drive-by malware installation. Trusted browsing virtual machines attempt to mitigate this problem, but fail to protect against many runtime and Trojan horse malware attacks. One option for securely acquiring sensitive input is TPM-verified trusted execution. While this method promises to provide the best security, it has serious usability limitations and would require extensive modifications to both the client and the server. We propose a new approach for securing network input that relies on a Trusted Input Proxy (TIP). The TIP runs as a module in a virtual machine architecture that proxies secure network connections. When a user wishes to enter sensitive data, he or she presses an escape sequence that triggers the TIP to display a secure input dialog. The TIP will automatically generate a placeholder value based on the input using regular expression approximation (e.g. 123-45-6789 for a SSN). It will then send key presses for the placeholder to the application. Finally, the TIP will substitute actual data for placeholders as it relays network messages to the server. Although the Trusted Input Proxy approach relies on a slightly larger trusted code base, it requires no modifications to the server, very few to the client, and is far more usable than TPM-verified execution. In this paper, we present the initial design of a Trusted Input Proxy and compare its merits and shortcomings to those of other approaches.
Constructive model selection for multi-output extreme learning machine

In this paper, a novel constructive model selection for multi-output extreme learning machine (CMS-MELM) is proposed to deal with multi-output regressions. The significant contributions to this paper feature the key characteristics as follows. 1) The initial candidate pool for CMS-MELM is randomly generated according to the ELM strategy, and ranked chunk-by-chunk based on a novel improved multi-response sparse regression (I-MRSR) incorporated with λ weighting. 2) Accordingly, the proposed constructive model selection works with fast speed due to chunk-type training process, which also benefits stable hidden node selection and corresponding generalization capability. 3) Furthermore, validation and retraining phases are conducted to enhance the overall performance of the resulting CMS-MELM scheme. Finally, the convincing performance of the complete CMS-MELM paradigm is verified by simulation studies on real-life benchmark multi-output regressions. Comprehensive comparisons of the CMS-MELM with other well-known strategies, i.e., ELM and OP-ELM, indicate the remarkable superiority in terms of generalization capability and stable compact structure. Clear conclusions are steadily drawn that the CMS-MELM method is feasibly effective for multi-output regressions.
A MULTI-MODEL DOCKING EXPERIMENT OF DYNAMIC SOCIAL NETWORK SIMULATIONS

Axtell, Axelrod, Epstein and Cohen [26] describe a docking or alignment process and experiment for verifying simulations. By comparing simulations built independently using different simulation tools, the docking or alignment process may discover bugs, misinterpretation of model specification, and inherent differences in toolkit implementations. If the behavior of the multiple simulations are similar, then verification confidence is increased. North and Macal [24] reported on such experiment using Mathematica, Swarm and RePast to simulation the Beer Distribution Game (originally simulated using system dynamics simulation methods). In this paper, we present the results of docking a Repast simulation and a Java/Swarm simulation of four social network models of the Open Source Software (OSS) community. Data about the SourceForge OSS developer site has been collected for over 2 years. Developer membership in projects is used to model the social network of developers. Social networks based on random graphs, preferential attachment, preference attachment with constant fitness, and preferential attachment with dynamic fitness are modeled and compared to collected data. We describe how properties of social networks such as degree distribution, diameter and clustering coefficient are used to dock Repast and Swarm simulations of four social network models. The simulations grow “artificial societies” representing the SourceForge developer/project community. As a by-product of the docking experiment, we provide observations on the advantages and disadvantages of the two toolkits for modeling such systems.
Combining Efforts for Improving Automatic Classification of Emotional User States

Classification performance of emotional user states found in realistic, spontaneous speech is not very high, compared to the performance reported for acted speech in the literature. This might be partly due to the difficulty of providing reliable annotations, partly due to suboptimal feature vectors used for classification, and partly due to the difficulty of the task. In this paper, we present a co-operation between several sites, using a thoroughly processed emotional database. For the four-class problem motherese/neutral/emphatic/angry, we first report classification performance computed independently at each site. Then we show that by using all the best features from each site in a combined classification, and by combining classifier outputs within the ROVER framework, classification results can be improved; all feature types and features from all sites contributed. Združevanje sil za boljse samodejno razvrscanje custvenih stanj uporabnika: Uspesnost samodejnega razvrsžanja custvenih stanj uporabnika, ki jih najdemo v realisticnem, spontanem govoru, je v primerjavi s kakovostjo, ki jo v literaturi navajajo za igrani govor, precej nižja. To je lahko delno posledica težav pri zagotavljanju zanesljive anotacije, delno posledica uporabe podoptimalnih vektorjev znacilk pri razvrsžanju, delno pa posledica težavnosti te naloge. V prispevku predstavljamo sodelovanje med razlicnimi ustanovami na temeljito obdelani bazi podatkov. Za stiristopenjski problem govor otroku/nevtralno/poudarjeno/jezno najprej navedemo kakovost razvrsžanja, kot so jo izracunali neodvisno na vsaki od sodelujocih ustanov. Nato poka-žemo, da lahko izboljsamo rezultate razvrsžanja z uporabo najboljsih znacilk vsake izmed ustanov in z združevanjem rezultatov razvrsževalnikov znotraj ogrodja ROVER.
A contemporary view of coronal heating

Determining the heating mechanism (or mechanisms) that causes the outer atmosphere of the Sun, and many other stars, to reach temperatures orders of magnitude higher than their surface temperatures has long been a key problem. For decades, the problem has been known as the coronal heating problem, but it is now clear that ‘coronal heating’ cannot be treated or explained in isolation and that the heating of the whole solar atmosphere must be studied as a highly coupled system. The magnetic field of the star is known to play a key role, but, despite significant advancements in solar telescopes, computing power and much greater understanding of theoretical mechanisms, the question of which mechanism or mechanisms are the dominant supplier of energy to the chromosphere and corona is still open. Following substantial recent progress, we consider the most likely contenders and discuss the key factors that have made, and still make, determining the actual (coronal) heating mechanism (or mechanisms) so difficult.
Theorising Student Identity as Fragmented: some implications for feminist critical pedagogy

Abstract In this paper, I explore the narratives of a group of British adolescent comprehensive school students, attending particularly to diversity. I provide a critique of those poststructural analyses which understand the student as a composite of self‐contained homogeneous parts, offering instead an analysis of the self which is highly fractured, contradictory and shifting. This paper suggests that analyses of diversity must account for inner and outer diversity, and that inner diversity may account for student narratives which appear highly contradictory. It goes on to explore various solutions offered by educational researchers to diversity and to suggest that negotiation might supply the most fruitful alternative. Finally, I suggest some implications for an alternative feminist critical pedagogy which incorporates diversity of the self.
Residential Mobility, Inhibitory Control, and Academic Achievement in Preschool

Research Findings: The present study investigated the direct effects of residential mobility on children's inhibitory control and academic achievement during the preschool year. It also explored fall inhibitory control and academic skills as mediators linking residential mobility and spring achievement. Participants included 359 preschool children (49% female) studied in the fall and spring of the preschool year (73% were enrolled in Head Start). Residential mobility was significantly and negatively associated with fall inhibitory control and fall math and literacy. Significant indirect effects of mobility were found for spring math and literacy through inhibitory control and fall achievement. Specifically, the negative relation between mobility and spring math and literacy was partially explained by lower scores on fall inhibitory control and academic skills. Practice or Policy: The current study contributes to the existing literature by specifying pathways linking frequent moves and achievement for young children. Policy implications are discussed.
Motivational Profiles and Achievement Goal Dominance in Physical Education

Abstract The main goal was to compare idiographic profiles of achievement goal dominance (AGD) and motivational profiles based on 2x2 achievement goals to improve our understanding of how the four achievement goals work in conjunction with one another, and to discern which profiles are most adaptive in the Physical Education context. A total of 351 students (203 males; 148 females) (M = 14.26 ± 1.37 years) from 3 different secondary schools agreed to participate. 86.6% (N = 303) showed AGD, mostly mastery-approach dominance (62.9%). We examined the four AGD groups’ idiographic profiles and how they relate to certain positive (autonomous motivation and positive affect) and negative variables (controlled motivation and amotivation). The results supported the hypotheses of AGD theory (MANOVA one-way, Wilks’ lambda = .609, F(24, 298) = 7.96, p < . 001, η2 = . 15). Subsequently, k-means cluster analysis was performed, yielding 4 distinct achievement goal profiles. The most adaptive was named “mastery goals”, while “high achievement goals” were the second most adaptive. AGD participants’distribution across the different motivational clusters was also ascertained (MANOVA one-way, Wilks’ lambda = .678, F(12, 910) = 12.01, p < . 001, η2 = . 12).
Response to Tregeagle (2012). Commentary on Computer-based Information Systems and Human Service Organisations: Emerging Problems and Future Possibilities (Gillingham, 2011)

I am grateful to Dr Susan Tregeagle for taking the time to comment on my article (Gillingham, 2011) and so draw further attention to what is increasingly being recognised as a serious problem. However, in her description of my article as an exploration of ‘‘the failure of electronic information systems (IS) to provide useful data on which social workers and policy makers could improve child welfare services’’, Tregeagle (2012) misconstrued my main argument, which concerned how IS have affected frontline practitioners in child protection services. Consequently, much of Tregeagle’s (2012) critique focused on issues that were, at best, marginal to my concerns. In principle, I agree that the data IS can capture about service activity should be able to be used to inform service reform. Tregeagle (2012) has raised an important point about the quality of data captured by IS, which deserves more thorough investigation. In my article, I mentioned, only briefly, Shaw et al.’s (2009) observation that problems with IS and their usage in human service organisations (in England) have raised doubts about the reliability of the data they can provide for evaluative purposes, and that concerns have also been raised by senior departmental staff in the Victorian Ombudsman’s (2009) investigation about data quality in the Client Relationship Information System (CRIS), the IS used in Victoria. However, returning to Australian sources used in my article (Gillingham, 2011), it appears that the Ombudsman’s (2009) comments deserve full quotation rather than brief paraphrasing:
Integrin αVβ5-mediated Removal of Apoptotic Cell Debris by the Eye Lens and Its Inhibition by UV Light Exposure*

Accumulation of apoptotic material is toxic and associated with cataract and other disease states. Identification of mechanisms that prevent accumulation of apoptotic debris is important for establishing the etiology of these diseases. The ocular lens is routinely assaulted by UV light that causes lens cell apoptosis and is associated with cataract formation. To date, no molecular mechanism for removal of toxic apoptotic debris has been identified in the lens. Vesicular debris within lens cells exposed to UV light has been observed raising speculation that lens cells themselves could act as phagocytes to remove toxic apoptotic debris. However, phagocytosis has not been confirmed as a function of the intact eye lens, and no mechanism for lens phagocytosis has been established. Here, we demonstrate that the eye lens is capable of phagocytizing extracellular lens cell debris. Using high throughput RNA sequencing and bioinformatics analysis, we establish that lens epithelial cells express members of the integrin αVβ5-mediated phagocytosis pathway and that internalized cell debris co-localizes with αVβ5 and with RAB7 and Rab-interacting lysosomal protein that are required for phagosome maturation and fusion with lysosomes. We demonstrate that the αVβ5 receptor is required for lens epithelial cell phagocytosis and that UV light treatment of lens epithelial cells results in damage to the αVβ5 receptor with concomitant loss of phagocytosis. These data suggest that loss of αVβ5-mediated phagocytosis by the eye lens could result in accumulation of toxic cell debris that could contribute to UV light-induced cataract formation.