Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential regulation of human papillomavirus type 6 and 11 early promoters in cultured cells derived from laryngeal papillomas

Cells cultured from laryngeal papillomas contain episomal human papillomavirus type 6 or type 11 (HPV-6/11) DNA. We developed a sensitive RNase protection assay to simultaneously measure expression from the HPV E6, E7, and E1 promoters (P1, P2 and P3, respectively) in this manipulable culture system and found that P1, P2 and P3 transcript abundances could be independently modulated by culture medium composition and culture substrate. In undifferentiated cells grown in a low-calcium, serum-free medium, P1 transcripts commonly predominated over those from P2, P3 transcripts were often undetectable, and high concentrations of retinoic acid were able to selectively decrease P2 transcript abundance. When cultures were allowed to stratify and differentiate by growth on a collagen gel at he air-liquid interface, total HPV RNA increased up to sixfold because of selective increases in abundances of P1 and P3 transcripts. High-calcium submerged cultures also showed easily detectable P3 transcripts, and isolated suprabasal cells contained almost exclusively these transcripts. Growth arrest alone was not sufficient to induce P3 transcripts. Thus, in contrast to the HPV-6/11 E6 and E7 promoters, the E1 promoter was utilized primarily in a differentiation-specific manner. We also show that increased HPV gene dosage will not necessary bring about increased HPV transcript abundance, suggesting that other viral and cellular factors are responsible for regulation of total transcript levels as well as specific promoter usage.
Non-Exponential Relaxation Time Scales in Disordered Systems: An Application to Protein Dynamics

We study the dynamics of a heteropolymeric chain relaxing toward a new equilibrium configuration after the action of an external perturbation. We compare the results from Monte Carlo simulations with the results of a Langevin normal-mode decomposition. We discuss, for the sake of comparison, the case of an ordered homopolymeric chain. We discuss the dependence of the relaxation stretching exponent on the system size by studying chains constituted by 15 and 30 points.
Parallel Knowledge Embedding with MapReduce on a Multi-core Processor

This article firstly attempts to explore parallel algorithms of learning distributed representations for both entities and relations in large-scale knowledge repositories with {\it MapReduce} programming model on a multi-core processor. We accelerate the training progress of a canonical knowledge embedding method, i.e. {\it translating embedding} ({\bf TransE}) model, by dividing a whole knowledge repository into several balanced subsets, and feeding each subset into an individual core where local embeddings can concurrently run updating during the {\it Map} phase. However, it usually suffers from inconsistent low-dimensional vector representations of the same key, which are collected from different {\it Map} workers, and further leads to conflicts when conducting {\it Reduce} to merge the various vectors associated with the same key. Therefore, we try several strategies to acquire the merged embeddings which may not only retain the performance of {\it entity inference}, {\it relation prediction}, and even {\it triplet classification} evaluated by the single-thread {\bf TransE} on several well-known knowledge bases such as Freebase and NELL, but also scale up the learning speed along with the number of cores within a processor. So far, the empirical studies show that we could achieve comparable results as the single-thread {\bf TransE} performs by the {\it stochastic gradient descend} (SGD) algorithm, as well as increase the training speed multiple times via adapting the {\it batch gradient descend} (BGD) algorithm for {\it MapReduce} paradigm.
Visualization and quantification of SPIO nanoparticles in intracellular spaces of macrophages for nanomedicine applications.

This work focuses on the visualization and quantification of Super-paramagnetic iron oxide nanoparticles (SPIO-NPs) inside macrophages using transmission electron microscope (TEM) images. Macrophages have been extensively used as probes for cell and subcellular structure labeling, as well as for drug and gene delivery. In order to track the macrophages movement inside the body, SPIO-NPs are introduced to help in the visualization of macrophages by MRI imaging and then to control process of the drug and gene delivery. The mechanism of interaction between macrophages and SPIO-NPs is still not fully understood by scientists. Estimating the quantity of NPs inside microphages will certainly improve the understanding of this mechanism. In this work a 3D reconstruction and visualization, using transmission electron microscopy (TEM), of macrophages filled with SPIO-NPs is being developed. An estimation of the quantities of the NPs inside macrophages has been achieved. The visual interaction between macrophages and SPIO-NPs had been discovered.
On Code Generation for Derived Associations

While the generation of executable code for explicit associations in UML models is well understood, it is less clear how executable code can be generated if the associations are derived. We discuss how this can be achieved for an important class of derived associations that are defined by means of derivation rules. The result is optimized and executable (as opposed to template) code. The generated code supports semantic reflection, that is, runtime access to the rules used to define the association. We relate these features to use cases from the area of business rules. We also present the Take rule compiler, a Java implementation of the principles discussed.
Evidence for Positive Selection on the Osteogenin (BMP3) Gene in Human Populations

Background Human skeletal system has evolved rapidly since the dispersal of modern humans from Africa, potentially driven by selection and adaptation. Osteogenin (BMP3) plays an important role in skeletal development and bone osteogenesis as an antagonist of the osteogenic bone morphogenetic proteins, and negatively regulates bone mineral density. Methodology/Principal Findings Here, we resequenced the BMP3 gene from individuals in four geographically separated modern human populations. Features supportive of positive selection in the BMP3 gene were found including the presence of an excess of nonsynonymous mutations in modern humans, and a significantly lower genetic diversity that deviates from neutrality. The prevalent haplotypes of the first exon region in Europeans demonstrated features of long-range haplotype homogeneity. In contrast with findings in European, the derived allele SNP Arg192Gln shows higher extended haplotype homozygosity in East Asian. The worldwide allele frequency distribution of SNP shows not only a high-derived allele frequency in Asians, but also in Americans, which is suggestive of functional adaptation. Conclusions/Significance In conclusion, we provide evidence for recent positive selection operating upon a crucial gene in skeletal development, which may provide new insight into the evolution of the skeletal system and bone development.
An Empirical Evaluation of Social Support and Psychological Well-being in Older Chinese and Korean Immigrants

Objectives. To examine, among older Chinese and Korean immigrants: (1) the concept and measurement of perceived social support; (2) levels of social support and psychological well-being by living arrangement; and (3) whether social support is positively related to psychological well-being. Design. A convenience sample of 200 self-identified Chinese and Koreans, aged 65 years and older, were interviewed. Psychometric analysis was conducted to examine the reliability and validity of a new social support measure. Bivariate and multivariate analyses were used to examine the relationship between social support and psychological well-being. Results. Factor analysis revealed a four-factor solution of social support and adequate psychometrics of all social support scales was found. Multivariate results suggest that Koreans have more depression than Chinese (p < 0.01). Those who lived with their spouse and adult children had lower overall psychological well-being (p < 0.05) and lower positive affect (p < 0.05) compared to those who lived alone. Having more emotional/companionship support significantly (p < 0.001) contributed to better overall psychological well-being, having less depression and higher positive affect. Conclusions. A new multidimensional social support measure for use with older Chinese and Koreans could be useful upon further validation. These results suggest that older Chinese and Koreans’ psychological well-being may be negatively affected when they live with their adult children. More depression in Koreans may be related to difficulties in expanding their social network beyond Korean-speaking people.
Static Mastermind

Static mastermind is like normal mastermind, except that the codebreaker must supply at one go a list of questions (candidate codes), the answers to which must uniquely determine the secret code. We confirm the minimum size list for some small values. Then we solve the game for up to 4 positions. In particular we show that for k sufficiently large the minimium size of a list for 4 positions and k colours is k − 1.
Designing collaborations: could design probes contribute to better communication between collaborators?

Digital Humanities is an inherently collaborative field of research. The wide range of stakeholders, as well as the ever changing methodologies, hold the potential for innovation but also carry a constant threat of miscommunication. Design is a fixed partner in Digital Humanities and their practices are closely intertwined. However on a practical level, design is most commonly regarded as an implementation technique rather than an equal part of the theoretical framework. We propose to utilize design as a research tool by developing a set of Design Probes which are created to address the specific needs and challenges of collaborative research in Digital Humanities. We describe design and technical implementation methods, as well as the theoretical context and the possible outcome of this proposal.
Durability of regenerated articular cartilage produced by free autogenous periosteal grafts in major full-thickness defects in joint surfaces under the influence of continuous passive motion. A follow-up report at one year.

An autogenous graft of tibial periosteum was sutured (with its cambium layer facing into the joint) to the base of a five by ten-millimeter full-thickness defect in the patellar groove of each of forty-five adolescent rabbits. The rabbits were randomly treated postoperatively by either four weeks of immobilization in a cast, intermittent active motion in a cage, or two weeks of continuous passive motion. One year postoperatively, the regenerated tissue from each rabbit was analyzed macroscopically, histologically, histochemically, and biochemically. Gross degenerative changes were seen in 57 per cent of the rabbits that had been immobilized in a cast, in 73 per cent of the rabbits that had been allowed intermittent active motion, and in 22 per cent of the rabbits that had been subjected to continuous passive motion (p less than 0.05). Out of a possible score of 7.0 points for the nature of the regenerated tissue, the scores for the three groups were: immobilization in a cast, 4.1 points; intermittent active motion, 4.0 points; and continuous passive motion, 5.9 points (p greater than 0.05). Out of a possible perfect combined score of 10.0 points for the structural characteristics of the regenerated tissue, the cast-immobilization group scored 3.8 points; the intermittent active-motion group, 2.5 points; and the continuous passive-motion group, 6.4 points (p less than 0.001). The total scores for freedom from cellular changes of degeneration, a perfect score being 5.0 points, were: immobilization in a cast, 2.4 points; intermittent active motion, 2.3 points; and continuous passive motion, 3.9 points (p less than 0.01). Degenerative changes in the adjacent cartilage, which were noted in 42 and 46 per cent of the knees in the immobilization and intermittent active-motion groups, respectively, were not found in the knees that had been subjected to continuous passive motion (p less than 0.05). The total indices, which were derived by combining the scores for all categories (maximum, 24.0 points), revealed that the index for the continuous passive-motion group was significantly better than the index for either of the other two groups: immobilization in a cast, 12.9 points; intermittent active motion, 11.2 points; and continuous passive motion, 19.2 points (p less than 0.0005). (ABSTRACT TRUNCATED AT 400 WORDS)
Low-leakage hybrid FinFET SRAM cell with asymmetrical gate overlap / underlap bitline access transistors for enhanced read data stability

The degraded read data stability and write ability of SRAM cells have become primary design concerns with CMOS technology scaling into the sub-22nm channel lengths. A new six-FinFET SRAM cell with asymmetrical bitline access transistors is proposed in this paper for enhancing the read data stability and suppressing the leakage power consumption in memory circuits. The bitline access transistor channel is underlapped on one side while overlapped by the gate terminal on the opposite side of the transistor. The asymmetrical bitline access transistors are weakened during read operations and strengthened during write operations as the direction of current flow is reversed. With the proposed asymmetrical six-FinFET SRAM cell, the read data stability is enhanced by up to 62% and the leakage power consumption is reduced by up to 49.3%, while maintaining similar write margin, cell layout area, read delay, and write delay as compared to a previously published asymmetrical six-FinFET SRAM cell in a 15nm FinFET technology.
Congenital brachial palsy: incidence, causes, and outcome in the United Kingdom and Republic of Ireland

Objectives: To determine the incidence and study the causes and outcome of congenital brachial palsy (CBP). Design: Active surveillance of newborn infants using the British Paediatric Surveillance Unit notification system and follow up study of outcome at 6 months of age. Setting: The United Kingdom and Republic of Ireland. Participants: Newborn infants presenting with a flaccid paresis of the arm (usually one, rarely both) born between April 1998 and March 1999. Main outcome measures: Extent of the lesion at birth and degree of recovery at 6 months of age. Findings: There were 323 confirmed cases giving an incidence of 0.42 per 1000 live births (1 in 2300). Significant associated risk factors in comparison with the normal population were shoulder dystocia (60% v 0.3%), high birth weight with 53% infants weighing more than the 90th centile, and assisted delivery (relative risk (RR) 3.4, 95% confidence interval (CI) 2.9 to 3.9, p = 0.0001). There was a considerably lower risk of CBP in infants delivered by caesarean section (RR 7, 95% CI 2 to 56, p = 0.002). At about 6 months of age, about half of the infants had recovered fully, but the remainder showed incomplete recovery including 2% with no recovery. The relative risk of partial or no recovery in infants with extensive lesions soon after birth compared with those with less extensive lesions was 11.28 (95% CI 2.38 to 63.66, p = 0.000005). Conclusions: The incidence of CBP in the United Kingdom and Republic of Ireland is strikingly similar to that previously reported nearly 40 years ago. Most cases are due to trauma at delivery, which is not necessarily excessive or inappropriate. Given the uncertainty about the appropriate management of these infants, serious consideration should be given to a formal clinical trial of microsurgical nerve repair.
Design of Biomimetic Vascular Grafts with Magnetic Endothelial Patterning

The development of small diameter vascular grafts with a controlled pluricellular organization is still needed for effective vascular tissue engineering. Here, we describe a technological approach combining a tubular scaffold and magnetically labeled cells to create a pluricellular and organized vascular graft, the endothelialization of which could be monitored by MRI prior to transplantation. A novel type of scaffold was developed with a tubular geometry and a porous bulk structure enabling the seeding of cells in the scaffold pores. A homogeneous distribution of human mesenchymal stem cells in the macroporous structure was obtained by seeding the freeze-dried scaffold with the cell suspension. The efficient covering of the luminal surface of the tube was then made possible thanks to the implementation of a magnetic-based patterning technique. Human endothelial cells or endothelial progenitors were magnetically labeled with iron oxide nanoparticles and successfully attracted to the 2-mm lumen where they attached and formed a continuous endothelium. The combination of imaging modalities [fluorescence imaging, histology, and 3D magnetic resonance imaging (MRI)] evidenced the integrity of the vascular construct. In particular, the observation of different cell organizations in a vascular scaffold within the range of resolution of single cells by 4.7 T MRI is reported.
Using reflective self-assessments in a learning management system to promote student engagement and academic success

Learning management systems have the capabilities of creating, fostering, delivering, and facilitating learning at anytime and anywhere, allowing students to engage in online discussion and collaborative activities. However, many researchers feel that the online space essentially remains a repository for content. However, the fact that some academics use such systems as a content dumping site cannot be generalized. No, such a blanket statement would be a grave injustice to those few academics that are trying to improve the teaching and learning process, especially through reflective practice. The purpose of this paper is to highlight how an academic in electrical engineering has effectively used BlackboardTM to promote student engagement and academic success through online reflective self-assessments. An ex-post facto study is used with descriptive statistics of the quantitative data. Two groups of students enrolled for different electronic communication modules were asked to complete biweekly online reflective self-assessments via BlackboardTM. Results indicate that those who completed more than 50% of these self-assessments were almost twice as likely to achieve academic success as compared to those who completed less than 50% of them. These results tend to suggest that some academics are using educational technology more effectively than other academics, to the benefit of students and higher educational institutions.
Understanding Privacy Settings in Facebook with an Audience View

Users of online social networking communities are disclosing large amounts of personal information, putting themselves at a variety of risks. Our ongoing research investigates mechanisms for socially appropriate privacy management in online social networking communities. As a first step, we are examining the role of interface usability in current privacy settings. In this paper we report on our first iterative prototype, where presenting an audience-oriented view of profile information significantly improved the understanding of privacy settings.
Priority-based delay mitigation for event-monitoring IEEE 802.15.4 LR-WPANs

IEEE 802.15. 4 slotted carrier-sense multiple access with collision avoidance (CSMA-CA) adopts periodic sleeping for energy efficiency support. However, such a periodic sleeping mechanism, especially with contention-based medium access, tends to cause additional sleep delay due to heavy contention. In this letter, we propose a priority-based scheme, comprising frame tailoring and priority toning, in order to relax such a problematic delay and guarantee time-bounded delivery of high priority packets in event-monitoring networks.
Chapter 21 Short Cut Fusion of Recursive Programs with Computational Effects

: Fusion is the process of improving the efﬁciency of modularly constructed programs by transforming them into monolithic equivalents. This paper deﬁnes a generalization of the standard build combinator which expresses uniform production of functorial contexts containing data of inductive types. It also proves correct a fusion rule which generalizes the fold / build and fold / buildp rules from the literature, and eliminates intermediate data structures of inductive types without disturbing the contexts in which they are situated. An important special case arises when this context is monadic. When it is, a second rule for fusing combinations of producers and consumers via monad operations, rather than via composition, is also available. We give examples illustrating both rules, and consider their coalgebraic duals as well.
Wrangling Galaxy’s reference data

Summary: The Galaxy platform has developed into a fully featured collaborative workbench, with goals of inherently capturing provenance to enable reproducible data analysis, and of making it straightforward to run one’s own server. However, many Galaxy platform tools rely on the presence of reference data, such as alignment indexes, to function efficiently. Until now, the building of this cache of data for Galaxy has been an error-prone manual process lacking reproducibility and provenance. The Galaxy Data Manager framework is an enhancement that changes the management of Galaxy’s built-in data cache from a manual procedure to an automated graphical user interface (GUI) driven process, which contains the same openness, reproducibility and provenance that is afforded to Galaxy’s analysis tools. Data Manager tools allow the Galaxy administrator to download, create and install additional datasets for any type of reference data in real time. Availability and implementation: The Galaxy Data Manager framework is implemented in Python and has been integrated as part of the core Galaxy platform. Individual Data Manager tools can be defined locally or installed from a ToolShed, allowing the Galaxy community to define additional Data Manager tools as needed, with full versioning and dependency support. Contact: dan@bx.psu. edu. or anton@bx.psu. edu Supplementary information: Supplementary data is available at Bioinformatics online.
Richer histories for more relevant policies: 42 years of tree cover loss and gain in Southeast Sulawesi, Indonesia

Understandings of contemporary forest cover loss are critical for policy but have come at the expense of long‐term, multidirectional analyses of land cover change. This is a critical gap given (i) profound reconfigurations in land use and land control over the past several decades and (ii) evidence of widespread ‘woodland resurgence’ throughout the tropics. In this study, we argue that recent advancements within the field of land change science provide new opportunities to address this gap. In turn, we suggest that multidecadal and multidirectional analyses of land cover change can facilitate richer social analyses of land cover change and more relevant conservation policies and practice. Our argument is grounded in a case study from Southeast Sulawesi, Indonesia. Using a novel analytical platform, Google Earth Engine, and open access to high‐quality Landsat data, we map land cover change in Southeast Sulawesi, Indonesia, from 1972 to 2014. We find that tree cover loss constitutes the single largest net change over the period 1972–2014 but that gross rates of tree cover gain were three times higher than gross loss rates from 1972 to 1995 and equivalent to loss rates from 1995 to 2014. We suggest the smallholder tree crop economy likely produced both forest loss and Imperata grassland restoration in this region. This case points to the need to expand rather than collapse the baselines used to study carbon and biodiversity change in tropical regions. It also demonstrates the possible utility of applying such methods to other regions.