Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the role of microfilaments and microtubules in acquisition of bipolarity and elongation of fibroblasts in hydrated collagen gels

Fibroblasts in situ reside within a collagenous stroma and are elongate and bipolar in shape. If isolated and grown on glass, they change from elongate to flat shape, lose filopodia, and acquire ruffles. This shape change can be reversed to resemble that in situ by suspending the cells in hydrated collagen gels. In this study of embryonic avian corneal fibroblasts grown in collagen gels, we describe for the first time the steps in the acquisition of the elongate shape and analyze the effect of cytoskeleton-disrupting drugs on filopodial activity, assumption of bipolarity, and cell elongation within extracellular matrix. We have previously shown by immunofluorescence that filopodia contain actin but not myosin and are free of organelles. The cell cortex is rich in actin and the cytosol, in myosin. By using antitubulin, we show in the present study that microtubules are aligned along the long axis of the bipolar cell body. The first step in assumption of the elongate shape is extension of filopodia by the round cells suspended in collagen, and this is not significantly affected by the drugs we used: taxol to stabilize microtubules; nocodazole to disassemble microtubules; and cytochalasin D to disrupt microfilaments. The second step, movement of filopodia to opposite ends of the cell, is disrupted by cytochalasin, but not by taxol or nocodazole. The third step, extension of pseudopodia and acquisition of bipolarity similarly requires intact actin, but not microtubules. If fibroblasts are allowed to become bipolar before drug treatment, moreover, they remain so in the presence of the drugs. To complete the fourth step, extensive elongation of the cell, both intact actin and microtubules are required. Retraction of the already elongated cell occurs on microtubule disruption, but retraction requires an intact actin cytoskeleton. We suggest that the cell interacts with surrounding collagen fibrils via its actin cytoskeleton to become bipolar in shape, and that microtubules interact with the actin cortex to bring about the final elongation of the fibroblast.
The saliency of anomalies in animated human characters

Virtual characters are much in demand for animated movies, games, and other applications. Rapid advances in performance capture and advanced rendering techniques have allowed the movie industry in particular to create characters that appear very human-like. However, with these new capabilities has come the realization that such characters are yet not quite “right. ” One possible hypothesis is that these virtual humans fall into an “Uncanny Valley”, where the viewer's emotional response is repulsion or rejection, rather than the empathy or emotional engagement that their creators had hoped for. To explore these issues, we created three animated vignettes of an arguing couple with detailed motion for the face, eyes, hair, and body. In a set of perceptual experiments, we explore the relative importance of different anomalies using two different methods: a questionnaire to determine the emotional response to the full-length vignettes, with and without facial motion and audio; and a 2AFC (two alternative forced choice) task to compare the performance of a virtual “actor” in short clips (extracts from the vignettes) depicting a range of different facial and body anomalies. We found that the facial anomalies are particularly salient, even when very significant body animation anomalies are present.
Primary fallopian tube malignancies in BRCA-positive women undergoing surgery for ovarian cancer risk reduction.

PURPOSE To review the frequency and location of malignancies detected after prophylactic salpingo-oophorectomy in women with BRCA mutations. METHODS Medical records and pathology findings were reviewed from BRCA-positive women undergoing prophylactic surgery for ovarian cancer risk reduction who underwent complete examination of the adnexa. Patients undergoing this procedure between January 1999 and January 2007 were identified. RESULTS From January 1999 to January 2007, 122 BRCA-positive patients underwent prophylactic surgery in the Division of Gynecologic Oncology at Brigham and Women's Hospital. The median age was 46.5 years (range, 33 to 76 years). Seven (5.7%) were found to have an early malignancy in the upper genital tract and all patients were age > or = 44 years at diagnosis. Of seven consecutive cancers culled between January 1999 and January 2007, all (100%) originated in the fimbrial or ampullary region of the tube; six had an early (intraepithelial) component. Two were associated with surface implants on the ovary and two required repeated sectioning to detect microscopic carcinomas in the fimbria. CONCLUSION The distal fallopian tube seems to be the dominant site of origin for early malignancies detected in approximately 6% of women undergoing ovarian cancer risk-reduction surgery. The greatest proportion of serous cancer risk in BRCA mutation-positive women should be assigned to the fimbria rather than the ovary, and future clinical and research protocols should employ thorough examination of the fimbria, including multiple sections from each tissue block, to maximize detection of early malignancies in this population.
A Performance Prediction Module for Work ow Scheduling

Through the years, scienti c applications have demanded more powerful and sophisticated computing environments and management techniques. Work ows facilitated the design and management of scienti c applications. The complexity of today's work ows demand a high amount of resources and mechanisms for provisioning them. The execution of scienti c work ow applications is a complex task and depends on how the resources are assigned. Scheduling is the name given to the process that assigns computing resources to the tasks comprised in a work ow. This work presents a scheduling algorithm (PPSA) for work ows tightly coupled to a performance prediction module (PEM). A set of experiments was developed for measuring the performance of the algorithm using the information provided by the proposed performance module. The proposed algorithm is compared with an algorithm included in the well-known work ow middlewares Condor DAGMan and ASKALON.
Electroencephalogram characteristics in patients with chronic fatigue syndrome

Objective To explore the electroencephalogram (EEG) characteristics in patients with chronic fatigue syndrome (CFS) using brain electrical activity mapping (BEAM) and EEG nonlinear dynamical analysis. Methods Forty-seven outpatients were selected over a 3-month period and divided into an observation group (24 outpatients) and a control group (23 outpatients) by using the non-probability sampling method. All the patients were given a routine EEG. The BEAM and the correlation dimension changes were analyzed to characterize the EEG features. Results 1) BEAM results indicated that the energy values of δ, θ, and α1 waves significantly increased in the observation group, compared with the control group (P<0.05, P<0.01, respectively), which suggests that the brain electrical activities in CFS patients were significantly reduced and stayed in an inhibitory state; 2) the increase of δ, θ, and α1 energy values in the right frontal and left occipital regions was more significant than other encephalic regions in CFS patients, indicating the region-specific encephalic distribution; 3) the correlation dimension in the observation group was significantly lower than the control group, suggesting decreased EEG complexity in CFS patients. Conclusion The spontaneous brain electrical activities in CFS patients were significantly reduced. The abnormal changes in the cerebral functions were localized at the right frontal and left occipital regions in CFS patients.
Summing Sudakov logarithms in B ---> X(s gamma) in effective field theory

We construct an effective field theory valid for processes in which highly energetic light-like particles interact with collinear and soft degrees of freedom, using the decay B → Xs near the endpoint of the photon spectrum, x = 2Eγ/mb → 1, as an example. Below the scale µ = mb both soft and collinear degrees of freedom are included in the effective theory, while below the scale µ = mb √ x − y, where 1 − y is the lightcone momentum fraction of the b quark in the B meson, we match onto a theory of bilocal operators. We show that at one loop large logarithms cancel in the matching conditions, and that we recover the well known renormalization group equations that sum leading Sudakov logarithms.
BAYESIAN ANALYSIS OF BINARY REGRESSION USING SYMMETRIC AND ASYMMETRIC LINKS

SUMMARY. Binary response regression is a useful technique for analyzing categorical data. Popular binary models use special link functions such as the logit or the probit link. In this article, the inverse link function H is modeled to be a scale mixture of cumulative distribution functions. Two dierent models for H are proposed: (i) H is a finite normal scale mixture with a Dirichlet distribution prior on the mixing distribution; and (ii) H is a scale mixture of truncated normal distributions with the mixing distribution having a Dirichlet prior. The second model allows symmetric as well as asymmetric links. Bayesian analyses of these models using data augmentation and Gibbs sampling are described. Model diagnostics by cross validation of the conditional predictive distributions are proposed. These analyses are illustrated in the Beetle mortality data and the Challenger o-ring distress data.
The Forward Kinematics of 3-R$\underline{P}$R Planar Robots: A Review and a Distance-Based Formulation

The standard forward-kinematics analysis of 3-RPR planar parallel robots boils down to computation of the roots of a sextic polynomial. There are many different ways to obtain this polynomial, but most of them include exceptions for which the formulation is not valid. Unfortunately, near these exceptions, the corresponding polynomial exhibits numerical instabilities. In this paper, we provide a way around this inconvenience by translating the forward-kinematics problem to be solved into an equivalent problem fully stated in terms of distances. Using constructive geometric arguments, an alternative sextic - which is not linked to a particular reference frame - is straightforwardly obtained with the need for neither variable eliminations nor tangent-half-angle substitutions. The presented formulation is valid, with no modification, for any planar 3-RPR parallel robot, including the special architectures and configurations - which ultimately lead to numerical instabilities - that cannot be directly handled by previous formulations.
Current methods for the isolation of extracellular vesicles

Abstract Extracellular vesicles (EVs), including microvesicles and exosomes, are nano- to micron-sized vesicles, which may deliver bioactive cargos that include lipids, growth factors and their receptors, proteases, signaling molecules, as well as mRNA and non-coding RNA, released from the cell of origin, to target cells. EVs are released by all cell types and likely induced by mechanisms involved in oncogenic transformation, environmental stimulation, cellular activation, oxidative stress, or death. Ongoing studies investigate the molecular mechanisms and mediators of EVs-based intercellular communication at physiological and oncogenic conditions with the hope of using this information as a possible source for explaining physiological processes in addition to using them as therapeutic targets and disease biomarkers in a variety of diseases. A major limitation in this evolving discipline is the hardship and the lack of standardization for already challenging techniques to isolate EVs. Technical advances have been accomplished in the field of isolation with improving knowledge and emerging novel technologies, including ultracentrifugation, microfluidics, magnetic beads and filtration-based isolation methods. In this review, we will discuss the latest advances in methods of isolation methods and production of clinical grade EVs as well as their advantages and disadvantages, and the justification for their support and the challenges that they encounter.
De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

Hevea brasiliensis (Willd. Ex Adr. Juss.) Muell. -Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection.
Inspection resistant memory: Architectural support for security from physical examination

The ability to safely keep a secret in memory is central to the vast majority of security schemes, but storing and erasing these secrets is a difficult problem in the face of an attacker who can obtain unrestricted physical access to the underlying hardware. Depending on the memory technology, the very act of storing a 1 instead of a 0 can have physical side effects measurable even after the power has been cut. These effects cannot be hidden easily, and if the secret stored on chip is of sufficient value, an attacker may go to extraordinary means to learn even a few bits of that information. Solving this problem requires a new class of architectures that measurably increase the difficulty of physical analysis. In this paper we take a first step towards this goal by focusing on one of the backbones of any hardware system: on-chip memory. We examine the relationship between security, area, and efficiency in these architectures, and quantitatively examine the resulting systems through cryptographic analysis and microarchitectural impact. In the end, we are able to find an efficient scheme in which, even if an adversary is able to inspect the value of a stored bit with a probabilistic error of only 5%, our system will be able to prevent that adversary from learning any information about the original un-coded bits with 99.9999999999% probability.
Improving Refactoring Speed by 10X

Refactoring engines are standard tools in today's Integrated Development Environments (IDEs). They allow programmers to perform one refactoring at a time, but programmers need more. Most design patterns in the Gang-of-Four text can be written as a refactoring script - a programmatic sequence of refactorings. In this paper, we present R3, a new Java refactoring engine that supports refactoring scripts. It builds a main-memory, non-persistent database to encode Java entity declarations (e.g., packages, classes, methods), their containment relationships, and language features such as inheritance and modifiers. Unlike classical refactoring engines that modify Abstract Syntax Trees (ASTs), R3 refactorings modify only the database; refactored code is produced only when pretty-printing ASTs that reference database changes. R3 performs comparable precondition checks to those of the Eclipse Java Development Tools (JDT) but R3's codebase is about half the size of the JDT refactoring engine and runs an order of magnitude faster. Further, a user study shows that R3 improved the success rate of retrofitting design patterns by 25% up to 50%.
Double Jeopardy? Age, Race, and HRQOL in Older Adults with Cancer

Understanding the post-treatment physical and mental function of older adults from ethnic/racial minority backgrounds with cancer is a critical step to determine the services required to serve this growing population. The double jeopardy hypothesis suggests being a minority and old could have compounding effects on health. This population-based study examined the physical and mental function of older adults by age (mean age = 75.7, SD = 6.1), ethnicity/race, and cancer (breast, prostate, colorectal, and gynecologic) as well as interaction effects between age, ethnicity/race and HRQOL. There was evidence of a significant age by ethnicity/race interaction in physical function for breast, prostate and all sites combined, but the interaction became non-significant (for breast and all sites combined) when comorbidity was entered into the model. The interaction persisted in the prostate cancer group after controlling for comorbidity, such that African Americans and Asian Americans in the 75–79 age group report lower physical health than non-Hispanic Whites and Hispanic Whites in this age group. The presence of double jeopardy in the breast and all sites combined group can be explained by a differential comorbid burden among the older (75–79) minority group, but the interaction found in prostate cancer survivors does not reflect this differential comorbid burden.
Effects of cognitive training based on metamemory and mental images

There is scant research evidence regarding training effects among elderly with limited educational experience. Research indicating an association between metamemory and memory performance is based on samples of older adults with at least 12 years of education. Objectives To test the efficacy of a cognitive training program based on the creation of mental images and changes in specific aspects of metamemory in individuals with 3 to 15 years of education (M=8.38, SD=4.24). Methods 37 older adults participated in five training sessions (Training Group (TG)) and 32 control subjects completed only pre and post test assessments (Control Group (CG)) including the Mini Mental Status Examination (MMSE), the Geriatric Depression Scale (GDS), the Brief Cognitive Screening Battery (BCSB)(naming and memorization of 10 pictures, animal category verbal fluency test, the Clock Drawing Test (CDT)), the Story subtest from the Rivermead Behavioural Memory Test (RBMT), the Memory Complaint Questionnaire (MAC-Q), and the Picture and Story domains from the Memory Self-Efficacy Questionnaire (MSEQ). Results The TG showed significant improvement between pre and post tests on the delayed recall of the 10 pictures and in self-efficacy for the memorization of stories. These same changes were not found in the CG. Conclusions Five-session cognitive training may lead to significant improvements in episodic memory and memory self-efficacy, an aspect of metamemory, in individuals with an average of 8 years of education.
Biodegradation of Synthetic and Natural Plastic by Microorganisms

Plastic disposal is one of the greatest problems facing the environment today, as vast amounts of synthetic plastic remain non degradable. A number of microorganisms have the ability to degrade different types of plastic under suitable conditions, but due to the hardness of these polymers and their non-solubility in water, biological decomposition is a slow process. Natural plastics are made from plant and animal sources, or produced by a range of microorganisms, must be introduced. Some bacterial strains can produce and store bioplastics using carbon sources under suitable fermentation conditions. Such biomaterials are called polyhydroxyalkanoates (PHA) or biological polyester. They are safe, have no toxic by-products and can be degraded easily by microorganisms.
Epidermal Cell Lines in Culture A Survey of Transformation Markers in Differentiating Updated

Primary mouse epidermal cells underwent spontaneous ma lignant transformation in culture. Twelve malignant epidermal cell lines were established which produced squamous cell carcinomas in syngeneic hosts. These lines were used to define criteria for recognizing transformed epidermal cells in vitro. Growth in suspension in agar, agarose, or Methocel was mini mal for 11 of the lines. All lines tested retained specific epider mal antigens (pemphigus, pemphigoid, keratin) by indirect immunofluorescence, but keratin content was reduced when quantified by radioimmunoassay. Basal activity of ornithine decarboxylase and activity induced by the tumor promoter 12O-tetradecanoylphorbol-13-acetate were variable among lines. All malignant lines as well as normal epidermal cells grew well at reduced extracellular calcium concentrations. When the extracellular calcium was elevated, normal cells ceased prolif eration, terminally differentiated, and sloughed from the culture dish, while malignant cells continued to proliferate although they expressed differentiate functions. These results indicate that malignant transformation in epidermis is associated with a fundamental alteration in the program of terminal differentiation which allows some cells to escape the proliferative block and cell death which accompanies differentiation in normal keratinocytes. This alteration should be useful to select for transformants during the process of carcinogenesis in vitro.
Constraint of anthropogenic NO x emissions in China from different sectors: a new methodology using multiple satellite retrievals

Abstract. A new methodology is developed to constrain Chinese anthropogenic emissions of nitrogen oxides (NOx) from four major sectors (industry, power plants, mobile and residential) in July 2008. It combines tropospheric NO2 column retrievals from GOME-2 and OMI, taking advantage of their different passing time over China (~10:00 a.m. LT (local time) versus ~02:00 p.m. ) and consistent retrieval algorithms. The approach is based on the difference of NOx columns at the overpass times of the two instruments; it thus is less susceptible to the likely systematic errors embedded in individual retrievals that are consistent with each other. Also, it explicitly accounts for diurnal variations and uncertainties of NOx emissions for individual sources. Our best top-down estimate suggests a national budget of 6.8 TgN/yr (5.5 TgN/yr for East China), close to the a priori bottom-up emission estimate from the INTEX-B mission for the year of 2006. The top-down emissions are lower than the a priori near Beijing, in the northeastern provinces and along the east coast; yet they exceed the a priori over many inland regions. Systematic errors in satellite retrievals are estimated to lead to underestimation of top-down emissions by at most 17% (most likely 10%). Effects of other factors on the top-down estimate are typically less than 15% each, including lightning, soil emissions, mixing in planetary boundary layer, anthropogenic emissions of carbon monoxide and volatile organic compounds, magnitude of a priori emissions, assumptions on emission diurnal variations, and uncertainties in the four sectors. The a posteriori emission budget is 5.7 TgN/yr for East China.