Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterned cortical tension mediated by N-cadherin controls cell geometric order in the Drosophila eye

Adhesion molecules hold cells together but also couple cell membranes to a contractile actomyosin network, which limits the expansion of cell contacts. Despite their fundamental role in tissue morphogenesis and tissue homeostasis, how adhesion molecules control cell shapes and cell patterns in tissues remains unclear. Here we address this question in vivo using the Drosophila eye. We show that cone cell shapes depend little on adhesion bonds and mostly on contractile forces. However, N-cadherin has an indirect control on cell shape. At homotypic contacts, junctional N-cadherin bonds downregulate Myosin-II contractility. At heterotypic contacts with E-cadherin, unbound N-cadherin induces an asymmetric accumulation of Myosin-II, which leads to a highly contractile cell interface. Such differential regulation of contractility is essential for morphogenesis as loss of N-cadherin disrupts cell rearrangements. Our results establish a quantitative link between adhesion and contractility and reveal an unprecedented role of N-cadherin on cell shapes and cell arrangements. DOI: http://dx.doi. org/10.7554/eLife.22796. 001
Genetic Diversity of the Coat Protein of Olive Mild Mosaic Virus (OMMV) and Tobacco Necrosis Virus D (TNV-D) Isolates and Its Structural Implications

The genetic variability among 13 isolates of Olive mild mosaic virus (OMMV) and of 11 isolates of Tobacco necrosis virus D (TNV-D) recovered from Olea europaea L. samples from various sites in Portugal, was assessed through the analysis of the coat protein (CP) gene sequences. This gene was amplified through reverse transcriptase polymerase chain reaction (RT-PCR), cloned, and 5 clone sequences of each virus isolate, were analysed and compared, including sequences from OMMV and TNV-D isolates originally recovered from different hosts and countries and available in the GenBank, totalling 131 sequences. The encoded CP sequences consisted of 269 amino acids (aa) in OMMV and 268 in TNV-D. Comparison of the CP genomic and amino acid sequences of the isolates showed a very low variability among OMMV isolates, 0.005 and 0.007, respectively, as well as among TNV-D isolates, 0.006 and 0.008. The maximum nucleotide distances of OMMV and TNV-D sequences within isolates were also low, 0.013 and 0.031, respectively, and close to that found between isolates, 0.018 and 0.034, respectively. In some cases, less variability was found in clone sequences between isolates than in clone sequences within isolates, as also shown through phylogenetic analysis. CP aa sequence identities among OMMV and TNV-D isolates ranged from 84.3% to 85.8%. Comparison between the CP genomic sequences of the two viruses, showed a relatively low variability, 0.199, and a maximum nucleotide distance between isolates of 0.411. Analysis of comparative models of OMMV and TNV-D CPs, showed that naturally occurring substitutions in their respective sequences do not seem to cause significant alterations in the virion structure. This is consistent with a high selective pressure to preserve the structure of viral capsid proteins.
Heavy Lifting at Work and Risk of Ischemic Heart Disease: Protocol for a Register-Based Prospective Cohort Study

Background There are theoretical grounds to suspect that heavy lifting at work is an important risk factor for ischemic heart disease (IHD). However the relationship has not been sufficiently acknowledged by empirical studies. Positive and statistically significant associations have been found in studies that utilize self-reported exposure data. Such studies are, however, prone to reporting bias. All else equal, people with a poor cardiovascular fitness/health may have a higher propensity to perceive their work environment as heavy. Objective The study described in the present protocol aims to investigate the relationship between heavy lifting at work and IHD by use of material and methods that are free from reporting bias. Methods This is a register-based prospective cohort study. Male blue-collar workers in Denmark will be identified and followed through national registers, from 2001-2010, for hospital treatment or death due to IHD. Relative rates of IHD between “workers in occupations likely to involve heavy lifting” and “other blue-collar workers” will be estimated through Poisson regression. Results Results are expected to be ready in mid-2015. Conclusions Since this is not a randomized study, it cannot confirm etiological hypotheses. It may, however, confirm that employment in occupations that involve heavy lifting is a predictor for IHD and thereby lend support to the hypothesis of a causal relationship.
Immunogenicity of a tetravalent meningococcal glycoconjugate vaccine in infants: a randomized controlled trial.

CONTEXT Immunization with a meningococcal tetravalent (serogroup ACWY) glycoconjugate vaccine is recommended for all US adolescents. However, the currently licensed vaccine is poorly immunogenic in infancy, when the highest rates of disease are observed. OBJECTIVE To determine the immunogenicity of a novel tetravalent CRM(197)-conjugated meningococcal vaccine (MenACWY) in infants. DESIGN, SETTING, AND PARTICIPANTS Randomized, open-label, controlled study of 225 UK and 196 Canadian 2-month-olds from August 2004 to September 2006. INTERVENTION UK infants received a primary course of MenACWY (at 2, 3, and 4 months or 2 and 4 months) or Neisseria meningitidis serogroup C monovalent meningococcal glycoconjugate vaccine (MenC) (at 2 and 4 months). All received MenACWY at 12 months. Canadian infants received MenACWY at 2, 4, and 6 months or 2 and 4 months; at 12 months they received MenACWY, a plain tetravalent polysaccharide vaccine, or no vaccine. MAIN OUTCOME MEASURE Percentage of infants with a human complement serum bactericidal activity (hSBA) titer >or=1:4 after a primary course of MenACWY and after a 12-month booster. Safety and reactogenicity of MenACWY were also assessed. RESULTS According to the prespecified per-protocol analysis, the percentages (95% CIs) of MenACWY 2-, 3-, and 4-month recipients with hSBA titers >or=1:4 after primary immunization were serogroup A, 93% (84%-98%); C, 96% (89%-99%); W-135, 97% (90%-100%); and Y, 94% (86%-98%). With a post hoc intention-to-treat analysis with imputed values for missing data, these values were unchanged for serogroups C and Y; for serogroup A, values were 92% (84%-97%), and for W-135, 97% (91%-99%). For the per-protocol analysis of MenACWY 2-, 4-, and 6-month recipients, the percentages (95% CIs) of responders were A, 81% (71%-89%); C, 98% (92%-100%); W-135, 99% (93%-100%); and Y, 98% (92%-100%). With the imputed value analysis, these values were A, 83% (74%-89%); C, 98% (93%-99%); W-135, 99% (94%-100%); and Y, 98% (92%-99%). At least 84% of MenACWY 2- and 4-month recipients achieved hSBA titers >or=1:4 for serogroups C, W-135, and Y after primary immunization, as did at least 60% for serogroup A (per-protocol and imputation analysis). At least 95% of primary and booster MenACWY recipients achieved hSBA titers >or=1:4 for serogroups C, W-135, and Y at 13 months, as did at least 84% for serogroup A (per-protocol and imputation analysis). During the primary immunization course, postimmunization pain on leg movement was observed in 2% of UK MenACWY 2- and 4-month recipients and 4% of MenC 2- and 4-month recipients; a temperature of 38 degrees C or greater was observed in 4% and 2% in these groups, respectively. CONCLUSION MenACWY is well tolerated and immunogenic in infancy. Trial Registration clinicaltrials.gov Identifier: NCT00262002.
Neuroengineering Original Research Article Early Interfaced Neural Activity from Chronic Amputated Nerves

Direct interfacing of transected peripheral nerves with advanced robotic prosthetic devices has been proposed as a strategy for achieving natural motor control and sensory perception of such bionic substitutes, thus fully functionally replacing missing limbs in amputees. Multi-electrode arrays placed in the brain and peripheral nerves have been used successfully to convey neural control of prosthetic devices to the user. However, reactive gliosis, micro hemorrhages, axonopathy and excessive infl ammation currently limit their long-term use. Here we demonstrate that enticement of peripheral nerve regeneration through a non-obstructive multi-electrode array, after either acute or chronic nerve amputation, offers a viable alternative to obtain early neural recordings and to enhance long-term interfacing of nerve activity. Non-restrictive electrode arrays placed in the path of regenerating nerve fi bers allowed the recording of action potentials as early as 8 days post-implantation with high signal-to-noise ratio, as long as 3 months in some animals, and with minimal infl ammation at the nerve tissue-metal electrode interface. Our fi ndings suggest that regenerative multi-electrode arrays of open design allow early and stable interfacing of neural activity from amputated peripheral nerves and might contribute towards conveying full neural control and sensory feedback to users of robotic prosthetic devices. Different types of multi-electrode arrays have been developed to obtain high spatial and temporal resolution sampling of motor neuronal activity (reviewed by Cheung, 2007). Unfortunately, irrespective of the probe design, current electrodes provide limited long-term effi cacy due to progressive reduction in the number of active sites over time. This reduction is presumably a result of poor tissue-electrode interface, tissue damage by probe micro-motion within the soft nerve tissue, and electrode insulation due to tissue scar formation (Biran et al., 2005, 2007; Leung et al., 2008; Williams et al., 2007). These limitations obligate the need for neurointerface recalibration prior to each recording session and gradual increase in the voltage needed to maintain neural responses over time, which in turn raise the risk of electrolytic tissue damage and further compromise the long-term stability of the neurointerface. Regenerative sieve electrodes were proposed more than three decades ago as a viable alternative to interface motor and sensory nerve fi bers (Dario et al., 1998; Edell et al., 1982; Mannard et al., 1974), and have been shown to be useful in obtaining neural recordings after long-term (i.e., 2–6 months) implantation (Klinge et al., 2001; Lago et al., 2007; Panetsos et al., 2008). Unfortunately, neural …
Design of automatic transabdominal ultrasound imaging system

The quality of ultrasound images highly depends on sonographer skills. This paper describes a platform for the reduction of operator dependency during transabdominal ultrasound examinations. The design includes a linear system to enable automatic transabdominal ultrasonography of the cervix. The system was integrated within APLIO MX SSA-780A TOSHIBA ultrasound machine. Results show operator independent ultrasonography within an area of 70 cm2. Our results enable panoramic ultrasound imaging up to 575 mm times 375 mm in the abdominal area.
Shrinking fermionic modes, on the lattice and in the continuum

Recent lattice data indicates that volume occupied by topological fermionic modes shrinks to zero in the continuum limit of vanishing lattice spacing. The data apparently cannot be accommodated within, say, conventional instanton model. We review field-theoretic arguments which demonstrate that the topological fermionic modes are to shrink to a vanishing submanifold of the whole four dimensional space provided that measurements are performed with high resolution. Moreover, the data fit well the emerging overall picture of lower-dimensional defects in the Euclidean vacuum of Yang-Mills theories. We also mention results on localization of scalar particles.
Affective Benchmarking of Movies Based on the Physiological Responses of a Real Audience

We propose here an objective study of the emotional impact of a movie on an audience. An affective benchmarking solution is introduced making use of a low-intrusive measurement of the well-known Electro Dermal Answer. A dedicated processing of this biosignal produces a time-variant and normalized affective signal related to the significant excitation variations of the audience. Besides the new methodology, the originality of this paper stems from the fact that this framework has been tested on a real audience during regular cinema shows and a film festival, for five different movies and a total of 128 audience members.
Evaluation of the Nuclisens HIV-1 QT Assay for Quantitation of Human Immunodeficiency Virus Type 1 RNA Levels in Plasma

ABSTRACT Nuclisens HIV-1 QT is a new version of the NASBA HIV-1 QT assay for quantitation of human immunodeficiency virus type 1 (HIV-1) RNA in plasma. The specificity of this assay was 100% in one laboratory and 99%—with nonrepeatability of the initial false positive—in another. The test was linear between 2.0 and 6.0 log RNA copies per ml. According to the input HIV-1 RNA concentration, accuracy varied from −0.11 to +0.10 log RNA copy per ml and precision varied from 0.66 to 0.14 log RNA copy per ml. Reproducibility decreased when the HIV-1 RNA level was near the lower limit of quantitation of the test. HIV-1 RNA could be quantitated by Nuclisens HIV-1 QT in 36% (laboratory 1) and 24% (laboratory 2) of clinical samples with HIV-1 RNA levels lower than the lower limit of quantitation by NASBA HIV-1 QT. Nuclisens HIV-1 QT was not suitable for measurement of RNA from clade G and group O HIV-1 strains.
Al–Cu–Fe QUASICRYSTALLINE PHASE FORMATION BY MECHANICAL ALLOYING

Al–Cu–Fe alloys were prepared from elemental powders in a high-energy planetary ball mill. A sequence of solid state reactions resulting in quasicrystal (QC) phase formation takes place during heating of the as-milled powder. These reactions were studied by both differential scanning calorimetry and x-ray diffraction methods. Mechanically alloyed powders were consolidated by cold and hot pressing, as well as by explosive compaction. After annealing at sufficiently high temperatures, the consolidated samples are single-phase QC, except the ones consolidated by explosion. The high reactivity of the as-milled alloys causes the appearance of high porosity of the consolidated samples after the annealing.
Permeation of hydrocarbons through polyvinyl chloride (PVC) and polyethylene (PE) pipes and pipe gaskets

Plastic pipes have been used increasingly as a means for the conveyance of drinking water in water distribution systems. Although there are research and case studies documenting the permeation of organic compounds through plastic pipes, there is still a lack of understanding on the performance of PE and PVC pipe materials in hydrocarboncontaminated soils commonly encountered under field conditions. A microscopic visualization technique was developed to investigate the permeation of organic solvents through PVC pipes by observing the formation and propagation of organic fronts in pipe materials with a light microscope. The threshold concentrations of toluene where a moving front was formed were 25% (v/v) of toluene in polyethylene glycol and 40% (v/v) of toluene in NIST reference fuel. For a combination of BTEX compounds in NIST reference fuel, a BTEX concentration of 40% (v/v) or higher was required to initiate a moving front and potentially cause permeation. This implies that new PVC pipe materials are an effective barrier to resist the permeation of typical commercial gasoline. Permeation of benzene, toluene and trichloroethylene (TCE) through 1-inch diameter PVC pipes from vapor and aqueous phases was further investigated by using pipe-bottle tests, gravimetric sorption tests and microscopic visualization tests. Saturated organic vapors penetrated through 1-inch PVC pipes within 30 days. Organic compounds in saturated aqueous solutions also permeated through PVC pipes but the breakthrough times were significantly delayed. The breakthrough times of saturated aqueous solutions of TCE and benzene were found to range from 60 days to 240 days, depending on the experimental mixing conditions. Insignificant sorption and no moving front were detected when exposed to the organic vapors that were in equilibrium with ≤ 40% (v/v) benzene or toluene in NIST
The burden of cancer in 25-29 year olds in New Zealand: a case for a wider adolescent and young adult age range?

AIMS New Zealand currently defines the adolescent and young adult (AYA) group for cancer services as young people 12-24 years of age, while other countries favour a designation of 15-29 years. This study was undertaken to compare cancer incidence and survival among 25-29 year olds to New Zealand's younger AYA population and to assess survival for our 15-29 year population against international benchmarks. METHODS Diagnostic and demographic information for cancer registrations between 2000 and 2009 for 25-29 year olds was obtained from the New Zealand Cancer Registry. Incidence rates (IR) and five-year relative survival estimates were calculated according to AYA diagnostic group/sub-group, sex and prioritised ethnicity. RESULTS 1,541 new primary malignant cancers were diagnosed (IR: 588 per million). Five-year relative survival was 85%, but was significantly lower for Māori and Pacific peoples (both 77%) compared to non-Māori/non-Pacific peoples (88%). In the overall 15-29 year AYA cohort, disease-specific outcomes for bone tumours (46%) and breast cancer (64%) were inferior to international standards. CONCLUSION New Zealand 25 to 29 year olds are at twice the risk of developing cancer as those 15-24 years. Given that the survival disparities identified were remarkably consistent with those for younger AYA, consideration should be given widening New Zealand's AYA age range.
Effects of Anesthetics on the Renal Sympathetic Response to Anaphylactic Hypotension in Rats

The autonomic nervous system plays an important role in rat anaphylactic hypotension. It is well known that sympathetic nerve activity and cardiovascular function are affected by anesthetics. However, the effects of different types of anesthesia on the efferent renal sympathetic nerve activity (RSNA) during anaphylactic hypotension remain unknown. Therefore, we determined the renal sympathetic responses to anaphylactic hypotension in anesthetized and conscious rats and the roles of baroreceptors in these responses. Sprague-Dawley rats were randomly allocated to anesthetic groups that were given pentobarbital, urethane, or ketamine-xylazine and to a conscious group. The rats were sensitized using subcutaneously injected ovalbumin. The systemic arterial pressure (SAP), RSNA and heart rate (HR) were measured. The effects of sinoaortic baroreceptor denervation on RSNA during anaphylaxis were determined in pentobarbital-anesthetized and conscious rats. In all of the sensitized rats, the RSNA increased and SAP decreased after antigen injection. At the early phase within 35 min of the antigen injection, the antigen-induced sympathoexcitation in the conscious rats was significantly greater than that in the anesthetized rats. Anaphylactic hypotension was attenuated in the conscious rats compared to the anesthetized rats. The anesthetic-induced suppression of SAP and RSNA was greater in the order ketamine-xylazine >urethane = pentobarbital. Indeed, in the rats treated with ketamine-xylazine, RSNA did not increase until 40 min, and SAP remained at low levels after the antigen injection. The baroreceptor reflex, as evaluated by increases in RSNA and HR in response to the decrease in SAP induced by sodium nitroprusside (SNP), was suppressed in the anesthetized rats compared with the conscious rats. Consistent with this finding, baroreceptor denervation attenuated the excitatory responses of RSNA to anaphylaxis in the conscious rats but not in the pentobarbital-anesthetized rats. RSNA was increased markedly in conscious rats during anaphylactic hypotension. Anesthetics attenuated this antigen-induced renal sympathoexcitation through the suppression of baroreceptor function.
A support vector machine classifier from a bit-constrained, sparse and localized hypothesis space

Choosing an appropriate hypothesis space in classification applications, according to the Structural Risk Minimization (SRM) principle, is of paramount importance to train effective models: in fact, properly selecting the the space complexity allows to optimize the learned functions performance. This selection is not straightforward, especially (though not solely) when few samples are available for deriving an effective model (e.g. in bioinformatics applications). In this paper, by exploiting a bit-based definition for Support Vector Machine (SVM) classifiers, selected from an hypothesis space described according to sparsity and locality principles, we show how the complexity of the corresponding space of functions can be effectively tuned through the number of bits used for the function representation. Real world datasets are exploited to show how the number of bits and the degree of sparsity/locality imposed to define the hypothesis space affect the complexity of the space of classifiers and, consequently, the performance of the model, picked up from this set.
Gaining efficiency and flexibility in the simple temporal problem

Deals with the problem of managing quantitative temporal networks without disjunctive constraints. This problem is known as the "simple temporal problem". Dynamic management algorithms are considered to be coupled with incremental constraint posting approaches for planning and scheduling. A basic algorithm for incremental propagation of a new time constraint is presented which is a modification of the Bellman-Ford algorithm for the single-source shortest-path problem. For this algorithm, a sufficient condition for inconsistency is given, based on cycle detection in the shortest-paths graph. Moreover, the problem of constraint retraction from a consistent situation is considered, and properties for repropagating the network locally are exploited. Some experiments are also presented that show the usefulness of these properties.
Prostaglandin D2 mediates neuronal protection via the DP1 receptor

Cyclo‐oxygenases (COXs) catalyze the first committed step in the synthesis of the prostaglandins PGE2, PGD2, PGF2α, PGI2 and thomboxane A2. Expression and enzymatic activity of COX‐2, the inducible isoform of COX, are observed in several neurological diseases and result in significant neuronal injury. The neurotoxic effect of COX‐2 is believed to occur through downstream effects of its prostaglandin products. In this study, we examined the function of PGD2 and its two receptors DP1 and chemoattractant receptor‐homologous molecule expressed on Th2 cells (CRTH2) (DP2) in neuronal survival. PGD2 is the most abundant prostaglandin in brain and regulates sleep, temperature and nociception. It signals through two distinct G protein‐coupled receptors, DP1 and DP2, that have opposing effects on cyclic AMP (cAMP) production. Physiological concentrations of PGD2 potently and unexpectedly rescued neurons in paradigms of glutamate toxicity in cultured hippocampal neurons and organotypic slices. This effect was mimicked by the DP1‐selective agonist BW245C but not by the PGD2 metabolite 15d‐PGJ2, suggesting that neuroprotection was mediated by the DP1 receptor. Conversely, activation of the DP2 receptor promoted neuronal loss. The protein kinase A inhibitors H89 and KT5720 reversed the protective effect of PGD2, indicating that PGD2‐mediated neuroprotection was dependent on cAMP signaling. These studies indicate that activation of the PGD2 DP1 receptor protects against excitotoxic injury in a cAMP‐dependent manner, consistent with recent studies of PGE2 receptors that also suggest a neuroprotective effect of prostaglandin receptors. Taken together, these data support an emerging and paradoxical neuroprotective role of prostaglandins in the CNS.