Miracle-dz/UniFAR-FTUs huggingface dataset:
Integration of stress-related and reactive oxygen species-mediated signals by Topoisomerase VI in Arabidopsis thaliana

Environmental stress often leads to an increased production of reactive oxygen species that are involved in plastid-to-nucleus retrograde signaling. Soon after the release of singlet oxygen (1O2) in chloroplasts of the flu mutant of Arabidopsis, reprogramming of nuclear gene expression reveals a rapid transfer of signals from the plastid to the nucleus. We have identified extraplastidic signaling constituents involved in 1O2-initiated plastid-to-nucleus signaling and nuclear gene activation after mutagenizing a flu line expressing the luciferase reporter gene under the control of the promoter of a 1O2-responsive AAA-ATPase gene (At3g28580) and isolating second-site mutations that lead to a constitutive up-regulation of the reporter gene or abrogate its 1O2-dependent up-regulation. One of these mutants, caa39, turned out to be a weak mutant allele of the Topoisomerase VI (Topo VI) A-subunit gene with a single amino acid substitution. Transcript profile analysis of flu and flu caa39 mutants revealed that Topo VI is necessary for the full activation of AAA-ATPase and a set of 1O2-responsive transcripts in response to 1O2. Topo VI binds to the promoter of the AAA-ATPase and other 1O2-responsive genes, and hence could directly regulate their expression. Under photoinhibitory stress conditions, which enhance the production of 1O2 and H2O2, Topo VI regulates 1O2-responsive and H2O2-responsive genes in a distinct manner. These results suggest that Topo VI acts as an integrator of multiple signals generated by reactive oxygen species formed in plants under adverse environmental conditions.
Detecting Surgical Tools by Modelling Local Appearance and Global Shape

Detecting tools in surgical videos is an important ingredient for context-aware computer-assisted surgical systems. To this end, we present a new surgical tool detection dataset and a method for joint tool detection and pose estimation in 2d images. Our two-stage pipeline is data-driven and relaxes strong assumptions made by previous works regarding the geometry, number, and position of tools in the image. The first stage classifies each pixel based on local appearance only, while the second stage evaluates a tool-specific shape template to enforce global shape. Both local appearance and global shape are learned from training data. Our method is validated on a new surgical tool dataset of 2 476 images from neurosurgical microscopes, which is made freely available. It improves over existing datasets in size, diversity and detail of annotation. We show that our method significantly improves over competitive baselines from the computer vision field. We achieve 15% detection miss-rate at 10-1 false positives per image (for the suction tube) over our surgical tool dataset. Results indicate that performing semantic labelling as an intermediate task is key for high quality detection.
Transcript Profiling and Identification of Molecular Markers for Early Microspore Embryogenesis in Brassica napus1[W][OA]

Isolated microspores of Brassica napus are developmentally programmed to form gametes; however, microspores can be reprogrammed through stress treatments to undergo appropriate divisions and form embryos. We are interested in the identification and isolation of factors and genes associated with the induction and establishment of embryogenesis in isolated microspores. Standard and normalized cDNA libraries, as well as subtractive cDNA libraries, were constructed from freshly isolated microspores (0 h) and microspores cultured for 3, 5, or 7 d under embryogenesis-inducing conditions. Library comparison tools were used to identify shifts in metabolism across this time course. Detailed expressed sequence tag analyses of 3 and 5 d cultures indicate that most sequences are related to pollen-specific genes. However, semiquantitative and real-time reverse transcription-polymerase chain reaction analyses at the initial stages of embryo induction also reveal expression of embryogenesis-related genes such as BABYBOOM1, LEAFY COTYLEDON1 (LEC1), and LEC2 as early as 2 to 3 d of microspore culture. Sequencing results suggest that embryogenesis is clearly established in a subset of the microspores by 7 d of culture and that this time point is optimal for isolation of embryo-specific expressed sequence tags such as ABSCISIC ACID INSENSITIVE3, ATS1, LEC1, LEC2, and FUSCA3. Following extensive polymerase chain reaction-based expression profiling, 16 genes were identified as unequivocal molecular markers for microspore embryogenesis in B. napus. These molecular marker genes also show expression during zygotic embryogenesis, underscoring the common developmental pathways that function in zygotic and gametic embryogenesis. The quantitative expression values of several of these molecular marker genes are shown to be predictive of embryogenic potential in B. napus cultivars (e.g. ‘Topas’ DH4079, ‘Allons,’ ‘Westar,’ ‘Garrison’).
Programación de operaciones en planta en entornos cambiantes

Los metodos clasicos de programacion de operaciones en planta resultan poco eficaces en las plantas de produccion reales ya que presuponen hipotesis escasamente realistas que dificilmente se cumplen en la practica. Fundamentalmente, estas hipotesis estan relacionadas con la consideracion del entorno de fabricacion como estatico. Pero en la vida real las instalaciones productivas estan sujetas a numerosos sucesos imprevistos que, si no se tienen adecuadamente en cuenta, desembocan en planes de produccion inaceptables. Por otra parte, es necesario reaccionar con celeridad, dada la importancia economica de los costes indirectos asociados a las interrupciones que originan. De hecho, la capacidad de reaccion rapida y la flexibilidad son requisitos clave a tener en cuenta en los sistemas de control, ya que contribuyen a reducir los tiempos de flujo, mejorar las tasas de utilizacion y el servicio al cliente. Por consiguiente, es preciso extender los modelos de scheduling clasicos con el fin de representar la fabrica de una manera mas fidedigna. Los algoritmos geneticos constituyen una de las tecnicas mas prometedoras como alternativa a las tecnicas clasicas, por su robustez y flexibilidad. Aunque los algoritmos geneticos se disenaron originalmente para resolver problemas de optimizacion sin restricciones, se han utilizado con exito en problemas de planificacion de operaciones en planta. Por otra parte, la calidad y el tiempo de proceso depende del numero de generaciones a probar y del numero de organismos de la poblacion. En el presente articulo, se describe la utilizacion de algoritmos geneticos para la planificacion de operaciones en planta en un entorno real. Se han representado en el modelo eventos imprevistos tales como indisponibilidad de recursos o cambios en las ordenes de fabricacion. En el contexto de un proyecto europeo perteneciente al programa de Crecimiento Competitivo y Sostenible del V Programa Marco, se describe un prototipo para la planificacion dinamica de operaciones en planta utilizando algoritmos geneticos y se extraen algunas conclusiones acerca de la viabilidad y calidad de la solucion.
Imaging cortical lesions in multiple sclerosis with ultra-high-field magnetic resonance imaging.

OBJECTIVE To determine the sensitivity of T2*-weighted gradient-echo (T2*GRE) and inversion recovery turbo-field-echo (TFE) sequences for cortical multiple sclerosis lesions at 7 T. DESIGN, SETTING, AND PARTICIPANTS Autopsied brain tissue from individuals with multiple sclerosis was scanned with 3-dimensional T2*GRE and 3-dimensional inversion recovery white matter-attenuated TFE sequences at 7 T. Cortical lesions visible with either sequence were scored for each anatomical lesion type. Imaged brain tissue was then processed for immunohistochemical analysis, and cortical lesions were identified by labeling with antibody against myelin basic protein and CD68 for microglia. Magnetic resonance images were matched with corresponding histological sections and scored retrospectively to determine the sensitivity for each cortical lesion type. Main Outcome Measure Cortical lesion detection by 3-dimensional T2*GRE and white matter-attenuated TFE sequences. RESULTS The 3-dimensional T2*GRE and white matter-attenuated TFE sequences retrospectively detected 93% and 82% of all cortical lesions, respectively (with varying sensitivities for different lesion types). Lesion visibility was primarily determined by size as all undetected lesions were smaller than 1.1 mm at their smallest diameter. The T2*GRE images showed hypointense rings in some cortical lesions that corresponded with increased density of activated microglia. CONCLUSIONS Three-dimensional T2*GRE and white matter-attenuated TFE sequences at a 7-T field strength detect most cortical lesions in postmortem multiple sclerosis tissue. This study indicates the potential of T2*GRE and white matter-attenuated TFE sequences in ultra-high-field magnetic resonance imaging for cortical lesion detection in patients with multiple sclerosis.
Attitude and gyro bias estimation using GPS and IMU measurements

We propose an attitude and gyro-bias estimation scheme for accelerated rigid body systems using an inertial measurement unit (IMU) and a global positioning system (GPS). The proposed scheme allows to obtain attitude estimates directly on the Special Orthogonal group SO(3) while estimating the gyro bias and the unknown apparent acceleration of the vehicle. We prove semi-global exponential stability of the estimation errors. Furthermore, a new switching technique for the attitude state is introduced which results in a velocity-aided hybrid attitude observer with proven global exponential stability.
Demography of Dietary Restriction and Death in Drosophila

Dietary restriction (DR) increases life-span in organisms from yeast to mammals, presumably by slowing the accumulation of aging-related damage. Here we show that in Drosophila, DR extends life-span entirely by reducing the short-term risk of death. Two days after the application of DR at any age for the first time, previously fully fed flies are no more likely to die than flies of the same age that have been subjected to long-term DR. DR of mammals may also reduce short-term risk of death, and hence DR instigated at any age could generate a full reversal of mortality.
Expression and Characterization of Inactivating and Activating Mutations in the Human Ca2+o-sensing Receptor*

Nearly 30 mutations have been identified to date in the coding region of the extracellular calcium-sensing receptor (CaR) that are associated with inherited human hypo- and hypercalcemic disorders. To understand the mechanisms by which the mutations alter the function of the receptor may help to discern the structure-function relationships in terms of ligand-binding and G protein coupling. In the present studies, we transiently expressed eight known CaR mutations in HEK293 cells. The effects of the mutations on extracellular calcium- and gadolinium-elicited increases in the cytosolic calcium concentration were then examined. Seven inactivating mutations, which cause familial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism, show a reduced functional activity of the receptor because they may 1) reduce its affinity for agonists; 2) prevent conversion of the receptor from a putatively immature, high mannose form into the fully glycosylated and biologically active form of the CaR, in addition to lowering its affinity for agonists; or 3) fail to couple the receptor to and/or activate its respective G protein(s). Conversely, one activating mutation, which causes a form of autosomal dominant hypocalcemia, appears to increase the affinity of the receptor for its agonists.
Significance of Cyclooxygenase-2 Induced via p38 Mitogen-Activated Protein Kinase in Mechanical Stimulus-Induced Peritoneal Adhesion in Mice

Postoperative peritoneal adhesion represents a major complication of surgery, but the molecular mechanism underlying pathogenesis of adhesion is not fully understood. The present study investigated the roles of cyclooxygenase (COX)-1 and COX-2 in peritoneal adhesion induced by scraping the surface of the cecum and abdominal wall in mice. Slight, but macroscopically observable, peritoneal adhesion was induced even on day 1, and the extent of adhesion reached a maximum on day 7 and beyond. COX-1 mRNA was constitutively expressed in the intact cecum, and its expression level was not altered after the mechanical stimulus. In contrast, expression of the COX-2 gene was markedly increased after the stimulus, and maximum expression was observed on days 3 to 7. Mofezolac, a specific COX-1 inhibitor, had no effect on peritoneal adhesion at 30 mg/kg and had only marginal effects on prostaglandin (PG)E2 levels in the cecum or peritoneal fluid. On the other hand, two highly selective inhibitors for COX-2, NS-398 (N-[2-(cyclohexyloxy)-4-nitrophenyl]-methanesulfonamide) and CAY10404 [3-(4-methylsulphonylphenyl)-4-phenyl-5-trifluoromethylisoxazole], dose-dependently inhibited both adhesion formation and the increase in PGE2 levels (3-30 mg/kg). The effects of NS-398 were eliminated when PGE2 or (R)-butaprost was administered exogenously. A COX-2 antisense oligonucleotide also attenuated adhesion formation. Activation of p38 mitogen-activated protein (MAP) kinase was observed in the traumatized cecum, and an MAP kinase inhibitor, SB202190 [4-(4-fluorophenyl)-2-(4-hydroxyphenyl)-5-(4-pyridyl)-1H-imidazole], inhibited adhesion formation (54% inhibition at 15 μM) and also reduced the COX-2 mRNA level and PGE2 levels. In conclusion, COX-2, but not COX-1, plays a significant role in mechanical stimulus-induced peritoneal formation in the mouse cecum.
Regional changes in ventricular excitability during load manipulation of the in situ pig heart.

1. The effect of load manipulation on myocardial excitability was studied in the anaesthetized, in situ pig heart. 2. A 33% increase in systolic left ventricular pressure achieved by aortic clamping reduced the mean effective refractory period by 11 ms (7.6%, P less than 0.01); whereas a 15% reduction in ventricular pressure achieved by intravenous infusion of sodium nitroprusside increased the mean effective refractory period by 4 ms (3.2%, P less than 0.05). 3. Changes in action potential duration, measured to 70% repolarization, roughly paralleled those of the effective refractory period. 4. The changes in effective refractory period were inhomogeneous, with a greater change occurring at the apex compared to the base in response to an increase in load, i.e. there was an increase in regional dispersion of refractoriness across the left ventricle. 5. Since inhomogeneity of repolarization and refractoriness is known to be potentially arrhythmogenic, these findings suggest that mechanical factors may contribute directly to the arrhythmias commonly seen clinically in high load states such as congestive cardiac failure and may also have consequences for the treatment of such arrhythmias.
Decreased mortality associated with the use of metformin compared with sulfonylurea monotherapy in type 2 diabetes.

OBJECTIVE The aim of this study was to examine the relationship between use of metformin and sulfonylurea and mortality in new users of these agents. RESEARCH DESIGN AND METHODS Saskatchewan Health databases were used to examine population-based mortality rates for new users of oral antidiabetic agents. Individuals with prescriptions for sulfonylurea or metformin in 1991-1996 and no use in the year prior were identified as new users. Prescription records were prospectively followed for 1-9 years; subjects with any insulin use were excluded. Causes of death were identified based on ICD-9 codes in an electronic vital statistics database. Multivariate logistic regression and survival analyses were used to assess the differences in mortality between drug cohorts, after adjusting for potential confounding variables. RESULTS The total study sample comprised 12,272 new users of oral antidiabetic agents; the average length of follow-up was 5.1 (SD 2.2) years. In subjects with at least 1 year of drug exposure and no insulin use, mortality rates were 750/3,033 (24.7%) for those receiving sulfonylurea monotherapy, 159/1,150 (13.8%) for those receiving metformin monotherapy, and 635/4,683 (13.6%) for those receiving combination therapy over an average 5.1 (SD 2.2) years of follow-up. The adjusted odds ratio (OR) for all-cause mortality for metformin monotherapy was 0.60 (95% CI 0.49-0.74) compared with sulfonylurea monotherapy. Sulfonylurea plus metformin combination therapy was also associated with reduced all-cause mortality (OR 0.66, 95% CI 0.58-0.75). Reduced cardiovascular-related mortality rates were also observed in metformin users compared with sulfonylurea monotherapy users. CONCLUSIONS Metformin therapy, alone or in combination with sulfonylurea, was associated with reduced all-cause and cardiovascular mortality compared with sulfonylurea monotherapy among new users of these agents.
Competition and Increasing Returns to Scale: A Model of Bank Size

This study examines the causal effects of bank size on banks' survival, asset quality and leverage. Two forces drive these effects: increasing returns to scale derived from banks' expertise and competition. The first enables bigger banks to survive competition better, have higher asset quality and be more leveraged. It drives banks into a race for expansion. This race toughens competition between banks, which edges out small banks and may worsen all banks' asset quality. Consequently, the banking industry will be dominated by a small number of highly leveraged banks. In this study, financial intermediation arises endogenously and co‐exists with direct finance.
Pathogenesis of haemophilic arthropathy

Summary. The pathogenetic mechanism of haemophilic arthropathy is multifactorial and includes degenerative cartilage‐mediated and inflammatory synovium‐mediated components. Intra‐articular blood first has a direct effect on cartilage, as a result of the iron‐catalysed formation of destructive oxygen metabolites (resulting in chondrocyte apoptosis), and subsequently affects the synovium, in addition to haemosiderin‐induced synovial triggering. Both processes occur in parallel, and while they influence each other they probably do not depend on each other. This concept resembles degenerative joint damage as found in osteoarthritis as well as inflammatory processes in rheumatoid arthritis. These processes finally result in a fibrotic and destroyed joint.
Synthesis of social surveys on noise annoyance.

Since noise was first recognized as a serious environmental pollutant, a number of social surveys have been conducted in order to assess the magnitude of the problem and to develop suitable noise ratings, such that, from a measurement of certain physical characteristics of community noise, one could reliably predict the community's subjective response to the noise. Recently, the author has reviewed the data from social surveys concerning the noise of aircraft, street traffic, expressway traffic, and railroads. Going back to the original published data, the various survey noise ratings were translated to day-night average sound level, and an independent judgment was make, where choice was possible, as to which respondents should be counted as "highly annoyed. " The results of 11 of these surveys show a remarkable consistency. It is proposed that the average of these curves is the best currently available relationship for predicting community annoyance due to transportation noise of all kinds.
Parameterised verification of randomised distributed systems using state-based models

Model checking is a powerful technique for the verification of distributed systems but is limited to verifying systems with a fixed number of processes. The verification of a system for an arbitrary number of processes is known as the parameterised model checking problem and is, in general, undecidable. Parameterised model checking has been studied in depth for non-probabilistic distributed systems. We extend some of this work in order to tackle the parameterised model checking problem for distributed protocols that exhibit probabilistic behaviour, a problem that has not been widely addressed to date. In particular, we consider the application of network invariants and explicit induction to the parameterised verification of state-based models of randomised distributed systems. We demonstrate the use of network invariants by constructing invariant models for non-probabilistic and probabilistic forms of a simple counter token ring protocol. We show that proving properties of the invariants equates to proving properties of the token ring protocol for any number of processes. The use of induction is considered for the verification of a class of randomised distributed systems. These systems, termed degenerative, have the property that a model of a system with given communication graph eventually behaves like a model of a system with a reduced graph, where reduction is by removal of a set of nodes. We distinguish between deterministically, probabilistically and semi-degenerative systems, according to the manner in which a system degenerates. For the former two classes we describe induction schemas for reasoning about models of these systems over arbitrary communication graphs. We show that certain properties hold for models of such systems with any graph if they hold for all models of a system with some base graph and demonstrate this via case studies: two randomised leader election protocols. We illustrate how induction can also be employed to prove properties of semi-degenerative systems by considering a simple gossip protocol.
Fine-grained indoor tracking by fusing inertial sensor and physical layer information in WLANs

Indoor positioning has become an emerging research area because of huge commercial demands for location-based services in indoor environments. Channel State Information (CSI) as a fine-grained physical layer information has been recently proposed to achieve high positioning accuracy by using range-based methods, e.g., trilateration. In this work, we propose to fuse the CSI-based ranges and velocity estimated from inertial sensors by an enhanced particle filter to achieve highly accurate tracking. The algorithm relies on some enhanced ranging methods and further mitigates the remaining ranging errors by a weighting technique. Additionally, we provide an efficient method to estimate the velocity based on inertial sensors. The algorithms are designed in a network-based system, which uses rather cheap commercial devices as anchor nodes. We evaluate our system in a complex environment along three different moving paths. Our proposed tracking method can achieve 1.3m for mean accuracy and 2.2m for 90% accuracy, which is more accurate and stable than pedestrian dead reckoning and range-based positioning.
Scheduling in a cognitive radio network

In this paper, we consider the channel access and power allocation problem for secondary users in a time division multiple access (TDMA) cognitive radio network. An algorithm is proposed to minimize the total transmit power while ensuring that SU queue lengths are stable. Simulation results show that the proposed algorithm can achieve a good tradeoff between the power consumption and the queue length.
Singularity of nonlinear feedback control scheme for robots

The author investigates the singular problem of a robot-control scheme with u sin theta as the orientation error, where u and theta are, respectively, the unit vector of the rotational axis and the rotational angle from the current orientation of the end effector to the desired one. It is rigorously found that the singularity points of the control scheme are at theta =+or- pi /2 and +or- pi , and, for a step into theta , pi /2 >