Miracle-dz/UniFAR-FTUs huggingface dataset:
Suppression of Ku70/80 or Lig4 leads to decreased stable transformation and enhanced homologous recombination in rice

Summary Evidence for the involvement of the nonhomologous end joining (NHEJ) pathway in Agrobacterium-mediated transferred DNA (T-DNA) integration into the genome of the model plant Arabidopsis remains inconclusive. Having established a rapid and highly efficient Agrobacterium-mediated transformation system in rice (Oryza sativa) using scutellum-derived calli, we examined here the involvement of the NHEJ pathway in Agrobacterium-mediated stable transformation in rice. Rice calli from OsKu70,OsKu80 and OsLig4 knockdown (KD) plants were infected with Agrobacterium harboring a sensitive emerald luciferase (LUC) reporter construct to evaluate stable expression and a green fluorescent protein (GFP) construct to monitor transient expression of T-DNA. Transient expression was not suppressed, but stable expression was reduced significantly, in KD plants. Furthermore, KD-Ku70 and KD-Lig4 calli exhibited an increase in the frequency of homologous recombination (HR) compared with control calli. In addition, suppression of OsKu70,OsKu80 and OsLig4 induced the expression of HR-related genes on treatment with DNA-damaging agents. Our findings suggest strongly that NHEJ is involved in Agrobacterium-mediated stable transformation in rice, and that there is a competitive and complementary relationship between the NHEJ and HR pathways for DNA double-strand break repair in rice.
A comprehensive robotic model for neural & acoustic signal processing in bats

A scale-accurate robotic model of a bat biosonar head which reproduces all known functional characteristics of its biological paragon is being build in the CIRCE project. The heads of bats are a set of intelligent, adaptively controlled sonar antennae, where signal processing is carried out both in the acoustic and in the neural domain. The primary project goal is to identify hypotheses of high explanatory power for the function of these biological systems. The progress report given here outlines involved engineering challenges and explains design decisions in the areas of ultrasonic transducers, antennae shapes, actuation and neuromimetic signal processing.
An Effective Algorithm for the Minimum Set Cover Problem

In this paper, a learning algorithm of the Hopfield neural network, which can escape from local minimum, is proposed. The learning algorithm adjusts the balance between constraint term and cost term of the energy function so that the local minimum that the network once falls into vanishes and the network can continue updating in a gradient descent direction of energy. Approximation performance is experimentally determined on random instances of hypergraphs by comparing it to several known algorithms. The experimental results show that the proposed algorithm works much better than the existing algorithms for the problem
Quality of Life among Cancer Patients

Introduction: Cancer is a leading cause of death. People living with cancer experience a variety of symptoms. Quality of life (QOL) is a major concern of patients with terminal cancer. Symptoms affect their QOL. Management of symptoms improves distress and QOL. Objective: The objective of the study was to assess the QOL among cancer patients. Materials and Methods: A survey was conducted among 768 cancer patients selected by a convenient sampling technique. Data was collected from cancer patients by interview technique using structured and validated interviewed schedule. Results: Out of 768 cancer patients, 30.2% patients were in the age group of 51–60 years, majority with head–and-neck cancer (40.1%), and 57.7% had stage III disease. QOL of majority of patients was influenced by their symptoms. 82.3% of them had low QOL scores. Conclusion: Cancer patients experienced many symptoms that affected their QOL. There is a need to develop interventions for effective management of symptoms that will empower the patients to have a greater sense of control over their illness and treatment and to improve the QOL.
Combining topology and sequence design for the discovery of potent antimicrobial peptide dendrimers against multidrug-resistant Pseudomonas aeruginosa.

Multidrug-resistant opportunistic bacteria, such as Pseudomonas aeruginosa, represent a major public health threat. Antimicrobial peptides (AMPs) and related peptidomimetic systems offer an attractive opportunity to control these pathogens. AMP dendrimers (AMPDs) with high activity against multidrug-resistant clinical isolates of P. aeruginosa and Acinetobacter baumannii were now identified by a systematic survey of the peptide sequences within the branches of a distinct type of third-generation peptide dendrimers. Combined topology and peptide sequence design as illustrated here represents a new and general strategy to discover new antimicrobial agents to fight multidrug-resistant bacterial pathogens.
Sources and Fluids in the Mantle Wedge below Kamchatka, Evidence from Across-arc Geochemical Variation

Major and trace element and Sr–Nd–Pb isotopic variations in of melting changes from >20% at the arc front to <10% below mafic volcanic rocks hve been studied in a 220 km transect across the back-arc region. The rocks from volcanoes of the northern part the Kamchatka arc from the Eastern Volcanic Front, over the Central of the Central Kamchatka Depression—to the north of the transect Kamchatka Depression to the Sredinny Ridge in the back-arc. considered in this study—are significantly different in their trace Thirteen volcanoes and lava fields, from 110 to 400 km above the element compositions compared with the other rocks of the transect subducted slab, were sampled. This allows us to characterize spatial and their source appears to have been enriched by a component variations and the relative amount and composition of the slab derived from melting of the edge of the ruptured slab. fluid involved in magma genesis. Typical Kamchatka arc basalts, normalized for fractionation to 6% MgO, display a strong increase in large ion lithophile, light rare earth and high field strength
Water vapor correction to improve the operational calibration for NOAA AVHRR/3 channel 2 (0.85 µm) over a desert target

The Advanced Very High Resolution Radiometers (AVHRRs) flown on the National Oceanic and Atmospheric Administration (NOAA) and the European Organisation for the Exploitation of Meteorological Satellites (EUMETSAT) polar satellites have been providing invaluable data for Earth system science and global change studies. However, the use of AVHRR solar reflectance products (e.g., normalized difference vegetation index (NDVI)) is constrained by calibration uncertainty, largely owing to the lack of an on-orbit calibration device for solar reflectance channels. Since the mid-1990s, NOAA has been applying operational calibration to these channels using the time series of top-of-atmosphere (TOA) measurements of the Libyan Desert site. However, the assumed radiometric stability of Libyan Desert TOA measurements can be disrupted by short-term variations in atmospheric components, especially for AVHRR channel 2, which has a spectral response function covering water vapor absorption lines in the near-infrared (NIR) spectra. This study aims to improve the calibration accuracy of AVHRR channel 2 data by applying water vapor correction over the homogeneous desert target surface using the water vapor content (W) derived from the linear relationships between the AVHRR split-window temperature difference (ΔT) and the Moderate Resolution Imaging Spectroradiometer (MODIS) NIR water vapor product. Results show that the linear ΔT–W relationship is affected by the temperature lapse rate at the satellite over-passing time and the spectral response functions of AVHRR split-window channels. Water vapor correction reduces the calibration uncertainty from 2.6%–3.5% to 1.7%–1.8%, and about 1.0% surface-based relative calibration accuracy is independent of the water vapor uncertainty introduced by the ΔT–W regression. Furthermore, the short-term variations in the channel 2 operational degradation rate are largely reduced after water vapor correction. Thus, implementing water vapor correction can improve the operational calibration accuracy for AVHRR channel 2.
Objective function design for robust optimality of linear control under state-constraints and uncertainty

We consider a model for the control of a linear network flow system with unknown but bounded demand and polytopic bounds on controlled flows. We are interested in the problem of finding a suitable objective function that makes robust optimal the policy represented by the so-called linear saturated feedback control. We regard the problem as a suitable differential game with switching cost and study it in the framework of the viscosity solutions theory for Bellman and Isaacs equations.
Aurora-A and p16 Polymorphisms Contribute to an Earlier Age at Diagnosis of Pancreatic Cancer in Caucasians

Purpose: Aurora-A and p16 play a major role in cell cycle checkpoint regulation. Both of them are important in the maintenance of centrosome duplication. Therefore, we hypothesized that polymorphisms in the two genes may interact or work together to influence the finely tuned mechanisms of cell cycle regulation that these proteins regulate. The purpose of this study was to investigate the association of the Aurora-A (T91A), and p16 (C540G and C580T) polymorphisms with age at diagnosis of pancreatic cancer. Experimental Design: We genotyped 148 Caucasian patients with a diagnosis of pancreatic cancer for the Aurora-A and p16 polymorphisms using pyrosequencing. We tested the association between age at diagnosis and the Aurora-A and p16 genotypes by comparing Kaplan-Meier curves, evaluating the homogeneity of the curves using the log-rank test. We used Cox proportional hazard regression analysis to estimate the association between time to diagnosis and genotype, adjusting for gender. Results: Patients with the Aurora-A polymorphic genotypes had a median age at diagnosis with pancreatic cancer that was 2.8 years earlier than those with the wild-type genotype [log-rank, P = 0.015; hazard ratio (HR), 1.55; 95% confidence intervals (95% CI), 1.09-2.20]. There was no significant association between the p16 genotypes and age at diagnosis. However, the Aurora-A and p16 C580T polymorphisms combined had a synergistic effect on age-associated risk for early diagnosis of pancreatic cancer. Compared with patients with wild-type genotypes for both genes, the median age at diagnosis for patients with one or two polymorphic alleles for both genes was 12.6 years earlier (log-rank, P = 0.0002; HR, 3.88; 95% CI, 1.94-7.76). No significant associations between the polymorphisms and the cancer metastatic status or survival after diagnosis were found. Conclusions: Our findings suggest that the Aurora-A polymorphism contributes to a significantly earlier age at diagnosis of pancreatic cancer, and that Aurora-A and p16 C580T polymorphisms synergistically contribute to an earlier age at diagnosis of pancreatic cancer.
Giant flute-like scour and other erosional features formed by the 1929 Grand Banks turbidity current

Erosional features on the floor of Eastern Valley of the Laurentian Fan, in 2800 m water depth, have been mapped with SeaMARC I side-scan sonar images and Seabeam multi-beam echo-soundings, and were directly observed during a dive with the deep submersible Alvin. The most spectacular feature is a 100-m-deep flute-shaped scour, more than 1 km long. The surrounding valley is floored by an unconsolidated coarse conglomerate, which was moulded into transverse bedforms by the turbidity current that was triggered by the 1929 Grand Banks earthquake. Direct observations and seismic-reflection profiles show that the flute-shaped scour cuts through this conglomerate and into Plio-Pleistocene valley-floor sediments, thereby exposing a section through the 1929 deposit. Application of the Allen defect theory suggests that the flute is unusually deep because general channel-floor erosion was inhibited by the conglomerate veneer. Valley-floor channels typically 1 km wide and 10m deep contain series of closed depressions that occasionally deepen to 30 m. These are also interpreted as erosional scours, analogous to pools cut on the beds of bedrock rivers. The large flute was probably formed by detached flow enlarging an initial scour depression. Such scours probably play an important role in channel-floor erosion, increasing the volume of sediment transported by large turbidity currents.
Reservoir Geology of the Morecambe Field

Summary The Morecambe Gas Field, located in the Irish Sea Basin, came on stream on 1 January 1985 and is to be used as a seasonal storage facility. Structurally the field is a northwest-southeast trending faulted anticline divided into two parts by a narrow southwest-northeast graben system. Gas is produced from the upper part of the Lower Triassic Sherwood Sandstone Group. The reservoir sandstones were deposited predominantly by the action of low sinuosity braided streams during periods of high stage flow. Facies associations recognised from core and wireline log data include: Channel Sandstones, Secondary and Ephemeral Channel Sandstones, Sheetflood Sandstones, Floodplain fine member and Channel abandonment deposits. Reservoir quality is dependent on grain size, shape, sorting, facies control and the distribution and abundance of authigenic cements. Quartz and dolomite cements are a major factor in causing porosity reduction, whilst authigenic illite controls effective permeability. Platy illite only occurs below an identifiable datum believed to represent a ‘paleo’ gas-water contact. Below the illite datum permeability is impaired by up to one hundred fold. A change in illite crystal morphology in the lower parts of the reservoir results in a basal zone which exhibits improved quality. The main producing horizons are stacked sandbodies within the Keuper Waterstones and Keuper Sandstone Frodsham Member. On the basis of facies modelling a three dimensional reservoir model has been developed for simulation purposes. A simplified three layer model which incorporates the influence of authigenic illite has also been erected and will control future field development. A phased development programme is planned for the field over the next ten years. The first stage is currently underway, utilising slant drilling technology to economically drain the reservoir. Maximum gas production from the field will be 1200 million cubic feet per day.
Short- or long-rest intervals during repeated-sprint training in soccer?

The present study compared the effects of two repeated-sprint training (RST) programs, differing in duration of the between-sprint rest intervals, on various soccer-related exercise performances. For 5 weeks during the competitive season, twenty-nine young trained male soccer players either replaced two of their habitual fitness conditioning sessions with RST characterized by short (5–15; n = 9) or long (5–30; n = 10) rest intervals, or served as control (n = 10). The 5–15 and 5–30 protocols consisted of 6 repetitions of 30-m (~5 s) straight-line sprints interspersed with 15 s or 30 s of passive recovery, respectively. 5–15 improved 200-m sprint time (2.0±1.5%; p<0.05) and had a likely positive impact on 20-m sprint performance, whereas 5–30 lowered the 20-m sprint time (2.7±1.6%; p<0.05) but was only possibly effective for enhancing the 200-m sprint performance. The distance covered during the Yo-Yo Intermittent Recovery Test Level 2 increased following 5–15 (11.4±5.0%; p<0.05), which was possibly better than the non-significant 6.5% enhancement observed in 5–30. Improvements in the total time of a repeated-sprint ability test were possibly greater following 5–30 (3.6±0.9%; p<0.05) compared to 5–15 (2.6±1.1%; p<0.05). Both RST interventions led to similar beneficial (p<0.05) reductions in the percentage decrement score (~30%) of the repeated-sprint ability test as well as in blood lactate concentration during submaximal exercise (17–18%). No changes occurred in the control group. In soccer players, RST over a 5-week in-season period is an efficient means to simultaneously develop different components of fitness relevant to match performance, with different benefits induced by shorter compared to longer rest intervals.
Protected Carotid Stenting: Clinical Advantages and Complications of Embolic Protection Devices in 442 Consecutive Patients

Background and Purpose— Periprocedural embolization of debris during carotid stenting interventions may result in neurological deficit. This study was designed to evaluate in-hospital and 30-day adverse events in patients percutaneously treated for carotid artery disease with embolic protection devices. Methods— From 1999 to June 2002, a total of 442 consecutive patients underwent percutaneous angioplasty and/or stenting of the extracranial carotid artery. The endovascular procedure was conducted under embolic protection devices. Results— The percutaneous procedure was successful in 440 of 442 patients (99.5%). No periprocedural death occurred with any embolic protection device. All in-hospital stroke/death and 30-day ipsilateral stroke/death rate was 1.1%. The overall complication rate was 3.4%. Major adverse events included 1 major stroke (0.2%), 4 intracranial hemorrhages (0.9%), 1 carotid artery wall fissuration (0.2%), and 1 diffuse cardioembolism (0.2%). Minor adverse events included 4 minor strokes (0.9%) and 4 transient ischemic attacks (0.9%). The cerebral protection device–related complications were 4 (0.9%): 1 case of abrupt closure of the internal carotid artery because of spiral dissection (0.2%), 1 case of trapped guide wire (0.2%), and 2 cases of intimal dissection (0.5%). Transient loss of consciousness, tremors, and fasciculations were present in 6 of 40 patients (15%) in whom occlusive protection devices were used. Conclusions— Our data suggest that percutaneous stenting of the carotid artery when a cerebral protection device is used is feasible and effective but not without potential complications. However, a long learning curve may exist for the proper use of some embolic protection devices.
A Pointwise Approach for Vietnamese Diacritics Restoration

The automatic insertion of diacritics in electronic texts is necessary for a number of languages, including French, Romanian, Croatian, Sindhi, Vietnamese, etc. When diacritics are removed from a word and the resulting string of characters is not a word, it is easy to recover the diacritics. However, sometimes the resulting string is also a word, possibly with different grammatical properties or a different meaning, and this makes recovery of the missing diacritics a difficult task for software as well as for human readers. This paper is the first to study automatic diacritic restoration in Vietnamese texts. Modern Vietnamese is a complex language with many diacritical marks, and white space does not always function as a word separator. This paper proposes a point wise approach for automatically recovering missing diacritics, using three features for classification: n-grams of syllables, n-grams of syllable types, and dictionary word features. Our experiments show that the proposed method can recover diacritics with a 94.7% accuracy rate.
CYP72B1 Inactivates Brassinosteroid Hormones: An Intersection between Photomorphogenesis and Plant Steroid Signal Transduction1

Active brassinosteroids, such as brassinolide (BL) and castasterone, are growth promoting plant hormones. An Arabidopsis cytochrome P450 monooxygenase encoded by CYP72B1 has been implicated in brassinosteroid catabolism as well as photomorphogenesis. We expressed CYP72B1 in yeast, coupled with brassinosteroid feeding, and established the biochemical function to be the hydroxylation of BL and castasterone, to give 26-hydroxybrassinolide and 26-hydroxycastasterone, respectively. Brassinosteroid feeding experiments with wild-type Arabidopsis, a CYP72B1 null mutant, and a CYP72B1 overexpression line demonstrated that carbon 26 hydroxylation of active brassinosteroids is an endogenous function of CYP72B1. Seedling growth assays demonstrated that 26-hydroxybrassinolide is an inactive brassinosteroid. Genetic and physiological analysis of the hypocotyl response to exogenous BL and varying intensities of white and monochromatic light suggested that CYP72B1 modulates photomorphogenesis primarily through far-red light and to a lesser extent through blue- and red-light pathways. CYP72B1 transcript accumulation in dark-grown seedlings was organ specific and down-regulated after 1 h of illumination in dim white, red, and blue light, but not far-red light. CYP72B1 translational fusions with the β-glucuronidase reporter gene demonstrated that protein levels increased in the hypocotyl elongation zone when shifted from the dark to far-red light, but not blue or red light. We propose a model in which Arabidopsis seedling development switches from dark-grown development (skotomorphogenesis) to light-grown development (photomorphogenesis) in part by rapid modulation of brassinosteroid sensitivity and levels. CYP72B1 provides an intersection between the light and brassinosteroid pathways mainly by far-red-light-dependent modulation of brassinosteroid levels.
Retreat signature of a polar ice stream: sub-glacial geomorphic features and sediments from the Ross Sea, Antarctica

Abstract Three research expeditions to the Ross Sea, Antarctica resulted in collection of a dataset of more than 270 km of side-scan and chirp-sonar data, more than 330 km of swath bathymetry and 3.5 kHz data, and 24 cores within a glacially-carved trough. The former ice-stream flow path is divided into six zones, covering a distance of approximately 370 km, distinguished by unique stratigraphic signatures and geomorphic features. An erosional surface with thin, patchy lodgement till characterizes Zone 1. This region is interpreted as having experienced relatively high basal shear stress conditions. Zones 2, 3, and 4 are characterized by an erosional surface and thin, time-transgressive subglacial and grounding-line proximal deposits that include back-stepping moraines, flutes, transverse moraines, and corrugation moraines. These zones represent the transition between erosional and depositional regimes under the expanded LGM ice sheet; material eroded from the inner shelf was transported toward the outer shelf, possibly as a thin deforming till layer. The two outer zones are depositional and include maximum grounding-line (Zone 5) and pro-glacial deposits that were overridden subsequently by the ice sheet (Zone 6). Surface features include mega-scale glacial lineations, corrugation moraines, and iceberg furrows. Ice in these zones is interpreted as having experienced relatively lower basal shear stress, an extensional regime, and faster flow. This advance may have destabilized the ice sheet, initiating local draw-down and production of icebergs that furrowed the sea floor. Corrugation moraines are thought to represent annual retreat moraines, constraining the retreat rate of the ice sheet across the continental shelf to a consistent 40 to 100 m a−1.
Factors Affecting Technology Uses in Schools: An Ecological Perspective

Why is technology not used more in schools? Many researchers have tried to solve this persistent puzzle. The authors of this article report on their study of technology uses in 19 schools. They suggest an ecological metaphor, using the example of the introduction of the zebra mussel into the Great Lakes, to integrate and organize sets of factors that affect implementation of computer uses. Their findings suggest that an ecological perspective can provide a powerful analytical framework for understanding technology uses in schools. That perspective points out new directions for research and has significant policy and practical implications for implementing innovations in schools.