Miracle-dz/UniFAR-FTUs huggingface dataset:
An optimized somatic embryo transformation system assisted homozygous edited rubber tree generation method mediated by CRISPR/Cas9

Previously, we have realized the CRISPR/Cas9-RNP and plasmid mediated protoplast transient transformation genome editing in the rubber tree (Hevea brasiliensis), but no gene editing plants were acquired due to the bottleneck of genetic transformation. In present study, antibiotic sensitivity tests against kanamycin, hygromycin and basta were analyzed for embryo screening, the results demonstrated that 10 mg/L hygromycin is the best for transformation. Then Agrobacterium mediated transformation of H. brasiliensis embryos was carried out using a pCAMBIA1300-based CRISPR/Cas9 vector targeting Phytoene desaturase gene (HbPDS). High-throughput sequencing of T0 generation positive embryos which were used as regeneration materials in typical transformation procedure showed that more than 90% T0 edited embryos are chimeric with a 3.2% transformation efficiency. A T0 embryo with 9.8% edited cells was sliced into small pieces for one more cycle embryogenesis to produce T1 generation embryos in order to improve the ratio of homozygous embryos. Subsequently, next-generation sequencing (NGS) demonstrated that 29 out of 33 T1 embryos were edited, nearly 50% of which were found homozygous. At last, besides four chimeric plantlets with partial albino leaves, four plantlets with complete albino phenotype were regenerated from the 29 T1 generation edited embryos, among which one is a homozygous mono-allelic mutant and the other three are homozygous bi-allelic mutants. NGS demonstrated that the threshold for the proportion of edited cells with expected albino phenotype is between 70-85%. Additionally, Tail-PCR indicate that the T-DNA was inserted into different genome positions in the four homozygous edited plantlets, combined with the different genotypes are considered, the four homozygous plantlets can be confirmed as independently derived from single transformed cells. Overall, this is the first edited rubber trees with expected phenotype reported publicly, which shows the potential in genetic improvement of H. brasiliensis by CRISPR/Cas9 gene editing, and subculture of T0 positive transformed somatic embryos into T1 generation is proved to be an effective and necessary procedure to produce homozygous transgenic plantlets. This study presents a significant advancement in transgenic and gene editing for rubber tree.
Endosomal sorting protein SNX4 limits synaptic vesicle docking and release

Sortin-Nexin 4 (SNX4) is an evolutionary conserved organizer of membrane recycling. In neurons, SNX4 accumulates in synapses, but how SNX4 affects synapse function remains unknown. We generated a conditional SNX4 knock-out mouse model and report that SNX4 cKO synapses show enhanced neurotransmission during train stimulation, while the first evoked EPSC was normal. SNX4 depletion did not affect vesicle recycling or the levels and localization of SNARE-protein VAMP2/synaptobrevin-2. However, SNX4 depletion affected synapse ultrastructure: an increase in docked synaptic vesicles at the active zone, while the overall vesicle number was normal, and a decreased active zone length. These effects together lead to a substantially increased density of docked vesicles per release site. In conclusion, SNX4 is a negative regulator of synaptic vesicle docking and release. These findings suggest a role for SNX4 in synaptic vesicle recruitment at the active zone.
Discovery of active mouse, plant and fungal cytochrome P450s in endogenous proteomes and upon expression in planta

Eukaryotes produce a large number of cytochrome P450s that mediate the synthesis and degradation of diverse endogenous and exogenous metabolites. Yet, most of these P450s are uncharacterized and global tools to study these challenging, membrane-resident enzymes remain to be exploited. Here, we applied activity profiling of plant, mouse and fungal P450s with chemical probes that become reactive when oxidized by P450 enzymes. Identification by mass spectrometry revealed labeling of a wide range of active P450s, including six plant P450s, 40 mouse P450s and 13 P450s of the fungal wheat pathogen Zymoseptoria tritici. We next used transient expression of GFP-tagged P450s by agroinfiltration to show ER-targeting and NADPH-dependent, activity-based labeling of plant, mouse and fungal P450s. Both global profiling and transient expression can be used to detect a broad range of active P450s to study e.g. their regulation and discover selective inhibitors.
Investigation of Feature Selection Techniques for Face Recognition Using Feature Fusion Model

This study investigates various feature selection techniques for face recognition. Biometric based authentication system protects access to resources and has gained importance, because of their reliable, invariant and discriminating features. An automated biometric system is based on physiological or behavioral human characteristics for protected access. Biometric trait such as palmprint, iris, hand, voice, face fingerprint, or signature is used to authenticate a person's claim. Of the biometrics, face recognition is gaining popularity due to its simple method of capturing the image using cameras. However the number of features generated is high leading to higher computation time. Using feature selection technique it is shown that recognition rate improves.
CYCLIC ISOGENIES OF ELLIPTIC CURVES OVER A FIXED QUADRATIC FIELD

Building on the work of Mazur on prime degree isogenies, Kenku determined in 1981 all the possible cyclic isogeny degrees of elliptic curves over Q . Although more than 40 years have passed, the possible isogeny degrees have not been determined over a single number ﬁeld since. In this paper we determine such a classiﬁcation of all possible cyclic isogeny degrees for the quadratic ﬁeld Q ( √ 213), assuming the Generalised Riemann Hypothesis. Along the way we determine all of the ﬁnitely many quadratic points on the modular curves X 0 (125) and X 0 (169).
Variations of the Antarctic Ice Sheet in a Coupled Ice Sheet‐Earth‐Sea Level Model: Sensitivity to Viscoelastic Earth Properties

A coupled ice sheet‐solid Earth‐sea level model is applied to long‐term variations of the Antarctic ice sheet. A set of radially varying viscoelastic profiles in the global Earth model is used to explore feedbacks on ice sheet variability, including one with a very weak upper mantle zone and thin lithosphere representative of West Antarctic regions. Simulations are performed for (1) the deglacial retreat over the last ~20,000 years, (2) the future 5,000 years with greenhouse‐gas scenario Representative Concentration Pathway 8.5 (RCP8.5), and (3) the warm Pliocene ~3 Ma. For the deglacial period a large ensemble of 625 simulations is analyzed, with a score computed for each run based on comparisons to geologic and modern data. For each of the five Earth profiles, the top‐scoring combinations of the other model parameters in the ensemble are used to perform future and Pliocene simulations. For the last deglacial retreat, the viscoelastic Earth profiles produce relatively small differences in overall ice volume and equivalent sea level. In contrast, profiles with weak upper mantle and thin lithosphere produce strong negative feedback and less ice retreat in the future and Pliocene runs. This is due to the faster pace of ice sheet retreat in these runs, leading to greater lags in the viscous bedrock rebound behind the unloading, which allows for greater influence of the viscosity profiles. However, the differences in grounding‐line retreat are located primarily in East Antarctic basins, where a weak upper mantle and thin lithosphere may not be realistic, emphasizing the need for lateral heterogeneity in the Earth model.
Using product line techniques to build adaptive systems

Adaptive systems are able to adapt their properties and resource requirements at runtime in response to dynamically varying user needs and resource constraints. With the emergence of mobile and service oriented computing, such variation is becoming increasingly common, and the need for adaptivity is increasing accordingly. Software product line engineering has proved itself as an efficient way to deal with varying user needs and resource constraints. In this paper we present an approach to building adaptive systems based on product line oriented techniques such as variability modeling and component based architectures. By representing the product line architecture at runtime, we are able to delegate much of the complexity of adaptation to a reusable adaptation platform. To validate our approach we have built a prototype adaptation platform and developed a few pilot applications exploiting the platform to achieve adaptivity
The investigational new drug XK469 induces G(2)-M cell cycle arrest by p53-dependent and -independent pathways.

PURPOSE XK469 (2-[4-(7-chloro-2-quinoxalinyloxy) phenoxy]propionic acid), a synthetic quinoxaline phenoxypropionic acid derivative, has broad activity against murine tumors and is entering Phase I clinical development as a topoisomerase IIbeta inhibitor. This study investigated the underlying molecular mechanism of XK469's effects on the cell cycle. EXPERIMENTAL DESIGN Growth inhibition, cell cycle arrest, induction of p53 and p21 mRNA and protein, and cdc2 phosphorylation and kinase activity were studied in treated cells from the H460 lung cancer line and p21 and p53 knockout cells of the HCT 116 colon cancer line. RESULTS XK469 arrested H460 cells at G(2)-M, which was associated with cdc2 phosphorylation and decreased cdc2 kinase activity. Moreover, XK469 stabilized p53 and subsequently increased p21(WAF1/CIP1). Furthermore, HCT116 p21(-/-) cells were less sensitive than wild-type cells to XK469-induced growth inhibition, but p53(+/+) and p53(-/-) cells were equally sensitive despite the absence of p21 induction in the p53(-/-) cells. CONCLUSIONS When considered with published data, our study suggests a complex mechanism of XK469-mediated anticancer activity involving multiple pathways, including p53-dependent and -independent G(2)-M arrest via inactivation of cdc2-cyclin B1 kinase activity.
Blood Pressure Is Lower in Children and Adolescents With a Low-Saturated-Fat Diet Since Infancy: The Special Turku Coronary Risk Factor Intervention Project

Blood pressure was measured in the prospective randomized Special Turku Coronary Risk Factor Intervention Project Study with an oscillometric method every year from 7 months to 15 years of age in 540 children receiving a low-saturated-fat, low-cholesterol diet and in 522 control children. Dietary intakes, family history of parental hypertension, and grandparental vascular disease were recorded. Systolic and diastolic blood pressures were 1.0 mm Hg lower (95% CI for systolic: −1.7 to −0.2 mm Hg; 95% CI for diastolic: −1.5 to −0.4 mm Hg) in children receiving low-saturated-fat counseling through childhood than in control children. Intakes of saturated fat were lower (P<0.001), those of polyunsaturated fat higher (P<0.001), and intakes of potassium slightly higher (P=0.002) in the intervention group, but sodium intakes were not influenced by the intervention (P=0.76). Children whose parents were hypertensive had 4- to 6-mm Hg higher systolic and 3- to 4-mm Hg higher diastolic blood pressures than children of normotensive parents (P<0.001). Diastolic blood pressure of children with grandparental vascular disease, ie, early cardiovascular or cerebrovascular disease, tended to be higher than that of children with no grandparental disease (P=0.051). We conclude that restriction of saturated fat from infancy until 15 years of age decreases childhood and adolescent blood pressure with a meaningful population-attributable amount. The importance of childhood lifestyle counseling and primary prevention of hypertension should be emphasized, especially in those children with a family history of hypertension or atherosclerotic vascular disease.
Implant stability in the treatment of MRSA bone implant infections with linezolid versus vancomycin in a rabbit model

The increasing prevalence of methicillin‐resistant Staphylococcus aureus (MRSA) infections represents a significant healthcare burden. Vancomycin and linezolid exhibit potent clinical and microbiological activity in MRSA infections. Our purpose was to investigate the efficacy of linezolid versus vancomycin in experimental implant infections and the influence on implant stability in a rabbit model. Thirty‐six female New Zealand White rabbits received surgical insertion of titanium implants into their distal femurs and were randomly assigned to six groups (A: infected, no treatment; B: infected, vancomycin; C: infected, linezolid; D: no infection, no treatment; E/F: no infection, vancomycin or linezolid, respectively). Antibiotics were administered, and plasma levels determined. Bone‐implant specimens were tested for mechanical stability of fixation. Quantitative histomorphometry of bone and soft tissue was performed using computerized image analysis. Plasma levels of linezolid and vancomycin were within the respective therapeutic ranges. Microbiological analysis of specimens from infected rabbits showed MRSA tissue colonization in all untreated animals, in two of six vancomycin‐treated animals, and in none of the linezolid‐treated animals. Antibiotic treatment improved mechanical stability significantly (p = 0.004) with both vancomycin and linezolid. Mechanical testing correlated with histomorphometry results. A significant negative correlation was found between displacement of the implant and the percentage of calcified tissue around the implant, and a significant positive correlation was found between displacement of the implant and the amount of noncalcified tissue. Our data indicate that both treatment regimens improved implant stability. © 2011 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 30:190–195, 2012
Macular Hole and Intravitreal Injection of Triamcinolone Acetonide for Macular Edema Due to Central Retinal Vein Occlusion

Purpose. To report a case of macular hole progression after intravitreal injection of triamcinolone acetonide (IVTA) for chronic macular edema secondary to nonischemic central retinal vein occlusion (CRVO). Methods. A 33-year-old woman with massive macular edema after CRVO underwent IVTA. Optical coherence tomography (OCT) and fluorescein angiography were performed before and after the procedure. Results. At the 1-week IVTA injection control, the patient's best-corrected visual acuity improved from 20/400 to 20/200 and OCT detected a progression of macular hole stage. Conclusions. IVTA steroid injection may provide a significant improvement in macular edema, but injection-related complications may occur such as this uncommon macular reaction resulting in permanent visual loss.
Sat>IP client integration in a DVB software stack

In order to leverage the full potential of video playback capabilities in modern connected devices new protocols for content delivery are emerging. Sat>IP protocol is gaining popularity as a new IP-based architecture for reception and distribution of satellite signal. In this paper we present one solution for integration of Sat>IP client in an existing DVB broadcast software stack. Seamless integration is enabled by using virtual IP tuner concept for content acquisition. The solution is implemented on an Android based embedded DTV platform.
Joint Cascade Optimization Using A Product Of Boosted Classifiers

The standard strategy for efficient object detection consists of building a cascade composed of several binary classifiers. The detection process takes the form of a lazy evaluation of the conjunction of the responses of these classifiers, and concentrates the computation on difficult parts of the image which cannot be trivially rejected. We introduce a novel algorithm to construct jointly the classifiers of such a cascade, which interprets the response of a classifier as the probability of a positive prediction, and the overall response of the cascade as the probability that all the predictions are positive. From this noisy-AND model, we derive a consistent loss and a Boosting procedure to optimize that global probability on the training set. Such a joint learning allows the individual predictors to focus on a more restricted modeling problem, and improves the performance compared to a standard cascade. We demonstrate the efficiency of this approach on face and pedestrian detection with standard data-sets and comparisons with reference baselines.
Evidence for a Spinal Central Pattern Generator in Humans a

Abstract: Non‐patterned electrical stimulation of the posterior structures of the lumbar spinal cord in subjects with complete, long‐standing spinal cord injury, can induce patterned, locomotor‐like activity. We show that epidural spinal cord stimulation can elicit step‐like EMG activity and locomotor synergies in paraplegic subjects. An electrical train of stimuli applied over the second lumbar segment with a frequency of 25 to 60 Hz and an amplitude of 5‐9 V was effective in inducing rhythmic, alternating stance and swing phases of the lower limbs. This finding suggests that spinal circuitry in humans has the capability of generating locomotor‐like activity even when isolated from brain control, and that externally controlled sustained electrical stimulation of the spinal cord can replace the tonic drive generated by the brain.
A claim in search of evidence: reply to Manger’s thermogenesis hypothesis of cetacean brain structure

In a recent publication in Biological Reviews, Manger (2006) made the controversial claim that the large brains of cetaceans evolved to generate heat during oceanic cooling in the Oligocene epoch and not, as is the currently accepted view, as a basis for an increase in cognitive or information‐processing capabilities in response to ecological or social pressures. Manger further argued that dolphins and other cetaceans are considerably less intelligent than generally thought. In this review we challenge Manger’s arguments and provide abundant evidence that modern cetacean brains are large in order to support complex cognitive abilities driven by social and ecological forces.
Reliability and Security in the CoDeeN Content Distribution Network

With the advent of large-scale, wide-area networking testbeds, researchers can deploy long-running distributed services that interact with other resources on the Web. The CoDeeN Content Distribution Network, deployed on PlanetLab, uses a network of caching Web proxy servers to intelligently distribute and cache requests from a potentially large client population. We have been running this system nearly continuously since June 2003, allowing open access from any client in the world. In that time, it has become the most heavily-used long-running service on PlanetLab, handling over four million accesses per day. In this paper, we discuss the design of our system, focusing on the reliability and security mechanisms that have kept the service in operation. Our reliability mechanisms assess node health, preventing failing nodes from disrupting the operation of the overall system. Our security mechanisms protect nodes from being exploited and from being implicated in malicious activities, problems that commonly plague other open proxies. We believe that future services, especially peer-to-peer systems, will require similar mechanisms as more services are deployed on non-dedicated distributed systems, and as their interaction with existing protocols and systems increases. Our experiences with CoDeeN and our data on its availability should serve as an important starting point for designers of future systems.
Molecular Identification of Echinococcus multilocularis Infection in Small Mammals from Northeast, Iran

Background Alveolar echinococcosis is a zoonotic disease caused by the metacestode of Echinococcus multilocularis. Many species of small mammals, including arvicolid rodents or Ochotona spp. , are natural intermediate hosts of the cestode. The main aim of this study was to identify natural intermediate hosts of E. multilocularis in Chenaran County, Razavi Khorasan Province, northeastern Iran, where the prevalence of infected wild and domestic carnivores is high. Methodology/Principal Findings A program of trapping was carried out in five villages in which this cestode was reported in carnivores. The livers of 85 small mammals were investigated for the presence of E. multilocularis infection using multiplex PCR of mitochondrial genes. Infections were identified in 30 specimens: 23 Microtus transcaspicus, three Ochotona rufescens, two Mus musculus, one Crocidura gmelini, and one Apodemus witherbyi. Conclusions/Significance A range of small mammals therefore act as natural intermediate hosts for the transmission of E. multilocularis in Chenaran County, and the prevalence suggested that E. multilocularis infection is endemic in this region. The existence of the life cycle of this potentially lethal cestode in the vicinity of human habitats provides a significant risk of human infection.
Modelling colour appearance : applications in skin image perception

Humans are trichromatic, and yet their perception of colours is rich and complex. The research presented in this thesis explores the process of colour appearance of uniform patches and natural polychromatic stimuli. This is done through the measurement and analysis of the achromatic locus (Chapter 2), modelling of chromatic adaptation in a large dataset of unique hues settings (Chapter 3), and measurement of thresholds for uniform and polychromatic stimuli derived from simulated skin images (Chapter 4). Chapter 2 proposes a novel navigation scheme based on unique hues for traversing colour space. The results show that when colour adjustments are made using this novel scheme, the variability of achromatic settings made by observers is reduced compared to the classical method of making colour adjustments along the cardinal axes of the CIELUV colour space. This result holds across the tested luminance levels (5,20,50 cd/m^2) in each of the three tested ambient illumination conditions – dark, simulated daylight and cool white fluorescent lighting. The analysis also shows that the direction of maximum variance of the achromatic settings lies along the daylight locus. Chapter 3 evaluates models of chromatic adaptation by using unique hues settings measured under different ambient illumination conditions. It is shown that a simple diagonal model in cone excitation space is the most efficient in terms of the trade-off between accuracy and degrees of freedom. It is also found that diagonal and linear models show similar performances, reiterating their theoretical equivalence. Performances of these diagonalisable models are found to be worse for UR and UG unique hue planes compared to UY and UB planes. Chapter 4 presents a set of three experiments reporting estimations of perceptual thresholds for polychromatic and uniform stimuli in a 3-D chromaticity-luminance colour space. The first experiment reports thresholds for simulated skin images and uniform stimuli of the corresponding mean CIELAB colour. The second and third experiments investigate the effect of ambient illumination and the location of the stimuli in colour space. The thresholds for the polychromatic stimuli are found to be consistently higher than those for the uniform patches, for both the chromatic, and the luminance projections. The area of the chromaticity ellipses shows a gradual increase with distance from the illuminant chromaticity. The orientations of these ellipses for simulated skin are found to align with the vector joining the mean patch chromaticity and the illuminant chromaticity.