Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening seven common mitochondrial mutations in 28 Egyptian patients with suspected mitochondrial disease

AimIn this research, we aimed to study the clinical findings in a group of 28 Egyptian patients with suspected mitochondrial disease and to test whether seven common mitochondrial DNA (mtDNA) mutations causing mitochondrial disorders in different populations are the same ones causing mutations in Egyptian patients. Patients and methodsTwenty-eight Egyptian patients with suspected mtDNA disorders were subjected to a thorough clinical examination, pedigree analysis, and biochemical investigations. Neurophysiologic investigations were carried out including electroencephalogram, electromyelogram, nerve conduction velocities, a complete eye evaluation including electroretinogram and visual-evoked potential, a hearing test, brain MRI, and magnetic resonance spectroscopy. Pathological examination on muscle biopsy stained by the modified Gomori trichrome stain was also carried out. PCR-RFLP analyses were carried out for the detection of seven (3243A>G, 3271T>C, 8334A>G, 8993T>G/C, 3256C>T, 4332G>A, and 12147G>A) mtDNA point mutations. ResultsAll 28 patients showed variable multisystem affection. We divided the patients into three groups according to the main findings and investigations. Group 1 included four patients with suspected Leigh’s syndrome, group 2 included two patients with suspected MELAS, and group 3 included 22 patients with suspected general mitochondrial disorder. The molecular study indicated that the chosen point mutations (3243A>G, 3271T>C, 8334A>G, 8993T>G/C, 3256C>T, 4332G>A, and 12147G>A) were not detected in this group of Egyptian patients. ConclusionThe presence of other different mutations in either the nuclear or the mitochondrial genomes might be the reason for the negative results obtained in this research. Further confirmation by sequencing of mitochondrial and genomic genes is recommended.
Oscillating positive expiratory pressure (OPEP) device therapy in Canadian respiratory disease management: Review, care gaps and suggestion for use

Abstract Oscillating positive expiratory pressure (OPEP) devices are a non-pharmacologic therapy that can increase mobilization and elimination of airway mucus hypersecretions. In respiratory diseases such as chronic obstructive pulmonary disease, cystic fibrosis and others, mucus clearance can improve pulmonary mechanics and facilitate gas exchange, reduce breathlessness, prevent recurring infection, reduce exacerbations and hospitalization and improve quality of life. Several OPEP devices are available, although only a few have published evidence of efficacy, cost effectiveness and benefit to patients. We review the evidence and provide suggestions on inclusion of some OPEP devices in mucus clearance therapy regimens.
Morphological comparison of Calochortus howellii and a new species from Southwestern Oregon, C. umpquaensis (Liliaceae)

Calochortus umpquaensis (Liliaceae), a new species from Oregon, is from a very limited area in Douglas County. Morphological comparisons are made between it and the closely related C. howellii, which is endemic to the Illinois River drainage of Josephine County, Oregon. Differences include petal coloration and size, capsule length and position, and seed shape, size, surface ornamentation, and cell shape. Morphological and cytological evidence support placement of C. umpquaensis with C. howellii in subsection Nitidi of section Calochortus. Since the time of its discovery by Thomas Howell in the late 1880's, Calochortus howellii Watson was presumed to have a disjunct distribution, with a number of populations known from the Illinois River valley of Josephine County, Oregon, and a single collection purportedly made by Howell near Roseburg in Douglas County, 130 km to the northeast. However, there were no further discoveries of C. howellii-like plants in Douglas County until 1976, when a population was found along the Little River, a tributary of the North Umpqua, approximately 26 km east of Roseburg. These plants were notably different in morphology from the typical C. howellii. A thorough morphological comparison of several populations in, the Illinois River drainage with the Little River population, together with phenological, cytological, and chemical studies, support their status as a separate species. In this paper, I present a morphological comparison of the two species and describe Calochortus umpquaensis, named for the area in which it occurs. A nomenclatural problem involving the type specimen of C. howellii is clarified and the probable cause of the confusion between the two distinctive species is discussed (appendix). MATERIALS AND METHODS Collection and Analysis of Morphological Data. For both species, 50 flowering individuals from each of two sites were measured in the field for leaf length, stem length, petal length, capsule length, and number of flowers per individual. All flowering individuals in a given area were measured. Because no statistically significant difference in measurements was found between the two sites for either species, the two subsamples were combined. Additional measurements were taken later following maturation of the capsules. To achieve an adequate sample size, a greater sample area was required to collect capsule measurements. Fresh petals were collected for scanning electron microscopy and were fixed, dehydrated, and critical-point dried, then coated with goldpalladium. Preparations were examined using an AMRAY 1000A scanning electron micro-
Discussion of methodology

Primary school children in Sweden are seven to sixteen years old, which means that they represent over half of the years belonging to childhood and ages by which children have often already suffered an acute head injury associated with primary cerebral symptoms. For these children, unlike children of other ages, it is possible to quickly obtain such information as name, date of birth, address and telephone number. It was therefore natural to choose a primary school population as the primary material in the investigation. To be sure, a primary school population is selected, since oligophrenic children are usually taught in separate schools. This selection is unfortunate, as it is stated that oligophrenic children suffer accidents and acute head injuries more often than other children (9, 12, 84). However an alternative primary material with less built-in selection was not available to the author. Children attending primary school in Umei whose home address was not in Umei proper were excluded from the primary material because the pattern of childhood accidents in a rural area differs from that in a city (53) and because the author considered it advantageous for the primary material to be as uniform as possible with respect to risk of accidents and access to a hospital earlier in the children’s lives. Children who had not moved into Umei (3682) and children who had moved from another city of similar size (797) dominated in the primary material over children who had moved from a big city (Stockholm, Malmo or Gothenburg) (216) or from small towns or rural areas (410), according to information obtained by questionnaire. In the city of Umei it is possible to distinguish four large school districts serving four parts of the city that differ in character and with respect to traffic density (See Fig. 1). When the urban children in these school districts were compared with respect to the frequency of reported acute head injuries and the frequency of positive answers to questions of pilot-study type on the questionnaire, there proved to be no important differences between the school districts, and the children were therefore treated as a single material. The author regards the primary material as representative of nonoligophrenic children, seven to sixteen years of age, raised in a densely populated area.
Effect of Close-to-Nature Management on Species Diversity in a Cunninghamia lanceolata Plantation

The study was conducted in a Cunninghamia lanceolata stand under close-to-nature management,with three different thinning densities( 75%,55%,and 35%) and three repetitions,in the Experimental Center of Tropical Forestry,Pingxiang,Guangxi. Four broad-leaved species Castanopsis hystrix,Mytilaria laosensis,Castanopsis fissa and Machilus pingii were randomly inter-planted into the Cunninghamia lanceolata stand. The impact of close-to-nature management with different thinning densities on community composition,species diversity and growth status were studied. The results showed that after five years of the close-to-nature management,the number of species in tree layer,shrub layer and herb layer highly increased. The dominant species in shrub layer and herb layer varied before and after thinning operation,but they were mostly the same in different thinning intensities. In the shrub layer,there was no significant difference in diversity indexes between the thinning stands and the unthinned pure stands. In the herb layer,the diversity indexes in the thinning stands were higher than that of the unthinned pure stands,while the Simpson index and Pielous evenness index were significantly higher than the pure stand. Theaverage DBH of Cunninghamia lanceolata was significantly increased with the thinning intensities,but no significant difference was found in tree height. The DBH and height of the broad-leaved trees grew as the thinning density increasing. Significant differences were found in the DBH and height of Castanopsis fissa and Castanopsis hystrix in different thinning intensities. Intolerant species such as Castanopsis fissa and Mytilaria laosensis,as well as neutral species Castanopsis hystrix were good for inter-planted in high thinning intensity during close-to-nature management in Cunninghamia lanceolata plantation,while the shade tolerant species like Machilus pingii performed better in medium thinning stands.
A report of 5 unrecorded bacterial species of the Deinococcus genus in Korea

The genus Deinococcus was first proposed by Brooks & Murray (1981) when the type species Deinococcus radiodurans was isolated from gamma-ray-irradiated food. At the time of writing, the genus Deinococcus comprises 53 species with validly names isolated from diverse environments such as air, a hot spring, continental Antarctica, desert soil, fish, and water (http://www.bacterio. cict.fr/d/deinococcus.html). Members of the genus Deinococcus are Gram-positive (Brooks & Murray, 1981; Srinivasan et al., 2012a; 2012b) or Gram-negative (Suresh et al., 2004; Zhang et al., 2007; Im et al., 2008; Chen et al., 2012), have L-ornithine as the di-amino acid in the cell-wall peptidoglycan, and have cell colors ranging from yellow to red. They are characterized by their extreme resistant to UV light, gamma radiation and desiccation (Mattimore et al., 1996; Hirsch et al., 2004; de Groot et al., 2005; Rainey et al., 2005; Callegan et al., 2008; Srinivasan et al., 2012a, 2012b). The ionizing radiation and deciccation induced DNA damage and it has been reported that the members of the genus Deinococcus showed resistance and had ability to repair the damaged DNA (Mattimore & Battista, 1996). In 2014, we collected diverse local forest soil samples and isolated novel bacterial species and unrecorded bacterial species in Korea. The identified bacterial species belonged to the (class/phylum) Deinococci/ Deinococcus-Thermus. As a subset of this study, the present report focuses on the description of unrecorded radiation-resistant species belonging to the genus Deinococcus. Here we report 5 unrecorded bacterial species in Korea belonging to familiy Deinococcaceae of order Deinococcales in the Deinococcus-Thermus.
Reply

Reply Petar Podlesniy, PhD, Joana Figueiro-Silva, PhD, Albert Llado, MD, PhD, Anna Antonell, PhD, Raquel Sanchez-Valle, MD, PhD, Daniel Alcolea, MD, Alberto Lleo, MD, PhD, Jose Luis Molinuevo, MD, PhD, Nuria Serra, BS, and Ramon Trullas, PhD As indicated in our article, we adhered to the MIQE guidelines to perform real time quantitative polymerase chain reaction (qPCR) assays. Consequently, we used both nontemplate and positive controls. For nontemplate control, we used deionized double-distilled water. For positive control, we used the targeted amplicons cloned into a pJET1.2 plasmid. The F1-R2 primer combination, which generates a long amplicon of 515bp, was designed to assess the possible influence of oxidative or structural damage to mitochondrial DNA (mtDNA). Accordingly, this primer set was neither our major amplification strategy, as stated by Sondheimer et al, nor was it intended for absolute mtDNA quantification. The efficiency of the PCR reaction with the F1-R2 primer set is lower than with the other 3 primer combinations, which are obviously a better choice for quantification assays, because they produce shorter amplicons. In contrast to Sondheimer et al, we detect mtDNA in cerebrospinal fluid (CSF) with all the above primer combinations without any signal above threshold in negative controls, although clearly at high amplification cycles due to the low concentration of mtDNA in CSF (Fig). Moreover, we do not observe additional PCR products in our dissociation analyses, which show a single peak after the PCR reaction with F2-R2 (mtDNA-85), F3-R3 (mtDNA-73), and F1-R1 (mtDNA-153) primer sets. We do observe a bimodal peak in the dissociation analysis of the PCR product of the F1-R2 (mtDNA-515) primer combination, but this melting curve profile is typical of long PCR fragments and is due to internal sequence inhomogeneity. Moreover, we confirmed both the presence of mtDNA in CSF and the absence of signal in the negative control using a different PCR strategy with a hydrolysis probe and digital PCR. Finally, sequencing of PCR products from CSF of subjects carrying mtDNA polymorphisms in the amplified regions confirmed that our qPCR assay specifically amplifies mtDNA from these subjects. The discrepancy between our results and those of Sondheimer et al could be due to many factors, including:
Dozens of virtual impactor orbits eliminated by the EURONEAR VIMP DECam data mining project

Context. Massive data mining of image archives observed with large etendue facilities represents a great opportunity for orbital amelioration of poorly known virtual impactor asteroids (VIs). There are more than 1000 VIs known today; most of them have very short observed arcs and many are considered lost as they became extremely faint soon after discovery. Aims. We aim to improve the orbits of VIs and eliminate their status by data mining the existing image archives. Methods. Within the European Near Earth Asteroids Research (EURONEAR) project, we developed the Virtual Impactor search using Mega-Precovery (VIMP) software, which is endowed with a very effective (fast and accurate) algorithm to predict apparitions of candidate pairs for subsequent guided human search. Considering a simple geometric model, the VIMP algorithm searches for any possible intersection in space and time between the positional uncertainty of any VI and the bounding sky projection of any image archive. Results. We applied VIMP to mine the data of 451,914 Blanco/DECam images observed between 12 September 2012 and 11 July 2019, identifying 212 VIs that possibly fall into 1286 candidate images leading to either precovery or recovery events. Following a careful search of candidate images, we recovered and measured 54 VIs in 183 DECam images. About 4,000 impact orbits were eliminated from both lists, 27 VIs were removed from at least one list, while 14 objects were eliminated from both lists. The faintest detections were around V ∼ 24.0, while the majority fall between 21 < V < 23. The minimal orbital intersection distances remains constant for 67% detections, increasing for eight objects and decreasing for ten objects. Most eliminated VIs (70%) had short initial arcs of less than five days. Some unexpected photometric discovery has emerged regarding the rotation period of 2018 DB, based on the close inspection of longer trailed VIs and the measurement of their fluxes along the trails. Conclusions. Large etendue imaging archives represent great assets to search for serendipitous encounters of faint asteroids and VIs.
Measuring and Modelling Whole-Tree Gas Exchange

Diurnal patterns of CO2 and water vapour exchange were determined for Macadamia integrifolia and Litchi chinensis trees enclosed in whole-tree gas exchange chambers at Alstonville, New South Wales (28.5oS) during October and November 1991. Whole-tree gas exchange responses to photon irradiance (I), ambient partial pressure of CO2 (Ca) and vapour pressure deficit (D) were similar to those normally observed for individual leaves. Nevertheless, at a given I (above approximately 500 μmol quanta m-2, s-1) stomatal conductances (gs) and CO2 assimilation rates (A) were higher under overcast, as opposed to clear sky conditions. This difference was maintained even when A and gs were examined as a function of sun angle. Combined with a simple light interception model, nested quadratic equations combining stomatal responses and biochemical characteristics of individual leaves were found to provide excellent descriptions of the gas exchange responses of the isolated trees. This indicates a close to optimal partitioning of photosynthetic machinery throughout the canopy. From the whole-tree gas exchange model it was found that higher A and gs under overcast conditions are attributable to both lower T1 and D as well as to a more uniform distribution of irradiance across the canopy surface.
Diet of larvae and juvenile perch, Perca fluviatilis performing diel vertical migrations in a deep reservoir

Feeding behaviour of two functional groups of 0+ perch Perca fluviatilis (epilimnetic, staying all 24 hours in epilimnion; hypolimnetic, daily migrating between hypolimnion and epilimnion) were investigated in the deep canyon-shaped Slapy Reservoir ( c zech Republic)
Singling out modified gravity parameters and data sets reveals a dichotomy between Planck and lensing

An important route to testing general relativity (GR) at cosmological scales is usually done by constraining modified gravity (MG) parameters added to the Einstein perturbed equations. Most studies have analysed so far constraints on pairs of MG parameters, but here, we explore constraints on one parameter at a time while fixing the other at its GR value. This allows us to analyse various models while benefiting from a stronger constraining power from the data. We also explore which specific data sets are in tension with GR. We find that models with (μ = 1, η) and (μ, η = 1) exhibit a 3. 9σ and 3. 8σ departure from GR when using Planck18 + Supernovae type Ia (SNe) + Baryon acoustic oscillation (BAO), while (μ, η) shows a tension of 3. 4σ. We find no tension with GR for models with the MG parameter Σ fixed to its GR value. Using a Bayesian model selection analysis, we find that some one-parameter MG models are moderately favoured over ΛCDM when using all data set combinations except Planck cosmic microwave background lensing and dark energy survey data. Namely, Planck18 shows a moderate tension with GR that only increases when adding any combination of redshift space distortion, SNe, or BAO. However, adding lensing diminishes or removes these tensions, which can be attributed to the ability of lensing in constraining the MG parameter Σ. The two overall groups of data sets are found to have a dichotomy when performing consistency tests with GR, which may be due to systematic effects, lack of constraining power, or modelling. These findings warrant further investigation using more precise data from ongoing and future surveys.
Iris Liveness Detection Competition (LivDet-Iris) - The 2020 Edition

Launched in 2013, LivDet-Iris is an international competition series open to academia and industry with the aim to assess and report advances in iris Presentation Attack Detection (PAD). This paper presents results from the fourth competition of the series: LivDet-Iris 2020. This year's competition introduced several novel elements: (a) incorporated new types of attacks (samples displayed on a screen, cadaver eyes and prosthetic eyes), (b) initiated LivDet-Iris as an on-going effort, with a testing protocol available now to everyone via the Biometrics Evaluation and Testing (BEAT)* open-source platform to facilitate reproducibility and benchmarking of new algorithms continuously, and (c) performance comparison of the submitted entries with three baseline methods (offered by the University of Notre Dame and Michigan State University), and three open-source iris PAD methods available in the public domain. The best performing entry to the competition reported a weighted average APCER of 59.10% and a BPCER of 0.46% over all five attack types. This paper serves as the latest evaluation of iris PAD on a large spectrum of presentation attack instruments.
A revision of the vdB 130 cluster stellar content based on Gaia DR2 data: interstellar extinction toward the Cyg OB1 supershell

Two star-forming regions are studied: the young embedded open cluster vdB 130 and the protocluster neighbourhood observed in the head and tail of the cometary molecular cloud located in the wall of the expanding supershell surrounding the Cyg OB1 association. The GAIA DR2 catalogue is employed to verify the stellar composition of the vdB 130 cluster whose members were earlier selected using the UCAC4 catalogue. The new sample of vdB 130 members contains 68 stars with close proper motions (within 1 mas yr$^{-1}$) and close trigonometric parallaxes (ranging from 0.50 to 0.70 mas). The relative parallax error is shown to increase with distance to objects and depend on their magnitude. At a distance of 1.5-2 kpc it is of about 3-7 per cent and 20-30 per cent for bright and faint stars, respectively. The cluster is not older than ~10 Myr. New spectroscopic and photometric observations carried out on Russian telescopes are combined with GAIA DR2 to search for optical components in the protocluster region - a new starburst. An analysis of 20 stars in the vicinity of the protocluster revealed no concentration of either proper motions or parallaxes. According to spectroscopic, photometric, and trigonometric estimates, the distances to these stars range from 0.4 to 2.5 kpc, and colour excess is shown to increase with a distance D (kpc) in accordance with the law: $E(B-V)\simeq 0.6\times D$ mag.
MetaSimulator: Simulating Unknown Target Models for Query-Efficient Black-box Attacks

Many adversarial attacks have been proposed to investigate the security issues of deep neural networks. For the black-box setting, current model stealing attacks train a substitute model to counterfeit the functionality of the target model. However, the training requires querying the target model. Consequently, the query complexity remains high and such attacks can be defended easily by deploying the defense mechanism. In this study, we aim to learn a generalized substitute model called MetaSimulator that can mimic the functionality of the unknown target models. To this end, we build the training data with the form of multi-tasks by collecting query sequences generated in the attack of various existing networks. The learning consists of a double-network framework, including the task-specific network and MetaSimulator network, to learn the general simulation capability. Specifically, the task-specific network computes each task's meta-gradient, which is further accumulated from multiple tasks to update MetaSimulator to improve generalization. When attacking a target model that is unseen in training, the trained MetaSimulator can simulate its functionality accurately using its limited feedback. As a result, a large fraction of queries can be transferred to MetaSimulator in the attack, thereby reducing the high query complexity. Comprehensive experiments conducted on CIFAR-10, CIFAR-100, and TinyImageNet datasets demonstrate the proposed approach saves twice the number of queries on average compared with the baseline method. The source code is released on this https URL .