Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella is supported as sister and Observed Variability is biased

Identifying the extant sister group to the remaining angiosperms has been a subject of long debate, for which the primary currently competing hypotheses are that Amborella alone is sister or that the clade (Amborella, Nymphaeales) is sister. Both Xi et al. (Syst. Biol., 2014, 63, 919) and Goremykin et al. (Syst. Biol., 2015, 64, 879) identified Amborella as sister in concatenation‐based phylogenetic analyses of their 310 nuclear genes and 78 plastid genes, respectively. But after application of Observed Variability‐based character subsampling, both papers reported the clade (Amborella, Nymphaeales) as sister. Hence alternative character‐sampling strategies may produce highly supported yet mutually exclusive phylogenetic inferences when applied to nuclear and plastid genomic data sets. Edwards et al. (Mol. Phylogenet. Evol., 2016, 94, 447) defended Observed Variability and the (Amborella, Nymphaeales) hypothesis. In this study I respond to Edwards et al.'s (Mol. Phylogenet. Evol., 2016, 94, 447) criticisms of Simmons and Gatesy (Mol. Phylogenet. Evol., 2015, 91, 98) and use Edwards et al.'s (Mol. Phylogenet. Evol., 2016, 94, 447) and Goremykin et al.'s (Syst. Biol., 2015, 64, 879) own data to demonstrate that the best‐supported phylogenetic hypothesis is that Amborella alone is sister and that the competing evidence in favour of the (Amborella, Nymphaeales) hypothesis is caused primarily by methodological artifacts (biased character deletion by Observed Variability, MP‐EST and STAR generally not being robust to the highly divergent and mis‐rooted gene trees that were used).
Addressing the Long-Lineage Bottleneck in Apache Spark

Apache Spark employs lazy evaluation [11, 6]; that is, in Spark, a dataset is represented as Resilient Distributed Dataset (RDD), and a single-threaded application (driver) program simply describes transformations (RDD to RDD), referred to as lineage [7, 12], without performing distributed computation until output is requested. The lineage traces computation and dependency back to external (and assumed durable) data sources, allowing Spark to opportunistically cache intermediate RDDs, because it can recompute everything from external data sources. To initiate computation on worker machines, the driver process constructs a directed acyclic graph (DAG) representing computation and dependency according to the requested RDD’s lineage. Then the driver broadcasts this DAG to all involved workers requesting they execute their portion of the result RDD. When a requested RDD has a long lineage, as one would expect from iterative convergent or streaming applications [9, 15], constructing and broadcasting computational dependencies can become a significant bottleneck. For example, when solving matrix factorization using Gemulla’s iterative convergent algorithm [3], and taking tens of data passes to converge, each data pass is slowed down by 30-40% relative to the prior pass, so the eighth data pass is 8.5× slower than the first. The current practice to avoid such performance penalty is to frequently checkpoint to durable storage device which truncates lineage size. Checkpointing as a performance speedup is difficult for a programmer to anticipate and fundamentally contradicts Spark’s philosophy that the working set should stay in memory and not be replicated across the network. Since Spark caches intermediate RDDs, one solution is to cache constructed DAGs and broadcast only new DAG elements. Our experiments show that with this optimization, per iteration execution time is almost independent of growing lineage size and comparable to the execution time provided by optimal checkpointing. On 10 machines using 240 cores in total, without checkpointing we observed a 3.8× speedup when solving matrix factorization and 16× speedup for a streaming application provided in the Spark distribution.
Nonlinear correlation method for the separation of couplings in EEG experiments with neural ensembles

In the present paper the nonlinear association analysis of the EEG brain data in the process of bistable image perception are realized. Brain functional connectivity can be characterized by the temporal evolution of correlation between signals recorded from spatially-distributed regions. Numerous techniques were introduced for assessing this connectivity. Among nonlinear regression analysis methods, we chose a method introduced in the field of EEG analysis by Pijn, Lopes da Silva and colleagues, based on the fitting of a nonlinear curve by piecewise linear approximation, and more recently evaluated in a model of coupled neuronal populations. This method has some major advantages over other signal analysis methods such as coherence and cross-correlation functions because it can be applied independently of whether the type of relationship between the two signals is linear or nonlinear. In the capacity of bistable image we used a set of images based on a well-known bistable object, the Necker cube, as a visual stimulus. This is a cube with transparent faces and visible ribs. Bistability in perception consists in the interpretation of this 3D-object as to be oriented in two different ways, in particular, if the different ribs of the Necker cube are drawn with different intensity. It was shown that the structure of connections in the brain is different for cases without visual stimulation and with stimulation with the help of the Necker cube.
Portrait of Transcriptional Expression Profiles Displayed by Different Glioblastoma Cell Lines

Glioblastoma multiforme (GBM) is among the most lethal of all human tumors, with the average survival of approximately 1 year from diagnosis (Avgeropoulos and Batchelor, 1999). In glioblastomas, LOH 10q is the most frequent genetic alteration (69%), followed by EGFR amplification (34%), TP53 mutations (31%), p16INK4a deletion (31%), and PTEN mutations (24%)(Ohgaki and Kleihues, 2005). Treatments of patients with GBM include surgery, radiotherapy and parallel adjuvant chemotherapy (Stupp et al., 2005). While radiotherapy has been found to significantly prolong survival rates for GBM patients, a poor prognosis and radioresistance are typical characteristics of this disease (Stupp et al., 2007). The antitumoral drug Temozolomide (TMZ) constitutes, in combination with radiotherapy, the current standard of care for glioblastoma (Stupp et al., 2005). However, the action of TMZ may be counteracted in tumors by the expression of the DNA repair enzyme MGMT, which repairs TMZ-induced DNA lesions (Hegi et al., 2005). MGMT activity and resistance to TMZ were highly correlated, indicating that MGMT is a major predictor of response to TMZ in glioma cells (Hermisson et al., 2006). According to the authors, collectively, MGMT expression and TP53 status may become valuable parameters to predict cell responses to TMZ treatment in patients with GBM. Modulation of MSH6, PARP1 and NTL1, DNA repair genes involved in mismatch repair and base excision repair (BER), were found at transcription and protein levels in GBM cells resistant to TMZ (Zhang et al., 2010). Other genotoxic agents exert different effects in GBM cells with different TP53 status. UV light (UV-C) (Batista et al., 2009) and chloroethylating agents (ACNU and BCNU) (Batista et al., 2007), significantly induce apoptosis in TP53-mutated glioma cells, while WT TP53 cells are more sensitive to methylating agents, including TMZ (Hermisson et al., 2006; Roos et al., 2007). Efforts have been made to overcome drug and radio-resistance of GBM cells, but the heterogeneity of these tumors seems to be critical, and molecular analysis is an important tool to elucidate the mechanisms underlying cellular responses to antitumoral agents. Recently, application of genome-scale methodologies has opened the opportunity to study
Spin-
12
 Heisenberg antiferromagnet on the star lattice: Competing valence-bond-solid phases studied by means of tensor networks

Using the infinite Projected Entangled Pair States (iPEPS) algorithm, we study the ground-state properties of the spin-$1/2$ quantum Heisenberg antiferromagnet on the star lattice in the thermodynamic limit. By analyzing the ground-state energy of the two inequivalent bonds of the lattice in different unit-cell structures, we identify two competing Valence-Bond-Solid (VBS) phases for different antiferromagnetic Heisenberg exchange couplings. More precisely, we observe (i) a VBS state which respects the full symmetries of the Hamiltonian, and (ii) a resonating VBS state which, in contrast to previous predictions, has a six-site unit-cell order and breaks $C_3$ symmetry. We also studied the ground-state phase diagram by measuring the ground-state fidelity and energy derivatives, and further confirmed the continuous nature of the quantum phase transition in the system. Moreover, an analysis of the isotropic point shows that its ground state is also a VBS as in (i), which is as well in contrast with previous predictions.
Neurodegenerative Disease Monitoring Using a Portable Wireless Sensor Device

Neurodegenerative diseases are characterized by progressive loss of neurons in the central nervous system. The disorders are clinically well-defined as a disease-related dementia, Alzheimer's disease the most typical case, or as a movement disorder, Parkinson's disease (PD). The risk of developing these diseases increases significantly with age: Parkinson's disease affects 1% of the population over 65 years of age, rising to 2% for those over 80 years. Parkinson's disease is a common neurodegenerative disorder that often impairs motor skills and speech of the patient. PD is characterized by muscle rigidity, tremor, slowing of physical movement (bradykinesia) and in extreme cases, loss of physical movement (akinesia). In particular, PD is due to a loss of dopaminergic neurons (related to the neurotransmitter dopamine), and subcortical neurons in the brain. Replacement therapy with dopaminergic drugs (levodopa, pramipexole) effectively reverses all the symptoms and signs of the disease. After a changeable period of time, however, this excellent initial response to dopaminergic treatment is complicated by the appearance of disorders known as motor response complications (MRC). These complications are divided into two main categories: (i) fluctuations in motor response and (ii) the emergence of abnormal involuntary movements known as levodopa-induced dyskinesias (LID) (Konitsiotis, 2005). Generally, motor fluctuations appear first as a shortening of the initially soft and lasting dopaminergic response. For patients with advanced PD, a few hours after the administration of medication the patient begins to notice the reappearance of signs and symptoms of the disease. This is known as "end of dose deterioration" or "wearing off". This may happen several times a day, so the patient can actually spend several hours per day in an "off" state. During the short visit with the neurologist, the patient may appear to be well and thus the neurologist misses the symptoms related to wearing off. As a result, changes in the recent drug treatment availability do not take place in time. It is now well known that early treatment of wearing-off fluctuations delay the onset of more severe complications in the future, as well as the appearance of LID. Therefore any strategy that can detect early changes associated with wearing off would provide a valuable clinical tool that would allow early treatment interventions.
Retention patches maintain diversity of epiphytic and epixylic indicator lichens more effectively than solitary trees

ABSTRACT The effectiveness of retention trees and patches in preserving diversity of nine epiphytic and epixylic old-growth forest lichens was studied in north boreal spruce forests in Finland. We compared (1) 7–8-year-old retention cuts, with at least 5–10 living or dead retention trees per hectare, (2) 10–12-year-old clear-cuts, with some scattered living and dead retention trees on the sites, (3) old-growth spruce forests, and (4) 7-8-year-old retention patches (0.06–0.45 ha) representing the original tree species composition of old-growth forests. The occurrence of indicator lichens was studied on 150 deciduous trees and snags in each forest category. The species richness was significantly higher in old-growth forests than in the clear-cuts and retention cuts, but did not differ between old-growth forests and retention patches. Only three species were found in clear-cuts and two in retention cuts. Foliose cyanolichens Leptogium saturninum and Nephroma bellum thrived on solitary retention trees, whereas humidity-requiring pin lichens from the genus Chaenotheca were found only in old-growth forests and retention patches. Our results suggest that the ability of epiphytic and epixylic species to survive on retained trees depends on several factors: (1) substrate quality (tree species, tree type and diameter of a tree), (2) environmental factors (e.g. humidity, slope exposition), and (3) morphological and physiological characteristics of species. Besides of substrate trees, the retained conifers (esp. spruce) seem to be important in retention patches to provide the shading necessary to maintain humidity.
Efficiency modeling and evaluation of a resonant snubber based soft-switching inverter for motor drive applications

This paper establishes an analytical model for a resonant snubber based soft-switching inverter. The model adopts the loss separation method to evaluate losses in individual components. Because of symmetry of the inverter circuit, the developed model is suitable for both single-phase and three-phase inverters. A single-phase inverter has been built and tested with a single-phase induction motor driving a fan load to verify the developed model. The equivalent single-phase induction motor model was curve-fitted from experimental results. The analytical results demonstrated reasonable agreement with the experimental results. The same efficiency evaluation method was then applied to a nonzero-voltage turn-on hard-switching inverter, and the results were compared with that of the soft-switching inverter. The resonant snubber based soft-switching inverter shows substantial efficiency improvement over the hard-switching inverter, especially in low speed operation. <<ETX>>
The Study of the Correlation between Constipation and Fatigue in Patients with Multiple Sclerosis

Fatigue and constipation are among the most common factors in multiple sclerosis patients. From the perspective of Persian Medicine, constipated patients are prone to fatigue and we suspected that this problem in patients with multiple sclerosis becomes more severe. The Rome III questionnaire is a valid instrument that measures the existence and severity of constipation and FSS is a scale to assess the scale of fatigue. The objective was to assess if there is an association between constipation and fatigue symptoms in patients with multiple sclerosis. Hence, 355 patients with multiple sclerosis participated in this study. Patients were divided into a constipated or non-constipated group and compared to determine the association between constipation and fatigue scores. It was seen that the level of fatigue and depression in the constipated group was significantly higher than those without constipation (P value < 0.001). According to the observed association between constipation and fatigue, and traditional Persian Medicine theories, constipation can lead to fatigue; patients with constipation had worse scores on the FSS questionnaires and future studies should assess if the treatment of constipation with suitable laxative drugs in multiple sclerosis patients leads to a reduction of fatigue.
Facebook Acoustic Events Dataset

The introduction of large scale datasets such as ImageNet, AudioSet, YouTube-8M and Kinetics has greatly advanced the state-of-the-art in machine perception. These datasets primarily focus on single modalities of audio or visual cues. We seek to broaden the scope in machine perception to multimodal understanding with this work, which introduces the Facebook Acoustic Events dataset. This is a human labeled dataset which contains acoustic event labels of 500K segments from a random sample of public Facebook videos. Combined with its visual counterpart, labeled with scenes, objects and actions, we hope to make research in multi-modal learning and video understanding more accessible and convenient. We provide a well balanced dataset for acoustic event classification together with comprehensive benchmarks on both single and multimodal experiments on acoustic event detection using novel CNN based architectures.
Clinical-grade mesenchymal stromal cells produced under various GMP processes differ in their immunomodulatory properties : Standardization of immune quality controls

SITI Laboratory, Etablissement Français du Sang Bretagne, CHU Rennes, France; INSERM U917, Université Rennes 1, Rennes, France; Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Italy; Etablissement Français du Sang Pyrénées Méditerranée, Université Paul Sabatier UMR5273-INSERM U1031, Toulouse, France; and Institut für Klinische Transfusionmedizin und Immungenetik, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen and University of Ulm, Ulm, Germany.
Understanding Knowledge Sharing and Social Capital in Social Network Sites

This research is intended to explore whether the intensity of use of SNSs is related to users’ social capital dimension: structural (social interaction ties), relational social capital (trust, norms of reciprocity, and identification), cognitive (shared vision) and furthermore their relation with knowledge sharing. The result will be analyzed using PLS-SEM method to examine the hypotheses. We found that the use of SNSs raise all dimensions of social capital. We also found that structural and cognitive dimensions of social capital positively related to knowledge sharing.
CONVERGENCE RATES FOR ILL-POSED INVERSE PROBLEMS WITH AN UNKNOWN OPERATOR

This paper studies the estimation of a nonparametric function ϕ from the inverse problem r = Tϕ given estimates of the function r and of the linear transform T. We show that rates of convergence of the estimator are driven by two types of assumptions expressed in a single Hilbert scale. The two assumptions quantify the prior regularity of ϕ and the prior link existing between T and the Hilbert scale. The approach provides a unified framework that allows us to compare various sets of structural assumptions found in the econometric literature. Moreover, general upper bounds are also derived for the risk of the estimator of the structural function ϕ as well as that of its derivatives. It is shown that the bounds cover and extend known results given in the literature. Two important applications are also studied. The first is the blind nonparametric deconvolution on the real line, and the second is the estimation of the derivatives of the nonparametric instrumental regression function via an iterative Tikhonov regularization scheme.
Eat, Drink, Firms, Government: An Investigation of Corruption from the Entertainment and Travel Costs of Chinese Firms

We propose entertainment and travel costs (ETC) expenditures as a measure of corruption in Chinese firms. These expenses are publicly reported in firms’ accounting books, and on average they amount to about 3 percent of a firm’s total value added. We find that ETC is a mix that includes grease money to obtain better government services, protection money to lower tax rates, managerial excesses, and normal business expenditures to build relational capital with suppliers and clients. Entertainment and travel costs overall have a significantly negative effect on firm productivity, but we also find that some components of ETC have substantial positive returns to firms.
RNA Editing in Zebrafish Grin 1 b is Regulated by Age and Influenced by Gender

We recently described RNA editing in two sites of the Grin1b gene transcript of Danio rerio embryos. Upon further investigation, we discovered the editing of one of these sites changes with age (embryo vs. adult), as well as differing between male and female adults. RNA editing of this target represents an opportunity for dissection of the structural control elements that assist zebrafish ADARs in this coordinate regulation. We suggest that RNA editing research and genome editing strategies may be reinforcing and complementary.
Intelligent Feedback Scheduling of Control Tasks

, an efficient feedback scheduling scheme based on the proposed Feed Forward Neural Network (FFNN) scheme is employed to improve the overall control performance while minimizing the overhead of feedback scheduling which exposed using the optimal solutions obtained offline by mathematical optimization methods. The previously described FFNN is employed to adapt online the sampling periods of concurrent control tasks with respect to changes in computing resource availability. The proposed intelligent scheduler will be examined with different optimization algorithms. An inverted pendulum cost function is used in these experiments. Then, simulation of three inverted pendulums as intelligent Real Time System (RTS) is described in details. Numerical simulation results demonstrates that the proposed scheme can reduce the computational overhead significantly while delivering almost the same overall control performance as compared to optimal feedback scheduling
Mathematical approach to recover EEG brain signals with artifacts by means of Gram-Schmidt transform

A novel method for removing oculomotor artifacts on electroencephalographical signals is proposed and based on the orthogonal Gram-Schmidt transform using electrooculography data. The method has shown high efficiency removal of artifacts caused by spontaneous movements of the eyeballs (about 95-97% correct remote oculomotor artifacts). This method may be recommended for multi-channel electroencephalography data processing in an automatic on-line in a variety of psycho-physiological experiments.
Molecular characterization of salt stress in grapevine cultivars (Vitis vinifera L.) and rootstocks

Salt stress is an important factor inducing the expression of many genes; e.g. the osmotin gene is one of the very important genes responding to NaCl stress. After exposure to NaCl stress, the osmotin gene expression level was investigated in 6 grape cultivars grown in GAP (Southeast Anatolian region including the provinces Gaziantep, Şanliurfa, Diyarbakir, Mardin, Batman, Siirt and Şirnak) and in 4 grape cultivars and 7 rootstocks recommended to the GAP region. Expression levels were investigated by Northern blot analysis. The osmotin expression level was higher in scion cultivars than in rootstocks. Within grapevine cultivars, the highest osmotin gene expression level was observed in cv. Tahannebi, followed by Honusu, another GAP region cultivar. The osmotin gene expression levels of two grape cultivars, Ata sarisi and Alphonse Lavallee recommended to the GAP region, were lower than those of Honusu. On the other hand the GAP region cultivars Ag Besni, Rumi, Kabarcik, Dimiþki and the recommended cultivars Razaki and Italia were significantly different in their expression levels. Among rootstocks 1616 C displayed the highest expression level, followed by 99R; they were followed by 1613C. In 110R the expression level was slightly lower than in the above mentioned ones and 41B. In SO4 and 5C the level of expression remained at the control level.