Miracle-dz/UniFAR-FTUs huggingface dataset:
Conservative plumage masks extraordinary phylogenetic diversity in the Grallaria rufula (Rufous Antpitta) complex of the humid Andes

ABSTRACT The Grallaria rufula complex is currently considered to consist of 2 species, G. rufula (Rufous Antpitta) and G. blakei (Chestnut Antpitta). However, it has been suggested that the complex, populations of which occur in humid montane forests from Venezuela to Bolivia, comprises a suite of vocally distinct yet morphologically cryptic species. We sequenced nuclear and mitochondrial DNA for 80 individuals from across the distribution of the complex to determine the extent of genetic variation between and within described taxa. Our results revealed 18 geographically coherent clades separated by substantial genetic divergence: 14 within rufula, 3 within blakei, and 1 corresponding to G. rufocinerea (Bicolored Antpitta), a species with distinctive plumage found to be nested within the complex. Neither G. rufula nor G. blakei as presently defined was monophyletic. Although 6 of the 7 recognized subspecies of G. rufula were monophyletic, several subspecies contained substantial genetic differentiation. Genetic variation was largely partitioned across recognized geographic barriers, especially across deep river valleys in Peru and Colombia. Coalescent modeling identified 17 of the 18 clades as significantly differentiated lineages, whereas analyses of vocalizations delineated 16 biological species within the complex. The G. rufula complex seems unusually diverse even among birds of the humid Andes, a prime location for cryptic speciation; however, the extent to which other dispersal-limited Andean species groups exhibit similar degrees of cryptic differentiation awaits further study.
Neue Ausbreitungstendenzen von primär als Eisenbahn- wanderer aufgetretenen Pflanzenarten im Ruhrgebiet: Die Beispiele Eragrostis minor, Geranium purpureum und Saxifraga tridactylites *

Recent spreading trends of railway migrating plant species into areas outside railway ground in the Ruhrgebiet (Germany, Northrhine-Westphalia): Eragrostis minor, Geranium purpureum and Saxifraga tridactylites as exemplary species General tendencies of dispersal and demographic dynamics of the former nearly exclusive railway migrating plants Eragrostis minor, Geranium purpureum and Saxifraga tridactylites in the Ruhrge- biet (Germany, Northrhine-Westphalia) are pointed out. The first occurrences of the mentioned spe- cies were caused by railway migration. Nowadays, there is an additional spreading independent of railways at least partly. 1. Einleitung
Retromer Combinatorials for Gene-Therapy Across a Spectrum of Neurological Diseases

Endosomal trafficking is a biological pathway implicated in Alzheimer’s and Parkinson’s disease, and a growing number of other neurological disorders. For this category of diseases, the endosome’s trafficking complex retromer has emerged as a validated therapeutic target. Retromer’s core is a heterotrimeric complex composed of the scaffold protein VPS35 to which VPS26 and VPS29 bind. Unless it is deficient, increasing expression of VPS35 by viral vectors has a limited effect on other trimeric members and on retromer’s overall function. Here we set out to address these constraints and, based on prior insight, hypothesized that co-expressing VPS35 and VPS26 would synergistically interact and elevate retromer’s trimeric expression and function. Neurons, however, are distinct in expressing two VPS26 paralogs, VPS26a and VPS26b, and so to test the hypothesis we generated three novel AAV9 vectors harboring the VPS35, or VPS26a, or VPS26b transgene. First, we optimized their expression in neuroblastoma cell lines, then, in a comprehensive series of neuronal culture experiments, we expressed VPS35, VPS26a, and VPS26b individually and in all possible combinations. Confirming our hypothesis, expressing individual proteins failed to affect the trimer, while VPS35 and VPS26 combinatorials synergized the trimer’s expression. In addition, we illustrate functional synergy by showing that only VPS35 and VPS26 combinatorials significantly increase levels of Sorl1, a key retromer-receptor deficient in Alzheimer’s disease. Collectively, and together with other recent observations, these results suggest a precision-medicine logic when applying retromer gene therapy to a host of neurological disorders, depending on each disorder’s specific retromer-related molecular and anatomical phenotype.
The role of contraction in skeletal muscle development

Mazelet, L. , Parker, M.O. , Brennan, C. , Huq, N. , Ashworth, R. “Recovery from skeletal muscle paralysis: studies using embryonic zebrafish”. Journal of Muscle Research and Cell Motility 2013 Mazelet, L. , Teh, M.T. , Ashworth, R. “The role of contraction in skeletal muscle development: a study of focal adhesion kinase in vivo”. New Directions in Biology and Disease of Skeletal Muscle Conference, 2012, New Orleans USA. http://www.med.upenn.edu/muscle Mazelet, L. , Audebert, F. “La leishmaniose canine dans le bassin mediterranéen français“. [Canine leishmaniasis in the French mediterranean basin] Université Pierre et Marie Curie, PARIS VI, 2003. http://tipi.free. fr/savsite/divers/Lise_Mazelet. pdf
Metagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19

Broad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs (n = 45). ABSTRACT Broad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs (n = 45). mNGS identified all viruses detected by routine clinical testing (influenza A [n = 3], human metapneumovirus [n = 2], and human coronavirus OC43 [n = 2], and human coronavirus HKU1 [n = 1]). mNGS also identified both coinfections (1, 2.2%) and alternative viral infections (4, 13.3%) that were not detected by routine clinical workup (respiratory syncytial virus [n = 3], human metapneumovirus [n = 1], and human coronavirus NL63 [n = 1]). Among SARS-CoV-2 RT-PCR-positive PUIs, lower cycle threshold (CT) values correlated with greater SARS-CoV-2 read recovery by mNGS (R2, 0.65; P < 0.001). Our results suggest that current broad-spectrum molecular testing algorithms identify most respiratory viral infections among SARS-CoV-2 PUIs, when available and implemented consistently.
Segmental and prosodic improvements to speech generation

• A submitted manuscript is the author's version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers.
Emergence of stable motifs in consumer-resource communities

Understanding how and why complex communities can be stable has preoccupied ecologists for over a century. Data show that real communities tend to exhibit characteristic motifs and topologies. Despite a large body of theory investigating both ecological (niche partitioning) and evolutionary (speciation and extinction) mechanisms, a general explanation for why particular motifs are more common than others remains elusive. Here we develop a mechanistic framework that investigates the set of possible motifs that can emerge under minimal conditions of a nutrient-limited system with no external inputs, and no spatial heterogeneity. Focusing on consumer-resource communities structured by competition and predation, we find that the emergent motifs under these minimal conditions are vertical trophic chains that maximize energy transfer and biomass production. Not only are such motifs stable to perturbations of species’ abundances, but they are also robust to species additions and removals. Our findings provide a mechanistic explanation for why tri-trophic chains are overrepresented in real food webs. They suggest that, because they maximize energy transfer, and can emerge and persist under minimal conditions, vertical trophic chains may constitute the fundamental architecture of consumer-resource communities.
Analytic Confidence Level Calculations Using the Likelihood Ratio and Fourier Transform

The interpretation of new particle search results involves a confidence level calculation on either the discovery hypothesis or the background only(“null”)hypothesis. A typical approach uses toy Monte Carlo experiments to build an expected experiment estimator distribution against which an observed experiment's estimator may be compared. In this note, a new approach is presented which calculates analytically the experiment estimator distribution via a Fourier transform, using the likelihood ratio as an ordering estimator. The analytic approach enjoys an enormous speed advantage over the toy Monte Carlo method, making it possible to quickly and precisely calculate confidence level results.
Effect of temperature and photoperiod on the incidence of bulbing and bolting in seedlings of onion cultivars of diverse origin

Summary The effects of temperature and photoperiod on bulbing and bolting in onion (Allium cepa L.) cultivars: ‘Senshyu Yellow’, ‘Jaune Espagnol’, ‘Hygro’, ‘Sito’, ‘Delta’, ‘Australian Brown’, ‘Rijnsburger Balstora’, and ‘Phulkara’ from Japan, Turkey, The Netherlands, The United Kingdom, Australia, and Pakistan were examined under controlled environments in glasshouse conditions in the UK. Plants of each cultivar, at the three-leaf stage, were transferred to a wide range of photo-thermal regimes consisting of six-set point temperatures (6°, 10°, 14°, 18°, 22° or 26°C) and four photoperiods (8, 11, 14 or 17 h d–1). The bulbing ratio in all cultivars increased curvi-linearly with increasing temperature and lengthening photoperiod. Increasing photoperiod promoted bulbing, while under very short photoperiods (8 h d–1) no cultivars bulbed, even after 60 d of growth. The time to bulb maturity decreased linearly with increasing temperature and lengthening photoperiod. Under low temperatures, the time to floral initiation shortened with lengthening photoperiods (8 – 14 h d–1). Under photo-thermal regimes favouring floral initiation, leaf number increased with both increasing temperature and lengthening photoperiod.
Stochastic frontier analysis

Modern textbook presentations of production economics typically treat producers as successful optimizers. Conventional econometric practice has generally followed this paradigm, and least squares based regression techniques have been used to estimate production, cost, profit and other functions. In such a framework deviations from maximum output, from minimum cost and cost minimizing input demands, and from maximum profit and profit maximizing output supplies and input demands, are attributed exclusively to random statistical noise. However casual empiricism and the business press both make persuasive cases for the argument that, although producers may indeed attempt to optimize, they do not always succeed. This book develops econometric techniques for the estimation of production, cost and profit frontiers, and for the estimation of the technical and economic efficiency with which producers approach these frontiers. Since these frontiers envelop rather than intersect the data, and since the authors continue to maintain the traditional econometric belief in the presence of external forces contributing to random statistical noise, the work is titled Stochastic Frontier Analysis.
Quantitative Determination of Casein Mixtures by High-performance Ion-exchange Chromatography

DAVIES and LAW1) described a method for the quantitative fractionation of casein mixtures using ion-exchange chromatography. Although at present this method is considered to be most reliable, it is time-consuming and requires a relatively large amount of casein sample. Recently high-performance ion-exchange chromatography has been developed and make it possible to resolve a relatively small amount of protein efficiently in a short time. A few investigators2-4) have fractionated casein mix-
Advances in Very Early Time Electromagnetic (VETEM) System Data Analysis and Image Processing

The Very Early Time Electromagnetic (VETEM) system operates in a frequency band between electromagnetic (EM) conductivity systems and ground penetrating radar (GPR). VETEM survey data exhibit higher resolution than EM methods and better detection depth than GPR. A single computer application performs data analysis and image processing, yielding detailed images of transient response over the survey area, with the ability to discriminate between metallic and nonmetallic buried objects using a method based on the persistence of the received signal. Processing steps of field data from the Idaho National Engineering and Environmental Laboratory (INEEL) are presented, and data processing methods are discussed.
Detection of structural alterations in metal bodies: An approximation using Fourier transform and principal component analysis (PCA)

In this theme some advances have been developed, verified in the background, where attempts have been made to determine the existence of structural alterations such as perforations, defective welding and dents in metal structures; a pattern of mechanical vibration that allows to differentiate each alteration has not yet been clearly defined. In this work, the data taking was carried out taking into account the position of the sensors, two beams were added without alteration, in order to be able to interact with the five configurations, which were adopted for the experimental design. To the tests of repeated measurements, in each configuration, analysis (ANOVA) was used for the validation of NULL hypotheses, and thus to determine the number of test to be treated. After having the defined matrices representing each configuration, in each anomaly, it is necessary to apply the principal component Analysis (PCA), to the data obtained by the calculation of the fast Fourier transform (FFT). And thus determine the number of components by means of three Criteria (Jollife, Kaiser and PVA), using a classification algorithm, which evaluates the percentage of classification vs lower standard deviation. In this analysis the descriptors were not calculated but the main components of each criterion were taken as a description tool. The process of extraction of characteristics was fundamental to determine the proper configuration in each alteration (fissure, welded, perforated, deformed). On the other hand, statistical parameters were calculated (average, standard deviation, variation factor, Euclidean distance) of each anomaly. Taking as descriptors.
Robotic grasp detection using effective graspable feature selection and precise classification

It is necessary to implement real-time grasp detection in robotic grasping tasks. To this end, in this paper we propose a method for effective graspable feature selection and precise classification. In a robotic grasping scene, our method can effectively select graspable rectangles and further extract useful features from them to generate a feature set. A convolutional neural network (CNN) is then developed to score and classify the elements in the feature set. Finally, we compute the desired robotic grasp pose based on the graspable feature that gets the highest score. In the test phase the proposed CNN network achieves an accuracy of 96.5% on the Cornell Grasping Dataset. In real-world grasping experiments 105 frames per second (fps) for the object’s grasp detection and a grasp success rate of 89.9% have been achieved with our method.
IoT Attack Detection with Deep Learning Analysis

Internet traffic detection and classification has been thoroughly studied in the last decade, but this is still a hot topic as regards the Internet of Things (IoT), a communication paradigm that is going to involve different aspects of our daily life. As a consequence, researchers started applying traditional methods for traffic classification also to the traffic flows coming and addressed to smart devices. In this paper, we created a large integrated dataset of IoT traffic flows, coming from four different network scenarios, in order to have a benchmark for future research. Moreover, we used this dataset to test the effectiveness of a deep learning network model, made of different hidden layers, and we compare its outcomes with the ones obtained through traditional machine learning approaches, demonstrating the superiority of our deep learning architecture in both a binary and multinomial classification.
AlgT (ς22) Controls Alginate Production and Tolerance to Environmental Stress inPseudomonas syringae

ABSTRACT Pseudomonas aeruginosa and the phytopathogen P. syringae produce the exopolysaccharide alginate, which is a copolymer of d-mannuronic and l-guluronic acids. One of the key regulatory genes controlling alginate biosynthesis in P. aeruginosa is algT, which encodes the alternate sigma factor, ς22. In the present study, the algT gene product from P. syringaepv. syringae showed 90% amino acid identity with its P. aeruginosa counterpart, and sequence analysis of the region flanking algT in P. syringae revealed the presence of nadB, mucA, andmucB in an arrangement virtually identical to that ofP. aeruginosa. An algT mutant of P. syringae was defective in alginate production but could be complemented with wild-type algT from P. syringae or P. aeruginosa when expressed intrans. The algT mutant also displayed increased sensitivity to heat, paraquat, and hydrogen peroxide (H2O2); the latter two compounds are known to generate reactive oxygen intermediates. Signals for activation of algT gene expression in P. syringae were investigated with an algT::uidAtranscriptional fusion. Like that in P. aeruginosa,algT transcription in P. syringae was activated by heat shock. However, algT expression in P. syringae was also stimulated by osmotic stress and by exposure to paraquat, H2O2, and copper sulfate. The latter two compounds are frequently encountered during colonization of plant tissue and may be unique signals for algT activation inP. syringae.
Effects of Protein Micropatterns of Biomaterials Surfaces on Human Chondrocytes Morphology and Protein Expression

In order to study the effects of extracellular matrix(ECM) protein micropatterns on biomaterials surfaces fabricated by microcontact printingμCP) on human chondrocytes adhesion,spread and protein expression,the bone morphogenetic protein 2(BMP-2) was printed onto polystyrene(PS) surface to fabricate the ECM protein micropatterns byμCP. Three kinds of excellent micropattern were obtained successfully according to the fluorescent images.The human chondrocytes were seeded on PS(control samples),BMP-2 coated PS surface and PS surface with BMP-2 micropatterns,respectively.As compared with control samples,the human chondrocytes on BMP-2 coating exhibited better growth and spread behavior,at the same time,the BMP-2 coating also cannot promote expression of collagenⅡ and Ⅵ. On the other side,the results concerning BMP-2 micropattens indicated that the protein micropattern surfaces have significant influence on cell adhesion,spread,alignment and functions.The cells preferentially adhered on micropattern protein zones.The micropattern shape and its sizes affected not only the cell adhesion morphology and spread degree but also the typeⅡ and Ⅵcollagen expression.The spread behavior of cell has some positive connections with protein expression and the cell with more spread expressed more typeⅡ and Ⅵcollagen. These results suggested that the ECM protein micropatterns can effectively regulate human chondrocytes growth and functions.
Sudden Caffeine Withdrawal Triggers Migraine—A Randomized Controlled Trial

Objective: Assessing the effects of caffeine withdrawal on migraine. Background: The effects of caffeine withdrawal on migraineurs are at large unknown. Methods: This was a randomized, double-blind, crossover study (NCT03022838), designed to enroll 80 adults with episodic migraine and a daily consumption of 300–800 mg caffeine. Participants substituted their estimated dietary caffeine with either placebo capsules or capsulated caffeine tablets for 5 weeks before switching the comparators for 5 more weeks. Results: The study was terminated due to low recruitment. Ten subjects with a mean age of 46.3 ± 9.9 years, BMI of 24.9 ± 3.7, and a mean blood pressure of 134/83 ± 17/12 mmHg were enrolled. The average consumption of caffeine per day was 539 ± 196.3 mg. The average monthly headache days and migraine attack frequency at baseline was 11.5 ± 4.9 and 5.2 ± 1.2, respectively. At baseline Pittsburgh Sleep Quality Index was 5.8 ± 2.5 and HIT-6 was 62.8 ± 3.9. There were no differences in these or in parameters from actigraphy during the caffeine period compared with the placebo period. One subject withdrew just after entering the study. In the remaining nine, withdrawal triggered severe migraine attacks in seven, causing one more drop-out, and a typical caffeine withdrawal syndrome in two. Caffeine continuation did not trigger migraines, but one attack occurred in the wake of caffeine reintroduction. Conclusions: The study failed to answer how caffeine withdrawal affects migraineurs over time, but showed that abrupt withdrawal of caffeine is a potent trigger for migraine attacks.