Miracle-dz/UniFAR-FTUs huggingface dataset:
A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp. as a model

Abstract Integrated platforms for storage, management, analysis and sharing of large quantities of omics data have become fundamental to comparative genomics. CoGe (https://genomevolution.org/coge/) is an online platform designed to manage and study genomic data, enabling both data- and hypothesis-driven comparative genomics. CoGe’s tools and resources can be used to organize and analyse both publicly available and private genomic data from any species. Here, we demonstrate the capabilities of CoGe through three example workflows using 17 Plasmodium genomes as a model. Plasmodium genomes present unique challenges for comparative genomics due to their rapidly evolving and highly variable genomic AT/GC content. These example workflows are intended to serve as templates to help guide researchers who would like to use CoGe to examine diverse aspects of genome evolution. In the first workflow, trends in genome composition and amino acid usage are explored. In the second, changes in genome structure and the distribution of synonymous (Ks) and non-synonymous (Kn) substitution values are evaluated across species with different levels of evolutionary relatedness. In the third workflow, microsyntenic analyses of multigene families’ genomic organization are conducted using two Plasmodium-specific gene families—serine repeat antigen, and cytoadherence-linked asexual gene—as models. In general, these example workflows show how to achieve quick, reproducible and shareable results using the CoGe platform. We were able to replicate previously published results, as well as leverage CoGe’s tools and resources to gain additional insight into various aspects of Plasmodium genome evolution. Our results highlight the usefulness of the CoGe platform, particularly in understanding complex features of genome evolution. Database URL: https://genomevolution.org/coge/
Sperm DNA Fragmentation and Its Relation With Fertility

Sperm DNA integrity is vital for successful fertilization, embryo development, pregnancy, and transmission of genetic material to the offspring. DNA fragmentation is the most frequent DNA anomaly present in the male gamete that has been associated to poor semen quality, low fertilization rates, impaired embryo quality, and preim‐ plantation development and reduced clinical outcomes in assisted reproduction procedures. This work summarizes the causes of fragmentation in the spermatic DNA, and its relation with seminal parameters, male aging, and results in assisted repro‐ duction procedures.
Acoustic Gait Analysis using Support Vector Machines

Gait analysis, defined as the study of human locomotion, can provide valuable information for low-cost analytic and classification applications in security, medical diagnostics, and biomechanics. In comparison to visual-based gait analysis, audio-based gait analysis offers robustness to clothing variations, visibility issues, and angle complications. Current acoustic techniques rely on frequency-based features that are sensitive to changes in footwear and floor surfaces. In this research, we consider an approach to surface-independent acoustic gait analysis based on time differences between consecutive steps. We employ support vector machines (SVMs) for classification. Our approach achieves good classification rates with high discriminative one-vs-all capabilities and we believe that our technique provides a promising avenue for future development.
Upscaling from single cells to modules – fabrication of vacuum- and ITO-free polymer solar cells on flexible substrates with long lifetime

Fabrication of polymer solar cell (PSC) modules was done on a previously reported compact coating/printing machine and tested in a readily scalable roll process on flexible substrates without applying vacuum, ITO or spin coating. Our aim was to establish loss upon scaling from cells to small modules. We studied from single cells (1 cm2) to modules comprising four serially connected devices with a total active area of 8 cm2. Four different polymers (P3HT, PV-D4610, PDTSTTz-4 and PBDTTTz-4) were applied in the preparation of the modules and efficiencies of more than 3% were achieved which is comparable to single cell devices prepared using the same process. This proves that it is possible to scale up new materials in an ITO free device context to modules without having an efficiency drop, due to reliable and consistent processing. The main loss observed was due to the packaging using barrier materials. The photochemical stability of the materials was therefore studied using intense light along with the operational stability of the corresponding devices according to the ISOS-D-1 and ISOS-L-1 standards. For devices under constant illumination we found that barrier materials from Mitsubishi and 3M provide better operational stability over time, compared to the barrier foil obtained from Amcor, for all the polymers, which is ascribed to the cut-off at higher wavelengths thereby lowering the degree of UV light that reaches the device. When comparing the operational stability of the four polymers under constant illumination, P3HT generally retains its performance better with higher T80 values, while the polymer PV-D4610 shows the highest PCE (1.6%) after 300 hours of operation.
DEPOSITION OF NANO-CRYSTALLINE FLUOR-HYDROXYAPATITE COATINGS ON TITANIUM SUBSTRATES VIA SOL-GEL METHOD

In this investigation, fluor-hydroxyapatite (FHA) film was deposited on a titanium substrate by sol-gel method. Triethyl phosphite, ammonium fluoride and calcium nitrate in ethanol solutions were used respectively as P, F and Ca precursors. Typical apatite structures were obtained for all coatings after dipping and subsequent heat treatment at 550, 700 and 800 oC, the coating layers were investigated with Xray diffraction, Fourier transform infra-red and Scanning electron microscopy spectroscopy. Based on the results obtained from X-ray diffraction, the coatings heated at 550 oC were composed of hydroxyapatite (HA) and fluorapatite (FA). Rutile (TiO 2 ) phase was also found in the coatings heated at higher temperature. In addition, the formation of fluor-hydroxyapatite was confirmed by FT-IR results. SEM studies showed the samples heat treated at 550 oC and 700 oC have almost the same morphology. It seems the coating of samples heat treated in 800 oC was more homogenous and smooth without any considerable porosity.
Experiences with Publicly Open Human Activity Data Sets - Studying the Generalizability of the Recognition Models

In this article, it is studied how well inertial sensor-based human activity recognition models work when training and testing data sets are collected in different environments. Comparison is done using publicly open human activity data sets. This article has four objectives. Firstly, survey about publicly available data sets is presented. Secondly, one previously not shared human activity data set used in our earlier work is opened for public use. Thirdly, the genaralizability of the recognition models trained using publicly open data sets are experimented by testing them with data from another publicly open data set to get knowledge to how models work when they are used in different environment, with different study subjects and hardware. Finally, the challenges encountered using publicly open data sets are discussed. The results show that data gathering protocol can have a statistically significant effect to the recognition rates. In addition, it was noted that often publicly open human activity data sets are not as easy to apply as they should be.
Assessment of Hypoxia in the Stroma of Patient-Derived Pancreatic Tumor Xenografts

The unusually dense stroma of pancreatic cancers is thought to play an important role in their biological aggression. The presence of hypoxia is also considered an adverse prognostic factor. Although it is usually assumed that this is the result of effects of hypoxia on the epithelial component, it is possible that hypoxia exerts indirect effects via the tumor stroma. We therefore measured hypoxia in the stroma of a series of primary pancreatic cancer xenografts. Nine patient-derived pancreatic xenografts representing a range of oxygenation levels were labeled by immunohistochemistry for EF5 and analyzed using semi-automated pattern recognition software. Hypoxia in the tumor and stroma was correlated with tumor growth and metastatic potential. The extent of hypoxia varied from 1%–39% between the different models. EF5 labeling in the stroma ranged from 0–20% between models, and was correlated with the level of hypoxia in the tumor cell area, but not microvessel density. Tumor hypoxia correlated with spontaneous metastasis formation with the exception of one hypoxic model that showed disproportionately low levels of hypoxia in the stroma and was non-metastatic. Our results demonstrate that hypoxia exists in the stroma of primary pancreatic cancer xenografts and suggest that stromal hypoxia impacts the metastatic potential.
A Generic Framework to Perform Comprehensive Analysis of Tweets

Recently, there has been an increased interest in the use of social media data as important traffic information sources and as a data research in the field of Human and Social Sciences. Social media are used, for example, to identify Twitter user communities in the context of altmetrics. In this paper, we highlight the potential use of social media data analysis by non computer science researchers. We present an approach based on a multi-dimensional analysis which combines the thematic, temporal and spatial features of tweets. We detail an experimentation using different tools in order to create the “perfectible” toolbox for researchers in HSS (for example territorial marketing) or for local territory managers. This approach can be applied in the context of altmetrics.
Numerical modeling of stresses and buckling loads of isogrid lattice composite structure cylinders

Isogrid composite lattice cylindrical structure with or without skins which consists of a system of ±ϕ (with respect to the shell axis) helical ribs and circumferential ribs, and has no skins or has skins was studied in a numerical method using ANSYS software, where in this model axial compression and/or pressure loads are applied, to determine the different failure modes which are, failure due to stress exceeds material strength, failure due to local buckling of ribs (crippling), failure due to general buckling of the cylinder and failure due to local buckling skin if the skin is existed. An example was studied to compare the results obtained from the numerical method and other research article. Keywords: FEM, Composite Structures, Isogrid Lattice, Buckling Load
A Data-Gathering Scheme with Joint Routing and Compressive Sensing Based on Modified Diffusion Wavelets in Wireless Sensor Networks

Compressive sensing (CS)-based data gathering is a promising method to reduce energy consumption in wireless sensor networks (WSNs). Traditional CS-based data-gathering approaches require a large number of sensor nodes to participate in each CS measurement task, resulting in high energy consumption, and do not guarantee load balance. In this paper, we propose a sparser analysis that depends on modified diffusion wavelets, which exploit sensor readings’ spatial correlation in WSNs. In particular, a novel data-gathering scheme with joint routing and CS is presented. A modified ant colony algorithm is adopted, where next hop node selection takes a node’s residual energy and path length into consideration simultaneously. Moreover, in order to speed up the coverage rate and avoid the local optimal of the algorithm, an improved pheromone impact factor is put forward. More importantly, theoretical proof is given that the equivalent sensing matrix generated can satisfy the restricted isometric property (RIP). The simulation results demonstrate that the modified diffusion wavelets’ sparsity affects the sensor signal and has better reconstruction performance than DFT. Furthermore, our data gathering with joint routing and CS can dramatically reduce the energy consumption of WSNs, balance the load, and prolong the network lifetime in comparison to state-of-the-art CS-based methods.
Effective thermal conductivity and thermal properties of phthalonitrile‐terminated poly(arylene ether nitriles) composites with hybrid functionalized alumina

A polymer-based thermal conductive composite has been developed. It is based on a dispersion of micro- and nanosized alumina (Al2O3) in the phthalonitrile-terminated poly (arylene ether nitriles) (PEN-t-ph) via solution casting method. The Al2O3 with different particle sizes were functionalized with phthalocyanine (Pc) which was used as coupling agent to improve the compatibility of Al2O3 and PEN-t-ph matrix. The content of microsized functionalized Al2O3 (m-f-Al2O3) maintained at 30 wt % to form the main thermally conductive path in the composites, and the nanosized functionalized Al2O3 (n-f-Al2O3) act as connection role to provide additional channels for the heat flow. The thermal conductivity of the f-Al2O3/PEN-t-ph composites were investigated as a function of n-f-Al2O3 loading. Also, a remarkable improvement of the thermal conductivity from 0.206 to 0.467 W/mK was achieved at 30 wt % n-f-Al2O3 loading, which is nearly 2.7-fold higher than that of pure PEN-t-ph polymer. Furthermore, the mechanical testing reveals that the tensile strength increased from 99 MPa for pure PEN-t-ph to 105 MPa for composites with 30 wt % m-f-Al2O3 filler loading. In addition, the PEN-t-ph composites possess excellent thermal properties with glass transition temperature (Tg) above 184°C, and initial degradation temperature (Tid) over 490°C. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 41595.
Brain–computer symbiosis

The theoretical groundwork of the 1930s and 1940s and the technical advance of computers in the following decades provided the basis for dramatic increases in human efficiency. While computers continue to evolve, and we can still expect increasing benefits from their use, the interface between humans and computers has begun to present a serious impediment to full realization of the potential payoff. This paper is about the theoretical and practical possibility that direct communication between the brain and the computer can be used to overcome this impediment by improving or augmenting conventional forms of human communication. It is about the opportunity that the limitations of our body's input and output capacities can be overcome using direct interaction with the brain, and it discusses the assumptions, possible limitations and implications of a technology that I anticipate will be a major source of pervasive changes in the coming decades.
Clinical and Genetic Heterogeneity of Autism

Autism (MIM 209850) comprises a heterogeneous group of disorders with a complex genetic etiology, characterized by impairments in reciprocal social communication and presence of restricted, repetitive and stereotyped patterns of behavior [1]. With an early onset prior to age 3 and prevalence as high as 0.9–2.6% [2,3], autism occurs predominantly in males, with a ratio of male: female of 4 to 1. It is one of the leading causes of childhood disability and inflicts serious suffering and burden for the family and society [4].
The Diversity and Distribution of Fungi on Residential Surfaces

The predominant hypothesis regarding the composition of microbial assemblages in indoor environments is that fungal assemblages are structured by outdoor air with a moderate contribution by surface growth, whereas indoor bacterial assemblages represent a mixture of bacteria entered from outdoor air, shed by building inhabitants, and grown on surfaces. To test the fungal aspect of this hypothesis, we sampled fungi from three surface types likely to support growth and therefore possible contributors of fungi to indoor air: drains in kitchens and bathrooms, sills beneath condensation-prone windows, and skin of human inhabitants. Sampling was done in replicated units of a university-housing complex without reported mold problems, and sequences were analyzed using both QIIME and the new UPARSE approach to OTU-binning, to the same result. Surfaces demonstrated a mycological profile similar to that of outdoor air from the same locality, and assemblages clustered by surface type. “Weedy” genera typical of indoor air, such as Cladosporium and Cryptococcus, were abundant on sills, as were a diverse set of fungi of likely outdoor origin. Drains supported more depauperate assemblages than the other surfaces and contained thermotolerant genera such as Exophiala, Candida, and Fusarium. Most surprising was the composition detected on residents’ foreheads. In addition to harboring Malassezia, a known human commensal, skin also possessed a surprising richness of non-resident fungi, including plant pathogens such as ergot (Claviceps purperea). Overall, fungal richness across indoor surfaces was high, but based on known autecologies, most of these fungi were unlikely to be growing on surfaces. We conclude that while some endogenous fungal growth on typical household surfaces does occur, particularly on drains and skin, all residential surfaces appear – to varying degrees – to be passive collectors of airborne fungi of putative outdoor origin, a view of the origins of the indoor microbiome quite different from bacteria.
Frequent and parallel habitat transitions as driver of unbounded radiations in the Cape flora

The enormous species richness in the Cape Floristic Region (CFR) of Southern Africa is the result of numerous radiations, but the temporal progression and possible mechanisms of these radiations are still poorly understood. Here, we explore the macroevolutionary dynamics of the Restionaceae, which include 340 species that are found in all vegetation types in the Cape flora and are ecologically dominant in fynbos. Using an almost complete (i.e., 98%) species‐level time calibrated phylogeny and models of diversification dynamics, we show that species diversification is constant through the Cenozoic, with no evidence of an acceleration with the onset of the modern winter‐wet climate, or a recent density‐dependent slowdown. Contrary to expectation, species inhabiting the oldest (montane) and most extensive (drylands) habitats did not undergo higher diversification rates than species in the younger (lowlands) and more restricted (wetland) habitats. We show that the rate of habitat transitions is more closely related to the speciation rate than to time, and that more than a quarter of all speciation events are associated with habitat transitions. This suggests that the unbounded Restionaceae diversification resulted from numerous, parallel, habitat shifts, rather than persistence in a habitat stimulating speciation. We speculate that this could be one of the mechanisms resulting in the hyperdiverse Cape flora.
Power grid verification under transient constraints

Checking the power grid must begin early in the design. One way of doing this is using vectorless verification which, unlike standard simulation, only requires limited information about the currents drawn from the grid, in the form of DC local and global upper-bounds, or current constraints. We extend the standard vectorless verification to allow transient constraints, where circuit currents may be bounded by different values at different times. This is useful to check the validity of candidate sequences of chip operations, each having different current requirements. We show that this framework leads to a less pessimistic estimation of voltage drops.
The fabrication of microfluidic structures by means of full-wafer adhesive bonding using a poly(dimethylsiloxane) catalyst

In this work, we present the use of a PDMS (poly(dimethylsiloxane)) curing-agent as the intermediate layer for adhesive full-wafer bonding suitable for fabrication of microfluidic structures. The curing-agent of the two-component silicone rubber (Sylgard 184) is spin coated on a substrate, brought into contact with another PDMS layer and heat cured to create an irreversible seal which is as strong as or even stronger than plasma-assisted PDMS bonding. The maximum bond strength is measured to 800 kPa when bonding together PDMS and silicon. The applicability of the new PDMS adhesive bonding method is verified by means of fabricating microfluidic structures. Using this method allows for wafer-level bonding of PDMS to various materials such as PDMS, glass or silicon and more importantly to selectively bond different layers by using a patterned adhesive bonding technique. Moreover, precise alignment of the structural layers is facilitated since curing is initiated upon heat which is an advantage when fabricating multilayer microfluidic devices.
Sedimentary DNA Reveals Cyanobacterial Community Diversity over 200 Years in Two Perialpine Lakes

ABSTRACT We reconstructed cyanobacterial community structure and phylogeny using DNA that was isolated from layers of stratified sediments spanning 200 years of lake history in the perialpine lakes Greifensee and Lake Zurich (Switzerland). Community analysis based on amplification and sequencing of a 400-nucleotide (nt)-long 16S rRNA fragment specific to Cyanobacteria revealed operational taxonomic units (OTUs) capturing the whole phylum, including representatives of a newly characterized clade termed Melainabacteria, which shares common ancestry with Cyanobacteria and has not been previously described in lakes. The reconstruction of cyanobacterial richness and phylogenetic structure was validated using a data set consisting of 40 years of pelagic microscopic counts from each lake. We identified the OTUs assigned to common taxa known to be present in Greifensee and Lake Zurich and found a strong and significant relationship (adjusted R 2 = 0.89; P < 0.001) between pelagic species richness in water and OTU richness in the sediments. The water-sediment richness relationship varied between cyanobacterial orders, indicating that the richness of Chroococcales and Synechococcales may be underestimated by microscopy. PCR detection of the microcystin synthetase gene mcyA confirmed the presence of potentially toxic cyanobacterial taxa over recent years in Greifensee and throughout the last century in Lake Zurich. The approach presented in this study demonstrates that it is possible to reconstruct past pelagic cyanobacterial communities in lakes where the integrity of the sedimentary archive is well preserved and to explore changes in phylogenetic and functional diversity over decade-to-century timescales. IMPORTANCE Cyanobacterial blooms can produce toxins that affect water quality, especially under eutrophic conditions, which are a consequence of human-induced climate warming and increased nutrient availability. Lakes worldwide have suffered from regular cyanobacterial blooms over the last century. The lack of long-term data limits our understanding of how these blooms form. We successfully reconstructed the past diversity of whole cyanobacterial communities over two hundred years by sequencing genes preserved in the sediments of two perialpine lakes in Switzerland. We identified changes in diversity over time and validated our results using existing data collected in the same two lakes over the past 40 years. This work shows the potential of our approach for addressing important ecological questions about the effects of a changing environment on lake ecology.