Miracle-dz/UniFAR-FTUs huggingface dataset:
Topographical and physiological differences of the skin mycobiome in health and disease

ABSTRACT Skin constantly encounters external elements, including microbes. Culture-based studies have identified fungi present on human skin and have linked some species with certain skin diseases. Moreover, modern medical treatments, especially immunosuppressants, have increased the population at risk for cutaneous and invasive fungal infections, emphasizing the need to understand skin fungal communities in health and disease. A major hurdle for studying fungal flora at a community level has been the heterogeneous culture conditions required by skin fungi. Recent advances in DNA sequencing technologies have dramatically expanded our knowledge of the skin microbiome through culture-free methods. This review discusses historical and recent research on skin fungal communities – the mycobiome – in health and disease, and challenges associated with sequencing-based mycobiome research.
Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile

Abstract Chromatin immunoprecipitation followed by sequencing (ChIP-seq) can detect read-enriched DNA loci for point-source (e.g., transcription factor binding) and broad-source factors (e.g., various histone modifications). Although numerous quality metrics for ChIP-seq data have been developed, the ‘peaks’ thus obtained are still difficult to assess with respect to signal-to-noise ratio (S/N) and the percentage of false positives. We developed a quality-assessment tool for ChIP-seq data, SSP (strand-shift profile), that quantifies S/N and peak reliability without peak calling. We validated SSP in-depth using ≥ 1,000 publicly available ChIP-seq datasets along with virtual data to demonstrate that SSP is quantifiable and sensitive to different S/Ns for both pointand broad-source factors. Moreover, SSP is consistent among cell types and with respect to variance of sequencing depth, and identifies low-quality samples that cannot be identified by quality metrics currently available. Finally, we show that “hidden-duplicate reads” cause aberrantly high S/Ns, and SSP provides an additional metric to avoid them, which can also contribute to estimation of peak mode (pointor broad-source) of samples. Availability https://github.com/rnakato/SSP"
Irrigation practices and intestinal helminth infections in Southern and Central zones of Tigray.

Background: Irrigation practices have impact on the distribution of schistosomiasis; so, identifying newly established schistosomiasis transmission foci allows for designing prevention and control strategy. Objective: To establish schistosomiasis prevalence and intensity in relation to development of water bodies for irrigation. Methods: A survey of stool specimens of 2000 school children using Kato thick smear method was carried out in Central and Southern Tigray between October 2001 and January 2002. Results: Among the 1012 males and 998 females examined, 29% males and 27.5% females were found positive for one or more parasite. The prevalence of S. mansoni was 27% in longstanding irrigated, 10.8% in recently constructed irrigation schemes and 1.8% in the non-irrigated rural localities. In the urban setting, its prevalence was 15.5% in areas with water body nearby and 0.5% in areas with no water body nearby (P detected in Tumuga with a prevalence of 87%; Dibdibo (41%), Mariam Shewito (25%), Adiha (23%) and Lekia (9%). Conclusion: The increasing risk of schistosomiasis mansoni in the irrigation sites is high. Hence, designing preventive and control strategies concurrent with the development of the irrigation projects will be required to reduce prevalence of schistosomiasis.
EMS Painter: Co-creating Visual Art using Electrical Muscle Stimulation

We present a work in progress, enabling an audience to influence a painter, through electrical muscle stimulation (EMS) to co-create visual art works. Two sets of EMS pads are positioned on the painter's arm such that stimulation pulses, triggered on a collocated tablet interface by audience members, cause deviation in the ongoing brushstroke. LEDs co-located with the EMS pads provide additional visual feedback to the audience of stimulation delivery. In an initial trial, rather than focusing on co-creation, the audience amused themselves by mischievously diverting the painter from his work.
Intestinal Microbiota in Healthy Adults: Temporal Analysis Reveals Individual and Common Core and Relation to Intestinal Symptoms

Background While our knowledge of the intestinal microbiota during disease is accumulating, basic information of the microbiota in healthy subjects is still scarce. The aim of this study was to characterize the intestinal microbiota of healthy adults and specifically address its temporal stability, core microbiota and relation with intestinal symptoms. We carried out a longitudinal study by following a set of 15 healthy Finnish subjects for seven weeks and regularly assessed their intestinal bacteria and archaea with the Human Intestinal Tract (HIT)Chip, a phylogenetic microarray, in conjunction with qPCR analyses. The health perception and occurrence of intestinal symptoms was recorded by questionnaire at each sampling point. Principal Findings A high overall temporal stability of the microbiota was observed. Five subjects showed transient microbiota destabilization, which correlated not only with the intake of antibiotics but also with overseas travelling and temporary illness, expanding the hitherto known factors affecting the intestinal microbiota. We identified significant correlations between the microbiota and common intestinal symptoms, including abdominal pain and bloating. The most striking finding was the inverse correlation between Bifidobacteria and abdominal pain: subjects who experienced pain had over five-fold less Bifidobacteria compared to those without pain. Finally, a novel computational approach was used to define the common core microbiota, highlighting the role of the analysis depth in finding the phylogenetic core and estimating its size. The in-depth analysis suggested that we share a substantial number of our intestinal phylotypes but as they represent highly variable proportions of the total community, many of them often remain undetected. Conclusions/Significance A global and high-resolution microbiota analysis was carried out to determine the temporal stability, the associations with intestinal symptoms, and the individual and common core microbiota in healthy adults. The findings provide new approaches to define intestinal health and to further characterize the microbial communities inhabiting the human gut.
Thin single screen-printed bifunctional titania layer photoanodes for high performing DSSCs via a novel hybrid paste formulation and process

A novel hybrid titania paste comprising aqueous-synthesized anatase (A) nanocrystalites and submicrometer-sized “sea urchin”-like rutile (R) particles that enables the construction of thin (5–6 μm) single-layer photoanodes with competitive power conversion efficiency is described. Owing to the high surface area of the dye (N719)-coated anatase film, the scattering properties of the unique rutile particulates, and the incorporation of P25 particles, the constructed bifunctional electrode films exhibit excellent electron transport properties (long electron lifetime) and no electrolyte diffusion resistance. Dye-sensitized solar cell devices built with the thin (5–6 μm) hybrid electrodes showed greatly improved power conversion efficiency (PCE), namely 7.04%, when compared to devices based on single anatase (4.20%), double-layer (A + R), or double thickness commercial benchmark paste (6.74%). This is an impressive result as less than 1/2 material was used in a single printed layer. Thinner films as the ones built here may prove particularly advantageous in using new noniodide electrolytes associated with slow diffusion rates.
nfrared to Ultraviolet Measurements of Two- Absorption and n2 in Wide Bandgap Sol

The bound electronic nonlinear refractive index, n2. and two-photon absorption (2PA) coefficient, 0. are measured in a variety of inorganic dielectric solids at the four harmon- ics of the Nd:YAG laser using 2 scan. The specific materials studied are: barium fluoride (BaFZ), calcite (CaC03), potas- sium bromide (KBr), lithium fluoride (LiF), magnesium fluoride (MgF2), sapphire (Alz03), a tellurite glass (75%TeO2+ 20%Zn0 + 5%Na;.O) and fused silica (SO;.). We also report n2 and 3 in three second-order, ~('1, nonlinear crystals: potassium titanyl phosphate (KTiOPO4 or KTP), lithium niobate (LiNbOS), and 3-barium borate (O-BaB2 04 or BBO). Nonlinear absorption or refraction can alter the wavelength conversion efficiency in these materials. The results of this study are compared to a simple two- parabolic band model originally developed to describe zincblende semiconductors. This model gives the bandgap energy (E, ) scal- ing and spectrum of the change in absorption. The dispersion of n2 as obtained from a Kramers-Kronig transformation of this absorption change scales as ET4. The agreement of this theory to data for semiconductors was excellent. However, as could be expected, the agreement for these wide bandgap materials is not as good, although general trends such as increasing nonlinearity with decreasing bandgap energy can be seen.
A 15.2-ENOB continuous-time ΔΣ ADC for a 200mVpp-linear-input-range neural recording front-end

Closed-loop neuromodulation with simultaneous stimulation and sensing is desired to advance deep brain stimulation (DBS) therapies. However, stimulation generates large artifacts (∼100mV) at the recording sites that saturate traditional front-ends. We present a 15.2b-ENOB CT ΔΣΜ with 187dB FOM, which along with an 8x-gain capacitively coupled chopper instrumentation amplifier (CCIA), realizes a front-end that can digitize neural signals (<2mV<inf>pp</inf>) from 1Hz to 5kHz in the presence of 200mV<inf>pp</inf> artifacts. Neural recording front-ends need to function within a power budget of 10μW/ch, input-referred noise of 4–8μV<inf>rms</inf> in 1Hz-5kHz, DC input impedance Z<inf>in, DC</inf>>1GΩ and high-pass (HP) cutoff <1Hz [1]. Prior work has addressed power and noise [1]-[2], but has limited dynamic-range and bandwidth (BW), making them incapable of performing true closed-loop operation.
BRDF characterization of solar diffuser for JPSS J1 using PASCAL

The Visible/Infrared Imaging Radiometer Suite (VIIRS) is a key sensor on the Suomi National Polar-orbiting Partnership (NPP) satellite as well as the upcoming Joint Polar Satellite System (JPSS). VIIRS collects Earth radiometric and imagery data in 22 spectral bands from 0.4 to 12.5 μm. Radiometric calibration of the reflective bands in the 0.4 to 2.5 μm wavelength range is performed by measuring sunlight reflectance from Spectralon®. Reflected sun light is directly proportional to the Bidirectional Reflectance Distribution Function (BRDF) of the Spectralon®. This paper presents the BRDF measurements of the Spectralon® for JPSS-1 VIIIRS in the 0.4 – 1,63 μm wavelength using PASCAL (Polarization And Scatter Characterization Analysis of Lambertian materials) with an uncertainty better than 0.8%. PASCAL makes absolute measurements of BRDF in an analogous fashion to the National Institute of Standards and Technology (NIST) Spectral Tri-function Automated Reflectance Reflectometer (STARR) facility. BRDF is calculated on the basis of the measured incident power, reflected power and geometric factors thus eliminating the need for a standard. The detector rotates about the sample in the plane defined by the source beam and the azimuth rotation of the sample. Unique additional features of this instrument include the ability to vary the sample elevation and roll / clock the sample about its normal thus allowing BRDF measurements in the as use geometry. A description of PASCAL, validation and the BRDF results of the Solar Diffuser are presented. Part dependent non-uniformity of Spectralon® was also observed.
Demonstration of Autosomal Monoallelic Expression in Thyroid Tissue Assessed by Whole-Exome and Bulk RNA Sequencing.

BACKGROUND Congenital hypothyroidism due to thyroid dysgenesis (CHTD) is a disorder with a prevalence of 1/4000 live births, the cause of which remains unknown. The most common diagnostic category is thyroid ectopy, which occurs in up to 80% of CHTD cases. CHTD is predominantly not inherited and has a high discordance rate (>92%) between monozygotic (MZ) twins. The sporadic nature of CHTD might be explained by somatic events such as autosomal monoallelic expression (AME), given that genes expressed in a monoallelic way are more vulnerable to otherwise benign monoallelict genetic or epigenetic mutations. OBJECTIVE The aim of this study was to search for complete (90%) AME in normal and dysgenetic thyroid tissues. METHODS Aggregated analysis of whole-exome and bulk RNA sequencing was performed on two ectopic thyroids, four normal thyroids, and the human thyroid cell line Nthy-ori. RESULTS A median of 5062 (range 2081-5270) genes per sample showed sufficient numbers of heterozygous single nucleotide polymorphisms to be informative. The median monoallelic expression represented 22 (range 16-32) of the informative genes for each thyroid sample. Examples of genes displaying AME are FCGBP, ZNF331, USP10, BCLAF1, and some HLA genes; these genes are involved in epithelial-mesenchymal transition, cell migration, cancer, and immunity. CONCLUSIONS AME may account for the high discordance rate observed between MZ twins and for the sporadic nature of CHTD. These findings also have implications for other pathologies, including cancers and autoimmune disorders of the thyroid.
Reduced Polymorphism Associated with X Chromosome Meiotic Drive in the Stalk-Eyed Fly Teleopsis dalmanni

Sex chromosome meiotic drive has been suggested as a cause of several evolutionary genetic phenomena, including genomic conflicts that give rise to reproductive isolation between new species. In this paper we present a population genetic analysis of X chromosome drive in the stalk-eyed fly, Teleopsis dalmanni, to determine how this natural polymorphism influences genetic diversity. We analyzed patterns of DNA sequence variation at two X-linked regions (comprising 1325 bp) approximately 50 cM apart and one autosomal region (comprising 921 bp) for 50 males, half of which were collected in the field from one of two allopatric locations and the other half were derived from lab-reared individuals with known brood sex ratios. These two populations are recently diverged but exhibit partial postzygotic reproductive isolation, i.e. crosses produce sterile hybrid males and fertile females. We find no nucleotide or microsatellite variation on the drive X chromosome, whereas the same individuals show levels of variation at autosomal regions that are similar to field-collected flies. Furthermore, one field-caught individual collected 10 years previously had a nearly identical X haplotype to the drive X, and is over 2% divergent from other haplotypes sampled from the field. These results are consistent with a selective sweep that has removed genetic variation from much of the drive X chromosome. We discuss how this finding may relate to the rapid evolution of postzygotic reproductive isolation that has been documented for these flies.
RBMX is a component of the centromere noncoding RNP complex involved in cohesion regulation

Satellite I RNA, a noncoding (nc)RNA transcribed from repetitive regions in human centromeres, binds to Aurora kinase B and forms a ncRNP complex required for chromosome segregation. To examine its function in this process, we purified satellite I ncRNP complex from nuclear extracts prepared from asynchronized or mitotic (M) phase‐arrested HeLa cells and then carried out LC/MS to identify proteins bound to satellite I RNA. RBMX (RNA‐binding motif protein, X‐linked), which was isolated from M phase‐arrested cells, was selected for further characterization. We found that RBMX associates with satellite I RNA only during M phase. Knockdown of RBMX induced premature separation of sister chromatid cohesion and abnormal nuclear division. Likewise, knockdown of satellite I RNA also caused premature separation of sister chromatids during M phase. The amounts of RBMX and Sororin, a cohesion regulator, were reduced in satellite I RNA‐depleted cells. These results suggest that satellite I RNA plays a role in stabilizing RBMX and Sororin in the ncRNP complex to maintain proper sister chromatid cohesion.
Using Phylogenetic and Coalescent Methods to Understand the Species Diversity in the Cladia aggregata Complex (Ascomycota, Lecanorales)

The Cladia aggregata complex is one of the phenotypically most variable groups in lichenized fungi, making species determination difficult and resulting in different classifications accepting between one to eight species. Multi-locus DNA sequence data provide an avenue to test species delimitation scenarios using genealogical and coalescent methods, employing gene and species trees. Here we tested species delimitation in the complex using molecular data of four loci (nuITS and IGS rDNA, protein-coding GAPDH and Mcm-7), including 474 newly generated sequences. Using a combination of ML and Bayesian gene tree topologies, species tree inferences, coalescent-based species delimitation, and examination of phenotypic variation we assessed the circumscription of lineages. We propose that results from our analyses support a 12 species delimitation scenario, suggesting that there is a high level of species diversity in the complex. Morphological and chemical characters often do not characterize lineages but show some degree of plasticity within at least some of the clades. However, clades can often be characterized by a combination of several phenotypical characters. In contrast to the amount of homoplasy in the morphological characters, the data set exhibits some geographical patterns with putative species having distribution patterns, such as austral, Australasian or being endemic to Australia, New Zealand or Tasmania.
Butyrate production from high-fiber diet protects against lymphoma tumor

Abstract Gut microbiota and dietary fiber are critical for protecting body from obesity, diabetes and cancer. Butyrate, produced in the gut by bacterial fermentation of dietary fibers, is demonstrated to be protective against the development of colorectal cancer as a histone deacetylase (HDAC) inhibitor. We report that high-fiber diet and butyrate significantly inhibited the growth lymphoma tumors. Butyrate induced apoptosis of lymphoma tumor cells and significantly up-regulated histone 3 acetylation (H3ac) level and target genes such as Fas, P21, P27. Our results unravel an instrumental role of fiber diet and their metabolites on lymphoma tumor and demonstrate an intervention potential on the prevention and therapy of lymphoma.
A Decision Tree Based Method for Extracting Important Elements of In-Applications Purchase

With rapid development of mobile communications services and handheld devices, it led to explosive growth in mobile applications (App). Related works also indicated that game Apps have become the biggest source of revenue compared to other kinds of Apps. Recent surveys have found that the mobile games industry will account for ever increasing contributions, with a market share approaching 35% by 2020. Therefore, the game App providers need to know how to design products to satisfy consumer's needs and how to increase revenue from Apps. In particular, in-App purchase is the major revenue models for game Apps. Consequently, this study attempts to define the potential factors of influencing in-App purchase behaviors of game users. Then, we use decision trees (DT) to identify important factors. The findings can be used as a reference when designing game Apps for game developers and researchers to increase profit of game Apps.
Sex-biased dispersal patterns depend on the spatial scale in a social rodent

Dispersal is a fundamental process in ecology because it influences the dynamics, genetic structure and persistence of populations. Furthermore, understanding the evolutionary causes of dispersal pattern, particularly when they differ between genders, is still a major question in evolutionary ecology. Using a panel of 10 microsatellite loci, we investigated at different spatial scales the genetic structure and the sex-specific dispersal patterns in the common vole Microtus arvalis, a small colonial mammal. This study was conducted in an intensive agricultural area of western France. Hierarchical FST analyses, relatedness and assignment tests suggested (i) that females are strongly kin-clustered within colonies; (ii) that dispersal is strongly male-biased at a local scale; and (iii) long-distance dispersal is not rare and more balanced between genders. We conclude that males migrate continuously from colony to colony to reproduce, whereas females may disperse just once and would be mainly involved in new colony foundation.
Agent-based simulation of a shared, autonomous and electric on-demand mobility solution

Recent technological progress in automation and electrification gives room to create sustainable, costumer-orientated and economical transportation solutions. For vehicle-based systems, on-demand mobility services are considered to play an important role. To support decision making in an early stage of development, we propose a mobility on-demand simulation that reflects its system behavior on an operational level. Its core forms a discrete event simulation combined with a multi-agent approach. The main entities are fully-automated electric taxis, a central dispatcher and customers. All agents live in a shared environment consisting of a street network and charging infrastructure. The dispatching center handles matchmaking between customers and vehicles with the help of a Contract Net Protocol. Taxis compete for customer transportation requests broadcasted by the dispatcher. Routing and charging decisions are made individually by each agent. A simulation study evaluates three mobility on-demand services for Munich. The basic scenario analyzes a limited service area, where a shared vehicle fleet is responsible for the entire local traffic demand. The second scenario considers additional commuter trips entering or leaving this zone. The third scenario investigates a citywide operation. Key findings confirm the feasibility of operating a shared autonomous vehicle fleet with both high service levels and vehicle utilization.
A Wireless Multi-Channel Recording System for Freely Behaving Mice and Rats

To understand the neural basis of behavior, it is necessary to record brain activity in freely moving animals. Advances in implantable multi-electrode array technology have enabled researchers to record the activity of neuronal ensembles from multiple brain regions. The full potential of this approach is currently limited by reliance on cable tethers, with bundles of wires connecting the implanted electrodes to the data acquisition system while impeding the natural behavior of the animal. To overcome these limitations, here we introduce a multi-channel wireless headstage system designed for small animals such as rats and mice. A variety of single unit and local field potential signals were recorded from the dorsal striatum and substantia nigra in mice and the ventral striatum and prefrontal cortex simultaneously in rats. This wireless system could be interfaced with commercially available data acquisition systems, and the signals obtained were comparable in quality to those acquired using cable tethers. On account of its small size, light weight, and rechargeable battery, this wireless headstage system is suitable for studying the neural basis of natural behavior, eliminating the need for wires, commutators, and other limitations associated with traditional tethered recording systems.