Miracle-dz/UniFAR-FTUs huggingface dataset:
Crowdsourced study of children with autism and their typically developing siblings identifies differences in taxonomic and predicted function for stool-associated microbes using exact sequence variant analysis

Background The existence of a link between the gut microbiome and autism spectrum disorder (ASD) is well established in mice, but in human populations efforts to identify microbial biomarkers have been limited due to problems stratifying participants within the broad phenotype of ASD and a lack of appropriately matched controls. To overcome these limitations and investigate the relationship between ASD and the gut microbiome, we ran a crowdsourced study of families 2-7 year old sibling pairs, where one child of the pair had a diagnosis of ASD and the other child did not. Methods Parents of age-matched sibling pairs electronically consented and completed study procedures via a secure web portal (microbiome.stanford.edu). Parents collected stool samples from each child, responded to behavioral questionnaires about the ASD child’s typical behavior, and whenever possible provided a home video of their ASD child’s natural social behavior. We performed DNA extraction and 16S rRNA amplicon sequencing on 117 stool samples (60 ASD and 57 NT) that met all study design eligibility criteria,. Using DADA2, Exact Sequence Variants (ESVs) were identified as taxonomic units, and three statistical tests were performed on ESV abundance counts: (1) permutation test to determine differences between sibling pairs, (2) differential abundance test using a zero-inflated gaussian mixture model to account for the sparse abundance matrix, and (3) differential abundance test after modeling under a negative binomial distribution. The potential functional gene abundance for each sample was also inferred from the 16S rRNA data, providing KEGG Ortholog (KO), which were analyzed for differential abundance. Results In total, 21 ESVs had significantly differentially proportions in stool of children with ASD and their neurotypical siblings. Of these 21 ESVs, 11 were enriched in neurotypical children and ten were enriched in children with ASD. ESVs enriched in the ASD cohort were predominantly associated with Ruminococcaceae and Bacteroidaceae; while those enriched in controls were more diverse including taxa associated with Bifidobacterium, Porphyromonas, Slackia, Desulfovibrio, Acinetobacter johnsonii, and Lachnospiraceae. Exact Variant Analysis suggested that Lachnospiraceae was specific to the control cohort, while Ruminococcaceae, Tissierellaceae and Bacteroidaceae were significantly enriched in children with ASD. Metabolic gene predictions determined that while both cohorts harbor the butyrogenic pathway, the ASD cohort was more likely to use the 4-aminobutanoate (4Ab) pathway, while the control cohort was more likely to use the pyruvate pathway. The 4Ab pathway releases harmful by-products like ammonia and can shunt glutamate, affecting its availability as an excitatory neurotransmitter. Finally, we observed differences in the carbohydrate uptake capabilities of various ESVs identified between the two cohorts.
Highly differentiated CD4 T cells Unequivocally Identify Primary Resistance and Risk of Hyperprogression to PD-L1/PD-1 Immune Checkpoint Blockade in Lung Cancer

The majority of lung cancer patients are refractory to PD-L1/PD-1 blockade monotherapy. This therapy may even accelerate progression and death in a group of patients called hyperprogressors. Here we demonstrate that the efficacy of PD-L1/PD-1 blockade therapy relies on baseline circulating highly-differentiated CD28− CD27− CD4 T cells (THD cells), which segregate patients in two non-overlapping groups. THD cells in cancer patients mostly comprised of central memory subsets that potently co-upregulated PD-1 and LAG3 upon antigen recognition. Low baseline THD numbers unequivocally identified intrinsic non-responders and hyperprogressors, whom aberrantly responded to therapy with a potent systemic proliferative THD cell burst. Responder patients showed significant reductions in systemic CD4 THD cells throughout therapy linked to expansion of the CD28+ CD27+ CD4 T cell compartment. Quantification of THD cells from peripheral blood samples prior to therapy allows identification of non-responders, hyperprogressors and responders, a critical issue in clinical oncology. These results place CD4 T cell responses at the center of anti-tumor immunity.
Sensitivity Levels: Optimizing the Performance of Privacy Preserving DNA Alignment

The advent of high throughput next-generation sequencing (NGS) machines made DNA sequencing cheaper, but also put pressure on the genomic life-cycle, which includes aligning millions of short DNA sequences, called reads, to a reference genome. On the performance side, efficient algorithms have been developed, and parallelized on public clouds. On the privacy side, since genomic data are utterly sensitive, several cryptographic mechanisms have been proposed to align reads securely, with a lower performance than the former, which in turn are not secure. This manuscript proposes a novel contribution to improving the privacy performance product in current genomic studies. Building on recent works that argue that genomics data needs to be × treated according to a threat-risk analysis, we introduce a multi-level sensitivity classification of genomic variations. Our classification prevents the amplification of possible privacy attacks, thanks to promoting and partitioning mechanisms among sensitivity levels. Thanks to this classification, reads can be aligned, stored, and later accessed, using different security levels. We then extend a recent filter, which detects the reads that carry sensitive information, to classify reads into sensitivity levels. Finally, based on a review of the existing alignment methods, we show that adapting alignment algorithms to reads sensitivity allows high performance gains, whilst enforcing high privacy levels. Our results indicate that using sensitivity levels is feasible to optimize the performance of privacy preserving alignment, if one combines the advantages of private and public clouds.
Complete mitochondrial genomesequence of the hen harrier (Circus cyaneus)

Abstract In this study, the complete mitochondrial genome of the Hen Harrier (Circus cyaneus) was sequenced. The genome is found to be 18,754 bp in length and has a base composition of A (31.7%), G (13.0%), C (31.2%), and T (24.1%). Similar to other Circus species, it contains a typically conserved structure including 13 protein-coding genes, 2 rRNA genes, 2 control region (D-loop), and 22 tRNA genes. A phylogenetic analysis between 17 species using 12 protein-coding genes proved that Accipiter gentilis is the most close to Circus cyaneus.
New polymorphic microsatellite markers for the endangered fern Ceratopteris thalictroides (Parkeriaceae)

Ceratopteris thalictroides is a semi-aquatic fern with a circumtropical distribution. Because this species is designated internationally on the IUCN Red List as requiring at least some concern, Korean populations are of great concern for the species’ long-term survival, as they are at the northern limit of the species distribution. To establish an effective conservation strategy for those populations at the genetic level, we used the Mi-Seq platform to develop three sets of 25 polymorphic microsatellite markers for C. thalictroides, which is endangered in Korea. In populations sampled from Busan and Gochang, the number of alleles ranged from 2 to 13 (average of 5.64), and plants presented an expected heterozygosity of 0.000 to 0.860. These markers will be useful for evaluating the genetic status and conserving Korean populations of C. thalictroides more effectively.
Design and evaluation of a large sequence-capture probe set and associated SNPs for diploid and haploid samples of Norway spruce (Picea abies)

Massively parallel sequencing has revolutionized the field of genetics by providing comparatively high-resolution insights into whole genomes for large number of species so far. However, whole-genome resequencing of many conspecific individuals remains cost-prohibitive for most species. This is especially true for species with very large genomes with extensive genomic redundancy, such as the genomes of coniferous trees. The genome assembly for the conifer Norway spruce (Picea abies) was the first published draft genome assembly for any gymnosperm. Our goal was to develop a dense set of genome-wide SNP markers for Norway spruce to be used for assembly improvement and population studies. From 80,000 initial probe candidates, we developed two partially-overlapping sets of sequence capture probes: one developed against 56 haploid megagametophytes, to aid assembly improvement; and the other developed against 6 diploid needle samples, to aid population studies. We focused probe development within genes, as delineated via the annotation of ~67,000 gene models accompanying P. abies assembly version 1.0. The 31,277 probes developed against megagametophytes covered 19,268 gene models (mean 1.62 probes/model). The 40,018 probes developed against diploid tissue covered 26,219 gene modules (mean 1.53 probes/model). Analysis of read coverage and variant quality around probe sites showed that initial alignment of captured reads should be done against the whole genome sequence, rather than a subset of probe-containing scaffolds, to overcome occasional capture of sequences outside of designed regions. All three probe sets, anchored to the P. abies 1.0 genome assembly and annotation, are available for download.
Synthesis and in vitro anticancer activity of 6-chloro-7-methyl-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one derivatives: molecular docking and interaction with bovine serum albumin

ABSTRACT A novel series of 6-chloro-7-methyl-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one derivatives were synthesized. Structure of the newly synthesized compounds was established by their analytical and spectroscopic data. The title compounds were evaluated for their anticancer activity against human breast cancer (T-47D) and lung cancer (NCI-H226) cell lines. Effects of compounds on the cell morphology of these cell lines were studied. Among the series of compounds tested, 6-chloro-7-methyl-2-(4-((2-(piperidin-1-yl)ethylamino)methyl) phenyl)-[1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one [MTDP4(9)] exhibited good anticancer activity against both cell lines. Further, the binding interaction of [MTDP4(9)] with bovine serum albumin has been investigated by UV, fluorescence and molecular docking studies.
Mineral nitrogen in soils of Lithuania’s agricultural land: comparison of oven-dried and field-moist samples

Mineral nitrogen (Nmin = N-NH4 + + N-NO3 −) in oven-dried and field-moist samples was investigated in 2011– 2014 in five areas of Lithuania with soils of different texture (sand, sandy loam, loam and clay) and different mineral nitrogen (Nmin) content. The samples were taken in spring (from late March to early April) and autumn (late October – early November), from the 0–30, 30–60 and 60–90 cm as well as from 0–60 cm soil layers. The aim of the research was to determine the influence of different methods of soil sample preparation on the concentrations of ammonium (N-NH4 +) and nitrate (N-NO3 −) nitrogen in oven-dried and field-moist samples and to assess the suitability of the obtained results for the development of agricultural plant fertilisation plans. According to the research results, drying of soil samples at a temperature of 35°C for 12 hours resulted in significantly higher levels of N-NH4 + compared to those of field-moist samples. The N-NO3 − concentrations in the field-moist samples, when stored at a 4°C temperature for 3 days, increased marginally compared to the oven-dried soil samples. Weak or moderate, however, statistically significant correlations were observed between N-NH4 + concentrations in the oven-dried and field-moist samples. In order to perform faster chemical analyses of soil Nmin for making agricultural plant fertilisation plans, it is necessary to carry out analyses on oven-dried soil samples, and using the linear correlation equations, to convert the results of N-NH4 + analyses into field-moisture data.
STF-62247 blocks late stages of autophagy by disrupting lysosomal physiology

STF-62247 was previously identified as a promising compound able to selectively target the loss of the tumor suppressor gene von Hippel-Lindau (VHL) in renal cell carcinomas. This present work investigates the effect of STF-62247 on the autophagic flux. Our investigations show that STF-62247 blocks late stages of autophagy through lysosomal disruption. Indeed, STF-62247 localizes at lysosomes and causes unregulated swelling of these acidic compartments in VHL-mutated cells, linking a potential role for VHL in lysosomal integrity. Knock-outs of BECN1 and ATG5 were able to rescue the viability of VHL-mutated cells in response to STF-62247 but did not rescue the lysosomal swelling. In fact, neutralizing the lysosomal pH by inhibiting the vacuolar H+-ATPase completely rescued this phenotype. Moreover, we show that STF-62247 disrupts endocytic routes and causes cathepsin D trafficking defects. This mechanistic study is the first to characterize STF-62447 as a novel lysosomotropic compound. Importantly, our study re-classifies STF-62247 as a blocker of later stages of autophagy and highlights its potential usage as a powerful new tool for endocytic and autophagy-related research.
Using revegetation to suppress invasive plants in grasslands and forests

1. Following the removal of invasive plant species, most land managers rely on natural succession to re-establish native plant communities. However, insufficient native propagule pressure combined with legacy effects of invasive plant species means that passive approaches to restoration are often inadequate to establish native communities and prevent reinvasion. 2. In this paper, we review literature evaluating the ability of active revegetation to suppress
Estimating forest uniformity in Eucalyptus spp. and Pinus taeda L. stands using field measurements and structure from motion point clouds generated from unmanned aerial vehicle (UAV) data collection

Aim of study: In this study we applied 3D point clouds generated by images obtained from an Unmanned Aerial Vehicle (UAV) to evaluate the uniformity of young forest stands.Area of study: Two commercial forest stands were selected, with two plots each. The forest species studied were Eucalyptus spp. and Pinus taeda L. and the trees had an age of 1.5 years.Material and methods: The individual trees were detected based on watershed segmentation and local maxima, using the spectral values stored in the point cloud. After the tree detection, the heights were calculated using two approaches, in the first one using the Digital Surface Model (DSM) and a Digital Terrain Model, and in the second using only the DSM. We used the UAV-derived heights to estimate an uniformity index.Main results: The trees were detected with a maximum 6% of error. However, the height was underestimated in all cases, in an average of 1 and 0.7 m for Pinus and Eucalyptus stands. We proposed to use the models built herein to estimate tree height, but the regression models did not explain the variably within the data satisfactorily. Therefore, the uniformity index calculated using the direct UAV-height values presented results close to the field inventory, reaching better results when using the second height approach (error ranging 2.8-7.8%). Research highlights: The uniformity index using the UAV-derived height from the proposed methods was close to the values obtained in field. We noted the potential for using UAV imagery in forest monitoring.
A New Otiorhynchus Germar, 1822 Subgenus Tecutinus Reitter, 1912 From Anatolia (Coleoptera, Curculionidae)

Christoph Germann (2016): A new Otiorhynchus Germar, 1822 subgenus Tecutinus Reitter, 1912 from Anatolia (Coleoptera, Curculionidae). Contributions to Natural History 33: 1-10, DOI: 10.5281/zenodo.247244
Description and phylogenetic position of Plagiolemma distortum sp. nov., a new raphid diatom (Bacillariophyceae) from French coastal waters

A new marine raphid diatom, Plagiolemma distortum Nézan, sp. nov. is described from plankton samples from the Atlantic Ocean, south Brittany (north-western France), where it was regularly observed, but never in high abundances. Cells have an unusual and complex shape under light microscopy (LM) depending on their position and orientation. The two valves are highly vaulted and narrow in width (transapical axis). Cells contain four complexly lobed plastids and a variable number of refractive granules without particular localization. In addition, capsules containing motile cells were observed. Ultrastructural details of the frustules were investigated using scanning electron microscopy (SEM). The girdle bands are simple. Each valve possesses a sigmoid raphe raised on a ridge and ending in external large openings with elaborate internal helictoglossae. Moreover, each valve displays outer slit-like foramina and inner rounded hymenes, external terminal minute holes (micropyles) arranged in a row at the poles. In addition, on each valve face, one to several short transverse median costae are observed, terminating far away from the valve edges. Morphological comparisons with closely related taxa show that P. distortum is a new species. A video clip of a moving cell is provided for better understanding of the cell shape. The formation and function of capsules are discussed as well as the species habitat. A phylogenetic study, based on nuclear small subunit (SSU) ribosomal DNA (rDNA) sequence data, which includes new sequences relative to Plagiolemma and Plagiotropis, was performed. Furthermore, some morphological details observed with SEM are included in an emended generic diagnosis of Plagiolemma.
Modeling spatial variation in winter abundance to direct conservation actions for a vulnerable migratory songbird, the Bicknell's Thrush (Catharus bicknelli)

ABSTRACT The winter range of the Bicknell's Thrush (Catharus bicknelli), a globally vulnerable Nearctic–Neotropical migratory songbird, is restricted to the Greater Antilles. Most birds occur on Hispaniola, where the species exhibits sexual habitat segregation, and where the loss of its preferred wet broadleaf habitats has been severe. Conservation of female-dominated habitats has been identified as a top priority for the species' preservation. During 2010, we conducted standardized field surveys for the Bicknell's Thrush in forests of the Dominican Republic's Cordillera Septentrional, an area of high importance for females. We combined occurrence data with environmental variables to create a model of thrush distribution and habitat selection in the region. Elevation (densities peaked at ∼600 m), aspect (northeastern slopes), the amount of forest cover within 1 km, and forest density best described thrush presence and abundance. As an example of how predictive models of abundance can inform conservation, we used the best model that contained only spatially explicit covariates to map predicted winter abundance of the Bicknell's Thrush. With the highest elevations in the study area (∼600 m) and the most intact forest cover, 2 scientific reserves contained the largest areas of high thrush abundance, but many privately held lands contained forest fragments predicted to contain thrushes. Applying criteria from our abundance model to a region-wide assessment of available private properties, we identified a 400-ha abandoned farm situated along the Cordillera Septentrional between existing protected areas that contained environmental conditions suitable for Bicknell's Thrushes. We used this information to identify, purchase, and create the Dominican Republic's first-ever private reserve, the 400-ha Reserva Privada Zorzal. Our model can be used to identify and prioritize additional lands for conservation of the Bicknell's Thrush in the region. Our approach could also be used elsewhere to make informed conservation decisions.
A rapid visuomotor response on the human upper limb is selectively influenced by implicit, but not explicit, motor learning

How do humans learn to adapt their motor actions to achieve task success? Recent behavioral and patient studies have challenged the classic notion that motor learning arises solely from the errors produced during a task, suggesting instead that explicit cognitive strategies can act in concert with the implicit, error“based, motor learning component. Here, we show that the earliest wave of directionally-tuned neuromuscular activity that occurs within ~100 ms of peripheral visual stimulus onset is selectively influenced by the implicit component of motor learning. In contrast, the voluntary neuromuscular activity associated with reach initiation, which evolves ~100 to 200 ms later is influenced by both the implicit and explicit components of motor learning. The selective influence of the implicit, but not explicit, component of motor learning on the earliest cascade of neuromuscular activity supports the notion that these components of motor learning can differentially influence descending motor pathways.
Student Tracking System in School Bus using Face Recognition and IoT

School buses provide daily transportation for majority of children. To maintain students' safety while travelling, the proposed system will use face recognition model to identify students and track various parameters such as the number of passengers, adherence to the route and schedule, location, and other data required by the school and parents. This system will then send the relevant information via SMS to the parents. A camera is installed at the bus entrance to assist in identifying the child and tracking the child's location by using a GPS module. When a child boards or exits a bus, the camera recognizes the child, and the system sends a text message to the parents with relevant details, such as bus route, time, and location.
Understanding Motivations for Gardening Using a Qualitative General Inductive Approach

Although some benefits of gardening have been documented, motivations regarding participation in gardening are often considered based on anecdote. The purpose of this study was to use qualitative analysis to explore reasons gardeners from different genders and generations participate in gardening. The questions developed for this study were intentionally exploratory and left open-ended to gather a large variety of responses. Surveys were collected from 177 individuals between the ages of 7 and 94 years old. Responses were categorized into themes identified through the literature review, the pilot study, and through exploration of the data. Responses could fit into as many categories as were mentioned by the respondents and were categorized by three independent coders. Interrater reliability was assessed using a two-way mixed, absolute agreement, average measures intraclass correlation (ICC) and determined the degree to which coders provided consistency in their ratings across participants. Themes developed through this survey included “social interaction,” “aesthetics,” “food availability/health/nutrition,” “economics,” “therapeutic,” “environmental benefits,” “nostalgia,” and “personal productivity. ” Themes of personal productivity and nostalgia are those which have not occurred in previous research. Statistically significant differences were found in comparisons among males and females with more males gardening for food/health/nutrition and for reasons regarding nostalgia. More females reported gardening for personal productivity when compared with males. No significant difference was identified in comparisons of gardeners from various age groups indicating that gardeners across generations have similar intentions and receive similar benefits.