Miracle-dz/UniFAR-FTUs huggingface dataset:
Modular and efficient pre-processing of single-cell RNA-seq

Analysis of single-cell RNA-seq data begins with pre-processing of sequencing reads to generate count matrices. We investigate algorithm choices for the challenges of pre-processing, and describe a workflow that balances efficiency and accuracy. Our workflow is based on the kallisto (https://pachterlab.github.io/kallisto/) and bustools (https://bustools.github.io/) programs, and is near-optimal in speed and memory. The workflow is modular, and we demonstrate its flexibility by showing how it can be used for RNA velocity analyses. Documentation and tutorials for using the kallisto | bus workflow are available at https://www.kallistobus. tools/.
Causal Associations Between Body Mass Index and Mental Health: A Mendelian Randomization Study

Background Body Mass Index (BMI) is negatively correlated with subjective well-being and positively correlated with depressive symptoms. Whether these associations reflect causal effects or confounding is unclear. Methods We examined causal effects between BMI and subjective well-being/depressive symptoms with bi-directional, two-sample Mendelian randomization using summary-level data from large genome-wide association studies. Genetic variants robustly related to the exposure variable acted as instrumental variable (two thresholds were used; p<5e-08 and p<1e-05). These ‘instruments’ were then associated with the outcome variable. Pleiotropy was corrected for by two sensitivity analyses. Results Substantial evidence was found for a causal effect of BMI on mental health, such that a higher BMI decreased subjective well-being and increased depressive symptoms. No consistent evidence was found for causality in the other direction. Conclusions This study provides support for a higher BMI causing poorer mental health. Further research should corroborate these findings and consider non-linear effects and sex differences.
Investigating Affective and Motor Improvements with Dance in Parkinson’s Disease

Background Research has supported the notion that dance alleviates motor symptoms for people with Parkinson’s disease (PD) illustrated by observed improvements in gait, balance, and quality of life. However, what remains unclear is whether engaging in weekly dance classes also positively influences nonmotor symptoms of PD, such as affect regulation (mood). Objectives To examine depressive symptoms of participants in a dance program for people with PD, and to extend previous findings on the topics for motor symptoms. Methods People with PD (n=23) and age-matched healthy controls (n=11) between the ages of 58-75 (M=67.91, SD=5.43) participated in a weekly Dance for PD® class. Nonmotor symptoms of PD were assessed using the Geriatric Depression Scale (GDS), administered at three time points over the 1st year of a newly-developed dance program. The Berg Balance Scale (BBS) and the Timed Up and Go (TUG) were also administered at three time points to assess motor function. Results Longitudinal mixed methods analysis showed significant improvements in GDS scores, when examining effects of the dance class over the time, with a significant main effect of time (p < 0.01) and condition: pre/post dance class (p < 0.025). Significant improvements were also observed across the motor tests of BBS (p < 0.001) and TUG (p < 0.001) measurements. Conclusion Our findings suggest dance can facilitate positive improvements in both motor and mood related symptoms of PD. These findings show important nonmotor effects of dance as an adjunct treatment for mood that may reduce the burden of this disease.
A FRET-based biosensor for measuring Gα13 activation in single cells

Förster Resonance Energy Transfer (FRET) provides a way to directly observe the activation of heterotrimeric G-proteins by G-protein coupled receptors (GPCRs). To this end, FRET based biosensors are made, employing heterotrimeric G-protein subunits tagged with fluorescent proteins. These FRET based biosensors complement existing, indirect, ways to observe GPCR activation. Here we report on the insertion of mTurquoise2 at several sites in the human Gα13 subunit. Three variants were found to be functional based on i) plasma membrane localization and ii) ability to recruit p115-RhoGEF upon activation of the LPA2 receptor. The tagged Gα13 subunits were used as FRET donor and combined with cp173Venus fused to the Gγ2 subunit as the acceptor. We constructed Gα13 biosensors by generating a single plasmid that produces Gα13-mTurquoise2, Gβ1 and cp173Venus-Gγ2. The Gα13 activation biosensors showed a rapid and robust response when used in primary human endothelial cells that were treated with thrombin, triggering endogenous protease activated receptors (PARs). This response was efficiently inhibited by the RGS domain of p115-RhoGEF and from the biosensor data we inferred that this is due to GAP activity. Finally, we demonstrated that the Gα13 sensor could be used to dissect heterotrimeric G-protein coupling efficiency in single living cells. We conclude that the Gα13 biosensor is a valuable tool for live-cell measurements that probe Gα13 activation.
Efficient RNA-mediated reprogramming of human somatic cells to naïve pluripotency facilitated by tankyrase inhibition

In contrast to conventional human pluripotent stem cells (hPSC) that are related to post-implantation embryo stages, naïve hPSC exhibit features of pre-implantation epiblast. Naïve hPSC are established by resetting conventional hPSC, or are derived from dissociated embryo inner cell masses. Here we investigate conditions for transgene-free reprogramming of human somatic cells to naïve pluripotency. We find that tankyrase inhibition promotes RNA-mediated induction of naïve pluripotency. We demonstrate application to independent human fibroblast cultures and endothelial progenitor cells. We show that induced naïve hPSC can be clonally expanded with a diploid karyotype and undergo somatic lineage differentiation following formative transition. Induced naïve hPSC lines exhibit distinctive surface marker, transcriptome, and methylome properties of naïve epiblast identity. This system for efficient, facile, and reliable induction of transgene free naïve hPSC offers a robust platform, both for delineation of human reprogramming trajectories and for evaluating the attributes of isogenic naïve versus conventional hPSC.
Finding Paths in Video Sequences

This paper investigates the ta sk of identifying frequently-used pathways from video sequences of natural outdoor scenes. Path models are adaptively learnt from the accumulation of trajectory data over many image frames. Labelled paths are used as an efficient means for compressing the trajectory data for logging purposes. In addition, the path models are used to predict the object’s location many timesteps ahead, and to aid the recognition of unusual behaviour identified as atypical object motion.
Bacterial Protein Interaction Networks: Connectivity is Ruled by Gene Conservation, Essentiality and Function

Protein-protein interaction (PPI) networks are the backbone of all processes in living cells. In this work we relate conservation, essentiality and functional repertoire of a gene to the connectivity k of the corresponding protein in the PPI networks. Focusing on a set of 42 bacterial species with reasonably separated evolutionary trajectories, we investigate three issues: i) whether the distribution of connectivity values changes between PPI subnetworks of essential and nonessential genes; ii) how gene conservation, measured both by the evolutionary retention index (ERI) and by evolutionary pressures (evaluated through the ratio Ka/Ks and ENC plots) is related to the the connectivity of the corresponding protein; iii) how PPI connectivities are modulated by evolutionary and functional relationships, as represented by the Clusters of Orthologous Proteins (COGs). We show that conservation, essentiality and functional specialization of genes control in a quite universal way the topology of the emerging bacterial PPI networks. Noteworthy, a structural transition in the network is observed such that, for connectivities k ≥ 40, bacterial PPI networks are mostly populated by genes that are conserved, essential and which, in most cases, belong to the COG cluster J, related to ribosomal functions and to the processing of genetic information.
Evaluation of allelopathic competency of Lamium amplexicaule and identification of its allelopathic active substance

The weedy annual grass Lamium amplexicaule (L.) originated from the Mediterranean region, spreads quickly, and becomes naturalized in areas it invades. It was assumed that volatile phytotoxic substances are one of the invasive characteristics of L. amplexicaule. However, no volatile compound has been found. Therefore, we re-evaluated the allelopathic potential of L. amplexicaule and investigated the phytotoxic substances with allelopathic activity. An extract of L. amplexicaule inhibited the root and shoot growth of Lepidium sativum, Lactuca sativa, Arctium lappa, Lolium multiflorum Lam. , Echinochloa crus-galli, and Vulpia myuros, which indicates that the extract has an allelopathic effect. The extract was purified using bioassay-guided chromatographic separations, and a phytotoxic substance with allelopathic activity was isolated and characterized as methyl caffeate. The compound significantly inhibited the root and shoot growth of L. sativum and L. multiflorum. The present results suggest that methyl caffeate may contribute to the allelopathic effect of the L. amplexicaule extracts and consequently, may be partly responsible for the invasive characteristics of the species.
Interactive Qualitative Analysis: A Systems Method for Qualitative Research [Book Review]

Review(s) of: Interactive Qualitative Analysis: A Systems Method for Qualitative Research, By Northcutt, Norvell; McCoy, Danny, Sage, Thousand Oaks, California, 2004, ISBN 0-7619-2834-0, 441 pages plus CD, paperback. Includes photo.
Spore concentrations of Blumeria graminis f. sp. tritici in relation to weather factors and disease development in Gansu, China

Abstract Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is an important disease in China. In this study, airborne spore concentrations were monitored using spore samplers and real-time PCR during 2013– 2015 at three locations in Gangu, Gansu province of China. The effects of meteorological variables on spore concentration were analyzed and models were developed for forecasting dynamics of airborne conidia and disease progress. The temperature, solar radiation and rainfall were positively correlated to spore concentrations and disease development. Although there was a negative correlation between relative humidity and spore concentration, relative humidity was positively related with disease development. Stepwise regression models were obtained for predicting the dynamics of airborne conidia based on the positive degree days and accumulation of rainfall (R2 = 0.31, P < 0.01), the positive degree days (R2 = 0.16, P = 0.04) and mean temperatures (R2 = 0.24, P = 0.01) at three locations, respectively. Disease forecasting models were developed based on various meteorological variables and spore concentration, the most important variables being temperature and spore concentration. This knowledge can improve the disease forecasting of wheat powdery mildew in Gangu and help develop better disease control strategies.
Study of natural ventilation in a Gothic multi-tunnel greenhouse designed to produce rose (Rosa spp.) in the high-Andean tropic

In tropical regions the production of ornamentals is developed exclusively in naturally ventilated plastic greenhouses, which sometimes leads to inappropriate microclimates with high temperatures and humidity that limit the productive development of plants. The aim of this work was to study air flows, temperature distribution and relative humidity inside an alternative greenhouse designed to produce rose (Rosa spp.). Three configurations of ventilation, side ventilation (SV), roof ventilation (RC) and combined roof and side ventilation (RSV) were analyzed. The methodological development was based on the use of a previously validated CFD-2D numerical simulation model, which showed an adequate fit between the measured and simulated data, obtaining MAE and RMSE values for temperature and relative humidity of 0.44 and 0.47 °C, 3.99% and 4.04% respectively. The results obtained for the predominant climatic conditions of the study region showed that the highest ventilation rates were obtained for RSV, with values of 0.044 and 0.182 m3 m-2s-1, this ventilation efficiency propitiated the generation of a homogeneous microclimate, with temperature and relative humidity values adequate to produce rose (Rosa spp).
Effectiveness of hermetic maize grain storage technology in limiting aflatoxin exposure in women and children from smallholder farming areas

The longitudinal study assessed the effectiveness of hermetic storage technology in limiting aflatoxin exposure among women aged 15-45 years and children under five years of age from households in selected smallholder farming areas of Zimbabwe. Exposure levels were determined by measuring aflatoxin M1 (AFM1) in urine samples from women and children every three months during the 2015/2016 storage season for nine months. After extraction and immunoaffinity column clean up, AFM1 was determined by high performance liquid chromatography. Generally, the proportion of AFM1 positive urine samples from women increased throughout the grain storage season from 5.4% (n=23) (geometric mean (GM) 1.62 μg/l) at harvest to 75% (n=315) (GM 48.35 μg/l) nine months later (range <limit of quantification (LOQ)-217.29 μg/l). In urine samples from children, AFM1 positive samples increased from 2.2% (n=4) (GM 0.78 μg/l) at harvest to 72.5% (n=98) (GM 22.81 μg/l) nine months later (range <LOQ- 135.00 μg/l). Urinary AFM1 was significantly higher in samples from participants using conventional storage (GM 62.28 μg/l; range <LOQ-217.29 μg/l) compared with samples from participants using hermetic technology (GM 31.95 μg/l; range <LOQ-157.71 μg/l. There was no significant difference in AFM1 concentrations in urine samples from participants consuming grain from metal silos and hermetic bags (P>0.05) hence the two technologies are equally effective in limiting exposure to aflatoxins in humans. The study concluded that aflatoxin exposure levels among women and children from small-holder farming areas increase throughout the postharvest season and the use of hermetic storage technology resulted in up to 33.2% decrease in frequency of detection and 48.7% decrease in levels of AFM1 compared to conventional storage technologies. Thus hermetic grain storage can be an effective technology recommended for limiting aflatoxin exposure in smallholder farming populations.
Discovery of active secondary metabolites from Paenibacillus odorifer, a lichen-associated bacterium

Les bacteries qui sont des sources prolifiques d'antibiotiques et des fournisseurs importants d’agents pharmaceutiques peuvent produire une grande variete de metabolites. Ainsi, la decouverte de metabolites issus bacteries est un nouveau challenge pour les chimistes. Parmi ces sources, les lichens sont admis comme niches interessantes de nouvelles bacteries et de nouveaux composes bacteriens. Par consequent, les communautes de micro-organismes associees aux lichens sont devenues des sources prometteuses pour la production de composes naturels actifs. Dans cette these, nous avons concentre notre travail sur l'isolement des bacteries de Rhizocarpon geogaphicum, l'un des lichens crustaces les plus populaires vivant sur la roche. Parmi les souches isolees, Paenibacillus odorifer a ete selectionnee pour poursuivre les travaux visant a produire des composes actifs. Apres des etapes d’optimisation de culture, l’etude des extraits issus des cultures de P. odorifer soit par le bioreacteur soit en Erlenmeyer a permis l’isolement des metabolites : un polysaccharide antioxydant, deux derives tert-butylphenoliques cytotoxiques issus de la bioaccumulation et de la biotransformation de precurseurs, d'un nouvel alcaloide cytotoxique, de deux diols, de deux derives de type furfural et quelques autres composes connus. Des hypotheses de biosynthese ont pu etre proposes pour certains composes. La diversite des metabolites isoles de P. odorifer indique que cette espece possede un grand potentiel de production des composes actifs et est une bacterie utilisatrice de substrats tert-butyl phenoliques.
Distinct Contribution of DNA Methylation and Histone Acetylation to the Genomic Occupancy of Transcription Factors

Epigenetic modifications on chromatin play important roles in regulating gene expression. While chromatin states are often governed by multi-layered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor binding but also to recruit methyl-CpG binding proteins that affect chromatin structure through the activity of histone deacetylase complexes (HDACs). Both of these mechanisms can potentially affect gene expression, but the importance of each, and whether these activities are integrated to achieve appropriate gene regulation, remains largely unknown. To address this important question, we measured gene expression, chromatin accessibility, and transcription factor occupancy in wild-type or DNA methylation-deficient mouse embryonic stem cells following HDAC inhibition. Interestingly, we observe widespread increases in chromatin accessibility at repeat elements when HDACs are inhibited, and this is magnified when cells also lack DNA methylation. A subset of these elements have elevated binding of the YY1 and GABPA transcription factors and increased expression. The pronounced additive effect of HDAC inhibition in DNA methylation deficient cells demonstrate that DNA methylation and histone deacetylation act largely independently to suppress transcription factor binding and gene expression.
Co-administration and Evaluation of Immune Responses of Three DNA Vaccines Encoding Immunogenic Antigens from Mycobacterium tuberculosis

Background: Ineﬀectiveness of BCG vaccine in controlling tuberculosis (TB) and co-infection of TB and HIV have turned TB into a serious global threat. Therefore, the development of an alternative vaccine to BCG and/or antimycobacterial drugs is an urgent need. Here,threechimericDNAconstructsconsistingof Mtb32C-HBHA,Ag85a-Tb10.4,andAg85a-cfp10madeinourpreviousstudies were co-administered to BALB/c mice to evaluate their immune responses using a prime-boost regimen in which the animals were ﬁrst immunized with BCG and then administered with DNA vaccines. Methods: In order to evaluate the immunogenicity of three DNA constructs, the levels of several immunomodulatory cytokines were measured in vaccinated mice. Thirty female BALB/c mice were divided into the following groups (n = 10): control (receiving pcDNA 3.1+ intramuscularly), vaccine (receiving recombinant vectors intramuscularly), and vaccine-BCG (receiving BCG subcutaneously followed by recombinant vectors intramuscularly). Results: The levels of IL-4, IL-12, TGF- β , IFN- γ , and IL-10 were higher in the immunized groups than in the control group (P < 0.05). Besides, the levels of IL-12 and IFN- γ were much higher in the BCG-vaccine group than in the vaccine alone group. In the case of IFN- γ , a signiﬁcant diﬀerence was observed between the vaccine and BCG-vaccine groups at P < 0.001 while in the case of IL-12, the diﬀerence was signiﬁcant at P < 0.05. However, in the case of IL-10, IL-4, and TGF- β , the diﬀerences between the vaccine and BCG-vaccine groups were not signiﬁcant (P > 0.05). Conclusions: Our results proved that using a chimeric DNA vaccine as a booster in the prime-boost strategy could signiﬁcantly enhancetheeﬃcacyof BCG.Thisstudysuggeststhattheuseof suchDNAvaccinesencodingmycobacterialimmunogenicantigens as boosters enhances the eﬃcacy of BCG.
Prevalence of endoparasites infection in fatteners depending on maintenance system and season

The study was conducted on four farms localized in Wielkopolska Province, Poland, leading an intense pigs farming in closed cycle (all production groups were housed on the farm). The fatteners were maintained in conventional indoor herds for the whole fattening period, and the farms did not lead organic farming. McMaster method was used for eggs isolation from feces, while flotation was applied in cysts diagnostics from feces. The infection level of fatteners (n=320), kept on shallow and deep litter in the summer (July/August) and winter (January/February) period in 2013, was established. The occurrence of three varieties of parasites was observed: Oesophagostomum spp. , Ascaris suum and one protozoan – Balantidium coli. The most abundant parasite was Oesophagostomum spp. The study also demonstrated an increased prevalence on the farms maintaining the animals on shallow litter as compared to deep one. Higher values of selected parasitological indices were noted in the summer (farm C shallow litter 62.5 %, 764 EPG; farm B shallow litter 50 %, 267.5 EPG) as compared to the winter period (farm C 35%, 194.4 EPG, farm B 40%, 215.6 EPG). Ascaris suum was the next nematode of the highest extensiveness, i.e. on the level of 20 %. The study also demonstrated the presence of Ascaris suum exclusively in two farms – B and C, on shallow litter. The rarest was protozoan Balantidium coli. It was isolated and identified only on one farm, during the summer on a shallow litter (12.5 % once 39 mean number of cyst per sample).
Image to interpretation

﻿ The ink and stylus tablets discovered at the Roman Fort of Vindolanda have provided a unique resource for scholars of ancient history. However, the stylus tablets in particular have proved extremely difficult to read. The aim of this thesis is to explore the extent to which techniques from Artificial Intelligence can be used to develop a system that could aid historians in reading the stylus texts. This system would utilise image processing techniques that have been developed in Engineering Science to analyse the stylus tablets, whilst incorporating knowledge elicited from experts working on the texts, to propagate possible suggestions of the text contained within the tablets. This thesis reports on what appears to be the first system developed to aid experts in the process of reading an ancient document. There has been little previous research carried out to see how papyrologists actually carry out their task. This thesis studies closely how experts working with primary sources, such as the Vindolanda Texts, operate. Using Knowledge Elicitation Techniques, a model is proposed for how they read a text. Information regarding the letter forms and language used at Vindolanda is collated, A corpus of annotated images is built up, to provide a data set regarding the letter forms used in the ink and stylus texts. In order to relate this information to the work done on image processing, a stochastic Minimum Description Length (MDL) architecture is adopted, and adapted, to form the basis of a system that can propagate interpretations of the Vindolanda texts. In doing so a system is constructed that can read in image data and output textual interpretations of the writing that appears on the documents. It is demonstrated that knowledge elicitation techniques can be used to capture and mobilise expert information. The process of reading ancient, and ambiguous texts, is made explicit. It is also shown that MDL can be used as a basis to build large systems that reason about complex information effectively. This research presents the first stages towards developing a cognitive visual system that can propagate realistic interpretations from image data, and so aid the papyrologists in their task.