Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying Gene Expression Directly from FACS Using Hydrolysis (TaqMan) Probes on Flash-frozen Cells

[Abstract] The TaqMan Gene Expression Cells-to-CtTM Kit enables reverse transcription directly from cell lysates without the need for isolating RNA. The recommended input range for the lysis reaction is between 10-105 cells, though the upper limit may vary somewhat according to cell type. This protocol is partially adapted from the manufacturer’s protocol (TaqMan Gene Expression Cells-to-CtTM Kit User Guide) for gene expression for use with frozen cell pellets to allow for sample transfer among laboratories and involves experimentally confirmed dilution prior to lysis. Within this constraint, the recommended range for sample cell number for frozen cells is between 40-2 x 105 cells. This protocol is also designed for use with a ‘homebrew’ qPCR master mix as the volume of TaqMan Genotyping Master Mix included in the kit may be insufficient for analysis of large numbers of samples and/or assays (Smythe and Copren, 2008). Cell count is provided by fluorescence-activated cell sorting (FACS) and is a unique aspect of this protocol.
Innovative technology-based interventions in aphasia rehabilitation: a systematic review

ABSTRACT Background In the last decades technologies have started to be integrated into language rehabilitation, but more recently many innovations have been included in the health field, especially the use of virtual reality (VR) and mobile devices. Aim The present review aims to investigate the use and efficacy of innovative technology-based interventions for language rehabilitation in post-stroke patients. We consider innovative technologies as those implementing either virtual reality or mobile software applications. Methods For conducting this systematic review, we conformed to the PRISMA guidelines. The articles were selected by computer-based searches in three high-profile databases: PubMed, PsycINFO, and Web of Science. 13 studies met the inclusion criteria. Studies were also rated along the efficacy-effectiveness spectrum (RITES). Main Contribution Most of studies used a tablet to deliver the therapy, and only a few of them implemented VR-based treatments. Despite the paucity of literature, the results were encouraging, and showed efficacy and effectiveness of rehabilitation programs based on innovative technologies. Moreover, patients appeared compliant to treatments. Conclusions In future studies, more robust research designs should be implemented with larger sample sizes, more homogenous samples, and comparisons with “treatment-as-usual” control conditions. Finally, we suggest an innovative use of VR for language rehabilitation within an embodied cognition approach.
Ecological network assembly: how the regional metaweb influences local food webs

Local food webs result from a sequence of colonisations and extinctions by species from the regional pool or metaweb, i.e., the assembly process. Assembly is theorised to be a selective process: whether or not certain species or network structures can persist is partly determined by local processes including habitat filtering and dynamical constraints. Consequently, local food web structure should reflect these processes. The goal of this study was to test evidence for these selective processes by comparing the structural properties of real food webs to the expected distribution given the metaweb. We were particularly interested in ecological dynamics; if the network properties commonly associated with dynamical stability are indeed the result of stability constraints, then they should deviate from expectation in the direction predicted by theory. To create a null expectation, we used the novel approach of randomly assembling model webs by drawing species and interactions from the empirical metaweb. The assembly model permitted colonisation and extinction, and required a consumer species to have at least one prey, but had no habitat type nor population dynamical constraints. Three data sets were used: (1) the marine Antarctic metaweb, with 2 local food-webs; (2) the 50 lakes of the Adirondacks; and (3) the arthropod community from Florida Keys’ classic defaunation experiment. Contrary to our expectations, we found that there were almost no differences between empirical webs and those resulting from the null assembly model. Few empirical food webs showed significant differences with network properties, motif representations and topological roles. Network properties associated with stability did not deviate from expectation in the direction predicted by theory. Our results suggest that — for the commonly used metrics we considered — local food web structure is not strongly influenced by dynamical nor habitat restrictions. Instead, the structure is inherited from the metaweb. This suggests that the network properties typically attributed as causes or consequences of ecological stability are instead a by-product of the assembly process (i.e., spandrels), and may potentially be too coarse to detect the true signal of dynamical constraint.
Fast algorithms for model-based imaging through turbulence

Digital holography (DH) systems have the potential to perform single-shot imaging through deep turbulence by incorporating emerging algorithms, such as model-based iterative reconstruction (MBIR), that jointly estimate both the phase-errors and speckle-free image. However, the high computational cost of MBIR poses a challenge for use in practical applications. In this paper, we propose a method that makes MBIR feasible for real-time DH systems. Our method uses surrogate optimization techniques to simplify and speed up the reflectance and phase-error updates in MBIR. Further, our method accelerates computation of the surrogate-updates by leveraging cache-prefetching and SIMD vector processing units on each CPU core. We analyze the convergence and real CPU time of our method using simulated data sets, and demonstrate its dramatic speedup over the original MBIR approach.
Chinese women who use force against husbands in Hong Kong: their help seeking experience and implication on service development

ABSTRACT Many women who use force (WuF) against their husbands are driven by their emotions towards husbands’ physical abuse, coercive control or neglect. Despite the ongoing development and expansion of support for domestic violence in Hong Kong, the number of WuFs against their husbands has been increasing, indicating a gap between service availability and women’s participation in these services. This study aims to further our understanding of WuF’s motivating factors in seeking help from an anti-violence programme service by interviewing 20 participants of the programme. Our observation would enhance our understanding of this target group and provide us more insight in pinpointing the service contents and the corresponding promotion elements that will tally with WuF’s needs for emotional support and education about women using force and mutual violence in an intimate relationship.
Dunlin subspecies exhibit regional segregation and high site fidelity along the East Asian–Australasian Flyway

ABSTRACT The degree to which individuals migrate among particular breeding, migration, and wintering sites can have important implications for prioritizing conservation efforts. Four subspecies of Dunlin (Calidris alpina) migrate along the East Asian–Australasian Flyway. Each subspecies has a distinct and well-defined breeding range, but their migration and winter ranges are poorly defined or unknown. We assessed the migratory connectivity of 3 of these subspecies by evaluating a dataset that encompasses 57 yr (1960–2017), and comprises more than 28,000 Dunlin banding records and 818 observations (71 recaptures and 747 band resightings). We present some of the first evidence that subspecific segregation likely occurs, with arcticola Dunlin wintering in areas of Japan, and other arcticola, actites, and sakhalina Dunlin wintering in areas of the Yellow and China seas. Observations indicate that whether an arcticola Dunlin winters in Japan or the Yellow and China seas is independent of their breeding location, sex, or age. Furthermore, observations indicate that ≥83% of arcticola Dunlin exhibit interannual site fidelity to specific wintering sites. This suggests that the degradation of specific wetland areas may negatively affect particular individuals of a particular subspecies (or combination of subspecies), and, if widespread, could result in population declines. Given the possible biases inherent in analyzing band recovery data, we recommend additional flyway-wide collaboration and the use of lightweight tracking devices and morphological and genetic assignment techniques to better quantify subspecies' migratory movements and nonbreeding distributions. This information, when combined, will enable effective conservation efforts for this species across the East Asian–Australasian Flyway. LAY SUMMARY The East Asian–Australasian Flyway has more threatened and near-threatened migratory waterbird species than any other flyway in the world; however, developing flyway conservation plans has been challenging, in part due to limited information regarding population-specific migration patterns. Four subspecies of Dunlin migrate and winter along the East Asian–Australasian Flyway. Each has a well-defined breeding range; their migration and winter ranges are poorly defined or unknown. We assessed the migratory connectivity of 3 subspecies using data from 57 yr (1960–2017), which comprises more than 28,000 Dunlin banding records, 71 recaptures, and 747 band resightings. Subspecific segregation likely occurs, with arcticola Dunlin wintering in Japan, and other arcticola, actites, and sakhalina Dunlin wintering in the Yellow and China seas. It is likely that ≥83% of arcticola Dunlin exhibit interannual site fidelity to specific wintering sites. Our findings suggest that degradation of specific wetland areas may negatively affect particular individuals of a particular subspecies (or combination of subspecies) and could result in population declines.
Modeling and simulation of a 3-ф induction motor based on two types of WFA

This paper has been proposed to simulate the transient model of 3-Ф cage rotor induction motor based on winding function approach (WFA). According to this method the motor is assumed to be consist of an electrical circuits on both stator and rotor. The magneto motive forces (MMF) that have been generated by these circuits play a role for coupling them together. Then mutual and self-inductances will be easily computed using WFA. Two types of WFA have been used to build and simulate the model of the induction motor. In the one part type, it’s assumed that the coupling MMF between stator and rotor have a non-sinusoidal shapes according to the actual windings distribution over the motor slots. While in second part type the generated MMF in are assumed to have sinusoidal waveform. The suggested models may be used to simulate the dynamic as well as steady state performance of a faulty and non-faulty motor. A simulation of the suggested models that consists of m-rotor bars and n-stator phases multiple coupled circuit-based has been performed using matlab m.file and the results of the motor current have been proved in its nonlinear way by using WFA.
Deep reinforcement learning based path tracking controller for autonomous vehicle

Path tracking is an essential task for autonomous vehicles (AV), for which controllers are designed to issue commands so that the AV will follow the planned path properly to ensure operational safety, comfort, and efficiency. While solving the time-varying nonlinear vehicle dynamic problem is still challenging today, deep neural network (NN) methods, with their capability to deal with nonlinear systems, provide an alternative approach to tackle the difficulties. This study explores the potential of using deep reinforcement learning (DRL) for vehicle control and applies it to the path tracking task. In this study, proximal policy optimization (PPO) is selected as the DRL algorithm and is combined with the conventional pure pursuit (PP) method to structure the vehicle controller architecture. The PP method is used to generate a baseline steering control command, and the PPO is used to derive a correction command to mitigate the inaccuracy associated with the baseline from PP. The blend of the two controllers makes the overall operation more robust and adaptive and attains the optimality to improve tracking performance. In this paper, the structure, settings and training process of the PPO are described. Simulation experiments are carried out based on the proposed methodology, and the results show that the path tracking capability in a low-speed driving condition is significantly enhanced.
Late Silurian to early Devonian development of the Chingiz accretion arc, West Junggar: insights into accretion arc evolution in the Central Asia Orogenic Belt

ABSTRACT Early Palaeozoic evolution of the Kazakhstan orocline in the Central Asian Orogenic Belt (CAOB) is key to reconstructing the Palaeozoic tectonic framework in Central Asia. This study presents field mapping, geochemistry, and geochronological data from the Wulasitai area of northern West Junggar to constrain the subduction polarity and major tectonic events in the Chingiz arc of the Kazakhstan orocline during the Early Palaeozoic. The mapping area outcrops imbricated coherent turbidite slices and mélanges that consist of chert, limestone, silt, sandstone, and conglomerate blocks in mudstone matrix, representing an OPS (Ocean Plate Stratigraphy) mélange in an accretionary complex. Existing fossil ages from these blocks range from the Ordovician to Silurian, while our new detrital zircon U-Pb samples from the turbiditic matrix yield maximum depositional ages (MDTs) from 428 ± 2 Ma to 450 ± 1 Ma. Detrital zircon ages of ~510 to 430 Ma in the mélange suggest the Chingiz arc to the south of the study area as a major sediment source, providing an indirect constraint on the polarity of subduction. We suggest that the northern part of the Chingiz arc may be underlain by southward subduction, with the accretionary complex located on the Wulasitai area of the northern West Junggar. The Wulasitai mélange is overlain depostionally by volcanic rocks carrying depleted HFSE and enriched LILE, LREE. The andesite and tuff are dated to 415 ± 5 Ma, 414 ± 3 Ma, and 402 ± 6 Ma, which we interpret as reflecting the development of the volcanic arc onto the previous subduction complex. This model implies the generation of the arc (accretion arc) as the slab rolling back and trench retreating, which may play an important role in the evolutionary history of CAOB.
Identification and design of vinyl sulfone inhibitors against Cryptopain-1 – a cysteine protease from cryptosporidiosis-causing Cryptosporidium parvum

Cryptosporidiosis, a disease marked by diarrhea in adults and stunted growth in children, is associated with the unicellular protozoan pathogen Cryptosporidium; often the species parvum. Cryptopain-1, a cysteine protease characterized in the genome of Cryptosporidium parvum, had been earlier shown to be inhibited by a vinyl sulfone compound called K11777 (or K-777). Cysteine proteases have long been established as valid drug targets, which can be covalently and selectively inhibited by vinyl sulfones. This computational study was initiated to identify purchasable vinyl sulfone compounds, which could possibly inhibit cryptopain-1 with higher efficacy than K11777. Docking simulations screened a number of such possibly better inhibitors. The work was furthered to probe the enzymatic pocket of cryptopain-1, through in-silico mutations, to derive a map of receptor-ligand interactions in the docked complexes. The idea was to provide crucial clues to aid the design of inhibitors, which would be able to bind the protease well by making favorable interactions with important residues of the enzyme. The analyses dictated placement of ligands towards the front of the enzymatic cleft, and disfavored interactions deep within. The S1’ and S2 subsites of the enzyme preferred to remain occupied by polar ligand subgroups. Reasonably distanced ring systems and polar backbones of ligands were desired across the cleft. Large as well as inflexible subgroups were not tolerated. Double ringed systems such as substituted napthalene, especially in S1, were exceptions though. The S2 subsite, which is typically a specificity determinant in papain (C1) family cysteine proteases such as cathepsin L-like cryptopain-1, can possibly accommodate polar and hydrophobic ligand subgroups alike.
Combining molecular gut content analysis and functional response models shows how body size affects prey choice in soil predators

Predator-prey interactions are a core concept of animal ecology and functional response models provide a powerful tool to predict the strength of trophic links and assess motives for prey choice. However, due to their reductionist set-up, these models may not display field conditions, possibly leading to skewed results. We tested the validity of functional response models for multiple prey by comparing them with empirical data from DNA-based molecular gut content analysis of two abundant and widespread macrofauna soil predators, lithobiid and geophilomorph centipedes. We collected soil and litter dwelling centipedes, screened their gut contents for DNA of nine abundant decomposer and intraguild prey using specific primers and tested for different prey and predator traits explaining prey choice. In order to calculate the functional response of same predators, we used natural prey abundances and functional response parameters from published experiments and compared both approaches. Molecular gut content results showed that prey choice of centipedes is driven by predator body size and prey identity. Results of functional response models significantly correlated with results from molecular gut content analysis for the majority of prey species. Overall, the results suggest that functional response models are a powerful tool to predict trophic interactions in soil, however, species-specific traits have to be taken into account to improve predictions.
The Information Communication Technology, Social Media, International Migration and Migrants’ Relations with Kin in Nigeria

Studies abound on international migration and remittances across the world and studies are particularly not lacking on the subject in Africa. There are however few studies on the moderating roles of information communication technology (ICT) and social media in the relationships among international migration, remittances and relationships in Sub-Saharan Africa. This article examines the dimension of ICT and social media in migration studies. This is an aspect that has often been ignored and overlooked even though ICT and social media have great contributions in the international migration process particularly as migrants and relatives in sending and receiving countries both have the primary experience. Research objectives include: reasons for emigration; information technology/social media used by migrants and their kin as they relate across spaces; and how ICT affects relationships of kin and international migrants. Secondary data were gathered through journals, books, documents and reliable Internet sources. Primary data were gathered in Ibadan, Nigeria in 2018 through 30 in-depth interviews analysed through content analysis. Findings reveal the nature of ICT used by international migrants and their kin and purpose of utilization and the effects of ICT on international migration, remittances and kinship networks. The article presents detailed data, narratives, interpretations and implications of relationships among international migration, ICT/social media and kinship networks. This article argues that ICT/social media is central to international migration decision-making, access of migrants and kin to social forces and factors motivating international migration, and it is very important to how migrants and kin maintain and/or weaken relationships and access to remittances and utilization.
A New Method to Digitize DNA Sequence

The global description uses composition, transition and distribution to describe an amino acid sequence and has been widely adopted in various fields. Here we integrate it with properties of nucleic acid and form a new method to digitize DNA sequence. Through this method we can use a 39-dimession vector to represent a DNA sequence. We use the exon-1 of β-Globin genes of eight species to verify this method and compare with other methods. A similar result with other method proves that this method is persuading. This method provides a new strategy to digitize DNA sequence and generates DNA sequence descriptor vector. It is different from other methods and this method only produces a 39-dimession vector and not depends on the length of DNA sequence.
A demographic projection model to support conservation decision making for an endangered snake with limited monitoring data

Conservation planning for rare and threatened species is often made more difficult by a lack of research and monitoring data. In such cases, managers may rely on qualitative assessments of species risk that lack explicit acknowledgement of uncertainty. Snakes are a group of conservation concern that are also notoriously difficult to monitor. Here, we demonstrate a quantitative population projection for a data‐deficient species, the Puerto Rican boa (Chilabothrus inornatus) using expert knowledge and published information about species life history and threats to persistence. Using this model, we simulated population dynamics over 30 years under four scenarios of future urbanization and found that there was an increased probability of population decline as urbanization rates increased. We conduct a sensitivity analysis to evaluate the sensitivity of outcomes to model inputs, a practice that may also be useful in recovery planning. The sensitivity analyses also provide insight into how the future trajectories would change if the elicited demographic rates are incorrect. Even when data are sparse, quantitative methods can often be used to produce rigorous and reproducible estimates of future status with quantifiable uncertainty.
Asymmetric MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin

The Escherichia coli SMC complex, MukBEF, acts in chromosome segregation. MukBEF shares the distinctive architecture of other SMC complexes, with one prominent difference; unlike other kleisins, MukF forms dimers through its N-terminal domain. We show that a 4-helix bundle adjacent to the MukF dimerization domain interacts functionally with the MukB coiled-coiled ‘neck’ adjacent to the ATPase head, forming an asymmetric tripartite complex, as in other SMC complexes. Since MukF dimerization is preserved during this interaction, MukF directs the formation of dimer of dimers MukBEF complexes, observed previously in vivo. The MukF N- and C-terminal domains stimulate ATPase independently and additively, consistent with them each targeting only one of the two MukB ATPase active sites in the asymmetric complex. We demonstrate that MukF interaction with the MukB neck turns over during cycles of ATP binding and hydrolysis in vivo and that impairment of this interaction leads to MukBEF release from chromosomes.