Miracle-dz/UniFAR-FTUs huggingface dataset:
A practical identifier design of road variations for anti-lock brake system

ABSTRACT Emergency brake technologies have always been a major interest of vehicle active safety-related studies. On homogeneous surfaces, traditional anti-lock brake system (ABS) can achieve efficient braking performance and maintain the handling capability as well. However, when road conditions are time variant during the braking process, or different at the bilateral wheels, braking stability performance is likely to be degraded. To address this problem and enhance ABS performances, a practical identifier of road variations is developed in this study. The proposed identifier adopts a statechart-based approach and is hierarchically constructed with a wheel layer and a full vehicle layer identifier. Based on the identification results, modifications are made to a four-phase wheel-behaviour-based ABS controller to enhance its performance. The feasibility and effectiveness of the proposed identifier in collaborating with the modified ABS controller are examined via simulations and further validated by track tests under various practical braking scenarios.
An undergraduate genome research course using “big data”

The ability to analyze large data sets (“Big Data”) is an increasingly important skill in modern science. In Biochemistry, the increased volume and velocity of data is particularly evident in the rapid expansion of biological databases. We present a modular bioinformatics course to survey the analysis of genomic data for advanced undergraduates. Research activities include genome scanning for endogenous retroviruses, annotating genomic sequences and a brief exploration of programming in R. A summative poster session was used to disseminate their work. This course is amenable to remote or online instruction. Supplemental materials provided include a schedule and outline. This article reports a session from the virtual international 2021 IUBMB/ASBMB workshop, “Teaching Science on Big Data. ”
Acute inhibition of transient receptor potential vanilloid‐type 4 cation channel halts cytoskeletal dynamism in microglia

Microglia, the resident macrophages of the central nervous system, are highly motile cells that support brain development, provision neuronal signaling, and protect brain cells against damage. Proper microglial functioning requires constant cell movement and morphological changes. Interestingly, the transient receptor potential vanilloid 4 (TRPV4) channel, a calcium‐permeable channel, is involved in hypoosmotic morphological changes of retinal microglia and regulates temperature‐dependent movement of microglial cells both in vitro and in vivo. Despite the broad functions of TRPV4 and the recent findings stating a role for TRPV4 in microglial movement, little is known about how TRPV4 modulates cytoskeletal remodeling to promote changes of microglial motility. Here we show that acute inhibition of TRPV4, but not its constitutive absence in the Trpv4 KO cells, affects the morphology and motility of microglia in vitro. Using high‐end confocal imaging techniques, we show a decrease in actin‐rich filopodia and tubulin dynamics upon acute inhibition of TRPV4 in vitro. Furthermore, using acute brain slices we demonstrate that Trpv4 knockout microglia display lower ramification complexity, slower process extension speed and consequently smaller surveyed area. We conclude that TRPV4 inhibition triggers a shift in cytoskeleton remodeling of microglia influencing their migration and morphology.
Adaptive sequencing using nanopores and deep learning of mitochondrial DNA

Nanopore sequencing is an emerging technology that reads DNA by utilizing a unique method of detecting nucleic acid sequences and identifies the various chemical modifications they carry. Deep learning has increased in popularity as a useful technique to solve many complex computational tasks. 'Adaptive sequencing' is an implementation of selective sequencing, intended for use on the nanopore sequencing platform. In this study, we demonstrated an alternative method of software-based selective sequencing that is performed in real time by combining nanopore sequencing and deep learning. Our results showed the feasibility of using deep learning for classifying signals from only the first 200 nucleotides in a raw nanopore sequencing signal format. This was further demonstrated by comparing the accuracy of our deep learning classification model across data from several human cell lines and other eukaryotic organisms. We used custom deep learning models and a script that utilizes a 'Read Until' framework to target mitochondrial molecules in real time from a human cell line sample. This achieved a significant separation and enrichment ability of 2.3-fold. In a series of very short sequencing experiments (10, 30 and 120 min), we identified genomic and mitochondrial reads with accuracy above 90%, although mitochondrial DNA comprised only 0.1% of the total input material. The uniqueness of our method is the ability to distinguish two groups of DNA even without a labeled reference. This contrasts with studies that required a well-defined reference, whether of a DNA sequence or of another type of representation. Additionally, our method showed higher correlation to the theoretically possible enrichment factor, compared with other published methods. We believe that our results will lay the foundation for rapid and selective sequencing using nanopore technology and will pave the approach for clinical applications that use nanopore sequencing data.
A survey study of family members' encounters with healthcare services within the care of older people, psychiatric care, palliative care and diabetes care

Abstract The aim of this study was to describe and compare family members' experiences of approach in encounters with healthcare professionals and possible feelings of alienation in the professional care within four care contexts: the care of older people, psychiatric care, palliative care and diabetes care. The design was an explorative cross‐sectional survey study. Data were collected in Sweden using the Family Involvement and Alienation Questionnaire‐Revised (FIAQ‐R). It measures family members' experiences of the healthcare professionals' approach and the family members' feeling of alienation from the provision of professional care. A total of 1047 questionnaires were distributed to family members using convenient sampling method, of which 294 were included. Data were analysed using rank‐based, non‐parametric statistical methods. The results indicated that most respondents experienced a positive actual approach from the healthcare professionals. Many participants rated the importance of approach at a higher level than their actual experience. Participants in the context of diabetes care reported a more negative actual approach from the healthcare professionals than did participants in the other contexts and considered the healthcare professionals' approach towards them as being less important. The results for the entire group indicated that the participants felt a low level of alienation from the professional care. Participants in the context of the care of older people reported significantly lower level of feeling of being alienated than did participants in the contexts of psychiatric care and diabetes care. The differences between participants in diabetes care and other care contexts can possibly be explained by a more fully implemented self‐care approach among the patients in diabetes care than in the other care contexts. Even though the results are quite positive, it is still important that nurses consider a family‐centred approach to better adapt to the needs of both the family members and the patients.
Neurodegenerative phagocytes mediate synaptic stripping in Neuro-HIV

Abstract Glial cell activation is a hallmark of several neurodegenerative and neuroinflammatory diseases. During HIV infection, neuroinflammation is associated with cognitive impairment, even during sustained long-term suppressive antiretroviral therapy. However, the cellular subsets contributing to neuronal damage in the CNS during HIV infection remain unclear. Using post-mortem brain samples from eight HIV patients and eight non-neurological disease controls, we identify a subset of CNS phagocytes highly enriched in LGALS3, CTSB, GPNMB and HLA-DR, a signature identified in the context of ageing and neurodegeneration. In HIV patients, the presence of this phagocyte phenotype was associated with synaptic stripping, suggesting an involvement in the pathogenesis of HIV-associated neurocognitive disorder. Taken together, our findings elucidate some of the molecular signatures adopted by CNS phagocytes in HIV-positive patients and contribute to the understanding of how HIV might pave the way to other forms of cognitive decline in ageing HIV patient populations.
Elevated inbreeding in Heliconia tortuosa is determined by tropical forest stand age, isolation and loss of hummingbird functional diversity

Forest conversion and habitat loss are major threats to biological diversity. Forest regeneration can mitigate the negative effects of old‐growth forest loss on species diversity, but less is known about the extent to which forest loss reduces genetic diversity in remnant populations and whether secondary forests play a role in the maintenance of genetic diversity. We quantified genetic diversity in a tropical hummingbird‐pollinated understorey herb, Heliconia tortuosa, across a landscape mosaic of primary and secondary forest regrowth. Using microsatellite genotypes from >850 adult and juvenile plants within 33 forest patches and extensive bird surveys, we examined the effect of contemporary and historical landscape features including forest age (primary vs. secondary forest), stand isolation and pollinator assemblages on genetic diversity and levels of inbreeding in H. tortuosa. We found that inbreeding was up to three times higher in secondary forest, and this effect was amplified with reductions in primary forest in the surrounding landscape through reduced observed heterozygosity in isolated fragments. Inbreeding in forest patches was negatively correlated with the local frequency of specialist long‐distance foraging traplining hummingbirds. Traplining hummingbirds therefore appear to facilitate mating among unrelated plants—an inference we tested using empirically parameterized simulations. Higher levels of inbreeding in H. tortuosa are therefore associated with reduced functional diversity of hummingbirds in secondary forests and forest patches isolated from primary forests. Our findings suggest a cryptic consequence of primary forest loss and secondary forest regeneration through the disruption of mutualistic interactions resulting in the erosion of genetic diversity in a common understorey plant.
Altered fecal microbial and metabolic profile reveals potential mechanisms underlying iron deficiency anemia in pregnant women in China

The gut microbiome and its metabolism may provide crucial insight into the cause of iron deficiency anemia (IDA) in pregnant women. This study aimed to investigate the effect of the gut microbiome and its related metabolites on pregnant women with iron deficiency (ID) and IDA. Maternal cubital venous blood and stool samples were collected from healthy control pregnant women (HC, non-anemic, n = 10), pregnant women with ID non-anemia (ID, n = 10), and IDA (n = 10). All groups were subjected to fecal metagenomics and metabolomics. The composition and function of the gut microbiome were, then, compared in pregnant women with ID and IDA with HC after excluding the possibility of inflammation and insufficient iron absorption capacity. Whole-genome shotgun libraries were prepared by quantifying metagenomic DNA samples with Quant-iT PicoGreen dsDNA Assay. The levels of 41 microbial species, including 21 Streptococci and ten metabolites (catechol), which could serve as siderophores, were increased. In contrast, three Bacteroides and six metabolites were decreased in pregnant women with IDA (p < 0.05). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the bio-pathways, including biosynthesis of siderophore group non-ribosomal peptides (p < 0.01), ATP-binding cassette transporters (p < 0.05), and membrane transport of the gut microbiota (p < 0.01) in IDA patients were expressed differently compared with HC. Correlation analysis also indicates that these increased bacteria formed strong co-occurring relationships with metabolites in the occurrence and development of IDA in pregnant women. The present study identified that streptococci and catechol (fecal metabolite) were significantly increased in pregnant women with IDA. Therefore, adjusting the intestinal homeostasis using long-term living and eating habits on oral Streptococcus in pregnant women with IDA before iron supplementation may be more conducive to iron supplementation, thus providing novel therapies for IDA.
Gestational age at birth and outcome in monochorionic twins with different types of selective fetal growth restriction: A systematic literature review

This systematic review aims to assess the gestational age at birth and perinatal outcome [intrauterine demise (IUD), neonatal mortality and severe cerebral injury] in monochorionic twins with selective fetal growth restriction (sFGR), according to Gratacós classification based on umbilical artery Doppler flow patterns in the smaller twin. Seventeen articles were included. Gestational age at birth varied from 33.0 to 36.0 weeks in type I, 27.6–32.4 weeks in type II, and 28.3–33.8 weeks in type III. IUD rate differed from 0%–4% in type I to 0%–40% in type II and 0%–23% in type III. Neonatal mortality rate was between 0%–10% in type I, 0%–38% in type II, and 0%–17% in type III. Cerebral injury was present in 0%–2% of type I, 2%–30% of type II and 0%–33% of type III cases. The timing of delivery in sFGR varied substantially among studies, particularly in type II and III. The quality of evidence was moderate due to heterogenous study populations with varying definitions of sFGR and perinatal outcome parameters, as well as a lack of consensus on the use of the Gratacós classification, leading to substantial incomparability. Our review identifies the urgent need for uniform antenatal diagnostic criteria and definitions of outcome parameters.
A millennium of increasing diversity of ecosystems until the mid‐20th century

Land‐use change is widely regarded as a simplifying and homogenising force in nature. In contrast, analysing global land‐use reconstructions from the 10th to 20th centuries, we found progressive increases in the number, evenness, and diversity of ecosystems (including human‐modified land‐use types) present across most of the Earth's land surface. Ecosystem diversity increased more rapidly after ~1700 CE, then slowed or slightly declined (depending on the metric) following the mid‐20th century acceleration of human impacts. The results also reveal increasing spatial differentiation, rather than homogenisation, in both the presence‐absence and area‐coverage of different ecosystem types at sub‐global scales—at least, prior to the mid‐20th century. Nonetheless, geographic homogenization was revealed for a subset of analyses at a global scale, reflecting the now‐global presence of certain human‐modified ecosystem types. Our results suggest that, while human land‐use changes have caused declines in relatively undisturbed or “primary” ecosystem types, they have also driven increases in ecosystem diversity over the last millennium.
Evaluation of amotosalen and UVA pathogen‐reduced apheresis platelets after 7‐day storage

Amotosalen/UVA pathogen‐reduced platelet components (PRPCs) with storage up to 7 days are standard of care in France, Switzerland, and Austria. PRPCs provide effective hemostasis with reduced risk of transfusion‐transmitted infections and transfusion‐associated graft versus host disease, reduced wastage and improved availability compared with 5‐day‐stored PCs. This study evaluated the potency of 7‐day PRPCs by in vitro characterization and in vivo pharmacokinetic analysis of autologous PCs.
Patient‐derived renal cell carcinoma organoids for personalized cancer therapy

Abstract Background Kidney cancer is one of the most common solid tumors. The advancement of human kidney cancer research and treatment has been hindered by a lack of research models that faithfully recapitulate the diversity of the disease. Methods We established an effective three‐dimensional culture system for generating kidney cancer organoids from clinical renal cell carcinoma samples. Renal cell carcinoma (RCC) organoids were characterized by H&E staining, immunofluorescence, whole‐exome sequencing, RNA sequencing and single‐cell RNA sequencing. The use of RCC organoids in personalized cancer therapy was assessed by testing their responses to treatment drugs and chimeric antigen receptor T cells. Results Using this organoid culture system, 33 kidney cancer organoid lines from common kidney cancer subtypes, including clear cell renal cell carcinoma (ccRCC), papillary renal cell carcinoma (pRCC), and chromophobe renal cell carcinoma (chRCC), were generated. RCC organoids preserved the histological architectures, mutational landscapes, and transcriptional profile of the parental tumor tissues. Single‐cell RNA‐sequencing revealed inter‐ and intra‐tumoral heterogeneity in RCC organoids. RCC organoids allowed for in vitro drug screening and provided a tool for assessing the efficacy of chimeric antigen receptor T cells. Conclusions Patient‐derived RCC organoids are valuable pre‐clinical models for academic research and personalized medicine.
The stepwise Indian–Eurasian collision and uplift of the Himalayan‐Tibetan plateau drove the diversification of high‐elevation Scytodes spiders

The Cenozoic Indian–Eurasian collision and uplift of the Himalayan‐Tibetan Plateau (HTP) are among the most important geological events in the world. They have affected the diversification of regional biota of many taxonomic groups on and around the HTP. However, the exact timing and model of the collision and uplift events and speciation on and around the HTP are still in debate. The Himalayas group of Scytodes spitting spiders (Araneae: Scytodidae) are distributed at high elevations of the HTP and northern Indochina. Here, we reconstruct a dated molecular phylogeny for pan‐Himalayan Scytodes spiders, including the Himalayas group, with full geographical sampling of the species from the HTP and Indochina. We test a hypothesis to explain that the rich montane biodiversity of the region is uplift‐driven diversification—that orogeny drives rapid in situ speciation of the resident Scytodes lineages. Our findings revealed that the separation of the Himalayas clade from the Myanmar clade took place during the middle Oligocene, reflecting the final collision of India with Eurasia. The deep divergences among three clades (the Himalayas, the Myanmar and the Indochina clades) occurred from the middle Eocene to the middle Oligocene, corresponding to two early uplift events of the HTP. The evolutionary split between the Himalayas + Myanmar and Indochina clades were simultaneous with the rapid lateral extrusion of Indochina by the initial Himalayan uplift around the Eocene. This study highlights the importance of the diversification of dispersal‐limited, high‐elevation invertebrates as independent lines of evidence to reflect key tectonic events in the Himalayan‐Indochina region, supporting the stepwise model for the Indian–Eurasian collision and uplift of HTP.
Active-PET: a multifunctional PET scanner with dynamic gantry size featuring high-resolution and high-sensitivity imaging: a Monte Carlo simulation study

Organ-specific PET scanners have been developed to provide both high spatial resolution and sensitivity, although the deployment of several dedicated PET scanners at the same center is costly and space-consuming. Active-PET is a multifunctional PET scanner design exploiting the advantages of two different types of detector modules and mechanical arms mechanisms enabling repositioning of the detectors to allow the implementation of different geometries/configurations. Active-PET can be used for different applications, including brain, axilla, breast, prostate, whole-body, preclinical and pediatrics imaging, cell tracking, and image guidance for therapy. Monte Carlo techniques were used to simulate a PET scanner with two sets of high resolution and high sensitivity pixelated Lutetium Oxyorthoscilicate (LSO(Ce)) detector blocks (24 for each group, overall 48 detector modules for each ring), one with large pixel size (4 × 4 mm2) and crystal thickness (20 mm), and another one with small pixel size (2 × 2 mm2) and thickness (10 mm). Each row of detector modules is connected to a linear motor that can displace the detectors forward and backward along the radial axis to achieve variable gantry diameter in order to image the target subject at the optimal/desired resolution and/or sensitivity. At the center of the field-of-view, the highest sensitivity (15.98 kcps MBq−1) was achieved by the scanner with a small gantry and high-sensitivity detectors while the best spatial resolution was obtained by the scanner with a small gantry and high-resolution detectors (2.2 mm, 2.3 mm, 2.5 mm FWHM for tangential, radial, and axial, respectively). The configuration with large-bore (combination of high-resolution and high-sensitivity detectors) achieved better performance and provided higher image quality compared to the Biograph mCT as reflected by the 3D Hoffman brain phantom simulation study. We introduced the concept of a non-static PET scanner capable of switching between large and small field-of-view as well as high-resolution and high-sensitivity imaging.
Prediction of pain responses to subsequent cold pressor test via baseline heart rate variability in healthy adults

Baseline heart rate variability (HRV) that reflects parasympathetic nervous system (PNS) activity may serve as an objective, physiological index of pain assessment, but more research is warranted to examine the link between HRV and laboratory pain responses. This study examined whether baseline HRV would predict pain responses to subsequent cold pressor test (CPT) in healthy adults.
Interpersonal therapy versus antidepressant medication for treatment of postpartum depression and anxiety among women with HIV in Zambia: a randomized feasibility trial

Postpartum depression (PPD) is a prevalent and debilitating disease that may affect medication adherence and thus maternal health and vertical transmission among women with HIV. We assessed the feasibility of a trial of interpersonal psychotherapy (IPT) versus antidepressant medication (ADM) to treat PPD and/or anxiety among postpartum women with HIV in Lusaka, Zambia.