Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes

Rapid ecological speciation along depth gradients has taken place independently and repeatedly in freshwater fishes. While the extent of genomic divergence between ecomorphs is often well understood, the molecular mechanisms facilitating such rapid diversification are typically unclear. In Lake Masoko, an East African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow littoral and deep benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data from jaw tissue, we explore two major regulatory transcriptional mechanisms, expression and splicing QTL variants and examine their contribution to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 4.2% were regulated by cis-regulatory expression QTLs, and 6.4% were regulated by cis-regulatory splicing QTLs. There were also strong signals of divergent selection of differentially expressed genes that showed divergent regulation from expression, splicing or both QTL variants, including genes associated with major jaw plasticity and adaptation networks, adaptive immune system response, and oxidoreductase processes. These results suggest that transcriptome plasticity and modification have important roles during early-stage ecological speciation and demonstrate the role of regulatory-variants as important targets of selection driving ecologically-relevant divergence in gene expression that is associated with adaptive diversification.
Imaging Immune Cells Using Fc Domain Probes in Mouse Cancer Xenograft Models

Simple Summary The immune system responds to abnormal cell growth by sending immune cells to kill them. The immune cell response is very important since it can usually stop abnormal cells from growing and spreading. Immuno-therapeutics used to treat cancer require help from the immune system to be effective. A biopsy is typically performed to determine the therapeutic efficacy of cancer treatment which is invasive and difficult. A simpler and less invasive way to monitor therapeutic efficacy is needed. Here, we show a molecule that can be used as an imaging agent to determine immune cell recruitment to tumors. Abstract Tracking immune responses is complex due to the mixture of cell types, variability in cell populations, and the dynamic environment. Tissue biopsies and blood analysis can identify infiltrating and circulating immune cells; however, due to the dynamic nature of the immune response, these are prone to sampling errors. Non-invasive targeted molecular imaging provides a method to monitor immune response, which has advantages of providing whole-body images, being non-invasive, and allowing longitudinal monitoring. Three non-specific Fc-containing proteins were labeled with near-infrared dye IRDye800CW and used as imaging probes to assess tumor-infiltrating immune cells in FaDu and A-431 xenograft models. We showed that Fc domains localize to tumors and are visible by fluorescent imaging. This tumor localization appears to be based on binding tumor-associated immune cells and some xenografts showed higher fluorescent signals than others. The Fc domain alone bound to different human immune cell types. The Fc domain can be a valuable research tool to study innate immune response.
Experimental Study on the Temperature Features inside the Car Parking in Summer Outdoors

This paper aims at finding out the regularities of temperature variation inside the car during parking time and the measures to improve its internal environment through experiments on temperature variation after parking. The experimental results show that after parking, the average internal air temperature can reach 55℃ and even 71℃ on certain surface. The inside-car air temperature varies with places and rises with the height in space, presenting an obvious stratification. After the car gets started, the unbearable or uncomfortable time for people inside lasts 15 to 20 minutes. Meanwhile, the petrol consumption is increased. The experiment demonstrates that a relatively ideal effect can be achieved by means of installing solar film, taking unsophisticated sun-shading measures and choosing proper parking areas. 
4G and beyond in Australia: Technologies and opportunities in the NBN era

Fourth-generation cellular mobile wireless broadband systems are currently being trialled and deployed in Australia and around the world. This next generation is driven by increasing customer demand for ubiquitous access and higher data rates, the opportunity for increased revenues and lower costs for network operators, and the pursuit of more efficient, harmonised and profitable spectrum by regulators. Focusing on the 3GPP evolution path, we present an overview of technologies for 4G and beyond, and consider the opportunities in Australia in terms of spectrum, future wireless networks, and the National Broadband Network.
Land-Streamer vs. Conventional Seismic Data for High-Resolution Near-Surface Surveys

Near-surface high-resolution seismic mapping is very important in many applications such as engineering and environmental. However, the conventional setup of the seismic technique requires planting geophones, connecting cables, and then collecting all equipment after completing the survey, which is time-consuming. In this study, we suggest using a land-streamer setup rather than the conventional setup for fast, accurate, and high-resolution near-surface seismic surveys. Only one field data set is recorded using both the conventional and the land-streamer setups. The recorded data is then compared in terms of time, frequency, wavenumber domains, and acquisition time. Following this, we compared the accuracy of the subsurface mapping of both setups using a synthetic example. The results show that the conventional setup can reach deeper depths but with lower accuracy, where the errors in imaging the local anomalies’ widths and thicknesses are 77% to 145% and 35% to 50%, respectively. The land-streamer setup provides accurate near-surface results but shallower penetration depth, here the errors in the anomalies’ widths and thicknesses are 5% to 12% and 10% to 20%, respectively.
Impact of Respiratory Fluctuation on Hemodynamics in Human Cardiovascular System: A 0-1D Multiscale Model

To explore hemodynamic interaction between the human respiratory system (RS) and cardiovascular system (CVS), here we propose an integrated computational model to predict the CVS hemodynamics with consideration of the respiratory fluctuation (RF). A submodule of the intrathoracic pressure (ITP) adjustment is developed and incorporated in a 0-1D multiscale hemodynamic model of the CVS specified for infant, adolescent, and adult individuals. The model is verified to enable reasonable estimation of the blood pressure waveforms accounting for the RF-induced pressure fluctuations in comparison with clinical data. The results show that the negative ITP caused by respiration increases the blood flow rates in superior and inferior vena cavae; the deep breathing improves the venous return in adolescents but has less influence on infants. It is found that a marked reduction in ITP under pathological conditions can excessively increase the flow rates in cavae independent of the individual ages, which may cause the hemodynamic instability and hence increase the risk of heart failure. Our results indicate that the present 0-1D multiscale CVS model incorporated with the RF effect is capable of providing a useful and effective tool to explore the physiological and pathological mechanisms in association with cardiopulmonary interactions and their clinical applications.
Impact of Thyroid Tissue Status on the Cut-Off Value of Lymph Node Fine-Needle Aspiration Thyroglobulin Measurements in Papillary Thyroid Cancer

Objective: To study the optimal cut-off value of thyroglobulin measurement in a fine-needle aspiration (FNA-Tg) in diagnosing malignant lymph nodes and benign lymph nodes (LNs) according to the thyroid tissue status. Methods: A total of 517 LNs were aspirated: 401 preoperative LNs, 42 LNs after subtotal thyroidectomy and 74 suspected LNs after total thyroidectomy. The cut-off value of FNA-Tg was obtained from receiver operating characteristic (ROC) analysis. The cut-off value with the best diagnostic performance was then obtained by comparing different cut-off values from other studies. Results: LN FNA-Tg levels differed between preoperative and total thyroid disease (p < 0.001) and subtotal thyroidectomy and total thyroidectomy (p = 0.03), but not between preoperative and subtotal thyroidectomy (p = 1.00). Accordingly, those 443 LNs with preoperative and subtotal thyroidectomy were compared to those 74 without thyroid tissue. The optimal cut-off value in thyroid tissue group was 19.4 ng/ml and the area under the ROC curve (AUC) was 0.95 (95% CI 0.92–0.97). The optimal cut-off value in thyroid tissue absence group was 1.2 ng/ml and the AUC was 0.93 (0.85–0.98). After the analysis and comparison of multiple cut-off values, the optimal diagnostic performance was still found to be 19.4 ng/ml and 1.2 ng/ml. Conclusion: The influential factors of FNA-Tg are still controversial, and the optimal cut-off value of FNA-Tg can be determined based on the presence or absence of thyroid tissue. FNA-Tg can be used as an important auxiliary method for diagnosing cervical metastatic LNs of thyroid cancer.
Why optimize long term groundwater monitoring design? A multiobjective case study of Hill Air Force Base

Mathematical tools from the field of optimization have significant potential for reducing longterm monitoring costs and aiding site managers in making informed decisions on sampling strategies for sites undergoing long-term monitoring. A case study is presented that demonstrates the use of a Nondominated Sorted Genetic Algorithm (NSGA) for monitoring design at Hill Air Force Base (AFB). The method combines fate-and-transport simulation (although it can also be used only with historical data), plume interpolation, and adaptive search to identify the tradeoff between monitoring costs and mass estimation error. The method efficiently provides decision makers a direct representation of the tradeoff between monitoring objectives such as cost and error. Additionally, the most and least significant monitoring wells in a preexisting monitoring network are identified.
Fine-Scale Structures in the Mid-Level Eyewall of Super Typhoon Rammasun (2014) Simulated With the WRF-LES Framework

It has been numerically demonstrated that the turbulence above the boundary is important to tropical cyclone intensification and rapid intensification, but the three-dimensional structures of the sub-grid-scale (SGS) eddy have not been revealed due to the lack of observational data. In this study, two numerical simulations of Super Typhoon Rammasun (2014) were conducted with the Advanced Weather Research and Forecast (WRF) model by incorporating the large-eddy simulation (LES) technique, in which the enhanced eyewall convection and the process of rapid intensification are captured. Consistent with previous observational studies, the strong turbulent kinetic energy (TKE) is found throughout the whole eyewall inside of the radius of maximum wind in both experiments. The simulations indicate that the strong TKE is associated with horizontal rolls with the horizontal extent of 2–4 km, which are aligned azimuthally in the intense eyewall convection. It is indicated that the three-dimensional structures of the SGS eddy can be simulated with the vertical grid spacing of ∼100 m when the horizontal grid spacing is 74 m. It is suggested that there is considerable turbulence associated with azimuthally-aligned horizontal rolls in the mid-level eyewall of tropical cyclone.
HDAC1 Regulates Neuronal Differentiation

In adult hippocampal neurogenesis, chromatin modification plays an important role in neural stem cell self-renewal and differentiation by regulating the expression of multiple genes. Histone deacetylases (HDACs), which remove acetyl groups from histones, create a non-permissive chromatin that prevents transcription of genes involved in adult neurogenesis. HDAC inhibitors have been shown to promote adult neurogenesis and have also been used to treat nervous system disorders, such as epilepsy. However, most HDAC inhibitors are not specific and may have other targets. Therefore, it is important to decipher the role of individual HDACs in adult hippocampal neurogenesis. HDACs 1, 2, and 3 have been found expressed at different cellular stages during neurogenesis. Conditional deletion of HDAC2 in neural stem cells impairs neuronal differentiation in adult hippocampus. HDAC3 supports proliferation of adult hippocampal neural stem/progenitor cells. The role of HDAC1 in adult neurogenesis remains still open. Here, we used a conditional knock-out mouse to block HDAC1 expression in neural stem cells (Nestin+ cells) during hippocampal neurogenesis. Our results showed that both HDAC1 and HDAC2 are expressed in all cellular stages during hippocampal neurogenesis. Moreover, we found that deletion of HDAC1 by viral infection of neural stem cells is sufficient to compromise neuronal differentiation in vitro. However, we were unable to reduce the expression of HDAC1 in vivo using Nestin-CreERT2 mice. Understanding the role of HDAC1 may lead to ways to control stem cell proliferation and neuronal regeneration in the adult hippocampus, and to more specific HDAC therapeutics for neurological disorders.
Viral Coinfection and Nasal Cytokines in Children With Clinically Diagnosed Acute Sinusitis

Objective: Children with no pathogenic bacteria in the nasopharynx are unlikely to have acute bacterial sinusitis. We evaluated whether information on clinical presentation, viral co-detection, and mucosal cytokine levels could be used to predict presence of bacteria in the nasopharynx. Method: We obtained nasopharyngeal (NP) swabs from children diagnosed with acute sinusitis. NP swabs were processed for bacterial culture, viral PCR testing, and cytokine expression. We examined whether results of the bacterial culture could be predicted based on the presence of clinical information, presence of viruses or mucosal cytokine levels. Results: We enrolled 174 children; 123 (71%) had a positive culture for potentially pathogenic bacteria and 51 (29%) had normal flora. 122/174 (70%) tested positive for one or more viruses. Compared to children with normal flora, children with pathogenic bacteria were more likely to have viruses (p < 0.01), but this relationship disappeared when we adjusted for age. Children with pathogenic bacteria in their nasopharynx and children with normal flora had similar levels of nasal cytokines. Conclusion: In children with clinically diagnosed acute sinusitis, clinical presentation, levels of nasal cytokines, and presence of viruses do not differentiate children with and without pathogenic bacteria in their nasopharynx.
Variable Admittance Control of a Hand Exoskeleton for Virtual Reality-Based Rehabilitation Tasks

Robot-based rehabilitation is consolidated as a viable and efficient practice to speed up and improve the recovery of lost functions. Several studies highlight that patients are encouraged to undergo their therapies and feel more involved in the process when collaborating with a user-friendly robotic environment. Object manipulation is a crucial element of hand rehabilitation treatments; however, as a standalone process may result in being repetitive and unstimulating in the long run. In this view, robotic devices, like hand exoskeletons, do arise as an excellent tool to boost both therapy's outcome and patient participation, especially when paired with the advantages offered by interacting with virtual reality (VR). Indeed, virtual environments can simulate real-life manipulation tasks and real-time assign a score to the patient's performance, thus providing challenging exercises while promoting training with a reward-based system. Besides, they can be easily reconfigured to match the patient's needs by manipulating exercise intensity, e.g., Assistance-As-Needed (AAN) and the required tasks. Modern VR can also render interaction forces when paired to wearable devices to give the user some sort of proprioceptive force or tactile feedback. Motivated by these considerations, a Hand Exoskeleton System (HES) has been designed to be interfaced with a variable admittance control to achieve VR-based rehabilitation tasks. The exoskeleton assists the patient's movements according to force feedback and following a reference value calculated inside the VR. Whenever the patient grasps a virtual object, the HES provides the user with a force feedback sensation. In this paper, the virtual environment, developed within the Webots framework and rendering a HES digital-twin mapping and mimicking the actual HES motion, will be described in detail. Furthermore, the admittance control strategy, which continuously varies the control parameters to best render the force sensation and adapt to the user's motion intentions, will be investigated. The proposed approach has been tested on a single subject in the framework of a pilot study.
The Role of nmcR, ampR, and ampD in the Regulation of the Class A Carbapenemase NmcA in Enterobacter ludwigii

Various carbapenemases have been identified in the Enterobacteriaceae. However, the induction and corresponding regulator genes of carbapenemase NmcA has rarely been detected in the Enterobacter cloacae complex (ECC). The NmcA-positive isolate ECC NR1491 was first detected in Japan in 2013. It was characterized and its induction system elucidated by evaluating its associated regulator genes nmcR, ampD, and ampR. The isolate was highly resistant to all β-lactams except for third generation cephalosporins (3GC). Whole-genome analysis revealed that blaNmcA was located on a novel 29-kb putatively mobile element called EludIMEX-1 inserted into the chromosome. The inducibility of β-lactamase activity by various agents was evaluated. Cefoxitin was confirmed as a strong concentration-independent β-lactamase inducer. In contrast, carbapenems induced β-lactamase in a concentration-dependent manner. All selected 3GC-mutants harboring substitutions on ampD (as ampR and nmcR were unchanged) were highly resistant to 3GC. The ampD mutant strain NR3901 presented with a 700 × increase in β-lactamase activity with or without induction. Similar upregulation was also observed for ampC and nmcA. NR1491 (pKU412) was obtained by transforming the ampR mutant (135Asn) clone plasmid whose expression increased by ∼100×. Like NR3901, it was highly resistant to 3GC. Overexpression of ampC, rather than nmcA, may have accounted for the higher MIC in NR1491. The ampR mutant repressed nmcA despite induction and it remains unclear how it stimulates nmcA transcription via induction. Future experiments should analyze the roles of nmcR mutant strains.
Microbial Cell Factory of Baccatin III Preparation in Escherichia coli by Increasing DBAT Thermostability and in vivo Acetyl-CoA Supply

Given the rapid development of genome mining in this decade, the substrate channel of paclitaxel might be identified in the near future. A robust microbial cell factory with gene dbat, encoding a key rate-limiting enzyme 10-deacetylbaccatin III-10-O-transferase (DBAT) in paclitaxel biosynthesis to synthesize the precursor baccatin III, will lay out a promising foundation for paclitaxel de novo synthesis. Here, we integrated gene dbat into the wild-type Escherichia coli BW25113 to construct strain BWD01. Yet, it was relatively unstable in baccatin III synthesis. Mutant gene dbatS189V with improved thermostability was screened out from a semi-rational mutation library of DBAT. When it was over-expressed in an engineered strain N05 with improved acetyl-CoA generation, combined with carbon source optimization of fermentation engineering, the production level of baccatin III was significantly increased. Using this combination, integrated strain N05S01 with mutant dbatS189V achieved a 10.50-fold increase in baccatin III production compared with original strain BWD01. Our findings suggest that the combination of protein engineering and metabolic engineering will become a promising strategy for paclitaxel production.
Robust Speech Recognition Based on Vector Taylor Series

The vector Taylor series(VTS)expansion is an effective approach to noise robust speech recognition.How-ever,in the log-spectral domain,there exist the strong correlations among the different channels of Mel filter bank and thus it is difficult to estimate the noise variance from noisy speech proposes.A feature compensation algorithm in the cepstral domain based on vector Taylor series was proposed.In this algorithm,the distribution of speech cepstral features was represented by a Gaussian mixture model(GMM),and the mean and variance of noise were estimated from noisy speech by the VTS approximation.The experimental results show that the proposed algorithm can signifi-cantly improve the performance of speech recognition system,and outperforms the VTS-based feature compensation method in the log-spectral domain.
The role of mosque education in the integration of Turkish–Dutch youth: perspectives of Muslim parents, imams, mosque teachers and key stakeholders

ABSTRACT This study addresses the perceived role of mosque education in the integration of Turkish–Dutch Muslim children in the Netherlands. It is based on interviews with imams, mosque teachers, parents of mosque students, chairs of migrant organizations, policymakers and experts (N = 75). Most respondents (N = 49) view mosque education as potentially aiding the integration of the children, often depending on whether mosques adopt this as a policy and train imams and mosque teachers accordingly. Mosque education is perceived by many as contributing to integration by teaching the children values of respect and tolerance, offering positive identity affirmation to children’s stigmatized Islamic identity and countering youth radicalization by providing messages of moderation. While sixteen participants see mosque education as irrelevant for integration, ten participants voice concerns about the potential of mosque education to cause value confusion, alienate students from the Dutch society and indoctrinate them with Turkish state propaganda. Implications are discussed.
Progressive Multi-Scale Vision Transformer for Facial Action Unit Detection

Facial action unit (AU) detection is an important task in affective computing and has attracted extensive attention in the field of computer vision and artificial intelligence. Previous studies for AU detection usually encode complex regional feature representations with manually defined facial landmarks and learn to model the relationships among AUs via graph neural network. Albeit some progress has been achieved, it is still tedious for existing methods to capture the exclusive and concurrent relationships among different combinations of the facial AUs. To circumvent this issue, we proposed a new progressive multi-scale vision transformer (PMVT) to capture the complex relationships among different AUs for the wide range of expressions in a data-driven fashion. PMVT is based on the multi-scale self-attention mechanism that can flexibly attend to a sequence of image patches to encode the critical cues for AUs. Compared with previous AU detection methods, the benefits of PMVT are 2-fold: (i) PMVT does not rely on manually defined facial landmarks to extract the regional representations, and (ii) PMVT is capable of encoding facial regions with adaptive receptive fields, thus facilitating representation of different AU flexibly. Experimental results show that PMVT improves the AU detection accuracy on the popular BP4D and DISFA datasets. Compared with other state-of-the-art AU detection methods, PMVT obtains consistent improvements. Visualization results show PMVT automatically perceives the discriminative facial regions for robust AU detection.