Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of the best housekeeping gene for RT-qPCR analysis of human pancreatic organoids

In the last few years, there has been a considerable increase in the use of organoids, which is a new three-dimensional culture technology applied in scientific research. The main reasons for their extensive use are their plasticity and multiple applications, including in regenerative medicine and the screening of new drugs. The aim of this study was to better understand these structures by focusing on the choice of the best housekeeping gene (HKG) to perform accurate molecular analysis on such a heterogeneous system. This feature should not be underestimated because the inappropriate use of a HKG can lead to misleading data and incorrect results, especially when the subject of the study is innovative and not totally explored like organoids. We focused our attention on the newly described human pancreatic organoids (hPOs) and compared 12 well-known HKGs (ACTB, B2M, EF1α, GAPDH, GUSB, HPRT, PPIA, RNA18S, RPL13A TBP, UBC and YWHAZ). Four different statistical algorithms (NormFinder, geNorm, BestKeeper and ΔCt) were applied to estimate the expression stability of each HKG, and RefFinder was used to identify the most suitable genes for RT-qPCR data normalization. Our results showed that the intragroup and intergroup comparisons could influence the best choice of the HKG, making clear that the identification of a stable reference gene for accurate and reproducible RT-qPCR data normalization remains a critical issue. In summary, this is the first report on HKGs in human organoids, and this work provides a strong basis to pave the way for further gene analysis in hPOs.
The neurodevelopmental basis of humor appreciation: A fNIRS study of young children

Humor is crucial for social development. Despite this, very few studies have examined the neurodevelopment of humor in very young children, and none to date have used functional near-infrared spectroscopy (fNIRS) to study this important cognitive construct. The main aim of the current study was to characterize the neural basis of humor processing in young children between the ages of 6–8 years. Thirty-five healthy children (6–8 years old) watched funny and neutral video clips while undergoing fNIRS imaging. We observed activation increases in left temporo-occipito-parietal junction (TOPJ), inferior-parietal lobe (IPL), dorsolateral-prefrontal cortex (DLPFC) and right inferior frontal gyrus (IFG) and superior parietal lobe (SPL) regions. Activation in left TOPJ was positively correlated with age. In addition, we found that coherence increased in humor viewing compared to neutral content, mainly between remote regions. This effect was different for boys and girls, as boys showed a more pronounced increase in coherence for funny compared to neutral videos, more so in frontoparietal networks. These results expand our understanding of the neurodevelopment of humor by highlighting the effect of age on the neural basis of humor appreciation as well as emphasizing different developmental trajectories of boys and girls.
Type Synthesis Principle and Practice of Flexure Systems in the Framework of Screw Theory: Part III—Numerations and Synthesis of Flexure Mechanisms

In recent years, the increasing of application requirements call for development of a variety of flexure mechanisms with high precision or large motion and both. Therefore, in Part III of this series of papers we demonstrate how to use the methodology addressed in Part I to synthesize concepts for two kinds of flexure mechanisms, i.e. kinematics-type flexure mechanisms (KFMs) and constraint-type flexure mechanisms (CFMs) with the specified-DOF (Degree of Freedom) characteristics. Although most of them utilize parallel configurations and flexure elements, there is a clear difference in the behavior of flexures between KFMs and CFMs, The resultant type synthesis approaches fall into two distinct categories i.e. freedom-based and constraint-based one, both of which have presented in Part I. In order to derive useful flexure mechanism concepts available for different applications, a general design philosophy and rules are summarized firstly. As the main content of this part, the classifications, numerations, and synthesis for KFMs and CFMs are made in a systematic way. As a result, a majority of new precision flexure mechanisms are developed. In addition, qualitative comparisons are provided to demonstrate the performance and application differences between kinematic-type and constraint-type flexure mechanisms with the same DOF.Copyright © 2010 by ASME
On The Effect Of Coding Artifacts On Acoustic Scene Classification

Previous DCASE challenges contributed to an increase in the performance of acoustic scene classification systems. State-of-the-art classifiers demand significant processing capabilities and memory which is challenging for resource-constrained mobile or IoT edge devices. Thus, it is more likely to deploy these models on more powerful hardware and classify audio recordings previously uploaded (or streamed) from low-power edge devices. In such scenario, the edge device may apply perceptual audio coding to reduce the transmission data rate. This paper explores the effect of perceptual audio coding on the classification performance using a DCASE 2020 challenge contribution [1]. We found that classification accuracy can degrade by up to 57% compared to classifying original (uncompressed) audio. We further demonstrate how lossy audio compression techniques during model training can improve classification accuracy of compressed audio signals even for audio codecs and codec bitrates not included in the training process.
A Unified Architecture of Semantic Segmentation and Hierarchical Generative Adversarial Networks for Expression Manipulation

Editing facial expressions by only changing what we want is a long-standing research problem in Generative Adversarial Networks (GANs) for image manipulation. Most of the existing methods that rely only on a global generator usually suffer from changing unwanted attributes along with the target attributes. Recently, hierarchical networks that consist of both a global network dealing with the whole image and multiple local networks focusing on local parts are showing success. However, these methods extract local regions by bounding boxes centred around the sparse facial key points which are non-differentiable, inaccurate and unrealistic. Hence, the solution becomes sub-optimal, introduces unwanted artefacts degrading the overall quality of the synthetic images. Moreover, a recent study has shown strong correlation between facial attributes and local semantic regions. To exploit this relationship, we designed a unified architecture of semantic segmentation and hierarchical GANs. A unique advantage of our framework is that on forward pass the semantic segmentation network conditions the generative model, and on backward pass gradients from hierarchical GANs are propagated to the semantic segmentation network, which makes our framework an end-to-end differentiable architecture. This allows both architectures to benefit from each other. To demonstrate its advantages, we evaluate our method on two challenging facial expression translation benchmarks, AffectNet and RaFD, and a semantic segmentation benchmark, CelebAMask-HQ across two popular architectures, BiSeNet and UNet. Our extensive quantitative and qualitative evaluations on both face semantic segmentation and face expression manipulation tasks validate the effectiveness of our work over existing state-of-the-art methods.
Equivalent circuits for electrically small antennas using LS-decomposition with the method of moments

As part of an investigation into methods for accelerating the process of filling the method-of-moments impedance matrix (Z), it was found that (Z) could be decomposed into three parts: a real inductance matrix (L) from the magnetostatic vector potential, a real elastance matrix (S) from the electrostatic static scalar potential, and a complex impedance matrix (z( omega )) of residual frequency-dependent contributions. By neglecting (z( omega )) at sufficiently low frequencies, static and quasi-static charge and current distributions were obtained. For electrically small antennas, a complete RLC circuit was obtained directly from a single quasi-static solution rather than as an approximate characterization of the impedance as a function of frequency. This gives a precise definition of the circuit parameters limiting the performance of electrically small antennas. >
Whole-Genome Sequencing of Klebsiella pneumoniae BASUSDALSc45PDB48, a Unique Strain Capable of Growing in Pesticide-Containing Medium, Isolated from Soil in Bangladesh

We report the draft genome sequence of Klebsiella pneumoniae strain BASUSDALSc45PDB48, isolated from pesticide-contaminated soil; this strain showed the ability to grow in a medium with cypermethrin as the only carbon source. The genome assembly comprised 5,249,704 bp, with 128.17 Ns per 100 kbp, an N50 value of 5,035,968 bp, a GC content of 57.57%, and 5,349 annotated genes. ABSTRACT We report the draft genome sequence of Klebsiella pneumoniae strain BASUSDALSc45PDB48, isolated from pesticide-contaminated soil; this strain showed the ability to grow in a medium with cypermethrin as the only carbon source. The genome assembly comprised 5,249,704 bp, with 128.17 Ns per 100 kbp, an N50 value of 5,035,968 bp, a GC content of 57.57%, and 5,349 annotated genes.
Application of wavelet-Galerkin method to electrically-large optical waveguide problems

The wavelet-Galerkin method based on highly regular Daubechies' compactly supported scaling functions has been applied to two-dimensional time-domain optical waveguide problems. The simple local sampling and the small numerical dispersion properties have enabled full-wave analysis of electrically-large inhomogeneous structures in a reasonable computational effort.
Study protocol: the OxWell school survey investigating social, emotional and behavioural factors associated with mental health and well-being

Introduction Improving our understanding of the broad range of social, emotional and behavioural factors that contribute to mental health outcomes in adolescents will be greatly enhanced with diverse, representative population samples. We present a protocol for a repeated self-report survey assessing risk and protective factors for mental health and well-being in school pupils aged 8–18 years with different socioeconomic backgrounds in England. The survey will provide a comprehensive picture of mental health and associated risks at the community level to inform the development of primary and secondary prevention and treatment strategies in schools. Methods and analysis This protocol is for a large-scale online repeated self-report survey, representative of children and adolescents aged 8–18 years attending schools or further education colleges in participating counties in England. The survey consists of around 300 questions, including validated measures of mental health and well-being, risk and protective factors, and care-seeking behaviour and preferences. Additional questions each year vary to address current events and novel hypotheses, developed by the research team, collaborators and stakeholders. Primary analyses will investigate current and changing risk and protective factors, care-seeking behaviour and attitudes to allowing linkage of their sensitive data to other databases for research, and will compare measures of mental health to measures of well-being. Ethics and dissemination The study was approved by the University of Oxford Research Ethics Committee (Reference: R62366). Tailored data summaries will be provided to participating schools and stakeholders within 3 months of data collection. The main findings will be presented at scientific meetings, published in peer-reviewed journals and shared via digital and social media channels. At the end of the study, other researchers will be able to apply for access to anonymous data extracts.
Vascular cell-matrix adhesion in development and cancer.

The development and homeostasis of vertebrate organisms depend on the "tree of life", that is the intricate network of vascular tubes composed by endothelial cells attached to the basement membrane and surrounded by perivascular cells. Although many studies have revealed the fundamental role of cytokines, growth factors and Notch signalling in vascular morphogenesis, we still lack sufficient understanding of the molecular mechanisms controlling the various steps of the angiogenic processes. Emerging data highlight that cell adhesions are key players in vascular morphogenesis. In this review, we focus on endothelial cells and we present the current state of knowledge regarding the role of cell-matrix adhesions in developmental and tumour angiogenesis, attained mainly from genetic studies and animal models.
Shared familial risk factors between autism spectrum disorder and obesity - a register-based familial coaggregation cohort study.

BACKGROUND Meta-analyses suggest an association between autism spectrum disorder (ASD) and obesity, but the factors underlying this association remain unclear. This study investigated the association between ASD and obesity stratified on intellectual disability (ID). In addition, in order to gain insight into possible shared etiological factors, the potential role of shared familial liability was examined. METHOD We studied a cohort of 3,141,696 individuals by linking several Swedish nationwide registers. We identified 35,461 individuals with ASD and 61,784 individuals with obesity. Logistic regression models were used to estimate the association between ASD and obesity separately by ID and sex and by adjusting for parental education, psychiatric comorbidity, and psychotropic medication. Potential shared familial etiologic factors were examined by comparing the risk of obesity in full siblings, maternal and paternal half-siblings, and full- and half-cousins of individuals with ASD to the risk of obesity in relatives of individuals without ASD. RESULTS Individuals with ASD + ID (OR = 3.76 [95% CI, 3.38-4.19]) and ASD-ID (OR = 3.40 [95% CI, 3.23-3.58]) had an increased risk for obesity compared with individuals without ASD. The associations remained statistically significant when adjusting for parental education, psychiatric comorbidity, and medication. Sex-stratified analyses indicated a higher relative risk for males compared with females, with statistically significant interaction effects for ASD-ID, but not for ASD+ID in the fully adjusted model. First-degree relatives of individuals with ASD+ID and ASD-ID had an increased risk of obesity compared with first-degree relatives of individuals without ASD. The obesity risk was similar in second-degree relatives of individuals with ASD+ID but was lower for and ASD-ID. Full cousins of individuals with ASD+ID had a higher risk compared with half-cousins of individuals with ASD+ID). A similar difference in the obesity risk between full cousins and half-cousins was observed for ASD-ID. CONCLUSIONS Individuals with ASD and their relatives are at increased risk for obesity. The risk might be somewhat higher for males than females. This warrants further studies examining potential common pleiotropic genetic factors and shared family-wide environmental factors for ASD and obesity. Such research might aid in identifying specific risks and underlying mechanisms in common between ASD and obesity.
NANOCRYSTALLINE SILICON THIN FILM TRANSISTORS FOR HIGH PERFORMANCE LARGE AREA ELECTRONICS

Nanocrystalline silicon (nc-Si) thin film transistors (TFTs) have potential for high-performance applications in large area electronics, such as next generation of flat panel displays and medical x-ray imagers, for pixel drivers, readout circuits, as well as complementary channel logic circuits for system-on-panel integration. This potential stems from reduced threshold voltage shift and higher transconductance, compared to amorphous silicon counterpart. In this paper, we discuss various TFT structures, their associated design and performance considerations, including leakage current and threshold voltage stability mechanisms.
Maternal Vascular Lesions in the Placenta Predict Vascular Impairments a Decade After Delivery

Supplemental Digital Content is available in the text. Women with adverse pregnancy outcomes later experience excess hypertension and cardiovascular disease, but how the events are linked is unknown. Examination of the placenta may provide clues to vascular impairments after delivery. Maternal vascular malperfusion lesions (MVMs) were abstracted from clinical reports, validated and characterized using clinical guidelines and severity score. A total of 492 women (170 with MVMs and 322 without MVMs) participated in a study visit 8 to 10 years after delivery to assess blood pressure, cardiometabolic factors, and sublingual microvascular features using sidestream dark field imaging. Covariates included age, race, adverse pregnancy outcomes (preeclampsia, small for gestational age, and preterm birth), and health behaviors. Women with versus without MVM had a distinct sublingual microvascular profile comprised of (1) lower microvascular density (−410 μm/mm2, P=0.015), (2) higher red blood cell filling as a marker of perfusion (2%, P=0.004), and (3) smaller perfused boundary region (−0.07 µm, P=0.025) as a measure of glycocalyx integrity, adjusted for covariates including adverse pregnancy outcomes. Women with MVM also had higher adjusted diastolic blood pressure (+2.6 mm Hg, P=0.021), total and LDL (low-density lipoprotein)-cholesterol (+11.2 mg/dL, P=0.016; +8.7 mg/dL, P=0.031). MVM associations with subsequent cardiovascular measures did not vary by type of adverse pregnancy outcome, except among women with preterm births where blood pressure was higher only among those with MVM. Results were similar when evaluated as MVM severity. A decade after delivery, women with placental vascular lesions had an adverse cardiovascular profile comprised of microvascular rarefaction, higher blood pressure and more atherogenic lipids. Placental histopathology may reveal a woman’s early trajectory toward subsequent vascular disease.
Covid-19 and the Multidisciplinary Team Meeting: ‘Should Old Acquaintance be Forgot?'

to be secure and reliable. It also boasts other beneﬁ ts, all of which are designed to aid communication and networking. Commercial platforms such as Skype and Zoom tend to be less secure and currently not advocated for use in the NHS. Unfortunately, few data exist that support the notion that virtual MDT working should either remain or gradually metamorphose back into the traditional model. However, one small questionnaire study explored opinions after eight virtual MDTs. Of respondents (n = 36), 73% and 83% considered that the depth of discussion and decision-making processes had not changed versus the traditional MDT. 6 In a further study, 7 a questionnaire was distributed to all head and neck MDTs in the UK, of which there were 97 responses. Most respondents (70%) considered that decision-making was unchanged, while 85% felt that technology was and approximately three quarters felt that some aspects of communication (for example team
An Integrated Biosecurity Risk Assessment Model (IBRAM) For Evaluating the Risk of Import Pathways for the Establishment of Invasive Species

An important aspect of analyzing the risk of unwanted organisms establishing in an area is understanding the pathways by which they arrive. Evaluating the risks of these pathways requires use of data from multiple sources, which frequently are uncertain. To address the needs of agencies responsible for biosecurity operations, we present an Integrated Biosecurity Risk Assessment Model (IBRAM) for evaluating the risk of establishment and dispersal of invasive species along trade pathways. The IBRAM framework consists of multiple linked models which describe pest entry into the country, escape along trade pathways, initial dispersal into the environment, habitat suitability, probabilities of establishment and spread, and the consequences of these invasions. Bayesian networks (BN) are used extensively to model these processes. The model includes dynamic BN components and geographic data, resulting in distributions of output parameters over spatial and temporal axes. IBRAM is supported by a web‐based tool that allows users to run the model on real‐world pest examples and investigate the impact of alternative risk management scenarios, to explore the effect of various interventions and resource allocations. Two case studies are provided as examples of how IBRAM may be used: Queensland fruit fly (Bactrocera tryoni) (Diptera: Tephritidae) and brown marmorated stink bug (Halyomorpha halys) (Hemiptera: Pentatomidae) are unwanted organisms with the potential to invade Aotearoa New Zealand, and IBRAM has been influential in evaluating the efficacy of pathway management to mitigate the risk of their establishment in the country.
Bryostatin-1 Decreases HIV-1 Infection and Viral Production in Human Primary Macrophages

HIV-1 persists in a cellular latent form despite therapy that quickly propagates infection upon treatment interruption. Reversing latency would contribute to eradicate these cells, closing the gap to a cure. ABSTRACT While combination antiretroviral therapy maintains undetectable viremia in people living with HIV (PLWH), a lifelong treatment is necessary to prevent viremic rebound after therapy cessation. This rebound seemed mainly caused by long-lived HIV-1 latently infected cells reverting to a viral productive status. Reversing latency and elimination of these cells by the so-called shock-and-kill strategy is one of the main investigated leads to achieve an HIV-1 cure. Small molecules referred to as latency reversal agents (LRAs) proved to efficiently reactivate latent CD4+ T cells. However, the LRA impact on de novo infection or HIV-1 production in productively infected macrophages remains elusive. Nontoxic doses of bryostatin-1, JQ1, and romidepsin were investigated in human monocyte-derived macrophages (MDMs). Treatment with bryostatin-1 or romidepsin resulted in a downregulation of CD4 and CCR5 receptors, respectively, accompanied by a reduction of R5 tropic virus infection. HIV-1 replication was mainly regulated by receptor modulation for bryostatin-1, while romidepsin effects rely on upregulation of SAMHD1 activity. LRA stimulation of chronically infected cells did not enhance HIV-1 production or gene expression. Surprisingly, bryostatin-1 caused a major decrease in viral production. This effect was not viral strain specific but appears to occur only in myeloid cells. Bryostatin-1 treatment of infected MDMs led to decreased amounts of capsid and matrix mature proteins with little to no modulation of precursors. Our observations revealed that bryostatin-1-treated myeloid and CD4+ T cells respond differently upon HIV-1 infection. Therefore, additional studies are warranted to more fully assess the efficiency of HIV-1 eradicating strategies. IMPORTANCE HIV-1 persists in a cellular latent form despite therapy that quickly propagates infection upon treatment interruption. Reversing latency would contribute to eradicate these cells, closing the gap to a cure. Macrophages are an acknowledged HIV-1 reservoir during therapy and are suspected to harbor latency establishment in vivo. However, the impact of latency reversal agents (LRAs) on HIV-1 infection and viral production in human macrophages is poorly known but nonetheless crucial to probe the safety of this strategy. In this in vitro study, we discovered encouraging antireplicative features of distinct LRAs in human macrophages. We also described a new viral production inhibition mechanism by protein kinase C agonists that is specific to myeloid cells. This study provides new insights into HIV-1 propagation restriction potentials by LRAs in human macrophages and underline the importance of assessing latency reversal strategy on all HIV-1-targeted cells.