Miracle-dz/UniFAR-FTUs huggingface dataset:
Closed-loop control of a 2-D mems micromirror with sidewall electrodes for a laser scanning microscope system

ABSTRACT This article presents the development and implementation of a robust nonlinear control scheme for a 2-D micromirror-based laser scanning microscope system. The presented control scheme, built around sliding mode control approach and augmented an adaptive algorithm, is proposed to improve the tracking accuracy in presence of cross-axis effect. The closed-loop controlled imaging system is developed through integrating a 2-D micromirror with sidewall electrodes (SW), a laser source, NI field-programmable gate array (FPGA) hardware, the optics, position sensing detector (PSD) and photo detector (PD). The experimental results demonstrated that the proposed scheme is able to achieve accurate tracking of a reference triangular signal. Compared with open-loop control, the scanning performance is significantly improved, and a better 2-D image is obtained using the micromirror with the proposed scheme.
One-sided asymptotic inferences for a proportion

ABSTRACT Two-sided asymptotic confidence intervals for an unknown proportion p have been the subject of a great deal of literature. Surprisingly, there are very few papers devoted, like this article, to the case of one tail, despite its great importance in practice and the fact that its behavior is usually different from that of the case with two tails. This paper evaluates 47 methods and concludes that (1) the optimal method is the classic Wilson method with a correction for continuity and (2) a simpler option, almost as good as the first, is the new adjusted Wald method (Wald's classic method applied to the data increased in the values proposed by Borkowf: adding a single imaginary failure or success).
Maturases and Group II Introns in the Mitochondrial Genomes of the Deepest Jakobid Branch

Abstract Ophirinina is a recently described suborder of jakobid protists (Excavata) with only one described species to date, Ophirina amphinema. Despite the acquisition and analysis of massive transcriptomic and mitogenomic sequence data from O. amphinema, its phylogenetic position among excavates remained inconclusive, branching as sister group either to all Jakobida or to all Discoba. From a morphological perspective, it has not only several typical jakobid features but also unusual traits for this group, including the morphology of mitochondrial cristae (sac-shaped to flattened-curved cristae) and the presence of two flagellar vanes. In this study, we have isolated, morphologically characterized, and sequenced genome and transcriptome data of two new Ophirinina species: Ophirina chinija sp. nov. and Agogonia voluta gen. et sp. nov. Ophirina chinija differs from O. amphinema in having rounded cell ends, subapically emerging flagella and a posterior cell protrusion. The much more distantly related A. voluta has several unique ultrastructural characteristics, including sac-shaped mitochondrial cristae and a complex “B” fiber. Phylogenomic analyses with a large conserved-marker dataset supported the monophyly of Ophirina and Agogonia within the Ophirinina and, more importantly, resolved the conflicting position of ophirinids as the sister clade to all other jakobids. The characterization of the mitochondrial genomes showed that Agogonia differs from all known gene-rich jakobid mitogenomes by the presence of two group II introns and their corresponding maturase protein genes. A phylogenetic analysis of the diversity of known maturases confirmed that the Agogonia proteins are highly divergent from each other and define distant families among the prokaryotic and eukaryotic maturases. This opens the intriguing possibility that, compared to other jakobids, Ophirinina may have retained additional mitochondrial elements that may help to understand the early diversification of eukaryotes and the evolution of mitochondria.
Flow in a Viscous Trailing Vortex

The equations of motion for an isolated laminar viscous vortex at moderate to large Reynolds numbers are linearised, by assuming that both the rotational velocity and the deficit of longitudinal velocity are small compared with that in the free stream. The rotational motion and the longitudinal motion may then be superimposed and solutions are readily obtained for each. If the vortex is generated by a body with profile drag it is predicted that the deficit of longitudinal velocity will be positive, which is in agreement with experimental observation. Further details of the solution and its relation to the flow in real vortices are discussed; and the theory is compared with some measurements in a turbulent vortex.
Bridging the Buried Interface with Piperazine Dihydriodide Layer for High Performance Inverted Solar Cells.

Given that it is closely related to perovskite crystallization and interfacial trap densities, buried interfacial engineering is crucial for creating effective and stable perovskite solar cells. Compared with the in-depth studies on the defect at the top perovskite interface, exploring the defect of the buried side of perovskite film is relatively complicated and scanty owing to the non-exposed feature. Herein, the degradation process is probed from the buried side of perovskite films with continuous illumination and its effects on morphology and photoelectronic characteristics with a facile lift-off method. Additionally, a buffer layer of Piperazine Dihydriodide (PDI2 ) is inserted into the imbedded bottom interface. The PDI2 buffer layer is able to lubricate the mismatched thermal expansion between perovskite and substrate, resulting in the release of lattice strain and thus a void-free buried interface. With the PDI2 buffer layer, the degradation originates from the growing voids and increasing non-radiative recombination at the imbedded bottom interfaces are suppressed effectively, leading to prolonged operation lifetime of the perovskite solar cells. As a result, the power conversion efficiency of an optimized p-i-n inverted photovoltaic device reaches 23.47% (with certified 23.42%) and the unencapsulated devices maintain 90.27% of initial efficiency after 800 h continuous light soaking.
Postoperative Day 1 Discharge After Robotic Totally Endoscopic Coronary Bypass: The Ultimate in Enhanced Recovery After Surgery

Objective: The benefits of Enhanced Recovery After Surgery (ERAS) protocols are being recognized in multiple surgical specialties, including following coronary bypass surgery to improve quality of care and decrease costs. We developed a fast-track discharge protocol for patients undergoing robotic totally endoscopic coronary bypass surgery (TECAB) to be discharged on postoperative day (POD) 1, the subjects of this study. Methods: In a retrospective study of 720 patients undergoing robotic beating-heart TECAB over 8 years at our institution, 93 patients were selected for a fast-track POD1 discharge protocol. We compared the outcomes of this group to the remaining 627 patients who were discharged per standard protocol (non-POD1 discharge). Results: The early discharge group was significantly younger, had lower Society of Thoracic Surgeons (STS) risk of mortality, and had a lower prevalence of obesity, diabetes, and chronic kidney disease. Patients discharged on POD1 were more often extubated in the operating room (56% vs 42%, P = 0.010). The readmission rate for the early discharge group was 3.2%, which was similar to the readmission rate of 6.7% for the standard discharge protocol group (P = 0.329). Time to return to work was shorter in the early discharge group, although it did not quite reach statistical significance (12 vs 18 days, P = 0.051). There was no difference in midterm cardiac mortality. Conclusions: Early discharge on POD1 after robotic TECAB is appropriate in selected patients and is associated with low readmission rates and a trend towards earlier return to work. Patients suitable for this “ultrafast-track” approach were more likely to be younger, have lower STS risk, and fewer comorbidities. Visual abstract
Transversus Abdominis Plane Block as Part of a Multimodal Analgesic Regimen in Patients Undergoing Anterior Lumbar Interbody Fusion: A Retrospective Cohort Study

Background Opioids are a mainstay for pain control in patients undergoing lumbar spine surgery but are associated with a high risk of dependence and significant adverse effects. Efforts continue to be made to utilize non-narcotic agents such as regional nerve block for pain control as part of a multimodal analgesia regimen. Recently, transversus abdominis plane (TAP) blocks have proven beneficial for patients undergoing lumbar fusion procedures. The purpose of this study is to evaluate the efficacy of TAP blocks for postoperative pain control and the effect on opioid consumption and hospital length of stay (LOS) in patients undergoing anterior lumbar interbody fusion (ALIF). Methods A retrospective review of patients undergoing elective ALIF included collection of data on demographics, LOS, pain scores using visual analog scale (VAS), opioid consumption using morphine milligram equivalents (MME) from postoperative day (POD) 0 to 5, and any complications. Patients who underwent primary ALIF or ALIF with concomitant posterolateral lumbar fusion were included. Results A total of 99 patients met inclusion criteria; 47 had a preoperative TAP block and 52 did not. Demographic data and number of levels fused were equally distributed between the groups. The TAP group had significantly lower MME consumption postoperatively during POD 0 to 2 and 0 to 5. VAS pain scores were lower for TAP block patients on POD 3 and 4; otherwise, there was no significant difference. LOS and complication rates were not significantly different. A multiple regression analysis found male sex to be a predictor of increased postoperative MME, while age and TAP block were significant predictors of decreased MME. Conclusions The use of TAP block for patients undergoing ALIF was associated with less cumulative MME consumption in the immediate postoperative period. TAP block may be an effective tool for reducing postoperative opioid consumption in patients undergoing ALIF. Clinical Relevance The data in this study provide clinical relevance supporting the use of TAP blocks for patients undergoing ALIF procedures. Level of Evidence 3.
The unsteady flow due to an impulsively rotated sphere

We consider the flow induced by a sphere, contained in an otherwise quiescent body of fluid, that is suddenly imparted with angular momentum. This classical problem is known to exhibit a finite-time singularity in the boundary-layer equations, due to the viscous boundary layer, induced by the sudden rotation, colliding at the sphere's equator. We consider this flow from the perspective of the post-collision dynamics, showing that the collision gives rises to a radial jet headed by a swirling toroidal starting vortex pair. The starting vortex propagates away from the sphere and, in doing so, loses angular momentum. The jet, in turn, develops an absolute instability which propagates back towards the sphere's equator. The starting vortex pair detaches from the jet and expands as a coherent (non-swirling) toroidal vortex pair. We also present results of some new experiments which show good qualitative agreement with our computational results.
Smuggling in Humanity: Musicking through Prison Walls

In this article, the two authors talk about their vastly different trajectories that span international geographies and contrasting circumstances. By chance, their lives intersected in a music education program in an American prison. They trace their lifeworlds and how their musical engagement was a reciprocal learning experience for both of them. The article describes the “Empowering Song” music education approach that had its genesis in American prisons. The authors also share the experiential learning that has marked their collaboration, a relationship that has benefited them socially, emotionally, and politically. As a liberation pedagogy, the Empowering Song approach has wider implications, from general music and professional settings to community music in peace-building and forced migration circumstances.
An experimental comparison of the Digital Spatial Profiling and Visium spatial transcriptomics technologies for cancer research

Background Spatial transcriptomic technologies are powerful tools for resolving the spatial heterogeneity of gene expression in tissue samples. However, little evidence exists on relative strengths and weaknesses of the various available technologies for profiling human tumour tissue. In this study, we aimed to provide an objective assessment of two common spatial transcriptomics platforms, 10X Genomics’ Visium and Nanostring’s GeoMx DSP. Method The abilities of the DSP and Visium platforms to profile transcriptomic features were compared using matching cell line and primary breast cancer tissue samples. A head-to-head comparison was conducted using data generated from matching samples and synthetic tissue references. Platform specific features were also assessed according to manufacturers’ recommendations to evaluate the optimal usage of the two technologies. Results We identified substantial variations in assay design between the DSP and Visium assays such as transcriptomic coverage and composition of the transcripts detected. When the data was standardised according to manufacturers’ recommendations, the DSP platform was more sensitive in gene expression detection. However, its specificity was diminished by the presence of non-specific detection. Our results also confirmed the strength and weakness of each platform in characterising spatial transcriptomic features of tissue samples, in particular their application to hypothesis generation versus hypothesis testing. Conclusion In this study, we share our experience on both DSP and Visium technologies as end users. We hope this can guide future users to choose the most suitable platform for their research. In addition, this dataset can be used as an important resource for the development of new analysis tools.
Impact of diet on jejunal microbiota composition during broiler development with special focus on Enterococcus hirae and Enterococcus faecium

Modern broiler breeds allow for high feed efficiency and rapid growth, but come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are furthermore affected by the composition of the gut microbiota, which in turn is influenced by diet composition. In this study we therefore assessed how diet composition alters the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content jejunum was used for metagenomic shotgun sequencing to determine the microbiota composition on species level. Among all diet groups, a total of 104 differential abundant bacterial species were detected. Most notably were the changes in the jejunal microbiota induced by butyrate supplementation when compared to the control diet, resulting in the reduced relative abundance of mainly Enterococcus faecium and the opportunistic pathogen Enterococcus hirae in broilers 4 days post-hatch. At this early stage of development, the immune system is still immature thereby highlighting the importance to study the relation of diet and the jejunal microbiota. Future studies should furthermore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.
The super-enhancer landscape reflects molecular subgroups of adrenocortical carcinoma

Adrenocortical carcinoma (ACC) is a rare cancer of the adrenal gland with generally very unfavourable outcome. Two molecular subgroups, C1A and C1B, have been previously identified with a significant association with patient survival. In this work, we study chromatin state organization characterized by histone modifications using ChIP-sequencing in adult ACC. We describe the super-enhancer landscape of ACC, characterized by H3K27ac, and identify super-enhancer regulated genes that play a significant role in tumorigenesis. We show that the super-enhancer landscape reflects differences between the molecular sub-groups C1A and C1B and identify networks of master transcription factors mirroring these differences. Additionally, we study the effects of molecules THZ1 and JQ1 previously reported to affect super-enhancer-driven gene expression in ACC cell lines. Our results reveal that the landscape of histone modifications in ACC is linked to its molecular subgroups and thus provide the groundwork for future analysis of epigenetic reprogramming in ACC.
Diverging asymmetry of intrinsic functional organization in autism

Autism is a neurodevelopmental condition involving atypical sensory-perceptual functions together with language and socio-cognitive deficits. Previous work has reported subtle alterations in the asymmetry of brain structure and reduced laterality of functional activation in individuals with autism relative to non-autistic individuals (NAI). However, whether functional asymmetries show altered intrinsic systematic organization in autism remains unclear. Here, we computed inter- and intra-hemispheric asymmetry of intrinsic functional gradients capturing connectome organization along three axes, stretching between sensory-default, somatomotor-visual, and default-multiple demand networks, to study system-level hemispheric imbalances in autism. We observed decreased leftward functional asymmetry of language network organization in individuals with autism, relative to NAI. Whereas language network asymmetry varied across age groups in NAI, this was not the case in autism, suggesting atypical functional laterality in autism may result from altered developmental trajectories. Finally, we observed that intra-but not inter-hemispheric features were predictive of the severity of autistic traits. In sum, our findings illustrate how regional and patterned functional lateralization is altered in autism at the system level. Such differences may be rooted in altered developmental trajectories of functional organization asymmetry in autism.
ON 4-EQUIVALENCED ASSOCIATION SCHEMES

Let (Ω, S) be an association scheme where Ω is a non-empty finite set and S is a partition of Ω×Ω. For a positive integer k we say that (Ω, S) is k-equivalenced if each non-diagonal element of S has valency k. In this paper we focus on 4-equivalenced association schemes, and prove that they are transitive.
THAPBI PICT—a fast, cautious, and accurate metabarcoding analysis pipeline

THAPBI PICT is an open source software pipeline for metabarcoding analysis with multiplexed Illumina paired-end reads, including where different amplicons are sequenced together. We demonstrate using worked examples with our own and public data sets how, with appropriate primer settings and a custom database, THAPBI PICT can be applied to other amplicons and organisms, and used for reanalysis of existing datasets. The core dataflow of the implementation is (i) data reduction to unique marker sequences, often called amplicon sequence variants (ASVs), (ii) dynamic thresholds for discarding low abundance sequences to remove noise and artifacts (rather than error correction by default), before (iii) classification using a curated reference database. The default classifier assigns a label to each query sequence based on a database match that is either perfect, or a single base pair edit away (substitution, deletion or insertion). Abundance thresholds for inclusion can be set by the user or automatically using per-batch negative or synthetic control samples. Output is designed for practical interpretation by nonspecialists and includes a read report (ASVs with classification and counts per sample), sample report (samples with counts per species classification), and a topological graph of ASVs as nodes with short edit distances as edges. Source code available from https://github.com/peterjc/thapbi-pict/with documentation including installation instructions.
Dolphin social phenotypes vary in response to food availability but not 1 climate 2

13 Social behaviours can allow individuals to flexibly respond to environmental change, potentially 14 buffering adverse effects. However, individuals may respond differently to the same environmental 15 stimulus, complicating predictions for population-level response to environmental change. Here we 16 show that bottlenose dolphins ( Tursiops truncatus ) alter their social behaviour at yearly and monthly 17 scales in response to a proxy for food availability (salmon abundance) but do not respond to 18 variation in a proxy for climate (the North Atlantic Oscillation index). There was also individual 19 variation in plasticity for gregariousness and connectedness to distant parts of the social network, 20 although these traits showed limited repeatability. In contrast, individuals showed consistent 21 differences in clustering with their immediate social environment at the yearly scale but no 22 individual variation in plasticity for this trait at either time scale. These results indicate that social 23 behaviour in free-ranging cetaceans can be highly resource dependent with individuals increasing 24 their connectedness over short timescales but possibly reducing their wider range of connection at 25 longer timescales. Some social traits showed more individual variation in plasticity or mean 26 behaviour than others, highlighting how predictions for the responses of populations to 27 environmental variation must consider the type of individual variation present in the population.
Focus constructions and the focus criterion in gungbe

Cet article montre que la focalisation en gungbe est un processus syntaxique qui requiert l'anteposition des elements focalises vers la position de specifieur ou de tete d'une projection fonctionnelle FocP integere au systeme CP. Les elements focalises bougent necessairement dans ces positions pour satisfaire le critere focus, lequel exige qu'au niveau approprie de representation, tout constituant focalise (c.a d. XP[+f]) se trouve en relation specifieur-tete avec une tete X° marquee [+f] et vice versa. Le critere focus etant satisfait en structure de surface en gungbe, les constituants focalises (verbaux ou non) doivent bouger en [spec FocP]. En outre, la focalisation du verbe declenche un mouvement de tete, le critere focus etant realise par la relation specifieur-tete etablie entre le verbe en Foc° et un operateur focus nul en [spec FocP]
Understanding of Convolutional Neural Network (CNN): A Review

The application of deep learning technology has increased rapidly in recent years. Technologies in deep learning increasingly emulate natural human abilities, such as knowledge learning, problem-solving, and decision-making. In general, deep learning can carry out self-training without repetitive programming by humans. Convolutional neural networks (CNNs) are deep learning algorithms commonly used in wide applications. CNN is often used for image classification, segmentation, object detection, video processing, natural language processing, and speech recognition. CNN has four layers: convolution layer, pooling layer, fully connected layer, and non-linear layer. The convolutional layer uses kernel filters to calculate the convolution of the input image by extracting the fundamental features. The pooling layer combines two successive convolutional layers. The third layer is the fully connected layer, commonly called the convolutional output layer. The activation function defines the output of a neural network, such as 'yes' or 'no'. The most common and popular CNN activation functions are Sigmoid, Tanh, ReLU, Leaky ReLU, Noisy ReLU, and Parametric Linear Units. The organization and function of the visual cortex greatly influence CNN architecture because it is designed to resemble the neuronal connections in the human brain. Some of the popular CNN architectures are LeNet, AlexNet and VGGNet.