Miracle-dz/UniFAR-FTUs huggingface dataset:
Overleaf Example

We present a sampling-based approach to reasoning about the caging-based manipulation of rigid and a simplified class of deformable 3D objects subject to energy constraints. Towards this end, we propose the notion of soft fixtures extending earlier work on energy-bounded caging to include a broader set of energy function constraints and settings, such as gravitational and elastic potential energy of 3D deformable objects. Previous methods focused on establishing provably correct algorithms to compute lower bounds or analytically exact estimates of escape energy for a very restricted class of known objects with low-dimensional C-spaces, such as planar polygons. We instead propose a practical sampling-based approach that is applicable in higherdimensional C-spaces but only produces a sequence of upperbound estimates that, however, appear to converge rapidly to actual escape energy. We present 8 simulation experiments demonstrating the applicability of our approach to various complex quasi-static manipulation scenarios. Quantitative results indicate the effectiveness of our approach in providing upper-bound estimates for escape energy in quasi-static manipulation scenarios. Two real-world experiments also show that the computed normalized escape energy estimates appear to correlate strongly with the probability of escape of an object under randomized pose perturbation.
Gait optimization for a multilink anguilliform swimmer

Hyper-redundant mechanisms (HRMs), also known as snake-like robots, have been the target of a small but focused research push over the past four decades. Consisting of a simple kinematic chain with a large number of redundant degrees of freedom (DoF), they can act manipulators approximating the form and function of an elephant's trunk, or undulatory locomotors mimicking the motions of snakes, worms, and other creatures. Although past research on locomotion has largely restricted itself to land-based studies, hyper-redundant mechanisms are inherently well suited to aquatic propulsion. Their structural form allows them to directly mimic the swimming motions of anguilliform fish. Biological anguilliform swimmers are both maneuverable and extremely efficient, however, these properties hinge upon finely tuned body deformations. The current understanding of undulatory swimming does not provide a clear method to optimally define these deformations for a highly articulated system. The present study solves this issue by developing a scheme capable of producing optimal gaits for a hyper-redundant swimmer. The optimization process consists ofa self-propelled swimming model and a custom particle swarm algorithm. The proposed scheme is used to produce optimal gaits for efficient swimming over a range of different velocities and for high acceleration. Although the development of the gait generation process is an end in itself, the properties of the optimal swimming kinematics also provide insight on HRMs and undulatory swimming in a more general sense. Simple control strategies, key issues for design, and potential topics for future work are extracted from the results. %%%%Les recherches precedentes on montres que des mecanismes hyper-redondants (MHR)sont fortement adaptables en bougeant sur la terre. Cependant, leurs capacites pourraient aussi etre etendues aux environnements aquatiques par la propulsion semblable a celle de l'anguille. Les nageurs anguilliforme naturels sont autant manuvrables qu'extremement efficaces. Cependant, ces proprietes dependent de deformations tres specifiques du corps. La comprehension actuelle de la nage ondulatoire ne fournit pas de methode claire ou de facon optimale afin de definir ces deformations pour un systeme fortement articule. L'etude presentee ici resout cette question en developpant un processus informatique capable de produire des demarches optimales pour un robot hyper-redondant nageant. Le processus est compose d'un modele nageant et d'un algorithme d'essaim de particules faits sur mesure. Cette solution d'optimisation est utilisee pour produire des demarches efficaces pour la natation sur une gamme de vitesses differentes et pour la haute acceleration. Bien que le developpement du processus d'optimisation soit une fin en soi, les proprietes de la cinematique de la nage optimale fournis aussi un aperu sur les MHRs et sur la natation ondulatoire dans un sens plus general. Des strategies de controle simples, des problemes-cles pour le design, et des sujets potentiels pour le travail a…
Race, Masculinity, and Personality Development: Understanding the Black Male Experience in America

Although men from all racial backgrounds have several poor health outcomes, most of the research suggests that Black men have even worse health outcomes compared to White men (Bowman, 1989; Watkins & Neighbors, 2007; Williams, 2003). The majority of published research on masculinity, however, has primarily focused on samples of White men. The issue of how racism intersects with masculinity and its impact on Black men remains understudied and is a current area of focus in the field. The present study examined relationships between Black men on the cultural measures of masculinity and self-esteem, Dark Triad (narcissism, psychopathy, and Machiavellianism), and self-compassion. Black men (N = 278) were recruited from mTurk to participate in a brief online survey. Structural equation modeling revealed that adherence to traditional/hegemonic masculine norms was more strongly and positively associated with self-esteem, endorsement of Dark Triad traits, and self-compassion. The relationship between Black masculinity and self-esteem and self-compassion was also positive, although these relationships were weaker. Black masculinity was negatively related to endorsement of Dark Triad traits which may serve as a protective factor. These findings highlight the need to better understand the ways in which multiple factors integrate and inherently influence personality as well as adaptive and maladaptive coping mechanisms in particular contexts among Black men. Intervention and prevention implications include integration of discussion related to masculinity themes in the research and therapy process.
Deep Iterative Reconstruction for Phase Retrieval

The classical phase retrieval problem is the recovery of a constrained image from the magnitude of its Fourier transform. Although there are several well-known phase retrieval algorithms, including the hybrid input-output (HIO) method, the reconstruction performance is generally sensitive to initialization and measurement noise. Recently, deep neural networks (DNNs) have been shown to provide state-of-the-art performance in solving several inverse problems such as denoising, deconvolution, and superresolution. In this work, we develop a phase retrieval algorithm that utilizes two DNNs together with the model-based HIO method. First, a DNN is trained to remove the HIO artifacts, and is used iteratively with the HIO method to improve the reconstructions. After this iterative phase, a second DNN is trained to remove the remaining artifacts. Numerical results demonstrate the effectiveness of our approach, which has little additional computational cost compared to the HIO method. Our approach not only achieves state-of-the-art reconstruction performance but also is more robust to different initialization and noise levels.
Supplement to : Uncertainty quantification , propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models

S1 Model details S1.1 Additional information on the LTP LTD pathway autophosphorylation As described in the main text, the following elementary species are included in the model: calcium (Ca), calmodulin (CaM), protein phosphatase 2B (PP2B) and Ca/CaM-dependent protein kinase II (CaMKII) and protein phosphatase 1 (PP1). CaM is a Ca-binding protein involved in multiple signaling processes and is strongly implicated in synaptic plasticity. CaM contains four Ca-binding domains, each binding one Ca ion. The binding of Ca by CaM is a cooperative process. Ca-bound CaM activates PP2B, another protein implicated in molecular processes related to learning which also plays a role in striatal signaling. The third protein, CaMKII, is a kinase, which is activated by the binding of Ca-CaM. CaMKII molecules exist as dodecamers, consisting of two hexamer rings. A CaMKII unit that has bound CaM can autophosphorylate when sitting beside an active neighbouring unit in the same hexamer ring. The phosphorylated unit can remain active even in the absence of Ca-CaM.
Collaboration and competition between active sheets for self-propelled particles

Significance Chemical and density gradients produced by catalytic reactions provide effective means of propelling particles in fluid-filled microchambers. Using computer modeling, we show the rich dynamic behavior that emerges when catalyst-coated sheets are combined with chemoresponsive particles in solution. Catalytic reactions on the flexible sheets generate density variations that produce fluid flows, which deform the sheets and drive their movement. The same reactions yield the chemical gradients that direct the particles’ motion. The resulting synergistic interactions among the sheets, particles, and fluid lead to bioinspired behavior, such as crab-shaped sheets competitively grabbing or collaboratively sharing particles, which can also flee these predators. By identifying parameters that govern the systems’ behavior, we provide guidelines for creating chemically driven, flexible robots for fluidic environments. Biological species routinely collaborate for their mutual benefit or compete for available resources, thereby displaying dynamic behavior that is challenging to replicate in synthetic systems. Here we use computational modeling to design microscopic, chemically active sheets and self-propelled particles encompassing the appropriate synergistic interactions to exhibit bioinspired feeding, fleeing, and fighting. This design couples two different mechanisms for chemically generating motion in fluid-filled microchambers: solutal buoyancy and diffusiophoresis. Catalyst-coated sheets, which resemble crabs with four distinct claws, convert reactants in solution into products and thereby create local variations in the density and chemical composition of the fluid. Via the solutal buoyancy mechanism, the density variations generate fluid flows, which modify the shape and motility of the crabs. Concomitantly, the chemical variations propel the motion of the particles via diffusiophoresis, and thus, the crabs’ and particles’ motion becomes highly interconnected. For crabs with restricted lateral mobility, these two mechanisms can be modulated to either drive a crab to catch and appear to feed on all of the particles or enable the particles to flee from this sheet. Moreover, by adjusting the sheet’s size and the catalytic coating, two crabs can compete and fight over the motile, diffusiophoretic particles. Alternatively, the crabs can temporally share resources by shuttling the particles back and forth between themselves. With completely mobile sheets, four crabs can collaborate to perform a function that one alone cannot accomplish. These findings provide design rules for creating chemically driven soft robotic sheets that significantly expand the functionality of microfluidic devices.
Novel insights into the genetics and epigenetics of MALT lymphoma unveiled by next generation sequencing analyses

Mucosa-associated lymphoid tissue (MALT) lymphoma is the most common type of marginal zone lymphoma (MZL) representing 5-8% of all B-cell lymphomas and occurs at diverse anatomic sites with site-specific clinical and biological differences. Unique among the three MZL (extranodal MZL of MALT type, splenic MZL, and nodal MZL), MALT lymphomas have recurrent chromosomal translocations with the BIRC3-MALT1 being the most frequent event observed in 15-40% of cases, especially those occurring in the lung and stomach. We analyzed 72 cases of MALT lymphomas derived from different anatomic sites (lung 32%, ocular adnexa 28%, salivary glands 18%, thyroid 7%, stomach 5%, and other 10%) for DNA copy number variations (CNV) and for the mutational status of a large panel of genes previously reported to be mutated in B-cell lymphomas (Online Supplementary Methods). In addition, for a subset of cases, transcriptional (n=21, 29%) and methylation (n=19, 26%) profiling was evaluated. DNA sequencing achieved at least 100x coverage in > 90% of the target regions (Online Supplementary Table S1 and Online Supplementary Figure S1) with a mean coverage of ~700x. From this analysis, we identified an average of three mutated genes per patient (range: 0-11). Seventy patients (97%) had at least one event (mutations or genomic alteration) and
Transcriptome Dynamics of Double Recessive Mutant, o2o2o16o16, Reveals the Transcriptional Mechanisms in the Increase of Its Lysine and Tryptophan Content in Maize

In maize, pyramiding of o2 and o16 alleles can greatly improve the nutritional quality of grains. To dissect its molecular mechanism, we created a double recessive mutant line, o2o2o16o16, by introgression of the o2 and o16 alleles into the wild-type maize inbred line, by molecular marker-assisted backcross selection. The kernels (18 day after pollination (DAP), 28 DAP, and 38 DAP) of the o2o2o16o16 mutant and its parent lines were subject to RNA sequencing (RNA-Seq). The RNA-Seq analysis revealed that 59 differentially expressed genes (DEGs) were involved in lysine metabolism and 43 DEGs were involved in tryptophan metabolism. Among them, the genes encoding AK, ASADH, and Dap-F in the lysine synthesis pathway were upregulated at different stages of endosperm development, promoting the synthesis of lysine. Meanwhile, the genes encoding LKR/SDH and L-PO in the lysine degradation pathway were downregulated, inhibiting the degradation of lysine. Moreover, the genes encoding TAA and YUC in the tryptophan metabolic pathway were downregulated, restraining the degradation of tryptophan. Thus, pyramiding o2 and o16 alleles could increase the lysine and tryptophan content in maize. These above results would help to uncover the molecular mechanisms involved in the increase in lysine and the tryptophan content, through the introgression of o2 and o16 alleles into the wild-type maize.
Effect Partitioning in Cross-Sectionally Clustered Data Without Multilevel Models

Abstract Effect partitioning is almost exclusively performed with multilevel models (MLMs) – so much so that some have considered the two to be synonymous. MLMs are able to provide estimates with desirable statistical properties when data come from a hierarchical structure; but the random effects included in MLMs are not always integral to the analysis. As a result, other methods with relaxed assumptions are viable options in many cases. Through empirical examples and simulations, we show how generalized estimating equations (GEEs) can be used to effectively partition effects without random effects. We show that more onerous steps of MLMs such as determining the number of random effects and the structure for their covariance can be bypassed with GEEs while still obtaining identical or near-identical results. Additionally, violations of distributional assumptions adversely affect estimates with MLMs but have no effect on GEEs because no such assumptions are made. This makes GEEs a flexible alternative to MLMs with minimal assumptions that may warrant consideration. Limitations of GEEs for partitioning effects are also discussed.
A cytorhabdovirus phosphoprotein forms mobile inclusions trafficked on the actin/ER network for viral RNA synthesis

Abstract As obligate parasites, plant viruses usually hijack host cytoskeletons for replication and movement. Rhabdoviruses are enveloped, negative-stranded RNA viruses that infect vertebrates, invertebrates, and plants, but the mechanisms of intracellular trafficking of plant rhabdovirus proteins are largely unknown. Here, we used Barley yellow striate mosaic virus (BYSMV), a plant cytorhabdovirus, as a model to investigate the effects of the actin cytoskeleton on viral intracellular movement and viral RNA synthesis in a mini-replicon (MR) system. The BYSMV P protein forms mobile inclusion bodies that are trafficked along the actin/endoplasmic reticulum network, and recruit the N and L proteins into viroplasm-like structures. Deletion analysis showed that the N terminal region (aa 43–55) and the remaining region (aa 56–295) of BYSMV P are essential for the mobility and formation of inclusions, respectively. Overexpression of myosin XI-K tails completely abolishes the trafficking activity of P bodies, and is accompanied by a significant reduction of viral MR RNA synthesis. These results suggest that BYSMV P contributes to the formation and trafficking of viroplasm-like structures along the ER/actin network driven by myosin XI-K. Thus, rhabdovirus P appears to be a dynamic hub protein for efficient recruitment of viral proteins, thereby promoting viral RNA synthesis.
Superparamagnetic iron oxide nanoparticle for in vivo molecular and cellular imaging

Over recent years, the biomedical applications of nanoparticles (NPs) (e.g. cell tracking, biosensing, magnetic resonance imaging, targeted drug delivery and tissue engineering) have been increasingly developed. Among the various NP types, superparamagnetic iron oxide NPs (SPIONs) have attracted a considerable amount of attention for early detection of diseases owing to their specific physicochemical properties and their molecular imaging capability. A comprehensive review is presented on the recent in vitro and in vivo advances in the development of SPION applications for molecular imaging, with their possibilities and limitations. Copyright © 2014 John Wiley & Sons, Ltd.
Sleep-Disordered Breathing

ABSTRACT Purpose of Review: Sleep-disordered breathing encompasses a broad spectrum of sleep-related breathing disorders, including obstructive sleep apnea (OSA), central sleep apnea, as well as sleep-related hypoventilation and hypoxemia. Diagnostic criteria have been updated in the International Classification of Sleep Disorders, Third Edition and the American Academy of Sleep Medicine Manual for Scoring Sleep and Associated Events. Neurologic providers should have basic knowledge and skills to identify at-risk patients, as these disorders are associated with substantial morbidity, the treatment of which is largely reversible. Recent Findings: OSA is the most common form of sleep-disordered breathing and is highly prevalent and grossly underdiagnosed. Recent studies suggest that prevalence rates in patients with neurologic disorders including epilepsy and stroke exceed general population estimates. The physiologic changes that occur in OSA are vast and involve complex mechanisms that play a role in the pathogenesis of cardiovascular and metabolic disorders and, although largely unproven, likely impact brain health and disease progression in neurologic patients. A tailored sleep history and examination as well as validated screening instruments are effective in identifying patients with sleep-disordered breathing, although sleep testing is necessary for diagnostic confirmation. While continuous positive airway pressure therapy and other forms of noninvasive positive pressure ventilation remain gold standard treatments, newer therapies, including mandibular advancement, oral appliance devices, and hypoglossal nerve stimulation, have become available. Emerging evidence of the beneficial effects of treatment of sleep-disordered breathing on neurologic outcomes underscores the importance of sleep education and awareness for neurologic providers. Summary: Sleep-disordered breathing is highly prevalent and grossly underrecognized. The adverse medical and psychosocial consequences of OSA and other sleep-related breathing disorders are considerable. The impact of sleep therapies on highly prevalent neurologic disorders associated with substantial morbidity and health care costs is becoming increasingly recognized.
Triggering receptor expressed on myeloid cells‐2 fine‐tunes inflammatory responses in murine Gram‐negative sepsis

During infections, TLR‐mediated responses require tight regulation to allow for pathogen removal, while preventing overwhelming inflammation and immunopathology. The triggering receptor expressed on myeloid cells (TREM)‐2 negatively regulates inflammation by macrophages and impacts on phagocytosis, but the function of endogenous TREM‐2 during infections is poorly understood. We investigated TREM‐2's role in regulating TLR4‐mediated inflammation by studying wild‐type and TREM‐2‐/‐ mice challenged with LPS and found TREM‐2 to dampen early inflammation. Augmented early inflammation in TREM‐2‐/‐ animals was followed by an accelerated resolution and ultimately improved survival, associated with the induction of the negative regulator A20. Upon infection with Escherichia coli, the otherwise beneficial effect of an exaggerated early immune response in TREM‐2‐/‐ animals was counteracted by a 50% reduction in bacterial phagocytosis. In line with this, TREM‐2‐/‐ peritoneal macrophages (PMs) exhibited augmented inflammation following TLR4 stimulation, demonstrating the presence and negative regulatory functionality of TREM‐2 on primary PMs. Significantly, we identified a high turnover rate because TREM‐2 RNA is 25‐fold down‐regulated and the protein proteasomally degraded upon LPS encounter, thus ensuring a tightly regulated and versatile system that modulates inflammation. Our results illustrate TREM‐2's effects on infection‐triggered inflammation and identify TREM‐2 as a potential target to prevent overwhelming inflammation while preserving antibacterial‐effector functions. —Gawish, R. , Martins, R. , Böhm, B. , Wimberger, T. , Sharif, O. , Lakovits, K. , Schmidt, M. , Knapp, S. Triggering receptor expressed on myeloid cells‐2 fine‐tunes inflammatory responses in murine Gram‐negative sepsis. FASEB J. 29, 1247‐1257 (2015). www.fasebj. org
MAC Protocols for Terahertz Communication: A Comprehensive Survey

Terahertz communication is emerging as a future technology to support Terabits per second link with highlighting features as high throughput and negligible latency. However, the unique features of the Terahertz band such as high path loss, scattering, and reflection pose new challenges and results in short communication distance. The antenna directionality, in turn, is required to enhance the communication distance and to overcome the high path loss. However, these features in combine negate the use of traditional medium access protocols (MAC). Therefore, novel MAC protocol designs are required to fully exploit their potential benefits including efficient channel access, control message exchange, link establishment, mobility management, and line-of-sight blockage mitigation. An in-depth survey of Terahertz MAC protocols is presented in this paper. The paper highlights the key features of the Terahertz band which should be considered while designing an efficient Terahertz MAC protocol, and the decisions which if taken at Terahertz MAC layer can enhance the network performance. Different Terahertz applications at macro and nano scales are highlighted with design requirements for their MAC protocols. The MAC protocol design issues and considerations are highlighted. Further, the existing MAC protocols are also classified based on network topology, channel access mechanisms, and link establishment strategies as Transmitter and Receiver initiated communication. Open challenges and future research directions on Terahertz MAC protocols are also highlighted.