Miracle-dz/UniFAR-FTUs huggingface dataset:
Inheritance of self- and graft-incompatibility traits in an F1 apricot progeny

Floral self-incompatibility affecting yearly yield in a weather-dependent manner and graft incompatibility affecting longevity of mature trees are two important traits for apricot production. However, genetic control of graft compatibility and relationship between these traits are unknown. Here, we analyzed its inheritance in an F1 apricot progeny from a cross between self- and graft- incompatible and self- and graft-compatible cultivars. Hybrid individuals were genotyped for establishing self-incompatibility status and grafted on the plum rootstock ‘Marianna 2624’. Phenotyping of graft incompatibility was done at two time points, one month and one year after grafting. Anatomical (necrotic layer, bark and wood discontinuity for two consecutive years) and cytomorphological (cell proliferation, cell arrangement and cell shape one month after grafting) characteristics related to graft compatibility displayed continuous variation within the progeny, suggesting a polygenic inheritance. Using the Pearson correlation test, strong and significant correlations were detected between anatomical and cytomorphological traits that may reduce the number of characters for screening genotypes or progenies for graft compatibility in segregating crosses. Furthermore, no correlation existed between self- and graft incompatibility traits suggesting that they are independent inheritance traits. Hence, screening an extended hybrid population is required for pyramiding these traits in breeding programs.
Effects of Viscosupplementation on Quality of Knee Joint Arthrokinematic Motion Analyzed by Vibroarthrography

Objective To evaluate the influence of viscosupplementation on osteoarthritic knee arthrokinematics analyzed by VAG. It is considered that intra-articular hyaluronic acid injection may improve the function of synovial joints by recovery of friction-reducing properties of articular environment. Design Thirty-five patients with knee osteoarthritis (grade II according to the Kellgren-Lawrence system) and 50 asymptomatic subjects were enrolled in the study. Patients were analyzed at 3 time points: 1 day before and 2 weeks and 4 weeks after single injection of 1.5% cross-linked hyaluronate. Control subjects were tested once. The vibroarthrographic signals were collected during knee flexion/extension motion using an accelerator and described by variation of mean square (VMS), mean range (R5), and power spectral density for frequency of 50 to 250 Hz (P1), and 250 to 450 Hz (P2). Results Patients before viscosupplementation were characterized by about 2-fold higher values of vibroarthrographic parameters than controls. Two weeks after the procedure, the values of R5, P1, and P2 significantly decreased, in comparison to pre-injection. At 4 weeks post-injection, we noted a significant increase in R5, P1, and P2 values, when compared to 2 weeks post-injection. Finally, at 4 weeks post-injection, the level of VMS, R5, and P2 parameters did not differ from values obtained at pre-injection. Conclusions We showed that viscosupplementation may be effective in providing arthrokinematics improvement, but with a relatively short period of duration. This phenomenon is observed as decreased vibroacoustic emission, which reflects a more smooth movement in the joint.
Parents' Experiences Discussing Pediatric Vaccination with Healthcare Providers: A Survey of Canadian Naturopathic Patients

Background Parents who choose to selectively vaccinate or avoid vaccination for their children may do so at risk of compromising relations with their family physician or pediatrician. Groups that are associated with reduced rates of pedicatic vaccination, such as parents who access naturopathic care, may be particularly vulnerable to this issue. Methodology/Principal Findings In March through September 2010, we administered a 26-item cross-sectional survey to 129 adult patients, all of whom were parents with children ≤16 years of age, presenting for naturopathic care in Ontario, Canada. Ninety-five parents completed the survey (response rate 74%), and only 50.5% (48 of 95) reported that their children had received all recommended vaccines. Most parents (50.5%; 48 of 95) reported feeling pressure to vaccinate from their allopathic physician and, of those who discussed vaccination with their physician, 25.9% (21 of 81) were less comfortable continuing care as a result. Five percent (4 of 81) of respondents were advised by their physician that their children would be refused care if they decided against vaccination. In our adjusted generalized linear model, feeling pressure to vaccinate (odds ratio [OR] = 3.07; 95% confidence interval [CI] = 1.14 to 8.26) or endorsing a naturopathic physician as their most trusted source of information regarding vaccination (OR = 3.57; 95% CI = 1.22 to 10.44) were associated with greater odds of having a partially vaccinated or unvaccinated child. The majority (69.6%; 32 of 46) of parent's with partially vaccinated or unvaccinated children reported a willingness to re-consider this decision. Conclusions/Significance Use of naturopathic care should be explored among parents in order to identify this high-risk group and engage them in discussion regarding pediatric vaccination to encourage evidence-based, shared decision making. Physicians should ensure that discussions regarding vaccination are respectful, even if parents are determined not to vaccinate their children.
Human natural killer cells mediate adaptive immunity to viral antigens

Vaccination or childhood infection elicits antigen-specific, long-lived immunological memory in human natural killer cells. Recall responses by human NK cells One of the traditional dividing lines separating innate and adaptive immunity was the restriction of immune memory to adaptive immune cells. This paradigm has been challenged by accumulating evidence that memory responses can be evoked in natural killer (NK) cells from experimental animals, including mice and nonhuman primates. To determine whether human NK cells also exhibit memory responses, Nikzad et al. analyzed NK cells recovered from humanized mice or NK cells found in the viral antigen-challenged skin of adult volunteers who had chickenpox as children. Antigen-specific recall responses by human NK cells were observed in both experimental systems. These findings suggest that human NK memory responses contribute to acquired host protection after either natural infections or vaccine administration. Adaptive immune responses are defined as antigen sensitization–dependent and antigen-specific responses leading to establishment of long-lived immunological memory. Although natural killer (NK) cells have traditionally been considered cells of the innate immune system, mounting evidence in mice and nonhuman primates warrants reconsideration of the existing paradigm that B and T cells are the sole mediators of adaptive immunity. However, it is currently unknown whether human NK cells can exhibit adaptive immune responses. We therefore tested whether human NK cells mediate adaptive immunity to virally encoded antigens using humanized mice and human volunteers. We found that human NK cells displayed vaccination-dependent, antigen-specific recall responses in vitro, when isolated from livers of humanized mice previously vaccinated with HIV-encoded envelope protein. Furthermore, we discovered that large numbers of cytotoxic NK cells with a tissue-resident phenotype were recruited to sites of varicella-zoster virus (VZV) skin test antigen challenge in VZV-experienced human volunteers. These NK-mediated recall responses in humans occurred decades after initial VZV exposure, demonstrating that NK memory in humans is long-lived. Our data demonstrate that human NK cells exhibit adaptive immune responses upon vaccination or infection. The existence of human memory NK cells may allow for the development of vaccination-based approaches capable of establishing potent NK-mediated memory functions contributing to host protection.
Emerging Roles of Focal Adhesion Kinase in Cancer

Focal adhesion kinase (FAK) is a cytoplasmic nonreceptor tyrosine kinase that enables activation by growth factor receptors or integrins in various types of human cancers. The kinase-dependent and kinase-independent scaffolding functions of FAK modulate the authentic signaling and fundamental functions not only in cancer cells but also in tumor microenvironment to facilitate cancer progression and metastasis. The overexpression and activation of FAK are usually investigated in primary or metastatic cancers and correlated with the poor clinical outcome, highlighting FAK as a potential prognostic marker and anticancer target. Small molecule inhibitors targeting FAK kinase activity or FAK-scaffolding functions impair cancer development in preclinical or clinical trials. In this review, we give an overview for FAK signaling in cancer cells as well as tumor microenvironment that provides new strategies for the invention of cancer development and malignancy.
Design of a non-contact magnetic spring for vibration isolation

This document serves to summarise the research performed by the author undertaken in approximately the first six months of his doctorate. The aim of the project is to build a vibration isolation table using non-contact magnetic springs. The document is structured with an introduction to the project, followed by an introduction to the field of magnetic levitation, including a literature review. The majority of the document then focusses on the basics and findings thus far of the magnetic design of the spring, concluding with the future work and timeline of the project. Regarding the document This document has been typeset using pdfLATEX with margin kerning. PDF hyperlinks have been automatically inserted in all appropriate positions: at footnote, page number, bibliographical, figure, and table references. Furthuremore, bibliographies are appended with page number hyperlinks for convenience. All hyperlinks have been typeset black to ensure consistent output via screen or print. Page margins have been chosen to ensure the optimal number of characters per line (approximately 66) for ease of reading.
Generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids

Significance Rods and cones are photoreceptor cells with different distributions and functions in the human retina. Rods are dominant at the periphery, which is responsible for peripheral vision; cones are enriched in the macula, which is responsible for central vision and visual acuity. Macular degenerations affect vision the most and are currently incurable. Unique to primates, the macula is challenging to study. Retinal organoids are promising tools in retinal studies, but cone-rich retinal organoids have not been adequately demonstrated and rigorous transcriptome profiling of retinal organoids has not been sufficiently addressed. Here we report the generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids, which resemble the macula/fovea based on the ratio of cones to rods and single-cell transcriptomes. Rod and cone photoreceptors are light-sensing cells in the human retina. Rods are dominant in the peripheral retina, whereas cones are enriched in the macula, which is responsible for central vision and visual acuity. Macular degenerations affect vision the most and are currently incurable. Here we report the generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids differentiated from hESCs using an improved retinal differentiation system. Induced by extracellular matrix, aggregates of hESCs formed single-lumen cysts composed of epithelial cells with anterior neuroectodermal/ectodermal fates, including retinal cell fate. Then, the cysts were en bloc-passaged, attached to culture surface, and grew, forming colonies in which retinal progenitor cell patches were found. Following gentle cell detachment, retinal progenitor cells self-assembled into retinal epithelium—retinal organoid—that differentiated into stratified cone-rich retinal tissue in agitated cultures. Electron microscopy revealed differentiating outer segments of photoreceptor cells. Bulk RNA-sequencing profiling of time-course retinal organoids demonstrated that retinal differentiation in vitro recapitulated in vivo retinogenesis in temporal expression of cell differentiation markers and retinal disease genes, as well as in mRNA alternative splicing. Single-cell RNA-sequencing profiling of 8-mo retinal organoids identified cone and rod cell clusters and confirmed the cone enrichment initially revealed by quantitative microscopy. Notably, cones from retinal organoids and human macula had similar single-cell transcriptomes, and so did rods. Cones in retinal organoids exhibited electrophysiological functions. Collectively, we have established cone-rich retinal organoids and a reference of transcriptomes that are valuable resources for retinal studies.
Ripples and dunes in a turbulent stream . Part 2 : Evidences against the formation of river dunes by primary linear instability

It is widely accepted that both ripples and dunes form in rivers by primary linear instability, the wavelength of the former scaling on the grain size, that of the latter being controled by the water depth. We revisit here this problem, using the derivation of the turbulent flow over a wavy bottom performed in Part 1. A multi-scale description of the problem is proposed, in which the details of the different mechanisms controlling sediment transport are encoded into three quantities: the saturated flux, the saturation length and the threshold shear stress. Theses quantities are modelled in the case of erosion and momentum limited bed loads. This framework allows to give a clear picture of the instability in terms of dynamical mechanisms. The relation between the wavelength at which ripples form and the flux saturation length is quantitatively derived. It allows to explain the discrepancy between measured initial wavelengths and predictions that do not take this lag between flow velocity and sediment transport into account. Experimental data is used to determine the saturation length as a function of grain size and shear velocity. Finally, we show that the presence of a free surface always has a stabilising effect, whatever the choice of the turbulence closure and of the sand transport model. Consequently, the shape of the dispersion relation obtained from the linear stability analysis of a flat sand bed is such that dunes can not result from a primary linear instability. This suggests that dunes form by a non-linear pattern coarsening which is limited by the flow depth.
Defective Escape Behavior in DEAH-Box RNA Helicase Mutants Improved by Restoring Glycine Receptor Expression

RNA helicases regulate RNA metabolism, but their substrate specificity and in vivo function remain largely unknown. We isolated spontaneous mutant zebrafish that exhibit an abnormal dorsal bend at the beginning of tactile-evoked escape swimming. Similar behavioral defects were observed in zebrafish embryos treated with strychnine, which blocks glycine receptors (GlyRs), suggesting that the abnormal motor response in mutants may be attributable to a deficit in glycinergic synaptic transmission. We identified a missense mutation in the gene encoding RNA helicase Dhx37. In Dhx37 mutants, ribosomal RNA levels were unchanged, whereas GlyR α1, α3, and α4a subunit mRNA levels were decreased due to a splicing defect. We found that Dhx37 can interact with GlyR α1, α3, and α4a transcripts but not with the GlyR α2 subunit mRNA. Overexpression of GlyR α1, α3, or α4a subunits in Dhx37-deficient embryos restored normal behavior. Conversely, antisense-mediated knockdown of multiple GlyR α subunits in wild-type embryos was required to recapitulate the Dhx37 mutant phenotype. These results indicate that Dhx37 is specifically required for the biogenesis of a subset of GlyR α subunit mRNAs, thereby regulating glycinergic synaptic transmission and associated motor behaviors. To our knowledge, this is the first identification of pathologically relevant substrates for an RNA helicase.
Characterising Upper Limb Movements in Huntington's Disease and the Impact of Restricted Visual Cues

Background Voluntary motor deficits are a common feature in Huntington's disease (HD), characterised by movement slowing and performance inaccuracies. This deficit may be exacerbated when visual cues are restricted. Objective To characterize the upper limb motor profile in HD with various levels of difficulty, with and without visual targets. Methods Nine premanifest HD (pre-HD), nine early symptomatic HD (symp-HD) and nine matched controls completed a motor task incorporating Fitts' law, a model of human movement enabling the quantification of movement timing, via the manipulation of task difficulty (i.e., target size, and distance between targets). The task required participants to make reciprocal movements under cued and blind conditions. Dwell times (time stationary between movements), speed, accuracy and variability of movements were compared between groups. Results Symp-HD showed significantly prolonged and less consistent movement times, compared with controls and pre-HD. Furthermore, movement planning and online control were significantly impaired in symp-HD, compared with controls and pre-HD, evidenced by prolonged dwell times and deceleration times. Speed and accuracy were comparable across groups, suggesting that group differences observed in movement time, variability, dwell time and deceleration time were evident over and above simple performance measures. The presence of cues resulted in greater movement time variability in symp-HD, compared with pre-HD and controls, suggesting that the deficit in movement consistency manifested only in response to targeted movements. Conclusions Collectively, these findings provide evidence of a deficiency in both motor planning, particularly in relation to movement timing and online control, which became exacerbated as a function of task difficulty during symp-HD stages. These variables may provide a more sensitive measure of motor dysfunction than speed and/or accuracy alone in symp-HD.
The concerted actions of Tip1/CLIP-170, Klp5/Kinesin-8, and Alp14/XMAP215 regulate microtubule catastrophe at the cell end

Abstract Spatial regulation of microtubule catastrophe is important for controlling microtubule length and consequently contributes to the proper establishment of cell polarity and cell growth. The +TIP proteins including Tip1/CLIP-170, Klp5/Kinesin-8, and Alp14/XMAP215 reside at microtubule plus ends to regulate microtubule dynamics. In the fission yeast Schizosaccharomyces pombe, Tip1 and Alp14 serve as microtubule-stabilizing factors, while Klp5 functions oppositely as a catastrophe-promoting factor. Despite that Tip1 has been shown to play a key role in restricting microtubule catastrophe to the cell end, how Tip1 fulfills the role remains to be determined. Employing live-cell microscopy, we showed that the absence of Tip1 impairs the localization of both Klp5 and Alp14 at microtubule plus ends, but the absence of Klp5 prolongs the residence time of Tip1 at microtubule plus ends. We further revealed that Klp5 accumulates behind Tip1 at microtubule plus ends in a Tip1-dependent manner. In addition, artificially tethering Klp5 to microtubule plus ends promotes premature microtubule catastrophe, while tethering Alp14 to microtubule plus ends in the cells lacking Tip1 rescues the phenotype of short microtubules. These findings establish that Tip1 restricts microtubule catastrophe to the cell end likely by spatially restricting the microtubule catastrophe activity of Klp5 and stabilizing Alp14 at microtubule plus ends. Thus, the work demonstrates the orchestration of Tip1, Alp14, and Klp5 in ensuring microtubule catastrophe at the cell end.
Civil War

Most nations have experienced an internal armed conflict since 1960. Yet while civil war is central to many nations’ development, it has stood at the periphery of economics research and teaching. The past decade has witnessed a long overdue explosion of research into war’s causes and consequences. We summarize progress, identify weaknesses, and chart a path forward. Why war? Existing theory is provocative but incomplete, omitting advances in behavioral economics and making little progress in key areas, like why armed groups form and cohere, or how more than two armed sides compete. Empirical work finds that low per capita incomes and slow economic growth are both robustly linked to civil war. Yet there is little consensus on the most effective policies to avert conflicts or promote postwar recovery. Cross-country analysis of war will benefit from more attention to causal identification and stronger links to theory. We argue that micro-level analysis and case studies are also crucial to decipher war’s causes, conduct, and consequences. We bring a growth theoretic approach to the study of conflict consequences to highlight areas for research, most of all the study of war’s impact on institutions. We conclude with a plea for new and better data. ( JEL D72, D74, O17)
Novel stochastic framework for automatic segmentation of human thigh MRI volumes and its applications in spinal cord injured individuals

Severe spinal cord injury (SCI) leads to skeletal muscle atrophy and adipose tissue infiltration in the skeletal muscle, which can result in compromised muscle mechanical output and lead to health-related complications. In this study, we developed a novel automatic 3-D approach for volumetric segmentation and quantitative assessment of thigh Magnetic Resonance Imaging (MRI) volumes in individuals with chronic SCI as well as non-disabled individuals. In this framework, subcutaneous adipose tissue, inter-muscular adipose tissue and total muscle tissue are segmented using linear combination of discrete Gaussians algorithm. Also, three thigh muscle groups were segmented utilizing the proposed 3-D Joint Markov Gibbs Random Field model that integrates first order appearance model, spatial information, and shape model to localize the muscle groups. The accuracy of the automatic segmentation method was tested both on SCI (N = 16) and on non-disabled (N = 14) individuals, showing an overall 0.93±0.06 accuracy for adipose tissue and muscle compartments segmentation based on Dice Similarity Coefficient. The proposed framework for muscle compartment segmentation showed an overall higher accuracy compared to ANTs and STAPLE, two previously validated atlas-based segmentation methods. Also, the framework proposed in this study showed similar Dice accuracy and better Hausdorff distance measure to that obtained using DeepMedic Convolutional Neural Network structure, a well-known deep learning network for 3-D medical image segmentation. The automatic segmentation method proposed in this study can provide fast and accurate quantification of adipose and muscle tissues, which have important health and functional implications in the SCI population.
Optimal placement of FACTS devices by a Group Search Optimizer with Multiple Producer

This paper presents a group search optimizer with multiple producer (GSOMP) for reactive power dispatch incorporating with flexible AC transmission system (FACTS) devices, which is formulated as a nonlinear constrained multi-objective optimization problem. The optimal location of multi-type FACTS devices and their control parameters are optimized by GSOMP to minimize the real power loss and also to improve voltage profile. The performance of GSOMP has been evaluated on the standard IEEE 14-bus and New England 39-bus test systems respectively. Simulation results show that the performance of the power systems is improved with multi-type FACTS devices optimally placed in the reactive power planning model.