Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation

Eukaryotic centromeres contain the kinetochore, which connects chromosomes to the spindle allowing segregation. During meiosis, centromeres are suppressed for inter-homolog crossover, as recombination in these regions can cause chromosome missegregation and aneuploidy. Plant centromeres are surrounded by transposon-dense pericentromeric heterochromatin that is epigenetically silenced by histone 3 lysine 9 dimethylation (H3K9me2), and DNA methylation in CG and non-CG sequence contexts. However, the role of these chromatin modifications in control of meiotic recombination in the pericentromeres is not fully understood. Here, we show that disruption of Arabidopsis thaliana H3K9me2 and non-CG DNA methylation pathways, for example, via mutation of the H3K9 methyltransferase genes KYP/SUVH4 SUVH5 SUVH6, or the CHG DNA methyltransferase gene CMT3, increases meiotic recombination in proximity to the centromeres. Using immunocytological detection of MLH1 foci and genotyping by sequencing of recombinant plants, we observe that H3K9me2 and non-CG DNA methylation pathway mutants show increased pericentromeric crossovers. Increased pericentromeric recombination in H3K9me2/non-CG mutants occurs in hybrid and inbred backgrounds and likely involves contributions from both the interfering and noninterfering crossover repair pathways. We also show that meiotic DNA double-strand breaks (DSBs) increase in H3K9me2/non-CG mutants within the pericentromeres, via purification and sequencing of SPO11-1-oligonucleotides. Therefore, H3K9me2 and non-CG DNA methylation exert a repressive effect on both meiotic DSB and crossover formation in plant pericentromeric heterochromatin. Our results may account for selection of enhancer trap Dissociation (Ds) transposons into the CMT3 gene by recombination with proximal transposon launch-pads.
Congenital prosopagnosia without object agnosia? A literature review

ABSTRACT A longstanding controversy concerns the functional organization of high-level vision, and the extent to which the recognition of different classes of visual stimuli engages a single system or multiple independent systems. We examine this in the context of congenital prosopagnosia (CP), a neurodevelopmental disorder in which individuals, without a history of brain damage, are impaired at face recognition. This paper reviews all CP cases from 1976 to 2016, and explores the evidence for the association or dissociation of face and object recognition. Of the 238 CP cases with data permitting a satisfactory evaluation, 80.3% evinced an association between impaired face and object recognition whereas 19.7% evinced a dissociation. We evaluate the strength of the evidence and correlate the face and object recognition behaviour. We consider the implications for theories of functional organization of the visual system, and offer suggestions for further adjudication of the relationship between face and object recognition.
MicroRNA Microarray Profiling during Megakaryocyte Differentiation of Cord Blood CD133+ Hematopoietic Stem Cells

Objective In order to clarify the role of microRNAs (miRNA) in megakaryocyte differentiation, we ran a microRNA microarray experiment to measure the expression level of 961 human miRNA in megakaryocytes differentiated from human umbilical cord blood CD133+ cells. Materials and Methods In this experimental study, human CD133+ hematopoietic stem cells were collected from three human umbilical cord blood (UCB) samples, and then differentiated to the megakaryocytic lineage and characterized by flow cytometry, CFU-assay and ploidy analysis. Subsequently, microarray analysis was undertaken followed by quantitative polymerase chain reaction (qPCR) to validate differentially expressed miRNA identified in the microarray analysis. Results A total of 10 and 14 miRNAs were upregulated (e.g. miR-1246 and miR-148-a) and down-regulated (e.g. miR- 551b and miR-10a) respectively during megakaryocyte differentiation, all of which were confirmed by qPCR. Analysis of targets of these miRNA showed that the majority of targets are transcription factors involved in megakaryopoiesis. Conclusion We conclude that miRNA play an important role in megakaryocyte differentiation and may be used as targets to change the rate of differentiation and further our understanding of the biology of megakaryocyte commitment.
THE SMOOTH MUSCLE CELL

Smooth muscle derived from the inner media and intima of immature guinea pig aorta were grown for up to 8 wk in cell culture. The cells maintained the morphology of smooth muscle at all phases of their growth in culture. After growing to confluency, they grew in multiple overlapping layers. By 4 wk in culture, microfibrils (110 A) appeared within the spaces between the layers of cells. Basement membrane-like material also appeared adjacent to the cells. Analysis of the microfibrils showed that they have an amino acid composition similar to that of the microfibrillar protein of the intact elastic fiber. These investigations coupled with the radioautographic observations of the ability of aortic smooth muscle to synthesize and secrete extracellular proteins demonstrate that this cell is a connective tissue synthetic cell.
Conditional Reduction of Predation Risk Associated with a Facultative Symbiont in an Insect

Symbionts are widespread among eukaryotes and their impacts on the ecology and evolution of their hosts are meaningful. Most insects harbour obligate and facultative symbiotic bacteria that can influence their phenotype. In the pea aphid Acyrthosiphon pisum, an astounding symbiotic-mediated phenotype has been recently observed: when infected with the symbiotic bacteria Rickettsiella viridis, young red aphid larvae become greener at adulthood and even darker green when co-infected with Rickettsiella viridis and Hamiltonella defensa. As body colour affects the susceptibility towards natural enemies in aphids, the influence of the colour change due to these facultative symbionts on the host survival in presence of predators was tested. Our results suggested that the Rickettsiella viridis infection may impact positively host survival by reducing predation risk. Due to results from uninfected aphids (i.e., more green ones attacked), the main assumption is that this symbiotic infection would deter the predatory ladybird feeding by reducing the profitability of their hosts rather than decreasing host detection through body colour change. Aphids co-infected with Rickettsiella viridis and Hamiltonella defensa were, however, more exposed to predation suggesting an ecological cost associated with multiple infections. The underlying mechanisms and ecological consequences of these symbiotic effects are discussed.
Home alone: a systematic review and meta‐analysis on the effects of individual housing on body weight, food intake and visceral fat mass in rodents

Rats and mice are widely used to study environmental effects on psychological and metabolic health. Study designs differ widely and are often characterized by varying (social) housing conditions. In itself, housing has a profound influence on physiology and behaviour of rodents, affecting energy balance and sustainable metabolic health. However, evidence for potential long‐term consequences of individual versus social housing on body weight and metabolic phenotype is inconsistent. We conducted a systematic literature review and meta‐analyses assessing effects of individual versus social housing of rats and mice, living under well‐accepted laboratory conditions, on measures of metabolic health, including body weight, food intake and visceral adipose tissue mass. Seventy‐one studies were included in this review; 59 were included in the meta‐analysis. Whilst housing did not affect body weight, both food intake and visceral adipose tissue mass were significantly higher in individually compared with socially housed animals. A combination of emotional stress and lack of social thermoregulation likely contributed to these effects. Increased awareness of consequences and improved specifications of housing conditions are necessary to accurately evaluate efficacy of drugs, diets or other interventions on metabolic and other health outcomes because housing conditions are rarely considered as possible moderators of reported outcomes.
Exploring Linear Relationship in Feature Map Subspace for ConvNets Compression

While the research on convolutional neural networks (CNNs) is progressing quickly, the real-world deployment of these models is often limited by computing resources and memory constraints. In this paper, we address this issue by proposing a novel filter pruning method to compress and accelerate CNNs. Our work is based on the linear relationship identified in different feature map subspaces via visualization of feature maps. Such linear relationship implies that the information in CNNs is redundant. Our method eliminates the redundancy in convolutional filters by applying subspace clustering to feature maps. In this way, most of the representative information in the network can be retained in each cluster. Therefore, our method provides an effective solution to filter pruning for which most existing methods directly remove filters based on simple heuristics. The proposed method is independent of the network structure, thus it can be adopted by any off-the-shelf deep learning libraries. Experiments on different networks and tasks show that our method outperforms existing techniques before fine-tuning, and achieves the state-of-the-art results after fine-tuning.
Stable Water Use Efficiency of Tibetan Alpine Meadows in Past Half Century: Evidence from Wool δ13C Values

Understanding the influences of climatic changes on water use efficiency (WUE) of Tibetan alpine meadows is important for predicting their long-term net primary productivity (NPP) because they are considered very sensitive to climate change. Here, we collected wool materials produced from 1962 to 2010 and investigated the long-term WUE of an alpine meadow in Tibet on basis of the carbon isotope values of vegetation (δ 13Cveg). The values of δ 13Cveg decreased by 1.34‰ during 1962–2010, similar to changes in δ 13C values of atmospheric CO2. Carbon isotope discrimination was highly variable and no trend was apparent in the past half century. Intrinsic water use efficiency (W i) increased by 18 μmol·mol–1 (approximately 23.5%) during 1962–2010 because the increase in the intercellular CO2 concentration (46 μmol·mol–1) was less than that in the atmospheric CO2 concentration (C a, 73 μmol·mol–1). In addition, W i increased significantly with increasing growing season temperature and C a. However, effective water use efficiency (W e) remained relatively stable, because of increasing vapor pressure deficit. C a, precipitation, and growing season temperature collectively explained 45% of the variation of W e. Our findings indicate that the W e of alpine meadows in the Tibetan Plateau remained relatively stable by physiological adjustment to elevated C a and growing season temperature. These findings improve our understanding and the capacity to predict NPP of these ecosystems under global change scenarios.
Structural and Functional Brain Connectivity of People with Obesity and Prediction of Body Mass Index Using Connectivity

Obesity is a medical condition affecting billions of people. Various neuroimaging methods including magnetic resonance imaging (MRI) have been used to obtain information about obesity. We adopted a multi-modal approach combining diffusion tensor imaging (DTI) and resting state functional MRI (rs-fMRI) to incorporate complementary information and thus better investigate the brains of non-healthy weight subjects. The objective of this study was to explore multi-modal neuroimaging and use it to predict a practical clinical score, body mass index (BMI). Connectivity analysis was applied to DTI and rs-fMRI. Significant regions and associated imaging features were identified based on group-wise differences between healthy weight and non-healthy weight subjects. Six DTI-driven connections and 10 rs-fMRI-driven connectivities were identified. DTI-driven connections better reflected group-wise differences than did rs-fMRI-driven connectivity. We predicted BMI values using multi-modal imaging features in a partial least-square regression framework (percent error 15.0%). Our study identified brain regions and imaging features that can adequately explain BMI. We identified potentially good imaging biomarker candidates for obesity-related diseases.
Silicon Surface Morphologies after Femtosecond Laser Irradiation

In this article, we present summaries of the evolution of surface morphology resulting from the irradiation of single-crystal silicon with femtosecond laser pulses. In the first section, we discuss the development of micrometer-sized cones on a silicon surface irradiated with hundreds of femtosecond laser pulses in the presence of sulfur hexafluoride and other gases. We propose a general formation mechanism for the surface spikes. In the second section, we discuss the formation of blisters or bubbles at the interface between a thermal silicon oxide and a silicon surface after irradiation with one or more femtosecond laser pulses. We discuss the physical mechanism for blister formation and its potential use as channels in microfluidic devices.
A K-means-based network partition algorithm for controller placement in software defined network

Software Defined Networking (SDN), the novel paradigm of decoupling the control logic from packet forwarding devices, has been drawing considerable attention from both academia and industry. As the latency between a controller and switches is a significant factor for SDN, selecting appropriate locations for controllers to shorten the latency becomes one grand challenge. In this paper, we investigate multi-controller placement problem from the perspective of latency minimization. Distinct from previous works, the network partition technique is introduced to simplify the problem. Specifically, the network partition problem and the controller placement problem are first formulated. An optimized K-means algorithm is then proposed to address the problem. Extensive simulations are conducted and results demonstrate that the proposed algorithm can remarkably reduce the maximum latency between centroid and their nodes compared with the standard K-means. Specifically, the maximum latency can reach 2.437 times shorter than the average latency achieved by the standard K-means.
Tumor lymphangiogenesis promotes T cell infiltration and potentiates immunotherapy in melanoma

Tumor lymphangiogenesis, a driver of immunosuppression and metastasis, also potentiates immunotherapy. Unintentional immunotherapy inhibition Metastatic spread depends on lymphangiogenesis, and mediators of this pathway are targeted clinically for cancer treatment. Fankhauser et al. used mouse models of melanoma to show that blocking lymphangiogenesis actually disrupted recruitment of naïve T cells and subsequent antitumor immunity. Data from patients enrolled in clinical trials confirmed that indicators of lymphangiogenesis were associated with robust T cell responses. These findings have important implications for the use and predictions of response to immunotherapy. In melanoma, vascular endothelial growth factor–C (VEGF-C) expression and consequent lymphangiogenesis correlate with metastasis and poor prognosis. VEGF-C also promotes tumor immunosuppression, suggesting that lymphangiogenesis inhibitors may be clinically useful in combination with immunotherapy. We addressed this concept in mouse melanoma models with VEGF receptor–3 (VEGFR-3)–blocking antibodies and unexpectedly found that VEGF-C signaling enhanced rather than suppressed the response to immunotherapy. We further found that this effect was mediated by VEGF-C–induced CCL21 and tumor infiltration of naïve T cells before immunotherapy because CCR7 blockade reversed the potentiating effects of VEGF-C. In human metastatic melanoma, gene expression of VEGF-C strongly correlated with CCL21 and T cell inflammation, and serum VEGF-C concentrations associated with both T cell activation and expansion after peptide vaccination and clinical response to checkpoint blockade. We propose that VEGF-C potentiates immunotherapy by attracting naïve T cells, which are locally activated upon immunotherapy-induced tumor cell killing, and that serum VEGF-C may serve as a predictive biomarker for immunotherapy response.
Dissipativity based H∞ control for nonlinear stochastic systems with time-varying delays

This paper is concerned with the H∞ state feedback control problem for a class of nonlinear stochastic systems with time-varying state delays. Firstly, the stochastic dissipativity of the time-delay nonlinear system is established, based on which the H∞ state feedback controller is synthesized. We show that the closed-loop system rendered by the designed controller can achieve the L2-gain performance and exponential stability in the sense of mean square. Finally, these sufficient conditions are further specialized as solving a linear matrix inequality (LMI) and a bilinear matrix inequality (BMI) for a class of special stochastic nonlinear delayed systems.
Effects of gonadotropin-releasing hormone agonist on human chorionic gonadotropin activity in granulosa cells of immature female rats

Although the expression of gonadotropin-releasing hormone (GnRH) in the ovaries is well established, its physiological role remains unknown. The aim of this study was to determine whether ovarian GnRH mediates the actions of human chorionic gonadotropin (hCG) in the granulosa cells of immature female rats. Follicular growth was induced by administration of pregnant mare serum gonadotropin (PMSG, 15 IU/0.15 ml) on day 25 after birth, and hCG (20 IU/0.2 ml) was administered on day 27 revealing the increase of plasma progesterone level. Primary cultures of granulosa cells were established from large follicles 2 days after PMSG treatment. Progesterone synthesis was augmented by hCG in a dose-dependent manner. Annexin A5 (ANXA5), a biomarker of GnRH, was expressed in the granulosa-luteal cells after hCG treatment, as shown by immunohistochemistry, suggesting that hCG treatment induced GnRH action. The GnRH mRNA level was increased by hCG, and treatment with GnRH agonist (GnRHa) increased ANXA5 mRNA levels in the primary cultures of granulosa cells. Concomitant incubation of GnRH (10–7 M) or GnRHa (fertirelin acetate, 10–8 M) with hCG suppressed progesterone synthesis during a 3 h incubation period. The mRNA expression of luteinizing hormone receptor (LHR) and follicle-stimulating hormone receptor (FSHR) was synergistically stimulated and suppressed by hCG and GnRHa, respectively. GnRHa stimulated p21 expression, and GnRHa and hCG synergistically reduced the mRNA expression levels of p27 and FOXO1. These data suggest that GnRH induced by LH may have a role for the LH-mediated luteinization of granulosa cells. In addition, ANXA5 may be involved in GnRH action. GnRH-ANXA5 would be an important mechanism in cell differentiation.
Do adults with Down syndrome do the same amount of physical activity as adults without disability? A proof of principle study

BACKGROUND This study compared levels of physical activity completed by adults with and without Down syndrome. METHOD Fifteen adults with and 15 adults without Down syndrome matched for age and gender, took part. The intensity and duration of physical activity were measured using RT3 accelerometers worn for seven days. RESULTS Only, 12 participants with Down syndrome had complete physical activity data, and these participants and their matched controls (total: six females, 18 males; aged 25.8 ± 9.7) were included in the analyses. There were significantly lower levels of moderate and vigorous physical activity per day for people with Down syndrome (median = 27 min) compared to those without (median = 101 min) (p < .001). Participants without disability were twice more likely to achieve recommended levels of physical activity than people with Down syndrome. CONCLUSIONS Adults with Down syndrome appear to participate in lower levels of physical activity than adults without Down syndrome. Further research should validate these estimates.
Resected Brain Tissue, Seizure Onset Zone and Quantitative EEG Measures: Towards Prediction of Post-Surgical Seizure Control

Background Epilepsy surgery is a potentially curative treatment option for pharmacoresistent patients. If non-invasive methods alone do not allow to delineate the epileptogenic brain areas the surgical candidates undergo long-term monitoring with intracranial EEG. Visual EEG analysis is then used to identify the seizure onset zone for targeted resection as a standard procedure. Methods Despite of its great potential to assess the epileptogenicty of brain tissue, quantitative EEG analysis has not yet found its way into routine clinical practice. To demonstrate that quantitative EEG may yield clinically highly relevant information we retrospectively investigated how post-operative seizure control is associated with four selected EEG measures evaluated in the resected brain tissue and the seizure onset zone. Importantly, the exact spatial location of the intracranial electrodes was determined by coregistration of pre-operative MRI and post-implantation CT and coregistration with post-resection MRI was used to delineate the extent of tissue resection. Using data-driven thresholding, quantitative EEG results were separated into normally contributing and salient channels. Results In patients with favorable post-surgical seizure control a significantly larger fraction of salient channels in three of the four quantitative EEG measures was resected than in patients with unfavorable outcome in terms of seizure control (median over the whole peri-ictal recordings). The same statistics revealed no association with post-operative seizure control when EEG channels contributing to the seizure onset zone were studied. Conclusions We conclude that quantitative EEG measures provide clinically relevant and objective markers of target tissue, which may be used to optimize epilepsy surgery. The finding that differentiation between favorable and unfavorable outcome was better for the fraction of salient values in the resected brain tissue than in the seizure onset zone is consistent with growing evidence that spatially extended networks might be more relevant for seizure generation, evolution and termination than a single highly localized brain region (i.e. a “focus”) where seizures start.