Miracle-dz/UniFAR-FTUs huggingface dataset:
Epiblast cells gather onto the anterior mesendoderm and initiate brain development without the direct involvement of the node in avian embryos: Insights from broad-field live imaging

Live imaging of migrating and interacting cells in developing embryos has opened a new means for deciphering fundamental principles in morphogenesis and patterning, which was not possible with classic approaches of experimental embryology. In our recent study, we devised a new genetic tool to sparsely label cells with a green-fluorescent protein in the broad field of chicken embryos, enabling the analysis of cell migration during the early stages of brain development. Trajectory analysis indicated that anterior epiblast cells from a broad area gather to the head axis to form the brain primordia or brain-abutting head ectoderm. Grafting the mCherry-labeled stage (st.) 4 node in an anterior embryonic region resulted in the anterior extension of the anterior mesendoderm (AME), the precursor for the prechordal plate and anterior notochord, from the node graft at st. 5. Grafting the st. 4 node or st. 5 AME at various epiblast positions that otherwise develop into the head ectoderm caused local cell gathering to the graft-derived AME. The node was not directly associated with this local epiblast-gathering activity. The gathered anterior epiblast cells developed into secondary brain tissue consisting of consecutive brain portions, e.g., forebrain and midbrain or midbrain and hindbrain, reflecting the brain portion specificities inherent to the epiblast cells. The observations indicated the bipotentiality of all anterior epiblast cells to develop into the brain or head ectoderm. Thus, a new epiblast brain field map is proposed, allowing the reinterpretation of classical node graft data, and the role of the AME is highlighted. The new model leads to the conclusion that the node does not directly participate in brain development.
Bone regeneration materials and their application over 20 years: A bibliometric study and systematic review

Bone regeneration materials (BRMs) bring us new sights into the clinical management bone defects. With advances in BRMs technologies, new strategies are emerging to promote bone regeneration. The aim of this study was to comprehensively assess the existing research and recent progress on BRMs, thus providing useful insights into contemporary research, as well as to explore potential future directions within the scope of bone regeneration therapy. A comprehensive literature review using formal data mining procedures was performed to explore the global trends of selected areas of research for the past 20 years. The study applied bibliometric methods and knowledge visualization techniques to identify and investigate publications based on the publication year (between 2002 and 2021), document type, language, country, institution, author, journal, keywords, and citation number. The most productive countries were China, United States, and Italy. The most prolific journal in the BRM field was Acta Biomaterialia, closely followed by Biomaterials. Moreover, recent investigations have been focused on extracellular matrices (ECMs) (370 publications), hydrogel materials (286 publications), and drug delivery systems (220 publications). Research hotspots related to BRMs and extracellular matrices from 2002 to 2011 were growth factor, bone morphogenetic protein (BMP)-2, and mesenchymal stem cell (MSC), whereas after 2012 were composite scaffolds. Between 2002 and 2011, studies related to BRMs and hydrogels were focused on BMP-2, in vivo, and in vitro investigations, whereas it turned to the exploration of MSCs, mechanical properties, and osteogenic differentiation after 2012. Research hotspots related to BRM and drug delivery were fibroblast growth factor, mesoporous materials, and controlled release during 2002–2011, and electrospinning, antibacterial activity, and in vitro bioactivity after 2012. Overall, composite scaffolds, 3D printing technology, and antibacterial activity were found to have an important intersection within BRM investigations, representing relevant research fields for the future. Taken together, this extensive analysis highlights the existing literature and findings that advance scientific insights into bone tissue engineering and its subsequent applications.
Clinical efficacy and safety of ultrasound-assisted thrombolysis vs. standard catheter-directed thrombolysis in patients with acute pulmonary embolism: A study level meta-analysis of clinical trials

Aim To compare the clinical efficacy of ultrasound-assisted thrombolysis (USAT) vs. standard catheter-directed thrombolysis (SCDT) in patients with acute pulmonary embolism (aPE). Methods This study analyzed the clinical outcomes of patients with non-low-risk aPE who received USAT or SCDT. The primary outcomes were all-cause death, total bleeding, and major bleeding. Secondary outcomes included pulmonary thrombotic load score (Miller), improvement in right ventricular-to-left ventricular ratio (RV/LV), dose and duration of the thrombolytic drug tissue plasminogen activator (tPA), length of stay (LOS) in the ICU, and total LOS in the hospital. Results A total of seven articles and 451 patients were included in this study. 241 patients were in the USAT group and 210 patients were in the SCDT group. There were no significant differences in all-cause mortality, total bleeding, and major bleeding between the two groups. Miller scores for pulmonary thrombus also showed no difference between the two groups, but pulmonary artery systolic pressure (PASP) was lower in the SCDT group after-treatment. The reduction of RV/LV from baseline was more pronounced in the SCDT group than in the USAT group (OR: −0.14, 95%CI: −0.20 to 0.07, P < 0.0001, I2 = 0%). Total dose of tPA and duration of infusion in the USAT group were lower than those in the SCDT group, but there was no significant statistical difference. LOS in the ICU was similar between the two groups, while LOS in the hospital was lower in the SCDT group. Conclusion This study did not detect any differences in all-cause mortality, total bleeding, and major bleeding between non-low-risk aPE patients treated with USAT or SCDT. Improvement in right ventricular function was better in the SCDT group, and hospital LOS was lower in the SCDT group.
Development of an Optimization Model for Multiple Production Systems with Split and Merge

Assembly Production Systems (ASPS) are used to assemble complex components in manufacturing industries such as automobile production, aviation, mechanical equipment, electronic goods and household items. Importantly, ASPS may, in a single production process, merge two or more serial production lines. Contrastingly, disassembly systems (DisASPS), with split lines, are employed to disassemble/systematically remove constituent parts from the final product, without impairment. The buffer size of the bay in front of each machine tool should be optimized for an efficient ASPS or DisASPS. The characteristics of machine tools, including their uptimes and downtimes, have a significant impact on decisions concerning buffer size and subsequently on the production rate of an ASPS or DisASPS. Optimum buffer size can achieve a high production rate which enhances the performance and operation of the entire production system. This research presents an effective method for determining optimal and near optimal design for assembly and disassembly production systems. The proposed model optimizes the buffer size among each couple of machine tools in the ASPS and DisAPS for any given uptime and downtime parameters of the machine tools. A Genetic Algorithms (GA)-based optimization model is used to determine the optimal values of buffer size for serial production lines in the production systems. The numerical examples performed in the research validated the ability of the optimization model in determining the buffer size. Optimized selection can be carried out quickly as compared to previous selection techniques. Moreover, the proposed algorithm can back the manufacturing engineer’s decision-making while development stage of new ASPS or DisASPS.
Reducing sample variance: halo biasing, non-linearity and stochasticity

Comparing clustering of differently biased tracers of the dark matter distribution offers the opportunity to reduce the sample or cosmic variance error in the measurement of certain cosmological parameters. We develop a formalism that includes bias non-linearities and stochasticity. Our formalism is general enough that it can be used to optimize survey design and tracers selection and optimally split (or combine) tracers to minimize the error on the cosmologically interesting quantities. Our approach generalizes the one presented by McDonald & Seljak of circumventing sample variance in the measurement off ≡ d ln D/d ln a. We analyse how the bias, the noise, the non-linearity and stochasticity affect the measurements of Df and explore in which signal-to-noise regime it is significantly advantageous to split a galaxy sample in two differently biased tracers. We use N-body simulations to find realistic values for the parameters describing the bias properties of dark matter haloes of different masses and their number density. We find that, even if dark matter haloes could be used as tracers and selected in an idealized way, for realistic haloes, the sample variance limit can be reduced only by up to a factor σ 2tr /σ 1tr ≃ 0.6. This would still correspond to the gain from a three times larger survey volume if the two tracers were not to be split. Before any practical application one should bear in mind that these findings apply to dark matter haloes as tracers, while realistic surveys would select galaxies: the galaxy-host halo relation is likely to introduce extra stochasticity, which may reduce the gain further.
A UNIVERSAL MODEL FOR HALO CONCENTRATIONS

We present a numerical study of dark matter halo concentrations in ΛCDM and self-similar cosmologies. We show that the relation between concentration, c, and peak height, ν, exhibits the smallest deviations from universality if halo masses are defined with respect to the critical density of the universe. These deviations can be explained by the residual dependence of concentration on the local slope of the matter power spectrum, n, which affects both the normalization and shape of the c–ν relation. In particular, there is no well-defined floor in the concentration values. Instead, the minimum concentration depends on redshift: at fixed ν, halos at higher z experience steeper slopes n, and thus have lower minimum concentrations. We show that the concentrations in our simulations can be accurately described by a universal seven-parameter function of only ν and n. This model matches our ΛCDM results to ≲ 5% accuracy up to z = 6, and matches scale-free Ωm = 1 models to ≲ 15%. The model also reproduces the low concentration values of Earth–mass halos at z ≈ 30, and thus correctly extrapolates over 16 orders of magnitude in halo mass. The predictions of our model differ significantly from all models previously proposed in the literature at high masses and redshifts. Our model is in excellent agreement with recent lensing measurements of cluster concentrations.
FIR MEASUREMENTS OF Lyα EMITTERS AT z ≲ 1.0: DUST ATTENUATION FROM PACS-HERSCHEL

One remaining open question regarding the physical properties of Lyα emitters (LAEs) is their dust content and evolution with redshift. The variety of results is large and with those reported by now it is difficult to establish clear relations between dust, other fundamental parameters of galaxies (star formation rate, metallicity, or age), and redshift. In this Letter, we report Herschel PACS-100 μm, PACS-160 μm, and Spitzer MIPS-24 μm detections of a sample of spectroscopically GALEX selected LAEs at z ∼ 0.3 and ∼1.0. Five out of ten and one out of two LAEs are detected in, at least, one PACS band at z ∼ 0.3 and ∼1.0, respectively. These measurements have a great importance given that they allow us to quantify, for the first time, the dust content in LAEs from direct FIR observations. MIPS-24 μm detections allow us to determine the IR properties of the PACS-undetected LAEs. We obtain that mid-IR/FIR-detected star-forming (SF) LAEs at z ∼ 0.3 have dust content within 0.75 ≲ A1200 Å ≲ 2.0, with a median value of A1200 Å ∼ 1.1. This range broadens up to 0.75 ≲ A1200 Å ≲ 2.5 when considering the LAEs at z ∼ 1.0. Only one SF LAE is undetected both in MIPS-24 μm and PACS, with A1200 Å ≲ 0.75. These results seem to be larger than those reported for high-redshift LAEs and, therefore, although an evolutionary trend is not clearly seen, it could point out that low-redshift LAEs are dustier than high-redshift ones. However, the diverse methods used could introduce a systematic offset in the results.
On the relation between non-exponential scrape off layer profiles and the dynamics of filaments

A theoretical framework is developed to clarify the relation between the profiles of density and temperature in the scrape off layer (SOL) with the fluctuations (filaments) that generate them. The framework is based on the dynamics of independent filaments and on their statistical behaviour and can be used to rigorously understand the mechanisms that lead to the non-exponential nature of the radial SOL profiles as well as the increase of the relative fluctuation amplitude in the far SOL. Several models for the dynamics of the filaments, which can be applied to the framework, are derived and discussed for the purpose of identifying how different assumptions lead to the emergence of features in the profiles. It is found that multiple alternative models can explain the observations, thus motivating more stringent and focused experimental analysis. In particular, radially accelerating filaments, less efficient parallel exhaust and also a statistical distribution of the velocity of the filaments can all contribute to induce flatter profiles in the far SOL. A quite general result is the resiliency of the non-exponential nature of the profiles. At the same time, several of the models discussed can also capture the increase of the relative fluctuation amplitude observed in the far SOL. It is also shown that several scenarios are compatible with the broadening of the SOL, which could be caused by charge exchange interactions with neutral particles or by a significant radial acceleration of the filaments.
Transposon wave remodelled the epigenomic landscape in the rapid evolution of a novel X chromosome dosage compensation mechanism

Sex chromosome dosage compensation is a model to understand the coordinated regulation of transcription, however the advanced age of the sex chromosomes in model systems make it difficult to study how the complex regulatory mechanisms underlying chromosome-wide dosage compensation can evolve. The sex chromosomes of Poecilia picta have undergone recent and rapid divergence, resulting in widespread gene loss on the male Y, coupled with complete X chromosome dosage compensation, the first case reported in a fish. The de novo origin of a novel dosage compensation system presents a unique opportunity to discover new mechanisms of gene regulation and their evolutionary origins. By combining a new chromosome-level assembly of P. picta with whole-genome bisulfite sequencing and RNA-Seq data, we determine that the binding motif of Yin Yang 1 (YY1) is associated with male hypomethylated regions on the X, but not the autosomes. The male-specific hypomethylation of these motifs offers a putative model for male specific upregulation of genes on the X. These YY1 motifs are the result of a recent and rapid repetitive element expansion on the P. picta X chromosome, which is absent in closely related species that lack dosage compensation. Taken together, our results present compelling support that a disruptive wave of repetitive element insertions carrying YY1 motifs resulted in the remodeling of the X chromosome epigenomic landscape and the de novo origin of a new dosage compensation mechanism.
A Novel Missense Mutation in ERCC8 Co-Segregates with Cerebellar Ataxia in a Consanguineous Pakistani Family

Autosomal-recessive cerebellar ataxias (ARCAs) are heterogeneous rare disorders mainly affecting the cerebellum and manifest as movement disorders in children and young adults. To date, ARCA causing mutations have been identified in nearly 100 genes; however, they account for less than 50% of all cases. We studied a multiplex, consanguineous Pakistani family presenting with a slowly progressive gait ataxia, body imbalance, and dysarthria. Cerebellar atrophy was identified by magnetic resonance imaging of brain. Using whole exome sequencing, a novel homozygous missense mutation ERCC8:c.176T>C (p.M59T) was identified that co-segregated with the disease. Previous studies have identified homozygous mutations in ERCC8 as causal for Cockayne Syndrome type A (CSA), a UV light-sensitive syndrome, and several ARCAs. ERCC8 plays critical roles in the nucleotide excision repair complex. The p.M59T, a substitution mutation, is located in a highly conserved WD1 beta-transducin repeat motif. In silico modeling showed that the structure of this protein is significantly affected by the p.M59T mutation, likely impairing complex formation and protein-protein interactions. In cultured cells, the p.M59T mutation significantly lowered protein stability compared to wildtype ERCC8 protein. These findings expand the role of ERCC8 mutations in ARCAs and indicate that ERCC8-related mutations should be considered in the differential diagnosis of ARCAs.
Evolution of spatial and temporal cis-regulatory divergence between marine and freshwater sticklebacks

Cis-regulatory changes are thought to play a major role in adaptation. Threespine sticklebacks have repeatedly colonized freshwater habitats in the Northern Hemisphere, where they have evolved a suite of phenotypes that distinguish them from marine populations, including changes in physiology, behavior, and morphology. To understand the role of gene regulatory evolution in adaptive divergence, here we investigate cis-regulatory changes in gene expression between marine and freshwater ecotypes through allele-specific expression (ASE) in F1 hybrids. Surveying seven ecologically relevant tissues, including three sampled across two developmental stages, we identified cis-regulatory divergence affecting a third of genes, nearly half of which were tissue-specific. Next, we compared allele-specific expression in dental tissues at two timepoints to characterize cis-regulatory changes during development between marine and freshwater fish. Applying a genome-wide test for selection on cis-regulatory changes, we find evidence for lineage-specific selection on several processes, including the Wnt signaling pathway in dental tissues. Finally, we show that genes with ASE, particularly those that are tissue-specific, are enriched in genomic regions associated with marine-freshwater divergence, supporting an important role for cis-regulatory differences in adaptive evolution of sticklebacks. Altogether, our results provide insight into the cis-regulatory landscape of divergence between stickleback ecotypes and supports a fundamental role for cis-regulatory changes in rapid adaptation to new environments.
Multi-flow block interleaving applied to distributed speech recognition over IP networks

Abstract Interleaving has shown to be a useful technique to provide robustdistributed speech recognition over IP networks. This is due toits ability to disperse consecutive losses. However, this ability isrelated to the delay introduced by the interleaver. In this work,we propose a novel multi-ﬂow block interleaver which exploitsthe presence of several streams and allows to reduce the involveddelay. Experimental results have shown that this interleaver ap-proximates the performance of end-to-end interleavers but with afraction of their delay. As disadvantage, this interleaver must beplaced in a common node where more than one ﬂow are available. Index Terms : distributed speech recognition, IP networks, inter-leaving, active networks. 1. Introduction Since its beginning, Internet has been growing in size, incorporat-ing many new networks, as well as in functionality, adding newservices. As many other features have been integrated into In-ternet, such as mailing, instant messaging, telephony and so on,speech enabled services (SES) are also being incorporated. Theseservices provide ubiquitous speech recognition, allowing multipleusers to remotely access and share high performance recognitionengines.A very attractive approach to speech recognition over IP net-works is the distributed speech recognition (DSR) solution [1]. Asmany other services over Internet, it is based on a client-serverarchitecture. On one hand, a simple and low power client (
ezCoref : A Scalable Approach for Collecting Crowdsourced Annotations for Coreference Resolution

Large-scale high-quality corpora are critical 001 for advancing research in coreference resolu-002 tion. Coreference annotation is typically time-003 consuming and expensive, since researchers 004 generally hire expert annotators and train them 005 with an extensive set of guidelines. Crowd-006 sourcing is a promising alternative, but coref-007 erence includes complex semantic phenomena 008 difficult to explain to untrained crowdworkers, 009 and the clustering structure is difficult to ma-010 nipulate in a user interface. To address these 011 challenges, we develop and release ezCoref , 012 an easy-to-use coreference annotation tool and 013 annotation methodology that facilitates crowd-014 sourced data collection across multiple do-015 mains, currently in English. Instead of teaching 016 crowdworkers how to handle non-trivial cases 017 (e.g., near-identity coreferences), ezCoref 018 provides only a minimal set of guidelines suf-019 ficient for understanding the basics of the task. 020 To validate this decision, we deploy ezCoref 021 on Mechanical Turk to re-annotate 240 pas-022 sages from seven existing English coreference 023 datasets across seven domains, achieving an 024 average rate of 2530 tokens per hour, for one 025 annotator. This paper is the first to compare 026 the quality of crowdsourced coreference anno-027 tations against those of experts, and to identify 028 where their behavior differs to facilitate future 029 annotation efforts. We show that it is possi-030 ble to collect coreference annotations of a rea-031 sonable quality in a fraction of time it would 032 traditionally require. 033
Chemical and Enzymatic Fiber Modification to Enhance the Mechanical Properties of CMC Composite Films

Carboxymethyl cellulose (CMC) is a cellulose derivative that can be obtained from wood, bamboo, rattan, straw, and other cellulosic materials. CMC can be used to produce biofilms for many purposes, but the properties of these resulting films make them unsuitable for some applications. The effects of three kinds of plant fiber addition on CMC film properties was investigated using CMC derived from eucalyptus bark cellulose. Tensile strength (TS) and elongation at break (EB) of CMC/sodium alginate/glycerol composite films were 26.2 MPa and 7.35%, respectively. Tensile strength of CMC composite films substantially increased, reaching an optimum at 0.50 g of fiber. The enhancement due to industrial hemp hurd fiber on CMC composite films was more obvious. Pretreatment with hydrogen peroxide (H2O2) and glacial acetic acid (CH3COOH) produced films with a TS of 35.9 MPa and an EB of 1.61%. TS values with pectinase pretreated fiber films was 41.3 MPa and EB was 1.76%. TS of films pretreated with pectinase and hemicellulase was 45.2 MPa and EB was 4.18%. Chemical and enzymatic treatment both improved fiber crystallinity, but film tensile strength was improved to a greater extent by enzymatic treatment. Surface roughness and pyrolysis residue of the film increased after fiber addition, but Fourier transform infrared spectroscopy (FTIR), opacity, and water vapor transmission coefficients were largely unchanged. Adding fiber improved tensile strength of CMC/sodium alginate/glycerol composite films and broadened the application range of CMC composite films without adversely affecting film performance.