Miracle-dz/UniFAR-FTUs huggingface dataset:
Stoeckeria algicida n. gen., n. sp. (Dinophyceae) from the Coastal Waters off Southern Korea: Morphology and Small Subunit Ribosomal DNA Gene Sequence

Abstract. This paper presents a new description of the morphology of the planktonic dinoflagellate Stoeckeria algicida n. gen., n. sp. and a report of the sequence of the small subunit rDNA (SS rDNA) from cultured cells. The vegetative biflagellated cell, gametes, triflagellated planozygotes, and cyst stages of this heterotrophic species were observed in cultures. The vegetative biflagellated cells are oval, with the cell length being considerably larger than the cell width. The ranges (and mean, n=60) of cell length and width of live biflagellated cells satiated with the raphidophyte Heterosigma akashiwo were 14.4–20.8 μm (16.8) and 10.0–17.4 μm (12.9), respectively, while those of biflagellated cells starved for 3 d (n=60) were 7.3–15.9 μm (11.6) and 2.7–12.2 μm (7.3), respectively. Thin plates of the vegetative biflagellated cells were arranged in a Kofoidian series of Po, cp, X, 4′, 2a, 7″, 6c, 6s, 5″′, 0 (p), and 2″″. When properly aligned, the sequence of the SS rDNA of the biflagellated cells of S. algicida (GenBank Accession no. AJ841809) was 3% different from that of a dinoflagellate from Shepherd's Crook and 4% different from that of Cryptoperidiniopsoid sp. brodyi, Pfiesteria spp. , or Pfiesteria‐like species. In a maximum‐likelihood‐distance phylogenetic tree generated using the SS rDNA sequences, Pfiesteria spp. , Pfiesteria‐like species, and a dinoflagellate from Shepherd's Crook were closest to S. algicida, but these dinoflagellates were clearly divergent with S. algicida. Based on morphological and genealogical analyses, we suggest that this is a new species in a new genus.
Detecting code smells using machine learning techniques: Are we there yet?

Code smells are symptoms of poor design and implementation choices weighing heavily on the quality of produced source code. During the last decades several code smell detection tools have been proposed. However, the literature shows that the results of these tools can be subjective and are intrinsically tied to the nature and approach of the detection. In a recent work the use of Machine-Learning (ML) techniques for code smell detection has been proposed, possibly solving the issue of tool subjectivity giving to a learner the ability to discern between smelly and non-smelly source code elements. While this work opened a new perspective for code smell detection, it only considered the case where instances affected by a single type smell are contained in each dataset used to train and test the machine learners. In this work we replicate the study with a different dataset configuration containing instances of more than one type of smell. The results reveal that with this configuration the machine learning techniques reveal critical limitations in the state of the art which deserve further research.
Particle ejection mechanisms due to bubble eruptions in fluidized beds.

The mechanisms by which bubbles erupt at the free surface of a gas fluidized bed were studied experimentally. Two bed geometries were used. One was a two-dimensional bed with a rectangular cross section measuring 14.4 ,mm x 609.6 mm, and the other was a semicylindrical three-dimensional bed with an internal diameter at 288 mm. Five different types of particles are used with surface mean diameters ranging from 112 ym to 912 pm and densities ranging from 3 1,055 to 3,970 kg/m . In some experiments bubbles were created by injecting air into an incipiently fluidized bed; and in others, the bed was allowed to bubble freely. Fluidization velocities ranged from 1.05 to 2.44 Umf. The bubble eruptions were recorded using a high speed video system. Four mechanisms of particle ejection were identified; and the'results suggest that the relative importance of each mechanism depends on bed geometry^and the nature of the bubble interactions. From studies tq determine frequency of each mechanism, the most common type of eruption was found to be a single bubble breaking at the free surface, ejecting particles from the bulge o'r nose region of the bubble. No material from the bubble wake was ejected during the single bubble eruptions. This type of eruption was studied in detail and a universal non-dimensional curve for single bubbles is presented. r The average maximum height of ejected material in single bubble eruptions was found to be 60 percent of the free surface diameter in the three-dimensional bed and 57 percent of the free surface diameter in the two-dimensional bed. -1
A novel reduced graphene oxide decorated with halloysite nanotubes (HNTs-d-rGO) hybrid composite and its flame-retardant application for polyamide 6

The improvement of flame-retardant properties of polyamide 6 (PA6) was achieved by using reduced graphene oxide decorated with halloysite nanotubes (HNTs-d-rGO) hybrid composite as the additive in PA6 matrix. The intimate integration of reduced graphene oxide (rGO) and halloysite nanotubes (HNTs) through a three-step chemical functionaliza- tion, enabled the combination of their unique physical and chemical characteristics together. The nanostructure of HNTs-d- rGO was determined by Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM). A morphological study revealed that HNTs-d-rGO was dispersed uniformly in PA6 matrix. From the results of cone calorimetry measurements, the fire retardant properties of PA6 were further improved with the addition of HNTs-d-rGO when compared with that of either HNTs, or GO, or a mixture of HNTs and GO (HNTs- m-GO) used in PA6 matrix. The results indicate clearly that higher flame-retardant activity of the integrated HNTs-d-rGO nanostructures than that of the simple mixture verifies the importance of the intimate integration between HNTs and rGO, which ascribe to the combination of the stable silica layer created by HNT and the barrier effect of rGO.
Towards a Video Game Description Language

As participants in this Dagstuhl session address the challenge of General Video Game Playing (GVGP), we have recognised the need to create a Video Game Description Language (VGDL). Unlike General Game Playing, we have envisioned GVGP will not require a prescribed language to facilitate understanding of the logic of the game: requiring the computational agent to ascertain these facts for itself. However, we would still require means to define the wide range of problems the GVGP agents may face for the purpose of classification. Not only would such a language provide means to encapsulate the features and mechanics of a game for the purposes of human understanding, but also provide context for the evaluation of GVGP agents having completed playing. Outside of the issues of classification, there is also the opportunity for automatic game generation. Given the intent of the GVGP group to work within a framework akin to the one of the Physical Travelling Salesman Problem (PTSP), we aim to attach a code-base to the VGDL compiler that derives implementations of these games from the definition that can be used in conjunction with GVGP. Implementing such a compiler could provide numerous opportunities; users could modify existing games very quickly, or have a library of existing implementations defined within the language (e.g. an Asteroids ship or a Mario avatar) that have pre-existing, parameterised behaviours that can be customised for the users specific purposes. Provided the language is fit for purpose, automatic game creation could be explored further through experimentation with machine learning algorithms, furthering research in game creation and design. In order for both of these perceived functions to be realised and to ensure it is suitable for a large user base we recognise that the language carries several key requirements. Not only must it be human-readable, but retain the capability to be both expressive and extensible whilst equally simple as it is general. In our preliminary discussions, we sought to define the key requirements and challenges in constructing a new VGDL that will become part of the GVGP process. From this we have proposed an initial design to the semantics of the language and the components required to define a given game. Furthermore, we applied this approach to represent classic games such as Space Invaders, Lunar Lander and Frogger in an attempt to identify potential problems that may come to light. In summary, our group has agreed on a series of preliminary language components and started to experiment with forms of implementation for both the language and the attached framework. In future we aim to realise the potential of the VGDL for the purposes of Procedural Content Generation, Automatic Game Design and Transfer Learning and how the roadmap for GVGP can provide opportunities for these areas.
Deficits in Cognition and Synaptic Plasticity in a Mouse Model of Down Syndrome Ameliorated by GABAB Receptor Antagonists

Cognitive impairment in Down syndrome (DS) is characterized by deficient learning and memory. Mouse genetic models of DS exhibit impaired cognition in hippocampally mediated behavioral tasks and reduced synaptic plasticity of hippocampal pathways. Enhanced efficiency of GABAergic neurotransmission was implicated in those changes. We have recently shown that signaling through postsynaptic GABAB receptors is significantly increased in the dentate gyrus of Ts65Dn mice, a genetic model of DS. Here we examined a role for GABAB receptors in cognitive deficits in DS by defining the effect of selective GABAB receptor antagonists on behavior and synaptic plasticity of adult Ts65Dn mice. Treatment with the GABAB receptor antagonist CGP55845 restored memory of Ts65Dn mice in the novel place recognition, novel object recognition, and contextual fear conditioning tasks, but did not affect locomotion and performance in T-maze. The treatment increased hippocampal levels of brain-derived neurotrophic factor, equally in 2N and Ts65Dn mice. In hippocampal slices, treatment with the GABAB receptor antagonists CGP55845 or CGP52432 enhanced long-term potentiation (LTP) in the Ts65Dn DG. The enhancement of LTP was accompanied by an increase in the NMDA receptor-mediated component of the tetanus-evoked responses. These findings are evidence for a contribution of GABAB receptors to changes in hippocampal-based cognition in the Ts65Dn mouse. The ability to rescue cognitive performance through treatment with selective GABAB receptor antagonists motivates studies to further explore the therapeutic potential of these compounds in people with DS.
Preoperative short course radiotherapy with concurrent and consolidation chemotherapies followed by delayed surgery in locally advanced rectal cancer: preliminary results

Purpose This study aimed to assess complications and outcomes of a new approach, that is, combining short course radiotherapy (SRT), concurrent and consolidative chemotherapies, and delayed surgery. Materials and Methods In this single arm phase II prospective clinical trial, patients with T3-4 or N+ M0 rectal adenocarcinoma were enrolled. Patients who received induction chemotherapy or previous pelvic radiotherapy were excluded. Study protocol consisted of three-dimensional conformal SRT (25 Gy in 5 fractions in 1 week) with concurrent and consolidation chemotherapies including capecitabine and oxaliplatin. Total mesorectal excision was done at least 8 weeks after the last fraction of radiotherapy. Primary outcome was complete pathologic response and secondary outcomes were treatment related complications. Results Thirty-three patients completed the planned preoperative chemoradiation and 26 of them underwent surgery (24 low anterior resection and 2 abdominoperineal resection). Acute proctitis grades 2 and 3 were seen in 11 (33.3%) and 7 (21.2%) patients, respectively. There were no grades 3 and 4 subacute hematologic and non-hematologic (genitourinary and peripheral neuropathy) toxicities and perioperative morbidities such as anastomose leakage. Grade 2 or higher late toxicities were observed among 29.6% of the patients. Complete pathologic response was achieved in 8 (30.8%) patients who underwent surgery. The 3-year overall survival and local control rates were 65% and 94%, respectively. Conclusion This study showed that SRT combined with concurrent and consolidation chemotherapies followed by delayed surgery is not only feasible and tolerable without significant toxicity but also, associated with promising complete pathologic response rates.
Contrast-enhanced ultrasound in the follow-up of patients after endovascular abdominal aortic aneurysm repair (EVAR): A pictorial review

Poster: "ECR 2010 / C-3212 / Contrast-enhanced ultrasound in the follow-up of patients after endovascular abdominal aortic aneurysm repair (EVAR): A pictorial review" by: "R. Iezzi, F. Pirro, M. Nestola, A. Simeone, L. Bonomo; Rome/IT"
Sulfatase 2 facilitates lymphangiogenesis in breast cancer by regulating VEGF-D

In our previous studies, sulfatase 2 (Sulf2) was found to upregulate vascular endothelial growth factor-D (VEGF-D) expression in breast cancer. As VEGF-D plays an important role in lymphangiogenesis, we hypothesized that Sulf2 facilitates lymphangiogenesis in breast cancer by regulating VEGF-D. To evaluate the functions of Sulf2 on lymphangiogenesis in breast cancer, proliferation, apoptosis, cell cycle, cell mobility and tube-formation of lymphatic endothelial cells (LECs) were measured in vitro. Lymphangiogenesis in nude mouse ears and breast cancer xenografts were examined in vivo. Furthermore, the expression levels of related signaling pathway genes were screened and verified in LECs. We found that Sulf2 significantly increased the mobility and tube formation of the LECs, inhibited cisplatin-induced LEC apoptosis, but had no effect on cell proliferation and the cell cycle. Moreover, recombinant Sulf2 (rSulf2) combined with VEGF-D further promoted the proliferation, cell cycle, mobility and tube-like structure formation in the LECs, and at the same time inhibited cisplatin-induced apoptosis especially in the late stage. Sulf2 also significantly increased the density of lymphatic vessels in mouse ears and breast cancer xenografts in vivo. AKT1 was also shown to be upregulated and activated by Sulf2. Our results confirmed that Sulf2 facilitated lymphangiogenesis in breast cancer cells by regulating VEGF-D and that the AKT1-related signaling pathway was involved.
Precipitation behaviour of oxide in directionally solidified aerospace bearing steel

The directional solidification enables independently control of the holding temperature and withdrawal rate over a given range. This technology was used to investigate the precipitation behaviour of oxide in aerospace bearing steel M50NiL. Most of the oxides are Si–Al–Mn–Ti–O complex inclusions with spherical shape. With the increase of withdrawal rate, the size and volume fraction of oxides decrease. In contrast, the diameter and volume fraction increase remarkably with the increase of holding temperature. The composition of oxides with different sizes varies with holding temperature. The holding temperature of 1550°C accompanied with a cooling rate over 95.7°C min−1 is deemed as the optimal solidification parameters for M50NiL steel, which can significantly reduce the size and volume fraction of oxides.
Structured Uncertainty Prediction Networks

This paper is the first work to propose a network to predict a structured uncertainty distribution for a synthesized image. Previous approaches have been mostly limited to predicting diagonal covariance matrices [15]. Our novel model learns to predict a full Gaussian covariance matrix for each reconstruction, which permits efficient sampling and likelihood evaluation. We demonstrate that our model can accurately reconstruct ground truth correlated residual distributions for synthetic datasets and generate plausible high frequency samples for real face images. We also illustrate the use of these predicted covariances for structure preserving image denoising.
AllSome Sequence Bloom Trees

The ubiquity of next generation sequencing has transformed the size and nature of many databases, pushing the boundaries of current indexing and searching methods. One particular example is a database of 2,652 human RNA-seq experiments uploaded to the Sequence Read Archive. Recently, Solomon and Kingsford proposed the Sequence Bloom Tree data structure and demonstrated how it can be used to accurately identify SRA samples that have a transcript of interest potentially expressed. In this paper, we propose an improvement called the AllSome Sequence Bloom Tree. Results show that our new data structure significantly improves performance, reducing the tree construction time by 52.7% and query time by 39 - 85%, with a price of up to 3x memory consumption during queries. Notably, it can query a batch of 198,074 queries in under 8 hours (compared to around two days previously) and a whole set of k-mers from a sequencing experiment (about 27 mil k-mers) in under 11 minutes.
Towards gait modeling for fall prevention

This paper describes a monitoring system prototype dedicated to fall prevention for elderly. Our system designed in collaboration with physicians, aims at assessing the risk that a fall occurs, relying on the signature of the walk. The signature is defined as a set of relevant characteristics, computed from the observation through a video camera of the behavior at home of the elderly and can be viewed as a self reference for the telecared person. We model the deviation of this signature to determine an increase of the fall risk.
Video-Based Object Recognition Using Novel Set-of-Sets Representations

We address the problem of object recognition in egocentric videos, where a user arbitrarily moves a mobile camera around an unknown object. Using a video that captures variation in an object's appearance owing to camera motion (more viewpoints, scales, clutter and lighting conditions), can accumulate evidence and improve object recognition accuracy. Most previous work has taken a single image as input, or tackled a video simply by a collection i.e. sum of frame-based recognition scores. In this paper, beyond frame-based recognition, we propose two novel set-of-sets representations of a video sequence for object recognition. We combine the techniques of bag of words for a set of data spatially distributed thus heterogeneous, and manifold for a set of data temporally smooth and homogeneous, to construct the two proposed set-of-sets representations. We also propose methods to perform matching for the two representations respectively. The representations and matching techniques are evaluated on our video-based object recognition datasets, which contain 830 videos of ten objects and four environmental variations. The experiments on the challenging new datasets show that our proposed solution significantly outperforms the traditional frame-based methods.
Heparan sulfate antagonism alters bone morphogenetic protein signaling and receptor dynamics, suggesting a mechanism in hereditary multiple exostoses

Hereditary multiple exostoses (HME) is a pediatric disorder caused by heparan sulfate (HS) deficiency and is characterized by growth plate–associated osteochondromas. Previously, we found that osteochondroma formation in mouse models is preceded by ectopic bone morphogenetic protein (BMP) signaling in the perichondrium, but the mechanistic relationships between BMP signaling and HS deficiency remain unclear. Therefore, we used an HS antagonist (surfen) to investigate the effects of this HS interference on BMP signaling, ligand availability, cell-surface BMP receptor (BMPR) dynamics, and BMPR interactions in Ad-293 and C3H/10T1/2 cells. As observed previously, the HS interference rapidly increased phosphorylated SMAD family member 1/5/8 levels. FACS analysis and immunoblots revealed that the cells possessed appreciable levels of endogenous cell-surface BMP2/4 that were unaffected by the HS antagonist, suggesting that BMP2/4 proteins remained surface-bound but became engaged in BMPR interactions and SMAD signaling. Indeed, surface mobility of SNAP-tagged BMPRII, measured by fluorescence recovery after photobleaching (FRAP), was modulated during the drug treatment. This suggested that the receptors had transitioned to lipid rafts acting as signaling centers, confirmed for BMPRII via ultracentrifugation to separate membrane subdomains. In situ proximity ligation assays disclosed that the HS interference rapidly stimulates BMPRI–BMPRII interactions, measured by oligonucleotide-driven amplification signals. Our in vitro studies reveal that cell-associated HS controls BMP ligand availability and BMPR dynamics, interactions, and signaling, and largely restrains these processes. We propose that HS deficiency in HME may lead to extensive local BMP signaling and altered BMPR dynamics, triggering excessive cellular responses and osteochondroma formation.
A reference peptide database for proteome quantification based on experimental mass spectrum response curves

Abstract Motivation Mass spectrometry (MS) based quantification of proteins/peptides has become a powerful tool in biological research with high sensitivity and throughput. The accuracy of quantification, however, has been problematic as not all peptides are suitable for quantification. Several methods and tools have been developed to identify peptides that response well in mass spectrometry and they are mainly based on predictive models, and rarely consider the linearity of the response curve, limiting the accuracy and applicability of the methods. An alternative solution is to select empirically superior peptides that offer satisfactory MS response intensity and linearity in a wide dynamic range of peptide concentration. Results We constructed a reference database for proteome quantification based on experimental mass spectrum response curves. The intensity and dynamic range of over 2 647 773 transitions from 121 318 peptides were obtained from a set of dilution experiments, covering 11 040 gene products. These transitions and peptides were evaluated and presented in a database named SCRIPT-MAP. We showed that the best-responder (BR) peptide approach for quantification based on SCRIPT-MAP database is robust, repeatable and accurate in proteome-scale protein quantification. This study provides a reference database as well as a peptides/transitions selection method for quantitative proteomics. Availability and implementation SCRIPT-MAP database is available at http://www.firmiana. org/responders/. Supplementary information Supplementary data are available at Bioinformatics online.
Numerical Simulations of Gel Propellant Flow Through Orifices

A series of axisymmetric parametric investigations are conducted to assess the overall flowfield and discharge coefficient of power-law gelled fluids flowing within plain orifice atomizers. Steady calculations have been employed to assess discharge characteristics for various length-to-diameter ratios, inlet lip roundness and chamfer depths/sizes. Also, time-accurate computation for the baseline configuration is implemented as the first step to assess the injector dynamics for gel propellant flows. As a result, cases utilizing a generalized Reynolds number (Re gen ) as low as 1,000 generate laminar instabilities leading to periodic flow much like that of Newtonian liquids at Re = 10,000. This self-induced oscillation is characterized by its natural frequency and massflow pulsation amplitude for the limited unsteady results conducted thusfar. of the generalized Reynolds number, as well as the influence of geometric conditions will be studied. This will be compared with the flow characteristics of Newtonian liquids and help the understanding of the injector dynamics for the gel flows. Besides, for more realistic simulations, the Herschel-Bulkley or Carreau-Yasuda model, advanced rheological models than power-law model, will be used. Based on this model, the viscosity fluctuation will also be investigated and its influence of gel atomization with mass pulsations will be studied.