Miracle-dz/UniFAR-FTUs huggingface dataset:
Early developmental specification of the thyroid gland depends on han-expressing surrounding tissue and on FGF signals

The thyroid is an endocrine gland in all vertebrates that develops from the ventral floor of the anterior pharyngeal endoderm. Unravelling the molecular mechanisms of thyroid development helps to understand congenital hypothyroidism caused by the absence or reduction of this gland in newborn humans. Severely reduced or absent thyroid-specific developmental genes concomitant with the complete loss of the functional gland in the zebrafish hands off (han, hand2) mutant reveals the han gene as playing a novel, crucial role in thyroid development. han-expressing tissues surround the thyroid primordium throughout development. Fate mapping reveals that, even before the onset of thyroid-specific developmental gene expression, thyroid precursor cells are in close contact with han-expressing cardiac lateral plate mesoderm. Grafting experiments show that han is required in surrounding tissue, and not in a cell-autonomous manner, for thyroid development. Loss of han expression in the branchial arches and arch-associated cells after morpholino knock-down of upstream regulator genes does not impair thyroid development, indicating that other han-expressing structures, most probably cardiac mesoderm, are responsible for the thyroid defects in han mutants. The zebrafish ace (fgf8) mutant has similar thyroid defects as han mutants, and chemical suppression of fibroblast growth factor (FGF) signalling confirms that this pathway is required for thyroid development. FGF-soaked beads can restore thyroid development in han mutants, showing that FGFs act downstream of or in parallel to han. These data suggest that loss of FGF-expressing tissue in han mutants is responsible for the thyroid defects.
Modelling the water balance of Lake Victoria (East Africa) – Part 1: Observational analysis

Abstract. Lake Victoria is the largest lake in Africa and one of the two major sources of the Nile river. The water level of Lake Victoria is determined by its water balance, consisting of precipitation on the lake, evaporation from the lake, inflow from tributary rivers and lake outflow, controlled by two hydropower dams. Due to a scarcity of in situ observations, previous estimates of individual water balance terms are characterized by substantial uncertainties, which means that the water balance is often not closed independently. In this first part of a two-paper series, we present a water balance model for Lake Victoria, using state-of-the-art remote sensing observations, high-resolution reanalysis downscaling and outflow values recorded at the dam. The uncalibrated computation of the individual water balance terms yields lake level fluctuations that closely match the levels retrieved from satellite altimetry. Precipitation is the main cause of seasonal and interannual lake level fluctuations, and on average causes the lake level to rise from May to July and to fall from August to December. Finally, our results indicate that the 2004–2005 drop in lake level can be about half attributed to a drought in the Lake Victoria Basin and about half to an enhanced outflow, highlighting the sensitivity of the lake level to human operations at the outflow dam.
Fourth-order accurate finite-volume CWENO scheme for astrophysical MHD problems

In this work, a simple fourth-order accurate finite volume semi-discrete scheme is introduced to solve astrophysical magnetohydrodynamics (MHD) problems on Cartesian meshes. Hydrodynamic quantities like density, momentum and energy are discretised as volume averages. The magnetic field and electric field components are discretised as area and line averages respectively, so as to employ the constrained transport technique, which preserves the solenoidality of the magnetic field to machine precision. The present method makes use of a dimension-by-dimension approach employing a 1-D fourth-order accurate centrally weighted essentially non-oscillatory (1D-CWENO4) reconstruction polynomial. A fourth-order accurate, strong stability preserving (SSP) Runge-Kutta method is used to evolve the semi-discrete MHD equations in time. Higher-order accuracy of the scheme is confirmed in various linear and nonlinear multi-dimensional tests and the robustness of the method in avoiding unphysical numerical artifacts in the solution is demonstrated through several complex MHD problems.
Cannabidiol can improve complex sleep‐related behaviours associated with rapid eye movement sleep behaviour disorder in Parkinson's disease patients: a case series

Cannabidiol (CBD) is the main non‐psychotropic component of the Cannabis sativa plant. REM sleep behaviour disorder (RBD) is a parasomnia characterized by the loss of muscle atonia during REM sleep associated with nightmares and active behaviour during dreaming. We have described the effects of CBD in RBD symptoms in patients with Parkinson's disease.
Comparison of in-hospital outcomes between octogenarians and nonagenarians undergoing transcatheter aortic valve replacement: a propensity matched analysis

Background Aortic valve stenosis (AS) is very common in the elderly patients above 80 years. Transcatheter aortic valve replacement (TAVR) in such patients is being increasingly performed. This study sought to assess in-hospital outcome differences between octogenarians and nonagenarians and predictors of mortality in nonagenarians undergoing TAVR with severe AS. Method The study population was derived from the National Inpatient Sample (NIS) for the years 2012–2014 using ICD-9 CM procedure codes 35.05 and 35.06 for TAVR. Hospitalizations below 80 years of age were excluded. After performing propensity score matching (1: 2), in-hospital outcomes were compared in matched cohorts. Then, multivariate model was developed to analyze predictors of in-hospital mortality in nonagenarians. Results There were 11,630 hospitalizations in the octogenarian and 5815 hospitalizations in the nonagenarian group. Primary outcome of in-hospital mortality (6% vs. 4.1%, P ≤ 0.001) was higher in nonagenarians compared to octogenarians. Secondary outcomes including stroke (3.4% vs. 2.8%, P ≤ 0.001), renal failure (18.9% vs. 17.3%, P ≤ 0.001), blood transfusion (35% vs. 32.6%, P ≤ 0.001), vascular complications (4.5% vs. 3.5%, P ≤ 0.001), and pacemaker implantation (27.8% vs. 24.8%, P ≤ 0.001) were higher in nonagenarians. There was no difference in their length of stay. Median cost (70,374$ vs. 65,381$, P ≤ 0.001) was slightly higher with nonagenarian. Conclusions Although in-hospital mortality is slightly higher in nonagenarians, it is acceptable. This difference in mortality is at least partly explained by higher complications in nonagenarians. Efforts should be made to decrease the complications which can further narrow the difference in in-hospital mortality between the groups.
MiR-340 affects gastric cancer cell proliferation, cycle, and apoptosis through regulating SOCS3/JAK-STAT signaling pathway

Abstract Objective: Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway is closely related to tumorigenesis. Suppressors of cytokine signaling 3 (SOCS3) is a negative regulator of JAK-STAT signaling pathway. MiR-340 expression is significantly upregulated in gastric cancer (GC) tissue. This study investigated the role of miR-340 in regulating SOCS3 expression and affecting GC cell proliferation, cycle, and apoptosis. Patients and methods: Dual luciferase assay was used to verify the targeted relationship between miR-340 and SOCS3. GC tissue was collected from patients. Normal gastric mucosal tissue was selected as control. MiR-340, SOCS3, p-JAK, p-STAT3, and Survivin protein expressions were compared with GES-1 and MKN-28 cells. MKN-28 cells were cultured in vitro and divided into four groups, including miR-NC, anti-miR-340, pSicoR-Blank, and pSicoR-SOCS3 groups. Cell proliferation, cycle, and apoptosis were detected by flow cytometry. Results: Bioinformatics analysis revealed the targeted relationship between miR-340 and the 3′-UTR of SOCS3 mRNA. Dual luciferase assay demonstrated that miR-340 regulated SOCS3 expression. MiR-340 level was significantly elevated, while SOCS3 level was obviously declined in GC tissue compared with normal mucosal tissue. MiR-340, p-JAK, p-STAT3, and Survivin expressions were upregulated, whereas SOCS3 expression was reduced in MKN-28 cells compared with that in GES-1 cells. Anti-miR-340 or pSicoR-SOCS3 transfection markedly increased SOCS3 expression, reduced p-JAK, p-STAT3, and Survivin levels, attenuated cell proliferation, arrested cell cycle, and enhanced cell apoptosis in MKN-28 cells. Conclusions: Downregulation of miR-340 inhibited GC cell proliferation, arrested cell cycle, and facilitated apoptosis through upregulating SOCS3 expression to suppress JAK-STAT3 signaling pathway.
The relationship among breakfast time, morningness–eveningness preference and body mass index in Type 2 diabetes

Obesity is prevalent and related to poor outcomes in Type 2 diabetes. Evening preference and late meal times have been shown to be associated with obesity, but data are lacking in people with Type 2 diabetes. This study examined the relationship among meal timing, morningness–eveningness preference and BMI in Type 2 diabetes, using a mediation analysis.
Find the Conversation Killers: A Predictive Study of Thread-ending Posts

How to improve the quality of conversations in online communities has attracted considerable attention recently. Having engaged, civil, and reactive online conversations has a critical effect on the social life of Internet users. In this study, we are particularly interested in identifying a post in a multi-party conversation that is unlikely to be further replied to, which therefore kills that thread of the conversation. For this purpose, we propose a deep learning model called the ConverNet. ConverNet is attractive due to its capability of modeling the internal structure of a long conversation and its appropriate encoding of the contextual information of the conversation, through effective integration of attention mechanisms. Empirical experiments on real-world datasets demonstrate the effectiveness of the proposed model. For the widely concerned topic, our analysis also offers implications for how to improve the quality and user experience of online conversations, or how to engage users in a conversation with a chatbot.
Alterations in Root Morphology of Rootstock Peach Trees Caused by Mycorrhizal Fungi

© 2012 da Silva Nunes et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Alterations in Root Morphology of Rootstock Peach Trees Caused by Mycorrhizal Fungi
3D ultrasound guidance system for permanent breast seed implantation: integrated system performance and phantom procedure

Permanent breast seed implantation (PBSI) is a single visit accelerated partial breast irradiation method that uses needles inserted via a template to distribute Pd-103 radioactive seeds with two-dimensional (2D) ultrasound (US) guidance. This guidance approach is limited by its dependence on the operator and average seed placement errors greater than benchmark values established by dosimetric studies. We propose the use of a three-dimensional (3D) US imaging approach for needle guidance with integrated template tracking. We previously described the preliminary development and validation of the 3D US mechatronic system. The present work demonstrates the accuracy of the integrated system by quantifying agreement between tracking and imaging sub-systems and its use guiding a phantom procedure. Tracking error was measured by inserting a needle a known distance through the template and comparing expected tip position from tracking to observed tip position from imaging. Mean ± standard deviation differences in needle tip position and angle were 2.90 ± 0.76 mm and 1.77 ± 0.98°, respectively, validating the needle tracking accuracy of the developed system. The system was used to guide 15 needles into a patient-specific phantom according to the accompanying treatment plan and micro-CT images taken before and after to evaluate placement accuracy. Seed positions were modelled using needle positions and the resulting dosimetry compared to a procedure specific benchmark. The mean tip difference was 2.08 mm while the mean angular difference was 2.6°, resulting in acceptable dosimetric coverage. These results demonstrate 3D US as a potentially feasible technique for PBSI guidance.
Biogeosciences Improved modelling of atmospheric ammonia over Denmark using the coupled modelling system

A local-scale Gaussian dispersion-deposition model (OML-DEP) has been coupled to a regional chemistry-transport model (DEHM with a resolution of approximately 6 km× 6 km over Denmark) in the Danish Ammonia Modelling System, DAMOS. Thereby, it has been possible to model the distribution of ammonia concentrations and depositions on a spatial resolution down to 400 m× 400 m for selected areas in Denmark. DAMOS has been validated against measured concentrations from the dense measuring network covering Denmark. Here measured data from 21 sites are included and the validation period covers 2–5 years within the period 2005–2009. A standard time series analysis (using statistic parameters like correlation and bias) shows that the coupled model system captures the measured time series better than the regionalscale model alone. However, our study also shows that about 50 % of the modelled concentration level at a given location originates from non-local emission sources. The local-scale model covers a domain of 16 km× 16 km, and of the locally released ammonia (NH3) within this domain, our simulations at five sites show that 14–27 % of the locally (within 16 km × 16 km) emitted NH3 also deposits locally. These results underline the importance of including both high-resolution local-scale modelling of NH3 as well as the regional-scale component described by the regional model. The DAMOS system can be used as a tool in environmental management in relation to assessments of total nitrogen load of sensitive nature areas in intense agricultural regions. However, high spatio-temporal resolution in input parameters like NH 3 emissions and landuse data is required.
A Deubiquitinating Enzyme Ubp14 Is Required for Development, Stress Response, Nutrient Utilization, and Pathogenesis of Magnaporthe oryzae

Ubiquitination is an essential protein modification in eukaryotic cells, which is reversible. Deubiquitinating enzymes (DUBs) catalyze deubiquitination process to reverse ubiquitination, maintain ubiquitin homeostasis or promote protein degradation by recycling ubiquitins. In order to investigate effects of deubiquitination process in plant pathogenic fungus Magnaporthe oryzae, we generated deletion mutants of MoUBP14. Ortholog of MoUbp14 was reported to play general roles in ubiquitin-mediated protein degradation in Saccharomyces cerevisiae. The ΔMoubp14 mutant lost its pathogenicity and was severely reduced in mycelial growth, sporulation, carbon source utilization, and increased in sensitivity to distinct stresses. The mutant was blocked in penetration, which could due to defect in turgor generation. It is also blocked in invasive growth, which could due to reduction in stress tolerance and nutrient utilization. Deletion of UBP14 also led to accumulation of free polyubiquitin chains. Pulldown assay identified some proteins related to carbohydrate metabolism and stress response may putatively interact with MoUbp14, including two key rate-limiting enzymes of gluconeogenesis, MoFbp1 and MoPck1. These two proteins were degraded when the glucose was supplied to M. oryzae grown in low glucose media for a short period of time (∼12 h), and this process required MoUbp14. In summary, pleiotropic phenotypes of the deletion mutants indicated that MoUbp14 is required for different developments and pathogenicity of M. oryzae.
Managing Visibility and Validity of Distress Calls with an Ad-Hoc SOS System

The availability of ICT services can be severely disrupted in the aftermath of disasters. Ad-hoc assemblages of communication technology have the potential to bridge such breakdowns. This article investigates the use of an ad-hoc system for sending SOS signals in a large-scale exercise that simulated a terrorist attack. In this context, we found that the sensitivity that was introduced by the adversarial nature of the situation posed unexpected challenges for our approach, as giving away one's location in the immediate danger of a terrorist attack became an issue both for first responders and the affected people in the area. We show how practices of calling for help and reacting to help calls can be affected by such a system and affect the management of the visibility and validity of SOS calls, implying a need for further negotiation in situations where communication is sensitive and technically restrained.
Frustratingly Easy Meta-Embedding – Computing Meta-Embeddings by Averaging Source Word Embeddings

Creating accurate meta-embeddings from pre-trained source embeddings has received attention lately. Methods based on global and locally-linear transformation and concatenation have shown to produce accurate meta-embeddings. In this paper, we show that the arithmetic mean of two distinct word embedding sets yields a performant meta-embedding that is comparable or better than more complex meta-embedding learning methods. The result seems counter-intuitive given that vector spaces in different source embeddings are not comparable and cannot be simply averaged. We give insight into why averaging can still produce accurate meta-embedding despite the incomparability of the source vector spaces.
A system for online beam emittance measurements and proton beam characterization

A system for online measurement of the transverse beam emittance was developed. It is named 4PrOBεaM (4-Profiler Online Beam Emittance Measurement) and was conceived to measure the emittance in a fast and efficient way using the multiple beam profiler method. The core of the system is constituted by four consecutive UniBEaM profilers, which are based on silica fibers passing across the beam. The 4PrOBεaM system was deployed for characterization studies of the 18 MeV proton beam produced by the IBA Cyclone 18 MeV cyclotron at Bern University Hospital (Inselspital). The machine serves daily radioisotope production and multi-disciplinary research, which is carried out with a specifically conceived Beam Transport Line (BTL). The transverse RMS beam emittance of the cyclotron was measured as a function of several machine parameters, such as the magnetic field, RF peak voltage, and azimuthal angle of the stripper. The beam emittance was also measured using the method based on the quadrupole strength variation. The results obtained with both techniques were compared and a good agreement was found. In order to characterize the longitudinal dynamics, the proton energy distribution was measured. For this purpose, a method was developed based on aluminum absorbers of different thicknesses, a UniBEaM detector, and a Faraday cup. The results were an input for a simulation of the BTL developed in the MAD-X software. This tool allows machine parameters to be tuned online and the beam characteristics to be optimized for specific applications.
Oral health disparities among adolescents from urban and rural communities of central Chile.

PURPOSE Rural populations may be at increased risk for prevalent oral diseases. The aim of this study was to compare oral health status of adolescents of rural and urban areas from central Chile. METHODS A representative sample of 552 and 486 adolescents aged 12 and 15 years, respectively, was examined using WHO methods. Adolescents were chosen from schools belonging to urban and rural districts of the region. Caries status was obtained by decayed, missing, filled teeth (DMFT) and significant caries (SiC) indexes. The gingival exam included the oral hygiene index (OHI) of Silness and Löe and the gingival index (GI) of Löe and Silness. Clinical attachment loss and community periodontal index (CPI) were restricted to 15-year-old adolescents. Statistical comparisons of medians and means were performed with the Mann-Whitney U-test. To determine the association between caries experience and oral hygiene and gingival indexes, Spearman's correlation was used at p<0.05. RESULTS Twelve-year-old children from rural areas had caries prevalence of 67.50%, which was significantly higher (p<0.05) than children from urban areas, who had 54.04%. Caries experience of 12-year-old rural children was significantly higher (DMFT 3.36; standard deviation (SD) 2.71) than that of urban children (DMFT 2.29; SD 2.17) (p=0.0001). Rural adolescents also showed increased caries severity (SiC 6.21; SD 2.44), whereas urban children showed had a SiC of 4.71 (SD 1.74) (p=0.0001). For periodontal indexes, the average GI for 12-year-olds was 1.51 (SD 0.33), which corresponds to moderate inflammation, but rural subjects (GI 1.55; SD 0.34) had higher values (p=0.002) than their urban counterparts (GI 1.45; SD 0.29). In 15-year-old adolescents, caries prevalence was significantly higher in rural (73.58%) than in urban (64.59%) individuals (p<0.05). Although not significant, caries experience for 15-year-olds in rural areas, like in the other age group, was slightly higher than for urban 15-year-olds (DMFT 5.03; SD 3.61 and DMFT 4.65; SD 3.58, respectively) (p=0.238). The SiC in the rural subjects (9.16; SD 2.26) of this age group was significantly higher than for urban adolescents (8.51; SD 3.00). No significant differences either in the OHI (p=0.418) or in the GI (p=0.624) were observed between rural and urban participants. CONCLUSIONS Adolescents of central Chile show clear disparities in oral health, with rural communities more affected. Gingival health seems to be less impacted by rurality than caries experience. Other social determinants of oral health may also explain these results, and further research appears necessary.
Radiosensitization with Chemotherapeutic Agents and Hyperthermia: Effects on Linear-quadratic Parameters of Radiation Cell Survival Curves

The radio-sensitizing effects of several chemotherapeutic agents and hyperthermia have been investigated in several animal and human cell culture systems. Cells are first treated with Cisplatin, Gemcitabine, Halogenated pyrimidines or hyperthermia and thereafter irradiated with different dose of radiation up to 8 Gy. After treatment the clonogenic survival was determined and from the survival curves the values of the linear and quadratic parameters were determined using the formula S(D)/S(O)= exp-(αD+βD2). An increase in the value of the linear parameter, α, was observed in most cases, which corresponds to an enhanced (potentially) direct lethal damage (PLD) at low doses. The quadratic parameter β, which is assumed to depend on the interaction of sublethal lesions (SLD), was rarely affected. Furthermore, it appeared that more radioresistant cell lines were more sensitised than the radiosensitive lines. Furthermore it can be concluded that radiosensitization is also dependent on cell cycle stage like plateau or exponentially growing phase or post treatment plating conditions.