Miracle-dz/UniFAR-FTUs huggingface dataset:
Histone H3K36M mutation and trimethylation patterns in chondroblastoma

Histones are essential components of chromatin, and mutations in histones lead to alterations in methylation and acetylation, which play an important role in tumorigenesis. Most of the chondroblastomas harbour the H3K36M mutation. With the availability of a mutation‐specific antibody, we sought to assess the sensitivity of this antibody and the alterations of histone methylation in a series of chondroblastoma cases.
Efficient Software Implementation of Ring-LWE Encryption on IoT Processors

Embedded processors have been widely used for building up Internet of Things (IoT) platforms, in which the security issue is becoming critical. This paper studies efficient techniques of lattice-based cryptography on these processors and presents the first implementation of ring-LWE encryption on ARM NEON and MSP430 architectures. For ARM NEON architecture, we propose a vectorized version of Iterative Number Theoretic Transform (NTT) for high-speed computation of polynomial multiplication on ARM NEON platforms and a 32-bit variant of SAMS2 technique for fast reduction. For MSP430 architecture, we propose an optimized SWAMS2 reduction technique, which consists of five different basic operations, including Shifting, Swapping, Addition, and two Multiplication-Subtractions. Regarding of the sampling from the discrete Gaussian distribution, we adopt Knuth-Yao sampler, accompanied with optimized methods such as Look-Up Table (LUT) and byte-scanning. Subsequently, a full-fledged implementation of Ring-LWE is presented by both taking advantage of our proposed method and previous optimization techniques re-designed for desired platforms. Our ring-LWE implementation of encryption/decryption at a classical security level of 128 bits requires only <inline-formula><tex-math notation="LaTeX">$149.4k/32.8k$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>149</mml:mn><mml:mo>. </mml:mo><mml:mn>4</mml:mn><mml:mi>k</mml:mi><mml:mo>/</mml:mo><mml:mn>32</mml:mn><mml:mo>. </mml:mo><mml:mn>8</mml:mn><mml:mi>k</mml:mi></mml:mrow></mml:math><inline-graphic xlink:href="liu-ieq1-2750146.gif"/></alternatives></inline-formula> clock cycles on ARM NEON, and <inline-formula><tex-math notation="LaTeX">$2126.3k/244.5k$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>2126</mml:mn><mml:mo>. </mml:mo><mml:mn>3</mml:mn><mml:mi>k</mml:mi><mml:mo>/</mml:mo><mml:mn>244</mml:mn><mml:mo>. </mml:mo><mml:mn>5</mml:mn><mml:mi>k</mml:mi></mml:mrow></mml:math><inline-graphic xlink:href="liu-ieq2-2750146.gif"/></alternatives></inline-formula> clock cycles on MSP430. These results are roughly 7 times faster than the fastest ECC implementation on desired platforms with same security level.
Durum Wheat Quality, Yield and Sanitary Status under Conservation Agriculture

In Mediterranean environments the adoption of Conservation Agriculture (CA) would allow growers to achieve environmental, agronomic and economic sustainability. We investigated the effect of different combination of crop establishment treatments and crop sequence (conventional tillage (CT) and durum wheat monocropping (WW); conventional tillage (CT) and durum wheat following faba beans (WF); zero tillage (ZT) and durum wheat monocropping (WW); zero tillage (ZF) and durum wheat following faba beans (WF) on yield, grain quality traits as well as on disease incidence and severity in durum wheat (var. Saragolla). The results of two years of data of a long-term experiment (seven-year experiment; split-plot design) are discussed. The CA approach (ZT + WF), which always induced the highest grain yields (6.1 t ha−1 and 3.3 t ha−1 in 2016 and 2017) thanks to an increased number of spikes m−2 (296 vs. 269 and 303 vs. 287 spikes m−2 in 2016 and 2017, respectively) as well as a more pronounced ear length, demonstrated significantly positive influences in terms of grain quality. It promoted grain protein accumulation (12.1% for ZT + WF vs. 11.4% for ZT + WW and 12.4% for ZT + WF vs. 10.6% for ZT + WW in 2016 and 2017) and improved the gluten quality (in terms of sodium dodecyl sulphate (SDS) sedimentation test) and colour of the grain. The abundance of crop residues determined a higher incidence and severity of Zymoseptoria tritici leaf symptoms under the CA system; nevertheless, the late appearance of infection was the main reason for not affecting yield and quality traits. The presence of faba beans (WF) in the rotation significantly reduced leaf symptoms in Z. tritici.
Comparative Study of the Efficiency of Three Protein-Ligand Docking Programs

Structure-based lead optimization approaches are increasingly playing a role in the drug-discovery process. Virtual screening by molecular docking has become a largely used approach to lead discovery in the pharmaceutical industry when a high-resolution structure of the biological target of interest is available. The performance of three docking programs (Arguslab, Autodock and FlexX), for virtual database screening, is studied. Autodock and FlexX are well established commercial packages while Arguslab is distributed freely for Windows platforms by Planaria Software. Comparisons of these docking programs and scoring functions using a large and diverse data set of pharmaceutically interesting targets and active compounds are carried out. We focus on the problem of docking and scoring flexible compounds which are sterically capable of docking into a rigid conformation of the receptor. The three dimensional structures of a carefully chosen set of 126 pharmaceutically relevant proteinligand complexes were used for the comparative study. The Autodock methodology is shown to consistently yield enrichments superior to the two alternative methods, while FlexX outperforms largely Arguslab.
3 D Imaging of the Early Embryonic Chicken Heart After Altered Blood Flow with Focused Ion Beam Scanning Electron Microscopy

Introduction: Embryonic heart formation is a finely orchestrated interplay between genetic and environmental factors, with rapid transformations that occur at the tissue, cell, and subcellular levels. Myofibrils play an essential role in cardiac tissue remodeling as hemodynamic load increases throughout development. Myofibrils mature by aligning in the direction of stretch and increasing the amount of contractile units [1]. Concurrently in early development, a portion of endocardial cells in the cushion bulges of extracellular matrix transform into mesenchymal cells that invade the cardiac jelly through the process of endothelial mesenchymal transition (EMT). As EMT progresses, the original plump and tightly organized endocardium disassembles and rearranges to form an intact flattened layer [2]. Endocardial and myocardial cell changes during development ultimately shape the heart.
Phase shifts and stable states on coral reefs

Recent transitions from coral to macroalgal dominance on some tropical reefs have engendered debate about their causes and effects. A widely accepted view is that reef environments support stable, alternative coral or non-coral assemblages, despite the lack of evidence to support this hypothesis. Confusion in the literature stems from (1) misunderstanding theory; and (2) conflating a switch between alternative stable states with a shift in the phase portrait of a single equilibrial sys- tem caused by a persistent change, or trend, in the environment. In the present paper we outline the conceptual derivation of the hypothesis of alternative stable states, distinguish it from the phase-shift hypothesis, and discuss the evidence required to support each one. For cases in which firm conclu- sions can be drawn, data from fossil and modern reefs overwhelmingly support the phase-shift hypothesis rather than the hypothesis of alternative stable states. On tropical reefs, a given environ- ment evidently supports at most a single stable community. Corals dominate environments that are disturbed primarily by natural events and have small anthropogenic impacts. In such environments, macroalgae dominate a stage during some successional trajectories to the stable, coral-dominated community. In anthropogenically perturbed environments, the resilience of the coral-dominated community is lost, precipitating phase shifts to communities dominated by macroalgae or other non- coral taxa. The implication for reef management and restoration is both substantial and optimistic. To the extent that the environments of degraded reefs are restored, either passively or actively, the com- munities should return to coral dominance.
Bio-optical data integration based on a 4 D database system approach

Bio-optical characterization of water bodies requires spatio-temporal data about Inherent Optical Properties and Apparent Optical Properties which allow the comprehension of underwater light field aiming at the development of models for monitoring water quality. Measurements are taken to represent optical properties along a column of water, and then the spectral data must be related to depth. However, the spatial positions of measurement may differ since collecting instruments vary. In addition, the records should not refer to the same wavelengths. Additional difficulty is that distinct instruments store data in different formats. A data integration approach is needed to make these large and multi source data sets suitable for analysis. Thus, it becomes possible, even automatically, semi-empirical models evaluation, preceded by preliminary tasks of quality control. In this work it is presented a solution, in the stated scenario, based on spatial – geographic – database approach with the adoption of an object relational Database Management System – DBMS – due to the possibilities to represent all data collected in the field, in conjunction with data obtained by laboratory analysis and Remote Sensing images that have been taken at the time of field data collection. This data integration approach leads to a 4D representation since that its coordinate system includes 3D spatial coordinates – planimetric and depth – and the time when each data was taken. It was adopted PostgreSQL DBMS extended by PostGIS module to provide abilities to manage spatial/geospatial data. It was developed a prototype which has the mainly tools an analyst needs to prepare the data sets for analysis.
Two toe pedicle flaps combined with skin grafting for reconstructing the distal phalanx of the thumb

The distal phalanx of the thumb is reconstructed mainly with a wrap-around flap. However, this approach tends to cause the loss of the distal phalanx of the toe. In this study, the methods for reconstructing the distal phalanx of the thumb using a wrap-around flap from the great toe and a tibial flap from the second toe were analysed retrospectively. The clinical efficiency of this method was also investigated. Free wrap-around flap creation, tibial flap creation from the second toe, and iliac bone graft repair were performed on 12 patients with loss of the distal phalanx of the thumb. Conversely, a free wrap-around flap from the big toe of the same side and a tibial flap from the second toe were created to repair the degloving injury of the thumb of another eight patients. Thus, the study included a total of 20 patients. All 20 skin flaps successfully survived after 6-60 months. The patients were satisfied with the appearance of their thumb. They also reported being able to use their repaired thumbs to grasp, nip, and pick up needles. The donor sites did not show scars, contractures, or ulcerations. No toe deformity was reported, and the foot activity was not affected. The application of a wrap-around flap and a tibial flap from the second toe in the reconstruction of the distal phalanx of the thumb effectively restores the appearance and function of the thumb.
A Minimalistic Example and Quick Reminders Imagine

Statistics are tools to help end users accomplish their task. In research, to be qualified as usable, statistical tools should help researchers advance scientific knowledge by supporting and promoting the effective communication of research findings. Yet areas such as human-computer interaction (HCI) have adopted tools — i.e., p-values and dichotomous testing procedures — that have proven to be poor at supporting these tasks. The abusive use of these procedures has been severely criticized in a range of disciplines for several decades, suggesting that tools should be blamed, not end users. This chapter explains in a non-technical manner why it would be beneficial for HCI to switch to an estimation approach, i.e., reporting informative charts with effect sizes and interval estimates, and offering nuanced interpretations of our results. Advice is offered on how to communicate our empirical results in a clear, accurate, and transparent way without using any tests or p-values.
MicroRNA-214 suppresses propofol-induced neuroapoptosis through activation of phosphoinositide 3-kinase/protein kinase B signaling by targeting phosphatase and tensin homolog expression

The present study aimed to investigate the effects of microRNA (miR)-214 on neuroapoptosis induced by propofol and the possible mechanism of its anti-apoptotic effects. Initially, it was observed that miR-214 expression was upregulated in propofol-induced neuroapoptosis rats. Next, propofol-treated nerve cells were transfected with miR-214 mimics. The results revealed that miR-214 overexpression induced apoptosis, inhibited cell proliferation, inhibited cyclin D1 protein expression, promoted caspase-3 activity and B-cell lymphoma 2-associated X protein expression, and enhanced the levels of inflammation factors in nerve cells treated with propofol. In addition, miR-214 overexpression suppressed phosphoinositide 3-kinase/protein kinase B (PI3K/Akt) signaling by targeting the activation of phosphatase and tensin homolog (PTEN) and nuclear factor-κB expression in nerve cells treated with propofol. Treatment with a PTEN inhibitor successfully suppressed the PTEN protein expression and decreased the apoptosis of propofol-treated nerve cells subsequent to miR-214 overexpression through PI3K/Akt signaling. In conclusion, the present study data revealed that miR-214 suppressed propofol-induced neuroapoptosis through the activation of PI3K/Akt signaling by targeting PTEN expression.
Evaluation of Lactobacillus reuteri DSM17938 as starter in cheese production

The probiotic bacteria Lactobacillus reuteri DSM17938 was evaluated as a starter culture in cheese production, with the intention to produce a new interesting product within the functional food market. Growth and acidification rate in milk subjected to different heat treatments, as well as supplementation with growth promoting factors or support cultures was measured during controlled fermentations. The results showed that the weak proteolytic activity of L. reuteri could be compensated for by supplementation with 1% casamino acids or 5% MRS broth. Furthermore, a decrease in growth and acidification rate could be seen when using yoghurt culture or Lactobacillus delbrueckii as adjunct cultures. L. reuteri DSM 17938 was successfully incorporated into a fresh cheese with high viability during the storage period, suggesting that fresh cheese is an excellent carrier for the bacteria. The inhibitory activity of L. reuteri on a non-pathogenic mutant of Escherichia coli O157:H7 (EHEC) and Staphylococcus aureus was also tested. Both pathogens were inhibited in cheese with L. reuteri and the control, opening for further investigations in the field. A limited population of L. reuteri DSM 17938 was also successful incorporated in a hard cheese produced at Skogsbackens dairy. However, the survival was excellent during the storage period of 83 days, suggesting that the cheese could be a good carrier for L. reuteri.
Dynamic Ridesharing

Recent technological developments such as GPS, mobile devices and increases in data storage and computation capacity have greatly enhanced the communication capabilities of travelers, facilitating ridesharing in real-time. This opportunity has created a new ridesharing industry built on making use of the unused vehicle capacity moving about on the roads. There are however still important barriers for widespread dynamic ridesharing adoption. It therefore becomes important to better understand the problems and challenges of ridesharing, creating the need for novel research that explicitly takes into account dynamic ridesharing. In this tutorial we review recent research on new vehicle routing models, cost sharing mechanisms, and planning models that incorporate ridesharing.
Regulation of Myc oncoprotein function by E3 ubiquitin ligases

The Myc oncoprotein/transcription factor plays an important role in controlling cell proliferation, and is deregulated in many human cancers. Myc is a short-lived protein that is turned over via the ubiquitin-proteasome pathway. The major aim of this thesis was to identify E3 ubiquitin ligases that regulate Myc turnover and/or function. Further we aimed to understand the mechanisms behind IFN-γ-induced inactivation of Myc. Through this work we identified the first E3 ligase, SCFSkp2, interacting with Myc and promoting its ubiquitylation and proteasomal turnover. Surprisingly, Skp2 promotes Myc-induced S-phase entry and is required for transcriptional activation by Myc. We show that Myc recruits Skp2 and the proteasome to target promoters and that the proteasome subunit Sug1 is required for Myc transactivation, suggesting that both Skp2 and Sug1 act as coactivators for Myc-induced transcription. We further found an interaction between Myc and the tumour suppressor/E3 ligase von Hippel Lindau (VHL) that targets hypoxia-inducible factor (HIF) for degradation. Unlike HIF, Myc binds VHL also during hypoxia through a distinct binding site. VHL is shown to play a role in ubiquitylation of Myc, but surprisingly not in degradation, thus displaying a new non-proteasomal VHL function. Further, VHL interacts with a subset of Myc target promoters and is possibly involved in regulation of certain Myc target genes. We also present results showing that Cyclin E/Cdk2 regulates the stability of Myc by phosphorylating Ser-62 and functions as a Myc cofactor, increasing Myc transactivation and stability. We further show that this phosphorylation is inhibited by the growth inhibitory cytokine IFN-γ via upregulation of the Cdk inhibitor p27, resulting in increased Myc turnover via the ubiquitin/proteasome pathway. Taken together, this thesis presents three examples of regulation of Myc ubiquitylation with different consequences for Myc function and stability. These findings emphasise the importance of Myc regulation by E3 ligases at different biological levels and could potentially be of importance for the development of novel cancer therapeutics.
Modelling Hydrological Ecosystem Services — A state of the art model comparison

Abstract. Different simulation models are used in science and practice in order to incorporate hydrological ecosystem services in decision-making processes. This contribution compares three simulation models, the Soil and Water Assessment Tool, a traditional hydrological model, and two ecosystem services models, the Integrated Valuation of Ecosystem Services and Trade-offs model and the Resource Investment Optimization System model. The three models are compared on a theoretical and conceptual basis as well in a comparative case study application. The application of the models to a study area in Nicaragua reveals that a practical benefit to apply these models for different questions in decision-making generally exists. However, modelling of hydrological ecosystem services is associated with a high application effort and requires input data that may not always be available. The degree of detail in temporal and spatial variability in ecosystem service provision is higher when using the Soil and Water Assessment Tool compared to the two ecosystem service models. In contrast, the ecosystem service models have lower requirements on input data and process knowledge. A relationship between service provision and beneficiaries is readily produced and can be visualized as a model output. The latter is especially useful for a practical decision-making context.
Towards assimilation of crowdsourced observations for different levels of citizen engagement: the flood event of 2013 in the Bacchiglione catchment

Accurate flood predictions are essential to reduce the risk and damages over large urbanized areas. To improve prediction capabilities, hydrological measurements derived by traditional physical sensors are integrated in real-time within mathematic models. Recently, traditional sensors are complemented with low-cost social sensors. However, measurements derived by social sensors (i.e. crowdsourced observations) can be more spatially distributed but less accurate. In this study, we assess the usefulness for model performance of assimilating crowdsourced observations from a heterogeneous network of static physical, static social and dynamic social sensors. We assess potential effects on the model predictions to the extreme flood event occurred in the Bacchiglione catchment on May 2013. Flood predictions are estimated at the target point of Ponte degli Angeli (Vicenza), outlet of the Bacchiglione catchment, by means of a semi-distributed hydrological model. The contribution of the upstream sub-catchment is calculated using a conceptual hydrological model. The flow is propagated along the river reach using a hydraulic model. In both models, a Kalman filter is implemented to assimilate the real-time crowdsourced observations. We synthetically derived crowdsourced observations for either static social or dynamic social sensors because crowdsourced measures were not available. We consider three sets of experiments: (1) only physical sensors are available; (2) probability of receiving crowdsourced observations and (3) realistic scenario of citizen engagement based on population distribution. The results demonstrated the importance of integrating crowdsourced observations. Observations from upstream sub-catchments assimilated into the hydrological model ensures high model performance for high lead time values. Observations next to the outlet of the catchments provide good results for short lead times. Furthermore, citizen engagement level scenarios moved by a feeling of belonging to a community of friends indicated flood prediction improvements when such small communities are located upstream a particular target point. Effective communication and feedback is required between water authorities and citizens to ensure minimum engagement levels and to minimize the intrinsic low-variable accuracy of crowdsourced observations.
Development of PCR Diagnosis of Pathogenic Fungi of the Genus Septoria , Affecting Cereal Crops in Northern Kazakhstan

Traditional methods of complex diagnostics, including the selection of species in pure culture, selection environments and cultivation conditions, obtaining monoporosa isolates and microscopy are long, time-consuming and ineffective. Immune-enzyme analysis method takes a few hours, however, developed on the basis of the methodology of species-specific, predictive and quantification S. tritici and S. nodorum in the leaves and seeds of wheat insensitive do not always provide a clear identification of these species. The introduction of express methods of diagnostics of Septoria leaf blotch on the basis of the polymerase chain reaction (PCR) in modifications of Real-Time lets quickly and accurately diagnose the disease. A system of highly specific sensitive PCR diagnostics of pathogenic fungi Septoria tritici and Stagonospora nodorum, causing diseases of cereals in Northern Kazakhstan is developed. The primers and probes are designed based on partial sequences of the internal transcribed spacer of ribosomal DNA (ITS) provides a quick and accurate identification of pathogens Septoria by quantitative PCR without the risk of contamination of the work area with amplification products. Effectiveness of the test-system was also demonstrated in samples of total DNA isolated from the infected herbarium material.