Miracle-dz/UniFAR-FTUs huggingface dataset:
The Penetration Depth Derived from the Synthesis of ALOS/PALSAR InSAR Data and ASTER GDEM for the Mapping of Forest Biomass

The Global Digital Elevation Model produced from stereo images of Advanced Spaceborne Thermal Emission and Reflection Radiometer data (ASTER GDEM) covers land surfaces between latitudes of 83°N and 83°S. The Phased Array type L-band Synthetic Aperture Radar (PALSAR) onboard Advanced Land Observing Satellite (ALOS) collected many SAR images since it was launched on 24 January 2006. The combination of ALOS/PALSAR interferometric data and ASTER GDEM should provide the penetration depth of SAR data assuming ASTER GDEM was the elevation of vegetation canopy top. It would be correlated with forest biomass because penetration depth could be affected by forest density and forest canopy height. Their combination held great promises for the forest biomass mapping over large area. The feasibility of forest biomass mapping through the data synthesis of ALOS/PALSAR InSAR data and ASTER GDEM was investigated in this study. A procedure for the extraction of penetration depth was firstly proposed. Then three models were built for biomass estimation: (I) model only using backscattering coefficients of ALOS/PALSAR data; (II) model only using penetration depth; (III) model using both of them. The biomass estimated from Lidar data was taken as reference data to evaluate the three different models. The results showed that the combination of backscattering coefficients and penetration depth gave the best accuracy. The forest disturbance has to be considered in forest biomass estimation because of the long time span of ASTER data for generating ASTER GDEM. The spatial homogeneity could be used to improve estimation accuracy.
The Clinical Significance of MiR-148a as a Predictive Biomarker in Patients with Advanced Colorectal Cancer

Aim Development of robust prognostic and/or predictive biomarkers in patients with colorectal cancer (CRC) is imperative for advancing treatment strategies for this disease. We aimed to determine whether expression status of certain miRNAs might have prognostic/predictive value in CRC patients treated with conventional cytotoxic chemotherapies. Methods We studied a cohort of 273 CRC specimens from stage II/III patients treated with 5-fluorouracil-based adjuvant chemotherapy and stage IV patients subjected to 5-fluorouracil and oxaliplatin-based chemotherapy. In a screening set (n = 44), 13 of 21 candidate miRNAs were successfully quantified by multiplex quantitative RT-PCR. In the validation set comprising of the entire patient cohort, miR-148a expression status was assessed by quantitative RT-PCR, and its promoter methylation was quantified by bisulfite pyrosequencing. Lastly, we analyzed the associations between miR-148a expression and patient survival. Results Among the candidate miRNAs studied, miR-148a expression was most significantly down-regulated in advanced CRC tissues. In stage III and IV CRC, low miR-148a expression was associated with significantly shorter disease free-survival (DFS), a worse therapeutic response, and poor overall survival (OS). Furthermore, miR-148a methylation status correlated inversely with its expression, and was associated with worse survival in stage IV CRC. In multivariate analysis, miR-148a expression was an independent prognostic/predictive biomarker for advanced CRC patients (DFS in stage III, low vs. high expression, HR 2.11; OS in stage IV, HR 1.93). Discussion MiR-148a status has a prognostic/predictive value in advanced CRC patients treated with conventional chemotherapy, which has important clinical implications in improving therapeutic strategies and personalized management of this malignancy.
Porcine Adipose Tissue-Derived Mesenchymal Stem Cells Retain Their Proliferative Characteristics, Senescence, Karyotype and Plasticity after Long-Term Cryopreservation

We and others have provided evidence that adipose tissue-derived mesenchymal stem cells (ASCs) can mitigate rat cardiac functional deterioration after myocardial ischemia, even though the mechanism of action or the relevance of these findings to human conditions remains elusive. In this regard, the porcine model is a key translational step, because it displays heart anatomic-physiological features that are similar to those found in the human heart. Towards this end, we wanted to establish the cultural characteristics of porcine ASCs (pASCs) with or without long-term cryostorage, considering that allogeneic transplantation may also be a future option. Compared to fresh pASCs, thawed cells displayed 90–95% viability and no changes in morphological characteristics or in the expression of surface markers (being pASCs characterized by positive markers CD29+; CD90+; CD44+; CD140b+; CD105+; and negative markers CD31−; CD34−; CD45− and SLA-DR−; n = 3). Mean population doubling time was also comparable (64.26±15.11 hours to thawed cells vs. 62.74±18.07 hours to fresh cells) and cumulative population doubling increased constantly until Passage 10 (P10) in the entire cell population, with a small and gradual increase in senescence (P5, 3.25%±0.26 vs. 3.47%±0.32 and P10, 9.6%±0.29 vs. 10.67%±1.25, thawed vs. fresh; SA-β-Gal staining). Chromosomal aberrations were not observed. In addition, under both conditions pASCs responded to adipogenic and osteogenic chemical cues in vitro. In conclusion, we have demonstrated the growth characteristics, senescence, and the capacity of pASCs to respond to chemical cues in vitro and have provided evidence that these properties are not influenced by cryostorage in 10% DMSO solution.
Streaky Structures in a Wing Boundary Layer at High Free Stream Turbulence and Modelling of the Transition in Such Flow

Abstract : Raised interest of researchers to a problem of the laminar-turbulent transition at high free stream turbulence can be observed recently. The given interest is connected to a lot of reasons both of the scientific nature and requirements of the modern engineering with point of view its new opportunities. It is known that laminar-turbulent transition at low free stream turbulence is occurred caused by the process of generation and development of the instability waves so-called Tollmien-Schlichting (TS) waves. This type of transition was in details investigated by many researchers and continues to be studied in nowadays. A more complex way of understanding of the laminar flow breakdown mechanism into the turbulent state for the wall shear layers where the boundary layer flow modulated by longitudinal localized in spanwise direction structures. In this case the classical scenario of transition due to the mechanism of spatial evolution of a TS wave ceases to work and it is necessary to understand what processes result in occurrence of longitudinal structures and what mechanism of their breakdown. By one of such transition mechanisms is the transition mechanism at high free stream turbulence. Experiments in the natural conditions were shown that the flat plate boundary layer at high free stream turbulence was modulated by streaky structures in spanwise direction. It was shown that the spanwise scale of these structures correlated with a boundary layer thickness. On the other hand all researchers observed the turbulent spots origination at last stages of transition. However the more detailed development characteristics of the given structures as well as the mechanism of their generation development and breakdown was not investigated.
C-3MA: Tartu-Riga-Zurich Translation Systems for WMT17

This paper describes the neural machine translation systems of the University of Latvia, University of Zurich and University of Tartu. We participated in the WMT 2017 shared task on news translation by building systems for two language pairs: English ↔ German and English ↔ Latvian. Our systems are based on an attentional encoder-decoder, using BPE subword segmentation. We experimented with back-translating the monolingual news corpora and ﬁltering out the best translations as additional training data, enforcing named entity translation from a dictionary of parallel named entities, penalizing over-and under-translated sentences, and combining output from multiple NMT systems with SMT. The described methods give 0.7 - 1.8 BLEU point improvements over our base-line systems.
Regulatory Role of Ginsenoside Rp1, a Novel Ginsenoside Derivative, on CD29-Mediated Cell Adhesion

In this study, we examined the regulatory role of G-Rp1 on cell adhesion events mediated by beta1-integrins (CD29). Using a U937 cell-cell adhesion assay, we found that exogenous G-Rp1 down-regulates CD29 activation in a dose-dependent manner, whereas G-Rg3 did not cause the same effect. However, G-Rp1 increased cell-fibronectin adhesion comparable to cytochalasin B, an actin cytoskeleton disruptor. Furthermore, G-Rp1 also blocked the rearrangement of actin at sites of cell-cell contact, indicating that the actin cytoskeleton may be a target of G-Rp1 action. Interestingly, G-Rp1 suppressed dephosphorylation of vasodilator-stimulated phosphoprotein (VASP) at Ser-157, known to be an actin cytoskeleton modulatory protein. These results suggest that G-Rp1 may act as a novel regulator of CD29-mediated cell adhesion events, which are involved in numerous pathological symptoms.
Neural network-based interactive multicriteria decision making in a quality of perception-oriented management scheme

We address the problem of bridging the application-network gap from a multicriteria decision making perspective. We have sought to use this approach to integrate results from our work on user-level quality of perception with the move technical characterization of quality of service. For this purpose, we apply the multicriteria decision-making formalism by defining the criteria on the basis of which an appropriate tailored communication protocol is constructed, and we suggest a neural network-based scheme to solve the problem.
THREE-DIMENSIONAL RELATIVISTIC MAGNETOHYDRODYNAMIC SIMULATIONS OF THE KELVIN–HELMHOLTZ INSTABILITY: MAGNETIC FIELD AMPLIFICATION BY A TURBULENT DYNAMO

Magnetic field strengths inferred for relativistic outflows including gamma-ray bursts (GRBs) and active galactic nuclei are larger than naively expected by orders of magnitude. We present three-dimensional relativistic magnetohydrodynamic simulations demonstrating amplification and saturation of a magnetic field by a macroscopic turbulent dynamo triggered by the Kelvin–Helmholtz shear instability. We find rapid growth of electromagnetic energy due to the stretching and folding of field lines in the turbulent velocity field resulting from nonlinear development of the instability. Using conditions relevant for GRB internal shocks and late phases of GRB afterglow, we obtain amplification of the electromagnetic energy fraction to ϵB ∼ 5 × 10−3. This value decays slowly after the shear is dissipated and appears to be largely independent of the initial field strength. The conditions required for operation of the dynamo are the presence of velocity shear and some seed magnetization both of which are expected to be commonplace. We also find that the turbulent kinetic energy spectrum for the case studied obeys Kolmogorov's 5/3 law and that the electromagnetic energy spectrum is essentially flat with the bulk of the electromagnetic energy at small scales.
Meta‐analytically Quantifying the Reliability and Biasability of Forensic Experts

Abstract: In this paper we employ meta‐analytic procedures and estimate effect sizes indexing the degree of reliability and biasability of forensic experts. The data are based on within‐expert comparisons, whereby the same expert unknowingly makes judgments on the same data at different times. This allows us to take robust measurements and conduct analyses that compare variances within the same experts, and thus to carefully quantify the degree of consistency and objectivity that underlie expert performance and decision making. To achieve consistency, experts must be reliable, at least in the very basic sense that an expert makes the same decision when the same data are presented in the same circumstances, and thus be consistent with themselves. To achieve objectivity, experts must focus only on the data and ignore irrelevant information, and thus be unbiasable by extraneous context. The analyses show that experts are not totally reliable nor are they unbiasable. These findings are based on fingerprint experts decision making, but because this domain is so well established, they apply equally well (if not more) to all other less established forensic domains.
The Teacher as Warm Demander

Many teachers in high-poverty schools struggle to establish a positive classroom environment. These teachers know a great deal about their students, feel affection for them, and empathize with their struggles. Unfortunately, the way these teachers act on their caring is often not comprehensive enough to make a difference. The teachers work hard to design interesting lessons, but if students are disengaged, the quality of the lessons will be irrelevant and misbehavior will reveal students' underlying resistance.
Differential and Synergistic Effects of Selective Norepinephrine and Serotonin Reuptake Inhibitors in Rodent Models of Pain

There is increasing recognition that norepinephrine (NE) and serotonin (5-HT) reuptake inhibitors (NRIs and SRIs) are efficacious in treating some types of pain. To date, studies have not systematically evaluated the relative activity at the NE and/or 5-HT transporter required for maximal efficacy in rodent pain models. Known selective NE and 5-HT reuptake inhibitors reboxetine, desipramine, fluoxetine, and paroxetine were evaluated in both in vitro and in vivo assays. Using the spinal nerve ligation model of neuropathic pain, the compounds differentially reversed tactile allodynia. Evaluation of a broader spectrum of reuptake inhibitors in the para-phenylquinone (PPQ)-induced abdominal constriction model, a model of acute visceral pain, demonstrated that both the SRIs and the NRIs significantly blocked abdominal constrictions. However, the magnitude of this effect was greater following treatment with compounds having greater affinity for NRI compared with SRI affinity. In addition, isobolographic analyses indicated significant synergistic effects for all combinations of desipramine and fluoxetine in the PPQ model of visceral pain. Collectively, the present results support the hypothesis that compounds with greater NRI activity should be more effective for the treatment of pain than compounds having only SRI activity, and this hypothesis is also supported by clinical data. These studies also suggest that the potency and effectiveness of NRIs might be enhanced by the presence of 5-HT activity.
Tunable Chemokine Production by Antigen Presenting Dendritic Cells in Response to Changes in Regulatory T Cell Frequency in Mouse Reactive Lymph Nodes

Background Although evidence exists that regulatory T cells (Tregs) can suppress the effector phase of immune responses, it is clear that their major role is in suppressing T cell priming in secondary lymphoid organs. Recent experiments using two photon laser microscopy indicate that dendritic cells (DCs) are central to Treg cell function and that the in vivo mechanisms of T cell regulation are more complex than those described in vitro. Principal Findings Here we have sought to determine whether and how modulation of Treg numbers modifies the lymph node (LN) microenvironment. We found that pro-inflammatory chemokines—CCL2 (MCP-1) and CCL3 (MIP-la)—are secreted in the LN early (24 h) after T cell activation, that this secretion is dependent on antigen-specific DC–T cell interactions, and that it was inversely related to the frequency of Tregs specific for the same antigen. Furthermore, we demonstrate that Tregs modify the chemoattractant properties of antigen-presenting DCs, which, as the frequency of Tregs increases, fail to produce CCL2 and CCL3 and to attract antigen-specific T cells. Conclusions These results substantiate a major role of Tregs in LN patterning during antigen-specific immune responses.
Association of programmed cell death-1 (PDCD-1) gene polymorphisms with rheumatoid arthritis in Iranian patients.

OBJECTIVES Programmed cell death 1 (PDCD-1, also named PD-1, CD279, and SLEB2), a negative T cell regulator to maintain peripheral tolerance, induces negative signals to T cells during interaction with its ligands and is therefore a candidate gene in the development of autoimmune diseases such as rheumatoid arthritis (RA). Herein, we investigate the association of PDCD-1 polymorphisms with the risk of RA among Iranian patients and healthy controls. METHODS Genomic DNA was extracted from the whole blood samples using DNA Purification kit (DNG-plus). Using the PCR- RFLP method, 3 PDCD-1 SNPs, including PD1.1G/A, PD1.3G/A, and PD1.9C/T were genotyped in 120 RA patients as well as 188 healthy controls. The genotype and allele frequencies of these SNPs were analysed by statistical tests for the significant association between RA patients and controls. Haplotype constructions of these SNPs were performed. Clinical diagnosis of the RA patients was confirmed by the Rheumatology Research Centere of Tehran University of Medical Sciences. RESULTS Our study revealed that PD1.1 A allele at position -538 in the promoter region of PDCD-1 gene is associated with an increased risk of RA disease compared to controls (2.9% vs. 0.7%, OR= 3.735, 95% CI= 0.956-14.588, p=0.046). There were no significant differences in other alleles and genotypes of PDCD-1 SNPs between RA cases and controls. CONCLUSIONS Our results indicate that among the polymorphisms which we evaluated only the PD1.1A allele in the promoter region of PDCD-1 gene is significantly associated with RA susceptibility in Iranian patients.
Orientation of Pseudomonas aeruginosa ExsA Monomers Bound to Promoter DNA and Base-Specific Contacts with the PexoT Promoter

ABSTRACT ExsA is a transcriptional activator of the Pseudomonas aeruginosa type III secretion system (T3SS) and a member of the AraC/XylS protein family. Each of the 10 ExsA-dependent promoter regions that define the T3SS regulon has two adjacent binding sites for monomeric ExsA. Whereas the promoter-proximal sites (binding site 1) contain highly conserved GnC and TGnnA sequences that are separated by ∼10 bp, the promoter-distal sites (binding site 2) share no obvious sequence similarity to each other or to the binding site 1 consensus. In the present study, we used footprinting with Fe-BABE (a protein-labeling reagent that can be conjugated to cysteine residues) to demonstrate that the two ExsA monomers bind to the PexsC, PexsD, PexoT, and PpcrG promoters in a head-to-tail orientation. The footprinting data further indicate that the conserved GnC and TGnnA sequences constitute binding site 1. When bound to site 1, the first helix-turn-helix (HTH) motif of ExsA interacts with the conserved GnC sequence, and the second HTH interacts at or near the TGnnA sequences. Genetic data using the PexoT promoter indicate that residues L198 and T199 in the first HTH motif of ExsA contact the guanine in the GnC sequence and that residue K202, also in the first HTH motif, contacts the cytosine. Likewise, evidence is presented that residues Q248, Y250, T252, and R257 located in the second HTH motif contribute to the recognition of the TGnnA sequence. These combined data define interactions of ExsA with site 1 on the PexoT promoter and provide insight into the nature of the interactions involved in recognition of binding site 2.
Improving API Usage through Automatic Detection of Redundant Code

Software projects often rely on third-party libraries made accessible through Application Programming Interfaces (APIs). We have observed many cases where APIs are used in ways that are not the most effective. We developed a technique and tool support to automatically detect such patterns of API usage in software projects. The main hypothesis underlying our technique is that client code imitating the behavior of an API method without calling it may not be using the API effectively because it could instead call the method it imitates. Our technique involves analyzing software systems to detect cases of API method imitations. In addition to warning developers of potentially re-implemented API methods, we also indicate how to improve the use of the API. Applying our approach on 10 Java systems revealed over 400 actual cases of potentially suboptimal API usage, leading to many improvements to the quality of the code we studied.
Expression of the melanin‐concentrating hormone (MCH) receptor mRNA in the rat brain

The melanin‐concentrating hormone (MCH) system is thought to be an important regulator of food intake. Recently the orphan G protein‐coupled receptor SLC‐1 was identified as the MCH receptor (MCHR). Preliminary analyses of MCHR mRNA distribution have supported a role for the MCH system in nutritional homeostasis. We report here a complete anatomical distribution of the MCHR mRNA. We have found high levels of expression of MCHR mRNA in most anatomical areas implicated in control of olfaction, with the exception of the main olfactory bulb. Dense labeling was also detected in the hippocampal formation, subiculum, and basolateral amygdala, all of which are important in learning and memory, and in the shell of the nucleus accumbens, a substrate for motivated behavior and feeding. Within the hypothalamus, MCHR mRNA was moderately expressed in the ventromedial nucleus, arcuate nucleus, and zona incerta, all of which serve key roles in the neuronal circuitry of feeding. In the brainstem, strong expression was observed in the locus coeruleus, which is implicated in arousal, as well as in nuclei that contribute to orofacial function and mastication, including the facial, hypoglossal, motor trigeminal, and dorsal motor vagus nuclei. In most regions there was a good correspondence between MCHR mRNA distribution and that of MCH‐immunoreactive fibers. Taken together, these data suggest that MCH may act at various levels of the brain to integrate various aspects of feeding behavior. However, the extensive MCHR distribution throughout the brain suggests that this receptor may play a role in other functions, most notably reinforcement, arousal, sensorimotor integration, and autonomic control. J. Comp. Neurol. 435:26–40, 2001. © 2001 Wiley‐Liss, Inc.
DC-magnetoencephalography and time-resolved near-infrared spectroscopy combined to study neuronal and vascular brain responses

The temporal relation between vascular and neuronal responses of the brain to external stimuli is not precisely known. For a better understanding of the neuro–vascular coupling changes in cerebral blood volume and oxygenation have to be measured simultaneously with neuronal currents. With this motivation modulation dc-magnetoencephalography was combined with multi-channel time-resolved near-infrared spectroscopy to simultaneously monitor neuronal and vascular parameters on a scale of seconds. Here, the technique is described, how magnetic and optical signals can be measured simultaneously. In a simple motor activation paradigm (alternating 30 s of finger movement with 30 s of rest for 40 min) both signals were recorded non-invasively over the motor cortex of eight subjects. The off-line averaged signals from both modalities showed distinct stimulation related changes. By plotting changes in oxy- or deoxyhaemoglobin as a function of magnetic field a characteristic trajectory was created, which was similar to a hysteresis loop. A parametric analysis allowed quantitative results regarding the timing of coupling: the vascular signal increased significantly slower than the neuronal signal.