Miracle-dz/UniFAR-FTUs huggingface dataset:
ORGANIC CARBON DYNAMICS IN THE BALTIC SEA

Coastal seas constitute a link between land and the open ocean, and therefore play an important role in the global carbon cycle. Large amounts of carbon, of both terrestrial and marine origin, transit and are transformed in these waters, which belong to the more productive areas of the oceans. Despite much research has been done on the subject, there are still many unknown factors in the coastal sea carbon cycling. This doctoral thesis investigates the carbon dynamics in the Baltic Sea, with a focus on the production and fate of marine and terrestrial organic carbon and its influence on the air-sea CO2 exchange in its northernmost part, the Gulf of Bothnia. The main approach is the use of a coupled 3D physicalbiogeochemical model, in combination with a long series of measurements of physical and biogeochemical parameters. A new coupled 3D physical-biogeochemical model, which includes the stoichiometric flexibility of plankton and organic matter, is set up for the Gulf of Bothnia. It is found that phytoplankton stoichiometric flexibility in particular, with non-Redfieldian dynamics, is key to explaining seasonal pCO2, dissolved organic carbon (DOC), and nutrient dynamics. If the Redfield ratio is instead used to predict organic carbon production, as done in most biogeochemical models currently in use, the uptake of atmospheric CO2 is reduced by half. Furthermore, it is shown that the organic carbon production needed to reproduce the summer pCO2 drawdown is larger than measured estimates of primary production. This discrepancy is attributed to a substantial production of extracellular DOC, which seems not to be captured by measurements. The dynamics of terrestrial dissolved organic carbon (tDOC) is studied by the use of a passive tracer released from rivers into the physical model of the Baltic Sea. It is found that 80% of the tDOC released in the Baltic Sea is removed, and the rest is exported to the North Sea. Two different parameterisations of tDOC removal are tested. In the first one a decay rate with a timescale of 1 year applied to 80% of the tDOC, and the remaining 20% is assumed to be refractory. In the second one a decay rate with a timescale of 10 years applied to 100% of the tDOC. Trying these parameterisations in a full biogeochemical model shows that only the one with the faster decay is able to reproduce observations of pCO2 in the low-salinity region. A removal rate of one year agrees well with calculated removal rates from bacterial incubation experiments, indicating that bacteria have the potential to cause this remineralisation. It is not only remineralisation of tDOC that affects the pCO2; it is also suggested that a strong tDOC induced light extinction is needed to prevent a too large pCO2 drawdown by phytoplankton in the low salinity region.
Novel dose-finding designs and considerations on practical implementations in oncology clinical trials

ABSTRACT One of the main objectives in phase I oncology trials is to evaluate safety and tolerability of an experimental treatment by estimating the maximum tolerated dose (MTD) based on the rate of dose-limiting toxicities (DLT). To meet emerging challenges in dose-finding studies, over the past two decades, extensive research has been conducted by statistical and medical researchers to create innovative dose finding designs that perform better than the standard 3 + 3 design, which often exhibits undesirable statistical and operational properties. However, clinical implementation and practical usage of these new designs have been limited. This article begins with a review of the most recent literature and then provides some perspectives on implementing novel adaptive dose finding designs in oncology phase I trials from a pharmaceutical industry perspective. Statistical planning and logistical considerations on how to effectively execute such designs in multi-center clinical trials are discussed using two recent case studies.
Modern Markets and Guava Farmers in Mexico 1

-This paper analyzes the participation of small farmers in the fresh fruit and vegetable supply systems of supermarkets in Mexico, using the case of small-scale guava farmers in the state of Michoacán. Several findings emerge. The most important determinants of access of these farmers to “more modern markets” channels are their territorial context and the way in which those territories interact with different markets, and their quasi-fixed capital assets. Farm size, education, and participation in organizations are not significant determinants (except for farm size in the Central Region). Policies and projects aimed at promoting the inclusion in modern markets of small-scale farmers such as those producing guava in Michoacán, must act on the territorial dimension of the problem of inclusion/exclusion, and not restrict themselves to actions aimed at improving the supply chains or the capacities of the households or their farms and organizations.
ALN thin-films as heat spreaders in III–V photonics devices Part 2: Simulations

In the paper, we aim to solve the thermal problems appearing in integrated silicon photonics by using high thermal conductivity Aluminium Nitride (ALN) as a thermal spreading layer located around the ridge of a hybrid III-V laser on silicon in comparison to the existing encapsulation material benzocyclobutene (BCB). Here, to facilitate the design of reliable hybrid semiconductor lasers, we first develop and implement a multiphysics electro-thermo-mechanical model within a finite element environment COMSOL. A phenomenological model of laser operation is used to numerically capture all the thermal and electrical characteristics of the lasers. In terms of the hybrid devices, the simulated thermal resistance agrees well with our device measurements presented in Part 1 of this work. We also demonstrate that the use of the ALN heat spreader can significantly reduce the thermal resistance. Moreover, a linear elastic model is employed for a mechanical analysis of the entire laser structure. The maximum allowable stress is estimated using the Christensen criterion. We find that the process-dependent residual stress dictates the device stress field. In the current design, the BCB encapsulation layer is at risk of failure around the InP waveguide. For AlN spreaders, lower film processing temperatures are key to reduce the stress in the deposited film. We further perform a parametric study on Tref to determine the maximum allowable deposition temperature of AlN/BCB. The simulations suggest that Tref should not exceed 59 °C and 69 °C for ALN and BCB respectively to avoid mechanical failure in the devices.
Syndecan-4 Is a Major Syndecan in Primary Human Endothelial Cells In Vitro, Modulated by Inflammatory Stimuli and Involved in Wound Healing

Syndecans are important cell surface proteoglycans with many functions; yet, they have not been studied to a very large extent in primary human endothelial cells. The purpose of this study was to investigate syndecan-4 expression in cultured human umbilical vein endothelial cells (HUVECs) and assess its role in inflammatory reactions and experimental wound healing. qRT-PCR analysis revealed that syndecan-3 and syndecan-4 were highly expressed in HUVECs, whereas the expression of syndecan-1 and -2 was low. HUVECs were cultured with the inflammatory mediators lipopolysaccharide (LPS) and interleukin 1β (IL-1β). As a result, syndecan-4 expression showed a rapid and strong increase. Syndecan-1 and -2 expressions decreased, whereas syndecan-3 was unaffected. Knockdown of syndecan-4 using siRNA resulted in changes in cellular morphology and focal adhesion sites, delayed wound healing and tube formation, and increased secretion of the pro-inflammatory and angiogenic chemokine, CXCL8. These data suggest functions for syndecan-4 in inflammatory reactions, wound healing and angiogenesis in primary human endothelial cells.
Boosting algorithms with topic modeling for multi-label text categorization: A comparative empirical study

Boosting algorithms have received significant attention over the past several years and are considered to be the state-of-the-art classifiers for multi-label classification tasks. The disadvantage of using boosting algorithms for text categorization (TC) is the vast number of features that are generated using the traditional Bag-of-Words (BOW) text representation, which dramatically increases the computational complexity. In this paper, an alternative text representation method using topic modeling for enhancing and accelerating multi-label boosting algorithms is concerned. An extensive empirical experimental comparison of eight multi-label boosting algorithms using topic-based and BOW representation methods was undertaken. For the evaluation, three well-known multi-label TC datasets were used. Furthermore, to justify boosting algorithms performance, three well-known instance-based multi-label algorithms were involved in the evaluation. For completely credible evaluations, all algorithms were evaluated using their native software tools, except for data formats and user settings. The experimental results demonstrated that the topic-based representation significantly accelerated all algorithms and slightly enhanced the classification performance, especially for near-balanced and balanced datasets. For the imbalanced dataset, BOW representation led to the best performance. The MP-Boost algorithm is the most efficient and effective algorithm for imbalanced datasets using BOW representation. For topic-based representation, AdaBoost.MH with meta base learners, Hamming Tree (AdaMH-Tree) and Product (AdaMH-Product) achieved the best performance; however, with respect to the computational time, these algorithms are the slowest overall. Moreover, the results indicated that topic-based representation is more significant for instance-based algorithms; nevertheless, boosting algorithms, such as MP-Boost, AdaMH-Tree and AdaMH-Product, notably exceed their performance.
The light output and the detection ef fi ciency of the liquid scintillator

The light output response and the neutron and gamma-ray detection efficiency are determined for liquid scintillator EJ-309. The light output function is compared to those of previous studies. Experimental efficiency results are compared to predictions from GEANT4, MCNPX and PENELOPE Monte Carlo simulations. The differences associated with the use of different light output functions are discussed. & 2014 Elsevier Ltd. All rights reserved.
Face recognition using variance weightiness LBP based on single training image per person

A novel and efficient method for face recognition with only one training image is proposed in this paper. It combines both texture feature and global topological information, and merges different features with proper weightiness. Firstly, we partition facial images according to “Three courtyards and five eyes” theory. Secondly, LBP is used to exact texture feature, and then we choose variance for weightiness to merge features, here we make use of variance to estimate the scattered degree between classes. Finally, the Chi-square is used to measure similarity, and we send them to the nearest classifier for further recognition. On ORL facial database, experiments show a better effect and higher recognition accuracy of this method.
FACTORSYNTH : A MAX TOOL FOR SOUND ANALYSIS AND RESYNTHESIS BASED ON MATRIX FACTORIZATION

Factorsynth is a new software tool, developed in the Max environment, that implements sound processing based on matrix factorization techniques. In particular, Nonnegative Matrix Factorization is applied to the input sounds, which produces a set of temporal and spectral components that can be then freely manipulated and combined to produce new sounds. Based on a simple graphical interface that visualizes the factorization output, Factorsynth aims at bringing the ideas of matrix factorization to a wider audience of composers and sound designers.
Dementia: Stigma, Language, and Dementia-friendly

The incidence of dementia worldwide is rapidly increasing and Alzheimer’s Disease International (ADI) (2013) reported that ‘there are 7.7 million new cases of dementia each year, implying that there is a new case of dementia somewhere in the world every four seconds’. In Australia, there are over 332,000 people diagnosed with dementia, with an estimated 1700 new diagnoses per week (Alzheimer’s Australia, 2014c). As the incidence of dementia rises globally, the rate and scale at which it is currently escalating has forced governments to make it a health priority, and from a consumer’s perspective, it is therefore very timely to re-consider the language being used to represent people with dementia and its impact on stigma. I have also considered the presence of stigma within the stigma literature, and wonder if the presence of stigma towards people with dementia, within the dementia and stigma literature, exacerbates the stigma, or prevents the timely translation of good research into better practice. Finally, I will briefly discuss the concept of a dementia friendly community, and the challenges this presents to me as a person living with younger onset dementia.
Endothelial Cx 40 limits myocardial ischaemia / reperfusion injury in mice

Endothelial Cx40 limits myocardial ischaemia/ reperfusion injury in mice
Polarization properties of phase conjugation by degenerate four-wave mixing in a medium of rigidly held dye molecules

The saturation properties of dye molecules that are rigidly held in a solid host are qualitatively different from those of molecules that are free to rotate. We have found that these unique saturation characteristics can be exploited to achieve nearly perfect vector phase conjugation for field strengths near the saturation intensity. We have studied these properties experimentally by using fluorescein-doped boric acid glass as the nonlinear-optical material.
Total Synthesis of Aquatolide: Wolff Ring Contraction and Late-Stage Nozaki-Hiyama-Kishi Medium-Ring Formation.

A total synthesis of the highly strained natural product aquatolide has been achieved. The synthesis featured a photoinduced Wolff ring contraction reaction for the construction of bicyclo[2.1. 1]hexane from diazo compound with a bicyclo[2.2.1]heptane skeleton. The eight-membered enone was built by a late-stage intramolecular Nozaki-Hiyama-Kishi vinylation reaction of steric bulky vinyl iodide and aldehyde.
Purification and Characterization of a Chimeric Enzyme fromHaemophilus influenzae Rd That Exhibits Glutathione-dependent Peroxidase Activity*

While belonging to the same family of antioxidant enzymes, members of the peroxiredoxins do not necessarily employ one and the same method for their reduction. Most representatives become reduced with the aid of thioredoxin, whereas some members use AhpF, tryparedoxin, or cyclophilin A. Recent research on a new peroxiredoxin isoform (type C) from Populus trichocarpa has shown that these particular types may also use glutaredoxin instead of thioredoxin. This finding is supported by the occurrence of chimeric proteins composed of a peroxiredoxin and glutaredoxin region. A gene encoding such a fusion protein is enclosed in the Haemophilus influenzae Rd genome. We expressed the H. influenzaeprotein, denoted here as PGdx, in Escherichia coli and purified the recombinant enzyme. In vitro assays demonstrate that PGdx, in the presence of dithiothreitol or glutathione, is able to protect supercoiled DNA against the metal ion-catalyzed oxidation-system. Enzymatic assays did, indeed, characterize PGdx as a peroxidase, requiring the glutathione redox cycle for the reduction of hydrogen peroxide (k cat /K m 5.01 × 106 s−1 m −1) as well as the small organic hydroperoxide tert-butylhydroperoxide (k cat/K m 5.67 × 104 s−1 m −1). Enzymatic activity as function of the glutathione concentration deviated from normal Michaelis-Menten kinetics, giving a sigmoidal pattern with an apparent Hill coefficient of 2.9. Besides the formation of a disulfide-linked PGdx dimer, it was also shown by mass spectrometric analysis that cysteine 49, which is equivalent to the active site cysteine of the peroxiredoxins, undergoes glutathionylation during purification under nonreducing conditions. Based on these results, we propose a model for the catalytic mechanism.
Surface Reconstruction of the Brain based on Level Set Method

In this paper, a new method for 3D surface reconstruction of the brain is presented. The approach is based on the level set method. The 3D visual surface of the brain can be displayed accurately and quickly. Different with 3D model from MC (marching-cubes) algorithm, the results from the proposed method has many specific characteristics, such as direct, convenient and transparent.
Lexical familiarity and English-language experience affect Japanese adults' perception of / / and /l/.

This study assessed the influence of subjective lexical familiarity and English-language experience on Japanese adults' accuracy in identifying singleton word-initial tokens of English [symbol: see text] and /l/. The inexperienced Japanese (IJ) subjects had lived in the U.S. for 2 years, whereas the experienced Japanese (EJ) subjects had lived there for 21 years, on average. The native Japanese subjects correctly identified English [symbol: see text] and /l/ tokens less often than did a group of native English (NE) subjects, but they did not differ from the NE subjects in identifying the control consonants /w/ and /d/. The NE subjects, who were at ceiling, showed no effect of subjective lexical familiarity. However, the EJ and IJ subjects correctly identified [symbol: see text] and /l/ tokens more often in words that were more familiar than their minimal pairs than in words that were less familiar than their minimal pairs. The EJ subjects identified liquids more often than did the IJ subjects, but usually less often than the NE subjects. However, the EJ subjects managed to identify [symbol: see text] tokens at rates comparable to the NE subjects' rates in words that wer matched in subjective familiarity to their minimal pair (experiment 1), and when identifying [symbol: see text] tokens that had been edited out of their original word or nonword context (experiment 2).
Open-region, electromagnetic finite-element scattering calculations in anisotropic media on parallel computers

Open-region scattering calculations for complex, electrically large scatterers remains a difficult modeling and simulation problem. The finite-element method (FEM) has been shown to be a viable approach to solving such problems. However, conventional methods on serial computers limit the size which can be tackled with the FEM. In this paper, we demonstrate the use of both a PML boundary condition along with a parallel solver for tackling large, complex problems containing scatterers which are inhomogeneous and anisotropic.
Heap Leaching: Modelling and Forecasting Using CFD Technology

Heap leach operations typically employ some form of modelling and forecasting tools to predict cash flow margins and project viability. However, these vary from simple spreadsheets to phenomenological models, with more complex models not commonly employed as they require the greatest amount of time and effort. Yet, accurate production modelling and forecasting are essential for managing production and potentially critical for successful operation of a complex heap, time and effort spent in setting up modelling tools initially may increase profitability in the long term. A brief overview of various modelling approaches is presented, but this paper focuses on the capabilities of a computational fluid dynamics (CFD) model. Advances in computational capability allow for complex CFD models, coupled with leach kinetic models, to be applied to complex ore bodies. In this paper a comprehensive hydrodynamic CFD model is described and applied to chalcopyrite dissolution under heap operating conditions. The model is parameterized against experimental data and validated against a range of experimental leach tests under different thermal conditions. A three-dimensional ‘virtual’ heap, under fluctuating meteorological conditions, is simulated. Continuous and intermittent irrigation is investigated, showing copper recovery per unit volume of applied leach solution to be slightly increased for pulse irrigation.
Comparison of invasive and non-invasive measurement of spontaneous baroreflex during anesthesia.

BACKGROUND Many works have shown that beat-to-beat variations in systolic arterial pressure (SAP) could be used for the assessment of cardiac baroreflex function. The purpose of this study was to evaluate whether Finapres, a non-invasive device to measure systolic arterial pressure, could serve as an acceptable alternative to intra-arterial catheterization for assessing the spontaneous baroreflex during anesthesia. METHODS Thirty ASA class I patients scheduled for surgical hepatic and gastric tumor excisions were enrolled in this study. Spontaneous baroreflex sensitivity (SBR) during anesthesia was calculated by sequence analysis of beat-to-beat variations in systolic arterial pressure and R-R intervals. Data obtained from Finapres were compared with those from standard intra-arterial catheterization technique. RESULTS SBR values determined by non-invasive and invasive blood pressure measurement technique were precisely correlated (r = 0.96) and the mean difference was about 0.22 ms/mmHg (12.5%). However, the individual data might differ by -0.52 to +0.96 ms/mmHg (-35% to +60%). CONCLUSIONS Finapres may trace the changes of SBR during anesthesia and provides similar results as does invasive method but individual variation exists.
Advances in Prostate Cancer Diagnosis: Triggers for Prostate Biopsy

In the early years of screening for prostate cancer with serum PSA, absolute cutoffs were typically utilized such as greater than 4.0 ng/mL or even 2.5 ng/mL. A biopsy of the prostate would commonly be recommended in a man with greater than 10-year life expectancy who had a confirmed elevation above such a threshold or in the presence of an abnormal digital rectal examination. The unmet need, however, is to be more selective in recommending a prostate biopsy, due to the risk of complications and the high rate of false-positive PSAs. More recently, various clinical nomograms can be used to refine selection. In addition, clinicians can now utilize various advanced serum biomarkers that have enhanced specificity—especially for the patient with a rising PSA with prior negative biopsy. In this chapter, we will focus on the biomarkers PCA3, Prostate Health Index, and 4 K score to illustrate key concepts in biomarker develop‐ ment and clinical utility.