Miracle-dz/UniFAR-FTUs huggingface dataset:
The response of methane and nitrous oxide fluxes to forest change in Europe

Abstract. Forests in Europe are changing due to interactions between climate change, nitrogen (N) deposition and new forest management practices. The concurrent impact on the forest greenhouse gas (GHG) balance is at present difficult to predict due to a lack of knowledge on controlling factors of GHG fluxes and response to changes in these factors. To improve the mechanistic understanding of the ongoing changes, we studied the response of soil–atmosphere exchange of nitrous oxide (N2O) and methane (CH4) at twelve experimental or natural gradient forest sites, representing anticipated future forest change. The experimental manipulations, one or more per site, included N addition (4 sites), changes of climate (temperature, 1 site; precipitation, 2 sites), soil hydrology (3 sites), harvest intensity (1 site), wood ash fertilisation (1 site), pH gradient in organic soil (1 site) and afforestation of cropland (1 site). On average, N2O emissions increased by 0.06 ± 0.03 (range 0–0.3) g N2O-N m−2 yr−1 across all treatments on mineral soils, but the increase was up to 10 times higher in an acidic organic soil. Soil moisture together with mineral soil C / N ratio and pH were found to significantly influence N2O emissions across all treatments. Emissions were increased by elevated N deposition, especially in interaction with increased soil moisture. High pH reduced the formation of N2O, even under otherwise favourable soil conditions. Oxidation (uptake) of CH4 was on average reduced from 0.16 ± 0.02 to 0.04 ± 0.05 g CH4-C m−2 yr−1 by the investigated treatments. The CH4 exchange was significantly influenced by soil moisture and soil C / N ratio across all treatments, and CH4 emissions occurred only in wet or water-saturated conditions. For most of the investigated forest manipulations or natural gradients, the response of both N2O and CH4 fluxes was towards reducing the overall GHG forest sink. The most resilient forests were dry Mediterranean forests, as well as forests with high soil C / N ratio or high soil pH. Mitigation strategies may focus on (i) sustainable management of wet forest areas and forested peatlands, (ii) continuous forest cover management, (iii) reducing atmospheric N input and, thus, N availability, and (iv) improving neutralisation capacity of acid soils (e.g. wood ash application).
Possible involvement of transient receptor potential ankyrin 1 in Ca2+ signaling via T‐type Ca2+ channel in mouse sensory neurons

T‐type Ca2+ channels and TRPA1 are expressed in sensory neurons and both are associated with pain transmission, but their functional interaction is unclear. Here we demonstrate that pharmacological evidence of the functional relation between T‐type Ca2+ channels and TRPA1 in mouse sensory neurons. Low concentration of KCl at 15 mM (15K) evoked increases of intracellular Ca2+ concentration ([Ca2+]i), which were suppressed by selective T‐type Ca2+ channel blockers. RT‐PCR showed that mouse sensory neurons expressed all subtypes of T‐type Ca2+ channel. The magnitude of 15K‐induced [Ca2+]i increase was significantly larger in neurons sensitive to allylisothiocyanate (AITC, a TRPA1 agonist) than in those insensitive to it, and in TRPA1−/− mouse sensory neurons. TRPA1 blockers diminished the [Ca2+]i responses to 15K in neurons sensitive to AITC, but failed to inhibit 40 mM KCl‐induced [Ca2+]i increases even in AITC‐sensitive neurons. TRPV1 blockers did not inhibit the 15K‐induced [Ca2+]i increase regardless of the sensitivity to capsaicin. [Ca2+]i responses to TRPA1 agonist were enhanced by co‐application with 15K. These pharmacological data suggest the possibility of functional interaction between T‐type Ca2+ channels and TRPA1 in sensory neurons. Since TRPA1 channel is activated by intracellular Ca2+, we hypothesize that Ca2+ entered via T‐type Ca2+ channel activation may further stimulate TRPA1, resulting in an enhancement of nociceptive signaling. Thus, T‐type Ca2+ channel may be a potential target for TRPA1‐related pain.
iCub-HRI: A Software Framework for Complex Human–Robot Interaction Scenarios on the iCub Humanoid Robot

Generating complex, human-like behavior in a humanoid robot like the iCub requires the integration of a wide range of open source components and a scalable cognitive architecture. Hence, we present the iCub-HRI library which provides convenience wrappers for components related to perception (object recognition, agent tracking, speech recognition, and touch detection), object manipulation (basic and complex motor actions), and social interaction (speech synthesis and joint attention) exposed as a C++ library with bindings for Java (allowing to use iCub-HRI within Matlab) and Python. In addition to previously integrated components, the library allows for simple extension to new components and rapid prototyping by adapting to changes in interfaces between components. We also provide a set of modules which make use of the library, such as a high-level knowledge acquisition module and an action recognition module. The proposed architecture has been successfully employed for a complex human–robot interaction scenario involving the acquisition of language capabilities, execution of goal-oriented behavior and expression of a verbal narrative of the robot’s experience in the world. Accompanying this paper is a tutorial which allows a subset of this interaction to be reproduced. The architecture is aimed at researchers familiarizing themselves with the iCub ecosystem, as well as expert users, and we expect the library to be widely used in the iCub community.
Palliative sedation: The end of heated debate?

After more than 15 years of engagement in research on palliative sedation, we dare to pose that it is among the most challenging topics in end-of-life care. The first publications on palliative sedation appeared in this journal as early as 20 years ago. Chater et al.1 stressed the need for proper terminology and proposed to abandon the term “terminal sedation. ” While palliative sedation has remained the most commonly used term ever since, it has also become clear that simply using a common term does not guarantee the use of a common concept, leave alone common practices. [. ]
Pedestrian detection using integral channel detection and ADABOOST algorithm

Pedestrian detection and tracking is a challenging task in surveillance video system as there are variations in appearance, poses, color, shadow, interference. Past study reveals that several schemes have been developed for pedestrian detection and tracking, however there is a need for improvement in accuracy and robustness. This paper proposes a new concept to improve these measures to remove variations, in which the essential process is to extract features color, HOG and gradient as Integral Channels Features. These features form the estimated model from the feature and the estimated model is used as a detector for pedestrian detection using ADABOOST algorithm. From the results shown in this paper, it is clear that the technique of integral channel features and ADABOOST algorithm used for detection combine gives very prominent results for pedestrian detection. An experimental result illustrates the improvement in efficiency and is highly competitive in terms of misclassification error rate.
Studies on the efficacy of Silicosec against Oryzaephilus surinamensis L. and Tribolium castaneum Herbst using two bioassay methods

Laboratory experiments were conducted to determine the effect of Silicosec by using contact and oral bioassay methods on survival of 1-7 days old adults of Oryzaeohilus surinamensis (L.) and Tribolium castaneum (Herbst) at 27±2°C and 65±5% RH. For contact method adult of these species were exposed to five doses of Silicosec for 3 days on plastic Petri dishes while in the case of oral bioas- say technique the species were exposed to maize treated with five doses of Silicosec in small glass vials for 10 days. After exposure the initial mortality was recorded. For O. surinamensis in oral and contact methods 99% mortality was achieved at 8 333 ppm after 10 days and 165 ppm after 3 days, respectively, for T. castaneum 75% mortality achieved at 25 000 ppm after 10 days and 165 ppm after 3 days in the same order. For the oral method LC 50 values for O. surinamensis and T. castaneum were 50 and 133 ppm, respectively after 10 days, while for the contact method these criteria were 8 and 57 ppm, respectively after 3 days. The results revealed that Silicosec with contact method could have more deleterious effect compared to the other method, and O. surinamensis was more susceptible to Silicosec than T. castaneum in either bioassay methods.
The Response of Dark Septate Endophytes (DSE) to Heavy Metals in Pure Culture

Dark septate endophytes (DSE) occur widely in association with plants exposed to heavy metal stress. However, little is known about the response of DSE exposed to heavy metals. In this study, five DSE were isolated from the roots of Astragalus adsurgens Pall. seedlings growing on lead-zinc mine tailings in China. Based on morphological characteristics and DNA sequence analyses, the isolates were identified as Gaeumannomyces cylindrosporus, Paraphoma chrysanthemicola, Phialophora mustea, Exophiala salmonis, and Cladosporium cladosporioides. G. cylindrosporus was selected to explore responses to Pb stress. Scanning electron microscopic observations of G. cylindrosporus grown on solid medium revealed curling of hyphae and formation of hyphal coils in response to Pb. In contrast, in liquid medium, hyphae became thick and swollen with an increase in Pb (II) concentration. We interpret that these changes are related to the variation in cell wall components. We also demonstrated that fungal melanin content increased with the addition of Pb(II). Melanin, as an important component in the cell wall, is known to be an essential antioxidant responsible for decreasing heavy metal toxicity. We also measured the total soluble protein content and glutathione (GSH) concentrations in G. cylindrosporus and found that they initially increased and then decreased with the increase of Pb(II) concentrations. The antioxidant enzyme activities were also examined, and the results showed that superoxide dismutase (SOD) activity was significantly positively correlated with Pb(II) concentrations (r = 0.957, P<0.001). Collectively, our observations indicate that the intracellular antioxidant systems, especially fungal melanin, play an important role in abating the hazards of heavy metals.
Tides in the Weddell Sea

grano Bank and under the Ronne Ice Shelf near the ice front. Model performance was evaluated through comparisons with TOPEX/Poseidon altimetry, bottom pressure gauge records, and current meter data. The largest discrepancies between the model results and measurements occur over the continental slope and under the ice shelves. The principal error sources are believed to be inaccurate bathymetry in our model, tidal analysis limitations associated with short data record lengths, and omission of baroclinic tides. Model results indicate that tides play a significant role in the circulation and heat flux in the Weddell Sea. We discuss the influence of tides on mean flow through the modified effective bottom drag, and the generation of baroclinic tides and other internal gravity waves through interactions of the tide with topography.
Workflow assessment of 3T MRI-guided transperineal targeted prostate biopsy using a robotic needle guidance

Magnetic resonance imaging (MRI) guided transperineal targeted prostate biopsy has become a valuable instrument for detection of prostate cancer in patients with continuing suspicion for aggressive cancer after transrectal ultrasound guided (TRUS) guided biopsy. The MRI-guided procedures are performed using mechanical targeting devices or templates, which suffer from limitations of spatial sampling resolution and/or manual in-bore adjustments. To overcome these limitations, we developed and clinically deployed an MRI-compatible piezoceramic-motor actuated needle guidance device, Smart Template, which allows automated needle guidance with high targeting resolution for use in a wide closed-bore 3-Tesla MRI scanner. One of the main limitations of the MRI-guided procedure is the lengthy procedure time compared to conventional TRUS-guided procedures. In order to optimize the procedure, we assessed workflow of 30 MRI-guided biopsy procedures using the Smart Template with focus on procedure time. An average of 3.4 (range: 2~6) targets were preprocedurally selected per procedure and 2.2 ± 0.8 biopsies were performed for each target with an average insertion attempt of 1.9 ± 0.7 per biopsy. The average technical preparation time was 14 ± 7 min and the in-MRI patient preparation time was 42 ± 7 min. After 21 ± 7 min of initial imaging, 64 ± 12 min of biopsy was performed yielding an average of 10 ± 2 min per tissue sample. The total procedure time occupying the MRI suite was 138 ± 16 min. No noticeable tendency in the length of any time segment was observed over the 30 clinical cases.
Dose intensification of TRAIL-inducing ONC201 inhibits metastasis and promotes intratumoral NK cell recruitment

ONC201 is a first-in-class, orally active antitumor agent that upregulates cytotoxic TRAIL pathway signaling in cancer cells. ONC201 has demonstrated safety and preliminary efficacy in a first-in-human trial in which patients were dosed every 3 weeks. We hypothesized that dose intensification of ONC201 may impact antitumor efficacy. We discovered that ONC201 exerts dose- and schedule-dependent effects on tumor progression and cell death signaling in vivo. With dose intensification, we note a potent anti-metastasis effect and inhibition of cancer cell migration and invasion. Our preclinical results prompted a change in ONC201 dosing in all open clinical trials. We observed accumulation of activated NK+ and CD3+ cells within ONC201-treated tumors and that NK cell depletion inhibits ONC201 efficacy in vivo, including against TRAIL/ONC201-resistant Bax–/– tumors. Immunocompetent NCR1-GFP mice, in which NK cells express GFP, demonstrated GFP+ NK cell infiltration of syngeneic MC38 colorectal tumors. Activation of primary human NK cells and increased degranulation occurred in response to ONC201. Coculture experiments identified a role for TRAIL in human NK-mediated antitumor cytotoxicity. Preclinical results indicate the potential utility for ONC201 plus anti–PD-1 therapy. We observed an increase in activated TRAIL-secreting NK cells in the peripheral blood of patients after ONC201 treatment. The results offer what we believe to be a unique pathway of immune stimulation for cancer therapy.
Unique clinical characteristics, autoantibodies and medication use in Native American patients with systemic lupus erythematosus

Objective Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with varied morbidity and mortality. We assessed clinical presentations, autoantibody specificities and therapeutic interventions in Native American (NA) patients with SLE. Methods Patients with SLE meeting 1997 American College of Rheumatology classification criteria (n=3148) were enrolled between 1992 and 2010 in the multiethnic, cross-sectional Lupus Family Registry and Repository. Clinical, demographic and therapeutic information were extracted from medical records using a standardised form and formalised training. Autoantibodies were assessed by indirect immunofluorescence (antinuclear antibodies (ANA) and antidouble-stranded DNA), precipitin (ENA) and ELISA (IgG and IgM anticardiolipins). Results NA patients met SLE classification at a younger age (29.89±12.3 years) than European Americans (EA; 32.02±12.87, P=0.0157) and a similar age to African-Americans (AAs) and Hispanics (HIS). More NA patients had concurrent rheumatic diseases or symptoms, such as Raynaud’s phenomenon, interstitial lung disease, Sjӧgren’s syndrome and systemic sclerosis. Compared with EAs, NAs were more likely to have high-titre ANA (≥1:3240; P<0.0001) and had more SLE-associated autoantibodies. Autoantibodies with unknown specificities were more common in NAs (41%) compared with other racial/ethnic groups in this collection (AA: 24%, P=0.0006; EA: 17%, P<0.0001; HIS: 23%, P=0.0050). Fewer NA patients used hydroxychloroquine (68%) compared with others (AA: 74%, P=0.0308; EA: 79%, P=0.0001, HIS: 77%, P=0.0173); this was influenced by lower hydroxychloroquine use in NA patients from Latin America (32%). NA patients had higher rates of methotrexate use (28%) compared with AA (18%, P=0.0006) and HIS patients (14%, P=0.0003), higher azathioprine use (38%) compared with EA patients (30%, P=0.0105) and higher mycophenolate mofetil use (26%) compared with EA (17%, P=0.0012) and HIS patients (11%, P<0.0001). Conclusions NA patients are diagnosed with SLE earlier in life and present worse concurrent rheumatic disease symptoms than EA patients. NA patients also are more likely to have expanded autoantibody profiles and precipitins of unknown specificities.
Effect of Benzo[a]Pyrene on Spindle Misorientation and Fidelity of Chromosome Segregation in Lung Epithelial BEAS-2B Cells

Benzo[a]pyrene (B[a]P) is an environmental carcinogen found in tobacco smoke. It leads to high levels of DNA adducts in the lungs of cigarette smokers contributing to genomic instability. Alterations in the mitotic spindle apparatus play a major role in the generation of genomic instability through promoting chromosome mis-segregation and aneuploidy. To date, the effect of B[a]P exposure on altering the mitotic apparatus in normal lung epithelial cells remains unknown. In our study, BEAS-2B human bronchial epithelial cells were exposed to B[a]P and spindle dynamics were evaluated. Confocal imaging showed that B[a]P exposure significantly alters spindles misorientation, leading to chromosome mis-segregations in the form of chromosome lags and bridges. In addition, centrosome duplication and premature centriole disengagement were induced leading to misaligned and multipolar spindle formation. Comparative genomic analysis of mitotic spindle associated genes, revealed downregulation of AurA-Plk1-AurB signaling cascade by B[a]P. In addition, we analyzed the status of p53 and its downstream p21 in B[a]P-treated cells and showed a suppression of p53-p21 axis. When the extent of DNA damage associated with induced mitotic abnormalities was investigated using γ-H2AX, a significant increase and persistence in DNA damage was observed. Overall, our findings show that B[a]P potently induces mitotic abnormalities, DNA damage, and genetic instability.
Adaptation of Bordetella pertussis to the Respiratory Tract

There is a lack of insight into the basic mechanisms by which Bordetella pertussis adapts to the local host environment during infection. We analyzed B. pertussis gene expression in the upper and lower airways of mice and compared this to SO4-induced in vitro Bvg-regulated gene transcription. Approximately 30% of all genes were differentially expressed between in vitro and in vivo conditions. This included several novel potential vaccine antigens that were exclusively expressed in vivo. Significant differences in expression profile and metabolic pathways were identified between the upper versus the lower airways, suggesting distinct antigenic profiles. We found high-level expression of several Bvg-repressed genes during infection, and mouse vaccination experiments using purified protein fractions from both Bvg- and Bvg+ cultures demonstrated protection against intranasal B. pertussis challenge. This study provides novel insights into the in vivo adaptation of B. pertussis and may facilitate the improvement of pertussis vaccines.
On Methods Controlling the False Discovery Rate 1

A great upsurge in research has taken place during the last decade or so in the area of multiple testing due to its increased relevance in modern scientific investigations. A major portion of this research has been devoted to developing methods that control error rates more meaningful as well as powerful than traditional ones in the context of these investigations. The error rates measuring false discovery proportion, particulary the false discovery rate (FDR), and procedures controlling them have received the most attention. This article relates specifically to the FDR and is written with two basic objectives:
Criticality in Large-Scale Brain fMRI Dynamics Unveiled by a Novel Point Process Analysis

Functional magnetic resonance imaging (fMRI) techniques have contributed significantly to our understanding of brain function. Current methods are based on the analysis of gradual and continuous changes in the brain blood oxygenated level dependent (BOLD) signal. Departing from that approach, recent work has shown that equivalent results can be obtained by inspecting only the relatively large amplitude BOLD signal peaks, suggesting that relevant information can be condensed in discrete events. This idea is further explored here to demonstrate how brain dynamics at resting state can be captured just by the timing and location of such events, i.e., in terms of a spatiotemporal point process. The method allows, for the first time, to define a theoretical framework in terms of an order and control parameter derived from fMRI data, where the dynamical regime can be interpreted as one corresponding to a system close to the critical point of a second order phase transition. The analysis demonstrates that the resting brain spends most of the time near the critical point of such transition and exhibits avalanches of activity ruled by the same dynamical and statistical properties described previously for neuronal events at smaller scales. Given the demonstrated functional relevance of the resting state brain dynamics, its representation as a discrete process might facilitate large-scale analysis of brain function both in health and disease.
The Role of the Two-Component System BaeSR in Disposing Chemicals through Regulating Transporter Systems in Acinetobacter baumannii

Bacterial two-component regulatory systems (TCSs) facilitate changes in gene expression in response to environmental stimuli. TCS BaeR regulons influence tigecycline susceptibility in Acinetobacter baumannii through positively regulating the pump genes adeA and adeB. In this study, we demonstrate that an additional two transport systems, AdeIJK and MacAB-TolC, are also regulated by BaeSR. In the wild type and clinical tigecycline-resistant A. baumannii strains, gene expression of AdeIJK and MacAB-TolC increased after tigecycline induction, implicating their importance to tigecycline resistance in addition to AdeABC. Phenotypic microarray results showed that A. baumannii is vulnerable to certain chemicals, especially tannic acid, after deleting baeR, which was confirmed using the spot assay. The wild-type strain of A. baumannii also exhibited 1.6-fold and 4.4-fold increase in gene expression of adeJ and macB in the medium with 100 μg/mL tannic acid, but the increase was fully inhibited by baeR deletion. An electrophoretic motility shift assay based on an interaction between His-BaeR and the adeA, adeI and macA promoter regions did not demonstrate direct binding. In conclusion, A. baumannii can use the TCS BaeSR in disposing chemicals, such as tannic acid and tigecycline, through regulating the efflux pumps.