Miracle-dz/UniFAR-FTUs huggingface dataset:
Fungi Benefit from Two Decades of Increased Nutrient Availability in Tundra Heath Soil

If microbial degradation of carbon substrates in arctic soil is stimulated by climatic warming, this would be a significant positive feedback on global change. With data from a climate change experiment in Northern Sweden we show that warming and enhanced soil nutrient availability, which is a predicted long-term consequence of climatic warming and mimicked by fertilization, both increase soil microbial biomass. However, while fertilization increased the relative abundance of fungi, warming caused only a minimal shift in the microbial community composition based on the phospholipid fatty acid (PLFA) and neutral lipid fatty acid (NLFA) profiles. The function of the microbial community was also differently affected, as indicated by stable isotope probing of PLFA and NLFA. We demonstrate that two decades of fertilization have favored fungi relative to bacteria, and increased the turnover of complex organic compounds such as vanillin, while warming has had no such effects. Furthermore, the NLFA-to-PLFA ratio for 13C-incorporation from acetate increased in warmed plots but not in fertilized ones. Thus, fertilization cannot be used as a proxy for effects on warming in arctic tundra soils. Furthermore, the different functional responses suggest that the biomass increase found in both fertilized and warmed plots was mediated via different mechanisms.
Task-oriented programming in a pure functional language

Task-Oriented Programming (TOP) is a novel programming paradigm for the construction of distributed systems where users work together on the internet. When multiple users collaborate, they need to interact with each other frequently. TOP supports the definition of tasks that react to the progress made by others. With TOP, complex multi-user interactions can be programmed in a declarative style just by defining the tasks that have to be accomplished, thus eliminating the need to worry about the implementation detail that commonly frustrates the development of applications for this domain. TOP builds on four core concepts: tasks that represent computations or work to do which have an observable value that may change over time, data sharing enabling tasks to observe each other while the work is in progress, generic type driven generation of user interaction, and special combinators for sequential and parallel task composition. The semantics of these core concepts is defined in this paper. As an example we present the iTask3 framework, which embeds TOP in the functional programming language Clean.
P2Prec: a social-based P2P recommendation system

P2Prec is a social-based P2P recommendation system for large-scale content sharing that leverages content-based and social-based recommendation. The main idea is to recommend high quality documents related to query topics and contents held by useful friends (of friends) of the users, by exploiting friendship networks. We have implemented a prototype of P2Prec using the Shared-Data Overlay Network (SON), an open source development platform for P2P networks using web services, JXTA and OSGi. In this paper, we describe the demo of P2Prec's main services (installing P2Prec peers, initializing peers, gossiping topics of interest among friends, key-word querying for contents) using our prototype implemented as an application of SON.
Spatial Distribution and Partition Coefficient of Nutrient in Water and Sediment of Shatt Al-Basrah Canal, Iraq

The proposed water and sediment quality of Shatt Al-Basrah was assessed by (1) using Geographic Information Systems (GIS) using Inverse Distance Weighting (IDW) method for calculating nutrient concentrations of water and sediment samples, (2) evaluating Partition Coefficient (Kd) and cluster analysis for water and sediment samples. The GIS facilitates the explanations of the spatial relationships among key environmental processes. It employs spatial distribution modeling to analyze the nutrient concentrations of Nitrite as N (NO2-N), Nitrate as N (NO3-N), Ammonia as N (NH3-N), Ammonium (NH4), and Sulfate (SO4) in the water and sediment. This paper shows that the results of Partition Coefficient (Kd) is always less than 3 for all sites illustrating that the pollutants are present in liquid phase preferentially which have high solubility and are less sediment-associated.
Image Composition Using Deep Painterly Harmonization

: Superimposing a component from a photograph into a painting is a difficult assignment. Applying photograph compositing methods using existing painterly stylization computations, which are worldwide to outcome a photomontage, are performed ineffectively when applied locally. We address these issues with the appropriate rules that cautiously decides the neighbourhood measures need to be considered. We guarantee both spatial and in-scale measurable consistencies to show that the two properties are critical in producing quality outcomes. To adapt to the decent variety of deliberation levels and kinds of canvases, we present a procedure to change the parameters of the exchange contingent upon the artistic creation. We show that our calculation delivers essentially preferable outcomes over photograph compositing or worldwide stylization procedures and that it empowers imaginative painterly alters that would be in any case hard to accomplish.
The role of Self-efficacy, Positive Affect and Social Support on Drug Residents’ Resilience

Undergoing a rehabilitation program is a long process for drug residents, therefore resilience is needed to complete the program. This study aims to determine the effect of self-efficacy, positive affect, and social support on the resilience of drug residents. There were 221 drug residents at rehabilitation institutions in Bogor and Jakarta who participated in this research. They completed Connor-Davison Resilience Scale (CD-RISC) developed by Connor and Davidson [5], Generalized Self-efficacy Scale (GSE) developed by Schwarzer and Jerusalem [30], Positive and Negative Affect Schedule (PANAS) developed by Watson, Clark, & Tellegen [7], and The Social Provision Scale developed by Cutrona and Russell [28]. Confirmatory Factor Analysis was used to test the construct validity of measuremnets, and multiple regression analysis techniques to test the model. The results indicate that there was a significant effect of self-efficacy, positive affect, and social support on the resilience of drug residents (R2=.58). This finding suggest rehabilitation institution to maintain positive affect, develop self-efficacy and confidence among residents to enhance their resilience during rehabilition program. The result also revelad that guidance is the significant type of social support that influence resilience
Methane yield predictive model based on the composition of biomass: Focus on the anaerobic digestion mode and regression method

Nine kinds of biomass were used to investigate the correlation of organic composition with the methane yield in continuous anaerobic digestion (AD) mode with different organic loading rates (OLRs). The experimental results showed that the methane yields were different with the change of OLR; thus, only one model was unable to satisfy the prediction accuracy for all the operation conditions. A stepwise regression model and two self-defined models were used to determine the prediction accuracy for different operation OLRs in the present assay. The results showed that the self-defined models constituted by biodegradable components (protein, fat, and readily degradable sugars) obtained a higher determination coefficient (R2) than the model fitted by the traditional stepwise regression method. Biomass with a higher content of easily degradable matter had a lower predictive deviation. Based on this, it is recommended that the various biomasses be divided into two groups to obtain better model fitting and prediction accuracy. The biomass with a content of readily degradable section that was more than 47% or the content of lignin was less than 8% can be classified into one group, and the others can be classified into another group according to the present test results.
Design and Characterization of a Three-Axis Hall Effect-Based Soft Skin Sensor

This paper presents an easy means to produce a 3-axis Hall effect–based skin sensor for robotic applications. It uses an off-the-shelf chip and is physically small and provides digital output. Furthermore, the sensor has a soft exterior for safe interactions with the environment; in particular it uses soft silicone with about an 8 mm thickness. Tests were performed to evaluate the drift due to temperature changes, and a compensation using the integral temperature sensor was implemented. Furthermore, the hysteresis and the crosstalk between the 3-axis measurements were evaluated. The sensor is able to detect minimal forces of about 1 gf. The sensor was calibrated and results with total forces up to 1450 gf in the normal and tangential directions of the sensor are presented. The test revealed that the sensor is able to measure the different components of the force vector.
Whole Exome Sequencing in Patients with the Cuticular Drusen Subtype of Age-Related Macular Degeneration

Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in elderly people worldwide. Cuticular drusen (CD) is a clinical subtype of AMD, which typically displays an earlier age at onset, and has a strong genetic component. Genetic studies support a role for rare sequence variants in CD susceptibility, and rare sequence variants in the CFH gene have been identified in 8.8% of CD cases. To further explore the role of rare variants in CD, we performed whole exome sequencing (WES) in 14 affected members of six families and 12 sporadic cases with CD. We detected rare sequence variants in CFH and FBLN5, which previously were shown to harbor rare variants in patients with CD. In addition, we detected heterozygous rare sequence variants in several genes encoding components of the extracellular matrix (ECM), including FBLN1, FBLN3/EFEMP1, FBLN5, FBLN6/HMCN1, FBN2, and COL15A1. Two rare pathogenic variants were identified in the COL15A1 gene: one in a sporadic case and another was found to segregate in a family with six affected individuals with CD. In addition, two rare pathogenic variants were identified in the FGL1 gene in three unrelated CD cases. These findings suggest that alterations in the ECM and in the coagulation pathway may play a role in the pathogenesis of CD. The identified candidate genes require further analyses in larger cohorts to confirm their role in the CD subtype of AMD. No evidence was found of rare sequence variants in a single gene that segregate with CD in the six families, suggesting that the disease is genetically heterogeneous.
Prognostic impact of concurrent MYC and BCL6 rearrangements and expression in de novo diffuse large B-cell lymphoma

Double-hit B-cell lymphoma is a common designation for a group of tumors characterized by concurrent translocations of MYC and BCL2, BCL6, or other genes. The prognosis of concurrent MYC and BCL6 translocations is not well known. In this study, we assessed rearrangements and expression of MYC, BCL2 and BCL6 in 898 patients with de novo diffuse large B-cell lymphoma treated with standard chemotherapy (cyclophosphamide, doxorubicin, vincristine, and prednisone plus rituximab). Neither BCL6 translocation alone (more frequent in activated B-cell like diffuse large B-cell lymphoma) nor in combination with MYC translocation (observed in 2.0% of diffuse large B-cell lymphoma) predicted poorer survival in diffuse large B-cell lymphoma patients. Diffuse large B-cell lymphoma patients with MYC/BCL6 co-expression did have significantly poorer survival, however, MYC/BCL6 co-expression had no effect on prognosis in the absence of MYC/BCL2 co-expression, and had no additive impact in MYC+/BCL2+ cases. The isolated MYC+/BCL6+/BCL2− subset, more frequent in germinal center B-cell like diffuse large B-cell lymphoma, had significantly better survival compared with the isolated MYC+/BCL2+/BCL6− subset (more frequent in activated B-cell like diffuse large B-cell lymphoma). In summary, diffuse large B-cell lymphoma patients with either MYC/BCL6 rearrangements or MYC/BCL6 co-expression did not always have poorer prognosis; MYC expression levels should be evaluated simultaneously; and double-hit B-cell lymphoma needs to be refined based on the specific genetic abnormalities present in these tumors.
A small-molecule TrkB ligand restores hippocampal synaptic plasticity and object location memory in Rett syndrome mice

ABSTRACT Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutations in methyl-CpG-binding protein-2 (MECP2), a transcriptional regulator of many genes, including brain-derived neurotrophic factor (BDNF). BDNF levels are reduced in RTT autopsy brains and in multiple brain areas of Mecp2-deficient mice. Furthermore, experimental interventions that increase BDNF levels improve RTT-like phenotypes in Mecp2 mutant mice. Here, we characterized the actions of a small-molecule ligand of the BDNF receptor TrkB in hippocampal function in Mecp2 mutant mice. Systemic treatment of female Mecp2 heterozygous (HET) mice with LM22A-4 for 4 weeks improved hippocampal-dependent object location memory and restored hippocampal long-term potentiation (LTP). Mechanistically, LM22A-4 acts to dampen hyperactive hippocampal network activity, reduce the frequency and amplitude of miniature excitatory postsynaptic currents (mEPSCs), and reduce the frequency of spontaneous tetrodotoxin-resistant Ca2+ signals in Mecp2 mutant hippocampal neurons, making them comparable to those features observed in wild-type neurons. Together, these observations indicate that LM22A-4 is a promising therapeutic candidate for the treatment of hippocampal dysfunction in RTT. Editors' choice: The brain-penetrant BDNF loop domain mimetic LM22A-4 improves synaptic plasticity and spatial discrimination memory in Rett syndrome mice, making it a promising therapeutic candidate for the treatment of hippocampal dysfunction.
Cannabis Dampens the Effects of Music in Brain Regions Sensitive to Reward and Emotion

Abstract Background Despite the current shift towards permissive cannabis policies, few studies have investigated the pleasurable effects users seek. Here, we investigate the effects of cannabis on listening to music, a rewarding activity that frequently occurs in the context of recreational cannabis use. We additionally tested how these effects are influenced by cannabidiol, which may offset cannabis-related harms. Methods Across 3 sessions, 16 cannabis users inhaled cannabis with cannabidiol, cannabis without cannabidiol, and placebo. We compared their response to music relative to control excerpts of scrambled sound during functional Magnetic Resonance Imaging within regions identified in a meta-analysis of music-evoked reward and emotion. All results were False Discovery Rate corrected (P<.05). Results Compared with placebo, cannabis without cannabidiol dampened response to music in bilateral auditory cortex (right: P=.005, left: P=.008), right hippocampus/parahippocampal gyrus (P=.025), right amygdala (P=.025), and right ventral striatum (P=.033). Across all sessions, the effects of music in this ventral striatal region correlated with pleasure ratings (P=.002) and increased functional connectivity with auditory cortex (right: P< .001, left: P< .001), supporting its involvement in music reward. Functional connectivity between right ventral striatum and auditory cortex was increased by cannabidiol (right: P=.003, left: P=.030), and cannabis with cannabidiol did not differ from placebo on any functional Magnetic Resonance Imaging measures. Both types of cannabis increased ratings of wanting to listen to music (P<.002) and enhanced sound perception (P<.001). Conclusions Cannabis dampens the effects of music in brain regions sensitive to reward and emotion. These effects were offset by a key cannabis constituent, cannabidol.
Using Brain Potentials to Functionally Localise Stroop-Like Effects in Colour and Picture Naming: Perceptual Encoding versus Word Planning

The colour-word Stroop task and the picture-word interference task (PWI) have been used extensively to study the functional processes underlying spoken word production. One of the consistent behavioural effects in both tasks is the Stroop-like effect: The reaction time (RT) is longer on incongruent trials than on congruent trials. The effect in the Stroop task is usually linked to word planning, whereas the effect in the PWI task is associated with either word planning or perceptual encoding. To adjudicate between the word planning and perceptual encoding accounts of the effect in PWI, we conducted an EEG experiment consisting of three tasks: a standard colour-word Stroop task (three colours), a standard PWI task (39 pictures), and a Stroop-like version of the PWI task (three pictures). Participants overtly named the colours and pictures while their EEG was recorded. A Stroop-like effect in RTs was observed in all three tasks. ERPs at centro-parietal sensors started to deflect negatively for incongruent relative to congruent stimuli around 350 ms after stimulus onset for the Stroop, Stroop-like PWI, and the Standard PWI tasks: an N400 effect. No early differences were found in the PWI tasks. The onset of the Stroop-like effect at about 350 ms in all three tasks links the effect to word planning rather than perceptual encoding, which has been estimated in the literature to be finished around 200–250 ms after stimulus onset. We conclude that the Stroop-like effect arises during word planning in both Stroop and PWI.
FANCD2 binding identifies conserved fragile sites at large transcribed genes in avian cells

Abstract Common Chromosomal Fragile Sites (CFSs) are specific genomic regions prone to form breaks on metaphase chromosomes in response to replication stress. Moreover, CFSs are mutational hotspots in cancer genomes, showing that the mutational mechanisms that operate at CFSs are highly active in cancer cells. Orthologs of human CFSs are found in a number of other mammals, but the extent of CFS conservation beyond the mammalian lineage is unclear. Characterization of CFSs from distantly related organisms can provide new insight into the biology underlying CFSs. Here, we have mapped CFSs in an avian cell line. We find that, overall the most significant CFSs coincide with extremely large conserved genes, from which very long transcripts are produced. However, no significant correlation between any sequence characteristics and CFSs is found. Moreover, we identified putative early replicating fragile sites (ERFSs), which is a distinct class of fragile sites and we developed a fluctuation analysis revealing high mutation rates at the CFS gene PARK2, with deletions as the most prevalent mutation. Finally, we show that avian homologs of the human CFS genes despite their fragility have resisted the general intron size reduction observed in birds suggesting that CFSs have a conserved biological function.
Stimulus conflation and tuning selectivity in V4 neurons: a model of visual crowding

Visual crowding is a fundamental constraint on our ability to identify peripheral objects in cluttered environments. This study proposes a descriptive model for understanding crowding based on the tuning selectivity for stimuli within the receptive field (RF) and examines potential neural correlates in cortical area V4. For V4 neurons, optimally sized, letter-like stimuli are much smaller than the RF. This permits stimulus conflation, the fusing of separate objects into a single identity, to occur within the RF of single neurons. Flanking interactions between such stimuli were found to be limited to the RF. The response to an optimal stimulus centered in the neuron's RF, is suppressed by the simultaneous presentation of flanking stimuli within the RF. The degree of suppression is a function of the neuron's stimulus tuning properties and the position of the flanker within the RF. A single neuron may show suppression or facilitation depending on the detailed stimulus conditions and the relationship to tuning selectivity. Loss of activity in the set of neurons tuned to a particular stimulus alters its overall representation and potential identification, thus forming a basis for visual crowding effects. The mechanisms that determine the outcome of conflation are associated with object identification, and are not some other independent visual phenomena.
Dendritic cell immunotherapy followed by cART interruption during HIV-1 infection induces plasma protein markers of cellular immunity and neutrophil recruitment

Objectives To characterize the host response to dendritic cell-based immunotherapy and subsequent combined antiretroviral therapy (cART) interruption in HIV-1-infected individuals at the plasma protein level. Design An autologous dendritic cell (DC) therapeutic vaccine was administered to HIV-infected individuals, stable on cART. The effect of vaccination was evaluated at the plasma protein level during the period preceding cART interruption, during analytical therapy interruption and at viral reactivation. Healthy controls and post-exposure prophylactically treated healthy individuals were included as controls. Methods Plasma marker (‘analyte’) levels including cytokines, chemokines, growth factors, and hormones were measured in trial participants and control plasma samples using a multiplex immunoassay. Analyte levels were analysed using principle component analysis, cluster analysis and limma. Blood neutrophil counts were analysed using linear regression. Results Plasma analyte levels of HIV-infected individuals are markedly different from those of healthy controls and HIV-negative individuals receiving post-exposure prophylaxis. Viral reactivation following cART interruption also affects multiple analytes, but cART interruption itself only has only a minor effect. We find that Thyroxine-Binding Globulin (TBG) levels and late-stage neutrophil numbers correlate with the time off cART after DC vaccination. Furthermore, analysis shows that cART alters several regulators of blood glucose levels, including C-peptide, chromogranin-A and leptin. HIV reactivation is associated with the upregulation of CXCR3 ligands. Conclusions Chronic HIV infection leads to a change in multiple plasma analyte levels, as does virus reactivation after cART interruption. Furthermore, we find evidence for the involvement of TBG and neutrophils in the response to DC-vaccination in the setting of HIV-infection.