Miracle-dz/UniFAR-FTUs huggingface dataset:
Autoinducer-2 Plays a Crucial Role in Gut Colonization and Probiotic Functionality of Bifidobacterium breve UCC2003

In the present study we show that luxS of Bifidobacterium breve UCC2003 is involved in the production of the interspecies signaling molecule autoinducer-2 (AI-2), and that this gene is essential for gastrointestinal colonization of a murine host, while it is also involved in providing protection against Salmonella infection in Caenorhabditis elegans. We demonstrate that a B. breve luxS-insertion mutant is significantly more susceptible to iron chelators than the WT strain and that this sensitivity can be partially reverted in the presence of the AI-2 precursor DPD. Furthermore, we show that several genes of an iron starvation-induced gene cluster, which are downregulated in the luxS-insertion mutant and which encodes a presumed iron-uptake system, are transcriptionally upregulated under in vivo conditions. Mutation of two genes of this cluster in B. breve UCC2003 renders the derived mutant strains sensitive to iron chelators while deficient in their ability to confer gut pathogen protection to Salmonella-infected nematodes. Since a functional luxS gene is present in all tested members of the genus Bifidobacterium, we conclude that bifidobacteria operate a LuxS-mediated system for gut colonization and pathogen protection that is correlated with iron acquisition.
Developmentally Specific Associations Between CNR1 Genotype and Cannabis Use Across Emerging Adulthood.

OBJECTIVE Previous studies have found preliminary evidence for associations between common single-nucleotide polymorphisms (SNPs) in the cannabinoid receptor gene CNR1 and cannabis use and dependence. The present study examined a set of eight independent SNPs in or near CNR1 in relation to cannabis use measured longitudinally across emerging adulthood. METHOD Using latent growth curve modeling of 10 waves of longitudinal data spanning mean ages 18.4-23.8 years in a sample of non-Hispanic White individuals (n = 334), we tested if genotype at each CNR1 SNP was associated with both level and growth of cannabis use over time. Peer group drug use, a known correlate of individual use, was evaluated as a time-varying predictor of cannabis use and as a moderator of the relationship between SNPs and individual use. RESULTS After correction for multiple comparisons, one SNP, rs806374, was significantly associated with individual differences in level-but not growth-of cannabis use over time, such that C carriers were more likely to use cannabis more frequently at study onset (around age 18). Peer drug use was a predictor of individual cannabis use that grew in terms of effect size with time, but did not significantly moderate the effect of rs806374 genotype. CONCLUSIONS C carriers at rs806374 may be at specific risk for increased odds of use during the transition out of high school (around age 18). Future studies should investigate potential mechanisms at this developmental stage, including individual differences in subjective response, innate tolerance, reinforcement mechanisms, or general liability for substance misuse.
Prospective data from the Women’s Health Initiative on depressive symptoms, stress, and inflammation

This study examined the longitudinal association of depressive symptoms and stressful life events with inflammation in the Women’s Health Initiative. Women aged 50 years and older (N = 7477) completed questionnaires assessing depressive symptoms and stressful life events at baseline and 15 years later. Serum measures of C-reactive protein were collected at both assessments. In bivariate analyses, C-reactive protein predicted 15-year depressive symptoms and stressful life events (ps < .03) and baseline depressive symptoms and stressful life events predicted later C-reactive protein (ps < .03). These longitudinal relationships were not maintained in multivariate adjusted analyses. Combined with previous research, this suggests the relationship between depression, stressful life events and inflammation attenuates with time.
PMAnalyzer: a new web interface for bacterial growth curve analysis

Summary: Bacterial growth curves are essential representations for characterizing bacteria metabolism within a variety of media compositions. Using high‐throughput, spectrophotometers capable of processing tens of 96‐well plates, quantitative phenotypic information can be easily integrated into the current data structures that describe a bacterial organism. The PMAnalyzer pipeline performs a growth curve analysis to parameterize the unique features occurring within microtiter wells containing specific growth media sources. We have expanded the pipeline capabilities and provide a user‐friendly, online implementation of this automated pipeline. PMAnalyzer version 2.0 provides fast automatic growth curve parameter analysis, growth identification and high resolution figures of sample‐replicate growth curves and several statistical analyses. Availability and Implementation: PMAnalyzer v2.0 can be found at https://edwards.sdsu. edu/pmanalyzer/. Source code for the pipeline can be found on GitHub at https://github.com/dacuevas/PMAnalyzer. Source code for the online implementation can be found on GitHub at https://github.com/dacuevas/PMAnalyzerWeb. Contact: dcuevas08@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
eXtasy simplified-towards opening the black box

Exome sequencing remarkably simplifies the search for mutations causing rare monogenic disorders. Still, due to a big number of potential candidate variants, computational methods are needed to facilitate this process. Recently, an algorithm based on genomic data fusion has been proposed in this context (eXtasy), which exhibits highly competitive performances among the state of the art methods. Nonetheless, being based on a Random Forest classifier, its core model is characterized by a prohibitive size, slow execution speed and difficulties associated with gaining insights in the decision-making process. Here we propose a simplification of the original eXtasy algorithm that retains superior ranking capability of former without suffering from the both high complexity and low interpretability.
IFLT Based Real-Time Framework for Image Matching

In this paper we show that the features generated by the recently presented Invariant Features of Local Textures (IFLT) technique can be used in a SIFT like framework to deliver real-time point wise image matching with performance comparable to existing state-of-the-art image matching systems. The proposed framework is also capable of saving considerable amount of computation time.
Changes in Nematode Communities in Different Physiographic Sites of the Condor Seamount (North-East Atlantic Ocean) and Adjacent Sediments

Several seamounts are known as ‘oases’ of high abundances and biomass and hotspots of biodiversity in contrast to the surrounding deep-sea environments. Recent studies have indicated that each single seamount can exhibit a high intricate habitat turnover. Information on alpha and beta diversity of single seamount is needed in order to fully understand seamounts contribution to regional and global biodiversity. However, while most of the seamount research has been focused on summits, studies considering the whole seamount structure are still rather poor. In the present study we analysed abundance, biomass and diversity of nematodes collected in distinct physiographic sites and surrounding sediments of the Condor Seamount (Azores, North-East Atlantic Ocean). Our study revealed higher nematode biomass in the seamount bases and values 10 times higher in the Condor sediments than in the far-field site. Although biodiversity indices did not showed significant differences comparing seamount sites and far-field sites, significant differences were observed in term of nematode composition. The Condor summit harboured a completely different nematode community when compared to the other seamount sites, with a high number of exclusive species and important differences in term of nematode trophic diversity. The oceanographic conditions observed around the Condor Seamount and the associated sediment mixing, together with the high quality of food resources available in seamount base could explain the observed patterns. Our results support the hypothesis that seamounts maintain high biodiversity through heightened beta diversity and showed that not only summits but also seamount bases can support rich benthic community in terms of standing stocks and diversity. Furthermore functional diversity of nematodes strongly depends on environmental conditions link to the local setting and seamount structure. This finding should be considered in future studies on seamounts, especially in view of the potential impacts due to current and future anthropogenic threats.
Benchmarking Successional Progress in a Quantitative Food Web

Central to ecology and ecosystem management, succession theory aims to mechanistically explain and predict the assembly and development of ecological communities. Yet processes at lower hierarchical levels, e.g. at the species and functional group level, are rarely mechanistically linked to the under-investigated system-level processes which drive changes in ecosystem properties and functioning and are comparable across ecosystems. As a model system for secondary succession, seasonal plankton succession during the growing season is readily observable and largely driven autogenically. We used a long-term dataset from large, deep Lake Constance comprising biomasses, auto- and heterotrophic production, food quality, functional diversity, and mass-balanced food webs of the energy and nutrient flows between functional guilds of plankton and partly fish. Extracting population- and system-level indices from this dataset, we tested current hypotheses about the directionality of successional progress which are rooted in ecosystem theory, the metabolic theory of ecology, quantitative food web theory, thermodynamics, and information theory. Our results indicate that successional progress in Lake Constance is quantifiable, passing through predictable stages. Mean body mass, functional diversity, predator-prey weight ratios, trophic positions, system residence times of carbon and nutrients, and the complexity of the energy flow patterns increased during succession. In contrast, both the mass-specific metabolic activity and the system export decreased, while the succession rate exhibited a bimodal pattern. The weighted connectance introduced here represents a suitable index for assessing the evenness and interconnectedness of energy flows during succession. Diverging from earlier predictions, ascendency and eco-exergy did not increase during succession. Linking aspects of functional diversity to metabolic theory and food web complexity, we reconcile previously disjoint bodies of ecological theory to form a complete picture of successional progress within a pelagic food web. This comprehensive synthesis may be used as a benchmark for quantifying successional progress in other ecosystems.
A Reconfigurable Five-Stage Pipelined SAT Solver

Several approaches have been proposed to accelerate the NP-complete Boolean Satisfiability problem (SAT) using reconfigurable computing. In this paper, we present a five stage pipelined SAT solver. The first stage is a variable decider that, in the normal flow, assigns a free variable from a set of statically pre-ordered variables. In case of conflict, where one or more of the SAT CNF clauses is unsatisfied,the highest ordered variable from a pool of conflicting variables is reassigned or freed. The second stage fetches the effect of the current assigned variable on the SAT instance clauses from a memory pre-initialized with the effect of each variable on all clauses. This data is fed to the next stage, the clause evaluator. The fourth stage is the conflict detector that detects if there is a conflict and, if there is, it detects the index of the first unsatisfied clause.The last stage fetches the conflicting variables (variables in the unsatisfied clause) from a memory containing variables associated with each clause. Our approach’s feasibility is evaluated through instances from the DIMACS benchmarks suite. Pipelining allows retaining same clock frequency of an equivalent non-pipelined implementation while achieving an average of three times speedup in performance.
Bio-inspired control of joint torque and knee stiffness in a robotic lower limb exoskeleton using a central pattern generator

Robotic lower limb exoskeletons are becoming increasingly popular in therapy and recreational use. However, most exoskeletons are still rather limited in their locomotion speed and the activities of daily live they can perform. Furthermore, they typically do not allow for a dynamic adaptation to the environment, as they are often controlled with predefined reference trajectories. Inspired by human leg stiffness modulation during walking, variable stiffness actuators increase flexibility without the need for more complex controllers. Actuation with adaptable stiffness is inspired by the human leg stiffness modulation during walking. However, this actuation principle also introduces the stiffness setpoint as an additional degree of freedom that needs to be coordinated with the joint trajectories. As a potential solution to this issue a bio-inspired controller based on a central pattern generator (CPG) is presented in this work. It generates coordinated joint torques and knee stiffness modulations to produce flexible and dynamic gait patterns for an exoskeleton with variable knee stiffness actuation. The CPG controller is evaluated and optimized in simulation using a model of the exoskeleton. The CPG controller produced stable and smooth gait for walking speeds from 0.4 m/s up to 1.57 m/s with a torso stabilizing force that simulated the use of crutches, which are commonly needed by exoskeleton users. Through the CPG, the knee stiffness intrinsically adapted to the frequency and phase of the gait, when the speed was changed. Additionally, it adjusted to changes in the environment in the form of uneven terrain by reacting to ground contact forces. This could allow future exoskeletons to be more adaptive to various environments, thus making ambulation more robust.
Proportionate NLMS for adaptive feedback control in hearing aids

The proportionate normalized least-mean-squares (PNLMS) algorithm is commonly used in acoustic echo cancellation (AEC) context. It provides faster initial convergence and tracking rates compared to the NLMS algorithm for the case of sparse echo impulse responses. The improved PNLMS algorithm (IPNLMS) has been proven to be more powerful than PNLMS by exploiting new rules for computing the weight of each step-size corresponding to each adaptive filter coefficient. However, the application of the PNLMS and the IPNLMS algorithms for adaptive feedback control (AFC) in hearing aids (HAs) is still limited due to high correlation between the loudspeaker and incoming signals. This paper proposes implementations of the PNLMS/IPNLMS algorithms for AFC using the prediction error method (PEM) for hearing aids. The proposed methods have been evaluated for both speech and music incoming signals. Simulation shows that the proposed methods have faster initial convergence and tracking than the PEM using the NLMS algorithm (PEM-NLMS).
New interleukin-15 superagonist (IL-15SA) significantly enhances graft-versus-tumor activity

Interleukin-15 (IL-15) is a potent cytokine that increases CD8+ T and NK cell numbers and function in experimental models. However, obstacles remain in using IL-15 therapeutically, specifically its low potency and short in vivo half-life. To help overcome this, a new IL-15 superagonist complex comprised of an IL-15N72D mutation and IL-15RαSu/Fc fusion (IL-15SA, also known as ALT-803) was developed. IL-15SA exhibits a significantly longer serum half-life and increased in vivo activity against various tumors. Herein, we evaluated the effects of IL-15SA in recipients of allogeneic hematopoietic stem cell transplantation. Weekly administration of IL-15SA to transplant recipients significantly increased the number of CD8+ T cells (specifically CD44+ memory/activated phenotype) and NK cells. Intracellular IFN-γ and TNF-α secretion by CD8+ T cells increased in the IL-15SA-treated group. IL-15SA also upregulated NKG2D expression on CD8+ T cells. Moreover, IL-15SA enhanced proliferation and cytokine secretion of adoptively transferred CFSE-labeled T cells in syngeneic and allogeneic models by specifically stimulating the slowly proliferative and nonproliferative cells into actively proliferating cells. We then evaluated IL-15SA's effects on anti-tumor activity against murine mastocytoma (P815) and murine B cell lymphoma (A20). IL-15SA enhanced graft-versus-tumor (GVT) activity in these tumors following T cell infusion. Interestingly, IL-15 SA administration provided GVT activity against A20 lymphoma cells in the murine donor leukocyte infusion (DLI) model without increasing graft versus host disease. In conclusion, IL-15SA could be a highly potent T- cell lymphoid growth factor and novel immunotherapeutic agent to complement stem cell transplantation and adoptive immunotherapy.
Strengthening Borehole Configuration from the Retaining Roadway for Greenhouse Gas Reduction: A Case Study

A monitoring trial was carried out to investigate the effect of boreholes configuration on the stability and gas production rate. These boreholes were drilled from the retaining roadway at longwall mining panel 1111(1) of the Zhuji Coalmine, in China. A borehole camera exploration device and multiple gas parameter measuring device were adopted to monitor the stability and gas production rate. Research results show that boreholes 1~8 with low intensity and thin casing thickness were broken at the depth of 5~10 m along the casing and with a distance of 2~14 m behind the coal face, while boreholes 9~11 with a special thick-walled high-strength oil casing did not fracture during the whole extraction period. The gas extraction volume is closely related to the boreholes stability. After the stability of boreholes 9~11 being improved, the average gas flow rate increased dramatically 16-fold from 0.13 to 2.21 m3/min, and the maximum gas flow rate reached 4.9 m3/min. Strengthening boreholes configuration is demonstrated to be a good option to improve gas extraction effect. These findings can make a significant contribution to the reduction of greenhouse gas emissions from the coal mining industry.
Contrasting Prefrontal Cortex Contributions to Episodic Memory Dysfunction in Behavioural Variant Frontotemporal Dementia and Alzheimer’s Disease

Recent evidence has questioned the integrity of episodic memory in behavioural variant frontotemporal dementia (bvFTD), where recall performance is impaired to the same extent as in Alzheimer’s disease (AD). While these deficits appear to be mediated by divergent patterns of brain atrophy, there is evidence to suggest that certain prefrontal regions are implicated across both patient groups. In this study we sought to further elucidate the dorsolateral (DLPFC) and ventromedial (VMPFC) prefrontal contributions to episodic memory impairment in bvFTD and AD. Performance on episodic memory tasks and neuropsychological measures typically tapping into either DLPFC or VMPFC functions was assessed in 22 bvFTD, 32 AD patients and 35 age- and education-matched controls. Behaviourally, patient groups did not differ on measures of episodic memory recall or DLPFC-mediated executive functions. BvFTD patients were significantly more impaired on measures of VMPFC-mediated executive functions. Composite measures of the recall, DLPFC and VMPFC task scores were covaried against the T1 MRI scans of all participants to identify regions of atrophy correlating with performance on these tasks. Imaging analysis showed that impaired recall performance is associated with divergent patterns of PFC atrophy in bvFTD and AD. Whereas in bvFTD, PFC atrophy covariates for recall encompassed both DLPFC and VMPFC regions, only the DLPFC was implicated in AD. Our results suggest that episodic memory deficits in bvFTD and AD are underpinned by divergent prefrontal mechanisms. Moreover, we argue that these differences are not adequately captured by existing neuropsychological measures.
Sex and regional differences in rabbit right ventricular L‐type calcium current levels and mathematical modelling of arrhythmia vulnerability

What is the central question of this study? Regional variations of ventricular L‐type calcium current (ICa‐L) amplitude may underlie the increased arrhythmia risk in adult females. Current amplitude variations have been described for the left ventricle but not for the right ventricle. What is the main finding and its importance? Adult female rabbit right ventricular base myocytes exhibit elevated ICa‐L compared with female apex or male myocytes. Oestrogen upregulated ICa‐L in cultured female myocytes. Mathematical simulations modelling long QT syndrome type 2 demonstrated that elevated ICa‐L prolonged action potentials and induced early after‐depolarizations. Thus, ventricular arrhythmias in adult females may be associated with an oestrogen‐induced upregulation of ICa‐L.
Coherent Somatic Mutation in Autoimmune Disease

Background Many aspects of autoimmune disease are not well understood, including the specificities of autoimmune targets, and patterns of co-morbidity and cross-heritability across diseases. Prior work has provided evidence that somatic mutation caused by gene conversion and deletion at segmentally duplicated loci is relevant to several diseases. Simple tandem repeat (STR) sequence is highly mutable, both somatically and in the germ-line, and somatic STR mutations are observed under inflammation. Results Protein-coding genes spanning STRs having markers of mutability, including germ-line variability, high total length, repeat count and/or repeat similarity, are evaluated in the context of autoimmunity. For the initiation of autoimmune disease, antigens whose autoantibodies are the first observed in a disease, termed primary autoantigens, are informative. Three primary autoantigens, thyroid peroxidase (TPO), phogrin (PTPRN2) and filaggrin (FLG), include STRs that are among the eleven longest STRs spanned by protein-coding genes. This association of primary autoantigens with long STR sequence is highly significant (). Long STRs occur within twenty genes that are associated with sixteen common autoimmune diseases and atherosclerosis. The repeat within the TTC34 gene is an outlier in terms of length and a link with systemic lupus erythematosus is proposed. Conclusions The results support the hypothesis that many autoimmune diseases are triggered by immune responses to proteins whose DNA sequence mutates somatically in a coherent, consistent fashion. Other autoimmune diseases may be caused by coherent somatic mutations in immune cells. The coherent somatic mutation hypothesis has the potential to be a comprehensive explanation for the initiation of many autoimmune diseases.