Miracle-dz/UniFAR-FTUs huggingface dataset:
A meta‐analysis of temperature sensitivity as a microbial trait

Traits‐based approaches in microbial ecology provide a valuable way to abstract organismal interaction with the environment and to generate hypotheses about community function. Using macromolecular rate theory (MMRT), we recently identified that temperature sensitivity can be characterized as a distinct microbial trait. As temperature is fundamental in controlling biological reactions, variation in temperature sensitivity across communities, organisms, and processes has the potential to vastly improve understanding of microbial response to climate change. These microbial temperature sensitivity traits include the heat capacity ( ΔCP‡ ), temperature optimum (Topt), and point of maximum temperature sensitivity (TSmax), each of which provide unique insights about organismal response to changes in temperature. In this meta‐analysis, we analyzed the distribution of these temperature sensitivity traits from bacteria, fungi, and mixed communities across a variety of biological systems (e.g., soils, oceans, foods, wastewater treatment plants) in order to identify commonalities in temperature responses across these diverse organisms and reaction rates. Our analysis of temperature sensitivity traits from over 350 temperature response curves reveals a wide distribution of temperature sensitivity traits, with Topt and TSmax well within biological relevant temperatures. We find that traits vary significantly depending on organism type, microbial diversity, source environment, and biological process, with higher temperature sensitivity found in fungi than bacteria and in less diverse systems. Carbon dioxide production was found to be less temperature sensitive than denitrification, suggesting that changes in temperature will have a potentially larger impact on nitrogen‐related processes. As climate changes, these results have important implications for basic understanding of the temperature sensitivity of biological reactions and for ecological understanding of species’ trait distributions, as well as for improved treatment of temperature sensitivity in models.
Randomized optimal transport on a graph: framework and new distance measures

Abstract The recently developed bag-of-paths (BoP) framework consists in setting a Gibbs–Boltzmann distribution on all feasible paths of a graph. This probability distribution favors short paths over long ones, with a free parameter (the temperature T) controlling the entropic level of the distribution. This formalism enables the computation of new distances or dissimilarities, interpolating between the shortest-path and the resistance distance, which have been shown to perform well in clustering and classification tasks. In this work, the bag-of-paths formalism is extended by adding two independent equality constraints fixing starting and ending nodes distributions of paths (margins). When the temperature is low, this formalism is shown to be equivalent to a relaxation of the optimal transport problem on a network where paths carry a flow between two discrete distributions on nodes. The randomization is achieved by considering free energy minimization instead of traditional cost minimization. Algorithms computing the optimal free energy solution are developed for two types of paths: hitting (or absorbing) paths and non-hitting, regular, paths and require the inversion of an n × n matrix with n being the number of nodes. Interestingly, for regular paths on an undirected graph, the resulting optimal policy interpolates between the deterministic optimal transport policy (T → 0+) and the solution to the corresponding electrical circuit (T → ∞). Two distance measures between nodes and a dissimilarity between groups of nodes, both integrating weights on nodes, are derived from this framework.
Reduction of polycyclic aromatic hydrocarbons in common carp meat smoked in traditional conditions

ABSTRACT Common carp meat was smoked in traditional conditions without filter and with zeolite, granular activated carbon, and gravel filters. The aim of this study was to determine the influence of using different filters in traditional smoking conditions on 16 polycyclic aromatic hydrocarbons from the Environmental Protection Agency list (16 US-EPA PAHs). Determination and quantification of PAHs were performed by gas chromatography–mass spectrometry (GC-MS). According to the obtained results, all examined samples of common carp meat smoked in traditional conditions were safe for consumers regarding to the European Commission Regulation on PAH content. After statistical analysis, the zeolite filter appeared to be the best one based on food safety of traditional production of smoked common carp meat. Application of any of these filters to produce smoked common carp meat in traditional conditions resulted in a safer product, as lower levels of PAHs were obtained.
Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase

Bacterial lactate racemase is a nickel-dependent enzyme that contains a cofactor, nickel pyridinium-3,5-bisthiocarboxylic acid mononucleotide, hereafter named nickel-pincer nucleotide (NPN). The LarC enzyme from the bacterium Lactobacillus plantarum participates in NPN biosynthesis by inserting nickel ion into pyridinium-3,5-bisthiocarboxylic acid mononucleotide. This reaction, known in organometallic chemistry as a cyclometalation, is characterized by the formation of new metal–carbon and metal–sulfur σ bonds. LarC is therefore the first cyclometallase identified in nature, but the molecular mechanism of LarC-catalyzed cyclometalation is unknown. Here, we show that LarC activity requires Mn2+-dependent CTP hydrolysis. The crystal structure of the C-terminal domain of LarC at 1.85 Å resolution revealed a hexameric ferredoxin-like fold and an unprecedented CTP-binding pocket. The loss-of-function of LarC variants with alanine variants of acidic residues leads us to propose a carboxylate-assisted mechanism for nickel insertion. This work also demonstrates the in vitro synthesis and purification of the NPN cofactor, opening new opportunities for the study of this intriguing cofactor and of NPN-utilizing enzymes.
Hybrid Precoding Architecture for Massive Multiuser MIMO With Dissipation: Sub-Connected or Fully Connected Structures?

In this paper, we study the hybrid precoding structures over limited feedback channels for massive multiuser multiple-input multiple-output (MIMO) systems. We focus on the system performance of hybrid precoding under a more realistic hardware network model, particularly, with inevitable dissipation. The effect of quantized analog and digital precoding is characterized. We investigate the spectral efficiencies of two typical hybrid precoding structures, i.e., the sub-connected structure and the fully connected structure. It is revealed that increasing signal power can compensate for the performance loss incurred by quantized analog precoding. In addition, by capturing the nature of the effective channels for hybrid processing, we employ a channel correlation-based codebook and demonstrate that the codebook shows a great advantage over the conventional random vector quantization codebook. It is also discovered that, if the channel correlation-based codebook is utilized, the sub-connected structure always outperforms the fully connected structure in either massive MIMO or low signal-to-noise ratio scenarios; otherwise, the fully-connected structrue achieves better performance. Simulation results under both Rayleigh fading channels and millimeter wave (mm-wave) channels verify the conclusions above.
The Application of Cooperative Learning Think Pair Share (TPS) Model to Increase the Process Science Skills in Class IV Elementry School Number 81 Pekanbaru City

The aims of this study to analyze the implementation of cooperative learning Think Pair Share (TPS) model in enhancing science process skills of fourth grade students of SDN 81 Pekanbaru. Subjects were students of elementary school (SDN) 81 Pekanbaru City at year 2014/2015, with a total sample of 21 students (one class). Science process skills of students captured through science process skills test, which consists of seven aspects of evaluation (indicators), namely: observation/observation, question, hypothesis, communication, inference, planning, and implementation. The results showed that in general a significant increase, but to aspects of "question" has decreased the number of N-gain of 0.06. The highest increase was shown in the aspect of "application", the number of N-gain of 0.50 (medium category). Lowest increase shown in the aspect of "hypothesis", the number of N-gain of 0.16 (lower category).
Residual Dipolar Coupling-A Fundemental Tissue Parameter

Introduction Residual dipolar coupling (RDC) provides an important contrast mechanism when imaging fibrocartilage. The behavior of water imbedded in collagen was first described fifty years ago in a seminal paper by Berendsen where the NMR spectrum of bovine Achilles tendon displayed three discrete broad lines(1). The two outer lines were found to depend on the fiber to static magnetic field orientation, providing direct evidence of residual proton-proton dipolar coupling. When imaging tissues containing fibrocartilage, the details of the NMR spectrum are not given much consideration. The presence of RDC, however, produces change in T2 values and gives rise to the magic angle effect, providing angle dependent contrast between fiber structures. RDC should be viewed as a fundamental measureable tissue parameter, similar to a diffusion rate or T1 value. We have developed an imaging technique allowing the evaluation of this parameter on a per voxel basis. The RDC value provides a sensitive indicator reflecting the structure of fibrocartilage tissue, e.g. direction and distribution of fibers, how much collagen is present and state of hydration. Methods Images of tissue specimens were obtained in multiple equally spaced orientations relative to B0 using a GE 3T HDx scanner with small custom receiver coils. Images were registered using FLIRT software (FSL, Oxford) and intensity fluctuations computed on a per voxel basis using macros written in ImageJ. Simulations were performed in MatLab evaluating the number of sample orientations necessary to achieve a stable value for the coefficient of variation (related to RDC) for an arbitrary voxel. Results In our previous work with dipolar anisotropy fiber tracking(2) we reported intensity fluctuations for each voxel as a coefficient of variation (cv) parameter. Fig. 1 shows the expected intensity changes vs. orientation for a dipolar model. Computation of a cv value was done from the intensities indicated by the vertical lines. For a 2D distribution of fibers (requiring only one rotation axis to investigate) six equally spaced orientations provided a stable cv value. For a full 3D investigation at least 16 equally spaced orientations were found to be necessary.
Unshielded and Asymmetric RF Transmit Coil for Hyperpolarized 129 Xe Human Lung Imaging at 3 . 0 T

Introduction: Hyperpolarized He gas provides unprecedented imaging of lung anatomy and function. However, He is exceedingly rare and this is expected to limit its widespread clinical use. On the other hand, hyperpolarized Xe gas is more plentiful and has been shown to provide similar image quality and diagnostic utility. Furthermore, Xe has a high solubility in tissue and can reveal anomalies in pulmonary perfusion and gas exchange. Hyperpolarized gas imaging of human subjects is expected to benefit from parallel imaging approaches [1], requiring uniform transmit coils conforming to the human thorax. Asymmetric bird-cage resonators have previously been described for hyperpolarized He lung imaging at 1.5 T, allowing uniform, quadrature B1 transmission in the chest and room to accommodate multi-channel receive coil arrays [2]. In this work we describe a novel unshielded, asymmetric quadrature bird-cage transmit coil designed for hyperpolarized Xe imaging of human lungs at 3.0 T while allowing proton imaging without having to move the subject. The coil performance is also compared to a conventional linear coil on the basis of SNR, B1 homogeneity and patient comfort.
Promoter methylation of PGC1A and PGC1B predicts cancer incidence in a veteran cohort.

AIM Previous studies suggest telomere shortening represses PGC1A and PGC1B expression leading to mitochondrial dysfunction. Methylation of CpG sites within these genes may interact with these factors to affect cancer risk. MATERIALS & METHODS Among 385 men, we identified 84 incidents of cancers (predominantly prostate and nonmelanoma skin). We examined associations between leukocyte DNA methylation of 41 CpGs from PGC1A and PGC1B with telomere length, mitochondrial 8-OHdG lesions, mitochondrial abundance and cancer incidence. RESULTS Methylation of five and eight CpG sites were significantly associated with telomere length and mitochondrial abundance at p < 0.05. Two CpG sites were independently associated with cancer risk: cg27514608 (PGC1A, TSS1500; HR: 1.55, 95% CI: 1.19-2.03, FDR = 0.02), and cg15219393 (PGC1B, first exon/5'UTR; HR: 3.71, 95% CI: 1.82-7.58, FDR < 0.01). Associations with cg15219393 were observed primarily among men with shorter leukocyte telomeres. CONCLUSION PGC1A and PGC1B methylation may serve as early biomarkers of cancer risk.
Evaluating Testing, Profile Likelihood Confidence Interval Estimation, and Model Comparisons for Item Covariate Effects in Linear Logistic Test Models

The linear logistic test model (LLTM) has been widely applied to investigate the effects of item covariates on item difficulty. The LLTM was extended with random item residuals to account for item differences not explained by the item covariates. This extended LLTM is called the LLTM-R. In this article, statistical inference methods are investigated for these two models. Type I error rates and power are compared via Monte Carlo studies. Based on the simulation results, the use of the likelihood ratio test (LRT) is recommended over the paired-sample t test based on sum scores, the Wald z test, and information criteria, and the LRT is recommended over the profile likelihood confidence interval because of the simplicity of the LRT. In addition, it is concluded that the LLTM-R is the better general model approach. Inferences based on the LLTM while the LLTM-R is the true model appear to be largely biased in the liberal way, while inferences based on the LLTM-R while the LLTM is the true model are only biased in a very minor and conservative way. Furthermore, in the absence of residual variance, Type I error rate and power were acceptable except for power when the number of items is small (10 items) and also the number of persons is small (200 persons). In the presence of residual variance, however, the number of items needs to be large (80 items) to avoid an inflated Type I error and to reach a power level of . 90 for a moderate effect.
Eye-Tracking Provides a Sensitive Measure of Exploration Deficits After Acute Right MCA Stroke

The eye-tracking study aimed at assessing spatial biases in visual exploration in patients after acute right MCA (middle cerebral artery) stroke. Patients affected by unilateral neglect show less functional recovery and experience severe difficulties in everyday life. Thus, accurate diagnosis is essential, and specific treatment is required. Early assessment is of high importance as rehabilitative interventions are more effective when applied soon after stroke. Previous research has shown that deficits may be overlooked when classical paper-and-pencil tasks are used for diagnosis. Conversely, eye-tracking allows direct monitoring of visual exploration patterns. We hypothesized that the analysis of eye-tracking provides more sensitive measures for spatial exploration deficits after right middle cerebral artery stroke. Twenty-two patients with right MCA stroke (median 5 days after stroke) and 28 healthy controls were included. Lesions were confirmed by MRI/CCT. Groups performed comparably in the Mini–Mental State Examination (patients and controls median 29) and in a screening of executive functions. Eleven patients scored at ceiling in neglect screening tasks, 11 showed minimal to severe signs of unilateral visual neglect. An overlap plot based on MRI and CCT imaging showed lesions in the temporo–parieto–frontal cortex, basal ganglia, and adjacent white matter tracts. Visual exploration was evaluated in two eye-tracking tasks, one assessing free visual exploration of photographs, the other visual search using symbols and letters. An index of fixation asymmetries proved to be a sensitive measure of spatial exploration deficits. Both patient groups showed a marked exploration bias to the right when looking at complex photographs. A single case analysis confirmed that also most of those patients who showed no neglect in screening tasks performed outside the range of controls in free exploration. The analysis of patients’ scoring at ceiling in neglect screening tasks is of special interest, as possible deficits may be overlooked and thus remain untreated. Our findings are in line with other studies suggesting considerable limitations of laboratory screening procedures to fully appreciate the occurrence of neglect symptoms. Future investigations are needed to explore the predictive value of the eye-tracking index and its validity in everyday situations.
Green silver-nanoparticle-based dual sensor for toxic Hg(II) ions

The present study focuses on the utilization of green silver nanoparticles, as they are preferred for sensing applications due to their environmentally friendly nature. We have examined the optical and electrochemical sensing behavior of silver nanoparticles from Agaricus bisporus (AgNP-AB) towards Hg(II) ions. The AgNP-AB was prepared by microwave reactor. The synthesized AgNP was used for the sensing of Hg(II) ions without the use of modifiers or further sophisticated instrumentation. The synthesized nanoparticles were successfully characterized by different techniques. AgNP-AB leads to aggregation with the addition of Hg(II) ions in aqueous medium, and develops a color change from brown to black which leads to the formation of AgNP-AB-Hg(II) complex. Moreover, the metal sensing ability of AgNP has been explored using electrochemical studies. AgNP-AB modified platinum electrode (AgNP-AB/PE) was developed for the fast sensing of toxic Hg(II) ions. The sensor exhibits a good limit of detection at 2.1 × 10−6 M. The sensitivity of AgNP-AB/PE towards Hg(II) ions was analyzed with various metal ions. The sensing skill of the developed system was successfully checked with real water samples from Vembanade Lake, Kumarakom, Kerala. AgNP from A. bisporus is highly versatile and promising for different environmental applications.
The Ferredoxin-Like Proteins HydN and YsaA Enhance Redox Dye-Linked Activity of the Formate Dehydrogenase H Component of the Formate Hydrogenlyase Complex

Formate dehydrogenase H (FDH-H) and [NiFe]-hydrogenase 3 (Hyd-3) form the catalytic components of the hydrogen-producing formate hydrogenlyase (FHL) complex, which disproportionates formate to H2 and CO2 during mixed acid fermentation in enterobacteria. FHL comprises minimally seven proteins and little is understood about how this complex is assembled. Early studies identified a ferredoxin-like protein, HydN, as being involved in FDH-H assembly into the FHL complex. In order to understand how FDH-H and its small subunit HycB, which is also a ferredoxin-like protein, attach to the FHL complex, the possible roles of HydN and its paralogue, YsaA, in FHL complex stability and assembly were investigated. Deletion of the hycB gene reduced redox dye-mediated FDH-H activity to approximately 10%, abolished FHL-dependent H2-production, and reduced Hyd-3 activity. These data are consistent with HycB being an essential electron transfer component of the FHL complex. The FDH-H activity of the hydN and the ysaA deletion strains was reduced to 59 and 57% of the parental, while the double deletion reduced activity of FDH-H to 28% and the triple deletion with hycB to 1%. Remarkably, and in contrast to the hycB deletion, the absence of HydN and YsaA was without significant effect on FHL-dependent H2-production or total Hyd-3 activity; FDH-H protein levels were also unaltered. This is the first description of a phenotype for the E. coli ysaA deletion strain and identifies it as a novel factor required for optimal redox dye-linked FDH-H activity. A ysaA deletion strain could be complemented for FDH-H activity by hydN and ysaA, but the hydN deletion strain could not be complemented. Introduction of these plasmids did not affect H2 production. Bacterial two-hybrid interactions showed that YsaA, HydN, and HycB interact with each other and with the FDH-H protein. Further novel anaerobic cross-interactions of 10 ferredoxin-like proteins in E. coli were also discovered and described. Together, these data indicate that FDH-H activity measured with the redox dye benzyl viologen is the sum of the FDH-H protein interacting with three independent small subunits and suggest that FDH-H can associate with different redox-protein complexes in the anaerobic cell to supply electrons from formate oxidation.
The initiation of cannabis use in adolescence is predicted by sex‐specific psychosocial and neurobiological features

Cannabis use initiated during adolescence might precipitate negative consequences in adulthood. Thus, predicting adolescent cannabis use prior to any exposure will inform the aetiology of substance abuse by disentangling predictors from consequences of use. In this prediction study, data were drawn from the IMAGEN sample, a longitudinal study of adolescence. All selected participants (n = 1,581) were cannabis‐naïve at age 14. Those reporting any cannabis use (out of six ordinal use levels) by age 16 were included in the outcome group (N = 365, males n = 207). Cannabis‐naïve participants at age 14 and 16 were included in the comparison group (N = 1,216, males n = 538). Psychosocial, brain and genetic features were measured at age 14 prior to any exposure. Cross‐validated regularized logistic regressions for each use level by sex were used to perform feature selection and obtain prediction error statistics on independent observations. Predictors were probed for sex‐ and drug‐specificity using post‐hoc logistic regressions. Models reliably predicted use as indicated by satisfactory prediction error statistics, and contained psychosocial features common to both sexes. However, males and females exhibited distinct brain predictors that failed to predict use in the opposite sex or predict binge drinking in independent samples of same‐sex participants. Collapsed across sex, genetic variation on catecholamine and opioid receptors marginally predicted use. Using machine learning techniques applied to a large multimodal dataset, we identified a risk profile containing psychosocial and sex‐specific brain prognostic markers, which were likely to precede and influence cannabis initiation.