Miracle-dz/UniFAR-FTUs huggingface dataset:
Global patterns in leaf 13C discrimination and implications for studies of past and future climate

Fractionation of carbon isotopes by plants during CO2 uptake and fixation (Δleaf) varies with environmental conditions, but quantitative patterns of Δleaf across environmental gradients at the global scale are lacking. This impedes interpretation of variability in ancient terrestrial organic matter, which encodes climatic and ecological signals. To address this problem, we converted 3,310 published leaf δ13C values into mean Δleaf values for 334 woody plant species at 105 locations (yielding 570 species-site combinations) representing a wide range of environmental conditions. Our analyses reveal a strong positive correlation between Δleaf and mean annual precipitation (MAP; R2 = 0.55), mirroring global trends in gross primary production and indicating stomatal constraints on leaf gas-exchange, mediated by water supply, are the dominant control of Δleaf at large spatial scales. Independent of MAP, we show a lesser, negative effect of altitude on Δleaf and minor effects of temperature and latitude. After accounting for these factors, mean Δleaf of evergreen gymnosperms is lower (by 1–2.7‰) than for other woody plant functional types (PFT), likely due to greater leaf-level water-use efficiency. Together, environmental and PFT effects contribute to differences in mean Δleaf of up to 6‰ between biomes. Coupling geologic indicators of ancient precipitation and PFT (or biome) with modern Δleaf patterns has potential to yield more robust reconstructions of atmospheric δ13C values, leading to better constraints on past greenhouse-gas perturbations. Accordingly, we estimate a 4.6‰ decline in the δ13C of atmospheric CO2 at the onset of the Paleocene-Eocene Thermal Maximum, an abrupt global warming event ∼55.8 Ma.
Dispositional Hope as a Moderator of the Link Between Social Comparison With Friends and Eighth-Grade Students’ Perceptions of Academic Competence

We examined the link between social comparison with friends and self-perceptions of academic competence during adolescence and how personality may play a role in this link. Participants were 193 eighth-grade students who attended a rural, mid-Atlantic middle school. We used difference scores to measure the extent to which students’ nominated and reciprocated friends had higher academic performance in math and reading than the students themselves. Regression analyses revealed that, as students’ friends had higher math test scores than the students themselves, students’ academic self-competence decreased. For reading, however, a similar result only held for students with higher levels of dispositional hope. The role that hope plays in how students interpret unfavorable social comparisons, and in how they view their academic competence, may not be straightforward. The implications of social comparison may also vary across academic domains.
An Efficient Minibatch Acceptance Test for Metropolis-Hastings

We present a novel Metropolis-Hastings method for large datasets that uses small expected-size mini-batches of data. Previous work on reducing the cost of Metropolis-Hastings tests yields only constant factor reductions versus using the full dataset for each sample. Here we present a method that can be tuned to provide arbitrarily small batch sizes, by adjusting either proposal step size or temperature. Our test uses the noise-tolerant Barker acceptance test with a novel additive correction variable. The resulting test has similar cost to a normal SGD update. Our experiments demonstrate several order-of-magnitude speedups over previous work.
Fetal DNA in maternal plasma is elevated in pregnancies with aneuploid fetuses

Current non‐invasive screening methods for the prenatal diagnosis of fetal aneuploidies are hampered by low sensitivities and high false positive rates. Attempts to redress this situation include the enrichment of fetal cells from maternal blood, or the use of fetal DNA in the plasma of pregnant women. By the use of real‐time quantitative polymerase chain reaction (PCR) it has recently been shown that circulatory male fetal DNA in maternal plasma is elevated in pregnancies with trisomy 21 fetuses. In this independent study we confirm and extend upon these results by showing that the levels of fetal DNA are also elevated in pregnancies with other chromosomal aneuploidies (mean=185.8 genome equivalents/ml; range=62.2–471.7) when compared to pregnancies with normal male fetuses (mean=81.9 genome equivalents/ml; range=28.8–328.9), p=0.005. This elevation was greatest for fetuses with trisomy 21, whereas it was not significant for fetuses with trisomy 18, p=0.356. These data suggest that a quantitative analysis of such fetal DNA levels may serve as an additional marker for certain fetal chromosomal abnormalities, in particular for trisomy 21. Copyright © 2000 John Wiley & Sons, Ltd.
Efficient Approximation Algorithms for Chemical Mechanical Polishing Dummy Fill

To reduce chip-scale topography variation in chemical mechanical polishing process, dummy fill is widely used to improve the layout density uniformity. Previous researches formulated the density-driven dummy fill problem as a standard linear program (LP). However, solving the huge linear program formed by real-life designs is very expensive and has become the hurdle in deploying the technology. Even though there exist efficient heuristics, their performance cannot be guaranteed. Furthermore, dummy fill can also change the interconnect coupling capacitance which might lead to a significant influence on circuit delay, crosstalk, and power consumption. In this paper, we develop a dummy fill algorithm that can be applied to solve both the traditional density-driven problem and the problem considering fill-induced coupling capacitance impact. The proposed algorithm is both efficient and with provably good performance, which is based on a fully polynomial time approximation scheme by Fleischer for covering LP problems. Moreover, based on the approximation algorithm, we also propose a new greedy iterative algorithm to achieve high quality solutions more efficiently than previous Monte Carlo based heuristic methods. Final experimental results demonstrate the effectiveness and efficiency of our algorithms.
Context-related age changes in mothers' speech: joint book reading

The characteristics of motherese are well established by now. Also well established is the fact that mothers' speech to children becomes more adult-like as the child grows older (for example Snow & Ferguson 1977, Snow 1978). What is not agreed is the role speech to children plays in language acquisition. After analysing research on the subject, de Villiers & de Villiers point out that part of the problem may be that 'most of the studies have analyzed the mother's speech in isolation from her interaction with the child' (1978:342). This point becomes increasingly important within the current trend to view early language acquisition not so much as the learning of syntactic rules but as learning how to communicate, how to talk in particular contexts (e.g. Bruner 1980). It is hard to know what to make of the changes in mothers' speech if we do not tie them to the child's own communicative experiences. Moerk (1974) has shown that the types of activities and speech mothers engaged in were related to what the child spoke about at each age. The research reported on here stayed within one activity — looking at a picture book and analysed changes in mothers' speech with respect to the activity itself. Related work on another context, an object retrieval task, found age-related differences in the type of information offered by the mothers (Bridges 1979). Previous research in the book-reading context has shown that mothers seem to structure the activity to facilitate vocabulary learning (Ninio & Bruner 1978). By following what a mother and child said about a single picture across book-reading sessions (Snow & Goldfield 1980), and in different presentations of the same picture within one session (Ninio in press), it has been shown that what is said about a picture at any one time tends to be a development, addition to, or elaboration of what was said about it the last time it came around. In this study we use the book-reading context to focus on changes in the mothers' speech as the child gets older and himself changes the way
Biofilm Dynamics and Kinetics during High-Rate Sulfate Reduction under Anaerobic Conditions

The sulfate kinetics in an anaerobic, sulfate-reducing biofilm were investigated with an annular biofilm reactor. Biofilm growth, sulfide production, and kinetic constants (Km and Vmax) for the bacterial sulfate uptake within the biofilm were determined. These parameters were used to model the biofilm kinetics, and the experimental results were in good agreement with the model predictions. Typical zero-order volume rate constants for sulfate reduction in a biofilm without substrate limitation ranged from 56 to 93 μmol of SO24-cm−3 h−1 at 20�C. The temperature dependence (Q10) of sulfate reduction was equivalent to 3.4 at between 9 and 20�C. The measured rates of sulfate reduction could explain the relatively high sulfide levels found in sewers and wastewater treatment systems. Furthermore, it has been shown that sulfate reduction in biofilms just a few hundred micrometers thick is limited by sulfate diffusion into biofilm at concentrations below 0.5 mM. This observation might, in some cases, be an explanation for the relatively poor capacity of the sulfate-reducing bacteria to compete with the methanogenic bacteria in anaerobic wastewater treatment in submerged filters.
Automatic bioacoustic detection of Rhynchophorus ferrugineus

The goal of this project is to research and develop a bio-acoustic automatic detector of a devastating pest attacking palm trees, which has recently appeared in Mediterranean countries. The method is based on piezoelectric sensors that are inserted in the tree trunk and record locomotion and feeding vibrations of the insect. The obtained signals are amplified, filtered, parameterized and automatically classified by advanced machine learning methods on a portable computer. We report excellent detection results reaching 99.5% on real-field recordings.
Improving the performance of real-time communication services on high-speed LANs under topology changes

In this paper, we propose and evaluate a new protocol that provides topology change- and fault-tolerant real-time communication services on NOW and clusters. This protocol overcomes the main drawback of our previously proposed protocol, called Dynamically Re-established Real-Time Channels (DRRTC), which is physically limited by the number of virtual channels per port. The new protocol allows different real-time channels to share the same virtual channel. In this way, the new protocol allows us to establish a greater number of real-time channels than the previous one. Moreover, its only limitation is the bandwidth devoted to real-time traffic. However, this introduces two new problems that are successfully managed by the new protocol: the existence of cyclic dependencies among different real-time channels and the increased complexity of deadline requirements. We present and analyze the performance evaluation results when a single switch or a single link is deactivated/activated for different topologies and workloads. The new protocol overwhelms the DRRTC protocol while guaranteeing deadline requirements and channel recovery.
Performance Evaluation of Apriori Algorithm on a Hadoop Cluster

Frequent Itemset Mining is a well-known concept in data sciences. If we feed frequent itemset miner algorithms with large datasets they become resource hungry fast as their search space explodes. This problem is even more apparent when we try to use them on Big Data. Recent advances in parallel programming provides good solutions to deal with large datasets but they present their own problems when we try to modify existing data mining algorithms for the new paradigms. The Apriori-algorithm is a classic solution for mining frequent item-sets. In this paper, we provide a parallel implementation of the Apriori algorithm for the Hadoop platform. We introduce a method to measure the performance of the distributed algorithm. In our experimental results we find choke points in the algorithm and provide resolutions. Key–Words: Hadoop, MapReduce, Apriori-algorithm, Frequent itemset mining, Cloud computing
Common SNPs/haplotypes in IL18R1 and IL18 genes are associated with variations in humoral immunity to smallpox vaccination in Caucasians and African Americans.

BACKGROUND Identifying genetic factors that influence poxvirus immunity across races may assist in the development of better vaccines and approaches for vaccine development. METHODS We performed an extensive candidate-gene genetic screen (across 32 cytokine and cytokine receptor genes) in a racially diverse cohort of 1056 healthy adults after a single dose of smallpox vaccine. Associations between single-nucleotide polymorphisms (SNPs)/haplotypes and vaccinia virus-specific neutralizing antibodies were assessed using linear regression methodologies. RESULTS The combined analysis identified 63 associations between candidate SNPs and antibody levels after smallpox vaccination with P < . 05. Thirty-one of these were within the IL18R1 and IL18 genes. Five IL18R1 SNPs, including a coding synonymous polymorphism rs1035130 (Phe251Phe) and 2 promoter SNPs (rs6710885, rs2287037), all in linkage disequilibrium, were associated with significant variations in antibody levels in both Caucasians (P ≤ .016) and African Americans (P ≤ .025). Similarly, associations with 2 intronic IL18 SNPs (rs2043055 and rs5744280) were consistent in the Caucasian (P ≤ .023) and African American samples (P ≤ .014). Haplotype analysis revealed highly significant associations between IL18R1 haplotypes and vaccinia virus-specific antibody levels (P < .001, by combined analysis) that were consistent across races. CONCLUSIONS Our study provides evidence for IL18 and IL18R1 genes as plausible genes regulating the humoral immune response to smallpox vaccine in both Caucasians and African Americans.
Deterministic inference for stochastic systems using multiple shooting and a linear noise approximation for the transition probabilities

Estimating model parameters from experimental data is a crucial technique for working with computational models in systems biology. Since stochastic models are increasingly important, parameter estimation methods for stochastic modelling are also of increasing interest. This study presents an extension to the ‘multiple shooting for stochastic systems (MSS)’ method for parameter estimation. The transition probabilities of the likelihood function are approximated with normal distributions. Means and variances are calculated with a linear noise approximation on the interval between succeeding measurements. The fact that the system is only approximated on intervals which are short in comparison with the total observation horizon allows to deal with effects of the intrinsic stochasticity. The study presents scenarios in which the extension is essential for successfully estimating the parameters and scenarios in which the extension is of modest benefit. Furthermore, it compares the estimation results with reversible jump techniques showing that the approximation does not lead to a loss of accuracy. Since the method is not based on stochastic simulations or approximative sampling of distributions, its computational speed is comparable with conventional least‐squares parameter estimation methods.
A Practical Comparison of Ligation-Independent Cloning Techniques

The precise assembly of specific DNA sequences is a critical technique in molecular biology. Traditional cloning techniques use restriction enzymes and ligation of DNA in vitro, which can be hampered by a lack of appropriate restriction-sites and inefficient enzymatic steps. A number of ligation-independent cloning techniques have been developed, including polymerase incomplete primer extension (PIPE) cloning, sequence and ligation-independent cloning (SLIC), and overlap extension cloning (OEC). These strategies rely on the generation of complementary overhangs by DNA polymerase, without requiring specific restriction sites or ligation, and achieve high efficiencies in a fraction of the time at low cost. Here, we outline and optimise these techniques and identify important factors to guide cloning project design, including avoiding PCR artefacts such as primer-dimers and vector plasmid background. Experiments made use of a common reporter vector and a set of modular primers to clone DNA fragments of increasing size. Overall, PIPE achieved cloning efficiencies of ∼95% with few manipulations, whereas SLIC provided a much higher number of transformants, but required additional steps. Our data suggest that for small inserts (<1.5 kb), OEC is a good option, requiring only two new primers, but performs poorly for larger inserts. These ligation-independent cloning approaches constitute an essential part of the researcher's molecular-tool kit.
Recent advances on 3D printing in hard and soft tissue engineering

Abstract Three-dimensional (3D) printing is a versatile technique used for various tissue-engineering applications and regenerative medicine. Tissue engineering comprises three primary components used with the aim of restoring, maintaining, or replaceing organs. Three-dimensional printing techniques have significant capability in creating three-dimensional scaffolds for tissue engineering and employing variety of biomaterials for scaffold fabrication. Three-dimensional scaffolds have an important role in cellular attachment, proliferation, nutrient transportation and vascularization. This review aims to introduce 3D printing techniques in hard-tissue engineering (bones and teeth) and soft-tissue engineering (cardiovascular system, nerves, cartilage, liver, skin and trachea) including scaffolds, applications and recent advances. GRAPHICAL ABSTRACT
Hierarchical equilibria of branching populations

Abstract. The objective of this paper is the study of the equilibrium behavior of a population on the hierarchical group $\Omega_N$ consisting of families of individuals undergoing critical branching random walk and in addition these families also develop according to a critical branching process. Strong transience of the random walk guarantees existence of an equilibrium for this two-level branching system. In the limit $N\to\infty$ (called the hierarchical mean field limit ), the equilibrium aggregated populations in a nested sequence of balls $B^{(N)}_\ell$ of hierarchical radius $\ell$ converge to a backward Markov chain on $\mathbb{R_+}$. This limiting Markov chain can be explicitly represented in terms of a cascade of subordinators which in turn makes possible a description of the genealogy of the population.
Mitigating the Effects of Process Variations : Architectural Approaches for Improving Batch Performance

As transistor feature sizes continue to shrink into the sub-90nm range and beyond, the effects of process variations on critical path delay have amplified. A common concept to remedy the effects of variation is speed-binning, by which chips from a single batch are rated by a discrete range of frequencies. In this paper, we argue that under these conditions, architectural optimizations should consider their effect on the “batch” of microprocessors rather than aiming at increasing the performance of a single processor. We first show that the critical paths are mostly determined by the level 1 data caches on a set of manufactured microprocessors. Then, we propose three new microarchitectural techniques aimed at masking the effects of process variations on level 1 caches. The first two techniques allow individual highlatency cache lines spanning single or multiple sets to be disabled at the post-manufacture testing stage. The third approach introduces a small substitute cache associated with each cache way to replicate the data elements stored in the high latency lines. Our new schemes can be effectively used to boost up the overall chip yield and also shift the chip binning distribution towards higher frequencies. To make a quantitative comparison between the different schemes, we first define a metric called batchperformance that takes into account the chip yield and frequency of chips in each bin. We then analyze our proposed schemes and show that the resizing schemes and the substitute cache can increase the batch-performance by as much as 5.8% and 11.6%,
Inversions of sexual roles in women’s tourist experiences: mind, body, and language in sexual behaviour

Women’s sexual behaviour in leisure-travel contexts is an under-researched area. Most attention has focused on commercial forms of sex/romance tourism. The purpose of this study was to address women’s sexual behaviour in tourism, with both steady and casual sexual partner/s, by focusing on their perceptions and related meanings. Drawing upon constructivist grounded theory, 21 in-depth interviews with secular and traditional Israeli Jewish women were analysed using a Foucauldian lens, which incorporated technologies of self, inversions of sexual roles and heterotopia. The findings reveal that for some women, sexual behaviour in tourism is an arena for self-exploration, resistance and self-transformation. The complexity of the inversions of sexual roles is illustrated via the triplex of mind, language and body, that combined produce a counter-discourse to social stereotypes associated with women’s sexual behaviour in their home environments.
Improve the prevention of sudden cardiac arrest in emerging countries: the Improve SCA clinical study design

Aims This study aims to demonstrate that primary prevention (PP) patients with one or more additional risk factors are at a similar risk of life-threatening ventricular arrhythmias when compared with secondary prevention (SP) patients, and would receive similar benefit from an implantable cardioverter defibrillator (ICD), or cardiac resynchronization therapy-defibrillator (CRT-D) implant. The study evaluates the benefits of therapy for high-risk patients in countries where defibrillation therapy for PP of SCA is underutilized. Methods Enrolment will consist of 4800 ICD-eligible patients from Asia, Latin America, Eastern Europe, the Middle East, and Africa. Upon enrolment, patients will be categorized as SP or PP. Primary prevention patients will be assessed for additional risk factors: syncope/pre-syncope, non-sustained ventricular tachycardia, frequent premature ventricular contractions, and low left ventricular ejection fraction. Those PP patients with one or more risk factors will be categorized as ‘1.5’ patients. Implant of an ICD/CRT-D will be left to the patient and/or physician's discretion. The primary endpoint will compare the appropriate ICD therapy rate between SP and 1.5 patients. The secondary endpoint compares mortality between 1.5 implanted and non-implanted patients. Conclusion The Improve SCA study will investigate a subset of PP patients, believed to be at similar risk of life-threatening ventricular arrhythmias as SP patients. Results may help clinicians identify and refer the highest risk PP patients for ICDs, help local societies expand guidelines to include PP of SCA utilizing ICDs, and provide additional geographical-relevant evidence to allow patients to make an informed decision whether to receive an ICD. Trial registration NCT02099721.