Miracle-dz/UniFAR-FTUs huggingface dataset:
Vegetation dynamics and plant CO2 responses as positive feedbacks in a greenhouse world

An atmosphere‐ocean‐vegetation coupled model is used to quantify the biogeophysical feedback that emerges as vegetation adjusts dynamically to a quadrupling of atmospheric CO2. This feedback amplifies global warming by 13%. About half of it is due to climatically induced expansion of boreal forest into tundra, reinforced by reductions in snow and sea ice cover. The other half represents a global climatic effect of increased vegetative cover (an indirect consequence of plant physiological responses to CO2) in the semi‐arid subtropics. Enhanced absorption of shortwave radiation in these regions produces a net surface warming, which the atmosphere communicates poleward. The greatest vegetation‐induced warming is co‐located with large, vulnerable carbon stores in the north. These lose carbon, so that in the long term, the biospheric response to CO2 and climate change becomes dominated by positive feedbacks that overwhelm the effect of CO2 fertilization on terrestrial carbon stocks.
Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI

BsrDI and BtsI restriction endonucleases recognize and cleave double-strand DNA at the sequences GCAATG (2/0) and GCAGTG (2/0), respectively. We have purified and partially characterized these two enzymes, and analyzed the genes that encode them. BsrDI and BtsI are unusual in two respects: each cleaves DNA as a heterodimer of one large subunit (B subunit) and one small subunit (A subunit); and, in the absence of their small subunits, the large subunits behave as sequence-specific DNA nicking enzymes and only nick the bottom strand of the sequences at these respective positions: GCAATG (−/0) and GCAGTG (−/0). We refer to the single subunit, the bottom-strand nicking forms as ‘hemidimers’. Amino acid sequence comparisons reveal that BsrDI and BtsI belong to a family of restriction enzymes that possess two catalytic sites: a canonical PD-Xn-EXK and a second non-canonical PD-Xn-E-X12-QR. Interestingly, the other family members, which include BsrI (ACTGG 1/−1) and BsmI/Mva1269I (GAATGC 1/−1) are single polypeptide chains, i.e. monomers, rather than heterodimers. In BsrDI and BtsI, the two catalytic sites are found in two separate subunits. Site-directed mutagenesis confirmed that the canonical catalytic site located at the N-terminus of the large subunit is responsible for the bottom-strand cleavage, whereas the non-canonical catalytic site located in the small subunit is responsible for hydrolysis of the top strand. Top-strand specific nicking variants, Nt.BsrDI and Nt.BtsI, were successfully engineered by combining the catalytic-deficient B subunit with wild-type A subunit.
Towards combinatorial LP turbo decoding

We present a novel algorithm that solves the turbo code LP decoding problem in a finite number of steps by Euclidean distance minimizations, which in turn rely on repeated shortest path computations in the trellis graph representing the turbo code. Previous attempts to exploit the combinatorial graph structure only led to algorithms which are either of heuristic nature or do not guarantee finite convergence. A numerical study shows that our algorithm clearly beats the running time, up to a factor of 100, of generic commercial LP solvers for medium-sized codes, especially for high SNR values.
Domain-related Annotation of Polish Spoken Dialogue Corpus LUNA.PL

The paper presents a corpus of Polish spoken dialogues annotated on several levels, from transcription of dialogues and their morphosyntactic analysis, to semantic annotation. The LUNA.PL corpus is the first semantically annotated corpus of Polish spontaneous speech. It contains 500 dialogues recorded at the Warsaw Transport Authority call centre. For each dialogue, the corpus contains recorded audio signal, its transcription and five XML files with annotations on subsequent levels. Speech transcription was done manually. Text annotation was constructed using a combination of rule based programmes and computer-aided manual work. For morphological annotation we used the already existing analyzer and manually disambiguated the results. Morphologically annotated texts of dialogues were automatically segmented into elementary syntactic chunks. Semantic annotation was done by a set of specially designed rules and then manually corrected. The paper describes details of the domain related semantic annotation which consists of two levels - concept level at which around 200 attributes and their values are annotated, and predicate level at which 47 frame types are recognized. We describe the domain model accepted, and the statistics over the entire annotated set of dialogues.
Computationally Efficient Class-Prior Estimation under Class Balance Change Using Energy Distance

In many real-world classication problems, the class balance often changes between training and test datasets, due to sample selection bias or the non-stationarity of the environment. Naive classier training under such changes of class balance systematically yields a biased solution. It is known that such a systematic bias can be corrected by weighted training according to the test class balance. However, the test class balance is often unknown in practice. In this paper, we consider a semi- supervised learning setup where labeled training samples and unlabeled test samples are available and propose a class balance estimator based on the energy distance. Through experiments, we demonstrate that the proposed method is computationally much more efficient than existing approaches, with comparable accuracy.
Interpretable classification models for recidivism prediction

We investigate a long‐debated question, which is how to create predictive models of recidivism that are sufficiently accurate, transparent and interpretable to use for decision making. This question is complicated as these models are used to support different decisions, from sentencing, to determining release on probation to allocating preventative social services. Each case might have an objective other than classification accuracy, such as a desired true positive rate TPR or false positive rate FPR. Each (TPR, FPR) pair is a point on the receiver operator characteristic (ROC) curve. We use popular machine learning methods to create models along the full ROC curve on a wide range of recidivism prediction problems. We show that many methods (support vector machines, stochastic gradient boosting and ridge regression) produce equally accurate models along the full ROC curve. However, methods that are designed for interpretability (classification and regression trees and C5.0) cannot be tuned to produce models that are accurate and/or interpretable. To handle this shortcoming, we use a recent method called supersparse linear integer models to produce accurate, transparent and interpretable scoring systems along the full ROC curve. These scoring systems can be used for decision making for many different use cases, since they are just as accurate as the most powerful black box machine learning models for many applications, but completely transparent, and highly interpretable.
Open issues in Big Data Warehouse design

Data Warehouse and OLAP systems allow analyzing huge volumes of data represented according to the multidimensional model. In the era of Big Data, NoSQL systems have been proved to be an effective Business Intelligence solution. Some works recently study warehousing and OLAPing Big Data. (Un)Lucky these works exclusively investigate time performance related to the Volume and Velocity features of Big Data. Therefore, in this paper we investigate the impact of other Big Data features: Variety, Veracity and Value on warehousing and OLAP analysis. Then, we go beyond computation performance and we highlight new Big Data Warehouses design issues.
Explicit two-source extractors and resilient functions

We explicitly construct an extractor for two independent sources on n bits, each with polylogarithmic min-entropy. Our extractor outputs one bit and has polynomially small error. The best previous extractor, by Bourgain, required each source to have min-entropy . 499n. A key ingredient in our construction is an explicit construction of a monotone, almost-balanced Boolean functions that are resilient to coalitions. In fact, our construction is stronger in that it gives an explicit extractor for a generalization of non-oblivious bit-fixing sources on n bits, where some unknown n-q bits are chosen almost polylogarithmic-wise independently, and the remaining q bits are chosen by an adversary as an arbitrary function of the n-q bits. The best previous construction, by Viola, achieved q quadratically smaller than our result. Our explicit two-source extractor directly implies improved constructions of a K-Ramsey graph over N vertices, improving bounds obtained by Barak et al. and matching independent work by Cohen.
Hypertrophy, Fibrosis, and Sudden Cardiac Death in Response to Pathological Stimuli in Mice With Mutations in Cardiac Troponin T

Background—Transgenic mouse models expressing a missense mutation (R92Q) or a splice donor site mutation (trunc) in the cardiac troponin T (cTnT) model familial hypertrophic cardiomyopathy (FHC) in humans. Although males from these strains share the unusual property of having significantly smaller ventricles and cardiac myocytes, they differ with regard to systolic function, fibrosis, and gene expression. Little is known about how these phenotypes affect the responses to additional pathological stimuli. Methods and Results—We tested the ability of hearts of both sexes of wild-type and mutant mice to respond to defined pathological, pharmacological, hypertrophic stimuli in vivo. Hearts of mutant cTnT models of both sexes were able to undergo hypertrophy in response to at least one stimulus, but the extent differed between the 2 mutants and was sex specific. Interestingly, the trunc-mutant mouse heart was resistant to the development of fibrosis in response to pharmacological stimuli. Stimulation with 2 adrenergic agonists led to sudden cardiac death of all male but not female mutant animals, which suggests altered adrenergic responsiveness in these 2 models of FHC. Conclusions—Hypertrophic signaling is differentially affected by distinct mutations in cTnT and is sex modified. Hearts can respond with either an augmented hypertrophic and fibrotic response or a diminished hypertrophy and resistance to fibrosis. Sudden cardiac death is related to adrenergic stress and is independent of the development of fibrosis but occurred only in male mice. These results suggest that patients with certain TnT mutations may respond to certain pathological situations with a worsened phenotype.
Performance of a Limiting-Antigen Avidity Enzyme Immunoassay for Cross-Sectional Estimation of HIV Incidence in the United States

Background A limiting antigen avidity enzyme immunoassay (HIV-1 LAg-Avidity assay) was recently developed for cross-sectional HIV incidence estimation. We evaluated the performance of the LAg-Avidity assay alone and in multi-assay algorithms (MAAs) that included other biomarkers. Methods and Findings Performance of testing algorithms was evaluated using 2,282 samples from individuals in the United States collected 1 month to >8 years after HIV seroconversion. The capacity of selected testing algorithms to accurately estimate incidence was evaluated in three longitudinal cohorts. When used in a single-assay format, the LAg-Avidity assay classified some individuals infected >5 years as assay positive and failed to provide reliable incidence estimates in cohorts that included individuals with long-term infections. We evaluated >500,000 testing algorithms, that included the LAg-Avidity assay alone and MAAs with other biomarkers (BED capture immunoassay [BED-CEIA], BioRad-Avidity assay, HIV viral load, CD4 cell count), varying the assays and assay cutoffs. We identified an optimized 2-assay MAA that included the LAg-Avidity and BioRad-Avidity assays, and an optimized 4-assay MAA that included those assays, as well as HIV viral load and CD4 cell count. The two optimized MAAs classified all 845 samples from individuals infected >5 years as MAA negative and estimated incidence within a year of sample collection. These two MAAs produced incidence estimates that were consistent with those from longitudinal follow-up of cohorts. A comparison of the laboratory assay costs of the MAAs was also performed, and we found that the costs associated with the optimal two assay MAA were substantially less than with the four assay MAA. Conclusions The LAg-Avidity assay did not perform well in a single-assay format, regardless of the assay cutoff. MAAs that include the LAg-Avidity and BioRad-Avidity assays, with or without viral load and CD4 cell count, provide accurate incidence estimates.
CINNABAR DEPOSITION IN SUBMARINE COASTAL HYDROTHERMAL VENTS, PACIFIC MARGIN OF CENTRAL MEXICO

Cinnabar deposition was observed in submarine hydrothermal vents at about 10 m depth in the Punta Mita area in western Mexico. The vents occur in basaltic rocks and discharge a mixture of liquid and gas at a temperature of 85°C. Tertiary ignimbrites, basaltic lava flows, and mafic intrusions crop out in Punta Mita; however, at present there is no volcanic activity in the area, and the hydrothermal vents do not possess characteristics compatible with a magmatic heat source. The water discharged by the vents is more dilute than seawater, and precious and base metal contents are below detection limits. The gas is composed mostly of nitrogen and methane, and it contains only trace amounts of He, Ar, H2, CO2, H2S, and O2. Deposits of carbonates (calcite and aragonite), sulfides (pyrite, cinnabar, minor thallium sulfide, and galena), sulfates (barite), and phosphates (carbonate-hydroxyl apatite) were observed. Cinnabar occurs in association with thallium sulfide within pyrite crusts that line the upflow channels and cover the outflow areas near the vents. The hydrothermal activity in Punta Mita is related to deep circulation of ground water from onshore and convective heating in the high geothermal gradient of the area. The interaction of the hot water with organic matter in the layers of sedimentary rocks produces nitrogen and methane, and mercury and other elements are leached from the volcanic and sedimentary rocks. Mercury remains in solution in the thermal fluid until it reaches the sea floor.
Robust predictive control for linear systems subject to norm-bounded model uncertainty

A novel robust predictive control algorithm is presented for input-saturated uncertain discrete-time linear systems described by structured norm-bounded uncertainties. The solution is based on the minimization, at each time instant, of an LMI convex optimization problem obtained by a recursive use of the S-procedure. Stability and feasibility are proved and comparisons with robust multi-model (polytopic) MPC algorithms are reported.
Adaptive Covariance Matrix Estimation for Multi-Baseline InSAR Data Stacks

For many multidimensional applications of synthetic aperture radar (SAR) imaging, the estimation of the covariance matrix for each resolution cell is a critical processing step. The context of this work is the application of covariance matrix estimation for multi-baseline interferometric SAR data sets. In order to ensure local stationarity, which is needed for an unbiased estimation, adaptive techniques are necessary. In this paper, a new approach for adaptive covariance matrix estimation is proposed and evaluated based on measures known from the field of image processing. The procedure is centered around the idea of checking whether the neighboring pixels belong to the same statistical distribution as the currently investigated pixel by applying a threshold to the respective probability density function. All inlier pixels are then used to estimate the complex covariance matrix of the reference pixel. From this covariance matrix, both amplitude and interferometric phase values are extracted, which are then combined for all pixels in the stack in order to employ techniques for the evaluation of filtering efficiency that are typically used in image denoising research. It is found that the proposed algorithm provides high filtering efficiency and good detail preservation at the same time. Apart from that, it is found to be particularly suitable for small-sized stacks of coregistered SAR imagery.
A CSR-NL Interface Specification Version 1.51

Spoken Language Systems will require integration of continuous speech recognition and natural language processing. This is a proposed specification for an interface between a continuous speech recognizer (CSR) and a natural language processor (NLP) to form a spoken language system. Both components are integrated with a stack controller and contribute to the search control. The specification also defines a "Top-N" mode in which a "first part" outputs a list of top N scored sentences for postprocessing by a "second part". An additional use for this specification might be NLP evaluation testing: a common simulated CSR could be interfaced to each site's NLP to provide identical testing environments.
Evapotranspiration of Vitis vinifera L. cvs Sunred Seedless and Muscat Supreme in response to soil water depletion and irrigation cutoff during berry ripening

The effects of soil water depletion and irrigation cutoff during ripening on yield, quality and evapotranspiration (ET) of table grapes were studied to refine irrigation strategies needed during hot, dry summers. Six irrigation treatments were applied to two cultivars, viz. Sunred Seedless and Muscat Supreme, from the 1998/99 until 2000/01 seasons in a field trial in the Hex River valley of South Africa. Grapevines of all treatments were irrigated with micro-sprinklers at 40% plant available water (PAW) depletion before véraison and after harvest. Two treatments were irrigated at 20% and 40% PAW depletion from véraison to harvest. Four more treatments were applied by cutting off irrigation at these two depletion levels when total soluble solids reached 12°B and 15°B, respectively. According to earlier results, best overall performance for Sunred Seedless was obtained where irrigation at 40% PAW depletion was cut off at 15°B compared to the worst, i.e. where irrigation at 20% depletion was cut off at 15°B. For Muscat Supreme, irrigation at 20% PAW depletion, either continued until harvest, or cut off at 15°B, resulted in optimum overall performance. Although yield and quality responded differently, this study showed that the ET of the two cultivars responded in a similar way to the irrigation treatments under the given conditions. The ET of grapevines irrigated at 40% PAW increased from 1.6 mm day−1 in September to a maximum of 5.4 mm day−1 in January. Irrigation at 20% PAW depletion increased the maximum ET to 7.3 mm day−1. For both soil water depletion levels, irrigation cutoff at 12°B and 15°B resulted in, respectively, ca. 75% and 65% PAW depletion at harvest. Mean daily ET during January decreased to 4.1 mm day−1 and 5.0 mm day−1 after the irrigation had been cut off at 12°B and 15°B, respectively. The crop coefficients, which decreased accordingly, can be used to reduce irrigation to obtain optimum table grape yield and quality, particularly for Sunred Seedless.
Using wearable UWB radios to measure foot clearance during walking

Foot clearance above ground is a key factor for a better understanding of the complicated relationship between falls and gait. This paper proposes a wearable system using UWB transceivers to monitor the vertical heel/toe clearance during walking. First, a pair of very small and light antennas is placed on a point approximating to the heel/toe of the foot, acting as a transmitter and receiver. Then, the reflected signal from ground is captured and propagation delay is detected using noise suppressed Modified-Phase-Only-Correlator (MPOC). The performance of the UWB-based system was compared with an ultrasound system for stationary movements. The experimental results show that an overall mean difference between these two systems is about 0.634mm with correlation coefficient value of 0.9604. The UWB-based system is then used to measure foot clearance during walking which shows promising results for gait events detection.
Anonymity and fair-exchange in e-commerce protocol for physical products delivery

Fair exchange and customer's and merchant's anonymity are two important properties of e-commerce transactions. There is to date a variety of proposed e-commerce protocols to achieve fair exchange and customer's anonymity for transactions involving digital products. For physical products delivery there is no e-commerce protocol to provide fair exchange and customer's and merchant's anonymity. In this paper, we propose the first e-commerce protocol for physical products delivery that will provide fair exchange in all circumstances, anonymity of customer and merchant for any collusion that can be formed, non-repudiation, integrity and confidentiality of data exchanged between the parties.
Evolutionary Neural Gas (ENG): A Model of Self Organizing Network from Input Categorization

Despite their claimed biological plausibility, most self organizing networks have strict topological constraints and consequently they cannot take into account a wide range of external stimuli. Furthermore their evolution is conditioned by deterministic laws which often are not correlated with the structural parameters and the global status of the network, as it should happen in a real biological system. In nature the environmental inputs are noise afiected and \fuzzy". Which thing sets the problem to investigate the possibility of emergent behaviour in a not strictly constrained net and subjected to difierent inputs. It is here presented a new model of Evolutionary Neural Gas (ENG) with any topological constraints, trained by probabilistic laws depending on the local distortion errors and the network dimension. The network is considered as a population of nodes that coexist in an ecosystem sharing local and global resources. Those particular features allow the network to quickly adapt to the environment, according to its dimensions. The ENG model analysis shows that the net evolves as a scale-free graph, and justifles in a deeply physical sense- the term \gas" here used. c
Laser-vibrometric ultrasonic characterization of resonant modes and quality factors of Ge membranes

Abstract The vibrations of a single-crystal germanium (Ge) membrane are studied in air and vacuum using laser vibrometry, in order to determine mechanical properties such as Q-factors, tensile stress, anisotropy, and robustness to shock. Resonance modes up to 3:2 are identified, giving a residual stress measurement of 0.22 GPa, consistent with the value obtained from x-ray relaxation studies. The membrane is found to be isotropic, with Q-factors ranging from around 40 at atmospheric pressure to over 3200 at mbar, significantly lower than those found in polycrystalline Ge micromechanical devices. The robustness to shock is explained through the high resonance mode frequencies and the dissipation mechanism into the substrate, which is a direct consequence of having a high quality film with low residual tensile stress, giving the potential for such films to be used in optoelectronic devices.