Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparative study of salt tolerance parameters in 11 wild relatives of Arabidopsis thaliana

Salinity is an abiotic stress that limits both yield and the expansion of agricultural crops to new areas. In the last 20 years our basic understanding of the mechanisms underlying plant tolerance and adaptation to saline environments has greatly improved owing to active development of advanced tools in molecular, genomics, and bioinformatics analyses. However, the full potential of investigative power has not been fully exploited, because the use of halophytes as model systems in plant salt tolerance research is largely neglected. The recent introduction of halophytic Arabidopsis-Relative Model Species (ARMS) has begun to compare and relate several unique genetic resources to the well-developed Arabidopsis model. In a search for candidates to begin to understand, through genetic analyses, the biological bases of salt tolerance, 11 wild relatives of Arabidopsis thaliana were compared: Barbarea verna, Capsella bursa-pastoris, Hirschfeldia incana, Lepidium densiflorum, Malcolmia triloba, Lepidium virginicum, Descurainia pinnata, Sisymbrium officinale, Thellungiella parvula, Thellungiella salsuginea (previously T. halophila), and Thlaspi arvense. Among these species, highly salt-tolerant (L. densiflorum and L. virginicum) and moderately salt-tolerant (M. triloba and H. incana) species were identified. Only T. parvula revealed a true halophytic habitus, comparable to the better studied Thellungiella salsuginea. Major differences in growth, water transport properties, and ion accumulation are observed and discussed to describe the distinctive traits and physiological responses that can now be studied genetically in salt stress research.
The Conditional CAPM and the Cross-Section of Expected Returns

Most empirical studies of the static CAPM assume that betas remain constant over time and that the return on the value-weighted portfolio of all stocks is a proxy for the return on aggregate wealth. The general consensus is that the static CAPM is unable to explain satisfactorily the cross-section of average returns on stocks. We assume that the CAPM holds in a conditional sense, i.e., betas and the market risk premium vary over time. We include the return on human capital when measuring the return on aggregate wealth. Our specification performs well in explaining the cross-section of average returns.
SONS: The JCMT legacy survey of debris discs in the submillimetre

During the period of these observations the James Clerk Maxwell Telescope was operated by the Joint Astronomy Centre on behalf of the Science and Technology Facilities Council of the United Kingdom, the National Research Council of Canada and the Netherlands Organisation for Pure Research. Additional funds for the construction of SCUBA-2 were provided by the Canada Foundation for Innovation. MCW acknowledges the support of the European Union through ERC grant number 279973. GMK is supported by the Royal Society as a Royal Society University Research Fellow. MB acknowledges support from a FONDECYT Postdoctoral Fellowship, project no. 3140479 and the Deutsche Forschungsgemeinschaft through project Kr 2164/15-1. JPM is supported by a UNSW Vice Chancellor’s postdoctoral research fellowship. The work of OP is supported by the Royal Society through a Royal Society Dorothy Hodgkin fellowship. GJW gratefully acknowledges support from the Leverhulme Trust.
Chapter 4 e role of endophytic methane oxidizing bacteria in submerged Sphagnum in determining methane emissions of Northeastern Siberian tundra 1

e role of the microbial processes governing methane emissions from tundra ecosystem is receiving increasing attention. Recently, cooperation between methanotrophic bacteria and submerged Sphagnum was shown to reduce methane emissions but also to supply CO2 for photosynthesis for the plant. Although this process was shown to be important in the laboratory, the differences that exist in methane emissions from inundated vegetation types with or without Sphagnum in the field have not been linked to these bacteria before. In this study, chamber flux measurements, an incubation study and flux modeling were used to investigate the drivers and controls on the relative difference in methane emissions between a submerged Sphagnum/sedge vegetation and an inundated sedge vegetation without Sphagnum. It was found that methane emissions in the Sphagnum dominated vegetation type were 50% lower than in the vegetation type without Sphagnum. A model sensitivity analysis showed that these differences could not sufficiently be explained by differences in methane production and plant transport. e model, combined with an incubation study, indicated that methane oxidation by endophytic bacteria, living in cooperation with submerged Sphagnum, plays a significant role in methane cycling at this site. is result is important for spatial upscaling spatially as oxidation by these bacteria plays a large role in 15% of the net methane emissions at this tundra site. Our findings support the notion that methane oxidizing bacteria are an important factor in understanding the processes behind methane emissions in tundra. 1e content of this chapter has been submitted as "e role of endophytic methane oxidizing bacteria in submerged Sphagnum in determining methane emissions of Northeastern Siberian tundra" to Biogeosciences
Joint estimation of the target height and the reflecting surface height in low angle radar

For the presence of the multi-path propagation, it is difficult for us to estimate the elevation of a low-height target. In this paper, a new method for the joint estimation of the target height and the reflecting surface height is proposed based on multichannel digital array radar. According to the model of multi-path propagation in low angle tracking, the joint estimation is obtained by minimizing the cost function. Compared with the traditional height measuring methods, the reflecting surface height is taken into account in this method. Because the reflecting surface height has significant influence on the performance of height measuring, the performance of the proposed method is significantly improved. Furthermore, in order to reduce the computational burden, a projection gradient method instead of two-dimension search is adopted. Simulation results are presented to verify the effectiveness of this method.
Rule-based Named Entity Extraction For Ontology Population

Currently, Text analysis techniques such as named entity recognition rely mainly on ontologies which represent the semantics of an application domain. To build such an ontology from specialized texts, this article presents a tool which detects proper names, locations and dates from texts by using manually written linguistic rules. The most challenging task is to extract not only entities but also interpret the information and adapt in a specific corpus in French.
Testing for an Unusual Distribution of Rare Variants

Technological advances make it possible to use high-throughput sequencing as a primary discovery tool of medical genetics, specifically for assaying rare variation. Still this approach faces the analytic challenge that the influence of very rare variants can only be evaluated effectively as a group. A further complication is that any given rare variant could have no effect, could increase risk, or could be protective. We propose here the C-alpha test statistic as a novel approach for testing for the presence of this mixture of effects across a set of rare variants. Unlike existing burden tests, C-alpha, by testing the variance rather than the mean, maintains consistent power when the target set contains both risk and protective variants. Through simulations and analysis of case/control data, we demonstrate good power relative to existing methods that assess the burden of rare variants in individuals.
PKC-2 Phosphorylation of UNC-18 Ser322 in AFD Neurons Regulates Temperature Dependency of Locomotion

Diacylglycerol (DAG)/protein kinase C (PKC) signaling plays an integral role in the regulation of neuronal function. This is certainly true in Caenorhabditis elegans and in particular for thermosensory signaling and behavior. Downstream molecular targets for transduction of this signaling cascade remain, however, virtually uncharacterized. We investigated whether PKC phosphorylation of Munc18-1, an essential protein in vesicle trafficking and exocytosis, was the downstream effector for DAG regulation of thermosensory behavior. We demonstrate here that the C. elegans ortholog of Munc18-1, UNC-18, was phosphorylated in vitro at Ser322. Transgenic rescue of unc-18-null worms with Ser322 phosphomutants displayed altered thermosensitivity. C. elegans expresses three DAG-regulated PKCs, and blocking UNC-18 Ser322 phosphorylation was phenocopied only by deletion of calcium-activated PKC-2. Expression of nonphosphorylatable UNC-18 S322A, either pan-neuronally or specifically in AFD thermosensory neurons, converted wild-type worms to a pkc-2-null phenotype. These data demonstrate that an individual DAG-dependent thermosensory behavior of an organism is effected specifically by the downstream PKC-2 phosphorylation of UNC-18 on Ser322 in AFD neurons.
Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments

The last several years have seen the consolidation of high-throughput proteomics initiatives to identify and characterize protein interactions and macromolecular complexes in model organisms. In particular, more that 10,000 high-confidence protein-protein interactions have been described between the roughly 6,000 proteins encoded in the budding yeast genome (Saccharomyces cerevisiae). However, unfortunately, high-resolution three-dimensional structures are only available for less than one hundred of these interacting pairs. Here, we expand this structural information on yeast protein interactions by running the first-ever high-throughput docking experiment with some of the best state-of-the-art methodologies, according to our benchmarks. To increase the coverage of the interaction space, we also explore the possibility of using homology models of varying quality in the docking experiments, instead of experimental structures, and assess how it would affect the global performance of the methods. In total, we have applied the docking procedure to 217 experimental structures and 1,023 homology models, providing putative structural models for over 3,000 protein-protein interactions in the yeast interactome. Finally, we analyze in detail the structural models obtained for the interaction between SAM1-anthranilate synthase complex and the MET30-RNA polymerase III to illustrate how our predictions can be straightforwardly used by the scientific community. The results of our experiment will be integrated into the general 3D-Repertoire pipeline, a European initiative to solve the structures of as many as possible protein complexes in yeast at the best possible resolution. All docking results are available at http://gatealoy.pcb. ub.es/HT_docking/.
Low prevalence of the new variant of Chlamydia trachomatis in Denmark

We estimated the prevalence of the new variant of Chlamydia trachomatis in Denmark. Fifty consecutive C trachomatis urine samples from each of the 14 regional microbiology laboratories were initially tested and re-analysed with a real-time C trachomatis PCR assay targeting the 16S rRNA gene and with the Becton Dickinson ProbeTec with confirmation of positives with a plasmid PCR with the primers CTP200/CTP201 flanking the deletion. The positive rate for 691 samples was 17% by real-time C trachomatis PCR and by ProbeTec. One specimen was positive for the new variant of C trachomatis (0.14% of all samples; 0.8% of the positives). The prevalence of the new variant of C trachomatis is very low despite very close contact between Denmark and Sweden and extensive cross-border commuting.
COMPUTER SYNTHESIS OF BIRD SONGS AND CALLS

We describe the computer simulation of a one‐mass source together with a simple transmission line model for a psittacine bird. The syrinx is modeled as a lumped mass subject to elastic restoring forces and internal dissipation. Nonlinear interaction with the airflow follows the Ishizaka and Flanagan glottal model. This is also used to model complete closure of the syrinx: during closure an additional restoring force is added and dissipation is increased. During the whole closed phase the syringeal flow is zero, and consequently its spectrum is broadened and higher partials are generated. The vocal tract transmission lines are implemented with fractional delay lines and the transmission lines are assumed lossless. The beak is implemented as two complementary fifth order Butterworth filters. The pole trajectory for the filters approximates the nonlinear path of the beak cutoff as discussed by Fletcher. [M.K. was supported by the Fulbright Foundation as well as Tekes. F.A. was funded by the Sound Source Mode.
Modeling dyadic and interdependent data in the developmental and behavioral sciences

N.A. Card, T.D. Little, J.P. Selig, Modeling Dyadic and Interdependent Data in Developmental Research: An Introduction. B. Laursen, D. Popp, W.J. Burk, M. Kerr, H. Stattin, Incorporating Interdependence into Developmental Research: Examples from the Study of Homophily and Homogeneity. W.L. Cook, Application of the Social Relations Model Formulas to Developmental Research. A.H. N. Cillessen, C. Borch, Analyzing Social Networks in Adolescence. N. Ram, A.B. Pedersen, Dyadic Models Emerging from the Longitudinal Structural Equation Modeling Tradition: Parallels with Ecological Models of Interspecific Interactions. E. Ferrer, K.F. Widaman, Multilevel Structural Equation Models for Contextual Factors with Inter-Group Differences. P. Sadler, E. Woody, It Takes Two: A Dyadic, SEM-Based Perspective on Personality Development. D.A. Kashy, M.B. Donnellan, Comparing MLM and SEM Approaches to Analyzing Developmental Dyadic Data: Growth Curve Models of Hostility in Families. J.P. Selig, K.A. McNamara, N.A. Card, T.D. Little, Techniques for Modeling Dependency in Interchangeable Dyads. T.E. Malloy, A.H. N. Cillessen, Variance Component Analysis of Generalized and Dyadic Peer Perceptions in Adolescence. N.A. Card, T.D. Little, J.P. Selig, Using the Bivariate Social Relations Model to Study Dyadic Relationships: Early Adolescents' Perceptions of Friends' Aggression and Prosocial Behavior. S.J.T. Branje, C. Finkenauer, W.H. J. Meeus, Modeling Interdependence Using the Social Relations Model: The Investment Model in Family Relationships. J. Templin, Methods for Detecting Subgroups in Social Networks. T.A. Kindermann, Can We Use Causal Inferences about the Influence of Children's Naturally-Existing Social Networks on their School Motivation? B.J.H. Zijlstra, R. Veenstra, M.A.J. Van Duijn, An Application of the Multilevel Model for Binary Network Data on Bully-Victim Relationships. C.F. Bond, Jr., D. Cross, Beyond the Dyad: Prospects for Social Development. D.A. Kenny, Thinking about the Developmental Course of Relationships.
A Dense Disparity Estimation Method using Color Segmentation and Energy Minimization

This paper presents a new dense disparity estimation method using color segmentation and energy minimization. Segmentation-based methods have an advantage of clear representation of disparities on discontinuous region. This paper remodels the energy minimization method to fit with segmentation-based method. In the proposed method, the initial disparity map is obtained by variable block matching of the segmented plane and random sample consensus (RANSAC) fitting. Then energy minimization is performed on the small segmented planes and the overall segmented planes, respectively to refine the disparity map more accurately. At the end of the method, erroneous stripes that are not corrected by the segmentation-based approach are processed by a pixel-based method. Experimental results show that the error rate of the proposed method is comparable to other state-of-the-art matching methods on various stereo image pairs.
Visual perception and curve tracing in form and integrative agnosia

The work presented within this thesis has explored distinctions between form and integrative agnosia and figure ground perception in patients with dorsal and ventral extrastriate lesions. SA was distinguished as having a dorsal extrastriate lesion and a form agnosia - an impairment in coding basic aspects of shape and lesions of the dorsal extrastriate region. HJA, our case of integrative agnosia was able to code basic aspects of shape but impaired in segmenting and grouping more complex items. SA was impaired on object recognition but showed improved performance with animate objects relative to inanimate whilst HJA showed the opposite pattern. It was suggested SA was able to make use of top-down knowledge here. HJA demonstrated intact discrimination of simple shapes but struggled to separate figure from ground on line drawings with internal detail compared with outlines consistent with poor forming of parts into wholes. We identified curve tracing as a useful test of figure ground segmentation in these cases. SA was highly impaired on all such tasks. HJA in comparison, showed a similar pattern of performance to controls suggesting that he was serially scanning and shifting attention at a normal rate. HJA was found to have a strong global bias to identifying the overall letter when presented with hierarchical stimuli, while SA demonstrated a strong local bias. We suggested that this could be reflect global form proving more salient to HJA compared with local form in SA and that these biases have influenced figure ground segmentation.
Heterogeneous defects of platelet secretion and responses to weak agonists in patients with bleeding disorders

Summary. Eleven patients with mild bleeding disorders had as a common abnormality, impaired platelet aggregation and secretion with low concentrations (0.5–1.0 μg/ml) of collagen and, in most cases, an absence of second phase aggregation with epinephrine. Platelet granule contents were normal, ruling out storage pool deficiency. To characterize further the platelet abnormalities, we measured aggregation, 14C‐5HT secretion, and TxB2 formation induced by a variety of platelet agonists. In eight of the 11 patients we observed decreased initial rates as well as extents of aggregation with one or more weak agonists (ADP, epinephrine, thromboxane A2 and the endoperoxide analogue U44069), i.e. agonists which induced secretion only as a result of aggregation, but normal responses to strong agonists such as arachidonate and high (10 μg/ml) concentrations of collagen, which can induce secretion in the presence or absence of aggregation. In all of these patients. TxB2 formation with arachidonate and all concentrations of collagen was normal. The platelet defects in these eight patients have been designated as weak agonist response defects (WARDs). In contrast, the initial aggregation responses to all weak agonists were normal in the three other patients, while secretion and TxB2 formation induced by strong agonists were impaired. Thus, in contrast to the eight patients above, the platelet defects in these three patients were characteristic of defects in the secretion response per se. The results obtained in the 11 patients studied indicate that these types of platelet disorders, previously referred to as primary secretion defects, include defects in the initial platelet responses which precede secretion (WARD) as well as defects in the secretory mechanism per se. Both groups of defects appear to be heterogeneous in nature.
Dialysis prior to living donor kidney transplantation and rates of acute rejection.

BACKGROUND The relationship between transplantation prior to chronic dialysis initiation and the pattern of acute rejection of kidneys from living donors (LDKT) has not been fully explored. METHODS Using data provided by the United States Renal Data System, we performed a retrospective cohort study fitting multivariate proportional hazards models to characterize the association of chronic use of dialysis prior to transplantation [non-pre-emptive LDKT (non-PLDKT)] and acute rejection, and to examine if this association varies throughout the first year. RESULTS Non-PLDKT was associated with a 2.5-fold higher rate of biopsy-confirmed rejection during the first month [adjusted HR 2.5, 95% confidence interval (1.85-3.33)], compared with no dialysis prior to transplantation. Increasing duration of pre-transplant dialysis was associated with increasing rate of biopsy-confirmed acute rejection during the first month (P = 0.001 for trend). Over the first year, there was a diminishing relationship between non-PLDKT and acute rejection: 2.5-, 2.22-, 2.13- and 1.78-fold elevation in the episodes of biopsy-confirmed acute rejection during the first, second, third through to the sixth and seventh through to the twelfth month post-transplant, respectively (P = 0.05 for trend). CONCLUSIONS The waning of the association of non-PLDKT with acute rejection over time supports the hypothesis that dialysis exposure prior to transplantation may modulate the immune system to increase the rates of acute rejection.
The Language of Blood: The Making of Spanish-American Identity in New Mexico, 1880s-1930s

When the United States declared war on Spain in 1898, rumours abounded throughout the nation that the Spanish-speaking population of New Mexico secretly sympathised with the enemy. At the end of the war, The New York Times warned that New Mexico's "Mexicans professed a deep hostility to American ideas and American policies. " As long as Spanish remained the primary language of public instruction, the Times admonished, "the majority of the inhabitants will remain 'Mexican' and retain a pseudo-allegiance [to Spain]. " This perception of Spanish-speaking New Mexicans as 'un-American' was widely shared. Such allegations of disloyalty, coupled with the prevalent views that all Mexican peoples were racially non-white and 'unfit' to assume the rights and responsibilities of full citizenship, inspired powerful reactions among the Spanish-speaking people of New Mexico. Most sought to distinguish themselves from Mexican immigrants by emphasising their 'Spanish' roots. Tourism, too, began to foster the myth that nuevomexicanos were culturally and racially Spanish. Since the 1950s, historians, sociologists, and anthropologists have dismissed the ubiquitous Spanish heritage claimed by many New Mexicans.
Information fusion strategies from distributed filters in packet-drop networks

In this paper we study different distributed estimation schemes for stochastic discrete time linear systems where the communication between the sensors and the estimation center is subject to random packet loss. Sensors are provided with computational and memory resources so that they can potentially perform data processing of the measurements before sending their information. In particular, we explore three different strategies. The first, named measurement fusion (MF), optimally fuses the raw measurements received so far from all sensors. The second strategy, named optimal partial estimate fusion (OPEF), optimally fuses at the central node the last local state estimates received from each sensor. The last strategy, named open loop partial estimate fusion (OLPEF), simply sums local state estimates received from each sensor and replace the lost ones with their open loop prediction. We provide some analytical results about the performance of these three schemes in special regimes conditions, namely low and high process noise. We also show through numerical simulations that, although none of the three schemes achieves the ideal performance of a scheme with infinite bandwidth communication between sensors and the central node, the OPEF scheme provides almost ideal performance.