Miracle-dz/UniFAR-FTUs huggingface dataset:
Observationally based analysis of land–atmosphere coupling

Abstract. The temporal variance of soil moisture, vegetation and evapotranspiration over land has been recognized to be strongly connected to the temporal variance of precipitation. However, the feedbacks and couplings between these variables are still not well understood and quantified. Furthermore, soil moisture and vegetation processes are associated with a memory and therefore they may have important implications for predictability. In this study we apply a generalized linear method, specifically designed to assess the reciprocal forcing between connected fields, to the latest available observational data sets of global precipitation, evapotranspiration, vegetation and soil moisture content. For the first time a long global observational data set is used to investigate the spatial and temporal land variability and to characterize the relationships and feedbacks between land and precipitation. The variables considered show a significant coupling among each other. The analysis of the response of precipitation to soil moisture evidences a robust coupling between these two variables. In particular, the first two modes of variability in the precipitation forced by soil moisture appear to have a strong link with volcanic eruptions and El Nino–Southern Oscillation (ENSO) cycles, respectively, and these links are modulated by the effects of evapotranspiration and vegetation. It is suggested that vegetation state and soil moisture provide a biophysical memory of ENSO and major volcanic eruptions, revealed through delayed feedbacks on rainfall patterns. The third mode of variability reveals a trend very similar to the trend of the inter-hemispheric contrast in sea surface temperature (SST) and appears to be connected to greening/browning trends of vegetation over the last three decades.
Specialized attachment structure of the fish pathogenic oomycete Saprolegnia parasitica

The secondary cysts of the fish pathogen oomycete Saprolegnia parasitica possess bundles of long hooked hairs that are characteristic to this economically important pathogenic species. Few studies have been carried out on elucidating their specific role in the S. parasitica life cycle and the role they may have in the infection process. We show here their function by employing several strategies that focus on descriptive, developmental and predictive approaches. The strength of attachment of the secondary cysts of this pathogen was compared to other closely related species where bundles of long hooked hairs are absent. We found that the attachment of the S. parasitica cysts was around three times stronger than that of other species. The time sequence and influence of selected factors on morphology and the number of the bundles of long hooked hairs conducted by scanning electron microscopy study revealed that these are dynamic structures. They are deployed early after encystment, i.e., within 30 sec of zoospore encystment, and the length, but not the number, of the bundles steadily increased over the encystment period. We also observed that the number and length of the bundles was influenced by the type of substrate and encystment treatment applied, suggesting that these structures can adapt to different substrates (glass or fish scales) and can be modulated by different signals (i.e., protein media, 50 mM CaCl2 concentrations, carbon particles). Immunolocalization studies evidenced the presence of an adhesive extracellular matrix. The bioinformatic analyses of the S. parasitica secreted proteins showed that there is a high expression of genes encoding domains of putative proteins related to the attachment process and cell adhesion (fibronectin and thrombospondin) coinciding with the deployment stage of the bundles of long hooked hairs formation. This suggests that the bundles are structures that might contribute to the adhesion of the cysts to the host because they are composed of these adhesive proteins and/or by increasing the surface of attachment of this extracellular matrix.
Assistive technology in everyday living – A user survey of people with Parkinson's disease

The aim of this study was to explore the individual circumstances of people with Parkinson's disease, as well as their ideas and opinions about assistive technology that may be used for daily living. A self-reported, user survey was designed. The results of the study were derived from a postal survey of randomly chosen members of the Parkinson's Association of Ireland. Analysis were conducted on data from 59 people. According to the survey results the majority of the participants reported problems with mobility (88%), fatigue (54%), and getting tired fast (70%). Problems with mobility included changing location (59%) and body position (51%-53%). Thirty four and twenty five percent of respondents described their physical strength and flexibility, respectively, as 'poor' or 'very poor'. For 81% of participants it was important to be able to contact someone in a case of a fall. The results of this study indicate a possible underutilisation of assistive technologies and technology by people with Parkinson's disease. In addition, the study identifies areas in which there is a demand for assistive technologies.
Multistability in Large Scale Models of Brain Activity

Noise driven exploration of a brain network’s dynamic repertoire has been hypothesized to be causally involved in cognitive function, aging and neurodegeneration. The dynamic repertoire crucially depends on the network’s capacity to store patterns, as well as their stability. Here we systematically explore the capacity of networks derived from human connectomes to store attractor states, as well as various network mechanisms to control the brain’s dynamic repertoire. Using a deterministic graded response Hopfield model with connectome-based interactions, we reconstruct the system’s attractor space through a uniform sampling of the initial conditions. Large fixed-point attractor sets are obtained in the low temperature condition, with a bigger number of attractors than ever reported so far. Different variants of the initial model, including (i) a uniform activation threshold or (ii) a global negative feedback, produce a similarly robust multistability in a limited parameter range. A numerical analysis of the distribution of the attractors identifies spatially-segregated components, with a centro-medial core and several well-delineated regional patches. Those different modes share similarity with the fMRI independent components observed in the “resting state” condition. We demonstrate non-stationary behavior in noise-driven generalizations of the models, with different meta-stable attractors visited along the same time course. Only the model with a global dynamic density control is found to display robust and long-lasting non-stationarity with no tendency toward either overactivity or extinction. The best fit with empirical signals is observed at the edge of multistability, a parameter region that also corresponds to the highest entropy of the attractors.
Age-Related Long-Term Functional Results after Riboflavin UV A Corneal Cross-Linking

Purpose. To report a comparative prospective long-term functional analysis after Riboflavin UV A corneal cross-linking (CXL) in three different age groups of patients affected by progressive keratoconus (KC). Methods. Functional analysis comprised paediatric patients (≤18 years) included 152 eyes (29.5%); intermediate group (19–26 years) 286 eyes (55.4%), and adults (≥27 years) 78 eyes (15.1%). CXL was performed according to the Siena protocol by using the Vega CBM (Caporossi-Baiocchi-Mazzotta) X linker (CSO, Florence, Italy) at Siena University by the same authors. Pre- and post-op examinations included UCVA, BSCVA, corneal topography, and surface aberrometry (CSO Eye Top, Florence, Italy), at 48 months followup. Results. At 48 months followup paediatrics, intermediate, and adult patients showed a mean gain in UCVA of +0.2, +0.14 and +0.12 Snellen lines. BSCVA gained by a mean of +0.21, +0.2, and +0.1 Snellen lines. K max was reduced by a mean value of −0.9 D, −0.6 D, and −0.5 D, respectively. Coma values improved by a mean of −0.45 μm, −0.91 μm, and −0.19 μm, respectively. Treatment ensured a long-term keratoconus stabilization in over 90% of treated patients. Conclusion. According to our long-term comparative results, epithelium-off Riboflavin UV A cross-linking should be the first choice therapy of progressive KC, particularly in paediatric age and patients under 26 years.
The Unexpected Empirical Consensus Among Consensus Methods

In economics and political science, the theoretical literature on social choice routinely highlights worst-case scenarios and emphasizes the nonexistence of a universally best voting method. Behavioral social choice is grounded in psychology and tackles consensus methods descriptively and empirically. We analyzed four elections of the American Psychological Association using a state-of-the-art multimodel, multimethod approach. These elections provide rare access to (likely sincere) preferences of large numbers of decision makers over five choice alternatives. We determined the outcomes according to three classical social choice procedures: Condorcet, Borda, and plurality. Although the literature routinely depicts these procedures as irreconcilable, we found strong statistical support for an unexpected degree of empirical consensus among them in these elections. Our empirical findings stand in contrast to two centuries of pessimistic thought experiments and computer simulations in social choice theory and demonstrate the need for more systematic descriptive and empirical research on social choice than exists to date.
Enhancing Chinese Word Segmentation Using Unlabeled Data

This paper investigates improving supervised word segmentation accuracy with unlabeled data. Both large-scale in-domain data and small-scale document text are considered. We present a unified solution to include features derived from unlabeled data to a discriminative learning model. For the large-scale data, we derive string statistics from Gigaword to assist a character-based segmenter. In addition, we introduce the idea about transductive, document-level segmentation, which is designed to improve the system recall for out-of-vocabulary (OOV) words which appear more than once inside a document. Novel features result in relative error reductions of 13.8% and 15.4% in terms of F-score and the recall of OOV words respectively.
Learning and extraction of violin instrumental controls from audio signal

Acquisition of instrumental gestures in musical performances is an important task used in different fields ranging from acoustics and sound synthesis to motor learning or electroacoustic performances. The most common approach for acquiring gestures is by means of a sensing system. The direct measurement involves the use of usually expensive sensors with some degree of intrusivity and generally entails complex setups. Indirect acquisition is based on the processing of the audio signal and it is usually informed on acoustical or physical properties of the sound or sound production mechanism. In this paper we present an indirect acquisition method of violin controls from an audio signal based on learning of empirical data that is previously collected with a highly accurate sensing system. The learning consists of training of statistical models with a database of multimodal data from violin performances. The database includes audio spectral features and instrumental controls (bow tilt, bow force, bow velocity, bowing distance to the bridge and played string) and is designed to sample most part of the violin performance control space. We expect that once the indirect acquisition system is trained, no sensors should be required, so the indirect acquisition becomes a low-cost and non-intrusive acquisition method.
Children and adults differ in their strategies for social learning

Adults and children rely heavily on other people’s testimony. However, domains of knowledge where there is no consensus on the truth are likely to result in conflicting testimonies. Previous research has demonstrated that in these cases, learners look towards the majority opinion to make decisions. However, it remains unclear how learners evaluate social information, given that considering either the overall valence, or the number of testimonies, or both may lead to different conclusions. We therefore formalized several social learning strategies and compared them to the performance of adults and children. We find that children use different strategies than adults. This suggests that the development of social learning may involve the acquisition of cognitive strategies.
Neuropathology of older persons without cognitive impairment from two community-based studies

Objective: To examine the relation of National Institute on Aging–Reagan (NIA-Reagan) neuropathologic criteria of Alzheimer disease (AD) to level of cognitive function in persons without dementia or mild cognitive impairment (MCI). Methods: More than 2,000 persons without dementia participating in the Religious Orders Study or the Memory and Aging Project agreed to annual detailed clinical evaluation and brain donation. The studies had 19 neuropsychological performance tests in common that assessed five cognitive domains, including episodic memory, semantic memory, working memory, perceptual speed, and visuospatial ability. A total of 134 persons without cognitive impairment died and underwent brain autopsy and postmortem assessment for AD pathology using NIA-Reagan neuropathologic criteria for AD, cerebral infarctions, and Lewy bodies. Linear regression was used to examine the relation of AD pathology to level of cognitive function proximate to death. Results: Two (1.5%) persons met NIA-Reagan criteria for high likelihood AD, and 48 (35.8%) met criteria for intermediate likelihood; 29 (21.6%) had cerebral infarctions, and 18 (13.4%) had Lewy bodies. The mean Mini-Mental State Examination score proximate to death was 28.2 for those meeting high or intermediate likelihood AD by NIA-Reagan criteria and 28.4 for those not meeting criteria. In linear regression models adjusted for age, sex, and education, persons meeting criteria for intermediate or high likelihood AD scored about a quarter standard unit lower on tests of episodic memory (p = 0.01). There were no significant differences in any other cognitive domain. Conclusions: Alzheimer disease pathology can be found in the brains of older persons without dementia or mild cognitive impairment and is related to subtle changes in episodic memory.
Thermodynamic and kinetic characterization of a β‐hairpin peptide in solution: An extended phase space sampling by molecular dynamics simulations in explicit water

The folding of the amyloidogenic H1 peptide MKHMAGAAAAGAVV taken from the syrian hamster prion protein is explored in explicit aqueous solution at 300 K using long time scale all‐atom molecular dynamics simulations for a total simulation time of 1.1 μs. The system, initially modeled as an α‐helix, preferentially adopts a β‐hairpin structure and several unfolding/refolding events are observed, yielding a very short average β‐hairpin folding time of ∼200 ns. The long time scale accessed by our simulations and the reversibility of the folding allow to properly explore the configurational space of the peptide in solution. The free energy profile, as a function of the principal components (essential eigenvectors) of motion, describing the main conformational transitions, shows the characteristic features of a funneled landscape, with a downhill surface toward the β‐hairpin folded basin. However, the analysis of the peptide thermodynamic stability, reveals that the β‐hairpin in solution is rather unstable. These results are in good agreement with several experimental evidences, according to which the isolated H1 peptide adopts very rapidly in water β‐sheet structure, leading to amyloid fibril precipitates [Nguyen et al., Biochemistry 1995;34:4186–4192; Inouye et al., J Struct Biol 1998;122:247–255]. Moreover, in this article we also characterize the diffusion behavior in conformational space, investigating its relations with folding/unfolding conditions. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Identification of the novel KI Polyomavirus in paranasal and lung tissues

KI is a novel polyomavirus identified in the respiratory secretions of children with acute respiratory symptoms. Whether this reflects a causal role of the virus in the human respiratory disease remains to be established. To investigate the presence of KIV in the respiratory tissue, we examined 20 fresh lung cancer specimens and surrounding normal tissue along with one paranasal and one lung biopsy from two transplanted children. KIV‐VP1 gene was detected in 9/20 lung cancer patients and 2/2 transplanted patients. However, amplification of the sequence coding for the C‐terminal part of the early region of KIV performed on the 11 positive cases was successful only in two malignant lung tissues, one surrounding normal tissue, and 1/2 biopsies tested. Phylogenetic analysis performed on the early region of KIV (including the four Italian isolates), BKV and JCV revealed the presence of three distinct clades. Within the KIV clade two sub‐clades were observed. A sub‐clade A containing the four Italian strains, and a sub‐clade B comprising the Swedish and Australian isolates. Interestingly, the two Italian strains identified in normal tissue clustered together, whereas those detected in malignant tissue fell outside this cluster. In vitro studies are needed to investigate the transforming potential of KIV strains. J. Med. Virol. 81:558–561, 2009. © 2009 Wiley‐Liss, Inc.
Two phases of replacement replenish the olfactory ensheathing cell population after injury in postnatal mice

Olfactory ensheathing cells (OECs) support the regeneration of olfactory sensory neurons throughout life, however, it remains unclear how OECs respond to a major injury. We have examined the proliferation and migration of OECs following unilateral bulbectomy in postnatal mice. S100ß‐DsRed and OMP‐ZsGreen transgenic mice were used to visualize OECs and olfactory neurons, respectively, and we used the thymidine analogue ethynyl deoxyuridine (EdU) to identify cells that were proliferating at the time of administration. Following unilateral bulbectomy, there was an initial phase of OEC proliferation throughout the olfactory pathway with a peak of proliferation occurring 2 to 7 days after the injury. A second phase of proliferation also occurred in which precursors localized within the olfactory mucosa divided to replenish the OEC population. We then tracked the positions of OECs that had proliferated and found that there was a progressive increase in OECs in the cavity for at least 12 to 16 days after injury which could not be accounted for solely by local proliferation of OECs within the cavity. These results suggest that OECs migrated from the peripheral olfactory nerve to populate the mass of cells that filled cavity left by bulbectomy. Our results demonstrate that following injury to the olfactory nervous system, the OEC population is replenished by migration of cells that arise from both local proliferation of OECs throughout the olfactory nerve pathway as well as from precursor cells in the olfactory mucosa. © 2011 Wiley Periodicals, Inc.
Functional analyses of human and zebrafish 18–amino acid in‐frame deletion pave the way for domain mapping of the cerebral cavernous malformation 3 protein

Cerebral cavernous malformations (CCMs) may cause recurrent headaches, seizures, and hemorrhagic stroke and have been associated with loss‐of‐function mutations in CCM1/KRIT1, CCM2, and CCM3/programmed cell death 10 (PDCD10). The CCM3/PDCD10 amino acid sequence does not reveal significant homologies to protein domains with known structure. With the help of the only published human in‐frame deletion of the CCM3 gene (c.97‐? _150+? del), CCM3:p.L33_K50del, we have identified the interaction domain of CCM3 with the oxidant stress response serine/threonine kinase 25 (STK25, YSK1, SOK1) and with the mammalian Ste20‐like kinase 4 (MST4, MASK). Consistently, nano–liquid chromatography–tandem mass spectrometry (nano‐LC‐MS/MS) analyses revealed two STK25 phosphorylation sites at serine 39 and threonine 43. The corresponding in‐frame deletion of zebrafish ccm3a, dccm3:p.L31_K48del, also resulted in impaired interaction with STK25 and MST4. In agreement with the observed redundant biochemical functionality of zebrafish ccm3a and its duplicate ccm3b, simultaneous inactivation of both genes resulted in a progressive cardiovascular phenotype in zebrafish indistinguishable from ccm1 and ccm2 mutants. The pronounced cardiovascular dilatations could be recapitulated by morpholino‐induced in‐frame skipping of the exon encoding the STK25 and MST4 binding site of zebrafish Ccm3a if Ccm3b was repressed in parallel. Using a novel zebrafish model of CCM, we could thus demonstrate that the newly mapped STK25 and MST4 interaction domain within the CCM3 protein plays a crucial role for vascular development in zebrafish. Hum Mutat 30:1–9, 2009. © 2009 Wiley‐Liss, Inc.
MTL–Independent Phenotypic Switching in Candida tropicalis and a Dual Role for Wor1 in Regulating Switching and Filamentation

Phenotypic switching allows for rapid transitions between alternative cell states and is important in pathogenic fungi for colonization and infection of different host niches. In Candida albicans, the white-opaque phenotypic switch plays a central role in regulating the program of sexual mating as well as interactions with the mammalian host. White-opaque switching is controlled by genes encoded at the MTL (mating-type-like) locus that ensures that only a or α cells can switch from the white state to the mating-competent opaque state, while a/α cells are refractory to switching. Here, we show that the related pathogen C. tropicalis undergoes white-opaque switching in all three cell types (a, α, and a/α), and thus switching is independent of MTL control. We also demonstrate that C. tropicalis white cells are themselves mating-competent, albeit at a lower efficiency than opaque cells. Transcriptional profiling of C. tropicalis white and opaque cells reveals significant overlap between switch-regulated genes in MTL homozygous and MTL heterozygous cells, although twice as many genes are white-opaque regulated in a/α cells as in a cells. In C. albicans, the transcription factor Wor1 is the master regulator of the white-opaque switch, and we show that Wor1 also regulates switching in C. tropicalis; deletion of WOR1 locks a, α, and a/α cells in the white state, while WOR1 overexpression induces these cells to adopt the opaque state. Furthermore, we show that WOR1 overexpression promotes both filamentous growth and biofilm formation in C. tropicalis, independent of the white-opaque switch. These results demonstrate an expanded role for C. tropicalis Wor1, including the regulation of processes necessary for infection of the mammalian host. We discuss these findings in light of the ancestral role of Wor1 as a transcriptional regulator of the transition between yeast form and filamentous growth.