Miracle-dz/UniFAR-FTUs huggingface dataset:
New estimators for mixed stochastic and set theoretic uncertainty models: The general case

New filters are derived for estimating the n-dimensional state of a linear dynamic system based on uncertain m-dimensional observations, which suffer from two types of uncertainties simultaneously. The first uncertainty is a stochastic process with given distribution. The second uncertainty is only known to be bounded, the exact underlying distribution is unknown. The new estimators combine set theoretic and stochastic estimation in a rigorous manner and provide a continuous transition between the two classical estimation concepts. They converge to a set theoretic estimator, when the stochastic error goes to zero, and to a Kalman filter, when the bounded error vanishes. In the mixed noise case, solution sets are provided that are uncertain in a stochastic sense.
The pachner graph and the simplification of 3-sphere triangulations

It is important to have fast and effective methods for simplifying 3-manifold triangulations without losing any topological information. In theory this is difficult: we might need to make a triangulation super-exponentially more complex before we can make it smaller than its original size. Here we present experimental work suggesting that for 3-sphere triangulations the reality is far different: we never need to add more than two tetrahedra, and we never need more than a handful of local modifications. If true in general, these extremely surprising results would have significant implications for decision algorithms and the study of triangulations in 3-manifold topology. The algorithms behind these experiments are interesting in their own right. Key techniques include the isomorph-free generation of all 3-manifold triangulations of a given size, polynomial-time computable signatures that identify triangulations uniquely up to isomorphism, and parallel algorithms for studying finite level sets in the infinite Pachner graph.
The Th1/Th2 cytokine balance changes with the progress of the immunopathological lesion of Sjogren’s syndrome

Expression of type‐1 and type‐2 cytokines at the mRNA level in labial salivary glands (LSG) of patients with Sjogren’s syndrome (SS), as reported by several groups, have generated conflicting results. In the present study we have directly examined the production of IL‐4, IL‐13 and IFN‐γ by lymphocytes infiltrating the LSG of 44 consecutive patients referred for SS evaluation. Cytokines production was evaluated following in vitro culture of LSG in the presence of IL‐2. IFN‐γ and IL‐13 were detected in the majority of SN (24/44 and 26/44, respectively) while IL‐4 was present in 5/44 SN. The presence of IFN‐γ was significantly higher in SS patients, as opposed to patients who did not fulfil the criteria for SS (P < 0·01). In addition, almost all cultured lymphocytes expressed mRNA for IFN‐γ (17/19 cultures) and IL‐13 (18/19) while IL‐4 mRNA was also expressed at high frequency (14/19 cultures). Interestingly, the IFN‐γ mRNA copies in cultured lymphocytes correlated significantly with the intensity of lymphocytic infiltration as evaluated by Chisholm’s score (P < 0·01). Furthermore, RT‐PCR of RNA extracted from whole LSG from 14 SS patients also demonstrated the presence of all cytokines in the majority of the cases and the prevalence of IFN‐γ in LSG with high‐grade infiltration. Because IL‐13 was produced by the majority of the cultured LSG, IgE production was also evaluated. Interestingly, IgE was detected in 21/44 LSG culture SN and mainly in those biopsies that had Chisholm’s score less than 0·5 (P < 0·05). We conclude that lymphocytes infiltrating the LSG are capable of producing both Th1 and Th2 cytokines and that the balance between them shifts in favour of Th1 in LSG with high infiltration score and in patients with SS.
Carbon Dioxide Emissions and Implications for Environmental Policy: Evidence in Southeast Asia

The article attempts to investigate impacts of determinants on per capita carbon dioxide (CO2) emissions in six developing countries in Southeast Asia between 1985 and 2014 using a panel dataset. We found that electric power per capita, energy use, and gross domestic product have positive influences on per capita CO2 emissions in Southeast Asia. However, population and renewable energy consumption negatively affect per capita CO2 emissions in this region. Our results also addressed that per capita CO2 emissions of Indonesia and Viet Nam are higher than that of other countries in the region. Lastly, policies are recommended to reduce CO2 emissions and protect the environment in Southeast Asia, including improvement of energy efficiency of countries in the region, implementation of the Project in Clean Energy Investments, reduction of fuel and CO2 emissions applied to light duty vehicles and high duty vehicles, exploitation of advantages in exporting greenhouse gas emissions, and cooperation among countries in the region in order to reduce emissions. DOWNLOAD HISTORY | This article has been downloaded 250 times in Digital Commons before migrating into this platform.
Kinematics matters: A new eye-tracking investigation of animated triangles

Eye movements have been recently recorded in participants watching animated triangles in short movies that normally evoke mentalizing (Frith–Happé animations). Authors have found systematic differences in oculomotor behaviour according to the degree of mental state attribution to these triangles: Participants made longer fixations and looked longer at intentional triangles than at triangles moving randomly. However, no study has yet explored kinematic characteristics of Frith–Happé animations and their influence on eye movements. In a first experiment, we have run a quantitative kinematic analysis of Frith–Happé animations and found that the time triangles spent moving and the distance between them decreased with the mentalistic complexity of their movements. In a second experiment, we have recorded eye movements in 17 participants watching Frith–Happé animations and found that some differences in fixation durations and in the proportion of gaze allocated to triangles between the different kinds of animations were entirely explained by low-level kinematic confounds. We finally present a new eye-tracking measure of visual attention, triangle pursuit duration, which does differentiate the different types of animations even after taking into account kinematic cofounds. However, some idiosyncratic kinematic properties of the Frith–Happé animations prevent an entirely satisfactory interpretation of these results. The different eye-tracking measures are interpreted as implicit and line measures of the processing of animate movements.
Plasma membrane-bound AGC3 kinases phosphorylate PIN auxin carriers at TPRXS(N/S) motifs to direct apical PIN recycling

Polar membrane cargo delivery is crucial for establishing cell polarity and for directional transport processes. In plants, polar trafficking mediates the dynamic asymmetric distribution of PIN FORMED (PIN) carriers, which drive polar cell-to-cell transport of the hormone auxin, thereby generating auxin maxima and minima that control development. The Arabidopsis PINOID (PID) protein kinase instructs apical PIN localization by phosphorylating PINs. Here, we identified the PID homologs WAG1 and WAG2 as new PIN polarity regulators. We show that the AGC3 kinases PID, WAG1 and WAG2, and not other plant AGC kinases, instruct recruitment of PINs into the apical recycling pathway by phosphorylating the middle serine in three conserved TPRXS(N/S) motifs within the PIN central hydrophilic loop. Our results put forward a model by which apolarly localized PID, WAG1 and WAG2 phosphorylate PINs at the plasma membrane after default non-polar PIN secretion, and trigger endocytosis-dependent apical PIN recycling. This phosphorylation-triggered apical PIN recycling competes with ARF-GEF GNOM-dependent basal recycling to promote apical PIN localization. In planta, expression domains of PID, WAG1 and WAG2 correlate with apical localization of PINs in those cell types, indicating the importance of these kinases for apical PIN localization. Our data show that by directing polar PIN localization and PIN-mediated polar auxin transport, the three AGC3 kinases redundantly regulate cotyledon development, root meristem size and gravitropic response, indicating their involvement in both programmed and adaptive plant development.
The colR4 and colR15 beta-tubulin mutations in Chlamydomonas reinhardtii confer altered sensitivities to microtubule inhibitors and herbicides by enhancing microtubule stability

The colR4 and colR15 beta 2-tubulin missense mutations for lysine-350 in Chlamydomonas reinhardtii (Lee and Huang, 1990) were originally isolated by selection for resistance to the growth inhibitory effects of colchicine. The colR4 and colR15 mutants have been found to be cross resistant to vinblastine and several classes of antimitotic herbicides, including the dinitroanilines (oryzalin, trifluralin, profluralin, and ethafluralin); the phosphoric amide amiprophos methyl; and the dimethyl propynl benzamide pronamide. Like colchicine and vinblastine, the antimitotic effects of these plant-specific herbicides have been associated with the depolymerization of microtubules. In contrast to their resistance to microtubule-depolymerizing drugs, the mutants have an increased sensitivity to taxol, a drug which enhances the polymerization and stability of microtubules. This pattern of altered sensitivity to different microtubule inhibitors was found to cosegregate and corevert with the beta-tubulin mutations providing the first genetic evidence that the in vivo herbicidal effects of the dinitroanilines, amiprophos methyl, and pronamide are related to microtubule function. Although wild-type like in their growth characteristics, the colR4 and colR15 mutants were found to have an altered pattern of microtubules containing acetylated alpha-tubulin, a posttranslational modification that has been associated with stable subsets of microtubules found in a variety of cells. Microtubules in the interphase cytoplasm and those of the intranuclear spindle of mitotic cells, which in wild-type Chlamydomonas cells do not contain acetylated alpha-tubulin, were found to be acetylated in the mutants. These data taken together suggest that the colR4 and colR15 missense mutations increase the stability of the microtubules into which the mutant beta-tubulins are incorporated and that the altered drug sensitivities of the mutants are a consequence of this enhanced microtubule stability.
Tau pathology involves protein phosphatase 2A in Parkinsonism-dementia of Guam

Significance Parkinsonism-dementia (PD) of Guam is a classical tauopathy in which abnormal hyperphosphorylation of tau leads to neurodegeneration and dementia. A key unresolved question is the mechanism of abnormal hyperphosphorylation of tau in this disease. This study reports the involvement of a signaling pathway in which the inhibition of protein phosphatase 2A (PP2A) through phosphorylation of its catalytic subunit PP2Ac at Tyr307 induced by the activation of metabotropic glutamate receptor 5 (mGluR5) leads to hyperphosphorylation of tau. These findings suggest that the mGluR5–PP2A axis has a central role in neurofibrillary degeneration in Guam PD and thus may be a therapeutic target for the treatment of this disease and related tauopathies. Parkinsonism-dementia (PD) of Guam is a neurodegenerative disease with parkinsonism and early-onset Alzheimer-like dementia associated with neurofibrillary tangles composed of hyperphosphorylated microtubule-associated protein, tau. β-N-methylamino-l-alanine (BMAA) has been suspected of being involved in the etiology of PD, but the mechanism by which BMAA leads to tau hyperphosphorylation is not known. We found a decrease in protein phosphatase 2A (PP2A) activity associated with an increase in inhibitory phosphorylation of its catalytic subunit PP2Ac at Tyr307 and abnormal hyperphosphorylation of tau in brains of patients who had Guam PD. To test the possible involvement of BMAA in the etiopathogenesis of PD, we studied the effect of this environmental neurotoxin on PP2A activity and tau hyperphosphorylation in mouse primary neuronal cultures and metabolically active rat brain slices. BMAA treatment significantly decreased PP2A activity, with a concomitant increase in tau kinase activity resulting in elevated tau hyperphosphorylation at PP2A favorable sites. Moreover, we found an increase in the phosphorylation of PP2Ac at Tyr307 in BMAA-treated rat brains. Pretreatment with metabotropic glutamate receptor 5 (mGluR5) and Src antagonists blocked the BMAA-induced inhibition of PP2A and the abnormal hyperphosphorylation of tau, indicating the involvement of an Src-dependent PP2A pathway. Coimmunoprecipitation experiments showed that BMAA treatment dissociated PP2Ac from mGluR5, making it available for phosphorylation at Tyr307. These findings suggest a scenario in which BMAA can lead to tau pathology by inhibiting PP2A through the activation of mGluR5, the consequent release of PP2Ac from the mGluR5–PP2A complex, and its phosphorylation at Tyr307 by Src.
Identification of a Topological Characteristic Responsible for the Biological Robustness of Regulatory Networks

Attribution of biological robustness to the specific structural properties of a regulatory network is an important yet unsolved problem in systems biology. It is widely believed that the topological characteristics of a biological control network largely determine its dynamic behavior, yet the actual mechanism is still poorly understood. Here, we define a novel structural feature of biological networks, termed ‘regulation entropy’, to quantitatively assess the influence of network topology on the robustness of the systems. Using the cell-cycle control networks of the budding yeast (Saccharomyces cerevisiae) and the fission yeast (Schizosaccharomyces pombe) as examples, we first demonstrate the correlation of this quantity with the dynamic stability of biological control networks, and then we establish a significant association between this quantity and the structural stability of the networks. And we further substantiate the generality of this approach with a broad spectrum of biological and random networks. We conclude that the regulation entropy is an effective order parameter in evaluating the robustness of biological control networks. Our work suggests a novel connection between the topological feature and the dynamic property of biological regulatory networks.
Effects of livestock grazing on Anemone coronaria L. in drylands: Implications for nature conservation

Funding information Yad Hanadiv Foundation, Grant/Award Number: NA Grazing in nature reserves, or other sensitive lands, could affect the abundance of important plant species. In the Mediterranean basin, the Anemone coronaria is considered a flagship geophyte species. Studies conducted in the Mediterranean region of northern Israel showed that livestock grazing increased the abundance of A. coronaria. This was attributed to the consumption of other herbaceous vegetation species, resulting in better accessibility of A. coronaria to sunlight. Also, it was suggested that consumption of this species is limited due to its toxicity. The objective of this study was to investigate the impact of livestock on the abundance of A. coronaria, and on specific soil properties in a dryland environment, where primary productivity is determined by water availability. A long-term study was established in the Israeli Negev, where early-, mid-, and late-season grazing treatments took place over the course of a decade, and studied over three consecutive years between 2013/ 2014 and 2015/2016. The study revealed that the abundance of A. coronaria followed the order of non-grazing (control) > late-season grazing > mid-season grazing > early-season grazing. However, this effect was not significant (p = .0668). One way or another, the largest adverse impact of early-season grazing is attributed to consuming fresh and not yet toxic shoots of A. coronaria at that phenological stage. The soil properties were studied in summer 2016. The analysis showed a significant increase in bulk density under all of the grazing treatments compared with those in the control plots. It was concluded that, in drylands, trampling over wet soil during the growing season increases its compactability, degrading the soil-moisture status, and limiting A. coronaria abundance. Recommendations for nature conservation in drylands are, therefore, to negate grazing during A. coronaria’s early-growing season, as well as shortly after rain events when the soil moisture level is high.
Identification and Characterization of Cancer Stem Cells from Head and Neck Squamous Cell Carcinoma Cell Lines

Background/Aims: Head and neck squamous cell carcinoma (HNSCC) ranks sixth worldwide for tumor-related mortality. A subpopulation of tumor cells, termed cancer stem cells (CSCs), has the ability to support cancer growth. Therefore, profiling CSC-enriched populations could be a reliable tool to study cancer biology. Methods: We performed phenotypic characterization of 7 HNSCC cell lines and evaluated the presence of CSCs. CSCs from Hep-2 cell line and HNSCC primary cultures were enriched through sphere formation and sphere-forming cells have been characterized both in vitro and in vivo. In addition, we investigated the expression levels of Nicotinamide N-methyltransferase (NNMT), an enzyme overexpressed in several malignancies. Results: CSC markers were markedly expressed in Hep-2 cell line, which was found to be highly tumorigenic. CSC-enriched populations displayed increased expression of CSC markers and a strong capability to form tumors in vivo. We also found an overexpression of CSC markers in tumor formed by CSC-enriched populations. Interestingly, NNMT levels were significantly higher in CSC-enriched populations compared with parental cells. Conclusion: Our study provides an useful procedure for CSC identification and enrichment in HNSCC. Moreover, results obtained seem to suggest that CSCs may represent a promising target for an anticancer therapy.
Splicing of a group II intron in a functional transfer gene of Lactococcus lactis

A chromosomally located sex factor that controls conjugation in Lactococcus lactis 712 has been cloned and sequenced, leading to the discovery of an open reading frame with homology to the maturases of group II self‐splicing introns. Reverse transcriptase polymerase chain reaction amplification was used to demonstrate that the intron was spliced out of mRNA in vivo, and sequence analysis revealed the site of splicing. The intron was inserted within a sex‐factor gene which encodes a protein with homology to proteins involved in rolling‐circle DNA replication. Gene‐disruption experiments were used to demonstrate that this mobA gene was essential for sex‐factor transfer and this suggests that intron splicing is a necessary part of the conjugation process. The sequence of the intron was modelled to produce a secondary structure that exhibited several features characteristic of the IIA subgroup. Here we report the characterization of a new group II intron in the Gram‐positive bacterium L. lactis and demonstrate for the first time in bacteria both splicing in vivo and an active role for the gene carrying the intron.
Frontal lobe degeneration

The clinical, neuropsychological, and cerebral blood flow characteristics of eight patients with frontal lobe degeneration (FLD) were studied. Social withdrawal and behavioral disinhibition were the earliest and most common clinical presentations, and psychiatric symptoms typically preceded the onset of dementia by several years. Neuropsychological testing showed selective impairment of frontal and memory tasks with relative sparing of attention, language, and visuospatial skills. Single-photon emission computerized tomography demonstrated frontal and temporal hypoperfusion with relative sparing of parietal and occipital blood flow. Previous studies suggest that the neuropathologic findings in patients with FLD are varied; some demonstrate frontal gliosis, neuronal loss, and Pick bodies while others show only gliosis and neuronal loss.
Lung Cancer in Railroad Workers Exposed to Diesel Exhaust

Diesel exhaust has been suspected to be a lung carcinogen. The assessment of this lung cancer risk has been limited by lack of studies of exposed workers followed for many years. In this study, we assessed lung cancer mortality in 54,973 U.S. railroad workers between 1959 and 1996 (38 years). By 1959, the U.S. railroad industry had largely converted from coal-fired to diesel-powered locomotives. We obtained work histories from the U.S. Railroad Retirement Board, and ascertained mortality using Railroad Retirement Board, Social Security, and Health Care Financing Administration records. Cause of death was obtained from the National Death Index and death certificates. There were 43,593 total deaths including 4,351 lung cancer deaths. Adjusting for a healthy worker survivor effect and age, railroad workers in jobs associated with operating trains had a relative risk of lung cancer mortality of 1.40 (95% confidence interval, 1.30–1.51). Lung cancer mortality did not increase with increasing years of work in these jobs. Lung cancer mortality was elevated in jobs associated with work on trains powered by diesel locomotives. Although a contribution from exposure to coal combustion products before 1959 cannot be excluded, these results suggest that exposure to diesel exhaust contributed to lung cancer mortality in this cohort.
The Effect of Ciprofloxacin on Tendon, Paratenon, and Capsular Fibroblast Metabolism *

The pathologic mechanisms underlying fluoroquinolone-induced tendinopathy are poorly understood. The observed incidence of tendinitis and tendon rupture in patients treated with ciprofloxacin hydrochloride suggests that the fluoroquinolone antibiotics alter tendon fibroblast metabolism. The purpose of this study was to examine the effect of ciprofloxacin on fibroblast metabolism in vitro. Canine Achilles tendon, paratenon, and shoulder capsule specimens were maintained in culture with ciprofloxacin (5, 10, or 50 g/ml). Fibroblast proliferation, collagen synthesis, proteoglycan synthesis, and matrix-degrading activity were analyzed. Incubation of Achilles tendon, Achilles paratenon, and shoulder capsule fibroblasts with ciprofloxacin resulted in a statistically significant 66% to 68% decrease in cell proliferation compared with control cells at day 3 in culture. Ciprofloxacin caused a statistically significant 36% to 48% decrease in collagen synthesis compared with controls in all fibroblast cultures. Ciprofloxacin caused a statistically significant 14% to 60% decrease in proteoglycan synthesis in all fibroblast cell lines. Compared with unstimulated control fibroblasts, culture media from Achilles tendon, paratenon, and shoulder capsule cells that were exposed to ciprofloxacin demonstrated statistically significant increases in matrix-degrading proteolytic activity after 72 hours in culture. This study demonstrates that ciprofloxacin stimulates matrix-degrading protease activity from fibroblasts and that it exerts an inhibitory effect on fibroblast metabolism. The increase in protease activity and the inhibition of both cell proliferation and the synthesis of matrix ground substance may contribute to the clinically described tendinopathies associated with ciprofloxacin therapy.