Miracle-dz/UniFAR-FTUs huggingface dataset:
Visible foliar injury as a tool for the assessment of surface ozone impact on native vegetation: a case study from the Jizerské hory Mts

Surface ozone is considered to be a very phytotoxic gaseous air pollutant. Its negative impacts at both the cell and the organ level have been shown, mainly as a result of experiments. However, the demonstration of ozone negative impacts on native plants is not explicit. An assessment of ozone impact on vegetation and ecosystems using indicators based on ambient ozone concentrations is insufficient and assessment techniques based on internal ozone dose and on real plant damage are more appropriate. Such a possible technique is the mapping of ozone visible symptoms due to ozone influence. The ICP-Forest method concerning ozone visible symptoms and the assessment of ozone influence were applied for the purposes of this case study. The visible symptoms are characterized by a few typical signs. Nevertheless, the identification of visible symptoms in native conditions can be problematic and misleading conclusions could be drawn. Therefore it is necessary to complete the identification of visible symptoms with a validation in order to confirm ozone as the cause of plant injury.
Heuristics Entwined with Handlers Combined: From Functional Specification to Logic Programming Implementation

A long-standing problem in logic programming is how to cleanly separate logic and control. While solutions exist, they fall short in one of two ways: some are too intrusive, because they require significant changes to Prolog's underlying implementation; others are lacking a clean semantic grounding. We resolve both of these issues in this paper. We derive a solution that is both lightweight and principled. We do so by starting from a functional specification of Prolog based on monads, and extend this with the effect handlers approach to capture the dynamic search tree as syntax. Effect handlers then express heuristics in terms of tree transformations. Moreover, we can declaratively express many heuristics as trees themselves that are combined with search problems using a generic entwining handler. Our solution is not restricted to a functional model: we show how to implement this technique as a library in Prolog by means of delimited continuations.
Effect of Channel Estimation Errors on Arbitrary Transmit Antenna Selection for Cognitive MISO Systems

This letter analyzes the effect of channel estimation errors on the performance of cognitive multiple input and single output (MISO) systems with arbitrary transmit antenna selection. In particular, the channel estimation errors are caused by the partial channel information between the cognitive transmitter and the primary receiver. Utilizing the derived probability density function (PDF) of the received signal-to-noise ratio (SNR), the effective capacity of the considered systems is numerically evaluated, and a new closed-form expression for the case of perfect channel estimation is also derived. Simulation results show that the system performance is not sensitive to the channel estimation error, especially for strict delay quality of service (QoS) requirement of the cognitive user (CU).
Elo 1 p-Dependent Carboxy-Terminal Elongation of C 14 : 1 D 9 to C 16 : 1 D 11 Fatty Acids in Saccharomyces cerevisiae

Saccharomyces cerevisiae medium-chain acyl elongase (ELO1) mutants have previously been isolated in screens for fatty acid synthetase (FAS) mutants that fail to grow on myristic acid (C14:0)-supplemented media. Here we report that wild-type cells cultivated in myristoleic acid (C14:1D)-supplemented media synthesized a novel unsaturated fatty acid that was identified as C16:1D fatty acid by gas chromatography-mass spectroscopy. Synthesis of C16:1D was dependent on a functional ELO1 gene, indicating that Elo1p catalyzes carboxy-terminal elongation of unsaturated fatty acids (a-elongation). In wild-type cells, the C16:1D elongation product accounted for approximately 12% of the total fatty acids. This increased to 18% in cells that lacked a functional acyl chain desaturase (ole1D mutants) and hence were fully dependent on uptake and elongation of C14:1. The observation that ole1D mutant cells grew almost like wild type on medium supplemented with C14:1 indicated that uptake and elongation of unsaturated fatty acids were efficient. Interestingly, wildtype cells supplemented with either C14:1 or C16:1 fatty acids displayed dramatic alterations in their phospholipid composition, suggesting that the availability of acyl chains is a dominant determinant of the phospholipid class composition of cellular membranes. In particular, the relative content of the two major phospholipid classes, phosphatidylethanolamine and phosphatidylcholine, was strongly dependent on the chain length of the supplemented fatty acid. Moreover, analysis of the acyl chain composition of individual phospholipid classes in cells supplemented with C14:1 revealed that the relative degree of acyl chain saturation characteristic for each phospholipid class appeared to be conserved, despite the gross alteration in the cellular acyl chain pool. Comparison of the distribution of fatty acids that were taken up and elongated (C16:1D) to those that were endogenously synthesized by fatty acid synthetase and then desaturated by Ole1p (C16:1D) in individual phospholipid classes finally suggested the presence of two different pools of diacylglycerol species. These results will be discussed in terms of biosynthesis of different phospholipid classes via either the de novo or the Kennedy pathway.
Hardware acceleration for similarity measurement in natural language processing

The continuation of Moore's law scaling, but in the absence of Dennard scaling, motivates an emphasis on energy-efficient accelerator-based designs for future applications. In natural language processing, the conventional approach to automatically analyze vast text collections - using scale-out processing - incurs high energy and hardware costs since the central compute-intensive step of similarity measurement often entails pairwise, all-to-all comparisons. We propose a custom hardware accelerator for similarity measures that leverages data streaming, memory latency hiding, and parallel computation across variable-length threads. We evaluate our design through a combination of architectural simulation and RTL synthesis. When executing the dominant kernel in a semantic indexing application for documents, we demonstrate throughput gains of up to 42× and 58× lower energy per similarity-computation compared to an optimized software implementation, while requiring less than 1.3% of the area of a conventional core.
Secure remote matching with privacy: Scrambled support vector vaulted verification (S2V3)

As biometric authentication systems become common in everyday use, researchers are beginning to address privacy issues in biometric recognition. With the growing use of mobile devices, it is important to develop approaches that support remote mobile verification. This paper outlines the need for a mobile/remote SVM-based authentication system that does not compromise the privacy of the subject being recognized. We discuss limitations of earlier privacy-preserving authentication systems and present necessary privacy and security requirements that make a system attractive from both the server's security point of view and from the client's privacy-centric point of view. We then present a novel protocol we call “Vaulted Verification” that allows a server to remotely authenticate a client's biometric in a privacy preserving way. We conclude with a small evaluation of performance, discussion of security implications, and ideas for future work.
Morphometry of the Normal Cadaveric Cervical Spinal Cord

Study Design The authors measured the transverse area and diameters of the cadaveric cervical spinal cord without evidence of nervous system pathology and also investigated factors related to spinal cord size. Objectives This study attempted to provide basic data that affords an accurate morphometric analysis of the human cervical spinal cord. Summary of Background Data Several postmortem morphometric studies of the spinal cord have been performed, but the measurements are different among the reports, and no authorized standard has been established. Methods The authors measured the transverse area and diameters of the C7 segment in 152 cadaveric specimens and investigated the cord size in relation to age, body height, body weight, and brain weight. Of these, 14 cases were selected and their segments from C2 to T1 were measured. Results There was a considerable individual variation in spinal cord size. The transverse area of the C7 segment varied from 33.3 mm2 to 74.0 mm2 (mean 49.6 ± 7.4 mm2). The cord size showed a strong correlation with brain weight, and to a lesser degree with age and body height. Although the size of the spinal cord varied from case to case, the relative ratio of the transverse area of each segment to that of the C3 segment was almost the same among the cases examined. Conclusions This large variation in cord size should be taken under consideration in morphometric analyses of the spinal cord. When the pathologic cord conditions such as compression or atrophy exist, the normally expected transverse area of the affected segment in each individual is calculable from measurement of a given single normal segment.
On attaining maximal fitness or how to evolve virtual redwoods

An understanding of the evolutionary mechanisms that lead to increased genome capabilities is essential for determining the potentials and limits of living systems. We evolve abstract aesthetic imagery on the basis of an image connectivity trait that has a theoretically determined maximum value. This trait can be influenced by "development" genes. We investigate simulated evolution when the development genes are not present, when they are fused with the existing genotype, and when they function semi-autonomously by residing in symbionts. Genome fusing initially impedes evolution while symbiosis initially accelerates evolution. Our findings suggest that symbiosis events play a more important role than genome fusion events for sustaining open-ended evolution.
Upregulation of SOCS3 in lung CD4+ T cells in a mouse model of chronic PA lung infection and suppression of Th17-mediated neutrophil recruitment in exogenous SOCS3 transfer in vitro

Neutrophilic airway inflammation in chronic lung infections caused by Pseudomonas aeruginosa (PA) is associated with T helper (Th)17 responses. Suppressor of cytokine signaling 3 (SOCS3) is the major negative modulator of Th17 function through the suppression of signal transducer and activator of transcription (STAT)3 activation. The aim of the present study was to investigate the expression of SOCS3 in lung CD4+ T cells in a mouse model of chronic PA lung infection and the effect of exogenous SOCS3 on Th17-mediated neutrophil recruitment in vitro. A mouse model of chronic PA lung infection was established and the activation of STAT3 and Th17 response in lung tissues and lung CD4+ T cells was assessed. The protein and mRNA expression of SOCS3 in lung CD4+ T cells was analyzed by western blotting and reverse transcription-quantitative polymerase chain reaction. The authors constructed a recombinant lentivirus carrying the SOCS3 gene and transferred it into lung CD4+ T cells isolated from a mouse model. These transfected cells were stimulated with interleukin (IL)-23 in vitro and the protein level of p-STAT3 and retinoid-related orphan receptor (ROR)γt was determined by western blotting. The expression of IL-17A+ cells was analyzed by flow cytometry and the level of IL-17A in cell culture supernatant was measured by ELISA. The mouse lung epithelial cell line, MLE-12, was cocultured with lung CD4+ T cells that overexpressed the SOCS3 gene and the culture supernatant was harvested and used for a chemotaxis assay. Compared with control mice, mice with chronic PA lung infection had significantly higher level of p-STAT3 and Th17 response in both lung tissues and lung CD4+ T cells. The protein and mRNA level of SOCS3 in lung CD4+ T cells increased as the chronic PA lung infection developed. Exogenous SOCS3 gene transfer in PA-infected lung CD4+ T cells decreased p-STAT3 and RORγt expression and suppressed the level of IL-17A+ cells in vitro. MLE-12 cells cocultured with SOCS3-overexpressing lung CD4+ T cells expressed a significantly lower level of neutrophil chemoattractants chemokine (C-X-C motif) ligand (CXCL) 1 and CXCL5, and recruited significantly smaller numbers of migrating neutrophils than those cocultured with control cells. SOCS3 was upregulated in lung CD4+ T cells following the activation of STAT3/Th17 axis in a mouse model of chronic PA lung infection. Exogenous SOCS3 transfer in PA-infected lung CD4+ T cells suppresses Th17-mediated neutrophil recruitment in vitro.
Structure-aware XML Object Identification

The object identi cation problem is particu- larly hard for XML data, due to its struc- tural exibility. Tree edit distances have been proposed for approximate comparisons among XML trees. However, such distances ignore the semantics implicit in XML data structure, and their use is computationally infeasible for unordered data. In this paper, we de ne a new distance for XML data, the structure aware XML distance, that overcomes these issues, together with a polynomial-time algorithm to calculate it, and we present experimental re- sult that prove its e ectiveness and e ciency.
Reduced Calreticulin Levels Link Endoplasmic Reticulum Stress and Fas-Triggered Cell Death in Motoneurons Vulnerable to ALS

Cellular responses to protein misfolding are thought to play key roles in triggering neurodegeneration. In the mutant superoxide dismutase (mSOD1) model of amyotrophic lateral sclerosis (ALS), subsets of motoneurons are selectively vulnerable to degeneration. Fast fatigable motoneurons selectively activate an endoplasmic reticulum (ER) stress response that drives their early degeneration while a subset of mSOD1 motoneurons show exacerbated sensitivity to activation of the motoneuron-specific Fas/NO pathway. However, the links between the two mechanisms and the molecular basis of their cellular specificity remained unclear. We show that Fas activation leads, specifically in mSOD1 motoneurons, to reductions in levels of calreticulin (CRT), a calcium-binding ER chaperone. Decreased expression of CRT is both necessary and sufficient to trigger SOD1G93A motoneuron death through the Fas/NO pathway. In SOD1G93A mice in vivo, reductions in CRT precede muscle denervation and are restricted to vulnerable motor pools. In vitro, both reduced CRT and Fas activation trigger an ER stress response that is restricted to, and required for death of, vulnerable SOD1G93A motoneurons. Our data reveal CRT as a critical link between a motoneuron-specific death pathway and the ER stress response and point to a role of CRT levels in modulating motoneuron vulnerability to ALS.
Optimizing Early Rule-Out Strategies for Acute Myocardial Infarction: Utility of 1-Hour Copeptin.

BACKGROUND Combined testing of high-sensitivity cardiac troponin T (hs-cTnT) and copeptin at presentation provides a very high-although still imperfect-negative predictive value (NPV) for the early rule-out of acute myocardial infarction (AMI). We hypothesized that a second copeptin measurement at 1 h might further increase the NPV. METHODS In a prospective diagnostic multicenter study, we measured hs-cTnT and copeptin concentrations at presentation and at 1 h in 1439 unselected patients presenting to the emergency department with suspected AMI. The final diagnosis was adjudicated by 2 independent cardiologists blinded to copeptin concentrations. We investigated the incremental value of 1-h copeptin in the rule-out setting (0-h hs-cTnT negative and 0-h copeptin negative) and the intermediate-risk setting (0-h hs-cTnT negative and 0-h copeptin positive). RESULTS The adjudicated diagnosis was AMI in 267 patients (18.6%). For measurements obtained at presentation, the NPV in the rule-out setting was 98.6% (95% CI, 97.4%-99.3%). Whereas 1-h copeptin did not increase the NPV significantly, 1-h hs-cTnT did, to 99.6% (95% CI, 98.7%-99.9%, P = 0.008). Similarly, in the intermediate-risk setting (NPV 92.8%, 95% CI, 88.7%-95.8%), 1-h copeptin did not significantly increase the NPV (P = 0.751), but 1-h hs-cTnT did, to 98.6 (95% CI, 96%-99.7%, P < 0.001). CONCLUSIONS One-hour copeptin increased neither the safety of the rule-out process nor the NPV in the intermediate-risk setting. In contrast, the incremental value of 1-h hs-cTnT was substantial in both settings. ClinicalTrials.gov/NCT00470587.
The impact of priority generations in a multi-priority queueing system — A simulation approach

In this paper, we consider a preemptive (multiple) priority queueing model in which arrivals occur according to a Markovian arrival process (MAP). An arriving customer belongs to priority type i, 1 ≤ i ≤ m+1, with probability pi. The highest priority, labeled as 0, is generated by other priority customers while waiting in the system and not otherwise. Also, a customer of priority i can turn into a priority j, j ≠ i, 1 ≤ i, j ≤ m + 1, customer, after a random amount of time that is assumed to be exponentially distributed with parameter depending on the priority type. The waiting spaces for all but priority type m+1 are assumed to be finite. The (m+1)-st priority customers have unlimited waiting space. At any given time, the system can have at most one highest priority customer. Thus, all priority customers except the (m +1) — st are subject to loss. Customers are served on a first-come-first-served basis within their priority by a single server and the service times are assumed to follow a phase type distribution that may depend on the customer priority type. This queueing model, which is a level-dependent quasi-birth-and-death process, is amenable for investigation algorithmically through the well-known matrix-analytic methodology. However, here we propose to study through simulation using ARENA, a powerful simulation software as some key measures such as the waiting time distributions are highly complex to characterize analytically. The simulated results for a few scenarios are presented.
Digestibility and performance of steers fed varying inclusions of corn silage and modified distillers grains with solubles to partially replace corn in finishing diets

Abstract Two finishing and 1 digestibility experiment evaluated the partial substitution of corn with corn silage and corn modified distillers grains with solubles (MDGS). Steers were used in Exp. 1 (n = 295; 467 ± 52 kg) and Exp. 2 (n = 225; BW = 348 ± 27 kg) in a 2 × 2 + 1 factorial arrangement of treatments with factors including corn silage (15 or 45%) and MDGS (20 or 40%) plus a control diet consisting of 5% cornstalks and 40% MDGS. In Exp. 1, there were tendencies for a corn silage × MDGS interaction for ADG, final BW, and G:F (P ≤ 0.08). In the overall F-test for G:F, there were no differences between the control treatment and 15:20, 15:40, or 45:40 (P ≥ 0.15), however, steers fed the control treatment had increased G:F compared to steers fed 45:20 treatment diets (P = 0.03). In Exp. 2, there were no corn silage × MDGS interactions (P ≥ 0.12). As corn silage increased in the diet, ADG, final BW, and G:F decreased (P ≤ 0.01). As MDGS increased from 20 to 40%, ADG and G:F tended to improve (P ≤ 0.07). In the overall F-test, the control was not different for G:F from 15:20, 45:20, or 45:40 (P ≥ 0.15), but had a 4.8% poorer G:F compared to 15:40 (P < 0.01). In Exp. 3, ruminally fistulated steers (n = 6) were used in a 5 × 6 Latin rectangle design and fed 15 or 45% corn silage with 20 or 40% MDGS as a 2 × 2 factorial. An additional diet consisting of 95% corn silage and 5% supplement was fed. There were no corn silage × MDGS interactions for nutrient intake, total tract digestibility, ruminal pH measurements, acetate: propionate ratio (A:P), or in-situ disappearance data (P ≥ 0.31) for the 2 × 2 factorial. As corn silage increased in the diet, DMI, NDF intake, ruminal pH, A:P, in-situ NDF disappearance of corn bran, and DM disappearance of corn increased (P ≤ 0.09) with decreases in DM and OM digestibility (P ≤ 0.03). As MDGS increased in the diet, there was an increase in NDF intake, total volatile fatty acid concentration, and NDF disappearance of corn bran (P ≤ 0.03) with no differences for any other tested variables (P ≥ 0.13). In general, increasing corn silage in place of corn in finishing diets containing MDGS results in a modest reduction in ADG and G:F with increases in ruminal pH.
Different Sequence Strains of Streptococcus agalactiae Elicit Various Levels of Cytokine Production

Group B streptococcus (GBS) is the most common cause of neonatal and obstetric sepsis and an increasingly important cause of septicemia in elderly subjects and immunocompromised patients. Our aim was to evaluate whether different genotypes of GBS may induce a different production of pro-inflammatory and anti-inflammatory cytokines. We used multilocus sequence typing to identify 71 clones isolated from asymptomatic healthy carriers and symptomatic individuals. All these clinical isolates were used to infect purified human monocytes. TNF-alpha, IL-6, IL-8 and IL-10 secretion was measured. Fifteen allelic sequence types (STs) were identified. The MLST (multilocus sequence typing) anlaysis grouped the bacteria into four different lineages (clonal cluster) and two of these were closely involved in the infection of symptomatic subjects: CC17 and CC19. Furthermore, CC17 and CC19 stimulated TNF-α, IL-6 and IL-8 production significantly more than the other lineages, while CC17 induced a decreased IL-10 production. These results suggest the existence of differences in immune response to infection with particular genotypes of GBS.
Coronavirus phylogeny based on 2D graphical representation of DNA sequence

A novel coronavirus has been identified as the cause of the outbreak of severe acute respiratory syndrome (SARS). Previous phylogenetic analyses based on sequence alignments show that SARS‐CoVs form a new group distantly related to the other three groups of previously characterized coronaviruses. In this aritcle, a new approach based on the 2D graphical representation of the whole genome sequence is proposed to analyze the phylogenetic relationships of coronaviruses. The evolutionary distances are obtained through measuring the differences among the two‐dimensional curves. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1196–1202, 2006
The Association between Dietary Intake of Folate and Physical Activity with Psychological Dimensions of Depressive Symptoms among Students from Iran

Depression in students is a major public health problem. Although several risk factors associated with depression have been identified, the cause of depression is still not clear. Several studies have demonstrated that physical activity and nutrient intake, such as increased levels of B vitamins in serum, decrease symptoms of depression. The aim of this study was to investigate the association between physical activity and dietary intake of vitamins B6, B9, and B12 and symptoms of depression among postgraduate students. The results of this study suggest that intake of vitamin B9 may modulate the total score of Center for Epidemiological Studies Depression Scale (CES-D) and two subscales of the CES-D including depressive affect and interpersonal difficulties. This study also showed that moderate/high levels of physical activity were inversely and significantly associated with symptoms of depression (total scores) and three subscales of the CES-D including depressive affect, positive affect, and somatic complaints.