Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing the Spontaneous Blink Generator: An Animal Model

Although spontaneous blinking is one of the most frequent human movements, little is known about its neural basis. We developed a rat model of spontaneous blinking to identify and better characterize the spontaneous blink generator. We monitored spontaneous blinking for 55 min periods in normal conditions and after the induction of mild dry eye or dopaminergic drug challenges. The normal spontaneous blink rate was 5.3 ± 0.3 blinks/min. Dry eye or 1 mg/kg apomorphine significantly increased and 0.1 mg/kg haloperidol significantly decreased the blink rate. Additional analyses revealed a consistent temporal organization to spontaneous blinking with a median 750 s period that was independent of the spontaneous blink rate. Dry eye and dopaminergic challenges significantly modified the regularity of the normal pattern of episodes of frequent blinking interspersed with intervals having few blinks. Dry eye and apomorphine enhanced the regularity of this pattern, whereas haloperidol reduced its regularity. The simplest explanation for our data is that the spinal trigeminal complex is a critical element in the generation of spontaneous blinks, incorporating reflex blinks from dry eye and indirect basal ganglia inputs into the blink generator. Although human subjects exhibited a higher average blink rate (17.6 ± 2.4) than rats, the temporal pattern of spontaneous blinking was qualitatively similar for both species. These data demonstrate that rats are an appropriate model for investigating the neural basis of human spontaneous blinking and suggest that the spinal trigeminal complex is a major element in the spontaneous blink generator.
A Method for the Spatial Discretization of Parabolic Equations in One Space Variable

This paper is concerned with the design of a spatial discretization method for polar and nonpolar parabolic equations in one space variable. A new spatial discretization method suitable for use in a library program is derived. The relationship to other methods is explored. Truncation error analysis and numerical examples are used to illustrate the accuracy of the new algorithm and to compare it with other recent codes.
Dynamic Checking of Safe Concurrent Memory Access using Shared Ownership

In shared-memory concurrent programming, shared resources can be protected using synchronization mechanisms such as monitors or channels. The connection between these mechanisms and the resources they protect is, however, only given implicitly; this makes it difficult both for programmers to apply the mechanisms correctly and for compilers to check that resources are properly protected. This paper presents a mechanism to automatically check that shared memory is accessed properly, using a methodology called shared ownership. In contrast to traditional ownership, shared ownership offers more flexibility by permitting multiple owners of a resource. On the basis of this methodology, we define an abstract model of resource access that provides operations to manage data dependencies, as well as sharing and transfer of access privileges. The model is rigorously defined using a formal semantics, and shown to be free from data races. This property can be used to detect unsafe memory accesses when simulating the model together with the execution of a program. The expressiveness and efficiency of the approach is demonstrated on a variety of programs using common synchronization mechanisms.
A history of smoking is inversely correlated with the incidence of gemcitabine-induced neutropenia.

BACKGROUND Smoking may affect the efficacy of chemotherapy and the incidence of adverse events. We investigated the correlation between smoking history and gemcitabine-induced neutropenia. PATIENTS AND METHODS Data on smoking history and incidence of grade 3-4 neutropenia were retrospectively gathered for 103 chemo-naive patients treated with gemcitabine monotherapy (59 patients with pancreatic, 41 with hepatobiliary and three with other cancers). RESULTS There was a significantly higher incidence of grade 3-4 neutropenia among patients without a history of smoking (55.7%) than among those with a history of smoking (including current and ex-smokers; 23.6%) [odds ratio (OR) 0.244, 95% confidence interval (CI) 0.105-0.569; P < 0.001]. After adjustment for age, gender, platelet and baseline neutrophil counts, history of surgery for primary cancer, creatinine concentration, hemoglobin concentration, aspartate aminotransferase concentration, alanine aminotransferase concentration and total bilirubin concentration, logistic regression analysis identified a history of smoking as an independent inverse predictor of gemcitabine-induced neutropenia (OR 0.188, 95% CI 0.057-0.618; P = 0.006). CONCLUSION Patients without a history of smoking may be at higher risk of developing gemcitabine-induced neutropenia. The mechanism underlying this phenomenon is unclear at this point.
A framework for classifying denial of service attacks

Launching a denial of service (DoS) attack is trivial, but detection and response is a painfully slow and often a manual process. Automatic classification of attacks as single- or multi-source can help focus a response, but current packet-header-based approaches are susceptible to spoofing. This paper introduces a framework for classifying DoS attacks based on header content, and novel techniques such as transient ramp-up behavior and spectral analysis. Although headers are easily forged, we show that characteristics of attack ramp-up and attack spectrum are more difficult to spoof. To evaluate our framework we monitored access links of a regional ISP detecting 80 live attacks. Header analysis identified the number of attackers in 67 attacks, while the remaining 13 attacks were classified based on ramp-up and spectral analysis. We validate our results through monitoring at a second site, controlled experiments, and simulation. We use experiments and simulation to understand the underlying reasons for the characteristics observed. In addition to helping understand attack dynamics, classification mechanisms such as ours are important for the development of realistic models of DoS traffic, can be packaged as an automated tool to aid in rapid response to attacks, and can also be used to estimate the level of DoS activity on the Internet.
Functional Analysis of the Kinome of the Wheat Scab Fungus Fusarium graminearum

As in other eukaryotes, protein kinases play major regulatory roles in filamentous fungi. Although the genomes of many plant pathogenic fungi have been sequenced, systematic characterization of their kinomes has not been reported. The wheat scab fungus Fusarium graminearum has 116 protein kinases (PK) genes. Although twenty of them appeared to be essential, we generated deletion mutants for the other 96 PK genes, including 12 orthologs of essential genes in yeast. All of the PK mutants were assayed for changes in 17 phenotypes, including growth, conidiation, pathogenesis, stress responses, and sexual reproduction. Overall, deletion of 64 PK genes resulted in at least one of the phenotypes examined, including three mutants blocked in conidiation and five mutants with increased tolerance to hyperosmotic stress. In total, 42 PK mutants were significantly reduced in virulence or non-pathogenic, including mutants deleted of key components of the cAMP signaling and three MAPK pathways. A number of these PK genes, including Fg03146 and Fg04770 that are unique to filamentous fungi, are dispensable for hyphal growth and likely encode novel fungal virulence factors. Ascospores play a critical role in the initiation of wheat scab. Twenty-six PK mutants were blocked in perithecia formation or aborted in ascosporogenesis. Additional 19 mutants were defective in ascospore release or morphology. Interestingly, F. graminearum contains two aurora kinase genes with distinct functions, which has not been reported in fungi. In addition, we used the interlog approach to predict the PK-PK and PK-protein interaction networks of F. graminearum. Several predicted interactions were verified with yeast two-hybrid or co-immunoprecipitation assays. To our knowledge, this is the first functional characterization of the kinome in plant pathogenic fungi. Protein kinase genes important for various aspects of growth, developmental, and infection processes in F. graminearum were identified in this study.
The CNO Isotopes: Deep Circulation in Red Giants and First and Second Dredge-up

It is demonstrated that deep circulation mixing below the base of the standard convective envelope, and the consequent "cool bottom processing" (CBP) of the CNO isotopes, can reproduce the trend with stellar mass of the 12C/13C observations in low-mass red giants. (This trend is opposite to what is expected from standard first dredge-up.) Our models assume that extra mixing always reaches to the same distance in temperature from the H-burning shell and that CBP begins when the H-burning shell erases the molecular weight discontinuity ("μ-barrier") established by first dredge-up. For Population I stars, none of the other CNO isotopes except 15N are expected to be altered by CBP. (If 18O depletion occurs on the asymptotic giant branch [AGB], as some observations suggest, it would require that extra mixing reach closer to the H-burning shell on the AGB than on the red giant branch [RGB]—and should also result in a much lower 12C/13C ratio than is observed in the relevant AGB stars.) CBP increases dramatically as one reduces the stellar mass or metallicity—roughly as M-2 on the RGB, because of the longer RGB of low-mass stars, and roughly as Z-1, because of the higher H-shell burning temperatures of low-metallicity stars. In low-mass Population II stars, all the CNO isotopes are expected to be significantly altered by CBP. Field Population II stars exhibit RGB abundances consistent with the predictions of our CBP models that have been normalized to reproduce the Population I RGB abundances. On the other hand, globular cluster stars are observed to encounter much more extensive processing; additionally, CBP is observed to start near the base of the globular cluster RGB (overcoming any "μ-barrier"). For the CNO isotopes 12C, 13C, 14N, 16O, 17O, and 18O, we also present self-consistent calculations of the consequences of both first and second dredge-up, i.e., of standard convection during the RGB and AGB stages, over a wide range of stellar masses (0.8-9 M☉) and metallicities (Z=0.02-0.0001). We demonstrate that the common low- and intermediate-mass stars are a prime source of 13C, 14N, and 17O in the universe. The light elements (3He, 4He, 7Li, 9Be, 10B, and 11B) are discussed in a companion paper.
Argonautes ALG-3 and ALG-4 are required for spermatogenesis-specific 26G-RNAs and thermotolerant sperm in Caenorhabditis elegans

Gametogenesis is a thermosensitive process in numerous metazoans, ranging from worms to man. In Caenorhabditis elegans, a variety of RNA-binding proteins that associate with germ-line nuage (P granules), including the Piwi-clade argonaute PRG-1, have been implicated in maintaining fertility at elevated temperature. Here we describe the role of two AGO-class paralogs, alg-3 (T22B3.2) and alg-4 (ZK757.3), in promoting thermotolerant male fertility. A rescuing GFP::alg-3 transgene is localized to P granules beginning at the late pachytene stage of male gametogenesis. alg-3/4 double mutants lack a subgroup of small RNAs, the 26G-RNAs which target and appear to down-regulate numerous spermatogenesis-expressed mRNAs. These findings add to a growing number of AGO pathways required for thermotolerant fertility in C. elegans and support a model in which AGOs and their small RNA cofactors function to promote robustness in gene-expression networks.
Prevalence of peripheral vascular disease and its association with carotid intima-media thickness and arterial stiffness in type 2 diabetes: The Chennai Urban Rural Epidemiology Study (CURES 111)

We investigated the prevalence of peripheral vascular disease (PVD) and its association with preclinical atherosclerotic markers [intima-media thickness (IMT)] and arterial stiffness among 1755 urban south Indian type 2 diabetic subjects recruited from the Chennai Urban Rural Epidemiology Study (CURES). Doppler studies were performed, and PVD was defined as ankle–brachial index (ABI) of ≤0.9. IMT of the common carotid artery was determined using high-resolution B-mode ultrasonography, and augmentation index (AGI) was measured using the Sphygmocor apparatus. The overall prevalence of PVD was 8.3% (age-standardized 6.5%). The prevalence of PVD was higher among known diabetic subjects (n = 1401) compared to newly detected diabetic subjects (n = 354) (8.6% vs 6.8%, p = 0.250). The mean IMT and AGI in subjects with PVD were significantly higher compared to subjects without PVD (IMT: 0.99 ± 0.26 mm vs 0.83 ± 0.19 mm; AGI: 28.1 ± 9.6% vs 25.7 ± 9.8%, respectively). IMT was independently associated with PVD even after adjusting for age [odds ratio (OR) = 2.9 (1.2−6.7), p = 0.016 for second tertile and OR = 3.9 (1.7−9.3), p = 0.002 for third tertile compared to first tertile]. AGI was also associated with PVD in the unadjusted model [OR = 1.8 (1.1−3.1), p = 0.027 for second tertile compared to first tertile]. However, when adjusted for age, the significance was lost. In conclusion, among urban south Indian type 2 diabetic subjects, the prevalence of PVD is 8.3% and IMT is more strongly associated with PVD than AGI.
Implications of human macrophage metalloelastase and vascular endothelial growth factor gene expression in angiogenesis of hepatocellular carcinoma.

OBJECTIVE To determine molecular mechanisms involved in angiogenesis of hepatocellular carcinoma (HCC). SUMMARY BACKGROUND DATA Tumor angiogenesis is believed to derive from the balance between angiogenic stimulators and inhibitors. It has been suggested that the switch to the angiogenic phenotype requires both upregulation of the first and downregulation of the second. However, its molecular basis in vivo remains obscure. In this study the authors analyze the participation of two factors in angiogenesis of HCC- human macrophage metalloelastase (HME), a matrix metalloproteinase responsible for the generation of angiostatin, a potent angiogenesis inhibitor, and vascular endothelial growth factor (VEGF), the most potent endogenous angiogenic factor. METHODS Tumorous and contiguous nontumorous tissues from 25 patients with HCC who underwent curative partial hepatectomy were subjected to Northern blot analysis to detect HME and VEGF messenger RNA (mRNA) expression. Western blot analysis was used to detected angiostatin. Tumor vascularity was evaluated using hepatic angiography. RESULTS Eleven of the 15 cases expressing the HME gene showed hypovascular tumors, whereas hypervascular tumors were seen in 9 of the 10 HME-negative cases. The median of HME mRNA expression (tumorous/nontumorous ratio) was 6.5 (range 0-264.5) in the hypovascular group and 0 (range 0-3.2) in the hypervascular group. A stepwise logistic analysis revealed that HME and VEGF mRNA expression were two independent variables significantly affecting the vascularity of HCC tumors. CONCLUSION HME gene expression is significantly associated with hypovascular tumors; moreover, angiogenesis in HCC is not determined by a single factor, but depends on the net balance between HME and VEGF gene expressions.
Intranasal Immunization with Heat-InactivatedStreptococcus pneumoniae Protects Mice against Systemic Pneumococcal Infection

ABSTRACT In order to study the mucosal and serum antibody response to polysaccharide-encapsulated bacteria in mice, a preparation of heat-inactivated Streptococcus pneumoniae type 4 was administered, with and without cholera toxin, at various mucosal sites. It appeared that intranasal immunization of nonanesthesized animals was superior to either oral, gastric, or colonic-rectal antigen delivery with regard to the induction of serum immunoglobulin G (IgG) and IgA, as well as saliva IgA antibodies specific for pneumococci. The marked IgA antibody response in feces after intranasal, but not after oral or gastric, immunization is suggestive of a cellular link between the nasal induction site and the distant mucosal effector sites. Intranasal immunization also induced antibodies in serum and in mucosal secretions against type-specific capsular polysaccharide. IgA and IgG antibody levels in pulmonary lavage fluids correlated well with saliva IgA and serum IgG antibodies, respectively. Antibody determinations in pulmonary secretions may therefore be redundant in some cases, and the number of experimental animals may be reduced accordingly. After intraperitoneal challenge with type 4 pneumococci, mice immunized intranasally were protected against both systemic infection and death, even without the use of cholera toxin as a mucosal adjuvant. Thus, an efficient intranasal vaccine against invasive pneumococcal disease may be based on a very simple formulation with whole killed pneumococci.
Application of Artificial Intelligence Techniques for Dissolved Gas Analysis of Transformers-A Review

The gases generated in oil filled transformers can be used for qualitative determination of incipient faults. The Dissolved Gas Analysis has been widely used by utilities throughout the world as the primarily diagnostic tool for transformer maintenance. In this paper, various Artificial Intelligence Techniques that have been used by the researchers in the past have been reviewed, some conclusions have been drawn and a sequential hybrid system has been proposed. The synergy of ANN and FIS can be a good solution for reliable results for predicting faults because one should not rely on a single technology when dealing with real–life applications. Keywords—Dissolved Gas Analysis, Artificial Intelligence Techniques, Incipient Faults, Transformer Fault Diagnosis, and Hybrid Systems.
Reference Values for Normal Pulmonary Artery Dimensions by Noncontrast Cardiac Computed Tomography: The Framingham Heart Study

Background— Main pulmonary artery diameter (mPA) and ratio of mPA to ascending aorta diameter (ratio PA) derived from chest CT are commonly reported in clinical practice. We determined the age- and sex-specific distribution and normal reference values for mPA and ratio PA by CT in an asymptomatic community-based population. Methods and Results— In 3171 men and women (mean age, 51±10 years; 51% men) from the Framingham Heart Study, a noncontrast, ECG-gated, 8-slice cardiac multidetector CT was performed. We measured the mPA and transverse axial diameter of the ascending aorta at the level of the bifurcation of the right pulmonary artery and calculated the ratio PA. We defined the healthy referent cohort (n=706) as those without obesity, hypertension, current and past smokers, chronic obstructive pulmonary disease, history of pulmonary embolism, diabetics, cardiovascular disease, and heart valve surgery. The mean mPA diameter in the overall cohort was 25.1±2.8 mm and mean ratio PA was 0.77±0.09. The sex-specific 90th percentile cutoff value for mPA diameter was 28.9 mm in men and 26.9 mm in women and was associated with increase risk for self-reported dyspnea (adjusted odds ratio, 1.31; P=0.02). The 90th percentile cutoff value for ratio PA of the healthy referent group was 0.91, similar between sexes but decreased with increasing age (range, 0.82–0.94), though not associated with dyspnea. Conclusions— For simplicity, we established 29 mm in men and 27 mm in women as sex-specific normative reference values for mPA and 0.9 for ratio PA.
Stable isotopes, ecological integration and environmental change: wolves record atmospheric carbon isotope trend better than tree rings

Large-scale patterns of isotope ratios are detectable in the tissues of organisms, but the variability in these patterns often obscures detection of environmental trends. We show that plants and animals at lower trophic levels are relatively poor indicators of the temporal trend in atmospheric carbon isotope ratios (δ13C) when compared with animals at higher trophic levels. First, we tested how differences in atmospheric δ13C values were transferred across three trophic levels. Second, we compared contemporary δ13C trends (1961–2004) in atmospheric CO2 to δ13C patterns in a tree species (jack pine, Pinus banksiana), large herbivore (moose, Alces alces) and large carnivore (grey wolf, Canis lupus) from North America. Third, we compared palaeontological (approx. 30 000 to 12 000 14C years before present) atmospheric CO2 trends to δ13C patterns in a tree species (Pinus flexilis, Juniperus sp.), a megaherbivore (bison, Bison antiquus) and a large carnivore (dire wolf, Canis dirus) from the La Brea tar pits (southern California, USA) and Great Basin (western USA). Contrary to previous expectations, we found that the environmental isotope pattern is better represented with increasing trophic level. Our results indicate that museum specimens of large carnivores would best reflect large-scale spatial and temporal patterns of carbon isotopes in the palaeontological record because top predators can act as ecological integrators of environmental change.
Ecosystem Carbon Stock Influenced by Plantation Practice: Implications for Planting Forests as a Measure of Climate Change Mitigation

Uncertainties remain in the potential of forest plantations to sequestrate carbon (C). We synthesized 86 experimental studies with paired-site design, using a meta-analysis approach, to quantify the differences in ecosystem C pools between plantations and their corresponding adjacent primary and secondary forests (natural forests). Totaled ecosystem C stock in plant and soil pools was 284 Mg C ha−1 in natural forests and decreased by 28% in plantations. In comparison with natural forests, plantations decreased aboveground net primary production, litterfall, and rate of soil respiration by 11, 34, and 32%, respectively. Fine root biomass, soil C concentration, and soil microbial C concentration decreased respectively by 66, 32, and 29% in plantations relative to natural forests. Soil available N, P and K concentrations were lower by 22, 20 and 26%, respectively, in plantations than in natural forests. The general pattern of decreased ecosystem C pools did not change between two different groups in relation to various factors: stand age (<25 years vs. ≥25 years), stand types (broadleaved vs. coniferous and deciduous vs. evergreen), tree species origin (native vs. exotic) of plantations, land-use history (afforestation vs. reforestation) and site preparation for plantations (unburnt vs. burnt), and study regions (tropic vs. temperate). The pattern also held true across geographic regions. Our findings argued against the replacement of natural forests by the plantations as a measure of climate change mitigation.
Measuring immersion and edutainment in multimedia cultural heritage applications

In our research we address the common and important problem of measuring users' experience in multimedia cultural heritage applications. Our objective is to develop a simple and efficient instrument capable to highlight both main qualities and major difficulties in using such applications for different types of users. We address specific objectives of usability for multimedia cultural heritage applications: immersion and edutainment. In addition to identifying best features and flaws, the results of measurement provide a tool for a comparison of different applications.