Miracle-dz/UniFAR-FTUs huggingface dataset:
Competing risks modeling of cumulative effects of time-varying drug exposures

An accurate assessment of drug safety or effectiveness in pharmaco-epidemiology requires defining an etiologically correct time-varying exposure model, which specifies how previous drug use affects the hazard of the event of interest. An additional challenge is to account for the multitude of mutually exclusive events that may be associated with the use of a given drug. To simultaneously address both challenges, we develop, and validate in simulations, a new approach that combines flexible modeling of the cumulative effects of time-varying exposures with competing risks methodology to separate the effects of the same drug exposure on different outcomes. To account for the dosage, duration and timing of past exposures, we rely on a spline-based weighted cumulative exposure modeling. We also propose likelihood ratio tests to test if the cumulative effects of past exposure on the hazards of the competing events are the same or different. Simulation results indicate that the estimated event-specific weight functions are reasonably accurate, and that the proposed tests have acceptable type I error rate and power. In real-life application, the proposed method indicated that recent use of antihypertensive drugs may reduce the risk of stroke but has no effect on the hazard of coronary heart disease events.
Force-induced on-rate switching and modulation by mutations in gain-of-function von Willebrand diseases

Significance Binding of von Willebrand factor (VWF) to platelets is regulated by hydrodynamic forces in the vasculature. VWF can sense force and can bind when the hydrodynamics change due to bleeding. We show that force application switches the A1 domain in VWF to a second state with faster on-rate for its binding partner on platelets, GPIbα. This provides a physiological mechanism for activating VWF binding to platelets at sites of bleeding. Moreover, force increases the effects of gain-of-function mutations found in von Willebrand disease (VWD) and platelet-type VWD by mechanically stabilizing bond formation and strength. Mutations in the ultralong vascular protein von Willebrand factor (VWF) cause the common human bleeding disorder, von Willebrand disease (VWD). The A1 domain in VWF binds to glycoprotein Ibα (GPIbα) on platelets, in a reaction triggered, in part, by alterations in flow during bleeding. Gain-of-function mutations in A1 and GPIbα in VWD suggest conformational regulation. We report that force application switches A1 and/or GPIbα to a second state with faster on-rate, providing a mechanism for activating VWF binding to platelets. Switching occurs near 10 pN, a force that also induces a state of the receptor−ligand complex with slower off-rate. Force greatly increases the effects of VWD mutations, explaining pathophysiology. Conversion of single molecule kon (s−1) to bulk phase kon (s−1M−1) and the kon and koff values extrapolated to zero force for the low-force pathways show remarkably good agreement with bulk-phase measurements.
Deposition of aerosol particles in human lungs: in vivo measurement and modelling

The deposition dose and site of inhaled particles within the lung are the key determinants in health risk assessment of particulate pollutants. Accurate dose estimation, however, is a formidable task because aerosol transport and deposition in the lung are governed by many factors whose precise workings are often not fully understood. In vivo human data obtained under controlled environment are most important and provide the primary basis of estimating lung doses. The existing database, however, is not sufficient to cover widely varying exposure conditions encountered during daily activities. Mathematical models thus are used to fill the gap or to extend the range of experimental data and are further used as a tool for analysing the exposure–dose relationship under varying inhalation conditions. In this report we briefly review and discuss our recent studies of in vivo measurement of inhaled particles in normal subjects, subsequent analysis of the data for empirical modelling and an improved mathematical model that can be used for a wide range of applications.
Development of Electroactive and Anaerobic Ammonium-Oxidizing (Anammox) Biofilms from Digestate in Microbial Fuel Cells

Microbial Fuel cells (MFCs) have been proposed for nutrient removal and energy recovery from different wastes. In this study the anaerobic digestate was used to feed H-type MFC reactors, one with a graphite anode preconditioned with Geobacter sulfurreducens and the other with an unconditioned graphite anode. The data demonstrate that the digestate acts as a carbon source, and even in the absence of anode preconditioning, electroactive bacteria colonise the anodic chamber, producing a maximum power density of 172.2 mW/m2. The carbon content was also reduced by up to 60%, while anaerobic ammonium oxidation (anammox) bacteria, which were found in the anodic compartment of the reactors, contributed to nitrogen removal from the digestate. Overall, these results demonstrate that MFCs can be used to recover anammox bacteria from natural sources, and it may represent a promising bioremediation unit in anaerobic digestor plants for the simultaneous nitrogen removal and electricity generation using digestate as substrate.
Verbal fields in Hungarian simple sentences and infinitival clausal complements

The paper presents an analysis of Hungarian sentence articulation driven by discourse-semantic functions such as topic and focus, hence the information structure of the utterance. In this paper extensions of the standard LTAG framework are proposed to represent the information structure driven positions in simple sentences. The elementary trees are generated by the meta-grammar, using the XMG tool for grammar writing. The verbal fields will also be investigated in complex sentences with infinitival clausal complements. I will discuss challenging phenomena, such as scrambling of the different verbal fields, and verbal modifier climbing.
The Effect of Vitamin C on Endothelial Function of Children with Type 1 Diabetes: An Experimental Study

Background: Considering the importance of improvement of endothelial function in patients with type 1 diabetes mellitus (DM) and to prevent its related micro- and macro-vascular complications; in this study, the effect of vitamin C administration on improving endothelial function of children with type 1 diabetes was investigated. Methods: In this analytic-experimental study, children with type 1 DM aged 6-18 years and a group of healthy children enrolled. Vitamin C (250 mg/daily) administrated for the two studied groups for 1-month. Endothelial function evaluated by flow-mediated dilatation (FMD) and intima-media thickness (IMT) measurement using vascular Doppler ultrasonography, before and after trial. Results: In this study, 18 patients with type 1 diabetes (DM) and 19 normal children as the control group were studied. After vitamin C administration IMT reduced in all studied groups (P < 0.05). FMD increased in all studied groups, but it was significant only in the control group (P = 0.02 in the control group and P = 0.07 in patients with DM). Mean differences of IMT 2 – IMT 1, FMD 2 – FMD 1 and left ventricular (LV) mass 2 – LV mass 1 and blood pressure (BP) were not significantly different in two studied groups (P > 0.05). Mean differences of IMT 2 – IMT 1, FMD 2 – FMD 1, LV mass 2 – LV mass 1 and BP were not significantly different in patients with HbA1c ≤ 7 g/dl and those with HbA1c >7 g/dl and control group (P > 0.05). Conclusions: The findings of the current study indicated that vitamin C may have a protective effect on endothelial dysfunction, but regarding its effectiveness among the high-risk population such as diabetic patients with and without appropriate glycemic control the study was not sufficiently powered due to its small sample size.
Differential Alterations of Dopamine Transporter in the Striatum and Midbrain in Patients With Parkinsonian Syndrome

Objectives Differential vulnerabilities of subregional dopamine neurons have been suggested in movement disorders such as idiopathic Parkinson disease. In this study, we examined dopamine transporter (DaT) density in the striatum versus midbrain (MB) in patients with nigrostriatal denervation. Methods Brain SPECT was performed in 39 patients with parkinsonian syndrome (age 61 ± 15 years, 18 male patients) 4 hours after IV injection of 3 to 5 mCi 123I ioflupane using SPECT-CT acquisition. Images were reconstructed using OSEM with resolution recovery and correction for scatter and attenuation based on a low-dose CT. Peak pixel counts within the caudate head (CA), mid putamen (PT), and MB localized by sagittal CT, as well as averaged counts around the calcarine fissure as reference, were determined by region-of-interest analysis. Semiquantitative DaT values were expressed as CA, PT, or MB uptake relative to the reference. We then assessed the relationship between the MB measurements and independent clinical evaluation of motor symptoms in these patients. Results Averaged striatal DaT values for both hemispheres ranged from 1.67 to 6.59 for CA, 1.50 to 5.33 for PT, and 1.08 to 2.24 for MB. Within the high striatal DaT group (mean, 4.76 [SD, 0.55]) and low DaT group (mean, 2.71 [SD, 0.58]; dichotomy defined as a threshold of 4), mean DaT values in MB were 1.68 (SD, 0.32) and 1.53 (SD, 0.29), respectively, indicating nonsignificant 9% decrease (P > 0.15) in comparison to 43% decrease in the averaged striatal uptake. Within the high striatal DaT group, Pearson correlations between DaT values of CA and PT versus MB were highly significant at 0.81 and 0.82 (P ⩽ 0.001), respectively, but those correlations were not significant, 0.35 (P > 0.05) and 0.06 (P > 0.75), in the low striatal DaT group. Midbrain uptake measurements did not correlate with motor symptoms (bradykinesia, tremor, rigidity, and postural instability). Conclusions These findings indicate that reductions in DaT values in the striatum and MB are not necessarily simultaneous with the process of nigrostriatal denervation, and correlation of DaT values among CA/PT and MB becomes weaker as the denervation becomes more severe. Differential regional DaT loss may indicate differential vulnerability of DaT-containing neurons in these structures or could be in part related to tracer binding to non-DaT targets.
Building a Better Mousetrap

Routers in the network core are unable to maintain detailed statistics for every packet; thus, traffic statistics are often based on packet sampling, which reduces accuracy. Because tracking large (“heavy-hitter”) traffic flows is important both for pricing and for traffic engineering, much attention has focused on maintaining accurate statistics for such flows, often at the expense of small-volume flows. Eradicating these smaller flows makes it difficult to observe communication structure, which is sometimes more important than maintaining statistics about flow sizes. This paper presents FlexSample, a sampling framework that allows network operators to get the best of both worlds: For a fixed sampling budget, FlexSample can capture significantly more small-volume flows for only a small increase in relative error of large traffic flows. FlexSample uses a fast, lightweight counter array that provides a coarse estimate of the size (“class”) of each traffic flow; a router then can sample at different rates according to the class of the traffic using any existing sampling strategy. Given a fixed sampling rate and a target fraction of sampled packets to allocate across traffic classes, FlexSample computes packet sampling rates for each class that achieve these allocations online. Through analysis and trace-based experiments, we find that FlexSample captures at least 50% more mouse flows than strategies that do not perform class-dependent packet sampling. We also show how FlexSample can be used to capture unique flows for specific applications.
A Novel Approach for Allocating Mathematical Expressions to Visual Speech Signals

In this article, visual speech information modeling analysis by explicit mathematical expressions coupled with words’ phonemic structure is presented. The visual information is obtained from deformation of lips’ dimensions during articulation of a set of words that is called visual speech sample set. The continuous interpretation of the lips’ movement has been provided using Barycentric Lagrange Interpolation producing a unique mathematical expression named visual speech signal. Hierarchical analysis of the phoneme sequences has been applied for words’ categorization to organize the database properly. The visual samples were extracted from three visual feature points chosen on the lips via an experiment in which two individuals pronounced the aforementioned words. The simulation results show that each individual word can be represented by a mathematical expression or visual speech signal whereas the sample sets can also be derived from the same mathematical expression, and this is a significant improvement over the popular statistical methods.
Gene Entity Recognition of Full Text Articles

Biomedical scientific literature is an unexploited treasure. Due to the staggering number of publications it is literally intractable to gather manually all information. Automatized information extraction (IE) is therefore key. An important subtask is the recognition of names in the text as specific entities (named entity recognition, NER). NER for genes in biomedical literature is a challenging task. This paper reports preliminary results for the identification of gene names in full text with the naive Bayes, support vector machine and random forest algorithms, showing that there is no loss on performance compared to the gene NER restricted to abstracts.
Novel method of generation of Ca(HCO 3 ) 2 and CaCO 3 aerosols and first determination of hygroscopic and cloud condensation nuclei activation properties

Abstract. Atmospheric mineral aerosols contain CaCO3 as a reactive component. A novel method to produce CaCO3 aerosol was developed by spraying Ca(HCO3)2 solution, which was generated from a CaCO3 suspension and CO2. By aerosol mass spectrometry the freshly sprayed and dried aerosol was characterized to consist of pure Ca(HCO3)2 which under annealing in a tube furnace transformed into CaCO3. Transmission Electron Microscopy demonstrated that the particles produced were spherical. The method was able to generate aerosol of sufficient concentration and proper size for the study of physiochemical properties and investigations of heterogeneous reactions of mineral aerosol. The dried Ca(HCO3)2 particles were somewhat more hygroscopic than CaCO3 particles. However, during humidification a restructuring took place and ∼2/3 of the Ca(HCO3)2 was transformed to CaCO3. The mixed Ca(HCO3)2/CaCO3(s) particles were insoluble with a growth factor of 1.03 at 95% (hygroscopicity parameter κ=0.011±0.007) relative humidity. This compares to a corresponding growth factor of 1.01 for CaCO3(s) (κ=0.0016±0.0004). Mass spectrometric composition analysis, restructuring, and insolubility of the mixed particles suggested that solid Ca(HCO3)2(s) was observed. This would be in contrast to the current belief that Ca(HCO3)2(s) is thermodynamically instable. The CCN activity of Ca(HCO3)2(s) aerosol (κ≈0.15) is remarkably higher than that of CaCO3 aerosol (κ=0.0019±0.0007) and less than that of Ca(NO3)2. The noticeable but limited solubility of Ca(HCO3)2 of ≈0.01 mol/l explains limited hygroscopic growth and good CCN activity. Experiments in the Large Julich Aerosol Chamber indicated that Ca(HCO3)2(s) could exist for several hours under dry atmospheric conditions. However, it was likely buried in a protective layer of CaCO3(s). We conclude that Ca(HCO3)2 may be formed in the atmosphere in cloud droplets of activated mineral dust by reaction of CaCO3 with CO2 and H2O. The presence of Ca(HCO3)2 and as a consequence an enhanced CCN activity may alter the influence of mineral aerosol on global climate.
Content analysis of students’ journals in a percussion methods course

This article presents an empirical investigation of music education students’ journals within a percussion methods course at a Midwestern university in the United States. The findings of this investigation raise issues about music education students’ sense of self-awareness, specificity within the journals, and the predominance of discussions about concrete (e.g., technique) over abstract (e.g., musicianship) aspects of the course. The issues are discussed from a variety of perspectives, including a discussion of the potential shortcomings of verbal thinking within a music education course. Implications are offered regarding the design and pedagogy of music education courses.
Hrs recruits clathrin to early endosomes

The hepatocyte growth factor‐regulated tyrosine kinase substrate, Hrs, has been implicated in intracellular trafficking and signal transduction. Hrs contains a phosphatidylinositol 3‐phosphate‐binding FYVE domain that contributes to its endosomal targeting. Here we show that Hrs and EEA1, a FYVE domain protein involved in endocytic membrane fusion, are localized to different regions of early endosomes. We demonstrate that Hrs co‐localizes with clathrin, and that the C‐terminus of Hrs contains a functional clathrin box motif that interacts directly with the terminal β‐propeller domain of clathrin heavy chain. A massive recruitment of clathrin to early endosomes was observed in cells transfected with Hrs, but not with Hrs lacking the C‐terminus. Furthermore, the phosphatidylinositol 3‐kinase inhibitor wortmannin caused the dissociation of both Hrs and clathrin from endosomes. While overexpression of Hrs did not affect endocytosis and recycling of transferrin, endocytosed epidermal growth factor and dextran were retained in early endosomes. These results provide a molecular mechanism for the recruitment of clathrin onto early endosomes and suggest a function for Hrs in trafficking from early to late endosomes.
Cardiovascular events increased at normal and high-normal blood pressure in young and middle-aged Japanese male smokers but not in nonsmokers

Objective: To clarify whether the impact of normal and high-normal BP (BP) per se on cardiovascular disease (CVD) and all-cause death differs depending on smoking status. Methods and results: A prospective observational cohort study (median follow-up period: 7.5 years) was performed among 25 077 healthy nondiabetic Japanese men aged 20–61 years (mean age 37.3 years), whose BP was less than 150/95 mmHg and who were not on medication. Hazard ratios (HRs), adjusted by known risk factors and a change in annual BP during the follow-up, were calculated by the Cox proportional model with less than 119/75 mmHg as a reference. Among smokers, CVD events increased significantly from a SBP of 120 mmHg, with HRs of 2.68 (120–129 mmHg), 4.28 (130–139 mmHg), and 11.7 (140–149 mmHg). The CVD events also increased from a DBP of 75 mmHg (P for trend less than 0.0001), with 75–79 mmHg and 90–94 mmHg considered statistically significant. Among noncurrent smokers, 110–149 mmHg (SBP) and 75–89 mmHg (DBP) were not associated with elevated HRs for CVD. The relation between BP and all-cause mortality was similar among both current and noncurrent smokers: 140–149 mmHg (SBP) and 90–94 mmHg (DBP) were significantly associated with elevated risk, and 130–139 mmHg (SBP) among noncurrent smokers associated with elevated risk. Conclusion: Young and middle-aged healthy Japanese individuals with normal and high-normal BP (120–139/75–89 mmHg) were at risk for CVD among smokers, even after adjusting for an annual change in BP.
Spatial and Temporal Dynamics of Stink Bugs in Southeastern Farmscapes

ABSTRACT. A 3-yr study (2009–2011) was conducted to examine the spatial and temporal dynamics of stink bugs in three commercial farmscapes. Study locations were replicated in South Carolina and Georgia, in an agriculturally diverse region known as the southeastern coastal plain. Crops included wheat, Triticum aestivum (L.), corn, Zea mays (L.), soybean, Glycine max (L.), cotton, Gossypium hirsutum (L.), and peanut, Arachis hypogaea (L.). Farmscapes were sampled weekly using whole-plant examinations for corn, with all other crops sampled using sweep nets. The predominant pest species of phytophagous stink bugs were the brown stink bug, Euschistus servus (Say), the green stink bug, Chinavia hilaris (Say), and the southern green stink bug, Nezara viridula (L.). Chi-square tests indicated a departure from a normal distribution in 77% of analyses of the variance to mean ratio, with 37% of slopes of Taylor's power law and 30% of coefficient &bgr; of Iwao's patchiness regression significantly greater than one, indicating aggregated distributions. Spatial Analyses by Distance IndicEs (SADIE) indicated aggregated patterns of stink bugs in 18% of year-end totals and 42% of weekly counts, with 80% of adults and nymphs positively associated using the SADIE association tool. Maximum stink bug densities in each crop occurred when the plants were producing fruit. Stink bugs exhibited greater densities in crops adjacent to soybean in Barnwell and Lee Counties compared with crops adjacent to corn or fallow areas. The diversity of crops and relatively small size of fields in the Southeast leads to colonization of patches within a farmscape. The ecological and management implications of the spatial and temporal distribution of stink bugs within farmscapes are discussed.
Modeling Sequential Domain Shift through Estimation of Optimal Sub-spaces for Categorization

Domain adaptation (DA) is the process in which labeled training samples available from one domain is used to improve the performance of statistical tasks performed on test samples drawn from a different domain. The domain from which the training samples are obtained is termed as the source domain, and the counterpart consisting of the test samples is termed as the target domain. Few unlabeled training samples are also taken from the target domain in order to approximate its distribution. In this paper, we propose a new method of unsupervised DA, where a set of domain invariant sub-spaces are estimated using the geometrical and statistical properties of the source and target domains. This is a modification of the work done by Gopalan et al. [2], where the geodesic path from the principal components of the source to that of the target is considered in the Grassmann manifold, and the intermediary points are sampled to represent the incremental change in the geometric properties of the data in source and target domains. Instead of the geodesic path, we consider an alternate path of shortest length between the principal components of source and target, with the property that the intermediary sample points on the path form domain invariant sub-spaces using the concept of Maximum Mean Discrepancy (MMD) [3]. Thus we model the change in the geometric properties of data in both the domains sequentially, in a manner such that the distributions of projected data from both the domains always remain similar along the path. The entire formulation is done in the kernel space which makes it more robust to non-linear transformations. Let X and Y be the source and target domains having nX and nY number of instances respectively. If Φ(.) is a universal kernel function, then in kernel space the source and target domains are Φ(X) ∈ RnX×d and Φ(Y ) ∈ RnX×d respectively. Let KXX and KYY be the kernel gram matrices of Φ(X) and Φ(Y ) respectively. Let D = [X ;Y ] denote the combined source and target domain data, and the corresponding data in kernel space is given as Φ(D). The kernel gram matrix formed using D is given by