Miracle-dz/UniFAR-FTUs huggingface dataset:
Semiparametric Regression Analysis of Interval‐Censored Data

Summary. We propose a semiparametric approach to the proportional hazards regression analysis of interval‐censored data. An EM algorithm based on an approximate likelihood leads to an M‐step that involves maximizing a standard Cox partial likelihood to estimate regression coefficients and then using the Breslow estimator for the unknown baseline hazards. The E‐step takes a particularly simple form because all incomplete data appear as linear terms in the complete‐data log likelihood. The algorithm of Turnbull (1976, Journal of the Royal Statistical Society, Series B38, 290–295) is used to determine times at which the hazard can take positive mass. We found multiple imputation to yield an easily computed variance estimate that appears to be more reliable than asymptotic methods with small to moderately sized data sets. In the right‐censored survival setting, the approach reduces to the standard Cox proportional hazards analysis, while the algorithm reduces to the one suggested by Clayton and Cuzick (1985, Applied Statistics34, 148–156). The method is illustrated on data from the breast cancer cosmetics trial, previously analyzed by Finkelstein (1986, Biometrics42, 845–854) and several subsequent authors.
A deviation bound for α-dependent sequences with applications to intermittent maps

We prove a deviation bound for the maximum of partial sums of functions of α-dependent sequences as defined in Dedecker, Gouezel and Merlevede (2010). As a consequence, we extend the Rosenthal inequality of Rio (2000) for α-mixing sequences in the sense of Rosenblatt (1956) to the larger class of α-dependent sequences. Starting from the deviation inequality, we obtain upper bounds for large deviations and an Holderian invariance principle for the Donsker line. We illustrate our results through the example of intermittent maps of the interval, which are not α-mixing in the sense of Rosenblatt.
Classifying facial attributes using a 2-D Gabor wavelet representation and discriminant analysis

A method for automatically classifying facial images is proposed. Faces are represented using elastic graphs labelled with with 2D Gabor wavelet features. The system is trained from examples to classify faces on the basis of high-level attributes, such as sex, "race", and expression, using linear discriminant analysis (LDA). Use of the Gabor representation relaxes the requirement for precise normalization of the face: approximate registration of a facial graph is sufficient. LDA allows simple and rapid training from examples, as well as straightforward interpretation of the role of the input features for classification. The algorithm is tested on three different facial image datasets, one of which was acquired under relatively uncontrolled conditions, on tasks of sex, "race" and expression classification. Results of these tests are presented. The discriminant vectors may be interpreted in terms of the saliency of the input features for the different classification tasks, which we portray visually with feature saliency maps for node position as well as filter spatial frequency and orientation.
Serum Microarrays for Large Scale Screening of Protein Levels *S

There is a great need for comprehensive proteomic analysis of large patient cohorts of plasma and serum samples to identify biomarkers of human diseases. Here we describe a new antibody-based proteomic approach involving a reverse array format where serum samples are spotted on a microarray. This enables all samples to be screened for their content of a certain serum protein in a single experiment using target-recognizing antibodies and fluorescently labeled secondary antibodies. The procedure is illustrated with the analysis of the IgA levels in 2009 spotted serum samples, and the data are compared with clinical routine measurements. The results suggest that it is possible to simultaneously screen thousands of complex clinical serum samples for their content of the relative amount of specific serum proteins of clinical relevance.
Purification of DNA-binding proteins using tandem DNA-affinity column.

The development of DNA-affinity chromatography greatly facilitated purification of sequence-specific DNA-binding proteins (1). Here we describe a tandem DNA-affinity column that allows fast purification to homogeneity of sequence-specific DNAbinding proteins. We also describe a simple method for the synthesis and maintenance of DNA-affinity resins which enables the resins to be used repeatedly over extended periods of time with remarkable reliability. The first step in the purification scheme is an anion exchange chromatography. Fractions from the anion exchange column containing the sequence-specific DNA-binding protein are pooled, diluted in 50-100 ml binding buffer (25 mM NaCl, 5 mM Tris, 1.0 mM EDTA, 0.05% NP-40, pH = 7.5) and run by gravity at 0.5 -1 . 0 ml/min through a tandem DNA-affinity column which consists of 3 6 DNA-affinity modules connected in series. Each module contains 1 2 ml of DNA-affinity resins in 10 ml PolyPrep Chromatography columns (Bio-Rad Laboratories, Richmond, CA) overlayed with 4—6 ml buffer. The top 3—4 column modules contain DNA-affinity resin made up of agarose beads conjugated with double-stranded oligonucleotides containing DNA motif of interest with a mutation that eliminates sequence-specific binding. The bottom 1-2 modules contain beads with double stranded oligonucleotide containing the wildtype motif that specifically binds the protein to be purified. After running the load through the DNA-affinity column, modules containing the wild type DNA-resin are disconnected from the top modules containing the mutated DNA-resin. Sequencespecific DNA-binding proteins are simply eluted with buffer containing an appropriate salt concentration (0.2-1.0 M NaCl) after the module is washed with low salt buffer (25-200 mM NaCl).
Serum antibodies to periodontal pathogens and markers of systemic inflammation.

AIM We examined the relationship between serum antibodies against Porphyromonas gingivalis and Actinobacillus actinomycetemcomitans, and plasma fibrinogen and serum C-reactive protein (CRP) in a nationally representative sample. METHODS Data on 2,973 participants aged 40 years and older from the third National Health and Nutrition Examination Survey, second phase (1991-1994) were used. Three logistic regression models adjusted for gender, race, educational attainment, diabetes, cigarette smoking, body mass index (BMI), and other inflammatory conditions were constructed, based on three different assumptions: (A) no access to dental/periodontal data; (B) knowledge of number of teeth present but not of clinical periodontal status; and (C) knowledge of both dental and clinical periodontal status. RESULTS High fibrinogen (>400 mg/dl) was unrelated to P. gingivalis and A. actinomycetemcomitans antibodies in all models. High CRP (>0.4 mg/dl) was related to high antibody levels to P. gingivalis in models A [odds ratios (OR) 1.63, 95% confidence intervals (CI) 1.15-2.32], B (OR 1.69, 95% CI 1.18-2.41), and C (OR 1.58, 95% CI 1.12-2.23). In model C, high CRP was related to >30% extent of attachment loss of >or=3 mm (OR 1.58, 95% CI 1.19-2.08). Antibodies to A. actinomycetemcomitans were not associated with high CRP levels in any model. CONCLUSIONS High serum titre to P. gingivalis and the presence of periodontal disease are independently related to high CRP levels.
Interactive word cloud for analyzing reviews

A five-star quality rating is one of the most widely used systems for evaluating items. However, it has two fundamental limitations: 1) the rating for one item cannot describe crucial information in detail; 2) the rating is not on an absolute scale that can be used to compare items. Because of these limitations, users cannot make an optimal decision. In this paper, we introduce our sophisticated approach to extract useful information from user reviews using collapsed dependencies and sentiment analysis. We propose an interactive word cloud that can show grammatical relationships among words, explore reviews efficiently, and display positivity or negativity on a sentence. In addition, we introduce visualization for comparing multiple word clouds and illustrate the usage through test cases.
Bayesian nonparametric dependent model for partially replicated data: The influence of fuel spills on species diversity

We introduce a dependent Bayesian nonparametric model for the probabilistic modeling of membership of subgroups in a community based on partially replicated data. The focus here is on species-by-site data, i.e. community data where observations at different sites are classified in distinct species. Our aim is to study the impact of additional covariates, for instance environmental variables, on the data structure, and in particular on the community diversity. To that purpose, we introduce dependence a priori across the covariates, and show that it improves posterior inference. We use a dependent version of the Griffiths-Engen-McCloskey distribution defined via the stick-breaking construction. This distribution is obtained by transforming a Gaussian process whose covariance function controls the desired dependence. The resulting posterior distribution is sampled by Markov chain Monte Carlo. We illustrate the application of our model to a soil microbial dataset acquired across a hydrocarbon contamination gradient at the site of a fuel spill in Antarctica. This method allows for inference on a number of quantities of interest in ecotoxicology, such as diversity or effective concentrations, and is broadly applicable to the general problem of communities response to environmental variables.
Teaching for understanding/understanding for teaching.

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Assessment of in vivo fetal growth and placental vascular function in a novel intrauterine growth restriction model of progressive uterine artery occlusion in guinea pigs

Intrauterine growth restriction (IUGR) is associated with short‐ and long‐term detrimental cardiometabolic effects. Mice and rats are commonly used to assess IUGR, but differences in placental and fetal developmental physiology relative to those in humans highlight the need for alternative small animal IUGR models. We developed a guinea pig IUGR model by gradual occlusion of uterine arteries by ameroid constrictor implantation. In this model, reduced uterine blood flow was associated with IUGR, allowing in vivo assessment of fetal growth trajectory and umbilico‐placental vascular function in conscious animals. The intervention induces placental vascular dysfunction and remodelling, as well as altered fetal abdominal growth resulting in an asymmetric IUGR and preserved brain growth.
Silicon Integrated InGaAs/InAlAs/AlAs HBV Frequency Tripler

We present an integrated heterostructure barrier varactor frequency tripler on silicon substrate. The InGaAs/InAlAs/AlAs material structure is transferred onto the silicon wafer using low-temperature plasma-assisted bonding. The presented multiplier operates in the W-band (90-110 GHz). The module delivers 22.6 dBm, with a conversion loss of 6 dB, and 9% 3-dB bandwidth.
Development and validation of reversed phase highperformance liquid chromatographic method fordetermination of amlodipine

Purpose: To develop and validate a new sensitive and low-cost method for the analysis of amlodipine in tablet dosage form using reversed phase high performance liquid chromatography (RP-HPLC) with ultraviolet (UV) detection. Methods: Standards and samples were prepared by dissolving amlodipine besylate standard or amlodipine tablets in mobile phase and sonicated for 5 min. The samples were analysed by RP-HPLC equipped with quaternary pump and auto-injector. Separation was achieved using C18 column, and the mobile phase consisted of ammonium acetate buffer containing 0.02 % triethylamine TEA (pH = 4, adjusted using glacial acetic acid) and acetonitrile in the ratio 60:40 v/v. The flow rate was 1 ml/min and a UV detector was used for the detection of amlodipine at a wavelength of 248 nm. The method was validated according to International Conference of Harmonization (ICH) guidelines. Results: The retention time for amlodipine peak was 3.44 ± 0.41 min with a total run time of 6 min. The method was linear over the range of 0.5 - 40 μg/ml with coefficient of determination (R2) of 0.999. Recovery was 98.09 - 100.19 %, and the method showed high precision and repeatability. All validated parameters were within the range of ICH requirements. Conclusion: A new rapid sensitive and low-cost method has been developed and validated for the analysis of amlodipine in tablet dosage form.
Stability of dimeric interface in banana lectin: Insight from molecular dynamics simulations

Banana lectin (Banlec) is a homodimeric non‐glycosylated protein. It exhibits the β‐prism I structure. High‐temperature molecular dynamics simulations have been utilized to monitor and understand early stages of thermally induced unfolding of Banlec. The present study elucidates the behavior of the dimeric protein at four different temperatures and compares the structural and conformational changes to that of the minimized crystal structure. The process of unfolding was monitored by following the radius of gyration, the rms deviation of each residue, change in relative solvent accessibility and the pattern of inter‐ and intra‐subunit interactions. The overall study demonstrates that the Banlec dimer is a highly stable structure, and the stability is mostly contributed by interfacial interactions. It maintains its overall conformation during high‐temperature (400–500 K) simulations, with only the unstructured loop regions acquiring greater momentum under such condition. Nevertheless, at still higher temperatures (600 K) the tertiary structure is gradually lost which later extends to loss of secondary structural elements. The pattern of hydrogen bonding within the subunit and at the interface across different stages has been analyzed and has provided rationale for its intrinsic high stability. © 2009 IUBMB IUBMB Life 61(3): 252–260, 2009
Environmental factors and traits that drive plant litter decomposition do not determine home-fi eld advantage effects

decomposition do not determine home-field advantage effects G. F. (Ciska) Veen*, Maja K. Sundqvist and David A. Wardle Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-90183 Ume a, Sweden; Department of Terrestrial Ecology, Netherlands Institute of Ecology, PO Box 50, 6700 AB Wageningen, The Netherlands; Department of Ecology and Environmental Science, Ume a University, SE-901 87 Ume a, Sweden; and Center for Macroecology, Evolution and Climate, The Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen, Denmark
N-Acetylated Gemini Surfactants: Synthesis, Surface-Active Properties, Antifungal Activity, and Ecotoxicity Bioassays

A series of N-acetylated cationic gemini surfactants (3a-e) having dimeric structures derived from tertiary amines were synthesized. Their antifungal potency and surface properties were determined. It also studied the acute toxicity of the molecule with the best performance and the best water solubility (3e) through Chlorella vulgaris and Daphnia magna bioassays. The results were compared to those obtained for a commercially available reference compound 2-(thiocyanomethylthio) benzothiazole (TCMTB). Parameters such as surface tension (ϒCMC), critical micelle concentration (CMC), surface excess concentration (Γ), and area per molecule (A) were determined. The resulting values indicated that the five gemini surfactants are characterized by good surface-active and self-aggregation properties. All surfactants were tested to evaluate their antifungal activity. Six fungal strains were used to conduct the study. The minimum inhibitory concentration (MIC) value was measured by the fungal growth inhibition. The results of the MICs were compared with two commercially available reference compounds (Fluconazole and TCMTB). The least active molecule was 3e, but 3b and 3d were found to be the most potent compounds with a similar activity for all strains. Candida albicans was the most sensitive one. In contrast, Aspergillus niger was resistant. Ecotoxicity of gemini 3e was assessed: the commercial formulation (TCMTB) was between three and four orders of magnitude more toxic than the gemini one for the biological species tested.
Requirement of rapid Ca2+ entry and synaptic activation of metabotropic glutamate receptors for the induction of long‐term depression in adult rat hippocampus

1 During block of γ‐aminobutyric acid‐A‐mediated inhibition, low‐frequency stimulation (2 Hz, 900 pulses) to Schaffer collateral‐CA1 neuron synapses of adult rat hippocampus induced an N‐methyl‐D‐aspartate receptor‐independent, postsynaptic Ca2+‐dependent depression of synaptic strength (long‐term depression; LTD). 2 Ratio imaging with fura‐2 revealed moderate dendritic [Ca2+] increases (≈500 nM) during only the initial ≈30 s of the 7.5 min stimulation period. Conditioning for 30 s was, however, insufficient to induce LTD. 3 The [Ca2+] changes were insensitive to the metabotropic glutamate receptor (mGluR) antagonist (+)‐α‐methyl‐4‐carboxyphenylglycine (MCPG). MCPG, however, completely blocked LTD when present during conditioning. 4 The [Ca2+] changes were abolished by postsynaptic hyperpolarization (‐110 mV at the soma). Hyperpolarizing neurons to ‐110 mV during conditioning significantly attenuated LTD induction. 5 LTD induction was also blocked by the postsynaptic presence of the protein kinase C inhibitor peptide PKC(19‐36). 6 These results suggest that LTD induction in adult hippocampus by prolonged low‐frequency stimulation depends on both a rapid Ca2+ influx through voltage‐sensitive channels and synaptic stimulation of mGluRs which may be coupled to phospholipase C.
3-D Vector Flow Estimation With Row–Column-Addressed Arrays

Simulation and experimental results from 3-D vector flow estimations for a 62 + 62 2-D row-column (RC) array with integrated apodization are presented. A method for implementing a 3-D transverse oscillation (TO) velocity estimator on a 3-MHz RC array is developed and validated. First, a parametric simulation study is conducted, where flow direction, ensemble length, number of pulse cycles, steering angles, transmit/receive apodization, and TO apodization profiles and spacing are varied, to find the optimal parameter configuration. The performance of the estimator is evaluated with respect to relative mean bias B̃ and mean standard deviation σ. Second, the optimal parameter configuration is implemented on the prototype RC probe connected to the experimental ultrasound scanner SARUS. Results from measurements conducted in a flow-rig system containing a constant laminar flow and a straight-vessel phantom with a pulsating flow are presented. Both an M-mode and a steered transmit sequence are applied. The 3-D vector flow is estimated in the flow rig for four representative flow directions. In the setup with 90° beam-to-flow angle, the relative mean bias across the entire velocity profile is (-4.7, -0.9, 0.4)% with a relative standard deviation of (8.7, 5.1, 0.8)% for (Vx, Vy, Vz). The estimated peak velocity is 48.5 ± 3 cm/s giving a -3% bias. The out-of-plane velocity component perpendicular to the cross section is used to estimate volumetric flow rates in the flow rig at a 90° beam-to-flow angle. The estimated mean flow rate in this setup is 91.2 ± 3.1 L/h corresponding to a bias of -11.1%. In a pulsating flow setup, flow rate measured during five cycles is 2.3 ± 0.1 mL/stroke giving a negative 9.7% bias. It is concluded that accurate 3-D vector flow estimation can be obtained using a 2-D RC-addressed array.
Complete Genome Sequence of Burkholderia sp. Strain RPE64, Bacterial Symbiont of the Bean Bug Riptortus pedestris

ABSTRACT We isolated Burkholderia symbiont strain RPE64 from the bean bug Riptortus pedestris. Analysis of the complete 6.96-Mb genome, which consists of three chromosomes and two plasmids, will facilitate further understanding of insect–microbe symbiosis and the development of pest-control technologies.
The influence of hydrodynamic interactions on protein dynamics in confined and crowded spaces—assessment in simple models

We consider several systems that are confined within a softly repulsive sphere. The first one is a model protein, crambin, which is described by a structure-based coarse grained model. We demonstrate that the folding process is accelerated by the hydrodynamic interactions (HI) in a way that depends on the radius of the sphere. The tighter the encompassing sphere, the smaller the effect, independent of the nature of the starting conformations. The second system is a protein surrounded by protein-like softly repulsive spheres that make the confined space crowded. In this case, the HI shorten the folding times in a way which depends on the degree of crowdedness only weakly. The third system is a collection of spheres that are meant to represent molecules. We show that confinement increases association times. We also observe that the HI either facilitate or obstruct association of two spheres depending on the crowding conditions. The dependence of the association time on crowdedness in the confining sphere is qualitatively distinct from that derived by Wieczorek and Zielenkiewicz for a cube with the periodic boundary conditions.
Growth of MicroEnterprises : Empirical evidence from Ethiopia

The role of micro and small enterprises (MSEs) in employment and income generation is increasingly recognized and has become a major playing field for policy makers and donors with dual objective of enhancing growth and alleviating poverty. This study investigates some key determinants of success and particularly employment expansion among microenterprises based on a survey covering 974 randomly selected businesses in six major towns in Ethiopia. Empirical literature on MSEs growth is scant in the sub-Saharan Africa and the gap is even more evident when it comes to micro-enterprises. Growth of micro-enterprises measured in terms of employment since start is affected by a variety of factors. Firm’s initial size and age are inversely related with growth providing evidence that smaller and younger firms grow faster than larger and older firms and consistent with the learning hypothesis but contrary to the Gibrat’s law. Entrepreneurs with some business experience and high school complete and with some college years grow faster. Firms in manufacturing and service sectors, located at traditional market and those male-headed grow rapidly than their counterparts. Firms with business license also grow faster than those operating without license. In the absence of formal source of credit, informal networks such as, trade credit and other informal sources enhance business expansion. Policies and support programs that aim at promoting MSEs, therefore, need to take account of the heterogeneity nature of these enterprises and entrepreneurs. ---------------------------† The author is also a Research Associate at Department of Economics, Gothenburg University, Sweden. His email addresses are: mulu_yesus@yahoo.com or mulu.gebreeyesus@economics.gu. se