Miracle-dz/UniFAR-FTUs huggingface dataset:
Syringeal Specialization of Frequency Control during Song Production in the Bengalese Finch (Lonchura striata domestica)

Background Singing in songbirds is a complex, learned behavior which shares many parallels with human speech. The avian vocal organ (syrinx) has two potential sound sources, and each sound generator is under unilateral, ipsilateral neural control. Different songbird species vary in their use of bilateral or unilateral phonation (lateralized sound production) and rapid switching between left and right sound generation (interhemispheric switching of motor control). Bengalese finches (Lonchura striata domestica) have received considerable attention, because they rapidly modify their song in response to manipulations of auditory feedback. However, how the left and right sides of the syrinx contribute to acoustic control of song has not been studied. Methodology Three manipulations of lateralized syringeal control of sound production were conducted. First, unilateral syringeal muscular control was eliminated by resection of the left or right tracheosyringeal portion of the hypoglossal nerve, which provides neuromuscular innervation of the syrinx. Spectral and temporal features of song were compared before and after lateralized nerve injury. In a second experiment, either the left or right sound source was devoiced to confirm the role of each sound generator in the control of acoustic phonology. Third, air pressure was recorded before and after unilateral denervation to enable quantification of acoustic change within individual syllables following lateralized nerve resection. Significance These experiments demonstrate that the left sound source produces louder, higher frequency, lower entropy sounds, and the right sound generator produces lower amplitude, lower frequency, higher entropy sounds. The bilateral division of labor is complex and the frequency specialization is the opposite pattern observed in most songbirds. Further, there is evidence for rapid interhemispheric switching during song production. Lateralized control of song production in Bengalese finches may enhance acoustic complexity of song and facilitate the rapid modification of sound production following manipulations of auditory feedback.
A Paracrine Loop Between Adipocytes and Macrophages Aggravates Inflammatory Changes: Role of Free Fatty Acids and Tumor Necrosis Factor α

Objective—Weight gain is associated with infiltration of fat by macrophages, suggesting that they are an important source of inflammation in obese adipose tissue. Here we developed an in vitro coculture system composed of adipocytes and macrophages and examined the molecular mechanism whereby these cells communicate. Methods and Results—Coculture of differentiated 3T3-L1 adipocytes and macrophage cell line RAW264 results in the marked upregulation of proinflammatory cytokines, such as tumor necrosis factor α (TNF-α), and the downregulation of the antiinflammatory cytokine adiponectin. Such inflammatory changes are induced by the coculture without direct contact, suggesting the role of soluble factors. A neutralizing antibody to TNF-α, which occurs mostly in macrophages, inhibits the inflammatory changes in 3T3-L1, suggesting that TNF-α is a major macrophage-derived mediator of inflammation in adipocytes. Conversely, free fatty acids (FFAs) may be important adipocyte-derived mediators of inflammation in macrophages, because the production of TNF-α in RAW264 is markedly increased by palmitate, a major FFA released from 3T3-L1. The inflammatory changes in the coculture are augmented by use of either hypertrophied 3T3-L1 or adipose stromal vascular fraction obtained from obese ob/ob mice. Conclusions—We postulate that a paracrine loop involving FFAs and TNF-α between adipocytes and macrophages establishes a vicious cycle that aggravates inflammatory changes in the adipose tissue.
Characterization of Metacaspases with Trypsin-Like Activity and Their Putative Role in Programmed Cell Death in the Protozoan Parasite Leishmania

ABSTRACT In this report, we have characterized two metacaspases of Leishmania donovani, L. donovani metacaspase-1 (LdMC1) and LdMC2. These two proteins show 98% homology with each other, and both contain a characteristic C-terminal proline-rich domain. Both genes are transcribed in promastigotes and axenic amastigotes of L. donovani; however, LdMC1 shows increased mRNA levels in axenic amastigotes. An anti-LdMC antibody was obtained and showed reactivity with a single ∼42-kDa protein band in both promastigote and axenic amastigote parasite whole-cell lysates by Western blotting. Pulse-chase experiments suggest that LdMCs are not synthesized as proenzymes, and immunofluorescence studies show that LdMCs are associated with the acidocalcisome compartments of L. donovani. Enzymatic assays of immunoprecipitated LdMCs show that native LdMCs efficiently cleave trypsin substrates and are unable to cleave caspase-specific substrates. Consistently, LdMC activity is insensitive to caspase inhibitors and is efficiently inhibited by trypsin inhibitors, such as leupeptin, antipain, and Nα-tosyl-l-lysine-chloromethyl ketone (TLCK). In addition, our results show that LdMC activity was induced in parasites treated with hydrogen peroxide, a known trigger of programmed cell death (PCD) in Leishmania and that parasites overexpressing metacaspases are more sensitive to hydrogen peroxide-induced PCD. These findings suggest that Leishmania metacaspases are not responsible for the caspase-like activities reported in this organism and suggest a possible role for LdMCs as effector molecules in Leishmania PCD.
Estimating Terms of Trade Levels

This paper exploits bilateral product-level trade for a wide range of OECD countries to derive export and import PPPs and terms of trade levels. This is based on a hedonic regression model in which a product is characterized by the location of both the buyer and seller. Relative price levels of imports and exports are significantly different from one in most countries, confirming the widespread existence of barriers to arbitrage. Richer countries appear to benefit from higher terms of trade. JEL classification: C82, E31 and F19 Acknowledgements: We were lucky to benefit from outstanding statistical assistance by Ton van Moergastel and Robert Inklaar, which is gratefully acknowledged. We also wish to thank participants at workshops at the University of Groningen and University of California, Davis, in particular Bettina Aten, Erwin Diewert, Robert Feenstra and Prasada Rao for helpful discussions. * Corresponding author: Marcel P. Timmer, Faculty of Economics, University of Groningen, PO Box 800, 9700 AV Groningen, The Netherlands, tel. : 050-363 3653, fax: 050-363 7337, E-mail: m.p.timmer@eco.rug. nl
Endothelial Differentiation of Human Stem Cells Seeded onto Electrospun Polyhydroxybutyrate/Polyhydroxybutyrate-Co-Hydroxyvalerate Fiber Mesh

Tissue engineering is based on the association of cultured cells with structural matrices and the incorporation of signaling molecules for inducing tissue regeneration. Despite its enormous potential, tissue engineering faces a major challenge concerning the maintenance of cell viability after the implantation of the constructs. The lack of a functional vasculature within the implant compromises the delivery of nutrients to and removal of metabolites from the cells, which can lead to implant failure. In this sense, our investigation aims to develop a new strategy for enhancing vascularization in tissue engineering constructs. This study's aim was to establish a culture of human adipose tissue-derived stem cells (hASCs) to evaluate the biocompatibility of electrospun fiber mesh made of polyhydroxybutyrate (PHB) and its copolymer poly-3-hydroxybutyrate-co-3-hydroxyvalerate (PHB-HV) and to promote the differentiation of hASCs into the endothelial lineage. Fiber mesh was produced by blending 30% PHB with 70% PHB-HV and its physical characterization was conducted using scanning electron microscopy analysis (SEM). Using electrospinning, fiber mesh was obtained with diameters ranging 300 nm to 1.3 µm. To assess the biological performance, hASCs were extracted, cultured, characterized by flow cytometry, expanded and seeded onto electrospun PHB/PHB-HV fiber mesh. Various aspects of the cells were analyzed in vitro using SEM, MTT assay and Calcein-AM staining. The in vitro evaluation demonstrated good adhesion and a normal morphology of the hASCs. After 7, 14 and 21 days of seeding hASCs onto electrospun PHB/PHB-HV fiber mesh, the cells remained viable and proliferative. Moreover, when cultured with endothelial differentiation medium (i.e., medium containing VEGF and bFGF), the hASCs expressed endothelial markers such as VE-Cadherin and the vWF factor. Therefore, the electrospun PHB/PHB-HV fiber mesh appears to be a suitable material that can be used in combination with endothelial-differentiated cells to improve vascularization in engineered bone tissues.
Probing metabolite diffusion at ultra‐short time scales in the mouse brain using optimized oscillating gradients and “short”‐echo‐time diffusion‐weighted MRS

Measuring diffusion at ultra‐short time scales may yield information about short‐range intracellular structure and cytosol viscosity. However, reaching such time scales usually requires oscillating gradients, which in turn imply long echo times TE. Here we propose a new kind of stretched oscillating gradient that allows us to increase diffusion‐weighting b while preserving spectral and temporal properties of the gradient modulation. We used these optimized gradients to measure metabolite diffusion in the mouse brain down to effective diffusion times of 1 ms while keeping TE relatively short (60 ms). At such TE, a significant macromolecule signal could still be observed and used as an internal reference of approximately null diffusivity, which proved critical to discard datasets corrupted by some motion artifact. The methods introduced here may be useful to improve the accuracy and precision of metabolite apparent diffusion coefficient measurements with oscillating gradients.
Decoding fingerprints using the Markov Chain Monte Carlo method

This paper proposes a new fingerprinting decoder based on the Markov Chain Monte Carlo (MCMC) method. A Gibbs sampler generates groups of users according to the posterior probability that these users could have forged the sequence extracted from the pirated content. The marginal probability that a given user pertains to the collusion is then estimated by a Monte Carlo method. The users having the biggest empirical marginal probabilities are accused. This MCMC method can decode any type of fingerprinting codes. This paper is in the spirit of the `Learn and Match' decoding strategy: it assumes that the collusion attack belongs to a family of models. The Expectation-Maximization algorithm estimates the parameters of the collusion model from the extracted sequence. This part of the algorithm is described for the binary Tardos code and with the exploitation of the soft outputs of the watermarking decoder. The experimental body considers some extreme setups where the fingerprinting code lengths are very small. It reveals that the weak link of our approach is the estimation part. This is a clear warning to the `Learn and Match' decoding strategy.
Role of Growth Hormone Deficiency and Treatment in Chronic Kidney Disease

Malnutrition and inflammation are strong predictors of mortality in advanced kidney disease, especially in patients on renal replacement therapy. The complex relationship between kidney disease, uremia, and malnutrition significantly contributes to the increased morbidity and mortality in this patient population potentially through a relative deficiency in growth hormone (GH). With an approximate 26 million Americans currently affected by some stage of chronic kidney disease and a predicted 750,000 people to be on dialysis by 2020, there is a need to develop innovative strategies aimed at reducing the high mortality seen in dialysis patients. We will review evidence on one such intervention with infusion of recombinant GH to improve the nutritional and inflammatory state, thereby expecting to improve the mortality and morbidity in this patient population.
LeafletAnalyzer, an Automated Software for Quantifying, Comparing and Classifying Blade and Serration Features of Compound Leaves during Development, and among Induced Mutants and Natural Variants in the Legume Medicago truncatula

Diverse leaf forms ranging from simple to compound leaves are found in plants. It is known that the final leaf size and shape vary greatly in response to developmental and environmental changes. However, changes in leaf size and shape have been quantitatively characterized only in a limited number of species. Here, we report development of LeafletAnalyzer, an automated image analysis and classification software to analyze and classify blade and serration characteristics of trifoliate leaves in Medicago truncatula. The software processes high quality leaf images in an automated or manual fashion to generate size and shape parameters for both blades and serrations. In addition, it generates spectral components for each leaflets using elliptic Fourier transformation. Reconstruction studies show that the spectral components can be reliably used to rebuild the original leaflet images, with low, and middle and high frequency spectral components corresponding to the outline and serration of leaflets, respectively. The software uses artificial neutral network or k-means classification method to classify leaflet groups that are developed either on successive nodes of stems within a genotype or among genotypes such as natural variants and developmental mutants. The automated feature of the software allows analysis of thousands of leaf samples within a short period of time, thus facilitating identification, comparison and classification of leaf groups based on leaflet size, shape and tooth features during leaf development, and among induced mutants and natural variants.
Cerebral oxygen uptake in chronic schizophrenic reaction.

Since Kety and associates 1 reported that the cerebral blood flow (CBF) and cerebral metabolic rate for oxygen (CMR o2 ) are normal in schizophrenia, patients with this disorder have commonly been used as "normal subjects" for cerebral metabolic studies. In the course of such studies we have noted unusually low values for CMR o2 in approximately one-third of patients with chronic schizophrenic reactions. Using the original nitrous oxide technique of Kety and Schmidt,* we have made 29 determinations of CBF and CMR o2 upon 24 patients with chronic schizophrenic reactions of two or more years' duration and have compared these with the rates in 81 control cases. The experimental group consisted of 11 men and 13 women from 16 to 66 years of age, with an average age of 36 years. In these subjects the onset of clearly recognizable schizophrenic reactions had occurred from 2½ to 23 years prior to
The Major Subunit, CfaB, of Colonization Factor Antigen I from Enterotoxigenic Escherichia coli Is a Glycosphingolipid Binding Protein

ABSTRACT Bacterial adherence to mucosal surfaces is an important virulence trait of pathogenic bacteria. Adhesion of enterotoxigenic Escherichia coli (ETEC) to the intestine is mediated by a number of antigenically distinct colonization factors (CFs). One of the most common CFs is CFA/I. This has a fimbrial structure composed of a major repeating subunit, CfaB, and a single tip subunit, CfaE. The potential carbohydrate recognition by CFA/I was investigated by binding CFA/I-fimbriated bacteria and purified CFA/I fimbriae to a large number of variant glycosphingolipids separated on thin-layer chromatograms. For both fimbriated bacteria and purified fimbriae, specific interactions could be identified with a number of nonacid glycosphingolipids. These included glucosylceramide, lactosylceramide with phytosphingosine and/or hydroxy fatty acids, neolactotetraosylceramide, gangliotriaosylceramide, gangliotetraosylceramide, the H5 type 2 pentaglycosylceramide, the Lea-5 glycosphingolipid, the Lex-5 glycosphingolipid, and the Ley-6 glycosphingolipid. These glycosphingolipids were also recognized by recombinant E. coli expressing CFA/I in the absence of tip protein CfaE, as well as by purified fimbriae from the same strain. This demonstrates that the glycosphingolipid-binding capacity of CFA/I resides in the major CfaB subunit.
Hardware-in-the-Loop Simulation of Power Electronic Systems Using Adaptive Discretization

This paper presents the hardware-in-the-loop (HIL) simulation of power electronic systems using a unique adaptive discretization technique based on the input of the system, where the coefficient matrices and system equations are changed while the simulation is running. The voltage-source-converter (VSC)-based HVDC system is used as a case study. Two z-transform-based discretization techniques, known as the step-invariant transformation (SIT) and the ramp-invariant transformation, and one of their derivative time-shifted SIT are applied for simulating the VSC-HVDC system. Discrete switching synchronization algorithms are used to accommodate the asynchronous events that take place in between two discrete simulation points. The HIL simulation is implemented using an off-the-shelf PC cluster interfaced with a digital controller. The simulator and the controller are connected through I/O ports, which facilitate the exchange of analog and digital signals. A 4-kW VSC-HVDC experimental setup is used to validate the simulation results, using the same digital controller as that in the HIL simulation to supply the necessary gate pulses for the experimental VSCs. A comparative study of the results obtained through offline, HIL simulation, and the experiment is presented.
Scale Mixtures of Gaussians and the Statistics of Natural Images

The statistics of photographic images, when represented using multiscale (wavelet) bases, exhibit two striking types of non-Gaussian behavior. First, the marginal densities of the coefficients have extended heavy tails. Second, the joint densities exhibit variance dependencies not captured by second-order models. We examine properties of the class of Gaussian scale mixtures, and show that these densities can accurately characterize both the marginal and joint distributions of natural image wavelet coefficients. This class of model suggests a Markov structure, in which wavelet coefficients are linked by hidden scaling variables corresponding to local image structure. We derive an estimator for these hidden variables, and show that a nonlinear "normalization" procedure can be used to Gaussianize the coefficients.
Micro artificial muscle fiber using NiTi spring for soft robotics

For a new class of soft robotic platforms, development of flexible and robust actuators is quintessential. Remarkable resilience, shape memory effect, high energy density, and scalability are attributed to nickel titanium (NiTi) making it an excellent actuator candidate for meso-scale applications. This paper presents a micro-muscle fiber crafted from shape memory alloy (NiTi) coiled springs. An enhanced spring NiTi model describes the combination of martensite deformation and spring effect due to its geometry. This paper also describes a manufacturing process and characterization for micro-scale NiTi coil actuators in various annealing temperatures. The presented fiber is 400µm in diameter and 0.5m in length exhibiting 50% contraction and 1226J/kg of energy density with 40g of force. By changing the geometry of the spring, force-displacement characteristics can be tuned. An enhanced-performance inverted-spring manufacturing method is also described and characterized. A method of discrete displacement control is presented. Taking advantage of the flexibility of micro-coil spring, we present a novel mesh-worm prototype that utilizes bio-inspired antagonistic actuation for its body deformation and locomotion.
Consumption of Meat, Animal Products, Protein, and Fat and Risk of Breast Cancer: A Prospective Cohort Study in New York

Epidemiologic studies have focused on the association between diet and breast cancer with conflicting results. Whereas a majority of case-control studies indicate a role for the intake of total fat and saturated fat, most prospective cohort studies either are negative or indicate very modest associations. Only a few authors have examined the role of meat intake in relation to breast cancer risk. The aim of this study was to examine the relation between risk of breast cancer and dietary intake of meat, animal products, fat, and protein. Between 1985 and 1991, we recruited 14,291 New York City women in a prospective cohort study of endogenous hormones, diet, and cancer in which they reported on their recent diet using a food frequency questionnaire self-administered at enrollment. From the cohort, 180 invasive breast cancer cases diagnosed before December 1990 and five times as many controls, individually matched by age, calendar time at enrollment, menopausal status, and, if premenopausal, phase of menstrual cycle, were included in a nested case-control study. There was an evident increase in the relative risk (RR) of breast cancer for increasing consumption of meat. Women in the upper quintile of meat consumption, as compared with the lowest quintile, had an energy-adjusted RR of 1.87 (95% confidence interval = 1.09–3.21). There was a modest RR increase in the upper quintile of total and saturated fat and no apparent association for other types of fat, protein, dairy products, poultry, or fish. The study indicates that the elevated consumption of certain foods of animal origin, such as red meat, may be a factor in explaining the postulated role of diet in breast cancer etiology.
Analysis of fecal populations of bifidobacteria and lactobacilli and investigation of the immunological responses of their human hosts to the predominant strains

The bifidobacterial and lactobacillus populations of fecal samples collected from 10 human subjects were studied. The numbers of bifidobacteria were similar in the fecal samples of all of the subjects, but lactobacillus numbers varied, even between samples collected from the same individual. Analysis of the composition of the bacterial populations by ribotyping and pulsed-field gel electrophoresis to differentiate between strains showed that, at least for the numerically predominant strains, each subject harbored a unique collection of bifidobacteria and lactobacilli. Predominant bifidobacterial and lactobacillus strains detected in the feces of each subject were used in immunological assays (lymphocyte transformation, serum antibody titers) to determine the influence of the bacteria on the immune system of their host. Immunoglobulin G antibodies reactive with lactobacilli were detected at high concentrations; antibodies reactive with bifidobacteria were present at lower concentrations. The antibodies appeared to be genus specific rather than strain specific. The results of the study emphasized the complexity of the relationship that exists between the intestinal microflora and the human host.