Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for Absorption of Ionic Calcium and Soluble Calcium Complexes by the Duodenum and Cecum in the Rat

The absorption of dietary calcium (Ca) may in part be determined by the formation in the intestinal lumen of soluble Ca complexes and insoluble Ca salts. This study was undertaken to test the assumption that ionic Ca concentration (Ca2+) is the only species of Ca that is available for absorption. Bidirectional steady-state Ca fluxes were measured in vitro under short-circuit conditions across segments of the proximal duodenum and the cecum in the presence and absence of varying concentrations of soluble Ca citrate complexes. The presence of 5.0 mmol/L medium citrate reduced medium Ca2+ and cecal Ca mucosal-to-serosal fluxes (Jms) (29 ± 18 versus 108 ± 7 nmol Ca/cm2/h, P < .001), but did not reduce duodenal Ca Jms (31 ± 5 versus 23 ± 9, P not significant). Duodenal Ca Jms increased 106% as medium Ca citrate complex increased to 1.018 mmol/L and Ca2+ remained constant; cecal Jms increased by 48% under the same conditions. The formation of soluble Ca organic anion complexes with lactate, malate, and fumarate reduced medium Ca2+ and cecal Ca Jms decreased with the reduction of medium Ca2+. The results of this study indicate that Ca2+ is the form of Ca most readily absorbed by the small intestine and the colon. Soluble Ca citrate complexes are absorbed by the duodenum and, to a much lesser extent, by the cecum. The reduction of Ca Jms by citrate is caused by the reduction of medium Ca2+ through formation of Ca citrate complexes and not caused by a direct interaction of the anion with the intestinal epithelium.
Vascular Endothelial Growth Factor-A Specifies Formation of Native Collaterals and Regulates Collateral Growth in Ischemia

The density of native (preexisting) collaterals and their capacity to enlarge into large conduit arteries in ischemia (arteriogenesis) are major determinants of the severity of tissue injury in occlusive disease. Mechanisms directing arteriogenesis remain unclear. Moreover, nothing is known about how native collaterals form in healthy tissue. Evidence suggests vascular endothelial growth factor (VEGF), which is important in embryonic vascular patterning and ischemic angiogenesis, may contribute to native collateral formation and arteriogenesis. Therefore, we examined mice heterozygous for VEGF receptor-1 (VEGFR-1+/−), VEGF receptor-2 (VEGFR-2+/−), and overexpressing (VEGFhi/+) and underexpressing VEGF-A (VEGFlo/+). Recovery from hindlimb ischemia was followed for 21 days after femoral artery ligation. All statements below are P<0.05. Compared to wild-type mice, VEGFR-2+/− showed similar: ischemic scores, recovery of hindlimb perfusion, pericollateral leukocytes, collateral enlargement, and angiogenesis. In contrast, VEGFR-1+/− showed impaired: perfusion recovery, pericollateral leukocytes, collateral enlargement, worse ischemic scores, and comparable angiogenesis. Compared to wild-type mice, VEGFlo/+ had 2-fold lower perfusion immediately after ligation (suggesting fewer native collaterals which was confirmed by angiography) and blunted recovery of perfusion. VEGFhi/+ mice had 3-fold greater perfusion immediately after ligation, more native collaterals, and improved recovery of perfusion. These differences were confirmed in the cerebral pial cortical circulation where, compared to VEGFhi/+ mice, VEGFlo/+ formed fewer collaterals during the perinatal period when adult density was established, and had 2-fold larger infarctions after middle cerebral artery ligation. Our findings indicate VEGF and VEGFR-1 are determinants of arteriogenesis. Moreover, we describe the first signaling molecule, VEGF-A, that specifies formation of native collaterals in healthy tissues.
UDRF: Multi-Resource Fairness for Complex Jobs with Placement Constraints

In this paper, we study the problem of multi-resource fairness in systems with multiple users. Each user requires to run one or more complex jobs that consist of multiple interconnected tasks. A job is considered finished when all its corresponding tasks have been executed in the system. Tasks can have different resource requirements. Because of special demands on particular hardware or software, tasks can have placement constraints limiting the type of machines they can run on. We develop User-Dependence Dominant Resource Fairness (UDRF), a generalized version of max-min fairness that combines graph theory and the notion of dominant resource shares to ensure multi- resource fairness between users with complex jobs. UDRF satisfies several desirable properties including strategy proofness, which ensures that users do not benefit from misreporting their true resource demands. We propose an offline algorithm that computes optimal UDRF allocation while the scheduling process can be to be decentralize across multiple schedulers. But optimality comes at a cost, especially for systems where schedulers need to make thousands of online scheduling decisions per second. Therefore, we develop a lightweight online algorithm that closely approximates UDRF. Large-scale simulations driven by Google cluster- usage traces show that UDRF achieves better resource utilization and throughput compared to the current state-of-the-art in multi-resource fair allocation.
Identification, localization, and primary structure of CAP-23, a particle-bound cytosolic protein of early development

We report the identification of CAP-23, a novel particle-bound cytosolic protein associated with developing cells in both mammalian and avian tissues. CAP-23 was a substrate for purified protein kinase C (PKC) in vitro, and the protein was phosphorylated in a PMA-sensitive manner in cultured cells, indicating that it is a PKC substrate in situ. cDNA coding for chick CAP-23 was isolated. The deduced sequence revealed an unusual amino acid composition that strikingly resembled that of rat GAP-43, a growth-associated neuron-specific PKC substrate. Further predicted features of CAP-23 included a PKC phosphorylation site at Ser-6, and the presence of basic NH2- and COOH-terminal domains. CAP-23 was encoded by an mRNA of approximately 1.5 kb, whose distribution during chick development resembled that of the corresponding protein. Southern blot analysis revealed the presence of a single main hybridizing species in the chick genome. The distribution of CAP-23 during development was analyzed with Western blots and by immunofluorescence on tissue sections. In cultured cells the protein appeared to be distributed in a regular spotted pattern below the entire cell surface. In early chick embryos (E2), CAP-23 was present in most if not all cells. The protein then became progressively restricted to only some developing tissues and to only certain cells in these tissues. In most tissues CAP-23 levels fell below detection limits between E15 and E19. Highest levels of the protein were found in the nervous system, where CAP-23 levels peaked around E18, and where elevated levels were still detectable at birth.
Successive interference cancellation in downlink cooperative cellular networks

This work studies the improvement in the sum rate of downlink cellular networks using successive interference cancellation (SIC). First, we consider a two-cell cellular network and propose a cooperative SIC scheme, in which one user receives its data at the single-user capacity using SIC while the rate in the other cell is appropriately adapted to maximize the sum rate. Identifying the corner points of the rate region of a two-user interference channel, we derive conditions for which applying SIC increases the sum rate as compared to treating interference as noise (IaN). Conditions when both mobiles can perform SIC are also given. These conditions allow us to identify cell areas and user positions in which SIC gains can be achieved. Furthermore, a flexible user association policy is presented as a means to further increase the sum-rate gains by using SIC. Finally, we propose a centralized cell scheduling for performing cooperative SIC in multiuser multi-cell networks. Numerical results show that significant sum-rate improvement is achieved using SIC receivers, even with few users per cell and especially at the cell edge.
Differential contributions of connexin37 and connexin43 to oogenesis revealed in chimeric reaggregated mouse ovaries

The gap junction proteins connexin37 and connexin43 are required for ovarian folliculogenesis in the mouse. To define their respective roles in oogenesis, chimeric ovaries containing either null mutant oocytes and wild-type granulosa cells or the reverse combination were grafted to the renal capsules of immunodeficient female mice. After three weeks, the oocytes were tested for meiotic competence and fertilizability in vitro. Ovaries composed of connexin43-deficient oocytes and wild-type granulosa cells produced antral follicles enclosing oocytes that could develop to at least the two-cell stage, demonstrating that oocytes need not express connexin43 to reach maturity. Conversely, both follicle development and oocyte maturation were impaired in ovaries containing either wild-type oocytes and connexin43-deficient granulosa cells or connexin37-deficient oocytes and wild-type granulosa cells. Thus absence of connexin43 from granulosa cells or connexin37 from oocytes is sufficient to compromise both oocyte and follicle development. Wild-type oocytes paired with connexin37-deficient granulosa cells generated antral follicles containing oocytes that developed to at least the two-cell stage. Therefore, connexin37 absence from granulosa cells need not impair fertility in mice. Dye transfer experiments revealed persistent oocyte-granulosa cell coupling in those follicles, indicating functional compensation by another connexin. The results indicate that mouse oocytes do not need to express connexin43 in order to develop into meiotically competent, fertilizable gametes, but must express connexin37 for communication with granulosa cells, a requirement for oogenesis.
Perceptually based metrics for the evaluation of textural image retrieval methods

Texture is widely used in CBIR, and there have been a number of studies over the years to establish which features are perceptually significant. However it is still difficult to retrieve reliably images that the human user would agree are "similar". This paper reviews a range of computational methods, and compares their performance in classifying and retrieving images from the Brodatz set. Their performance is then related to the combined ranking of "similar" images from the same dataset, obtained from experiments where human volunteers were asked to identify which images were most like each of the Brodatz images. The full set of 112 images was used. We conclude that no one method consistently returns retrievals which the human user would agree were similar across the full range of textures, but that statistical methods appear to perform better overall. We propose a subset of the Brodatz images for comparison of retrieval methods, based on the correlation between individual rankings.
Brillouin Scattering in Polymer Optical Fibers: Fundamental Properties and Potential Use in Sensors

We review the fundamental properties of Brillouin scattering in a perfluorinated graded-index polymer optical fiber (PFGI-POF) with 120 μm core diameter. The experiments were performed at 1.55 μm telecommunication wavelength. The Brillouin frequency shift (BFS) and the Brillouin bandwidth were 2.83 GHz and 105 MHz, respectively. The Brillouin gain coefficient was calculated to be 3.09 × 10−11 m/W, which was comparable to that of fused silica fibers. The Brillouin threshold power of the 100 m POF was estimated to be as high as 24 W, which can be, for practical applications, reduced by using POFs with smaller cores. These properties were compared with those of silica-based graded-index multi-mode fibers. We also investigated the BFS dependences on strain and temperature. They showed negative dependences with coefficients of −121.8 MHz/% and −4.09 MHz/K, respectively, which are −0.2 and −3.5 times as large as those in silica fibers. These BFS dependences indicate that the Brillouin scattering in PFGI-POFs can be potentially applied to high-accuracy temperature sensing with reduced strain sensitivity.
A particle filtering approach to salient video object localization

We describe a novel fully automatic algorithm for identifying salient objects in video based on their motion. Spatially coherent clusters of optical flow vectors are sampled to generate estimates of affine motion parameters local to super-pixels identified within each frame. These estimates, combined with spatial data, form coherent point distributions in a 5D solution space corresponding to objects or parts there-of. These distributions are temporally denoised using a particle filtering approach, and clustered to estimate the position and motion parameters of salient moving objects in the clip. We demonstrate localization of salient object/s in a variety of clips exhibiting moving and cluttered backgrounds.
Benchmarking for large-scale placement and beyond

Over the last five years, the large scale integrated circuit placement community achieved great strides in the understanding of placement problems, developed new high-performance algorithms, and achieved impressive empirical results. These advances have been supported by a nontrivial benchmarking infrastructure, and future achievements are set to draw on benchmarking as well. In this paper, we review motivations for benchmarking, especially for commercial electronic design automation, analyze available benchmarks, and point out major pitfalls in benchmarking. Our empirical data offers perhaps the first comprehensive evaluation of several leading large-scale placers on multiple benchmark families. We outline major outstanding problems and discuss the future of placement benchmarking. Furthermore, we attempt to extrapolate our experience to circuit layout tasks beyond placement.
A fresh look at the validity of the diffusion approximation for modeling fluorescence spectroscopy in biological tissue

Fluorescence has become a widely used technique for applications in noninvasive diagnostic tissue spectroscopy. The standard model used for characterizing fluorescence photon transport in biological tissue is based on the diffusion approximation. On the premise that the total energy of excitation and fluorescent photon flows must be conserved, we derive the widely used diffusion equations in fluorescence spectroscopy and show that there must be an additional term to account for the transport of fluorescent photons. The significance of this additional term in modeling fluorescence spectroscopy in biological tissue is assessed.
Isavuconazonium sulfate: a new agent for the treatment of invasive aspergillosis and invasive mucormycosis

ABSTRACT Introduction: Invasive fungal infections are serious and life-threatening complications of many of today’s medical enhancements. While we have seen an insurgence of new antifungal therapies on the market since the early 1990s that have contributed significantly to saving lives, there are still important gaps including narrow spectrum of activity, dose-limiting toxicities, or unpredictable pharmacokinetics. Isavuconazonium sulfate hopes to fill several of these gaps. Areas covered: The in vitro and in vivo pharmacology, pharmacokinetic characteristics, and phase 3 clinical trials for isavuconazole are described with a specific focus on the treatment of invasive aspergillosis and mucormycosis. A literature search was conducted in PubMed as well as FDA and EMA websites, and abstracts from congress proceedings. Expert Commentary: Isavuconazole’s pharmacokinetic profile, broad-spectrum antifungal activity, and clinical trial data make this new triazole a welcome addition to the armamentarium.
Oxidative Stress and Regulation of Pink 1 in Zebrafish ( Danio rerio )

Oxidative stress-mediated neuronal dysfunction is characteristic of several neurodegenerative disorders, including Parkinson’s disease (PD). The enzyme tyrosine hydroxylase (TH) catalyzes the formation of L-DOPA, the ratelimiting step in the biosynthesis of dopamine. A lack of dopamine in the striatum is the most characteristic feature of PD, and the cause of the most dominant symptoms. Loss of function mutations in the PTEN-induced putative kinase (PINK1) gene cause autosomal recessive PD. This study explored the basic mechanisms underlying the involvement of pink1 in oxidative stress-mediated PD pathology using zebrafish as a tool. We generated a transgenic line, Tg(pink1:EGFP), and used it to study the effect of oxidative stress (exposure to H2O2) on pink1 expression. GFP expression was enhanced throughout the brain of zebrafish larvae subjected to oxidative stress. In addition to a widespread increase in pink1 mRNA expression, mild oxidative stress induced a clear decline in tyrosine hydroxylase 2 (th2), but not tyrosine hydroxylase 1 (th1) expression, in the brain of wild-type larvae. The drug L-Glutathione Reduced (LGR) has been associated with anti-oxidative and possible neuroprotective properties. Administration of LGR normalized the increased fluorescence intensity indicating pink1 transgene expression and endogenous pink1 mRNA expression in larvae subjected to oxidative stress by H2O2. In the pink1 morpholino oliogonucleotide-injected larvae, the reduction in the expression of th1 and th2 was partially rescued by LGR. The pink1 gene is a sensitive marker of oxidative stress in zebrafish, and LGR effectively normalizes the consequences of mild oxidative stress, suggesting that the neuroprotective effects of pink1 and LGR may be significant and useful in drug development. Citation: Priyadarshini M, Orosco LA, Panula PJ (2013) Oxidative Stress and Regulation of Pink1 in Zebrafish (Danio rerio). PLoS ONE 8(11): e81851. doi:10.1371/journal.pone. 0081851 Editor: Alexander J Whitworth, University of Sheffield MRC Centre for Developmental and Biomedical Genetics, United Kingdom Received June 12, 2013; Accepted October 21, 2013; Published November 26, 2013 Copyright: © 2013 Priyadarshini et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This project was funded by the Finnish Graduate School of Neuroscience, Magnus Ehrnrooth Foundation, Academy of Finland and Sigrid Juselius foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. * E-mail: pertti.panula@helsinki.fi ¤ Current address: Institute of Pediatric Regenerative Medicine Shriners, Hospitals for Children, Department of Medical Pathology and Laboratory Medicine, University of California Davis, Davis, California, United States of America
STUDIES ON IMPROVING TEXTURE SEGMENTATION PERFORMANCE USING GENERALIZED GAUSSIAN MIXTURE MODEL INTEGRATING DCT AND LBP

This paper addresses the performance evaluation of the texture segmentation integrating DCT with LBP. In this method, the whole image is converted in to local binary pattern domain. The LBP image is then divided into different non overlapping blocks. From each block, the DCT coefficients are selected in a zigzag pattern for each block. Assuming the feature vectors follow a multivariate generalized Gaussian mixture model, the model parameters are estimated using EM algorithm. The initialisation of the model parameters is carried using moment method of estimation and using Hierarchical clustering algorithm. The texture segmentation algorithm is developed under Bayesian frame with component maximum likelihood. The performance of the proposed algorithm is evaluated using performance measures such as GCE, PRI and VOI with randomly selected images from Brodatz database. It is observed that this algorithm outperforms existing texture segmentation algorithms with respect to performance measures.
Continuous Spatial Representations in the Olfactory Bulb may Reflect Perceptual Categories

In sensory processing of odors, the olfactory bulb is an important relay station, where odor representations are noise-filtered, sharpened, and possibly re-organized. An organization by perceptual qualities has been found previously in the piriform cortex, however several recent studies indicate that the olfactory bulb code reflects behaviorally relevant dimensions spatially as well as at the population level. We apply a statistical analysis on 2-deoxyglucose images, taken over the entire bulb of glomerular layer of the rat, in order to see how the recognition of odors in the nose is translated into a map of odor quality in the brain. We first confirm previous studies that the first principal component could be related to pleasantness, however the next higher principal components are not directly clear. We then find mostly continuous spatial representations for perceptual categories. We compare the space spanned by spatial and population codes to human reports of perceptual similarity between odors and our results suggest that perceptual categories could be already embedded in glomerular activations and that spatial representations give a better match than population codes. This suggests that human and rat perceptual dimensions of odorant coding are related and indicates that perceptual qualities could be represented as continuous spatial codes of the olfactory bulb glomerulus population.
Kernel Bayesian Inference with Posterior Regularization

We propose a vector-valued regression problem whose solution is equivalent to the reproducing kernel Hilbert space (RKHS) embedding of the Bayesian posterior distribution. This equivalence provides a new understanding of kernel Bayesian inference. Moreover, the optimization problem induces a new regularization for the posterior embedding estimator, which is faster and has comparable performance to the squared regularization in kernel Bayes' rule. This regularization coincides with a former thresholding approach used in kernel POMDPs whose consistency remains to be established. Our theoretical work solves this open problem and provides consistency analysis in regression settings. Based on our optimizational formulation, we propose a flexible Bayesian posterior regularization framework which for the first time enables us to put regularization at the distribution level. We apply this method to nonparametric state-space filtering tasks with extremely nonlinear dynamics and show performance gains over all other baselines.
Facilitate Insight by Non-Invasive Brain Stimulation

Our experiences can blind us. Once we have learned to solve problems by one method, we often have difficulties in generating solutions involving a different kind of insight. Yet there is evidence that people with brain lesions are sometimes more resistant to this so-called mental set effect. This inspired us to investigate whether the mental set effect can be reduced by non-invasive brain stimulation. 60 healthy right-handed participants were asked to take an insight problem solving task while receiving transcranial direct current stimulation (tDCS) to the anterior temporal lobes (ATL). Only 20% of participants solved an insight problem with sham stimulation (control), whereas 3 times as many participants did so (p = 0.011) with cathodal stimulation (decreased excitability) of the left ATL together with anodal stimulation (increased excitability) of the right ATL. We found hemispheric differences in that a stimulation montage involving the opposite polarities did not facilitate performance. Our findings are consistent with the theory that inhibition to the left ATL can lead to a cognitive style that is less influenced by mental templates and that the right ATL may be associated with insight or novel meaning. Further studies including neurophysiological imaging are needed to elucidate the specific mechanisms leading to the enhancement.