Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of Mrp1 (ABCc1) and Pgp (ABCb1) by Bilirubin at the Blood-CSF and Blood-Brain Barriers in the Gunn Rat

Accumulation of unconjugated bilirubin (UCB) in the brain causes bilirubin encephalopathy. Pgp (ABCb1) and Mrp1 (ABCc1), highly expressed in the blood-brain barrier (BBB) and blood-cerebrospinal fluid barrier (BCSFB) respectively, may modulate the accumulation of UCB in brain. We examined the effect of prolonged exposure to elevated concentrations of UCB on expression of the two transporters in homozygous, jaundiced (jj) Gunn rats compared to heterozygous, not jaundiced (Jj) littermates at different developmental stages (2, 9, 17 and 60 days after birth). BBB Pgp protein expression was low in both jj and Jj pups at 9 days (about 16–27% of adult values), despite the up-regulation in jj animals (2 and 1.3 fold higher than age matched Jj animals at P9 and P17–P60, respectively); Mrp1 protein expression was barely detectable. Conversely, at the BCSFB Mrp1 protein expression was rather high (60–70% of the adult values) in both jj and Jj at P2, but was markedly (50%) down-regulated in jj pups starting at P9, particularly in the 4th ventricle choroid plexuses: Pgp was almost undetectable. The Mrp1 protein down regulation was accompanied by a modest up-regulation of mRNA, suggesting a translational rather than a transcriptional inhibition. In vitro exposure of choroid plexus epithelial cells obtained from normal rats to UCB, also resulted in a down-regulation of Mrp1 protein. These data suggest that down-regulation of Mrp1 protein at the BSCFB, resulting from a direct effect of UCB on epithelial cells, may impact the Mrp1-mediated neuroprotective functions of the blood-cerebrospinal fluid barrier and actually potentiate UCB neurotoxicity.
Neonatal whisker clipping alters intracortical, but not thalamocortical projections, in rat barrel cortex

Retrograde axonal transport of cholera toxin B subunit (CTB) was used to compare the development of intracortical and thalamocortical connections in normal rats with those in rats in which all of the whiskers were trimmed continuously from birth. In normal animals, injections of CTB into a single barrel column resulted in an asymmetrical labeling of cells that were distributed preferentially within columns related to the same row in which the injection was placed. This anisotropy in the patterns of intracortical connections was not observed in whisker‐clipped animals. In these animals, there was a significant reduction in the mean number of labeled cells in the infragranular layers, and labeled cells were distributed symmetrically around the injection site. The same injections of CTB also labeled thalamocortical neurons in the ventrobasal thalamus. Analysis of the distribution of these cells revealed that, in both control and experimental animals, the vast majority of labeled cells were restricted to a homologous (i.e., corresponding to the injected cortical barrel) thalamic barreloid. These findings indicate that manipulations of sensory experience alter patterns of intracortical, but not thalamocortical, connections. J. Comp. Neurol. 412:83–94, 1999. © 1999 Wiley‐Liss, Inc.
The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase

Mutations in the brown midrib4 (bm4) gene affect the accumulation and composition of lignin in maize. Fine-mapping analysis of bm4 narrowed the candidate region to an approximately 105 kb interval on chromosome 9 containing six genes. Only one of these six genes, GRMZM2G393334, showed decreased expression in mutants. At least four of 10 Mu-induced bm4 mutant alleles contain a Mu insertion in the GRMZM2G393334 gene. Based on these results, we concluded that GRMZM2G393334 is the bm4 gene. GRMZM2G393334 encodes a putative folylpolyglutamate synthase (FPGS), which functions in one-carbon (C1) metabolism to polyglutamylate substrates of folate-dependent enzymes. Yeast complementation experiments demonstrated that expression of the maize bm4 gene in FPGS-deficient met7 yeast is able to rescue the yeast mutant phenotype, thus demonstrating that bm4 encodes a functional FPGS. Consistent with earlier studies, bm4 mutants exhibit a modest decrease in lignin concentration and an overall increase in the S:G lignin ratio relative to wild-type. Orthologs of bm4 include at least one paralogous gene in maize and various homologs in other grasses and dicots. Discovery of the gene underlying the bm4 maize phenotype illustrates a role for FPGS in lignin biosynthesis.
Spatial Defects in 5896 HG-U 133 A GeneChips

Motivation: Modern biology has moved from a science of individual measurements to a science where data are collected on an industrial scale. Foremost amongst the new tools for biochemistry are chip arrays which, in one operation, measure hundreds of thousands or even millions of DNA sequences or RNA transcripts. Whilst this is impressive, increasingly sophisticated analysis tools have been required to convert gene array data into gene expression levels. Despite the assumption that noise levels are low, since the number of measurements for an individual gene is small, identifying which signals are affected by noise is a priority. Results: 5896 raw data (Affymetrix CEL) files were obtained from ftp:// ftp.ebi. ac.uk/pub/databases/microarray/data/experiment/TABM/E-TABM-185/ Each CEL file was checked for spatial errors. In HG-U133A high-density oligonucleotide array (HDONAs) the mean error rate is only 1.6% which is amongst the best for human GeneChips. However some locations are much more error prone than others, with up to 28% of probes being affected. Removal of erroneous data improves breast cancer survival prediction.
Semantic Web-based Sentiment Analysis

1 The introduction of semantics in Sentiment Analysis research has proved to bring several benefits for what performances are concerned and has allowed to identify new challenging tasks to be accomplished. Semantics helps structuring the plain natural language text with formal representation. The current system we are developing performs sentiment analysis by hybridizing natural language processing techniques with Semantic Web technologies. Our system, called Sentilo, is able to recognize the holder of an opinion, to detect the topics and sub-topics in its scope, and to measure the sentiment expressed by them. This information is formally represented by means of RDF graphs according to an OWL opinion ontology, while holders and topics identity is resolved on the Linked Open Data cloud.
Radio and television information filtering through speech recognition

: The problem of information overload can be solved by the application of information (cid:12)ltering to the huge amount of data. Information on radio and television can be (cid:12)ltered using speech recognition of the audio track. A prototype system using closed captions has been developed on top of the INQUERY information access system. The challange of integrating speech recognition and information retrieval into a working system is a big one. The open problems are the selection of a document representation model, the recognition and selection of indexing features for speech retrieval and dealing with the erroneous output of recognition processes.
PAPER : COMPUTATIONAL LINGUISTICS

The observations regarding computational linguistics in this paper are limited to developments in the United States, and further, to work which employs some measure of linguistic (rather than purely statistical) analysis. The paper is not a survey, which would be redundant in view of the comprehensive reports on natural language processing provided by Walker (1973) and Damerau (1976), and in Sparck Jones and Kay (1973). Rather, it is organized around problems and solutions to problems, and it attempts to document the view that techniques of computational linguistics have reached the stage where applications in information science are now possible. *
An enhanced LSA-based approach for update summarization

Update summarization is a challenge in automatic text summarization. The task aims to distill evolved messages from a collection of new articles, under the assumption that the reader has already browsed the previous articles. In this paper, we reviewed some state-of-the-art approaches for extracting update summarization and then focused on a LSA-based one. After the analysis of LSA-based approach's framework, we improved the approach by enhancing the approach's performance in accuracy. First, we utilized TOPIC SIGNATURE algorithm to extract the terms' novel information and incorporated the information to the process of evaluating topic's novelty score, which makes the evaluation more accuracy. Second, we excluded the least novel and important topics when generating summary, which helps improving the quality of the summary. The evaluation result on the update summarization task of Text Analysis Conference (TAC) 2008 indicates the validity of our modification.
A 14-b 30MS/s 0.75mm2 Pipelined ADC with On-Chip Digital Self-Calibration

A 14-b 30 MS/s CMOS pipelined ADC is presented. To facilitate digital calibration, a simple 1-b per stage architecture with redundancy is used. The ADC fully integrates digital self-calibration, which performs overall sequence by one flag signal. Implemented in a 90 nm digital CMOS process, the prototype ADC achieves 83.7 dB SFDR and 69.3 dB SNDR with calibration. Its active area is 0.75 mm2 including the on-chip calibration logic and the total power consumes 106 mW with 3.3 V and 1.0 V supply.
Robotics for rehabilitation of hand movement in stroke survivors

This article aims to give an overall review of research status in hand rehabilitation robotic technology, evaluating a number of devices. The main scope is to explore the current state of art to help and support designers and clinicians make better choices among varied devices and components. The review also focuses on both mechanical design, usability and training paradigms since these parts are interconnected for an effective hand recovery. In order to study the rehabilitation robotic technology status, the devices have been divided in two categories: end-effector robots and exoskeleton devices. The end-effector robots are more flexible than exoskeleton devices in fitting the different size of hands, reducing the setup time and increasing the usability for new patients. They suffer from the control of distal joints and haptic aspects of object manipulation. In this way, exoskeleton devices may represent a new opportunity. Nevertheless their design is complex and a deep investigation of hand biomechanics and physical human–robot interaction is required. The main hand exoskeletons have been developed in the last decade and the results are promising demonstrated by the growth of the commercialized devices. Finally, a discussion on the complexity to define which design is better and more effective than the other one is summarized for future investigations.
Redactable vs. Sanitizable Signatures

Malleable signature schemes allow altering signed data in a controlled way while keeping the signature veriﬁable trusting the signer’s key. Several constructions exists. They can be grouped in two diﬀerent categories: (1) redactable signatures ( RSS ) and (2) sanitizable signatures ( SSS ). RSS s allow for removing blocks of a signed document, while SSS s oﬀer the possibility to change all admissible blocks to arbitrary strings. This paper shows that SSS s with a strenghted security deﬁnition can be transformed into RSS s with a weakened privacy deﬁ-nition. A transformation from a RSS into a SSS is not possible, even if we assume accountability for RSS . In particular, no unforgeable RSS can be transformed into a SSS . This work provides the ﬁrst rigorous proof that RSS s and SSS s are two diﬀerent concepts.
Banking (Conservatively) with Optimists

Commercial banks frequently encounter optimistic entrepreneurs whose perceptions are biased by wishful thinking. Bankers are left with a difficult screening problem: separating realistic entrepreneurs from optimists who may be clever, knowledgeable, and completely sincere. We build a game-theoretic model of the screening process. We show that although entrepreneurs may practice self-restraint to signal realism, competition may lead banks to be insufficiently conservative in their lending, thus reducing capital-market efficiency. High collateral requirements decrease efficiency further. We discuss bank regulation and bankruptcy rules in connection with the problems that optimistic entrepreneurs present.
Computation of Force Closure Grasps from Finite Contact Point Set

A Robot, from its very name, literally means “forced labor”. To live up to this title, an ability to interact with milieu is crucial. A robot should be able to manipulate objects. With a hand capable of grasping, a robot is blessed with greater degree of influent. Complex manipulation and maneuver are possible with grasping. Moreover, grasping allows robot to use tools readily available for human. For example, instead of having a robot with various switchable specialized end effectors, we can build a robot with dexterous hands and make available tools usable by both robot and human. The later situation is more robust than the first. Without a doubt, grasping is an essential ability of a robot, especially a humanoid one.
Vitamin A Intake and Risk of Melanoma: A Meta-Analysis

Background Mounting evidence from experimental and animal studies suggests that vitamin A may have a protective effect on melanoma, but the findings on the association of vitamin A intake with risk of melanoma have been inconsistently reported in epidemiologic studies. We attempted to elucidate the association by performing a meta-analysis. Methods Eligible studies were identified by searching PubMed and EMBASE databases, as well as by reviewing the references of retrieved publications. Summary odds ratios (OR) with corresponding 95% confidence interval (CI) were computed with a random-effects model. Study-specific ORs and 95% CIs for the highest vs. lowest categories of vitamin A intake were pooled. Results A total of 8 case-control studies and 2 prospective studies comprising 3,328 melanoma cases and 233,295 non-case subjects were included. The summary OR for the highest compared with the lowest intake of total vitamin A, retinol and beta-carotene was 0.86 (95% CI = 0.59–1.25), 0.80 (95% CI = 0.69–0.92) and 0.87 (95%CI = 0.62–1.20), respectively. Significant heterogeneity was observed among studies on vitamin A and beta-carotene intake, but not among studies on retinol intake. Subgroup and sensitivity analyses confirmed these findings. There was no indication of publication bias. Conclusion Findings from this meta-analysis suggest that intake of retinol, rather than of total vitamin A or beta-carotene, is significantly associated with reduced risk of melanoma.
Gene expression signatures differentiate ovarian/peritoneal serous carcinoma from breast carcinoma in effusions.

Ovarian/primary peritoneal carcinoma and breast carcinoma are the gynaecological cancers that most frequently involve the serosal cavities.With the objective of improving on the limited diagnostic panel currently available for the differential diagnosis of these two malignancies,as well as to define tumour-specific biological targets, we compared their global gene expression patterns. Gene expression profiles of 10 serous ovarian/peritoneal and eight ductal breast carcinoma effusions were analysed using the HumanRef-8 BeadChip from Illumina.Differentially expressed candidate genes were validated using quantitative real-time PCR and immunohistochemistry. Unsupervised hierarchical clustering using all 54,675 genes in the array separated ovarian from breast carcinoma samples. We identified 288 unique probes that were significantly differentially expressed in the two cancers by greater than 3.5-fold, of which 81 and 207 were overexpressed in breast and ovarian/peritoneal carcinoma, respectively. SAM analysis identified 1078 differentially expressed probes with false discovery rate less than 0.05. Genes overexpressed in breast carcinoma included TFF1, TFF3, FOXA1, CA12, GATA3, SDC1, PITX1, TH, EHFD1, EFEMP1, TOB1 and KLF2. Genes overexpressed in ovarian/peritoneal carcinoma included SPON1, RBP1, MFGE8, TM4SF12, MMP7, KLK5/6/7, FOLR1/3,PAX8, APOL2 and NRCAM. The differential expression of 14 genes was validated by quantitative real-time PCR, and differences in 5 gene products were confirmed by immunohistochemistry. Expression profiling distinguishes ovarian/peritoneal carcinoma from breast carcinoma and identifies genes that are differentially expressed in these two tumour types. The molecular signatures unique to these cancers may facilitate their differential diagnosis and may provide a molecular basis for therapeutic target discovery.
TrkB and Protein Kinase M ζ Regulate Synaptic Localization of PSD-95 in Developing Cortex

Postsynaptic density 95 (PSD-95), the major scaffold at excitatory synapses, is critical for synapse maturation and learning. In rodents, eye opening, the onset of pattern vision, triggers a rapid movement of PSD-95 from visual neuron somata to synapses. We showed previously that the PI3 kinase–Akt pathway downstream of BDNF/TrkB signaling stimulates synaptic delivery of PSD-95 via vesicular transport. However, vesicular transport requires PSD-95 palmitoylation to attach it to a lipid membrane. Also, PSD-95 insertion at synapses is known to require this lipid modification. Here, we show that BDNF/TrkB signaling is also necessary for PSD-95 palmitoylation and its transport to synapses in mouse visual cortical layer 2/3 neurons. However, palmitoylation of PSD-95 requires the activation of another pathway downstream of BDNF/TrkB, namely, signaling through phospholipase Cγ and the brain-specific PKC variant protein kinase M ζ (PKMζ). We find that PKMζ selectively regulates phosphorylation of the palmitoylation enzyme ZDHHC8. Inhibition of PKMζ results in a reduction of synaptic PSD-95 accumulation in vivo, which can be rescued by overexpressing ZDHHC8. Therefore, TrkB and PKMζ, two critical regulators of synaptic plasticity, facilitate PSD-95 targeting to synapses. These results also indicate that palmitoylation can be regulated by a trophic factor. Our findings have implications for neurodevelopmental disorders as well as aging brains.
Investigation of Slot-Burner Aerodynamics with Recessed-Type Nozzle Geometry

The aerodynamics of fully turbulent jets supplied from rectangular slot-burners was modelled using the Reynolds Averaged Navier–Stokes (RANS) model. Three different turbulent models were considered, such as standard k-e, RNG k-e and Reynolds stress turbulence models. The recessed-type nozzle geometry was investigated to determine the effect of burner geometry on jet development. The slot-burner was based on physical models, which were designed to be representative of typical burner geometries found in tangentially-fired coal boilers. The study was validated against the physical models. The detailed flow field obtained from the simulations was used to explain the aerodynamic development of jets in such burners. It was found that the addition of a recess section to the nozzle geometry introduced significant changes to the flow due to complex pressure and mixing fields being set up inside the recess, which altered the jets once they exited into the open atmosphere.
Using Crop Management Scenario Simulations to Evaluate the Sensitivity of the Ohio Phosphorus Risk Index

Phosphorus (P) risk indices are commonly used in the USA to estimate the field-scale risk of agricultural P runoff. Because the Ohio P Risk Index is increasingly being used to judge farmer performance, it is important to evaluate weighting/scoring of all P Index parameters to ensure Ohio farmers are credited for practices that reduce P runoff risk and not unduly penalized for things not demonstrably related to runoff risk. A sensitivity analysis provides information as to how sensitive the P Index score is to changes in inputs. The objectives were to determine 1) which inputs are most highly associated with P Index scores and 2) the relative impact of each input variable on resultant P Index scores. The current approach uses simulations across 6134 Ohio point locations and five crop management scenarios (CMSs), representing increasing soil disturbance. The CMSs range from all no-till, which is being promoted in Ohio, rotational tillage, which is a common practice in Ohio to full tillage to represent an extreme practice. Results showed that P Index scores were best explained by soil test P (31.9%) followed by connectivity to water (29.7%), soil erosion (13.4%), fertilizer application amount (11.3%), runoff class (9.5%), fertilizer application method (2.2%), and finally filter strip (2.0%). Ohio P Index simulations across CMSs one through five showed that >40% scored 45 points (very high). Given Ohio water quality problems, the Ohio P Index needs to be stricter. The current approach is useful for Ohio P Index evaluations and revision decisions by spatially illustrating the impact of potential changes regionally and state-wide.
Stimulation of endogenous cardioblasts by exogenous cell therapy after myocardial infarction

Controversy surrounds the identity, origin, and physiologic role of endogenous cardiomyocyte progenitors in adult mammals. Using an inducible genetic labeling approach to identify small non‐myocyte cells expressing cardiac markers, we find that activated endogenous cardioblasts are rarely evident in the normal adult mouse heart. However, myocardial infarction results in significant cardioblast activation at the site of injury. Genetically labeled isolated cardioblasts express cardiac transcription factors and sarcomeric proteins, exhibit spontaneous contractions, and form mature cardiomyocytes in vivo after injection into unlabeled recipient hearts. The activated cardioblasts do not arise from hematogenous seeding, cardiomyocyte dedifferentiation, or mere expansion of a preformed progenitor pool. Cell therapy with cardiosphere‐derived cells amplifies innate cardioblast‐mediated tissue regeneration, in part through the secretion of stromal cell‐derived factor 1 by transplanted cells. Thus, stimulation of endogenous cardioblasts by exogenous cells mediates therapeutic regeneration of injured myocardium.
Frequency-DOA joint estimation by Ant Colony Optimization

The Multiple Signal Classification (MUSIC) method is a typical method for high-resolution Direction Of Arrival(DOA) and frequency estimation. Usually it performs spectrum search in certain grid space, which inevitably leads to high computational cost in the muti-dimensional case, for example the search for frequency and azimuth at the same time. To overcome this problem, in this paper, we introduced Ant Colony Optimization(ACO) to work with MUSIC. A new kind of ACO for continuous domain featured by Gauss kernel function is used to sample the MUSIC spectrum, which is regarded as the fitness function in the process. The resulted estimator is called Ant Colony Optimization based MUSIC (ACO-MUSIC). Simulations show that ACO-MUSIC not only reduces the computational complexity greatly but also maintains the excellent performance of the original MUSIC estimator.
Spot Convenience Yield Models for the Energy Markets

We review that part of the literature on energy spot price models which involves convenience yield as a factor, our goal being to document the shortcomings of the most commonly used models. From a mathematical point of view, the introduction of the convenience yield is usually justified by the desire to reconciliate dynamical models for the time evolution of commodity prices with standard arbitrage theory. Since the convenience yield appears as a factor which cannot be observed directly, stochastic filtering has been proposed as a strategy of choice for its estimation from observed market prices. We implement these ideas on the models we review, and on some natural extensions. We illustrate the inconsistencies of the spot models on readily available data, paving the way for the empirical analysis of models of the term structure of convenience yield recently proposed as a viable alternative.