Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphorylation of Saccharomyces cerevisiae Choline Kinase on Ser30 and Ser85 by Protein Kinase A Regulates Phosphatidylcholine Synthesis by the CDP-choline Pathway*

The Saccharomyces cerevisiae CKI-encoded choline kinase is phosphorylated on a serine residue and stimulated by protein kinase A. We examined the hypothesis that amino acids Ser30 and Ser85 contained in a protein kinase A sequence motif in choline kinase are target sites for protein kinase A. The synthetic peptides SQRRHSLTRQ (V max/K m = 10.8 μm −1 nmol min−1mg−1) and GPRRASATDV (V max/K m = 0.15 μm −1 nmol min−1mg−1) containing the protein kinase A motif for Ser30 and Ser85, respectively, within the choline kinase protein were substrates for protein kinase A. Choline kinase with Ser30 to Ala (S30A) and Ser85 to Ala (S85A) mutations were constructed alone and in combination by site-directed mutagenesis and expressed in a cki1Δeki1Δ double mutant that lacks choline kinase activity. The mutant enzymes were expressed normally, but the specific activity of choline kinase in cells expressing the S30A, S85A, and S30A,S85A mutant enzymes was reduced by 44, 8, and 60%, respectively, when compared with the control. In vivo labeling experiments showed that the extent of phosphorylation of the S30A, S85A, and S30A,S85A mutant enzymes was reduced by 70, 17, and 83%, respectively. Phosphorylation of the S30A, S85A, and S30A,S85A mutant enzymes by protein kinase A in vitro was reduced by 60, 7, and 96%, respectively, and peptide mapping analysis of the mutant enzymes confirmed the phosphorylation sites in the enzyme. The incorporation of3H-labeled choline into phosphocholine and phosphatidylcholine in cells bearing the S30A, S85A, and S30A,S85A mutant enzymes was reduced by 56, 27, and 81%, respectively, and by 58, 33, and 84%, respectively, when compared with control cells. These data supported the conclusion that phosphorylation of choline kinase on Ser30 and Ser85 by protein kinase A regulates PC synthesis by the CDP-choline pathway.
Declarative Tuning for Locality in Parallel Programs

Optimized placement of data and computation for locality is critical for improving performance and reducing energy consumption on modern computing systems. However, for most programming models, modifying data and computation placements typically requires rewriting large portions of the application, thereby posing a huge performance portability challenge in today's rapidly evolving architecture landscape. In this paper we present TunedCnC, a novel, declarative and flexible CnC tuning framework for controlling the spatial and temporal placement of data and computation by specifying hierarchical affinity groups and distribution functions. TunedCnC emphasizes a separation of concerns: the domain expert specifies a parallel application by defining data and control dependences, while the tuning expert specifies how the application should be executed on a given architecture - defining when and where for data and computation placement. The application remains unchanged when tuned for a different platform or towards different performance goals. We evaluate the utility of TunedCnC on several applications, and demonstrate that varying the tuning specification can have a significant impact on an application's performance. Our evaluation is performed using an implementation of the Concurrent Collections (CnC) declarative parallel programming model, but our results should be applicable to tuning of other data-flow task-parallel programming models as well.
Micro-force measuring apparatus for robotic fish: Design, implementation and application

Robotic fish are widely studied for their high propulsive efficiency, maneuverability, speed, acceleration and stealth. Compared to the measurement of the speed and acceleration of robotic fish, the propulsion can hardly be detected because of the micro-force and the movement. In this paper, we designed a micro-force measuring apparatus consisting of a micro-force sensor and a fixing device for robotic fish. The sensor has an accuracy of 0.1mN and can transform the force to electronic signal which is convenience to measure. The designed fixing device can limit the lateral movements of robotic fish but have non drag force in the forward swimming direction. Through this apparatus we first measured different propelling models and then compared the propulsion of robotic fish with different shape and stiffness of caudal fins. Robotic fish designed with soft caudal fin can generate maximum propulsion when undulation in the carangiform model.
An Endogenous Foamy-like Viral Element in the Coelacanth Genome

Little is known about the origin and long-term evolutionary mode of retroviruses. Retroviruses can integrate into their hosts' genomes, providing a molecular fossil record for studying their deep history. Here we report the discovery of an endogenous foamy virus-like element, which we designate ‘coelacanth endogenous foamy-like virus’ (CoeEFV), within the genome of the coelacanth (Latimeria chalumnae). Phylogenetic analyses place CoeEFV basal to all known foamy viruses, strongly suggesting an ancient ocean origin of this major retroviral lineage, which had previously been known to infect only land mammals. The discovery of CoeEFV reveals the presence of foamy-like viruses in species outside the Mammalia. We show that foamy-like viruses have likely codiverged with their vertebrate hosts for more than 407 million years and underwent an evolutionary transition from water to land with their vertebrate hosts. These findings suggest an ancient marine origin of retroviruses and have important implications in understanding foamy virus biology.
Mechanisms mediating insulin resistance in transgenic mice overexpressing mouse apolipoprotein A-II Published, JLR Papers in Press, October 1, 2004. DOI 10.1194/jlr.M400345-JLR200

We previously demonstrated that transgenic mice overexpressing mouse apolipoprotein A-II (apoA-II) exhibit several traits associated with the insulin resistance (IR) syndrome, including increased atherosclerosis, hypertriglyceridemia, obesity, and IR. The skeletal muscle appeared to be the insulin-resistant tissue in the apoA-II transgenic mice. We now demonstrate a decrease in FA oxidation in skeletal muscle of apoA-II transgenic mice, consistent with reports that decreased skeletal muscle FA oxidation is associated with increased skeletal muscle triglyceride accumulation, skeletal muscle IR, and obesity. The decrease in FA oxidation is not due to decreased carnitine palmitoyltransferase 1 activity, because oxidation of palmitate and octanoate were similarly decreased. Quantitative RT-PCR analysis of gene expression demonstrated that the decrease in FA oxidation may be explained by a decrease in medium chain acyl-CoA dehydrogenase. We previously demonstrated that HDLs from apoA-II transgenic mice exhibit reduced binding to CD36, a scavenger receptor involved in FA metabolism. However, studies of combined apoA-II transgenic and CD36 knockout mice suggest that the major effects of apoA-II are independent of CD36. Rosiglitazone treatment significantly ameliorated IR in the apoA-II transgenic mice, suggesting that the underlying mechanisms of IR in this animal model may share common features with certain types of human IR.
Reversible Data Hiding in Encrypted Images Based on Progressive Recovery

This paper proposes a method of reversible data hiding in encrypted images (RDH-EI) based on progressive recovery. Three parties are involved in the framework, including the content owner, the data-hider, and the recipient. The content owner encrypts the original image using a stream cipher algorithm and uploads a ciphertext to the server. The data-hider on the server divides the encrypted image into three channels and, respectively, embeds different amount of additional bits into each one to generate a marked encrypted image. On the recipient side, additional message can be extracted from the marked encrypted image, and the original image can be recovered without any errors. While most of the traditional methods use one criterion to recover the whole image, we propose to do the recovery by a progressive mechanism. Rate-distortion of the proposed method outperforms state-of-the-art RDH-EI methods.
Effect of Electro-Acupuncture on Neuroplasticity of Spinal Cord-Transected Rats

Background This study aimed to evaluate the effects of electro-acupuncture (EA) on neuroplasticity associated with the expressions of neurotrophic factors (NTFs) and their receptors in rats subjected to spinal cord transection (SCT). Material/Methods A total of 144 rats were randomly divided into 3 groups (n=48 per group): sham-operated group, SCT group, and EA (electro-acupuncture) group. Rats in SCT and EA groups received spinal cord transection at T10–T11 vertebral levels. Then, EA group rats received EA treatment. Reverse transcription polymerase chain reaction was used to detect NTFs and receptors at the mRNA level. In situ hybridization (ISH) and immunohistochemistry (IHC) were used to detect the expression of NTFs and their receptors. Basso, Beattie, Bresnahan (BBB) scores and cortical somato-sensory evoked potentials (CSEP) were evaluated to assess the recovery of motor and sensory functions. We also measured BDA (Biotinylated dextran amine) axonal tracing, CGRP (Calcitonin gene-related peptide), GAP-43 (Growth-associated protein), and synaptophysin immunohistochemistry (IHC). Results EA treatment led to obvious improvement in hindlimb locomotor and sensory functions. CNTF, FGF-2, and TrkB mRNA were significantly upregulated, while NGF, PDGF, TGF-β1, IGF-1, TrkA, and TrkC mRNA were concomitantly downregulated in the caudal spinal segment (CSS) following EA. Immunohistochemistry demonstrated an increased number of CGRP fibers, GAP-43, and synaptophysin profiles in the CSS in the EA rats. Conclusions EA may promote the recovery of neuroplasticity in rats subjected to SCT. This could be attributed to the systematic regulation of NTFs and their receptors after EA.
Evaluation of Hepatic Tissue Blood Flow Using Xenon Computed Tomography with Fibrosis Progression in Nonalcoholic Fatty Liver Disease: Comparison with Chronic Hepatitis C

Aims The present study evaluated the utility of xenon computed tomography (Xe-CT) as a noninvasive diagnostic procedure for the measurement of hepatic tissue blood flow (TBF) in patients with nonalcoholic fatty liver disease (NAFLD) or chronic hepatitis C (CH-C). Methods Xe-CT was performed in 93 patients with NAFLD and in 109 patients with CH-C. Subjects were classified into one of three groups, based on fibrosis stage: group 1, no bridging fibrosis; group 2, bridging fibrosis; and group 3, liver cirrhosis. Correlations between hepatic TBFs in each fibrosis stage were examined. Results In group 1, portal venous TBF (PVTBF), hepatic arterial (HATBF), and total hepatic TBF (THTBF) were significantly lower in patients with in nonalcoholic steatohepatitis (NASH) than in those with CH-C (p < 0.001, p < 0.05, p < 0.001, respectively). In group 2, PVTBF and THTBF were significantly lower in patients with in NASH than in those with CH-C (p < 0.001, p < 0.05, respectively). In group 3, hepatic TBFs were not significantly different when comparing patients with NASH and those with CH-C. Conclusions PVTBF decreased due to fat infiltration. Therefore, hemodynamic changes occur relatively earlier in NAFLD than in CH-C. Patients with NASH should be monitored carefully for portal hypertensive complications in the early fibrosis stage.
GFScan: A Gene Family Search Tool at Genomic DNA Level

We have developed GFScan (Gene Family Scan), a tool that identifies members of a gene family by searching genomic DNA sequences with genomic DNA motifs (or matrices) that are representative of the family. We have tested GFScan on four human gene families including the neurotransmitter-gated ion-channels (NGIC) family, the carbonic anhydrases (CA) family, the Dbl homology (DH) domain family, and the ETS-domain family. All known members of these families with motifs mapped to sequenced genomic DNA regions were found, whereas some novel genomic locations were also found to match the motifs, which may indicate new members in these families. Compared with other methods, GFScan recognized all true positives with much fewer false positives. We also showed that motifs constructed based on human genes could be used to search the mouse genome to identify orthologous family members in mouse. This program is available at http://www.cshl. org/mzhanglab/.
Error analysis and modelling of double saturating exponential dose response curves from SAR OSL dating

Increasingly observed in single-aliquot regenerative dose (SAR) optically stimulated luminescence (OSL, also termed photon stimulated luminescence or PSL) dating studies of sedimentary quartz are dose response curves that at high doses are not satisfied by a single saturating exponential (SSE) regression model. Commonly these can appear to be satisfied by a SSE+Linear (E+L) regression model, but some authors have proposed that a double saturating exponential (DSE) model would more closely fit the observed dose response curves (DRCs), especially in the region of highest applied doses. As error analysis for SAR equivalent dose (De) values derived from a DSE model is not yet available through the widely available Riso supplied software (Analyst), we present here a regression and error analysis scheme for DSE SAR data, and also a simple charge traffic model that generates approximate DSE dose responses. To illustrate results from our error analysis, we employ two SAR high dose data sets for fine-grain quartz, and compare graphically the SSE, E+L and DSE fits for each data set. These comparisons show clearly that such data are more closely fitted by a DSE regression than by the other two models. This result, and the charge traffic model, lend validity to the physical reality of DSE regression models, and have implications for quartz SAR dating of older sediments.
“Soft” tissue patterning: Muscles and tendons of the limb take their form

The musculoskeletal system grants our bodies a vast range of movements. Because it is mainly composed of easily identifiable components, it serves as an ideal model to study patterning of the specific tissues that make up the organ. Surprisingly, although critical for the function of the musculoskeletal system, understanding of the embryonic processes that regulate muscle and tendon patterning is very limited. The recent identification of specific markers and the reagents stemming from them has revealed some of the molecular events regulating patterning of these soft tissues. This review will focus on some of the current work, with an emphasis on the roles of the muscle connective tissue, and discuss several key points that addressing them will advance our understanding of these patterning events. Developmental Dynamics 240:1100–1107, 2011. © 2011 Wiley‐Liss, Inc.
TakeLab at SemEval-2016 Task 6: Stance Classification in Tweets Using a Genetic Algorithm Based Ensemble

This paper describes our system for the detection of stances in tweets submitted to SemEval 2016 Task 6A. The system uses an ensemble of learning algorithms, ﬁne-tuned using a genetic algorithm. We experiment with various off-the-shelf classiﬁers and build our model using standard lexical and a number of task-speciﬁc features. Our system ranked 3rd among the 19 systems submitted to this task.
Optimal planning of building integrated photovoltaic system in urban energy internet

Urban Energy Internet based on urban distribution network integrates various forms of energy sources and internet participants. It is crucial for different participants to agree on specific technical standards as well as planning objectives. Since the siting and sizing of BIPV system may have significant influence on its independent power producer and local electric power supply company, a coordinated planning is undoubtedly required to balance the interests of related parties. Firstly, this research carries out an analytical method based on power circle diagram to generate sets of siting and sizing solutions. Secondly, an optimal planning model is proposed considering bilateral interests of related parties to obtain the optimal capacity of BIPV and its access position. A practical case study is demonstrated.
TelegraphCQ: Continuous Dataflow Processing for an Uncertain World

Increasingly pervasive networks are leading towards a world where data is constantly in motion. In such a world, conventional techniques for query processing, which were developed under the assumption of a far more static and predictable computational environment, will not be sufficient. Instead, query processors based on adaptive dataflow will be necessary. The Telegraph project has developed a suite of novel technologies for continuously adaptive query processing. The next generation Telegraph system, called TelegraphCQ, is focused on meeting the challenges that arise in handling large streams of continuous queries over high-volume, highly-variable data streams. In this paper, we describe the system architecture and its underlying technology, and report on our ongoing implementation effort, which leverages the PostgreSQL open source code base. We also discuss open issues and our research agenda.
Partial correction of the CFTR‐dependent ABPA mouse model with recombinant adeno‐associated virus gene transfer of truncated CFTR gene

Recently, we have developed a model of airway inflammation in a CFTR knockout mouse utilizing Aspergillus fumigatus crude protein extract (Af‐cpe) to mimic allergic bronchopulmonary aspergillosis (ABPA) 1 , an unusual IgE‐mediated hypersensitivity syndrome seen in up to 15% of cystic fibrosis (CF) patients and rarely elsewhere. We hypothesized that replacement of CFTR via targeted gene delivery to airway epithelium would correct aberrant epithelial cytokine signaling and ameliorate the ABPA phenotype in CFTR‐deficient (CFTR 489X − /−, FABP‐hCFTR + / +) mice. CFTR knockout mice underwent intra‐tracheal (IT) delivery of recombinant adeno‐associated virus serotype 5 (rAAV5Δ‐264CFTR) or rAAV5‐GFP at 2.58 × 1012 viral genomes/mouse. All mice were then sensitized with two serial injections (200 µg) of crude Af antigen via the intra‐peritoneal (IP) route. Untreated mice were sensitized without virus exposure. Challenges were performed 2 weeks after final sensitization, using a 0.25% solution containing Aspergillus fumigatus crude protein extract delivered by inhalation on three consecutive days. The rAAV5Δ‐264CFTR‐treated mice had lower total serum IgE levels (172513 ng/ml ± 1312) than rAAV5‐GFP controls (26 892 ng/ml ± 3715) (p = 0.037) and non‐treated, sensitized controls (24 816 ± 4219 ng/ml). Serum IgG1 levels also were lower in mice receiving the CFTR vector. Interestingly, splenocytes from rAAV5Δ‐264CFTR‐treated mice secreted less IL‐13, INFg, TNFa, RANTES and GM‐CSF after ConA stimulation. Gene therapy with rAAV5Δ‐264CFTR attenuated the hyper‐IgE response in this reproducible CF mouse model of ABPA, with systemic effects also evident in the cytokine response of stimulated splenocytes. Copyright © 2007 John Wiley & Sons, Ltd.
Accuracy of Self-assessed Tanner Staging Against Hormonal Assessment of Sexual Maturation in Overweight African-American Children

AIM To evaluate the accuracy of self-reported Tanner (SRT) staging against a proxy method of physician's assessment of sexual maturation, using pubertal hormones in overweight African-American (AA) children. METHODS Cross-sectional data from 196 children (113 girls, 83 boys) aged 9-11 years, who were 'overweight' (>85th and <95th percentile for age- and gender-matched BMI; n = 43) or 'obese' (>95th percentile; n = 153) were used. Children assessed their breast or genital and pubic hair development using standardized Tanner drawings representing different stages of sexual maturity. SRT data were compared to pubertal stage assessed by measuring fasting serum concentrations of luteinizing hormone (LH) in boys, and LH and estradiol (E2) in girls, which were used to stage children into pubertal stages 1-5. RESULTS SRT stages of genital and pubic hair assessments in boys, and breast and pubic hair assessments in girls, yielded 15-20% concordance (kappa statistic = 0.02-0.12) compared to their hormone-derived pubertal stages. CONCLUSIONS Among overweight AA 9-11 year-old children, self-assessment of Tanner staging did not accurately assess their pubertal development when compared to a hormone-derived pubertal assessment method.
What quantum technology will bring to our daily life?

The motivation of this talk is to investigate what quantum resources will bring about in our daily life. A kind of quantization for general bipartite games is first given and then applied to both the modified classical “cash in a hat” game and modified Prisoners Dilemma game with different distribution policies. It is shown that quantum entanglement can bring full cooperation with the help of fair distribution policies. It is further demonstrated that quantum networks will make possible playing quantum game between remote players. Two schemes are given to illustrate how to play distributed quantum games between two players on the nodes of quantum networks. In our opinion, it is a worthy research topic to investigate how quantum entanglement can be exploited to achieve full cooperation with equitable distribution polices.
Quiver theories, soliton spectra and Picard-Lefschetz transformations

Quiver theories arising on D3-branes at orbifold and del Pezzo singularities are studied using mirror symmetry. We show that the quivers for the orbifold theories are given by the soliton spectrum of massive 2d = 2 theory with weighted projective spaces as target. For the theories obtained from the del Pezzo singularities we show that the geometry of the mirror manifold gives quiver theories related to each other by Picard-Lefschetz transformations, a subset of which are simple Seiberg duals. We also address how one indeed derives Seiberg duality on the matter content from such geometrical transitions and how one could go beyond and obtain certain ``fractional Seiberg duals. '' Moreover, from the mirror geometry for the del Pezzos arise certain Diophantine equations which classify all quivers related by Picard-Lefschetz. Some of these Diophantine equations can also be obtained from the classification results of Cecotti-Vafa for the 2d = 2 theories.
TransChat: Cross-Lingual Instant Messaging for Indian Languages

We present TransChat 1 , an open source, cross platform, Indian language Instant Messaging (IM) application that facilitates cross lingual textual communication over English and multiple Indian Languages. The application is a client-server IM architecture based chat system with multiple Statistical Machine Translation (SMT) engines working towards efficient translation and transmission of messages. Tran-sChat allows users to select their preferred language and internally, selects appropriate translation engine based on the input configuration. For translation quality enhancement, necessary pre-and post-processing steps are applied on the input and output chat-texts. We demonstrate the efficacy of TransChat through a series of qualitative evaluations that test-(a) The usability of the system (b) The quality of the translation output. In a multilingual country like India, such applications can help overcome language barrier in domains like tourism, agriculture and health.