Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Sympathetic Nerves and Adipocyte Catecholamine Uptake in the Vasorelaxant Function of Perivascular Adipose Tissue

Objective— Healthy perivascular adipose tissue (PVAT) exerts an anticontractile effect on resistance arteries which is vital in regulating arterial tone. Activation of &bgr;3-adrenoceptors by sympathetic nerve–derived NA (noradrenaline) may be implicated in this effect and may stimulate the release of the vasodilator adiponectin from adipocytes. Understanding the mechanisms responsible is vital for determining how PVAT may modify vascular resistance in vivo. Approach and Results— Electrical field stimulation profiles of healthy C57BL/6J mouse mesenteric resistance arteries were characterized using wire myography. During electrical field stimulation, PVAT elicits a reproducible anticontractile effect, which is endothelium independent. To demonstrate the release of an anticontractile factor, the solution surrounding stimulated exogenous PVAT was transferred to a PVAT-denuded vessel. Post-transfer contractility was significantly reduced confirming that stimulated PVAT releases a transferable anticontractile factor. Sympathetic denervation of PVAT using tetrodotoxin or 6-hydroxydopamine completely abolished the anticontractile effect. &bgr;3-adrenoceptor antagonist SR59203A reduced the anticontractile effect, although the PVAT remained overall anticontractile. When the antagonist was used in combination with an OCT3 (organic cation transporter 3) inhibitor, corticosterone, the anticontractile effect was completely abolished. Application of an adiponectin receptor-1 blocking peptide significantly reduced the anticontractile effect in +PVAT arteries. When used in combination with the &bgr;3-adrenoceptor antagonist, there was no further reduction. In adiponectin knockout mice, the anticontractile effect is absent. Conclusions— The roles of PVAT are 2-fold. First, sympathetic stimulation in PVAT triggers the release of adiponectin via &bgr;3-adrenoceptor activation. Second, PVAT acts as a reservoir for NA, preventing it from reaching the vessel and causing contraction.
Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans

Despite conservation of the signal recognition particle (SRP) from bacteria to man, computational approaches have failed to identify SRP components from genomes of many lower eukaryotes, raising the possibility that they have been lost or altered in those lineages. We report purification and analysis of SRP in the human pathogen Cryptococcus neoformans, providing the first description of SRP in basidiomycetous yeast. The C. neoformans SRP RNA displays a predicted structure in which the universally conserved helix 8 contains an unprecedented stem-loop insertion. Guided by this sequence, we computationally identified 152 SRP RNAs throughout the phylum Basidiomycota. This analysis revealed additional helix 8 alterations including single and double stem-loop insertions as well as loop diminutions affecting RNA structural elements that are otherwise conserved from bacteria to man. Strikingly, these SRP RNA features in Basidiomycota are accompanied by phylum-specific alterations in the RNA-binding domain of Srp54, the SRP protein subunit that directly interacts with helix 8. Our findings reveal unexpected fungal SRP diversity and suggest coevolution of the two most conserved SRP features—SRP RNA helix 8 and Srp54—in basidiomycetes. Because members of this phylum include important human and plant pathogens, these noncanonical features provide new targets for antifungal compound development.
Report on Differential Privacy

Over the past decade the collection and analysis of personal data has increased a lot. This has also raised the question about loss of privacy. Privacy and (useful) data analysis are relatively conflicting terms and thus combining them is a difficult question. In order to discuss the problem, we need to define privacy. Various definitions have been proposed but in the current report we will talk about one of them. Namely differential privacy, which was introduced by Dwork in 2006 [1]. There has been active research of differential privacy after that. In 2014, Dwork and Roth published a comprehensive introduction [2] to the field of differential privacy, which the current report is also based on. Suppose a trusted curator (e.g. government) gathers sensitive information from a large number of respondents, with the goal of learning (and releasing to the public) statistical facts about the underlying population. The problem is, how to release statistical information without compromising the privacy of the individual respondents. The release phase can also be imagined as a data analyst querying the database. Roughly speaking, differential privacy ensures that the removal or addition of a single database item does not affect (much) the outcome of any analysis. Thus no privacy is lost by joining the database. In the current report, we firstly talk briefly about few naive privacy preserving methods and argue that they do not really work. In the second section we set up the model of computation and introduce the formal definition of differential privacy. In the third section, we describe few mechanisms that comply with the differential privacy definition. Finally, we will introduce the notion of composition and show how to analyze the privacy loss over several queries.
Distributed Log Analysis on the Cloud Using MapReduce

In this paper we describe our work on designing a web based, distributed data analysis system based on the popular MapReduce framework deployed on a small cloud; developed specifically for analyzing web server logs. The log analysis system consists of several cluster nodes, it splits the large log files on a distributed file system and quickly processes them using MapReduce programming model. The cluster is created using an open source cloud infrastructure, which allows us to easily expand the computational power by adding new nodes. This gives us the ability to automatically resize the cluster according to the data analysis requirements. We implemented MapReduce programs for basic log analysis needs like frequency analysis, error detection, busy hour detection etc. as well as more complex analyses which require running several jobs. The system can automatically identify and analyze several web server log types such as Apache, IIS, Squid etc. We use open source projects for creating the cloud infrastructure and running MapReduce jobs.
Transscleral Suture-Fixated Versus Intrascleral Haptic-Fixated Intraocular Lens: A Comparative Study

Purpose: To compare the clinical outcomes between sutured transscleral-fixated and intrascleral haptic-fixated posterior chamber intraocular lens (IOL). Setting: Dr Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi. Design: A comparative case series. Methods: Forty eyes of 40 patients were included; 20 in each group. Patients in group 1 underwent sutured transscleral-fixated IOL and those in group 2 underwent intrascleral haptic-fixated IOL augmented by fibrin glue. Parameters evaluated were uncorrected visual acuity (UCVA), best corrected visual acuity (BCVA), intraocular pressure (IOP), central macular thickness (CMT), IOL tilt on ultrasound biomicroscopy (UBM), and pseudophakodonesis on slitlamp and UBM. Results: The most common cause of aphakia was complicated cataract surgery (50%). The mean preoperative UCVA in logarithm of minimum angle of resolution (logMAR) was 1.59±0.24 and 1.63±0.26 in group 1 and 2, respectively (P=0.45). There was significant improvement in UCVA in both groups (P=0.001) at 6 months (group 1: 0.33±0.17; group 2: 0.22±0.10); the improvement being greater in group 2 (P<0.05). Mean percentage endothelial cell loss and IOP change were comparable. Mean CMT (&mgr;m) was 250.95±23.98 and 225.85±21.13 in group 1 and 2, respectively (P=0.009). Pseudophakodonesis was more in group 1 as assessed on slitlamp (P=0.037) and as assessed on UBM (P=0.046). Macular edema was the most common complication seen more in group 1. Conclusions: Intrascleral haptic-fixated IOL provides more stable fixation, better visual outcome, and lesser complication in comparison with sutured transscleral-fixated IOL.
Replication Study: Discovery and preclinical validation of drug indications using compendia of public gene expression data

In 2015, as part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Kandela et al., 2015) that described how we intended to replicate selected experiments from the paper “Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data“ (Sirota et al., 2011). Here we report the results of those experiments. We found that cimetidine treatment in a xenograft model using A549 lung adenocarcinoma cells resulted in decreased tumor volume compared to vehicle control; however, while the effect was in the same direction as the original study (Figure 4C; Sirota et al., 2011), it was not statistically significant. Cimetidine treatment in a xenograft model using ACHN renal cell carcinoma cells did not differ from vehicle control treatment, similar to the original study (Supplemental Figure 1; Sirota et al., 2011). Doxorubicin treatment in a xenograft model using A549 lung adenocarcinoma cells did not result in a statistically significant difference compared to vehicle control despite tumor volume being reduced to levels similar to those reported in the original study (Figure 4C; Sirota et al., 2011). Finally, we report a random effects meta-analysis for each result. These meta-analyses show that the inhibition of A549 derived tumors by cimetidine resulted in a statistically significant effect, as did the inhibition of A549 derived tumors by doxorubicin. The effect of cimetidine on ACHN derived tumors was not statistically significant, as predicted. DOI: http://dx.doi. org/10.7554/eLife.17044. 001
Evidence of Resistance to Cry34/35Ab1 Corn by Western Corn Rootworm (Coleoptera: Chrysomelidae): Root Injury in the Field and Larval Survival in Plant-Based Bioassays

Abstract Western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), is a serious pest of corn in the United States, and recent management of western corn rootworm has included planting of Bt corn. Beginning in 2009, western corn rootworm populations with resistance to Cry3Bb1 corn and mCry3A corn were found in Iowa and elsewhere. To date, western corn rootworm populations have remained susceptible to corn producing Bt toxin Cry34/35Ab1. In this study, we used single-plant bioassays to test field populations of western corn rootworm for resistance to Cry34/35Ab1 corn, Cry3Bb1 corn, and mCry3A corn. Bioassays included nine rootworm populations collected from fields where severe injury to Bt corn had been observed and six control populations that had never been exposed to Bt corn. We found incomplete resistance to Cry34/35Ab1 corn among field populations collected from fields where severe injury to corn producing Cry34/35Ab1, either singly or as a pyramid, had been observed. Additionally, resistance to Cry3Bb1 corn and mCry3A corn was found among the majority of populations tested. These first cases of resistance to Cry34/35Ab1 corn, and the presence of resistance to multiple Bt toxins by western corn rootworm, highlight the potential vulnerability of Bt corn to the evolution of resistance by western corn rootworm. The use of more diversified management practices, in addition to insect resistance management, likely will be essential to sustain the viability of Bt corn for management of western corn rootworm.
Gabapentin prevents synaptogenesis between sensory and spinal cord neurons induced by thrombospondin‐4 acting on pre‐synaptic Cavα2δ1 subunits and involving T‐type Ca2+ channels

Nerve injury induces concurrent up‐regulation of the voltage‐gated calcium channel subunit Cavα2δ1 and the extracellular matrix protein thrombospondin‐4 (TSP4) in dorsal root ganglia and dorsal spinal cord, leading to the development of a neuropathic pain state. Interactions of these proteins promote aberrant excitatory synaptogenesis that contributes to neuropathic pain state development through unknown mechanisms. We investigated the contributions of Cavα2δ1 subunits and TSP4 to synaptogenesis, and the pathways involved in vitro, and whether treatment with gabapentin could block this process and pain development in vivo.
Methanol independent induction in Pichia pastoris by simple derepressed overexpression of single transcription factors

Carbon source regulated promoters are well‐studied standard tools for controlling gene expression. Acquiring control over the natural regulation of promoters is important for metabolic engineering and synthetic biology applications. In the commonly used protein production host Komagataella phaffii (Pichia pastoris), methanol‐inducible promoters are used because of their tight regulation and exceptional strength. Yet, induction with toxic and flammable methanol can be a considerable safety risk and cannot be applied in many existing fermentation plants. Here we studied new regulatory circuits based on the most frequently used alcohol oxidase 1 promoter (PAOX1), which is tightly repressed in presence of repressing carbon sources and strongly induced by methanol. We compared different overexpression strategies for putative carbon source dependent regulators identified by a homology search in related yeasts and previously published literature in order to convert existing methanol dependent expression strains into methanol free systems. While constitutive overexpression showed only marginal or detrimental effects, derepressed expression (activated when the repressing carbon source is depleted) showed that three transcription factors (TFs) are single handedly suitable to strongly activate PAOX1 in P. pastoris without relying on any specifically engineered host strains. Transcriptome analyses demonstrated that Mxr1, Mit1, and Prm1 regulate partly overlapping and unique sets of genes. Derepressed overexpression of a single TF was sufficient to retrofit existing PAOX1 based expression strains into glucose/glycerol regulated, methanol‐free systems. Given the wide applicability of carbon source regulated promoters, the simplicity and low cost of controlling carbon source feed rates in large scale bioreactors, similar approaches as in P. pastoris may also be useful in other organisms.
Effects of ascorbic acid on plasma thyroxine concentrations and eggshell quality of Leghorn chickens treated with dietary thiouracil.

Because ascorbic acid (AA) and the thyroid hormones are known to influence eggshell formation, the effects of AA on body weight, total plasma thyroxine (T4), egg production, and eggshell quality of Single Comb White Leghorn (SCWL) hens concurrently and previously treated with thiouracil (TU) were determined. Hens were provided feed containing either 0 or 100 ppm AA from 47 to 67 wk of age and either 0 or . 1% TU from 47 to 57 wk of age. A three-way split-plot analysis was employed to test for the effects of AA, TU, and time, and their interactions. Dietary TU increased body weight between 53 and 59 wk, and increased thyroid weight at 67 wk; however, TU only depressed plasma T4 level at 51 wk. Dietary TU depressed egg production from 50 to 56 wk and egg weight at 49, 51, and 57 wk. Dietary TU depressed eggshell weight per unit surface area at 49 wk. There was no significant effect due to AA and no AA by TU interaction for any of the parameters examined. It was concluded that . 1% dietary TU from 47 to 57 wk of age did not alter eggshell quality and that dietary AA at the 100 ppm level did not influence the effects of . 1% TU on body weight, egg production, or egg weight of SCWL hens.
Scale-variance pedestrian detection via an integrated system

In this paper, we propose an integrated system for scale-variance pedestrian detection. It consists of two cascaded components: a multi-layer detection neural network (MLDNN) for scale-variance pedestrian detection, and a fast decision forest (FDF) for boosting detection performance with only a slight decrease in speed. Experimental results on the Caltech Pedestrian dataset show that our approach achieves state-of-the-art performance with a competitive speed.
Interlaboratory comparison of ultrasonic attenuation and speed measurements.

A set of test samples, all containing ultrasonically equivalent tissue‐mimicking material, was produced and measurements of ultrasonic speed and ultrasonic attenuation coefficients were made at seven laboratories using various techniques. The ultrasonic speed values agree well with one another, having a spread of about 0.3 per cent; thus, speed values for tissue parenchyma appearing in the literature are likely to be accurate. Values of ultrasonic attenuation coefficients agree fairly well with one another, with differences between individual values and the group mean of generally less than 20 per cent of the group mean.
Gene-specific mechanisms direct Glucocorticoid Receptor-driven 1 repression of inflammatory response genes in macrophages 2 3 4 5

4 5 Maria A. Sacta, Bowranigan Tharmalingam, Maddalena Coppo, David A. Rollins, 6 Dinesh K. Deochand, Bradley Benjamin, Li Yu, Bin Zhang, Xiaoyu Hu, Rong Li, 7 Yurii Chinenov and Inez Rogatsky* 8 9 Weill Cornell/ Rockefeller/ Sloan Kettering Tri-Institutional MD-PhD Program, 1300 York Avenue, 10 New York, NY 10021 USA 11 12 Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, 535 East 13 70th Street, New York, NY 10021 USA 14 15 Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of 16 Medical Sciences, 1300 York Avenue, New York, NY 10021 USA 17 18 Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084 China 19 20 Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084 China 21 22 Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, 23 San Antonio, Texas 78229 USA 24 25 26
Quantitative Phosphoproteomic and Metabolomic Analyses Reveal GmMYB173 Optimizes Flavonoid Metabolism in Soybean under Salt Stress*

Salinity causes osmotic stress to crops and limits their productivity. To understand the mechanism underlying soybean salt tolerance, proteomics approach was used to identify phosphoproteins altered by NaCl treatment. Results revealed that 412 of the 4698 quantitatively analyzed phosphopeptides were significantly up-regulated on salt treatment, including a phosphopeptide covering the serine 59 in the transcription factor GmMYB173. Our data showed that GmMYB173 is one of the three MYB proteins differentially phosphorylated on salt treatment, and a substrate of the casein kinase-II. MYB recognition sites exist in the promoter of flavonoid synthase gene GmCHS5 and one was found to mediate its recognition by GmMYB173, an event facilitated by phosphorylation. Because GmCHS5 catalyzes the synthesis of chalcone, flavonoids derived from chalcone were monitored using metabolomics approach. Results revealed that 24 flavonoids of 6745 metabolites were significantly up-regulated after salt treatment. We further compared the salt tolerance and flavonoid accumulation in soybean transgenic roots expressing the 35S promoter driven cds and RNAi constructs of GmMYB173 and GmCHS5, as well as phospho-mimic (GmMYB173S59D) and phospho-ablative (GmMYB173S59A) mutants of GmMYB173. Overexpression of GmMYB173S59D and GmCHS5 resulted in the highest increase in salt tolerance and accumulation of cyaniding-3-arabinoside chloride, a dihydroxy B-ring flavonoid. The dihydroxy B-ring flavonoids are more effective as anti-oxidative agents when compared with monohydroxy B-ring flavonoids, such as formononetin. Hence the salt-triggered phosphorylation of GmMYB173, subsequent increase in its affinity to GmCHS5 promoter and the elevated transcription of GmCHS5 likely contribute to soybean salt tolerance by enhancing the accumulation of dihydroxy B-ring flavonoids.
Metformin-induced activation of AMPK inhibits the proliferation and migration of human aortic smooth muscle cells through upregulation of p53 and IFI16

The proliferation and migration of vascular smooth muscle cells are significant in the development and progression of atherosclerosis and plaque rupture. Metformin is a widely used antidiabetic drug, which has been reported to inhibit cell growth and migration. The antiproliferative and antimigratory effects of metformin have been attributed to 5′ adenosine monophosphate-activated protein kinase (AMPK) activation. The purpose of the present study was to investigate the effects of metformin on primary human aortic muscle cells (HASMCs) in vitro and to clarify the underlying mechanism. We investigated the effectiveness of metformin in inhibiting the proliferation and migration of HASMCs in vitro using RNA extraction and reverse transcription-quantitative polymerase chain reaction (RT-qPCR), cell number counting, cell viability assay, cell cycle assay and cell migration assay. Through transfection with small interfering (si)RNA targeting p53 and interferon-inducible protein 16 (IFI16), the roles of p53 and IFI16 in these processes were evaluated. The present study demonstrated that p53, IFI16 and AMPK were upregulated in senescent primary HASMCs, which exhibited a decrease in proliferation and migration. In addition, metformin was able to activate p53, IFI16 and AMPK, in order to inhibit proliferation and migration of HASMCs. Furthermore, siRNA-mediated knockdown of p53 and IFI16 attenuated AMPK activation and reversed the suppressive effects of metformin. Notably, in response to metformin, the activation of AMPK was not observed in p53- and IFI16-silenced HASMCs. These results indicated that metformin-induced activation of AMPK suppresses the proliferation and migration of HASMCs by upregulating p53 and IFI16. These findings suggested that metformin may have potential use in the treatment of atherosclerosis.
Answerer in Questioner's Mind for Goal-Oriented Visual Dialogue

Goal-oriented dialogue has been paid attention for its numerous applications in artificial intelligence. To solve this task, deep learning and reinforcement learning have recently been applied. However, these approaches struggle to find a competent recurrent neural questioner, owing to the complexity of learning a series of sentences. Motivated by theory of mind, we propose "Answerer in Questioner's Mind" (AQM), a novel algorithm for goal-oriented dialogue. With AQM, a questioner asks and infers based on an approximated probabilistic model of the answerer. The questioner figures out the answerer's intent via selecting a plausible question by explicitly calculating the information gain of the candidate intentions and possible answers to each question. We test our framework on two goal-oriented visual dialogue tasks: "MNIST Counting Dialog" and "GuessWhat? " In our experiments, AQM outperforms comparative algorithms and makes human-like dialogue. We further use AQM as a tool for analyzing the mechanism of deep reinforcement learning approach and discuss the future direction of practical goal-oriented neural dialogue systems.
A Clustering Algorithm Based on Improved Minimum Spanning Tree

The algorithms of data mining need better efficiency as data scale becomes larger and larger and the dimension of data is more. Aiming at the lower efficiency of the former MST (minimum spanning tree) clustering algorithm based on gene expression, a modified IMST (improved minimum spanning tree) clustering algorithm applied to common problem is brought forward. The analyzing of theory and example show that new IMST clustering algorithm can enhance the efficiency of constructing spanning tree and can solve sorting problem for shorter edges of clustering in minimum spanning trees. At last, both the efficiency of clustering and its effect are improved whole.