Miracle-dz/UniFAR-FTUs huggingface dataset:
Somatostatin Inhibits Stem Cell Factor Messenger RNA Expression by Sertoli Cells and Stem Cell Factor-Induced DNA Synthesis in Isolated Seminiferous Tubules1

Abstract Immature porcine Sertoli cells have been reported to be targets for the regulatory peptide somatostatin (SRIF), which inhibits the basal and FSH-induced proliferation of Sertoli cells through a decrease of cAMP production. In the present study, we show that SRIF inhibits both basal and FSH-stimulated expression of the stem cell factor (SCF), a Sertoli cell-specific gene. The SRIF-mediated inhibition of forskolin-triggered, but not of 8-bromoadenosine-cAMP-triggered, SCF mRNA expression demonstrates the involvement of adenylyl cyclase in underlying peptide actions. Moreover, these effects require functional coupling of specific plasma membrane receptors to adenylyl cyclase via inhibitory G proteins, because pertussis toxin prevents SRIF-mediated inhibition of SCF mRNA expression. Reverse transcription-polymerase chain reaction (RT-PCR) and Western blot assays suggest the involvement of sst2 receptors in SRIF actions on Sertoli cells. The biological relevance of these data is supported by an SRIF-mediated decrease in SCF-induced incorporation of [3H]thymidine in isolated seminiferous tubules. In situ hybridization and confocal microscopy show that, in seminiferous tubules only, spermatogonia display both c-kit and sst2 receptors. Taken together, these results suggest that SCF-stimulated DNA synthesis can be inhibited by SRIF in spermatogonia, but not in Sertoli and peritubular cells. Combined RT-PCR and immunohistochemical approaches point toward spermatogonia and Leydig cells as the source of testicular SRIF. These data argue in favor of paracrine/autocrine SRIF actions in testis.
Vectorial insertion of apical and basolateral membrane proteins in polarized epithelial cells revealed by quantitative 3D live cell imaging

Although epithelial cells are known to exhibit a polarized distribution of membrane components, the pathways responsible for delivering membrane proteins to their appropriate domains remain unclear. Using an optimized approach to three-dimensional live cell imaging, we have visualized the transport of newly synthesized apical and basolateral membrane proteins in fully polarized filter-grown Madin-Darby canine kidney cells. We performed a detailed quantitative kinetic analysis of trans-Golgi network (TGN) exit, passage through transport intermediates, and arrival at the plasma membrane using cyan/yellow fluorescent protein-tagged glycosylphosphatidylinositol-anchored protein and vesicular stomatitis virus glycoprotein as apical and basolateral reporters, respectively. For both pathways, exit from the TGN was rate limiting. Furthermore, apical and basolateral proteins were targeted directly to their respective membranes, resolving current confusion as to whether sorting occurs on the secretory pathway or only after endocytosis. However, a transcytotic protein did reach the apical surface after a prior appearance basolaterally. Finally, newly synthesized proteins appeared to be delivered to the entire lateral or apical surface, suggesting-contrary to expectations-that there is not a restricted site for vesicle docking or fusion adjacent to the junctional complex.
Regulation of the ato operon by the atoC gene in Escherichia coli

The expression of the Ato enzymes, acetyl coenzyme A:acetoacetyl coenzyme A transferase and thiolase II, is required for growth of Escherichia coli on short-chain fatty acids. The structural genes for these enzymes, atoD, atoA, and atoB, respectively, make up the ato operon. A 48-kilodalton protein encoded by atoC was required for the synthesis or activation of the Ato enzymes. The expression of Ato enzyme activities was inducible in atoC+ strains, constitutive in atoCc strains, and noninducible in atoC mutants. Merodiploid studies demonstrated that the atoCc allele is trans-dominant to the atoC+ allele. To study the action of the trans-acting atoC-encoded activator, the promoter of the ato operon was fused to the promoterless galK gene and introduced into a low-copy-number vector. The resulting low-copy-number fusion plasmid was introduced into atoC+, atoC, and atoCc hosts. The expression of the fused galK gene was inducible in the atoC+ host, noninducible in atoC host strains, and constitutive when harbored in the atoCc host. This indicated that the atoC+ and atoCc gene products act at the level of transcription, stimulating the expression of the ato operon. A working model consistent with these results is presented.
Is Flow-Mediated Dilation Nitric Oxide Mediated?: A Meta-Analysis

Flow-mediated dilation (FMD) is a noninvasive index of endothelial function and vascular health in humans. Studies examining the role of nitric oxide (NO) are not conclusive. In this article, we quantified the contribution of NO in FMD of conduit arteries and explored the effect of the protocol (ie, distal cuff, ≈5-minute ischemia) and method of analysis (ie, automated and continuous edge detection) on the NO dependency of this test. A systematic review and 3-stage meta-analysis of published crossover studies that measured FMD under local infusion of saline or the NO synthase blocker NGmonomethyl-L-arginine (L-NMMA) was undertaken. Twenty studies met the inclusion criteria for stage 1 (374 individual comparisons). The meta-analyzed outcome was the difference in FMD between infusion of saline (ie, FMDsaline) and NO synthase blocker (ie, FMDL-NMMA). Overall, FMDsaline was 8.2% (95% confidence interval [CI], 6.8%–9.6%) compared with FMDL-NMMA of 3.7% (95% CI, 3.1%–4.3%; P<0.001). Stage 2 analysis focused on studies that used the most commonly adopted approach in healthy volunteers (ie, distal cuff placement, ≈5-minute occlusion), which similarly revealed a significant NO contribution to FMD (FMDsaline, 6.5% [95% CI, 5.7%–7.3%]; FMDL-NMMA, 0.9% [95% CI, 0.5%–1.3%]; P<0.001). Stage 3 meta-analyzed the studies that adopted the commonly adopted approach and automated, continuous method of analysis, which also revealed a significant contribution of NO to the FMD (FMDsaline, 6.9% [95% CI, 6.0%–7.8%]; FMDL-NMMA, 2.4% [95% CI, 1.1%–3.7%]; P<0.001). This comprehensive analysis demonstrates that FMD of conduit arteries in humans is, at least in part, mediated by NO.
Risk-Return Relationship in a Complex Adaptive System

For survival and development, autonomous agents in complex adaptive systems involving the human society must compete against or collaborate with others for sharing limited resources or wealth, by using different methods. One method is to invest, in order to obtain payoffs with risk. It is a common belief that investments with a positive risk-return relationship (namely, high risk high return and vice versa) are dominant over those with a negative risk-return relationship (i.e., high risk low return and vice versa) in the human society; the belief has a notable impact on daily investing activities of investors. Here we investigate the risk-return relationship in a model complex adaptive system, in order to study the effect of both market efficiency and closeness that exist in the human society and play an important role in helping to establish traditional finance/economics theories. We conduct a series of computer-aided human experiments, and also perform agent-based simulations and theoretical analysis to confirm the experimental observations and reveal the underlying mechanism. We report that investments with a negative risk-return relationship have dominance over those with a positive risk-return relationship instead in such a complex adaptive systems. We formulate the dynamical process for the system's evolution, which helps to discover the different role of identical and heterogeneous preferences. This work might be valuable not only to complexity science, but also to finance and economics, to management and social science, and to physics.
ControlIt! - A Software Framework for Whole-Body Operational Space Control

Whole Body Operational Space Control (WBOSC) enables floating-base highly redundant robots to achieve unified motion/force control of one or more operational space objectives while adhering to physical constraints. It is a pioneering algorithm in the field of human-centered Whole-Body Control (WBC). Although there are extensive studies on the algorithms and theory behind WBOSC, limited studies exist on the software architecture and APIs that enable WBOSC to perform and be integrated into a larger system. In this paper, we address this by presenting ControlIt! , a new open-source software framework for WBOSC. Unlike previous implementations, ControlIt! is multi-threaded to increase maximum servo frequencies using standard PC hardware. A new parameter binding mechanism enables tight integration between ControlIt! and external processes via an extensible set of transport protocols. To support a new robot, only two plugins and a URDF model is needed — the rest of ControlIt! remains unchanged. New WBC primitives can be added by writing Task or Constraint plugins. ControlIt! 's capabilities are demonstrated on Dreamer, a 16-DOF torque controlled humanoid upper body robot containing both series elastic and co-actuated joints, and using it to perform a product disassembly task. Using this testbed, we show that ControlIt! can achieve average servo latencies of about 0.5 ms when configured with two Cartesian position tasks, two orientation tasks, and a lower priority posture task. This is 10 times faster than the 5ms that was achieved using UTA-WBC, the prototype implementation of WBOSC that is both application and platform-specific. Variations in the product's position is handled by updating the goal of the Cartesian position task. ControlIt! 's source code is released under LGPL and we hope it will be adopted and maintained by the WBC community for the long term as a platform for WBC development and integration.
Scalable memory registration for high performance networks using helper threads

Remote DMA (RDMA) enables high performance networks to reduce data copying between an application and the operating system (OS). However RDMA operations in some high performance networks require communication memory explicitly registered with the network adapter and pinned by the OS. Memory registration and pinning limits the flexibility of the memory system and reduces the amount of memory that user processes can allocate. These issues become more significant on multicore platforms, since registered memory demand grows linearly with the number of processor cores. In this paper we propose a new memory registration/deregistration strategy to reduce registered memory on multicore architectures for HPC applications. We hide the cost of dynamic memory management by offloading all dynamic memory registration and deregistration requests to a dedicated memory management helper thread. We investigate design policies and performance implications of the helper thread approach. We evaluate our framework with the NAS parallel benchmarks, for which our registration scheme significantly reduces the registered memory (23.62% on average and up to 49.39%) and avoids memory registration/deregistration costs for reused communication memory. We show that our system enables the execution of problem sizes that could not complete under existing memory registration strategies.
Partitioned Global Address Space Languages

The Partitioned Global Address Space (PGAS) model is a parallel programming model that aims to improve programmer productivity while at the same time aiming for high performance. The main premise of PGAS is that a globally shared address space improves productivity, but that a distinction between local and remote data accesses is required to allow performance optimizations and to support scalability on large-scale parallel architectures. To this end, PGAS preserves the global address space while embracing awareness of nonuniform communication costs. Today, about a dozen languages exist that adhere to the PGAS model. This survey proposes a definition and a taxonomy along four axes: how parallelism is introduced, how the address space is partitioned, how data is distributed among the partitions, and finally, how data is accessed across partitions. Our taxonomy reveals that today’s PGAS languages focus on distributing regular data and distinguish only between local and remote data access cost, whereas the distribution of irregular data and the adoption of richer data access cost models remain open challenges.
A Network-Friendly Disk I/O Optimization Framework in a Virtualized Cloud System

In a typical virtualized cloud system, network-attached storage (NAS) is the common technology for storing the disk image files of virtual machine (VM). Although the client/server model on NAS is more reliable and manageable, a concurrent accessing behavior from multiple VMs on the shared NAS server may exhaust the underlying network bandwidth, thus hurting the disk I/O performance of VMs. In this paper, we improve this problem by a set of optimizations, which are designed around bridging the semantic gap between the file system of VM and NAS server. The experimental result shows that our work can effectively reduce the network traffic between the NAS server and client. Meanwhile, the disk I/O performance of VMs can be also improved.
Chemoenzymatic Synthesis of Prenylated Indole Derivatives by Using a 4‐Dimethylallyltryptophan Synthase from Aspergillus fumigatus

A 4‐dimethylallyltryptophan synthase, FgaPT2, has been identified in the genome of Aspergillus fumigatus. In a previous study, FgaPT2 was overexpressed in Saccharomyces cerevisiae and characterized biochemically. A higher protein yield (up to 100‐fold higher than that for S. cerevisiae) has now been achieved by overexpression in E. coli; this has permitted investigation into substrate specificity with alternative substances. FgaPT2 accepted 17 of 37 commercially available indole derivatives as substrates. Tryptophan derivatives that carry methyl groups at the indole ring showed a different acceptance from those with methyl groups on the side chain. 5‐Hydroxytryptophan was well accepted by FgaPT2, while the halogenated derivatives were not accepted. Decarboxylation, deamination, or oxidative deamination of tryptophan, as well as replacement of the NH2 group by OH, or of the COOH group by CH2COOH or CONHOH resulted in decreased but still significant enzymatic activity. None of the tested tryptophan‐containing dipeptides was accepted by FgaPT2. Structural elucidation of isolated enzymatic products by NMR and MS analyses proved unequivocally that the prenylation was regioselective at position C4 of the indole ring in the presence of dimethylallyl diphosphate. Determination of the kinetic parameters revealed that L‐tryptophan was accepted as the best substrate by the enzyme, followed by 5‐,6‐,7‐methyltryptophan and L‐abrine. The enzymatic rate constant (kcat Km−1) of nine selected substrates were found to be about 1.0 to 6.5 % of that for L‐tryptophan. Overnight incubation with eight substances showed that the conversion ratio to their prenylated derivatives was in the range 32.5 to 99.7 %. This provides evidence that 4‐dimethylallylated indole derivatives can be produced by chemoenzymatic synthesis with FgaPT2.
A neural-fuzzy walking control of an autonomous biped robot

In this paper, an adaptive neural-fuzzy walking control of an autonomous biped robot is proposed. This control system uses a feed forward neural network based on nonlinear regression. The general regression neural network is used to construct the base of an adaptive neuro-fuzzy system. The neural network uses an iterative grid partition method for the initial structure identification of the controller parameters. Comparison results are done between the proposed method and the ANFIS tool provided in the fuzzy MATLAB toolbox. The robot's control system uses an inverted pendulum to balance of the gaits. The effectiveness of the proposed control system is demonstrated by simulation and experimental tests
Users of Open Source Software - How Do They Get Help?

A study was conducted across multiple open source software online technical help communities. This paper presents the types of discussions that occur, the types of questions asked and the type of responses that are given. The implications for socio-technical design are considered, exploring how help requests and discussions can be used to improve future help-giving, documentation and interface and functionality redesign.
An intracytoplasmic injection of deionized bovine serum albumin immediately after somatic cell nuclear transfer enhances full-term development of cloned mouse embryos

In mouse somatic cell nuclear transfer (SCNT), polyvinylpyrrolidone (PVP) is typically included in the nuclear donor injection medium. However, the cytotoxicity of PVP, which is injected into the cytoplasm of oocytes, has recently become a cause of concern. In the present study, we determined whether bovine serum albumin deionized with an ion-exchange resin treatment (d-BSA) was applicable to the nuclear donor injection medium in SCNT as an alternative to PVP. The results obtained showed that d-BSA introduced into the cytoplasm of an enucleated oocyte together with a donor nucleus significantly enhanced the rate of in vitro development of cloned embryos to the blastocyst stage compared with that of a conventional nuclear injection with PVP in SCNT. We also defined the enhancing effects of d-BSA on the blastocyst formation rate when d-BSA was injected into the cytoplasm of oocytes reconstructed using the fusion method with a hemagglutinating virus of Japan envelope before oocyte activation. Furthermore, immunofluorescence experiments revealed that the injected d-BSA increased the acetylation levels of histone H3 lysine 9 and histone H4 lysine 12 in cloned pronuclear (PN) and 2-cell embryos. The injection of d-BSA before oocyte activation also increased the production of cloned mouse offspring. These results suggested that intracytoplasmic injection of d-BSA into SCNT oocytes before oocyte activation was beneficial for enhancing the in vitro and in vivo development of mouse cloned embryos through epigenetic modifications to nuclear reprogramming.
Speech enhancement based on L1 regularization in the cepstral domain

In this paper, a new speech enhancement algorithm using the L1 regularization method in the cepstral domain is proposed. Since voiced speeches have a quasi-periodic nature that allows them to be compactly represented in the cepstral domain, the L1 regularization technique can be applied to better control the optimization process required in speech enhancement applications. The proposed algorithm starts with the traditional temporal cepstral smoothing (TCS) method which gives the initial estimation of the power spectrum of the clean speech. It is then refined using a modified L1 regularizer which imposes further constraint to the penalty function based on the feature of speech signals in the cepstral domain. A notable improvement of the proposed algorithm over the traditional method is its adaptability to the non-stationary noise. Performance of the proposed algorithm is evaluated using standard measures such as segSNR and PESQ based on a large quantity of speech signals. Our results show that a significant improvement is achieved as compared to the conventional approaches especially in the case that the noise is non-stationary.
Declarative scheduling for active objects

Active objects are programming constructs that abstract distribution and help to handle concurrency. In this paper, we extend the multiactive object programming model to offer a priority specification mechanism. This mechanism allows programmers to have control on the scheduling of requests. The priority representation is based on a dependency graph which makes it very convenient to use. This article shows how to use this mechanism from the programmer side, and exposes the main properties of the dependency graph. The software architecture of our implementation is also presented, as it can be applied to various scheduling systems. Finally, we validate our approach through a microbenchmark that shows that the overhead of our priority representation is rather low. On the whole, we provide a general pattern to introduce a prioritized scheduling in active objects or in any other concurrent systems. The resulting framework is shown to be fine-grained, user-friendly, and efficient.
Selective Reduction in A2 Adenosine Receptor Desensitization Following Antisense‐Induced Suppression of G Protein‐Coupled Receptor Kinase 2 Expression

Phosphorylation of G protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) is considered to play a critical role in the desensitization of responses mediated by these receptors. To explore the role of GRK2 in A2 adenosine receptor desensitization, we attempted to reduce specifically GRK2 expression in NG108-15 cells by stable transfection with an antisense rat GRK2 cDNA sequence. This yielded up to a 69% loss of GRK2 when compared with plasmid-transfected control cells, which correlated with a reduction in kinase activity when measured by the ability of cell lysates to promote light-dependent phosphorylation of rhodopsin. Levels of GRK3 were the same in antisense and plasmid-transfected controls. On addition of the A2 adenosine receptor agonist 5'-(N-ethylcarboxamido)adenosine, cyclic AMP accumulation was greater in GRK2 antisense cells as compared with plasmid control cells. In contrast, cyclic AMP accumulation via agonist stimulation of either IP-prostanoid or secretin receptors or by addition of forskolin was not significantly different among all clones examined. The increase in A2 adenosine receptor response could not be explained by changes in A2A adenosine receptor expression, as assessed by ligand binding experiments with the radioligand 2-3H-labelled 4-[2-[7-amino-2-(2-furyl)[1,2,4]triazolo[2,3-a][1,3,5]triazin-5-++ +ylamino]ethyl]phenol ([3H]ZM241385). These data show for the first time a direct correlation between expression of GRK2 and desensitization of natively expressed A2 adenosine receptors in intact cells, suggesting that GRK2 plays a major role in the regulation of these receptors. Key Words: G protein-coupled receptor kinase-G protein-coupled receptor-Antisense-NG108-15 cells-A2 adenosine receptors-Desensitization.
Estimating Missing Features to Improve Multimedia Information Retrieval

Retrieval in a multimedia database usually involves combining information from different modalities of data, such as text and images. However, all modalities of the data may not be available to form the query. The retrieval results from such a partial query are often less than satisfactory. In this paper, we present an approach to complete a partial query by estimating the missing features in the query. Our experiments with a database of images and their associated captions show that, with an initial text-only query, our completion method has similar performance to a full query with both image and text features. In addition, when we use relevance feedback, our approach outperforms the results obtained using a full query.