Miracle-dz/UniFAR-FTUs huggingface dataset:
SketchDLC

With the fast development of deep learning (DL), the communication is increasingly a bottleneck for distributed workloads, and a series of optimization works have been done to scale out successfully. Nevertheless, the network behavior has not been investigated much yet. We intend to analyze the network behavior and then carry out some research through network simulation. Under this circumstance, an accurate communication measurement is necessary, as it is an effective way to study the network behavior and the basis for accurate simulation. Therefore, we propose to capture the deep learning communication (DLC) trace to achieve the measurement. To the best of our knowledge, we make the first attempt to capture the communication trace for DL training. In this article, we first provide detailed analyses about the communication mechanism of MXNet, which is a representative framework for distributed DL. Secondly, we define the DLC trace format to describe and record the communication behaviors. Third, we present the implementation of method for trace capturing. Finally, we make some statistics and analyses about the distributed DL training, including communication pattern, overlap ratio between computation and communication, computation overhead, synchronization overhead, update overhead, and so forth. Both the statistics and analyses are based on the trace files captured in a cluster with six machines. On the one hand, our trace files provide a sketch on the DLC, which contributes to understanding the communication details. On the other hand, the captured trace files can be used for figuring out various overheads, as they record the communication behaviors of each node.
A modified backward/forward sweep-based method for reconfiguration of unbalanced distribution networks

<span lang="EN-US">A three-phase unbalanced power flow method can provide a more realistic scenario of how distribution networks operate. The backward/forward sweep-based power flow method </span><span lang="EN-AU">(BF-PF)</span><span lang="EN-US"> has been used for many years as an important computational tool to solve the power flow for unbalanced and radial power systems. However, some of the </span><span lang="EN-AU">few </span><span lang="EN-US">available research tools produce many errors when </span><span lang="EN-AU">they </span><span lang="EN-US">are used for </span><span lang="EN-AU">network </span><span lang="EN-US">reconfiguration </span><span lang="EN-AU">because the </span><span lang="EN-US">topology change</span><span lang="EN-AU">s</span><span lang="EN-AU">after multiple switch actions</span><span lang="EN-US"> and the nodes are disorganized continually. </span><span lang="EN-AU">T</span><span lang="EN-US">his paper presents </span><span lang="EN-AU">a modified</span><span lang="EN-AU">BF-PF for </span><span lang="EN-US">three-phase unbalanced radial </span><span lang="EN-AU">distribution networks</span><span lang="EN-US"> that is capable </span><span lang="EN-AU">of arranging</span><span lang="EN-US"> the system topology when reconfiguration changes the branch connections. A binary search is used to determine the connections between nodes, allowing the algorithm to avoid those problems when reconfiguration is carried out, regardless of node numbers. Tests are made to verify the usefulness of the proposed algorithm in both the IEEE 13-node test feeder and the 123-node test feeder, converging in every run where constraints are accomplished. This approach can be used easily for a large-scale feeder network reconfiguration. </span><span lang="EN-AU"> The full version of this modified </span><span lang="EN-US">backward/forward sweep</span><span lang="EN-AU"> algorithm is available for research at MathWorks</span><span lang="EN-US">. </span>
Leukocyte-specific protein 1 targets the ERK/MAP kinase scaffold protein KSR and MEK1 and ERK2 to the actin cytoskeleton

The identification and characterization of scaffold and targeting proteins of the ERK/MAP kinase pathway is important to understand the function and intracellular organization of this pathway. The F-actin binding protein leukocyte-specific protein 1 (LSP1) binds to PKCβI and expression of B-LSP1, an LSP1 truncate containing the PKCβI binding residues, inhibits anti-IgM-induced translocation of PKCβI to the plasma membrane and anti-IgM-induced activation of ERK2. To understand the role of LSP1 in the regulation of PKCβI-dependent ERK2 activation, we investigated whether LSP1 interacts with ERK/MAP kinase pathway components and targets these proteins to the actin cytoskeleton. We show that LSP1 associates with the ERK scaffold protein KSR and with MEK1 and ERK2. LSP1-associated MEK1 is activated by anti-IgM treatment and this activation is inhibited by expression of B-LSP1, suggesting that the activation of LSP1-associated MEK1 is PKCβI dependent. Confocal microscopy showed that LSP1 targets KSR, MEK1 and ERK2 to peripheral actin filaments. Thus our data show that LSP1 is a cytoskeletal targeting protein for the ERK/MAP kinase pathway and support a model in which MEK1 and ERK2 are organized in a cytoskeletal signaling complex together with KSR, PKCβI and LSP1 and are activated by anti-IgM in a PKCβI-dependent manner.
Effective Extensible Programming: Unleashing Julia on GPUs

GPUs and other accelerators are popular devices for accelerating compute-intensive, parallelizable applications. However, programming these devices is a difficult task. Writing efficient device code is challenging, and is typically done in a low-level programming language. High-level languages are rarely supported, or do not integrate with the rest of the high-level language ecosystem. To overcome this, we propose compiler infrastructure to efficiently add support for new hardware or environments to an existing programming language. We evaluate our approach by adding support for NVIDIA GPUs to the Julia programming language. By integrating with the existing compiler, we significantly lower the cost to implement and maintain the new compiler, and facilitate reuse of existing application code. Moreover, use of the high-level Julia programming language enables new and dynamic approaches for GPU programming. This greatly improves programmer productivity, while maintaining application performance similar to that of the official NVIDIA CUDA toolkit.
Breeding latitude predicts timing but not rate of spring migration in a widespread migratory bird in South America

Abstract Identifying the processes that determine avian migratory strategies in different environmental contexts is imperative to understanding the constraints to survival and reproduction faced by migratory birds across the planet. We compared the spring migration strategies of Fork‐tailed Flycatchers (Tyrannus s. savana) that breed at south‐temperate latitudes (i.e., austral migrants) vs. tropical latitudes (i.e., intratropical migrants) in South America. We hypothesized that austral migrant flycatchers are more time‐selected than intratropical migrants during spring migration. As such, we predicted that austral migrants, which migrate further than intratropical migrants, will migrate at a faster rate and that the rate of migration for austral migrants will be positively correlated with the onset of spring migration. We attached light‐level geolocators to Fork‐tailed Flycatchers at two tropical breeding sites in Brazil and at two south‐temperate breeding sites in Argentina and tracked their movements until the following breeding season. Of 286 geolocators that were deployed, 37 were recovered ~1 year later, of which 28 provided useable data. Rate of spring migration did not differ significantly between the two groups, and only at one site was there a significantly positive relationship between date of initiation of spring migration and arrival date. This represents the first comparison of individual migratory strategies among conspecific passerines breeding at tropical vs. temperate latitudes and suggests that austral migrant Fork‐tailed Flycatchers in South America are not more time‐selected on spring migration than intratropical migrant conspecifics. Low sample sizes could have diminished our power to detect differences (e.g., between sexes), such that further research into the mechanisms underpinning migratory strategies in this poorly understood system is necessary.
Pin1 Promotes Transforming Growth Factor-β-induced Migration and Invasion*

Transforming growth factor-β (TGF-β) regulates a wide variety of biological activities. It induces potent growth-inhibitory responses in normal cells but promotes migration and invasion of cancer cells. Smads mediate the TGF-β responses. TGF-β binding to the cell surface receptors leads to the phosphorylation of Smad2/3 in their C terminus as well as in the proline-rich linker region. The serine/threonine phosphorylation sites in the linker region are followed by the proline residue. Pin1, a peptidyl-prolyl cis/trans isomerase, recognizes phosphorylated serine/threonine-proline motifs. Here we show that Smad2/3 interacts with Pin1 in a TGF-β-dependent manner. We further show that the phosphorylated threonine 179-proline motif in the Smad3 linker region is the major binding site for Pin1. Although epidermal growth factor also induces phosphorylation of threonine 179 and other residues in the Smad3 linker region the same as TGF-β, Pin1 is unable to bind to the epidermal growth factor-stimulated Smad3. Further analysis suggests that phosphorylation of Smad3 in the C terminus is necessary for the interaction with Pin1. Depletion of Pin1 by small hairpin RNA does not significantly affect TGF-β-induced growth-inhibitory responses and a number of TGF-β/Smad target genes analyzed. In contrast, knockdown of Pin1 in human PC3 prostate cancer cells strongly inhibited TGF-β-mediated migration and invasion. Accordingly, TGF-β induction of N-cadherin, which plays an important role in migration and invasion, is markedly reduced when Pin1 is depleted in PC3 cells. Because Pin1 is overexpressed in many cancers, our findings highlight the importance of Pin1 in TGF-β-induced migration and invasion of cancer cells.
Long‐Term Ethanol Exposure Decreases the Endotoxin‐Induced Hepatic Acute Phase Response in Rats

BACKGROUND Long-term excessive alcohol intake predisposes to infectious diseases. The hepatic acute-phase response is a component of the innate immune system and is part of the first line of defense against invading pathogens, which may be compromised by alcohol. We aimed to investigate whether an induced acute-phase response is impaired in long-term ethanol (EtOH)-fed rats. METHODS For 6 weeks, rats were either fed a Lieber-DeCarli EtOH-containing (36% as calories) liquid diet ad libitum or calorically pair-fed. Then, the rats were injected intraperitoneally with a low dose of lipopolysaccharide (LPS) (0.5 mg/kg) to induce an acute-phase response. Two hours after LPS, we measured the plasma concentrations of an array of inflammatory cytokines. Twenty-four hours after LPS, we measured the hepatic mRNA expression and serum concentrations of prominent rat acute-phase proteins. RESULTS EtOH-fed rats showed either no liver histopathological changes or varying degrees of steatosis. EtOH feeding decreased the spontaneous liver mRNA expression of the prevailing acute-phase protein alpha-2-macroglobulin (α2M) by 30% (p < 0.01). LPS immediately increased plasma tumor necrosis factor-alpha and interleukin-6 more than 100-fold in both feeding groups (p < 0.001, all) and approximately twice as much in the EtOH-fed rats (p < 0.05 and p = 0.08, respectively). LPS also induced a variable but marked amplification of (α2M), haptoglobin, alpha-1-acid glycoprotein, and lipocalin-2 liver mRNA expression levels and serum concentrations in both feeding groups (p ≤ 0.01 to 0.001). However, the LPS-induced increases in serum (α2M) and haptoglobin were less pronounced in the EtOH-fed rats, averaging approximately 60% of the concentrations in the pair-fed rats (p < 0.01 and p < 0.001, respectively). CONCLUSIONS Long-term EtOH exposure in rats reduces the spontaneous hepatic mRNA expression of (α2M) and markedly impairs the hepatic acute-phase response to endotoxin, despite higher pro-inflammatory cytokine release. The same phenomenon may contribute to the increased susceptibility to infections observed in humans with long-term excessive alcohol intake.
Safe receding horizon path planning for autonomous vehicles

A flat topped support useable as a table and as a seat is made of lumber. A top is made of a plurality of short boards side-by-side and two spaced apart wood strips which extend across the undersides of the boards and is secured to all of them. The edges of the strips that face each other are undercut to form channels or recesses. Two or more pairs of crossed wooden legs support the top. A pivot bolt pivotally secures the legs of each pair together. Outside the legs at the top of the leg pairs a brace board connects the adjacent pairs and seat in the recesses. A locking bar is suspended from the top midway between the strips by a coiled spring and has its ends notched to provide seats for the lower edges of the brace boards. The spring is of such length that it is under tension when the notches of the bar seat on the lower edges of the brace boards. Lower brace boards may be used to hold the spacing between adjacent pairs.
Multiple object tracking by multi-feature combination based on min-cost network flow

Multiple object tracking has been modelled as minimum cost network flow (MCNF) optimization problem recently. It is one of the most popular tracking-by-detection algorithm. MCNF is particularly effective due to its simple model and optimal solutions. However, complex scenarios, such as noisy detections and multi-objective interactions, make it difficult to track multi-objects in consecutive frames of video sequence. To effectively handle such situations, we proposed a novel method. The idea is a combination of multiple features and min-cost network flows (MF-MCNF). Experimental results on public tracking datasets demonstrate that our approach achieves a greater improvement comparing with existing MNCF algorithms.
The Transmeta Code Morphing#8482; Software: using speculation, recovery, and adaptive retranslation to address real-life challenges

Transmeta's Crusoe microprocessor is a full, system-level implementation of the x86 architecture, comprising a native VLIW microprocessor with a software layer, the Code Morphing Software (CMS), that combines an interpreter, dynamic binary translator, optimizer, and runtime system. In its general structure, CMS resembles other binary translation systems described in the literature, but it is unique in several respects. The wide range of PC workloads that CMS must handle gracefully in real-life operation, plus the need for full system-level x86 compatibility, expose several issues that have received little or no attention in previous literature, such as exceptions and interrupts, I/O, DMA, and self-modifying code. In this paper we discuss some of the challenges raised by these issues, and present the techniques developed in Crusoe and CMS to meet those challenges. The key to these solutions is the Crusoe paradigm of aggressive speculation, recovery to a consistent x86 state using unique hardware commit-and-rollback support, and adaptive retranslation when exceptions occur too often to be handled efficiently by interpretation.
A high-sensitivity battery-less wake-up receiver for 915 MHz ISM band applications

A high-sensitivity fully passive 902-928MHz ISM band wake-up radio (WuRx) receiver for implantable biomedical devices is presented. The WuRx does not have an external power source and harvests the entire energy from the radio-frequency (RF) signal received at the antenna. A high-efficiency differential RF-to-DC converter rectifies the input RF signal and supplies the circuit blocks including a low-power comparator and reference generators; and at the same time retrieves the envelope of the On-Off Keying (OOK) wake-up signal. To enhance the power conversion efficiency (PCE) of the proposed rectifier when the input power is low, appropriate gate-drive voltages for each stage of the rectifier are generated using a chain of auxiliary cells. The WuRx is designed and implemented in 0.13 μm CMOS and achieves a sensitivity of -43 dBm for a 100 kbps wake-up signal.
Microengineered Vascular Systems for Drug Development

Recent advances in microfabrication technologies and advanced biomaterials have allowed for the development of in vitro platforms that recapitulate more physiologically relevant cellular components and function. Microengineered vascular systems are of particular importance for the efficient assessment of drug candidates to physiological barriers lining microvessels. This review highlights advances in the development of microengineered vascular structures with an emphasis on the potential impact on drug delivery studies. Specifically, this article examines the development of models for the study of drug delivery to the central nervous system and cardiovascular system. We also discuss current challenges and future prospects of the development of microengineered vascular systems.
Azo-dye adsorption activity of iron(III) loaded novolac-based network sorbents

Iron(III) loaded novolac-based network adsorbents 1 and 2 were studied for efficient removal of azo-dye pollutants from aqueous solutions. The adsorption behavior was evaluated by using methyl orange and orange-G as model azo dyes. The effect of parameters such as contact time and initial dye concentration on the adsorption of azo dyes was studied. The results showed that loading of Fe(III) onto the sorbent networks has noticeable effect on azo-dye sorption capacity. The adsorption equilibrium data were fitted to Freundlich isotherm model. Besides, the reusability of the dye loaded sorbents was investigated on adjusting pH of solutions.
Experimental comparison of four FAIR arterial spin labeling techniques for quantification of mouse cerebral blood flow at 4.7 T

Pulsed arterial spin labeling (ASL) is an attractive and robust method for quantification of rodent cerebral blood flow (CBF) in particular, although there is a need for sensitivity optimization. Look–Locker flow‐sensitive alternating inversion recovery (FAIR) echo planar imaging (EPI) (LLFAIREPI) was expected to be a likely candidate for assessing sensitivity, although it has not yet been applied to rodents. In this study, the performance of two FAIR techniques and two Look–Locker FAIR techniques were compared in mouse brain at 4.7 T. FAIR‐EPI (single inversion time, FAIREPI‐1TI), FAIR‐EPI (eight inversion times, FAIREPI‐8TI), LLFAIREPI and Look–Locker FAIR gradient echo (LLFAIRGE) sequences were implemented with equal spatial resolution and equal FAIR preparation modules. Measurements were carried out sequentially on the brain in 10 healthy mice, and quantitative CBF maps were obtained after different acquisition times up to 23 min. All methods gave similar group variability in CBF. Especially at shorter acquisition times, LLFAIREPI gave lower relative variations in CBF within selected brain regions than the other techniques at the same acquisition time. The Look–Locker techniques, however, overestimated CBF compared with classical FAIR‐EPI, which was attributed to bulk flow in arterioles and T2 effects. The image quality with LLFAIREPI was less reproducible within the group. Both FAIREPI‐1TI and LLFAIREPI appear to be good candidates for serial rapid measurement of CBF, but LLFAIREPI has the additional advantage that apparent T1 can be measured simultaneously with CBF. Copyright © 2008 John Wiley & Sons, Ltd.
Climate response and radiative forcing from mineral aerosols during the last glacial maximum, pre‐industrial, current and doubled‐carbon dioxide climates

Mineral aerosol impacts on climate through radiative forcing by natural dust sources are examined in the current, last glacial maximum, pre‐industrial and doubled‐carbon dioxide climate. Modeled globally averaged dust loadings change by +88%, +31% and −60% in the last glacial maximum, pre‐industrial and future climates, respectively, relative to the current climate. Model results show globally averaged dust radiative forcing at the top of atmosphere is −1.0, −0.4 and +0.14 W/m2 for the last glacial maximum, pre‐industrial and doubled‐carbon dioxide climates, respectively, relative to the current climate. Globally averaged surface temperature changed by −0.85, −0.22, and +0.06 °C relative to the current climate in the last glacial maximum, pre‐industrial and doubled carbon dioxide climates, respectively, due solely to the dust radiative forcing changes simulated here. These simulations only include natural dust source response to climate change, and neglect possible impacts by human land and water use.
Heuristic procedures for probabilistic project scheduling

In this paper we analyze the resource-constrained project scheduling problem under uncertainty. Project activities are assumed to have known deterministic renewable resource requirements and probabilistic activity durations described by random variables with a given density function. We develop heuristic algorithms for building a schedule with protected starting times, obtained using a buffering mechanism guided by probabilistic information.
Engineering self-regulated synthetic gene expression systems and its application on controlled protein expression

One of the limiting factor in industrial biotechnology is the lack of cost-effective and regulated gene expression systems at large-scale. Thus current approaches suffer of suboptimal gene expression levels and/or they require of expensive inducer metabolites. The emergent of synthetic biology including new highthrouput DNA assembly methods and sophisticated biosensors now allow the redesign of complex bacterial trait including automata and full pre-programed gene expression control systems. This high level of control allows save inducers in bioprocesses and/or reducing the time where the cells and toxic intermediates are in contact by generating an auto-regulated expression system. With the aim to address this important shortcoming in industrial biotechnology and provide a cheap and highly controlled gene expression system at large scale, in this work we firstly have developed a new highthrouput DNA assembly system based on GoldenGate´s MoClo [1] adapted to the Standard European Vector Architecture (pSEVA) [2]. The new methods was further used to generate a large array of complex circuits capable of regulate genetic expression according to phosphate concentration by taking advantage of an existing collection of synthetic promoter available at SBG group [3]. The circuits were generated by assembling synthetic transcriptional units using random assembly of synthetic promoters and ribosome binding sites driving the expression of well-known reporter fluorescent proteins such as GFP and RFP, thus resulting on a wide variety of circuits. The circuits obtained where subsequently analyzed by following the fluorescent profile under different phosphate concentrations media. Those that showed a more promissing behavior where selected to be further studied and sequenced to determine those random elements. Ongoing efforts have focus on the construction of a set of well-characterized synthetic circuits driving the a la carte and self-regulated expression of a given gene, even a whole metabolic pathway. In summary, we have obtained a way number of different plasmids, circuits and components that can be used to elaborate new circuits and constructions with all new applications and functions such as the above mentioned genetic expression self-regulation based on externals factors like phosphate concentration and its application to large scale production systems.
Two-dimensional orthogonal tiling: from theory to practice

In pipelined parallel computations the inner loops are often implemented in a block fashion. In such programs, an important compiler optimization involves the need to statically determine the grain size. This paper presents extensions and experimental validation of the previous results of Andonov and Rajopadhye (1994) on optimal grain size determination.