Proteus: Simulating the Performance of Distributed DNN Training

DNN models are becoming increasingly larger to achieve unprecedented accuracy, and the accompanying increased computation and memory requirements necessitate the employment of massive clusters and elaborate parallelization strategies to accelerate DNN training. In order to better optimize the performance and analyze the cost, it is indispensable to model the training throughput of distributed DNN training. However, complex parallelization strategies and the resulting complex runtime behaviors make it challenging to construct an accurate performance model. In this paper, we present Proteus, the first standalone simulator to model the performance of complex parallelization strategies through simulation execution. Proteus first models complex parallelization strategies with a unified representation named Strategy Tree. Then, it compiles the strategy tree into a distributed execution graph and simulates the complex runtime behaviors, comp-comm overlap and bandwidth sharing, with a Hierarchical Topo-Aware Executor (HTAE). We finally evaluate Proteus across a wide variety of DNNs on three hardware configurations. Experimental results show that Proteus achieves $3.0\%$ average prediction error and preserves order for training throughput of various parallelization strategies. Compared to state-of-the-art approaches, Proteus reduces prediction error by up to $133.8\%$

Reproductive toxicity of low level bisphenol A exposures in a two-generation zebrafish assay: Evidence of male-specific effects

Bisphenol A (BPA), a high-volume chemical used to make polycarbonate plastic and epoxy resins, is a ubiquitous contaminant in environment and human body. To investigate the reproductive effects of long-term exposure to low concentrations of BPA, a two-generation study was conducted using the aquatic model species of zebrafish. Our findings revealed that exposure to 1 nM (0.228 μg/L) BPA for continuous two generations resulted in female-biased sex ratio in both F1 and F2 adult population, decreased sperm density, and decreased sperm quality as measured by motility, velocity, ATP content and lipid peroxidation in F1 and F2 males. Females were less sensitive to BPA exposures than males as no adverse effects were found in female gonads or gametes. Delayed hatching at 48 hpf and increased malformation and mortality were found in the offspring from BPA exposed F2, but not F1 parents. Most importantly, the adverse effect on larval development and survival from BPA exposed F2 parents was paternal-specific, resulting mainly from BPA exposed males. Subsequent transcription analysis of F2 male gonads revealed dysregulated mitochondrial biogenesis and significant activation of non-canonical Wnt/planar cell polarity and Wnt/Calcium signaling pathways. Gene expression analysis of larvae from BPA exposed F2 parents showed significant reduced expression of DNA methyltransferases such as dnmt1, dnmt3, and dnmt5. In conclusion, low level BPA exposures for continuous two generations not only affects sex ratio and sperm quantity/quality in F1 and F2 adults, reproductive success in offspring from F2 parents, but also perturbs various molecular pathways potentially contributing to these BPA induced male-specific reproductive defects.This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/aquatic-toxicology/Keywords: Wnt signaling, BPA, Zebrafish, Chronic exposure, Sperm, Mitochondrial biogenesisKeywords: Wnt signaling, BPA, Zebrafish, Chronic exposure, Sperm, Mitochondrial biogenesi

pH-Responsive Host–Guest Complexation in Pillar[6]arene-Containing Polyelectrolyte Multilayer Films

A water-soluble, anionic pillar[6]arene derivative (WP6) is applied as monomeric building block for the layer-by-layer self-assembly of thin polyelectrolyte multilayer films, and its pH-dependent host–guest properties are employed for the reversible binding and release of a methylviologen guest molecule. The alternating assembly of anionic WP6 and cationic diazo resin (DAR) is monitored in-situ by a dissipative quartz crystal microbalance (QCM-D). In solution, the formation of a stoichiometric inclusion complex of WP6 and cationic methylviologen (MV) as guest molecule is investigated by isothermal titration calorimetry and UV-vis spectroscopy, respectively, and attributed to electrostatic interactions as primary driving force of the host–guest complexation. Exposure of WP6-containing multilayers to MV solution reveals a significant decrease of the resonance frequency, confirming MV binding. Subsequent release is achieved by pH lowering, decreasing the host–guest interactions. The dissociation of the host–guest complex, release of the guest from the film, as well as full reversibility of the binding event are identified by QCM-D. In addition, UV-vis data quantify the surface coverage of the guest molecule in the film after loading and release, respectively. These findings establish the pH-responsiveness of WP6 as a novel external stimulus for the reversible guest molecule recognition in thin films

New Method to Evaluate the Crosslinking Degree of Resin Finishing Agent with Cellulose Using Kjeldahl Method and Arrhenius Formula

In anti-wrinkle finishing, the crosslinking degree of fabric is mainly determined by wrinkle recovery angle, stiffness, and viscosity, these indicators can only reflect the finishing effect from a macro perspective, which cannot reflect whether the crosslinking is sufficient, and it is difficult to quantify the crosslinking degree. In this paper, we combined the Kjeldahl method with the Arrhenius formula and proposed a method to analyze the crosslinking degree of dimethyloldihydroxyethyleneurea (two-dimensional (2D) resin) with cotton cellulose during delayed-cure finishing for the first time. The nitrogen content of completed fabrics during storage was measured by the Kjeldahl method, and the reaction rate equation of the 2D resin and cellulose under normal temperature conditions was calculated. The results show that the nitrogen content is more suitable to indicate the crosslinking degree, and the apparent activation energy was 28.271 kJ/mol and the pre-finger factor was 0.622, which indicated that the 2D resin was prone to cross-linking with cotton fabrics during storage. During long-term storage, the relative errors between the calculated and measured values of the nitrogen content were within ±5%, and the accuracy was higher than the traditional evaluation method. The stability of 2D resins during the storage of delayed-curing finishing was also analyzed through this method

Characteristics and possible mechanisms of 46, XY differences in sex development caused by novel compound variants in NR5A1 and MAP3K1

Abstract Background Dozens of genes are involved in 46, XY differences in sex development (DSD). Notably, about 3/4 of patients cannot make a clear etiology diagnosis and single gene variant identified cannot fully explain the clinical heterogeneity of 46, XY DSD. Materials and methods We conducted a systematic clinical analysis of a 46, XY DSD patient, and applied whole-exome sequencing for the genetic analysis of this pedigree. The identified variants were analyzed by bioinformatic analysis and in vitro studies were performed in human embryonic kidney 293T (HEK-293T) cells which were transiently transfected with wild type or variant NR5A1 and MAP3K1 plasmid. Furthermore, protein production of SRY-box transcription factor 9 (SOX9) was analyzed in cell lysates. Results A novel NR5A1 variant (c.929A > C, p. His310Pro) and a rare MAP3K1 variant (c.2282T > C, p. Ile761Thr) were identified in the proband, whereas the proband's mother and sister who only carry rare MAP3K1 variant have remained phenotypically healthy to the present. These two variants were predicted to be pathogenic by bioinformatic analysis. In vitro, NR5A1 variant decreased the SOX9 production by 82.11% compared to wild type NR5A1, while MAP3K1 variant had little effect on the SOX9 production compared to wild type MAP3K1. Compared to wild type NR5A1 transfection, the SOX9 production of cells transfected with both wild type plasmids decreased by about 17.40%. Compared to variant NR5A1 transfection, the SOX9 production of cells transfected with both variant plasmids increased by the 36.64%. Conclusions Our findings suggested the novel compound variants of NR5A1 and MAP3K1 can alter the expression of SOX9 and ultimately lead to abnormality of sex development

The complete chloroplast genome of a Cladrastis yunchunii X.W.Li et G.S

Cladrastis yunchunii X.W.Li et G.S is a plant species belonged to the family Papilionaceae. Cladrastis yunchunii is currently found in broad-leaved forests in the limestone area of Luxi County, Yunnan Province. It is suitable for afforestation and urban greening in limestone areas. In this study, for the first time, we report the complete chloroplast genome sequence of C. yunchunii. We sequenced and assembled the entire chloroplast genome of C. yunchuniii. The chloroplast genome was determined to be 158,250 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 84,930 bp and 12,664 bp, respectively, which were separated by a pair of inverted repeats (IR) regions of 30,328 bp. The genome contained 132 genes, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The overall GC content of the whole genome is 38.1%, and the corresponding values of the LSC, SSC, and IR regions were 36.4%, 33.6%, and 41.3%, respectively. Phylogenetic analysis suggested that C. yunchunii is closely related to the genus Ormosia in the Papilionaceae

The complete chloroplast genome of Keteleeria evelyniana

Here, we report the complete chloroplast genome of Keteleeria evelyniana. The genome is 116,940 bp in size, which is comprised of a large single-copy (LSC) region of 74,075 bp, a small single-copy (SSC) region of 40,425 bp, and two short inverted repeat (IR) regions of 1,220 bp. The overall GC content of the plastome was 38.5%. The new sequence comprised 103 unique genes, including 74 protein-coding genes, 4 rRNA genes, and 25 tRNA genes. Phylogenetic analysis showed that K.evelyniana was close to Keteleeria hainanensis and Keteleeria davidiana

The complete chloroplast genome of Pinus densata

Here, we report the complete chloroplast (cp) genome of Pinus densata. The complete chloroplast genome is 119,617 bp in length. There were 112 genes in the genome, including 73 protein-coding genes, 35 tRNA genes, and 4 rRNA genes. The overall GC was 38.5%, and the base of A, C, G, and T were 30.6, 19.3, 19.2, and 30.9%, respectively. Phylogenetic analysis showed that P. densata was relatively closely related to Pinus tabuliformis. These data may providing useful information for the phyletic evolution of P. densata within the Pinaceae family

Parcae: Proactive, Liveput-Optimized DNN Training on Preemptible Instances

Deep neural networks (DNNs) are becoming progressively large and costly to train. This paper aims to reduce DNN training costs by leveraging preemptible instances on modern clouds, which can be allocated at a much lower price when idle but may be preempted by the cloud provider at any time. Prior work that supports DNN training on preemptive instances employs a reactive approach to handling instance preemptions and allocations after their occurrence, which only achieves limited performance and scalability. We present Parcae, a system that enables cheap, fast, and scalable DNN training on preemptible instances by proactively adjusting the parallelization strategy of a DNN training job to adapt to predicted resource changes before instance preemptions and allocations really happen, which significantly reduces the cost of handling these events. Parcae optimizes liveput, a novel metric that measures the expected training throughput of a DNN job under various possible preemption scenarios. Compared to existing reactive, throughput-optimized systems, Parcae's proactive, live-optimized solution considers both the throughput of a job and its robustness under preemptions. To optimize liveput, Parcae supports lightweight instance migration and uses an availability predictor to forecast future preemptions. It then uses a liveput optimizer to discover an optimal strategy to parallelize DNN training under predicted preemptions. We evaluate Parcae on a variety of DNNs and preemption traces and show that Parcae outperforms existing spot-instance DNN training systems by up to 10$\times$. More importantly, Parcae achieves near-optimal performance for training large DNNs under frequent preemptions, in which case existing approaches cannot make any progress.Comment: NSDI '2