Miracle-dz/UniFAR-FTUs huggingface dataset:
GossipGraD: Scalable Deep Learning using Gossip Communication based Asynchronous Gradient Descent

In this paper, we present GossipGraD - a gossip communication protocol based Stochastic Gradient Descent (SGD) algorithm for scaling Deep Learning (DL) algorithms on large-scale systems. The salient features of GossipGraD are: 1) reduction in overall communication complexity from {\Theta}(log(p)) for p compute nodes in well-studied SGD to O(1), 2) model diffusion such that compute nodes exchange their updates (gradients) indirectly after every log(p) steps, 3) rotation of communication partners for facilitating direct diffusion of gradients, 4) asynchronous distributed shuffle of samples during the feedforward phase in SGD to prevent over-fitting, 5) asynchronous communication of gradients for further reducing the communication cost of SGD and GossipGraD. We implement GossipGraD for GPU and CPU clusters and use NVIDIA GPUs (Pascal P100) connected with InfiniBand, and Intel Knights Landing (KNL) connected with Aries network. We evaluate GossipGraD using well-studied dataset ImageNet-1K (~250GB), and widely studied neural network topologies such as GoogLeNet and ResNet50 (current winner of ImageNet Large Scale Visualization Research Challenge (ILSVRC)). Our performance evaluation using both KNL and Pascal GPUs indicates that GossipGraD can achieve perfect efficiency for these datasets and their associated neural network topologies. Specifically, for ResNet50, GossipGraD is able to achieve ~100% compute efficiency using 128 NVIDIA Pascal P100 GPUs - while matching the top-1 classification accuracy published in literature.
Photonic Metasurfaces for Spatiotemporal and Ultrafast Light Control

Shaltout, Amr M. Ph.D., Purdue University, December 2015. Photonic Metasurfaces for Spatiotemporal and Ultrafast Light Control. Major Professors: Vladimir Shalaev and Alexander Kildishev. The emergence of photonic metasurfaces planar arrays of nano-antennas has enabled a new paradigm of light control through wave-front engineering. Space-gradient metasurfaces induce spatially varying phase and/or polarization to propagating light. As a consequence, photons propagating through space-gradient metasurfaces can be engineered to undergo a change to their momentum, angular momentum and/or spin states. In our study, we implement metasurface-based devices that break the spin symmetry of light to obtain Photonic Spin Hall Effect (PSHE). We utilized PSHE to design a realtime circular dichroism spectrometer, a device vital in bio-sensing, and an optical rotator used in secure quantum communications. In addition, we developed metasurface based Fabry–Pérot nano-cavities, which go beyond the diffraction limit of light, a requirement to enhance photonic spontaneous emission using the Purcell effect. In addition, we demonstrate that the field of flat photonics is further empowered by utilizing time-gradient metasurfaces with dynamic responses to propagating light. A new genus of optical devices and physical effects can be realized. Photons experience inelastic interactions with time-varying metasurfaces resulting in a Doppler-like wavelength-shift. Furthermore, Snell’s relations are modified to a more universal form not limited by Lorentz reciprocity, hence meeting all the requirements to build magnetic-free optical isolators. Finally, we construct the concept of ultrafast metasurfaces. We integrate spatial interference methodology delivered by metasurfaces and temporal interference of phase-
Impact of homologous recombination deficiency biomarkers on outcomes in patients with triple-negative breast cancer treated with adjuvant doxorubicin and cyclophosphamide (SWOG S9313)

Background Homologous recombination deficiency (HRD)-causing alterations have been reported in triple-negative breast cancer (TNBC). We hypothesized that TNBCs with HRD alterations might be more sensitive to anthracycline plus cyclophosphamide-based chemotherapy and report on HRD status and BRCA1 promoter methylation (PM) as prognostic markers in TNBC patients treated with adjuvant doxorubicin (A) and cyclophosphamide (C) in SWOG9313. Patients and methods In total, 425 TNBC patients were identified from S9313. HRD score, tumor BRCA1/2 sequencing, and BRCA1 PM were carried out on DNA isolated from formalin-fixed paraffin-embedded tissue. Positive HRD status was defined as either a deleterious tumor BRCA1/2 (tBRCA) mutation or a pre-defined HRD score ≥42. Markers were tested for prognostic value on disease-free survival (DFS) and overall survival (OS) using Cox regression models adjusted for treatment assignment and nodal status. Results HRD status was determined in 89% (379/425) of cases. Of these, 67% were HRD positive (27% with tBRCA mutation, 40% tBRCA-negative but HRD score ≥42). HRD-positive status was associated with a better DFS [hazard ratio (HR) 0.72; 95% confidence interval (CI) 0.51-1.00; P = 0.049] and non-significant trend toward better OS (HR = 0.71; 95% CI 0.48-1.03; P = 0.073). High HRD score (≥42) in tBRCA-negative patients (n = 274) was also associated with better DFS (HR = 0.64; 95% CI 0.43-0.94; P = 0.023) and OS (HR = 0.65; 95% CI 0.42-1.00; P = 0.049). BRCA1 PM was evaluated successfully in 82% (348/425) and detected in 32% of cases. The DFS HR for BRCA1 PM was similar to that for HRD but did not reach statistical significance (HR = 0.79; 95% CI 0.54-1.17; P = 0.25). Conclusions HRD positivity was observed in two-thirds of TNBC patients receiving adjuvant AC and was associated with better DFS. HRD status may identify TNBC patients who receive greater benefit from AC-based chemotherapy and should be evaluated further in prospective studies. Clinical Trials Number Int0137 (The trial pre-dates Clinicaltrial.Gov website establishment).
Haemophilus ducreyi Seeks Alternative Carbon Sources and Adapts to Nutrient Stress and Anaerobiosis during Experimental Infection of Human Volunteers

ABSTRACT Haemophilus ducreyi causes the sexually transmitted disease chancroid in adults and cutaneous ulcers in children. In humans, H. ducreyi resides in an abscess and must adapt to a variety of stresses. Previous studies (D. Gangaiah, M. Labandeira-Rey, X. Zhang, K. R. Fortney, S. Ellinger, B. Zwickl, B. Baker, Y. Liu, D. M. Janowicz, B. P. Katz, C. A. Brautigam, R. S. Munson, Jr., E. J. Hansen, and S. M. Spinola, mBio 5:e01081-13, 2014, http://dx.doi.org/10.1128/mBio.01081-13) suggested that H. ducreyi encounters growth conditions in human lesions resembling those found in stationary phase. However, how H. ducreyi transcriptionally responds to stress during human infection is unknown. Here, we determined the H. ducreyi transcriptome in biopsy specimens of human lesions and compared it to the transcriptomes of bacteria grown to mid-log, transition, and stationary phases. Multidimensional scaling showed that the in vivo transcriptome is distinct from those of in vitro growth. Compared to the inoculum (mid-log-phase bacteria), H. ducreyi harvested from pustules differentially expressed ∼93 genes, of which 62 were upregulated. The upregulated genes encode homologs of proteins involved in nutrient transport, alternative carbon pathways (l-ascorbate utilization and metabolism), growth arrest response, heat shock response, DNA recombination, and anaerobiosis. H. ducreyi upregulated few genes (hgbA, flp-tad, and lspB-lspA2) encoding virulence determinants required for human infection. Most genes regulated by CpxRA, RpoE, Hfq, (p)ppGpp, and DksA, which control the expression of virulence determinants and adaptation to a variety of stresses, were not differentially expressed in vivo, suggesting that these systems are cycling on and off during infection. Taken together, these data suggest that the in vivo transcriptome is distinct from those of in vitro growth and that adaptation to nutrient stress and anaerobiosis is crucial for H. ducreyi survival in humans.
HIV-1 Exploits a Dynamic Multi-aminoacyl-tRNA Synthetase Complex To Enhance Viral Replication

ABSTRACT A hallmark of retroviruses such as human immunodeficiency virus type 1 (HIV-1) is reverse transcription of genomic RNA to DNA, a process that is primed by cellular tRNAs. HIV-1 recruits human tRNALys3 to serve as the reverse transcription primer via an interaction between lysyl-tRNA synthetase (LysRS) and the HIV-1 Gag polyprotein. LysRS is normally sequestered in a multi-aminoacyl-tRNA synthetase complex (MSC). Previous studies demonstrated that components of the MSC can be mobilized in response to certain cellular stimuli, but how LysRS is redirected from the MSC to viral particles for packaging is unknown. Here, we show that upon HIV-1 infection, a free pool of non-MSC-associated LysRS is observed and partially relocalized to the nucleus. Heat inactivation of HIV-1 blocks nuclear localization of LysRS, but treatment with a reverse transcriptase inhibitor does not, suggesting that the trigger for relocalization occurs prior to reverse transcription. A reduction in HIV-1 infection is observed upon treatment with an inhibitor to mitogen-activated protein kinase that prevents phosphorylation of LysRS on Ser207, release of LysRS from the MSC, and nuclear localization. A phosphomimetic mutant of LysRS (S207D) that lacked the capability to aminoacylate tRNALys3 localized to the nucleus, rescued HIV-1 infectivity, and was packaged into virions. In contrast, a phosphoablative mutant (S207A) remained cytosolic and maintained full aminoacylation activity but failed to rescue infectivity and was not packaged. These findings suggest that HIV-1 takes advantage of the dynamic nature of the MSC to redirect and coopt cellular translation factors to enhance viral replication. IMPORTANCE Human tRNALys3, the primer for reverse transcription, and LysRS are essential host factors packaged into HIV-1 virions. Previous studies found that tRNALys3 packaging depends on interactions between LysRS and HIV-1 Gag; however, many details regarding the mechanism of tRNALys3 and LysRS packaging remain unknown. LysRS is normally sequestered in a high-molecular-weight multi-aminoacyl-tRNA synthetase complex (MSC), restricting the pool of free LysRS-tRNALys. Mounting evidence suggests that LysRS is released under a variety of stimuli to perform alternative functions within the cell. Here, we show that HIV-1 infection results in a free pool of LysRS that is relocalized to the nucleus of target cells. Blocking this pathway in HIV-1-producing cells resulted in less infectious progeny virions. Understanding the mechanism by which LysRS is recruited into the viral assembly pathway can be exploited for the development of specific and effective therapeutics targeting this nontranslational function.
Molecular Cloning and Expression Analysis of Cyclin H from Black Tiger Shrimp (Penaeus monodon)

Cyclin H is an important cell protein that plays a crucial role in cell division. In the present study, the cDNA of cyclin H (designated as Pmcyclin H) was identified from black tiger shrimp (Penaeus monodon) by expressed sequence tag (EST) analysis, and RACE techniques. The full length cDNA of Pmcyclin H is 1280bp, including a 5’-terminal un-translated region (5’UTR) of 63 bp, a 3’UTR of 218 bp with a poly (A) tail, and an open reading frame (ORF) of 999 bp encoding a polypeptide of 332 amino acids with a predicted molecular weight of 39 kDa, predicted pI of 6.39. Both Blast, and phylogenetic analysis, confirmed that Pmcyclin H is a new member of the shrimp cyclin H family. Using real-time PCR the mRNA expression of Pmcyclin H in eight tissues was examined, and mRNA transcript of Pmcyclin H was predominantly detectable in ovarian tissue, and to a lesser degree in the tissues of intestine, testis, stomach, and heart, but almost undetectable in the tissues of liver (hepar), brain, and muscle. The temporal expression of Pmcyclin H in different developmental stages of the ovaries was investigated by real-time PCR. During the six stages of ovarian development, one peak expression of Pmcyclin H was detected in stage II. All these results indicated that Pmcyclin H might be involved in the regulation of cell cycle and ovarian development of P. monodon. The IJA appears exclusively as a peer-reviewed on-line open-access journal at http://www.siamb. org.il/. To read papers free of charge, please register online at registration form. Sale of IJA papers is strictly forbidden.
Rapid Publication Inactivation of Streptococcus pyogenes Extracellular Cysteine Protease Significantly Decreases Mouse Lethality of Serotype M 3 and M 49 Strains

Cysteine proteases have been implicated as important virulence factors in a wide range of prokaryotic and eukaryotic pathogens, but little direct evidence has been presented to support this notion. Virtually all strains of the human bacterial pathogen Streptococcus pyogenes express a highly conserved extracellular cysteine protease known as streptococcal pyrogenic exotoxin B (SpeB). Two sets of isogenic strains deficient in SpeB cysteine protease activity were constructed by integrational mutagenesis using nonreplicating recombinant plasmids containing a truncated segment of the speB gene. Immunoblot analyses and enzyme assays confirmed that the mutant derivatives were deficient in expression of enzymatically active SpeB cysteine protease. To test the hypothesis that the cysteine protease participates in host mortality, we assessed the ability of serotype M3 and M49 wild-type strains and isogenic protease-negative mutants to cause death in outbred mice after intraperitoneal inoculation. Compared to wild-type parental organisms, the serotype M3 speB mutant lost virtually all ability to cause mouse death ( P , 0.00001), and similarly, the virulence of the M49 mutant was detrimentally altered ( P , 0.005). The data unambiguously demonstrate that the streptococcal enzyme is a virulence factor, and thereby provide additional evidence that microbial cysteine proteases are critical in host–pathogen interactions. ( J. Clin. Invest. 1997. 99:2574– 2580.)
Assessment of fluid responsiveness: recent advances

Purpose of reviewIn the field of prediction of fluid responsiveness, the most recent studies have focused on validating new tests, on clarifying the limitations of older ones, and better defining their modalities. Recent findingsThe limitations of pulse pressure/stroke volume variations are numerous, but recent efforts have been made to overcome these limitations, like in case of low tidal volume ventilation. Following pulse pressure/stroke volume variations, new tests have emerged which assess preload responsiveness by challenging cardiac preload through heart–lung interactions, like during recruitment manoeuvres and end-expiratory/inspiratory occlusions. Given the risk of fluid overload that is inherent to the ‘classical’ fluid challenge, a ‘mini’ fluid challenge, made of 100 ml of fluid only, has been developed and investigated in recent studies. The reliability of the passive leg raising test is now well established and the newest publications have mainly aimed at defining several noninvasive estimates of cardiac output that can be monitored to assess its effects. SummaryResearch in this field is still very active, such that several indices and tests of fluid responsiveness are now available. They may contribute to reduce excessive fluid balance by avoiding unnecessary fluid administration and, also, by ensuring safe fluid removal.
Activation of cannabinoid CB1 receptor contributes to suppression of spinal nociceptive transmission and inhibition of mechanical hypersensitivity by A&bgr;-fiber stimulation

Abstract Activation of A&bgr;-fibers is an intrinsic feature of spinal cord stimulation (SCS) pain therapy. Cannabinoid receptor type 1 (CB1) is important to neuronal plasticity and pain modulation, but its role in SCS-induced pain inhibition remains unclear. In this study, we showed that CB1 receptors are expressed in both excitatory and inhibitory interneurons in substantia gelatinosa (SG). Patch-clamp recording of the evoked excitatory postsynaptic currents (eEPSCs) in mice after spinal nerve ligation (SNL) showed that electrical stimulation of A&bgr;-fibers (A&bgr;-ES) using clinical SCS-like parameters (50 Hz, 0.2 millisecond, 10 &mgr;A) induced prolonged depression of eEPSCs to C-fiber inputs in SG neurons. Pretreatment with CB1 receptor antagonist AM251 (2 &mgr;M) reduced the inhibition of C-eEPSCs by A&bgr;-ES in both excitatory and inhibitory SG neurons. We further determined the net effect of A&bgr;-ES on spinal nociceptive transmission in vivo by recording spinal local field potential in SNL rats. Epidural SCS (50 Hz, A&bgr;-plateau, 5 minutes) attenuated C-fiber-evoked local field potential. This effect of SCS was partially reduced by spinal topical application of AM251 (25 &mgr;g, 50 &mgr;L), but not CB2 receptor antagonist AM630 (100 &mgr;g). Finally, intrathecal pretreatment with AM251 (50 &mgr;g, 15 &mgr;L) in SNL rats blocked the inhibition of behavioral mechanical hypersensitivity by SCS (50 Hz, 0.2 millisecond; 80% of motor threshold, 60 minutes). Our findings suggest that activation of spinal CB1 receptors may contribute to synaptic depression to high-threshold afferent inputs in SG neurons after A&bgr;-ES and may be involved in SCS-induced inhibition of spinal nociceptive transmission after nerve injury.
VP8, the Major Tegument Protein of Bovine Herpesvirus 1, Interacts with Cellular STAT1 and Inhibits Interferon Beta Signaling

ABSTRACT The UL47 gene product, VP8, is the most abundant tegument protein of bovine herpesvirus 1 (BoHV-1). Previously, we demonstrated that a UL47-deleted BoHV-1 mutant (BoHV1-ΔUL47) exhibits 100-fold-reduced virulence in vitro and is avirulent in vivo. In this study, we demonstrated that VP8 expression or BoHV-1 infection inhibits interferon beta (IFN-β) signaling by using an IFN-α/β-responsive plasmid in a luciferase assay. As transducer and activator of transcription (STAT) is an essential component in the IFN-signaling pathways, the effect of VP8 on STAT was investigated. An interaction between VP8 and STAT1 was established by coimmunoprecipitation assays in both VP8-transfected and BoHV-1-infected cells. Two domains of VP8, amino acids 259 to 482 and 632 to 686, were found to be responsible for its interaction with STAT1. The expression of VP8 did not induce STAT1 ubiquitination or degradation. Moreover, VP8 did not reduce STAT1 tyrosine phosphorylation to downregulate IFN-β signaling. However, the expression of VP8 or a version of VP8 (amino acids 219 to 741) that contains the STAT1-interacting domains but not the nuclear localization signal prevented nuclear accumulation of STAT1. Inhibition of nuclear accumulation of STAT1 also occurred during BoHV-1 infection, while nuclear translocation of STAT1 was observed in BoHV1-ΔUL47-infected cells. During BoHV-1 infection, VP8 was detected in the cytoplasm at 2 h postinfection without any de novo protein synthesis, at which time STAT1 was already retained in the cytoplasm. These results suggest that viral VP8 downregulates IFN-β signaling early during infection, thus playing a role in overcoming the antiviral response of BoHV-1-infected cells. IMPORTANCE Since VP8 is the most abundant protein in BoHV-1 virions and thus may be released in large amounts into the host cell immediately upon infection, we proposed that it might have a function in the establishment of conditions suitable for viral replication. Indeed, while nonessential in vitro, it is critical for BoHV-1 replication in vivo. In this study, we determined that VP8 plays a role in downregulation of the antiviral host response by inhibiting IFN-β signaling. VP8 interacted with and prevented nuclear accumulation of STAT1 at 2 h postinfection in the absence of de novo viral protein synthesis. Two domains of VP8, amino acids 259 to 482 and 632 to 686, were found to be responsible for this interaction. These results provide a new functional role for VP8 in BoHV-1 infection and a potential explanation for the lack of viral replication of the UL47 deletion mutant in cattle.
Wikipedia-Based Entity Semantifying in Open Information Extraction

In the recent years, Open Information Extraction (OIE), an unsupervised strategy which extracts open-domain facts of knowledge from massive heterogeneous text corpora, has achieved impressive improvements. However, the facts (generally represented by a triple) extracted by OIE systems are in lack of clear semantics and then difficult for computer systems to understand. In this paper, we present a new method to semantify the facts by mapping the string arguments in the triples to the corresponding real-world entities based on the existing knowledge base Wikipedia. First, for each query of string argument, we consider a set of its most likely mapping entities and assign each candidate a fused prior probability. Then we calculate the graph-based similarity between candidates as the contextual evidence by propagating semantics on the neighborhood graph of candidates. Finally, we transform the mapping task into an optimization problem and find the maximum a posteriori (MAP) mapping by combining the prior information and contextual evidence through Bayes' theorem. Due to the fusion of multiple cues and the semantics propagation over the graph, our approach improves the performance of the entity semantifying. Experimental results demonstrate the effectiveness of our approach.
Topic-aware Network Visualisation to Explore Large Email Corpora

Nowadays, more and more large datasets exhibit an intrinsic graph structure. While there exist special graph databases to handle ever increasing amounts of nodes and edges, visualising this data becomes infeasible quickly with growing data. In addition, looking at its structure is not sufficient to get an overview of a graph dataset. Indeed, visualising additional information about nodes or edges without cluttering the screen is essential. In this paper, we propose an interactive visualisation for social networks that positions individuals (nodes) on a two-dimensional canvas such that communities defined by social links (edges) are easily recognisable. Furthermore, we visualise topical relatedness be-tween individuals by analysing information about social links, in our case email communication. To this end, we utilise document embeddings, which project the content of an email message into a high dimensional semantic space and graph embeddings, which project nodes in a network graph into a latent space reflecting their relatedness.
The effect of plasticizer and cellulose nanowhisker content on the dispersion and properties of cellulose acetate butyrate nanocomposites

We studied the effects of plasticizer and cellulose nanowhisker content on the dispersion and properties of cellulose acetate butyrate (CAB)-based bionanocomposites. The cellulose nanowhiskers in an aqueous medium were solvent-exchanged to nonaqueous polar solvent (acetone) and used for nanocomposite processing by solution casting. The plasticized and unplasticized nanocomposites with 5 and 10 wt % cellulose nanowhisker content were prepared. Atomic force microscopy indicated nanoscale dispersion of whiskers in the CAB matrix. The dynamic mechanical analysis showed an increase in storage modulus with addition of cellulose nanowhiskers, especially above the glassy-rubbery transition region. Thermogravimetric analysis showed an improvement in thermal stability with increased whisker content for both unplasticized and plasticized nanocomposites. The plasticized nanocomposites showed better transparency than the unplasticized composites, indicating a better dispersion of cellulose nanowhiskers in CAB, in the presence of a plasticizer. The dynamic mechanical properties and thermal stability increased, whereas transparency decreased with increased CNW content.