Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast Stochastic Variance Reduced Gradient Method with Momentum Acceleration for Machine Learning

Recently, research on accelerated stochastic gradient descent methods (e.g., SVRG) has made exciting progress (e.g., linear convergence for strongly convex problems). However, the best-known methods (e.g., Katyusha) requires at least two auxiliary variables and two momentum parameters. In this paper, we propose a fast stochastic variance reduction gradient (FSVRG) method, in which we design a novel update rule with the Nesterov's momentum and incorporate the technique of growing epoch size. FSVRG has only one auxiliary variable and one momentum weight, and thus it is much simpler and has much lower per-iteration complexity. We prove that FSVRG achieves linear convergence for strongly convex problems and the optimal $\mathcal{O}(1/T^2)$ convergence rate for non-strongly convex problems, where $T$ is the number of outer-iterations. We also extend FSVRG to directly solve the problems with non-smooth component functions, such as SVM. Finally, we empirically study the performance of FSVRG for solving various machine learning problems such as logistic regression, ridge regression, Lasso and SVM. Our results show that FSVRG outperforms the state-of-the-art stochastic methods, including Katyusha.
Open humerus shaft fracture with ipsilateral anterior shoulder fracture-dislocation and posterior elbow dislocation: a case report.

Fracture of the shaft of the humerus or femur associated with the dislocation of the adjacent proximal or distal joints is a rare but serious injury in adults. The magnitude of the force required is greater in the lower limb than that in the upper limb. Humerus shaft fracture associated with anterior or posterior dislocation of the shoulder joint is an uncommon injury and 20 cases have been reported in the literature since 1940. Humerus shaft fracture associated with an elbow dislocation is an extremely rare injury and ipsilateral forearm fracture has also been coexisting in all three cases reported in the literature. Besides these, three cases with ipsilateral shoulder and elbow dislocations without a humerus shaft fracture have been reported in the literature. Nevertheless, simultaneous humerus shaft fracture with ipsilateral both shoulder and elbow dislocations is an extraordinary injury and to our knowledge, such an injury has not been previously reported in the literature. The aim of this study is to report such a case and to discuss its management and possible complications. The patient was informed that data concerning this case would be submitted for publication.
DRDB: An Online Date Palm Genomic Resource Database

Background: Date palm (Phoenix dactylifera L.) is a cultivated woody plant with agricultural and economic importance in many countries around the world. With the advantages of next generation sequencing technologies, genome sequences for many date palm cultivars have been released recently. Short sequence repeat (SSR) and single nucleotide polymorphism (SNP) can be identified from these genomic data, and have been proven to be very useful biomarkers in plant genome analysis and breeding. Results: Here, we first improved the date palm genome assembly using 130X of HiSeq data generated in our lab. Then 246,445 SSRs (214,901 SSRs and 31,544 compound SSRs) were annotated in this genome assembly; among the SSRs, mononucleotide SSRs (58.92%) were the most abundant, followed by di- (29.92%), tri- (8.14%), tetra- (2.47%), penta- (0.36%), and hexa-nucleotide SSRs (0.19%). The high-quality PCR primer pairs were designed for most (174,497; 70.81% out of total) SSRs. We also annotated 6,375,806 SNPs with raw read depth≥3 in 90% cultivars. To further reduce false positive SNPs, we only kept 5,572,650 (87.40% out of total) SNPs with at least 20% cultivars support for downstream analyses. The high-quality PCR primer pairs were also obtained for 4,177,778 (65.53%) SNPs. We reconstructed the phylogenetic relationships among the 62 cultivars using these variants and found that they can be divided into three clusters, namely North Africa, Egypt – Sudan, and Middle East – South Asian, with Egypt – Sudan being the admixture of North Africa and Middle East – South Asian cultivars; we further confirmed these clusters using principal component analysis. Moreover, 34,346 SSRs and 4,177,778 SNPs with PCR primers were assigned to shared cultivars for cultivar classification and diversity analysis. All these SSRs, SNPs and their classification are available in our database, and can be used for cultivar identification, comparison, and molecular breeding. Conclusion: DRDB is a comprehensive genomic resource database of date palm. It can serve as a bioinformatics platform for date palm genomics, genetics, and molecular breeding. DRDB is freely available at http://drdb.big. ac.cn/home.
Direct evidence for the role of COOH terminus of mouse mammary tumor virus superantigen in determining T cell receptor V beta specificity

It has recently been shown that open reading frames in the 3' long terminal repeats of mouse mammary tumor viruses encode superantigens. These viral superantigens (vSAGs) stimulate most T cells expressing appropriate V beta s almost regardless of the rest of the variable components of the T cell receptors (TCR) expressed by those cells. vSAGs produce a type II integral membrane protein with a nonessential short cytoplasmic domain and a large glycosylated extracellular COOH- terminal domain, which is predicted to interact with major histocompatibility complex class II molecules and the TCR. The transmembrane region of vSAG also has an internal positively charged lysine residue of unknown significance. A set of chimeric and mutant vSAG genes has been used in transfection experiments to show that only the extreme COOH-terminal portion of vSAGs determine their TCR V beta specificities, and to show that the lysine residue in the transmembrane domain is not essential for the function of vSAG.
Effect of abutment height on interproximal implant bone level in the early healing: A randomized clinical trial

OBJECTIVE The aim of this randomized clinical trial was to compare the effect on the interproximal implant bone loss (IBL) of two different heights (1 and 3 mm) of definitive abutments placed at bone level implants with a platform switched design. MATERIAL AND METHODS Twenty-two patients received forty-four implants (6.5-10 mm length and 3.5-4 mm diameter) to replace at least two adjacent missing teeth, one bridge set to each patient-two implants per bridge. Patients were randomly allocated, and two different abutment heights, 1 and 3 mm using only one abutment height per bridge, were used. Clinical and radiological measurements were performed at 3 and 6 months after surgery. Interproximal bone level changes were compared between treatment groups. The association between IBL and categorical variables (history of periodontitis, smoking, implant location, implant diameter, implant length, insertion torque, width of keratinized mucosa, bone density, gingival biotype and antagonist) was also performed. RESULTS At 3 months, implants with a 1-mm abutment had significantly greater IBL (0.83 ± 0.19 mm) compared to implants with a 3-mm abutment (0.14 ± 0.08 mm). At 6 months, a greater IBL was observed at implants with 1-mm abutments compared to implants with 3-mm abutments (0.91 ± 0.19 vs. 0.11 ± 0.09 mm). The analysis of the relation between patient characteristics and clinical variables with IBL revealed no significant differences at any moment except for smoking. CONCLUSIONS Abutment height is an important factor to maintain interproximal implant bone level in early healing. Short abutments led to a greater interproximal bone loss in comparison with long abutments after 6 months. Other variables except smoking showed no relation with interproximal bone loss in early healing.
Induction of somatic embryogenesis as an example of stress-related plant reactions

In this review, we address the role of stress as one of the principal causes for a cell or tissue to change its pre-existing somatic program, reprogramming itself to express the embryogenic pathway. The focus of this paper is the effect of different stress conditions on the induction phase of plant somatic embryogenesis, as well as the development of embryogenic competence as a result of the applied stresses. We also present a variety of data that link plant somatic embryogenesis, DNA methylation and oxidative stress response.
On Deep Representation Learning from Noisy Web Images

The keep-growing content of Web images may be the next important data source to scale up deep neural networks, which recently obtained a great success in the ImageNet classification challenge and related tasks. This prospect, however, has not been validated on convolutional networks (convnet) -- one of best performing deep models -- because of their supervised regime. While unsupervised alternatives are not so good as convnet in generalizing the learned model to new domains, we use convnet to leverage semi-supervised representation learning. Our approach is to use massive amounts of unlabeled and noisy Web images to train convnets as general feature detectors despite challenges coming from data such as high level of mislabeled data, outliers, and data biases. Extensive experiments are conducted at several data scales, different network architectures, and data reranking techniques. The learned representations are evaluated on nine public datasets of various topics. The best results obtained by our convnets, trained on 3.14 million Web images, outperform AlexNet trained on 1.2 million clean images of ILSVRC 2012 and is closing the gap with VGG-16. These prominent results suggest a budget solution to use deep learning in practice and motivate more research in semi-supervised representation learning.
An in Vitro Antimicrobial Activity of Ten Iranian-Made Toothpastes

Background: Antimicrobial agents have been used as a chemotherapeutic agent to improve oral health. This in vitro study was carried out to determine the antimicrobial activity of ten Iranian-made toothpastes against commonly found bacteria in the oral cavity. Methods: The microorganisms used in this study were Streptococcus mutans, Streptococcus sanguis, Actinomyces viscosus and Candida albicans. Sterile discs impregnated with 10 Iranian-made toothpastes; Paveh, Saviz, Latifeh II, Bath, Darugar II, Darugar I, Close up, Tage, Pooneh III and Nasim, which were separately used on agar plates. Crest Cavity Protection toothpaste and Sterile pyrogenfree distilled water were used as positive and negative controls, respectively. The samples were tested in triplicate, at full strength, 1:1 and 1:3 dilutions. Inhibition zones were measured in millimeter after 48 hr. The data were analyzed by the ANOVA and t-test. Results: All tested toothpastes demonstrated an antimicrobial activity. The antimicrobial activity of Bath on S. mutans, Paveh on S. sanguis, Paveh, Saviz, Latifeh III and Darugar II on C. albicans were similar to the activity of Crest Cavity Protection. The antimicrobial activity of Pooneh III and Nasim on S. mutans, Bath on S. sanguis and A. viscosus, and Bath and Pooneh III on C. albicans were significantly higher and the others were significantly lower than the positive control. While, the activity of Crest Cavity Protection was the same as Pooneh III, it showed a weaker activity compared with Bath. Conclusion: Apart from Bath and Pooneh III, the other Iranian-made toothpastes tested in this study showed a lower antimicrobial activity compared to Crest Cavity Protection.
Lincomycin at Subinhibitory Concentrations Potentiates Secondary Metabolite Production by Streptomyces spp

ABSTRACT Antibiotics have either bactericidal or bacteriostatic activity. However, they also induce considerable gene expression in bacteria when used at subinhibitory concentrations (below the MIC). We found that lincomycin, which inhibits protein synthesis by binding to the ribosomes of Gram-positive bacteria, was effective for inducing the expression of genes involved in secondary metabolism in Streptomyces strains when added to medium at subinhibitory concentrations. In Streptomyces coelicolor A3(2), lincomycin at 1/10 of its MIC markedly increased the expression of the pathway-specific regulatory gene actII-ORF4 in the blue-pigmented antibiotic actinorhodin (ACT) biosynthetic gene cluster, which resulted in ACT overproduction. Intriguingly, S. lividans 1326 grown in the presence of lincomycin at a subinhibitory concentration (1/12 or 1/3 of its MIC) produced abundant antibacterial compounds that were not detected in cells grown in lincomycin-free medium. Bioassay and mass spectrometry analysis revealed that some antibacterial compounds were novel congeners of calcium-dependent antibiotics. Our results indicate that lincomycin at subinhibitory concentrations potentiates the production of secondary metabolites in Streptomyces strains and suggest that activating these strains by utilizing the dose-response effects of lincomycin could be used to effectively induce the production of cryptic secondary metabolites. In addition to these findings, we also report that lincomycin used at concentrations for markedly increased ACT production resulted in alteration of the cytoplasmic protein (FoF1 ATP synthase α and β subunits, etc.) profile and increased intracellular ATP levels. A fundamental mechanism for these unique phenomena is also discussed.
- 1-Task-specific shaping of feature-based attention in area MT

Visual perception depends on the effective prioritization of visual information in order to concur with the current behavioral context. Depending on the context’s requirements, it is important to facilitate the processing of a certain feature (e.g. motion) in some situations, while in others another feature (e.g. color) is more crucial. We here address the question whether and how the specific requirements of a visual task influence modulation of neuronal activity by featurebased attention (FBA). We recorded neuronal responses from monkey motion-sensitive mediotemporal area (MT) in response to spatially attended or unattended motion stimuli, while monkeys were required to detect an instantaneous speedor color-change of a pre-cued target stimulus. We found a strong influence of task requirements on several parameters of MT single cell responses: If the task required attention to speed, mean firing rates were higher, and response variability and latency to otherwise identical visual stimuli was lower as compared to the task requiring attention to color. This was evident even with attention directed to the stimulus outside the receptive field (RF) of the recorded neuron, moving in a direction 180 deg away from the preferred direction inside the RF. Importantly, this task-specific response modulation in the . CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was . http://dx.doi. org/10.1101/058693 doi: bioRxiv preprint first posted online Jun. 13, 2016;
Using ontology for the representational analysis of process modelling techniques

Selecting an appropriate business process modelling technique forms an important task within the methodological challenges of a business process management project. While a plethora of available techniques has been developed over the last decades, there is an obvious shortage of well-accepted reference frameworks that can be used to evaluate and compare the capabilities of the different techniques. Academic progress has been made at least in the area of representational analyses that use ontology as a benchmark for such evaluations. This paper reflects on the comprehensive experiences with the application of a model based on the Bunge ontology in this context. A brief overview of the underlying research model characterises the different steps in such a research project. A comparative summary of previous representational analyses of process modelling techniques over time gives insights into the relative maturity of selected process modelling techniques. Based on these experiences suggestions are made as to where ontology-based representational analyses could be further developed and what limitations are inherent to such analyses.
Journal of Cardiovascular Magnetic Resonance Open Access High Resolution Carotid Black-blood 3t Mr with Parallel Imaging and Dedicated 4-channel Surface Coils

Background: Most of the carotid plaque MR studies have been performed using black-blood protocols at 1.5 T without parallel imaging techniques. The purpose of this study was to evaluate a multi-sequence, black-blood MR protocol using parallel imaging and a dedicated 4-channel surface coil for vessel wall imaging of the carotid arteries at 3 T.
Regulation of a Novel Androgen Receptor Target Gene, the Cyclin B1 Gene, through Androgen-Dependent E2F Family Member Switching

ABSTRACT The malignant transformation of human prostatic epithelium is associated with the loss of androgen receptor (AR) in the surrounding stroma. However, the function and mechanisms of AR signaling in prostate cancer (PCa) stroma remain elusive. Here we report, by using proteomics pathway array analysis (PPAA), that androgen and its receptor inhibit the proliferation of prostate stromal cells through transcriptional suppression of cyclin B1, and we confirmed our findings at mRNA and protein levels using AR-negative or -positive primary prostate stromal cells. Furthermore, AR showed a negative correlation with cyclin B1 expression in stroma of human PCa samples in vivo. Mechanistically, we identify cyclin B1 as a bona fide AR target gene in prostate stromal cells. The negative regulation of cyclin B1 by AR is mediated through switching between E2F1 and E2F4 on the promoter of cyclin B1. E2F1 binds to the cyclin B1 promoter and maintains its expression and subsequent cell cycle progression in AR-negative stromal cells or AR-positive stromal cells when androgens are depleted. Upon stimulation with androgen in AR-positive stromal cells, E2F1 is displaced from the binding site by AR and replaced with E2F4, leading to the recruitment of the silencing mediator for retinoid and thyroid hormone receptor (SMRT)/histone deacetylase 3 (HDAC3) corepressor complex and repression of cyclin B1 at the chromatin level. The switch between E2F1 and E2F4 at the E2F binding site of the cyclin B1 promoter coincides with an androgen-dependent interaction between AR and E2F1 as well as the cytoplasmic-to-nuclear translocation of E2F4. Thus, we identified a novel mechanism for E2F factors in the regulation of cell cycle gene expression and cell cycle progression under the control of AR signaling.
An automatic thread decomposition approach for pipelined multithreading

Thread decomposition is critical for pipelined multithreading PMT to gain higher performance on target multi-core processors. This paper presents an automatic thread decomposition approach, which maps the decomposition problem onto a graph-theoretic framework to construct an optimised directed acyclic graph DAG with minimal bottleneck node size and balanced node size. In this approach, control dependence is treated as special data dependence and then an effective approach is proposed to remove redundant control dependences. A weighted DAG is constructed by assigning appropriate weights to all nodes and all dependences according to profile information. An automatic thread decomposition algorithm is given to generate an optimised pipeline based on the weighted DAG. The algorithm has been evaluated on a commodity multi-core processor, and experimental results show that it has achieved speedup ranging from 113% to 174% on some SPEC CPU 2000 benchmark programs.
Evaluation of an educational program to improve communication with patients about early-phase trial participation.

BACKGROUND Discussing early-phase cancer trials is challenging; most offer little personal benefit to patients with life-limiting illnesses who frequently have a poor understanding of and misconceptions about the therapeutic aims. We evaluated an evidence-based training program aimed at enhancing communication. METHODS Prior to and after the intervention, 47 health care professionals (HCPs) experienced in early-phase trial recruitment were audio taped discussing trials with patient simulators who completed postinterview evaluations. Coders rated the interviews for the presence of information areas required to elicit ethical consent. HCPs reported their self-confidence on 15 different aspects of trial discussion. RESULTS Significant objective and subjective improvements in communication were found after the workshop. Analyses of audio tapes showed positive shifts in: establishing the patient's knowledge of their prognosis (odds ratio [OR], 2.7; p = .002), discussing symptomatic care (OR, 3.8; p < .001), the aims of the trial (OR, 2.6; p =.002), and the unlikelihood of medical benefit (OR, 3.0; p = .021). Patient simulator ratings showed improvements in: the awareness of palliative care and symptom control (OR, 2.1; p = .004), the voluntariness of participation (OR, 3.7; p = .015), the opportunity to ask questions (OR, 2.9; p = .044), and the time to consider participation (OR, 6.1; p = .009). HCPs' self-confidence increased significantly for all 15 items (OR range, 1.5-2.9; p ≤ .001). CONCLUSION This short, intensive workshop changed communication skills competency and self-efficacy in ways likely to promote valid, ethically informed consent from patients contemplating trial entry.
Differential expression of sphingosine‐1‐phosphate receptors 1‐5 in the developing nervous system

Sphingosine‐1‐phosphate (S1P) binds to G protein–coupled receptors and can regulate a wide range of cellular functions. In a previous study, we isolated two key enzymes in the S1P pathway that were expressed in migrating neural crest cells. To determine if S1P receptors are present in neural crest cells or peripheral nervous system, we examine the expression patterns of S1P receptors (S1pr1‐5) in mouse, and s1pr1 and s1pr3 in chick embryos. Here, we present a comprehensive expression analysis of these receptors using in situ hybridizations, which provide spatiotemporal information. We showed that S1pr2 was expressed in migrating cranial neural crest cells and enteric neurons. S1pr1 was prominently expressed in the neuroepithelium whereas S1pr4 and S1pr5 were in neurons at later stages. On the contrary, S1pr3 was predominantly detected in non‐neuronal cells within and surrounding neural structures. We also described novel expression sites for S1P receptors in the developing nervous system. Developmental Dynamics 238:487–500, 2009. © 2009 Wiley‐Liss, Inc.