Miracle-dz/UniFAR-FTUs huggingface dataset:
A DAG Model of Synchronous Stochastic Gradient Descent in Distributed Deep Learning

With huge amounts of training data, deep learning has made great breakthroughs in many artificial intelligence (AI) applications. However, such large-scale data sets present computational challenges, requiring training to be distributed on a cluster equipped with accelerators like GPUs. With the fast increase of G PU computing power, the data communications among GPUs have become a potential bottleneck on the overall training performance. In this paper, we first propose a general directed acyclic graph (DAG) model to describe the distributed synchronous stochastic gradient descent (S-SG D) algorithm, which has been widely used in distributed deep learning frameworks. To understand the practical impact of data communications on training performance, we conduct extensive empirical studies on four state-of-the-art distributed deep learning frameworks (i.e., Caffe-MPI, CNTK, MXNet and TensorFlow) over multi-GPU and multi-node environments with different data communication techniques, including PCIe, NVLink, 10GbE, and InfiniBand. Through both analytical and experimental studies, we identify the potential bottlenecks and overheads that could be further optimized. At last, we make the data set of our experimental traces publicly available, which could be used to support simulation-based studies.
The BER theoretical model and properties of SiPM‐based receiver for OOK optical communication

The bit error rate (BER) theory of silicon photomultiplier (SiPM) based on‐off keying optical communication receiver, which introduces photon equivalent threshold is established. The optical crosstalk effect, the dark counts, the amplitude fluctuations of output pulses of SiPM, the baseline fluctuation, the shape of the incident light pulse, the adjacent symbol interference as well as the photon detection efficiency (PDE) are considered in the theory model. The numerical result shows that the average minimum optical power required is much smaller than that of the avalanche photodiode‐based receivers under the same conditions. The BER of SiPM‐based optical communication receiver is very sensitive to the PDE and optical crosstalk (OC) probability of SiPM. For the application of digital optical communication, a SiPM with high PDE but low OC probability and low dark count rate is a preference, under the premise that the output pulse is fast enough. For the state‐of‐the‐art SiPMs, the dark count rate is small enough to obtain adequate BER, and the OC effect is not a big limitation of the performance of SiPM‐based receiver. Moreover, the amplitude fluctuation and the baseline fluctuation of the SiPM‐based receiver are not bottlenecks of the performance in practice.
A PEAR1 polymorphism (rs12041331) is associated with risk of coronary artery aneurysm in Kawasaki disease

Kawasaki disease (KD) is an acute systemic vasculitis that is most seriously complicated by coronary artery aneurysm (CAA). The polymorphisms of platelet endothelial aggregation receptor 1 (PEAR1), notably rs12041331 and rs12566888, were found to be closely related to cardiac disease. However, little is known regarding the connection between PEAR1 and KD. In this study, we genotyped PEAR1 rs12566888 and rs12041331 in 637 healthy infants and 694 KD patients (74 with CAA). Subsequently, odds ratio (OR) and 95% confidence interval (CI) were calculated to assess the strength of their relationships. No significant differences in the frequency of rs12566888 or rs12041331 in PEAR1 were observed between KD and healthy controls. However, regardless of the statistical combination of rs12566888 genotype, the rs12041331 recessive inheritance model was associated with an increased risk of CAA after Bonferroni correction (for rs12041331, AA vs. GG/GA: adjusted OR = 2.37, 95% CI = 1.41–4.01, P = 0.009; combination of two recessive genotypes vs. combination of 0–1 recessive genotypes: adjusted OR = 2.39, 95% CI = 1.42–4.04, P = 0.009). This study suggests for the first time that PEAR1 polymorphisms did not indicate susceptibility for KD occurrence but the rs12041331 polymorphism was associated with increased risk of CAA formation in KD, and the functions of the gene warrant further research.
Integration of firefly optimization and Pearson service correlation for efficient cloud resource utilization

Cloud Computing (CC) environment presents a simplified, centralized platform or resources to usage while necessitated at minimum cost. In CC, the main processes in is the allocation of resources of web applications. However, with the increasing demands of Cloud User (CU), an efficient resource allocation technique for web applications is required. According to the request made by the user and response obtained, the cost of resources has also to be optimized. To overcome such limitations, Pearson service correlation‐based firefly resource cost optimization (PSC‐FRCO) technique is designed. Pearson service correlation‐based firefly resource cost optimization technique not only improves the performance of cost aware resource allocation but also achieves higher efficiency while rendering services in cloud computing environment for web applications. Pearson service correlation‐based firefly resource cost optimization technique initially uses Pearson service correlation in which the user‐required service is identified by correlating the available services provided by cloud owner. This helps in improving the Response Time (RT) of cloud service provisioning. Next, firefly resource cost optimization algorithm is applied to identify and allocate the cost‐optimized cloud resources to users to afford required service from the cloud server. Thus, PSC‐FRCO technique improves the Resource Utilization Efficiency (RUE) of web applications with minimal computational cost. This technique conducts experimental works on parameters such as RT, Bandwidth Utilization Rate (BUR) computational cost, Energy Consumption (EC), and RUE. Experimental analysis reveals that PSC‐FRCO technique enhances enhances RUE and lessens RT as compared to state‐of‐the‐art works.
Single-molecule optical absorption imaging by nanomechanical photothermal sensing

Significance Absorption microscopy is a promising technique that can detect single nonfluorescent molecules. However, fundamental limitations of existing optical absorption methods result in noisy detection signals for single molecules, which has hindered many anticipated applications. A promising method is to optically measure the photothermal heating of single molecules. In this paper, we present a photothermal microscopy technique where we detect the photothermal heating of single molecules mechanically with a temperature-sensitive nanomechanical drum. With our method, we achieve an unprecedented optical absorption sensitivity, enabling the detection of single molecules with large signal-to-noise ratios. This enables interesting applications such as the accurate localization of naturally occurring marker molecules or the identification of single molecules by measuring their absorption spectrum. Absorption microscopy is a promising alternative to fluorescence microscopy for single-molecule imaging. So far, molecular absorption has been probed optically via the attenuation of a probing laser or via photothermal effects. The sensitivity of optical probing is not only restricted by background scattering but it is fundamentally limited by laser shot noise, which minimizes the achievable single-molecule signal-to-noise ratio. Here, we present nanomechanical photothermal microscopy, which overcomes the scattering and shot-noise limit by detecting the photothermal heating of the sample directly with a temperature-sensitive substrate. We use nanomechanical silicon nitride drums, whose resonant frequency detunes with local heating. Individual Au nanoparticles with diameters from 10 to 200 nm and single molecules (Atto 633) are scanned with a heating laser with a peak irradiance of 354 ± 45 µW/µm2 using 50× long-working-distance objective. With a stress-optimized drum we reach a sensitivity of 16 fW/Hz1/2 at room temperature, resulting in a single-molecule signal-to-noise ratio of >70. The high sensitivity combined with the inherent wavelength independence of the nanomechanical sensor presents a competitive alternative to established tools for the analysis and localization of nonfluorescent single molecules and nanoparticles.
Triple Trustworthiness Measurement for Knowledge Graph

The Knowledge graph (KG) uses the triples to describe the facts in the real world. It has been widely used in intelligent analysis and applications. However, possible noises and conflicts are inevitably introduced in the process of constructing. And the KG based tasks or applications assume that the knowledge in the KG is completely correct and inevitably bring about potential deviations. In this paper, we establish a knowledge graph triple trustworthiness measurement model that quantify their semantic correctness and the true degree of the facts expressed. The model is a crisscrossing neural network structure. It synthesizes the internal semantic information in the triples and the global inference information of the KG to achieve the trustworthiness measurement and fusion in the three levels of entity level, relationship level, and KG global level. We analyzed the validity of the model output confidence values, and conducted experiments in the real-world dataset FB15K (from Freebase) for the knowledge graph error detection task. The experimental results showed that compared with other models, our model achieved significant and consistent improvements.
Qualitative and quantitative evaluation of TPM transcripts and proteins in developing striated chicken muscles indicate TPM4α is the major sarcomeric cardiac tropomyosin from early embryonic life to adulthood

The chicken has been used since the 1980s as an animal model for developmental studies regarding tropomyosin isoform diversity in striated muscles, however, the pattern of expression of transcripts as well as the corresponding TPM proteins of various tropomyosin isoforms in avian hearts are not well documented. In this study, using conventional and qRT‐PCR, we report the expression of transcripts for various sarcomeric TPM isoforms in striated muscles through development. Transcripts of both TPM1α and TPM1κ, the two sarcomeric isoforms of the TPM1 gene, are expressed in embryonic chicken hearts but disappear in post hatch stages. TPM1α transcripts are expressed in embryonic and adult skeletal muscle. The sarcomeric isoform of the TPM2 gene is expressed mostly in embryonic skeletal muscles. As reported earlier, TPM3α is expressed in embryonic heart and skeletal muscle but significantly lower in adult striated muscle. TPM4α transcripts are expressed from embryonic to adult chicken hearts but not in skeletal muscle. Our 2D Western blot analyses using CH1 monoclonal antibody followed by mass spectra evaluations found TPM4α protein is the major sarcomeric tropomysin expressed in embryonic chicken hearts. However, in 7‐day‐old embryonic hearts, a minute quantity of TPM1α or TPM1κ is also expressed. This finding suggests that sarcomeric TPM1 protein may play some important role in cardiac contractility and/or cardiac morphogenesis during embryogenesis. Since only the transcripts of TPM4α are expressed in adult chicken hearts, it is logical to presume that TPM4α is the only sarcomeric TPM protein produced in adult cardiac tissues.
A pseudo nearest centroid neighbour classifier

In this paper, we propose a new reliable classification approach, called the pseudo nearest centroid neighbour rule, which is based on the pseudo nearest neighbour rule (PNN) and nearest centroid neighbourhood (NCN). In the proposed PNCN, the nearest centroid neighbours rather than nearest neighbours per class are first searched by means of NCN. Then, we calculate k categorical local mean vectors corresponding to k nearest centroid neighbours, and assign a weight to each local mean vector. Using the weighted k local mean vectors for each class, PNCN designs the corresponding pseudo nearest centroid neighbour and decides the class label of the query pattern according to the closest pseudo nearest centroid neighbour among all classes. The classification performance of the proposed PNCN is evaluated on real and artificial datasets in terms of the classification accuracy. The experimental results demonstrate the effectiveness and robustness of PNCN over the competing methods in many practical classification problems.
Improvement of Sexual and Reproductive Function in Men with Spinal Cord Lesion

SUMMARY – The aim of the review is to establish sexual and reproductive functions in men with spinal cord lesion (SCL). Many sexual and reproductive dysfunctions may be found in these patients including individual’s low self-esteem, delay of orgasm, erectile or ejaculatory disorder and abnormalities of semen, which are characterized by lower sperm motility or viability. Owing to improvements in physical medicine and rehabilitation, the focus has been shifted from keeping patients alive towards ensuring the quality of life and improvements of sexual dysfunctions and later reproduction. Erectile dysfunction can be treated by using phosphodiesterase-5 inhibitors, intracavernosal injections, vacuum devices and penile prostheses. Semen can be retrieved from anejaculatory patients by medically assisted methods utilizing penile vibratory stimulation, electroejaculation, prostate massage, or surgically. Although there is low chance for pregnancy in natural way in most of SCL patients, fatherhood is possible through the introduction of assisted medical management. By use of various medical, technical and surgical procedures for sperm retrieval combined with assisted reproductive methods, high pregnancy rates have been reported comparable to those in able-bodied subfertile patients. Nevertheless, future studies are needed to improve semen quality and methods of assisted ejaculation in patients with SCL.
QTL Mapping of the Shape of Type VI Glandular Trichomes in Tomato

Glandular trichomes contribute to the high resistance of wild tomato species against insect pests not only thanks to the metabolites they produce but also because of morphological and developmental features which support the high production of these defense compounds. In Solanum habrochaites, type VI trichomes have a distinct spherical shape and a large intercellular storage cavity where metabolites can accumulate and are released upon breaking off of the glandular cells. In contrast, the type VI trichomes of S. lycopersicum have a four-leaf clover shape corresponding to the four glandular cells and a small internal cavity with limited capacity for storage of compounds. To better characterize the genetic factors underlying these trichome morphological differences we created a back-cross population of 116 individuals between S. habrochaites LA1777 and S. lycopersicum var. cerasiforme WVa106. A trichome score that reflects the shape of the type VI trichomes allowing the quantification of this trait was designed. The scores were distributed normally across the population, which was mapped with a total of 192 markers. This resulted in the identification of six quantitative trait locus (QTLs) on chromosomes I, VII, VII, and XI. The QTL on chromosome I with the highest LOD score was confirmed and narrowed down to a 500 gene interval in an advanced population derived from one of the back-cross lines. Our results provide the foundation for the genetic dissection of type VI trichome morphology and the introgression of these trichome traits into cultivated tomato lines for increased insect resistance. Key Message: This work shows that the shape of type VI glandular trichomes in tomato is a genetically defined trait controlled by multiple QTLs with one on chromosome I being the major contributor.
One-Handed Input Through Rotational Motion for Smartwatches

ABSTRACT One-handed input for smartwatches is crucial when users’ hands are occupied. A rotational motion is leveraged, which can be detected by built-in motion sensors in most smartwatches, as input to provide item selection. Users control a cursor by rotating the smartwatch into different orientations using the proposed item selection gestures. To understand human wrist dexterity and the ability to perform rotational motion input along each degree of freedom on smartwatches, a human-factor study was performed. Except dexterity, users’ consensus and agreement of user-defined rotational motion input gestures for selection and commitment on smartwatches in an exploratory user study were also observed. Based on both the studies, gestures roll and tilt are proposed as selection gestures, and shake and nod are used as commitment gestures. The item selection performance using the proposed gestures in 2D layouts in a user study was further evaluated. The study results showed that tilt-nod and tilt-shake are suitable for item numbers (4 × 3) and (5 × 5), respectively. Furthermore, due to high error rate for tilt-shake in (2 × 2) caused by false positive in shake detection, roll-shake with better social acceptance can be used as an alternative for smartwatches without a built-in front camera in (2 × 2).
Radiomic MRI Phenotyping of Glioblastoma: Improving Survival Prediction.

Purpose To investigate whether radiomic features at MRI improve survival prediction in patients with glioblastoma multiforme (GBM) when they are integrated with clinical and genetic profiles. Materials and Methods Data in patients with a diagnosis of GBM between December 2009 and January 2017 (217 patients) were retrospectively reviewed up to May 2017 and allocated to training and test sets (3:1 ratio). Radiomic features (n = 796) were extracted from multiparametric MRI. A random survival forest (RSF) model was trained with the radiomic features along with clinical and genetic profiles (O-6-methylguanine-DNA-methyltransferase promoter methylation and isocitrate dehydrogenase 1 mutation statuses) to predict overall survival (OS) and progression-free survival (PFS). The RSF models were validated on the test set. The incremental values of radiomic features were evaluated by using the integrated area under the receiver operating characteristic curve (iAUC). Results The 217 patients had a mean age of 57.9 years, and there were 87 female patients (age range, 22-81 years) and 130 male patients (age range, 17-85 years). The median OS and PFS of patients were 352 days (range, 20-1809 days) and 264 days (range, 21-1809 days), respectively. The RSF radiomics models were successfully validated on the test set (iAUC, 0.652 [95% confidence interval {CI}, 0.524, 0.769] and 0.590 [95% CI: 0.502, 0.689] for OS and PFS, respectively). The addition of a radiomics model to clinical and genetic profiles improved survival prediction when compared with models containing clinical and genetic profiles alone (P = .04 and .03 for OS and PFS, respectively). Conclusion Radiomic MRI phenotyping can improve survival prediction when integrated with clinical and genetic profiles and thus has potential as a practical imaging biomarker. © RSNA, 2018 Online supplemental material is available for this article.
Association of physical activity and sedentary time with blood cell counts: National Health and Nutrition Survey 2003-2006

Objective To assess the association of objectively measured levels of physical activity and sedentary time with major blood cell counts (e.g. white blood cells, red blood cells, platelets) among adults. Methods Data collected from the 2003–2004 and 2005–2006 cycles of the National Health and Nutrition Examination Survey (NHANES) was used to assess blood cell counts in relation to objectively measured physical activity and sedentary time (accelerometer). A series of linear regressions modes were used to assess these associations adjusting for a range of factors known to be associated with blood cell counts, including age, body mass index, dietary factors, and previous infections. Results Higher levels of moderate-vigorous physical activity (ptrend<0.001) and lower sedentary time (ptrend = 0.040) were associated with lower white blood cell counts. Conclusion These results suggest that modifiable health behaviors, such as physical activity and sedentary time, may be associated with inflammatory status through white blood cell counts, which may be important for future disease risk.
Mll‐COMPASS complexes mediate H3K4me3 enrichment and transcription of the osteoblast master gene Runx2/p57 in osteoblasts

Expression of Runx2/p57 is a hallmark of the osteoblast‐lineage identity. Although several regulators that control the expression of Runx2/p57 during osteoblast‐lineage commitment have been identified, the epigenetic mechanisms that sustain this expression in differentiated osteoblasts remain to be completely determined. Here, we assess epigenetic mechanisms associated with Runx2/p57 gene transcription in differentiating MC3T3 mouse osteoblasts. Our results show that an enrichment of activating histone marks at the Runx2/p57 P1 promoter is accompanied by the simultaneous interaction of Wdr5 and Utx proteins, both are components of COMPASS complexes. Knockdown of Wdr5 and Utx expression confirms the activating role of both proteins at the Runx2‐P1 promoter. Other chromatin modifiers that were previously described to regulate Runx2/p57 transcription in mesenchymal precursor cells (Ezh2, Prmt5, and Jarid1b proteins) were not found to contribute to Runx2/p57 transcription in full‐committed osteoblasts. We also determined the presence of additional components of COMPASS complexes at the Runx2/p57 promoter, evidencing that the Mll2/COMPASS‐ and Mll3/COMPASS‐like complexes bind to the P1 promoter in osteoblastic cells expressing Runx2/p57 to modulate the H3K4me1 to H3K4me3 transition.
Volume of urea cleared as a therapy dosing guide for more frequent hemodialysis

Introduction: With dialysis delivery systems that operate at low dialysate flow rates, prescriptions for more frequent hemodialysis (HD) employ dialysate volume as the primary parameter for small solute removal rather than blood‐side urea dialyzer clearance (K). Such delivery systems, however, yield dialysate concentrations that almost completely saturate with blood (water), suggesting that the volume of urea cleared (the product of K and treatment time or Kt) can be readily estimated from the prescribed dialysate volume to target small solute removal.
Endophytic fungal community of Dysphania ambrosioides from two heavy metal‐contaminated sites: evaluated by culture‐dependent and culture‐independent approaches

Endophytic fungal communities of Dysphania ambrosioides, a hyperaccumulator growing at two Pb‐Zn‐contaminated sites, were investigated through culture‐dependent and culture‐independent approaches. A total of 237 culturable endophytic fungi (EF) were isolated from 368 tissue (shoot and roots) segments, and the colonization rate (CR) ranged from 9.64% to 65.98%. The isolates were identified to 43 taxa based on morphological characteristics and rDNA ITS sequence analysis. Among them, 13 taxa (30.23%) were common in plant tissues from both sites; however, dominant EF were dissimilar. In culture‐dependent study, 1989 OTUs were obtained through Illumina Miseq sequencing, and dominant EF were almost same in plant tissues from both sites. However, some culturable EF were not observed in total endophytic communities. We suggest that combination of both culture‐dependent and culture‐independent methods will provide more chances for the precise estimation of endophytic fungal community than using either of them. The tissue had more influence on the culturable fungal community structure, whereas the location had more influence on the total fungal community structure (including culturable and unculturable). Both culture‐dependent and culture‐independent studies illustrated that endophytic fungal communities of D. ambrosioides varied across the sites, which suggested that HM concentration of the soil may have some influence on endophytic fungal diversity.