Miracle-dz/UniFAR-FTUs huggingface dataset:
Is folic acid safe for non-muscle-invasive bladder cancer patients? An evidence-based cohort study.

Background Patients with cancer are highly concerned about food choices and dietary supplements that may affect their treatment outcomes. Excess folic acid (synthetic folate) from supplements or fortification can lead to accumulation of unmetabolized folic acid in the systemic circulation and urine and may promote cancer growth, especially among those with neoplastic alterations. Objective We investigated the prospective association between synthetic compared with natural folate intake and clinical outcomes in non-muscle-invasive bladder cancer (NMIBC), which is a highly recurrent disease. Design In a cohort of 619 NMIBC patients, folate intake at diagnosis was assessed with a previously validated food-frequency questionnaire and categorized according to tertiles. After a median follow-up of 5.2 y, 303 tumor recurrence and 108 progression events were documented from medical record review. Multivariable Cox proportional hazards and logistic models were used to estimate adjusted HRs and ORs with 95% CIs. Results Synthetic folic acid intake was positively associated with a risk of recurrence among NMIBC patients (medium compared with low intake-HR: 1.72; 95% CI: 1.20, 2.48; P = 0.003; high compared with low intake-HR: 1.80; 95% CI: 1.14, 2.84; P = 0.01). Patients with a higher folic acid intake were more likely to have multifocal tumors at diagnosis (medium or high compared with low-OR: 2.08; 95% CI: 1.08, 4.02; P = 0.03). In contrast, natural folate intake tended to be inversely associated with the risk of progression (medium or high compared with low-HR: 0.68; 95% CI: 0.44, 1.04; P = 0.08). Conclusions A high intake of synthetic folic acid, in contrast to the natural forms, is associated with an increased risk of recurrence in NMIBC and multifocal tumors at diagnosis, which suggests that folic acid may be unsafe for NMIBC patients. These findings provide some evidence for nutritional consultation with regard to folate intake among NMIBC patients.
Building-Based Damage Detection From Postquake Image Using Multiple-Feature Analysis

Damaged building detection from high spatial resolution remote sensing image helps to rapid disaster losses assessment. However, the majority of traditional methods relies on only a single category feature of the damaged building. This letter presents a new strategy for detecting damaged buildings from postquake remote sensing image by multiple-feature analysis, in which the integrity of the building edge and the interior roof was both considered. The intactness of the building edge was assessed by proposing a new feature parameter, edge significance (ES), ES using significance test to quantify the difference between the gradient values on the edge and in the edge buffer. In addition, the gradient orientation inside the building was analyzed and local gradient orientation entropy (LOE) parameter was adopted to determine whether the interior roof was damaged. In general, damaged buildings have lower ES values because of broken edges and higher LOE values owing to debris, final decision was made on the basis of both feature parameters. A Quickbird image of Yushu, China, was used in the experiment and, among a total of 327 buildings, 266 were detected correctly. The overall accuracy was 84.10%, which is better than traditional methods.
Molecular and serologic markers of HPV 16 infection are associated with local recurrence in patients with oral cavity squamous cell carcinoma

Human papillomavirus (HPV) infections predict mortality in Taiwanese patients with oral cavity squamous cell carcinoma (OCSCC). To address their prognostic significance for local recurrence (LR), in this retrospective cohort study we investigated different serologic and molecular markers of HPV 16 infection in 85 consecutive patients with primary OCSCC who received standard treatment and had their sera stored before treatment. Resected tumor specimens were examined with PCR-based assays for HPV 16 E6/E7 mRNA expression. Sera were tested with suspension arrays for the presence of HPV-specific antibodies using synthetic L1 and E6 peptides as well as a synthetic E7 protein. HPV 16 E6/E7 mRNA, anti-L1, anti-E6, and anti-E7 antibodies tested positive in 12%, 25%, 38%, and 41% of the study patients, respectively. Multivariate analysis identified pathological T3/T4, E6/E7 mRNA, and anti-E7 antibodies as independent risk factors for LR, whereas anti-E6 antibodies were an independent protective factor. In patients with ≥ 3 (high-risk group), 2 (intermediate-risk), and ≤ 1 (low-risk) independent risk factors (predictors), the 5-year LR rates were 75%, 42%, and 4%, respectively. Results were validated in an independent cohort. Together, our preliminary data indicate that HPV 16 infections as well as low and high serum levels of anti-E6 and anti-E7 antibodies, respectively, can serve as biomarkers of LR in patients with OCSCC, whereas the clinical usefulness of anti-HPV 16 antibodies for risk stratification of newly diagnosed cases deserves further scrutiny.
Feedback for reinforcement learning based brain–machine interfaces using confidence metrics

Objective. For brain–machine interfaces (BMI) to be used in activities of daily living by paralyzed individuals, the BMI should be as autonomous as possible. One of the challenges is how the feedback is extracted and utilized in the BMI. Our long-term goal is to create autonomous BMIs that can utilize an evaluative feedback from the brain to update the decoding algorithm and use it intelligently in order to adapt the decoder. In this study, we show how to extract the necessary evaluative feedback from a biologically realistic (synthetic) source, use both the quantity and the quality of the feedback, and how that feedback information can be incorporated into a reinforcement learning (RL) controller architecture to maximize its performance. Approach. Motivated by the perception–action–reward cycle (PARC) in the brain which links reward for cognitive decision making and goal-directed behavior, we used a reward-based RL architecture named Actor–Critic RL as the model. Instead of using an error signal towards building an autonomous BMI, we envision to use a reward signal from the nucleus accumbens (NAcc) which plays a key role in the linking of reward to motor behaviors. To deal with the complexity and non-stationarity of biological reward signals, we used a confidence metric which was used to indicate the degree of feedback accuracy. This confidence was added to the Actor’s weight update equation in the RL controller architecture. If the confidence was high (>0.2), the BMI decoder used this feedback to update its parameters. However, when the confidence was low, the BMI decoder ignored the feedback and did not update its parameters. The range between high confidence and low confidence was termed as the ‘ambiguous’ region. When the feedback was within this region, the BMI decoder updated its weight at a lower rate than when fully confident, which was decided by the confidence. We used two biologically realistic models to generate synthetic data for MI (Izhikevich model) and NAcc (Humphries model) to validate proposed controller architecture. Main results. In this work, we show how the overall performance of the BMI was improved by using a threshold close to the decision boundary to reject erroneous feedback. Additionally, we show the stability of the system improved when the feedback was used with a threshold. Significance: The result of this study is a step towards making BMIs autonomous. While our method is not fully autonomous, the results demonstrate that extensive training times necessary at the beginning of each BMI session can be significantly decreased. In our approach, decoder training time was only limited to 10 trials in the first BMI session. Subsequent sessions used previous session weights to initialize the decoder. We also present a method where the use of a threshold can be applied to any decoder with a feedback signal that is less than perfect so that erroneous feedback can be avoided and the stability of the system can be increased.
Experimental Investigation of ERSFQ Circuit for Parallel Multibit Data Transmission

We present test results for parallel data communication ERSFQ circuits with clock recovery. We experimentally study on-chip and chip-to-chip parallel data communication circuits with 4-, 8- and 16-bit word lengths. The largest circuit is a 16-bit chip-to-chip communication test circuit embedded into a testbed with clock distributed over a combination of active and passive transmission lines with transmitter/receiver pairs, and is comprised of 3464 Josephson junctions in total. All ERSFQ circuits are fabricated using MITLL 10-kA/cm2 SFQ5ee process. For the chip-to-chip communication experiment, a multi-chip module (MCM) is assembled using Hypres' MCM flip-chip bonding process which connected the MIT-LL-made flip-chip to the Hypres-made MCM carrier using 220 signal bumps with 50 um pitch. We experimentally confirmed correct functionality of 4-, 8- and 16-bit circuits and measured their current bias margins. For the 16- bit chip-to-chip communication circuit mounted to a MCM, we measured ±12% dc bias margins similar to the margins measured for the on-chip version of the same circuit. The MCM circuit is also evaluated at high clock speed generated by an external source, while the data words are changed at low speed. The correct functionality is observed without significant reduction in the bias margins using average-voltage test approach.
The Influence of Intense Chemical Pollution on the Community Composition, Diversity and Abundance of Anammox Bacteria in the Jiaojiang Estuary (China)

Continuous chemical pollution is one of the most serious environmental problems in the Jiaojiang Estuary of the East Sea (China). This chemical pollution has significantly changed the estuarine environmental conditions and may have profoundly influenced the distribution of anammox bacterial communities in this estuary. Here, we investigated the influence of chemical pollution on the community composition, diversity and abundance of anammox bacteria in Jiaojiang estuarine sediments. Phylogenetic analysis of 16S rRNA genes showed that the majority of anammox bacterial sequences retrieved from the estuarine intertidal sediments were associated with Kuenenia. In contrast, different anammox communities composed of Brocadia, Kuenenia, Scalindua and Jettenia were found in the estuarine subtidal sediments. Redundancy analysis (RDA) indicated that the sediment nitrobenzene and organic content had significant impacts on the distribution of anammox communities in the intertidal sediments. Pearson correlation analysis showed that the diversity of anammox bacteria in the intertidal sediments was positively correlated with the organic content. In contrast, RDA results showed that the nitrobenzene content, NO3 − concentration and salinity significantly influenced the distribution of anammox communities in the subtidal sediments. The diversity and relative abundance of anammox bacteria in the subtidal sediments were positively correlated with NO3 − concentration.
TUNGSTEN CONTAINING HYDROGENATED DLC COATINGS ON GREASE LUBRICATED HARMONIC DRIVE GEAR FOR SPACE APPLICATION

Harmonic Drive gears are commonly used in space mechanisms. The performance degradation and even failure of grease-lubricated-type HD gear may be mainly caused by the wear of flexspline, circular spline, especially the interface between the wave generator and flexspline. Tungsten containing hydrogenated DLC (WC:H) coatings have the potential to improve the wear resistance and working life of HD gears. In this paper, the tribological behaviors of W-C:H coatings deposited with different C2H2 flow were assessed. Coating composition was optimized based on ball-on-disc tribotester under grease lubrication in vacuum environment. The results show that the coatings exhibited a very low friction coefficient of 0.08 and good wear resistance. New in this work is that optimized coating was applied to existing grease lubricated HD gears for space application verification. Two HD gears have been carried out life test in space simulator. The result show that the coated grease lubricated HD gears can work more than 5,000 hours, which was beyond twice times that of original ones. The improved life owing to the W-C:H coating using was a statistically significant result.
Extent of linkage disequilibrium and effective population size of the Landrace population in Korea

Objective The genetic diversity of the Landrace population, a representative maternal pig breed in Korea, is important for genetic improvement. Previously, the effective population size (Ne) has been used to infer the genetic diversity of a population of interest. In this study, we aimed to use single nucleotide polymorphism (SNP) data to characterize linkage disequilibrium (LD) and the Ne of the Korean Landrace population. Methods We genotyped 1,128 Landrace individuals from three representative Korean major grand-grand-parent (GGP) farms using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 SNPs located across all autosomes and mitochondrial and sex chromosomes. We estimated the expected LD and current Ne, as well as ancestral Ne. Results In the Korean Landrace population, the mean LD (r2) of 3.698 million SNP pairs was 0.135±0.204. The mean r2 decreased slowly with as the distance between SNPs increased, and remained constant beyond 3 Mb. According to the r2 calculations, 8,085 of 3.698 million SNP pairs were in complete LD. The current Ne (±standard deviation) of the Korean Landrace population is approximately 92.27 [79.46; 105.07] individuals. The ancestral Ne exhibited a slow and steady decline from 186.61 to 92.27 over the past 100 generations. Additionally, we observed more a rapid Ne decrease from the past 20 to 10 generations ago, compared with other intervals. Conclusion We have presented an overview of LD and the current and ancestral Ne values in the Korean Landrace population. The mean LD and current Ne for the Korean Landrace population confirm the genetic diversity and reflect the history of this pig population in Korea.
LSH Microbatches for Stochastic Gradients: Value in Rearrangement

Metric embeddings are immensely useful representation of interacting entities such as videos, users, search queries, online resources, words, and more. Embeddings are computed by optimizing a loss function of the form of a sum over provided associations so that relation of embedding vectors reflects strength of association. Moreover, the resulting embeddings allow us to predict the strength of unobserved associations. Typically, the optimization performs stochastic gradient updates on minibatches of associations that are arranged independently at random. We propose and study here the antithesis of {\em coordinated} arrangements, which we obtain efficiently through {\em LSH microbatching}, where similar associations are grouped together. Coordinated arrangements leverage the similarity of entities evident from their association vectors. We experimentally study the benefit of tunable minibatch arrangements, demonstrating consistent reductions of 3-15\% in training. Arrangement emerges as a powerful performance knob for SGD that is orthogonal and compatible with other tuning methods, and thus is a candidate for wide deployment.
Maternal and fetal effects of chocolate consumption during pregnancy: a systematic review

Abstract Objectives: The purpose of this review is to explore the effects of chocolate consumption during pregnancy on fetus and mother herself. Methods: Randomized controlled trials/quasi-experimental/observational/controlled before and after studies involving chocolate/cocoa/cacao consumption (irrespective of type or dose, composition, exposure period, and method of administration) among pregnant women/animals; and measuring any outcome (beneficial or harmful) related to fetus or mother after chocolate exposure were included. Databases searched were PubMed, Web of Science and Scopus; between April and May 2017. Risk of bias within each human randomized controlled trial (RCT) and animals’ experimental studies was evaluated by “The Cochrane Collaboration’s tool” and SYRCLE’s tool respectively. Results: Fourteen human studies including a total of 6639 participants and nine animal studies were selected. Outcome variables investigated in human studies were maternal blood pressure, fetal heart rate, and striae gravidarum. Animal studies explored chocolate-induced teratogenicity and fetal metabolic derangements. Ten out of these 23 studies reported chocolate to be “beneficial”; five studies reported adverse effects, whereas eight studies declared chocolate as “neutral”. Conclusions: Maternal chocolate intake has acute stimulatory effects on fetal reactivity and chronic blood pressure reducing effect in mothers. Chocolate is nonteratogenic and does not affect reproductive indices. Metabolic derangements in offsprings born to chocolate fed dams have been reported. Pregnant females must be careful about consumption of cocoa and chocolate. Future studies should be planned, keeping in view heterogeneities identified across the selected studies in this review.
Circle and arrow traffic light recognition

Car accident has been one of the accidents that occur the most in every part of the world and one of the main reasons is the negligence of the driver whether he is feeling sleepy or not paying attention to the traffic light. In this paper, we build a prototype that is able to tell the driver in advance about the upcoming traffic lights so he/she will be able react appropriately. The main steps for traffic light recognitions include color segmentation, feature extraction using Histogram of Oriented Gradients (HOG), training the features using Support Vector Machine (SVM), Artificial Neural Network (ANN), and Random Forest (RF), then classification. Performance was evaluated using 10-fold cross validation using videos taken during morning and night. The experiment results reveal that the best model is delivered using SVM with polynomial kernel. Its accuracy achieves 98.5% for morning data and 98.8% for night data.
Approximate Query Matching for Image Retrieval

Traditional image recognition involves identifying the key object in a portrait-type image with a single object focus (ILSVRC, AlexNet, and VGG). More recent approaches consider dense image recognition - segmenting an image with appropriate bounding boxes and performing image recognition within these bounding boxes (Semantic segmentation). The Visual Genome dataset [5] is an attempt to bridge these various approaches to a cohesive dataset for each subtask - bounding box generation, image recognition, captioning, and a new operation: scene graph generation. Our focus is on using such scene graphs to perform graph search on image databases to holistically retrieve images based on a search criteria. We develop a method to store scene graphs and metadata in graph databases (using Neo4J) and to perform fast approximate retrieval of images based on a graph search query. We process more complex queries than single object search, e.g. "girl eating cake" retrieves images that contain the specified relation as well as variations.
Colony-stimulating factor 2 acts from days 5 to 7 of development to modify programming of the bovine conceptus at day 86 of gestation

Abstract Colony-stimulating factor 2 (CSF2) is an embryokine that improves competence of the embryo to establish pregnancy and which may participate in developmental programming. We tested whether culture of bovine embryos with CSF2 alters fetal development and alleviates abnormalities associated with in vitro production (IVP) of embryos. Pregnancies were established by artificial insemination (AI), transfer of an IVP embryo (IVP), or transfer of an IVP embryo treated with 10 ng/ml CSF2 from day 5 to 7 of development (CSF2). Pregnancies were produced using X-sorted semen. Female singleton conceptuses were collected on day 86 of gestation. There were few morphological differences between groups, although IVP and CSF2 fetuses were heavier than AI fetuses. Bicarbonate concentration in allantoic fluid was lower for IVP than for AI or CSF2. Expression of 92 genes in liver, placenta, and muscle was determined. The general pattern for liver and placenta was for IVP to alter expression and for CSF2 to sometimes reverse this effect. For muscle, CSF2 affected gene expression but did not generally reverse effects of IVP. Levels of methylation for each of the three tissues at 12 loci in the promoter of insulin-like growth factor 2 (IGF2) and five in the promoter of growth factor receptor bound protein 10 were unaffected by treatment except for CSF2 effects on two CpG for IGF2 in placenta and muscle. In conclusion, CSF2 can act as a developmental programming agent but alone is not able to abolish the adverse effects of IVP on fetal characteristics. Summary Sentence Production of embryos in vitro (IVP) is associated with alterations in fetal morphology and gene expression at day 86 of gestation; addition of CSF2 to embryo culture altered features of the fetus but did not abolish abnormalities associated with IVP.
Adsorption Behavior of Selective Recognition Functionalized Biochar to Cd(II) in Wastewater

Biochar is an excellent absorbent for most heavy metal ions and organic pollutants with high specific surface area, strong aperture structure, high stability, higher cation exchange capacity and rich surface functional groups. To improve the selective adsorption capacity of biochar to designated heavy metal ions, biochar prepared by agricultural waste is modified via Ionic-Imprinted Technique. Fourier transform infrared (FT-IR) spectra analysis and X-ray photoelectron spectroscopy (XPS) analysis of imprinted biochar (IB) indicate that 3-Mercaptopropyltrimethoxysilane is grafted on biochar surface through Si–O–Si bonds. The results of adsorption experiments indicate that the suitable pH range is about 3.0–8.0, the dosage is 2.0 g·L−1, and the adsorption equilibrium is reached within 960 min. In addition, the data match pseudo-second-order kinetic model and Langmuir model well. The computation results of adsorption thermodynamics and stoichiometric displacement theory of adsorption (SDT-A) prove that the adsorption process is spontaneous and endothermic. Finally, IB possesses a higher selectivity adsorption to Cd(II) and a better reuse capacity. The functionalized biochar could solidify designated ions stably.
Development of Highly Polymorphic Pentanucleotide Tandem Repeat Loci with Low Stutter By

INTRODUCTION All eukaryotic genomes contain regions of simple repetitive DNA, called short tandem repeats (STR*) or microsatellites, which consist of tandem repeats of a small number of bases (1-3). The number of repeats at a STR locus can be highly variable among individuals, resulting in length polymorphisms that can be detected by relatively simple PCR-based assays. Thousands of these highly informative STR loci have been identified in the human genome. Consequently, STRs provide an abundant class of polymorphic markers that have gained popularity for use in genetic linkage analysis, mapping, identity testing and many other applications (3-6).