Miracle-dz/UniFAR-FTUs huggingface dataset:
Delay Monitoring System With Multiple Generic Monitors for Wide Voltage Range Operation

As the semiconductor process technology continuously scales down, circuit delay variations due to manufacturing and environmental variations become more and more serious. These delay variations are hardly predictable and thus require an additional design margin, which impedes the chance to reduce the area and power consumption of a chip. One of the best solutions to alleviate this problem is to measure circuit delays at run time and control the supply voltage accordingly through a closed-loop dynamic voltage and frequency scaling (DVFS) scheme. The key issue of this scheme is the delay mismatch between the monitoring circuit and the target block. A large delay mismatch might lose the advantage of the closed-loop DVFS. It becomes much worse as a circuit block operates in wider voltage range, from near-threshold voltage to super-overdrive voltage. This paper proposes novel delay monitoring systems with multiple generic monitors for wide voltage range operation, which provide a better delay correlation between the monitoring circuit and the target block compared to conventional monitoring approaches. The proposed approaches reduce the maximum error by up to 91% for a popular processor core in a 14-nm FinFET process technology, thereby bring a decrease of design margin, lower-power, and/or lower-cost design.
Cumulative impact analysis of wetlands using hydrologic indices

Abstract : In order to make informed decisions concerning cumulative impact analysis of wetlands, the Corps of Engineers Districts and other wetlands professionals need data often not directly available. Cumulative impact assessment of wetlands includes relating historic patterns of flow, derived from the stream's flow record, to changes in the watershed associated with that stream. Harmonic analysis and time-scale analysis were applied to selected stream records to ascertain their potential for describing cumulative impacts. The study area chosen included selected streams in the White River basin, Arkansas/Missouri. The Cache River received particular emphasis because a significant amount of information was readily available concerning it and its surroundings. Daily flow values were retrieved from each of the streams. Using nonlinear, harmonic analysis as well as time-scale analysis (a technique adapted from fractal geometry) to reveal the time-dependent patterns in the respective samples, the results were compared decade-by-decade to discern changes in the historic, seasonal patterns. Other streams in the White River basin were analyzed in the same manner and compared with the Cache River, noting historic changes in land use and stream regulation. The study identifies methods with the potential to differentiate historic time frames in which disruptions were likely to have occurred.
Epigenome-Wide Tumor DNA Methylation Profiling Identifies Novel Prognostic Biomarkers of Metastatic-Lethal Progression in Men Diagnosed with Clinically Localized Prostate Cancer

Purpose: Aside from Gleason sum, few factors accurately identify the subset of prostate cancer patients at high risk for metastatic progression. We hypothesized that epigenetic alterations could distinguish prostate tumors with life-threatening potential. Experimental Design: Epigenome-wide DNA methylation profiling was performed in surgically resected primary tumor tissues from a population-based (n = 430) and a replication (n = 80) cohort of prostate cancer patients followed prospectively for at least 5 years. Metastasis was confirmed by positive bone scan, MRI, CT, or biopsy, and death certificates confirmed cause of death. AUC, partial AUC (pAUC, 95% specificity), and P value criteria were used to select differentially methylated CpG sites that robustly stratify patients with metastatic-lethal from nonrecurrent tumors, and which were complementary to Gleason sum. Results: Forty-two CpG biomarkers stratified patients with metastatic-lethal versus nonrecurrent prostate cancer in the discovery cohort, and eight of these CpGs replicated in the validation cohort based on a significant (P < 0.05) AUC (range, 0.66–0.75) or pAUC (range, 0.007–0.009). The biomarkers that improved discrimination of patients with metastatic-lethal prostate cancer include CpGs in five genes (ALKBH5, ATP11A, FHAD1, KLHL8, and PI15) and three intergenic regions. In the validation dataset, the AUC for Gleason sum alone (0.82) significantly increased with the addition of four individual CpGs (range, 0.86–0.89; all P <0.05). Conclusions: Eight differentially methylated CpGs that distinguish patients with metastatic-lethal from nonrecurrent tumors were validated. These novel epigenetic biomarkers warrant further investigation as they may improve prognostic classification of patients with clinically localized prostate cancer and provide new insights on tumor aggressiveness. Clin Cancer Res; 23(1); 311–9. ©2016 AACR.
Trends in the Incidence, Prevalence, and Survival Outcomes in Patients With Neuroendocrine Tumors in the United States

Importance The incidence and prevalence of neuroendocrine tumors (NETs) are thought to be rising, but updated epidemiologic data are lacking. Objective To explore the evolving epidemiology and investigate the effect of therapeutic advances on survival of patients with NETs. Design, Setting, and Participants A retrospective, population-based study using nationally representative data from the Surveillance, Epidemiology, and End Results (SEER) program was conducted to evaluate 64 971 patients with NETs from 1973 to 2012. Associated population data were used to determine annual age-adjusted incidence, limited-duration prevalence, and 5-year overall survival (OS) rates. Trends in survival from 2000 to 2012 were evaluated for the entire cohort as well as specific subgroups, including distant-stage gastrointestinal NETs and pancreatic NETs. Analyses were conducted between December 2015, and February 2017. Main Outcomes and Measures Neuroendocrine tumor incidence, prevalence, and OS rates. Results Of the 64 971 cases of NETs, 34 233 (52.7%) were women. The age-adjusted incidence rate increased 6.4-fold from 1973 (1.09 per 100 000) to 2012 (6.98 per 100 000). This increase occurred across all sites, stages, and grades. In the SEER 18 registry grouping (2000-2012), the highest incidence rates were 1.49 per 100 000 in the lung, 3.56 per 100 000 in gastroenteropancreatic sites, and 0.84 per 100 000 in NETs with an unknown primary site. The estimated 20-year limited-duration prevalence of NETs in the United States on January 1, 2014, was 171 321. On multivariable analyses, the median 5-year OS rate varied significantly by stage, grade, age at diagnosis, primary site, and time period of diagnosis. The OS rate for all NETs improved from the 2000-2004 period to the 2009-2012 period (hazard ratio [HR], 0.79; 95% CI, 0.73-0.85). Even larger increases in OS between these periods were noted in distant-stage gastrointestinal NETs (HR, 0.71; 95% CI, 0.62-0.81) and distant-stage pancreatic NETs (HR, 0.56; 95% CI, 0.44-0.70). Conclusions and Relevance The incidence and prevalence of NETs are steadily rising, possibly owing to detection of early-stage disease and stage migration. Survival for all NETs has improved over time, especially for distant-stage gastrointestinal NETs and pancreatic NETs in particular, reflecting improvement in therapies. These data will help to prioritize future research directions.
Evaluation of Project P.A.T.H.S. in Hong Kong: Triangulation of Findings Based on Different Evaluation Strategies

There are different adolescent developmental issues in Hong Kong, such as mental health problems, abuse of psychotropic substances, adolescent suicide, school violence, and drop in family solidarity, that deserve the attention of helping professionals[1]. With reference to these problems, primary prevention programs that target specific adolescent developmental problems and positive youth development programs are called for. Furthermore, attempts to identify the "at-risk" adolescents at an earlier stage are important. However, research findings show that there are very few systematic and multiyear positive youth development programs in Hong Kong. Even if such programs exist, they commonly deal with isolated problems and issues in adolescent development (i.e., deficits-oriented programs) and they are relatively short term in nature. In addition, systematic and long-term evaluation of the available programs does not exist[2].
A Randomized Controlled Trial of Postoperative Thoracic Epidural Analgesia Versus Intravenous Patient-controlled Analgesia After Major Hepatopancreatobiliary Surgery

Objectives: The primary objective of this randomized trial was to compare thoracic epidural analgesia (TEA) to intravenous patient-controlled analgesia (IV-PCA) for pain control over the first 48 hours after hepatopancreatobiliary (HPB) surgery. Secondary endpoints were patient-reported outcomes, total narcotic utilization, and complications. Background: Although adequate postoperative pain control is critical to patient and surgeon success, the optimal analgesia regimen in HPB surgery remains controversial. Methods: Using a 2.5:1 randomization strategy, 140 patients were randomized to TEA (N = 106) or intravenous patient-controlled analgesia (N = 34). Patient-reported pain was measured on a Likert scale (0–10) at standard time intervals. Cumulative pain area under the curve was determined using the trapezoidal method. Results: Between the study groups key demographic, comorbidity, clinical, and operative variables were equivalently distributed. The median area under the curve of the postoperative time 0- to 48-hour pain scores was lower in the TEA group (78.6 vs 105.2 pain-hours, P = 0.032) with a 35% reduction in patients experiencing ≥7/10 pain (43% vs 62%, P = 0.07). Patient-reported outcomes and total opiate use further supported the benefit of TEA on patient experience. Anesthesia-related events requiring change in analgesic therapy were comparable (12.2% vs 2.9%, respectively, P = 0.187). Grade 3 or higher surgical complications (6.6% vs 9.4%), median length of stay (6 days vs 6 days), readmission (1.9% vs 3.1%), and return to the operating room (0.9% vs 3.1%) were similar (all P > 0.05). There were no mortalities in either group. Conclusions: In major HPB surgery, TEA provides a superior patient experience through improved pain control and less narcotic use, without increased length of stay or complications.
Logical Matrix Factorization With Application to Topological Structure Analysis of Boolean Network

This note investigates the logical matrix factorization with application to the topological structure analysis of Boolean networks. First, the concepts of both factorization and rank are defined for logical matrices, and two factorization problems are then studied. Using nonsingular logical matrix transformations, several necessary and sufficient conditions for the factorization of a given logical matrix are presented. Second, the logical matrix factorization is applied to the topological structure analysis of a given Boolean network, and a size-reduced structure-equivalent logical network is constructed for the given system. It is shown that the topological structure (including all the fixed points and cycles) of the resulting size-reduced logical network is the same as that of the original Boolean network. The study of an illustrative example shows that the new results presented in this note are effective in analyzing the topological structure of Boolean networks.
Bayesian sparse‐based reconstruction in bioluminescence tomography improves localization accuracy and reduces computational time

Bioluminescence tomography (BLT) provides fundamental insight into biological processes in vivo. To fully realize its potential, it is important to develop image reconstruction algorithms that accurately visualize and quantify the bioluminescence signals taking advantage of limited boundary measurements. In this study, a new 2‐step reconstruction method for BLT is developed by taking advantage of the sparse a priori information of the light emission using multispectral measurements. The first step infers a wavelength‐dependent prior by using all multi‐wavelength measurements. The second step reconstructs the source distribution based on this developed prior. Simulation, phantom and in vivo results were performed to assess and compare the accuracy and the computational efficiency of this algorithm with conventional sparsity‐promoting BLT reconstruction algorithms, and results indicate that the position errors are reduced from a few millimeters down to submillimeter, and reconstruction time is reduced by 3 orders of magnitude in most cases, to just under a few seconds. The recovery of single objects and multiple (2 and 3) small objects is simulated, and the recovery of images of a mouse phantom and an experimental animal with an existing luminescent source in the abdomen is demonstrated. Matlab code is available at https://github.com/jinchaofeng/code/tree/master.
Low‐level ultrahigh‐frequency and ultrashort‐pulse blue laser irradiation enhances osteoblast extracellular calcification by upregulating proliferation and differentiation via transient receptor potential vanilloid 1

Low‐level laser irradiation (LLLI) exerts various biostimulative effects, including promotion of wound healing and bone formation; however, few studies have examined biostimulation using blue lasers. The purpose of this study was to investigate the effects of low‐level ultrahigh‐frequency (UHF) and ultrashort‐pulse (USP) blue laser irradiation on osteoblasts.
Efficient Tag Identification in Mobile RFID Systems

In this paper we consider how to efficiently identify tags on the moving conveyor. Considering conditions like the path loss and multi-path effect in realistic settings, we first propose a probabilistic model for RFID tag identification. Based on this model, we propose efficient solutions to identify moving RFID tags, according to the fixed-path mobility on the conveyor. A dynamic program based solution and an adaptive solution are proposed to select optimized frame sizes during the query cycles. Simulation results indicate that by leveraging the probabilistic model our solutions can achieve much better performance than using parameters for the ideal propagation situations.
Dietary Patterns Are Associated with Metabolic Outcomes among Adult Samoans in a Cross-Sectional Study.

Background: The Samoan population has been undergoing a nutrition transition toward more imported and processed foods and a more sedentary lifestyle.Objectives: We aimed to identify dietary patterns in Samoa and to evaluate their associations with metabolic outcomes.Methods: The sample of this cross-sectional study includes 2774 Samoan adults recruited in 2010 (1104 with metabolic syndrome compared with 1670 without). Principal component analysis on food items from a 104-item food-frequency questionnaire was used to identify dietary patterns. Adjusted least squares means of each component of metabolic syndrome were estimated by quintiles of factor scores for each dietary pattern. Metabolic syndrome status was regressed on quintiles of scores by using log-binomial models to obtain prevalence ratios.Results: We identified a modern pattern, a mixed-traditional pattern, and a mixed-modern pattern. The modern pattern included a high intake of imported and processed foods, including pizza, cheeseburgers, margarine, sugary drinks, desserts, snacks, egg products, noodles, nuts, breads, and cakes and a low intake of traditional agricultural products and fish. The mixed-traditional pattern had a high intake of neotraditional foods, including fruits, vegetables, soup, poultry, and fish, and imported and processed foods, including dairy products, breads, and cakes. The mixed-modern pattern was loaded with imported and processed foods, including pizza, cheeseburgers, red meat, egg products, noodles, and grains, but also with neotraditional foods, such as seafood and coconut. It also included a low intake of fish, tea, coffee, soup, and traditional agricultural staples. Higher adherence to the mixed-modern pattern was associated with lower abdominal circumference (P-trend < 0.0001), lower serum triglycerides (P-trend = 0.03), and higher serum HDL cholesterol (P-trend = 0.0003). The mixed-modern pattern was inversely associated with prevalence of metabolic syndrome (the highest quintile: prevalence ratio = 0.79; 95% CI: 0.69, 0.91; P-trend = 0.006). Conclusion: Mixed dietary patterns containing healthier foods, rather than a largely imported and processed modern diet, may help prevent metabolic syndrome in Samoa.
Cell Phone Information Seeking Explains Blood Pressure in African American Women

Although cell phone use and Internet access via cell phone is not marked by racial disparities, little is known about how cell phone use relates to blood pressure and health information seeking behaviors. The purposes of this study were to (a) describe Internet activities, cell phone use, and information seeking; (b) determine differences in blood pressure and information seeking between cell phone information seekers and nonseekers; and (c) examine cell phone information seeking as a predictor of blood pressure in African American women. Participants (N = 147) completed a survey and had their blood pressure measured. Independent-sample t tests showed a significant difference in systolic blood pressure in cell phone information seekers and nonseekers. Linear regression revealed cell phone information seeking as an independent predictor of systolic blood pressure, despite confounders. It is possible that cell phone information seekers were using health information to make decisions about self-management of blood pressure.
Calmodulin antagonist enhances DR5‐mediated apoptotic signaling in TRA‐8 resistant triple negative breast cancer cells

Patients with triple negative breast cancer (TNBC) have no successful “targeted” treatment modality, which represents a priority for novel therapy strategies. Upregulated death receptor 5 (DR5) expression levels in breast cancer cells compared to normal cells enable TRA‐8, a DR5 specific agonistic antibody, to specifically target malignant cells for apoptosis without inducing normal hepatocyte apoptosis. Drug resistance is a common obstacle in TRAIL‐based therapy for TNBC. Calmodulin (CaM) is overexpressed in breast cancer. In this study, we characterized the novel function of CaM antagonist in enhancing TRA‐8 induced cytotoxicity in TRA‐8 resistant TNBC cells and its underlying molecular mechanisms. Results demonstrated that CaM antagonist(s) enhanced TRA‐8 induced cytotoxicity in a concentration and time‐dependent manner for TRA‐8 resistant TNBC cells. CaM directly bound to DR5 in a Ca2+ dependent manner, and CaM siRNA promoted DR5 recruitment of FADD and caspase‐8 for DISC formation and TRA‐8 activated caspase cleavage for apoptosis in TRA‐8 resistant TNBC cells. CaM antagonist, trifluoperazine, enhanced TRA‐8 activated DR5 oligomerization, DR5‐mediated DISC formation, and TRA‐8 activated caspase cleavage for apoptosis, and decreased anti‐apoptotic pERK, pAKT, XIAP, and cIAP‐1 expression in TRA‐8 resistant TNBC cells. These results suggest that CaM could be a key regulator to mediate DR5‐mediated apoptotic signaling, and suggests a potential strategy for using CaM antagonists to overcome drug resistance of TRAIL‐based therapy for TRA‐8 resistant TNBC.
A Comprehensive Reliability Assessment of Fault-Resilient Network-on-Chip Using Analytical Model

The component’s failure in network-on-chips (NoCs) has been a critical factor on the system’s reliability. In order to alleviate the impact of faults, fault tolerance has been investigated in the recent years to enhance NoC’s robustness. Due to the vast selection of fault-tolerance mechanisms and critical design constraints, selecting and configuring an appropriate mechanism to satisfy the fault-tolerance requirements constitute new challenges for designers. Consequently, reliability assessment has become prominent for the early stages of manufacturing process to solve these problems. This paper approaches the fault-tolerance analysis by providing an analytical model to approximate the lifetime reliability and compares it with a system-level simulation. Based on the proposed approach, we measure the fault-tolerance efficiency using a new parameter, named reliability acceleration factor. The goal of this paper is to provide an efficient and accurate reliability assessment to help designers easily understand and evaluate the advantages and drawbacks of their potential fault-tolerance methods.
A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts

Next-generation sequencing (NGS) can identify and validate new biomarkers of cancer onset, progression and therapy resistance. Substantial archives of formalin-fixed, paraffin-embedded (FFPE) cancer samples from patients represent a rich resource for linking molecular signatures to clinical data. However, performing NGS on FFPE samples is limited by poor RNA purification methods. To address this hurdle, we developed an improved methodology for extracting high-quality RNA from FFPE samples. By briefly integrating a newly-designed micro-homogenizing (mH) tool with commercially available FFPE RNA extraction protocols, RNA recovery is increased by approximately 3-fold while maintaining standard A260/A280 ratios and RNA quality index (RQI) values. Furthermore, we demonstrate that the mH-purified FFPE RNAs are longer and of higher integrity. Previous studies have suggested that pancreatic ductal adenocarcinoma (PDAC) gene expression signatures vary significantly under in vitro versus in vivo and in vivo subcutaneous versus orthotopic conditions. By using our improved mH-based method, we were able to preserve established expression patterns of KRas-dependency genes within these three unique microenvironments. Finally, expression analysis of novel biomarkers in KRas mutant PDAC samples revealed that PEAK1 decreases and MST1R increases by over 100-fold in orthotopic versus subcutaneous microenvironments. Interestingly, however, only PEAK1 levels remain elevated in orthotopically grown KRas wild-type PDAC cells. These results demonstrate the critical nature of the orthotopic tumor microenvironment when evaluating the clinical relevance of new biomarkers in cells or patient-derived samples. Furthermore, this new mH-based FFPE RNA extraction method has the potential to enhance and expand future FFPE-RNA-NGS cancer biomarker studies.
Manipulating nanoparticle transport within blood flow through external forces: an exemplar of mechanics in nanomedicine

A large number of nanoparticles (NPs) have been raised for diverse biomedical applications and some of them have shown great potential in treatment and imaging of diseases. Design of NPs is essential for delivery efficacy due to a number of biophysical barriers, which prevents the circulation of NPs in vascular flow and their accumulation at tumour sites. The physiochemical properties of NPs, so-called ‘4S’ parameters, such as size, shape, stiffness and surface functionalization, play crucial roles in their life journey to be delivered to tumour sites. NPs can be modified in various ways to extend their blood circulation time and avoid their clearance by phagocytosis, and efficiently diffuse into tumour cells. However, it is difficult to overcome these barriers simultaneously by a simple combination of ‘4S’ parameters for NPs. At this moment, external triggerings are necessary to guide the movement of NPs, which include light, ultrasound, magnetic field, electrical field and chemical interaction. The delivery system can be constructed to be sensitive to these external stimuli which can reduce the non-specific toxicity and improve the efficacy of the drug-delivery system. From a mechanics point of view, we discuss how different forces play their roles in the margination of NPs in blood flow and tumour microvasculature.