Miracle-dz/UniFAR-FTUs huggingface dataset:
Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data

We discuss the identification of features that are associated with an outcome in RNA-Sequencing (RNA-Seq) and other sequencing-based comparative genomic experiments. RNA-Seq data takes the form of counts, so models based on the normal distribution are generally unsuitable. The problem is especially challenging because different sequencing experiments may generate quite different total numbers of reads, or ‘sequencing depths’. Existing methods for this problem are based on Poisson or negative binomial models: they are useful but can be heavily influenced by ‘outliers’ in the data. We introduce a simple, non-parametric method with resampling to account for the different sequencing depths. The new method is more robust than parametric methods. It can be applied to data with quantitative, survival, two-class or multiple-class outcomes. We compare our proposed method to Poisson and negative binomial-based methods in simulated and real data sets, and find that our method discovers more consistent patterns than competing methods.
Reconstruction of bandlimited signals from noisy data by thresholding

The problem of recovering bandlimited signals from discrete and noisy data is studied. A nonlinear signal processing algorithm based on thresholding noisy data prior to reconstruction is proposed for improving the accuracy and robustness of reconstruction. The upper bound and the exact formula for mean integrated squared error of the proposed reconstruction scheme is established. The performance of the proposed reconstruction scheme is compared to that of the classical Whittaker-Shannon interpolation scheme.
High-Dimensional Feature Matching: Employing the Concept of Meaningful Nearest Neighbors

Matching of high-dimensional features using nearest neighbors search is an important part of image matching methods which are based on local invariant features. In this work we highlight effects pertinent to high-dimensional spaces that are significant for matching, yet have not been explicitly accounted for in previous work. In our approach, we require every nearest neighbor to be meaningful, that is, sufficiently close to a query feature such that it is an outlier to a background feature distribution. We estimate the background feature distribution from the extended neighborhood of a query feature given by its k nearest neighbors. Based on the concept of meaningful nearest neighbors, we develop a novel high-dimensional feature matching method and evaluate its performance by conducting image matching on two challenging image data sets. A superior performance in terms of accuracy is shown in comparison to several state-of-the-art approaches. Additionally, to make search for k nearest neighbors more efficient, we develop a novel approximate nearest neighbors search method based on sparse coding with an overcomplete basis set that provides a ten-fold speed-up over an exhaustive search even for high dimensional spaces and retains excellent approximation to an exact nearest neighbors search.
Renormalization Flow of Bound States

A renormalization group flow equation with a scale-dependent transformation of field variables gives a unified description of fundamental and composite degrees of freedom. In the context of the effective average action, we study the renormalization flow of scalar bound states which are formed out of fundamental fermions. We use the gauged Nambu–Jona-Lasinio model at weak gauge coupling as an example. Thereby, the notions of bound state or fundamental particle become scale dependent, being classified by the fixed-point structure of the flow of effective couplings.
Prognostic significance of the micropapillary pattern in patients with serous borderline ovarian tumors

Background. The impact of micropapillary histology on survival in patients with serous borderline ovarian tumors is not established. The purpose of this study was to evaluate the significance and influence of micropapillary pattern on clinical outcome of patients with serous borderline ovarian tumors. Methods. Eighty‐five patients who underwent surgery and were diagnosed with serous borderline ovarian tumors were retrospectively studied. Among these patients, 18 patients showed micropapillary pattern on histologic examination, while the remaining 67 patients did not. The significance of the presence of micropapillary pattern and relationship with various clinicopathologic findings and progression‐free survival were evaluated by statistical analysis. Results. No differences with regard to age, parity, body mass index, pretreatment CA‐125 level, tumor size, bilaterality, and the duration of follow‐up were observed between the two groups, but there was a significant difference in terms of FIGO stage (p<0.001), invasive implants (p = 0.004), performing lymphadenectomy (p = 0.009), operation time (p = 0.003), estimated blood loss (p<0.001), residual disease>1 cm (p = 0.001), adjuvant chemotherapy (p<0.001), and the length of hospital stay (p = 0.013). Progression‐free survival was found to be significantly decreased in patients with invasive implants (HR, 5.06; p = 0.025) and micropapillary pattern (HR, 4.20; p = 0.056) on multivariate analysis. Conclusions. Micropapillary serous borderline ovarian tumors were associated with a more aggressive clinical course compared with typical serous borderline ovarian tumor. The presence of invasive implants and micropapillary pattern were significant prognostic factors in patients with serous borderline ovarian tumors.
Parent Perception of Newborn Hearing Screening: Results of a US National Survey.

IMPORTANCE An unacceptably high number of children who do not pass universal newborn hearing screening (UNHS) are lost to follow-up. OBJECTIVES To provide insight into parent recall of UNHS. DESIGN, SETTING, AND PARTICIPANTS In this nationally representative cross-sectional survey, 2144 US parent households were surveyed in May 2012 using the Knowledge Panel. Responses of parents whose children were born before vs after UNHS implementation were compared. MAIN OUTCOMES AND MEASURES Outcome measures included recall of hearing screen at birth, hearing screen results, and recommendations for follow-up. All outcome measures were based on parent recall and report. Descriptive statistics and multiple logistic regression analyses were used. RESULTS The study participants included 1539 parent households and 605 nonparent households. Of the 1539 parent households surveyed, the mean age of the parents was 38.8 years (range, 18-88 years), the mean age of the children was 10.2 years (range, 0-17 years), and the mean age of children with hearing loss was 12.1 years (range, 0-17 years). A total of 1539 parents (55.8%) were women. Only 62.9% of parents (unweighted n = 950) recalled a newborn hearing screen, and among those children with risk indicators for hearing loss (n = 587), only 68.6% (unweighted n = 385) recalled a hearing screen. Higher parent educational level (odds ratio [OR], 2.27; 95% CI, 1.17-4.41, for some college and OR, 2.41; 95% CI, 1.22-4.78, for a bachelor's degree; P = .03), younger age of the child (OR, 1.16; 95% CI, 1.11-1.23; P < .001), and the presence of any risk indicator for hearing loss (OR, 1.5; 95% CI, 1.13-2.13; P = .007) were associated with parent recall of hearing screen. Reported pass rates were higher than expected. Parent recall of follow-up recommendations was not always consistent with guidelines. CONCLUSIONS AND RELEVANCE Although this study is inherently limited by recall bias, the findings indicate a lack of parent awareness of UNHS. Changes in the system of reporting UNHS results are necessary to improve parent recall of screen results and improve follow-up for children who do not pass the screen.
Fair Energy-Efficient Scheduling in Wireless Powered Full-Duplex Mobile-Edge Computing Systems

Prolonging battery lifetime, enhancing computation capability and improving spectral efficiency have been the key design challenges in Internet of Things (IoT) era. This paper provides a novel solution to jointly optimize the allocation of the communication, computing and energy resources in IoT, with the aid of some advanced wireless communication technologies including Wireless Energy Transfer (WET), Mobile-Edge Computing (MEC) and Full-Duplex (FD). Specifically, the Hybrid Access-Point (HAP) (integrated with a MEC server) operates in FD mode to simultaneously broadcast energy and receive computation tasks to/from the mobile devices in the same band. Each mobile relies on the harvested energy to accomplish computation tasks by locally executing or (partial) offloading to the HAP. We concentrate on max-min energy efficiency optimization problem (MMEP) with the joint the optimization of the transmission power at the HAP, computation energy consumption and offloaded bits at each mobile device, time slots for energy transfer and computation offloading. We study the cases with perfect and imperfect self-interference cancellation at the HAP. To solve the non-convex MMEP, we apply the fractional programming theory and Block Coordinate Descent (BCD) method to design the algorithms with low complexity. Numerical results demonstrate that the proposed solutions outperform the baseline scheme in terms of the worst-case mobile EE. Moreover, the proposed algorithms can converge to the optimal solution through a few iterations.
On the Design of Mutually Aware OptimalPricing and Load Balancing Strategiesfor Grid Computing Systems

Managing resources and cleverly pricing them on computing systems is a challenging task. Resource sharing demands careful load balancing and often strives to achieve a win-win situation between resource providers and users. Toward this goal, we consider a joint treatment of load balancing and pricing. We do not assume static pricing to determine load balancing, or vice versa. Instead, we study the relationship between the price that a computing node is charged and the load and revenue that it receives. We find that there exists an optimal price which maximizes the revenue. We then consider a multi-user environment and explore how the load from a user can be balanced on processors with existing loads. Finally, we derive an optimal price that maximizes the revenue in the multi-user environment. We evaluate the performance of the proposed algorithms through simulations.
Differentiated Therapy with Prostaglandin E1 (Alprostadil) after Orthotopic Liver Transplantation: the Usefulness of Procalcitonin (PCT) and Hepatic Artery Resistive Index (RI) for the Evaluation of Early Graft Function and Clinical Course

Abstract Increasing demand for donor organs has led to new pharmacological concepts for reducing ischemiareperfusion injury (I/R) of the graft after liver transplantation to prevent primary non-functioning of the organ. Prostaglandins have proved to be cytoprotective in several experimental models of ischemia and transplantation. The prophylactic administration after orthotopic liver transplantation is still a subject of controversial discussion. The aim of our study was the evaluation of the post-transplant hepatic artery resistive index (RI) measured by color Doppler imaging, in combination with postoperative elevation of transaminases, as parameters indicating the need for a differentiated systemic therapy with prostaglandin E1 (PGE1) (alprostadil). In addition, the value of serum procalcitonin (PCT) as a postoperative parameter for the extent of I/R is investigated. In the case of post-transplant elevated hepatic artery RI (RI > 0.75), the administration of PGE1 led to a significant reduction of transaminases (p < 0.05) and a decline of the RI. In addition, postoperative PCT levels could be reduced significantly by PGE1 application. These results suggest that determination of RI is feasible for indicating a need for therapy with PGE1. Its targeted application reduces hepatocellular damage due to I/R after liver transplantation.
The effect of surface coating and fibre loading on thermo-mechanical properties of recycled polyethylene terephthalate (RPET)/epoxy-coated kenaf fibre composites

Natural fibres have low degradation temperatures, which are inadequate for the processing with engineering thermoplastics at above 200°C. This research is aimed at improving the thermal stability of natural fibres by surface coating the fibres with thermosetting resin in order to be processed with engineering thermoplastics without degradation. A composite of recycled polyethylene terephthalate (RPET) reinforced with uncoated and epoxy-coated kenaf fibre of 5, 10 and 15 weight% was prepared by twin screw extruder and compression moulding at an optimised processing temperature of 240°C. Differential scanning calorimetry and thermogravimetric analysis were used to evaluate the thermal phase and decomposition characteristics of the composites. Mechanical tests were conducted to examine the mechanical properties of the composite. It was found that coated kenaf composite were thermally stable, indicating the non-existence of fibre degradation as compared to the uncoated. The mechanical properties of coated kenaf composites were better as compared to uncoated and apparently improved with increased fibre content. The morphological studies also revealed strong fibre/matrix interfacial bonding for coated fibre composites and the poor mechanical performance of uncoated fibre composite is attributed to thermal degradation of kenaf fibres in the composite system.
Chemical inhibition of acetyl-CoA carboxylase suppresses self-renewal growth of cancer stem cells

Cancer stem cells (CSC) may take advantage of the Warburg effect-induced siphoning of metabolic intermediates into de novo fatty acid biosynthesis to increase self-renewal growth. We examined the anti-CSC effects of the antifungal polyketide soraphen A, a specific inhibitor of the first committed step of lipid biosynthesis catalyzed by acetyl-CoA carboxylase (ACACA). The mammosphere formation capability of MCF-7 cells was reduced following treatment with soraphen A in a dose-dependent manner. MCF-7 cells engineered to overexpress the oncogene HER2 (MCF-7/HER2 cells) were 5-fold more sensitive than MCF-7 parental cells to soraphen A-induced reductions in mammosphere-forming efficiency. Soraphen A treatment notably decreased aldehyde dehydrogenase (ALDH)-positive CSC-like cells and impeded the HER2's ability to increase the ALDH+-stem cell population. The following results confirmed that soraphen A-induced suppression of CSC populations occurred through ACACA-driven lipogenesis: a. ) exogenous supplementation with supraphysiological concentrations of oleic acid fully rescued mammosphere formation in the presence of soraphen A and b. ) mammosphere cultures of MCF-7 cells with stably silenced expression of the cytosolic isoform ACACA1, which specifically participates in de novo lipogenesis, were mostly refractory to soraphen A treatment. Our findings reveal for the first time that ACACA may constitute a previously unrecognized target for novel anti-breast CSC therapies.
Multiobjective Monitoring for SLA Compliance

Service level agreements (SLAs) define performance guarantees made by service providers, e.g., in terms of packet loss, delay, delay variation, and network availability. In this paper, we describe a new active measurement methodology to accurately monitor whether measured network path characteristics are in compliance with performance targets specified in SLAs. Specifically, we: 1) introduce a new methodology for measuring mean delay along a path that improves accuracy over existing methodologies, and a method for obtaining confidence intervals on quantiles of the empirical delay distribution without making any assumption about the true distribution of delay; 2) introduce a new methodology for measuring delay variation that is more robust than prior techniques; 3) describe a new methodology for estimating packet loss rate that significantly improves accuracy over existing approaches; and 4) extend existing work in network performance tomography to infer lower bounds on the quantiles of a distribution of performance measures along an unmeasured path given measurements from a subset of paths. Active measurements for these metrics are unified in a discrete time-based tool called SLAm. The unified probe stream from SLAm consumes lower overall bandwidth than if individual streams are used to measure path properties. We demonstrate the accuracy and convergence properties of SLAm in a controlled laboratory environment using a range of background traffic scenarios and in one- and two-hop settings, and examine its accuracy improvements over existing standard techniques.
Controllability and Observability of Linear Time-Invariant Uncertain Systems Irrespective of Bounds of Uncertain Parameters

In this paper, the controllability and observability of linear time-invariant uncertain systems are investigated. The systems under consideration contain time-invariant uncertain parameters that may take arbitrarily large values. In such a situation, the locations of uncertain parameters in system matrices play an important role. We examine the permissible locations of uncertain parameters in system matrices for a linear uncertain system to be controllable and observable independently of the bounds of the uncertain parameters. The objective of this paper is to show that a linear uncertain system is controllable and observable, irrespective of the bounds of uncertain parameters, if and only if the system has a particular configuration called a complete generalized antisymmetric stepwise configuration (CGASC). Furthermore, the dual configuration of a CGASC is introduced and studied here.
High-Speed Electrical Machines: Technologies, Trends, and Developments

This paper reviews the current technologies used in high-speed electrical machines through an extensive survey of different topologies developed and built in the industry and academia for several applications. Developments in materials and components, including electrical steels and copper alloys, are discussed, and their impact on the machines' operating physical boundaries is investigated. The main application areas pulling the development of high-speed machines are also reviewed to better understand the typical performance requirements.
A time domain characterization of finite frequency properties for multi-dimensional behaviors

Many of practical design specifications are provided by finite frequency properties described by inequalities over restricted finite frequency intervals. In this paper, we consider a time domain characterization of the finite frequency domain inequalities (FFDIs) for multi-dimensional behaviors using quadratic differential forms (QDFs), which are useful algebraic tools for the dissipation theory based on the behavioral approach. Based on QDFs, result, we derive a characterization of the FFDIs using the compensating rate which guarantees the dissipativity of some behavior with some rate constraints as a main result. This is a generalization of previous works for one-dimensional systems to the multi-dimensional case.
Characterization of Oxacillinase and Metallo-β-Lactamas Genes and Molecular Typing of Clinical Isolates of Acinetobacter baumannii in Ahvaz, South-West of Iran

Background: Carbapenem resistant Acinetobacter baumannii is an important nosocomial pathogen associated with a variety of infections. Objectives: The current study aimed to characterize the antimicrobial susceptibility, analyze the prevalence of oxacillinase and metallo-β-lactamase (MBL) genes and molecular typing of clinical isolates of A. baumannii. Materials and Methods: A total of 124 non-repetitive isolates of A. baumannii were collected from various clinical specimens in two teaching hospitals in Ahvaz, south-west of Iran. Antimicrobial susceptibility test was carried out by disk diffusion method. The minimum inhibitory concentrations (MICs) of imipenem, meropenem, colistin and tigecycline were determined using E-test. To screen for MBL production, double disk synergy (DDs) test and MBL E-test were performed. The presence of blaOXA-23-like, blaOXA-24-like, blaOXA-51-like, blaOXA-58-like, blaVIM, blaIMP and blaSPM genes was assessed by polymerase chain reaction (PCR). To identify clonal relatedness, all isolates were subjected to repetitive sequence-based PCR (rep-PCR) Results: Based on disk diffusion results, the highest rate of resistance was observed in rifampin (96.8%). Colistin and polymyxin-B were the most effective agents in vitro. According to the MIC results, the rate of resistance to imipenem, meropenem, colistin and tigecycline were 78.2%, 73.4%, 0.8% and 0, respectively. Metallo-β-lactamase production was positive in 42.3% and 79.4% of the isolates by DDs test and E-test, respectively. All isolates (100%) carried blaOXA-51-like gene. According to the results of multiplex PCR, blaOXA-23-like and blaOXA-24-like genes were detected in 85.6% and 6.2% of carbapenem resistant isolates, respectively. No blaOXA-58- like, blaVIM, blaIMP and blaSPM were detected. By rep-PCR, carbapenem resistant isolates were separated into six genotypes (A to F). Genotype A (30.9%) was the most prevalent (P value < 0.001). Genotypes B and C were found in 28.9% and 26.8% of the isolates, respectively. Conclusions: The rate of carbapenem resistant A. baumannii isolates were high in this study. Since, blaOXA-58-like or MBL genes were not detected, it seems that resistance to carbapenems is related to blaOXA-23-like and blaOXA-24-like. Moreover, blaOXA-23-like was the most prevalent oxacillinase (OXA) gene. Most of the isolates belonged to one of the four dominant genotypes indicating clonal dissemination in the hospitals under study. In order to control the spread of carbapenem-resistant A. baumannii, infection- control strategies are needed.
Phonological similarity judgments in ASL: Evidence for maturational constraints on phonetic perception in sign

We created a novel paradigm to investigate phonological processing in sign and asked how age of acquisition (AoA) may affect it. Participants indicated which of two signs was more phonologically similar to a target, and estimated the strength of the resemblance with a mouse click along a continuous scale. We manipulated AoA by testing deaf native and non-native signers, and hearing L2 signers and sign-naive participants. Consistent with previous research, judgments by the native and L2 signers reflected similarity based on shared phonological features between signs. By contrast, judgments by the non-native signers and sign-naive participants were influenced by other (potentially visual or somatosensory) properties of signs that native and L2 signers ignored. These results suggest that early exposure to language helps a learner discern which aspects of a linguistic signal are most likely to matter for language learning, even if that language belongs to a different modality.
Towards Recycled Paper Based Impedance Biosensor with Wireless Readout

Results are presented regarding the development of recycled paper based impedance biosensors with screen printed interdigitated electrode structures (IDES). The sensors show a response to increasing salt concentrations in the range 30–100 mM NaCl. To prove the feasibility of using recycled paper, biofunctionalization with a glucose sensitive enzyme mixture was performed by inkjet printing. The quantification of the glucose sensitive colour change reaction in paper was investigated and a trend is found in the range of 6–90 mg/dL. Subsequently, measurements with a wireless electronic readout system were performed on an electrochemical assay showing a decrease of the normalized sensor response dependent from the glucose concentration in the range 0–80 mg/dL.