Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinct Transcriptional Changes and Epithelial–Stromal Interactions Are Altered in Early-Stage Colon Cancer Development

Although the progression of mutated colonic cells is dependent upon interactions between the initiated epithelium and surrounding stroma, the nature of these interactions is poorly understood. Here, the development of an ultrasensitive laser capture microdissection (LCM)/RNA-seq approach for studying the epithelial and stromal compartments of aberrant crypt foci (ACF) is described. ACF are the earliest identifiable preneoplastic lesion found within the human colon and are detected using high-definition endoscopy with contrast dye spray. The current analysis focused on the epithelium of ACF with somatic mutations to either KRAS, BRAF, or APC, and expression patterns compared with normal mucosa from each patient. By comparing gene expression patterns among groups, an increase in a number of proinflammatory NF-κB target genes was identified that was specific to ACF epithelium, including TIMP1, RELA, and RELB. Distinct transcriptional changes associated with each somatic mutation were observed and a subset of ACF display BRAFV600E-mediated senescence-associated transcriptome characterized by increased expression of CDKN2A. Finally, LCM-captured ACF-associated stroma was found to be transcriptionally distinct from normal-appearing stroma, with an upregulation of genes related to immune cell infiltration and fibroblast activation. Immunofluorescence confirmed increased CD3+ T cells within the stromal microenvironment of ACF and an abundance of activated fibroblasts. Collectively, these results provide new insight into the cellular interplay that occurs at the earliest stages of colonic neoplasia, highlighting the important role of NF-κB, activated stromal fibroblasts, and lymphocyte infiltration. Implications: Fibroblasts and immune cells in the stromal microenvironment play an important role during the earliest stages of colon carcinogenesis. Mol Cancer Res; 14(9); 795–804. ©2016 AACR.
Word Error Rate Minimization Using an Integrated Confidence Measure

This paper describes a new criterion for speech recognition using an integrated confidence measure to minimize the word error rate (WER). The conventional criteria for WER minimization obtain the expected WER of a sentence hypothesis merely by comparing it with other hypotheses in an n-best list. The proposed criterion estimates the expected WER by using an integrated confidence measure with word posterior probabilities for a given acoustic input. The integrated confidence measure, which is implemented as a classifier based on maximum entropy (ME) modeling or support vector machines (SVMs), is used to acquire probabilities reflecting whether the word hypotheses are correct. The classifier is comprised of a variety of confidence measures and can deal with a temporal sequence of them to attain a more reliable confidence. Our proposed criterion for minimizing WER achieved a WER of 9.8% and a 3.9% reduction, relative to conventional n-best rescoring methods in transcribing Japanese broadcast news in various environments such as under noisy field and spontaneous speech conditions.
ADAMTS1, CRABP1, and NR3C1 Identified as Epigenetically Deregulated Genes in Colorectal Tumorigenesis

Background: Gene silencing through CpG island hypermethylation is a major mechanism in cancer development. In the present study, we aimed to identify and validate novel target genes inactivated through promoter hypermethylation in colorectal tumor development. Methods: With the use of microarrays, the gene expression profiles of colon cancer cell lines before and after treatment with the demethylating agent 5-aza-2′-deoxycytidine were identified and compared. The expression of the responding genes was compared with microarray expression data of primary colorectal carcinomas. Four of these down-regulated genes were subjected to methylation-specific PCR, bisulphite sequencing, and quantitative gene expression analysis using tumors (n=198), normal tissues (n=44), and cell lines (n=30). Results: Twenty-one genes with a CpG island in their promoter responded to treatment in cell lines, and were simultaneously down-regulated in primary colorectal carcinomas. Among 20 colon cancer cell lines, hypermethylation was subsequently identified for three of four analyzed genes, ADAMTS1 (85%), CRABP1 (90%), and NR3C1 (35%). For the latter two genes, hypermethylation was significantly associated with absence or reduced gene expression. The methylation status of ADAMTS1, CRABP1, and NR3C1 was further investigated in 116 colorectal carcinomas and adenomas. Twenty-three of 63 (37%), 7/60 (12%), and 2/63 (3%) adenomas, as well as 37/52 (71%), 25/51 (49%), and 13/51 (25%) carcinomas were hypermethylated for the respective genes. These genes were unmethylated in tumors (n=82) from three other organs, prostate, testis, and kidney. Finally, analysis of normal colorectal mucosa demonstrated that the observed promoter hypermethylation was cancer-specific. Conclusion: By using a refined microarray screening approach we present three genes with cancer-specific hypermethylation in colorectal tumors, ADAMTS1, CRABP1, and NR3C1.
On Detection of Faint Edges in Noisy Images

A fundamental question for edge detection in noisy images is how faint can an edge be and still be detected. In this paper we offer a formalism to study this question and subsequently introduce computationally efficient multiscale edge detection algorithms designed to detect faint edges in noisy images. In our formalism we view edge detection as a search in a discrete, though potentially large, set of feasible curves. First, we derive approximate expressions for the detection threshold as a function of curve length and the complexity of the search space. We then present two edge detection algorithms, one for straight edges, and the second for curved ones. Both algorithms efficiently search for edges in a large set of candidates by hierarchically constructing difference filters that match the curves traced by the sought edges. We demonstrate the utility of our algorithms in both simulations and applications involving challenging real images. Finally, based on these principles, we develop an algorithm for fiber detection and enhancement. We exemplify its utility to reveal and enhance nerve axons in light microscopy images.
Stochastic Channel Allocation for Networked Control Systems

In this letter, we study a channel scheduling problem for a class of networked nonlinear control systems. The controller, sensors, and actuators of a group of dynamically decoupled nonlinear subsystems are connected through a digital communication channel, and due to the limited capacity, only one sensor and actuator can communicate with the controller at each time instant. To alleviate the negative effects of the limited communication capacity, we adopt a predictive control framework for controller/scheduler co-design. Instead of sending a single control value, the controller sends a sequence of predicted control values to a selected actuator so that there are control input candidates which can be fed to the subsystem when the actuator does not communicate with the controller. A stochastic algorithm is designed to schedule the sensors and actuators and we show that stochastic stability can be achieved under some mild assumptions and properly chosen design parameters.
A Toolbox for Easily Calibrating Omnidirectional Cameras

In this paper, we present a novel technique for calibrating central omnidirectional cameras. The proposed procedure is very fast and completely automatic, as the user is only asked to collect a few images of a checker board, and click on its corner points. In contrast with previous approaches, this technique does not use any specific model of the omnidirectional sensor. It only assumes that the imaging function can be described by a Taylor series expansion whose coefficients are estimated by solving a four-step least-squares linear minimization problem, followed by a non-linear refinement based on the maximum likelihood criterion. To validate the proposed technique, and evaluate its performance, we apply the calibration on both simulated and real data. Moreover, we show the calibration accuracy by projecting the color information of a calibrated camera on real 3D points extracted by a 3D sick laser range finder. Finally, we provide a Toolbox which implements the proposed calibration procedure
Profitability and the Lifecycle of Firms Missaka Warusawitharana

Using data on listed and unlisted firms in the U.K., this study documents that average profitability changes systematically with age. In their early years, firms realize substantial profitability increases, while mature firms face slow declines in profitability. A model of endogenous profitability changes arising from product development captures this pattern. Investment in product development generates profitability increases for young firms while competitive pressures from new entrants lead to profitability declines for mature firms. In addition, the model predicts that young firms realize profitability jumps more frequently and that the effect of age on firms’ policies would be stronger for young firms. Empirical tests support these predictions. Taken together, these findings show that changes in profitability influences the lifecycle of firms.
Multiple mutations in human immunodeficiency virus-1 integrase confer resistance to the clinical trial drug S-1360

Objectives: Study of HIV-1 resistance development to the diketo analogue S-1360, the first HIV-1 integrase strand transfer inhibitor that has entered clinical development. Design: HIV-1(IIIB) was passaged in cell culture in the presence of increasing concentrations of S-1360 (IIIB/S-1360res). Methods: The IIIB/S-1360res strains selected for 30, 50 and 70 passages in the presence of S-1360 were evaluated genotypically by sequencing analysis and phenotypically using the MT-4/MTT assay. Results: Multiple mutations, nine in total, emerged progressively in the catalytic domain of integrase as a result of the selection process. They included T66I and L74M that have both been associated with resistance against the diketo acid L-708,906. After 30, 50 and 70 passages in the presence of S-1360, IIIB/S-1360res displayed a four-, eight- and more than 62-fold reduced susceptibility for S-1360, respectively. Phenotypic cross-resistance to L-708,906 was modest for the IIIB/S-1360res strain selected during 50 passages, but pronounced for the strain selected during 70 passages. Interesting, all IIIB/S-1360res strains remained fully susceptible to the pyranodipyrimidine V-165, an integrase DNA binding inhibitor. Recombination of the mutant integrase genes into wild-type background by integrase-chimeric virus technology entirely reproduced the resistance profile of the IIIB/S-1360res strains. As for the replication kinetics of the selected and recombined strains, reduced replication fitness was measured for all strains when compared with their respective wild-type strains. Conclusions: The accumulation of integrase mutations coincided with an increasing level of (cross-)resistance of IIIB/S-1360res. Integrase-chimeric virus technology confirmed that the integrase mutations are indeed fully responsible for the resistance phenotype of IIIB/S-1360res.
Modelling and control of cholera on networks with a common water source

A mathematical model is formulated for the transmission and spread of cholera in a heterogeneous host population that consists of several patches of homogeneous host populations sharing a common water source. The basic reproduction number ℛ0 is derived and shown to determine whether or not cholera dies out. Explicit formulas are derived for target/type reproduction numbers that measure the control strategies required to eradicate cholera from all patches.
Development of analytical techniques for studies on dispersion of actinides in the environment and characterization of environmental radioactive particles

Radioactive particles from three locations were investigated for elemental composition, oxidation states of matrix elements, and origin. Instrumental techniques applied to the task were scanning electron microscopy, X-ray and gamma-ray spectrometry, secondary ion mass spectrometry, and synchrotron radiation based microanalytical techniques comprising X-ray fluorescence spectrometry, X-ray fluorescence tomography, and Xray absorption near-edge structure spectroscopy. Uranium-containing low activity particles collected from Irish Sea sediments were characterized in terms of composition and distribution of matrix elements and the oxidation states of uranium. Indications of the origin were obtained from the intensity ratios and the presence of thorium, uranium, and plutonium. Uranium in the particles was found to exist mostly as U(IV). Studies on plutonium particles from Runit Island (Marshall Islands) soil indicated that the samples were weapon fuel fragments originating from two separate detonations: a safety test and a low-yield test. The plutonium in the particles was found to be of similar age. The distribution and oxidation states of uranium and plutonium in the matrix of weapon fuel particles from Thule (Greenland) sediments were investigated. The variations in intensity ratios observed with different techniques indicated more than one origin. Uranium in particle matrixes was mostly U(IV), but plutonium existed in some particles mainly as Pu(IV), and in others mainly as oxidized Pu(VI). The results demonstrated that the various techniques were effectively applied in the characterization of environmental radioactive particles. An on-line method was developed for separating americium from environmental samples. The procedure utilizes extraction chromatography to separate americium from light lanthanides, and cation exchange to concentrate americium before the final separation in an ion chromatography column. The separated radiochemically pure americium fraction is measured by alpha spectrometry. The method was tested with certified sediment and soil samples and found to be applicable for the analysis of environmental samples containing a wide range of Am activity. Proceeding from the on-line method developed for americium, a method was also developed for separating plutonium and americium. Plutonium is reduced to Pu(III), and separated together with Am(III) throughout the procedure. Pu(III) and Am(III) are eluted from the ion chromatography column as anionic dipicolinate and oxalate complexes, respectively, and measured by alpha spectrometry.
Unsteady motion of two solid spheres in Stokes flow

This study is concerned with the unsteady motion of two solid spherical particles in an unbounded incompressible Newtonian flow. The background flow is uniform and can be time dependent. In addition, the particle Reynolds numbers 2aVa∕ν and 2bVb∕ν, based on characteristic particles velocities Va and Vb, are assumed to remain small throughout the motion. Here, a and b denote the particle radii and ν is the kinematic viscosity of the fluid. Two approximate methods are employed in order to calculate the unsteady force exerted on each particle. In the first approach, a simplified method of reflections in combination with the point-force method is employed. In the second approach, a simplified method of reflections combined with Burger’s unsteady flow solution is considered. The forces due to the background flow and the disturbed flow created by the presence of particles are treated separately. The equation of motion for each particle is derived and some special cases are presented in detail including the moti.
Software Engineering Job Productivity - a Systematic Review

Productivity is a key element in organizational management. Although it can be measured at different levels (country, sector, organization …) this research focuses on productivity at the job level. The aim of this paper is to obtain an overview of the state of the art in productivity measurement in software engineering, including the inputs and outputs of the production process used for this measurement at the job level in the workplace. To do so, a systematic literature review protocol was adapted from literature review protocol standards, and subsequently carried out. The objective is to assess the current inputs and outputs present in the literature in order to create new productivity measures for software practitioners. This paper reveals that two different measures are used to assess software engineering professionals: traditional SLOC/Time and planning projects units per time unit.
Factors Influencing Knowledge-Sharing Behavior in Virtual Communities: A Longitudinal Investigation

This article examines the change of the roles of trust, commitment, and self-efficacy with time. Data were collected from 150 members of a technical virtual community. The results reveal that trust and knowledge-sharing self-efficacy influence knowledge-sharing intention at two points of measurement significantly, while commitment significantly affects knowledge-sharing intention at the second point of measurement. The relationship between trust and knowledge-sharing intention decrease over time, whereas the link between commitment and knowledge-sharing intention increases with time.
Effects of aerobic exercise on mild cognitive impairment: a controlled trial.

OBJECTIVES To examine the effects of aerobic exercise on cognition and other biomarkers associated with Alzheimer disease pathology for older adults with mild cognitive impairment, and assess the role of sex as a predictor of response. DESIGN Six-month, randomized, controlled, clinical trial. SETTING Veterans Affairs Puget Sound Health Care System clinical research unit. PARTICIPANTS Thirty-three adults (17 women) with amnestic mild cognitive impairment ranging in age from 55 to 85 years (mean age, 70 years). Intervention Participants were randomized either to a high-intensity aerobic exercise or stretching control group. The aerobic group exercised under the supervision of a fitness trainer at 75% to 85% of heart rate reserve for 45 to 60 min/d, 4 d/wk for 6 months. The control group carried out supervised stretching activities according to the same schedule but maintained their heart rate at or below 50% of their heart rate reserve. Before and after the study, glucometabolic and treadmill tests were performed and fat distribution was assessed using dual-energy x-ray absorptiometry. At baseline, month 3, and month 6, blood was collected for assay and cognitive tests were administered. MAIN OUTCOME MEASURES Performance measures on Symbol-Digit Modalities, Verbal Fluency, Stroop, Trails B, Task Switching, Story Recall, and List Learning. Fasting plasma levels of insulin, cortisol, brain-derived neurotrophic factor, insulinlike growth factor-I, and beta-amyloids 40 and 42. RESULTS Six months of high-intensity aerobic exercise had sex-specific effects on cognition, glucose metabolism, and hypothalamic-pituitary-adrenal axis and trophic activity despite comparable gains in cardiorespiratory fitness and body fat reduction. For women, aerobic exercise improved performance on multiple tests of executive function, increased glucose disposal during the metabolic clamp, and reduced fasting plasma levels of insulin, cortisol, and brain-derived neurotrophic factor. For men, aerobic exercise increased plasma levels of insulinlike growth factor I and had a favorable effect only on Trails B performance. CONCLUSIONS This study provides support, using rigorous controlled methodology, for a potent nonpharmacologic intervention that improves executive control processes for older women at high risk of cognitive decline. Moreover, our results suggest that a sex bias in cognitive response may relate to sex-based differences in glucometabolic and hypothalamic-pituitary-adrenal axis responses to aerobic exercise.
Analysis acceleration in the design of frequency selective surfaces using parametric techniques

The design of multi-layer frequency selective surfaces often requires characterising the behaviour of the structure in wide frequency and angle ranges. Moreover, a fine tuning of the design leads to a large parameter space and results in a long computational time. To address this problem, an efficient parameterisation and interpolation technique has been implemented within the multimode equivalent network approach based on the integral equation formulation, a technique developed for the analysis of multi-layer periodic structures. The paper describes this technique and shows for a test case consisting of an array integrated with an FSS how the calculation time can be drastically reduced.
The structure of public opinion on crime policy: Evidence from seven Caribbean nations

A long tradition of research has examined public opinion on crime policy. Much of this research focuses on identifying the determinants and correlates of public opinion; few studies have examined the dimensional structure of public attitudes toward crime policy. This study posits and tests a multidimensional conceptualization of attitudes toward crime policy. We hypothesize that two general dimensions – punitiveness and progressiveness – are the minimum necessary to account for people’s opinions on crime policy. We test this multidimensional conceptualization and examine the structure of public opinion on crime policy using exploratory and confirmatory factor analyses and survey data from more than 11,000 residents in seven Caribbean nations. Our findings indicate that public opinion in all seven nations is multidimensional.
Enhanced-Power Saving Semi-Persistent Scheduler for VoLTE in LTE-Advanced

Power saving-semipersistent scheduler (PS-SPS) for voice over LTE (VoLTE) traffic was proposed in the downlink of LTE-A cell to reduce the energy consumption of the eNodeB. PS-SPS introduces the energy saving ability through a modification of traditional SPS (T-SPS) in allocating downlink Physical Resource Block (PRBs) to VoLTE users. In this paper, we first identify the drawbacks of PS-SPS that might curtail its energy saving capability and also degrade its capacity (maximum number of calls that can be supported simultaneously) compared with T-SPS. We then propose a novel SPS scheduler called enhanced-PS-SPS (E-PS-SPS) to allocate downlink PRBs to VoLTE users more efficiently compared with PS-SPS. Next, we build analytical models to derive expressions for capacity and eNodeB energy consumption for both PS-SPS and E-PS-SPS. Our analytical results show that E-PS-SPS not only outperforms PS-SPS in capacity by a substantial margin, but also considerably improves the energy saving. The analysis results are validated using simulations. Furthermore, owing to the modeling complexity of T-SPS, we bound its performance in terms of PS-SPS and E-PS-SPS through heuristic arguments. Simulation results validate our analytical bounds and also show that the proposed E-PS-SPS outperforms T-SPS also both in capacity and energy consumption, unlike PS-SPS whose capacity is lower than T-SPS.