Miracle-dz/UniFAR-FTUs huggingface dataset:
An integrated approach to validating ChIP-Seq using A * Lasso for Sparse Bayesian Network Learning

Mapping the transcription network is integral to our understanding of the transcriptional regulation in cells. Recently, ChIP-Seq experiments have become popular to determine the regulatory relationships between transcription factors (TF) and its target genes by detecting physical binding. However, these experiments are noisy and many binding events are not actually functional. Instead of doing further laboratory experiments which are expensive and not realistic for humans, we propose to estimate a sparse Bayesian network structure of the TFs and target genes, and detect SNPs that perturb the network. These SNP perturbations provide evidence of functional bindings. To learn the sparse Bayesian network, we present A* lasso, a single stage method that recovers the optimal sparse Bayesian network structure by solving a single optimization problem with A* search algorithm that uses lasso in its scoring system. Our approach substantially improves the computational efficiency of the well-known exact methods based on dynamic programming. In addition, to make the method more practical for settings that have a large number of variables, we suggest a heuristic scheme that dramatically reduces computational time without substantially compromising the quality of solutions. We apply our method to integrate SNP, expression and ChIP-Seq data. We detect several influential SNPs in our network, and are able to provide evidence for TF binding and characterize the effect on the surrounding network.
Hoard Behavior During Commodity Bubbles

Hoarding by large speculators is often blamed for contributing to commodity market panics and bubbles. Using supermarket scanner data on US household purchases during the 2008 Rice Bubble, we show that hoarding is in fact more systemic, affecting even households who have no resale motive. Export bans led to a spike in prices worldwide in the first half of 2008, which spilled over into US markets. Anticipating shortages, US households with previous purchases of rice, especially those of Asian ethnicity, nearly doubled their buying around the peak of the bubble. We document transmission mechanisms through over-extrapolation from high prices and contagion, as many households bought rice for the first and last time during the bubble.
SiGe V-band 1:32 frequency divider using dynamic and static division stages

In this paper, we present a fully integrated differential, compact frequency divider with a divide ratio of 32. The circuit utilizes a Si/SiGe 0.25 mum BiCMOS technology and operates beyond 75 GHz. The divider has a die area of 655 mum times 475 mum and consumes 202 mA at 5 V supply voltage. The frequency divider consists of the first stage of a dynamic divider with transimpedance topology and a static divider for the following four stages. The dynamic frequency divider operates from 22 GHz to 93 GHz with 5 V voltage supply and consumes 35 mA current. The static frequency divider operates up to 50 GHz and consumes 43 mA.
Queue Management for Network Coding in Ad Hoc Networks

Network Coding has been proven to be a method that will increase the throughput of network. Network coding will perform an XOR operation in the intermediate nodes to improve the throughput of the network. The simulation of network coding in AODV to search for the route to destination will be conducted in MATLAB. This paper introduces the development of simulation to illustrate the performance of network coding in wireless ad hoc network. The simulation will calculate the transmit packet time according to the size of the packet. Lastly, average network throughput performance between AODV network without network coding and network with network coding is shown and compared.
There and back again: Can you compile that snapshot?

A broken snapshot represents a snapshot from a project's change history that cannot be compiled. Broken snapshots can have significant implications for researchers, as they could hinder any analysis of the past project history that requires code to be compiled. Noticeably, while some broken snapshots may be observable in change history repositories (e.g., no longer available dependencies), some of them may not necessarily happen during the actual development. In this paper, we systematically study the compilability of broken snapshots in 219 395 snapshots belonging to 100 Java projects from the Apache Software Foundation, all relying on Maven as an automated build tool. We investigated broken snapshots from 2 different perspectives: (1) how frequently they happen and (2) likely causes behind them. The empirical results indicate that broken snapshots occur in most (96%) of the projects we studied and that they are mainly due to problems related to the resolution of dependencies. On average, only 38% of the change history of the analyzed systems is currently successfully compilable.
A Comparison of Approaches to Calculating Confidence Intervals for Benefit Measures from Dichotomous Choice Contingent Valuation Surveys

This paper compares the performance of four approaches to calculating confidence intervals around dichotomous choice contingent valuation method (DC CVM) benefit estimates. The performance of the approaches is compared using Monte Carlo simulation techniques for the two most common specifications for the welfare estimate. The results indicate that all four methods tended to perform well on average but the methods differed in the frequency with which they performed well. The results indicate the best choice depends on the sample size, on the distribution of the welfare estimate, and on the choice of functional form for the welfare estimate.
Tomographic analysis of reflectometry data: II. The phase derivative

A tomographic technique has been used in the past to decompose complex signals into their components. The technique is based on spectral decomposition and projection on the eigenvectors of a family of unitary operators. Here this technique is also shown to be appropriate to obtain the instantaneous phase derivative of the signal components. The method is illustrated on simulated data and on data obtained from plasma reflectometry experiments in the Tore Supra.
An InP MMIC Process Optimized for Low Noise at Cryo

An InP MMIC process was developed and optimized for ultra-low noise amplifiers (LNAs) operating at cryogenic temperature. The amplifiers from the process are working up to 100 GHz. The processed wafers are 4" and can carry more than 4000 3-stage units. For a significant number of 6-20 GHz 3-stage LNAs we have measured an average noise temperature of 5.8 K at ambient temperature of 10 K, state of the art in this frequency range, and 66.3 K at 300K. Associated gain was 35.9 dB (10K) and 33.2 dB (300 K). The standard deviation at room temperature for 47 LNAs was 1.5 K for the noise and 0.3 dB for the gain.
No effect of embryo culture media on birthweight and length of newborns.

STUDY QUESTION Does the type of media used to culture embryos for IVF influence the birthweight and length of neonates? SUMMARY ANSWER No significant differences were observed in birthweight and length among the three embryo culture media used for in vitro embryo culture. WHAT IS KNOWN ALREADY Since the establishment of IVF as an assisted reproductive technology (ART), many different culture systems have been used for the development of human embryos. Some studies have shown that the types of culture media influence the newborn birthweight; however, other studies have shown no effect. To further explore this contradictory issue, we compared the birthweight and length of neonates born after the transfer of embryos cultured in one of three commercially available media. STUDY DESIGN, SIZE AND DURATION This retrospective analysis of birthweight and length of newborns included 1201 women who delivered singletons and 445 women who delivered twins. The following three commercially available culture media were used: G5™, Global and Quinn's advantage media. Women who underwent IVF-ET cycles between 2008 and 2010 were analyzed. PARTICIPANTS/MATERIALS, SETTING AND METHODS Patients younger than 40 years of age with a body mass index (BMI) <30 kg/m(2) were analyzed. Only data from singletons and twins born alive after the 20th week of gestation were included in the data analysis. Patients who received preimplantation genetic diagnosis (PGD) and donor oocytes were excluded. MAIN RESULTS AND THE ROLE OF CHANCE The analysis of 1201 singletons and 445 sets of twins showed no significant association between mean birthweight or mean birth length and the type of embryo culture medium. Inter-twin mean birthweight and length disparities were analyzed, but were not shown to be significantly different. Multiple linear regression analysis showed that maternal weight, maternal height, gestational age and infant gender were significantly related to birthweight, and paternal height, gestational age and newborn complications were significantly associated with birth length. LIMITATIONS AND REASONS FOR CAUTION The current study showed that birthweight and length of newborns were not associated with the embryo culture medium. More research needs to be performed to analyze the effects of other culture medium formulations and to evaluate the long-term effects of embryo culture medium on the health of children conceived through ART. WIDER IMPLICATIONS OF THESE FINDINGS: Our retrospective study suggests that embryo culture medium does not influence neonatal birthweight and length; however, the effects of culture medium on epigenetic variation of embryos need to be studied further.
Chapter 9: Vertical Imbalance and Fiscal Behavior in a Welfare State: Norway

In the unitary Scandinavian welfare states, central governments are in control of all public finances. Decentralized government is designed from the center, and local and county governments are an integrated part of the general public sector. They are an important part, however, since they provide the main public welfare services (schooling and health care). The design is better described as delegation rather than decentralization, and can be called ‘administrative federalism’. Local and county governments primarily are agents of the central government. They have their own political systems based on elections to local and county councils, but the model allows little room for local democracy and accountability. As we will see, the local public sector certainly represents a challenge for central government control, but more in terms of broad spending pressure and cost control than strategic behavior. Interestingly, the central government is vulnerable in this centralized environment. A major objective of the welfare state is to provide uniform welfare services across the country. Decentralized governments can exploit the national political concern for the access to and quality of the welfare services they provide. Centralized financing, mandating, and detailed service
A novel role for the nuclear membrane protein emerin in association of the centrosome to the outer nuclear membrane

The type II inner nuclear membrane protein emerin is a component of the LINC complex that connects the nuclear lamina to the actin cytoskeleton. In emerin-null or -deficient human dermal fibroblasts we find that the centrosome is detached from the nucleus. Moreover, following siRNA knockdown of emerin in wild-type fibroblasts, the centrosome also becomes detached from the nucleus. We show that emerin interacts with tubulin, and that nocadozole-treated wild-type cells phenocopy the detached centrosome characteristic of emerin-null/deficient cells. We also find that a significant fraction of emerin is located at the outer nuclear membrane and peripheral ER, where it interacts directly with the centrosome. Our data provide the first evidence in mammalian cells as to the nature of the linkage of the centrosome, and therefore the tubulin cytoskeleton, with the outer nuclear membrane.
Prognostic Value of Pleural Lavage Cytology in Patients with Lung Cancer Resection: An Updated Meta-Analysis

Objective Pleural lavage cytology (PLC) is considered as a possible tool for assessing prognosis of lung cancer patients. We aimed to comprehensively review the prognosis value of PLC in patients undergoing surgical resection. Methods We searched 4 electronic databases for relevant studies comparing positive PLC and negative PLC. The primary outcomes included survival rate and recurrence rate at maximum follow-up. Results The meta-analysis included 28 studies, with a total of 20,714 patients. For the overall survival rate of all stages, the results demonstrated that positive pre-resection, post-resection and pooled PLC were associated with unfavorable survival: hazard ratio (HR) 2.89 (95% confidence interval [CI] 2.48–3.37), 2.70 (1.90–3.83), and 2.89 (2.52–3.31), respectively. For the stage I survival rate, the combined results also suggested that positive pre-resection, post-resection and pooled PLC were associated with unfavorable survival: HR 3.29 (95% CI 2.55–4.25), 4.85 (2.31–10.20), and 3.16 (2.53–3.94), respectively. Furthermore, a meta-analysis of 14 studies included 14,279 patients showed that positive pre-resection, post-resection and pooled PLC were associated with an increased risk of overall recurrence: risk ratio (RR) 2.45 (95% CI 1.91–3.15), 2.37 (1.11–5.09), and 2.37 (95% CI 2.00–2.80), respectively. Positive PLC was also associated with a high pleural recurrence (RR 4.77; 95% CI 3.13–7.26) or distant recurrence (RR 2.33; 95% CI 1.65–3.29). Conclusions Both positive pre- resection and post-resection PLC are associated with not only higher tumor recurrence but also unfavorable survival outcomes in patients with lung cancer resection. This technique can therefore act as a strong prognostic factor for tumor recurrence and adverse survival rates.
Peritoneal repairing cells: a type of bone marrow derived progenitor cells involved in mesothelial regeneration

The peritoneal mesothelium exhibits a high regenerative ability. Peritoneal regeneration is concomitant with the appearance, in the coelomic cavity, of a free‐floating population of cells whose origin and functions are still under discussion. We have isolated and characterized this cell population and we have studied the process of mesothelial regeneration through flow cytometry and confocal microscopy in a murine model lethally irradiated and reconstituted with GFP‐expressing bone marrow cells. In unoperated control mice, most free cells positive for mesothelin, a mesothelial marker, are green fluorescent protein (GFP). However, 24 hrs after peritoneal damage, free mesothelin+/ GFP+ cells appear in peritoneal lavages. Cultured lavage peritoneal cells show colocalization of GFP with mesothelial (mesothelin, cytokeratin) and fibroblastic markers. Immunohistochemical staining of the peritoneal wall also revealed colocalization of GFP with mesothelial markers and with procollagen‐1 and smooth muscle α‐actin. This was observed in the injured area as well as in the surrounding not‐injured peritoneal surfaces. These cells, which we herein call peritoneal repairing cells (PRC), are very abundant 1 week after surgery covering both the damaged peritoneal wall and the surrounding uninjured area. However, they become very scarce 1 month later, when the mesothelium has completely healed. We suggest that PRC constitute a type of monocyte‐derived cells, closely related with the tissue‐repairing cells known as ‘fibrocytes’ and specifically involved in peritoneal reparation. Thus, our results constitute a synthesis of the different scenarios hitherto proposed about peritoneal regeneration, particularly recruitment of circulating progenitor cells and adhesion of free‐floating coelomic cells.
Querying geo-social data by bridging spatial networks and social networks

Recording the location of people using location-acquisition technologies, such as GPS, allows generating life patterns, which associate people to places they frequently visit. Considering life patterns as edges that connect users of a social network to geographical entities on a spatial network, enriches the social network, providing an integrated socio-spatial graph. Queries over such graph extract information on users, in correspondence with their location history, and extract information on geographical entities in correspondence with users who frequently visit these entities. In this paper we present the concept of a socio-spatial graph that is based on life patterns, where users are connected to geographical entities using life-pattern edges. We provide a set of operators that form a query language suitable for the integrated data. We consider two implementations of a socio-spatial graph storage---one implementation uses a relational database system as the underline data storage, and the other employs a graph database system. The two implementations are compared, experimentally, for various queries and data. An important contribution of this work is in illustrating the usefulness and the feasibility of maintaining and querying integrated socio-spatial graphs.
Stereo Acoustic Echo Control Using A Simplified Echo Path Model

In handsfree tele- or video-communication, acoustic echoes arise due to the coupling between the loudspeakers and microphones. It is much more challenging to remove the undesired acoustic echoes for stereo or multi-channel tele-communication systems than for mono systems due to the non-uniqueness problem. While non-uniqueness can be prevented by introducing independent distortions into the left and right loudspeaker signals, stereo echo cancellation is more challenging in terms of convergence speed and computational complexity than mono echo cancellation. The proposed stereo echo control algorithm circumvents the non-uniqueness problem by using simplified echo path models consisting of delays and short-time spectral modification. It is shown that for reasonably symmetric systems the left and right echo path models are similar enough that a single echo path model can be used for estimating the total echo power spectrum and a gain filter for removing the echo from the microphone channels. The proposed algorithm is also applicable to multi-channel systems and the computational complexity is very low.
Application of statistical cancer atlas for 3D biopsy

Prostate cancer is the most commonly diagnosed cancer in males in the United States and the second leading cause of cancer death. While the exact cause is still under investigation, researchers agree on certain risk factors like age, family history, dietary habits, lifestyle and race. It is also widely accepted that cancer distribution within the prostate is inhomogeneous, i.e. certain regions have a higher likelihood of developing cancer. In this regard extensive work has been done to study the distribution of cancer in order to perform biopsy more effectively. Recently a statistical cancer atlas of the prostate was demonstrated along with an optimal biopsy scheme achieving a high detection rate. In this paper we discuss the complete construction and application of such an atlas that can be used in a clinical setting to effectively target high cancer zones during biopsy. The method consists of integrating intensity statistics in the form of cancer probabilities at every voxel in the image with shape statistics of the prostate in order to quickly warp the atlas onto a subject ultrasound image. While the atlas surface can be registered to a pre-segmented subject prostate surface or instead used to perform segmentation of the capsule via optimization of shape parameters to segment the subject image, the strength of our approach lies in the fast mapping of cancer statistics onto the subject using shape statistics. The shape model was trained from over 38 expert segmented prostate surfaces and the atlas registration accuracy was found to be high suggesting the use of this method to perform biopsy in near real time situations with some optimization.
Graffiti : A Framework for Testing Collaborative Distributed File System Metadata

Managing storage in the face of relentless growth in the numb er and variety of files on storage systems creates demand for rich file s ystem metadata as is made evident by the recent emergence of rich metada ta support in many applications as well as file systems. Yet, little suppor t exists for sharing metadata across file systems even though it is not uncommo n for users to manage multiple file systems and to frequently share copie s of files across devices and with other users. Encouraged by the surge in popu larity for collaborative bookmarking sites that share the burden of creat ing metadata for online content [21] we present Graffiti, a distributed organ iz tion layer for collaboratively sharing rich metadata across heterogeneo us file systems. The primary purpose of Graffiti is to provide a research and rapid prototyping platform for managing metadata across file systems and users .
Will Quantitative Proteomics Redefine Some of the Key Concepts in Skeletal Muscle Physiology?

Molecular and cellular biology methodology is traditionally based on the reasoning called “the mechanistic explanation”. In practice, this means identifying and selecting correlations between biological processes which result from our manipulation of a biological system. In theory, a successful application of this approach requires precise knowledge about all parameters of a studied system. However, in practice, due to the systems’ complexity, this requirement is rarely, if ever, accomplished. Typically, it is limited to a quantitative or semi-quantitative measurements of selected parameters (e.g., concentrations of some metabolites), and a qualitative or semi-quantitative description of expression/post-translational modifications changes within selected proteins. A quantitative proteomics approach gives a possibility of quantitative characterization of the entire proteome of a biological system, in the context of the titer of proteins as well as their post-translational modifications. This enables not only more accurate testing of novel hypotheses but also provides tools that can be used to verify some of the most fundamental dogmas of modern biology. In this short review, we discuss some of the consequences of using quantitative proteomics to verify several key concepts in skeletal muscle physiology.
Institutional Variation in Credential Completion: Evidence from Washington State Community and Technical Colleges

As community colleges search for models of organizational success, new attention is being paid to technical colleges—institutions that primarily offer terminal programs in specific career-related fields rather than focusing on more general academic credentials and transfer programs as many comprehensive institutions do. Recent research observes that in some states, technical colleges have substantially higher completion rates than do comprehensive community colleges. Yet there is scant research available that systematically compares similar students in similar programs at technical and comprehensive colleges. This study uses administrative data from Washington State to compare the outcomes of young, career-technical students across institutions, with and without extensive controls for student characteristics, educational intent, and area of study. This generates three key findings: first, technical and comprehensive colleges tend to serve quite different populations, so a true apples-to-apples comparison requires limiting the analysis to a relatively small fraction (less than 10%) of students enrolled at either institution. Second, at least for this limited subset of career-technical students, technical schools have significantly higher certificate completion rates after three years, with no apparent deficit in associate degree completion. Our third main finding is that the differences in student outcomes within the two types of schools are much larger than differences between them. Even within this limited group, institution type alone explains a relatively small fraction of the overall variation in student outcomes across institutions. It would thus be unwise for research and policymakers to fixate on this one dimension of