Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational approaches to phenotyping: high-throughput phenomics.

The recent completion of the Human Genome Project has made possible a high-throughput "systems approach" for accelerating the elucidation of molecular underpinnings of human diseases, and subsequent derivation of molecular-based strategies to more effectively prevent, diagnose, and treat these diseases. Although altered phenotypes are among the most reliable manifestations of altered gene functions, research using systematic analysis of phenotype relationships to study human biology is still in its infancy. This article focuses on the emerging field of high-throughput phenotyping (HTP) phenomics research, which aims to capitalize on novel high-throughput computation and informatics technology developments to derive genomewide molecular networks of genotype-phenotype associations, or "phenomic associations. " The HTP phenomics research field faces the challenge of technological research and development to generate novel tools in computation and informatics that will allow researchers to amass, access, integrate, organize, and manage phenotypic databases across species and enable genomewide analysis to associate phenotypic information with genomic data at different scales of biology. Key state-of-the-art technological advancements critical for HTP phenomics research are covered in this review. In particular, we highlight the power of computational approaches to conduct large-scale phenomics studies.
Estimating population size by spatially explicit capture–recapture

The number of animals in a population is conventionally estimated by capture–recapture without modelling the spatial relationships between animals and detectors. Problems arise with non-spatial estimators when individuals differ in their exposure to traps or the target population is poorly defined. Spatially explicit capture–recapture (SECR) methods devised recently to estimate population density largely avoid these problems. Some applications require estimates of population size rather than density, and population size in a defined area may be obtained as a derived parameter from SECR models. While this use of SECR has potential benefits over conventional capture–recapture, including reduced bias, it is unfamiliar to field biologists and no study has examined the precision and robustness of the estimates. We used simulation to compare the performance of SECR and conventional estimators of population size with respect to bias and confidence interval coverage for several spatial scenarios. Three possible estimators for the sampling variance of realised population size all performed well. The precision of SECR estimates was nearly the same as that of the null-model conventional population estimator. SECR estimates of population size were nearly unbiased (relative bias 0–10%) in all scenarios, including surveys in randomly generated patchy landscapes. Confidence interval coverage was near the nominal level. We used SECR to estimate the population of a species of skink Oligosoma infrapunctatum from pitfall trapping. The estimated number in the area bounded by the outermost traps differed little between a homogeneous density model and models with a quadratic trend in density or a habitat effect on density, despite evidence that the latter models fitted better. Extrapolation of trend models to a larger plot may be misleading. To avoid extrapolation, a large region of interest should be sampled throughout, either with one continuous trapping grid or with clusters of traps dispersed widely according to a probability-based and spatially representative sampling design.
Efficient Substitution of Multiple Constant Multiplications by Shifts and Additions Using Iterative Pairwise Matching

Many numerically intensive applications have computations that involve a large number of multiplications of one variable with several constants. A proper optimization of this part of the computation, which we call the multiple constant multiplication (MCM) problem, often results in a significant improvement in several key design metrics. After defining the MCM problem, we formulate it as a special case of common subexpression elimination. The algorithm for common subexpression elimination is based on an iterative pairwise matching heuristic. The flexibility of the MCM problem formulation enables the application of the iterative pairwise matching algorithm to several other important high level synthesis tasks. All applications are illustrated by a number of benchmarks.
Blind separation of speech mixtures based on nonstationarity

This paper presents a method for blind separation of convolutive mixtures of speech signals, based on the joint diagonalization of the time varying spectral matrices of the observation records and a novel technique to handle the problem of permutation ambiguity in the frequency domain. Simulations show that our method works well even for rather realistic mixtures in which the mixing filter has a quite long impulse response and strong echoes.
Using a Class on Compiler Design to Teach Software Construction

A class on compiler design is offered by many departments because it allows a student to see the interplay between theory (finite state machines, grammars, formal languages) and practice (language translation, problematic features of modern programming languages). Yet this purpose, although important, is not the only reason to include a compiler class in the curriculum. This paper reports how a compiler class can also provide the base to teach other subjects that students should be exposed to: software reuse, re-engineering, experience with patterns and software architectures, and reverse engineering. These topics are important even if the student never writes a language translator later on in his or her career.
Simple DRAM and Virtual Memory Abstractions to Enable Highly Efficient Memory Systems

In most modern systems, the memory subsystem is managed and accessed at multiple different granularities at various resources. We observe that such multi-granularity management results in significant inefficiency in the memory subsystem. Specifically, we observe that 1) page-granularity virtual memory unnecessarily triggers large memory operations, and 2) existing cache-line granularity memory interface is inefficient for performing bulk data operations and operations that exhibit poor spatial locality. To address these problems, we present a series of techniques in this thesis. First, we propose page overlays, a framework augments the existing virtual memory framework with the ability to track a new version of a subset of cache lines within each virtual page. We show that this extension is powerful by demonstrating its benefits on a number of applications. Second, we show that DRAM can be used to perform more complex operations than just store data. We propose RowClone, a mechanism to perform bulk data copy and initialization completely inside DRAM, and Buddy RAM, a mechanism to perform bulk bitwise operations using DRAM. Both these techniques achieve an order-of-magnitude improvement in the efficiency of the respective operations. Third, we propose Gather-Scatter DRAM, a technique that exploits DRAM organization to effectively gather/scatter values with a power-of-2 strided access patterns. For these access patterns, GS-DRAM achieves near-ideal bandwidth and cache utilization, without increasing the latency of fetching data from memory. Finally, we propose the Dirty-Block Index, a new way of tracking dirty blocks. In addition to improving the efficiency of bulk data coherence, DBI has several applications including high-performance memory scheduling, efficient cache lookup bypassing, and enabling heterogeneous ECC.
Sparse Signal Recovery via Generalized Entropy Functions Minimization

Compressive sensing relies on the sparse prior imposed on the signal of interest to solve the ill-posed recovery problem in an under-determined linear system. The objective function used to enforce the sparse prior information should be both effective and easily optimizable. Motivated by the entropy concept from information theory, in this paper we propose the generalized Shannon entropy function and Rényi entropy function of the signal as the sparsity promoting regularizers. Both entropy functions are nonconvex, non-separable. Their local minimums only occur on the boundaries of the orthants in the Euclidean space. Compared to other popular objective functions, minimizing the generalized entropy functions adaptively promotes multiple high-energy coefficients while suppressing the rest low-energy coefficients. The corresponding optimization problems can be recasted into a series of reweighted $l_1$-norm minimization problems and then solved efficiently by adapting the FISTA. Sparse signal recovery experiments on both the simulated and real data show that the proposed entropy functions minimization approaches perform better than other popular approaches and achieve state-of-the-art performances.
AND COMPARISON OF TECHNIQUES FOR TERRESTRIAL 3 D-VIEW

In the paper a presentation of existing georeferencing technique and a comparison between them is given. This is based on general considerations as well as on results two test applications carried out in the university laboratory, and at the ancient church of San Pietro al Monte in Civate (Lombardia, Italy). Two main ground constraints are currently used for the cultural heritage laser scanning survey: the use of targets as Ground Control Points, and the Direct Georeferencing approach, based on fixing the instrument position and attitude derived by external information (stationing over known points, levelling, azimuth orientation, use of INS/GPS in case of open and wide settlements). Moreover, nowadays several instruments can be used themselves as a total station to directly determine the stand-points coordinates as well. Both techniques can be adopted in a separate way, but they can be also integrated. The selection of a specific solution will depend upon the required accuracy for georeferencing, but can be driven also by special operational needs (available time, number of people involved, difficulty to get the site). On the other hand, an alternative solution to compute scan registration with a minimum ground control is given by the surface matching algorithms.
Contribution of parvalbumin and somatostatin-expressing GABAergic neurons to slow oscillations and the balance in beta-gamma oscillations across cortical layers

Cortical interneurons are classified into several subtypes that contribute to cortical oscillatory activity. Parvalbumin (PV)-expressing cells, a type of inhibitory interneuron, are involved in the gamma oscillations of local field potentials (LFPs). Under ketamine-xylazine anesthesia or sleep, mammalian cortical circuits exhibit slow oscillations in which the active-up state and silent-down state alternate at ~1 Hz. The up state is composed of various high-frequency oscillations, including gamma oscillations. However, it is unclear how PV cells and somatostatin (SOM) cells contribute to the slow oscillations and the high-frequency oscillations nested in the up state. To address these questions, we used mice lacking glutamate decarboxylase 67, primarily in PV cells (PV-GAD67 mice) or in SOM cells (SOM-GAD67 mice). We then compared LFPs between PV-GAD67 mice and SOM-GAD67 mice. PV cells target the proximal regions of pyramidal cells, whereas SOM cells are dendrite-preferring interneurons. We found that the up state was shortened in duration in the PV-GAD67 mice, but tended to be longer in SOM-GAD67 mice. Firing rate tended to increase in PV-GAD67 mice, but tended to decrease in SOM-GAD67 mice. We also found that delta oscillations tended to increase in SOM-GAD67 mice, but tended to decrease in PV-GAD67 mice. Current source density and wavelet analyses were performed to determine the depth profiles of various high-frequency oscillations. High gamma and ripple (60–200 Hz) power decreased in the neocortical upper layers specifically in PV-GAD67 mice, but not in SOM-GAD67. In addition, beta power (15–30 Hz) increased in the deep layers, specifically in PV-GAD67 mice. These results suggest that PV cells play important roles in persistence of the up state and in the balance between gamma and beta bands across cortical layers, whereas SOM and PV cells may make an asymmetric contribution to regulate up-state and delta oscillations.
COMPUTER AIDED DETECTION OF MAMMOGRAPHIC MASSES ON DIGITAL MAMMOGRAMS

This paper presents an automated system for detecting masses in mammogram images. The proposed method is based on a two-step procedure: a. regions of interest (ROI) specification, b. rule based classification of regions of interest. In the first step, the intensity values of pixels in mammogram images are used and scanning the pixels in 8 directions is evaluated. By using various thresholds while scanning the pixels, ROIs are specified. In the second step, all ROIs are labeled using Connected Component Labeling (CCL) and two rules are used to categorize ROIs as true masses or not. These rules are based on euclidean distance and regularity values of the ROIs. To test the system’s efficiency, we applied it to images from the Mammographic Image Analysis Society database. The accuracy of the system reaches 88.37% with 0.292 false positives per image.
Inhibition of inducible nitric oxide synthase reverses the loss of functional hyperemia in diabetic retinopathy

Neuronal activity leads to arteriole dilation and increased blood flow in retinal vessels. This response, termed functional hyperemia, is diminished in the retinas of diabetic patients, possibly contributing to the development of diabetic retinopathy. The mechanism responsible for this loss is unknown. Here we show that light‐evoked arteriole dilation was reduced by 58% in a streptozotocin‐induced rat model of type 1 diabetes. Functional hyperemia is believed to be mediated by glial cells and we found that glial‐evoked vasodilation was reduced by 60% in diabetic animals. The diabetic retinas showed neither a decrease in the thickness of the retinal layers nor an increase in neuronal loss, although signs of early glial reactivity and an upregulation of inducible nitric oxide synthase (iNOS) were detected. Inhibition of iNOS restored both light‐ and glial‐evoked dilations to control levels. These findings suggest that high NO levels resulting from iNOS upregulation alters glial control of vessel diameter and may underlie the loss of functional hyperemia observed in diabetic retinopathy. Restoring functional hyperemia by iNOS inhibition may limit the progression of retinopathy in diabetic patients. © 2010 Wiley‐Liss, Inc.
Workload characteristics of DNA sequence analysis: from storage systems' perspective

The recent development of NGS (Next Generation Sequencing) methods has greatly increased the amount of genome data and created the need for high-performance computing and high-performance storage systems. The key issue in developing high-performance storage systems is building a storage system that is optimized for NGS analysis pipeline. In this paper, we implemented a tool to collect and analyze I/O workload in NGS analysis pipeline. Using this tool, we executed NGS analysis pipeline and analyzed the characteristics of I/Os collected in the experiment.
Intergenerational Parenting Styles: The Consistency Of Parenting Styles Across Generations In A Rural Community

In the past half-century, research linking parenting styles with various child outcomes has led to a desire to understand how parents acquire the skills and behaviors they use towards their children. Research on intergenerational continuity of parenting practices/styles has produced varied results, such that multiple studies have found evidence of intergenerational continuity, whereas others have not. Accordingly, the purpose of the current study was to examine the relationship between the parenting style that parents report using with their own children and those they report their parents to have employed. In the present research, 22 participants (16 females, 6 males) were surveyed regarding perceptions of their own parenting styles and their perceptions of their parents’ parenting behaviors. Low return rate and sample size impact the generalizability of the results; nonetheless, the data suggests that perceived intergenerational continuity from mothers to daughters may exist for permissive parenting. However, same-gender continuities in parenting styles were not evident among men and cross-gender continuities in parenting styles were not observed for men or women. Although the data obtained is not generalizable and may not add to the existing literature on intergenerational continuity, this study highlights a key barrier to conducting research in rural communities: participation.
Are there good reasons for protecting mobile phones with hypervisors?

Security threats on consumer devices such as mobile phones are increasing as the software platforms become more open and complex. Therefore, hypervisors, which bring potential new secure services to embedded systems, are becoming increasingly important. In this paper, we look into how to design a hypervisor-based security architecture for an advanced mobile phone. Key security components of the architecture have been verified through a hypervisor implemented on an emulated ARM platform. We compare the hypervisor security architecture with TrustZone and summarize the major benefits and limitations of the hypervisor approach. In short, hypervisors exhibit several advantages such as support of multiple secure execution domains and monitoring of non-trusted domains; however, this comes at the cost of larger legacy system porting efforts.
Making Cases: On the Processuality of Casings in Social Research

Zusammenfassung Was ist der ‚Fall‘ in empirischen Fallstudien? Jenseits gebräuchlicher Handbuchdefinitionen schlagen wir vor, die (Re-)Konstruktion von Fällen als eine kontinuierliche Anstrengung zu verstehen und als casing zu charakterisieren. In diesem Beitrag heben wir die Rolle von casings für den Forschungsprozess hervor und fragen, wie, wann und warum in sozialwissenschaftlicher Forschung ‚gefällt‘ wird—Fragen, die ein pragmatisches Verständnis davon eröffnen, was Fälle und casings eigentlich sind und was sie leisten können. Anhand einer Diskussion zweier klassischer Fallstudien unterscheiden wir zwei Formen des casings (theoretisch vs. empirisch geleitetes casing) und stellen ein prozessuales Fallverständnis vor, das den gegenwärtigen Diskurs über ‚Prozessuale Soziologie‘ und ‚sozialwissenschaftliches Theoretisieren‘ methodologisch komplementieren möchte.
Censorship-resistant Collaboration with a Hybrid DTN/P2P Network

Acknowledgments My thanks go to Marc Fontaine for asking stupid questions that turned out to be quite clever, and for pointing out that correctness is essential both in the real and the physical world. I also thank Paul Baade for demanding impossible features which turned out to be the last piece in the puzzle. Julius Römmler has notified me of orthographical, typographical, and (inadvertently) semantical errors. And told me to use fewer big words. Thanks! I wish to thank Denis Lütke-Wiesmann for proofreading the thesis, and the footnotes. Sven Hager found lots of overly short, overly long, and overly wrong statements. Thanks! Thanks to Prof. Martin Mauve for coming up with the idea, shielding us from bureaucracy, asking for explanation and rationale at every step, and finding all the errors nobody else found.
Building High-Performance Application Protocol Parsers on Multi-core Architectures

Parsing packet payloads according to the syntax and semantics of an application protocol is a key step in analyzing network traffic. However, it is still a challenge to fulfill this task with high speed(10Gbps+) because parsing packets through deep-content analysis to build a corresponding syntax tree requires tremendous computing resources. Multi-core architectures provide a viable solution for building high-performance parsers for application protocols. Existing sequential application protocol parsers are hard to be reused, and building a new protocol parser from scratch is error-prone and time-consuming. This paper proposes a general and efficient approach to building high-performance parallel application protocol parsers on multi-core platforms. First, the open-source lexical analyzer FLEX is used to describe a protocol and generate a sequential parser. Then a source-to-source translation is performed to transform the sequential parser into a parallel one. Finally, an efficient parallel run-time system is built by employing lock-free design principles from top to bottom to support multi-threaded execution on multi-core processors. Experimental results show that our parsers achieve nearly 20Gbps for average HTTP packets and 5Gbps for the challenging smaller FIX packets.
Real-time rendering of procedural multiscale materials

We present a stable shading method and a procedural shading model that enables real-time rendering of sub-pixel glints and anisotropic microdetails resulting from irregular microscopic surface structure to simulate a rich spectrum of appearances ranging from sparkling to brushed materials. We introduce a biscale Normal Distribution Function (NDF) for microdetails to provide a convenient artistic control over both the global appearance as well as over the appearance of the individual microdetail shapes, while efficiently generating procedural details. Our stable rendering approach simulates a hierarchy of scales and accurately estimates pixel footprint at multiple levels of detail to achieve good temporal stability and antialiasing, making it feasible for real-time rendering applications.
Functional MRI Limitations and Aspirations

Most would agree that knowing precisely what was happening in the brain during the act of thinking would help in our pursuit to understand what thinking really is. This chapter describes the basics, limits, and future directions of one of the more effective tools we have to observe the human brain while it is functioning – functional MRI. Functional MRI emerged in the early 1990s, and has since grown explosively in utility. In this chapter, an in-depth exploration is carried out of what limits functional MRI to a spatial resolution of millimeters and a temporal resolution of seconds. In addition, issues of how sensitive functional MRI is in detecting brain activity and how deeply we can interpret the signal changes are explored. Lastly, the chapter ends with a discussion on how imaging might be essential, or perhaps irrelevant, to understanding thinking.
The CatSper channel controls chemosensation in sea urchin sperm

Sperm guidance is controlled by chemical and physical cues. In many species, Ca2+ bursts in the flagellum govern navigation to the egg. In Arbacia punctulata, a model system of sperm chemotaxis, a cGMP signaling pathway controls these Ca2+ bursts. The underlying Ca2+ channel and its mechanisms of activation are unknown. Here, we identify CatSper Ca2+ channels in the flagellum of A. punctulata sperm. We show that CatSper mediates the chemoattractant‐evoked Ca2+ influx and controls chemotactic steering; a concomitant alkalization serves as a highly cooperative mechanism that enables CatSper to transduce periodic voltage changes into Ca2+ bursts. Our results reveal intriguing phylogenetic commonalities but also variations between marine invertebrates and mammals regarding the function and control of CatSper. The variations probably reflect functional and mechanistic adaptations that evolved during the transition from external to internal fertilization.