Miracle-dz/UniFAR-FTUs huggingface dataset:
Using hints to reduce the read miss penalty for flat COMA protocols

In flat cache-only memory architectures (COMA), an attraction-memory miss must first interrogate a directory before a copy of the requested data can be located, which often involves three network traversals. By keeping track of the identity of a potential holder of the copy-called a hint-one network traversal can be saved, which reduces the read penalty. We have evaluated the reduction of the read-miss penalty provided by hints using detailed architectural simulations and four benchmark applications. The results show that a previously proposed protocol using hints can actually make the read-miss penalty larger, because when the hint is not correct, an extra network traversal is needed. This has motivated us to study a new protocol using hints that simultaneously sends a request to the potential holder and to the directory. This protocol reduces the read-miss penalty for all applications, but the protocol complexity does not seem to justify the performance improvement. <<ETX>>
“Beijing Region” (3pter-D3S3397) of the Human Genome: Complete sequence and analysis

The goal of the Human Genome Project (HGP) is to determine a complete and high-quality sequence of the human genome. China, as one of the six member states, takes a region between 3pter and D3S3397 of the human chromosome 3 as its share of this historic project, referred as “Beijing Region”. The complete sequence of this region comprises of 17.4 megabasepairs (Mb) with an average GC content of 42% and an average recombination rate of 2.14 cM/Mb. Within Beijing Region, 122 known and 20 novel genes are identified, as well as 42607 single nucleotide polymorphisms (SNPs). Comprehensive analyses also reveal: (i) gene density and GC-content of Beijing Region are in agreement with human cytogenetic maps, i.e. G-minus bands are GC-rich and of a high gene density, whereas G-plus bands are GC-poor and of a relatively low gene density; (ii) the average recombination rate within Beijing Region is relatively high compared with other regions of chromosome 3, with the highest recombination rate of 6.06 cM/Mb in the subtelomeric area; (iii) it is most likely that a large gene, associated with the mammary gland, may reside in the 1.1 Mb gene-poor area near the telomere; (iv) many disease-related genes are genetically mapped to Beijing Region, including those associated with cancers and metabolic syndromes. All make Beijing Region an important target for in-depth molecular investigations with a purpose of medical applications.
Design patterns for tunable and efficient SSD-based indexes

A number of data-intensive systems require using random hash-based indexes of various forms, e.g., hash tables, Bloom filters, and locality sensitive hash tables. In this paper, we present general SSD optimization techniques that can be used to design a variety of such indexes while ensuring higher performance and easier tunability than specialized state-of-the-art approaches. We leverage two key SSD innovations: a) rearranging the data layout on the SSD to combine multiple read requests into one page read, and b) intelligently reordering requests to exploit inherent parallelism in the architecture of SSDs. We build three different indexes using these techniques, and we conduct extensive studies showing their superior performance, lower CPU/memory footprint, and tunability compared to state-of-the-art systems.
MAPPING LAND COVER IN THE TAITA HILLS, SE KENYA, USING AIRBORNE LASER SCANNING AND IMAGING SPECTROSCOPY DATA FUSION

Abstract. The Taita Hills, located in south-eastern Kenya, is one of the world’s biodiversity hotspots. Despite the recognized ecological importance of this region, the landscape has been heavily fragmented due to hundreds of years of human activity. Most of the natural vegetation has been converted for agroforestry, croplands and exotic forest plantations, resulting in a very heterogeneous landscape. Given this complex agro-ecological context, characterizing land cover using traditional remote sensing methods is extremely challenging. The objective of this study was to map land cover in a selected area of the Taita Hills using data fusion of airborne laser scanning (ALS) and imaging spectroscopy (IS) data. Land Cover Classification System (LCCS) was used to derive land cover nomenclature, while the height and percentage cover classifiers were used to create objective definitions for the classes. Simultaneous ALS and IS data were acquired over a 10 km × 10 km area in February 2013 of which 1 km × 8 km test site was selected. The ALS data had mean pulse density of 9.6 pulses/m2, while the IS data had spatial resolution of 1 m and spectral resolution of 4.5–5 nm in the 400–1000 nm spectral range. Both IS and ALS data were geometrically co-registered and IS data processed to at-surface reflectance. While IS data is suitable for determining land cover types based on their spectral properties, the advantage of ALS data is the derivation of vegetation structural parameters, such as tree height and crown cover, which are crucial in the LCCS nomenclature. Geographic object-based image analysis (GEOBIA) was used for segmentation and classification at two scales. The benefits of GEOBIA and ALS/IS data fusion for characterizing heterogeneous landscape were assessed, and ALS and IS data were considered complementary. GEOBIA was found useful in implementing the LCCS based classification, which would be difficult to map using pixel-based methods.
Effectiveness of additional supervised exercises compared with conventional treatment alone in patients with acute lateral ankle sprains: systematic review

Objective To summarise the effectiveness of adding supervised exercises to conventional treatment compared with conventional treatment alone in patients with acute lateral ankle sprains. Design Systematic review. Data sources Medline, Embase, Cochrane Central Register of Controlled Trials, Cinahl, and reference screening. Study selection Included studies were randomised controlled trials, quasi-randomised controlled trials, or clinical trials. Patients were adolescents or adults with an acute lateral ankle sprain. The treatment options were conventional treatment alone or conventional treatment combined with supervised exercises. Two reviewers independently assessed the risk of bias, and one reviewer extracted data. Because of clinical heterogeneity we analysed the data using a best evidence synthesis. Follow-up was classified as short term (up to two weeks), intermediate (two weeks to three months), and long term (more than three months). Results 11 studies were included. There was limited to moderate evidence to suggest that the addition of supervised exercises to conventional treatment leads to faster and better recovery and a faster return to sport at short term follow-up than conventional treatment alone. In specific populations (athletes, soldiers, and patients with severe injuries) this evidence was restricted to a faster return to work and sport only. There was no strong evidence of effectiveness for any of the outcome measures. Most of the included studies had a high risk of bias, with few having adequate statistical power to detect clinically relevant differences. Conclusion Additional supervised exercises compared with conventional treatment alone have some benefit for recovery and return to sport in patients with ankle sprain, though the evidence is limited or moderate and many studies are subject to bias.
An Event Algebra for Specifying and Scheduling Workflows

Heterogeneous systems arise when preexisting or legacy information systems are integrated in such a way as to preserve their autonomy and past applications. Workflows are the semantically appropriate units of activity in such environments. They involve a variety of tasks and are best represented by different extended transaction models or combinations thereof. We present an approach by which workflows can be efficiently scheduled. Oux novel contribution is an event algebra in which dependencies characterizing workflows can be declaratively expressed. We show how to symbolically process these dependencies to determine which events can or must occur, and when. Our approach can represent dependencies compactly and reason with them efficiently.
β2-Adrenergic Receptor Redistribution in Heart Failure Changes cAMP Compartmentation

Heart Cell Signaling in 3D A healthy heart relies on the proper transduction of cellular signals through the β1- and β2-adrenergic receptors (βARs), which are located on the surface of the heart's muscle cells (cardiomyocytes). The surface of these cells resembles a highly organized series of hills and valleys and it has been unclear whether this topography plays a role in the βAR signaling events that are critical to cell function. Nikolaev et al. (p. 1653, published online 25 February; see Perspective by Dorn) monitored the cyclic adenosine monophosphate (cAMP) signals generated by the βARs in living cardiomyocytes. In cells from healthy rats and from rats with heart failure, the β1ARs were localized across the entire cell surface. In contrast, the spatial localization of the β2ARs differed in healthy and failing cells. In healthy cardiomyocytes, the β2ARs resided exclusively within surface invaginations called transverse tubules, thereby producing spatially confined cAMP signals, whereas in failing cardiomyocytes, the β2ARs redistributed to other cell surface areas, thereby producing diffuse cAMP signals. Thus, changes in the spatial localization of β2AR-induced cAMP signaling may contribute to heart failure. A change in the distribution of a signaling molecule on the surface of heart muscle cells may contribute to heart failure. The β1- and β2-adrenergic receptors (βARs) on the surface of cardiomyocytes mediate distinct effects on cardiac function and the development of heart failure by regulating production of the second messenger cyclic adenosine monophosphate (cAMP). The spatial localization in cardiomyocytes of these βARs, which are coupled to heterotrimeric guanine nucleotide–binding proteins (G proteins), and the functional implications of their localization have been unclear. We combined nanoscale live-cell scanning ion conductance and fluorescence resonance energy transfer microscopy techniques and found that, in cardiomyocytes from healthy adult rats and mice, spatially confined β2AR-induced cAMP signals are localized exclusively to the deep transverse tubules, whereas functional β1ARs are distributed across the entire cell surface. In cardiomyocytes derived from a rat model of chronic heart failure, β2ARs were redistributed from the transverse tubules to the cell crest, which led to diffuse receptor-mediated cAMP signaling. Thus, the redistribution of β2ARs in heart failure changes compartmentation of cAMP and might contribute to the failing myocardial phenotype.
The role of anomalous phenomena in the therapeutic process: an exploration of counselling psychologists' experience

The main focus of this research was to explore how counselling psychologists experience what that they cannot understand in the therapeutic process. The study focuses on how counselling psychologists make sense of and manage these experiences, as well as the role such experiences play in therapy. Although the existence of such occurrences are acknowledged in the foundations of many therapeutic approaches (Bion, 1970; Bugental, 1990; Freud 1915; Jung, 1923; Maslow, 1971; Ogden, 1999; Perls, 1973; Rogers, 1961; Stern, 2004) , there seems to be a lack of research in relation to how these phenomena are experienced and what role they play in the therapeutic process. Eight counselling psychologists with ten years of experience in clinical practice were recruited and interviewed using semi-structured interviews. Different aspects of these experiences were explored through applying the qualitative method known as Interpretative Phenomenological Analysis (Smith, 2004). The findings suggest that the way counselling psychologists experience phenomena that cannot be understood strongly relates to anxiety, fear and uncertainty, drawing attention to deep feelings of vulnerability and insecurity. The results demonstrate the ambivalent meanings of such experiences in the therapeutic process, and their significance in the process of therapy. The thesis also comprises the way in which counselling psychologists spoke about these phenomena and how these occurrences were managed by counselling psychologists. Some conclusions were made about what kind of knowledge counselling psychologists relied on while making sense of such phenomena. The recommendations made as a result of the research show validity as they closely relate to the way counselling psychologists explore their own identity as professionals. Also, the research highlighted the essentiality of exploring the role of theoretical knowledge and reflexivity for counselling psychologists. The research also explores unanticipated findings such as the existence of those experiences that need to remain undefinable and the ability of counselling psychologists to let go of the need to make sense of phenomena. The study also addresses the limitations and implications of the research, and suggestions for further research are indicated.
Authigenic uranium in foraminiferal coatings: A proxy for ocean redox chemistry

The rate of uranium accumulation in oceanic sediments from seawater is controlled by bottom water oxygen concentrations and organic carbon fluxes—two parameters that are linked to deep ocean storage of CO2. To investigate glacial-interglacial changes in what is known as authigenic U, we have developed a rapid method for its determination as a simple addition to a procedure for foraminiferal trace element analysis. Foraminiferal calcite acts as a low U substrate (U/Ca < 15 nmol/mol) upon which authigenic U accumulates in reducing sediments. We measured a downcore record of foraminiferal U/Ca from ODP Site 1090 in the South Atlantic and found that U/Ca ratios increase by 70–320 nmol/mol during glacial intervals. There is a significant correlation between U/Ca records of benthic and planktonic foraminiferal species and between U/Ca and bulk sediment authigenic U. These results indicate that elevated U/Ca ratios are attributable to the accumulation of authigenic U coatings in sediments. Foraminiferal Mn/Ca ratios were lower during the glacial intervals, suggesting that the observed U accumulation on the shells is not directly linked to U incorporation into secondary manganese phases. Thus, foraminiferal U/Ca ratios may provide useful information on past changes in sediment redox conditions.
The Physical Interaction of Myoblasts with the Microenvironment during Remodeling of the Cytoarchitecture

Integrins, focal adhesions, the cytoskeleton and the extracellular matrix, form a structural continuum between the external and internal environment of the cell and mediate the pathways associated with cellular mechanosensitivity and mechanotransduction. This continuum is important for the onset of muscle tissue generation, as muscle precursor cells (myoblasts) require a mechanical stimulus to initiate myogenesis. The ability to sense a mechanical cue requires an intact cytoskeleton and strong physical contact and adhesion to the microenvironment. Importantly, myoblasts also undergo reorientation, alignment and large scale remodeling of the cytoskeleton when they experience mechanical stretch and compression in muscle tissue. It remains unclear if such dramatic changes in cell architecture also inhibit physical contact and adhesion with the tissue microenvironment that are clearly important to myoblast physiology. In this study, we employed interference reflection microscopy to examine changes in the close physical contact of myoblasts with a substrate during induced remodeling of the cytoarchitecture (de-stabilization of the actin and microtubule cytoskeleton and inhibition of acto-myosin contractility). Our results demonstrate that while each remodeling pathway caused distinct effects on myoblast morphology and sub-cellular structure, we only observed a ∼13% decrease in close physical contact with the substrate, regardless of the pathway inhibited. However, this decrease did not correlate well with changes in cell adhesion strength. On the other hand, there was a close correlation between cell adhesion and β1-integrin expression and the presence of cell-secreted fibronectin, but not with the presence of intact focal adhesions. In this study, we have shown that myoblasts are able to maintain a large degree of physical contact and adhesion to the microenvironment, even during shot periods (<60 min) of large scale remodeling and physiological stress, which is essential to their in-vivo functionality.
Validation of the Charcot–Marie–Tooth disease pediatric scale as an outcome measure of disability

Charcot–Marie–Tooth disease (CMT) is a common heritable peripheral neuropathy. There is no treatment for any form of CMT, although clinical trials are increasingly occurring. Patients usually develop symptoms during the first 2 decades of life, but there are no established outcome measures of disease severity or response to treatment. We identified a set of items that represent a range of impairment levels and conducted a series of validation studies to build a patient‐centered multi‐item rating scale of disability for children with CMT.
Using Associations and Fuzzy Ontologies for Modeling Chemical Safety Information

In this paper we propose a novel approach for domain modeling that combines two different types of models: (1) fuzzy ontology that describes the concepts of the domain and their relations in a formal way, and (2) association model that presents the associations between the terms of the domain. We utilize the combined model for query expansion by finding both highly associative and related concepts for the query terms. To demonstrate the feasibility of the model and its utilization, we use the query expansion in a search engine of chemical safety cards.
Inductive Bias of Deep Convolutional Networks through Pooling Geometry

Our formal understanding of the inductive bias that drives the success of convolutional networks on computer vision tasks is limited. In particular, it is unclear what makes hypotheses spaces born from convolution and pooling operations so suitable for natural images. In this paper we study the ability of convolutional networks to model correlations among regions of their input. We theoretically analyze convolutional arithmetic circuits, and empirically validate our findings on other types of convolutional networks as well. Correlations are formalized through the notion of separation rank, which for a given partition of the input, measures how far a function is from being separable. We show that a polynomially sized deep network supports exponentially high separation ranks for certain input partitions, while being limited to polynomial separation ranks for others. The network's pooling geometry effectively determines which input partitions are favored, thus serves as a means for controlling the inductive bias. Contiguous pooling windows as commonly employed in practice favor interleaved partitions over coarse ones, orienting the inductive bias towards the statistics of natural images. Other pooling schemes lead to different preferences, and this allows tailoring the network to data that departs from the usual domain of natural imagery. In addition to analyzing deep networks, we show that shallow ones support only linear separation ranks, and by this gain insight into the benefit of functions brought forth by depth - they are able to efficiently model strong correlation under favored partitions of the input.
Antidermatophytic and Toxicological Evaluations of Dichloromethane-Methanol Extract, Fractions and Compounds Isolated from Coula edulis

Background: Coula edulis Bail (Olacaceae), is an evergreen tree growing to a height of 25. This study aimed at evaluating the antidermatophytic and toxicological properties of the stem bark of C. edulis extract as well as fractions and compounds isolated from it. Methods: The plant extract was prepared by maceration in CH2Cl2-MeOH (1:1 v/v). The fractionation of this extract was done by silica gel column chromatography. Antidermatophytic activities were assayed using agar dilution method. The acute and sub-acute toxicities of oral administrations of the extract were studied in rodents. Results: The crude extract of C. edulis displayed antidermatophytic activity against the tested microorganisms with highest activity against Microsporum audouinii and Trichophyton mentagrophytes. The fractionation enhanced the antidermatophytic activity in fraction F3 (MIC=0.62-1.25 mg/ml) compared to the crude extract (MIC=1.25-5 mg/ml). Further fractionation and purification of the fractions F2 and F3 gave respectively 3-O-β-D-glucopyranoside of sitosterol (MIC=0.20-0.40 mg/ml) and a mixture of β-sitosterol, stigmasterol and n-hexadecanoid acid (MIC=0.80 mg/ml). The median lethal doses (LD50) of the crude extract were 16.8 and 19.6 g/kg body weight (BW) in male and female mice, respectively. At 200 mg/kg BW, there was a decrease in body weight gain, food and water consumptions. Gross anatomical analysis revealed white vesicles on the liver of the rats treated with the extract at 200 mg/kg BW. This dose also induced significant (P<0.05) changes on hematological and biochemical parameters in rats after 28 days of treatment. Conclusion: These data suggest that the CH2Cl2-MeOH (1:1 v/v) extract of C. edulis stem bark possesses antidermatophytic properties. They also show that at high doses (≥ 200 mg/kg BW), the extract has significant hepatotoxic and nephrotoxic activities.
UNC-CH at DUC 2007: Query Expansion, Lexical Simplification and Sentence Selection Strategies for Multi-Document Summarization

This paper describes the approach used in the UNC-CH system to generate a topicfocused summary of information reported in multiple news articles. We explored query expansion, lexical simplification and sentence simplification. Results suggest that cluster membership plays an important role in improving summarization performance, while query expansion does not. The UNC-CH system performed well in both automated and manual evaluations, achieving the 12 th highest ROUGE2 score and a score greater than or equal to the average system responsiveness score for 30 of the 45 DUC 2007 topics.
A File By Any Other Name: Managing File Names with Metadata

File names are one of the earliest computing abstractions, a string of characters to uniquely identify a file for the system, and to help users remember the contents when they look for it later. They are also a rich source of semantic metadata about files. However, this metadata is unstructured and opaque to the rest of the system. As a result, metadata in file names is often error-prone, and hard to search for. File names can and should be more meaningful and reliable, while simplifying application design and encouraging users and applications to provide more metadata for search. We describe a POSIX compliant prototype file system, TrueNames, which demonstrates an alternate approach to naming and metadata, called metadata aware naming. TrueNames separates the task of uniquely identifying a file from the task of helping the user remember its contents. It captures metadata in a structured format for later indexing, and uses it to generate file names which are correct, regenerable, and disambiguatable by design. TrueNames simplifies application design by providing a consistent interface for metadata aware naming, incurs a low overhead of approximately 15% under realistic workloads, and can simplify a wide variety of data management tasks for both applications and users.