Miracle-dz/UniFAR-FTUs huggingface dataset:
Chain functions and scoring functions in genetic networks

One of the grand challenges of system biology is to reconstruct the network of regulatory control among genes and proteins. High throughput data, particularly from expression experiments, may gradually make this possible in the future. Here we address two key ingredients in any such 'reverse engineering' effort: The choice of a biologically relevant, yet restricted, set of potential regulation functions, and the appropriate score to evaluate candidate regulatory relations. We propose a set of regulation functions which we call chain functions, and argue for their ubiquity in biological networks. We analyze their complexity and show that their number is exponentially smaller than all boolean functions of the same dimension. We define two new scores: one evaluating the fitness of a candidate set of regulators of a particular gene, and the other evaluating a candidate function. Both scores use established statistical methods. Finally, we test our methods on experimental gene expression data from the yeast galactose pathway. We show the utility of using chain functions and the improved inference using our scores in comparison to several extant scores. We demonstrate that the combined use of the two scores gives an extra advantage. We expect both chain functions and the new scores to be helpful in future attempts to infer regulatory networks.
Pathophysiological topography of acute ischemia by combined diffusion-weighted and perfusion MRI.

BACKGROUND AND PURPOSE Combined echoplanar MRI diffusion-weighted imaging (DWI), perfusion imaging (PI), and magnetic resonance angiography (MRA) can be used to visualize acute brain ischemia and predict lesion evolution and functional outcome. The appearance of a larger lesion by PI than by DWI quantitatively defines a mismatch of potential clinical importance. Qualitative lesion variations exist in the topographic concordance of this mismatch. We examined both the topographic heterogeneity and relative frequency of mismatched patterns in acute stroke using these MRI techniques. METHODS Acute DWI, PI, and MRA studies of 34 prospectively recruited patients with supratentorial ischemic lesions scanned within 24 hours of stroke onset (range 2.5 to 23.3 hours, 12 patients <6 hours) were analyzed. RESULTS Ischemic lesions were predominantly in the middle cerebral artery (MCA) territory (94%), with DWI lesions most commonly affecting the insular region. Mismatched patterns with PI lesion larger than DWI lesion occurred in 21 patients (62% overall), in all 4 patients imaged within 3 hours, and in 44% of patients imaged after 18 hours. A patient with a large PI but no DWI lesion and severe clinical deficit at 2.5 hours after stroke onset recovered completely. Regional variations in DWI and PI lesion loci were found, inferring site of proximal MCA occlusion, embolic pathogenesis, and regional arterial reperfusion. CONCLUSIONS Analysis of the topographic concordance of PI and DWI lesions in acute stroke reveals regional PI lesions without concomitant DWI lesions, which do not necessarily progress to infarction but may suggest stroke pathogenesis and site of current arterial occlusion. Location of DWI lesions may suggest an earlier site of arterial occlusion and regions of maximal perfusion deficit.
Optimal assignment kernels for attributed molecular graphs

We propose a new kernel function for attributed molecular graphs, which is based on the idea of computing an optimal assignment from the atoms of one molecule to those of another one, including information on neighborhood, membership to a certain structural element and other characteristics for each atom. As a byproduct this leads to a new class of kernel functions. We demonstrate how the necessary computations can be carried out efficiently. Compared to marginalized graph kernels our method in some cases leads to a significant reduction of the prediction error. Further improvement can be gained, if expert knowledge is combined with our method. We also investigate a reduced graph representation of molecules by collapsing certain structural elements, like e.g. rings, into a single node of the molecular graph.
Functional Evaluation of Plasmodium Export Signals in Plasmodium berghei Suggests Multiple Modes of Protein Export

The erythrocytic stage development of malaria parasites occurs within the parasitophorous vacuole inside the infected-erythrocytes, and requires transport of several parasite-encoded proteins across the parasitophorous vacuole to several locations, including the cytosol and membrane of the infected cell. These proteins are called exported proteins; and a large number of such proteins have been predicted for Plasmodium falciparum based on the presence of an N-terminal motif known as the Plasmodium export element (PEXEL) or vacuolar transport signal (VTS), which has been shown to mediate export. The majority of exported proteins contain one or more transmembrane domains at the C-terminus and one of three types of N-terminus domain architectures. (1) The majority, including the knob-associated histidine rich protein (KAHRP), contain a signal/hydrophobic sequence preceding the PEXEL/VTS motif. (2) Other exported proteins, including the P. berghei variant antigen family bir and the P. falciparum skeleton binding protein-1, do not appear to contain a PEXEL/VTS motif. (3) The P. falciparum erythrocyte membrane protein-1 (PfEMP1) family lacks a signal/hydrophobic sequence before the motif. These different domain architectures suggest the presence of multiple export pathways in malaria parasites. To determine if export pathways are conserved in plasmodia and to develop an experimental system for studying these processes, we investigated export of GFP fused with N- and C-terminus putative export domains in the rodent malaria parasite P. berghei. Export was dependent on specific N- and C-terminal domains. Constructs with a KAHRP-like or bir N-terminus, but not the PfEMP1 N-terminus, exported GFP into the erythrocyte. The C-terminus of a P. falciparum variant antigen rifin prevented GFP export by the KAHRP-like N-terminus. In contrast, GFP chimeras containing KAHRP-like N-termini and the PfEMP1 C-terminus were exported to the surface of erythrocytes. Taken together, these results suggest that proteins with KAHRP-like architecture follow a common export pathway, but that PfEMP1s utilize an alternative pathway. Functional validation of common putative export domains of malaria parasites in P. berghei provides an alternative and simpler system to investigate export mechanisms.
Histogram-Based Attribute Profiles for Classification of Very High Resolution Remote Sensing Images

Morphological attribute profiles (APs) obtained by the sequential application of morphological attribute filters to images have been found very effective in remote sensing (RS) to characterize spatial properties of objects in a scene. However, a direct use of the APs can be insufficient to provide a complete characterization of spatial information when complex texture is present in the considered images. To overcome this problem, in this paper, we present the novel histogram-based morphological APs (HAPs). The HAPs model the marginal local distribution of attribute filter responses to better characterize the texture information, and they are obtained based on a three-step algorithm. In the first step, the standard APs are constructed by sequentially applying attribute filters to the considered image. In the second step, a local histogram is calculated for each sample of each image in the APs. Then, in the final step, the local histograms of the same pixel locations in the APs are stacked, resulting in a texture descriptor whose components represent local distributions of the filter responses for the related pattern. Finally, the very-high-dimensional HAPs are classified by a support vector machine (SVM) classifier with histogram intersection kernel. Experimental results obtained by considering two very high resolution panchromatic images show the effectiveness of the proposed HAPs, which sharply improve the accuracy of the SVM classifier with respect to standard AP-based methods.
Improve the performance to implement region based statistical traffic pattern discovery system for MANET

Many privacy improving techniques have been proposed based on packet encryption to protect the communication privacy of mobile ad hoc networks (MANETs). However, we show that MANETs are still vulnerable under passive statistical traffic analysis attacks. To demonstrate how to discover the communication patterns without decrypting the captured packets, we present Region based statistical traffic pattern discovery system for MANETs. Region based statistical traffic pattern discovery system for MANETs works passively to perform traffic analysis based on statistical characteristics of raw traffic. Region based statistical traffic pattern discovery system for MANETs are capable of discovering the sources, the destinations, and the end-to-end communication relations. Region based statistical traffic pattern discovery system for MANETs perform the traffic analysis as divide the entire network into multiple regions geographically. Empirical studies demonstrate that Region based statistical traffic pattern discovery system for MANETs achieves good accuracy in disclosing the hidden traffic patterns.
The Effect of the Connectivity of Rigid Phases on Strength of AlSi Alloys

The load carrying capacity of the eutectic Si in AlSi alloys depends on its volume fraction, distribution, morphology and connectivity, namely its internal architecture. This can be modified by heat treatment at temperatures close to the eutectic point causing the spheroidisation and loss of connectivity of the eutectic Si. This decreases the load carrying capacity of the eutectic Si and, consequently, the room and high temperature strength of AlSi alloys is reduced. The presence of other phases such as ceramic short fibres and aluminides in AlSi alloys can result in the formation of hybrid three‐dimensional structures that strongly delay and/or suppress the morphological changes and the loss of connectivity of the eutectic Si. As a result, the thermo‐mechanical behaviour of these heterogeneous lightweight materials is improved and stable. These effects have been explored in the last years by the authors and the main results are compiled and presented in the present work with special emphasis in the relationship between the architecture and the strength of different AlSi‐based materials.
Teachers’ and parents’ views on the Internet and social media usage by pupils with intellectual disabilities

This article reports experiences from a Swedish study, discussing teachers’ and parents’ views on how young people with intellectual disabilities use the Internet and social media. Five semi-structured focus group interviews were conducted with teachers (n = 8) in special programmes in upper secondary schools for pupils with intellectual disabilities and parents (n = 5) of pupils in the same form of schooling, and they were analysed with thematic analysis. Teachers more strongly emphasize a pupil’s use of the Internet for interactive purposes. Parents had expectations that the Internet could be a tool for gaining more awareness of one’s own disability and a way to meet other peer group pupils. Teachers’ and parents’ perspectives on the Internet and social media usage are important since it is imperative to show how support can be provided for young people with intellectual disabilities.
Copyright 2009 by Human Factors and Ergonomics Society, Inc. All rights reserved. 10.1518/107118109X12524443344790

Users interact with mobile devices through menus, which can include many items. Auditory menus can supplement or even replace visual menus. Unfortunately, little research has been devoted to enhancing the usability of large auditory menus. We evaluated a novel auditory menu enhancement called a “spindex" (i.e., speech index), in which brief audio cues inform the user where she is in a long menu. In the current implementation, each item in a menu is preceded by a sound based on the item’s initial letter. 25 undergraduates navigated through an alphabetized contact list of 50 or 150 names. The menu was presented with text-to-speech (TTS) alone, or TTS plus spindex, and with the visual menu displayed or not. Search time was faster with the spindex-enhanced menu, especially for long lists. Subjective ratings also favored the spindex. Results are discussed in terms of theory and practical applications.
EntityRank: Searching Entities Directly and Holistically

As the Web has evolved into a data-rich repository, with the standard "page view," current search engines are becoming increasingly inadequate for a wide range of query tasks. While we often search for various data "entities" (e.g., phone number, paper PDF, date), today's engines only take us indirectly to pages. While entities appear in many pages, current engines only find each page individually. Toward searching directly and holistically for finding information of finer granularity, we study the problem of entity search, a significant departure from traditional document retrieval. We focus on the core challenge of ranking entities, by distilling its underlying conceptual model Impression Model and developing a probabilistic ranking framework, EntityRank, that is able to seamlessly integrate both local and global information in ranking. We evaluate our online prototype over a 2TB Web corpus, and show that EntityRank performs effectively.
Systolic Blood Pressure Response to Exercise Stress Test and Risk of Stroke

Background and Purpose— Systolic blood pressure (SBP) during exercise has been found to predict a future diagnosis of hypertension, coronary heart disease, and cardiovascular disease death. No studies have been conducted to show a relationship between SBP during exercise test and stroke. The aim of the present study was to study the associations between SBP rise, percent maximum SBP at 2 minutes after exercise, and the risk of stroke in a population-based sample of men with no prior coronary heart disease. Methods— SBP was measured every 2 minutes during and after the exercise test. The subjects were a population-based sample of 1026 men without clinical coronary heart disease, antihypertensive medication, or prior stroke at baseline. During an average follow-up of 10.4 years, there were 46 cases of stroke (38 ischemic strokes). Results— Men with SBP rise >19.7 mm Hg per minute of exercise duration had a 2.3-fold increased risk of any stroke and a 2.3-fold increased risk of ischemic stroke compared with men whose SBP rise was <16.1 mm Hg/min. Similarly, percent maximum SBP at 2 minutes after exercise (SBP at 2 minutes’ recovery divided by maximum SBP) was associated (highest tertile) with a 4.6-fold increased risk of any stroke and a 5.2-fold increased risk of ischemic stroke. Conclusions— SBP rise during exercise and percent maximum SBP at 2 minutes after exercise were directly and independently associated with the risk of all stroke and ischemic stroke. Exercise SBP testing may be recommended as an additional tool in the prediction of future stroke.
Approximation for minimum total dominating set

A total dominating set is a dominating set which induces a subgraph without isolated vertices. In this paper, we study the approximation of minimum total dominating set problem. First, we present a new analysis for one-step greedy algorithm with approximation ratio ln(δ-0.5)+1.5, where δ is the maximum degree of the given graph. Second, we prove some approximation hardness of this problem on various classes of graphs, including sparse graphs, small degree graphs, directed graphs, etc.
The adverse selection risk of equipment support outsourcing and its prevention strategy

Support outsourcing is the new development of the equipment support ability construction. Support outsourcing is a “double-edged sword”, which brings about many risks despite the enhanced supporting ability. Adverse selection is the risk we must face in the process of signing contract of support outsourcing. This paper deals with the principle of mechanism to prevent the risk of adverse selection in the process of equipment support outsourcing, and gives a kind of mechanism design with the view of optimization to the payment structure.
A Critical Role of the Strychnine-Sensitive Glycinergic System in Spontaneous Retinal Waves of the Developing Rabbit

In the developing vertebrate retina, spontaneous electric activity occurs rhythmically in the form of propagating waves and is believed to play a critical role in activity-dependent visual system development, including the establishment of precise retinal and geniculate circuitry. To elucidate how spontaneous retinal waves encode specific developmental cues at various developmental stages, it is necessary to understand how the waves are generated and regulated. Using Ca2+ imaging and patch clamp in a flat-mount perinatal rabbit retinal preparation, this study demonstrates that, in addition to the cholinergic system, a strychnine-sensitive system in the inner retina plays an obligatory and developmentally regulated role in the initiation and propagation of spontaneous retinal waves. This system, which is believed to be the glycinergic network, provided an excitatory drive during early retinal development. It then became inhibitory after postnatal day 1 (P1) to P2, an age when a number of coordinated transitions in neurotransmitter systems occurred concomitantly, and finally contributed to the complete inhibition and disappearance of spontaneous waves after P7–P9. This glycinergic contribution was notably distinct from that of the ionotropic GABAergic system, which was found to exert an inhibitory but nonessential influence on the early wave formation. Blocking glycine- and GABA-gated anion currents had opposing effects on spontaneous retinal waves between embryonic day 29 and P0, suggesting that Cl− transporters, particularlyR(+)-butylindazone-sensitive K-Cl cotransporters, may have a synapse- and/or cell type-specific distribution pattern, in addition to an age-dependent expression pattern in the inner retina. Overall, the results revealed an important reliance of spontaneous retinal waves on dynamic and coordinated interactions among multiple, nonredundant neurotransmitter systems.
Adhesion dynamics and durotaxis in migrating cells

When tissue cells are plated on a flexible substrate, durotaxis, the directed migration of cells toward mechanically stiff regions, has been observed. Environmental mechanical signals are not only important in cell migration but also seem to influence all aspects of cell differentiation and development, including the metastatic process in cancer cells. Based on a theoretical model suggesting that this mechanosensation has a mechanical basis, we introduce a simple model of a cell by considering the contraction of F-actin bundles containing myosin motors (stress fibers) mediated by the movement of adhesions. We show that, when presented with a linear stiffness gradient, this simple model exhibits durotaxis. Interestingly, since stress fibers do not form on soft surfaces and since adhesion sliding occurs very slowly on hard surfaces, the model predicts that the expected cell velocity reaches a maximum at an intermediate stiffness. This prediction can be experimentally tested. We therefore argue that stiffness-dependent cellular adaptations (mechanosensation) and durotaxis are intimately related and may share a mechanical basis. We therefore identify the essential physical ingredients, which combined with additional biochemical mechanisms can explain durotaxis and mechanosensation in cells.
The circumbinary disc around the J-type C-star IRAS 18006-3213

Context: In the generally accepted, but poorly documented model, silicate J-type C-stars are binary objects for which the silicate emission originates from a circumbinary or a circumcompanion disc. Aims: We aim at testing this hypothesis by a thorough spectral and spatial observational study of one object: IRAS 18006-3213 . Methods: We obtained, analysed and modeled high spatial resolution interferometric VLTI/MIDI observations on multiple baselines ranging from 45 m to 100 m. Results: All observations resolved the object and show the very compact nature of the N-band emission (~30 mas). In addition, the highest spatial resolution data show a significant differential phase jump around 8.3 mum. This demonstrates the asymmetric nature of the N-band emission. Moreover, the single telescope N-band spectrum shows the signature of highly processed silicate grains. These data are used to confirm the model on silicate J-type C-stars for IRAS 18006-3213 . We show that the most favourable model of the dust geometry is a stable circumbinary disc around the system, seen under an intermediate inclination. Conclusions: The data presented on the silicate J-type C-star IRAS 18006-3213 provide evidence that the oxygen rich dust is trapped in a circumbinary disc. The formation of this disc is probably linked to the binary nature of the central star. Based on observations collected at the European Southern Observatory, Chile. Program ID: 073.D-610(A).
Genome-Wide Association Study of Coronary Heart Disease and Its Risk Factors in 8,090 African Americans: The NHLBI CARe Project

Coronary heart disease (CHD) is the leading cause of mortality in African Americans. To identify common genetic polymorphisms associated with CHD and its risk factors (LDL- and HDL-cholesterol (LDL-C and HDL-C), hypertension, smoking, and type-2 diabetes) in individuals of African ancestry, we performed a genome-wide association study (GWAS) in 8,090 African Americans from five population-based cohorts. We replicated 17 loci previously associated with CHD or its risk factors in Caucasians. For five of these regions (CHD: CDKN2A/CDKN2B; HDL-C: FADS1-3, PLTP, LPL, and ABCA1), we could leverage the distinct linkage disequilibrium (LD) patterns in African Americans to identify DNA polymorphisms more strongly associated with the phenotypes than the previously reported index SNPs found in Caucasian populations. We also developed a new approach for association testing in admixed populations that uses allelic and local ancestry variation. Using this method, we discovered several loci that would have been missed using the basic allelic and global ancestry information only. Our conclusions suggest that no major loci uniquely explain the high prevalence of CHD in African Americans. Our project has developed resources and methods that address both admixture- and SNP-association to maximize power for genetic discovery in even larger African-American consortia.
INDOL STUDIES

The production of indol by bacteria has received considerable attention throughout the development of the science of bacteriology. Norton and Sawyer (1921) claimed that, with the exception of Vibrio cholerae, all species which have been reported as indolpositive have also been found by some to be indol-negative. Because of this variation among strains of the same species, the indol reaction per se cannot be considered as a good species differentiating test. NicoUe and others (1919) studied a number of strains of Coccobacillus acridiorum, probably all from the same source, which showed considerable variation in indol formation. Many laboratory workers in bacteriology have met with indolnegative strains of Bact. coli and indol-positive strains of Bact. aerogenes. However, because indol production by any given strain of bacterium appears to be constant and fixed (Neisser, 1921), this reaction has some value in the study of individual strains, although an apparent flaw in this argument is brought out in the work of Fabry (1922) who stated that continued cultivation of an indol-positive strain of Bact. coli in a medium containing 0.05 per cent phenol developed a strain which did not produce indol. In this instance might not the phenol, by inhibiting growth of the predominating indol-positive cells, bring into prominence an indol-negative bio-type originally present in the same strain? Granting Neisser's claims, the production of indol by bacteria is of some practical value.