Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytomegalovirus (CMV) strain differences between the eye and blood in AIDS patients with CMV retinitis

Objective:To investigate possible differences in cytomegalovirus (CMV) strain distribution between the eye and blood in AIDS patients with CMV retinitis. Methods:CMV DNA sequences from aqueous humour and peripheral blood leukocytes (PBL), obtained from 13 AIDS patients with CMV retinitis, were compared. DNA was isolated and the CMV IE-1 sequence (part of the immediate early-1 gene) and the a-sequence (located in the a-region) were amplified by polymerase chain reaction (PCR). The PCR products of the a-sequence were analysed by Southern blotting for amplified fragment-length polymorphisms. The level of divergence between the a-sequences of aqueous humour- and PBL-derived CMV was studied in two patients by cloning these sequences followed by sequence analysis. Results:CMV DNA could be detected in all aqueous humour samples and in 10 out of 13 paired blood samples. In the 10 patients, with CMV DNA detectable in both aqueous humour and PBL, seven cases showed differences between the amplified products of both compartments. Sequence analysis in two patients revealed that the aqueous humour and PBL of the same patient can harbour both identical, similar and highly divergent CMV a-sequences. Conclusion:These results indicate that despite the haematogenous spread of CMV, the eye, being a relatively shielded organ, may contain CMV strains different from those found in the blood.
Mitral Annular Dynamics in Myxomatous Valve Disease: New Insights With Real-Time 3-Dimensional Echocardiography

Background— Mitral annulus is a complex structure of poorly understood physiology. Full-volume real-time 3-dimensional transesophageal echocardiography offers a unique opportunity to completely image and quantify mitral annulus size and motion. Methods and Results— Real-time 3-dimensional transesophageal echocardiography of the mitral valve was acquired in 32 patients with myxomatous valve disease (MVD) and moderate to severe regurgitation, 15 normal control subjects, and 10 patients with ischemic mitral regurgitation of identical body surface area. Mitral annular dimensions (circumference, area, anteroposterior and intercommissural diameters, height, and ratio of height to intercommissural diameter ratio, which appraises annular saddle-shape depth) were measured throughout the cardiac cycle with dedicated quantification software. Compared with direct surgical measurement, 3-dimensional anterior annular dimension provided reliable measurements (mean difference, 0.1±0.1 mm; P=0.73; 95% confidence interval, ±4.4 mm). Annular dimensions were larger in MVD patients compared with control subjects in diastole (all P<0.05). Normal annulus displayed early-systolic anteroposterior (P<0.001) and area (P=0.04) contraction, increased height (P<0.001), and deeper saddle shape (ratio of height to intercommissural diameter, 15±1% to 21±1%; P<0.001), whereas intercommissural diameter was unchanged (P=0.30). In contrast, MVD showed early-systolic intercommissural dilatation (P=0.02) and no area contraction (P=0.99), height increase (P=0.11), or saddle-shape deepening (P=0.35). Late-systolic MVD annular saddle shape deepened but annular area excessively enlarged (P<0.04) as a result of persistent intercommissural widening (P<0.02). MVD annulus also contrasts with ischemic mitral regurgitation annulus, which, despite similar anteroposterior enlargement, is narrower and essentially adynamic. After MVD repair, the annulus remained dynamic without systolic saddle-shape accentuation (P=0.30). Conclusions— Real-time 3-dimensional transesophageal echocardiography provides insights into normal, dynamic mitral annulus function with early-systolic area contraction and saddle-shape deepening contributing to mitral competency. MVD annulus is also dynamic but considerably different with loss of early-systolic area contraction and saddle-shape deepening despite similar magnitude of ventricular contraction, suggestive of ventricular-annular decoupling. Subsequent area enlargement may contribute to mitral incompetence. After mitral repair, MVD annulus remains dynamic without systolic saddle-shape accentuation. Thus, real-time 3-dimensional transesophageal echocardiography provides new insights that allow the refining of mitral pathophysiology concepts and repair strategies.
Bistatic scattering from a 3D target above randomly rough surface

This paper presents a hybrid iterative algorithm of analytic Kirchhoff Approximation (KA) and numerical method of moment (MoM) for scattering computation from a three-dimensional (3D) perfect conducting target above a randomly rough surface. The coupling integral equations (IEs) are derived based on the Green's function and the boundary conditions. The MoM with the Conjugate Gradient (CG) approach is used to solve the target's IE, and the KA is applied to scattering from the rough surface. The coupling iteration takes account the interactions between the target and the underlying rough surface. Convergence of the hybrid KA-MoM algorithm is numerically validated. Since is only one numerical integral of induced current on the target performed by KA computation, much memory and computation time is reduced. Bistatic scattering from a PEC cubic or spheroid target above a Gaussian rough surface are numerically simulated.
A Cockroach Inspired Robot With Artificial Muscles

A robot, Robot V (Ajax) has been constructed based on the death head cockroach, Blaberus discoidalis. In an attempt to further take advantage of the neuromechanics of the animal, actuators with muscle-like properties have been employed that demonstrate a superior force to weight ratio over conventional actuation devices. Although it is not feasible to capture the entire range of motion displayed by the animal (seven degrees of freedom per leg), research has shown that twenty-four degrees of freedom provide a sufficiently close approximation for agile walking and climbing. The fifteen kilogram robot has an offboard power source and control system
Dense Gas in the Milky Way

We present a study of dense gas emission in the Milky Way to serve as a basis for comparison with extragalactic results. This study combines new observations of HCN, CS, and CO in individual giant molecular clouds (GMCs) and in the Milky Way plane with published studies of emission from these molecules in the inner 500 pc of the Milky Way. We find a strong trend in the fraction of emission from dense gas tracers as a function of location in the Milky Way: in the bulge, IHCN/ICO = 0.081 ± 0.004, in the plane, IHCN/ICO = 0.026 ± 0.008 on average, and over the full extent of nearby GMCs, IHCN/ICO = 0.014 ± 0.020. Similar trends are seen in ICS/ICO: in the bulge, ICS/ICO = 0.027 ± 0.006, in the plane, ICS/ICO = 0.018 ± 0.008 on average, and over the full extent of nearby GMCs, ICS/ICO = 0.013 ± 0.02. The low intensities of the HCN and CS emission in the plane suggest that these lines are produced by gas at moderate densities; thus, they are not like the emission produced by the dense, parsec-scale star-forming cores in nearby GMCs. The contrast between the bulge and the disk ratios in the Milky Way is likely to be caused by a combination of higher kinetic temperatures as well as a higher dense gas fraction in the bulge of the Milky Way. We show that the ratio IHCN/ICO is correlated quantitatively with the total hydrostatic gas pressure in the Milky Way as IHCN/ICO ∝ P0.19±0.04.
Diet assessment based on type‐2 fuzzy ontology and fuzzy markup language

Nowadays most people can get enough energy to maintain one‐day activity, while few people know whether they eat healthily or not. It is quite important to analyze nutritional facts for foods eaten for those who are losing weight or suffering chronic diseases such as diabetes. This paper proposes a novel type‐2 fuzzy ontology, including a type‐2 fuzzy food ontology and a type‐2 fuzzy markup language (FML)‐based ontology, for diet assessment. In addition, we also present a type‐2 FML (FML2) to describe the type‐2 fuzzy ontology and the FML2‐based diet assessment agent, including a type‐2 knowledge engine, a type‐2 fuzzy inference engine, a diet assessment engine, and a semantic analysis engine. In the proposed approach, first, the nutrition facts of various kinds of food are collected from the Internet and the convenience stores. Next, the domain experts construct the type‐2 fuzzy ontology, and then the involved subjects are requested to input the different food eaten. Finally, the proposed FML2‐based diet assessment agent displays the diet assessment of the food eaten based on the constructed type‐2 fuzzy ontology. Using the generated semantic analysis, people can obtain health information about what they eat, which can lead to a healthy lifestyle and healthy diet. Experimental results show that the proposed approach works effectively where the proposed system can provide a diet health status, which can act as a reference to promote healthy living. © 2010 Wiley Periodicals, Inc.
Comparing Methodologies: Linked Open Data and Digital Libraries

This paper reports the outcomes of the conversation moderated by Anna Maria Tammaro, which took place in Bologna during the third AIUCD (Associazione per l'Informatica Umanistica e la Cultura Digitale) conference, between Karen Coyle and Gianmaria Silvello about convergences and divergences of Cultural Heritage (CH) and Computer Science (CS) communities about digital libraries and the Linked Open Data (LOD) paradigm. The conversation has been stimulated in the context of the community of Digital Humanities (DH) scholars, in order to actively engaging them in the linked open data and digital libraries services. The LOD paradigm is a promising technology not only for opening up digital libraries resources, but also for augmenting the discoverability, re-use, enrichment and sharing of their resources on the Web. For the digital libraries LOD can represent a quite significant shift from a "closed paradigm" where the domain expert (e.g. the librarian) has the control of the resources to an "open paradigm" where the resources are free to circulate and evolve "without" explicit control of domain experts. In this paper we report some existing positive experiences of integration of the LOD paradigm in the digital library context where the LOD has been used as a publishing paradigm. We also discuss some limitations of the current approach by presenting some open problems that should be investigated to fully realize the LOD paradigm potentialities.
THE DISCOURSE OF SOUND

Abstract This article offers a short overview of the development of listening theories concerning Western art music since the end of the eighteenth century. Referring to Michel Foucault, I consider such theories as discourses which produce ‘power effects', such as the training of listening attitudes, or the construction of specific spaces, such as the Festspielhaus in Bayreuth. During the eighteenth century, predominant discourses considered musical pieces as orations and, since the nineteenth century, as complex organisms or structures. In the last third of the twentieth century a focus on sound, evinced for instance by the field of ‘sound studies', has produced a new configuration that dissolves the prevailing model of structural listening. This perspective may shed light on some technical features of contemporary compositional styles, which I examine by considering the use of melodies, gestures and loops in two compositions by Fausto Romitelli and Simon Steen-Andersen.
Psychometric Properties of the Malay Version of the Dutch Eating Behaviour Questionnaire (DEBQ) in a Sample of Malaysian Adults Attending a Health Care Facility.

OBJECTIVE This study aims to investigate the psychometric properties of the Malay version of the Dutch Eating Behaviour Questionnaire (DEBQ) among Malaysian adults. METHOD The Malay version of the DEBQ instrument was administered to 398 outpatients (269 women and 129 men) at the University of Malaya Medical Centre (UMMC). Confirmatory Factor Analysis (CFA) was conducted to study the construct validity of the instrument. Composite reliability coefficient, Raykov's rho, was used to determine the internal consistency. RESULTS The proposed three-factor structure for the DEBQ instrument was appropriate, although three items (Items 21, 14 and 27) showed problematic loadings with inappropriate model fit and were removed. The modified version had an appropriate model fit χ2/df = 2.129, TLI = 0.908, CFI = 0.918, RMSEA = 0.053 (90%CI = 0.048-0.058), close-fit P-value = 0.136 and satisfactory internal consistency of 0.914 for emotional eating scale, 0.819 for external eating scale and 0.856 for restrained eating scale. DISCUSSION The Malay version of the DEBQ is a valid instrument to study eating behaviour traits among Malaysian adults. Further research is warranted to determine if Items 14 and 27 are appropriate for the Malaysian population.
Dynamic resource brokering for multi-user query execution

We propose a new framework for resource allocation based on concepts from microeconomics. Specifically, we address the difficult problem of managing resources in a multiple-query environment composed of queries with widely varying resource requirements. The central element of the framework is a resource broker that realizes a profit by "selling" resources to competing operators using a performance-based "currency. " The guiding principle for brokering resources is profit maximization. In other words, since the currency is derived from the performance objective, the broker can achieve the best performance by making the scheduling and resource allocation decisions that maximize profit. Moreover, the broker employs dynamic techniques and adapts by changing previous allocation decisions while queries are executing. In a first validation study of the framework, we developed a prototype broker that manages memory and disk bandwidth for a multi-user query workload. The performance objective for the prototype broker is to minimize slowdown with the constraint of fairness. Slowdown measures how much higher the response time is in a multi-user environment than a single-user environment, and fairness measures how even is the degradation in response time among all queries as the system load increases, Our simulation results show the viability of the broker framework and the effectiveness of our query admission and resource allocation policies for multi-user workloads.
A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.

We surveyed the sequenced Saccharomyces cerevisiae genome (strain S288C) comprehensively for open reading frames (ORFs) that could encode full-length proteins but contain obvious mid-sequence disablements (frameshifts or premature stop codons). These pseudogenic features are termed disabled ORFs (dORFs). Using homology to annotated yeast ORFs and non-yeast proteins plus a simple region extension procedure, we have found 183 dORFs. Combined with the 38 existing annotations for potential dORFs, we have a total pool of up to 221 dORFs, corresponding to less than approximately 3% of the proteome. Additionally, we found 20 pairs of annotated ORFs for yeast that could be merged into a single ORF (termed a mORF) by read-through of the intervening stop codon, and may comprise a complete ORF in other yeast strains. Focussing on a core pool of 98 dORFs with a verifying protein homology, we find that most dORFs are substantially decayed, with approximately 90% having two or more disablements, and approximately 60% having four or more. dORFs are much more yeast-proteome specific than live yeast genes (having about half the chance that they are related to a non-yeast protein). They show a dramatically increased density at the telomeres of chromosomes, relative to genes. A microarray study shows that some dORFs are expressed even though they carry multiple disablements, and thus may be more resistant to nonsense-mediated decay. Many of the dORFs may be involved in responding to environmental stresses, as the largest functional groups include growth inhibition, flocculation, and the SRP/TIP1 family. Our results have important implications for proteome evolution. The characteristics of the dORF population suggest the sorts of genes that are likely to fall in and out of usage (and vary in copy number) in a strain-specific way and highlight the role of subtelomeric regions in engendering this diversity. Our results also have important implications for the effects of the [PSI+] prion. The dORFs disabled by only a single stop and the mORFs (together totalling 35) provide an estimate for the extent of the sequence population that can be resurrected readily through the demonstrated ability of the [PSI+] prion to cause nonsense-codon read-through. Also, the dORFs and mORFs that we find have properties (e.g. growth inhibition, flocculation, vanadate resistance, stress response) that are potentially related to the ability of [PSI+] to engender substantial phenotypic variation in yeast strains under different environmental conditions. (See genecensus.org/pseudogene for further information.)
An alternative leukocyte homotypic adhesion mechanism, LFA-1/ICAM-1- independent, triggered through the human VLA-4 integrin

The VLA-4 (CD49d/CD29) integrin is the only member of the VLA family expressed by resting lymphoid cells that has been involved in cell-cell adhesive interactions. We here describe the triggering of homotypic cell aggregation of peripheral blood T lymphocytes and myelomonocytic cells by mAbs specific for certain epitopes of the human VLA alpha 4 subunit. This anti-VLA-4-induced cell adhesion is isotype and Fc independent. Similar to phorbol ester-induced homotypic adhesion, cell aggregation triggered through VLA-4 requires the presence of divalent cations, integrity of cytoskeleton and active metabolism. However, both adhesion phenomena differed at their kinetics and temperature requirements. Moreover, cell adhesion triggered through VLA-4 cannot be inhibited by cell preincubation with anti-LFA-1 alpha (CD11a), LFA-1 beta (CD18), or ICAM-1 (CD54) mAb as opposed to that mediated by phorbol esters, indicating that it is a LFA-1/ICAM-1 independent process. Antibodies specific for CD2 or LFA-3 (CD58) did not affect the VLA-4-mediated cell adhesion. The ability to inhibit this aggregation by other anti-VLA-4-specific antibodies recognizing epitopes on either the VLA alpha 4 (CD49d) or beta (CD29) chains suggests that VLA-4 is directly involved in the adhesion process. Furthermore, the simultaneous binding of a pair of aggregation-inducing mAbs specific for distinct antigenic sites on the alpha 4 chain resulted in the abrogation of cell aggregation. These results indicate that VLA-4- mediated aggregation may constitute a novel leukocyte adhesion pathway.
The NAD-dependent ligase encoded by yerG is an essential gene of Bacillus subtilis.

DNA ligases are grouped into two families, ATP-dependent and NAD-dependent, according to the cofactor required for their activity. A surprising capability of both kinds of ligases to complement for one another in vivo has been observed. Bacillus subtilis harbours one NAD-dependent ligase, YerG, and two ATP-dependent ligases, YkoU and YoqV, this last one being encoded by the 134 kb lysogenic bacteriophage SPss and consisting of a single adenylation domain typical of ATP-dependent ligases. Because the genetics of ligases in B.subtilis had not been studied previously, the genes encoding for one ligase of each kind, yerG and yoqV, were investigated. We found that the yerG gene was essential in B.subtilis. This suggests that none of the ATP-dependent ligases was able to complement the yerG defect. In addition, the ATP-dependent ligase encoded by yoqV, when cloned on a plasmid under appropriate expression signals, was unable to rescue a yerG mutant strain. The two B.subtilis ligase genes yerG and yoqV were also introduced in an Escherichia coli strain encoding a thermosensitive ligase (ligts), and whereas yoqV did not complement the ligts defects, yerG fully complemented the growth and UV sensitivity defects of the lig mutant. We propose to rename the yerG and yoqV genes of B.subtilis ligA and ligB respectively.
UNSUPERVISED LEARNING OF SEMANTIC CONCEPTS

Given a large number of articles comprising of natural text we intend to train on the text and extract clusters of words which are semantically related. When I query the system with a word it will return all the words which are very related to the same theme. For example our training set could be all the articles appearing in a magazine. If I query the system with war it would return all the words like soldiers, aircrafts, Iraq etc. Note that all the words do not mean the same they are related by a common unifying theme of war. We want to apply the techniques of nonlinear manifold learning to this unsupervised learning task. We experimented with two techniques, a linear technique Principal Component Analysis and and non-linear manifold learning technique called Isomap [11]
An examination of successful soldier postdeployment transition from combat to garrison life.

Previous studies have shown that combat exposures and deployment-related stressors have negative implications on soldiers' postdeployment health and well-being. The current study aimed to examine the individual and combined effects of organizational and social support on the success of soldiers' postdeployment reintegration. In this study, 2,922 U.S. soldiers were surveyed from a brigade combat team at 90-120 days postdeployment, measuring soldiers' perceptions of postdeployment transition home, occupational and social support, stigma and barriers associated with accessing behavioral health care, and previous behavioral health care. Logistic regression analysis indicated that soldiers reporting a positive postdeployment transition home (n = 1,776; 61%) was significantly associated with leadership perceptions, adjusted odds ratio (AOR) = 1.19, 95% confidence interval (CI) [1.02, 1.39], unit cohesion, AOR = 1.29, 95% CI [1.09, 1.53], personal support, AOR = 1.37, 95% CI [1.23, 1.52], perceived levels of stigma, AOR = 0.73, 95% CI [0.65, 0.82] barriers to accessing care, AOR = 0.86, 95% CI [0.76, 0.97], and previously accessing behavioral health care, AOR = 0.34, 95% CI [0.28, 0.43]. These findings suggest redeploying soldiers may benefit from programs aimed at improving self-efficacy and coping through fostering occupational and social support, with special concern taken to reduce stigma and barriers to care across the Army.
Local Volume Preservation for Skinned Characters

Generating plausible deformations of a character skin within the standard production pipeline is a challenge. This paper presents a volume preservation method dedicated to skinned characters. As usual, the character is defined by a skin mesh at some rest pose and an animation skeleton. At each animation step, skin deformations are first computed using standard SSD. Our method corrects the result using a set of local deformations which model the fold‐over‐free, constant volume behavior of soft tissues. This is done geometrically, without the need of any physically‐based simulation. To make the method easily applicable, we also provide automatic ways to extract the local regions where volume is to be preserved and to compute adequate skinning weights, both based on the character's morphology.