Miracle-dz/UniFAR-FTUs huggingface dataset:
Osteogenic comparison of expanded and uncultured adipose stromal cells.

BACKGROUND AIMS Adipose stromal cells (ASC) are a promising alternative to progenitor cells from other tissue compartments because of their multipotential and capacity to retrieve significantly more progenitor cells. Initial cell samples are heterogeneous, containing a collection of cells that may contribute to tissue repair, but the sample becomes more homogeneous with each passage. Therefore, we hypothesized that the osteogenic potential of culture-expanded ASC would differ from uncultured ASC. METHODS Adipose tissue was collected from a yearling colt, and ASC were isolated and expanded using standard protocols or prepared by a commercial vendor using proprietary technology (proprietary stromal vascular fraction, SVFp). Cells were seeded on collagen sponges and maintained in osteogenic culture conditions for up to 21 days to assess osteogenic potential. The ability of each population to stimulate neovascularization and bone healing was determined upon implanting cell-loaded sponges into a rodent calvarial bone defect. Neovascularization was measured 3 weeks post-implantation, while bone formation was monitored over 12 weeks using in vivo microcomputed tomography (microCT). RESULTS SVFp exhibited increased intracellular alkaline phosphatase activity compared with cultured ASC but proliferated minimally. Histologic analysis of explanted tissues demonstrated greater vascularization in defects treated with cultured ASC compared with SVFp. We detected increases in bone volume for defects treated with cultured cells while observing similar values for bone mineral density, regardless of cell type. CONCLUSIONS These results suggest that expanded ASC are advantageous for neovascularization and bone healing in this model compared with SVFp, and provide additional evidence of the utility of ASC in bone repair.
Mechanistic Information and Causal Continuity

Some biological processes (our examples are DNA expression and a reflex response in the leech) move from step to step in a way that cannot be completely understood solely in terms of causes and correlations. This paper develops a notion of mechanistic information that can be used to explain the continuities of such processes. We compare them to processes (including the Krebs cycle) that do not involve information. We compare our conception of mechanistic information to some familiar notions including Crick’s idea of genetic information, Shannon-Weaver information, and Millikan’s biosemantic information.
Differentiation of smallpox and camelpox viruses in cultures of human and monkey cells

SUMMARY The cytopathic effect of smallpox and camelpox viruses has been compared in cell cultures derived from human and monkey tissues. The two viruses could easily be distinguished in HeLa, GMK–AH1, BSC–1 and WISH cells, camelpox producing multinucleate giant cells and smallpox producing rounding up of individual cells. In other cells (LLC–MK2, HEK and 2RhK) the differences were not so marked, and in some (VERO, HEL, K and HuTh) no differences were seen.
The USDA Automated Multiple-Pass Method accurately assesses population sodium intakes.

BACKGROUND Given current sodium-reduction strategies, accurate and practical methods to monitor sodium intake in the US population are critical. Although the gold standard for estimating sodium intake is the 24-h urine collection, few studies have used this biomarker to evaluate the accuracy of a dietary instrument. OBJECTIVE Our objective was to compare self-reported dietary intake of sodium with 24-h urinary excretion obtained in the USDA Automated Multiple-Pass Method (AMPM) Validation Study. DESIGN Subjects were healthy, weight-stable volunteers aged 30-69 y recruited from the Washington, DC, area. Data from 465 subjects who completed at least one 24-h recall and collected a complete 24-h urine sample during the same period were used to assess the validity of sodium intake. Reporting accuracy was calculated as the ratio of reported sodium intake to that estimated from the urinary biomarker (24-h urinary sodium/0.86). Estimations of sodium intake included salt added in cooking but did not include salt added at the table. RESULTS Overall, the mean (95% CI) reporting accuracy was 0.93 (0.89, 0.97) for men (n = 232) and 0.90 (0.87, 0.94) for women (n = 233). Reporting accuracy was highest for subjects classified as normal weight [body mass index (in kg/m(2)) <25]: 1.06 (1.00, 1.12) for men (n = 84) and 0.99 (0.94, 1.04) for women (n = 115). For women only, reporting accuracy was higher in those aged 50-69 y than in those who were younger. CONCLUSION Findings from this study suggest that the USDA AMPM is a valid measure for estimating sodium intake in adults at the population or group level.
Multiple Subject Barycentric Discriminant Analysis (MUSUBADA): How to Assign Scans to Categories without Using Spatial Normalization

We present a new discriminant analysis (DA) method called Multiple Subject Barycentric Discriminant Analysis (MUSUBADA) suited for analyzing fMRI data because it handles datasets with multiple participants that each provides different number of variables (i.e., voxels) that are themselves grouped into regions of interest (ROIs). Like DA, MUSUBADA (1) assigns observations to predefined categories, (2) gives factorial maps displaying observations and categories, and (3) optimally assigns observations to categories. MUSUBADA handles cases with more variables than observations and can project portions of the data table (e.g., subtables, which can represent participants or ROIs) on the factorial maps. Therefore MUSUBADA can analyze datasets with different voxel numbers per participant and, so does not require spatial normalization. MUSUBADA statistical inferences are implemented with cross-validation techniques (e.g., jackknife and bootstrap), its performance is evaluated with confusion matrices (for fixed and random models) and represented with prediction, tolerance, and confidence intervals. We present an example where we predict the image categories (houses, shoes, chairs, and human, monkey, dog, faces,) of images watched by participants whose brains were scanned. This example corresponds to a DA question in which the data table is made of subtables (one per subject) and with more variables than observations.
PI Control Plus Electric Current Loops for PM Synchronous Motors

We present a solution for velocity control in permanent magnet synchronous motors. We formally prove that velocity converges to the constant desired value from any initial condition. Our controller is so simple that it only differs from the linear control strategy commonly implemented in commercial drives by two simple adaptive terms. Moreover, identical velocity responses are obtained with both controllers. Hence, our results explain how the linear control strategy implemented in most commercial drives works and also provide tuning guidelines for that control strategy. We remark that this has been a long standing unsolved problem.
Ecological measurement of fatigue and fatigability in older adults with osteoarthritis.

BACKGROUND Fatigue is associated with loss of independence in older adults; however, little is known about optimal treatment or how fatigue manifests in daily life activities. "Fatigability" was recently proposed to clarify the fatigue-activity relationship. The purpose of this study was to present a new measurement method of fatigability and begin to test its validity. METHODS Our sample included 40 adults with knee or hip osteoarthritis (OA) and 20 healthy controls. Fatigue was measured by ecological momentary assessment several times a day along with continuous measurement of physical activity using a wrist-worn accelerometer. Fatigability was measured as the fatigue increase after a period of high activity. RESULTS Compared with controls, participants with OA were approximately four times more likely to have an increase in fatigue after a high activity interval (37.0% vs 9.8%). Among people with OA, average fatigue and fatigability were not highly related (r = .13). Fatigue was most strongly associated with reported physical function, pain, and vitality, whereas fatigability was most strongly associated with body mass index, OA severity, and knee strength. CONCLUSIONS Although fatigue among people with OA was more associated with subjective reports of physical function and symptoms, pairing fatigue reports with physical activity tapped objective factors that may be related to the biomechanical demands of daily life activities. Thus, fatigability measurement may help discern how symptoms relate to daily life function and help to refine treatment approaches in OA.
Premature Collagen Fibril Formation, Fibroblast-Mast Cell Interactions and Mast Cell-Mediated Phagocytosis of Collagen in Keloids

Abstract Keloids are benign hyper-proliferative growths of fibrous tissue where increased fibroblast activity results in abnormal collagen deposition. Excessive inflammation is a characteristic feature of keloids, but little is known about the underlying ultrastructural features of keloids related to collagen processing, fibril and fiber formation, the interaction between fibroblasts and associated collagen fibers and mast cells. In this study, the ultrastructure of the dermis of keloid patients was evaluated using light and transmission electron microscopy techniques. Abnormal intracellular premature collagen fibril formation was observed. Phagocytosis of collagen fibrils by mast cells was a common ultrastructural feature of keloid tissue as was a close or direct association between fibroblasts and mast cells. Based on these findings and recent advances in knowledge related to collagen synthesis, fibril formation and processing, we hypothesize that keloid formation is primarily due to abnormal collagen synthesis where the consequent accumulation of collagen fibers causes increased mast cell recruitment and collagen phagocytosis. Subsequent release of mast cell-derived mediators then promotes further collagen synthesis. The observation of early formation in keloid tissue of premature insoluble collagen fibrils supports previous studies that enzymes such as procollagen C-proteinase are important early therapeutic targets.
BugBuilder - An Automated Microbial Genome Assembly and Analysis Pipeline

Summary BugBuilder is a framework for hands-free assembly and annotation of microbial genomes. It produces outputs suitable either for database submission or downstream finishing processes. It is configurable to work with most command-line assembly and scaffolding tools which are selectable at run-time, and supports all common sequence types used in microbial genome assembly. Availability and Implementation BugBuilder is implemented in Perl and is available under the Artistic License from http://www.imperial.ac.uk/bioinformatics-data-science-group/resources/software/bugbuilder, A virtual machine image is available pre-configured with the relevant freely-redistributable dependencies. Contact j.abbott@imperial.ac.uk
Analysis of cost functions and setpoints for predictive speed control of PMSM drives

Performance of the PMSM numerical predictive control on very long horizon is studied in simulation. It is shown that the trajectories of optimally controlled system follow the well known trajectories of maximum torque per ampere and maximum torque per volt. Significant difference from these trajectories is observed only at rapid request for maximum current. We compare the numerical solution with analytically obtained solution of minimum time current control. We show that available minimum time current control algorithm do not match the observed trajectory. An idea how to achieve the same behavior using only one step ahead prediction is proposed. The time optimal current control is approximated using ad-hoc arguments. The challenge for future research is to design better minimum time current control strategy.
SHED

Computing similarities or distances between 3D shapes is a crucial building block for numerous tasks, including shape retrieval, exploration and classification. Current state-of-the-art distance measures mostly consider the overall appearance of the shapes and are less sensitive to fine changes in shape structure or geometry. We present shape edit distance (SHED) that measures the amount of effort needed to transform one shape into the other, in terms of re-arranging the parts of one shape to match the parts of the other shape, as well as possibly adding and removing parts. The shape edit distance takes into account both the similarity of the overall shape structure and the similarity of individual parts of the shapes. We show that SHED is favorable to state-of-the-art distance measures in a variety of applications and datasets, and is especially successful in scenarios where detecting fine details of the shapes is important, such as shape retrieval and exploration.
Compressive Stepped-Frequency Continuous-Wave Ground-Penetrating Radar

Data acquisition speed is an inherent problem of stepped-frequency continuous-wave (SFCW) radars, which may discourage further usage and development of this technology. We propose an emerging paradigm called compressed sensing (CS) to overcome this problem. In CS, a signal can be reconstructed exactly based on only a few samples below the Nyquist rate. Accordingly, the data acquisition speed can be increased significantly. A novel design of an SFCW ground-penetrating radar (GPR) with high acquisition speed is proposed and evaluated. Simulation by a monocycle waveform and actual measurement by a vector network analyzer at a GPR test range indicate the applicability of the proposed system.
A Probabilistic Approach to Tactile Shape Reconstruction

In this paper, we present a probabilistic spatial approach to build compact 3-D representations of unknown objects probed by tactile sensors. Our approach exploits the high frame rates provided by modern tactile sensors and utilizes Kalman filters to build a probabilistic model of the contact point cloud that is efficiently stored in a kd-tree. The quality of generated shape representations is compared with a naive averaging approach, and we show that our method provides superior accuracy. We also evaluate the feasibility of object classification combining the generated object representations, together with the iterative closest point algorithm.
mosR, a Novel Transcriptional Regulator of Hypoxia and Virulence in Mycobacterium tuberculosis

ABSTRACT Latent tuberculosis represents a high-risk burden for one-third of the world population. Previous analysis of murine tuberculosis identified a novel transcriptional regulator encoded by Rv0348 that could control the establishment of persistent tuberculosis. Disruption of the Rv0348 gene from the genome of the virulent H37Rv strain of Mycobacterium tuberculosis revealed a global impact on the transcriptional profiles of 163 genes, including induction of the mammalian cell entry (mce1) operon and the repression of a significant number of genes involved in hypoxia and starvation responses. Nonetheless, gel shift assays did not reveal direct binding between Rv0348 and a set of regulated promoters, suggesting an indirect regulatory role. However, when expressed in Mycobacterium smegmatis, the Rv0348 transcripts were significantly responsive to different levels of hypoxia and the encoded protein was shown to regulate genes involved in hypoxia [e.g., Rv3130c (tgs1)] and intracellular survival (e.g., mce1), among other genes. Interestingly, the colonization level of the ΔmosR mutant strain was significantly lower than that of the wild-type strain of M. tuberculosis, suggesting its attenuation in the murine model of tuberculosis. Taken together, our analyses indicated that the Rv0348 gene encodes a novel transcriptional factor that regulates several operons involved in mycobacterial survival, especially during hypoxia; hence, we propose that Rv0348 be renamed mosR for regulator of mycobacterial operons of survival.
Ex vivo accuracy of three electronic apex locators: Root ZX, Elements Diagnostic Unit and Apex Locator and ProPex.

AIM To compare ex vivo the accuracy of three electronic apex locators (EALs): Root ZX, Elements Diagnostic Unit and Apex Locator and ProPex. METHODOLOGY Electronic working length determination was carried out in 40 extracted teeth using an ex vivo model. After access preparation, a first operator determined the reference length (AL) for each tooth under a 30x stereomicroscope using the apical constriction as the apical landmark. All teeth were then measured with each EAL and the results obtained were compared with the corresponding AL. The AL was subtracted from the electronically determined distance. The measurements exceeding the AL were recorded as positive (long) and the measurements short of the AL were recorded as negative. Data were analyzed using the Friedman Test and Tukey multiple range test for nonparametric correlation amongst groups. Statistical significance was considered at P < 0.05. RESULTS Comparing the differences between measurements obtained with the three EALs and those obtained with the stereomicroscope, the percentage of measurements within +/-0.5 mm of the AL was 97.37% (84.22% within 0.5 mm short of AL) for the Root ZX, 94.28% (88.57% within 0.5 mm short of AL) for the Elements and 100% (35.9% within 0.5 mm short of AL) for the ProPex. The mean difference between the AL and the lengths measured by the Root ZX, the Elements and the ProPex were, respectively, -0.157 +/- 0.228, -0.103 +/- 0.359 and 0.307 +/- 0.271 mm. CONCLUSIONS The results of the present study confirm that the EALs determined the canal length within +/-0.5 mm from the apical constriction in the majority of cases. The majority of the ProPex readings were long.
An anisotropic PML absorbing boundary condition using for waves propagating in dispersive medium

In this paper, an anisotropic perfectly matched layer (PML) absorbing boundary condition is presented for the finite difference-time domain (FDTD) method to simulate waves propagating in a dispersive medium. Numerical results show that by properly choosing the constitutive parameters of the anisotropic PML, the method provides a nearly reflectionless absorbing boundary and it is an effective method in the simulation of waves propagating in a dispersive medium.
Explaining Proenvironmental Intention and Behavior by Personal Norms and the Theory of Planned Behavior1

The value of personal norms (Schwartz, 1977) for proenvironmental behavior has been demonstrated in previous studies (e.g., Vining & Ebreo, 1992), but not in addition to the theory of planned behavior (Ajzen & Madden, 1986). In the present study, this combination was investigated by means of a mail survey among a sample of 305 Dutch citizens who were enlisted to participate in a behavioral change intervention program on environmentally relevant behavior. Personal norms appear to increase the proportion of explained variance in 5 intentions and 4 self-reported measures of performed environmentally relevant behaviors beyond that explained by three of the theory of planned behavior constructs (i.e., attitude, subjective norm, and perceived behavioral control). Issues evoked by these results are discussed.
Example Overflow: Using social media for code recommendation

Modern Q&A websites, such as Stack Overflow, use social media to provide concise answers, and offer rich technical context with quality assessment capabilities. Although some of the answers may include executable code snippets, they are entangled in free text and are not easily extracted. Q&A websites are not designed for such direct code reuse. We present Example Overflow, a code search and recommendation tool which brings together social media and code recommendation systems. Example Overflow enables crowd-sourced software development by utilizing both textual and social information, which accompany source code on the Web. Its browsing mechanism minimizes the context switch associated with other code search tools. In this paper we describe the development of the tool, provide preliminary evaluation, and discuss its contribution to an example centric programming paradigm.
Inter-enterprise contract architecture for open distributed systems: security requirements

An important element of electronic inter-enterprise interactions is support for a rapid and cost-effective establishment of contracts, monitoring of parties' performance to the contract and possible enforcement capability. We have previously developed a business contract architecture to address these requirements. This paper presents an extension of the earlier work. The concept of binding is used to describe the interactions between the components of the contract architecture so that standard contract sequences can be stored in a public repository for future reuse. Various security requirements of the architecture are identified from the application and distributed infrastructure perspectives. It is then shown how a secure contract architecture can be derived to address these requirements.
Mutations in SUPPRESSOR OF VARIEGATION1, a Factor Required for Normal Chloroplast Translation, Suppress var2-Mediated Leaf Variegation in Arabidopsis[W]

The Arabidopsis thaliana yellow variegated2 (var2) mutant is variegated due to lack of a chloroplast FtsH-like metalloprotease (FtsH2/VAR2). We have generated suppressors of var2 variegation to gain insight into factors and pathways that interact with VAR2 during chloroplast biogenesis. Here, we describe two such suppressors. Suppression of variegation in the first line, TAG-FN, was caused by disruption of the nuclear gene (SUPPRESSOR OF VARIEGATION1 [SVR1]) for a chloroplast-localized homolog of pseudouridine (Ψ) synthase, which isomerizes uridine to Ψ in noncoding RNAs. svr1 single mutants were epistatic to var2, and they displayed a phenotypic syndrome that included defects in chloroplast rRNA processing, reduced chloroplast translation, reduced chloroplast protein accumulation, and elevated chloroplast mRNA levels. In the second line (TAG-IE), suppression of variegation was caused by a lesion in SVR2, the gene for the ClpR1 subunit of the chloroplast ClpP/R protease. Like svr1, svr2 was epistatic to var2, and clpR1 mutants had a phenotype that resembled svr1. We propose that an impairment of chloroplast translation in TAG-FN and TAG-IE decreased the demand for VAR2 activity during chloroplast biogenesis and that this resulted in the suppression of var2 variegation. Consistent with this hypothesis, var2 variegation was repressed by chemical inhibitors of chloroplast translation. In planta mutagenesis revealed that SVR1 not only played a role in uridine isomerization but that its physical presence was necessary for proper chloroplast rRNA processing. Our data indicate that defects in chloroplast rRNA processing are a common, but not universal, molecular phenotype associated with suppression of var2 variegation.
On the Ergodic Capacity of the Wideband MIMO Channel

In the ergodic capacity literature, the majority of results preserve the assumption of a flat-fading Gaussian channel. However, the actual wireless channels in current communication systems are often wideband and therefore time dispersive and frequency selective. In this direction, we study the ergodic capacity of a wideband MIMO channel. Starting from a tapped delay line model for the time domain, the frequency domain model is derived by employing the Fourier transform. However, in both cases the resulting channel matrix is characterised by non- separable correlation amongst the Gaussian blocks. The asymp- totic eigenvalue probability density function and the channel capacity are calculated by specializing a theorem originating in operator-valued free probability. Finally, numerical results are presented to verify the validity of the approach and study the effect of the channel model parameters.