Miracle-dz/UniFAR-FTUs huggingface dataset:
Microfluidic Diffusion-Based Separation and Detection

Most fluids show laminar behavior in miniature flow structures with channel cross-sections below 0.5 mm. Different layers of miscible fluids and particles can flow next to each other in a microchannel without any mixing other than by diffusion. Small particles diffuse faster than larger ones, which allows separation of particles by size. It is possible to design fluidic microchips in which separations, chemical reactions, and calibration-free analytical measurements can be performed directly in very small quantities of complex samples such as whole blood and contaminated environmental samples.
Astroglial Inhibition of NF-κB Does Not Ameliorate Disease Onset and Progression in a Mouse Model for Amyotrophic Lateral Sclerosis (ALS)

Motor neuron death in amyotrophic lateral sclerosis (ALS) is considered a “non-cell autonomous” process, with astrocytes playing a critical role in disease progression. Glial cells are activated early in transgenic mice expressing mutant SOD1, suggesting that neuroinflammation has a relevant role in the cascade of events that trigger the death of motor neurons. An inflammatory cascade including COX2 expression, secretion of cytokines and release of NO from astrocytes may descend from activation of a NF-κB-mediated pathway observed in astrocytes from ALS patients and in experimental models. We have attempted rescue of transgenic mutant SOD1 mice through the inhibition of the NF-κB pathway selectively in astrocytes. Here we show that despite efficient inhibition of this major pathway, double transgenic mice expressing the mutant SOD1G93A ubiquitously and the dominant negative form of IκBα (IκBαAA) in astrocytes under control of the GFAP promoter show no benefit in terms of onset and progression of disease. Our data indicate that motor neuron death in ALS cannot be prevented by inhibition of a single inflammatory pathway because alternative pathways are activated in the presence of a persistent toxic stimulus.
Comparison of Solubilization Capacity of Resveratrol in Sodium 3α,12α-Dihydroxy-7-oxo-5β-cholanoate and Sodium Dodecyl Sulfate

In this study we investigated resveratrol (trans-3,5,4′-trihydroxystilbene) solubilization with sodium 3α,12α-dihydroxy-7-oxo-5β-cholanoate (S7-OD) and sodium dodecyl sulfate (SDS). The investigation was aimed at determining whether large spherical micelles (SDS) or small longitudinal micelles (S7-OD) are more convenient for incorporation of resveratrol. Also, we studied resveratrol behavior in mixed micelles with mentioned surfactants using spectroflourimetric method as well as the effects of sodium chloride and urea on resveratrol solubilization capacity in the applied surfactants. Resveratrol solubilization curve was different in the investigated surfactants. Resveratrol solubilization curve for sodium 3α,12α-dihydroxy-7-oxo-5β-cholanoate at concentration 0.9 CMC reached saturation level of 60% dissolved resveratrol. The curve for sodium dodecyl sulfate was linear within the whole range of the investigated concentration; resveratrol solubilization rate reached 13% at 2 CMC. In S7-OD, NaCl increased capacity of resveratrol solubilization up to 1.4 CMC surfactant concentration, whilst maximum level of dissolved resveratrol (90%) was observed at 0.9 CMC. In SDS, NaCl decreased resveratrol solubilization capacity. Urea reduced resveratrol solubilization rate in sodium 3α,12α-dihydroxy-7-oxo-5β-cholanoate, whereas it had inverse effect in sodium dodecyl sulfate. The obtained results strongly suggest that structure, that is, shape, of the surfactant micelles significantly affects their capacity of resveratrol solubilization. Also, presence of NaCl and urea influences solubilization capacities of investigated surfactants.
The relationship of nonalcoholic fatty liver disease and metabolic syndrome for colonoscopy colorectal neoplasm

Abstract Colorectal neoplasm is considered to have a strong association with nonalcoholic fatty liver disease (NAFLD) and metabolic syndrome (MetS), respectively. The relationship among NAFLD, MetS, and colorectal neoplasm was assessed in 1793 participants. Participants were divided into 4 groups based on the status of NAFLD and MetS. Relative excess risks of interaction (RERI), attributable proportion (AP), and synergy index (SI) were applied to evaluate the additive interaction. NAFLD and MetS were significantly correlated with colorectal neoplasm and colorectal cancer (CRC), respectively. The incidence of CRC in NAFLD (+) MetS (+) group was significantly higher than other 3 groups. The result of RERI, AP, and SI indicated the significant additive interaction of NAFLD and MetS on the development of CRC. NAFLD and MetS are risk factors for colorectal neoplasm and CRC, respectively. And NAFLD and MetS have an additive effect on the development of CRC.
Scheduling support for concurrency and parallelism in the Mach operating system

The shared use of general-purpose uniprocessors is examined. Support for common uniform-memory-access architectures that have all memory equidistant from all processors in terms of access time is emphasized. This work is also applicable to non-uniform-memory-access machines, whose memory access times depend on the physical distance between the processor and the accessed memory, but it does not provide a complete solution to load-balancing problems for this class of machine. The discussion covers time-sharing scheduling, the Mach scheduler, programming models, scheduling concurrency support, processor allocation, and related work. <<ETX>>
On the Development and Identification of Phenomenological Damage Models - Application to Industrial Wire Drawing and Rolling Processes

The continuum thermodynamics-based Lemaitre damage model is nowadays widely used to deal with coupled damage analyses for various mechanical applications (e.g. forming process simulations). However, such a model, which only accounts for the stress triaxiality (the ratio between the first and the second invariants of stress tensor) has been found to give incorrect results under shear dominated loading (in terms of damage location as well as risk of crack). Several recent studies have demonstrated the importance of the third stress invariant in damage prediction; the Lode angle parameter is generally used to include it. The idea is to describe completely the stress state in damage model’s formulations, which is defined by the equivalent stress, the stress triaxiality ratio and the Lode angle parameter. This later parameter has proved to have an important influence on ductile damage under low stress triaxiality. Xue’s coupled damage model accounts for the third invariant of the deviatoric stress tensor, allowing a better balance between respective effects of shear and elongation on damage. Some extensions of more physically based damage models, such as the Gurson-Tvergaard-Needleman model, have also been presented to account for this influence of the third stress invariant. In the present work, the phenomenological damage models have been implemented in Forge® Finite Element (FE) software to investigate ductile damage occurring during industrial forming processes. This paper presents the comparative study of Xue’s model and Lemaitre’s model. A complete procedure is detailed to identify the material and damage parameters from experimental mechanical tests on high carbon steel. This identification process has been carried out both for Lemaitre’s coupled damage model and Xue’s coupled damage model. Application to wire drawing followed by flat rolling shows that in such shear-inducing processes, these models predict damage at different locations, due to their different emphasis on shear with respect to elongational strain damage.
MICROSCOPIC STUDY OF ICE PROPAGATION IN CONCRETE

This paper introduces a new procedure to examine ice formation and propagation in concrete. The technique, using the concept of "directional solidification," allows the controlled cooling and warming of relatively large specimens and also permits continuous monitoring of the solid/liquid interface. An experimental program was initiated to study ice formation in the following materials: ionic solutions, normal and lightweight aggregate, cement paste, and concrete. The study reveals that, generally, ice does not completely fill up the pores in cement paste and supercooled water always exists due to the alkalinity of cement paste. The velocity of ice propagation differs in various components of concrete, and ice propagation in aggregate particles is faster than that in the matrix. Sequential images of ice formation in air-entrained voids give insight into the freezing mechanism of concrete.
Restless legs syndrome in multiple sclerosis: A case‐control study

The aim of our study was to explore restless legs syndrome (RLS) frequency in multiple sclerosis (MS)‐patients and establish whether RLS could be a symptom of MS. Over a period of 1 year, we consecutively enrolled 202 MS‐patients and 212 healthy controls, matched for sex and age, in a case‐control study. All of them filled in a structured questionnaire according to IRLSSG criteria. Those patients who fit the diagnostic criteria were subsequently examined by a neurologist to verify the effective presence of RLS. A total of 91 MS‐patients (45%) responded positively to the questionnaires. The diagnosis of RLS was carried out in 29subjects (14.4%). Among the healthy controls, a definite diagnosis of RLS was achieved only in 6 subjects (2.8%). The risk of MS patients to present RLS was significantly higher (OR.5.76 P:0.00002) than the general population. None of them was affected by other medical conditions related to RLS developing. The 62 remaining patients presented numbness and weakness of the legs not suggestive of RLS. Our findings confirm a significant correlation between MS and RLS. In our opinion, MS must be definitively included among RLS causes. © 2008 Movement Disorder Society
Dimensionality of the Short Form of the Beck Depression Inventory: A Study with Iranian College Students

The abridged form of the Beck Depression Inventory was administered to 537 Iranian college students in the United States and in Iran. The results of factor analysis for students in Iranian colleges were similar to those in the United States. The rotated factor pattern of the combined data indicated two dimensions (negative self-view and physical withdrawal) embedded in the inventory that were similar to those reported by the author of the scale.
T2*-sensitized high-resolution magnetic resonance venography using 3D-PRESTO technique.

PURPOSE We evaluated the ability of the PRESTO (principles of echo shifting with a train of observations) technique to reveal small veins and microbleeds in the human brain. MATERIALS AND METHODS In an experimental study, we calculated contrast-to-noise ratio (CNR) between a cerebral parenchymal phantom and human venous blood using 3 sequences of 3-dimensional (3D)-PRESTO, 3D-gradient recalled echo (GRE), and 3D-GRE echo-planar imaging (EPI). Then, we examined 7 healthy volunteers and 5 patients with venous angiomas or traumatic brain injuries using the 3D-PRESTO technique. In volunteer studies, MR venographies were reconstructed from 10-mm, 15-mm, and 20-mm thickness data using the minimum-intensity-projection (MinIP) technique. Three radiologists identified deep brain venous anatomy and counted the visible left medullary veins. In clinical studies, we evaluated the lesion conspicuity of small venous diseases and microbleeds. RESULTS In the phantom study, 3D-PRESTO showed the highest CNR. In all volunteer studies, the deep brain venous anatomy was readily identified in the MinIP images at each thickness. The mean numbers of counted left medullary veins were 5.1 for 10 mm, 5.9 for 15 mm, and 6.7 for 20 mm in the MinIP images. The difference was significant between 10-mm and 20-mm MinIP images (P=0.02). In patient studies, abnormal small veins and microbleeds were clearly revealed. CONCLUSION High-resolution MR venography using 3D-PRESTO technique can clearly depict small veins and microbleeds in the human brain.
Preference based Filtering and Recommendations for Running Routes

With the current trend of fitness and health tracking and quantified self, hundreds of relevant apps and devices are being released to the consumer market. Remarkably, some platforms were created to collect running-route data from these different sources in order to provide a better value for users. Such data could be employed in finding running routes based on the user’s preferences rather than being limited to the proximity to the user’s location. In this work, a classification system for running routes is introduced considering performance factors, visual factors and the nature of route. A running-route content-based recommender system is built on top of this classification enabling learning user preferences from their performance history. The system was evaluated using data from active runners and attained a promising recommendation accuracy averaging 84% among all subject users.
Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age

Differentiating pluripotent cells from fibroblast progenitors is a potentially transformative tool in personalized medicine. We previously identified relatively greater success culturing dura-derived fibroblasts than scalp-derived fibroblasts from postmortem tissue. We hypothesized that these differences in culture success were related to epigenetic differences between the cultured fibroblasts by sampling location, and therefore generated genome-wide DNA methylation and transcriptome data on 11 intrinsically matched pairs of dural and scalp fibroblasts from donors across the lifespan (infant to 85 years). While these cultured fibroblasts were several generations removed from the primary tissue and morphologically indistinguishable, we found widespread epigenetic differences by sampling location at the single CpG (N=101,989), region (N=697), “block” (N=243), and global spatial scales suggesting a strong epigenetic memory of original fibroblast location. Furthermore, many of these epigenetic differences manifested in the transcriptome, particularly at the region-level. We further identified 7,265 CpGs and 11 regions showing significant epigenetic memory related to the age of the donor, as well as an overall increased epigenetic variability, preferentially in scalp-derived fibroblasts -83% of loci were more variable in scalp, hypothesized to result from cumulative exposure to environmental stimuli in the primary tissue. By integrating publicly available DNA methylation datasets on individual cell populations in blood and brain, we identified significantly increased inter-individual variability in our scalp- and other skin-derived fibroblasts on a similar scale as epigenetic differences between different lineages of blood cells. Lastly, these epigenetic differences did not appear to be driven by somatic mutation – while we identified 64 probable de-novo variants across the 11 subjects, there was no association between mutation burden and age of the donor (p=0.71). These results depict a strong component of epigenetic memory in cell culture from primary tissue, even after several generations of daughter cells, related to cell state and donor age.
Investigation of the Galvanic Mechanism for Localized Carbon Dioxide Corrosion Propagation Using the Artificial Pit Technique

Abstract Localized carbon dioxide (CO2) corrosion is the most dangerous type of internal corrosion to mild steel pipelines in the oil and gas industry since the penetration rate of localized corrosion can be one or more magnitudes higher than that of uniform corrosion. In this study, the focus is on propagation of localized CO2 corrosion on mild steel that occurs by a galvanic mechanism. A galvanic cell is established by the coupling of two distinct areas in a conductive CO2 solution: a bare steel surface and an iron carbonate (FeCO3) layer-covered steel surface. It was found that localized CO2 corrosion propagates when a stable difference in corrosion potential is established between the anode (bare steel surface) and the cathode (FeCO3-covered surface). Stable propagation will occur only when the conditions are in the “gray zone,” i.e., close to saturation with respect to FeCO3, when no significant FeCO3 dissolution nor precipitation is expected. Practically, this corresponds to when FeCO3 supersaturati.
Spectral Analysis of Accelerometry Signals From a Directed-Routine for Falls-Risk Estimation

Injurious falls are a prevalent and serious problem faced by a growing elderly population. Accurate assessment and long-term monitoring of falls-risk could prove useful in the prevention of falls, by identifying those at risk of falling early so targeted intervention may be prescribed. Previous studies have demonstrated the feasibility of using triaxial accelerometry to estimate the risk of a person falling in the near future, by characterizing their movement as they execute a restricted sequence of predefined movements in an unsupervised environment, termed a directed routine. This study presents an improvement on this previously published system, which relied explicitly on time-domain features extracted from the accelerometry signals. The proposed improvement incorporates features derived from spectral analysis of the same accelerometry signals; in particular the harmonic ratios between signal harmonics and the fundamental frequency component are used. Employing these additional frequency-domain features, in combination with the previously reported time-domain features, an increase in the observed correlation with the clinical gold-standard risk of falling, from ρ = 0.81 to ρ = 0.96, was achieved when using manually annotated event segmentation markers; using an automated algorithm to segment the signals gave corresponding results of ρ = 0.73 and ρ = 0.99, before and after the inclusion of spectral features. The strong correlation with falls-risk observed in this preliminary study further supports the feasibility of using an unsupervised assessment of falls-risk in the home environment.
Exploring human activity annotation using a privacy preserving 3D model

Annotating activity recognition datasets is a very time consuming process. Using lay annotators (e.g. using crowd-sourcing) has been suggested to speed this up. However, this requires to preserve privacy of users and may preclude relying on video for annotation. We investigate to which extent using a 3D human model animated from the data of inertial sensors placed on the limbs allows for annotation of human activities. We animate the upper body of the 3D model with the data from 5 inertial measurement sensors obtained from the OPPORTUNITY dataset. The animated model is shown to 6 people in a suite of experiments in order to understand to which extent it can be used for labelling. We present 3 experiments where we investigate the use of a 3D model for i) activity segmentation, ii) for "open-ended" annotation where users freely describe the activity they see on screen, and iii) traditional annotation, where users pick one activity among a pre-defined list of activities. In the latter case, results show that users recognise the model's activities with 56% accuracy when picking from 11 possible activities.
Kinetics of the CRISPR-Cas9 effector complex assembly and the role of 3′-terminal segment of guide RNA

CRISPR-Cas9 is widely applied for genome engineering in various organisms. The assembly of single guide RNA (sgRNA) with the Cas9 protein may limit the Cas9/sgRNA effector complex function. We developed a FRET-based assay for detection of CRISPR–Cas9 complex binding to its targets and used this assay to investigate the kinetics of Cas9 assembly with a set of structurally distinct sgRNAs. We find that Cas9 and isolated sgRNAs form the effector complex efficiently and rapidly. Yet, the assembly process is sensitive to the presence of moderate concentrations of non-specific RNA competitors, which considerably delay the Cas9/sgRNA complex formation, while not significantly affecting already formed complexes. This observation suggests that the rate of sgRNA loading into Cas9 in cells can be determined by competition between sgRNA and intracellular RNA molecules for the binding to Cas9. Non-specific RNAs exerted particularly large inhibitory effects on formation of Cas9 complexes with sgRNAs bearing shortened 3′-terminal segments. This result implies that the 3′-terminal segment confers sgRNA the ability to withstand competition from non-specific RNA and at least in part may explain the fact that use of sgRNAs truncated for the 3′-terminal stem loops leads to reduced activity during genomic editing.
Algorithms for limited-view computed tomography: an annotated bibliography and a challenge.

In many applications of computed tomography, it may not be possible to acquire projection data at all angles, as required by the most commonly used algorithm of convolution backprojection. In such a limited-data situation, we face an ill-posed problem in attempting to reconstruct an image from an incomplete set of projections. Many techniques have been proposed to tackle this situation, employing diverse theories such as signal recovery, image restoration, constrained deconvolution, and constrained optimization, as well as novel schemes such as iterative object-dependent algorithms incorporating a priori knowledge and use of multispectral radiation. We present an overview of such techniques and offer a challenge to all readers to reconstruct images from a set of limited-view data provided here.
In vivo Survivors of Transformed Mouse Ovarian Surface Epithelial Cells Display Diverse Phenotypes for Gene Expression and Tumorigenicity

Ovarian cancer is the fifth most common cause of cancer death in women. Due to a lack of appropriate animal models, studies involving tumorigenicity, tumor progression and immune response at the molecular level are limited. We isolated many clones derived from thesurvivors of a transformed mouse ovarian epithelial cell line IG-10 in immune- competent mice and found that the clones displayed diverse phenotypes. Most clones were deficient in components of the MHC-I antigen presentation pathway. Soft-agarose colony assays showed different growth rates among clones. However, this did not completely correlate with each clone’s in vivo tumorigenicity regarding growth, tumor mass and ascites formation, suggesting the possibility that the clones may display contrasting intrinsic gene expression. We therefore performed two types of arrays to evaluate gene expression at transcriptional and translational levels. The results showed differences in expression of COL4α5, NOS-2, and SOCS-1 genes at the transcriptional level, MIP-2 gene at the protein level and CCL5, CXCL-10, IL-1α genes at both transcriptional and protein levels between low and high tumorigenic clones. Thus, our animal cell model together with the identified genes may provide a useful tool to study ovarian cancer immune response, tumorigenicity and tumor-host cell interactions in the tumor microenvironment.
The era of big spatial data

The recent explosion in the amount of spatial data calls for specialized systems to handle big spatial data. In this paper, we discuss the main features and components that needs to be supported in a system to handle big spatial data efficiently. We review the recent work in the area of big spatial data according to these four components, namely, language, indexing, query processing, and visualization. We describe each component, in details, and give examples of how it is implemented in existing work. After that, we describe a few case studies of systems for big spatial data and show how they support these four components. This assists researchers in understanding the different design approaches and highlights the open research problems in this area. Finally, we give examples of real applications that make use of these systems to handle big spatial data.