Miracle-dz/UniFAR-FTUs huggingface dataset:
Western blot analysis of BK channel β1‐subunit expression should be interpreted cautiously when using commercially available antibodies

Large conductance Ca2+‐activated K+ (BK) channels consist of pore‐forming α‐ and accessory β‐subunits. There are four β‐subunit subtypes (β1–β4), BK β1‐subunit is specific for smooth muscle cells (SMC). Reduced BK β1‐subunit expression is associated with SMC dysfunction in animal models of human disease, because downregulation of BK β1‐subunit reduces channel activity and increases SMC contractility. Several anti‐BK β1‐subunit antibodies are commercially available; however, the specificity of most antibodies has not been tested or confirmed in the tissues from BK β1‐subunit knockout (KO) mice. In this study, we tested the specificity and sensitivity of six commercially available antibodies from five manufacturers. We performed western blot analysis on BK β1‐subunit enriched tissues (mesenteric arteries and colons) and non‐SM tissue (cortex of kidney) from wild‐type (WT) and BK β1‐KO mice. We found that antibodies either detected protein bands of the appropriate molecular weight in tissues from both WT and BK β1‐KO mice or failed to detect protein bands at the appropriate molecular weight in tissues from WT mice, suggesting that these antibodies may lack specificity for the BK β1‐subunit. The absence of BK β1‐subunit mRNA expression in arteries, colons, and kidneys from BK β1‐KO mice was confirmed by RT‐PCR analysis. We conclude that these commercially available antibodies might not be reliable tools for studying BK β1‐subunit expression in murine tissues under the denaturing conditions that we have used. Data obtained using commercially available antibodies should be interpreted cautiously. Our studies underscore the importance of proper negative controls in western blot analyses.
Engineering Muscle Networks in 3D Gelatin Methacryloyl Hydrogels: Influence of Mechanical Stiffness and Geometrical Confinement

In this work, the influence of mechanical stiffness and geometrical confinement on the 3D culture of myoblast-laden gelatin methacryloyl (GelMA) photo-crosslinkable hydrogels was evaluated in terms of in vitro myogenesis. We formulated a set of cell-laden GelMA hydrogels with a compressive modulus in the range 1 ÷ 17 kPa, obtained by varying GelMA concentration and degree of cross-linking. C2C12 myoblasts were chosen as the cell model to investigate the supportiveness of different GelMA hydrogels toward myotube formation up to 2 weeks. Results showed that the hydrogels with a stiffness in the range 1 ÷ 3 kPa provided enhanced support to C2C12 differentiation in terms of myotube number, rate of formation, and space distribution. Finally, we studied the influence of geometrical confinement on myotube orientation by confining cells within thin hydrogel slabs having different cross sections: (i) 2,000 μm × 2,000 μm, (ii) 1,000 μm × 1,000 μm, and (iii) 500 μm × 500 μm. The obtained results showed that by reducing the cross section, i.e., by increasing the level of confinement—myotubes were more closely packed and formed aligned myostructures that better mimicked the native morphology of skeletal muscle.
Acceptance of Disability and the Risk of Frailty*

Background The objectives are to determine if: 1) accepting disability as a part of aging is associated with frailty; and 2) accepting disability is associated with becoming frail over a five-year period. Methods Secondary analysis of a prospective cohort study of 1,751 community-dwelling adults aged 65+. Participants were asked to rate their agreement with the statement: “When you reach my age, you have to accept a fair degree of discomfort and physical disability” on a five-point scale. Frailty was categorized as not frail or frail. The sample was re-interviewed five years later. Results The mean age was 75.5 years, 62.3% were women, and the mean education was 10.2 years. Accepting disability as a part of aging was strongly associated with frailty at time 1; the unadjusted Odds Ratio (OR) and 95% confidence interval (CI) was 1.47 (1.25, 1.72) and this association persisted after adjusting for confounding factors. Accepting disability was also associated with becoming frail; the unadjusted OR and 95% CI was 1.51 (1.20, 1.90), and this association also persisted after adjusting for potential confounding factors. Conclusions Accepting disability as a part of aging is associated with being frail and becoming frail.
Think before you Act! Minimising Action Execution in Wrappers

Web wrappers access databases hidden in the deep web by first interacting with web sites by, e.g., filling forms or clicking buttons, to extract the relevant data from the thus unearthed result pages. Though the (semi-)automatic induction and maintenance of such wrappers has been extensively studied, the efficient execution and optimization of wrappers has seen far less attention. We demonstrate that static and adaptive optimisation techniques, as used for query languages, significantly improve the wrapper execution performance. At the same time, we highlight difference between wrapper optimisation and common query optimisation for databases: (1) The runtime of wrappers is entirely dominated by page loads, while other operations (such as querying DOMs) have almost no impact, requiring a new cost model to guide the optimisation. (2) While adaptive query planning is otherwise often considered inessential, wrappers need to be optimised during runtime, since crucial information on the structure of the visited pages becomes only accessible at runtime. We introduce two basic, but highly effective optimisation techniques, one static, one adaptive, and show that they can easily cut wrapper evaluation time by one order of magnitude. We demonstrate our approach with wrappers specified in OXPath.
Relational Gaussian Processes for Learning Preference Relations

Preference learning has received increasing attention in both machine learning and information retrieval. The goal of preference learning is to automatically learn a model to rank entities (e.g., documents, webpages, products, music, etc.) according to their degrees of relevance. The particularity of preference learning might be that the training data is a set of pairwise preferences between entities, instead of explicit entity-wise values. For example, we may only know that a user prefers an item to another one ei ≻ ej , but we do not know the exact preference degrees of items.
Method for visualizing undone operations based on changes on desktop screen

The undo operation of graphical user interfaces is widely used. However, conventional implementations of undo have two problems: 1) users may not notice undone parts since the operation is instantaneous, and 2) it is difficult to know the undone contents if the user temporarily interrupts a work the user works on multiple operations in parallel. Although there have been several methods developed that improve undo operations, they are for specific applications. Here, we devised a visualization for undone operations that, is independent of the running applications and based on the idea that an undo operation causes display to change. Our method specifies the area affected by the undo operation by screens. We implementedseveral visualization methods including emphasizing the undone area, presenting the undone content, and notifying the user that the undone is not visible.
Deadlock-free joins in DB-mesh, an asynchronous systolic array accelerator

Previous database accelerator proposals such as the Q100 provide a fixed set of database operators, chosen to support a target query workload. Some queries may not be well-supported by a fixed accelerator, typically because they need more resources/operators of a particular kind than the accelerator provides. By Amdahl's law, these queries become relatively more expensive as they are not fully accelerated. We propose a second-level accelerator, DB-Mesh, to take up some of this workload. DB-Mesh is an asynchronous systolic array that is more generic than the Q100, and can be configured to run a variety of operators with configurable parameters such as record widths. We demonstrate DB-Mesh applied to nested loops joins, an operator that is not directly supported on the Q100. We show that a naïve implementation has the potential for deadlock, and show how to avoid deadlock with a careful design. We also demonstrate how the data flow policy used in the array influences system throughput.
Mobile Sensing Towards Context Awareness

In recent years, mobile technologies suffered a great development and became increasingly widespread, creating new opportunities and challenges to a large variety of areas, namely mobile sensing. Mobile sensing is an interesting and recent research topic, as nowadays mobile devices are used not only for communicating, but also for accessing the Internet, purchasing goods, exchanging information, and organizing our everyday life. In addition to continuously providing connectivity through multiple wireless interfaces (e.g. 3G, Wi-Fi, and Bluetooth), these devices also integrate various types of sensors, from microphones and cameras to accelerometers and positioning systems (GPS), allowing to capture useful real-time information about the user’s context. Therefore, the main goal of this work is to use that data and develop advanced algorithms for context estimation, inference and prediction, in order to provide the user with content tailored to his context, current activity, and preferences.
Assessment of the airway alterations by means of a fractal ladder network model

Abstract Ladder network models have been successfully employed to assess electrical and mechanical properties in tissue engineering applications, showing phase-locking features of fractal structures. In this study, we simulate an anatomically-based fractal mechanical model of the airways in the 0.016–1.6 Hz frequency range to understand how the phase is affected by structural changes in the airways. With concepts from the non-rigid wall framework, airway geometry and wall structure are included in the model. We found that variations in constriction and heterogeneity led to variations in the stress-strain relation and in the elastic modulus of the airway tissue. The results indicate that constriction plays the dominant role in the stress-strain context, while heterogeneity prevalently affects the elastic modulus. Additionally, we show that a lumped parameter fractional-orders model can capture the frequency dependence of the elastic modulus.
Mutual Exclusion between Fungal Species of the Fusarium Head Blight Complex in a Wheat Spike

ABSTRACT Fusarium head blight (FHB) is one of the most damaging diseases of wheat. FHB is caused by a species complex that includes two genera of Ascomycetes: Microdochium and Fusarium. Fusarium graminearum, Fusarium culmorum, Fusarium poae, and Microdochium nivale are among the most common FHB species in Europe and were chosen for these experiments. Field studies and surveys show that two or more species often coexist within the same field or grain sample. In this study, we investigated the competitiveness of isolates of different species against isolates of F. graminearum at the scale of a single spike. By performing point inoculations of a single floret, we ensured that each species was able to establish independent infections and competed for spike colonization only. The fungal colonization was assessed in each spike by quantitative PCR. After establishing that the spike colonization was mainly downwards, we compared the relative colonization of each species in coinoculations. Classical analysis of variance suggested a competitive interaction but remained partly inconclusive because of a large between-spike variance. Further data exploration revealed a clear exclusion of one of the competing species and the complete absence of coexistence at the spike level.
Costs and effectiveness of community postnatal support workers: randomised controlled trial

Abstract Objectives: To establish the relative cost effectiveness of postnatal support in the community in addition to the usual care provided by community midwives. Design: Randomised controlled trial with six month follow up. Setting: Recruitment in a university teaching hospital and care provided in women's homes. Participants: 623 postnatal women allocated at random to intervention (311) or control (312) group. Intervention: Up to 10 home visits in the first postnatal month of up to three hours duration by a community postnatal support worker. Main outcome measure: General health status as measured by the SF-36 and risk of postnatal depression. Breast feeding rates, satisfaction with care, use of services, and personal costs. Results: At six weeks there was no significant improvement in health status among the women in the intervention group. At six weeks the mean total NHS costs were £635 for the intervention group and £456 for the control group (P=0.001). At six months figures were £815 and £639 (P=0.001). There were no differences between the groups in use of social services or personal costs. The women in the intervention group were very satisfied with the support worker visits. Conclusions: There was no health benefit of additional home visits by community postnatal support workers compared with traditional community midwifery visiting as measured by the SF-36. There were no savings to the NHS over six months after the introduction of the community postnatal support worker service.
Evidence of Social Understanding Impairment in Patients with Amyotrophic Lateral Sclerosis

The present study aims at clarifying the nature of the Theory of Mind (ToM) deficits associated with Amyotrophic Lateral Sclerosis (ALS). ToM is the ability to attribute mental states such as intentions and beliefs to others in order to understand and predict their behaviour and to behave accordingly. Several neuroimaging studies reported the prefrontal cortices as the brain region underlying a key ToM ability, i.e. the comprehension of social intentions. Dysfunction of the prefrontal cortices in patients with ALS has been indicated by a range of neuroimaging studies. The frontal syndrome that appears to characterize up to 50% of ALS has been noted to be similar to the profile that characterizes patients with frontotemporal dementia (FTD), a neurodegenerative condition characterised by ToM deficits. In the present paper, we hypothesize that the performance of patients with ALS is significantly worse than healthy controls' performance on tasks requiring the comprehension of social contexts, whereas patients' performance is comparable to healthy controls' performance on tasks not requiring the comprehension of social contexts. To this end, we tested 15 patients with ALS with an experimental protocol that distinguishes between private (non-social) intentions and social intentions. The pattern of results followed the experimental hypothesis: the performance of patients with ALS and healthy controls significantly differed on the comprehension of social context only, with an impairment in patients with ALS. Single case analysis confirmed the findings at an individual level. The present study is the first which has examined and compared the understanding of social and non-social contexts in patients with ALS and shown a specific and selective deficit in the former only. The current findings further support the notion of a continuum of cognitive dysfunction ranging from ALS to FTD, with parallel cognitive profiles in both disorders.
Immune response in progressive multifocal leukoencephalopathy: An overview

Progressive multifocal leukoencephalopathy (PML) is a disease usually ocurring in immunosuppressed patients. By far the most common underlying immunosuppressive illness is the acquired immune deficiency snydrome, accounting for about 85% of PML cases currently seen in clinical practice. PML may occur in patients with deficits in the humoral and/or cellular immune response such as lymphoproliferative diseases, myeloproliferative diseases, carcinomatous diseases and acquired immunodeficiency due to autoimmune diseases and immunosuppressive therapy. The humoral immune response in PML is indicative of a persistent, reactivated infection with a prominent immunoglobulin (lgG) G synthesis to virus protein 1 (VP1). An lgM synthesis in serum is rarely found. In about 76% of PML cases, an intrathecal humoral immune response to recombinant VP1 can be found as compared to only 3.2% in healthy controls. The detection of intrathecally synthesized lgG antibodies to VP1 can be used as an additional diagnostic test for the diagnosis of PML. The magnitude of the intrathecal humoral immune response appears to rise over time and may be associated with a decrease of viral load in cerebrospinal fluid (CSF) and possibly the central nervous system (CNS). Compared to healthy controls, proliferation of peripheral blood mononuclear cells (PBMC) is reduced in PML patients. Immunological studies suggest a general impairment of the Th1-type T-helper cell function of cell-mediated immunity. Furthermore, the appearance of JCV-specific cytotoxic T-lymphocytes appears to be associated with a favorable clinical outcome.
Physical performance and muscular characteristics in different stages of COPD

This study has examined exercise capacity and muscle morphology in patients with different severities of chronic obstructive pulmonary disease (COPD). Twenty‐three patients and 12 healthy matched controls were recruited. Based on the severity of airflow obstruction, patients were divided into two subgroups. Exercise capacity was determined using a 6‐min walk test. Muscle fiber composition, fiber area and number of satellite cells/muscle fiber were determined in muscle biopsies using immunohistochemistry. A progressive decline in exercise capacity was noted with ascending disease severity. Furthermore, a correlation between reduction in exercise capacity and changes in muscle fiber composition was observed in COPD. The group with severe and very severe COPD had a lower proportion of type I and a higher proportion of type IIa fibers compared with the other groups. In severe and very severe COPD, a reduction in fiber area of type IIa fibers was also seen. The number of satellite cells/muscle fiber did not differ between the groups. In conclusion, a decline in exercise capacity occurs already in mild and moderate COPD, indicating that the 6‐min walk test is a reliable indicator of disease severity. Furthermore, changes in skeletal muscle morphology are associated with disease severity while muscle regenerative capacity is not altered.
A Data Partitioning Approach for Parallelizing Rule Based Inferencing for Materialized OWL Knowledge Bases

Materialized knowledge bases perform inferencing when data is loaded into them, so that answering queries is reduced to simple lookup and thus are faster. A major bottleneck of such a system is the inferencing process, which is slow and memory intensive. In this work we examine the problem of speeding up as well as scaling the inferencing process for OWL Knowledge Bases, that employ rule based reasoners. We propose a data partitioning approach for this problem, in which the input data is partitioned into smaller chunks that are then processed independently. We propose a parallel reasoning algorithm and show the correctness of our technique for the class of rule-sets obtained from OWL ontologies. We present two optimizations of this algorithm to further improve the performance. Finally, we present an implementation based on a popular open source tool. In our experiments using a standard OWL benchmark we have observed speedups of upto 18x, on a parallel cluster of 16 processors.
Genomic analysis of P elements in natural populations of Drosophila melanogaster

The Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in their P element composition mate and produce offspring. Despite extensive research on many aspects of P element biology, many questions remain about the genomic basis of variation in P-M dysgenesis phenotypes in natural populations. Here we compare gonadal dysgenesis phenotypes and genomic P element predictions for isofemale strains obtained from three worldwide populations of D. melanogaster to illuminate the molecular basis of natural variation in cytotype status. We show that the number of predicted P element insertions in genome sequences from isofemale strains is highly correlated across different bioinformatics methods, but the absolute number of insertions per strain is sensitive to method and filtering strategies. Regardless of method used, we find that the number of euchromatic P element insertions predicted per strain varies significantly across populations, with strains from a North American population having fewer P element insertions than strains from populations sampled in Europe or Africa. Despite these geographic differences, numbers of euchromatic P element insertions are not strongly correlated with the degree of gonadal dysgenesis exhibited by an isofemale strain. Thus, variation in P element insertion numbers across different populations does not necessarily lead to corresponding geographic differences in gonadal dysgenesis phenotypes. Additionally, we show that pool-seq samples can uncover population differences in the number of P element insertions observed from isofemale lines, but that efforts to rigorously detect differences in the number of P elements across populations using pool-seq data must properly control for read depth per strain. Our work supports the view that euchromatic P element copy number is not sufficient to explain variation in gonadal dysgenesis across strains of D. melanogaster, and informs future efforts to decode the genomic basis of geographic and temporal differences in P element induced phenotypes.
Shape, albedo, and illumination from a single image of an unknown object

We address the problem of recovering shape, albedo, and illumination from a single grayscale image of an object, using shading as our primary cue. Because this problem is fundamentally underconstrained, we construct statistical models of albedo and shape, and define an optimization problem that searches for the most likely explanation of a single image. We present two priors on albedo which encourage local smoothness and global sparsity, and three priors on shape which encourage flatness, outward-facing orientation at the occluding contour, and local smoothness. We present an optimization technique for using these priors to recover shape, albedo, and a spherical harmonic model of illumination. Our model, which we call SAIFS (shape, albedo, and illumination from shading) produces reasonable results on arbitrary grayscale images taken in the real world, and outperforms all previous grayscale “intrinsic image” - style algorithms on the MIT Intrinsic Images dataset.