Miracle-dz/UniFAR-FTUs huggingface dataset:
Pre‐embedding immunolabeling for electron microscopy: An evaluation of permeabilization methods and markers

For scarce antigens or antigens which are embedded in a dense macromolecular structure, on‐section labeling, the first method of choice, is not always successful. Often, the antigen can be localized by immunofluorescence microscopy, usually by a pre‐embedding labeling method. Most of these methods lead to loss of ultrastructural details and, hence, labeling at electron microscope resolution does not add essential information. The scope of this paper is to compare five permeabilization methods for pre‐embedding labelling for electron microscopy. We aim for a method that is easy to use and suitable for routine investigations. For our ongoing work, special attention is given to labeling of the cell nucleus. Accessibility of cytoplasmic and nuclear antigens is monitored with a set of different marker antibodies.
Induction of regulatory T cells by the immunomodulating cytokines α‐melanocyte‐stimulating hormone and transforming growth factor‐β2

Recently, we have reported that the cytokines α‐melanocyte‐stimulating hormone (α‐MSH) and transforming growth factor‐β2 (TGF‐β2) work in synergy to induce the activation of regulatory T (Treg) cells. When we used α‐MSH and TGF‐β2 to generate ocular autoantigen‐specific Treg cells and adoptively transferred them into mice susceptible to experimental autoimmune uveoretinitis (EAU), there was suppression in the incidence and severity of EAU. Specificity to a retinal autoantigen was required for the Treg cells to suppress EAU. When stimulated, these Treg cells produced TGF‐β1, and their production of interferon‐γ, interleukin (IL)‐10, and IL‐4 was suppressed. Also, the Treg cells are suppressed in their proliferative response. Our results demonstrate that α‐MSH with TGF‐β2 induce Treg cells that can subdue a tissue‐specific autoimmune response. This also promotes the possibility of using these immunomodulating cytokines to purposely induce antigen‐specific Treg cells to prevent and suppress autoimmune disease.
The possibilities of X‐ray holographic microscopy *

There has been a great deal of discussion over the past few years on the possibilities of adapting holography to ultra-high-resolution microscopy using X-rays. The main step forward has been the publication by Stroke (1966) of his method of Fourier holography. This has potentially a very high resolving power, provided the necessary conditions can be satisfied. It is of interest to microscopists to examine these conditions, and also to investigate the field of view which can be obtained. The focal depth of holographic techniques is known to be high, owing to their peculiar property of post-focusing in the reconstruction stage. Fig. 1 represents the simplest procedure for taking a Fourier hologram, and has been drawn to bring out the salient points. The generating system (Plane I) is
Profilin 2 promotes migration, invasion, and stemness of HT29 human colorectal cancer stem cells

We investigated the role of profilin 2 in the stemness, migration, and invasion of HT29 cancer stem cells (CSCs). Increased and decreased levels of profilin 2 significantly enhanced and suppressed the self-renewal, migration, and invasion ability of HT29 CSCs, respectively. Moreover, profilin 2 directly regulated the expression of stemness markers (CD133, SOX2, and β-catenin) and epithelial mesenchymal transition (EMT) markers (E-cadherin and snail). CD133 and β-catenin were up-regulated by overexpression of profilin 2 and down-regulated by depletion of profilin 2. SOX2 was decreased by profilin 2 depletion. E-cadherin was not influenced by profilin 2- overexpression but increased by profilin 2- knockdown. The expression of snail was suppressed by profilin 2- knockdown. We speculated that stemness and the EMT are closely linked through profilin 2-related pathways. Therefore, this study indicates that profilin 2 affects the metastatic potential and stemness of colorectal CSCs by regulating EMT- and stemness-related proteins. Graphical abstract Profilin 2 promotes migration, invasion, and stemness by regulating EMT markers and stemness markers in human colorectal cancer stem cells.
Phosphatidylserine and Phosphatidylethanolamine Bind to Protein Z Cooperatively and with Equal Affinity

Protein Z (PZ) is an anticoagulant that binds with high affinity to Protein Z-dependent protease inhibitor (ZPI) and accelerates the rate of ZPI-mediated inhibition of factor Xa (fXa) by more than 1000-fold in the presence of Ca2+ and phospholipids. PZ promotion of the ZPI-fXa interaction results from the anchoring of the Gla domain of PZ onto phospholipid surfaces and positioning the bound ZPI in close proximity to the Gla-anchored fXa, forming a ternary complex of PZ/ZPI/fXa. Although interaction of PZ with phospholipid membrane appears to be absolutely crucial for its cofactor activity, little is known about the binding of different phospholipids to PZ. The present study was conceived to understand the interaction of different phospholipids with PZ. Experiments with both soluble lipids and model membranes revealed that PZ binds to phosphatidylserine (PS) and phosphatidylethanolamine (PE) with equal affinity (Kd~48 μM); further, PS and PE bound to PZ synergistically. Equilibrium dialysis experiments revealed two lipid-binding sites for both PS and PE. PZ binds with weaker affinity to other phospholipids, e.g., phosphatidic acid, phosphatidylglycerol, phosphatidylcholine and binding of these lipids is not synergistic with respect to PS. Both PS and PE -containing membranes supported the formation of a fXa-PZ complex. PZ protection of fXa from antithrombin inhibition were also shown to be comparable in presence of both PS: PC and PE: PC membranes. These findings are particularly important and intriguing since they suggest a special affinity of PZ, in vivo, towards activated platelets, the primary membrane involved in blood coagulation process.
Open source libraries and frameworks for biological data visualisation: A guide for developers

Recent advances in high‐throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories.
Structural Modeling and DNA Binding Autoinhibition Analysis of Ergp55, a Critical Transcription Factor in Prostate Cancer

Background The Ergp55 protein belongs to Ets family of transcription factor. The Ets proteins are highly conserved in their DNA binding domain and involved in various development processes and regulation of cancer metabolism. To study the structure and DNA binding autoinhibition mechanism of Ergp55 protein, we have produced full length and smaller polypeptides of Ergp55 protein in E. coli and characterized using various biophysical techniques. Results The Ergp55 polypeptides contain large amount of α-helix and random coil structures as measured by circular dichorism spectroscopy. The full length Ergp55 forms a flexible and elongated molecule as revealed by molecular modeling, dynamics simulation and structural prediction algorithms. The binding analyses of Ergp55 polypeptides with target DNA sequences of E74 and cfos promoters indicate that longer fragments of Ergp55 (beyond the Ets domain) showed the evidence of auto-inhibition. This study also revealed the parts of Ergp55 protein that mediate auto-inhibition. Significance The current study will aid in designing the compounds that stabilize the inhibited form of Ergp55 and inhibit its binding to promoter DNA. It will contribute in the development of drugs targeting Ergp55 for the prostate cancer treatment.
A behavior-based control architecture

The presented control architecture is designed to support the development of intelligent control systems that are connected to the real world via sensors and actuators, and deal with dynamic and partly unpredictable environments, for instance to control an autonomous mobile robot. With quite an implementational effort, existing control architectures allow us to implement navigation facilities on a certain mobile robot. However, additional criteria that interfere with the navigational movements can usually not be added subsequently. Note that this situation occurs, e.g. if active sensing is requested, a handling device is added or other additional requirements arise. The purpose of the presented architecture is, first to allow easy implementation and second to obtain a modular control system that displays a kind of superposition characteristic. Considering a typical behavior based architecture, we focus on the method to coordinate the different mechanisms. The question is, how to combine commands or preferences of several running mechanisms. In our approach, we solve this merging problem by using a utility based approach. Each mechanism continuously evaluates sensory data with respect to its special sub-task in order to rate all actions of a certain actuator. These ratings result in a utility function, that also includes the priority of the performed sub-task of the mechanism. A fusion component then merges these distributions for each actuator, following a theorem of R.L. Keeny and H. Raiffa (1976).
The SciMED RADIUS™ Stent-Artery Interaction

Main cause of restenosis after balloon angioplasty is due to the stresses generated in the artery as well as from the stent artery interaction. Understanding the factors that are involved in this interaction and the ability to evaluate the stresses that are formed in the artery, could help to lessen the number of failures. The goal of the present study is to develop computationally efficient analytical model for estimating the potential damage factor as the contact stresses, and to investigate their influence upon stent design, artery and plaque parameters. The artery was stipulated to be thick walled cylinder and its stress-strain state was determined from analytic solution of Lame problem. An analytic model based on the analysis of the beams deformation in the framework Euler-Bernoulli assumptions was formulated for the stent. The radial pressure, which is exerted on the inner surface of the artery, is assumed to be an average of contact stresses applied by the stent and the blood pressure. The variation in the Potential Damage Factor value as a function of the mismatch between stent’s and artery’s diameters is linear, and as much as the diameter of the artery increases, the Potential Damage Factor for the same mismatch decreases. For arteries with 75% blocking and mismatch of 1mm, the potential damage factor is 4.5. Copyright © 2008 by ASME
Power Allocation and Feedback Reduction for MIMO-OFDMA Opportunistic Beamforming

MIMO-OFDMA systems using opportunistic beamforming are a promising solution to satisfy the increasing demand in terms of data rate and quality-of-service (QoS). An important practical issue in MIMO-OFDMA systems is the feedback load. As a large number of carriers (e.g. 2048 for WiMax) is usually used in such systems, feeding back full channel state information at the transmitter (CSIT) for each carrier is prohibitive. In this paper, the problem of feedback reduction in MIMO-OFDMA opportunistic beamforming is addressed. We present different partial CSIT schemes that reduce significantly the feedback overload at little expense of system throughput. We additionally investigate different power control strategies that show significant capacity gain for low to moderate number of users over standard opportunistic beamforming approaches
Recent genetic findings in schizophrenia and their therapeutic relevance

Over 100 loci are now associated with schizophrenia risk as identified by single nucleotide polymorphisms (SNPs) in genome-wide association studies. These findings mean that ‘genes for schizophrenia’ have unquestionably been found. However, many questions remain unanswered, including several which affect their therapeutic significance. The SNPs individually have minor effects, and even cumulatively explain only a modest fraction of the genetic predisposition. The remainder likely results from many more loci, from rare variants, and from gene–gene and gene–environment interactions. The risk SNPs are almost all non-coding, meaning that their biological significance is unclear; probably their effects are mediated via an influence on gene regulation, and emerging evidence suggests that some key molecular events occur during early brain development. The loci include novel genes of unknown function as well as genes and pathways previously implicated in the pathophysiology of schizophrenia, e.g. NMDA receptor signalling. Genes in the latter category have the clearer therapeutic potential, although even this will be a challenging process because of the many complexities concerning the genetic architecture and mediating mechanisms. This review summarises recent schizophrenia genetic findings and some key issues they raise, particularly with regard to their implications for identifying and validating novel drug targets.
Learning Transformation Rules to Find Grammatical Relations

Grammatical relationships are an important level of natural language processing. We present a trainable approach to find these relationships through transformation sequences and-error-driven learning. Our approach finds grammatical relationships between core syntax groups and bypasses much of the parsing phase. On our training and test set, our procedure achieves 63.6% recall and 77.3% precision (f-score = 69.8).
An image-based visual servoing scheme for following paths with nonholonomic mobile robots

We present an image-based visual servoing controller enabling nonholonomic mobile robots with a fixed pinhole camera to reach and follow a continuous path on the ground. The controller utilizes only a small set of features extracted from the image plane, without using the complete geometric representation of the path. A Lyapunov-based stability analysis is carried out. The performance of the controller is validated and compared by simulations and experiments on a car-like robot equipped with a pinhole camera.
A study on the structure of the sudoriferous duct traversing the epidermis in man with fresh material by phase contrast microscopy.

1) The lumen of the sudoriferous duct, all along its passage from the surface of the skin to the deepest level of the stratum corneum, is lined by concentrically and epithelially arranged flattened cells, the layers of which are presumably three in number (fig. 1). 2) An additional proof for the fact that the duct in the stratum corneum is a tubular structure with a wall of its own is afforded by an experiment, in which a fairly thick slice taken from the surface of the skin is heated in a solution of caustic potash. The cells constituting the wall of the duct are more resistant than the general cells of the stratum corneum, so that a tubular form remains (fig. 2). 3) In the stratum germinativum, nucleated and epithelially arranged cells, presumably in three layers, surround the lumen of the sudoriferous duct, some of them containing keratohyalin granules in the cytoplasm (fig. 3). 4) The sudoriferous duct in the corium has an epithelium consisting definitely of three layers of cells. The innermost layer is made up of cuboidal cells, while the outer two layers are constituted by more flattened cells. All the cell layers are continued, without any observable change in arrangement and character of cells, to those of the sudoriferous duct in the stratum germinativum. Hence, it is assumed that the cell layers of the duct in the stratum germinativum and at the upper levels of the epidermis are also three in number, although this is obscured by the circumstances that the neighboring epidermal cells are flattened by pressure and so deformed to appear as if they form more layers of cells over the proper wall of the duct (fig. 4). 5) The duct in the epidermis is thought to be continually regenerated by multiplication of its cells presumably at the deeper levels of the stratum germinativum. The duct cells, as they reach the upper levels of the epidermis, undergo keratinization, which is more precocious than in the epidermal cells at the same level. Moreover, the innermost layer of them precedes the outer two layers in that process.
Revisiting the impact of phenylephrine hydrochloride on static and dynamic accommodation

Purpose: Phenylephrine hydrochloride (PHCl), a commonly used mydriatic agent, causes a small but significant deterioration of accommodation. The relative roles of pharmacology and optics in this deterioration, however, remain unascertained. The study determined the combined impact of PHCl concentration (pharmacology) and pupil size (optics) on the static and dynamic characteristics of accommodation. Materials and Methods: A total of 16 emmetropic Indian adults viewed a high-contrast visual target that switched between 67 and 33 cm viewing distance (1.5D stimulus) with their right eye (left eye occluded using infrared transmitting filter) through natural pupils and through 8, 6, 4, and 1 mm diameter artificial pupils. This protocol was repeated once without PHCl and once each with 2.5%, 5%, and 10% PHCl. Consensual accommodation of the left eye was recorded using infrared photorefraction (60 Hz). Results: Relative to no PHCl, the horizontal pupil diameter of left eye was significantly larger (P < 0.001) and the response magnitude and peak velocity of accommodation and disaccommodation were modestly but significantly smaller (P < 0.02 for all) for all concentrations of PHCl tested. There was no significant difference in these parameters across the three drug concentrations (P > 0.4 for all). The response magnitude and peak velocity also decreased significantly with pupil diameter, at similar rates for the no PHCl and the three PHCl conditions (P < 0.001 for all). Conclusion: The reduction in accommodative performance with all drug concentrations and with pupil diameter suggests independent roles of pharmacology and optics in determining accommodative performance with PHCl. The reduction in accommodative performance is, however, modest and may be clinically irrelevant in Indian eyes.
The Arabidopsis D-type Cyclins CycD2 and CycD3 Both Interact in Vivo with the PSTAIRE Cyclin-dependent Kinase Cdc2a but Are Differentially Controlled*

D-type cyclins (CycD) play key roles in linking the Arabidopsis cell cycle to extracellular and developmental signals, but little is known of their regulation at the post-transcriptional level or of their cyclin-dependent kinase (CDK) partners. Using new antisera to CycD2 and CycD3, we demonstrate that the CDK partner of these Arabidopsiscyclins is the PSTAIRE-containing CDK Cdc2a. Previous analysis has shown that transcript levels of CycD2 and CycD3are regulated in response to sucrose levels and that both their mRNA levels and kinase activity are induced with different kinetics during the G1 phase of cells reentering the division cycle from quiescence (1). Here we analyze the protein levels and kinase activity of CycD2 and CycD3. We show that CycD3 protein and kinase activity parallel the abundance of its mRNA and that CycD3 protein is rapidly lost from cells in stationary phase or following sucrose removal. In contrast to both CycD3 and the regulation of its own mRNA levels, CycD2 protein is present at constant levels. CycD2 kinase activity is regulated by sequestration of CycD2 protein in a form inaccessible to immunoprecipitation and probably not complexed to Cdc2a.
Effects of moisture content and clothing fit on clothing apparent ‘wet’ thermal insulation: A thermal manikin study

‘Wet’ thermal insulation, defined as the thermal insulation when clothing gets partially or fully wet, is an important physical parameter to quantify clothing thermal comfort. As the water/sweat gradually occupies the intra-yarn and inter-yarn air voids of the clothing material, the clothing intrinsic thermal insulation will be diminished and, hence, contribute to the loss of total insulation. In cold conditions, a loss in total thermal insulation caused by sweating may result in an inadequate thermal insulation to keep thermal balance and eventually leads to the development of hypothermia and cold injuries. Therefore, it is imperative to investigate the effect of clothing fit and moisture content on clothing ‘wet’ insulation. In this study, the ‘wet’ thermal insulation of three two-layer clothing ensembles was determined using a Newton thermal manikin. Four levels of moisture content were added to the underwear: 100, 200, 500 and 700 g. The clothing apparent ‘wet’ thermal insulation under different testing scenarios was calculated and compared. A third-degree polynomial relationship between the reduction in ‘wet’ thermal insulation and the moisture content added to underwear was obtained. Further, it was evident that the clothing fit has a minimal effect on the apparent ‘wet’ thermal insulation. The findings may have important applications in designing and engineering functional cold weather clothing and immersion suits.
Transcriptome Analysis of Arabidopsis thaliana in Response to Plasmodiophora brassicae during Early Infection

Clubroot disease is a serious threat to cruciferous plants worldwide, especially to oilseed rape. However, knowledge on pathogenic molecular mechanisms and host interaction is limited. We presume that the recognition between Arabidopsis thaliana and Plasmodiophora brassicae occurs at the early stage of infection and within a relatively short period. In this study, we demonstrated changes on gene expression and pathways in A. thaliana during early infection with P. brassicae using transcriptome analysis. We identified 1,903 and 1,359 DEGs at 24 and 48 h post-inoculation (hpi), respectively. Flavonoids and the lignin synthesis pathways were enhanced, glucosinolates, terpenoids, and proanthocyanidins accumulated and many hormonal- and receptor-kinase related genes were expressed, caused by P. brassicae infection during its early phase. Therefore, the early interaction between A. thaliana and P. brassicae plays an important role in the entire infection process. The results provide a new contribution to a better understanding of the interaction between host plants and P. brassicae, as well as the development of future measures for the prevention of clubroot.