Miracle-dz/UniFAR-FTUs huggingface dataset:
Size-Invariant Detection of Cell Nuclei in Microscopy Images

Accurate detection of individual cell nuclei in microscopy images is an essential and fundamental task for many biological studies. In particular, multivariate fluorescence microscopy is used to observe different aspects of cells in cultures. Manual detection of individual cell nuclei by visual inspection is time consuming, and prone to induce subjective bias. This makes automatic detection of cell nuclei essential for large-scale, objective studies of cell cultures. Blur, clutter, bleed-through, imaging noise and touching and partially overlapping nuclei with varying sizes and shapes make automated detection of individual cell nuclei a challenging task using image analysis. In this paper we propose a new automated method for fast and robust detection of individual cell nuclei based on their radial symmetric nature in fluorescence in-situ hybridization (FISH) images obtained via confocal microscopy. The main contributions are two-fold. 1) This work presents a more accurate cell nucleus detection system using the fast radial symmetry transform (FRST). 2) The proposed cell nucleus detection system is robust against most occlusions and variations in size and moderate shape deformations. We evaluate the performance of the proposed algorithm using precision/recall rates, Fβ-score and root-mean-squared distance (RMSD) and show that our algorithm provides improved detection accuracy compared to existing algorithms.
Localization of presenilin–nicastrin complexes and γ‐secretase activity to the trans‐Golgi network

Abundant biochemical and genetic evidence suggests that presenilins are catalytic components of γ‐secretase, the protease responsible for generating the Alzheimer amyloid β‐protein. However, the differential localization of presenilins to early secretory compartments and γ‐secretase substrates to late secretory compartments and the plasma membrane (the ‘spatial paradox’) argues against this view. We investigated this issue by studying the localization of nicastrin, another putative γ‐secretase component, and its association with presenilin‐1 into proteolytically active complexes. Glycosidase digests revealed that nicastrin exists in multiple glycoforms and is terminally sialylated, a modification often associated with the trans‐Golgi network. Trafficking of nicastrin to the trans‐Golgi network was confirmed by density gradient fractionation and immunofluorescence microscopy. In presenilin‐deficient cells, however, nicastrin trafficking and maturation were abnormal, as the protein was restricted to early secretory compartments and failed to be sialylated. Mature sialylated nicastrin in trans‐Golgi network fractions was complexed quantitatively with N‐ and C‐terminal fragments of presenilin‐1, whereas immature nicastrin present in early secretory compartments was not. Additionally, trans‐Golgi network fractions contained the γ‐secretase substrate β‐amyloid precursor protein C83 and were enriched in presenilin‐dependent γ‐secretase proteolytic activity. The results resolve the apparent spatial paradox by demonstrating that presenilin–nicastrin complexes and presenilin‐dependent γ‐secretase activity are co‐localized to a late secretory compartment. The findings provide further evidence that presenilin‐containing complexes are the γ‐secretase, and indicate that presenilins also regulate γ‐secretase assembly.
Production of unique immunotoxin cancer therapeutics in algal chloroplasts

The idea of targeted therapy, whereby drug or protein molecules are delivered to specific cells, is a compelling approach to treating disease. Immunotoxins are one such targeted therapeutic, consisting of an antibody domain for binding target cells and molecules of a toxin that inhibits the proliferation of the targeted cell. One major hurdle preventing these therapies from reaching the market has been the lack of a suitable production platform that allows the cost-effective production of these highly complex molecules. The chloroplast of the green alga Chlamydomonas reinhardtii has been shown to contain the machinery necessary to fold and assemble complex eukaryotic proteins. However, the translational apparatus of chloroplasts resembles that of a prokaryote, allowing them to accumulate eukaryotic toxins that otherwise would kill a eukaryotic host. Here we show expression and accumulation of monomeric and dimeric immunotoxin proteins in algal chloroplasts. These fusion proteins contain an antibody domain targeting CD22, a B-cell surface epitope, and the enzymatic domain of exotoxin A from Pseudomonas aeruginosa. We demonstrated that algal-produced immunotoxins accumulate as soluble and enzymatically active proteins that bind target B cells and efficiently kill them in vitro. We also show that treatment with either the mono- or dimeric immunotoxins significantly prolongs the survival of mice with implanted human B-cell tumors.
Specific detection of Campylobacter jejuni and Campylobacter coli by using polymerase chain reaction

Development of a routine detection assay for Campylobacter jejuni and Campylobacter coli in clinical specimens was undertaken by using the polymerase chain reaction (PCR). An oligonucleotide primer pair from a conserved 5' region of the flaA gene of C. coli VC167 was used to amplify a 450-bp region by PCR. The primer pair specifically detected 4 strains of C. coli and 47 strains of C. jejuni; but it did not detect strains of Campylobacter fetus, Campylobacter lari, Campylobacter upsaliensis, Campylobacter cryaerophila, Campylobacter butzleri, Campylobacter hyointestinalis, Wolinella recta, Helicobacter pylori, Escherichia coli, Shigella spp. , Salmonella spp. , Vibrio cholerae, Citrobacter freundii, or Aeromonas spp. By using a nonradioactively labeled probe internal to the PCR product, the assay could detect as little as 0.0062 pg of purified C. coli DNA, or the equivalent of four bacteria. In stools seeded with C. coli cells, the probe could detect between 30 and 60 bacteria per PCR assay. The assay was also successfully used to detect C. coli in rectal swab specimens from experimentally infected rabbits and C. jejuni in human stool samples.
Dense, mixed-use, walkable urban precinct to support sustainable transport or vice versa? A model for consideration from Perth, Western Australia

ABSTRACT Within the majority of the literature on sustainable transport, it is accepted as ideal to arrange new urban growth in close proximity to major public transit services. While the literature on this subject of transit-oriented developments (TOD) is positive and optimistic, for the most part such assertions are conjectural. This article will attempt to fill this gap by revealing a modeling process undertaken for a local area's reurbanization project to understand the potential and limitations of several modes of transport to support the increased activity density in the precincts. Several of the most standardized policy levers were employed, such as parking ratios and mix of use and building height, and contrasted with the trip generation and transit mode's hourly capacity to reveal potential real-estate yields. The outcomes indicate not only the immediate yields but also the capacity for urban transformation due to each level of sustainable transport investments. The model is unique in that the capacity, parking ratios, and assumptions are highly transparent.
Enzymatic Degradation of Starch Based Thermoplastic Compounds Used in Protheses

Apart from favourable physico-chemical and mechanical properties, the most important requirement for a biodegradable polymer to be used in medical applications is its biocompatibility and the non-cytotoxicity of its degradation products. Their combined effect should assure the safe material degradation under controlled kinetics. The present work analyses the degradation behaviour of blends of corn starch with poly(ethylene-vinyl alcohol) copolymer (SEVA-C). The characterization included long-term degradation trials on simulated physiological solution with alpha-amylase up to 200 days. The degradation solutions were analysed by several techniques. High-performance liquid chromatography (HPLC) and colorimetric methods were used to monitor the liberation of carbohydrate as a consequence of starch hydrolysis by alpha-amylase. The hydration degree was followed by thermogravimetric analysis (TGA). Several degradation products such as carbohydrates ranging from C6 to C18 were identified. After alpha-amylase action, biodegradation was more pronounced in the first 100 days, after which the biodegradation rate decreased probably due to the structure and porosity of the material. The action of alpha-amylase solely led to the starch degradation, in contrast with other assays without enzymes where no carbohydrates were found in the degradation solutions.
Spironolactone and Chlorthalidone in Uncontrolled Elderly Hypertensive Patients Treated with Calcium Antagonists and Angiotensin II Receptor-Blocker: Effects on Endothelial Function, Inflammation, and Oxidative Stress

The side effects of thiazide-type diuretics include metabolic abnormality and increased oxidative stress, which might cause endothelial dysfunction despite blood pressure reduction. In hypertensive patients with heart failure, treatment with an aldosterone antagonist resulted in improvements in endothelial function and significant blood pressure reduction. The purpose of the present study was to evaluate the differences between spironolactione and chlorthalidone in hypertensive elderly patients treated with calcium antagonists and angiotensin II receptor blockers. Fourteen uncontrolled hypertensive patients treated with amlodipine and candesartan were included in this study. The study was an open-label randomized crossover comparison of 16 weeks treatment with spironolactone against chlorthalidone added to amlodipine and candesartan. blood pressure significantly decreased in patients treated with both spironolactone and chlorthalidone. Chlortalidone reduced flowmediated dilation significantly compared to the baseline condition and spironolactone. serum highsensitively C-reactive protein and uric acid increased significantly in chlorthalidone-treated patients compared to spironolactonetreated patients. We conclude that spironolactone may be a more useful add-on therapy than chlorthalidone in hypertensive patients inadequately controlled on candesartan and amlodipine, because spironolactone preserves endothelial function and reduces inflammation compared to chlorthalidone.
Effect of Blast Injury on Auditory Localization in Military Service Members

Objectives: Among the many advantages of binaural hearing are the abilities to localize sounds in space and to attend to one sound in the presence of many sounds. Binaural hearing provides benefits for all listeners, but it may be especially critical for military personnel who must maintain situational awareness in complex tactical environments with multiple speech and noise sources. There is concern that Military Service Members who have been exposed to one or more high-intensity blasts during their tour of duty may have difficulty with binaural and spatial ability due to degradation in auditory and cognitive processes. The primary objective of this study was to assess the ability of blast-exposed Military Service Members to localize speech sounds in quiet and in multisource environments with one or two competing talkers. Design: Participants were presented with one, two, or three topic-related (e.g., sports, food, travel) sentences under headphones and required to attend to, and then locate the source of, the sentence pertaining to a prespecified target topic within a virtual space. The listener’s head position was monitored by a head-mounted tracking device that continuously updated the apparent spatial location of the target and competing speech sounds as the subject turned within the virtual space. Measurements of auditory localization ability included mean absolute error in locating the source of the target sentence, the time it took to locate the target sentence within 30 degrees, target/competitor confusion errors, response time, and cumulative head motion. Twenty-one blast-exposed Active-Duty or Veteran Military Service Members (blast-exposed group) and 33 non-blast-exposed Service Members and beneficiaries (control group) were evaluated. Results: In general, the blast-exposed group performed as well as the control group if the task involved localizing the source of a single speech target. However, if the task involved two or three simultaneous talkers, localization ability was compromised for some participants in the blast-exposed group. Blast-exposed participants were less accurate in their localization responses and required more exploratory head movements to find the location of the target talker. Conclusions: Results suggest that blast-exposed participants have more difficulty than non-blast-exposed participants in localizing sounds in complex acoustic environments. This apparent deficit in spatial hearing ability highlights the need to develop new diagnostic tests using complex listening tasks that involve multiple sound sources that require speech segregation and comprehension.
HIPPOCAMPAL CYTOCHROME OXIDASE ACTIVITY OF RATS IN EASY AND DIFFICULT VISUAL DISCRIMINATION LEARNING

The present study investigated the functional involvement of the rat hippocampal formation in easy and difficult visual discrimination learning by measuring regional brain cytochrome oxidase (C.O.) activity, an index of neuronal metabolic activity. The results showed that learning was related to C.O. activity in the CA field and the dentate gyrus of the hippocampal formation of rats in the difficult discrimination, whereas learning was related to C.O. activity only in the dentate gyrus of rats in the easy discrimination. The results suggest that difficult visual discrimination learning required greater involvement of the hippocampal formation than easy visual discrimination learning.
Knee Stability after Articulated External Fixation

Background Articulated external fixation has been proposed as a method to protect ligament reconstructions while allowing aggressive and early postoperative rehabilitation after knee dislocation. However, the ability of these fixators to protect and stabilize the knee joint has not been clearly determined. Hypothesis Articulated external fixation can reduce anteroposterior translation in the cruciate-deficient knee and reduce cruciate ligament strain in cases of intact or reconstructed ligaments. Study Design Controlled laboratory study. Methods Knee stability was assessed by 3 standard clinical stability tests (Lachman, anterior drawer, and posterior drawer) on 7 human cadaveric lower extremities. Instrumented forces of 100 N were applied to the tibia to measure cruciate ligament forces and tibiofemoral displacement in intact and cruciate-deficient specimens with and without articulated external fixation to determine the degree to which a fixator can protect cruciate ligaments and stabilize the knee. Articulated external fixation was applied using monolateral and bilateral fixators to comparatively analyze the effectiveness of each construct. Statistical analysis was performed using 2-tailed, paired Student t tests. Results Application of the monolateral articulated external fixator to specimens with intact ligaments significantly reduced cruciate ligament forces by 1.0 N (P =. 011), 1.7 N (P =. 046), and 1.4 N (P =. 009) for Lachman, anterior drawer, and posterior drawer tests, respectively. In the cruciate ligament-deficient knees, the application of a monolateral fixator significantly reduced tibiofemoral translation by 49%, 70%, and 46% for Lachman, anterior drawer, and posterior drawer tests, respectively. No significant differences between the monolateral and bilateral fixator frames, in terms of ligament protection and joint stabilization, were observed. Conclusion and Clinical Relevance Articulated external fixation of the knee can reduce stress in the cruciate ligaments after multiligament reconstructions and can decrease anteroposterior translation in the cruciate-deficient knee.
Prospective Mediation Models of Sleep, Pain, and Daily Function in Children With Arthritis Using Ecological Momentary Assessment

Objectives:Sleep is an emerging area of concern in children with juvenile idiopathic arthritis (JIA). Research shows the presence of poor sleep quality and related adverse outcomes in pediatric pain populations, including JIA, but few studies have examined the prospective patterns of association between sleep and associated outcomes. This prospective study evaluated the direction and magnitude of associations between subjective sleep characteristics (sleep quality, difficulty initiating sleep, and sleep duration), pain intensity, and functional limitations in children with JIA. We hypothesized that pain intensity would partially mediate the relationship between sleep and functional limitations. Methods:Children and adolescents with JIA (n=59; age range, 8 to 18 y) recruited during clinic visits, completed smartphone-based diaries for 1 month. Subjective sleep characteristics were reported each morning; pain and functioning were assessed 3 times daily. Results:As hypothesized, the associations between sleep quality and functional limitations and between difficulty initiating sleep and functional limitations were partially mediated by pain intensity, at any given moment (z=−3.27, P=0.001, z=2.70, P<0.05). Mediation was not detected in a model testing the association between sleep duration, pain intensity, and functional limitations (z=−0.58, P=0.56). Discussion:Results suggest that sleep is integral to understanding the momentary association between pain intensity and functioning in children with JIA.
Manipulating the Expression Rate and Enantioselectivity of an Epoxide Hydrolase by Using Directed Evolution

We describe here a strategy to improve the expression efficiency and enantioselectivity of Aspergillus niger epoxide hydrolase (ANEH) by directed evolution. Based on a blue‐colony screening system using the LacZα (β‐galactosidase α peptide) complementation solubility reporter, several ANEH variants out of 15 000 transformants from a random‐mutagenesis library were identified that show improved recombinant expression in E. coli. Among them, Pro221Ser was subsequently used as a template for iterative saturation mutagenesis (ISM) at sites around the ANEH binding pocket. Following four rounds of ISM, a highly enantioselective mutant was identified that catalyzes the hydrolytic kinetic resolution of racemic glycidyl phenyl ether with a selectivity factor of E=160 in favor of the (S)‐diol compared to WT ANEH characterized by E=4.6. Expression of this mutant is 50 times higher than that of WT ANEH. It also serves as an excellent stereoselective catalyst in the hydrolytic kinetic resolution and desymmetrization of several other structurally diverse epoxides.
μ‐Opioid Receptor Ligands Lack Receptor Subtype Selectivity in the Aequorin Luminescence‐based Calcium Assay

The aim of the present study was to characterize the binding selectivity of the μ‐opioid receptor ligands, endomorphin‐1, endomorphin‐2, and DAMGO, in the in vitro functional assay, based on the changes in intracellular calcium levels. For the experiments Chinese hamster ovary cells, stably expressing human μ‐receptor, were used. The μ‐agonist‐induced calcium responses were significantly inhibited by naloxone, an opioid antagonist with high preference for the μ‐opioid receptors. Naloxonazine, a μ1‐non‐peptide antagonist, inhibited the effect of all tested μ‐agonists. However, there was no significant difference in the antagonist effect of naloxonazine on the calcium response induced by μ1‐ (endomorphin‐2) and μ2‐agonists (endomorphin‐1, DAMGO). [d‐Pro2]endomorphin‐1 and [d‐Pro2]endomorphin‐2, putative peptide μ2‐ and μ1‐antagonists, respectively, which had been shown in vivo to inhibit the antinociception induced by μ‐agonists, produced no inhibitory effect in our in vitro experiments. Our results demonstrated that there is only one population of the μ‐opioid receptors expressed in the Chinese hamster ovary cells. We suggest that the μ‐opioid receptors form a homogenous population in the in vitro systems. However, the existence of μ‐receptor subtypes in vivo is still pharmacologically possible.
Microarray analysis of spaceflown murine thymus tissue reveals changes in gene expression regulating stress and glucocorticoid receptors

The detrimental effects of spaceflight and simulated microgravity on the immune system have been extensively documented. We report here microarray gene expression analysis, in concert with quantitative RT‐PCR, in young adult C57BL/6NTac mice at 8 weeks of age after exposure to spaceflight aboard the space shuttle (STS‐118) for a period of 13 days. Upon conclusion of the mission, thymus lobes were extracted from space flown mice (FLT) as well as age‐ and sex‐matched ground control mice similarly housed in animal enclosure modules (AEM). mRNA was extracted and an automated array analysis for gene expression was performed. Examination of the microarray data revealed 970 individual probes that had a 1.5‐fold or greater change. When these data were averaged (n = 4), we identified 12 genes that were significantly up‐ or down‐regulated by at least 1.5‐fold after spaceflight (P ≤ 0.05). The genes that significantly differed from the AEM controls and that were also confirmed via QRT‐PCR were as follows: Rbm3 (up‐regulated) and Hsph110, Hsp90aa1, Cxcl10, Stip1, Fkbp4 (down‐regulated). QRT‐PCR confirmed the microarray results and demonstrated additional gene expression alteration in other T cell related genes, including: Ctla‐4, IFN‐α2a (up‐regulated) and CD44 (down‐regulated). Together, these data demonstrate that spaceflight induces significant changes in the thymic mRNA expression of genes that regulate stress, glucocorticoid receptor metabolism, and T cell signaling activity. These data explain, in part, the reported systemic compromise of the immune system after exposure to the microgravity of space. J. Cell. Biochem. 110: 372–381, 2010. © 2010 Wiley‐Liss, Inc.
Using views to maintain Petri-net-based process models

A software process model is a complex entity describing activities, products and quality aspects of the "real" software-production process. The ever-changing nature of the software process imposes a continuous control of its evolution; maintenance should adapt the process model to accurately reflect the state of the real process. Presently, process model maintainers have to make evolve these complex models under time pressure and with very little assistance. In this paper we present a preliminary approach for improving maintainability of Petri-net-based process models using the concept of view. A view can be seen as the sub-model capturing the perception a participant has about the process. We show how views can structure a model as a set of more abstract modules which are easy to make evolve. After evolution, views can be composed using a set of formally defined operators to obtain a new process model in an automatic way. Our study is applied to the Process Weaver modelling language. After a short presentation of the Process Weaver formalism, we illustrate view definition with an example of a review process model. View evolution and view composition are also introduced through a scenario of process model change based on the above example.