Miracle-dz/UniFAR-FTUs huggingface dataset:
NanoString, a novel digital color-coded barcode technology: current and future applications in molecular diagnostics

ABSTRACT Introduction: Formalin-fixed, paraffin-embedded (FFPE) tissue sample is a gold mine of resources for molecular diagnosis and retrospective clinical studies. Although molecular technologies have expanded the range of mutations identified in FFPE samples, the applications of existing technologies are limited by the low nucleic acids yield and poor extraction quality. As a result, the routine clinical applications of molecular diagnosis using FFPE samples has been associated with many practical challenges. NanoString technologies utilize a novel digital color-coded barcode technology based on direct multiplexed measurement of gene expression and offer high levels of precision and sensitivity. Each color-coded barcode is attached to a single target-specific probe corresponding to a single gene which can be individually counted without amplification. Therefore, NanoString is especially useful for measuring gene expression in degraded clinical specimens. Areas covered: This article describes the applications of NanoString technologies in molecular diagnostics and challenges associated with its applications and the future development. Expert commentary: Although NanoString technology is still in the early stages of clinical use, it is expected that NanoString-based cancer expression panels would play more important roles in the future in classifying cancer patients and in predicting the response to therapy for better personal therapeutic care.
Effects of a community-based multimodal exercise program on physical function and quality of life in cancer survivors: a pilot study

Abstract The purpose of this single-arm pilot study was to examine the effects of a community-based multimodal exercise program on: physical function (Timed-Up-and-Go [TUG], 6-min walk test [6MWT], leg and chest press strength, and functional reach [FR]); and quality of life, QoL [FACT-G]), in cancer survivors. Fifty-nine cancer survivors (91.5% female; mean age 59 ± 12 years) completed supervised exercise training for 90 min twice weekly for 12 weeks. Exercise training consisted of 30 min of each of the following: (1) aerobic conditioning; (2) resistance training; and (3) balance and flexibility training. Pre-post-outcome measures were compared for statistically significant differences (p < 0.01) and were related to the International Classification of Functioning, Disability and Health Model. Effect sizes (ES), minimal clinically important differences, and minimal detectable change at 90% confidence intervals were calculated. Participants decreased TUG time by 21.1% and walked 15.5% farther during 6-MWT (p < 0.001). Leg and chest press strength increased by 34.5% and 32.7%, respectively (p < 0.001). FR increased by 15.1% (p < 0.001). Significant improvements for physical well-being (13.9%), emotional well-being (6.7%), functional well-being (13.0%), and total well-being (9.6%) were found (p < 0.01). Improvements in physical function and QoL showed “moderate to large” ESs indicating improvements in physical function and QoL are clinically meaningful.
FROST DURABILITY OF CONCRETE CONTAINING VISCOSITY-MODIFYING ADMIXTURES

The use of viscosity-modifying admixtures in special concrete intended for underwater placement/repair and land-based applications has increased, yet limited information exists about the frost susceptibility of such concrete. The effect of an adding sequence of the air-entraining admixture, in relation to the viscosity-modifying admixture and the high-range water reducer on an air-void system, is evaluated. The impact of two commonly used viscosity-modifying admixtures, welan gum and hydroxypropyl methylcellulose, on frost durability and scaling resistance is determined for fluid mixes made with w/c ratios of 0.32, 0.40, and 0.45. Findings indicate that the air-entraining admixture is most effective when added after the viscosity-modifying admixture and high-range water reducer. Assuming that a sufficient air-void system is secured, concrete made with welan gum or hydroxypropyl methylcellulose can display adequate frost durability similar to that of conventional concrete.
Average field‐aligned current configuration parameterized by solar wind conditions

We present the first large‐scale comparison of the spatial distribution of field‐aligned currents as measured by the Active Magnetosphere and Planetary Electrodynamics Response Experiment, with the location and brightness of the average auroral oval, determined from the Imager for Magnetopause‐to‐Aurora Global Exploration far ultraviolet instrument. These distributions are compared under the same interplanetary magnetic field magnitude and clock angle conditions. The field‐aligned currents and auroral oval drop to lower latitudes, as the interplanetary magnetic field becomes both increasingly stronger in magnitude and increasingly southward. We find that the region 2 currents are more closely aligned with the distribution of auroral UV emission, whether that be in the discrete auroral zone about dusk or in the postmidnight diffuse aurora sector. The lack of coincidence between the region 1 field‐aligned currents with the auroral oval in the dusk sector is contrary to expectation.
Paternal inheritance of classic X‐linked bilateral periventricular nodular heterotopia

Periventricular nodular heterotopia (PNH) is a developmental disorder of the central nervous system, characterized by heterotopic nodules of gray matter resulting from disturbed neuronal migration. The most common form of bilateral PNH is X‐linked dominant inherited, caused by mutations in the Filamin A gene (FLNA) and associated with a wide variety of other clinical findings including congenital heart disease. The typical patient with FLNA‐associated PNH is female and presents with difficult to treat seizures. In contrast, hemizygous FLNA loss of function mutations in males are reported to be perinatally lethal. In X‐linked dominant traits like FLNA‐associated PNH the causal mutation is commonly inherited from the mother. Here, we present an exceptional family with paternal transmission of classic bilateral FLNA‐associated PNH from a mildly affected father with somatic and germline mosaicism for a c.5686G>A FLNA splice mutation to both daughters with strikingly variable clinical manifestation and PNH extent in cerebral MR imaging. Our observations emphasize the importance to consider in genetic counseling and risk assessment the rare genetic constellation of paternal transmission for families with X‐linked dominant inherited FLNA‐associated PNH. © 2013 Wiley Periodicals, Inc.
Design of Nanostructured Functional Coatings by Using Wet-Chemistry Methods

This review reports the implementation of novel nanostructured functional coatings by using different surface engineering techniques based on wet chemistry. In the first section, the theoretical fundaments of three techniques such as sol-gel process, layer-by-layer (LbL) assembly and electrospinning will be briefly described. In the second section, selected applications in different potential fields will be presented gathering relevant properties such as superhydrophobicity, biocide behavior or applications in the field of optical fiber sensors.
Structure/Function Studies of the α4 Subunit Reveal Evolutionary Loss of a GlyR Subtype Involved in Startle and Escape Responses

Inhibitory glycine receptors (GlyRs) are pentameric ligand-gated anion channels with major roles in startle disease/hyperekplexia (GlyR α1), cortical neuronal migration/autism spectrum disorder (GlyR α2), and inflammatory pain sensitization/rhythmic breathing (GlyR α3). However, the role of the GlyR α4 subunit has remained enigmatic, because the corresponding human gene (GLRA4) is thought to be a pseudogene due to an in-frame stop codon at position 390 within the fourth membrane-spanning domain (M4). Despite this, a recent genetic study has implicated GLRA4 in intellectual disability, behavioral problems and craniofacial anomalies. Analyzing data from sequenced genomes, we found that GlyR α4 subunit genes are predicted to be intact and functional in the majority of vertebrate species—with the exception of humans. Cloning of human GlyR α4 cDNAs excluded alternative splicing and RNA editing as mechanisms for restoring a full-length GlyR α4 subunit. Moreover, artificial restoration of the missing conserved arginine (R390) in the human cDNA was not sufficient to restore GlyR α4 function. Further bioinformatic and mutagenesis analysis revealed an additional damaging substitution at K59 that ablates human GlyR α4 function, which is not present in other vertebrate GlyR α4 sequences. The substitutions K59 and X390 were also present in the genome of an ancient Denisovan individual, indicating that GLRA4 has been a pseudogene for at least 30,000–50,000 years. In artificial synapses, we found that both mouse and gorilla α4β GlyRs mediate synaptic currents with unusually slow decay kinetics. Lastly, to gain insights into the biological role of GlyR α4 function, we studied the duplicated genes glra4a and glra4b in zebrafish. While glra4b expression is restricted to the retina, using a novel tol2-GAL4FF gene trap line (SAIGFF16B), we found that the zebrafish GlyR α4a subunit gene (glra4a) is strongly expressed in spinal cord and hindbrain commissural neurones. Using gene knockdown and a dominant-negative GlyR α4aR278Q mutant, we found that GlyR α4a contributes to touch-evoked escape behaviors in zebrafish. Thus, although GlyR α4 is unlikely to be involved in human startle responses or disease states, this subtype may contribute to escape behaviors in other organisms.
The diabetes-linked transcription factor PAX4 promotes β-cell proliferation and survival in rat and human islets

The mechanism by which the β-cell transcription factor Pax4 influences cell function/mass was studied in rat and human islets of Langerhans. Pax4 transcripts were detected in adult rat islets, and levels were induced by the mitogens activin A and betacellulin. Wortmannin suppressed betacellulin-induced Pax4 expression, implicating the phosphatidylinositol 3-kinase signaling pathway. Adenoviral overexpression of Pax4 caused a 3.5-fold increase in β-cell proliferation with a concomitant 1.9-, 4-, and 5-fold increase in Bcl-xL (antiapoptotic), c-myc, and Id2 mRNA levels, respectively. Accordingly, Pax4 transactivated the Bcl-xL and c-myc promoters, whereas its diabetes-linked mutant was less efficient. Bcl-xL activity resulted in altered mitochondrial calcium levels and ATP production, explaining impaired glucose-induced insulin secretion in transduced islets. Infection of human islets with an inducible adenoviral Pax4 construct caused proliferation and protection against cytokine-evoked apoptosis, whereas the mutant was less effective. We propose that Pax4 is implicated in β-cell plasticity through the activation of c-myc and potentially protected from apoptosis through Bcl-xL gene expression.
Research on Mining Water-Rich Fly-Ash-Based Filling Material

It had decades of history that cementing material was used for filling in coal mine or metal mine goaf, which was a common filling material in recently filling mining. Paste and high water material have excellent performance, but the price was too high, which restricted the development of cemented filling technology severely. Later, fly ash and other industrial waste were mixed into the cementing material in order to reduce the cost, but because of which early activity was low, the early strength was reduced by mixing too much fly ash and other industrial waste, the setting time was extended, which affected the filling effect seriously. Therefore, it becomes a key problem that how to excite the early activity of fly ash. It was a breakthrough to select the appropriate activator and activation method, because of the difference mechanism of action and effects for different activators of fly ash, the complexity composition of filling material mixed with large number of fly ash, and the early and late physical and mechanical properties [1,2]. Four salts are used for activators in this paper, which are mixed with fly ash and water, and a display method was selected to maximum activate the activity of fly ash, increase the early strength of the material, and reduce the cost of the material.
Experimental and Analytical Studies for Impedance-Based Smart Health Monitoring of Concrete Structures

This paper presents a feasibility study of an impedance-based damage detection technique using PZT (Lead-Zirconate-Titanate) patches for real-time health monitoring of concrete structures. The PZT patches are used to detect progressive surface damage on a plain concrete beam. Both experimental and analytical studies are carried out. For damage quantification, root-mean square deviations (RMSD) before and after damage are used as a damage indicator.
Advances in the research of autologous fibroblast injections for aging skin

With the development of autologous stem cells transplantation, the application of autologous fibroblast graft has been an important therapy in defect repair. In the past decade, amounts of studies have reported favorable treatment effect and safety about the therapy. The material has the ability to produce human collagen in vivo. This article details recent scientific work of the cases, effect, injection technique, complications and safety of autologous fibroblast injection treatment.
Mortality and Length of Stay of Very Low Birth Weight and Very Preterm Infants: A EuroHOPE Study

The objective of this paper was to compare health outcomes and hospital care use of very low birth weight (VLBW), and very preterm (VLGA) infants in seven European countries. Analysis was performed on linkable patient-level registry data from seven European countries between 2006 and 2008 (Finland, Hungary, Italy (the Province of Rome), the Netherlands, Norway, Scotland, and Sweden). Mortality and length of stay (LoS) were adjusted for differences in gestational age (GA), sex, intrauterine growth, Apgar score at five minutes, parity and multiple births. The analysis included 16,087 infants. Both the 30-day and one-year adjusted mortality rates were lowest in the Nordic countries (Finland, Sweden and Norway) and Scotland and highest in Hungary and the Netherlands. For survivors, the adjusted average LoS during the first year of life ranged from 56 days in the Netherlands and Scotland to 81 days in Hungary. There were large differences between European countries in mortality rates and LoS in VLBW and VLGA infants. Substantial data linkage problems were observed in most countries due to inadequate identification procedures at birth, which limit data validity and should be addressed by policy makers across Europe.
Morphologic Spectrum of Papillary Carcinoma of the Thyroid

OBJECTIVE To evaluate the efficacy of fine needle aspiration cytology (FNAC) in the diagnosis of morphologic variants of papillary carcinoma of the thyroid (PCT) and to determine the reasons for misdiagnosis in discrepant cases on cytology. STUDY DESIGN Fine needle aspiration smears from 158 histologically proven cases of PCT were blindly reviewed and an attempt made to subclassify them into different variants on the basis of various architectural and morphologic features. Cytohistologic correlation was performed to assess the efficacy of cytology in correctly identifying these variants. RESULTS In cases with satisfactory aspirates, the diagnosis of papillary carcinoma was correctly made in 112 of 139 (80.5%) histologically proven cases of PCT. Subclassification was correct in 87 of 96 (90.6%) cases of classic papillary carcinoma and in 25 of 43 (58.1%) of the other variants of PCT with adequate aspirates. Cytohistologic agreement was 100% in columnar cell variant (CCV) and high grade variant (HGV). Although there was overlap in the morphologic features of tall cell variant (TCV) and Hürthle cell variant, cytology correctly identified 60% and 76.4% of these cases, respectively. The accuracy of cytology was limited in diagnosing follicular variant as only 50% of these cases could be correctly typed on cytology. Nodular fascitis-like stroma and diffuse sclerosis variants could not be diagnosed on cytology. CONCLUSION Though FNAC is of limited value in typing the variants of PCT due to overlapping morphologic features, it can provide clues to the diagnosis in certain aggressive variants such as TCV, CCV and HGV. Early diagnosis in these cases can assist clinicians with management.
Effect of rainfall and fire frequency on tree--grass dynamics: Capturing the forest--savanna distributions along biogeographic gradients

In this work, we improve a previous minimalistic tree-grass savanna model by taking into account water availability, in addition to fire, since both factors are known to be important for shaping savanna physiognomies along a climatic gradient. As in our previous models, we consider two nonlinear functions of grass and tree biomasses to respectively take into account grass-fire feedbacks, and the response of trees to fire of a given intensity. The novelty is that rainfall is taken into account in the tree and grass growth functions and in the biomass carrying capacities. Then, we derive a qualitative analysis of the ODE model, showing existence of equilibria, and studying their stability conditions. We also construct a two dimension bifurcation diagram based on rainfall and fire frequency. This led to summarize different scenarios for the model including multi-stabilities that are proven possible. Next, to bring more realism in the model, pulsed fire events are modelled as part of an IDE (Impulsive differential Equations) system analogous to the ODE system. Numerical simulations are provided and we discuss some important ecological outcomes that our ODE and IDE models are able to predict. Notably, the expansion of forest into tree-poor physiognomies (grassland and savanna) is systematically predicted when fire return period increases, especially in mesic and humid climatic areas.
Combining Linear Non-Gaussian Acyclic Model with Logistic Regression Model for Estimating Causal Structure from Mixed Continuous and Discrete Data

Estimating causal models from observational data is a crucial task in data analysis. For continuous-valued data, Shimizu et al. have proposed a linear acyclic non-Gaussian model to understand the data generating process, and have shown that their model is identifiable when the number of data is sufficiently large. However, situations in which continuous and discrete variables coexist in the same problem are common in practice. Most existing causal discovery methods either ignore the discrete data and apply a continuous-valued algorithm or discretize all the continuous data and then apply a discrete Bayesian network approach. These methods possibly loss important information when we ignore discrete data or introduce the approximation error due to discretization. In this paper, we define a novel hybrid causal model which consists of both continuous and discrete variables. The model assumes: (1) the value of a continuous variable is a linear function of its parent variables plus a non-Gaussian noise, and (2) each discrete variable is a logistic variable whose distribution parameters depend on the values of its parent variables. In addition, we derive the BIC scoring function for model selection. The new discovery algorithm can learn causal structures from mixed continuous and discrete data without discretization. We empirically demonstrate the power of our method through thorough simulations.
Effect of an Educational and Psychological Intervention on Knowledge and Quality of Life among Patients with Psoriasis

Background: Psoriasis is one of the most common skin disorders with a prevalence rate of 0.1%–3%. Chronic nature, frequent relapses, absence of permanent cure, and the cosmetic disfigurement of psoriasis have a negative impact on quality of life (QoL) by causing psychological stress. Patients with psoriasis often have unambiguous ideas about the causes, controllability, consequences, and expected time-course of their disease. Aim: The aim of this study is to assess the effectiveness of a video-assisted teaching program regarding psoriasis on the level of knowledge and relaxation therapy on QoL among patients with psoriasis. Materials and Methods: Experimental design was adapted. One hundred and four participants diagnosed with psoriasis were randomly allocated either to an experimental or to a control group. Fifty-two participants were included in each group by simple random sampling. A video-assisted teaching program on psoriasis and relaxation exercises was taught to the participants over a period of 3 months. The tools used were: Psoriasis Knowledge Assessment Questionnaire, modified psoriasis disability index, and modified psoriasis life stress inventory. Results: In the experimental group, the knowledge score was increased significantly from 9 ± 2.2 at baseline to 23.6 ± 1.5 after the intervention. The disability score was decreased from 15.6 to 9.9 and the stress score related to the illness was decreased from 22.8 to 16.9 after the intervention. Conclusion: Educational intervention about disease process and relaxation exercises was effective in improving the knowledge and QoL of patients with psoriasis.
The Inhibitory Effect of Salmon Calcitonin on Tri-Iodothyronine Induction of Early Hypertrophy in Articular Cartilage

Objective Salmon calcitonin has chondroprotective effect both in vitro and in vivo, and is therefore being tested as a candidate drug for cartilage degenerative diseases. Recent studies have indicated that different chondrocyte phenotypes may express the calcitonin receptor (CTR) differentially. We tested for the presence of the CTR in chondrocytes from tri-iodothyronin (T3)-induced bovine articular cartilage explants. Moreover, investigated the effects of human and salmon calcitonin on the explants. Methods Early chondrocyte hypertrophy was induced in bovine articular cartilage explants by stimulation over four days with 20 ng/mL T3. The degree of hypertrophy was investigated by molecular markers of hypertrophy (ALP, IHH, COLX and MMP13), by biochemical markers of cartilage turnover (C2M, P2NP and AGNxII) and histology. The expression of the CTR was detected by qPCR and immunohistochemistry. T3-induced explants were treated with salmon or human calcitonin. Calcitonin down-stream signaling was measured by levels of cAMP, and by the molecular markers. Results Compared with untreated control explants, T3 induction increased expression of the hypertrophic markers (p<0.05), of cartilage turnover (p<0.05), and of CTR (p<0.01). Salmon, but not human, calcitonin induced cAMP release (p<0.001). Salmon calcitonin also inhibited expression of markers of hypertrophy and cartilage turnover (p<0.05). Conclusions T3 induced early hypertrophy of chondrocytes, which showed an elevated expression of the CTR and was thus a target for salmon calcitonin. Molecular marker levels indicated salmon, but not human, calcitonin protected the cartilage from hypertrophy. These results confirm that salmon calcitonin is able to modulate the CTR and thus have chondroprotective effects.