Miracle-dz/UniFAR-FTUs huggingface dataset:
Nuclear Gene Variation in Wild Brown Rats

Although the brown rat (Rattus norvegicus) is widely used as a model mammal throughout biological sciences, little is known about genetic variation in wild rat populations or the relationship of commonly used inbred strains to their wild relatives. We sampled wild brown rats from the species’ presumed ancestral range in NW China and from a derived population in the UK and estimated nucleotide diversity and population subdivision, based on the sequences of 30 autosomal protein-coding loci. Neutral genetic diversity was close to 0.2% in both populations, which is about five times lower than diversity at the orthologous sites in a population of wild house mice from the species’ putative ancestral range in India. We found significant population differentiation between UK and Chinese populations, as assessed by Fst and the program STRUCTURE. Based on synonymous diversity and divergence between the brown rat and house mouse, we estimate that the recent effective population size in brown rats is approximately 130,000 (approximate 95% confidence interval 85,000-184,000), about fivefold lower than wild house mice.
PACAP and VIP Inhibit the Invasiveness of Glioblastoma Cells Exposed to Hypoxia through the Regulation of HIFs and EGFR Expression

Pituitary adenylate cyclase-activating polypeptide (PACAP) and vasoactive intestinal peptide (VIP) through the binding of vasoactive intestinal peptide receptors (VIPRs), perform a wide variety of effects in human cancers, including glioblastoma multiforme (GBM). This tumor is characterized by extensive areas of hypoxia, which triggers the expression of hypoxia-inducible factors (HIFs). HIFs not only mediate angiogenesis but also tumor cell migration and invasion. Furthermore, HIFs activation is linked to epidermal growth factor receptor (EGFR) overexpression. Previous studies have shown that VIP interferes with the invasive nature of gliomas by regulating cell migration. However, the role of VIP family members in GBM infiltration under low oxygen tension has not been clarified yet. Therefore, in the present study we have investigated, for the first time, the molecular mechanisms involved in the anti-invasive effect of PACAP or VIP in U87MG glioblastoma cells exposed to hypoxia induced by treatment with desferrioxamine (DFX). The results suggest that either PACAP or VIP exert an anti-infiltrative effect under low oxygen tension by modulating HIFs and EGFR expression, key elements involved in cell migration and angiogenesis. These peptides act through the inhibition of PI3K/Akt and MAPK/ERK signaling pathways, which are known to have a crucial role in HIFs regulation.
Intolerance of Uncertainty, Anxiety and Worry in Response to a Novel Induction of Uncertainty

by NICOLE PUCCI Intolerance of uncertainty (IU) is the tendency to react negatively on an emotional, cognitive, and behavioral level to uncertain situations (Dugas, Buhr, Ladouceur, 2004). IU is theorized to be one of the cornerstones of Generalized Anxiety Disorder (GAD). Various methods have been used to manipulate uncertainty, but the validity of these methods has not been ideal. The purpose of the current study was to use ambiguous scenarios to induce uncertainty and to examine changes in state anxiety, worry, and uncertainty in selected samples of individuals high and low in anxiety. Results revealed main effects of time, indicating that the scenarios were effective in increasing uncertainty, anxiety and worry from pre to post manipulation. Furthermore, there was an effect of condition for post scenario anxiety. There were no main effects of group and no significant interactions. Results are outlined and implications are discussed.
Identification of human papillomavirus type 18 transforming genes in immortalized and primary cells

The selective retention and expression of the E6-E7 region of human papillomavirus (HPV) types 16 and 18 in cervical carcinomas suggests that these viral sequences play a role in the development of genital neoplasia. Each of three possible gene products, E6, E6*, and E7, from this region of HPV-18 were examined for transforming properties in several types of rodent cells. We have found that in immortalized fibroblasts, both E6 and E7 (but not E6*) are capable of inducing anchorage-independent growth. In rat embryo cells, the HPV-18 E7 open reading frame was an effective immortalizing agent and complemented an activated ras oncogene for transformation. In both immortalized and primary cells, transformation was observed when the HPV-18 sequences were expressed from either the HPV-18 promoter or a heterologous promoter. The E6-E7 region is not, however, the sole transforming domain of HPV-18, since another portion of the early region, possibly E5, also exhibited transforming capability in immortalized fibroblasts. The development of human cervical carcinomas may therefore involve a series of steps involving multiple viral and cellular gene products.
Relationship between depth and age in the North Pacific Ocean

[1] The North Pacific contains active mid-oceanic ridges and the oldest, Jurassic (166.8 ± 4 Ma), drilled oceanic crust. Its bathymetry is therefore critical to studies of the applicability of thermal contraction models (e.g., the infinite half-space and cooling plate) to the subsidence of seafloor with crustal age. The bathymetry, however, contains seamounts and oceanic islands (e.g., Mid-Pacific Mountains), oceanic plateaus (e.g., Hess, Magellan, and Shatsky), and midplate topographic swells (e.g., Hawaii), which are unrelated to the current plate-scale thermal state of the oceanic lithosphere. We use here a regional-residual separation algorithm called MiMIC to remove these features and to isolate the depths associated with the subsidence of North Pacific oceanic crust. These depths, z (m), increase with time, t (Ma), as z = 3010 + 307 until 85 Ma. For greater ages the depths “flatten” and asymptotically approach ∼6.1 km and are well described by z = 6120 − 3010 exp(−0.026t). The flattening is not “abrupt” as recently described in z-t curves produced using the mean, median, and mode. As a result, the depths of both young and old seafloor are fit well (mean difference between and observed and calculated depths of 75 ± 54 m 1σ) by a single cooling plate model. Using a thermal conductivity, k, of 3.138 mW m−2 as previous studies, however, gives a plate of similar thickness (i.e., thermal thickness, L, of ∼115 km) but one which is unreasonably hot (i.e., temperature at the base of the plate, Tb, of 1522 °C) and inexpansive (i.e., coefficient of thermal expansion, α, of 2.57×10−5 °C−1). More reasonable values (i.e., Tb = 1363°C, k = 3.371 W m−1 °C−1, α = 2.77×10−5 °C−1, and L = 120 km) are obtained if the crustal thickness is used to constrain Tb and a certain amount of the surface heat flow is allowed to be radiogenically generated within the oceanic lithosphere.
Expression of the breast cancer resistance protein and 5-fluorouracil resistance in clinical breast cancer tissue specimens

The breast cancer resistance protein (BCRP) is a recently characterized xenobiotic half-transporter protein that acts as an energy-dependent efflux pump and may be associated with the multidrug-resistant phenotype. The aim of this study was to determine the association between BCRP expression and 5-fluorouracil (5-FU) resistance in clinical breast cancer tissue specimens. The BCRP expression was investigated using quantitative reverse-transcriptase polymerase chain reaction (RT-PCR) by use of the Master SYBR-Green I reagent and immunohistochemistry (IHC) by use of the BXP-21 anti-BCRP monoclonal antibody in clinical breast cancer tissue specimens. Chemosensitivity to 5-FU for BCRP-positive clinical breast cancer tissue specimens was colorimetrically assessed with the cytotoxicity assay through methyl thiazolyl tetrazolium (MTT) reduction. A total of 37 BCRP-positive clinical breast cancer tissue specimens were identified with quantitative RT-PCR and IHC. There was a significant correlation in BCRP expression between the results of quantitative RT-PCR and IHC in the specimens. The fold resistance to 5-FU was 7–12 compared to sensitivity to paclitaxel as determined by the colorimetric assay through MTT reduction in the 37 specimens. Our study results indicated that 5-FU resistance may be mediated by BCRP expression in clinical breast cancer tissue specimens, which may help optimize the design of breast cancer clinical chemotherapy schemes in BCRP-positive specimens.
Influence of hot water extraction on the physical and mechanical behavior of OSB

This study evaluated the influence of hot water extraction on hemicellulose removal, the concomitant change in wood properties, and finally production of oriented strandboard (OSB) from the modified wood. Three red maple (Acer rubrum L.) trees were felled, debarked, and their butt logs used to produce strands of 4-in length with a target thickness of either 0.025 inches, 0.035 inches, and 0.045 inches. Two hot water extraction procedures (320 °F, 90 psig) of 45 and 90 minutes duration (plus 50 minutes of preheating) were used, resulting in an average weight loss of 16.4 and 17.2 percent, respectively. Weight loss was significantly influenced by extraction time (p = 0.0011) and tree source (p = 0.0001) while the influence of strand thickness was not statistically significant (p = 0.1026). One OSB panel (17.6 inches by 12.4 inches by 0.5 inches) was manufactured for each of the 27 material combinations (2 extraction conditions and unextracted control, 3 trees, and 3 strand thickness). Panels were blended individually with a resin load of 3.2 percent pMDI resin, no wax, and an average density of 41.8 pcf (test volume basis). Physical and mechanical properties were determined following ASTM D1037-06 A procedures. Water absorption by OSB produced from both extraction treatments was significantly higher than the control for both 2 and 24 hours immersion while the thickness swell of panels from extracted material was slightly improved after 24 hours. The modulus of rupture (MOR) was not statistically significantly different between the control (5,966 psi) and the 45 minutes of extraction time (6,162 psi) panels, while the 90 minutes extraction time was significantly lower (4,093 psi). Internal bond strength in dry conditions from both extraction times (29 and 45 psi) were significantly lower than the control (117 psi), and similar results were obtained in wet condition (35 and 15 psi).
Cytokinin Inhibits a Subset of Diageotropica-Dependent Primary Auxin Responses in Tomato1

Many aspects of plant development are regulated by antagonistic interactions between the plant hormones auxin and cytokinin, but the molecular mechanisms of this interaction are not understood. To test whether cytokinin controls plant development through inhibiting an early step in the auxin response pathway, we compared the effects of cytokinin with those of the dgt(diageotropica) mutation, which is known to block rapid auxin reactions of tomato (Lycopersicon esculentum) hypocotyls. Long-term cytokinin treatment of wild-type seedlings phenocopied morphological traits of dgt plants such as stunting of root and shoot growth, reduced elongation of internodes, reduced apical dominance, and reduced leaf size and complexity. Cytokinin treatment also inhibited rapid auxin responses in hypocotyl segments: auxin-stimulated elongation, H+ secretion, and ethylene synthesis were all inhibited by cytokinin in wild-type hypocotyl segments, and thus mimicked the impaired auxin responsiveness found in dgt hypocotyls. However, cytokinin failed to inhibit auxin-induced LeSAUR gene expression, an auxin response that is affected by the dgt mutation. In addition, cytokinin treatment inhibited the auxin induction of only one of two 1-aminocyclopropane-1-carboxylic acid synthase genes that exhibited impaired auxin inducibility in dgt hypocotyls. Thus, cytokinin inhibited a subset of the auxin responses impaired indgt hypocotyls, suggesting that cytokinin blocks at least one branch of the DGT-dependent auxin response pathway.
A silicon carbide nanowire field effect transistor for DNA detection

This work reports on the label-free electrical detection of DNA molecules for the first time, using silicon carbide (SiC) as a novel material for the realization of nanowire field effect transistors (NWFETs). SiC is a promising semiconductor for this application due to its specific characteristics such as chemical inertness and biocompatibility. Non-intentionally n-doped SiC NWs are first grown using a bottom-up vapor–liquid–solid (VLS) mechanism, leading to the NWs exhibiting needle-shaped morphology, with a length of approximately 2 μm and a diameter ranging from 25 to 60 nm. Then, the SiC NWFETs are fabricated and functionalized with DNA molecule probes via covalent coupling using an amino-terminated organosilane. The drain current versus drain voltage (Id–Vd) characteristics obtained after the DNA grafting and hybridization are reported from the comparative and simultaneous measurements carried out on the SiC NWFETs, used either as sensors or references. As a representative result, the current of the sensor is lowered by 22% after probe DNA grafting and by 7% after target DNA hybridization, while the current of the reference does not vary by more than ±0.6%. The current decrease confirms the field effect induced by the negative charges of the DNA molecules. Moreover, the selectivity, reproducibility, reversibility and stability of the studied devices are emphasized by de-hybridization, non-complementary hybridization and re-hybridization experiments. This first proof of concept opens the way for future developments using SiC-NW-based sensors.
Energy-balanced Sleep Scheduling Based on Particle Swarm Optimization in Wireless Sensor Network

In order to conserve battery power in wireless sensor networks, some sensor nodes may be put into the sleep state while other sensor nodes remain active for the sensing and communication tasks. However, determining which of the sensor nodes should be put into the sleep state is non-trivial. In this paper, an Energy-balanced Sleep Scheduling scheme based on Particle Swarm Optimization (EBSS-PSO) in the context of cluster-based sensor networks is proposed. The scheme aims to balance the energy load of the sensing and communication tasks among all the nodes in the cluster while provide adequate sensing coverage area and reduce the overlapping area. Analytical and simulation results are presented to evaluate the proposed EBSS-PSO scheme. It is shown that the EBSS-PSO scheme can extends the cluster's overall network lifetime and reduce the overlapping area effectively while maintaining a similar sensing coverage compared with three related sleep scheduling schemes, the Randomized Scheduling (RS) scheme, the Neighbor-based Scheduling (NS) scheme and the Energy-Neighbor-based Scheduling (ENS) scheme.
Dummies and SIDS: Causality has not been established

Editor—The relative risk for associated factors should not be confused with the attributable risk for causative factors. Li et al express the risk associated with sudden infant death syndrome (SIDS) and use of a dummy (pacifier) during sleep as a 90% reduction in risk, which could be potentially misunderstood and brings unwarranted media attention to what otherwise …
How Are Firms’ Wages and Prices Linked: Survey Evidence In Europe

This paper presents new evidence on the patterns of price and wage adjustment in European firms and on the extent of nominal rigidities. It uses a unique dataset collected through a firm-level survey conducted in a broad range of countries and covering various sectors. Several conclusions are drawn from this evidence. Firms adjust wages less frequently than prices: the former tend to remain unchanged for about 15 months on average, the latter for around 10 months. The degree of price rigidity varies substantially across sectors and depends strongly on economic features, such as the intensity of competition, the exposure to foreign markets and the share of labour costs in total cost. Instead, country specificities, mostly related to the labour market institutional setting, are more relevant in characterising the pattern of wage adjustment. The latter exhibits also a substantial degree of time-dependence, as firms tend to concentrate wage changes in a specific month, mostly January in the majority of countries. Wage and price changes feed into each other at the micro level and there is a relationship between wage and price rigidity.
Effect of Pacing‐Induced Tachycardia and Myocardial Ischemia on Ventricular Pressure‐Velocity Relationships in Man

Ventricular function was evaluated in 18 patients prior to left ventriculography and selective coronary arteriography. Simultaneous left ventricular pressure (catheter-tip manometer) and dP/dt were recorded at resting heart rates and during tachycardia induced by right atrial pacing. Pressure-velocity curves were constructed from which Vmax and maximum measured contractile element velocity (max VCE) were obtained. Vmax and max VCE initially increased with pacing-induced tachycardia in 17 of the 18 patients. Eight patients developed evidence of myocardial ischemia during atrial pacing. During the period of myocardial ischemia there was a decrease in Vmax and max VCE in all eight patients despite constant or increasing heart rate. In the 10 patients who did not develop evidence of myocardial ischemia with pacing-induced tachycardia, Vmax and max VCE continued to increase or remained constant with increasing rate. Peak left ventricular dP/dt increased coincident with the onset of myocardial ischemia in six of eight patients despite a fall in Vmax and max VCE in all eight patients during the ischemic period. A highly significant difference was demonstrated between Vmax values of patients with normal ejection fractions and patients with low ejection fractions, both at rest and during pacing-induced tachycardia.
Sequence Variants of ADIPOQ and Association with Type 2 Diabetes Mellitus in Taiwan Chinese Han Population

Diabetes is a serious global health problem. Large-scale genome-wide association studies identified loci for type 2 diabetes mellitus (T2DM), including adiponectin (ADIPOQ) gene and transcription factor 7-like 2 (TCF7L2), but few studies clarified the effect of genetic polymorphisms of ADIPOQ and TCF7L2 on risk of T2DM. We attempted to elucidate association between T2DM and polymorphic variations of both in Taiwan's Chinese Han population, with our retrospective case-control study genotyping single nucleotide polymorphisms (SNPs) in ADIPOQ and TCF7L2 genes both in 149 T2DM patients and in 139 healthy controls from Taiwan. Statistical analysis gauged association of these polymorphisms with risk of T2DM to show ADIPOQ rs1501299 polymorphism variations strongly correlated with T2DM risk (P = 0.042), with rs2241766 polymorphism being not associated with T2DM (P = 0.967). However, both polymorphisms rs7903146 and rs12255372 of TCF7L2 were rarely detected in Taiwanese people. This study avers that ADIPOQ rs1501299 polymorphism contributes to risk of T2DM in the Taiwanese population.
Time-dependent changes in membrane excitability during glucose-induced bursting activity in pancreatic β cells

In our companion paper, the physiological functions of pancreatic β cells were analyzed with a new β-cell model by time-based integration of a set of differential equations that describe individual reaction steps or functional components based on experimental studies. In this study, we calculate steady-state solutions of these differential equations to obtain the limit cycles (LCs) as well as the equilibrium points (EPs) to make all of the time derivatives equal to zero. The sequential transitions from quiescence to burst–interburst oscillations and then to continuous firing with an increasing glucose concentration were defined objectively by the EPs or LCs for the whole set of equations. We also demonstrated that membrane excitability changed between the extremes of a single action potential mode and a stable firing mode during one cycle of bursting rhythm. Membrane excitability was determined by the EPs or LCs of the membrane subsystem, with the slow variables fixed at each time point. Details of the mode changes were expressed as functions of slowly changing variables, such as intracellular [ATP], [Ca2+], and [Na+]. In conclusion, using our model, we could suggest quantitatively the mutual interactions among multiple membrane and cytosolic factors occurring in pancreatic β cells.
IL-6-driven STAT signalling in circulating CD4+ lymphocytes is a marker for early anticitrullinated peptide antibody-negative rheumatoid arthritis

Objectives A previously identified signal transduction and activator of transcription-3 (STAT3) target-enriched gene signature in circulating CD4+ T cells of patients with early rheumatoid arthritis (RA) was prominent in autoantibody-negative individuals. Here, interleukin (IL)-6-mediated STAT signalling was investigated in circulating lymphocytes of an independent early arthritis patient cohort, seeking further insight into RA pathogenesis and biomarkers of potential clinical utility. Methods Constitutive and IL-6-induced expression of phosphorylated STAT1 (pSTAT1) and pSTAT3 was determined in T and B cells using Phosflow cytometric analysis in patients with RA and controls. Contemporaneous levels of serum cytokines were measured by immunoassay. Induced gene expression was measured in cultured CD4+T cells by quantitative real-time PCR. Results Among circulating lymphocytes of 187 patients with early arthritis, constitutive pSTAT3 correlated with serum IL-6 levels maximally in CD4+ T cells. Increased constitutive pSTAT3, but not pSTAT1, was observed in circulating CD4+ T cells of patients with early anticitrullinated peptide autoantibody (ACPA)-negative RA compared with disease controls, and these levels decreased alongside markers of disease activity with IL-6R-targeted treatment. Among patients presenting with seronegative undifferentiated arthritis (UA) the ratio of constitutive pSTAT3:pSTAT1 in CD4+ T cells contributed substantially to an algorithm for predicting progression to classifiable RA during a median of 20 months follow-up (area under receiver operator characteristic curve=0.84; p<0.001). Conclusions Our findings support a particular role for IL-6-driven CD4+ T cell activation via STAT3 during the induction of RA, particularly as a feature of ACPA-negative disease. CD4+ T cell pSTAT measurements show promise as biomarkers of UA–RA progression and now require independent validation.
Nanotoxicology and nanoparticle safety in biomedical designs

Nanotechnology has wide applications in many fields, especially in the biological sciences and medicine. Nanomaterials are applied as coating materials or in treatment and diagnosis. Nanoparticles such as titania, zirconia, silver, diamonds, iron oxides, carbon nanotubes, and biodegradable polymers have been studied in diagnosis and treatment. Many of these nanoparticles may have toxic effects on cells. Many factors such as size, inherent properties, and surface chemistry may cause nanoparticle toxicity. There are methods for improving the performance and reducing toxicity of nanoparticles in medical design, such as biocompatible coating materials or biodegradable/biocompatible nanoparticles. Most metal oxide nanoparticles show toxic effects, but no toxic effects have been observed with biocompatible coatings. Biodegradable nanoparticles are also used in the efficient design of medical materials, which will be reviewed in this article.