Miracle-dz/UniFAR-FTUs huggingface dataset:
RORγ directly regulates the circadian expression of clock genes and downstream targets in vivo

In this study, we demonstrate that the lack of retinoic acid-related orphan receptor (ROR) γ or α expression in mice significantly reduced the peak expression level of Cry1, Bmal1, E4bp4, Rev-Erbα and Per2 in an ROR isotype- and tissue-selective manner without affecting the phase of their rhythmic expression. Analysis of RORγ/RORα double knockout mice indicated that in certain tissues RORγ and RORα exhibited a certain degree of redundancy in regulating clock gene expression. Reporter gene analysis showed that RORγ was able to induce reporter gene activity through the RORE-containing regulatory regions of Cry1, Bmal1, Rev-Erbα and E4bp4. Co-expression of Rev-Erbα or addition of a novel ROR antagonist repressed this activation. ChIP-Seq and ChIP–Quantitative real-time polymerase chain reaction (QPCR) analysis demonstrated that in vivo RORγ regulate these genes directly and in a Zeitgeber time (ZT)-dependent manner through these ROREs. This transcriptional activation by RORs was associated with changes in histone acetylation and chromatin accessibility. The rhythmic expression of RORγ1 by clock proteins may lead to the rhythmic expression of RORγ1 target genes. The presence of RORγ binding sites and its down-regulation in RORγ−/− liver suggest that the rhythmic expression of Avpr1a depends on RORγ consistent with the concept that RORγ1 provides a link between the clock machinery and its regulation of metabolic genes.
Meta-Recognition: The Theory and Practice of Recognition Score Analysis

In this paper, we define meta-recognition, a performance prediction method for recognition algorithms, and examine the theoretical basis for its postrecognition score analysis form through the use of the statistical extreme value theory (EVT). The ability to predict the performance of a recognition system based on its outputs for each match instance is desirable for a number of important reasons, including automatic threshold selection for determining matches and nonmatches, and automatic algorithm selection or weighting for multi-algorithm fusion. The emerging body of literature on postrecognition score analysis has been largely constrained to biometrics, where the analysis has been shown to successfully complement or replace image quality metrics as a predictor. We develop a new statistical predictor based upon the Weibull distribution, which produces accurate results on a per instance recognition basis across different recognition problems. Experimental results are provided for two different face recognition algorithms, a fingerprint recognition algorithm, a SIFT-based object recognition system, and a content-based image retrieval system.
Initiation of Purinergic Signaling by Exocytosis of ATP-containing Vesicles in Liver Epithelium*

Extracellular ATP represents an important autocrine/paracrine signaling molecule within the liver. The mechanisms responsible for ATP release are unknown, and alternative pathways have been proposed, including either conductive ATP movement through channels or exocytosis of ATP-enriched vesicles, although direct evidence from liver cells has been lacking. Utilizing dynamic imaging modalities (confocal and total internal reflection fluorescence microscopy and luminescence detection utilizing a high sensitivity CCD camera) at different scales, including confluent cell populations, single cells, and the intracellular submembrane space, we have demonstrated in a model liver cell line that (i) ATP release is not uniform but reflects point source release by a defined subset of cells; (ii) ATP within cells is localized to discrete zones of high intensity that are ∼1 μm in diameter, suggesting a vesicular localization; (iii) these vesicles originate from a bafilomycin A1-sensitive pool, are depleted by hypotonic exposure, and are not rapidly replenished from recycling of endocytic vesicles; and (iv) exocytosis of vesicles in response to cell volume changes depends upon a complex series of signaling events that requires intact microtubules as well as phosphoinositide 3-kinase and protein kinase C. Collectively, these findings are most consistent with an essential role for exocytosis in regulated release of ATP and initiation of purinergic signaling in liver cells.
Factors affecting the incidence of flystrike in sheep - a description and analysis of data from three separate areas in eastern Australia

Summary This paper presents a brief review of the factors affecting flystrike (cutaneous myiasis) as background to the on-going analysis of information on strike incidence, flock management, weather conditions and fly abundance in three discrete sheep grazing areas in eastern Australia (Flinders Island, Gunning and Inverell). These data were assembled in the late 1980s - early 1990s as part of a program aimed at the development of a strike management model. Information on weather, fly abundance and flock management was provided weekly by 30-40 graziers in each area over 3-4 years. Sheep data were collected using a questionnaire survey providing information on flock size, drenching practice, crutching, shearing, dagging, number of animals checked for strike, number struck in each age class and the type and method of insecticide usage. Previous studies have assessed strike incidence on the basis of the number of animals struck relative to the number of animals in the survey. The latter figure invariably includes sheep that, by reason of recent management (e.g., shearing, crutching or jetting), are not liable to infection. The extent to which such a procedure imparts an overall bias in regional estimates of strike is unknown, but its effect between weeks at the individual flock level is often quite marked (e.g., strike incidence after jetting may decrease to 0% even though prevailing fly and weather conditions would suggest that a high proportion of sheep were still technically susceptible). Hence in order to properly assess the inherent effects of weather and fly abundance, confounding influences associated with flock management need to be removed or minimised prior to data analysis. This paper describes the methods that have been adopted to transform weekly flock numbers into estimates of the number of sheep that are susceptible to fly attack as a first stage in the process of developing a strike management model.
Increased leukocyte ABCA1 gene expression in post-menopausal women on hormone replacement therapy

Objective. The ATP binding cassette A1 (ABCA1) is a key participant in the reverse cholesterol process whereby mediates cholesterol efflux directly to HDL particles. The aim of this study was to investigate whether long-term treatment with conventional hormone replacement therapy (HRT) in post-menopausal women could affect their leukocytes ABCA1 expression. Changes in various serum lipids and lipoprotein fractions were also investigated. Material and Methods. A total of 60 non-obese normolipidaemic post-menopausal women treated with oral oestrogen together with progestin therapy for 3 months were selected. Leukocytes ABCA1 gene expression and serum lipid and lipoprotein concentrations were measured at the start and end of the HRT. Results. HRT led to significant increases in HDL cholesterol (P = 0.001) and apoA-I (P = 0.046) and significant decrease in apoB (P = 0.049) and LDL cholesterol (P = 0.022) when compared with the baseline levels. Analysis of leukocytes ABCA1 mRNA showed a significant increase in ABCA1 gene expression after HRT (P = 0.001). There was also a significant inverse association (r = −0.28, P = 0.03) between ABCA1 gene expression and log TG/HDL cholesterol changes related to HRT. Conclusion. The beneficial cardiovascular effects of HRT could be explained, at least in part, by increasing the ABCA1 gene expression.
Spread of SHV-1 beta-lactamase in Escherichia coli isolated from fecal samples in Africa

Ninety-seven (42%) Escherichia coli strains isolated in Senegal from fecal samples produced beta-lactamases. Among them, 29 (30%) isolates produced SHV-1 beta-lactamase that was plasmid mediated. The plasmids belonged to four incompatibility groups. Various degrees of TEM-1 expression in the presence of SHV-1 were observed.
Loss of Heterozygosities in Five Tumor Suppressor Genes (FHIT Gene, p16, pRb, E-Cadherin and p53) in Thyroid Tumors

Objectives To evaluate the loss of heterozygosities (LOH) of chromosomes 3p14 (FHIT gene), 9p21 (p16), 13q21 (pRb), 6q22 (E-cadherin) and 17p13 (p53) in various thyroid tumors. Methods Eighty thyroid tumor cases (20 follicular adenomas, 10 follicular carcinomas, and 50 papillary carcinomas) have been analyzed for the presence of LOH in chromosomes 3p14, 9p21, 13q21, 6q22, and 17p13 allelic loss, using microsatellite markers and DNA obtained from formalin-fixed paraffin-embedded archival tissues. Results LOH on 3p14 was found in 10.5%, 33.3%, and 30.4% of follicular adenomas, follicular carcinomas, and papillary carcinomas, respectively. LOH on 9p21 was detected in 6%, 44.4%, and 47.8%, respectively. LOH on pRb gene was found in 5.3%, 20.0%, and 35.4%, respectively. LOH on E-cadherin gene was found in 5.3%, 22.2%, and 43.8%, respectively. LOH on 17p13 was detected in 0%, 40%, and 45.8%, respectively. LOH in FHIT gene, p16, pRb, E-cadherin, and p53 genes were more frequently identified in follicular carcinoma and papillary carcinoma than in follicular adenoma. Conclusion LOH results of the five tumor suppressor genes (FHIT gene, p16, pRb, E-cadherin, and p53) showed statistical differences between benign tumor and malignant tumor. Among papillary carcinoma, LOH in p16, E-cadherin and p53 genes well correlated with poorly differentiated grade, and LOH of E-cadherin was associated with lymph node metastasis.
Phenotypic Consequences of Purine Nucleotide Imbalance in Saccharomyces cerevisiae

Coordinating homeostasis of multiple metabolites is a major task for living organisms, and complex interconversion pathways contribute to achieving the proper balance of metabolites. AMP deaminase (AMPD) is such an interconversion enzyme that allows IMP synthesis from AMP. In this article, we show that, under specific conditions, lack of AMPD activity impairs growth. Under these conditions, we found that the intracellular guanylic nucleotide pool was severely affected. In vivo studies of two AMPD homologs, Yjl070p and Ybr284p, indicate that these proteins have no detectable AMP, adenosine, or adenine deaminase activity; we show that overexpression of YJL070c instead mimics a loss of AMPD function. Expression of the yeast transcriptome was monitored in a AMPD-deficient mutant in a strain overexpressing YJL070c and in cells treated with the immunosuppressive drug mycophenolic acid, three conditions that lead to severe depletion of the guanylic nucleotide pool. These three conditions resulted in the up- or downregulation of multiple transcripts, 244 of which are common to at least two conditions and 71 to all three conditions. These transcriptome results, combined with specific mutant analysis, point to threonine metabolism as exquisitely sensitive to the purine nucleotide balance.
Risk of Rebleeding After Treatment of Acute Hydrocephalus in Patients With Aneurysmal Subarachnoid Hemorrhage

Background and Purpose— Cerebrospinal fluid drainage is often indicated in patients with acute hydrocephalus after aneurysmal subarachnoid hemorrhage but is believed to increase the risk of rebleeding. We studied the risk of rebleeding in patients with subarachnoid hemorrhage during treatment for acute hydrocephalus. Methods— We included patients with hydrocephalus treated with external ventricular drainage or lumbar punctures within 4 days after the hemorrhage and before aneurysm occlusion. Each treated patient was matched with a control patient with untreated hydrocephalus and a control patient without ventricular enlargement. Patients and controls were matched for interval since subarachnoid hemorrhage, duration of exposure, use of tranexamic acid, clinical condition on admission, and age. We used Cox regression to calculate hazard ratios and we adjusted for rebleeding that had occurred before starting the cerebrospinal fluid drainage. Results— In the group treated with external ventricular drainage, rebleeding occurred in seven of 34 patients (21%) with treatment, in seven of 34 controls (21%) with untreated hydrocephalus, and in six of 34 controls (18%) without hydrocephalus. In the group treated with one or more lumbar punctures, rebleeding occurred in one of 21 patients (5%) with treatment, in three of 21 controls (14%) with untreated hydrocephalus, and in none of the 21 controls without hydrocephalus. The hazard ratios for rebleeding were 1.0 (95% CI: 0.4 to 2.7) for external ventricular drainage treatment and 0.7 (95% CI: 0.1 to 6.4) for lumbar puncture treatment. Conclusion— This study does not confirm an importantly increased risk of rebleeding during external ventricular drainage or lumbar punctures for acute hydrocephalus after aneurysmal subarachnoid hemorrhage.
A Study on the Effects of Breathing Cycle Training Technique Together with Dzikr Recitation towards Achievement of Students' HRV

This experiment put emphasis on slow breathing exercise while reciting dzikr. The HRV readings of the students involved were recorded throughout the experiment. Slow breathing or resonant breathing exercises have been proven to be able to lower the heart rate and thus increase the HRV. Recitation of ‘dzikr’ (Islamic recitation) is known to have positive impacts towards emotion. When properly recited, ‘dzikr’ could bring calmness to the mind and emotions. An emotion at peace could then bring better results from any actions. Forty secondary school students with behavioral problems were chosen to undergo a biofeedback procedure that incorporated ‘dzikr’ recitation together with slow breathing technique. ‘Dzikr’ intervention enabled the students to make changes themselves using the technique of "Heart Rate Variability" (HRV). Students were instructed to perform resonant breathing while chanting slowly and loudly of the ‘la ilaha illa Allah’ ‘dzikr’. The study found that students who successfully completed the resonant breathing and ‘dzikr’ training were able to make changes within themselves. The students had successfully achieved the change score "HRV Coherence" of the VLF spectrum of LF and HF spectrum conditions. The study had found that this technique was very effective and suitable to be implemented to assist students in making behavioral changes. This technique can be used in schools to help improve the students’ behavior and thus enabling education programs to be implemented successfully.
Respiration signal as a promising diagnostic tool for late onset sepsis in premature newborns

The purpose of this study was to find out differences between septicemic and healthy premature newborns from the respiratory signal. An statistical analysis of breathing trace's temporal features showed significant differences between the inspiration/expiration ratio, being its average value shorter in healthy patients. All patient's total respiratory cycle time exceeding the apnea threshold were classified, and two different distributions had been found: log-normal for non septicemic and GEV (Generalized Extreme Value) distribution for septicemic. Finally, assessing fractal signal properties, we found an increased Hurst exponent (H) in non infected population. Results suggest that respiratory parameters could be helpful in sepsis diagnosis together with heart rate variability (HRV), demonstrated a relevant marker by our research team.
A Cyclical Model of Exchange Rate Volatility

In this paper, we investigate the long run dynamics of the intraday range of the GBP/USD, JPY/USD and CHF/USD exchange rates. We use a non-parametric filter to extract the low frequency component of the intraday range, and model the cyclical deviation of the range from the long run trend as a stationary autoregressive process. We find that the long run trend is time-varying but highly persistent, while the cyclical component is strongly mean reverting. This has important implications for modelling and forecasting volatility over both short and long horizons. As an illustration, we use the cyclical volatility model to generate out-of-sample forecasts of exchange rate volatility for horizons of up to one year under the assumption that the long run trend is fully persistent. As a benchmark, we compare the forecasts of the cyclical volatility model with those of the two-factor intraday range-based EGARCH model of Brandt and Jones (2006). Not only is the cyclical volatility model significantly easier to estimate than the EGARCH model, but it also offers a substantial improvement in out-of-sample forecast performance.
A Mechanism-Based PK/PD Model for Hematological Toxicities Induced by Antibody-Drug Conjugates

Antibody-drug conjugates (ADCs) are complex drug platforms composed of monoclonal antibodies (mAbs) conjugated to potent cytotoxic drugs (payloads) via chemical linkers, enabling selective payload delivery to neoplastic cells, resulting in improved efficacy and reduced toxicity. Brentuximab vedotin (Adcetris®, SGN-35) and adotrastuzumab emtansine (Kadcyla®, T-DM1) are the two FDA-approved and commercially available ADCs, and both drugs exhibit ADC-related thrombocytopenia and neutropenia. A pharmacokinetic/pharmacodynamic (PK/PD) model for ADCs was developed to identify the analyte from each ADC that is most associated with the observed hematopoietic toxicities and to determine the role of the apparent in vivo payload release rate on the severity of thrombocytopenia and neutropenia. Murine xenograft experiments and data from literature were combined, and the PK of both ADCs and their analytes were described with two-compartment models, with linear elimination and first-order payload release rate constants (krel). ADC-associated hematotoxicities were captured with a previously published PD model for myelosuppression driven by various analytes. ADC half-lives were about 5 days, and krel values were 0.46 (T-DM1) and 0.12 h−1 (SGN-35). The lifespans of platelets following T-DM1 and neutrophils following SGN-35 were 3.73 and 4.72 days. Comparison of alternate model structures suggested that mechanisms of myelosuppression are payload-driven for SGN-35 and ADC pinocytosis-dependent for T-DM1. Model simulations suggested that a 4-fold increase (T-DM1) and 70% decrease (SGN-35) in krel would improve hematotoxicity to grade 1. The proposed model successfully captured the PK and associated myelosuppression of both ADCs and might serve as a general PK/PD platform for assessing hematological toxicities to ADCs.
Dynamics of near-critical polymer gels.

We report the viscosity and the modulus of near-critical polyester gels. Previous work has shown that these gels lie in the middle of the static crossover between mean-field and critical percolation. Above the gel point, the modulus data are well described by the scaling law attributing kT of stored elastic energy per unentangled network strand. Below the gel point, the viscosity data disagree with both the de Gennes conductivity analogy and the Rouse model, possibly due to a subtleeffect of chain entanglement
The temporal scour progress downstream of low-head stilling basins under unsteady flow

This paper deals with the temporal evolution of local scour downstream of low-head stilling basins. In comparison to previous companion papers the most real conditions of unsteady approach flow are considered here. In this aim, experiments were carried out in a 1 m wide and 20 m long rectangular channel. Free overfall jets plunging into a horizontal apron were caused by an ogee-crested spillway. A nearly-uniform sediment with median grain size d 50  9 mm was used as mobile bed. The temporal effect of six different hydrographs on local scour depth was investigated under clear-water scour condition. Based on the data collected and the previous results for steady flow conditions a predictive model is proposed to simulate the temporal progress of the scour depth along the channel axis as function of tailwater densimetric Froude number, relative submergence, and dimensionless
Polynomial texture mapping and 3D representations

The results of a multi-image photographic technique are compared with those obtained by close-range scanning of the same object by a 3D colour laser scanner. The 3D representation achieved by the polynomial texture map (PTM) is compared with the extraction of normals from the same image set by photometric stereo. It is shown that the median of each of the X,Y,Z distributions of normal components for a large number of 3-light combinations is a good estimator of the true normal at each point. Using an incised Egyptian stone tablet, normals derived from these two techniques are compared with those generated by a 3D laser scanner. It is shown that the photometric stereo method produces the highest quality rendering of the surface.
The influence of transition metal solutes on the dislocation core structure and values of the Peierls stress and barrier in tungsten

Several transition metals were examined to evaluate their potential for improving the ductility of tungsten. The dislocation core structure and Peierls stress and barrier of 1/2〈111〉 screw dislocations in binary tungsten–transition metal alloys (W1−xTMx) were investigated using density functional theory calculations. The periodic quadrupole approach was applied to model the structure of the 1/2〈111〉 dislocation. Alloying with transition metals was modeled using the virtual crystal approximation and the applicability of this approach was assessed by calculating the equilibrium lattice parameter and elastic constants of the tungsten alloys. Reasonable agreement was obtained with experimental data and with results obtained from the conventional supercell approach. Increasing the concentration of a transition metal from the VIIIA group, i.e. the elements in columns headed by Fe, Co and Ni, leads to reduction of the C′ elastic constant and increase of the elastic anisotropy A = C44/C′. Alloying W with a group VIIIA transition metal changes the structure of the dislocation core from symmetric to asymmetric, similarly to results obtained for W1−xRex alloys in the earlier work of Romaner et al (2010 Phys. Rev. Lett. 104 195503). In addition to a change in the core symmetry, the values of the Peierls stress and barrier are reduced. The latter effect could lead to increased ductility in a tungsten-based alloy. Our results demonstrate that alloying with any of the transition metals from the VIIIA group should have a similar effect to alloying with Re.
Neural-Network-Based Decentralized Adaptive Output-Feedback Control for Large-Scale Stochastic Nonlinear Systems

This paper focuses on the problem of neural-network-based decentralized adaptive output-feedback control for a class of nonlinear strict-feedback large-scale stochastic systems. The dynamic surface control technique is used to avoid the explosion of computational complexity in the backstepping design process. A novel direct adaptive neural network approximation method is proposed to approximate the unknown and desired control input signals instead of the unknown nonlinear functions. It is shown that the designed controller can guarantee all the signals in the closed-loop system to be semiglobally uniformly ultimately bounded in a mean square. Simulation results are provided to demonstrate the effectiveness of the developed control design approach.
Learning to be prepared

Behavioral economics provides several motivations for the common observation that agents appear somewhat unwilling to deviate from recent choices. More recent choices can be more salient than other choices, or more readily available in the agent’s mind. Alternatively, agents may have formed habits, or use rules of thumb. This paper provides discrete-time adjustment processes for strategic games in which players display such a bias towards recent choices. In addition, players choose best replies to beliefs supported by observed play in the recent past. We characterize the limit behavior of these processes by showing that they eventually settle down in minimal prep sets (Voorneveld in Games Econ Behav 48:403–414, 2004).