Miracle-dz/UniFAR-FTUs huggingface dataset:
Consistency of Eating Rate, Oral Processing Behaviours and Energy Intake across Meals

Faster eating has been identified as a risk factor for obesity and the current study tested whether eating rate is consistent within an individual and linked to energy intake across multiple meals. Measures of ad libitum intake, eating rate, and oral processing at the same or similar test meal were recorded on four non-consecutive days for 146 participants (117 male, 29 female) recruited across four separate studies. All the meals were video recorded, and oral processing behaviours were derived through behavioural coding. Eating behaviours showed good to excellent consistency across the meals (intra-class correlation coefficients > 0.76, p < 0.001) and participants who ate faster took larger bites (β ≥ 0.39, p < 0.001) and consistently consumed more energy, independent of meal palatability, sex, body composition and reported appetite (β ≥ 0.17, p ≤ 0.025). Importantly, eating faster at one meal predicted faster eating and increased energy intake at subsequent meals (β > 0.20, p < 0.05). Faster eating is relatively consistent within individuals and is predictive of faster eating and increased energy intake at subsequent similar meals consumed in a laboratory context, independent of individual differences in body composition.
Gene Expression Analysis of Ex Vivo Expanded and Freshly Isolated NK Cells From Cancer Patients

The infusion of natural killer (NK) cells is a promising therapy for patients with advanced malignancies. Clinical expanded NK-cell products were compared with freshly isolated NK cells. Autologous peripheral blood mononuclear cells were collected by apheresis from 8 patients. NK cells were isolated by anti-CD3-negative selection followed by anti-CD56-positive selection. They were then expanded by co-culture with interleukin-2 and an irradiated Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line (EBV-TM-LCL) to produce 14 NK-cell products. Molecular changes in the 14 NK-cell products were characterized using gene and microRNA expression microarrays. EBV-TM-LCL feeder cells from 3 lots were also analyzed as they were expanded for over 90 days and each lot was used for multiple NK-cell expansions. The gene expression profiles among the 3 EBV-TM-LCL lots used showed no differences and were not affected by their time in culture. Freshly isolated and expanded NK cells had distinct gene and microRNA expression profiles. Compared with fresh NK cells, expanded NK cells overexpressed 1098 genes and 28 human microRNAs. Genes in the crosstalk between dendritic and NK cells and metabolic pathways were up-regulated in expanded NK cells, whereas genes in a number of immune function pathways were down-regulated. Among all the most up-regulated genes were the NK cell-activating receptor natural cytotoxicity triggering receptor 3, myxovirus restistance 1, lymphotoxin β, and BCL2-associated X protein. Although some expanded NK-cell product variability was observed, perhaps related to patient factors, further studies on larger numbers of products will be needed to determine the impact of these differences on clinical outcomes.
Clinical validation of the European Panel on the Appropriateness of Gastrointestinal Endoscopy (EPAGE) II criteria in an open-access unit: a prospective study

Background and study aims: The European Panel on the Appropriateness of Gastrointestinal Endoscopy (EPAGE I) criteria were recently updated (EPAGE II), but no prospective studies have used these criteria in clinical practice. The aim of the current study was to validate the EPAGE II criteria in an open-access endoscopy unit. Patients and methods: A prospective observational study was conducted in an open-access endoscopy unit at a tertiary care referral center. Consecutive outpatients (n = 1004; mean age 58.9 ± 13.1 years; 45 % men) were referred for diagnostic colonoscopy between September 2009 and February 2010. The appropriateness of colonoscopy was assessed based on EPAGE II criteria, and the relationship between appropriateness and both referral doctor and detection of significant lesions was examined. The effectiveness of EPAGE II criteria in assessing appropriateness was measured by means of sensitivity, specificity, and positive and negative predictive values for detecting significant lesions. Results: Colonoscopic cecal intubation was achieved in 956 patients (95.2 %). Most referral doctors were gastroenterologists (58.0 %) and the most common indication was colorectal cancer (CRC) screening (35.2 %). EPAGE II criteria were applicable in 968 patients (96.4 %); of these patients, the indication was appropriate in 778 (80.4 %), inappropriate in 102 (10.5 %), and uncertain in 88 (9.1 %). Patients with appropriate or uncertain indications based on EPAGE II criteria had more relevant endoscopic findings than those with inappropriate indications (38.8 % vs. 24.5 %; OR 1.95, 95 %CI 1.22 – 3.13; P < 0.005). Sensitivity and negative predictive value of EPAGE II criteria for detecting significant lesions were 93.1 % (95 %CI 90 % – 96 %) and 75.5 % (95 %CI 67 % – 84 %), respectively, whereas for advanced neoplastic lesions these values were 98.0 % (95 %CI 95 % – 100 %) and 98.0 % (95 % CI 95 % – 100 %), respectively. Adherence to EPAGE II recommendations was an independent predictor of finding a significant lesion (OR 1.93, 95 %CI 1.20 – 3.11; P = 0.007). Conclusions: EPAGE II is a simple, valid score for detecting inappropriate colonoscopies in clinical practice.
COPI Complex Is a Regulator of Lipid Homeostasis

Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets.
Preparation of Magnetic Molecularly Imprinted Polymer for Melamine and its application in milk sample analysis by HPLC

In this work, a simple and selective method was successfully developed for the determination of melamine (MEL) in milk sample using magnetic surface molecularly imprinted polymer (MMIPs) as sorbent. The MMIPs has been prepared by using MEL as template molecule, methacrylic acid (MAA) as functional monomer and Fe3O4@ SiO2 as magnetic support. The polymer was characterized by means of fourier transform infrared(FT-IR) analysis, X-ray diffraction (XRD) analysis, thermogravimetric Analysis (TGA) ,scanning electron microscope(SEM) and vibrating sample magnetometer (VSM). The results demonstrated that an imprinted polymer layer was successfully coated onto the surface of modified Fe3O4 nanomaterials, resulting in a good magnetic responsibility. The UV spectrophotometry was used to demonstrate the interaction between MEL and MAA. It was found that one MELwas entrapped by two MAA molecules. Binding selectivity, adsorption capacity and the reusability for MMIPs were also evaluated in details. Results indicated the prepared MMIPs exhibited high adsorption capacity, fast binding ability and high selectivity for melamine. Detection limits for melamine were within the range of 0.15-3.00 μg/mL, which could meet the analysis of trace melamine in milk. Calibration curve was established with R of 0.9997. The limit of detection (LOD) of this new method was 15 μg/L. The obtained results revealed that the extraction recoveries of melamine from real samples were in the range of 85.6% to 104.2%. This work proposed a sensitive, rapid, reliable and convenient approach for the determination of trace melamine in complicated milk sample.
Nus transcription elongation factors and RNase III modulate small ribosome subunit biogenesis in Escherichia coli

Escherichia coli NusA and NusB proteins bind specific sites, such as those in the leader and spacer sequences that flank the 16S region of the ribosomal RNA transcript, forming a complex with RNA polymerase that suppresses Rho‐dependent transcription termination. Although antitermination has long been the accepted role for Nus factors in rRNA synthesis, we propose that another major role for the Nus‐modified transcription complex in rrn operons is as an RNA chaperone insuring co‐ordination of 16S rRNA folding and RNase III processing that results in production of proper 30S ribosome subunits. This contrarian proposal is based on our studies of nusA and nusB cold‐sensitive mutations that have altered translation and at low temperature accumulate 30S subunit precursors. Both phenotypes are suppressed by deletion of RNase III. We argue that these results are consistent with the idea that the nus mutations cause altered rRNA folding that leads to abnormal 30S subunits and slow translation. According to this idea, functional Nus proteins stabilize an RNA loop between their binding sites in the 5′ RNA leader and on the transcribing RNA polymerase, providing a topological constraint on the RNA that aids normal rRNA folding and processing.
Organization of sensory neocortex in prairie voles (Microtus ochrogaster)

In the current investigation, the functional organization of visual, auditory, and somatosensory cortex was examined in prairie voles (Microtus ochrogaster) by using electrophysiological recording techniques. Functional boundaries of cortical fields were directly related to myeloarchitectonic boundaries. Our results demonstrated that most of the neocortex is occupied by the visual, auditory, and somatosensory areas. Specifically, a small area 17, or primary visual area (V1), was located on the caudomedial pole of the neocortex; a large auditory cortex (AC), which contains the primary auditory area (A1) and other auditory fields, encompassed almost the entire temporal pole; and a large area 3b, or primary somatosensory area (S1), contained a complete representation of the contralateral body surface. Furthermore, these areas were coextensive with distinct myeloarchitectonic appearances. We also observed that the AC appeared to be disproportionately large in the prairie vole compared with other rodents. In addition, we found that both primary and nonprimary areas contained neurons that responded to auditory stimulation. Finally, we observed within S1 a disproportionate amount of cortex that was devoted to representing the perioral hairs and the snout and also that neurons within this representation had very small receptive fields. We discuss the expanded auditory domain and the enlarged representation of perioral hairs as they relate to the specialized life style of the prairie vole. J. Comp. Neurol. 502:414–426, 2007. © 2007 Wiley‐Liss, Inc.
Molecular dynamics study of the RNA ring nanostructure: a phenomenon of self-stabilization

We study mechanical and thermodynamic properties of RNA nanostructures focusing on a hexagonal nanoring discussed in Yingling and Shapiro (2007 Nano Lett. 7 2328). We are concerned with the following main issues: (i) the stability of the nanoring versus temperature; (ii) the effect of the environment (solvent, counterions) on its stability; (iii) conformations and dynamics under external force. The process of evaporation of the ions from the ring upon temperature drop has been found, demonstrating a surprising feature—the uptake of ions by the nanoring increases with the temperature. The connection of this behavior to the dielectric constant of water, hydration and structural changes in the nanoring is discussed. Several properties of the nanoring, such as elastic and transport coefficients, have been determined. A measure of the tensile elasticity of the ring against its uniform 2D in-plane compression has been given, as Keff ⩽ 0.01 GPa, which is a much lower value compared to typical values found for soft matter other than RNA.
Necrotizing Enterocolitis in Infants with Ductal-Dependent Congenital Heart Disease

Abstract Objective Infants with congenital heart disease (CHD) receiving prostaglandins (PGEs) may be at an increased risk for necrotizing enterocolitis (NEC). Enteral feeding may further increase the risk of NEC in these patients. We evaluated the incidence of NEC and its association with enteral feeding in infants with ductal-dependent CHD. Study Design We examined a cohort of infants with CHD receiving PGE in neonatal intensive care units managed by the Pediatrix Medical Group (Sunrise, FL) between 1997 and 2010. We used logistic regression to evaluate the association between NEC and enteral feeding, as well as other risk factors, including antacid medications, inotropic and ventilator support, and anatomic characteristics, controlling for gestational age. Results We identified 6,710 infants with ductal-dependent CHD receiving PGE for 17,158 infant days. NEC occurred in 21 of the 6,710 (0.3%) infants, of whom 12/21 (57%) were < 37 weeks gestational age. The incidence of NEC was 1.2/1,000 infant days while on enteral feeds versus 0.4/1,000 infant days while not on enteral feeds (p = 0.27). Enteral feeding was not associated with a statistically significant increased odds of NEC on the day of diagnosis (odds ratio [OR] 2.08; 95% confidence interval [CI] 0.38, 11.7). Risk factors associated with a significant increased odds of NEC included a diagnosis of single-ventricle heart defect (OR 2.82; 95% CI 1.23, 6.49), although the overall risk in this population remained low (8/1,631, 0.5%). Conclusion The incidence of NEC in our cohort of infants with ductal-dependent CHD on PGE therapy was low and did not increase with enteral feeding.
Elevated atmospheric carbon dioxide concentrations promote ant tending of aphids

Animal mutualisms, which involve beneficial interactions between individuals of different species, are common in nature. Insect-insect mutualism, for example, is widely regarded as a keystone ecological interaction. Some mutualisms are anticipated to be modified by climate change, but the focus has largely been on plant-microbe and plant-animal mutualisms rather than those between animals. Ant-aphid mutualisms, whereby ants tend aphids to harvest their honeydew excretions and, in return, provide protection for the aphids, are widespread. The mutualism is heavily influenced by the quality and quantity of honeydew produced by aphids, which is directly affected by host plant quality. As predicted increases in concentrations of atmospheric carbon dioxide (eCO2 ) are widely reported to affect plant nutritional chemistry, this may also alter honeydew quality and hence the nature of ant-aphid mutualisms. Using glasshouse chambers and field-based open-top chambers, we determined the effect of eCO2 on the growth and nutritional quality (foliar amino acids) of lucerne (Medicago sativa). We determined how cowpea aphid (Aphis craccivora) populations and honeydew production were impacted when feeding on such plants and how this affected the tending behaviour of ants (Iridomyrmex sp.). eCO2 stimulated plant growth but decreased concentrations of foliar amino acids by 29% and 14% on aphid-infested plants and aphid-free plants, respectively. Despite the deterioration in host plant quality under eCO2 , aphids maintained performance and populations were unchanged by eCO2 . Aphids induced higher concentrations of amino acids (glutamine, asparagine, glutamic acid and aspartic acid) important for endosymbiont-mediated synthesis of essential amino acids. Aphids feeding under eCO2 also produced over three times more honeydew than aphids feeding under ambient CO2 , suggesting they were imbibing more phloem sap at eCO2 . The frequency of ant tending of aphids more than doubled in response to eCO2 . To our knowledge, this is the first study to demonstrate the effects of atmospheric change on an ant-aphid mutualism. In particular, these results highlight how impending changes to concentrations of atmospheric CO2 may alter mutualistic behaviour between animals. These could include positive impacts, as reported here, shifts from mutualism to antagonism, partner switches and mutualism abandonment.
Metformin can enhance the radiosensitivity of cholangiocarcinoma through AMPK-FOXO 3 a axis

This study aims to evaluate the potential of metformin in enhancing the radiosensitivity of cholangiocarcinoma. In this study, we used the methods of proliferation, clonogenic, transfection, western blotting, and cell apoptosis assays to test the human cholangiocarcinoma cells. The Orthotopic tumors in SCID mice were treated with ionizing radiation (IR) and metformin. Our study showed that metformin (5 mM-50 mM) inhibited the proliferation, induced apoptosis and radio-sensitised cholangiocarcinoma cells. Metformin can phosphorylate and activate AMP activated kinase (AMPK), therefore activated the Forkhead Box O3a (FOXO3a) and down-regulated the Forkhead Box M1 (FOXM1) at last. However, the FOXM1 expression was up-regulated when we knocked down the FOXO3a. Metformin or radiotherapy inhibited orthotopic tumor growth and the combined treatment enhanced this effect further than each treatment alone. Metformin can induce the apoptosis of cholangiocacinoma cells, inhibit tumor growth and sensitise them to IR. Metformin mediated its radiosensitivity enhancement action through the AMPKFOXO3a-FOXM1 pathway. Our results suggest that metformin can be a useful radiosensitizer in cholangiocarcinoma.
Learning to Hash on Structured Data

Hashing techniques have been widely applied for large scale similarity search problems due to the computational and memory efficiency.However, most existing hashing methods assume data examples are independently and identically distributed.But there often exists various additional dependency/structure information between data examplesin many real world applications. Ignoring this structure information may limit theperformance of existing hashing algorithms.This paper explores the research problemof learning to Hash on Structured Data (HSD) and formulates anovel framework that considers additional structure information.In particular, the hashing function is learned in a unified learning framework by simultaneously ensuring the structural consistency and preserving the similarities between data examples.An iterative gradient descent algorithm is designed as the optimization procedure. Furthermore, we improve the effectiveness of hashing function through orthogonal transformation by minimizing the quantization error.Experimentalresults on two datasets clearly demonstrate the advantages ofthe proposed method over several state-of-the-art hashing methods.
Parallelizing the Linkage Tree Genetic Algorithm and Searching for the Optimal Replacement for the Linkage Tree

The recently introduced Linkage Tree Genetic Algorithm (LTGA) has shown to exhibit excellent scalability on a variety of optimization problems. LTGA employs Linkage Trees (LTs) to identify and exploit linkage information between problem variables. In this work we present two parallel implementations of LTGA that enable us to leverage the computational power of a multi-processor architecture. These algorithm extensions for LTGA enable us to solve a problem that previously could not be solved, being the problem of finding high-quality predetermined linkage models that result in a better performance of LTGA for intricate problems by replacing the online-learned LTs. This is done by learning high-quality LTs offline by optimizing LTGAs performance as a function of static LTs. This results in a better performance of LTGA than with online-learned LTs as the problem complexity increases. A parameter-free implementation is used to search optimal subsets of linkage sets in the offline-learned LTs. This pruning of the LT results in a further performance improvement of the LTGA by, on average, removing about 50% of the linkage sets from the offline-learned LTs. This suggests that LTs contain redundancies that may possibly still be exploited to improve the performance of LTGA with online-learned LTs.
Respiratory toxicity and immunotoxicity evaluations of microparticle and nanoparticle C60 fullerene aggregates in mice and rats following nose-only inhalation for 13 weeks

Abstract C60 fullerene (C60), or buckminsterfullerene, is a spherical arrangement of 60 carbon atoms, having a diameter of approximately 1 nm, and is produced naturally as a by-product of combustion. Due to its small size, C60 has attracted much attention for use in a variety of applications; however, insufficient information is available regarding its toxicological effects. The effects on respiratory toxicity and immunotoxicity of C60 aggregates (50 nm [nano-C60] and 1 μm [micro-C60] diameter) were examined in B6C3F1/N mice and Wistar Han rats after nose-only inhalation for 13 weeks. Exposure concentrations were selected to allow for data evaluations using both mass-based and particle surface area-based exposure metrics. Nano-C60 exposure levels selected were 0.5 and 2 mg/m3 (0.033 and 0.112 m2/m3), while micro-C60 exposures were 2, 15 and 30 mg/m3 (0.011, 0.084 and 0.167 m2/m3). There were no systemic effects on innate, cell-mediated, or humoral immune function. Pulmonary inflammatory responses (histiocytic infiltration, macrophage pigmentation, chronic inflammation) were concentration-dependent and corresponded to increases in monocyte chemoattractant protein (MCP)-1 (rats) and macrophage inflammatory protein (MIP)-1α (mice) in bronchoalveolar lavage (BAL) fluid. Lung overload may have contributed to the pulmonary inflammatory responses observed following nano-C60 exposure at 2 mg/m3 and micro-C60 exposure at 30 mg/m3. Phenotype shifts in cells recovered from the BAL were also observed in all C60-exposed rats, regardless of the level of exposure. Overall, more severe pulmonary effects were observed for nano-C60 than for micro-C60 for mass-based exposure comparisons. However, for surface-area-based exposures, more severe pulmonary effects were observed for micro-C60 than for nano-C60, highlighting the importance of dosimetry when evaluating toxicity between nano- and microparticles.
Expression of a Protein Phosphatase 1 Inhibitor, cdNIPP1, Increases CDK9 Threonine 186 Phosphorylation and Inhibits HIV-1 Transcription*

CDK9/cyclin T1, a key enzyme in HIV-1 transcription, is negatively regulated by 7SK RNA and the HEXIM1 protein. Dephosphorylation of CDK9 on Thr186 by protein phosphatase 1 (PP1) in stress-induced cells or by protein phosphatase M1A in normally growing cells activates CDK9. Our previous studies showed that HIV-1 Tat protein binds to PP1 through the Tat Q35VCF38 sequence, which is similar to the PP1-binding RVXF motif and that this interaction facilitates HIV-1 transcription. In the present study, we analyzed the effect of expression of the central domain of nuclear inhibitor of PP1 (cdNIPP1) in an engineered cell line and also when cdNIPP1 was expressed as part of HIV-1 pNL4-3 in place of nef. Stable expression of cdNIPP1 increased CDK9 phosphorylation on Thr186 and the association of CDK9 with 7SK RNA. The stable expression of cdNIPP1 disrupted the interaction of Tat and PP1 and inhibited HIV-1 transcription. Expression of cdNIPP1 as a part of the HIV-1 genome inhibited HIV-1 replication. Our study provides a proof-of-concept for the future development of PP1-targeting compounds as inhibitors of HIV-1 replication.