Miracle-dz/UniFAR-FTUs huggingface dataset:
HetNet capacity with reduced power subframes

The time domain inter-cell interference coordination (eICIC) mechanism specified in LTE Rel. 10 improves the throughput of picocell-edge users by protecting them from macrocell interference. On the other hand, it also degrades the aggregate capacity in macrocell because the macro base station (MBS) does not transmit data during the coordinated subframes (CSFs). The MBS data transmission at a reduced power level during CSFs, which is referred to as FeICIC in LTE Rel. 11, can improve the capacity in macrocell while not causing high interference to the picocell users. Using stochastic geometry, this paper lays a theoretical foundation for analyzing the heterogeneous networks (HetNets) with reduced power subframes and range expansion bias (REB). The analytic expression for average capacity is derived and validated through Monte Carlo simulations. Our analysis shows that with optimum parameter settings FeICIC can provide substantially better performance than eICIC in terms of both aggregate capacity in a cell and fairness among the users.
Tree species of the central amazon and soil moisture alter stable isotope composition of nitrogen and oxygen in nitrous oxide evolved from soil

The use of stable isotopes of N and O in N2O has been proposed as a way to better constrain the global budget of atmospheric N2O and to better understand the relative contributions of the main microbial processes (nitrification and denitrification) responsible for N2O formation in soil. This study compared the isotopic composition of N2O emitted from soils under different tree species in the Brazilian Amazon. We also compared the effect of tree species with that of soil moisture, as we expected the latter to be the main factor regulating the proportion of nitrifier- and denitrifier-derived N2O and, consequently, isotopic signatures of N2O. Tree species significantly affected δ 15N in nitrous oxide. However, there was no evidence that the observed variation in δ 15N in N2O was determined by varying proportions of nitrifier- vs. denitrifier-derived N2O. We submit that the large variation in δ 15N-N2O is the result of competition between denitrifying and immobilizing microorganisms for NO 3 m . In addition to altering δ 15N-N2O, tree species affected net rates of N2O emission from soil in laboratory incubations. These results suggest that tree species contribute to the large isotopic variation in N2O observed in a range tropical forest soils. We found that soil water affects both 15N and 18O in N2O, with wetter soils leading to more depleted N2O in both 15N and 18O. This is likely caused by a shift in biological processes for 15N and possible direct exchange of 18O between H2O and N2O.
Do Performance Targets Affect Behaviour? Evidence from Discontinuities in Test Scores in England

Performance targets are ubiquitous in all areas of an individual's life such as education, jobs, sport competitions and charity donations. In this paper I assess whether meeting performance targets in tests at school has an effect on students' subsequent behaviour. This is helpful to test whether motivation and effort by students, parents and schools that the targets may induce, contribute to explain observed behaviour. I address potentially spurious correlations between test scores and behaviour by exploiting a regression discontinuity design in tests and a linked dataset of test scores and subsequent behaviour by students in compulsory education in England. I find that meeting a target that the government sets for students at age 11 has an insignificant effect on outcomes such as the probability of absence from school or of a police warning. I also find that meeting other targets for high and low ability students decreases the probability of being bullied by up to 34% with respect to the mean probability of such outcomes. The effects are heterogeneous as they vary by gender, parents' education level and type of behaviour. Overall, the research design offers a valuable test to assess unintended consequences that meeting the target or failing to meet it may lead to. The lack of a significant effect of targets on suspension and expulsion from school, as well as police warnings, suggests no adverse behavioural effect of performance targets, which is reassuring evidence on the design of tests in compulsory education. By using Probit estimates, one would conclude that meeting a target has an impact on behaviour. Regression discontinuity estimates show instead an insignificant effect at the expected target and a significant one at other targets for certain outcomes, although smaller than Probit estimates.
In the Staphylococcus aureus Two-Component System sae, the Response Regulator SaeR Binds to a Direct Repeat Sequence and DNA Binding Requires Phosphorylation by the Sensor Kinase SaeS

ABSTRACT Staphylococcus aureus uses the SaeRS two-component system to control the expression of many virulence factors such as alpha-hemolysin and coagulase; however, the molecular mechanism of this signaling has not yet been elucidated. Here, using the P1 promoter of the sae operon as a model target DNA, we demonstrated that the unphosphorylated response regulator SaeR does not bind to the P1 promoter DNA, while its C-terminal DNA binding domain alone does. The DNA binding activity of full-length SaeR could be restored by sensor kinase SaeS-induced phosphorylation. Phosphorylated SaeR is more resistant to digestion by trypsin, suggesting conformational changes. DNase I footprinting assays revealed that the SaeR protection region in the P1 promoter contains a direct repeat sequence (GTTAAN6GTTAA [where N is any nucleotide]). This sequence is critical to the binding of phosphorylated SaeR. Mutational changes in the repeat sequence greatly reduced both the in vitro binding of SaeR and the in vivo function of the P1 promoter. From these results, we concluded that SaeR recognizes the direct repeat sequence as a binding site and that binding requires phosphorylation by SaeS.
Calibrationless Parallel Magnetic Resonance Imaging: A Joint Sparsity Model

State-of-the-art parallel MRI techniques either explicitly or implicitly require certain parameters to be estimated, e.g., the sensitivity map for SENSE, SMASH and interpolation weights for GRAPPA, SPIRiT. Thus all these techniques are sensitive to the calibration (parameter estimation) stage. In this work, we have proposed a parallel MRI technique that does not require any calibration but yields reconstruction results that are at par with (or even better than) state-of-the-art methods in parallel MRI. Our proposed method required solving non-convex analysis and synthesis prior joint-sparsity problems. This work also derives the algorithms for solving them. Experimental validation was carried out on two datasets—eight channel brain and eight channel Shepp-Logan phantom. Two sampling methods were used—Variable Density Random sampling and non-Cartesian Radial sampling. For the brain data, acceleration factor of 4 was used and for the other an acceleration factor of 6 was used. The reconstruction results were quantitatively evaluated based on the Normalised Mean Squared Error between the reconstructed image and the originals. The qualitative evaluation was based on the actual reconstructed images. We compared our work with four state-of-the-art parallel imaging techniques; two calibrated methods—CS SENSE and l1SPIRiT and two calibration free techniques—Distributed CS and SAKE. Our method yields better reconstruction results than all of them.
Study the Response of Cucumber Plant to Different Magnetic Fields

Magnetic fields (MF) are widely distributed in the environment and their effects are increasing due to various instruments that are used in industry and medicine. In the present experiment, the growth and productivity of cucumber plants of seeds in which affected by different magnetic fields was investigated. The soaked seed samples of cucumber were exposed to a 20μT AC magnetic field for 30 minutes. Similar seed samples also were treated with DC magnetic fields of 5μT for 30 min. To compare the effect of different magnetic fields, control samples with three replications were placed in gape out of magnetic field for 30 min. Results of study showed that the germination of seeds was significantly influenced by different magnetic fields depending on the days after treatment application. The first germinated seeds were observed two days after beginning of test in DC magnetic field (0.7 seed) treatment. In the last days of experiments (day ninth), no difference was observed among treatments. The growth behavior of seedling of cucumber affected by different magnetic field in comparison with control plants in greenhouse showed that seeds in which treated with AC magnetic field have better growth rate. The results of evaluation of plants in the field showed that parameters like fruit length (FL), the diameter of fruit (FMD), Fruit weight (FW), number of side stem (NSS), flower number (NF) and the number of flower per main stem were not significantly different at different times of experiment. Contrary to that, parameters such as the number of fruits per plant (NF) and the length of main stem (LMS) were significantly increased by time. Based on the obtained results of the germination, greenhouse and field trials it can be concluded that direct magnetic field stimulates seed germination and increases the growth rate and vigor of seedling especially at the beginning of germination. Generally, it can be indicated that the initial effect of magnetic field on the germination rate and the growth of seedling is very positive since it induces an improved capacity for nutrient and water uptake, providing greater physical support to the developing shoot.
Greater abnormalities of brain cerebrospinal fluid volumes in younger than in older patients with Alzheimer's disease.

OBJECTIVE This study used a semiautomated analysis technique to quantify differences in regional brain cerebrospinal fluid volumes observed with computed tomography between healthy adults and patients with Alzheimer's disease (AD). DESIGN Cross-sectional, between-subject design, using an age-regression model. SETTING Palo Alto (Calif) Department of Veterans Affairs Medical Center. PATIENTS AND OTHER PARTICIPANTS The 117 patients with probable or definite AD were recruited from the Geriatric Psychiatry Research Unit and National Institute of Mental Health Clinical Research Center of the Palo Alto Department of Veterans Affairs Medical Center. The 114 healthy volunteers were recruited from the local community. MAIN OUTCOME MEASURES Cerebrospinal fluid volumes estimated from computed tomographic scans and neuropsychological test scores. RESULTS The computed tomographic estimates of ventricular and sulcal cerebrospinal fluid volumes increased significantly in all sampled brain regions in normal aging and were vastly larger in AD than in normal aging. Furthermore, younger patients with AD had significantly greater cerebrospinal fluid volume enlargement than did older patients with AD compared with healthy controls of their age. When the AD group was divided on the basis of reported age at symptom onset, patients in the early-onset group (onset before age 65 years) were quantitatively more abnormal than and showed a different pattern of abnormality from the patients in the late-onset group. This onset difference was also evident in neuropsychological test performance. CONCLUSIONS This cross-sectional study revealed a number of converging findings that suggested greater abnormality in the early-onset than in the late-onset group of patients with AD. The possibility remains, however, that the two onset groups represent different stages along a continuum of pathologic changes.
Prevalence and Reasons for Introducing Infants Early to Solid Foods: Variations by Milk Feeding Type

OBJECTIVE: To examine the prevalence of, and mothers’ self-reported reasons for, introducing solid foods to infants earlier than recommended (aged <4 months) and the variation in reasons for early introduction by milk feeding type. METHODS: The study included 1334 mothers who participated in the national longitudinal Infant Feeding Practices Study II (2005–2007). Monthly 7-day food-frequency questions throughout infancy were used to determine infant age at solid food introduction and to classify infant’s milk feeding at introduction as breast milk only, formula only, or mixed. Reasons for introducing solid foods at age <4 months were assessed through maternal responses to a list of 12 potential reasons. Analyses included descriptive statistics and multivariable logistic regression. RESULTS: Overall, 40.4% of mothers introduced solid foods before age 4 months. Prevalence varied by milk feeding type (24.3%, 52.7%, and 50.2% for breastfed, formula-fed, and mixed-fed infants, respectively). The most commonly cited reasons for early introduction of solid food were as follows: “My baby was old enough,” “My baby seemed hungry,” “I wanted to feed my baby something in addition to breast milk or formula,” “My baby wanted the food I ate,” “A doctor or other health care professional said my baby should begin eating solid food,” and “It would help my baby sleep longer at night. ” Four of these reasons varied by milk feeding type. CONCLUSIONS: Our findings highlight the high prevalence of early introduction of solids and provide details on why mothers introduced solid foods early.
Physicochemical and Antioxidant Properties of Algerian Honey

The aim of the present study was to characterize the physical, biochemical and antioxidant properties of Algerian honey samples (n = 4). Physical parameters, such as pH, moisture content, electrical conductivity (EC), total dissolved solids (TDS), color intensity, total sugar and sucrose content were measured. Several biochemical and antioxidant tests were performed to determine the antioxidant properties of the honey samples. The mean pH was 3.84 ± 0.01, and moisture the content was 13.21 ± 0.16%. The mean EC was 0.636 ± 0.001, and the mean TDS was 316.92 ± 0.92. The mean color was 120.58 ± 0.64 mm Pfund, and the mean 5-hydroxymethylfurfural (HMF) content was 21.49 mg/kg. The mean total sugar and reducing sugar contents were 67.03 ± 0.68 g/mL and 64.72 ± 0.52 g/g, respectively. The mean sucrose content was 2.29 ± 0.65%. High mean values of phenolic (459.83 ± 1.92 mg gallic acid/kg), flavonoid (54.23 ± 0.62 mg catechin/kg), ascorbic acid (159.70 ± 0.78 mg/kg), AEAC (278.15 ± 4.34 mg/kg), protein (3381.83 ± 6.19 mg/kg) and proline (2131.47 ± 0.90) contents, as well as DPPH (39.57% ± 4.18) and FRAP activities [337.77 ± 1.01 µM Fe (II)/100 g], were also detected, indicating that Algerian honey has a high antioxidant potential. Strong positive correlations were found between flavonoid, proline and ascorbic acid contents and color intensity with DPPH and FRAP values. Thus, the present study revealed that Algerian honey is a good source of antioxidants.
Variable power broadcasting based on local information for source-dependent broadcasting protocols

A typical broadcasting protocol for wireless network usually involves fixed transmission power that covers, for example an area within 250 meters (m). However, it is often unnecessary to broadcast using fixed power because a node that needs to be covered may just be 100m away. By reducing the transmission power enough to cover this node, energy expenditure would be reduced, thus, prolonging the lifetime of battery-powered wireless networks such as Mobile Ad Hoc Networks (MANETs) and Wireless Sensor Networks (WSNs). Existing source-dependent broadcasting protocols do not have any mechanisms for adjusting the transmission power of nodes. Therefore, this paper proposes some effective mechanisms based on local neighborhood knowledge, while ensuring the overall network is still covered. Results of extensive simulations confirm the effectiveness of the proposed protocols in reducing energy consumption.
Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests.

The comparison of several statistical methods currently used for detection of differentially expressed genes was attempted both by a simulation approach and by the analysis of data sets of human expressed sequence tags, obtained from UniGene. In the simulated mixed case, mimicking a situation close to reality, the general chi(2) test was unexpectedly the most efficient in multiple tag sampling experiments, especially when dealing with variations affecting weakly expressed genes. On the other hand, Audic and Claverie's method proved the most efficient for detecting differences in gene expression when dealing with pairwise comparisons. By applying the above methods on UniGene-based data sets concerning two human kidney tumours compared with normal kidney tissue, three novel genes overexpressed in these tumours were identified. Software and additional information on statistical methodologies, simulation approach and data are available at http://telethon.bio. unipd.it/bioinfo/IDEG6/.
Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer

Molecular research in cancer is one of the largest areas of bioinformatic investigation, but it remains a challenge to understand biomolecular mechanisms in cancer-related pathways from high-throughput genomic data. This includes the Nuclear-factor-kappa-B (NFκB) pathway, which is central to the inflammatory response and cell proliferation in prostate cancer development and progression. Despite close scrutiny and a deep understanding of many of its members’ biomolecular activities, the current list of pathway members and a systems-level understanding of their interactions remains incomplete. Here, we provide the first steps toward computational reconstruction of interaction mechanisms of the NFκB pathway in prostate cancer. We identified novel roles for ATF3, CXCL2, DUSP5, JUNB, NEDD9, SELE, TRIB1, and ZFP36 in this pathway, in addition to new mechanistic interactions between these genes and 10 known NFκB pathway members. A newly predicted interaction between NEDD9 and ZFP36 in particular was validated by co-immunoprecipitation, as was NEDD9's potential biological role in prostate cancer cell growth regulation. We combined 651 gene expression datasets with 1.4M gene product interactions to predict the inclusion of 40 additional genes in the pathway. Molecular mechanisms of interaction among pathway members were inferred using recent advances in Bayesian data integration to simultaneously provide information specific to biological contexts and individual biomolecular activities, resulting in a total of 112 interactions in the fully reconstructed NFκB pathway: 13 (11%) previously known, 29 (26%) supported by existing literature, and 70 (63%) novel. This method is generalizable to other tissue types, cancers, and organisms, and this new information about the NFκB pathway will allow us to further understand prostate cancer and to develop more effective prevention and treatment strategies.
Misidentification of a Rare Species, Cryptococcus laurentii, by Commonly Used Commercial Biochemical Methods and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Systems: Challenges for Clinical Mycology Laboratories

ABSTRACT Forty-two putative Cryptococcus laurentii isolates identified by the Vitek 2 system were collected in China. The gold standard, internal transcribed spacer (ITS) sequencing, confirmed that only two isolates were genuine C. laurentii. Bruker Biotyper matrix-assisted laser desorption ionization–time of flight mass spectrometry was able to identify the C. laurentii isolates with an expanded custom database.
Functional diversity of bitter taste receptor TAS2R16 in primates

In mammals, bitter taste is mediated by TAS2R genes, which belong to the large family of seven transmembrane G protein-coupled receptors. Because TAS2Rs are directly involved in the interaction between mammals and their dietary sources, it is likely that these genes evolved to reflect species-specific diets during mammalian evolution. Here, we investigated the sensitivities of TAS2R16s of various primates by using a cultured cell expression system, and found that the sensitivity of each primate species varied according to the ligand. Especially, the sensitivity of TAS2R16 of Japanese macaques to salicin was much lower than that of human TAS2R16, which was supported by behavioural tests. These results suggest the possibility that bitter-taste sensitivities evolved independently by replacing specific amino acid residues of TAS2Rs in different primate species to adapt to food items they use.
New DNA Methylation Markers and Global DNA Hypomethylation Are Associated with Oral Cancer Development

DNA promoter methylation of tumor suppressor genes and global DNA hypomethylation are common features of head and neck cancers. Our goal was to identify early DNA methylation changes in oral premalignant lesions (OPL) that may serve as predictive markers of developing oral squamous cell carcinoma (OSCC). Using high-throughput DNA methylation profiles of 24 OPLs, we found that the top 86 genes differentially methylated between patients who did or did not develop OSCC were simultaneously hypermethylated, suggesting that a CpG island methylation phenotype may occur early during OSCC development. The vast majority of the 86 genes were nonmethylated in normal tissues and hypermethylated in OSCC versus normal mucosa. We used pyrosequencing in a validation cohort of 44 patients to evaluate the degree of methylation of AGTR1, FOXI2, and PENK promoters CpG sites that were included in the top 86 genes and of LINE1 repetitive element methylation, a surrogate of global DNA methylation. A methylation index was developed by averaging the percent methylation of AGTR1, FOXI2, and PENK promoters; patients with a high methylation index had a worse oral cancer–free survival (P = 0.0030). On the other hand, patients with low levels of LINE1 methylation had a significantly worse oral cancer–free survival (P = 0.0153). In conclusion, AGTR1, FOXI2, and PENK promoter methylation and LINE1 hypomethylation may be associated with an increased risk of OSCC development in patients with OPLs. Cancer Prev Res; 8(11); 1027–35. ©2015 AACR.
3 H ]-8-Cyclopentyl-1 , 3-dipropylxanthine Binding to Ax Adenosine Receptors of Intact Rat Ventricular Myocytes

The purpose of the present study was the identification of A, adenosine receptors in intact rat ventricular myocytes, which are thought to mediate the negative inotropic effects of adenosine. The adenosine receptor antagonist [H]-8-cydopentyl-l,3-dipropylxanthine was used as radioligand. Binding of the radioligand to intact myocytes was rapid, reversible, and saturable with a binding capacity of 40,000 binding sites per cell. The dissociation constant of the radioligand was 0.48 nM. The adenosine receptor antagonists 8-cyclopentyl-1,3-dipropylxanthine, "xanthine amine congener," and theophyUine were competitive inhibitors with affinities in agreement with results obtained for A, receptors in other tissues. Competition experiments using the adenosine receptor agonists A-N-phenylisopropyladenosine, S'-JV-ethylcarboxamidoadenosine, and S-N'-phenylisopropyladenosine gave monophasic displacement curves with A, values of 50 nM, 440 nM, and 4,300 nM, which agreed well with the GTP-inducable low affinity state in cardiac membranes. The low affinity for agonists was not due to agonist-induced desensitization, and correlated well with the corresponding ICM values for the inhibition of cyclic AMP accumulation by isoprenaline. It is suggested that only a low affinity state of A, receptors can be detected in intact rat myocytes due to the presence of high concentrations of guanine nucleotides in intact cells. (Circulation Research 1988;63:613-620)