Miracle-dz/UniFAR-FTUs huggingface dataset:
High-resolution mapping of the 11q13 amplicon and identification of a gene, TAOS1, that is amplified and overexpressed in oral cancer cells

Amplification of chromosomal band 11q13 is a common event in human cancer. It has been reported in about 45% of head and neck carcinomas and in other cancers including esophageal, breast, liver, lung, and bladder cancer. To understand the mechanism of 11q13 amplification and to identify the potential oncogene(s) driving it, we have fine-mapped the structure of the amplicon in oral squamous cell carcinoma cell lines and localized the proximal and distal breakpoints. A 5-Mb physical map of the region has been prepared from which sequence is available. We quantified copy number of sequence-tagged site markers at 42–550 kb intervals along the length of the amplicon and defined the amplicon core and breakpoints by using TaqMan-based quantitative microsatellite analysis. The core of the amplicon maps to a 1.5-Mb region. The proximal breakpoint localizes to two intervals between sequence-tagged site markers, 550 kb and 160 kb in size, and the distal breakpoint maps to a 250 kb interval. The cyclin D1 gene maps to the amplicon core, as do two new expressed sequence tag clusters. We have analyzed one of these expressed sequence tag clusters and now report that it contains a previously uncharacterized gene, TAOS1 (tumor amplified and overexpressed sequence 1), which is both amplified and overexpressed in oral cancer cells. The data suggest that TAOS1 may be an amplification-dependent candidate oncogene with a role in the development and/or progression of human tumors, including oral squamous cell carcinomas. The approach described here should be useful for characterizing amplified genomic regions in a wide variety of tumors.
Agroforestry practices, runoff, and nutrient loss: a paired watershed comparison.

A paired watershed study consisting of agroforestry (trees plus grass buffer strips), contour strips (grass buffer strips), and control treatments with a corn (Zea mays L.)-soybean [Glycine max (L.) Merr. ] rotation was used to examine treatment effects on runoff, sediment, and nutrient losses. During the (1991-1997) calibration and subsequent three-year treatment periods, runoff was measured in 0.91- and 1.37-m H-flumes with bubbler flow meters. Composite samples were analyzed for sediment, total phosphorus (TP), total nitrogen (TN), nitrate, and ammonium. Calibration equations developed to predict runoff, sediment, and nutrients losses explained 66 to 97% of the variability between treatment watersheds. The contour strip and agroforestry treatments reduced runoff by 10 and 1% during the treatment period. In both treatments, most runoff reductions occurred in the second and third years after treatment establishment. The contour strip treatment reduced erosion by 19% in 1999, while erosion in the agroforestry treatment exceeded the predicted loss. Treatments reduced TP loss by 8 and 17% on contour strip and agroforestry watersheds. Treatments did not result in reductions in TN during the first two years of the treatment period. The contour strip and agroforestry treatments reduced TN loss by 21 and 20%, respectively, during a large precipitation event in the third year. During the third year of treatments, nitrate N loss was reduced 24 and 37% by contour strip and agroforestry treatments. Contour strip and agroforestry management practices effectively reduced nonpoint-source pollution in runoff from a corn-soybean rotation in the clay pan soils of northeastern Missouri.
Compressed full-text indexes

Full-text indexes provide fast substring search over large text collections. A serious problem of these indexes has traditionally been their space consumption. A recent trend is to develop indexes that exploit the compressibility of the text, so that their size is a function of the compressed text length. This concept has evolved into self-indexes, which in addition contain enough information to reproduce any text portion, so they replace the text. The exciting possibility of an index that takes space close to that of the compressed text, replaces it, and in addition provides fast search over it, has triggered a wealth of activity and produced surprising results in a very short time, which radically changed the status of this area in less than 5 years. The most successful indexes nowadays are able to obtain almost optimal space and search time simultaneously. In this article we present the main concepts underlying (compressed) self-indexes. We explain the relationship between text entropy and regularities that show up in index structures and permit compressing them. Then we cover the most relevant self-indexes, focusing on how they exploit text compressibility to achieve compact structures that can efficiently solve various search problems. Our aim is to give the background to understand and follow the developments in this area.
Working Paper No . 2012 / 34 Mapping the Impacts of Food Aid Current Knowledge and Future Directions

This paper provides an overview on the impacts of food aid. We consider its effects on consumption, nutrition, food markets and labour supply, as well as the extent to which it exacerbates or mitigates conflict. We also consider the comparative evidence on alternatives to food aid including evidence on cost, impact, relative risks and beneficiary preferences. We note that there are two large gaps in the extant literature: the comparative effects of food and cash assistance at the household level; and the causal links between food aid and conflict.
Sensorless Control of PMSM in a High-Speed Region Considering Iron Loss

In a very high-speed operation (≥ 50 kr/min), the iron loss is not sufficiently small to be neglected. The iron loss alters the angle and magnitudes of the back electromotive force (EMF). The resistance representing the iron loss is calculated a priori from a finite-element analysis and incorporated into a lookup table, because it is dependent on the current magnitudes. Utilizing the extended EMF method, a sensorless control method is developed for a model that takes the iron loss into account. The proposed method overcomes the angle difference in the high-speed region, and the performance is demonstrated through simulation and experimental results.
นพินธต์น้ฉบบั : : Comparisons of pharmacokinetic parameters of valproic acid between responsive and resistant adult epileptic

Objectives To determine whether there are valproic acid (VPA) pharmacokinetic (PK) parameters differences between the VPA-responsive and VPA-resistant patient groups. Methods Thirty-three subjects (14 patients were in VPA-resistant group and 19 patients in VPA-responsive group) who were epileptic patients were recruited from the Neurology Clinic, Neurology Institute, Bangkok. Their ages were 15 65 years old. They were either treated with VPA (Depakine Chrono) monotherapy or polytherapy in which the combined drug did not have the same metabolic pathways as VPA. At steady state condition, two blood samples were collected from the subjects during elimination phase, approximately five hours apart. Individual PK parameter values of VPA were estimated using the equations for a linear one-compartment model with a first-order declining of drug concentration after the end of 14 hours zero-order drug release. Chi-square test and the odds ratio were used to analize the data. นพินธต์น้ฉบบั
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing

Gene expression is regulated by combinations of transcription factors, which can be mapped to regulatory elements on a genome-wide scale using ChIP experiments. In a previous ChIP-chip study of USF1 and USF2 we found evidence also of binding of GABP, FOXA2 and HNF4a within the enriched regions. Here, we have applied ChIP-seq for these transcription factors and identified 3064 peaks of enrichment for GABP, 7266 for FOXA2 and 18783 for HNF4a. Distal elements with USF2 signal was frequently bound also by HNF4a and FOXA2. GABP peaks were found at transcription start sites, whereas 94% of FOXA2 and 90% of HNF4a peaks were located at other positions. We developed a method to accurately define TFBS within peaks, and found the predicted sites to have an elevated conservation level compared to peak centers; however the majority of bindings were not evolutionary conserved. An interaction between HNF4a and GABP was seen at TSS, with one-third of the HNF4a positive promoters being bound also by GABP, and this interaction was verified by co-immunoprecipitations.
Novel S = 1 / 2 Kagome Lattice Materials : Cs 2 TiCu 3 F 12 and Rb 2 TiCu 3 F 12

Two new members of the A2B′Cu3F12 family of kagome-related materials have been prepared, in order to further understand the crystal-chemical relationships, phase transitions and magnetic behaviour within this family of potentially frustrated S = 1⁄2 two-dimensional quantum magnets. Cs2TiCu3F12 adopts a crystal structure with the ideal kagome lattice topology (space group R3̅m) at ambient temperature. Diffraction studies reveal different symmetry-lowering structural phase transitions in single crystal and polycrystalline forms at sub-ambient temperatures, with the single crystal form retaining rhombohedral symmetry OPEN ACCESS Crystals 2015, 5 227 and the powder form being monoclinic. In both cases, long-range antiferromagnetic order occurs in the region 16–20 K. Rb2TiCu3F12 adopts a distorted triclinic structure even at ambient temperatures.
Dynamical Simulation and Statistical Analysis of Velocity Fluctuations of a Turbulent Flow behind a Cube

A statistical approach for the treatment of turbulence data generated by computer simulations is presented. A model for compressible flows at large Reynolds numbers and low Mach numbers is used for simulating a backward-facing step airflow. A scaling analysis has justified the commonly used assumption that the internal energy transport due to turbulent velocity fluctuations and the work done by the pressure field are the only relevant mechanisms needed to model subgrid-scale flows. From the numerical simulations, the temporal series of velocities are collected for ten different positions in the flow domain, and are statistically treated. The statistical approach is based on probability averages of the flow quantities evaluated over several realizations of the simulated flow. We look at how long of a time average is necessary to obtain well-converged statistical results. For this end, we evaluate the mean-square difference between the time average and an ensemble average as the measure of convergence. This is an interesting question since the validity of the ergodic hypothesis is implicitly assumed in every turbulent flow simulation and its analysis. The ergodicity deviations from the numerical simulations are compared with theoretical predictions given by scaling arguments. A very good agreement is observed. Results for velocity fluctuations, normalized autocorrelation functions, power spectra, probability density distributions, as well as skewness and flatness coefficients are also presented.
Academic Ignorance and Black Intelligence.

The controversy over why children in the inner-city schools show such low educational achievement has been examined in several recent issues of The Atlantic. In the September, 1971, Atlantic, R. J. Herrnstein summarized the position of psychologists and others who believe that heredity is substantially more important than environment in determining intelligence, as measured by IQ tests. In its issue of December, 1971, The Atlantic published a number of letters (the correspondents included sociologists, anthropologists, economists, educators, and a few psychologists) taking issue with Professor Herrnstein's article. Many of those who wrote maintained that environmental factors, rather than any genetic deficit, explain the poor performance of lower-class inner-city children. A third position held by linguists and many anthropologists locates the problem not in the children, but in the relations between them and the school system. This position holds that inner-city children do not necessarily have inferior mothers, language, or experience, but that the language, family style, and ways of living of inner-city children are significantly different from the standard culture of the classroom, and that this difference is not always properly understood by teachers and psychologists. Linguists believe that we must begin to adapt our school system to the language and learning styles of the majority in the inner-city schools. They argue that everyone has the right to learn the standard languages and culture in reading and writing (and speaking, if they are so inclined); but this is the end result, not the beginning of the educational process. They do not believe that the standard language is the only medium in which teaching and learning can take place, or that the first step in education is to convert all first-graders to replicas of white middle-class suburban children. This article grew out of my own attempt to state the linguistic position on these issues at a Georgetown Round Table in 1968. While psychologists are obviously divided, linguists find (somewhat to their own surprise) that they all agree. My own statement here is based on research carried out in South Central Harlem from 1965 to 1968 by a team of two white and two black investigators, supported by the Office of Education. Our aim was to describe the differences between the standard English of the classroom and the vernacular language used by members of the street culture. We carried out long-term participant-observation with a number of black adolescent It is important to …
Regulation of (cid:2) cell glucokinase by S-nitrosylation and association with nitric oxide synthase

lucokinase (GK) activity plays a key role in glucose-stimulated insulin secretion from pancreatic (cid:2) cells. Insulin regulates GK activity by modulating its association with secretory granules, although little is known about the mechanisms involved in regulating this association. Using quantitative imaging of multicolor ﬂuorescent proteins fused to GK, we found that the dynamic association of GK with secretory granules is modulated through nitric oxide (NO). Our results in cultured (cid:2) cells show that insulin stim-ulates NO production and leads to S-nitrosylation of GK. Furthermore, inhibition of NO synthase (NOS) activity blocks insulin-stimulated changes in both GK association G with secretory granules and GK conformation. Mutation of cysteine 371 to serine blocks S-nitrosylation of GK and causes GK to remain tightly bound to secretory granules. GK was also found to interact stably with neuronal NOS as detected by coimmunoprecipitation and ﬂuorescence resonance energy transfer. Finally, attachment of a nuclear localization signal sequence to NOS drives GK to the nucleus in addition to its normal cytoplasmic and granule targeting. Together, these data suggest that the regulation of GK localization and activity in pancreatic (cid:2) cells is directly related to NO production and that the association of GK with secretory granules occurs through its interaction with 0.1 mM neocuproine) using 0.5% Triton X-100 and 0.5% cholate before protection of free cys- teines with methyl methanethiosulfonate (Pierce Chemical Co.) and de-rivatization of S-nitrosylated cysteines with ascorbic acid and biotin-HPDP (Pierce Chemical Co.). Biotinylated proteins were isolated by binding to neutravidin-agarose (Pierce Chemical Co.) followed by five washes with a high salt buffer (20 mM Hepes, pH 7.7, 600 mM NaCl, 1 mM EDTA, 0.5% Triton X-100) and elution in HNE buffer (20 mM Hepes, pH 7.7, 100 mM NaCl, 1 mM EDTA) plus 100 mM 2-mercaptoethanol. Alternatively, GK-YFPs were isolated by immunoprecipitation with A.v. Peptide Antibody (BD BioSciences, Clontech Laboratories, Inc.) preconjugated to IgG agarose (Sigma-Aldrich). Western blots were then performed on eluted pro- teins to detect GK and nitrosylated proteins.
Poly(alcian blue) Modified Carbon Paste Electrode for the Determination of Catechol in Presence of Hydroquinone: A Voltammetric Study

The carbon paste electrode (CPE) was modified by electropolymerisation of alcian blue in 0.2 M phosphate buffer solution (PBS) of pH 7.4 by using cyclic voltammetric (CV) technique. The fabricated electrode was employed for the electrochemical analysis of catechol (CC) and hydroquinone (HQ). The effect of scan rate suggests the adsorption controlled electrode process. A good analytical performance was observed in terms of sensitivity, selectivity, linearity and observed detection limits. The lower limit of detection of CC and HQ was found to be 0. 104μM and 0. 142μM by cyclic voltammetric technique. Because of the catalytic capability of the fabricated electrode the simultaneous separation was observed in a binary mixture containing CC and HQ.
Ultra-low duty cycle MAC with scheduled channel polling

Energy is a critical resource in sensor networks. MAC protocols such as S-MAC and T-MAC coordinate sleep schedules to reduce energy consumption. Recently, lowpower listening (LPL) approaches such as WiseMAC and B-MAC exploit very brief polling of channel activity combined with long preambles before each transmission, saving energy particularly during low network utilization. Synchronization cost, either explicitly in scheduling, or implicitly in long preambles, limits all these protocols to duty cycles of 1-2%. We demonstrate that ultra-low duty cycles of 0.1% and below are possible with a new MAC protocol called scheduled channel polling (SCP). This work prompts three new contributions: First, we establish optimal configurations for both LPL and SCP under fixed conditions, developing a lower bound of energy consumption. Under these conditions, SCP can extend lifetime of a network by a factor of 3-6 times over LPL. Second, SCP is designed to adapt well to variable traffic. LPL is optimized for known, periodic traffic, and long preambles become very costly when traffic varies. In one experiment, SCP reduces energy consumption by a factor of 10 under bursty traffic. We also show how SCP adapts to heavy traffic and streams data in multi-hop networks, reducing latency by 85% and energy by 95% at 9 hops. Finally, we show that SCP can operate effectively on recent hardware such as 802.15. 4 radios. In fact, power consumption of SCP decreases with faster radios, but that of LPL increases.
Genotypes and Pathogenicity of Cellulitis Isolates Reveal Traits That Modulate APEC Virulence

We characterized 144 Escherichia coli isolates from severe cellulitis lesions in broiler chickens from South Brazil. Analysis of susceptibility to 15 antimicrobials revealed frequencies of resistance of less than 30% for most antimicrobials except tetracycline (70%) and sulphonamides (60%). The genotyping of 34 virulence-associated genes revealed that all the isolates harbored virulence factors related to adhesion, iron acquisition and serum resistance, which are characteristic of the avian pathogenic E. coli (APEC) pathotype. ColV plasmid-associated genes (cvi/cva, iroN, iss, iucD, sitD, traT, tsh) were especially frequent among the isolates (from 66.6% to 89.6%). According to the Clermont method of ECOR phylogenetic typing, isolates belonged to group D (47.2%), to group A (27.8%), to group B2 (17.4%) and to group B1 (7.6%); the group B2 isolates contained the highest number of virulence-associated genes. Clonal relationship analysis using the ARDRA method revealed a similarity level of 57% or higher among isolates, but no endemic clone. The virulence of the isolates was confirmed in vivo in one-day-old chicks. Most isolates (72.9%) killed all infected chicks within 7 days, and 65 isolates (38.1%) killed most of them within 24 hours. In order to analyze differences in virulence among the APEC isolates, we created a pathogenicity score by combining the times of death with the clinical symptoms noted. By looking for significant associations between the presence of virulence-associated genes and the pathogenicity score, we found that the presence of genes for invasins ibeA and gimB and for group II capsule KpsMTII increased virulence, while the presence of pic decreased virulence. The fact that ibeA, gimB and KpsMTII are characteristic of neonatal meningitis E. coli (NMEC) suggests that genes of NMEC in APEC increase virulence of strains.
The zCOSMOS survey: the role of the environment in the evolution of the luminosity function of different galaxy types

(Abridged) We studied the evolution in the B band luminosity function to z~1 in the zCOSMOS 10k sample, for which both accurate galaxy classifications and a detailed description of the local density field are available. The global LF exhibits a brightening of ~0.7 mag in M* from z~0.2 to z~0.9. At low z, late types dominate at faint magnitudes, while the bright end is populated mainly by early types. At higher z, late-type galaxies evolve significantly and, at z~1, the contribution from the various types to the bright end of the LF is comparable. The evolution for early types is in both luminosity and normalization. A similar behaviour is exhibited by late types, but with an opposite trend for the normalization. Studying the role of the environment, we find that the global LF of galaxies in overdense regions has always a brighter M* and a flatter slope. In low density environments, the main contribution to the LF is from blue galaxies, while for high density environments there is an important contribution from red galaxies to the bright end. The differences between the global LF in the two environments are not due to only a difference in the relative numbers of red and blue galaxies, but also to their relative luminosity distributions: the value of M* for both types in underdense regions is always fainter than in overdense environments. The "specular" evolution of late- and early-type galaxies is consistent with a scenario where a part of blue galaxies is transformed in red galaxies with increasing cosmic time, without significant changes in the fraction of intermediate-type galaxies. The bulk of this tranformation in overdense regions probably happened before z~1, while it is still ongoing at lower z in underdense environments.