Sao Paulo State University

About: Sao Paulo State University is a education organization based out in São Paulo, Brazil. It is known for research contribution in the topics: Population & Large Hadron Collider. The organization has 55715 authors who have published 100436 publications receiving 1375332 citations.

RNA-Seq differential expression analysis: An extended review and a software tool.

Abstract: The correct identification of differentially expressed genes (DEGs) between specific conditions is a key in the understanding phenotypic variation. High-throughput transcriptome sequencing (RNA-Seq) has become the main option for these studies. Thus, the number of methods and softwares for differential expression analysis from RNA-Seq data also increased rapidly. However, there is no consensus about the most appropriate pipeline or protocol for identifying differentially expressed genes from RNA-Seq data. This work presents an extended review on the topic that includes the evaluation of six methods of mapping reads, including pseudo-alignment and quasi-mapping and nine methods of differential expression analysis from RNA-Seq data. The adopted methods were evaluated based on real RNA-Seq data, using qRT-PCR data as reference (gold-standard). As part of the results, we developed a software that performs all the analysis presented in this work, which is freely available at https://github.com/costasilvati/consexpression. The results indicated that mapping methods have minimal impact on the final DEGs analysis, considering that adopted data have an annotated reference genome. Regarding the adopted experimental model, the DEGs identification methods that have more consistent results were the limma+voom, NOIseq and DESeq2. Additionally, the consensus among five DEGs identification methods guarantees a list of DEGs with great accuracy, indicating that the combination of different methods can produce more suitable results. The consensus option is also included for use in the available software.

Constraints on the spin-parity and anomalous HVV couplings of the Higgs boson in proton collisions at 7 and 8 TeV

Abstract: The study of the spin-parity and tensor structure of the interactions of the recently discovered Higgs boson is performed using the H to ZZ, Z gamma*, gamma* gamma* to 4 l, H to WW to l nu l nu, and H to gamma gamma decay modes. The full dataset recorded by the CMS experiment during the LHC Run 1 is used, corresponding to an integrated luminosity of up to 5.1 inverse femtobarns at a center-of-mass energy of 7 TeV and up to 19.7 inverse femtobarns at 8 TeV. A wide range of spin-two models is excluded at a 99% confidence level or higher, or at a 99.87% confidence level for the minimal gravity-like couplings, regardless of whether assumptions are made on the production mechanism. Any mixed-parity spin-one state is excluded in the ZZ and WW modes at a greater than 99.999% confidence level. Under the hypothesis that the resonance is a spin-zero boson, the tensor structure of the interactions of the Higgs boson with two vector bosons ZZ, Z gamma, gamma gamma, and WW is investigated and limits on eleven anomalous contributions are set. Tighter constraints on anomalous HVV interactions are obtained by combining the HZZ and HWW measurements. All observations are consistent with the expectations for the standard model Higgs boson with the quantum numbers J[PC]=0[++].

Evaluating distributed generation impacts with a multiobjective index

Abstract: Evaluating the technical impacts associated with connecting distributed generation to distribution networks is a complex activity requiring a wide range of network operational and security effects to be qualified and quantified. One means of dealing with such complexity is through the use of indices that indicate the benefit or otherwise of connections at a given location and which could be used to shape the nature of the contract between the utility and distributed generator. This paper presents a multiobjective performance index for distribution networks with distributed generation which considers a wide range of technical issues. Distributed generation is extensively located and sized within the IEEE-34 test feeder, wherein the multiobjective performance index is computed for each configuration. The results are presented and discussed.

Follicular deviation and acquisition of ovulatory capacity in bovine follicles

Abstract: Selection of dominant follicles in cattle is associated with a deviation in growth rate between the dominant and largest subordinate follicle of a wave (diameter deviation). To determine whether acquisition of ovulatory capacity is temporally associated with diameter deviation, cows were challenged with purified LH at known times after a GnRH-induced LH surge (experiment 1) or at known follicular diameters (experiments 2 and 3). A 4-mg dose of LH induced ovulation in all cows when the largest follicle was ≥12 mm (16 of 16), in 17% (1 of 6) when it was 11 mm, and no ovulation when it was ≤10 mm (0 of 19). To determine the effect of LH dose on ovulatory capacity, follicular dynamics were monitored every 12 h, and cows received either 4 or 24 mg of LH when the largest follicle first achieved 10 mm in diameter (experiment 2). The proportion of cows ovulating was greater (P < 0.05) for the 24-mg (9 of 13; 69.2%) compared with the 4-mg (1 of 13; 7.7%) LH dose. To determine the effect of a higher LH dose on follicles near diameter deviation, follicular dynamics were monitored every 8 h, and cows received 40 mg of LH when the largest follicle first achieved 7.0, 8.5, or 10.0 mm (experiment 3). No cows with a follicle of 7 mm (0 of 9) or 8.5 mm (0 of 9) ovulated, compared with 80% (8 of 10) of cows with 10-mm follicles. Thus, follicles acquired ovulatory capacity at about 10 mm, corresponding to about 1 day after the start of follicular deviation, but they required a greater LH dose to induce ovulation compared with larger follicles. We speculate that acquisition of ovulatory capacity may involve an increased expression of LH receptors on granulosa cells of the dominant follicle and that this change may also be important for further growth of the dominant follicle.

Juvenile localized scleroderma: clinical and epidemiological features in 750 children. An international study

Abstract: Objective. Juvenile localized scleroderma (JLS) includes a number of conditions often grouped together. With the long-term goal of developing uniform classification criteria, we studied the epidemiological, clinical and immunological features of children with JLS followed by paediatric rheumatology and dermatology centres. Methods. A large, multicentre, multinational study was conducted by collecting information on the demographics, family history, triggering environmental factors, clinical and laboratory features, and treatment of patients with JLS. Results. Seven hundred and fifty patients with JLS from 70 centres were enrolled into the study. The disease duration at diagnosis was 18 months. Linear scleroderma (LS) was the most frequent subtype (65%), followed by plaque morphea (PM) (26%), generalized morphea (GM) (7%) and deep morphea (DM) (2%). As many as 15% of patients had a mixed subtype. Ninety-one patients (12%) had a positive family history for rheumatic or autoimmune diseases; 100 (13.3%) reported environmental events as possible trigger. ANA was positive in 42.3% of the patients, with a higher prevalence in the LS-DM subtype than in the PM-GM subtype. Scl70 was detected in the sera of 3% of the patients, anticentromere antibody in 2%, anti-double-stranded DNA in 4%, anti-cardiolipin antibody in 13% and rheumatoid factor in 16%. Methotrexate was the drug most frequently used, especially during the last 5 yr. Conclusion. This study represents the largest collection of patients with JLS ever reported. The insidious onset of the disease, the delay in diagnosis, the recognition of mixed subtype and the better definition of the other subtypes should influence our efforts in educating trainees and practitioners and help in developing a comprehensive classification system for this syndrome.