Miracle-dz/UniFAR-FTUs huggingface dataset:
Chapter 27 -- Breast Cancer Genomics, Section VI, Pathology and Biological Markers of Invasive Breast Cancer

Section IV Pathology and Biological Markers of Invasive Breast Cancer Chapter 27 Breast Cancer Genomics Paul T. Spellman, Laura Heiser, and Joe W. Gray Affiliation(s): Lawrence Berkeley National Laboratory, Life Sciences Division Breast cancer is predominantly a disease of the genome with cancers arising and progressing through accumulation of aberrations that alter the genome—by changing DNA sequence, copy number, and structure in ways that that contribute to diverse aspects of cancer pathophysiology. Classic examples of genomic events that contribute to breast cancer pathophysiology include inherited mutations in BRCA1, BRCA2, TP53, and CHK2 that contribute to the initiation of breast cancer, amplification of ERBB2 (formerly HER2) and mutations of elements of the PI3‐kinase pathway that activate aspects of epidermal growth factor receptor (EGFR) signaling and deletion of CDKN2A/B that contributes to cell cycle deregulation and genome instability. It is now apparent that accumulation of these aberrations is a time‐ dependent process that accelerates with age (1). Although American women living to an age of 85 have a 1 in 8 chance of developing breast cancer, the incidence of cancer in women younger than 30 years is uncommon. This is consistent with a multistep cancer progression model whereby mutation and selection drive the tumor’s development, analogous to traditional Darwinian evolution (2, 3). In the case of cancer, the driving events are changes in sequence, copy number, and structure of DNA and alterations in chromatin structure or other epigenetic marks. Our understanding of the genetic, genomic, and epigenomic events that influence the development and progression of breast cancer is increasing at a remarkable rate through application of powerful analysis tools that enable genome‐wide analysis of DNA sequence and structure, copy number, allelic loss, and epigenomic modification. Application of these techniques to elucidation of the nature and timing of these events is enriching our understanding of mechanisms that increase breast cancer susceptibility, enable tumor initiation and progression to metastatic disease, and determine therapeutic response or resistance. These studies also reveal the molecular differences between cancer and normal that may be exploited to therapeutic benefit or that provide targets for molecular assays that may enable early cancer detection, and predict individual disease progression or response to treatment. This chapter reviews current and future directions in genome analysis and summarizes studies that provide insights into breast cancer pathophysiology or that suggest strategies to improve breast cancer management. CANCER GENOME SEQUENCE Mutations and Polymorphisms The discovery of germ‐line and somatic mutations has long been a critical component of cancer research. Driven by increasingly powerful normal and tumor DNA sequencing capabilities, a substantial
Suppression of Meloidogyne javanica and M. incognita on Tomato with Ground Seed of Castor, Crotalaria, Hairy Indigo, and Wheat

Two greenhouse trials were conducted to determine the influence of ground seed of castor (Ricinus communis), crotalaria (Crotalaria spectabilis), hairy indigo (Indigofera hirsuta), and wheat (Triticum aestivum) on tomato (Lycopersicon esculentum) growth and egg mass production of Meloidogyne javanica (test 1) or M. incognita (test 2). Ground seed from each plant species was individually mixed with an air-dried, fine sandy soil at rates of 0, 0.5, 1.0, and 2.0% (w/w). The mixtures were placed in one-liter plastic pots, and water was added to bring soil to field capacity. After ten days, 0 or 10 000 M. javanica or M. incognita eggs and juveniles were added to each pot. A single 'Homestead tomato seedling was transplanted into each pot and allowed to grow for 70 days in test 1 and 75 days in test 2. Compared to the nonamended control, egg mass production was significantly reduced by all treatments except the 0.5% levels of wheat and castor and the 1.0% castor treatment. The 2.0% levels
Sulfate reduction at low pH in organic wastewaters

The objective of the research described in this thesis was to investigate the operational window of dissimilatory sulfate reduction at low pH (6, 5 and 4) during the acidification of organic wastewaters. High sulfate reduction efficiencies at low pH are desirable for a more sustainable operation of acidification reactors in a two-phase wastewater treatment system, as pH control requires less caustic and/or the effluent recirculation from the second (methanogenic) reactor can be skipped. The low pH would also facilitate the removal of sulfide by stripping, as the fraction of gaseous sulfide increases with decreasing pH
Bioethics and Intersex: "Time out". A paradigm shift on Intersex Management in the Spanish context

In medical literature about management of Intersex, there has been considerable debate addressing ethical issues on medical practice ―informed consent, parents' rights to make decisions about surgery on infants or whether children should be surgically altered to suit the binary gender norms of society―. Selecting the best management for the various intersex situations can be complex, and several proposals concerning ethical principles have emerged. During the annual meeting of the Spanish support group Grapsia, we coordinated a "Bioethics and Intersex/DSD" discussion group, with the aim to identify some key elements to enhance socio-health care for people with intersex variations and their families. On the one hand, it is necessary to consider the particularities of each context and the constraints imposed by the structure and organization of each country's health systems. On the other hand, it is crucial to include insights of patients taking part in support groups and their families.
Electron transport chains of lactic acid bacteria

Lactic acid bacteria are generally considered facultative anaerobic obligate fermentative bacteria. They are unable to synthesize heme. Some lactic acid bacteria are unable to form menaquinone as well. Both these components are cofactors of respiratory (electron transport) chains of prokaryotic bacteria. Lactococcus lactis, and several other lactic acid bacteria, however respond to the addition of heme in aerobic growth conditions. This response includes increased biomass and robustness. In this study we demonstrate that heme-grown Lactococcus lactis in fact do have a functional electron transport chain that is capable of generating a proton motive force in the presence of oxygen. In other words, heme addition induces respiration in Lactococcus lactis. This aerobic electron transport chain contains a NADH-dehydrogenase, a menaquinone-pool and a bd-type cytochrome. A phenotypic and genotypic screening revealed a similar response, induced by heme (and menaquinone) supplementation, in other lactic acid bacteria. The genome of Lactobacillus plantarum WCFS1 was predicted to encode a nitrate reductase A complex. We have found that Lactobacillus plantarum is capable of using nitrate as terminal electron acceptor, when heme and menaquinone are provided. Nitrate can be used by Lactobacillus plantarum as effective electron sink and allows growth on a extended range of substrates. The impact of both the aerobic and anaerobic electron transport chain, on the metabolism and global transcriptome of Lactobacillus plantarum were studied in detail. This work has resulted in the discovery of novel electron transport chains and respiratory capabilities of lactic acid bacteria. The potential respiratory capabilities of other, previously considered (strictly) anaerobic prokaryotic bacteria, were reviewed.
Morphological identification and analysis of EMS mutants from hexaploid wheat cultivar Yanzhan 4110.

【Objective】 The mutant library is the basic material of functional genomics.In wheat,this kind of mutant library was rarely reported.In this study,two wheat mutant libraries with EMS were constructed for laying a foundation for wheat functional genomics research. 【Method】 EMS was used as chemical mutagen to build the mutant library with early mature spring wheat Yanzhan 4110.Biological characters and agronomic traits were investigated in M2 generation.Some of mutants identified from M2 plants will be validated through M3 generation. 【Result】 During the growth period after sowing the M2 seeds,all the phenotypic changes of plants were observed and recorded.Phenotype mutants such as seedling habits,leaf appearance,plant height,spike appearance and mature period were obtained.Some of them were related to important agronomic traits and biological characters,specifically,some mutants were rarely observed in natural variation,such as extremely dwarf,with plant height at about 10-15cm.The rate of M2 phenotype mutation was 6.6%. 【Conclusion】 Two libraries of Yanzhan 4110 induced with EMS are ideal mutant libraries and they will be efficiently used in wheat functional genomic research and wheat improvement.
Effect of High Dosage of Methylprednisolone on Rat Retinal Ganglion Cell Apoptosis after Optic Nerve Crush

Purpose: To investigate the effect of high dose methylprednisolone (MP) on retinal ganglion cells (RGC) apoptosis.Methods: One hundred and twenty six Wistar rats were divided into normal control,crush control and MP treatment groups. High dose MP and 0.9% sodium chloride were injected intravenously at 1 h after injury in the treatment group and crush control group,respectively. Apoptotic cells, Bcl-2 and Bax positive cells were located and calculated by terminal-deoxynucleotidyl transferase mediated dUTP-biotin nick end labeling (TUNEL), immunohistochemical method and retinal whole-mount combined with section technique at day 4, 7, 14 after crush, respectively.Results: The TUNEL-labeling cells, Bcl-2 and Bax positive cells were detected in the ganglion cell layer of retina. Few apoptotic cells, a few of Bcl-2 and Bax positive cells were observed in normal control groups. The numbers of positive cells increased gradually after crush. The number of apoptotic cells and Bax positive cells in treatment groups was less than that in crush group significantly (P ＜ 0.05), while the number of Bcl-2 positive cells in treatment group was more than that in crush group at day 4, 7 and 14 after crush significantly (P ＜ 0.05)Conclusions: These results suggest that high dose MP can inhibit the apoptosis of RGC after optic nerve crush probably through up-regulation of Bcl-2 expression and downregulation of Bax expression.
Initial Interactions of Chlamydiae with the Host Cell

Chlamydiae are taken up by host cells so efficiently that the process has been termed "parasite-specified endocytosis" by Byrne and Moulder. This chapter focuses upon the active interactions of chlamydiae with the host cell and covers the stage of development up to the division of reticulate bodies (RBs). Surprisingly, different mutant cell lines displayed unique patterns of susceptibility or resistance to different C. trachomatis serovars or to C. pneumoniae. Despite the difficulties of comparing studies between different chlamydial species or serovars, conditions, and cell types, there is sufficient evidence to suggest that individual chlamydiae are capable of utilizing different mechanisms for entry. Translocation of Tarp and its tyrosine phosphorylation appear to be one of the first means of communication with the host cell to actively subvert host processes for parasite purposes. Identification of the kinases mediating Tarp phosphorylation is an initial step in mapping the signal transduction networks initiated by C. trachomatis to establish residence within an intracellular niche. Endocytosed elementary bodies (EBs) are rapidly transported to the peri-Golgi region of the host cell and become fusogenic with Golgi-derived vesicles. The Inc proteins do not share structural similarities to eukaryotic proteins, except for SNARE-like motifs, and homology searches do not provide substantial clues about their function. An improved understanding of the complex interactions of the important pathogens with the host cell should provide great potential for improved chemotherapeu-tic and immunoprophylactic interventions.
POTENCIAL OVICIDA DE Origanum vulgare (Lamiaceae) EM NEMATÓDEOS GASTRINTESTINAIS DE BOVINOS

Due to anthelmintic resistance in nematodes, several research studies have been developed seeking control alternatives to these parasites. This study evaluated the in vitro action of Origanum vulgare on gastrointestinal nematode eggs of cattle. In order to evaluate the ability to inhibit egg hatch, different dried leaves extracts of this plant were tested, such as dye, hydroalcoholic and aqueous extracts at concentrations varying from 0.62 to 80 mg/mL. Each assay was accompanied by control containing levamisole hydrochloride (0.2 mg/mL), distilled water and 70o GL grain alcohol at the same concentration of the extracts. Test results showed that the different O. vulgare extracts inhibited egg hatch of cattle gastrointestinal nematodes at a percentage that varied from 8.8 to 100%; dye and hydroalcoholic extract were the most promising inhibitors. In view of this ovicidal property, O. vulgare may be an important source of viable antiparasitic compounds for nematodiosis control in ruminants. KEYWORDS: Haemonchus spp. ; in vitro; oregano; phytotherapic.
Cladistics: A Practical Course in Systematics

Part 1 Cladistic theory: form - homology and analogy special similarity conflicting similarities and parsimony the relations between similarities homoplasty and the interpretation of character conflict monophyletic, paraphyletic and polyphyletic groups sister groups and ancestor-descendant relationships the transformation of cladistics phenetics eclectic of evolutionary taxonomy. Part 2 Character coding: character types binary characteristics multistate characters transformation between character states unordered and ordered characters additive binary coding branched character state trees other user-defined models of transformation character popularity cladograms and roots. Part 3 The determination of character polarity: outgroup comparison - the indirect method ontogeny - the direct method inadequate criteria ingroup commonality a priori models - Robertsonian changes, allelic dominance hierarchy, functional morphology, underlying synapomorphy. Part 4 Tree building techniques: parsimony criteria - Wagner, Fitch, Dollo, Camin-Sokal, polymorphism, generalized delayed and accelerated transformations optimization of "missing" values x-coding searching for the most parsimonious trees - exact algorithms, heuristic methods. Part 5 Tree statistics, trees and "confidence", concensus trees, alternatives to parsimony, character weighting, character conflict and its resolution: tree statistics - tree length, measures of fit between trees and data trees and confidence - bootstrap and jackknife, randomization, data decisiveness consensus trees - strict consensus, combinable components consensus, Nelson consensus, Adams consensus alternatives to parsimony - cliques, maximum likelihood, three-taxon statements phenetics character weighting character conflict and its resolution - re-evaluation of characters, consensus trees. Part 6 DNA analysis - theory: homology, homology testing - similarity, conjunction, congruence, results of testing for homology, orthology, paralogy, xenology, paraxenology, plerology nucleotide sequence data - the characters - substitutions, gaps, insertions and deletions (indels) tree construction - preliminaries note on rooting trees. Part 7 DNA analysis - methods: matrix methods - definitions, distance measures, metrics, tree reconstruction - phenetic methods, distance methods, problems parsimony methods - weighing, a priori weighting, a posteriori weighting, problems, invariants. Part 8 Fossils and cladistic analysis: fossils and ancestors age and rank stem groups and crown groups influence of fossils on classification of recent organisms - missing data, basal taxa, fossils and stratigraphy. Part 9 Cladistics and biogeography: life and earth together cladistics and biogeography - the progression rule, vacariance biogeography. (part contents)
Circulating nucleic acids: possible inherited effects

The presence of circulating nucleic acids in man, animals and plants is well documented. It is clear that such nucleic acids can not only circulate freely within an organism, but can also enter cells when their biology may be changed either epigenetically or genetically. Evidence is presented concerning a possible influence of these nucleic acid fragments on the genetics of the F1 generation of man, animals and plants. The data presented also offer a mechanism by which the incorporation of horizontally transferred genes between organisms may be achieved. The role that circulating nucleic acids might play in modifying the F1 generation and possibly the evolutionary process is considered. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110, 931–948.
Design and Implementation of High Efficiency Control Scheme of Dual Active Bridge Based 10 kV/1 MW Solid State Transformer for PV Application

One promising topology for solid state transformer (SST) is a modular multilevel cascaded converter, in which submodule is composed of dual active bridge (DAB) and H-bridge. For SST application in PV system, the efficiency could be severely affected especially for DAB due to the wide voltage and power range of PV panels. Thus, the motivation of this paper is to deal with the control strategy to improve DAB efficiency inside SST for PV application. Instead of utilizing time-domain based analysis method, which requires complex modeling process, this paper models DAB under frequency domain by fully considering the effect of both fundamental and harmonic frequency component. To achieve high efficiency operation, a multiorder reactive-current suppression (MRS) strategy is proposed by controlling phase shift angle as well as the duty cycles of primary and secondary side H-bridges. In terms of DAB controller design inside SST, the small signal model under MRS is established and a notch filter is implemented to suppress the second order line frequency fluctuation in the control loop. Finally, a 10 kV/1 MW SST prototype is introduced along with the system control structure and implementation method. The experiment of the submodule and SST confirms the effectiveness of proposed method.
A Least Mean Square Algorithm Based Single-Phase Grid Voltage Parameters Estimation Method

Grid-synchronization may be the most significant task in order to integrate renewable energy sources (RESs) and electric vehicles (EVs) into the power grid. The popular technique for grid synchronization is the power based phase locked loop (PLL). The major challenges that one encounters to design a robust power based PLL is the filter design inside the power based PLL control loop, and estimating the grid voltage parameters under frequency drift conditions. A wide bandwidth should be considered during filter design if a wide range of frequency variations are predicted in the grid voltage. The traditional filters cause a large phase delay if a wide bandwidth is considered during filter design. As a result, it degrades the transient performance of the power based PLL. In order to improve the transient performance of the PLL, this paper adopted a Fourier linear combiner (FLC) filter inside the PLL control loop. Moreover, a feedback loop is used to make the FLC frequency adaptive in order to estimate the grid voltage parameter when grid frequency drift occurs. Simulation and experimental results are provided to verify the proposed technique.
Path analysis of Cherry tomato during post-harvest

RESUMEN El objetivo de este trabajo fue analizar las principales variables asociadas a la resistencia poscosecha del tomate Cherry (tomate tipo cereza (Solanum lycopersicum var. cerasiforme), y con base en ello, orientar la seleccion de materiales para programas de mejoramiento. Se utilizo un diseno experimental en bloques completos aleatorizados, con tres repeticiones y 10 frutos por parcela. Para el analisis de los datos se adopto un diagrama causal ilustrativo, considerando la resistencia poscosecha como variable basica, y las siguientes variables explicativas: peso medio de los frutos, diametro de la cicatriz del pedunculo, grosor del mesocarpio, contenido de solidos solubles y pH. Se realizaron analisis de varianza, correlaciones genotipicas y multicolinealidad; y desdoblamiento de las correlaciones genotipicas por medio de analisis de ruta (portugues: “analise de trilha”). Considerando separadamente los caracteres estudiados, el grosor del mesocarpio y el peso medio de los frutos son los que contribuyen en una mayor medida a explicar las variaciones en la resistencia poscosecha del tomate Cherry. Es posible obtener ganancias en resistencia poscosecha por medio de seleccion indirecta via grosor del mesocarpio. Esta ganancia sera mayor si entre los frutos de mayor grosor del mesocarpio se seleccionan los que presentan menor peso. The current study was aimed at analyzing key variables involved in post-harvest resistance of Cherry tomato (Solanum lycopersicum var. cerasiforme) that are useful for guiding the selection of new materials in breeding programs. A completely randomized block design with three replications and 10 fruits per plot was applied. The data were analyzed by means of a causal diagram considering post-harvest resistance as the basic variable, and the following explanatory variables: fruit mean weight, peduncle scar diameter, mesocarp thickness, soluble solids content and pH. Further analyses were: Anova, genotypic correlations, diagnosis of multicollinearity, and the display of genotypic correlations through path analysis (portuguese: “analise de triha”). Mesocarp thickness and fruit mean weight are the characters that explained Cherry tomato post-harvest resistance variations to a greater extent. Gains in this feature could be obtained through indirect selection of mesocarp thickness. Such improvement could be optimized by further selecting lighter fruits out of those having a thicker mesocarp.
In Vitro Control of Enterococcus faecalis by Zataria multilfolira Boiss, Origanum vulgare L and Mentha pulegium Essential Oils

This study evaluates the antioxidant properties of the essential oils (EOs) from Zataria multiflora Boiss (ZMB), Origanum vulgare L (OVL) and Mentha pulegium (MP) and their influence on the growth, membrane permeability and cell surface characteristics of Enterococcus faecalis. Disk diffusion and micro-well dilution were tested for the antimicrobial activity of EOs. The minimum inhibitory concentrations (MICs) of ZMB, OVL and MP were 2, 8 and 42 mg/mL, respectively. The mechanism of the antimicrobial action of EOs against E. faecalis was also studied by measurement of the release of cell constituents and observations of cells by electron microscopy. The antioxidant activities, as evaluated by inhibition of free radicals using 2, 2-diphenyl-1-picrylhydrazyl method, was 26.47, 3.20 and 34.67, for ZMB, OVL and MP, respectively. These three EOs have the potential to be applied in food products both to inhibit the growth of E. faecalis and to suppress the activity of carcinogenic O2–, produced by this bacterium. Practical Application The use of essential oils (EOs) from Zataria multi flora Boiss, Origanum vulgare L and Mentha pulegium as natural antimicrobial agents would be appreciated in foodstuffs. Considering extracellular superoxide produced by Enterococcus faecalis, which damages colonic epithelial cells DNA associated with colorectal cancer, these EOs can be used as bacteria inhibitors. They can be used alone or in combination with other preservative factors in food products. Moreover, EOs recognize as interesting natural compounds with great potential as alternatives to synthetic additives. These useful properties could be improved food safety and shelf life.