Molecular tumor grading of non muscle invasive bladder cancer based on whole transcriptome analysis

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Background: There is an unmet need for a comprehensive genomic characterization of non muscle invasive bladder cancer (NMIBC). NMIBC comprise over 70% of all bladder cancers at presentation. They have highly variable clinical behavior that is not always adequately predicted on the basis of their histological grade (2004 World Health Organization low and high grade, LG-HG). The discrepancy between phenotype and genotype is compounded further by interobserver variability in pathological grading. We have previously established methods for whole transcriptome RNAseq from formalin fixed paraffin embedded tissues (FFPE). Methods: Whole transcriptomic analysis of 110 NMI FFPE BC both LG and HG was performed incorporating messenger RNA expression, splice variants, gene fusion, and pathway perturbation. We used a discovery (n = 40) and a validation cohort (n = 70). These data were integrated and tested for correlation with both pathological grading and clinical outcomes. Grade Risk Index (GRI) score quantifying how closely a patient's transcriptome is related to a reference set of LG NMIBC samples was established. Conventional pathological grading was reviewed by 3 different expert uro-pathologists and interobserver variability calculated. Results: Unsupervised clustering of data from RNA sequencing uncovered classification of three robust - - nonoverlapping, prognostically significant subtypes of NMIBC with distinct GRIs and signatures. When applied by expert pathologists, interobserver variability in histological grading was observed in 17.5%. In the intermediate group (GRI 0.13 to 0.19), pathologists disagreed in 37.5% whether BC was LG or HG. HG NMIBC clustered with MIBC. LG NMIBC in the intermediate GRI group included either very bulky tumors or extremely rare metastatic LG BC (n = 4). HG disease was associated with a shift in BMP signaling and a germ stem cell-like phenotype. Multiple components of the centromere complex and APOBEC3B were upregulated in HG BC. FGFR3::TACC3 fusion events were observed in LG NMIBC only (11.5%). Conclusions: Whole transcriptomic sequencing data delineated three molecular classes of NMIBC.

Mechanistic insights into nitrogen fixation by nitrogenase enzymes

Biological nitrogen fixation by nitrogenase enzymes is a process that activates dinitrogen (N2) one of the most inert molecules in nature, within the confines of a living organism and at ambient conditions. Despite decades of study, there are still no complete explanations as to how this is possible. Here we describe a model of N2 reduction using the Mo-containing nitrogenase (FeMoco) that can explain the reactivity of the active site via a series of electrochemical steps that reversibly unseal a highly reactive Fe edge site. Our model can explain the 8 proton-electron transfers involved in biological ammonia synthesis within the kinetic scheme of Lowe and Thorneley, the obligatory formation of one H2 per N2 reduced, and the behavior of known inhibitors.

Outcome of patients with pregnancy during or after breast cancer: a review of the recent literature

BACKGROUND

An increasing number of young women are delaying childbearing; hence, more are diagnosed with breast cancer (bca) before having a family. No clear recommendations are currently available for counselling such a population on the safety of carrying a pregnancy during bca or becoming pregnant after treatment for bca.

METHODS

Using a Web-based search of PubMed we reviewed the recent literature about bca and pregnancy. Our objective was to report outcomes for patients diagnosed with bca during pregnancy, comparing them with outcomes for non-pregnant women, and to evaluate prognosis in women diagnosed with and treated for bca who subsequently became pregnant.

RESULTS

"Pregnancy and bca" should be divided into two entities. Pregnancy-associated bca tends to be more aggressive and advanced in stage at diagnosis than bca in control groups; hence, it has a poorer prognosis. With respect to pregnancy after bca, there is, despite the bias in reported studies and meta-analyses, no clear evidence for a different or worse disease outcome in bca patients who become pregnant after treatment compared with those who do not.

CONCLUSIONS

Pregnancy-associated bca should be treated as aggressively as and according to the standards applicable in nonpregnant women; pregnancy after bca does not jeopardize outcome. The guidelines addressing risks connected to pregnancy and bca lack a high level of evidence for better counselling young women about pregnancy considerations and preventing unnecessary abortions. Ideally, evidence from large prospective randomized trials would set better guidelines, and yet the complexity of such studies limits their feasibility.

Denis RD, Stahlman J, Stamen R, Stanecka E, Stanek RW, Stanescu C, Stanescu-Bellu M, Stanitzki MM, Stapnes S, Starchenko EA, Stark J, Staroba P, Starovoitov P, Staszewski R, Stavina P, Steele G, Steinbach P, Steinberg P, Stekl I, Stelzer B, Stelzer HJ, Stelzer-Chilton O, Stenzel H, Stern S, Stewart GA, Stillings JA, Stockton MC, Stoebe M, Stoerig K, Stoicea G, Stonjek S, Stradling AR, Straessner A, Strandberg J, Strandberg S, Strandlie A, Strauss E, Strauss M, Strizenec P, Ströhmer R, Strom DM, Stroynowski R, Stucci SA, Stugu B, Stumer I, Stupak J, Sturm P, Styles NA, Su D, Su J, Subramania HS, Subramaniam R, Succurro A, Sugaya Y, Suhr C, Suk M, Sulin VV, Sultansoy S, Sumida T, Sun X, Sundermann JE, Suruliz K, Susinno G, Sutton MR, Suzuki Y, Svatos M, Swedish S, Swiatlowski M, Sykora I, Sykora T, Ta D, Tackmann K, Taenzer J, Taffard A, Tafirout R, Taiblum N, Takahashi Y, Takai H, Takashima R, Takeda H, Takeshita T, Takubo Y, Talby M, Talyshev AA, Tam JYC, Tamsett MC, Tan KG, Tanaka J, Tanaka R, Tanaka S, Tanaka S, Tanasijczuk AJ, Tani K, Tannoury N, Tapprogge S, Tarem S, Tarrade F, Tartarelli GF, Tas P, Tasevsky M, Tashiro T, Tassi E, Tavares Delgado A, Tayalati Y, Taylor C, Taylor FE, Taylor GN, Taylor W, Teischinger FA, Teixeira Dias Castanheira M, Teixeira-Dias P, Temming KK, Ten Kate H, Teng PK, Terada S, Terashi K, Terron J, Terzo S, Testa M, Teuscher RJ, Therhaag J, Theveneaux-Pelzer T, Thoma S, Thomas JP, Thompson EN, Thompson PD, Thompson PD, Thompson AS, Thomsen LA, Thomson E, Thomson M, Thong WM, Thun RP, Tian F, Tibbetts MJ, Tic T, Tikhomirov VO, Tikhonov YA, Timoshenko S, Tiouchichine E, Tipton P, Tisserant S, Todorov T, Todorova-Nova S, Toggerson B, Tojo J, Tokár S, Tokushuku K, Tollefson K, Tomlinson L, Tomoto M, Tompkins L, Toms K, Topilin ND, Torrence E, Torres H, Torró Pastor E, Toth J, Touchard F, Tovey DR, Tran HL, Trefzger T, Tremblet L, Tricoli A, Trigger IM, Trincaz-Duvoid S, Tripiana MF, Triplett N, Trischuk W, Trocmé B, Troncon C, Trottier-McDonald M, Trovatelli M, True P, Trzebinski M, Trzupek A, Tsarouchas C, Tseng JCL, Tsiareshka PV, Tsionou D, Tsipolitis G, Tsirintanis N, Tsiskaridze S, Tsiskaridze V, Tskhadadze EG, Tsukerman II, Tsulaia V, Tsung JW, Tsuno S, Tsybychev D, Tua A, Tudorache A, Tudorache V, Tuggle JM, Tuna AN, Tupputi SA, Turchikhin S, Turecek D, Turk Cakir I, Turra R, Tuts PM, Tykhonov A, Tylmad M, Tyndel M, Uchida K, Ueda I, Ueno R, Ughetto M, Ugland M, Uhlenbrock M, Ukegawa F, Unal G, Undrus A, Unel G, Ungaro FC, Unno Y, Urbaniec D, Urquijo P, Usai G, Usanova A, Vacavant L, Vacek V, Vachon B, Valencic N, Valentinetti S, Valero A, Valery L, Valkar S, Valladolid Gallego E, Vallecorsa S, Valls Ferrer JA, Van Berg R, Van Der Deijl PC, van der Geer R, van der Graaf H, Van Der Leeuw R, van der Ster D, van Eldik N, van Gemmeren P, Van Nieuwkoop J, van Vulpen I, van Woerden MC, Vanadia M, Vandelli W, Vaniachine A, Vankov P, Vannucci F, Vardanyan G, Vari R, Varnes EW, Varol T, Varouchas D, Vartapetian A, Varvell KE, Vassilakopoulos VI, Vazeille F, Vazquez Schroeder T, Veatch J, Veloso F, Veneziano S, Ventura A, Ventura D, Venturi M, Venturi N, Venturini A, Vercesi V, Verducci M, Verkerke W, Vermeulen JC, Vest A, Vetterli MC, Viazlo O, Vichou I, Vickey T, Vickey Boeriu OE, Viehhauser GHA, Viel S, Vigne R, Villa M, Villaplana Perez M, Vilucchi E, Vincter MG, Vinogradov VB, Virzi J, Vitells O, Viti M, Vivarelli I, Vives Vaque F, Vlachos S, Vladoiu D, Vlasak M, Vogel A, Vokac P, Volpi G, Volpi M, Volpini G, von der Schmitt H, von Radziewski H, von Toerne E, Vorobel V, Vos M, Voss R, Vossebeld JH, Vranjes N, Vranjes Milosavljevic M, Vrba V, Vreeswijk M, Vu Anh T, Vuillermet R, Vukotic I, Vykydal Z, Wagner W, Wagner P, Wahrmund S, Wakabayashi J, Walch S, Walder J, Walker R, Walkowiak W, Wall R, Waller P, Walsh B, Wang C, Wang H, Wang H, Wang J, Wang J, Wang K, Wang R, Wang SM, Wang T, Wang X, Warburton A, Ward CP, Wardrope DR, Warsinsky M, Washbrook A, Wasicki C, Watanabe I, Watkins PM, Watson AT, Watson IJ, Watson MF, Watts G, Watts S, Waugh AT, Waugh BM, Webb S, Weber MS, Weber SW, Webster JS, Weidberg AR, Weigell P, Weingarten J, Weiser C, Weits H, Wells PS, Wenaus T, Wendland D, Weng Z, Wengler T, Wenig S, Wermes N, Werner M, Werner P, Wessels M, Wetter J, Whalen K, White A, White MJ, White R, White S, Whiteson D, Whittington D, Wicke D, Wickens FJ, Wiedenmann W, Wielers M, Wienemann P, Wiglesworth C, Wiik-Fuchs LAM, Wijeratne PA, Wildauer A, Wildt MA, Wilhelm I, Wilkens HG, Will JZ, Williams HH, Williams S, Willis W, Willocq S, Wilson JA, Wilson A, Wingerter-Seez I, Winkelmann S, Winklmeier F, Wittgen M, Wittig T, Wittkowski J, Wollstadt SJ, Wolter MW, Wolters H, Wong WC, Wosiek BK, Wotschack J, Woudstra MJ, Wozniak KW, Wraight K, Wright M, Wu SL, Wu X, Wu Y, Wulf E, Wyatt TR, Wynne BM, Xella S, Xiao M, Xu C, Xu D, Xu L, Yabsley B, Yacoob S, Yamada M, Yamaguchi H, Yamaguchi Y, Yamamoto A, Yamamoto K, Yamamoto S, Yamamura T, Yamanaka T, Yamauchi K, Yamazaki Y, Yan Z, Yang H, Yang H, Yang UK, Yang Y, Yanush S, Yao L, Yasu Y, Yatsenko E, Yau Wong KH, Ye J, Ye S, Yen AL, Yildirim E, Yilmaz M, Yoosoofmiya R, Yorita K, Yoshida R, Yoshihara K, Young C, Young CJS, Youssef S, Yu DR, Yu J, Yu J, Yuan L, Yurkewicz A, Zabinski B, Zaidan R, Zaitsev AM, Zaman A, Zambito S, Zanello L, Zanzi D, Zaytsev A, Zeitnitz C, Zeman M, Zemla A, Zengel K, Zenin O, Ženiš T, Zerwas D, Zevi della Porta G, Zhang D, Zhang H, Zhang J, Zhang L, Zhang X, Zhang Z, Zhao Z, Zhemchugov A, Zhong J, Zhou B, Zhou L, Zhou N, Zhu CG, Zhu H, Zhu J, Zhu Y, Zhuang X, Zibell A, Zieminska D, Zimine NI, Zimmermann C, Zimmermann R, Zimmermann S, Zimmermann S, Zinonos Z, Ziolkowski M, Zitoun R, Zobernig G, Zoccoli A, zur Nedden M, Zurzolo G, Zutshi V, Zwalinski L. Jet energy measurement and its systematic uncertainty in proton-proton collisions at [Formula: see text] TeV with the ATLAS detector

The jet energy scale (JES) and its systematic uncertainty are determined for jets measured with the ATLAS detector using proton-proton collision data with a centre-of-mass energy of [Formula: see text] TeV corresponding to an integrated luminosity of [Formula: see text][Formula: see text]. Jets are reconstructed from energy deposits forming topological clusters of calorimeter cells using the anti-[Formula: see text] algorithm with distance parameters [Formula: see text] or [Formula: see text], and are calibrated using MC simulations. A residual JES correction is applied to account for differences between data and MC simulations. This correction and its systematic uncertainty are estimated using a combination of in situ techniques exploiting the transverse momentum balance between a jet and a reference object such as a photon or a [Formula: see text] boson, for [Formula: see text] and pseudorapidities [Formula: see text]. The effect of multiple proton-proton interactions is corrected for, and an uncertainty is evaluated using in situ techniques. The smallest JES uncertainty of less than 1 % is found in the central calorimeter region ([Formula: see text]) for jets with [Formula: see text]. For central jets at lower [Formula: see text], the uncertainty is about 3 %. A consistent JES estimate is found using measurements of the calorimeter response of single hadrons in proton-proton collisions and test-beam data, which also provide the estimate for [Formula: see text] TeV. The calibration of forward jets is derived from dijet [Formula: see text] balance measurements. The resulting uncertainty reaches its largest value of 6 % for low-[Formula: see text] jets at [Formula: see text]. Additional JES uncertainties due to specific event topologies, such as close-by jets or selections of event samples with an enhanced content of jets originating from light quarks or gluons, are also discussed. The magnitude of these uncertainties depends on the event sample used in a given physics analysis, but typically amounts to 0.5-3 %.

Strategies of sequential therapies in unresectable metastatic colorectal cancer: a meta-analysis

BACKGROUND

Before the emergence of first-line combination chemotherapy, the standard of care for unresectable metastatic colorectal cancer (mcrc) was first-line monotherapy with modulated 5-fluorouracil. Several large phase iii randomized controlled trials, now completed, have assessed whether a planned sequential chemotherapy strategy-beginning with fluoropyrimidine monotherapy until treatment failure, followed by another regimen (either monotherapy or combination chemotherapy) until treatment failure-could result in the same survival benefit produced with an upfront combination chemotherapy strategy, but with less toxicity for patients.

METHODS

The medline and embase databases, and abstracts from meetings of the American Society for Clinical Oncology and the European Society for Medical Oncology, were searched for reports comparing a sequential strategy of chemotherapy with an upfront combination chemotherapy in adult patients with mcrc. Publications that reported efficacy or toxicity data (or both) were included.

RESULTS

The five eligible trials that were identified included 4532 patients. A meta-analysis of those trials demonstrates a statistically significant survival advantage for combination chemotherapy (hazard ratio: 0.92; 95% confidence interval: 0.86 to 0.99). However, the median survival advantage (3-6 weeks in most trials) is small and of questionable clinical significance. Three trials reported first-line toxicities. Upfront combination chemotherapy results in significantly more neutropenia, febrile neutropenia, thrombocytopenia, diarrhea, nausea, vomiting, and sensory neuropathy. Sequential chemotherapy results in significantly more hand-foot syndrome.

CONCLUSIONS

Given the small survival advantage associated with upfront combination chemotherapy, planned sequential chemotherapy and upfront combination chemotherapy can both be considered treatment strategies. Treatment should be chosen on an individual basis considering patient and tumour characteristics, toxicity of each strategy, and patient preference.

Family environment and attention-deficit/hyperactivity disorder in adopted children: associations with family cohesion and adaptability

BACKGROUND

Positive family environments are crucial in promoting children's emotional and behavioural well-being, and may also buffer development of attention-deficit/hyperactivity disorder (ADHD). ADHD is highly heritable, but psychosocial factors in the family environment, particularly family cohesion and communication, may mediate genetic predispositions. The purpose of the current study is to examine the mediating influence of the adoptive family environment between pre-adoptive risk factors and youths' ADHD symptomatology at 14 years post adoption.

METHODS

The data used in this study were obtained from the fourth wave of the California Long-Range Adoption Study (CLAS) (n = 449). Using structural equation modelling (SEM), family sense of coherence and family adaptability were tested as possible mediators between environmental and biological predictors and ADHD symptomatology. Predictors included birthweight, gender, age at adoption, adoption from foster care, transracial adoption status, ethnicity and having a previous diagnosis of ADHD.

RESULTS

Results show that, while adoption from foster care is negatively associated with family functioning, higher family cohesion and adaptability mediate this influence on children's ADHD symptomatology. Older age of adoption directly predicts greater ADHD symptoms with no mediating influence of the family environment.

CONCLUSIONS

The mediating influence of the family environment between children's risk factors and ADHD symptoms suggests that family intervention strategies may be helpful in improving adopted children's outcomes. Once children are adopted, targeting family communication patterns and dynamics may be an additional part of developing an evidence-based, post-adoption services toolkit.

Evidence for electroweak production of W±W±jj in pp collisions at sqrt[s] = 8 TeV with the ATLAS detector

This Letter presents the first study of W(±)W(±)jj, same-electric-charge diboson production in association with two jets, using 20.3 fb(-1) of proton-proton collision data at sqrt[s] = 8  TeV recorded by the ATLAS detector at the Large Hadron Collider. Events with two reconstructed same-charge leptons (e(±)e(±), e(±)μ(±), and μ(±)μ(±)) and two or more jets are analyzed. Production cross sections are measured in two fiducial regions, with different sensitivities to the electroweak and strong production mechanisms. First evidence for W(±)W(±)jj production and electroweak-only W(±)W(±)jj production is observed with a significance of 4.5 and 3.6 standard deviations, respectively. The measured production cross sections are in agreement with standard model predictions. Limits at 95% confidence level are set on anomalous quartic gauge couplings.

Muon reconstruction efficiency and momentum resolution of the ATLAS experiment in proton-proton collisions at [Formula: see text] TeV in 2010

This paper presents a study of the performance of the muon reconstruction in the analysis of proton-proton collisions at [Formula: see text] TeV at the LHC, recorded by the ATLAS detector in 2010. This performance is described in terms of reconstruction and isolation efficiencies and momentum resolutions for different classes of reconstructed muons. The results are obtained from an analysis of [Formula: see text] meson and [Formula: see text] boson decays to dimuons, reconstructed from a data sample corresponding to an integrated luminosity of 40 pb[Formula: see text]. The measured performance is compared to Monte Carlo predictions and deviations from the predicted performance are discussed.