An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

'Education, education, education' : legal, moral and clinical

This article brings together Professor Donald Nicolson's intellectual interest in professional legal ethics and his long-standing involvement with law clinics both as an advisor at the University of Cape Town and Director of the University of Bristol Law Clinic and the University of Strathclyde Law Clinic. In this article he looks at how legal education may help start this process of character development, arguing that the best means is through student involvement in voluntary law clinics. And here he builds upon his recent article which argues for voluntary, community service oriented law clinics over those which emphasise the education of students

Loss of haptic feedback impairs control of hand posture: a study in chronically deafferented individuals when grasping and lifting objects.

Previous work has highlighted the role of haptic feedback for manual dexterity, in particular for the control of precision grip forces between the index finger and thumb. It is unclear how fine motor skills involving more than just two digits might be affected, especially given that loss of sensation from the hand affects many neurological patients, and impacts on everyday actions. To assess the functional consequences of haptic deficits on multi-digit grasp of objects, we studied the ability of three rare individuals with permanent large-fibre sensory loss involving the entire upper limb. All three reported difficulties in everyday manual actions (ABILHAND questionnaire). Their performance in a reach-grasp-lift task was compared to that of healthy controls. Twenty objects of varying shape, mass, opacity and compliance were used. In the reach-to-grasp phase, we found slower movement, larger grip aperture and less dynamic modulation of grip aperture in deafferented participants compared to controls. Hand posture during the lift phase also differed; deafferented participants often adopted hand postures that may have facilitated visual guidance, and/or reduced control complexity. For example, they would extend fingers that were not in contact with the object, or fold these fingers into the palm of the hand. Variability in hand postures was increased in deafferented participants, particularly for smaller objects. Our findings provide new insights into how the complex control required for whole hand actions is compromised by loss of haptic feedback, whose contribution is, thus, highlighted

A search for prompt lepton-jets in pp collisions at root s=8 TeV with the ATLAS detector

A search is presented for a new, light boson with a mass of about 1 GeV and decaying promptly to jets of collimated electrons and/or muons (lepton-jets). The analysis is performed with 20.3 fb−1 of data collected by the ATLAS detector at the Large Hadron Collider in proton-proton collisions at a centre-of-mass energy of 8 TeV. Events are required to contain at least two lepton-jets. This study finds no statistically significant deviation from predictions of the Standard Model and places 95% confidence-level upper limits on the contribution of new phenomena beyond the SM, incuding SUSY-portal and Higgs-portal models, on the number of events with lepton-jets.We acknowledge the support of ANPCyT, Argentina; YerPhI, Armenia; ARC, Australia; BMWFW and FWF, Austria; ANAS, Azerbaijan; SSTC, Belarus; CNPq and FAPESP, Brazil; NSERC, NRC and CFI, Canada; CERN; CONICYT, Chile; CAS, MOST and NSFC, China; COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Republic; DNRF, DNSRC and Lundbeck Foundation, Denmark; IN2P3-CNRS, CEADSM/IRFU, France; GNSF, Georgia; BMBF, HGF, and MPG, Germany; GSRT, Greece; RGC, Hong Kong SAR, China; ISF, I-CORE and Benoziyo Center, Israel; INFN, Italy; MEXT and JSPS, Japan; CNRST, Morocco; FOM and NWO, Netherlands; RCN, Norway; MNiSW and NCN, Poland; FCT, Portugal; MNE/IFA, Romania; MES of Russia and NRC KI, Russian Federation; JINR; MESTD, Serbia; MSSR, Slovakia; ARRS and MIZ. S, Slovenia; DST/NRF, South Africa; MINECO, Spain; SRC and Wallenberg Foundation, Sweden; SERI, SNSF and Cantons of Bern and Geneva, Switzerland; MOST, Taiwan; TAEK, Turkey; STFC, United Kingdom; DOE and NSF, United States of America. In addition, individual groups and members have received support from BCKDF, the Canada Council, CANARIE, CRC, Compute Canada, FQRNT, and the Ontario Innovation Trust, Canada; EPLANET, ERC, FP7, Horizon 2020 and Marie Sklodowska-Curie Actions, European Union; Investissements d'Avenir Labex and Idex, ANR, Region Auvergne and Fondation Partager le Savoir, France; DFG and AvH Foundation, Germany; Herakleitos, Thales and Aristeia programmes co-financed by EU-ESF and the Greek NSRF; BSF, GIF and Minerva, Israel; BRF, Norway; the Royal Society and Leverhulme Trust, United Kingdom

Measurement of jet charge in dijet events from √s = 8 TeV pp collisions with the ATLAS detector

The momentum-weighted sum of the charges of tracks associated to a jet is sensitive to the charge of the initiating quark or gluon. This paper presents a measurement of the distribution of momentum-weighted sums, called jet charge, in dijet events using 20.3 fb−¹ of data recorded with the ATLAS detector at √s = 8 TeV in pp collisions at the LHC. The jet charge distribution is unfolded to remove distortions from detector effects and the resulting particle-level distribution is compared with several models. The pT dependence of the jet charge distribution average and standard deviation are compared to predictions obtained with several leading-order and next-to-leading-order parton distribution functions. The data are also compared to different Monte Carlo simulations of QCD dijet production using various settings of the free parameters within these models. The chosen value of the strong coupling constant used to calculate gluon radiation is found to have a significant impact on the predicted jet charge. There is evidence for a pT dependence of the jet charge distribution for a given jet flavor. In agreement with perturbative QCD predictions, the data show that the average jet charge of quark-initiated jets decreases in magnitude as the energy of the jet increases

Search for the production of single vector-like and excited quarks in the Wt final state in pp collisions at √s=8 TeV with the ATLAS detector

A search for vector-like quarks and excited quarks in events containing a top quark and a W boson in the final state is reported here. The search is based on 20.3 fb−1 of proton-proton collision data taken at the LHC at a centre-of-mass energy of 8 TeV recorded by the ATLAS detector. Events with one or two leptons, and one, two or three jets are selected with the additional requirement that at least one jet contains a b-quark. Single-lepton events are also required to contain at least one large-radius jet from the hadronic decay of a high-pTW boson or a top quark. No significant excess over the expected background is observed and upper limits on the cross-section times branching ratio for different vector-like quark and excited-quark model masses are derived. For the excited-quark production and decay to Wt with unit couplings, quarks with masses below 1500 GeV are excluded and coupling-dependent limits are set

The Two-Dimensional Content of Consciousness

In this paper I put forward a representationalist theory of conscious experience based on Robert Stalnaker's version of two-dimensional modal semantics. According to this theory the phenomenal character of an experience correlates with a content equivalent to what Stalnaker calls the diagonal proposition. I show that the theory is closely related both to functionalist theories of consciousness and to higher-order representational theories. It is also more compatible with an anti-Cartesian view of the mind than standard representationalist theories.</p

Linfoma canino: clínica, hematologia e tratamento com o protocolo de Madison-Wisconsin

O linfoma é uma neoplasia de elevada incidência na população canina mundial, e que apresenta sinais clínicos diversos, dependentes da classificação anatômica e da extensão da doença. Este estudo objetivou avaliar as características clínicas e hematológicas de cães com linfoma no momento do diagnóstico, além da evolução clínica dos mesmos ao longo do tratamento com o protocolo de Madison-Wisconsin. Dos 18 cães inseridos no estudo, 50% apresentaram a forma multicêntrica da doença e 33% a forma cutânea. A manifestação clínica mais comum foi a linfadenomegalia superficial, acompanhada dos sinais sistêmicos de hiporexia, apatia e perda de peso. As principais alterações hematólogicas foram anemia normocítica normocrômica, trombocitopenia e leucocitose, associadas às síndromes paraneoplásicas. Vinte e sete por cento dos animais atingiram remissão completa da doença e apenas 22% atingiram sobrevida de um ano. Houve correlação positiva entre o valor do hematócrito e o tempo de sobrevida para os cães que morreram, demonstrando a influência da anemia no prognóstico dos animais. Sugere-se que o estágio avançado da doença no momento do diagnóstico tenha influenciado as baixas taxas de remissão e sobrevida obtidas neste estudo.Lymphoma is a neoplasm of high incidence in dogs, and has several clinical signs, depending on the tumor anatomical area and the extent of the disease. This study aimed to evaluate the clinical and hematological findings in dogs with lymphoma at diagnosis, and the clinical evolution during Madison-Wisconsin chemotherapy protocol. of the 18 dogs that underwent the study, 50% of the dogs had the multicentric form and 33% the cutaneous forms of the disease. The most common clinical sign was superficial lymphadenomegaly, combined to systemic signs of hyporexia, apathy and weight loss. The main hematological changes were anemia, thrombocytopenia and leukocytosis, associated with paraneoplastic syndromes. Complete remission was achieved in 27% of the animals and the one-year survival rate was 22%. There was a positive correlation between the hematocrit and survival time in dogs that died, which indicates the importance of anemia in the prognosis. It is suggested that the advanced stage of the disease may have contributed to the low remission and survival rates observed in this study.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Centro Universitário Barão de MauáUniversidade Estadual Paulista Faculdade de Ciências Agrárias e VeterináriasUniversidade Estadual Paulista Faculdade de Ciências Agrárias e Veterinárias Departamento de Clínica e Cirurgia VeterináriaUniversidade Estadual Paulista Faculdade de Ciências Agrárias e VeterináriasUniversidade Estadual Paulista Faculdade de Ciências Agrárias e Veterinárias Departamento de Clínica e Cirurgia VeterináriaFAPESP: 05/01718-6FAPESP: 06/03300-