Streaming sparse Gaussian process approximations

Sparse pseudo-point approximations for Gaussian process (GP) models provide a suite of methods that support deployment of GPs in the large data regime and enable analytic intractabilities to be sidestepped. However, the field lacks a principled method to handle streaming data in which both the posterior distribution over function values and the hyperparameter estimates are updated in an online fashion. The small number of existing approaches either use suboptimal hand-crafted heuristics for hyperparameter learning, or suffer from catastrophic forgetting or slow updating when new data arrive. This paper develops a new principled framework for deploying Gaussian process probabilistic models in the streaming setting, providing methods for learning hyperparameters and optimising pseudo-input locations. The proposed framework is assessed using synthetic and real-world datasets

Deep Gaussian processes for regression using approximate expectation propagation

Deep Gaussian processes (DGPs) are multi-layer hierarchical generalisations of Gaussian processes (GPs) and are formally equivalent to neural networks with multiple, infinitely wide hidden layers. DGPs are nonparametric probabilistic models and as such are arguably more flexible, have a greater capacity to generalise, and provide better calibrated uncertainty estimates than alternative deep models. This paper develops a new approximate Bayesian learning scheme that enables DGPs to be applied to a range of medium to large scale regression problems for the first time. The new method uses an approximate Expectation Propagation procedure and a novel and efficient extension of the probabilistic backpropagation algorithm for learning. We evaluate the new method for non-linear regression on eleven real-world datasets, showing that it always outperforms GP regression and is almost always better than state-of-the-art deterministic and sampling-based approximate inference methods for Bayesian neural networks. As a by-product, this work provides a comprehensive analysis of six approximate Bayesian methods for training neural networks

Trends in breast cancer incidence in Ho Chi Minh City 1996-2015: A registry-based study.

The burden of breast cancer in Vietnam has not been documented. This study sought to estimate the incidence of breast cancer in Ho Chi Minh City, the largest economic center of Vietnam, from 1996 to 2015. This was a population-based study using the Ho Chi Minh City Cancer Registry as a source of data (coverage period: 1996-2015). The Registry adopted the International Classification of Diseases for Oncology, 3rd Edition for the classification of primary sites and morphology, and guidelines from the International Agency for Research on Cancer and the International Association of Cancer Registries. Using the population statistics from census data of Ho Chi Minh City, the point incidence of breast cancer for 5-year period was estimated. Based on the national population, we calculated the age-standardized rate (ASR) of breast cancer between 1996 and 2015. Overall 14,222 new cases of breast cancer (13,948 women, or 98%) had been registered during the 1996-2015 period; among whom, just over half (52%) were in the 2nd stage and 26% in the 3rd and 4th stages. In women, the median age at diagnosis was 50 years and there was a slight increase over time. The ASR of breast cancer during the 2011-2015 period was 107.4 cases per 100,000 women, representing an increase of 70% compared to the rate during the 1996-2000 period. In men, there was also a significant increase in the ASR: from 1.13 during the 1996-2001 period to 2.32 per 100,000 men during the 2011-2015 period. These very first data from Vietnam suggest that although the incidence of breast cancer in Vietnam remains relatively low, it has increased over time

Black-Box α-divergence minimization

Black-box alpha (BB-α) is a new approximate inference method based on the minimization of α-divergences. BB-α scales to large datasets because it can be implemented using stochastic gradient descent. BB-α can be applied to complex probabilistic models with little effort since it only requires as input the likelihood function and its gradients. These gradients can be easily obtained using automatic differentiation. By changing the divergence parameter α, the method is able to interpolate between variational Bayes (VB) (α → 0) and an algorithm similar to expectation propagation (EP) (α = 1). Experiments on probit regression and neural network regression and classification problems show that BB-a with non-standard settings of α, such as α = 0.5, usually produces better predictions than with α → 0 (VB) or α = 1 (EP).JMHL acknowledges support from the Rafael del Pino Foundation. YL thanks the Schlumberger Foundation Faculty for the Future fellowship on supporting her PhD study. MR acknowledges support from UK Engineering and Physical Sciences Research Council (EPSRC) grant EP/L016516/1 for the University of Cambridge Centre for Doctoral Training, the Cambridge Centre for Analysis. TDB thanks Google for funding his European Doctoral Fellowship. DHL acknowledge support from Plan National I+D+i, Grant TIN2013-42351-P and TIN2015- 70308-REDT, and from Comunidad de Madrid, Grant S2013/ICE-2845 CASI-CAM-CM. RET thanks EPSRC grant #EP/L000776/1 and #EP/M026957/1

Expression of Wnt5a is downregulated by extracellular matrix and mutated c-Ha-ras in the human mammary epithelial cell line MCF-10A

Wnt genes are involved in tumour growth and regulate cell adhesion. Some (Wnt5a and Wnt7b) are more highly expressed in human breast cancer compared to normal tissues. Wnt5a is involved in the regulation of cell movement in Xenopus and is upregulated in several human cancers. Factors regulating Wnt gene expression in human breast epithelium are poorly understood, but c-erbB2 is amplified in many breast cancers and associated with rapid growth and metastasis, as is high expression of c-Ha-ras. To further understand the regulation of Wnt gene expression, this study investigated the effect of proto-oncogenes c-Ha-ras and c-erbB2, and collagen on Wnt mRNA expression, in a normal spontaneously immortalised human mammary epithelial cell line MCF-10A. Out of nine human Wnt genes investigated, Wnt5a and Wnt7b were expressed in the parental cell line, and neomycin-, c-Ha-ras- and c-erbB2-transfected cell lines. The level of Wnt5a mRNA expression was decreased 40-fold and 3-fold when parental cells were grown on collagen and in collagen, respectively. This downregulation correlated with cell branching. However, Wnt7b was not regulated by collagen. In the presence of activated c-Ha-ras, the level of Wnt5a mRNA expression was markedly decreased (> 200-fold) and cell growth rate was elevated. When treated with p21ras inhibitor, BZA-5B, there was a moderate reversal of Wnt5a mRNA expression (2-fold) with a parallel decrease in cell growth. The data indicate that c-Ha-ras is an upstream inhibitory regulator of Wnt5a, and provide further evidence of an inverse relationship between Wnt5a mRNA expression and cell branching. This demonstrates selectivity of regulation of individual members of the Wnt gene family by the ras pathway. Overexpression of c-erbB2 had no effect on Wnt5a or Wnt7b mRNA expression. Thus, extracellular matrix and ras regulate Wnt5a, providing a mechanism for feedback of morphogenetic movements, which is relevant also to cancer biology

Trends in incidence and histological pattern of thyroid cancer in Ho Chi Minh City, Vietnam (1996–2015): a population-based study

Background The burden and trend of thyroid cancer in Vietnam have not been well documented. This study aimed to investigate the trends in incidence and histological pattern of thyroid cancer in Ho Chi Minh City from 1996 to 2015. Methods A population-based study retrieved data from the Ho Chi Minh City Cancer Registry during 1996–2015. Trends in the incidence of thyroid cancer were investigated based on age, gender, and histology for each 5-year period. Annual percentage change (APC) in incidence rates was estimated using Joinpoint regression analysis. Results In the study period, there were 5953 thyroid cancer cases (men-to-women ratio 1:4.5) newly diagnosed in Ho Chi Minh City with the mean age of 42.9 years (±14.9 years). The age-standardized incidence rate of thyroid cancer increased from 2.4 per 100,000 during 1996–2000 (95% confidence interval [95% CI]: 2.2–2.6) to 7.5 per 100,000 during 2011–2015 (95% CI: 7.3–7.9), corresponded to an overall APC of 8.7 (95% CI 7.6–9.9). The APC in men and women was 6.2 (95% CI: 4.2–8.2) and 9.2 (95% CI: 8.0–10.4), respectively. The incidence rate in the < 45 years age group was the highest diagnosed overall and increased significantly in both men (APC 11.0) and women (APC 10.1). Both genders shared similar distribution of subtype incidences, with papillary thyroid cancer constituted the most diagnosed (73.3% in men and 85.2% in women). The papillary thyroid cancer observed a markedly increase overall (APC of 10.7 (95% CI 9.3–12.0)). Conclusions There were appreciable increases in the age-standardized incidence rate of thyroid cancer in both genders, mainly contributed by the papillary subtype. The age of patients at diagnosis decreased gradually. The widespread utilization of advanced diagnostic techniques and healthcare accessibility improvement might play a potential role in these trends. Further investigations are needed to comprehend the risk factors and trends fully

A double shunt technique for the prevention of ischaemia of a congenital, solitary, pelvic kidney during abdominal aortic aneurysm repair: a case report

<p>Abstract</p> <p>Introduction</p> <p>Congenital solitary pelvic kidney is a rare condition, and its association with an abdominal aortic aneurysm is even more unusual. To the best of our knowledge, only two such cases have been reported in the literature to date.</p> <p>Case presentation</p> <p>We report the case of a 59-year-old Caucasian man with a congenital solitary pelvic kidney, who was found to have an abdominal aortic aneurysm 83 mm in diameter. Abdominal computed tomography angiography clearly identified two renal arteries, one originating from the aortic bifurcation. and the other from the proximal portion of the right common iliac artery. At surgery, renal ischaemia was prevented by introduction of an axillofemoral shunt (consisting of two femoral cannulas and a vent tube of extracorporeal circulation) from the right axillary to the right femoral artery, and a second Argyle shunt from the right common iliac artery to the origin of the left renal artery. A 20 mm Dacron tube graft was then implanted. Our patient's postoperative renal function was normal.</p> <p>Conclusion</p> <p>The renal preservation double shunt technique used in this case seems to be effective during abdominal aortic aneurysm repair.</p

Presenting patient data in the electronic care record: the role of timelines

OBJECTIVE: To establish the current level of awareness and investigate the use of timelines within clinical computing systems as an organized display of the electronic patient record (EPR). DESIGN: Multicentre survey conducted using questionnaires and interview. SETTING: Seven UK hospitals and several general practice surgeries. PARTICIPANTS: A total of 120 healthcare professionals completed a questionnaire which directed structured interviews. Participants fell into two cohorts according to whether or not they had used clinical timelines, which gave 60 timeline users and 60 prospective timeline users. MAIN OUTCOME MEASURES: To investigate the awareness of timelines, and the potential benefits of timelines within clinical computing systems. RESULTS: Fifty-eight percent of participants had not heard of the specific term timelines despite 75% of users utilizing a form of timeline on a daily basis. The potential benefits of future timelines were clinical audit (95%CI 77.6-91.6), increased time efficiency (95%CI 77.7-91.6%), reduced clinical error (95%CI 71.0-86.7) and improved patient safety (95%CI 70.0-85.9). One continuous timeline view between primary and secondary care was considered to be of great potential benefit in allowing communication via a unified patient record. CONCLUSIONS: The concept of timelines has enjoyed proven success in healthcare in the USA and in other sectors worldwide. Clinicians are supportive of timelines in healthcare. Formal input from clinicians should be sought when designing and implementing computer systems in healthcare. Timelines in healthcare support clinicians cognitive processes by improving the amount of data available and improving the way in which data are presented

Relationship between the magnitude of intraocular pressure during an episode of acute elevation and retinal damage four weeks later in rats

PURPOSE: To determine relationship between the magnitude of intraocular pressure (IOP) during a fixed-duration episode of acute elevation and the loss of retinal function and structure 4 weeks later in rats. METHODS: Unilateral elevation of IOP (105 minutes) was achieved manometrically in adult Brown Norway rats (9 groups; n = 4 to 8 each, 10-100 mm Hg and sham control). Full-field ERGs were recorded simultaneously from treated and control eyes 4 weeks after IOP elevation. Scotopic ERG stimuli were white flashes (-6.04 to 2.72 log cd.s.m(-2)). Photopic ERGs were recorded (1.22 to 2.72 log cd.s.m(-2)) after 15 min of light adaptation (150 cd/m(2)). Relative amplitude (treated/control, %) of ERG components versus IOP was described with a cummulative normal function. Retinal ganglion cell (RGC) layer density was determined post mortem by histology. RESULTS: All ERG components failed to recover completely normal amplitudes by 4 weeks after the insult if IOP was 70 mmHg or greater during the episode. There was no ERG recovery at all if IOP was 100 mmHg. Outer retinal (photoreceptor) function demonstrated the least sensitivity to prior acute IOP elevation. ERG components reflecting inner retinal function were correlated with post mortem RGC layer density. CONCLUSIONS: Retinal function recovers after IOP normalization, such that it requires a level of acute IOP elevation approximately 10 mmHg higher to cause a pattern of permanent dysfunction similar to that observed during the acute event. There is a 'threshold' for permanent retinal functional loss in the rat at an IOP between 60 and 70 mmHg if sustained for 105 minutes or more