Bayesian neural networks via MCMC: a Python-based tutorial

Bayesian inference provides a methodology for parameter estimation and uncertainty quantification in machine learning and deep learning methods. Variational inference and Markov Chain Monte-Carlo (MCMC) sampling techniques are used to implement Bayesian inference. In the past three decades, MCMC methods have faced a number of challenges in being adapted to larger models (such as in deep learning) and big data problems. Advanced proposals that incorporate gradients, such as a Langevin proposal distribution, provide a means to address some of the limitations of MCMC sampling for Bayesian neural networks. Furthermore, MCMC methods have typically been constrained to use by statisticians and are still not prominent among deep learning researchers. We present a tutorial for MCMC methods that covers simple Bayesian linear and logistic models, and Bayesian neural networks. The aim of this tutorial is to bridge the gap between theory and implementation via coding, given a general sparsity of libraries and tutorials to this end. This tutorial provides code in Python with data and instructions that enable their use and extension. We provide results for some benchmark problems showing the strengths and weaknesses of implementing the respective Bayesian models via MCMC. We highlight the challenges in sampling multi-modal posterior distributions in particular for the case of Bayesian neural networks, and the need for further improvement of convergence diagnosis

Outcomes of four-point suture fixated and two-point sutureless posterior chamber IOLs combined with pars plana vitrectomy

Background While each scleral fixation method has its own advantages, there is a lack of strong evidence to suggest a superior technique. Advances in cataract surgery expand patient eligibility for successful cataract extraction, benefitting a growing population of pseudophakic patients. However, implantation of secondary intraocular lens (IOL) with compromised anterior or posterior capsule is a more challenging task. Each method of scleral fixation has its own advantages and none of them has strong evidence to be superior. This paper describes postsurgical outcomes of two scleral intraocular(IOL) fixation techniques combined with pars plana vitrectomy(PPV) from a single tertiary referral eye center. Methods Patients underwent PPV and IOL implantation with either four-point sutured scleral fixation (Akreos AO60(AK); n = 24) or two-point sutureless flanged intrascleral fixation (CT Lucia(CTL); n = 7). Reports include IOL and sclerotomy placement, fixation techniques, and IOL model. Results Thirty-one eyes of thirty patients were analyzed. Average change in vision from baseline measurement was LogMAR − 0.68 ± 0.66 and − 0.90 ± 0.63 for AK and CTL groups, respectively. Average postoperative refractive error was − 0.3 ± 1.03 D (AK) and 0.4 ± 0.60 D (CTL). No opacification cases of Akreos lens were found in this study with the longest follow up of 53 months. Conclusions Both methods of implantation (sutured and sutureless) could provide good visual and refractive outcomes. Minimal complication rates were reported despite including patients with multiple comorbidities, making both techniques an attractive choice for secondary IOL implantation

Cancer Screening Rates in Individuals With Different Life Expectancies

IMPORTANCE: Routine cancer screening has unproven net benefit for patients with limited life expectancy. OBJECTIVE: To examine the patterns of prostate, breast, cervical, and colorectal cancer screening in the United States in individuals with different life expectancies. DESIGN, SETTING, AND PARTICIPANTS: Data from the population-based National Health Interview Survey (NHIS) from 2000 through 2010 were used and included 27 404 participants aged 65 years or older. Using a validated mortality index specific for NHIS, participants were grouped into those with low (<25%), intermediate (25%-49%), high (50%-74%), and very high (≥75%) risks of 9-year mortality. MAIN OUTCOMES AND MEASURES: Rates of prostate, breast, cervical, and colorectal cancer screening. RESULTS: In participants with very high mortality risk, 31% to 55% received recent cancer screening, with prostate cancer screening being most common (55%). For women who had a hysterectomy for benign reasons, 34% to 56% had a Papanicolaou test within the past 3 years. On multivariate analysis, very high vs low mortality risk was associated with less screening for prostate (odds ratio [OR], 0.65 [95% CI, 0.50-0.85]), breast (OR, 0.43 [95% CI, 0.35-0.53]), and cervical (OR, 0.50 [95% CI, 0.36-0.70]) cancers. There was less screening for prostate and cervical cancers in more recent years compared with 2000, and there was no significant interaction between calendar year and mortality risk for any cancer screening (P > .05 for all cancers). Our sensitivity analysis showed that screening was also common in individuals with less than 5-year life expectancy. CONCLUSIONS AND RELEVANCE: A substantial proportion of the US population with limited life expectancy received prostate, breast, cervical, and colorectal cancer screening that is unlikely to provide net benefit. These results suggest that overscreening is common in both men and women, which not only increases health care expenditure but can lead to net patient harm

An improved ultrasound-assisted extraction process of gossypol acetic acid from cottonseed soapstock

To investigate the extracted process of gossypol acetic acid (G-AA) from cottonseed soapstock and explore the improvement of its yield and purity, a novel ultrasound-assisted extraction and crystallization method was introduced to this process. Under the optimized conditions, preliminary G-AA with the yield of 1300 mg and the purity of 95.9% could be obtained from 100 g of fresh soapstock by ultrasound-assisted extraction. In addition, UV, IR, and NMR spectrum further confirmed the detailed chemical structure of G-AA. Assay of inhibiting human prostate tumor cell line PC-3 and human breast cancer cell line MDA-MB-231 revealed its biological activity, the values of IC 50 are 9.096 Μmol/L and 14.37 Μmol/L respectively. In comparison with the conventional solvent extraction, this novel process increases the content of G-AA over 90%, reduces the time of crystallization by 75%, and retains the anticancer activity of gossypol. © 2009 American Institute of Chemical Engineers AIChE J, 2009Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/61872/1/11700_ftp.pd

Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3

Background: Alternative splicing (AS) of maturing mRNA can generate structurally and functionally distinct transcripts from the same gene. Recent bioinformatic analyses of available genome databases inferred a positive correlation between intron length and AS. To study the interplay between intron length and AS empirically and in more detail, we analyzed the diversity of alternatively spliced transcripts (ASTs) in the Drosophila RNA-binding Bruno-3 (Bru-3) gene. This gene was known to encode thirteen exons separated by introns of diverse sizes, ranging from 71 to 41,973 nucleotides in D. melanogaster. Although Bru-3's structure is expected to be conducive to AS, only two ASTs of this gene were previously described. Results: Cloning of RT-PCR products of the entire ORF from four species representing three diverged Drosophila lineages provided an evolutionary perspective, high sensitivity, and long-range contiguity of splice choices currently unattainable by high-throughput methods. Consequently, we identified three new exons, a new exon fragment and thirty-three previously unknown ASTs of Bru-3. All exon-skipping events in the gene were mapped to the exons surrounded by introns of at least 800 nucleotides, whereas exons split by introns of less than 250 nucleotides were always spliced contiguously in mRNA. Cases of exon loss and creation during Bru-3 evolution in Drosophila were also localized within large introns. Notably, we identified a true de novo exon gain: exon 8 was created along the lineage of the obscura group from intronic sequence between cryptic splice sites conserved among all Drosophila species surveyed. Exon 8 was included in mature mRNA by the species representing all the major branches of the obscura group. To our knowledge, the origin of exon 8 is the first documented case of exonization of intronic sequence outside vertebrates. Conclusion: We found that large introns can promote AS via exon-skipping and exon turnover during evolution likely due to frequent errors in their removal from maturing mRNA. Large introns could be a reservoir of genetic diversity, because they have a greater number of mutable sites than short introns. Taken together, gene structure can constrain and/or promote gene evolution

Multidrug resistant pulmonary tuberculosis treatment regimens and patient outcomes: an individual patient data meta-analysis of 9,153 patients.

Treatment of multidrug resistant tuberculosis (MDR-TB) is lengthy, toxic, expensive, and has generally poor outcomes. We undertook an individual patient data meta-analysis to assess the impact on outcomes of the type, number, and duration of drugs used to treat MDR-TB

Characterization of Outer Retinal Morphology with HighSpeed, Ultrahigh-Resolution Optical Coherence Tomography

PURPOSE. To visualize, quantitatively assess, and interpret outer retinal morphology by using high-speed, ultrahigh-resolution (UHR) OCT. METHODS. Retinal imaging was performed in the ophthalmic clinic in a cross-section of 43 normal subjects with a 3.5-m, axial-resolution, high-speed, UHR OCT prototype instrument, using a radial scan pattern (24 images, 1500 axial scans). Outer retinal layers were automatically segmented and measured. High-definition imaging was performed with a 2.8-m axialresolution, high-speed, UHR OCT research prototype instrument, to visualize the finer features in the outer retina. RESULTS. Quantitative maps of outer retinal layers showed clear differences between the cone-dominated fovea and the roddominated parafovea and perifovea, indicating that photoreceptor morphology can explain the appearance of the outer retina in high-speed, UHR OCT images. Finer, scattering bands were visualized in the outer retina using high-definition imaging and were interpreted by comparison to known anatomy. CONCLUSIONS. High-speed UHR OCT enables quantification of scattering layers in the outer retina. An interpretation of these features is presented and supported by quantitative measurements in normal subjects and comparison with known anatomy. The thick scattering region of the outer retina previously attributed to the retinal pigment epithelium (RPE) is shown to consist of distinct scattering bands corresponding to the photoreceptor outer segment tips, RPE, and Bruch&apos;s membrane. These results may advance understanding of the outer retinal appearance in OCT images. The normative measurements may also aid in future investigations of outer retinal changes in age-related macular degeneration and other diseases. (Inves

High Dose “HDR-Like” Prostate SBRT: PSA 10-Year Results From a Mature, Multi-Institutional Clinical Trial

Purpose/Objective(s)Although ample intermediate-term prostate stereotactic body radiotherapy (SBRT) outcomes have been reported, 10-year results remain relatively sparse.Materials/MethodsEighteen institutions enrolled 259 low- and intermediate-risk patients. Median follow-up is 5.5 years, with 66 patients followed ≥ 10 years. This SBRT regimen specifically emulated an existing HDR brachytherapy dose schedule and isodose morphology, prescribed to 38 Gy/4 fractions, delivered daily by robotic SBRT, mandating &gt; 150% dose escalation in the peripheral zone. Androgen deprivation therapy was not allowed, and a hydrogel spacer was not available at that time.ResultsMedian pre-SBRT PSA 5.12 ng/mL decreased to 0.1 ng/mL by 3.5 years, with further decrease to a nadir of &lt; 0.1 ng/mL by 7 years, maintained through 10 years. Ten-year freedom from biochemical recurrence measured 100% for low-risk, 84.3% for favorable intermediate risk (FIR), and 68.4% for unfavorable intermediate (UIR) cases. Multivariable analysis revealed that the UIR group bifurcated into two distinct prognostic subgroups. Those so classified by having Gleason score 4 + 3 and/or clinical stage T2 (versus T1b/T1c) had a significantly poorer 10 year freedom from biochemical recurrence rate, 54.8% if either or both factors were present, while UIR patients without these specific factors had a 94.4% 10-year freedom from biochemical recurrence rate. The cumulative incidence of grade 2 GU toxicity modestly increased over time – 16.3% at 5 years increased to 19.2% at 10 years-- while the incidence of grade 3+ GU and GI toxicity remained low and stable to 10 years - 2.6% and 0%, respectively. The grade 2 GI toxicity incidence also remained low and stable to 10 years – 4.1% with no further events after year 5.ConclusionThis HDR-like SBRT regimen prescribing 38 Gy/4 fractions but delivering much higher intraprostatic doses on a daily basis is safe and effective. This treatment achieves a median PSA nadir of &lt;0.1 ng/mL and provides high long-term disease control rates without ADT except for a subgroup of unfavorable intermediate-risk patients

High Dose “HDR-Like” Prostate SBRT: PSA 10-Year Results From a Mature, Multi-Institutional Clinical Trial

Purpose/Objective(s)Although ample intermediate-term prostate stereotactic body radiotherapy (SBRT) outcomes have been reported, 10-year results remain relatively sparse.Materials/MethodsEighteen institutions enrolled 259 low- and intermediate-risk patients. Median follow-up is 5.5 years, with 66 patients followed ≥ 10 years. This SBRT regimen specifically emulated an existing HDR brachytherapy dose schedule and isodose morphology, prescribed to 38 Gy/4 fractions, delivered daily by robotic SBRT, mandating > 150% dose escalation in the peripheral zone. Androgen deprivation therapy was not allowed, and a hydrogel spacer was not available at that time.ResultsMedian pre-SBRT PSA 5.12 ng/mL decreased to 0.1 ng/mL by 3.5 years, with further decrease to a nadir of < 0.1 ng/mL by 7 years, maintained through 10 years. Ten-year freedom from biochemical recurrence measured 100% for low-risk, 84.3% for favorable intermediate risk (FIR), and 68.4% for unfavorable intermediate (UIR) cases. Multivariable analysis revealed that the UIR group bifurcated into two distinct prognostic subgroups. Those so classified by having Gleason score 4 + 3 and/or clinical stage T2 (versus T1b/T1c) had a significantly poorer 10 year freedom from biochemical recurrence rate, 54.8% if either or both factors were present, while UIR patients without these specific factors had a 94.4% 10-year freedom from biochemical recurrence rate. The cumulative incidence of grade 2 GU toxicity modestly increased over time – 16.3% at 5 years increased to 19.2% at 10 years-- while the incidence of grade 3+ GU and GI toxicity remained low and stable to 10 years - 2.6% and 0%, respectively. The grade 2 GI toxicity incidence also remained low and stable to 10 years – 4.1% with no further events after year 5.ConclusionThis HDR-like SBRT regimen prescribing 38 Gy/4 fractions but delivering much higher intraprostatic doses on a daily basis is safe and effective. This treatment achieves a median PSA nadir of <0.1 ng/mL and provides high long-term disease control rates without ADT except for a subgroup of unfavorable intermediate-risk patients

Prior alcohol use enhances vulnerability to compulsive cocaine self-administration by promoting degradation of HDAC4 and HDAC5

Addiction to cocaine is commonly preceded by experiences with legal or decriminalized drugs, such as alcohol, nicotine, and marijuana. The biological mechanisms by which these gateway drugs contribute to cocaine addiction are only beginning to be understood. We report that in the rat, prior alcohol consumption results in enhanced addiction-like behavior to cocaine, including continued cocaine use despite aversive consequences. Conversely, prior cocaine use has no effect on alcohol preference. Long-term, but not short-term, alcohol consumption promotes proteasome-mediated degradation of the nuclear histone deacetylases HDAC4 and HDAC5 in the nucleus accumbens, a brain region critical for reward-based memory. Decreased nuclear HDAC activity results in global H3 acetylation, creating a permissive environment for cocaine-induced gene expression. We also find that selective degradation of HDAC4 and HDAC5, facilitated by the class II–specific HDAC inhibitor MC1568, enhances compulsive cocaine self-administration. These results parallel our previously reported findings that the gateway drug nicotine enhances the behavioral effects of cocaine via HDAC inhibition. Together, our findings suggest a shared mechanism of action for the gateway drugs alcohol and nicotine, and reveal a novel mechanism by which environmental factors may alter the epigenetic landscape of the reward system to increase vulnerability to cocaine addiction