GPU-based Low-dose 4DCT Reconstruction via Temporal Non-local Means

Four-dimensional computed tomography (4DCT) has been widely used in cancer radiotherapy for accurate target delineation and motion measurement for tumors in thorax and upper abdomen areas. However, 4DCT simulation is associated with much higher imaging dose than conventional CT simulation, which is a major concern in its clinical application. Conventionally, each phase of 4DCT is reconstructed independently using the filtered backprojection (FBP) algorithm. The basic idea of our new algorithm is that, by utilizing the common information among different phases, the input information required to reconstruct image of high quality, and thus the imaging dose, can be reduced. We proposed a temporal non-local means (TNLM) method to explore the inter-phase similarity. All phases of the 4DCT images are reconstructed simultaneously by minimizing a cost function consisting of a data fidelity term and a TNLM regularization term. We utilized a forward-backward splitting algorithm and a Gauss-Jacobi iteration method to efficiently solve the minimization problem. The algorithm was also implemented on graphics processing unit (GPU) to achieve a high computational speed. Our reconstruction algorithm has been tested on a digital NCAT thorax phantom in three low dose scenarios. Our new algorithm generates visually much better CT images containing less image noise and streaking artifacts compared with the standard FBP algorithm. Quantitative analysis shows that much higher contrast-to-noise ratio and signal-to-noise ratio can be obtained using our algorithm. The total reconstruction time for all 10 phases of a slice ranges from 90 to 140 seconds on an NVIDIA Tesla C1060 GPU card.Comment: 14 pages, 4 figures, and 2 tables, accepted by Med. Phy

Silver nanowire-based transparent, flexible, and conductive thin film

The fabrication of transparent, conductive, and uniform silver nanowire films using the scalable rod-coating technique is described in this study. Properties of the transparent conductive thin films are investigated, as well as the approaches to improve the performance of transparent silver nanowire electrodes. It is found that silver nanowires are oxidized during the coating process. Incubation in hydrogen chloride (HCl) vapor can eliminate oxidized surface, and consequently, reduce largely the resistivity of silver nanowire thin films. After HCl treatment, 175 Ω/sq and approximately 75% transmittance are achieved. The sheet resistivity drops remarkably with the rise of the film thickness or with the decrease of transparency. The thin film electrodes also demonstrated excellent flexible stability, showing < 2% resistance change after over 100 bending cycles

Disparities and risks of sexually transmissible infections among men who have sex with men in China: a meta-analysis and data synthesis.

BACKGROUND: Sexually transmitted infections (STIs), including Hepatitis B and C virus, are emerging public health risks in China, especially among men who have sex with men (MSM). This study aims to assess the magnitude and risks of STIs among Chinese MSM. METHODS: Chinese and English peer-reviewed articles were searched in five electronic databases from January 2000 to February 2013. Pooled prevalence estimates for each STI infection were calculated using meta-analysis. Infection risks of STIs in MSM, HIV-positive MSM and male sex workers (MSW) were obtained. This review followed the PRISMA guidelines and was registered in PROSPERO. RESULTS: Eighty-eight articles (11 in English and 77 in Chinese) investigating 35,203 MSM in 28 provinces were included in this review. The prevalence levels of STIs among MSM were 6.3% (95% CI: 3.5-11.0%) for chlamydia, 1.5% (0.7-2.9%) for genital wart, 1.9% (1.3-2.7%) for gonorrhoea, 8.9% (7.8-10.2%) for hepatitis B (HBV), 1.2% (1.0-1.6%) for hepatitis C (HCV), 66.3% (57.4-74.1%) for human papillomavirus (HPV), 10.6% (6.2-17.6%) for herpes simplex virus (HSV-2) and 4.3% (3.2-5.8%) for Ureaplasma urealyticum. HIV-positive MSM have consistently higher odds of all these infections than the broader MSM population. As a subgroup of MSM, MSW were 2.5 (1.4-4.7), 5.7 (2.7-12.3), and 2.2 (1.4-3.7) times more likely to be infected with chlamydia, gonorrhoea and HCV than the broader MSM population, respectively. CONCLUSION: Prevalence levels of STIs among MSW were significantly higher than the broader MSM population. Co-infection of HIV and STIs were prevalent among Chinese MSM. Integration of HIV and STIs healthcare and surveillance systems is essential in providing effective HIV/STIs preventive measures and treatments. TRIAL REGISTRATION: PROSPERO NO: CRD42013003721

Mini percutaneous nephrolithotomy is a noninferior modality to standard percutaneous nephrolithotomy for the management of 20-40 mm renal calculi: A Multicenter randomized controlled trial

Background: High quality of evidence comparing mini percutaneous nephrolithotomy (mPNL) with standard percutaneous nephrolithotomy (sPNL) for the treatment of larger-sized renal stones is lacking. Objective: To compare the efficacy and safety of mPNL and sPNL for the treatment of 20–40 mm renal stones. Design, setting, and participants: A parallel, open-label, and noninferior randomized controlled trial was performed at 20 Chinese centers (2016–2019). The inclusion criteria were patients 18–70 yr old, with normal renal function, and 20–40 mm renal stones. Intervention: Percutaneous nephrolithotomy PNL was performed using either 18 F or 24 F percutaneous nephrostomy tracts. Outcome measurements and statistical analysis: The primary outcome was the one-session stone-free rate (SFR). The secondary outcomes included operating time, visual analog pain scale (VAS) score, blood loss, complications as per the Clavien-Dindo grading system, and length of hospitalization. Results and limitations: The 1980 intention-to-treat patients were randomized. The mPNL group achieved a noninferior one-session SFR to the sPNL group by the one-side noninferiority test (0.5% [difference], p < 0.001). The transfusion and embolization rates were comparable; however, the sPNL group had a higher hemoglobin drop (5.2 g/l, p < 0.001). The sPNL yielded shorter operating time (–2.2 min, p = 0.008) but a higher VAS score (0.8, p < 0.001). Patients in the sPNL group also had longer hospitalization (0.6 d, p < 0.001). There was no statistically significant difference in fever or urosepsis occurrences. The study's main limitation was that only 18F or 24F tract sizes were used. Conclusions: Mini mPNL achieves noninferior SFR outcomes to sPNL, but with reduced bleeding, less postoperative pain, and shorter hospitalization. Patient summary: We evaluated the surgical outcomes of percutaneous nephrolithotomy using two different sizes of nephrostomy tracts in a large population. We found that the smaller tract might be a sensible alternative for patients with 20–40 mm renal stones. This multicenter, parallel, open-label, and noninferior randomized controlled trial showed that mini percutaneous nephrolithotomy achieved noninferior stone-free rate with advantages of reduced blood loss, less postoperative pain, and shorter hospitalization. Mini percutaneous nephrolithotomy should be considered a sensible alternative treatment of 20–40 mm renal stones.grants from high-level development funding of Guangzhou Medical Universit

Loss of LMO4 in the Retina Leads to Reduction of GABAergic Amacrine Cells and Functional Deficits

BACKGROUND: LMO4 is a transcription cofactor expressed during retinal development and in amacrine neurons at birth. A previous study in zebrafish reported that morpholino RNA ablation of one of two related genes, LMO4b, increases the size of eyes in embryos. However, the significance of LMO4 in mammalian eye development and function remained unknown since LMO4 null mice die prior to birth. METHODOLOGY/PRINCIPAL FINDINGS: We observed the presence of a smaller eye and/or coloboma in ∼40% LMO4 null mouse embryos. To investigate the postnatal role of LMO4 in retinal development and function, LMO4 was conditionally ablated in retinal progenitor cells using the Pax6 alpha-enhancer Cre/LMO4flox mice. We found that these mice have fewer Bhlhb5-positive GABAergic amacrine and OFF-cone bipolar cells. The deficit appears to affect the postnatal wave of Bhlhb5+ neurons, suggesting a temporal requirement for LMO4 in retinal neuron development. In contrast, cholinergic and dopaminergic amacrine, rod bipolar and photoreceptor cell numbers were not affected. The selective reduction in these interneurons was accompanied by a functional deficit revealed by electroretinography, with reduced amplitude of b-waves, indicating deficits in the inner nuclear layer of the retina. CONCLUSIONS/SIGNIFICANCE: Inhibitory GABAergic interneurons play a critical function in controlling retinal image processing, and are important for neural networks in the central nervous system. Our finding of an essential postnatal function of LMO4 in the differentiation of Bhlhb5-expressing inhibitory interneurons in the retina may be a general mechanism whereby LMO4 controls the production of inhibitory interneurons in the nervous system

Nonparametric Dynamic Panel Data Models: Kernel Estimation and Specification Testing

Published in Journal of Econometrics, https://doi.org/10.1016/j.jeconom.2013.04.020</p

The draft genomes of five agriculturally important African orphan crops

Background: Continuous growth of the world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries current face a serious burden of malnutrition, especially in Africa and South and South-East Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize and rice provide the majority of calories. Therefore, to diversify and stabilize global food supply, enhance agricultural productivity and tackle malnutrition, greater use of neglected or underutilized local plants (so-called 'orphan crops‘, but also including a few plants of special significance to agriculture, agroforestry and nutrition) could be a partial solution.Results: Here, we present draft genome information from five agriculturally, biologically, medicinally and economically important underutilized plants native to Africa; Vigna subterranea, Lablab purpureus, Faidherbia albida, Sclerocarya birrea, and Moringa oleifera. Assembled genomes range in size from 217 to 654 Mb. In V. subterranea, L. purpureus, F. albida, S. birrea and M. oleifera we have predicted 31707, 20946, 28979, 18937, 18451 protein-coding genes, respectively. By further analysing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors and starch biosynthesis-related genes in these genomes.Conclusions: These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused and predictable crop improvement programs

The nutritional and cardiovascular health benefits of rapeseed oil-fed farmed salmon in humans are not decreased compared with those of traditionally farmed salmon: a randomized controlled trial

Purpose: Farmed fish are increasingly raised on feeds containing vegetable oils, which affects their composition and possibly health properties. We investigated the effects of consuming farmed salmon, raised on different feeding regimes, on nutrient status and health outcomes in healthy subjects.  Methods: Salmon were grown on feeds containing mainly fish oil (FO) or rapeseed oil (RO), resulting in an eicosapentaenoic acid (EPA) + docosahexaenoic acid (DHA) content of fillets of 2.1 or 0.9 g/100 g, respectively. In a randomized parallel controlled trial, 51 healthy subjects were allocated to consume 2 portions/week of FO salmon (n = 17), RO salmon (n = 17) or no additional salmon (Control, n = 17) as part of their habitual diet, for 18 weeks. We collected blood at 0, 9 and 18 weeks to measure omega-3 index (O3I) in red blood cells, plasma markers of cardiovascular risk, serum 25(OH)-vitamin D 3 (25(OH)D 3) and plasma trace elements.  Results: After 18 weeks, O3I was similarly increased in subjects consuming 2 portions/week of FO or RO salmon compared to control (both p < 0.05). Serum 25(OH)D 3 was significantly higher, whereas plasma triacylglycerols were significantly lower in subjects consuming RO salmon compared to control (both p < 0.05). Heart rate was significantly lower in subjects consuming FO salmon after 9 weeks, compared to control (p < 0.01). Salmon consumption did not affect other markers.  Conclusion: Consuming two portions/week of salmon raised on rapeseed oil rather than fish oil increased the O3I and vitamin D status, and decreased plasma triacylglycerols. These outcomes endorse opportunities for developing more sustainable feeds within aquaculture food systems. Clinical trial registry: This trial was registered at clinicaltrials.gov as NCT01916434

Inferring causal molecular networks: empirical assessment through a community-based effort

Inferring molecular networks is a central challenge in computational biology. However, it has remained unclear whether causal, rather than merely correlational, relationships can be effectively inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge that focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results constitute the most comprehensive assessment of causal network inference in a mammalian setting carried out to date and suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess the causal validity of inferred molecular networks

Inferring causal molecular networks: empirical assessment through a community-based effort

It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess inferred molecular networks in a causal sense