Miracle-dz/UniFAR-FTUs huggingface dataset:
Review and comparison of methodologies for indirect comparison of clinical trial results: an illustration with ranibizumab and aflibercept

ABSTRACT Aim: To review and compare methods for indirect comparison of aflibercept and ranibizumab in patients with diabetic macular edema. Methods: Post-stratification, inverse probability weighting based on simulated data, weight optimization, and regression model techniques were used to compare pooled individual patient-level data from the RESTORE and RESPOND (ranibizumab 0.5 mg as needed after 3 initial monthly doses) studies with summary-level data from the VIVID and VISTA (aflibercept 2.0 mg every 8 weeks after 5 initial monthly doses, 2q8) studies. The impact of adjusting for up to two baseline characteristics was assessed. Results: All methods provided similar results. After adjustment for baseline best-corrected visual acuity and central retinal thickness, no statistically significant difference in average gain in baseline best-corrected visual acuity from baseline at month 12 was found between ranibizumab 0.5 mg and aflibercept 2q8. Conclusions: Weight optimization and regression methods are useful options to adjust for more than one baseline characteristic.
Expression of Myelin Protein Genes and Other Myelin Components in an Oligodendrocytic Cell Line Conditionally Immortalized with a Temperature‐Sensitive Retrovirus

Abstract: We have conditionally immortalized oligodendrocytes isolated from normal and shiverer primary mouse brain cultures through the use of the retroviral vector ZIPSVtsA58. This vector encodes an immortalizing thermolabile simian virus 40 large T antigen (Tag) and allows for clonal selection by conferring neomycin (G418) resistance. We isolated 14 shiverer and 10 normal lines that expressed the early oligodendrocyte marker 2′,3′‐cyclic nucleotide 3′‐phosphodiesterase mRNA. These cell lines grew continuously at the permissive temperature (34°C) and displayed Tag nuclear immunostaining. On shifting to nonpermissive temperatures (39°C), the cells showed rapid arrested cell growth and loss of Tag staining. One line (N20.1) engineered from normal oligodendrocytes also expressed myelin basic protein (MBP) and proteolipid protein (PLP) mRNAs, genes normally expressed by mature, differentiated oligodendrocytes. No differences in any of the myelin‐specific protein mRNA levels were observed in N20.1 cells grown at 39°C for >9 days compared with cells maintained at 34°C. Immunocytochemical staining revealed N20.1 cells to be positive for the oligodendrocyte surface markers—galactocerebroside, A007, and A2B5. However, MBP and PLP polypeptides could not be detected by western blot or immunocytochemical staining at either the permissive or nonpermissive temperature. Cell‐free protein synthesis experiments indicated that the MBP mRNAs isolated from N20.1 cells were translatable and directed the synthesis of the 17‐, 18.5‐, and 21.5‐kDa MBP isoforms. Analysis of the PLP/DM20 gene splice products by polymerase chain reaction indicated that the expression of DM20 mRNA predominated over that of PLP mRNA in this cell line. Because the cell line expressed the MBP and PLP genes, it represents a “mature” oligodendrocyte, but the splicing patterns of these genes indicate that it is at an early stage of “maturation’. This cell line has now been passaged >40 times with fidelity of phenotype and genotype.
The role of human papillomavirus in head and neck squamous cell carcinoma: A case control study on a southern Chinese population

HPV plays a role in the development of a portion of head and neck squamous cell carcinoma (HNSCC), but only limited information on its role in southern Chinese population is available. A multicenter case‐control study was conducted. HPV type, viral integration, E6/7 mRNA expression status, and TP53 mutation were determined. A total of 228 HNSCC were recruited including 137 (60.1%) oral SCC, 34 (14.9%) oropharyngeal SCC, 31 (13.6%) laryngeal SCC, 21 (9.2%) hypopharyngeal SCC, and 5 (2.2%) lip and paranasal sinus SCC. High‐risk HPV infection was found in 7.5% (17/228) of HNSCC, but only a small proportion of samples had evidence of viral integration (5.3%, 12/228) or E6/7 mRNA expression (4.4%, 10/228). HPV infection with oncogenic phenotype (integration and E6/7 mRNA expression) was significantly more common in oropharyngeal SCC than controls (9/34, 26.5% vs. 0/42, 0.0%, P < 0.001). Smoking showed a significant association with HNSCC, oropharyngeal SCC, and laryngeal SCC. TP53 mutation was associated with HNSCC (P < 0.001). Older age, TP53 mutation, and HPV16 infection with oncogenic phenotypes were independently associated factors for HNSCC with odds ratios of 1.03 (1.02–1.05), 3.38 (1.71–6.66), and 9.19 (1.13–74.68), respectively. High‐risk HPV infection of head and neck mucosa is not uncommon in the Hong Kong population. This study found that 26–30% of oropharyngeal carcinoma was associated with HPV infection, mostly HPV16, and that smoking which predisposes to TP53 mutations was another important risk factor. J. Med. Virol. 88:877–887, 2016. © 2015 Wiley Periodicals, Inc.
A systematic review and meta‐analysis of epidemiologic observational evidence on the effect of periodontitis on diabetes An update of the EFP‐AAP review

AIM To update the available evidence on the impact of periodontitis on diabetes control, incidence and complications. METHODS Observational studies on the effect of periodontitis on diabetes, published after 2012, were identified through electronic databases and hand-searched journals. Findings were summarized by evidence tables, using PRISMA statement. Quality of the included studies was evaluated through the Newcastle Ottawa scale. RESULTS Healthy individuals with periodontitis exhibit a poor glycaemic control and a higher risk of developing diabetes. Individuals affected by diabetes show a deterioration of glycaemic control if also affected by periodontitis and significantly higher prevalence of diabetes-related complications. Limited evidence is available on gestational diabetes and type 1 diabetes. CONCLUSIONS Periodontitis has a significant impact on diabetes control, incidence and complications. Nevertheless, the heterogeneity and quality of the included publications suggest that caution should be exercised when interpreting the data and that there remains an important need for additional evidence.
Partial convolution for total variation deblurring and denoising by new linearized alternating direction method of multipliers with extension step

In this paper, we propose a partial convolution model for image deblurring and denoising. We also devise a new linearized alternating direction method of multipliers (ADMM) with an extension step. As the computation of its subproblem is simple enough to have closed-form solutions, its per-iteration cost is low; however, the relaxed parameter condition together with the extra extension step inspired by Ye and Yuan's ADMM enables faster convergence than the original linearized ADMM. Preliminary experimental results show that our algorithm can produce better quality results than some existing efficient algorithms within a similar computation time. The performance advantage of our algorithm is particularly evident at high noise ratios.
Antiarrhythmic drug therapy for atrial fibrillation: Are the guidelines guiding clinical practice?

The AFFIRM study showed no clear survival advantage for a rhythm versus rate control strategy in patients with atrial fibrillation (AF). However, rhythm control with antiarrhythmic drugs (AADs) is appropriate in a large number of patients with AF. The American College of Cardiology/American Heart Association/European Society of Cardiology AF management guidelines include a safety‐based algorithm for selection of AAD therapy. Class 1C agents are recommended as first‐line therapy in patients without or with minimal structural heart disease. However, market research and clinical study data indicate a growing use of class III agents (mainly amiodarone) despite long‐term safety and tolerability concerns, suggesting that clinical practice does not adhere to current guidelines.
Microcatheter contrast injections during intra-arterial thrombolysis increase intracranial hemorrhage risk

Background and purpose Combined analysis of the Interventional Management of Stroke I and II trials demonstrated a significant association between microcatheter contrast injections and both intracranial hemorrhage (ICH) and contrast extravasation following combined intravenous (IV) and intra-arterial (IA) thrombolysis. The reliability of these observations was tested in our local registry of IA cases. Design/methods Treatment angiograms and post-procedure CTs of patients treated with combined IV/IA or IA only recombinant tissue plasminogen activator for ICA-T, M1 or M2 occlusions (n=77) were reviewed. The number of microcatheter injections (MCIs) within/distal to the target occlusion was assigned for every case. The association of MCIs to total ICH, total parenchymal hematoma (PH1+PH2) and PH2 after adjusting for significant covariates was tested. Results MCIs were used in 21 (27%) cases (range MCI 0–6). Any ICH occurred in 38 (49%) cases, including eight (10%) PH1s and eight (10%) PH2s. The use of MCIs was associated with increased PH (p=0.04), PH2 (p=0.07) and total ICH (p=0.03). MCIs were associated with increased contrast extravasation (CEx) (p=0.02). ICH was observed in all CEx cases (n=5, 100% vs 46% non-CEx; p=0.03), and four (80%) CEx cases developed PH2s (p<0.01). MCIs remained associated with total ICH after adjustment for significant covariates of Thromolysis in Cerebral Infarction score, glucose level and presence of atrial fibrillation (OR 3.60; 95% CI 1.12 to 11.49, p=0.03). MCI use was the only significantly associated covariate for total PHs. Conclusions MCI use was associated with ICH and with clinically significant PHs in this cohort, providing further evidence that MCIs be reduced during IA thrombolysis.
A dual-colored bio-marker made of doped ZnO nanocrystals

Bio-compatible ZnO nanocrystals doped with Co, Cu and Ni cations, surface capped with two types of aminosilanes and titania are synthesized by a soft chemical process. Due to the small particle size (2–5 nm), surface functional groups and the high photoluminescence emissions at the UV and blue-violet wavelength ranges, bio-imaging on human osteosarcoma (Mg-63) cells and histiocytic lymphoma U-937 monocyte cells showed blue emission at the nucleus and bright turquoise emission at the cytoplasm simultaneously. This is the first report on dual-color bio-images labeled by one semiconductor nanocrystal colloidal solution. Bright green emission was detected on mung bean seedlings labeled by all the synthesized ZnO nanocrystals. Cytotoxicity tests showed that the aminosilanes capped nanoparticles are non-toxic. Quantum yields of the nanocrystals varied from 79% to 95%. The results showed the potential of the pure ZnO and Co-doped ZnO nanocrystals for live imaging of both human cells and plant systems.
ECVQ and EVVQ video quality databases

The lack of publicly available video quality databases motivated us to create two new free available video quality databases, ETFOS CIF Video Quality (ECVQ) database and ETFOS VGA Video Quality database. They differ in resolution (CIF, VGA) and content type. Each database contains 90 videos distorted with H.264/AVC and MPEG-4 Part compression. The overall subjective scores for both databases are computed using few different approaches for processing of subjective scores. The performed analysis shows that there is no significant difference in overall scores when different processing of subjective scores approaches are used.
Advanced Risk Theory — a Self Contained Introduction, by F. Etienne de Vylder (Editions de L'Université de Bruxelles, 1996)

The opening sentence of the preface to this book gives considerable indication of what lies ahead for the reader: "Risk Theory is based on Probability Theory and Statistics, Stochastic Processes, Renewal Theory, Functional Analysis, Optimization Theory and Hilbert Space Theory". Practising actuaries will be pleased to know that the author then states: "It is not realistic to require that the nonacademic reader is familiar with all the indicated topics". The author's aim, as suggested by the second part of the book's title, is to guide the reader through advanced topics in risk theory, assuming very little prior knowledge. This is rather a bold aim. Topics are covered in some depth, and I feel that the reader with little knowledge of the above mentioned topics will struggle with some parts of the book. The book is written in three parts — ruin theory, optimisation theory and credibility theory, and additionally contains eleven appendices and thirteen pages of references and reading items. The choice of these three topics reflects the author's own substantial contributions to the field of actuarial science. Part I deals with many classical problems in ruin theory. After a couple of introductory chapters covering topics such as convolutions, renewal equations and conditional expectation, there are chapters on risk models and point processes. The main topic of this part is then covered, including finite and infinite time ruin problems for the classical surplus process. Variations on this process are introduced, such as stochastic premium income, and the author discusses how discrete time risk models can be used to approximate continuous time ones. Numerical illustrations are given of how to use ruin probabilities for the former as approximations to the corresponding quantities for the latter. Part II covers optimisation theory. Much of this part is not specifically actuarial, covering general optimisation problems, linear programming and games. It is only in the final two chapters that the focus is very much on insurance applications, including premium calculation, reinsurance and ruin theory. The final part of the book covers credibility theory. Unlike many other texts which include this subject, the author develops ideas in the framework of Hilbert spaces. Most classical topics of credibility theory are covered, including limited fluctuation credibility theory, the Biihlmann-Straub framework, hierarchical credibility, exact credibility and credibility regression models. The concluding chapter considers applications of simple credibility models to IBNR problems. Overall, this is a considerable volume containing many interesting ideas. Despite its title, I do not see it as a text from which a novice could confidently learn about many topics. I believe that it is much more suited to readers who already have a reasonably strong background in the material.
Peripubertal exposure to the antiandrogenic fungicide, vinclozolin, delays puberty, inhibits the development of androgen-dependent tissues, and alters androgen receptor function in the male rat

Vinclozolin is a well-characterized antiandrogenic fungicide. It produces adverse effects when administered during sexual differentiation, and it alters reproductive function in adult male rats by acting as an androgen-antagonist. Two active metabolites of vinclozolin, M1 and M2, compete with natural androgens for the rat and human androgen receptors (ARs), an effect that blocks androgen-induced gene expression in vivo and in vitro. In addition to their effects during perinatal life, androgens play a key role in pubertal maturation in young males. In this regard, the present study was designed to examine the effects of peripubertal oral administration of vinclozolin (0, 10, 30, or 100 mg kg−1 day−1) on morphological landmarks of puberty, hormone levels, and sex accessory gland development in male rats. In addition, as binding of the M1 and M2 to AR alter the subcellular distribution of AR by inhibiting AR-DNA binding, we examined the effects of vinclozolin on AR distribution in the target cells after in vivo treatment. We also examined serum levels of vinclozolin, M1, and M2 in the treated males so that these could be related to the effects on the reproductive tract and AR distribution. Vinclozolin treatment delayed pubertal maturation (at 30 and 100 mg kg−1 day−1) and retarded sex accessory gland and epididymal growth. Serum luteinizing hormone (LH; significant at all dosage levels) and testosterone and 5α-androstane,3α,17β-diol (at 100 mg kg−1 day−1) levels were increased. Testis size and sperm production, however, were unaffected. It was apparent that these effects were concurrent with subtle alterations in the subcellular distribution of AR. In control animals, most AR were in the high salt cell fraction, apparently bound to the natural ligand and DNA. Vinclozolin treatment reduced the amount of AR in the high salt (bound to DNA) fraction and it increased AR levels in the low salt (inactive, not bound to DNA) fraction. M1 and M2 were found in the serum of animals from the two highest dosage groups, but they were present at levels well below their K i values. In summary, these results suggest that when the vinclozolin metabolites occupy a small percentage of AR in the cell, this prevents maximal AR-DNA binding and alters in vivo androgen-dependent gene expression and protein synthesis, which in turn results in obvious alterations of morphological development and serum hormone levels. It is noteworthy that similar exposures during prenatal life result in a high incidence of malformations in male rats.
The serine/threonine protein phosphatase SIT4 modulates yeast‐to‐hypha morphogenesis and virulence in Candida albicans

SIT4 encodes the multifunctional catalytic subunit of a type 2A‐related protein phosphatase of Saccharomyces cerevisiae and has been implicated in cell cycle regulation and nitrogen sensing. We have identified the Candida albicans homologue of SIT4, and we show that its disruption caused a significant reduction in general growth rate, in hyphal outgrowth and in virulence in a mouse infection model. These phenotypes were reversed by the reintroduction of the wild‐type SIT4 gene. We used glass DNA microarrays to measure the transcriptional profiles of 6287 open reading frames in sit4 cells undergoing the yeast‐to‐hypha transition induced by serum. Although differential expression of many of the hyphae‐specific genes was not affected by the SIT4 deletion, the transcription of two new hyphae‐induced genes, XOG1 and YNR67, was entirely reliant upon Sit4p. Both genes represent glucanases, indicating that SIT4 may play a role in controlling cell wall biogenesis. Furthermore, sit4 cells exhibited a reduced heat shock response to treatment with serum/37°C, suggesting that SIT4 acts to co‐ordinate the stress response signals during morphological switching. Finally, sit4 cells displayed reduced transcript levels for the genes encoding the Hog1p MAP kinase and several modulators of protein biosynthesis. Sit4p thus plays important roles during hyphal growth in Candida albicans through the regulation of cell wall biogenesis, osmosensing and protein translation.
Anatolian origins and diversification of Aethionema, the sister lineage of the core Brassicaceae.

PREMISE OF THE STUDY The Irano-Turanian region harbors three biodiversity hotspots and ∼25% of Brassicaceae species are endemic to the region. Aethionema (∼61 species) is the sister lineage to the core Brassicaceae and occurs mainly in the Irano-Turanian region. The evolutionary important position of Aethionema makes it an ideal reference for broader comparative genetics and genomics. To understand the evolution of Aethionema, and for a broader understanding of crucifer evolution, a time-calibrated phylogenetic tree and biogeographical history of the genus is needed. METHODS Seventy-six plastome coding regions and nuclear rDNA genes, mainly from herbarium material, covering 75% of all Aethionema species, were used to resolve a time-calibrated Aethionema phylogeny. The different clades were characterized based on four morphological characters. The ancestral area of Aethionema was estimated with historical biogeographical analyses. KEY RESULTS Three well-supported major clades within Aethionema were resolved. The ancestral area reconstruction and divergence-time estimates are consistent with major dispersal events during the Pliocene from the Anatolian Diagonal. CONCLUSIONS We find that most Aethionema lineages originated along the Anatolian Diagonal, a floristic bridge connecting the east to the west, during the Pliocene. The dispersal of Aethionema correlates with the local geological events, such as the uplift of the Anatolian and Iranian plateaus and the formation of the major mountain ranges of the Irano-Turanian region. Knowing the paleo-ecological context for the evolution of Aethionema, in addition to the other lineages of Brassicaceae, facilitates our broader understanding for trait evolution and species diversification across the Brassicaceae.
Energy-Efficient Load-Balanced Heterogeneous Mobile Cloud

Today's integration of mobile technologies and traditional cloud computing exploits the abundant computation and storage resources in the cloud, to enhance the capabilities of end-user mobile devices. The designs that rely on remote cloud services, however, sometimes overlook the abundant resources (e.g., storage, communication, and computation) on mobile devices. In particular, when the remote cloud services are unavailable (due to service downtime or network issues), these smart devices can no longer function. We propose a Heterogeneous Mobile Cloud (HMC) computing design that efficiently utilizes the communication and computation resources to support data storage and data processing services in a group of mobile devices. Each mobile device may have different energy, communication and computation capabilities, but our Mobile Storage \& Processing System (\emph{MSPS}) ensures that: i) the communication and computation tasks are executed in an energy-efficient manner, ii) task allocation considers device heterogeneity and achieves system-wide load balancing, and iii) the stored data are fault-tolerant. Through extensive simulations and real hardware implementations on Android devices, we demonstrate the performance and feasibility of deploying \emph{MSPS} in a real heterogeneous mobile environment.
Optimization of Savitzky-Golay smoothing filter for salivary surface enhanced Raman spectra of non structural protein 1

Raman spectroscopy is a vibration based spectroscopic technique for identifying chemical constituent. The Raman signal can be enhanced by binding with metal nanostructures, resulting in so-called surface-enhanced Raman scattering (SERS). Non-structural protein 1 (NS1), a biomarker for flavivirus origin diseases, is found to present in saliva in low concentration. SERS is promising as an early detection method for NS1 in saliva. However, unwanted features are found to embed in the SERS spectrum, making the characteristic features undetected with visual or automated means. In particular, at low concentration of NS1, the intensity at characteristic peak (Imax) and its signal-to-noise ratio (SNR) is so low that the noisy features actually bury the fingerprint characteristics. In addition to background subtraction and baseline removal, spectrum smoothing using suitable filter is found to improve the spectra SNR. In this study, NS1 dilution dataset from the UiTM-NMRR-12868-NS1-DENV spectral database is used. It is found that SG smoothing filter optimized with a span of 13 and a polynomial degree of order 3 produces the most intense smoothing effect while preserving most of the characteristics of the original spectral waveform, with SNR of 3.76, %RMSE of 33.49% and maximum intensity (Imax) of 98%.