Predicting RNA-binding residues from evolutionary information and sequence conservation

Abstract Background RNA-binding proteins (RBPs) play crucial roles in post-transcriptional control of RNA. RBPs are designed to efficiently recognize specific RNA sequences after it is derived from the DNA sequence. To satisfy diverse functional requirements, RNA binding proteins are composed of multiple blocks of RNA-binding domains (RBDs) presented in various structural arrangements to provide versatile functions. The ability to computationally predict RNA-binding residues in a RNA-binding protein can help biologists reveal important site-directed mutagenesis in wet-lab experiments. Results The proposed prediction framework named “ProteRNA” combines a SVM-based classifier with conserved residue discovery by WildSpan to identify the residues that interact with RNA in a RNA-binding protein. Although these conserved residues can be either functionally conserved residues or structurally conserved residues, they provide clues on the important residues in a protein sequence. In the independent testing dataset, ProteRNA has been able to deliver overall accuracy of 89.78%, MCC of 0.2628, F-score of 0.3075, and F0.5-score of 0.3546. Conclusions This article presents the design of a sequence-based predictor aiming to identify the RNA-binding residues in a RNA-binding protein by combining machine learning and pattern mining approaches. RNA-binding proteins have diverse functions while interacting with different categories of RNAs because these proteins are composed of multiple copies of RNA-binding domains presented in various structural arrangements to expand the functional repertoire of RNA-binding proteins. Furthermore, predicting RNA-binding residues in a RNA-binding protein can help biologists reveal important site-directed mutagenesis in wet-lab experiments.</p

Donorâ Acceptorâ Acceptor’s Molecules for Vacuumâ Deposited Organic Photovoltaics with Efficiency Exceeding 9%

Three vacuumâ deposited donorâ acceptorâ acceptor (dâ aâ a’) small molecule donors are studied with different side chains attached to an asymmetric heterotetracene donor block for use in high efficiency organic photovoltaics (OPVs). The donor with an isobutyl side chain yields the highest crystal packing density compared to molecules with 2â ethylhexyl or nâ butyl chains, leading to the largest absorption coefficient and short circuit current in an OPV. It also exhibits a higher fill factor, consistent with its preferred outâ ofâ plane molecular Ï â Ï stacking arrangement that facilitates charge transport in the direction perpendicular to the substrate. A power conversion efficiency of 9.3 ± 0.5% is achieved under 1 sun intensity, AM 1.5 G simulated solar illumination, which is significantly higher than 7.5 ± 0.4% of the other two molecules. These results indicate that side chain modification of dâ aâ a’ small molecules offers an effective approach to control the crystal packing configuration, thereby improving the device performance.Three vacuumâ deposited donorâ acceptorâ acceptor’s small molecule donors with different alkyl chain configurations (R1â R3) are synthesized and characterized to understand the side chain effect on organic photovoltaic (OPV) performance. The donor with an isobutyl (R3) chain yields the highest crystal packing density and largest short circuit current among the three molecules. Its preferred faceâ on molecular stacking orientation on the substrate leads to the highest fill factor. The optimized OPV structure achieves a power conversion efficiency (PCE) = 9.3 ± 0.5%.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/144608/1/aenm201703603.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144608/2/aenm201703603-sup-0001-S1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144608/3/aenm201703603_am.pd

Comparison of domiciliary oxygen using liquid oxygen and concentrator in northern Taiwan

Background/PurposeLong-term oxygen therapy has become standard treatment for patients with chronic respiratory insufficiency. However, patterns of long-term home oxygen therapy have not been well studied in Taiwan. Oxygen concentrator systems are commonly used in Taiwan, but liquid oxygen delivery systems are portable and may provide advantages over the concentrator system. This study compared oxygen usage between patients from a liquid oxygen group (LOG) and an oxygen concentrator group (OCG). The authors also assessed the physiologic responses of patients with chronic obstructive pulmonary disease (COPD) to ambulatory oxygen use at home.MethodsThe study used a retrospective, cross-sectional, observational survey design. The LOG comprised 42 patients, and the OCG comprised 102 patients. We recruited participants in northern Taiwan from July 2009 to April 2010. The questionnaire instruments that were used to collect data consisted of three parts: demographic characteristics, devices used in respiratory care, and activity status with portable oxygen. Two-minute walking tests were performed on COPD patients in their homes.ResultsCOPD was the most common diagnosis in our study, with more than 50% of patients who received oxygen long term in both groups having received this diagnosis. The LOG used oxygen for an average of 21.7 hours per day, whereas OCG averaged 15.2 hours per day (p<0.001). In the OCG, 92.2% of patients used a concentrator alone, whereas 23.8% of the LOG used liquid oxygen alone (p<0.001). The LOG patients were involved in significantly more outdoors activities (p=0.002) and reported traveling with oxygen more often (p<0.001) than the OCG patients. For patients with the same dyspnea level of COPD severity, those using liquid oxygen had a lower increase in pulse rate after the walking test, in comparison with the concentrator users.ConclusionPatients in the LOG used oxygen for longer hours, went on more outings, and were more likely to travel with oxygen than patients in the OCG. Being ambulatory with liquid oxygen might enable patients with COPD to walk more effectively

Extensive Reading with Guidance

A language learning mode called “word-focused extensive reading” has been proposed to facilitate word-usage learning. The user inputs a word in the computer program designed and implemented for reading to find its usage in the context of a sentence. The computer program then searches for the knowledge base for the word and provides guidance to show a summary of the salient features of word collocation. Sentences with the word in question are displayed one at a time. For each sentence the relevant collocating words are highlighted. In this way the reader sees the word collocation so as to recognize the salient features of the word and thus incrementally acquires the knowledge of word usage. The program works with large Chinese and English collections of texts. For Chinese the knowledge of word collocation was built on the basis of the Balanced Corpus of Academia Sinica. The English collocation features were collected from the British National Corpus. The program can also be useful for learning to differentiate near-synonyms

Necrotizing fasciitis in liver cirrhosis

SummaryBackgroundNecrotizing fasciitis (NF) is associated with a high mortality rate. Hepatitis is endemic in Taiwan, and liver cirrhosis is associated with the development of NF. The characteristics of these patients, however, have not been well documented or the predictors of mortality clearly identified. The purpose of this study is to identify predictors of mortality in patients with liver cirrhosis and necrotizing fasciitis.MethodsThis study was conducted at the Chi-Mei Medical Center in southern Taiwan. Demographic data, clinical characteristics, and the microorganisms responsible for NF in patients with liver cirrhosis were recorded. To identify independent predictors associated with mortality, univariate analysis followed by multivariate logistic regression modeling was performed.ResultsDuring the period 2003–2011, a total of 55 patients with liver cirrhosis and NF were treated at the Chi-Mei Medical Center. Most patients had infections by monomicrobial Gram-negative bacilli. Univariate analysis revealed that severity of liver cirrhosis, shock, band polymorphonuclear neutrophil (>10%), international normalized ratio (>1.5), serum creatinine (>2.0 mg/dL), serum albumin (<2.5 g/dL), and activated partial thromboplastin time (>60 seconds) were significantly associated with mortality. However, multivariate logistic regression analysis revealed that serum albumin of <2.5 g/dL was the only independent predictor of mortality in patients with liver cirrhosis and NF.ConclusionNF in the vast majority of cirrhotic patients was caused by Gram-negative bacilli. Hypoalbuminemia (serum albumin <2.5 g/dL) was associated with mortality in patients with liver cirrhosis and NF. Further studies are needed to assess whether resuscitation with albumin-containing solutions lowers the mortality rate in such patients

Insights into Chinese perspectives on do-not-resuscitate (DNR) orders from an examination of DNR order form completeness for cancer patients

PURPOSE: Discussing end-of-life care with patients is often considered taboo, and signing a do-not-resuscitate (DNR) order is difficult for most patients, especially in Chinese culture. This study investigated distributions and details related to the signing of DNR orders, as well as the completeness of various DNR order forms. METHODS: Retrospective chart reviews were performed. We screened all charts from a teaching hospital in Taiwan for patients who died of cancer during the period from January 2010 to December 2011. A total of 829 patient records were included in the analysis. The details of the DNR order forms were recorded. RESULTS: The DNR order signing rate was 99.8 %. The percentage of DNR orders signed by patients themselves (DNR-P) was 22.6 %, while the percentage of orders signed by surrogates (DNR-S) was 77.2 %. The percentage of signed DNR forms that were completely filled out was 78.4 %. The percentage of DNR-S forms that were completed was 81.7 %, while the percentage of DNR-P forms that were completely filled out was only 67.6 %. CONCLUSION: Almost all the cancer patients had a signed DNR order, but for the majority of them, the order was signed by a surrogate. Negative attitudes of discussing death from medical professionals and/or the family members of patients may account for the higher number of signed DNR-S orders than DNR-P orders. Moreover, early obtainment of signed DNR orders should be sought, as getting the orders earlier could promote the quality of end-of-life care, especially in non-oncology wards

Fabrication of blue top-emitting organic light-emitting devices with highly saturated color

Abstract Blue top-emitting organic light-emitting devices (TOLEDs) with highly saturated color were developed by microcavity effect. The device structure studied was glass/reflective silver/indium-tin oxide (ITO)/organic electroluminescent stack/semi-transparent cathode (calcium/silver). By changing the thicknesses of ITO and organic layers in the microcavity structure device doped with p-bis(p-N, Ndi-phenyl-aminostyryl)benzene (DSA-ph), highly saturated color with Commission Internationale de L&apos;Eclairage chromaticity coordinates (CIE x;y ) of (0.14, 0.08) was obtained

Absorption and fluorescence of dissolved organic matter in submarine hydrothermal vents off NE Taiwan

National Natural Science Foundation of China [40810069004]; Xiamen University [211-III]; National Science Council of Taiwan [NSC 98-2621-M-110-001-MY3]; "Aim for the Top" University Program of TaiwanThe role of hydrothermal vents as either a source or a sink for chromophoric and fluorescent dissolved organic matter (CDOM and FDOM) in the oceans is unknown, since DOM absorption and fluorescence have not been reported for submarine hydrothermal vents. Water samples were collected from two shallow submarine hydrothermal vents off NE Taiwan, the white vent and the yellow vent, during two cruises in August, 2010. Absorption and excitation-emission-matrix fluorescence spectroscopy were used to characterize the optical properties of DOM from such extremely special environments. The absorption coefficients at wavelength 300 nm (a(300)) were much higher at the white vent mouth and 1 m below it (2.52 +/- 0.88 m(-1)) than in the background (0.34 +/- 0.12 m(-1)). This indicated that the white vent was a source of CDOM for seawater. Three fluorescent components were identified using parallel factor analysis: humic-like C1, tyrosine-like C3, and C2 as a combination of tryptophan-like and marine humic-like components. Both C1 and C3 (but not C2) had their highest fluorescence intensity at the white vent mouth and 1 m below it, suggesting the role of the vent as a source for both humic-like and tyrosine-like DOM. Samples from the yellow vent mouth also had a higher 0300 than the ambient seawater in our first cruise, but had fluorescence intensities of C(1-3) similar to the ambient seawater. Overall, the low humification index (HIX: 1.40 +/- 0.30) and the high autochthonous index (BIX: 1.27 +/- 0.63) indicated that the DOM likely had low humic contents and was mainly autochthonous of biological or bacterial origin in the study area. A biplot of HIX and BIX showed that DOM from the hydrothermal vents had a characteristic similar to terrestrial cave and spring waters, but was distinct from isolated humics. (C) 2011 Elsevier B.V. All rights reserved