Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins

<p>Abstract</p> <p>Background</p> <p>While occurring enzymatically in biological systems, O-linked glycosylation affects protein folding, localization and trafficking, protein solubility, antigenicity, biological activity, as well as cell-cell interactions on membrane proteins. Catalytic enzymes involve glycotransferases, sugar-transferring enzymes and glycosidases which trim specific monosaccharides from precursors to form intermediate structures. Due to the difficulty of experimental identification, several works have used computational methods to identify glycosylation sites.</p> <p>Results</p> <p>By investigating glycosylated sites that contain various motifs between Transmembrane (TM) and non-Transmembrane (non-TM) proteins, this work presents a novel method, GlycoRBF, that implements radial basis function (RBF) networks with significant amino acid pairs (SAAPs) for identifying O-linked glycosylated serine and threonine on TM proteins and non-TM proteins. Additionally, a membrane topology is considered for reducing the false positives on glycosylated TM proteins. Based on an evaluation using five-fold cross-validation, the consideration of a membrane topology can reduce 31.4% of the false positives when identifying O-linked glycosylation sites on TM proteins. Via an independent test, GlycoRBF outperforms previous O-linked glycosylation site prediction schemes.</p> <p>Conclusion</p> <p>A case study of Cyclic AMP-dependent transcription factor ATF-6 alpha was presented to demonstrate the effectiveness of GlycoRBF. Web-based GlycoRBF, which can be accessed at <url>http://GlycoRBF.bioinfo.tw</url>, can identify O-linked glycosylated serine and threonine effectively and efficiently. Moreover, the structural topology of Transmembrane (TM) proteins with glycosylation sites is provided to users. The stand-alone version of GlycoRBF is also available for high throughput data analysis.</p

Existence theorems for a crystal surface model involving the p-Laplace operator

The manufacturing of crystal films lies at the heart of modern nanotechnology. How to accurately predict the motion of a crystal surface is of fundamental importance. Many continuum models have been developed for this purpose, including a number of PDE models, which are often obtained as the continuum limit of a family of kinetic Monte Carlo models of crystal surface relaxation that includes both the solid-on-solid and discrete Gaussian models. In this paper we offer an analytical perspective into some of these models. To be specific, we study the existence of a weak solution to the boundary value problem for the equation - \Delta e^{-\mbox{div}\left(|\nabla u|^{p-2}\nabla u\right)}+au=f, where $p>1, a>0$ are given numbers and $f$ is a given function. This problem is derived from a crystal surface model proposed by J.L.~Marzuola and J.~Weare (2013 Physical Review, E 88, 032403). The mathematical challenge is due to the fact that the principal term in our equation is an exponential function of a p-Laplacian. Existence of a suitably-defined weak solution is established under the assumptions that $p\in(1,2], \ N\leq 4$, and $f\in W^{1,p}$. Our investigations reveal that the key to our existence assertion is how to control the set where -\mbox{div}\left(|\nabla u|^{p-2}\nabla u\right) is $\pm\infty$

Axillary accessory breast carcinoma masquerading as axillary abscess: a case report

Accessory breast is a frequently seen developmental breast abnormality, commoner among Asians than Caucasians. This ectopic breast tissue shares many similarities as the normal breast tissue, and although subjected to the same pathological processes, accessory breast carcinoma is rare. As locations of the accessory breast may be variable, detection of pathological lesions through clinical examinations and standard diagnostic tools (i.e., mammogram) can be difficult. Staging and management should be tailored-made according to the location of the accessory breast as well as its known pattern of lymphatic drainage. We report a case of an intra-ductal carcinoma occurring in an axillary accessory breast

Axillary accessory breast carcinoma masquerading as axillary abscess: a case report

Accessory breast is a frequently seen developmental breast abnormality, commoner among Asians than Caucasians. This ectopic breast tissue shares many similarities as the normal breast tissue, and although subjected to the same pathological processes, accessory breast carcinoma is rare. As locations of the accessory breast may be variable, detection of pathological lesions through clinical examinations and standard diagnostic tools (i.e., mammogram) can be difficult. Staging and management should be tailored-made according to the location of the accessory breast as well as its known pattern of lymphatic drainage. We report a case of an intra-ductal carcinoma occurring in an axillary accessory breast

EXPLORING E-LEARNING BEHAVIOR THROUGH LEARNING DISCOURSES

As many studies predict e-learning behaviors through intention, few of them investigate user’s learning behaviors directly. In addition to intention, individual’s e-learning behaviors may be influenced by technology readiness and group influences, such as social identity and social bond. This research-in-progress study explores how e-learning behaviors vary with intention, technology readiness, social identity and social bond. Our investigation was based on analyzing the speech acts embedded in fourteen learners’ online discourses in an eighteen-week e-learning course. We then compared how speech acts varied among groups with different degree of intention, technology readiness, social identity, and social bond. Our findings contribute e-learning research by clarifying how intention, technology readiness, social identity, and social bond influence learning behaviors in e-learning context

Discussion on the Relevance of Old Low-lying Land Reclamation and Soil Liquefaction

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchive

A multi-transition molecular line study of inward motions towards massive star-forming cores

A multi-transition 3$$mm molecular line single-pointing and mapping survey was carried out towards 29 massive star-forming cores in order to search for the signature of inward motions. Up to seven different transitions, optically thick lines HCO$^+$(1-0), CS(2-1), HNC(1-0), HCN(1-0), $^{12}$CO(1-0) and optically thin lines C$^{18}$O(1-0), $^{13}$CO(1-0) were observed towards each source. The normalized velocity differences ($\delta$V$_{\rm CS}$, $\delta$V$_{\rm HCO^{+}}$) between the peak velocities of optically thick lines and optically thin line C$^{18}$O(1-0) for each source were derived. Prominent inward motions are probably present in either HCO$^+$(1-0) or CS(2-1) or HNC(1-0) observations in most sources. Our observations show that there is a significant difference in the incidence of blue shifted line asymmetric line profiles between CS(2-1) and HCO$^+$(1-0). The HCO$^+$(1-0) shows the highest occurrence of obvious asymmetric feature, perhaps owing to different optical depth between CS(2-1) and HCO$^+$(1-0). HCO$^+$(1-0) appears to be the best inward motion tracer. The mapping observations of multiple line transitions enable us to identify six strong infall candidates G123.07-6.31, W75(OH), S235N, CEP-A, W3(OH), NGC7538. The infall signature is extended up to a linear scale $>0.2 \:$pc.Comment: 11 pages, 10 figures, 3 tables, accepted for publication in MNRA