Miracle-dz/UniFAR-FTUs huggingface dataset:
The immune epitope database (IEDB) 3.0

The IEDB, www.iedb. org, contains information on immune epitopes—the molecular targets of adaptive immune responses—curated from the published literature and submitted by National Institutes of Health funded epitope discovery efforts. From 2004 to 2012 the IEDB curation of journal articles published since 1960 has caught up to the present day, with >95% of relevant published literature manually curated amounting to more than 15 000 journal articles and more than 704 000 experiments to date. The revised curation target since 2012 has been to make recent research findings quickly available in the IEDB and thereby ensure that it continues to be an up-to-date resource. Having gathered a comprehensive dataset in the IEDB, a complete redesign of the query and reporting interface has been performed in the IEDB 3.0 release to improve how end users can access this information in an intuitive and biologically accurate manner. We here present this most recent release of the IEDB and describe the user testing procedures as well as the use of external ontologies that have enabled it.
On the barriers to the development of e-government in China

Governments around the world have recognized the opportunities provided by the Internet and the worldwide web and are exploring new ways of delivering services and interacting with citizens. Since the entrance to WTO, Chinese government has achieved a lot in transforming its functions in order to adapt to the new environment. Governments at all levels actively make plans and policies to improve administrative informatization and develop e-government. However, because of the unique situation of China, compared with developed countries, Chinese e-government is still at a relatively low stage. So it's vital for us to make a detail study of the current situation of e-government development in China, find out the factors that prevent its development and seek for the corresponding solutions.
Space/time trade-offs in hash coding with allowable errors

In this paper trade-offs among certain computational factors in hash coding are analyzed. The paradigm problem considered is that of testing a series of messages one-by-one for membership in a given set of messages. Two new hash-coding methods are examined and compared with a particular conventional hash-coding method. The computational factors considered are the size of the hash area (space), the time required to identify a message as a nonmember of the given set (reject time), and an allowable error frequency. The new methods are intended to reduce the amount of space required to contain the hash-coded information from that associated with conventional methods. The reduction in space is accomplished by exploiting the possibility that a small fraction of errors of commission may be tolerable in some applications, in particular, applications in which a large amount of data is involved and a core resident hash area is consequently not feasible using conventional methods. In such applications, it is envisaged that overall performance could be improved by using a smaller core resident hash area in conjunction with the new methods and, when necessary, by using some secondary and perhaps time-consuming test to “catch” the small fraction of errors associated with the new methods. An example is discussed which illustrates possible areas of application for the new methods. Analysis of the paradigm problem demonstrates that allowing a small number of test messages to be falsely identified as members of the given set will permit a much smaller hash area to be used without increasing reject time.
Improved calvarial bone repair by hASCs engineered with Cre/loxP‐based baculovirus conferring prolonged BMP‐2 and MiR‐148b co‐expression

Repairing large calvarial bone defects remains a challenging task. Previously, it was discovered that that miR‐148b, when acting in concert with bone morphogenetic protein 2 (BMP‐2), enhanced the osteogenesis of human adipose‐derived stem cells (hASCs) and improved calvarial bone healing in nude mice. However, the molecular target of miR‐148b remained elusive. Here it is revealed that miR‐148b directly targets NOG, whose gene product (noggin) is an antagonist to BMPs and negatively regulates BMP‐induced osteogenic differentiation and bone formation. A new Cre/loxP‐based baculovirus system was employed to drive prolonged BMP‐2 and miR‐148b overexpression in hASCs, wherein the BMP‐2 overexpression induced noggin expression but the concurrent miR‐148b expression downregulated noggin, thus relieving the negative regulatory loop and ameliorating hASC osteogenesis without hindering hASC proliferation or triggering appreciable cytotoxicity. Implantation of the engineered hASCs coexpressing BMP‐2 and miR‐148b into nude mice enabled substantial repair of critical‐size calvarial bone defects (4 mm diameter) at 12 weeks post‐transplantation, filling 83% of the defect area, 75% of bone volume and restoring the bone density to 89% of the original bone density. Such superior healing effects indicate the potential of the Cre/loxP‐based baculovirus‐mediated BMP‐2/miR‐148b expression for calvarial bone repair. Copyright © 2016 John Wiley & Sons, Ltd.
CAMA: Efficient Modeling of the Capture Effect for Low-Power Wireless Networks

Network simulation is an essential tool for the design and evaluation of wireless network protocols, and realistic channel modeling is essential for meaningful analysis. Recently, several network protocols have demonstrated substantial network performance improvements by exploiting the capture effect, but existing models of the capture effect are still not adequate for protocol simulation and analysis. Physical-level models that calculate the signal-to-interference-plus-noise ratio (SINR) for every incoming bit are too slow to be used for large-scale or long-term networking experiments, and link-level models such as those currently used by the NS2 simulator do not accurately predict protocol performance. In this article, we propose a new technique called the capture modeling algorithm (CAMA) that provides the simulation fidelity of physical-level models while achieving the simulation time of link-level models. We confirm the validity of CAMA through comparison with the empirical traces of the experiments conducted by various numbers of CC1000 and CC2420-based nodes in different scenarios. Our results indicate that CAMA can accurately predict the packet reception, corruption, and collision detection rates of real radios, while existing models currently used by the NS2 simulator produce substantial prediction error.
Clinical Evaluation of the NiTiBOND Stapes Prosthesis, an Optimized Shape Memory Alloy Design

Objective To prospectively analyze short-term (3 mo) results in patients with otosclerosis who underwent stapedotomy with the newly designed NiTiBOND prosthesis and compare them with patients that underwent SMart piston stapedotomy. We aimed to assess “noninferiority” for the new prosthesis. Study Design Prospective controlled trial. Setting Tertiary referral center. Patients Thirty-eight patients were included in the NiTiBOND group (41 ears), and 74 patients were included in the SMart Piston group (75 ears). Intervention(s) Stapedotomy. Main Outcome Measure(s) Pure-tone audiometry 3 months after surgery, intraoperative prosthesis handling as assessed using a questionnaire, and complications were analyzed. Results Pure-tone audiometry showed postoperative air-bone gap means (standard deviation) of 8.1 (8.3) and 9.9 (5.4) dB; air-bone gap closure within 10 dB was achieved in 71% and 72% and within 20 dB in 93% and 96% for the NiTiBOND and the SMart piston prosthesis, respectively. Noninferiority was shown at all frequencies and in the pure-tone average. The NiTiBOND prosthesis provides excellent intraoperative handling, and no adverse reactions were reported. Conclusion Preliminary short-term results suggest safety and reliability for the new NiTiBOND stapes prosthesis.
Management options for the treatment of benign prostatic hyperplasia with or without erectile dysfunction: a focus on tadalafil and patient considerations

Lower urinary tract symptoms (LUTS) and erectile dysfunction increase with age. Several studies have identified a true association between these two disorders. Basic research studies have shown a significant decrease in the nitric oxide/cyclic guanosine monophosphate pathway with age that leads to decreased relaxation of the bladder wall and prostate and worsening LUTS. In this review article, we will focus on the potential use and clinical significance of phosphodiesterase-5 inhibitors in the treatment of LUTS secondary to benign prostate hyperplasia.
The bacterial colonization of the large bowel of pre-term low birth weight neonates

SUMMARY The bacterial colonization of the large bowel of 11 pre-term, low birth weight neonates who were nourished by expressed breast milk was examined by culturing serial faecal samples and compared to that observed in eight breast-fed and seven formula-fed full-term neonates. Pre-term neonates were colonized by high counts of facultatively anaerobic bacteria from the first days of life while bifidobacteria colonized only six babies during the first week and appeared in only one baby before day 5. Bacteroides spp. and clostridia were isolated from seven and six pre-term babies respectively during week 1 and were first observed on day 2. The intestinal colonization of pre-term infants differed from that in full-term breast-fed infants in the high counts of facultatively anaerobic bacteria and late appearance of bifidobacteria, and from both groups of full-term infants in the early stable colonization by Bacteroides spp. It is postulated that the composition of the normal intestinal microflora of pre-term low birth weight babies contributes to their predisposition to neonatal necrotizing enterocolitis. Results are discussed in relation to the effect of infant feeding regimens on intestinal microbial populations.
Towards Automatic Detection of Applicable Diatheses

The valency behavior (argument structure) of lexical items is so varied that it cannot be described by general rules and must be captured in lexicons separately for each lexical item. For verbs, lexicons typically describe only unmarked usage—the active form—while natural languages allow for certain regular changes in the number, type and/or realization of complementations (e.g. passivization). Thanks to their regularity, such changes may be described in a separate rule component of the lexicon; however, they are typically seen in many but not all verbs and their applicability to a given lexical unit (verb meaning) is not predictable from its valency alone. In this paper, we describe our initial experiments with using a large morphologically annotated corpus of Czech for determining which diatheses are applicable to a given lexical unit.
CAFIIR: An image based CBR/IR application

In this paper we describe a multimedia application called Computer Aided Facial Image Inferencing and Retrieval (CAFIIR) system. This system uses both Case Based Reasoning and Information Retrieval Techniques. In CAFIIR we use fuzzy measures to represent characteristic features of a human face. This paper describes a method designed to implement inferencing using fuzzy measures. It also describes how CAFIIR handles CHFs values that may span across two or more Fuzzy sets. The paper illustrates how Dempster Sharer theory can be useful for extracting weights for individual characteristic features when weights are given for combined features. Some parts of the application have been implemented while others are still under implementation.
Dendritic cells pulsed with RNA are potent antigen-presenting cells in vitro and in vivo

Immunization with defined tumor antigens is currently limited to a small number of cancers where candidates for tumor rejection antigens have been identified. In this study we investigated whether pulsing dendritic cells (DC) with tumor-derived RNA is an effective way to induce CTL and tumor immunity. DC pulsed with in vitro synthesized chicken ovalbumin (OVA) RNA were more effective than OVA peptide-pulsed DC in stimulating primary, OVA-specific CTL responses in vitro. DC pulsed with unfractionated RNA (total or polyA+) from OVA-expressing tumor cells were as effective as DC pulsed with OVA peptide at stimulating CTL responses. Induction of OVA-specific CTL was abrogated when polyA+ RNA from OVA-expressing cells was treated with an OVA- specific antisense oligodeoxynucleotide and RNase H, showing that sensitization of DC was indeed mediated by OVA RNA. Mice vaccinated with DC pulsed with RNA from OVA-expressing tumor cells were protected against a challenge with OVA-expressing tumor cells. In the poorly immunogenic, highly metastatic, B16/F10.9 tumor model a dramatic reduction in lung metastases was observed in mice vaccinated with DC pulsed with tumor-derived RNA (total or polyA+, but not polyA- RNA). The finding that RNA transcribed in vitro from cDNA cloned in a bacterial plasmid was highly effective in sensitizing DC shows that amplification of the antigenic content from a small number of tumor cells is feasible, thus expanding the potential use of RNA-pulsed DC- based vaccines for patients bearing very small, possibly microscopic, tumors.
Learning Artificial Neural Networks multiclassifiers by evolutionary multiobjective differential evolution guided by statistical distributions

This work presents an Evolutionary Artificial Neural Network (EANN) approach based on the Pareto Differential Evolution (PDE) algorithm where the crossover operator is determined using a Gaussian distribution associated with the best models in the evolutionary population. The crossover operator used in a real-coded genetic algorithm is based on confidence intervals. The PDE is used to localize the most promising search regions for locating the best individuals. Confidence intervals use mean localization and standard deviation estimators that are highly recommendable when the distribution of the random variables is Gaussian. It has always been an issue to find good ANN architecture in both multiclassification problems and in the field of ANNs. EANNs provide a better method to optimize simultaneously both network performance (based on the Correct Classification Rate, C) and the network performance of each class (Minimum Sensitivity, MS). The proposal with respect to methodology performance is evaluated using a well characterized set of multiclassification benchmark problems. The results show that crossover performance based on confidence intervals is less dependent on the problem than crossover performance based on a random selection of three parents in the PDE.
Gases/Odors Identification With Artificial Immune Recognition System Using Thick Film Gas Sensor Array Responses

This paper discusses the robustness of the artificial immune recognition system (AIRS) for the gases/odors identification problem. The steady state responses of a thick-film sensor array with four sensor elements with exposure of four gases, viz., H2, CO, CH4, and LPG, are used as input data. The AIRS algorithm with its versions including AIRS1, AIRS2, and parallel AIRS is applied to classify the unseen gases/odors data with duly trained networks. The classification accuracy of the AIRS algorithm is compared with radial basis function neural network, naive bayes, and learning vector quantization methods. The results obtained with the AIRS are found more promising in this experiment. The results are verified using a cross-validation scheme.
Low Versus High Sensation-seeking Tourists: a Study of Backpackers' Experience Risk Perception

This study investigates the relationships between the personality trait of sensation seeking and backpackers' risk perceptions by relying on a survey of 579 Israeli students who experienced backpacking. Some of the findings suggest that sensation seeking and travel risk perceptions are negatively correlated. For example, backpackers who were characterized as high social stimulus seekers were less concerned with socially oriented threats, such as crowded and commercialized places. However, other findings indicate that the relationships between the two concepts are more complex and might not be negatively correlated. For instance, the findings also indicate that the respondents were concerned about risks they were most likely to confront, given their anticipated behavior and nature of experiences that might be determined by their personality trait of sensation seeking. Copyright © 2011 John Wiley & Sons, Ltd.
Direct evidence for rapid degradation of Bacillus thuringiensis toxin mRNA as a cause of poor expression in plants.

It is well established that the expression of Bacillus thuringiensis (B.t.) toxin genes in higher plants is severely limited at the mRNA level, but the cause remains controversial. Elucidating whether mRNA accumulation is limited transcriptionally or posttranscriptionally could contribute to effective gene design as well as provide insights about endogenous plant gene-expression mechanisms. To resolve this controversy, we compared the expression of an A/U-rich wild-type cryIA(c) gene and a G/C-rich synthetic cryIA(c) B.t. -toxin gene under the control of identical 5' and 3' flanking sequences. Transcriptional activities of the genes were equal as determined by nuclear run-on transcription assays. In contrast, mRNA half-life measurements demonstrated directly that the wild-type transcript was markedly less stable than that encoded by the synthetic gene. Sequences that limit mRNA accumulation were located at more than one site within the coding region, and some appeared to be recognized in Arabidopsis but not in tobacco (Nicotiana tabacum). These results support previous observations that some A/U-rich sequences can contribute to mRNA instability in plants. Our studies further indicate that some of these sequences may be differentially recognized in tobacco cells and Arabidopsis.
A Qualitative Visual Servoing to ensure the Visibility Constraint

This paper describes an original control law called qualitative servoing. The particularity of this method is that no specific desired value is specified for the visual features involved in the control scheme. Indeed, visual features are only constrained to belong to a confident interval, which gives more flexibility to the system. While this formalism can be used for several types of visual features, it is used in this paper for improving the on-line control of the visibility of a target. The principle is to make a compromise between the classical positioning task and the visibility constraint. Experimental results obtained with a six degrees of freedom robot arm are presented, demonstrating the performance of the proposed method
Intravenously Administered Alphavirus Vector VA7 Eradicates Orthotopic Human Glioma Xenografts in Nude Mice

Background VA7 is a neurotropic alphavirus vector based on an attenuated strain of Semliki Forest virus. We have previously shown that VA7 exhibits oncolytic activity against human melanoma xenografts in immunodeficient mice. The purpose of this study was to determine if intravenously administered VA7 would be effective against human glioma. Methodology/Principal Findings In vitro, U87, U251, and A172 human glioma cells were infected and killed by VA7-EGFP. In vivo, antiglioma activity of VA7 was tested in Balb/c nude mice using U87 cells stably expressing firefly luciferase in subcutaneous and orthotopic tumor models. Intravenously administered VA7-EGFP completely eradicated 100% of small and 50% of large subcutaneous U87Fluc tumors. A single intravenous injection of either VA7-EGFP or VA7 expressing Renilla luciferase (VA7-Rluc) into mice bearing orthotopic U87Fluc tumors caused a complete quenching of intracranial firefly bioluminescence and long-term survival in total 16 of 17 animals. In tumor-bearing mice injected with VA7-Rluc, transient intracranial and peripheral Renilla bioluminescence was observed. Virus was well tolerated and no damage to heart, liver, spleen, or brain was observed upon pathological assessment at three and ninety days post injection, despite detectable virus titers in these organs during the earlier time point. Conclusion VA7 vector is apathogenic and can enter and destroy brain tumors in nude mice when administered systemically. This study warrants further elucidation of the mechanism of tumor destruction and attenuation of the VA7 virus.
Simulation of the Expected Performance of a Seamless Scanner for Brain PET Based on Highly Pixelated CdTe Detectors

The aim of this work is the evaluation of the design for a nonconventional PET scanner, the voxel imaging PET (VIP), based on pixelated room-temperature CdTe detectors yielding a true 3-D impact point with a density of 450 channels/cm3, for a total 6 336 000 channels in a seamless ring shaped volume. The system is simulated and evaluated following the prescriptions of the NEMA NU 2-2001 and the NEMA NU 4-2008 standards. Results show that the excellent energy resolution of the CdTe detectors (1.6% for 511 keV photons), together with the small voxel pitch (1 × 1 × 2 mm3), and the crack-free ring geometry, give the design the potential to overcome the current limitations of PET scanners and to approach the intrinsic image resolution limits set by physics. The VIP is expected to reach a competitive sensitivity and a superior signal purity with respect to values commonly quoted for state-of-the-art scintillating crystal PETs. The system can provide 14 cps/kBq with a scatter fraction of 3.95% and 21 cps/kBq with a scatter fraction of 0.73% according to NEMA NU 2-2001 and NEMA NU 4-2008, respectively. The calculated NEC curve has a peak value of 122 kcps at 5.3 kBq/mL for NEMA NU 2-2001 and 908 kcps at 1.6 MBq/mL for NEMA NU 4-2008. The proposed scanner can achieve an image resolution of ~ 1 mm full-width at half-maximum in all directions. The virtually noise-free data sample leads to direct positive impact on the quality of the reconstructed images. As a consequence, high-quality high-resolution images can be obtained with significantly lower number of events compared to conventional scanners. Overall, simulation results suggest the VIP scanner can be operated either at normal dose for fast scanning and high patient throughput, or at low dose to decrease the patient radioactivity exposure. The design evaluation presented in this work is driving the development and the optimization of a fully operative prototype to prove the feasibility of the VIP concept.
Blur kernel estimation using sparsity and local smoothness prior

Abstract. Since blur kernel estimation is an ill-posed problem, it is essential that it be constrained by parametric image priors. However, the previous normalized sparsity measure alters the kernel structure during estimation. To address the problem of single-image blur kernel estimation, a local smoothness prior is introduced to the normalized sparsity model to constrain the blurred image gradient to be similar to the unblurred one. Moreover, based on the inequality constraints, a kernel optimization algorithm is proposed to weaken the noise. Experimental results show that the proposed method is robust against noise and is able to estimate a stable blur kernel. It outperforms other state-of-the-art methods on both synthetic and real data.