Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments*

Targeted mass spectrometry is an essential tool for detecting quantitative changes in low abundant proteins throughout the proteome. Although selected reaction monitoring (SRM) is the preferred method for quantifying peptides in complex samples, the process of designing SRM assays is laborious. Peptides have widely varying signal responses dictated by sequence-specific physiochemical properties; one major challenge is in selecting representative peptides to target as a proxy for protein abundance. Here we present PREGO, a software tool that predicts high-responding peptides for SRM experiments. PREGO predicts peptide responses with an artificial neural network trained using 11 minimally redundant, maximally relevant properties. Crucial to its success, PREGO is trained using fragment ion intensities of equimolar synthetic peptides extracted from data independent acquisition experiments. Because of similarities in instrumentation and the nature of data collection, relative peptide responses from data independent acquisition experiments are a suitable substitute for SRM experiments because they both make quantitative measurements from integrated fragment ion chromatograms. Using an SRM experiment containing 12,973 peptides from 724 synthetic proteins, PREGO exhibits a 40–85% improvement over previously published approaches at selecting high-responding peptides. These results also represent a dramatic improvement over the rules-based peptide selection approaches commonly used in the literature.
Children at Risk from Domestic Violence and their Educational Attainment: Perspectives of Education Welfare Officers, Social Workers and Teachers

Children who witness domestic violence may have impaired educational attainment as well as facing other challenges such as struggles with self-esteem and forming relationships. This qualitative study set in Northern Ireland explored the perceptions of Education Welfare Officers, child protection social workers and teachers in post-primary schools regarding the impact of domestic violence on schooling and educational attainment, and of service responses to this. The survey used semi-structured interviews with four professionals in each of the above categories. Findings confirmed the major effect that domestic violence can have on children's schooling and relationships. Two typical types of responses by children were identified: those who became quiet and withdrawn, and those who became loud and aggressive. There seemed to have been progress in terms of professional understanding and service responses regarding domestic violence, but there seemed to be limited structured cooperation between the professional groups in addressing the effects of domestic violence on children. Sharing of information is hindered by confidentiality issues, some of which might be addressed by integrated teams of appropriate professionals. Greater investment in inter-agency training and development of the preventive role of the Education Welfare Service are recommended.
Effects of Heating Rate During ACFs Curing Process on Material Properties and Thermal Cycling Reliability of Flip Chip Assembly

In this study, effects of heating rate during ACF curing processes on material properties such as thermo-mechanical properties and rheological properties of ACFs were investigated. Generally, material properties of polymers change with the process conditions such as temperature, time, frequency, and so on. As the heating rate increased, coefficient of thermal expansion (CTE) of ACFs increased, and storage modulus and glass transition temperature (Tg) of ACFs decreased. ACF material property changes were due to cross-linking density which is related with ACFs density. Contact resistance of ACFs flip chip assembly was dependent on heating rates. As the heating rate increased, the contact resistances of ACFs flip chip assemblies decreased. The decrease in contact resistance was due to larger ACFs conductive particle deformation. In addition, effects of heating rates of ACFs on thermal cycling (T/C) reliability of flip chip assemblies were also investigated. As the heating rate increased, the contact resistances of ACF flip chip assemblies rapidly increased during the T/C test. T/C reliability test result was analyzed by the shear strain estimation which is closely related with ACFs material properties and the gap between a chip bump and a substrate pad. As a summary, effects of heating rate on ACFs material properties and thermal cycling reliability were investigated. T/C reliability test result was analyzed in terms of the shear strain. Based on the results, the guidelines of ACFs curing process during flip chip bonding processes were suggested.
Escaping from ancient Rome! Applications and challenges for designing smart cities

From ancient Europe, the renaissance and industrialisation eras, to the modern times, urban planning paradigms have evolved in many ways, advancing the environments where people live in. Nevertheless, the recent development of wireless and wired communication network technologies and low‐power miniature sensors for various application domains provide us with another chance of revolutionising cities by making them smarter. Smart cities, propelled by a city‐scale infrastructure, where information provided from different application systems integrate together, will initiate the development of new applications that can benefit our everyday lives. This article presents an overview of representative applications that consist a smart city with their respective challenges and application requirements. Furthermore, we share our experiences obtained from designing and deploying examples of such smart systems in multiple application domains and summarise the remaining challenges for making the vision of designing smart cities a reality. Copyright © 2014 John Wiley & Sons, Ltd.
An Analytical Model for the Effects of the Spatial Resolution of Electrode Systems on the Spectrum of Cardiac Signals

It has been suggested that the spatiotemporal characteristics of complex cardiac arrhythmias can be extracted from the spectrum of cardiac signals. However, the analysis of simple bioelectric models indicates that the spectrum of cardiac signals can be affected by the spatial resolution of the electrode system. In this paper, we derive exact measurement transfer functions relating the spectrum of cardiac signals to the spatiotemporal dynamics of cardiac sources. The analysis of the measurement transfer bandwidths for dynamics with different degrees of spatiotemporal correlation shows that as the spatial resolution decreases, the bandwidth of the measurement transfer function decreases until it reaches a constant value. Moreover, this transition from decreasing to constant values is determined by the degree of spatiotemporal correlation of the underlying cardiac source. Motivated by our analytical results, we investigate in a realistic computer simulation environment the impact of additive noise on the accuracy of body-surface dominant frequency (DF) maps. Our simulation results show that meaningful DF values are obtained on those locations where the analytical measurement transfer bandwidth is wide. These findings suggest that the accuracy of body-surface DF maps can be limited by the low spatial resolution of body-surface electrode systems.
Physical and Organoleptic Properties of Fish Sausage Prepared from Bull's Eye (priacanthus Hamrur)

Priacanthus hamrur is an underutilized non-commercial species which is relatively less preferable for direct consumption. For efficient utilization of the species, an attempt was made to convert the fish meat in to sausage. The sausages prepared, showed good quality and textural properties. Hence the meat of Priacanthus hamrur can be used for increasing its value by preparing sausage. INTRODUCTION Fish and fishery products play an important role in human nutrition as a source of proteins, fatty acids, fat soluble vitamins and micronutrients (Altschul, 1989 and Belitz 2009). Fish meat contains significantly low lipid and higher water content than bovine/ chicken meat and is favored over other white or red meats. Seafood is being used as the dish of choice owing to its healthy image and delicious taste. In particular, the fishery industry has been developing processed or minced fish products such as fish burgers, fish fingers and sausages which add cooking convenience and value to nutritional benefits (Mohammed 2007) Fish flesh can be used as raw material for sausage production because its muscle protein can form gel and act as an emulsifying agent (Yada and Jackman 1994) Fish sausage paste has decisive influence on quality factors of the final product, such as texture, flavor, appearance and nutritive value. At present the bull's eye (Priacanthus hamrur) does not possess good consumer demand in raw condition. Hence an attempt is made to investigate it's suitability for the preparation of sausage and its quality evaluation.
A Continuous Space Rule Selection Model for Syntax-based Statistical Machine Translation

One of the major challenges for statistical machine translation (SMT) is to choose the appropriate translation rules based on the sentence context. This paper proposes a continuous space rule selection (CSRS) model for syntax-based SMT to perform this context-dependent rule selection. In contrast to existing maximum entropy based rule selection (MERS) models, which use discrete representations of words as features, the CSRS model is learned by a feed-forward neural network and uses real-valued vector representations of words, allowing for better generalization. In addition, we propose a method to train the rule selection models only on minimal rules, which are more frequent and have richer training data compared to non-minimal rules. We tested our model on different translation tasks and the CSRS model outperformed a base-line without rule selection and the previous MERS model by up to 2 . 2 and 1 . 1 points of BLEU score respectively.
Neurons of the ascidian larval nervous system in Ciona intestinalis: II. Peripheral nervous system

The peripheral nervous system of the ascidian tadpole larva comprises a distributed population of isolated receptor neurons, most of unproved function, organized along the trunk or tail epithelium. Previous reports using immunocytochemical methods failed to resolve the detailed morphology of the neurons and their axon pathways. Precleavage embryos of Ciona intestinalis transfected with the promoter of the neuron‐specific synaptotagmin gene fused to a green fluorescent protein (GFP) gene yielded clearly labelled GFP profiles. These we examined in confocal image stacks of 31 larvae. Anchor cells, at least eight in each adhesive apical papilla, contribute axons to the papillar nerves that terminate in the sensory vesicle of the central nervous system. Two nerve bundles projected from each papilla, suggesting that at least two subpopulations of papillar neurons exist. Each bundle fasciculated with axons of the rostral trunk epidermal neurons (RTEN) in a stereotyped pattern. The RTEN had a hitherto unreported elaborate arbor of sensory dendrites within the tunic, suggesting that each has an extended sensorial field. Two subpopulations of apical trunk epidermal neurons (ATEN), anterior and posterior, were distinguished. As with the RTEN, these neurons extended dendritic arbors into the tunic. Two additional types of tail neuron, the caudal epidermal neurons (dorsal and ventral) as well as a novel bipolar interneuron, were identified. These identified neuron types are the substrate for the ascidian larva's entire peripheral sensory input, important during larval swimming and settlement. J. Comp. Neurol. 501:335–352, 2007. © 2007 Wiley‐Liss, Inc.
Content-based image retrieval using the heterogeneous features

The effectiveness of the content-based image retrieval can be enhanced using the heterogeneous features embedded in the images. However, since the features in color and shape are generated using different computation methods and thus may require different similarity measurements, the integration of the retrieval on heterogeneous features is a non-trivial task. In this paper, present a semantics-based clustering approach, to support visual queries on heterogeneous features of images. Using this approach, the database images are classified based on their heterogeneous features. Each semantic image cluster contains a set of sub clusters, which are represented by the heterogeneous features that the images contain. A database image is included into a feature sub cluster, only if, the image contains all the features under the same cluster. A visual query processing strategy is then presented, to support visual queries, on heterogeneous features.
Preclinical Development Molecular Mechanisms Involved in the Synergistic Interaction of the EZH 2 Inhibitor 3-Deazaneplanocin A with Gemcitabine in Pancreatic Cancer Cells

Pancreatic ductal adenocarcinoma (PDAC) is characterized by overexpression of enhancer of Zeste homolog-2 (EZH2), which plays a pivotal role in cancer stem cell (CSC) self-renewal through methylation of histone H3 lysine-27 (H3K27me3). Against this background, EZH2 was identified as an attractive target, and we investigated the interaction of the EZH2 inhibitor DZNeP with gemcitabine. EZH2 expression was detected by quantitative PCR in 15 PDAC cells, including seven primary cell cultures, showing that expression values correlated with their originator tumors (Spearman R 1⁄4 0.89, P 1⁄4 0.01). EZH2 expression in cancer cells was significantly higher than in normal ductal pancreatic cells and fibroblasts. The 3deazaneplanocin A (DZNeP; 5 mmol/L, 72-hour exposure) modulated EZH2 and H3K27me3 protein expression and synergistically enhanced the antiproliferative activity of gemcitabine, with combination index values of 0.2 (PANC-1), 0.3 (MIA-PaCa-2), and 0.7 (LPC006). The drug combination reduced the percentages of cells in G2–M phase (e.g., from 27% to 19% in PANC-1, P < 0.05) and significantly increased apoptosis compared with gemcitabine alone. Moreover, DZNeP enhanced the mRNA and protein expression of the nucleoside transporters hENT1/hCNT1, possibly because of the significant reduction of deoxynucleotide content (e.g., 25% reduction of deoxycytidine nucleotides in PANC-1), as detected by liquid chromatography/tandem mass spectrometry. DZNeP decreased cell migration, which was additionally reduced by DZNeP/gemcitabine combination (–20% in LPC006, after 8-hour exposure, P < 0.05) and associated with increased E-cadherin mRNA and protein expression. Furthermore, DZNeP and DZNeP/gemcitabine combination significantly reduced the volume of PDAC spheroids growing in CSC-selective medium and decreased the proportion of CD133þ cells. All these molecular mechanisms underlying the synergism of DZNeP/gemcitabine combination support further studies on this novel therapeutic approach for treatment of PDACs. Mol Cancer Ther; 11(8); 1735–46. 2012 AACR.
Pivotal issues on relativistic electrons in ITER

The transfer of the plasma current from thermal to relativistic electrons is a threat to ITER achieving its mission. This danger is significantly greater in the nuclear than in the non-nuclear phase of ITER operations. Two issues are pivotal. The first is the extent and duration of magnetic surface breaking in conjunction with the thermal quenches. The second is the exponential sensitivity of the current transfer to three quantities: (1) the poloidal flux change required to e-fold the number of relativistic electrons, (2) the time τa after the beginning of the thermal quench before the accelerating electric field exceeds the Connor-Hastie field for runaway, and (3) the duration of the period τop in which magnetic surfaces remain open. Adequate knowledge does not exist to devise a reliable strategy for the protection of ITER. Uncertainties are sufficiently large that a transfer of neither a negligible nor the full plasma current to relativistic electrons can be ruled out during the non-nuclear phase of ITER. Tritium decay can provide a sufficiently strong seed for a dangerous relativistic-electron current even if τa and τop are sufficiently long to avoid relativistic electrons during non-nuclear operations. The breakup of magnetic surfaces that is associated with thermal quenches occurs on a time scale associated with fast magnetic reconnection, which means reconnection at an Alfvénic rather than a resistive rate. Alfvénic reconnection is well beyond the capabilities of existing computational tools for tokamaks, but its effects can be studied using its property of conserving magnetic helicity. Although the dangers to ITER from relativistic electrons have been known for twenty years, the critical issues have not been defined with sufficient precision to formulate an effective research program. Studies are particularly needed on plasma behavior in existing tokamaks during thermal quenches, behavior which could be clarified using methods developed here.
An Adaptive, Semi-Structured Language Model Approach to Spam Filtering on a New Corpus

Motivated by current efforts to construct more realistic spam filtering experimental corpora, we present a newly assembled, publicly available corpus of genuine and unsolicited (spam) email, dubbed GenSpam. We also propose an adaptive model for semi-structured document classification based on language model component interpolation. We compare this with a number of alternative classification models, and report promising results on the spam filtering task using a specifically assembled test set to be released as part of the GenSpam corpus.
Hepatitis B virus immunization with an adjuvant containing vaccine after liver transplantation for hepatitis B‐related disease: failure of humoral and cellular immune response

Long‐term hepatitis B reinfection prophylaxis after liver transplantation with hepatitis B immunoglobulin (HBIG) and nucleoside analogues is expensive and inconvenient. Studies evaluating humoral immune responses to hepatitis B virus (HBV) vaccines showed conflicting results. Best results were achieved under continuous HBIG administration with an adjuvant–containing HBsAg vaccine. In the present study, 8 patients who had been HBsAg positive and HBV DNA negative prior to liver transplantation were immunized with HBsAg‐vaccine containing the adjuvant 3‐deacylated monophosphoryl‐lipid‐A. Vaccination was started after discontinuation of HBIG. Six vaccinations were administered at weeks 0, 2, 4, 12, 16 and 24. Humoral (anti‐HBs titres) and cellular (enzyme‐linked immunospot assay and fluorescence‐activated cell sorting analysis) immune responses were studied. Only one of eight patients responded with a humoral immune response (maximum anti‐HBs titre 561 U/l). In this patient, decrease of anti‐HBs titre before vaccination was significantly slower than in the other seven patients and anti‐HBs did not become negative before first vaccination. A T‐cell response to HBsAg could not be detected in any of the patients. The responder was the only patient who showed a T‐cell response to HBcAg. In conclusion, the adjuvant‐containing vaccine did not induce a humoral or a detectable cellular immune response in most patients. Patient‐related preconditions and concomitant HBIG administration should be further investigated as possible predictors for response.
Latest News on Arabidopsis Brassinosteroid Perception and Signaling

Brassinosteroids (BRs) are plant hormones regulating growth and development. In interaction with other hormones, they are involved in environmental cue responses. The present model of the BR response pathway in Arabidopsis includes the perception of the hormone by the plasma membrane (PM) receptor brassinosteroid insensitive 1 (BRI1) and its hetero-oligomerization with the co-receptor BRI1-associated receptor kinase 1 (BAK1), followed by the activation of a signaling-cascade finally resulting in the expression of BR-responsive genes. New findings have shed light on the receptor density in the PM and on the molecular mechanism of BR perception, which includes the hormone-induced formation of a platform in the BRI1 extracellular domain for interaction with BAK1. Furthermore, new knowledge on early, BRI1-initiated signaling events at the PM–cytoplasm interface has recently been gained. In addition, a fast BR response pathway that modifies the membrane potential and the expansion of the cell wall – both crucial processes preceding cell elongation growth – have been identified. In this review, these latest findings are summarized and discussed against the background of the present model of BRI1 signaling.
Reengineering Thesauri for New Applications: The AGROVOC Example

Existing classification schemes and thesauri are lacking in well-defined semantics and structural consistency. Empowering end users in searching collections of ever increasing magnitudes with performance far exceeding plain free-text searching (as used in many Web search engines), and developing systems that not only find but also process information for action, requires far more powerful and complex knowledge organization systems (KOSs). The paper presents a conceptual structure and transition procedure to support the shift from a traditional KOS towards a full-fledged and semantically rich KOS. The proposed structure also complies with other interoperability approaches like RDFS and XML in the Web environment. AGROVOC, a traditional thesaurus developed and maintained by the Food and Agriculture Organization (FAO) of the United Nations, serves as a case study for exploring the reengineering of a traditional thesaurus into a fully-fledged ontology. We start the process of developing an inventory of specific relationship types with well-defined semantics for the agricultural domain and explore the rules-as-you-go approach to streamlining the reengineering process.
Facilitated detection of angry faces: Initial orienting and processing efficiency

In a visual search task, displays of four schematic faces (angry, sad, happy, or neutral) were presented. Participants decided whether the faces were all the same or whether one was different. A discrepant angry face in a context of three neutral faces was detected faster than other faces. This occurred in the absence of a higher probability of first fixation on the angry face. Moreover, angry faces were more accurately detected even when presented parafoveally. These results are not consistent with the hypothesis that angry faces are detected faster because they are looked at earlier. In contrast, angry faces were looked at less than other faces during the search process and were more accurately detected than other faces when the display duration was reduced to 150 ms. These results support the processing efficiency hypothesis, according to which fewer attentional resources are needed to identify angry faces, which would account for their speeded detection time. In addition, parafoveal analysis of the angry faces may start preattentively, which would account for the fewer and shorter fixations that they need later, when they come under the focus of attention.