Miracle-dz/UniFAR-FTUs huggingface dataset:
Monoclonal antibodies to enterobacterial common antigen and to Escherichia coli lipopolysaccharide outer core: demonstration of an antigenic determinant shared by enterobacterial common antigen and E. coli K5 capsular polysaccharide

We established hybridoma cell lines producing monoclonal antibodies against enterobacterial common antigen (ECA) and a substructure of the outer core of different Escherichia coli lipopolysaccharides (LPSs). Anti-ECA antibodies 865 and 898 reacted with ECA in extracts of heated E. coli and with ECA-bound R1 and R4 core-containing LPS preparations, as well as with a purified sample of ECA from Salmonella montevideo. Antibody 865, but not antibody 898, cross-reacted with K5 capsular polysaccharide, suggesting that 4-linked alpha-N-acetylglucosamine is part of an antigenic determinant shared by both K5 polysaccharide and ECA. Anti-LPS antibody 786 recognized an outer core structure common to E. coli K-12, B, R2, and R4 core type LPS, but not to R1 and R3 core type LPS. Its most probable target is the trisaccharide sequence Hexp(1----2)-alpha-D -Glcp(1----3) alpha-D-Glcp----(Hepp) (where Hex is hexose, p is phosphate, Glc is glucose, and Hep is heptose), the first glucose being the immunodominant moiety. These monoclonal antibodies may be used not only for the detection of ECA, K5, and LPS core structures but also for analysis of the molecular forms resolved on polyacrylamide gels (banding patterns) of both ECA and LPS, independently of one another.
Comparative study of the complete mitochondrial genomes of the bronze gudgeon (Coreius heterodon) and largemouth bronze gudgeon (Coreius guichenoti)

The bronze gudgeon (Coreius heterodon) and the congeneric species largemouth bronze gudgeon (Coreius guichenoti), two endemic fish species in China, are important economic fishes in local areas. The bronze gudgeon is distributed in Yangtze River and Huanghe River basin, whereas the largemouth bronze gudgeon is distributed only in the middle and upper reaches of Yangtze River. Here, we sequenced the complete mitochondrial genomes of the two species and compared the evolutionary rate differences between the two species. The complete mitochondrial genomes of C. heterodon and C. guichenoti are 16,611 and 16,612 bp, respectively. Both of the complete mitogenome sequences contain 13 protein-coding genes, 2 rRNA subunits, 22 tRNAs and 1 non-coding control region, which are typical vertebrate mitogenomes. The relative rate test shows that the mitochondrial genome of C. heterodon evolves nearly threefold faster than that of C. guichenoti, which is mostly caused by the higher substitution rates in rRNAs and especially in tRNAs in C. heterodon.
Predicting the effectiveness of queries and retrieval systems

We consider users' attempts to express their information needs through queries, or search requests and try to predict whether those requests will be of high or low quality. The second type of methods under investigation are those which attempt to estimate the quality of search systems themselves. Given a number of search systems to consider, these methods estimate how well or how poorly the systems will perform in comparison to each other. First, pre-retrieval predictors are investigated, which predict a query's effectiveness before the retrieval step and are thus independent of the ranked list of results. Such predictors base their predictions solely on query terms, collection statistics and possibly external sources. Twenty-two prediction algorithms are categorized and their quality is assessed on three different TREC test collections. A number of newly applied methods for combining various predictors are examined to obtain a better prediction of a query's effectiveness. Building on the analysis of pre-retrieval predictors, post-retrieval approaches are then investigated, which estimate a query's effectiveness on the basis of the retrieved results. The thesis focuses in particular on the Clarity Score approach and provides an analysis of its sensitivity towards different variables such as the collection, the query set and the retrieval approach. Adaptations to Clarity Score are introduced which improve the estimation accuracy of the original algorithm. The utility of query effectiveness prediction methods is commonly evaluated by reporting correlation coefficients, such as Kendall's Tau. Largely unexplored though is the question of the relationship between the current evaluation methodology for query effectiveness prediction and the change in effectiveness of retrieval systems that employ a predictor. We investigate this question by examining how the observed quality of predictors (with respect to Kendall's Tau) affects the retrieval effectiveness in two adaptive system settings: selective query expansion and meta-search. The last part of the thesis is concerned with the task of estimating the ranking of retrieval systems according to their retrieval effectiveness without relying on costly relevance judgments. Five different system ranking estimation approaches are evaluated on a wide range of data sets which cover a variety of retrieval tasks and test collections. It is shown that under certain conditions, automatic methods yield a highly accurate ranking of systems. Available online at http://www.cs. utwente.nl/~hauffc/phd/thesis.pdf.
Neighbor Joining Plus - algorithm for phylogenetic tree reconstruction with proper nodes assignment

Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such assumptions forms therefore a binary tree, with all the nodes labeled as leaves. However, these constraints are unduly restrictive as there are numerous data sets with multiple offspring of the same ancestors. Here we propose a solution to analyze and visualize such sets in a more intuitive manner. The method reconstructs phylogenetic tree by assigning the sequences with offspring as internal nodes, and the sequences without offspring as leaf nodes. In the resulting tree there is no constraint for the number of adjacent nodes, which means that the solution tree needs not to be a binary graph only. The subsequent derivation of evolutionary pathways, and pair-wise mutations, are then an algorithmically straightforward, with edge's length corresponding directly to the number of mutations. Other tree reconstruction algorithms can be extended in the proposed manner, to also give unbiased topologies.
A typechecker plugin for units of measure: domain-specific constraint solving in GHC Haskell

Typed functional programming and units of measure are a natural combination, as F# ably demonstrates. However, encoding statically-checked units in Haskell’s type system leads to inevitable disappointment with the usability of the resulting system. Extending the language itself would produce a much better result, but it would be a lot of work! In this paper, I demonstrate how typechecker plugins in the Glasgow Haskell Compiler allow users to define domain-specific constraint solving behaviour, making it possible to implement units of measure as a type system extension without rebuilding the compiler. This paves the way for a more modular treatment of constraint solving in GHC.
The Role of the Frank–Starling Law in the Transduction of Cellular Work to Whole Organ Pump Function: A Computational Modeling Analysis

We have developed a multi-scale biophysical electromechanics model of the rat left ventricle at room temperature. This model has been applied to investigate the relative roles of cellular scale length dependent regulators of tension generation on the transduction of work from the cell to whole organ pump function. Specifically, the role of the length dependent Ca2+ sensitivity of tension (Ca50), filament overlap tension dependence, velocity dependence of tension, and tension dependent binding of Ca2+ to Troponin C on metrics of efficient transduction of work and stress and strain homogeneity were predicted by performing simulations in the absence of each of these feedback mechanisms. The length dependent Ca50 and the filament overlap, which make up the Frank-Starling Law, were found to be the two dominant regulators of the efficient transduction of work. Analyzing the fiber velocity field in the absence of the Frank-Starling mechanisms showed that the decreased efficiency in the transduction of work in the absence of filament overlap effects was caused by increased post systolic shortening, whereas the decreased efficiency in the absence of length dependent Ca50 was caused by an inversion in the regional distribution of strain.
Fast Failure Detection of OpenFlow Channels

We propose a mechanism to detect OpenFlow channel failures quickly in switches and controllers where multiple controllers are running. In OpenFlow networks, it is important to maintain OpenFlow channels between controllers and switches are up and to detect channel failures immediately, so that messages to notify events such as port down and modification of flow tables are always delivered to the other side surely and immediately. Exchanging keep-alive messages frequently is undesirable for controllers because the controllers should handle many keep-alive messages from switches. This would be a significant overhead when the rate of other messages than keep-alive ones is low, because the controllers are forced to handle many keep-alive messages although such keep-alive messages do not affect network control directly. Our proposed mechanism adaptively sends keep-alive messages to detect quickly that a message is not reached to the other side, instead of checking whether a channel is up. A controller shares a message received from a switch with other controllers in a timely manner, and the controller regards a channel has been unavailable if the message notified by other controllers has not arrived via the channel. A switch sends keep-alive messages to all channels just after sending an important asynchronous message such as a port status message, and regards all channels have been gone down if the switch does not receive any response. The evaluation shows that our proposed mechanism reduces failure detection delay to timeout until receiving a response, and that overhead on latency is negligible.
Applicability of different scoring systems in outcome prediction of patients with mixed drug poisoning-induced coma

Background: Mixed drugs poisoning (MDP) is common in the emergency departments. Because of the limited number of intensive care unit beds, recognition of risk factors to divide the patients into different survival groups is necessary. Poisoning due to ingestion of different medications may have additive or antagonistic effects on different parameters included in the scoring systems; therefore, the aim of the study was to compare applicability of the different scoring systems in outcomes prediction of patients admitted with MDP-induced coma. Methods: This prospective, observational study included 93 patients with MDP-induced coma. Clinical and laboratory data conforming to the Acute Physiology and Chronic Health Evaluation (APACHE II), Modified APACHE II Score (MAS), Mainz Emergency Evaluation Scores (MEES) and Glasgow Coma Scale (GCS) were recorded for all patients on admission (time0) and 24 h later (time24). The outcome was recorded in two categories: Survived with or without complication and non-survived. Discrimination was evaluated using receiver operating characteristic (ROC) curves and area under the ROC curve (AUC). Results: The mortality rate was 9.7%. Mean of each scoring system was statistically significant between time0 and time24 in the survivors. However, it was not significant in non-survivors. Discrimination was excellent for GCS24 (0.90±0.05), APACHE II24 (0.89±0.01), MAS24 (0.86±0.10), and APACHE II0 (0.83±0.11) AUC. Conclusion: The GCS24, APACHE II24, MAS24, and APACHE II0 scoring systems seem to predict the outcome in comatose patients due to MDP more accurately. GCS and MAS may have superiority over the others in being easy to perform and not requiring laboratory data.
Cytogenetic Analysis of Ten Human Seminomas 1

A cytogenetic analysis of ten seminomas has been carried out after direct harvesting of the tumor cells. Modal chromosome numbers ranged from 63 to 112. These numbers were in agreement with flow cytometric determination of the DNA content of the tumors. Eight tumors had at least one copy of an i(12p) among other chromosomal abnormalities. Two seminomas lacked the i(12p).
Striatins Contain a Noncanonical Coiled Coil That Binds Protein Phosphatase 2A A Subunit to Form a 2:2 Heterotetrameric Core of Striatin-interacting Phosphatase and Kinase (STRIPAK) Complex*

Background: Striatins are novel regulatory subunits of PP2A in the striatin-interacting phosphatase and kinase (STRIPAK) complex. Results: The striatin coiled coil forms a noncanonical dimer required for PP2A A subunit binding. Conclusion: The coiled coil of striatins bind PP2A A subunits to form a 2:2 heterotetrameric core of the STRIPAK complex. Significance: The current structural analysis provides insights into the assembly of the STRIPAK complex. The protein phosphatase 2A (PP2A) and kinases such as germinal center kinase III (GCKIII) can interact with striatins to form a supramolecular complex called striatin-interacting phosphatase and kinase (STRIPAK) complex. Despite the fact that the STRIPAK complex regulates multiple cellular events, it remains only partially understood how this complex itself is assembled and regulated for differential biological functions. Our recent work revealed the activation mechanism of GCKIIIs by MO25, as well as how GCKIIIs heterodimerize with CCM3, a molecular bridge between GCKIII and striatins. Here we dissect the structural features of the coiled coil domain of striatin 3, a novel type of PP2A regulatory subunit that functions as a scaffold for the assembly of the STRIPAK complex. We have determined the crystal structure of a selenomethionine-labeled striatin 3 coiled coil domain, which shows it to assume a parallel dimeric but asymmetric conformation containing a large bend. This result combined with a number of biophysical analyses provide evidence that the coiled coil domain of striatin 3 and the PP2A A subunit form a stable core complex with a 2:2 stoichiometry. Structure-based mutational studies reveal that homodimerization of striatin 3 is essential for its interaction with PP2A and therefore assembly of the STRIPAK complex. Wild-type striatin 3 but not the mutants defective in PP2A binding strongly suppresses apoptosis of Jurkat cells induced by the GCKIII kinase MST3, most likely through a mechanism in which striatin recruits PP2A to negatively regulate the activation of MST3. Collectively, our work provides structural insights into the organization of the STRIPAK complex and will facilitate further functional studies.
Negative Outcome Studies in End-Stage Renal Disease

The mortality rates which we have seen now over several decades of routine provision of renal replacement therapy are truly remarkable – even if, with time, we have become familiar, if not comfortable, with them. The remarkable nature of this mortality issue is its severity, and persistence, despite numerous efforts to combat it with ‘active interventions’. These have included, in no particular order, correction of anaemia, better provision of dialysis adequacy, use of more permeable dialysis membranes, better control of dyslipidaemia, better control of mineral and bone metabolic parameters, correction of hyperhomocysteinaemia, and use of ACE inhibitors. One can now in 2008 be forgiven for some pessimism, nihilism (sometimes known as ‘renalism’) about the prospects for useful prolongation of life on dialysis except of course by transplantation. In this article (a fuller version of which appears also in Nephrology Dialysis and Transplantation, I discuss the reasons for the failure of the trials to date, the likely obstacles to future trials succeeding, and some suggestions for alternative strategies to try to grapple with this immense burden of vascular and all-cause morbidity and mortality.
On mechanical properties and bioactivity of PVDF-BCP composites

Abstract A ceramic/polymer biocomposite with high potential for multifunctional practical applications in bone tissue engineering was synthesized by using a well-known piezoelectric polymer, polyvinylidene fluoride (PVDF), and a high bioactive biphasic calcium phosphate (BCP) ceramic obtained from recycled fish bones. High-bioactivity was observed for the PVDF-BCP composite when it was subjected to conditions that simulate the animal body once a very thick apatite layer (9 μm) was grown on its surface in an immersion experiment (7 days) in simulated body fluid. The structural characteristics of the PVDF-BCP composite showed similarities with highly bioactive young animal bones, overlapped with PVDF polymorphic phases. Mechanical tests revealed properties very similar to those of the human bone tissue with a resistance strength reaching 80 MPa. Together, all these factors indicated a very promising material for application in osseous implants/replacement with postoperative recovery controlled/accelerated by external stimuli.
A new double trust regions SQP method without a penalty function or a filter

A new trust-region SQP method for equality constrained optimization is considered. This method avoids using a penalty function or a filter, and yet can be globally convergent to first-order critical points under some reasonable assumptions. Each SQP step is composed of a normal step and a tangential step for which different trust regions are applied in the spirit of Gould and Toint [Math. Program. , 122 (2010), pp. 155-196]. Numerical results demonstrate that this new approach is potentially useful. Mathematical subject classification: 65K05, 90C30, 90C55.
153 Focus 3 D : Compressive Accommodation Display

We present a glasses-free 3D display design with the potential to provide viewers with nearly correct accommodative depth cues, as well as motion parallax and binocular cues. Building on multilayer attenuator and directional backlight architectures, the proposed design achieves the high angular resolution needed for accommodation by placing spatial light modulators about a large lens: one conjugate to the viewer’s eye, and one or more near the plane of the lens. Nonnegative tensor factorization is used to compress a high angular resolution light field into a set of masks that can be displayed on a pair of commodity LCD panels. By constraining the tensor factorization to preserve only those light rays seen by the viewer, we effectively steer narrow high-resolution viewing cones into the user’s eyes, allowing binocular disparity, motion parallax, and the potential for nearly correct accommodation over a wide field of view. We verify the design experimentally by focusing a camera at different depths about a prototype display, establish formal upper bounds on the design’s accommodation range and diffraction-limited
Experimental Evaluation of a Microwave Tomography System for Breast Cancer Detection

Microwave tomography is a potential candidate for future breast-cancer screening or diagnosis. Contrary to x-rays, microwaves are non-ionizing and therefore not a health risk by their own. The examination procedure would also be more comfortable for the patient compared to conventional mammography since no compression of the breast is needed. The examination is performed by irradiating the breast with microwaves from multiple directions. The collected data is then processed by an iterative algorithm that reconstructs the permittivity and conductivity distribution in the interrogated region. Ideally, tumors could be identified in these reconstructed images due to their different properties compared to normal tissue. In this thesis, a prototype system for microwave tomographic imaging is experimentally evaluated. The system consists of 16 monopole antennas and utilize a mixture of water and glycerin as coupling liquid. As a tool for the assessment, two phantoms have been studied. One is a simplistic phantom consisting of a cylinder in which smaller cylindrical inclusions can be inserted. The other is a 3D printed structure made to resemble a human breast geometrically. This particular phantom consists of two shells, representing the different tissues of the breast. The system is found to produce well reconstructed images of both the interrogated phantoms. However, the interior geometry of the 3D printed phantom was more challenging. Furthermore, two different reconstruction algorithms are tested. The first is a Gauss-Newton based FEM algorithm and the second is a gradient-descent based FDTD method. Both of the studied algorithms proved to yield good reconstructions.
The effects of a compatibiliser on processing, tensile properties and morphology of polystyrene (PS)/styrene–butadiene rubber (SBR)/wollastonite composites

Thermoplastic elastomer composites of polystyrene (PS) blended with styrene–butadiene rubber (SBR)–filled wollastonite were prepared using a laboratory scale internal mixer. The compatibiliser used in this study was maleic anhydride (MAH). The torque developments, morphology, and mechanical properties such as tensile strength, elongation at break, Young’s modulus and impact strength were studied. PS/SBR/wollastonite composites with the addition of MAH had higher torque than PS/SBR/wollastonite composites without MAH. Tensile strength, impact strength and elongation at break were reduced by increasing filler loading, both for composites with and without MAH. Composites with MAH had higher tensile strength but lower impact strength and elongation at break as compared with composites without MAH. The Young’s modulus increased with the wollastonite loading, whereas at a similar wollastonite loading, composites with MAH exhibited higher values of Young’s modulus than composites without MAH. Scanning electron microscopy on fracture surfaces showed better filler–matrix adhesion for composites with MAH.
Server-based code obfuscation scheme for APK tamper detection

It is easy to decompile Android applications or apps owing to the structural characteristics of the app building process, but this ease makes them quite vulnerable to forgery or modification attacks. In particular, users may suffer direct financial loss if this vulnerability is exploited in security-critical private and business applications, such as online banking. One of the solutions to these problems is a code obfuscation technique. In this regard, DexGuard, which is based on ProGuard, which is integrated into the Android software development kit build system, has recently been introduced. Although DexGuard protects Android applications more effectively, an attacker is still able to analyze the hex code of a Dalvix Executable file. To resolve this weakness, we begin by analyzing the DexGuard tool from both a static and dynamic point of view. Our analysis reveals that DexGuard has some weaknesses. In this paper, we propose an obfuscation technique based on a client/server model with one-time secret key delivery using short message service or network protocol. The main concept is to store the core execute class file through obfuscation on the server, so when a program needs to execute core routines, it must request these routines from the server. In this way, we can protect Android apps from reverse engineering. Copyright © 2014 John Wiley & Sons, Ltd.