Miracle-dz/UniFAR-FTUs huggingface dataset:
Management of ErbB2-positive Breast Cancer: Insights from Preclinical and Clinical Studies with Lapatinib

The management of human epidermal growth factor receptor 2-positive (ErbB2+) breast cancer is challenging; patients with ErbB2+ breast tumors have more aggressive disease and a poor prognosis. The increasing incidence of breast cancer in Asia and the limitations of existing treatments pose additional challenges. In this review, we summarize the preclinical and clinical evidence that indicates how lapatinib, a novel inhibitor that targets the human epidermal growth factor receptor (ErbB1) and ErbB2 may help clinicians address four particularly challenging issues in the management of ErbB2+ breast cancer. These issues are: (i) trastuzumab therapy failure, (ii) development of central nervous system metastases, (iii) minimizing toxicity and (iv) selecting the most appropriate partners (chemotherapy and non-chemotherapy) for combination therapy with lapatinib. Lapatinib, in combination with chemotherapeutic agents, such as capecitabine, provides clinical benefits to patients with ErbB2+ breast cancer, including patients who develop progressive disease on trastuzumab. Lapatinib, in combination with non-chemotherapeutic agents, such as letrozole, may also provide a chemotherapy-free treatment option for postmenopausal patients with estrogen receptor-positive/ErbB2+ metastatic breast cancer. Encouraging results have also emerged regarding the synergistic effects of lapatinib in combination with other agents for the treatment of ErbB2+ breast cancer. Promising findings have also been reported for the use of lapatinib to prevent and treat central nervous system metastases. Collectively, these results indicate that the judicious use of lapatinib, an effective oral therapy with a manageable toxicity profile, can enhance the management of patients with ErbB2+ breast cancer.
Comparative Analysis of Fatty Acid Desaturases in Cyanobacterial Genomes

Fatty acid desaturases are enzymes that introduce double bonds into the hydrocarbon chains of fatty acids. The fatty acid desaturases from 37 cyanobacterial genomes were identified and classified based upon their conserved histidine-rich motifs and phylogenetic analysis, which help to determine the amounts and distributions of desaturases in cyanobacterial species. The filamentous or N2-fixing cyanobacteria usually possess more types of fatty acid desaturases than that of unicellular species. The pathway of acyl-lipid desaturation for unicellular marine cyanobacteria Synechococcus and Prochlorococcus differs from that of other cyanobacteria, indicating different phylogenetic histories of the two genera from other cyanobacteria isolated from freshwater, soil, or symbiont. Strain Gloeobacter violaceus PCC 7421 was isolated from calcareous rock and lacks thylakoid membranes. The types and amounts of desaturases of this strain are distinct to those of other cyanobacteria, reflecting the earliest divergence of it from the cyanobacterial line. Three thermophilic unicellular strains, Thermosynechococcus elongatus BP-1 and two Synechococcus Yellowstone species, lack highly unsaturated fatty acids in lipids and contain only one Δ9 desaturase in contrast with mesophilic strains, which is probably due to their thermic habitats. Thus, the amounts and types of fatty acid desaturases are various among different cyanobacterial species, which may result from the adaption to environments in evolution.
Chemical genetic algorithms: coevolution between codes and code translation

A chemical genetic algorithm (CGA) in which several types of molecules (information units) react with each other in a cell is proposed. Translation from codons (short substrings of bits) in DNA to amino acids (real value units) is specified by a particular set of translation molecules created by the reaction between tRNA units and amino acid units. This adaptively changes and optimizes the fundamental genotype-phenotype mapping during evolution. Through the struggle between cells containing a DNA unit and small molecular units, the codes in DNA and the translation table described by the small molecular units coevolve, and a specific output function (protein), which is used to evaluate a cell's fitness, is optimized. To demonstrate the effectiveness of the CGA, the algorithm is applied to a set of deceptive problems, and the results by using the CGA are compared to those by using a simple GA. It is shown that the CGA has far better performance for the tested functions than the conventional simple GA.
Time series discord discovery using WAT algorithm and iSAX representation

Among several existing algorithms proposed to solve the problem of time series discord discovery, HOT SAX and WAT are two widely used algorithms. Especially, WAT can make use of the multi-resolution property in Haar wavelet transform. In this work, we employ state-of-the-art iSAX representation rather than SAX representation in WAT algorithm. To apply iSAX in WAT algorithm, we have to devise two new auxiliary functions and also modify iSAX index structure to adapt Haar transform that is used in WAT algorithm. We empirically evaluate our algorithm with a set of experiments. Experimental results show that WATiSAX algorithm is more effective than original WAT algorithm.
A computational study of Shewanella oneidensis MR-1: structural prediction and functional inference of hypothetical proteins.

The genomes of many organisms have been sequenced in the last 5 years. Typically about 30% of predicted genes from a newly sequenced genome cannot be given functional assignments using sequence comparison methods. In these situations three-dimensional structural predictions combined with a suite of computational tools can suggest possible functions for these hypothetical proteins. Suggesting functions may allow better interpretation of experimental data (e.g., microarray data and mass spectroscopy data) and help experimentalists design new experiments. In this paper, we focus on three hypothetical proteins of Shewanella oneidensis MR-1 that are potentially related to iron transport/metabolism based on microarray experiments. The threading program PROSPECT was used for protein structural predictions and functional annotation, in conjunction with literature search and other computational tools. Computational tools were used to perform transmembrane domain predictions, coiled coil predictions, signal peptide predictions, sub-cellular localization predictions, motif prediction, and operon structure evaluations. Combined computational results from all tools were used to predict roles for the hypothetical proteins. This method, which uses a suite of computational tools that are freely available to academic users, can be used to annotate hypothetical proteins in general.
Fast Proxy Re-Encryption for Publish/Subscribe Systems

We develop two IND-CPA-secure multihop unidirectional Proxy Re-Encryption (PRE) schemes by applying the Ring-LWE (RLWE) key switching approach from the homomorphic encryption literature. Unidirectional PRE is ideal for secure publish-subscribe operations where a publisher encrypts information using a public key without knowing upfront who the subscriber will be and what private key will be used for decryption. The proposed PRE schemes provide a multihop capability, meaning that when PRE-encrypted information is published onto a PRE-enabled server, the server can either delegate access to specific clients or enable other servers the right to delegate access. Our first scheme (which we call NTRU-ABD-PRE) is based on a variant of the NTRU-RLWE homomorphic encryption scheme. Our second and main PRE scheme (which we call BV-PRE) is built on top of the Brakerski-Vaikuntanathan (BV) homomorphic encryption scheme and relies solely on the RLWE assumption. We present an open-source C++ implementation of both schemes and discuss several algorithmic and software optimizations. We examine parameter selection tradeoffs in the context of security, runtime/latency, throughput, ciphertext expansion, memory usage, and multihop capabilities. Our experimental analysis demonstrates that BV-PRE outperforms NTRU-ABD-PRE in both single-hop and multihop settings. The BV-PRE scheme has a lower time and space complexity than existing IND-CPA-secure lattice-based PRE schemes and requires small concrete parameters, making the scheme computationally efficient for use on low-resource embedded systems while still providing 100 bits of security. We present practical recommendations for applying the PRE schemes to several use cases of ad hoc information sharing for publish-subscribe operations.
RADIAL BASIS FUNCTION NETWORK AIDED WIDE-BAND BEAMFORMING FOR DISPERSIVE FADING ENVIRONMENTS

A novel Radial Basis Function Network (RBFN) assisted Decision-Feedback aided Space-Time Equalizer (DF-STE) designed for receivers employing multiple antennas is introduced. The proposed receiver structure outperforms the linear Minimum Mean-Squared Error benchmarker and it is less sensitive to both error propagation and channel estimation errors.
A Pontryagin Minimum Principle-Based Adaptive Equivalent Consumption Minimum Strategy for a Plug-in Hybrid Electric Bus on a Fixed Route

When developing a real-time energy management strategy for a plug-in hybrid electric vehicle, it is still a challenge for the Equivalent Consumption Minimum Strategy to achieve near-optimal energy consumption, because the optimal equivalence factor is not readily available without the trip information. With the help of realistic speeding profiles sampled from a plug-in hybrid electric bus running on a fixed commuting line, this paper proposes a convenient and effective approach of determining the equivalence factor for an adaptive Equivalent Consumption Minimum Strategy. Firstly, with the adaptive law based on the feedback of battery SOC, the equivalence factor is described as a combination of the major component and tuning component. In particular, the major part defined as a constant is applied to the inherent consistency of regular speeding profiles, while the second part including a proportional and integral term can slightly tune the equivalence factor to satisfy the disparity of daily running cycles. Moreover, Pontryagin’s Minimum Principle is employed and solved by using the shooting method to capture the co-state dynamics, in which the Secant method is introduced to adjust the initial co-state value. And then the initial co-state value in last shooting is taken as the optimal stable constant of equivalence factor. Finally, altogether ten successive driving profiles are selected with different initial SOC levels to evaluate the proposed method, and the results demonstrate the excellent fuel economy compared with the dynamic programming and PMP method.
On the Role of Explicit Morphological Feature Representation in Syntactic Dependency Parsing for German

We investigate the question whether an explicit feature representation for morphological features is necessary when parsing German with a fully lexicalized, statistical dependency parser. We use two morphosyntactic phenomena of German to show that while lexicalization does indeed suffice to a large extent when recovering the internal structure of noun phrases, an accurate explicit representation can support the correct selection of its grammatical function.
The HBx Oncoprotein of Hepatitis B Virus Deregulates the Cell Cycle by Promoting the Intracellular Accumulation and Re-Compartmentalization of the Cellular Deubiquitinase USP37

The HBx oncoprotein of hepatitis B Virus has been accredited as one of the protagonists in driving hepatocarcinogenesis. HBx exerts its influence over the cell cycle progression by potentiating the activity of cyclin A/E-CDK2 complex, the Cyclin A partner of which is a well-known target of cellular deubiquitinase USP37. In the present study, we observed the intracellular accumulation of cyclin A and USP37 proteins under the HBx microenvironment. Flow cytometry analysis of the HBx-expressing cells showed deregulation of cell cycle apparently due to the enhanced gene expression and stabilization of USP37 protein and deubiquitination of Cyclin A by USP37. Our co-immunoprecipitation and confocal microscopic studies suggested a direct interaction between USP37 and HBx. This interaction promoted the translocation of USP37 outside the nucleus and prevented its association and ubiquitination by E3 ubiquitin ligases - APC/CDH1 and SCF/β-TrCP. Thus, HBx seems to control the cell cycle progression via the cyclin A-CDK2 complex by regulating the intracellular distribution and stability of deubiquitinase USP37.
Citation for Published Item: Use Policy Colouring of Graphs with Ramsey-type Forbidden Subgraphs

other quality control mechanisms may not be reected in this document. Changes may have been made to this work since it was submitted for publication. A denitive version was subsequently published in The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full DRO policy for further details. Abstract. A colouring of a graph G = (V, E) is a mapping c : V → {1, 2,. } such that c(u) = c(v) if uv ∈ E; if |c(V)| ≤ k then c is a k-colouring. The Colouring problem is that of testing whether a given graph has a k-colouring for some given integer k. If a graph contains no induced subgraph isomorphic to any graph in some family H, then it is called H-free. The complexity of Colouring for H-free graphs with |H| = 1 has been completely classified. When |H| = 2, the classification is still wide open, although many partial results are known. We continue this line of research and forbid induced subgraphs {H1, H2}, where we allow H1 to have a single edge and H2 to have a single non-edge. Instead of showing only polynomial-time solvability, we prove that Colouring on such graphs is fixed-parameter tractable when parame-terized by |H1| + |H2|. As a by-product, we obtain the same result both for the problem of determining a maximum independent set and for the problem of determining a maximum clique.
Optimality Zone Algorithms for Hybrid Systems Computation and Control: From Exponential to Linear Complexity

In [1], [2], [3], [4] necessary conditions were obtained for hybrid optimal control problems (HOCPs) which resulted in a general Hybrid Maximum Principle (HMP); further, in [4], [5], a class of effficient, provably convergent Hybrid Maximum Principle (HMP) algorithms were obtained based up on the HMP. In [3], [4] the notion of optimality zones (OZs) was introduced as a theoretical framework for the computation of optimal location (i.e. discrete state) sequence for HOCPs (i.e. discrete state sequences with the associated switching times and states). This paper presents the algorithm HMPZ which fully integrates the prior computation of the OZs into the HMP algorithms of [4], [5]. Adding (a) the computational investment in the construction of the OZs for a given HOCP, and (b) the complexity of (i) the computation of the optimal schedule, (ii) the optimal switching time and optimal switching state sequence, and (iii) the optimal continuous control input, yields a complexity estimate for the algorithm (HMPZ) which is linear (i.e.O(L)) in the number of switching times L; this is to be compared with the geometric (i.e. O(|Q|L)) growth of a direct combinatoric search over the set of location sequence, where Q denotes the discrete state set of the hybrid system.
High performance support for OO traversals in monet

In this paper we discuss how Monet, a novel multimodel database system, can be used to efficiently support OODB applications. We show how Monet''s offbeat view on key issues in database architecture provides both challenges and opportunities in building a high-performance ODMG-compliant programming system on top of it. In particular, we show how an OO datamodel can be mapped onto Monet''s decomposed storage scheme, and how OO queries are translated into an algebraic language. A generic model for specifying OO class-attribute traversals is presented, that permits the OODB to algebraicly optimize and parallelize their execution. The complete OO7 benchmark has been implemented to measure the success of our approach. The results show that Monet achieves minimally the performance published for the fastest OODBs on the market place today.
Distinguishing features and potential roles of the RTO.k object model

In recent years, searching for a proper extension of the basic object model to meet the needs present in hard-real-time system development environments has become a serious research issue. The first co-author and Hermann Kopetz at the Technical University of Vienna formulated an extension of the basic object model, called the RTO.k object model, as one attempt to meet such needs. In the past two years, we have been making efforts to develop practical easy-to-use tools which assist the system engineers in (1) RTO.k structured description and simulation of application environments and (2) RTO.k structured hierarchical design of control computer systems. Unique features of the RTO.k model which distinguish it from other extensions of the basic object model as well as common features are presented. The roles which the RTO.k model can play during various steps of the real-time system engineering process are then discussed.
Functional connectivity changes in adults with developmental stuttering: a preliminary study using quantitative electro-encephalography

Introduction: Stuttering is defined as speech characterized by verbal dysfluencies, but should not be seen as an isolated speech disorder, but as a generalized sensorimotor timing deficit due to impaired communication between speech related brain areas. Therefore we focused on resting state brain activity and functional connectivity. Method: We included 11 patients with developmental stuttering and 11 age matched controls. To objectify stuttering severity and the impact on quality of life (QoL), we used the Dutch validated Test for Stuttering Severity-Readers (TSS-R) and the Overall Assessment of the Speaker’s Experience of Stuttering (OASES), respectively. Furthermore, we used standardized low resolution brain electromagnetic tomography (sLORETA) analyses to look at resting state activity and functional connectivity differences and their correlations with the TSS-R and OASES. Results: No significant results could be obtained when looking at neural activity, however significant alterations in resting state functional connectivity could be demonstrated between persons who stutter (PWS) and fluently speaking controls, predominantly interhemispheric, i.e., a decreased functional connectivity for high frequency oscillations (beta and gamma) between motor speech areas (BA44 and 45) and the contralateral premotor (BA6) and motor (BA4) areas. Moreover, a positive correlation was found between functional connectivity at low frequency oscillations (theta and alpha) and stuttering severity, while a mixed increased and decreased functional connectivity at low and high frequency oscillations correlated with QoL. Discussion: PWS are characterized by decreased high frequency interhemispheric functional connectivity between motor speech, premotor and motor areas in the resting state, while higher functional connectivity in the low frequency bands indicates more severe speech disturbances, suggesting that increased interhemispheric and right sided functional connectivity is maladaptive.
Helper effects on breeder allocations to direct care

Mothers receive childcare and productive assistance from allomaternal helpers in many societies. Although much effort has been aimed toward showing helper effects on maternal reproductive success, less has been directed toward highlighting the full range of potential effects on breeder behavior. I present a model of optimal maternal care with helpers, and tests of derived hypotheses with data collected among the Karo Batak—a group of Indonesian agriculturalists.
Algebraic Factorization Applied to Geometric Problems

This paper describes an optimized method for factorizing multivariate polynomials over algebraic extension fields. The proposed method is applied to solving several selected problems in automated geometry theorem proving, decomposition and implicitization of geometric objects, and verification of geometric conditions. Some performance comparisons between this and other related methods are reported. This work demonstrates the practical value and need of algebraic factorization in geometric problem-solving.
Guidelines for estimating the real cost of an objective structured clinical examination

A major impediment to the use of the objective structured clinical examination (OSCE) is that it is a labor-intensive and costly form of assessment. The cost of an OSCE is highly dependent on the particular model used, the extent to which hidden costs are reported, and the purpose of the examination. The authors detail hypothetical costs of running a four-hour OSCE for 120 medical students at one medical school. Costs are reported for four phases of this process: development, production, administration, and post-examination reporting and analysis. Costs are reported at two ends of the spectrum: the high end, where it is assumed that little is paid for by the institution and that faculty receive honoraria for work put into the examination; and the low end, where it is assumed that the sponsoring institution defrays basic costs and that faculty do not receive honoraria for their participation. The total costs reported for a first-time examination were $104,400 and $59,460 (Canadian dollars) at the high and low ends, respectively. These translate to per-student costs of $870 and $496. The cost of running an OSCE is high. However, the OSCE is uniquely capable of assessing many fundamental clinical skills that are presently not being assessed in a rigorous way in most medical schools.
Biometrics via Oculomotor Plant Characteristics: Impact of Parameters in Oculomotor Plant Model

This article proposes and evaluates a novel biometric approach utilizing the internal, nonvisible, anatomical structure of the human eye. The proposed method estimates the anatomical properties of the human oculomotor plant from the measurable properties of human eye movements, utilizing a two-dimensional linear homeomorphic model of the oculomotor plant. The derived properties are evaluated within a biometric framework to determine their efficacy in both verification and identification scenarios. The results suggest that the physical properties derived from the oculomotor plant model are capable of achieving 20.3% equal error rate and 65.7% rank-1 identification rate on high-resolution equipment involving 32 subjects, with biometric samples taken over four recording sessions; or 22.2% equal error rate and 12.6% rank-1 identification rate on low-resolution equipment involving 172 subjects, with biometric samples taken over two recording sessions.