Miracle-dz/UniFAR-FTUs huggingface dataset:
Study on Replication of Micro Channel Structures onto Polytetrafluoroethylene (PTFE) Substrate Employing Two-Stage Hot Embossing

Replication of micro structures on a polymer substrate employing two-stage hot embossing is described in this paper. Linear channels with rectangular cross section were fabricated on a master mold of a brass plate by means of a computer numerical control (CNC) machining center using a micro end mill. In the first embossing process, the master mold with concavity features was embossed on a polycarbonate (PC) plate in order to make a “polymer replication mold”. Polytetrafluoroethylene (PTFE) was chosen as a material of polymer substrate used in the second embossing process. The replicated structure on PTFE substrate was observed and each dimension of its cross-sectional shape was also measured in order to assess the replication accuracy. According to the results, it was found that the depth of a replicated channel was near 90 % of that on the master mold. But roundness at each corner could be also found due to the insufficiency of plastic flow. Furthermore the deformation of the structures on a replication mold of PC before and after 2nd hot embossing process was also examined. As a result, it was found that the deformation ratio at temperatures below 145 oC was roughly smaller than 10 %.
Modeling and Simulation of Plug-In Hybrid Electric Powertrain System for Different Vehicular Application

Plug-in hybrid electric vehicle (PHEV) presents the new trend of clean energy vehicle development due to their advantage of all electric driving, allowable external charging, lower emissions, and lower petroleum fuel consumption, comparing to the maturing HEV. Applications of advanced plug-in hybrid powertrain system technology to different type of vehicles lead to the need to identify the key characteristics of these different vehicular applications, and to develop more systematic and effective powertrain design methods. In this work two different types of PHEV powertrain architecture were investigated: a) pre-trans series-parallel multiregime plug-in hybrid electric commercial vehicle (SPMRPHEV), and b) post-trans parallel plug-in hybrid electric formula racing car. Model-based design (MBD) methods were used for powertrain system modelling of the two PHEV applications. With the powertrain system models developed using MATLAB Simulink and dSPACE Automotive Simulation Models (ASM), the powertrain configurations, control strategies and key features were investigated. The simulation results on standard driving cycles for each model using different rule-based control strategies were compared. The differences and key features of two types of vehicle in design and calibration were presented and analyzed.
Distinct Roles for N-Ethylmaleimide-sensitive Fusion Protein (NSF) Suggested by the Identification of a Second Drosophila NSF Homolog (*)

The N-ethylmaleimide-sensitive fusion protein (NSF) is a cytoplasmic protein implicated in the fusion of intracellular transport vesicles with their target membranes. NSF is thought to function in the fusion of essentially all types of vesicles, including endoplasmic reticulum, Golgi, and endocytic vesicles, as well as secretory vesicles undergoing regulated fusion (for review see Rothman, J. E.(1994) Nature 372, 55-63). However, little [Medline] experimental evidence exists to address the possibility that organisms might have multiple NSF proteins serving distinct functions in the same or different cells. We previously cloned a neurally expressed Drosophila homolog, dNSF-1 (Ordway, R. W., Pallanck, L., and Ganetzky, B.(1994) Proc. Natl. Acad. Sci. U. S. A. 91, 5715-5719), and have subsequently identified mutations in this gene that confer an apparent failure of synaptic transmission at elevated temperature (Pallanck, L., Ordway, R. W., and Ganetzky, B.(1995) Nature, 376, 25; Siddiqi, O. , and Benzer, S. (1976) Proc. Natl. Acad. Sci. U. S. A. 73, 3253-3257). Here we report that 1) Drosophila contains a second NSF homolog, termed dNSF-2, that exhibits 84% amino acid identity to dNSF-1, 2) dNSF-1 and dNSF-2 display overlapping but different temporal expression, and 3) multiple transcripts are derived from the dNSF-2 gene. These findings raise the possibility that different NSF gene products serve distinct or overlapping functions within the organism.
Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach

Systematic identification of binding partners for modular domains such as Src homology 2 (SH2) is important for understanding the biological function of the corresponding SH2 proteins. We have developed a worldwide web-accessible computer program dubbed SMALI for scoring matrix-assisted ligand identification for SH2 domains and other signaling modules. The current version of SMALI harbors 76 unique scoring matrices for SH2 domains derived from screening oriented peptide array libraries. These scoring matrices are used to search a protein database for short peptides preferred by an SH2 domain. An experimentally determined cut-off value is used to normalize an SMALI score, therefore allowing for direct comparison in peptide-binding potential for different SH2 domains. SMALI employs distinct scoring matrices from Scansite, a popular motif-scanning program. Moreover, SMALI contains built-in filters for phosphoproteins, Gene Ontology (GO) correlation and colocalization of subject and query proteins. Compared to Scansite, SMALI exhibited improved accuracy in identifying binding peptides for SH2 domains. Applying SMALI to a group of SH2 domains identified hundreds of interactions that overlap significantly with known networks mediated by the corresponding SH2 proteins, suggesting SMALI is a useful tool for facile identification of signaling networks mediated by modular domains that recognize short linear peptide motifs.
Path integral control and bounded rationality

Path integral methods [1], [2],[3] have recently been shown to be applicable to a very general class of optimal control problems. Here we examine the path integral formalism from a decision-theoretic point of view, since an optimal controller can always be regarded as an instance of a perfectly rational decision-maker that chooses its actions so as to maximize its expected utility [4]. The problem with perfect rationality is, however, that finding optimal actions is often very difficult due to prohibitive computational resource costs that are not taken into account. In contrast, a bounded rational decision-maker has only limited resources and therefore needs to strike some compromise between the desired utility and the required resource costs [5]. In particular, we suggest an information-theoretic measure of resource costs that can be derived axiomatically [6]. As a consequence we obtain a variational principle for choice probabilities that trades off maximizing a given utility criterion and avoiding resource costs that arise due to deviating from initially given default choice probabilities. The resulting bounded rational policies are in general probabilistic. We show that the solutions found by the path integral formalism are such bounded rational policies. Furthermore, we show that the same formalism generalizes to discrete control problems, leading to linearly solvable bounded rational control policies in the case of Markov systems. Importantly, Bellman's optimality principle is not presupposed by this variational principle, but it can be derived as a limit case. This suggests that the information-theoretic formalization of bounded rationality might serve as a general principle in control design that unifies a number of recently reported approximate optimal control methods both in the continuous and discrete domain.
A variational framework for joint segmentation and registration

Traditionally, segmentation and registration have been solved as two independent problems, even though it is often the case that the solution to one impacts the solution to the other. In this paper, we introduce a geometric, variational framework that uses active contours to simultaneously segment and register features from multiple images. The key observation is that multiple images may be segmented by evolving a single contour as well as the mappings of that contour into each image. To the best of our knowledge, this is the first attempt at interleaving segmentation and registration in such a framework.
RELATIVE CONTRIBUTIONS OF THE FIVE MAJOR HUMAN CYTOCHROMES P450, 1A2, 2C9, 2C19, 2D6, AND 3A4, TO THE HEPATIC METABOLISM OF THE PROTEASOME INHIBITOR BORTEZOMIB

VELCADE (bortezomib, PS-341), reversibly inhibits the 20S proteasome and exhibits cytotoxic and antitumor activities. Pretreatment of cancer cells with bortezomib increases the chemosensitivity of these cells, suggesting that bortezomib may be used in combination chemotherapy. The relative contributions of the five major human cytochromes P450 (P450s), 1A2, 2C9, 2C19, 2D6, and 3A4 (the focus of the present study), to the metabolism of bortezomib are an important aspect of potential drug interactions. Relative activity factor (RAF), chemical inhibition, and immunoinhibition using monoclonal antibodies were three approaches employed to determine the relative contributions of the major human P450s to the net hepatic metabolism of bortezomib. RAFs for the P450 isoform-selective substrates were determined; the ratio of the rate of metabolism of bortezomib with cDNA-expressed P450s versus rate of metabolism with human liver microsomes was normalized with respect to the RAF for each P450 isoform to determine the percentage contributions of the P450s to the net hepatic metabolism of bortezomib. CYP3A4 followed by CYP2C19 were determined to be the major contributors to the metabolism of bortezomib. Chemical inhibition and immunoinhibition confirmed that CYP3A4 and CYP2C19 were the major P450s responsible for the hepatic metabolism of bortezomib. The studies were conducted with 2 μM bortezomib, and the disappearance of bortezomib, rather than appearance of a specific metabolite, was quantified to determine the contributions of the P450s to the overall hepatic metabolism of bortezomib in humans.
Evolution of Retinoid and Steroid Signaling: Vertebrate Diversification from an Amphioxus Perspective

Although the physiological relevance of retinoids and steroids in vertebrates is very well established, the origin and evolution of the genetic machineries implicated in their metabolic pathways is still very poorly understood. We investigated the evolution of these genetic networks by conducting an exhaustive survey of components of the retinoid and steroid pathways in the genome of the invertebrate chordate amphioxus (Branchiostoma floridae). Due to its phylogenetic position at the base of chordates, amphioxus is a very useful model to identify and study chordate versus vertebrate innovations, both on a morphological and a genomic level. We have characterized more than 220 amphioxus genes evolutionarily related to vertebrate components of the retinoid and steroid pathways and found that, globally, amphioxus has orthologs of most of the vertebrate components of these two pathways, with some very important exceptions. For example, we failed to identify a vertebrate-like machinery for retinoid storage, transport, and delivery in amphioxus and were also unable to characterize components of the adrenal steroid pathway in this invertebrate chordate. The absence of these genes from the amphioxus genome suggests that both an elaboration and a refinement of the retinoid and steroid pathways took place at the base of the vertebrate lineage. In stark contrast, we also identified massive amplifications in some amphioxus gene families, most extensively in the short-chain dehydrogenase/reductase superfamily, which, based on phylogenetic and genomic linkage analyses, were likely the result of duplications specific to the amphioxus lineage. In sum, this detailed characterization of genes implicated in retinoid and steroid signaling in amphioxus allows us not only to reconstruct an outline of these pathways in the ancestral chordate but also to discuss functional innovations in retinoid homeostasis and steroid-dependent regulation in both cephalochordate and vertebrate evolution.
Tropical Medicine and Hygiene

IT has long been recognized that a number of diseases are peculiar to, if not confined to, warm climates. Many hypotheses in explanation of this circumstance have been advaiced, but it is only of late years-only since we have been able to recognize the germ causes of many of tllese diseases, or the media by or in which they are conveyedthat it has become possible to arrive at the true explanation. Almost without exception, tropical diseasesthat is to say, those diseases whiclh require for their successful propagation a warm climate-are caused' either by a protozoal organism or by a helminth, whichl, in their turn, in order to pass from one vertebrate host to another, demand either an animal vector peculiar to warm climates, or require a warm medium in wwhich to qualify for such passage. Hence, althouglh tropical disease once acquired can run its usual course even if the person remove to a cold or even frigid climate, that person cannot spread the disease there, nor, under natural conditions, can the disease be acquired tlhere. On the other lhand, bacterial diseases naIy be acquired and spread in any climate, as the germs in their passage from one human host to anothei do not necessarily demand any special animal intermediary, nor are they destroyed in their passage by ordinary temperatures. In the following summary relating to British contributions to tropical medicine bacterial diseases are therefore not considered. It is true
Automatic Hilghter of Lengthy Legal Documents

Legal documents are known for being lengthy. To our knowledge, some categories of legal documents contain duplicated information that do not require our attention. However, manually extracting non-duplicate information from documents requires considerable amount of effort. Thus, we want to use machine learning algorithms to pick up unordinary sentences for us. In this paper, we propose a set of algorithms that filters out duplicate information and returns useful information to the user. We are able to train a learner that can mark unordinary parts of a legal document for manual scrutinization. Our learning process contains two phases. At the first phase, we pick some legal documents that contain common patterns, e.g. software user agreements, to form a knowledge base for the trainer. We then run LDA [1] model on these documents. The LDA model will return us with a set of common topics across the knowledge base. At the second phase, we take a new piece of legal document as the test sample. We first remove common topic words from the test document to increase differences between sentences. We then use Word2Vec [2], [3] to convert sentences into vectors. After generating the feature space, we run Agglomerative Clustering and Local Outlier Factor(LOF) [4] algorithms on the feature vectors to detect special sentences in the given document. Last, we use PCA and t-SNE to visualize our result.
The trajectory of gait speed preceding mild cognitive impairment.

OBJECTIVES To compare the trajectory of motor decline, as measured by gait speed and finger-tapping speed, between elderly people who developed mild cognitive impairment (MCI) and those who remained cognitively intact. We also sought to determine the approximate time at which the decline in motor function accelerated in persons who developed MCI. DESIGN Longitudinal cohort study. PARTICIPANTS Participants were 204 healthy seniors (57.8% women) from the Oregon Brain Aging Study evaluated for up to 20 years using annual neurologic, neuropsychological, and motor examinations. MAIN OUTCOME MEASURES The pattern of motor decline with aging was compared using a mixed-effects model with an interaction term for age and a clinical diagnosis of MCI. The time before diagnosis of MCI, when the change in gait or finger-tapping speed accelerates, was assessed using a mixed-effects model with a change point for men and women, separately and combined, who developed MCI. RESULTS The rates of change, with aging, in gait speed (P < .001) and finger-tapping speed in the dominant hand (P = .003) and nondominant hand (P < .001) were significantly different between participants who developed MCI (converters) and those who did not (nonconverters). Using a change point analysis for MCI converters, the decrease in gait speed accelerated by 0.023 m/s/y (P < .001), occurring 12.1 years before the onset of MCI. An acceleration in gait speed decline occurred earlier in men than women. For tapping speed, the change point occurred after the onset of MCI for both dominant and nondominant hands when men and women were combined. CONCLUSIONS Motor decline as indexed by gait speed accelerates up to 12 years before MCI. Longitudinal changes in motor function may be useful in the early detection of dementia during preclinical stages, when the utility of disease-modifying therapies would be greatest.
EFFICIENT MULTICAST ROUTING PROTOCOL FOR MANETS

Mobile ad hoc networks (MANETs) have several prominent features because of which MANETs are visualized to support advanced applications. Multicast routing reduces the communication costs of applications. Several multicast routing protocols have been proposed for MANET. While previous MANET multicast protocols focused on the reductions of control overhead, the multicast protocol investigated in this research attempts to reduce the amount of bandwidth used by the network both in terms of control overhead and data rebroadcasts by. Unlike previously proposed MANET multicast algorithms, this new protocol will focus on reducing the amount of unnecessary data rebroadcast by considering QOS constraints like bandwidth, power and end to end delay considering though the creation of a more efficient multicast tree.
In-situ assessment of the stress-dependent stiffness of unbound aggregate bases: application in inverted base pavements

Unbound aggregate bases are the primary structural components in many flexible pavements. The response of the unbound aggregate base is critical to the overall performance of the pavement, particularly in inverted base pavements given the proximity of the base to the traffic loads. The behaviour of granular materials such as unbound aggregate bases is inherently nonlinear and anisotropic. An experimental methodology is developed to assess the in-situ stress-dependent small-strain stiffness of unbound aggregate bases under controlled load using wave propagation techniques. CODA wave analysis is used to detect small changes in travel time. The methodology is applied in two distinct case histories of inverted base pavements. Results show that field-compacted granular bases exhibit higher stiffness, lower stress sensitivity and more pronounced anisotropy than laboratory-compacted specimens. The discrepancy in stiffness observed among the two field case histories is primarily attributed to traffic preconditioning sustained by the older pavement. Additional results show that the effect of suction on the stiffness of coarse-grained granular bases is insignificant.
Preparation of multifunctional upconversion nanoconstruct for in vitro and in vivo imaging and photodynamic therapy induced by near-infrared light

Upconversion nanoparticles (UCNPs) have attracted much attention as novel contrast agents for low-background biomedical imaging and potential photosensitizer carriers for photodynamic therapy (PDT) in deep tissues. In this work, firstly we synthesized NaYF4:Yb3+,Tm3+@NaYF4:Yb3+,Er3+ core-shell structured UCNPs with multiple emission peaks (e.g. 480, 539, 654 and 800 nm) by a seeded growth approach. By coating folate-modified amphiphilic chitosan (FASOC) on UCNPs, the as-prepared UCNPs were favorably endowed with good water solubility and the enhanced tumor-selectivity to cancer cells that overexpressed folate receptor. Then, water-insoluble photosensitizer zinc(II) phthalocyanine (ZnPc) was loaded into the FASOC-UCNPs via hydrophobic interactions for potential near-infrared light induced photodynamic therapy (PDT). Our results indicate that the multifunctional FASOC-UCNP-ZnPc nanoconstruct has efficient NIR-to-NIR upconversion luminescence and PDT abilities, which could be potentially employed as a theranostic platform for cancer treatment.
Scaling Semantic Graph Databases in Size and Performance

GEMS is a full software system that implements a large-scale, semantic graph database on commodity clusters. Its framework comprises a SPARQL-to-C++ compiler, a library of distributed data structures, and a custom multithreaded runtime library. The authors evaluated their software stack on the Berlin SPARQL benchmark with datasets of up to 10 billion graph edges, demonstrating scaling in dataset size and performance as they added cluster nodes.
Synthesising verified access control systems through model checking

We present a framework for evaluating and generating access control policies. The framework contains a modelling formalism called RW, which is supported by a model checking tool. RW is designed for modelling access control policies, and verifying their properties. The RW language is very expressive, allowing us to model complex access conditions which can depend on data values, other permissions, and agent roles. A property expresses the capability of a coalition of agents to achieve a goal, which may include reading and overwriting certain information. Given a model built based on a policy and a property, the model-checking algorithm decides whether the goal defined by the property is achievable by the coalition within the permissions the policy provides. In the case that the goal is achievable, the algorithm outputs strategies which may be used by the coalition to achieve the goal. The unachievability of legitimate goals may suggest that the policy does not provide the users enough permissions to carry out their actions. The achievability of malicious goals may reveal certain security holes in the policy. When malicious goals are achievable, the resulting strategies help to provide clues on amending the policy. The tool implements the algorithm and thus performs the RW model-checking. It can also convert a policy written in the RW language into a policy file in XACML. An access control system can then be built on the converted policy file.
Defining the autism minimum candidate gene region on chromosome 7

Previous genetic and cytogenetic studies provide evidence that points to one or more autism susceptibility genes residing on chromosome 7q (AUTS1, 115–149 cM on the Marshfield map). However, further localization using linkage analysis has proven difficult. To overcome this problem, we examined the Collaborative Linkage Study of Autism (CLSA) data‐set to identify only the families potentially linked to chromosome 7. Out of 94, 47 families were identified and 17 markers were used to generate chromosomal haplotypes. We performed recombination breakpoint analysis to determine if any portion of the chromosome was predominately shared across families. The most commonly shared region spanned a 6 cM interval between D7S501 and D7S2847. Additional markers at 1 cM intervals within this region were genotyped and association and recombination breakpoint analysis was again performed. Although no significant allelic association was found, the recombination breakpoint data points to a shared region between D7S496–D7S2418 (120–123 cM) encompassing about 4.5 Mb of genomic DNA containing over 50 genes. © 2003 Wiley‐Liss, Inc.