Miracle-dz/UniFAR-FTUs huggingface dataset:
The Processes and Mechanisms of Cardiac and Pulmonary Fibrosis

Fibrosis is the formation of fibrous connective tissue in response to injury. It is characterized by the accumulation of extracellular matrix components, particularly collagen, at the site of injury. Fibrosis is an adaptive response that is a vital component of wound healing and tissue repair. However, its continued activation is highly detrimental and a common final pathway of numerous disease states including cardiovascular and respiratory disease. Worldwide, fibrotic diseases cause over 800,000 deaths per year, accounting for ~45% of total deaths. With an aging population, the incidence of fibrotic disease and subsequently the number of fibrosis-related deaths will rise further. Although, fibrosis is a well-recognized cause of morbidity and mortality in a range of disease states, there are currently no viable therapies to reverse the effects of chronic fibrosis. Numerous predisposing factors contribute to the development of fibrosis. Biological aging in particular, interferes with repair of damaged tissue, accelerating the transition to pathological remodeling, rather than a process of resolution and regeneration. When fibrosis progresses in an uncontrolled manner, it results in the irreversible stiffening of the affected tissue, which can lead to organ malfunction and death. Further investigation into the mechanisms of fibrosis is necessary to elucidate novel, much needed, therapeutic targets. Fibrosis of the heart and lung make up a significant proportion of fibrosis-related deaths. It has long been established that the heart and lung are functionally and geographically linked when it comes to health and disease, and thus exploring the processes and mechanisms that contribute to fibrosis of each organ, the focus of this review, may help to highlight potential avenues of therapeutic investigation.
Comparison of cell lines for stable production of fucose‐negative antibodies with enhanced ADCC

Several methods have been described to enhance antibody‐dependent cellular cytotoxicity (ADCC) using different host cells that produce antibody with reduced levels of fucose on their carbohydrates. We compared the suitability of these methods for the serum‐free fed‐batch production of antibody for clinical trials and commercial uses. Recombinant anti‐human CD20 chimeric IgG1‐producing clones were established from host‐cells that have been shown to produce more than 90% fucose‐negative antibody. The cell lines were a FUT8 (α‐1,6‐fucosyltransferase) knockout Chinese hamster ovary (CHO) cell line, Ms704, and two Lens culinaris agglutinin (LCA)‐resistant cell lines, one derived from a variant CHO line, Lec13 and the other from a rat hybridoma cell line, YB2/0. The amount of fucose‐negative antibody produced by Lec13 and YB2/0 significantly decreased with the culture. The increase in fucosylation was due to remaining synthesis of GDP‐fucose via de novo pathway for the CHO line and the elevation of FUT8 expression by the YB2/0 cells. In contrast, Ms704 cells stably produced fucose‐negative antibody with a consistent carbohydrate structure until the end of the culture. The productivity of the Ms704 cells reached 1.76 g/L with a specific production rate (SPR) of 29 pg/cell/day for 17 days in serum‐free fed‐batch culture using a 1 L spinner bioreactor. Our results demonstrate that FUT8 knockout has the essential characteristics of host cells for robust manufacture of fucose‐negative therapeutic antibodies with enhanced ADCC. © 2006 Wiley Periodicals, Inc.
Single-cell-type Proteomics: Toward a Holistic Understanding of Plant Function*

Multicellular organisms such as plants contain different types of cells with specialized functions. Analyzing the protein characteristics of each type of cell will not only reveal specific cell functions, but also enhance understanding of how an organism works. Most plant proteomics studies have focused on using tissues and organs containing a mixture of different cells. Recent single-cell-type proteomics efforts on pollen grains, guard cells, mesophyll cells, root hairs, and trichomes have shown utility. We expect that high resolution proteomic analyses will reveal novel functions in single cells. This review provides an overview of recent developments in plant single-cell-type proteomics. We discuss application of the approach for understanding important cell functions, and we consider the technical challenges of extending the approach to all plant cell types. Finally, we consider the integration of single-cell-type proteomics with transcriptomics and metabolomics with the goal of providing a holistic understanding of plant function.
The Morphology of Poly(3,4-Ethylenedioxythiophene)

Poly(3,4-ethylene dioxythiophene) (PEDOT) is a chemically stable, conjugated polymer that is of considerable interest for a variety of applications including coatings for interfacing electronic biomedical devices with living tissue. Here, we describe recent work from our laboratory and elsewhere to investigate the morphology of PEDOT in the solid state. We discuss the importance of oxidative chemical and electrochemical polymerization, as well as the critical role of the counterion used during synthesis and film deposition. We have obtained information about the morphology of PEDOT from a number of different complimentary techniques including X-ray diffraction, optical microscopy, scanning electron microscopy, transmission high-resolution electron microscopy, and low-voltage electron microscopy. We also discuss results from ultraviolet-visible light spectroscopy (UV-Vis), Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS). PEDOT is a relatively rigid polymer that packs in the solid state at a characteristic face-to-face distance (010) of ∼0.34 nm, similar to graphite. These sheets of oriented PEDOT molecules are separated from one another by ∼1.4 nm laterally, with the (100) distance between layers quite sensitive to the choice of counterion used during sample preparation. The order in the films is typically modest, although this also depends on the counterion used and the method of film deposition. The films can be organized into useful structures with a variety of nanoscale dissolvable templates (including fibers, particles, and lyotropic mesophases). When PEDOT is electrochemically deposited in the presence of bromine counterions, highly ordered crystalline phases are observed. It is also possible to deposit PEDOT around living cells, both in vitro and in vivo.
QSAR Study of the Anti-Cancer Activity of 38 Compounds in Different Cancer Cell Lines Based on Gene Expression Programming

Using the GEP,the QSAR model for anti-cancer activity of 38 compounds in 5 cancer cell lines was establish. These compounds are a novel class of anticarcinogen named tricyclic 5:7:5-fused diimidazo [4, 5-d:4, 5-f ][1, diazepines. The carcinoma cell lines involved in this research are A549 lung cancer, MCF-7 breast cancer, MDA-MB-231 breast cancer, OVCAR-3 ovarian cancer and PC-3 prostate cancer. Accuracies of these models in training group and test group are over 90%, showing perfect predictive ability. This QSAR model will be great valuable in providing guidance for future designing and synthesizing of anticancer drugs.
Mixed-metal MIL-100(Sc,M) (M=Al, Cr, Fe) for Lewis acid catalysis and tandem C-C bond formation and alcohol oxidation.

The trivalent metal cations Al(3+) , Cr(3+) , and Fe(3+) were each introduced, together with Sc(3+) , into MIL-100(Sc,M) solid solutions (M=Al, Cr, Fe) by direct synthesis. The substitution has been confirmed by powder X-ray diffraction (PXRD) and solid-state NMR, UV/Vis, and X-ray absorption (XAS) spectroscopy. Mixed Sc/Fe MIL-100 samples were prepared in which part of the Fe is present as α-Fe2 O3 nanoparticles within the mesoporous cages of the MOF, as shown by XAS, TGA, and PXRD. The catalytic activity of the mixed-metal catalysts in Lewis acid catalysed Friedel-Crafts additions increases with the amount of Sc present, with the attenuating effect of the second metal decreasing in the order Al>Fe>Cr. Mixed-metal Sc,Fe materials give acceptable activity: 40 % Fe incorporation only results in a 20 % decrease in activity over the same reaction time and pure product can still be obtained and filtered off after extended reaction times. Supported α-Fe2 O3 nanoparticles were also active Lewis acid species, although less active than Sc(3+) in trimer sites. The incorporation of Fe(3+) into MIL-100(Sc) imparts activity for oxidation catalysis and tandem catalytic processes (Lewis acid+oxidation) that make use of both catalytically active framework Sc(3+) and Fe(3+) . A procedure for using these mixed-metal heterogeneous catalysts has been developed for making ketones from (hetero)aromatics and a hemiacetal.
Hepatitis B Virus e Antigen Variants

More than 300 million people worldwide are chronically infected with hepatitis B virus (HBV). Considering the very short generation time for a virus, and the high error rate associated with the reverse transcription step of HBV replication, decades of HBV infection are probably equivalent to million years of human evolution. The most important selective force during the natural course of HBV infection appears to be the immune response. The development of anti-HBe antibody in hepatitis B patients usually correlates with reduction of HBV viremia. As a consequence, escape mutants of anti-HBe are selected. The core promoter mutants express less HBe antigen (HBeAg) through transcriptional down regulation, while precore mutants express truncated products. We recently identified additional mutations that modulate HBeAg translation initiation, proteolytic cleavage, and secondary structure maintenance through a disulfide bond. The core promoter mutants have been associated with the development of fulminant hepatitis during acute infection and liver cancer during chronic infection. Consistent with their enhanced pathogenicity, core promoter mutants were found to replicate at up to 10-fold higher levels in transfected human hepatoma cells than the wild-type virus. Moreover, some core promoter mutants are impaired in virion secretion due to missense mutations in the envelope gene. These virological properties may help explain enhanced pathogenicity of core promoter mutants in vivo.
Mucosal Administration of Flagellin Protects Mice from Streptococcus pneumoniae Lung Infection

ABSTRACT Streptococcus pneumoniae is a major cause of pneumonia in infants and the elderly. Innate defenses are essential to the control of pneumococcal infections, and deficient responses can trigger disease in susceptible individuals. Here we showed that flagellin can locally activate innate immunity and thereby increase the resistance to acute pneumonia. Flagellin mucosal treatment improved S. pneumoniae clearance in the lungs and promoted increased survival of infection. In addition, lung architecture was fully restored after the treatment of infected mice, indicating that flagellin allows the reestablishment of steady-state conditions. Using a flagellin mutant that is unable to signal through Toll-like receptor 5 (TLR5), we established that TLR5 signaling is essential for protection. In the respiratory tract, flagellin induced neutrophil infiltration into airways and upregulated the expression of genes coding for interleukin 6 (IL-6), tumor necrosis factor alpha (TNF-α), CXCL1, CXCL2, and CCL20. Using depleting antibodies, we demonstrated that neutrophils are major effectors of protection. Further, we found that B- and T-cell-deficient SCID mice clear S. pneumoniae challenge to the same extent as immunocompetent animals, suggesting that these cell populations are not required for flagellin-induced protection. In conclusion, this study emphasizes that mucosal stimulation of innate immunity by a TLR not naturally engaged by S. pneumoniae can increase the potential to cure pneumococcal pneumonia.
Modeling of the reversible effect of the axial strain on the critical current of superconducting REBCO films

A modified lattice model, which combines the axial strain and misorientation of grain boundaries (GBs) in the REBCO film has been developed to model the reversible effect of the axial strain on the critical current. The calculated results is showed to be well agree with the experimental data. The model can interpret the mechanism of the reversible effect of the axial strain on the critical current. Moreover, the irreversible strain of the polycrystalline REBCO film can be theoretical determined by comparing the calculating critical current-strain curve of the model with the experimental data.
Low-Level Program Verification using Matching Logic Reachability

Matching logic reachability is an emerging verification approach which uses a language-independent proof system to prove program properties based on the operational semantics. In this paper we apply this approach in the context of a low-level real-time language with interrupts, in which each instruction takes a specified time to execute. In particular, we verify that if the interrupts are scheduled with large enough intervals, the program execution terminates yielding the correct result. Surprisingly, it turns out that matching logic reachability can handle the low-level and real-time features of the language just by using their operational semantics, and that language specific reasoning is unnecessary. 1 Matching Logic Reachability In this section we give background on matching logic reachability [6–10]. The matching logic reachability approach to program verification is to directly use the operation semantics of the target language, together with an appropriate language-independent proof system, in order to prove that a program meets its specifications. Both the operational semantics and the program specifications are given as reachability rules. No axiomatic (or Hoare), dynamic, or other auxiliary semantics of the same language is needed for verification purposes, the language-independent proof system offers all the good properties of these formalisms, including small size and compositionality of proof derivations.
Measurement and evaluating frameworks in electronic government quality management

This paper deals with the key factors that would impact upon the implementation of e-government towards achieving quality services based on measurement and evaluation systems strategies. There are different views on the concept of e-government. However, the adoption of ICT by the public sector will almost consistently affect: Public service delivery; Structure and organizational settings; Ethical, social and political systems; Social needs in the Information era, considering the term "Citizen-centered approach to governing" (e-Governance); Converting the government into a competitive entity through innovation using ICT; Reinventing relations with citizens and the private sector and Team working and collaboration towards Good Government. The paper considers how access to quality measurement and evaluation systems in the public sector can be achieved through the combination of right technology based on social, cultural values and ethical consideration. Finally, it discusses how to build a sustainable evaluation model for Electronic Government quality management.
Tree as a Pivot: Syntactic Matching Methods in Pivot Translation

Pivot translation is a useful method for translating between languages with little or no parallel data by utilizing parallel data in an intermediate language such as English. A popular approach for pivot translation used in phrase-based or tree-based translation models combines source-pivot and pivot-target translation models into a source-target model, as known as triangulation . However, this combination is based on the constituent words’ surface forms and often produces incorrect source-target phrase pairs due to semantic ambiguity in the pivot language, and interlingual differences. This degrades translation accuracy. In this paper, we propose a approach for the triangulation using syntactic subtrees in the pivot language to distinguish pivot language words by their syntactic roles to avoid incorrect phrase combinations. Experimental results on the United Nations Parallel Corpus show the proposed method gains in all tested combinations of language, up to 2.3 BLEU points. 1
Comparative Analysis of Plasmids in the Genus Listeria

Background We sequenced four plasmids of the genus Listeria, including two novel plasmids from L. monocytogenes serotype 1/2c and 7 strains as well as one from the species L. grayi. A comparative analysis in conjunction with 10 published Listeria plasmids revealed a common evolutionary background. Principal Findings All analysed plasmids share a common replicon-type related to theta-replicating plasmid pAMbeta1. Nonetheless plasmids could be broadly divided into two distinct groups based on replicon diversity and the genetic content of the respective plasmid groups. Listeria plasmids are characterized by the presence of a large number of diverse mobile genetic elements and a commonly occurring translesion DNA polymerase both of which have probably contributed to the evolution of these plasmids. We detected small non-coding RNAs on some plasmids that were homologous to those present on the chromosome of L. monocytogenes EGD-e. Multiple genes involved in heavy metal resistance (cadmium, copper, arsenite) as well as multidrug efflux (MDR, SMR, MATE) were detected on all listerial plasmids. These factors promote bacterial growth and survival in the environment and may have been acquired as a result of selective pressure due to the use of disinfectants in food processing environments. MDR efflux pumps have also recently been shown to promote transport of cyclic diadenosine monophosphate (c-di-AMP) as a secreted molecule able to trigger a cytosolic host immune response following infection. Conclusions The comparative analysis of 14 plasmids of genus Listeria implied the existence of a common ancestor. Ubiquitously-occurring MDR genes on plasmids and their role in listerial infection now deserve further attention.
Some formal considerations on the generation of hierarchically structured expressions

In this note we define a machine that generates nests. The basic relations commonly attributed to linguistic expressions in configurational syntactic models as well as the device of chains postulated in current transformational grammar to represent distance relations can be naturally derived from the assumption that the combinatorial syntactic procedure is a nesting machine. Accordingly, the core of the transformational generative syntactic theory of language can be solidly constructed on the basis of nests, in the same terms as the general theory of order, an important methodological step that provides a rigorization of Chomsky’s minimalist intuition that the simplest way to generate hierarchically organized linguistic expressions is by postulating a combinatorial operation called Merge, which can be internal or external. Importantly, there is reason to think that nests are a useful representative tool in other domains besides language where either some recursive algorithm or evolutionary process is at work, which suggests the unifying force of the mathematical abstraction this note is based on.
On the unfair channel access phenomenon in wireless LANs

This paper shows that the relative collision probability for packets in Wireless LAN 802.11 networks decreases with increasing load offered by the respective station. This denotes a clearly unfair channel access which is important to be aware of, e.g., when collision probabilities are measured and used for reactive control of contention windows. We model the unfair channel access phenomenon analytically and semi-analytically for bidirectional constant bit rate and unidirectional TCP traffic and compare the results with those from simulations.
CONSTRUCTING THE YELLOW BRICK ROAD: ROUTE BRICKS ON VIRTUAL TACTILE MAPS

Tactile maps are the standard media to convey geographical information to blind people. An approach for an interactive substitute for tactile maps is presented, called virtual tactile maps. It is based on an image processing system tracking fingers and game piece-like objects. Output is done through speech and sound. Users learn routes by constructing them with route bricks.
Optimisation of suction pressure for iron ore sintering by genetic algorithm

Abstract Iron ore sintering is a complex thermochemical process for bulk production of blast furnace raw material. The quality of sinter is very important for smooth operation and high productivity of the blast furnace since it improves the permeability and reducibility of the burden material. A detailed mathematical model for the process, considering all the important phenomena such as gas–solid reaction, melting and solidification, flow through the porous bed, heat and mass transfer, etc., has been used for process simulation and analysis. Optimisation using a genetic algorithm has then been applied to evaluate the operating condition of suction pressure at different bed positions for optimum quality, productivity and thermal efficiency of the process. The genetic algorithm has several advantages over traditional optimisation techniques, since it can identify global optima under multimodal conditions, and do away with the need for gradient evaluation.
A Level-SetApproachto 3D ReconstructionFromRangeData

This paperpresentsa methodthat usesthe level setsof volumesto reconstructthe shapesof 3D objectsfrom rangedata.Thestrategy is to formulate3D reconstructionasa statisticalproblem:find thatsurfacewhich is mostly likely, giventhedataandsomeprior knowledgeabouttheapplicationdomain.Theresultingoptimizationproblemis solved by an incrementalprocessof deformation.We representa deformablesurfaceasthe level setof a discretely sampledscalarfunctionof 3 dimensions,i.e. avolume.Suchlevel-setmodelshavebeenshown to mimic conventional deformablesurfacemodelsby encodingsurfacemovementsaschangesin the greyscalevaluesof the volume. The result is a voxel-basedmodeling technology that offers several advantagesover conventional parametricmodels, includingflexible topology, noneedfor reparameterization, concisedescriptionsof differentialstructure,andanatural scalespacefor hierarchicalrepresentations. This paper builds on previouswork in both3D reconstructionandlevelsetmodeling. It presentsa fundamental result in surfaceestimationfrom rangedata: an analyticalcharacterization of the surfacethat maximizesthe posteriorprobability. It alsopresentsa novel computationaltechnique for levelset modeling, called the sparse-fieldalgorithm, which combines the advantagesof a level-setapproach with the computationalefficiency andaccuracy of a parametricrepresentation. The sparse-fieldalgorithmis moreefficient thanotherapproaches,andbecauseit assignsthe level setto a specificsetof grid points, it positionsthe level-set model more accuratelythan the grid itself. Theseproperties,computational efficiency and sub-cellaccuracy, are essential whentrying to reconstructheshapesof 3D objects.Resultsareshown for thereconstructionobjectsfrom setsof noisyandoverlapping rangemaps. Appears in: TheInternationalJournal of Computer Vision , 29(3), October, 1998, pp. 203–231. i