Miracle-dz/UniFAR-FTUs huggingface dataset:
The Inherent Complexity of Agglomeration: Essays on the self-organization of urban economies

This doctoral thesis combines complexity science and economic geography in order to explore bottom-up, self-organizing principles within urban economies, in particular in relation to the flow of information and knowledge between people. The thesis consists of a kappa that covers the general theoretical framework and four papers. The papers cover urban scaling and intra-urban scaling analysis, local interactions and informational spillovers , collective information processing, productivity benefits related to city size, diversity and specialization externalities, social capital and urban interactions.
Blocking of Bacterial Biofilm Formation by a Fish Protein Coating

ABSTRACT Bacterial biofilm formation on inert surfaces is a significant health and economic problem in a wide range of environmental, industrial, and medical areas. Bacterial adhesion is generally a prerequisite for this colonization process and, thus, represents an attractive target for the development of biofilm-preventive measures. We have previously found that the preconditioning of several different inert materials with an aqueous fish muscle extract, composed primarily of fish muscle α-tropomyosin, significantly discourages bacterial attachment and adhesion to these surfaces. Here, this proteinaceous coating is characterized with regards to its biofilm-reducing properties by using a range of urinary tract infectious isolates with various pathogenic and adhesive properties. The antiadhesive coating significantly reduced or delayed biofilm formation by all these isolates under every condition examined. The biofilm-reducing activity did, however, vary depending on the substratum physicochemical characteristics and the environmental conditions studied. These data illustrate the importance of protein conditioning layers with respect to bacterial biofilm formation and suggest that antiadhesive proteins may offer an attractive measure for reducing or delaying biofilm-associated infections.
Symptom reports in severe chronic insomnia.

STUDY OBJECTIVES To describe patterns and severities of the daytime and nighttime symptoms of chronic insomnia patients. DESIGN Exploratory chart review from clinicians' evaluation summaries, a self-report screening instrument, the Pittsburgh Sleep Quality Index, the Beck Depression Inventory, the Epworth Sleepiness Scale, and the Hopkins Symptom Checklist-90 (HSCL90). SETTING A regional sleep disorders referral clinic. PATIENTS OR PARTICIPANTS 94 patients with chronic insomnia (DSM-IV code 307.42), classified into the subgroups "Primary Insomnia," "Depression-Related," "Anxiety-Related," and "Other". INTERVENTIONS N/A. MEASUREMENTS AND RESULTS Frequent symptoms occurred not only in nocturnal domains (e.g., sleep disturbances, environmental sensitivity), but also in daytime domains (e.g., cognitive difficulties, sleepiness). Compared to primary insomnia patients, those with depression-related insomnia endorsed more severe symptoms. All subgroups endorsed a generally similar symptom profile when single symptoms were considered in isolation. When considered conjointly, severe symptoms typical of depression and generalized social alienation had a high negative predictive value for primary insomnia. The number of severe symptoms on the HSCL90 was related to fewer sleep hours in the nonprimary insomnia subgroup but not in the primary insomnia subgroup. CONCLUSIONS Patients with chronic insomnia report significant daytime as well as nighttime symptoms. Depression-related and primary insomnias were separable only by some highly characteristic symptoms of depression. Diagnostic subgroups of insomnia patients may vary in how their overall distress relates to diminished self-reported sleep. Nighttime and daytime symptoms need to be assessed together when measuring insomnia severity.
An examination of user behaviour during web information tasks

The goal of this work is to gain a greater understanding of user behaviour during web information tasks in order to better support users on the Web. We have completed a field study examining information seeking behaviour on the Web and propose two further studies: an exploration of monitoring behaviour on the Web through semi-structured interviews and the development and validation of recommendations for the design of future web browser tools.
Monitoring the status of iBeacons with crowd sensing

Since Apple introduced the iBeacons in Worldwide Developers Conference (WWDC) 2013, the iBeacon has been rapidly accepted and generalized in the market. For the deployed iBeacons, it is necessary to monitor their status. In this paper, we design a crowd sensing based monitoring framework which combines the moving and static schemas of participants to monitor the real status of iBeacons. In such a system, the inaccuracy and conflict of the collected signal information, commonly caused by the error rate of participants or the differences of sensing context, have received more and more attention. Estimating the real status of iBeacons according to the uploaded signal information becomes a big challenge for our monitoring system. Towards this end, we propose a context-aware estimation approach in this paper. We first model the effects of sensing context, and then propose an iterative method to infer the error rate of participants and estimate the real status of iBeacons with high precision. Our method is tested via extensive simulations, and verified by our monitoring system which has been applied in the teaching building. The results demonstrate that the proposed estimation approach outperforms recent popular three-estimates algorithm and OtO EM algorithm. At last, we develop the review mechanism, which ensures the efficiency of our monitoring system.
Cytotoxic effects of antibodies to proteinase 3 (C‐ANCA) on human endothelial cells

Autoantibodies directed against cytoplasmic antigens of neutrophils (ANCA), especially those with specificity for proteinase 3 (PR‐3) and myeloperoxidase, are valuable markers for differential diagnosis and monitoring of disease activity in Wegener's granulomatosis (WG) and other vasculitides. Till now, several concepts concerning a direct role of antibodies against PR‐3 in the pathogenesis of WG have been discussed. Recently we were able to show that these antibodies recognize PR‐3 translocated into the membrane of human endothelial cells. The aim of this study was to investigate putative cytotoxic effects of antibodies to PR‐3 on human endothelial cells. Antibodies were obtained by affinity purification of sera from patients with active WG, Purified antibodies to Ro (SS‐A), La (SS‐B) and RNP served as controls. Purified antibodies to PR‐3 displayed a lytic activity against endothelial cells treated with tumour necrosis factor‐alpha (TNF‐α:) with the help of cytokine‐primed neutrophils as measured in a Cr‐release assay. About 100% specific cytotoxicity occurred after 4 h and was independent of complement, Cytotoxic effects were inhibited by coincubation with unprimed ncutrophils or preincubation of PR‐3 antibodies with purified antigen. Antibodies to Ro (SS‐A), La (SS‐B) or RNP had no cytotoxic effect. In summary, PR‐3 antibody‐induced cytotoxicity required (i) expression of PR‐3 on the surface of TNF‐α‐treated endothelial cells: and (ii) co‐cultivation of cytokine‐primed neutrophils. This is to the best of our knowledge the first report on direct cytotoxic effects of PR‐3 antibodies on vascular endothelium. Our data give a hint at a PR‐3 antibody‐mediated mechanism of endothelial injury via antibody‐dependent cellular cytotoxicity in WG and other ANCA‐related vasculitides.
The effect of anabolic implants on intramuscular lipid deposition in finished beef cattle.

Two experiments were conducted to determine the effects of anabolic implants on performance, changes in ultrasound measurements, carcass quality, cellularity of i.m. and s.c. adipose depots, and mRNA expression of acetyl CoA carboxylase (ACC), stearoyl CoA desaturase (SCD), and lipoprotein lipase (LPL) in i.m. adipose tissue of finished beef cattle. Angus heifers (experiment 1: n = 10; 411 kg of BW) and steers (experiment 2: n = 18; 279 kg of BW) were randomly allotted as control (C) or implanted with Synovex-Plus (SP) at d 0 and midway through the finishing period. The cattle were fed a high-concentrate diet and were weighed at approximately 28-d intervals. Heifers and steers were finished for 108 and 133 d, respectively. At slaughter, a section of the LM (sixth to ninth rib) was removed, and i.m. adipose tissue was dissected for mRNA analysis. Subcutaneous and i.m. adipose tissues also were collected for determination of cellularity. At 48 h postmortem, carcass data were collected, and a steak (12th rib) was removed for analysis of lipid and fatty acid composition. Body weight did not differ (P > 0.10) between treatments until after reimplanting of the heifers (d 55) or steers (d 73). Average daily gain was 36 and 16% faster (P < or = 0.01) for implanted heifers and steers, respectively, compared with their control counterparts. Implanting resulted in larger (P < or = 0.10) HCW and LM area for heifers and steers. However, implanting did not affect (P > 0.10) dressing percent, fat thickness, percentage of KPH, yield grade, or marbling score. Intramuscular lipid content and concentrations of major fatty acids did not differ (P > 0.10) between treatments. Percentage of SC adipocytes was greater at larger diameters ( > 150 microm), whereas the majority of i.m. adipocytes were at small to middle diameters (50 to 150 microm). The number of i.m. adipocytes per gram of tissue was greater (P < 0.05) for SP than C and also were greater (P < 0.05) than the number of s.c. adipocytes in SP heifers. In experiment 2, adipocytes per gram of tissue tended to be greater (P = 0.07) for SP than C and were greater (P < 0.01) for i.m. than s.c. In experiment 1, average cell diameter and volume did not differ (P > 0.10) between treatments and tissues, but in experiment 2 both cellularity traits were greater (P < 0.01) for s.c. than for i.m. Implanting did not alter mRNA expression of ACC, SCD, or LPL in i.m. adipose tissue. This study shows that anabolic implants do not appear to have direct effects on i.m. lipid deposition.
SHY1, the Yeast Homolog of the MammalianSURF-1 Gene, Encodes a Mitochondrial Protein Required for Respiration*

C173 and W125 are pet mutants ofSaccharomyces cerevisiae, partially deficient in cytochrome oxidase but with elevated concentrations of cytochrome c. Assays of electron transport chain enzymes indicate that the mutations exert different effects on the terminal respiratory pathway, including an inefficient transfer of electrons between thebc 1 and the cytochrome oxidase complexes. A cloned gene capable of restoring respiration in C173/U1 and W125 is identical to reading frame YGR112w of yeast chromosome VII (GenBankZ72897). The encoded protein is homologous to the product of the mammalian SURF-1 gene. In view of the homology, the yeast gene has been designated SHY1 (SurfHomolog of Yeast). An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane. Deletion of part ofSHY1 produces a phenotype similar to that of G91 mutants. Disruption of SHY1 at a BamHI site, located approximately 2/3 of the way into the gene, has no obvious phenotypic consequence. This evidence, together with the ability of a carboxyl-terminal coding sequence starting from the BamHI site to complement a shy1 mutant, suggests that the Shy1p contains two domains that can be separately expressed to form a functional protein.
Clonal derivatives of the RD-114 cell line differ in their antiviral and gene-inducing responses to interferons

The human rhabdomyosarcoma cell line RD-114 is partially responsive to interferons (IFNs). In these cells, alpha interferon (IFN-alpha) or gamma interferon (IFN-gamma) inhibits the replication of some viruses but not of others. Similarly, some of the IFN-inducible mRNAs are induced poorly, whereas others are induced well. Here we report the isolation of clonal derivatives of this line which display different spectra of responses to IFNs. Among the eight extensively characterized clonal lines, one, C10, did not respond to IFN-alpha or IFN-gamma at all. Retrovirus production by each of the seven other lines was inhibited by both IFN-alpha and IFN-gamma. Replication of vesicular stomatitis virus was inhibited strongly by IFN-alpha in clone B1 but not in others, whereas it was not appreciably affected by IFN-gamma in any clone. Replication of encephalomyocarditis virus was inhibited strongly by IFN-gamma in clones A1, A2, A3, B3, and B8 and by IFN-alpha in clone A2. Neither IFN inhibited the multiplication of these clones greatly, although their doubling times were slightly increased. Five mRNAs were induced by IFNs to varying degrees in the seven clones. mRNA 2A was most strongly induced by IFN-gamma in clone A3. mRNA 1-8 was strongly induced by IFN-alpha in clone A1 and by either IFN in clones A2 and A3. The highest concentrations of 2',5'-oligoadenylate synthetase mRNA, mRNA 561, and mRNA 6-16 were in IFN-alpha-treated clones A1 and A2. These results demonstrated the existence of clonal heterogeneity in IFN responses in a cell line and strengthened the view that IFN treatment of cells generates multiple signals leading to a variety of IFN-induced phenotypes.
The ventral portion of the anterior pretectal nucleus controls descending mechanisms that initiate neuropathic pain in rats

Stimulating the dorsal anterior pretectal nucleus (dAPtN) in rats is more effective than stimulating the ventral APtN (vAPtN) at reducing tail‐flick latency, whereas stimulation of the vAPtN is more effective at reducing postoperative pain behaviour. This study examines whether a cell lesion caused by injecting N‐methyl‐D‐aspartate into the dAPtN or vAPtN changes the withdrawal threshold of a rat hind paw during different phases of the tactile hypersensitivity induced by a chronic constriction injury (CCI) of the contralateral sciatic nerve. The number of Fos immunoreactive cells in the APtN was also evaluated. The rats whose vAPtN was lesioned 2 days before CCI had more intense tactile hypersensitivity 2 days after CCI than that of the control group, but the groups were not different 7 days after the CCI. The rats whose vAPtN was lesioned 5 days after CCI had withdrawal thresholds that did not differ significantly 7 days after the CCI. The tactile hypersensitivity of the rats whose dAPtN was lesioned 2 days before or 5 days after CCI was not different from that of the control on the second and seventh days after the CCI. The number of Fos immunoreactive cells in the vAPtN and dAPtN increased 2 days after CCI, but did not differ from that in the control 7 days after CCI. We conclude that vAPtN and dAPtN cells are activated by nerve injury; the vAPtN exerts inhibitory control of the initial phase of neuropathic pain whereas the dAPtN does not appear to exert an inhibitory effect in neuropathic processing.
Charging Current Compensation for Distance Protection

One difficulty of the application of line protections to long transmission lines is the influence of the large capacitance of the line. When a fault occurs on a long line, relatively large magnitude harmonic components of current and voltage are superimposed on the fundamental frequency component due to the large capacitance of the line. This harmonic component can cause oscillation of the distance measurement. It is difficult to remove the harmonic component completely because the order of the harmonic component varies with several conditions. Our research has shown that the degree of oscillation can be reduced significantly by compensating for the charging current in the impedance calculation. This proposed charging current compensation (CCC) method provides an excellent result under all conditions. In this paper, the calculation method of CCC is introduced and good performance of CCC for the application to long overhead lines and to the long cable line is proven based on Alternative Transient Program simulations.
Longitudinal and transversal propagation of excitation along the tubular system of rat fast‐twitch muscle fibres studied by high speed confocal microscopy

Non‐technical summary Contraction of the vertebrate skeletal muscle is dependent on the excitation of the highly specialized plasma membrane of individual muscle fibres. Most of the plasma membrane covers an extensive, structured network of narrow invaginating tubules, but little is known about how excitation propagates along the tubular network of mammalian skeletal muscle fibres in the radial and longitudinal directions with respect to the fibre axis. Here we show that excitation can take multiple pathways through the internal network of tubules in fast‐twitch muscle fibres of the rat and determine the rates that excitation can spread within the internalized membrane tubules and show how this can change during muscle fatigue. Our results increase our understanding of mammalian skeletal muscle function in health, fatigue and some disease states.
Gene Transfer between Salmonella enterica Serovar Typhimurium inside Epithelial Cells

ABSTRACT Virulence and antibiotic resistance genes transfer between bacteria by bacterial conjugation. Conjugation also mediates gene transfer from bacteria to eukaryotic organisms, including yeast and human cells. Predicting when and where genes transfer by conjugation could enhance our understanding of the risks involved in the release of genetically modified organisms, including those being developed for use as vaccines. We report here that Salmonella enterica serovar Typhimurium conjugated inside cultured human cells. The DNA transfer from donor to recipient bacteria was proportional to the probability that the two types of bacteria occupied the same cell, which was dependent on viable and invasive bacteria and on plasmid tra genes. Based on the high frequencies of gene transfer between bacteria inside human cells, we suggest that such gene transfers occur in situ. The implications of gene transfer between bacteria inside human cells, particularly in the context of antibiotic resistance, are discussed.
Sox17‐2A‐iCre: A knock‐in mouse line expressing Cre recombinase in endoderm and vascular endothelial cells

Sox17 encodes an SRY‐related high‐mobility group (HMG) box transcription factor that is essential for endoderm formation and fetal hematopoietic stem cell maintenance. In the mouse, expression of Sox17 is first observed in the extraembryonic endoderm and is subsequently seen in the definitive endoderm as well as in blood and the endothelial cells of the developing vasculature. To conditionally inactivate genes in these domains, we have targeted the Sox17 locus to generate a bicistronic mRNA linking Sox17 to a codon improved Cre recombinase (iCre) via a viral 2A sequence. Here we report a new Cre knock‐in mouse line, Sox17‐2A‐iCre, with activity in the developing endoderm, the vascular endothelial cells of the cardiovascular system and the hematopoietic system. Our results indicate that the Sox17‐2A‐iCre is active in an early endoderm progenitor and recombination of the Rosa26 reporter was observed in all previously reported expression domains of Sox17. The Sox17‐2A‐iCre line will be an excellent tool to conditionally inactivate genes in the definitive endoderm as well as in the vasculature and hematopoietic system. genesis 47:603–610, 2009. © 2009 Wiley‐Liss, Inc.
INVOLVEMENT OF PEPTIDOGLYCAN RECOGNITION PROTEIN L6 IN ACTIVATION OF IMMUNE DEFICIENCY PATHWAY IN THE IMMUNE RESPONSIVE SILKWORM CELLS.

The immune deficiency (Imd) signaling pathway is activated by Gram-negative bacteria for producing antimicrobial peptides (AMPs). In Drosophila melanogaster, the activation of this pathway is initiated by the recognition of Gram-negative bacteria by peptidoglycan (PGN) recognition proteins (PGRPs), PGRP-LC and PGRP-LE. In this study, we found that the Imd pathway is involved in enhancing the promoter activity of AMP gene in response to Gram-negative bacteria or diaminopimelic (DAP) type PGNs derived from Gram-negative bacteria in an immune responsive silkworm cell line, Bm-NIAS-aff3. Using gene knockdown experiments, we further demonstrated that silkworm PGRP L6 (BmPGRP-L6) is involved in the activation of E. coli or E. coli-PGN mediated AMP promoter activation. Domain analysis revealed that BmPGRP-L6 contained a conserved PGRP domain, transmembrane domain, and RIP homotypic interaction motif like motif but lacked signal peptide sequences. BmPGRP-L6 overexpression enhances AMP promoter activity through the Imd pathway. BmPGRP-L6 binds to DAP-type PGNs, although it also binds to lysine-type PGNs that activate another immune signal pathway, the Toll pathway in Drosophila. These results indicate that BmPGRP-L6 is a key PGRP for activating the Imd pathway in immune responsive silkworm cells.
Therapeutic uses of furin and its inhibitors: a patent review

Introduction: Since the discovery of furin, numerous reports have studied its role in health and diseases, including cancer, inflammatory and infectious diseases. This interest has led to the development of both large protein- and peptide-based inhibitors aiming to control furin activity to treat these disorders. The most recent advances include the development of potent peptidomimetic furin inhibitors, considerably expanding the field of therapeutic applications. Area covered: In this review, the use of furin or its inhibitors for therapeutic conditions is described through the patent literature since 1994. Only compounds with biological efficacy or augmented properties demonstrated within the patent literature or the associated publications concerning their claimed uses are discussed. Expert opinion: Considering the diseases that may benefit from furin inhibition, several patents detail the use of the restricted number of furin inhibitors. However, there have been recent reports of new scaffolds, and even the use of furin itself, as a therapeutic agent. Despite considerable evidence of in vivo efficacy, limited confirmation from clinical trials supports or refutes the further use of these compounds in a therapeutic context. The most advanced application is the use of furin knockdown in the generation of an autologous cancer vaccine, which has initiated clinical trials.
Lutibacter oricola sp. nov., a marine bacterium isolated from seawater.

A bacterial strain, UDC377(T), was isolated from seawater samples collected at Seo-do on the coast of Dokdo island in the East Sea, and was subjected to taxonomic study using a polyphasic approach. Strain UDC377(T) was pale-yellow, Gram-staining-negative, non-motile, rod-shaped and aerobic. The strain grew optimally at 25-28 °C, in the presence of 2 % (w/v) NaCl and at pH 7.0-7.5. Strain UDC377(T) produced carotenoid pigments; however, it did not produce flexirubin-type pigments. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain UDC377(T) clustered with members of the genus Lutibacter and appeared most closely related to Lutibacter agarilyticus KYW566(T) (96.0 % 16S rRNA gene sequence similarity) followed by L. aestuarii MA-My1(T) (95.0 %), L. litoralis CL-TF09(T) (94.9 %), L. maritimus S7-2(T) (94.1 %) and L. flavus IMCC1507(T) (94.0 %). The DNA G+C content of strain UDC377(T) was 30.8 mol%. Strain UDC377(T) contained MK-6 as the predominant menaquinone, iso-C15 : 0 3-OH, iso-C15 : 0 and iso-C16 : 0 3-OH as the major fatty acids, and phosphatidylethanolamine, two unknown aminolipids and six unknown lipids as the major polar lipids. Based on phenotypic properties and phylogenetic data presented, strain UDC377(T) is considered to represent a novel species of the genus Lutibacter, for which the name Lutibacter oricola sp. nov. is proposed. The type strain is UDC377(T) ( = DSM 24956(T) = KCTC 23668(T)).