Miracle-dz/UniFAR-FTUs huggingface dataset:
The Dynamics of a Spatial Cyclic Competition System

We analyze the long term behavior of a system involved in cyclic competition similar to the rock-paper-scissors game. Previous studies have used cellular autonoma simulations to model the stochastic interactions and mean field equations to approximate this stochastic model. However, mean field approximation does not properly account for spatial correlations, leading to loss of spatial significance. We use pair approximations to model the local interactions with a system of differential equations. We then investigate the outcome of various initial conditions of the pair approximation model using numerical integration. Three categories of initial conditions are found that lead to three distinct behaviors: one species is present, all three species oscillate around the fixed point resulting in a heteroclinic cycle, or convergence to an interior fixed point. We also explore the relative importance of initial conditions and lattice size on fixation probabilities for each species. We finally discuss the implications of these results in a biological context.
Antibacterial susceptibility of uropathogens in 3 hospitals, Sari, Islamic Republic of Iran, 2002-2003.

To determine the frequency and pattern of antibiotic susceptibility of uropathogens in urinary tract infection (UTI) from 3 university hospitals we carried out a retrospective review of urine culture and antibiotic sensitivity testing from symptomatic outpatients and inpatients during 2002-2003. Of 5600 samples, 703 (12.6%) were culture positive, 38.7% of which were from hospitalized patients. Escherichia coli was the leading cause of UTI in both groups of patients. The rates and roles of other pathogens, including Pseudomonas spp. (5.3%-10.4%), Enterobacter spp. (0%-5.7%), Staphylococcus spp. ) 5.4%-26.4%), differed in each hospital. Differences in antibacterial susceptibility patterns were observed. Ampicillin (82%-100%) and co-trimoxazole (50%-90%) resistance were the most frequent. Methicillin resistance in Staphylococcus spp. ranged from 17% to 60%.
Roots, Cycles and Leaves. Expression of the Phosphoenolpyruvate Carboxylase Kinase Gene Family in Soybean1

Phosphorylation of phosphoenolpyruvate carboxylase (PEPc; EC 4.1.1.31) plays an important role in the control of central metabolism of higher plants. This phosphorylation is controlled largely at the level of expression of PEPc kinase (PPCK) genes. We have analyzed the expression of both PPCK genes and the PEPC genes that encode PEPc in soybean (Glycine max). Soybean contains at least four PPCK genes. We report the genomic and cDNA sequences of these genes and demonstrate the function of the gene products by in vitro expression and enzyme assays. For two of these genes, GmPPCK2 and GmPPCK3, transcript abundance is highest in nodules and is markedly influenced by supply of photosynthate from the shoots. One gene, GmPPCK4, is under robust circadian control in leaves but not in roots. Its transcript abundance peaks in the latter stages of subjective day, and its promoter contains a sequence very similar to the evening element found in Arabidopsis genes expressed at this time. We report the expression patterns of five PEPC genes, including one encoding a bacterial-type PEPc lacking the phosphorylation site of the plant-type PEPcs. The PEPc expression patterns do not match those of any of the PPCK genes, arguing against the existence of specific PEPc-PPCK expression partners. The PEPC and PPCK gene families in soybean are significantly more complex than previously understood.
A single conservative amino acid substitution in the reverse transcriptase of human immunodeficiency virus-1 confers resistance to (+)-(5S)-4,5,6,7-tetrahydro-5-methyl-6-(3-methyl-2-butenyl)imidazo[4,5, 1- jk][1,4]benzodiazepin-2(1H)-thione (TIBO R82150).

Tetrahydroimidazo[4,5,1-jk][1,4]benzodiazepin-2(1H)-one and -thione (TIBO) derivatives (e.g., R82150) are potent, human immunodeficiency virus-1 (HIV-1)-specific, inhibitors of reverse transcriptase (RT) that are undergoing initial evaluation in clinical trials. Because HIV-1 has become resistant to other RT inhibitors, we investigated the potential for viral resistance to TIBO R82150 by serial in vitro passage of HIV-1IIIB in the presence of drug. R82150-resistant variants (> 100-fold increase in IC50) dominated the replicating virus population after only three or four passages. R82150-resistant virus was partially cross-resistant to other HIV-1-specific RT inhibitors, including nevirapine (approximately 10-fold increase in IC50) and 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (approximately 3.5-fold increase) but remained susceptible to 2',3'-dideoxynucleosides and phosphonoformate. DNA sequencing of cloned resistant RT, combined with site-specific mutational analyses and construction of mutant recombinant proviruses, demonstrated that a single, conservative amino acid substitution (Leu100 to Ile) in HIV-1 RT is responsible for high level R82150 resistance and partial nevirapine resistance. These studies indicate that a subtle mutation in HIV-1 RT can dramatically affect viral susceptibility to an HIV-1-specific RT inhibitor. The clinical efficacy of TIBO derivatives and other HIV-1-specific RT inhibitors may be limited by the emergence of drug-resistant viral strains.
Measles Virus-Induced Immunosuppression In Vitro Is Independent of Complex Glycosylation of Viral Glycoproteins and of Hemifusion

ABSTRACT Expression of the measles virus (MV) F/H complex on the surface of viral particles, infected cells, or cells transfected to express these proteins (presenter cells [PC]) is necessary and sufficient to induce proliferative arrest in both human and rodent lymphoid cells (responder cells [RC]). This inhibition was found to occur independent of apoptosis and soluble mediators excluded by a pore size filter of 200 nm released from either PC or RC. We now show that reactive oxygen intermediates which might be released by RC or PC also do not contribute to MV-induced immunosuppression in vitro. Using an inhibitor of Golgi-resident mannosidases (deoxymannojirimycin), we found that complex glycosylation of the F and H proteins is not required for the induction of proliferative arrest of RC. As revealed by our previous studies, proteolytic cleavage of the MV F protein precursor into its F1 and F2 subunits, but not of F/H-mediated cellular fusion, was found to be required, since fusion-inhibitory peptides such as Z-d-Phe-l-Phe-Gly (Z-fFG) did not interfere with the induction of proliferative inhibition. We now show that Z-fFG inhibits cellular fusion at the stage of hemifusion by preventing lipid mixing of the outer membrane layer. These results provide strong evidence for a receptor-mediated signal elicited by the MV F/H complex which can be uncoupled from its fusogenic activity is required for the induction of proliferative arrest of human lymphocytes.
A mixed co‐culture of mesenchymal stem cells and transgenic chondrocytes in alginate hydrogel for cartilage tissue engineering

To regenerate articular cartilage tissue from degeneration and trauma, synovial mesenchymal stem cells (SMSCs) were used in this study as therapeutic progenitor cells to induce therapeutic chondrogenesis. To accomplish this, chondrocytes pre‐transduced with adenoviral vectors carrying the transforming growth factor (TGF) β3 gene were selected as transgenic companion cells and co‐cultured side‐by‐side with SMSCs in a 3D environment to provide chondrogenic growth factors in situ. We adopted a mixed co‐culture strategy for this purpose. Transgenic delivery of TGF‐β3 in chondrocytes was performed via recombinant adenoviral vectors. The mixed co‐culture of SMSCs and transgenic chondrocytes was produced in alginate gel constructs. Gene expression in both SMSCs and chondrocytes were characterized. Biochemical assays in vitro and in vivo showed that release of TGF‐ß3 from transgenic chondrocytes not only induced SMSC differentiation into chondrocytic cells but also preserved the chondrocytic phenotype of chondrocytes from suspected dedifferentiation. As a result, this mixed co‐culture strategy in conjunction with TGF‐ß3 gene delivery could be a promising approach in cartilage tissue engineering. Copyright © 2012 John Wiley & Sons, Ltd.
Interactive surface in the PapD chaperone cleft is conserved in pilus chaperone superfamily and essential in subunit recognition and assembly.

The assembly of adhesive pili in Gram‐negative bacteria is modulated by specialized periplasmic chaperone systems. PapD is the prototype member of the superfamily of periplasmic pilus chaperones. Previously, the alignment of chaperone sequences superimposed on the three dimensional structure of PapD revealed the presence of invariant, conserved and variable amino acids. Representative residues that protruded into the PapD cleft were targeted for site directed mutagenesis to investigate the pilus protein binding site of the chaperone. The ability of PapD to bind to fiber‐forming pilus subunit proteins to prevent their participation in misassembly interactions depended on the invariant, solvent‐exposed arginine‐8 (R8) cleft residue. This residue was also essential for the interaction between PapD and a minor pilus adaptor protein. A mutation in the conserved methionine‐172 (M172) cleft residue abolished PapD function when this mutant protein was expressed below a critical threshold level. In contrast, radical changes in the variable residue glutamic acid‐167 (E167) had little or no effect on PapD function. These studies provide the first molecular details of how a periplasmic pilus chaperone binds to nascently translocated pilus subunits to guide their assembly into adhesive pili.
Asymmetric Dimethylarginine at Sea Level Is a Predictive Marker of Hypoxic Pulmonary Arterial Hypertension at High Altitude

Background: Prolonged exposure to altitude-associated chronic hypoxia (CH) may cause high-altitude pulmonary hypertension (HAPH). Chronic intermittent hypobaric hypoxia (CIH) occurs in individuals who commute between sea level and high altitude. CIH is associated with repetitive acute hypoxic acclimatization and conveys the long-term risk of HAPH. As nitric oxide (NO) regulates pulmonary vascular tone and asymmetric dimethylarginine (ADMA) is an endogenous inhibitor of NO synthesis, we investigated whether ADMA concentration at sea level predicts HAPH among Chilean frontiers personnel exposed to 6 months of CIH. Methods: In this prospective study, 123 healthy army draftees were subjected to CIH (5 days at 3,550 m, 2 days at sea level) for 6 months. In 100 study participants with complete data, ADMA, symmetric dimethylarginine (SDMA), L-arginine, arterial oxygen saturation (SaO2), systemic blood pressure, and hematocrit were assessed at months 0 (sea level), 1, 4, and 6. Acclimatization to altitude was determined using the Lake Louise Score (LLS) and the presence of acute mountain sickness (AMS). Echocardiography was performed after 6 months of CIH in 43 individuals with either good (n = 23) or poor (n = 20) acclimatization. Results: SaO2 acutely decreased at altitude and plateaued at 90% thereafter. ADMA increased and SDMA decreased during the study course. The incidence of AMS and the LLS was high after the first ascent (53 and 3.1 ± 2.4) and at 1 month of CIH (47 and 3.0 ± 2.6), but decreased to 20 and 1.4 ± 2.0 at month 6 (both p < 0.001). Eighteen participants (42%) showed a mean pulmonary arterial pressure (mPAP) >25 mm Hg, out of which 9 (21%) were classified as HAPH (mPAP ≥ 30 mm Hg). ADMA at sea level was significantly associated with mPAP at high altitude in month 6 (R = 0.413; p = 0.007). In ROC analysis, a cutoff for baseline ADMA of 0.665 μmol/L was determined to predict HAPH (mPAP > 30 mm Hg) with a sensitivity of 100% and a specificity of 63.6%. Conclusions: ADMA concentration increases during CIH. ADMA at sea level is an independent predictive biomarker of HAPH. SDMA concentration decreases during CIH and shows no association with HAPH. Our data support a role of impaired NO-mediated pulmonary vasodilation in the pathogenesis of HAPH.
Decontamination of Cu2+ - Tainted Water through Biosorption onto Palm Tree Leaf Particles

In this study, the potential use of Palm Tree Leaf (PTL) particles for the removal of copper ions from aqueous solution was investigated. The effects of shaking time, Cu2+ concentration and equilibrium pH on the biosorption of copper ions from aqueous solution were studied. Batch biosorption experiments proved the technical feasibility of using PTL particles to remove copper ions from aqueous solutions, where Cu2+ uptake of 17.6 mg/g was observed. The biosorption of copper on PTL particles was pH dependent and maximum copper sorption was found to occur at an equilibrium pH of 5.5. The equilibrium sorption data of copper on PTL particles was described by 2 two-parameter isotherm models: the Freundlich and the Langmuir models, as well as by the three-parameter Redlich-Peterson model. While all three models proved a good fit for the equilibrium sorption data, CFEF non-linear regression analysis indicated that the Redlich-Peterson model resulted in the best fit. Dynamic studies revealed that the initial uptake of copper on PTL particles was rapid, where equilibrium was established within 15 minutes and that the data followed the pseudo second-order reaction.
Shear flow-induced motility of Dictyostelium discoideum cells on solid substrate

Application of a mild hydrodynamic shear stress to Dicytostelium discoideum cells, unable to detach cells passively from the substrate, triggers a cellular response consisting of steady membrane peeling at the rear edge of the cell and periodic cell contact extensions at its front edge. Both processes require an active actin cytoskeleton. The cell movement induced by the hydrodynamic forces is very similar to amoeboid cell motion during chemotaxis, as for its kinematic parameters and for the involvement of phosphatidylinositol(3,4,5)-trisphosphate internal gradient to maintain cell polarity. Inhibition of phosphoinositide 3-kinases by LY294002 randomizes the orientation of cell movement with respect to the flow without modifying cell speed. Two independent signaling pathways are, therefore, induced in D. discoideum in response to external forces. The first increases the frequency of pseudopodium extension, whereas the second redirects the actin cytoskeleton polymerization machinery to the edge opposite to the stressed side of the cell.
The Effect of a Communications Campaign on Middle School Students' Nutrition and Physical Activity: Results of the HEALTHY Study

The HEALTHY Study was a 3-year school-based intervention designed to change the behaviors of middle school students to reduce their risk for developing type 2 diabetes mellitus. This report examines the relation between exposure to communications campaign materials and behavior change among students in the HEALTHY intervention schools. Using data from campaign tracking logs and student interviews, the authors examined communications campaign implementation and exposure to the communications campaign as well as health behavior change. Campaign tracking documents revealed variability across schools in the quantity of communications materials disseminated. Student interviews confirmed that there was variability in the proportion of students who reported receiving information from the communication campaign elements. Correlations and regression analysis controlling for semester examined the association between campaign exposure and behavior change across schools. There was a significant association between the proportion of students exposed to the campaign and the proportion of students who made changes in health behavior commensurate with study goals. The results suggest that, in the context of a multifaceted school-based health promotion intervention, schools that achieve a higher rate of exposure to communication campaign materials among the students may stimulate greater health behavior change.
Customer-centric relationship management system development: A generative knowledge integration perspective

Purpose – This study aims to create and deploy new configurations of resources via understanding issues concerning generative knowledge integration (KI) to create a customer‐centric relationship management system.Design/methodology/approach – A qualitative case study of a public‐listed housing developer was conducted to analyze its main issues and conceptualize the underlying generative knowledge integration process.Findings – Issues concerning generating KI were identified from the case study. The conceptualization of generative KI encompasses three main generative KI mechanisms, knowledge conceptualization, knowledge convergence, and knowledge assimilation, that are connected by three generative KI processes: accessing and exchanging knowledge, articulating and exchanging knowledge, and combining and exchanging knowledge.Practical implications – The importance of understanding the concept of generative knowledge integration for practitioners is emphasized, and suggestions are given to promote the deploy.
Atypical Fibrous Histiocytoma of the Skin: Clinicopathologic Analysis of 59 Cases With Evidence of Infrequent Metastasis

Atypical fibrous histiocytoma is an uncommon, poorly documented variant of cutaneous fibrous histiocytoma. We studied 59 cases of atypical fibrous histiocytoma to better characterize the clinicopathologic spectrum. There were 33 males and 26 females (median age 38 years; range 5–79 years) with solitary lesions arising on lower (25 cases) and upper (17 cases) extremities, trunk (6 cases), head and neck (4 cases), and vulva (1 case); anatomic location was not stated in six cases. Lesions measured 0.4–8 cm in diameter (median 1.5 cm) and clinically were nodules (40 cases), polypoid tumors (18 cases), or a slightly elevated plaque (1 case). Histologically, the lesions were primarily dermal with superficial involvement of the subcutis in one third of the cases. Salient features included a proliferation of pleomorphic, plump, spindle, and/or polyhedral cells with mainly large, hyperchromatic, irregular, or bizarre nuclei, set in a background of classic features of fibrous histiocytoma, including spindle cell areas showing a storiform pattern and entrapped thickened, hyaline collagen bundles, especially at the periphery. Multinucleated giant cells, often with bizarre nuclei and foamy, sometimes hemosiderin-rich, cytoplasm were also variably present. The degree of pleomorphism varied from only focal and minimal (14 cases) or moderate (24 cases) to marked (21 cases). Mitotic activity was observed in 55 lesions, and the number of mitotic figures ranged from 1 to 15 per 10 high power fields. Atypical mitoses were noted in 20 lesions. Furthermore, some cases of atypical fibrous histiocytoma displayed other worrisome features less often observed in ordinary FH, including unusually large size (diameter >2 cm, 8 cases), involvement of the superficial subcutis (19 cases), and geographic necrosis (7 cases). Immunohistochemical studies performed in 42 cases showed only focal smooth muscle actin (10 cases) and CD34 (4 cases) positivity, whereas CD68, S-100 protein, desmin, pan-keratin, and epithelial membrane antigen were negative. Clinical follow-up data available in 21 patients (mean duration of follow-up 50.6 months, median 43 months) revealed local recurrences in three patients (one repeated); two patients developed distant metastases, one of whom died after 96 months. These two cases were not histologically distinct from the group as a whole. We conclude that atypical fibrous histiocytoma has a broader clinicopathologic spectrum than previously realized. Lesions with floridly atypical features represent potential pitfalls for overinterpretation as pleomorphic sarcoma, which would appear to be inappropriate in most cases. Provided that atypical fibrous histiocytoma is treated by complete excision, a benign outcome is to be expected in most cases. However, similar to the cellular and aneurysmal variants of fibrous histiocytoma, atypical fibrous histiocytoma shows a higher tendency to recur locally than ordinary fibrous histiocytoma and may rarely metastasize.
Fatal thyroid carcinoma: Anaplastic transformation of adenocarcinoma

Prognosis of well‐differentiated carcinoma of the thyroid gland is generally favorable, while that of anaplastic carcinoma, extremely poor. Well‐differentiated carcinoma may sometimes be fatal; the most common underlying cause is considered to be due to anaplastic transformation of the original well‐differentiated carcinoma to a less differentiated form. We studied 27 consecutive autopsy cases of fatal thyroid cancer treated at the Ito Hospital, Tokyo, during a five‐year period, 1969–1973. We found uniform histological features of anaplastic carcinoma in 10 cases and of well differentiated carcinoma in four cases. In addition, co‐existence of well‐differentiated and anaplastic carcinomas was observed in nine cases and well‐differentiated and squamous cell carcinomas in four. Circumstantial evidence strongly suggests that malignant transformation is a part of the natural history of thyroid carcinoma, from well‐differentiated carcinoma to less differentiated forms, either squamous cell or anaplastic carcinoma.
Resilience challenges for textile enterprises in a transitional economy and regional trade perspective – a study of Kyrgyz conditions

This paper aims to contribute to the resilience development of the textile sector in a transitional economy, based on a case study of the Kyrgyz Republic, where the transition to a free market system generated broken supply chains, low diversification, a high open economy level of the textile sector and dependence on international trade regulations. The approach used is based on theories of organisational resilience, literature studies and fieldwork. Scenarios are developed and analysed by event tree and SWOT analysis, to identify resilience properties of the textile sector. Findings focus on the implications of future membership or non-membership, respectively, in the Customs Union of Belarus, Kazakhstan and Russia, where both supportive and adverse effects have been identified. The results contribute to the knowledge of the transitional economy conditions and serve as a guideline for stakeholders about enhancing resilience, both at the industrial and organisational levels, of the Kyrgyz textile sector.
A generalization of weighted subspace fitting to full-rank models

The idea of subspace fitting provides a popular framework for different applications of parameter estimation and system identification. Previously, some algorithms have been suggested based on similar ideas, for a sensor array processing problem where the underlying data model is not low rank. We show that two of these algorithms (DSPE and DISPARE) fail to give consistent estimates and introduce a general class of subspace fitting-like algorithms for consistent estimation of parameters from a possibly full-rank data model. The asymptotic performance is analyzed, and an optimally weighted algorithm is derived. The result gives a lower bound on the estimation performance for any estimator based on a low-rank approximation of the linear space spanned by the sample data. We show that in general, for full-rank data models, no subspace-based method can reach the Cramer-Rao lower bound (CRB).
BIOLOGY Correction for ‘ ‘ Dissection of the high rate constant for the binding of a ribotoxin to the ribosome

Correction for ‘‘Extensive remyelination of the CNS leads to functional recovery,’’ by I. D. Duncan, A. Brower, Y. Kondo, J. F. Curlee, Jr., and R. D. Schultz, which appeared in issue 16, April 21, 2009, of Proc Natl Acad Sci USA (106:6832–6836; first published April 2, 2009; 10.1073/pnas.0812500106). The authors note that on page 6836, right column, first paragraph, the fourth line appears incorrectly in part. The dose amount ‘‘25.0 and 50.0 Gy’’ should instead appear as ‘‘25–50 kGy. ’’ This error does not affect the conclusions of the article.