Miracle-dz/UniFAR-FTUs huggingface dataset:
Initial Phases of Biofilm Formation in Shewanella oneidensis MR-1

ABSTRACT Shewanella oneidensis MR-1 is a facultative Fe(III)- and Mn(IV)-reducing microorganism and serves as a model for studying microbially induced dissolution of Fe or Mn oxide minerals as well as biogeochemical cycles. In soil and sediment environments, S. oneidensis biofilms form on mineral surfaces and are critical for mediating the metabolic interaction between this microbe and insoluble metal oxide phases. In order to develop an understanding of the molecular basis of biofilm formation, we investigated S. oneidensis biofilms developing on glass surfaces in a hydrodynamic flow chamber system. After initial attachment, growth of microcolonies and lateral spreading of biofilm cells on the surface occurred simultaneously within the first 24 h. Once surface coverage was almost complete, biofilm development proceeded with extensive vertical growth, resulting in formation of towering structures giving rise to pronounced three-dimensional architecture. Biofilm development was found to be dependent on the nutrient conditions, suggesting a metabolic control. In global transposon mutagenesis, 173 insertion mutants out of 15,000 mutants screened were identified carrying defects in initial attachment and/or early stages in biofilm formation. Seventy-one of those mutants exhibited a nonswimming phenotype, suggesting a role of swimming motility or motility elements in biofilm formation. Disruption mutations in motility genes (flhB, fliK, and pomA), however, did not affect initial attachment but affected progression of biofilm development into pronounced three-dimensional architecture. In contrast, mutants defective in mannose-sensitive hemagglutinin type IV pilus biosynthesis and in pilus retraction (pilT) showed severe defects in adhesion to abiotic surfaces and biofilm formation, respectively. The results provide a basis for understanding microbe-mineral interactions in natural environments.
An Improved Model for Prediction of Retention Times of Tryptic Peptides in Ion Pair Reversed-phase HPLC

The proposed model is based on the measurement of the retention times of 346 tryptic peptides in the 560- to 4,000-Da mass range, derived from a mixture of 17 protein digests. These peptides were measured in HPLC-MALDI MS runs, with peptide identities confirmed by MS/MS. The model relies on summation of the retention coefficients of the individual amino acids, as in previous approaches, but additional terms are introduced that depend on the retention coefficients for amino acids at the N-terminal of the peptide. In the 17-protein mixture, optimization of two sets of coefficients, along with additional compensation for peptide length and hydrophobicity, yielded a linear dependence of retention time on hydrophobicity, with an R2 value about 0.94. The predictive capability of the model was used to distinguish peptides with close m/z values and for detailed peptide mapping of selected proteins. Its applicability was tested on columns of different sizes, from nano- to narrow-bore, and for direct sample injection, or injection via a pre-column. It can be used for accurate prediction of retention times for tryptic peptides on reversed-phase (300-Å pore size) columns of different sizes with a linear water-ACN gradient and with TFA as the ion-pairing modifier.
On the multi-decadal oscillation of Atlantic tropical storm activity

Long term Atlantic tropical storm activity is described by the time series of the yearly Accumulated Cyclone Energy (ACE) Index for the time interval 1851-2007. ACE is a measure of total wind energy for North Atlantic basin and land falling tropical cyclone activity. Since the ACE index reflects a combination of storm intensity and duration it is a better measure of overall activity and likely damage than the number of either basin or land falling tropical storms or hurricanes. The yearly ACE time series is non-stationary, and one step toward detecting possible long-term quasi-periods is to detrend the original data. In this paper we use a procedure for data transformation by which ACE index is fitted in least square sense with polynomials of increasing order, followed by detrend. It is shown that, with some approximation, the obtained time series is cyclostationary, and a multi-decadal oscillation is detectable, as indicated by the power spectrum analysis.
The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development

The phytohormones auxin and cytokinin interact to regulate many plant growth and developmental processes. Elements involved in the biosynthesis, inactivation, transport, perception, and signaling of these hormones have been elucidated, revealing the variety of mechanisms by which signal output from these pathways can be regulated. Recent studies shed light on how these hormones interact with each other to promote and maintain plant growth and development. In this review, we focus on the interaction of auxin and cytokinin in several developmental contexts, including its role in regulating apical meristems, the patterning of the root, the development of the gynoecium and female gametophyte, and organogenesis and phyllotaxy in the shoot.
Inet-3.0: Internet Topology Generator

In this report we present version 3.0 of Inet, an Autonomous System (AS) level Internet topology generator. Our understanding of the Internet topology is quickly evolving, and thus, our understanding of how synthetic topologies should be generated is changing too. We document our analysis of Inet2.2, which highlighted two shortcommings in its topologies. Inet-3.0 improves upon Inet-2.2’s two main weaknesses by creating topologies with more accurate degree distributions and minimum vertex covers as compared to Internet topologies. We also examine numerous other metrics to show that Inet3.0 better approximates the actual Internet AS topology than does Inet-2.2. Inet-3.0’s topologies still do not well represent the Internet in terms of maximum clique size and clustering coefficient. These related problems stress a need for a better understanding of Internet connectivity and will be addressed in future work.
Molecular studies on the mechanism of tetracycline resistance mediated by Tet(O)

The mechanism of resistance to tetracycline in Escherichia coli mediated by the Campylobacter jejuni-derived resistance determinant Tet(O) was investigated. The cloned Tet(O) protein had no detectable effect on the intracellular accumulation of tetracycline. The presence of Tet(O) markedly diminished the inhibitory effect of tetracycline on protein synthesis both in vivo and in vitro. Ribosomes prepared from tetracycline-resistant and susceptible E. coli cells bound almost identical amounts of radiolabeled tetracycline. Thus, a reduction in the binding of the antibiotic to its target site on the ribosome is not the primary mechanism of resistance. Poly(U)-directed polyphenylalanine synthesis revealed that an S-100 fraction prepared from tetracycline-resistant cells made the ribosomes prepared from susceptible cells considerably more resistant to the inhibitory action of tetracycline. The N-terminal portion (1 to 150 residues) of Tet(O) is highly homologous to the GTP-binding domain of elongation factor Tu and to elongation factor G, indicating that the Tet(O) protein has the potential to bind GTP. These data suggest that the Tet(O) protein could function either as a tetracycline-resistant analog of this elongation factor(s) or by modifying the target sites on the ribosomes in a catalytic fashion.
Body mass index in young adults: Associations with parental body size and education in the CARDIA Study.

OBJECTIVES Associations of parental education, parental body size, and offspring's education with body mass index and 7-year change in body mass index were examined among participants in the Coronary Artery Risk Development in Young Adults (CARDIA) study. METHODS CARDIA is a study of coronary artery disease risk factors in 5115 Black and White persons aged 18 to 30 at baseline. Analyses of covariance were carried out with body mass index and change in body mass index as the dependent variables, and with parental education, parental body size, and participant education as the major independent variables. RESULTS Father's body size was positively associated with participant's baseline body mass index among Black men, White men, and White women. Mother's body size was positively associated with baseline body mass index among all race-sex groups, and with change in body mass index among White women. Father's education was inversely associated with baseline body mass index among Black men and White women, and with change among White women. CONCLUSIONS Parental education may influence body mass index and changes in young adulthood, especially among White women. Such associations may be both genetic and environmental and may be important for obesity prevention efforts.
Fucoidan Does Not Exert Anti-Tumorigenic Effects on Uveal Melanoma Cell Lines

Background. The polysaccharide fucoidan is widely investigated as an anti-cancer agent. Here, we tested the effect of fucoidan on uveal melanoma cell lines. Methods. The effect of 100 µM fucoidan was investigated on five cell lines (92.1, Mel270 OMM1, OMM2.3, OMM2.5) and of 1 µg/mL–1 mg/mL fucoidan in two cell lines (OMM1, OMM2.3). Cell proliferation and viability were investigated with a WST-1 assay, migration in a wound healing (scratch) assay. Vascular Endothelial Growth Factor (VEGF) was measured in ELISA. Angiogenesis was evaluated in co-cultures with endothelial cells. Cell toxicity was induced by hydrogen-peroxide. Protein expression (Akt, ERK1/2, Bcl-2, Bax) was investigated in Western blot. Results. Fucoidan increased proliferation in two and reduced it in one cell line. Migration was reduced in three cell lines. The effect of fucoidan on VEGF was cell type and concentration dependent. In endothelial co-culture with 92.1, fucoidan significantly increased tubular structures. Moreover, fucoidan significantly protected all tested uveal melanoma cell lines from hydrogen-peroxide induced cell death. Under oxidative stress, fucoidan did not alter the expression of Bcl-2, Bax or ERK1/2, while inducing Akt expression in 92.1 cells but not in any other cell line. Conclusion. Fucoidan did not show anti-tumorigenic effects but displayed protective and pro-angiogenic properties, rendering fucoidan unsuitable as a potential new drug for the treatment of uveal melanoma.
Lifespan Extension and Rescue of Spongiform Encephalopathy in Superoxide Dismutase 2 Nullizygous Mice Treated with Superoxide Dismutase–Catalase Mimetics

Superoxide is produced as a result of normal energy metabolism within the mitochondria and is scavenged by the mitochondrial form of superoxide dismutase (sod2). Mice with inactivated SOD2 (sod2 nullizygous mice) die prematurely, exhibiting several metabolic and mitochondrial defects and severe tissue pathologies, including a lethal spongiform neurodegenerative disorder (Li et al., 1995; Melov et al., 1998, 1999). We show that treatment ofsod2 nullizygous mice with synthetic superoxide dismutase (SOD)–catalase mimetics extends their lifespan by threefold, rescues the spongiform encephalopathy, and attenuates mitochondrial defects. This class of antioxidant compounds has been shown previously to extend lifespan in the nematode Caenorhabditis elegans (Melov et al., 2000). These new findings in mice suggest novel therapeutic approaches to neurodegenerative diseases associated with oxidative stress such as Friedreich ataxia, spongiform encephalopathies, and Alzheimer's and Parkinson's diseases, in which chronic oxidative damage to the brain has been implicated.
Using Association Rules Mining for Retrieving Genre-Specific Music Files

Retrieving a music file from a large database is a non-trivial task. To support this task, many mechanisms have been developed over the years. However, indexing files remains one of the most popular mechanisms. Several algorithms allow feature extraction from audio signals. Usually, these features are used to describe music content. In this paper, we demonstrate that associations between content-based descriptors can be used as well. We have developed a processing chain which uses association rules mining to find significant relations between content-based descriptors of music files. The significant relations are used to index music files. Experiments conducted demonstrates that the proposed approach can yield interesting results especially with classical music.
Production of alumina based porous ceramics using naphthalene as the pore former

The present work focuses on the production of alumina based porous ceramics and its characterization. Five different alumina samples having naphthalene wt% between (0 - 50)% were prepared by die pressing. Pellets were fired at different range of temperatures (1500 – 1600oC) and time (2 – 4 hrs). It was found that with increase in the weight percentage (wt%) of naphthalene, the porosity increases. The pore size distribution also changes to larger pore sizes. CCS, bi-axial flexural strength decreases with increase in the porosity level and increases with the increase in sintering temperature and time. The strength vs porosity plots showed that the strength decreases exponentially with temperature and ln (CCS) vs porosity plots showed a linear fit with a negative slope. The SEM microstructure could describe briefly the distribution of the porosity inside those pellets and the average size of pores.
Identification of Host-Specificity Determinants in Betanodaviruses by Using Reassortants between Striped Jack Nervous Necrosis Virus and Sevenband Grouper Nervous Necrosis Virus

ABSTRACT Betanodaviruses, the causal agents of viral nervous necrosis in marine fish, have bipartite positive-sense RNAs as genomes. The larger genomic segment, RNA1 (3.1 kb), encodes an RNA-dependent RNA polymerase, and the smaller genomic segment, RNA2 (1.4 kb), codes for the coat protein. Betanodaviruses have marked host specificity, although the primary structures of the viral RNAs and encoded proteins are similar among betanodaviruses. However, no mechanism underlying the host specificity has yet been reported. To evaluate viral factors that control host specificity, we first constructed a cDNA-mediated infectious RNA transcription system for sevenband grouper nervous necrosis virus (SGNNV) in addition to that for striped jack nervous necrosis virus (SJNNV), which was previously established by us. We then tested two reassortants between SJNNV and SGNNV for infectivity in the host fish from which they originated. When striped jack and sevenband grouper larvae were bath challenged with the reassortant virus comprising SJNNV RNA1 and SGNNV RNA2, sevenband groupers were killed exclusively, similar to inoculation with SGNNV. Conversely, inoculations with the reassortant virus comprising SGNNV RNA1 and SJNNV RNA2 killed striped jacks but did not affect sevenband groupers. Immunofluorescence microscopic studies using anti-SJNNV polyclonal antibodies revealed that both of the reassortants multiplied in the brains, spinal cords, and retinas of infected fish, similar to infections with parental virus inoculations. These results indicate that viral RNA2 and/or encoded coat protein controls host specificity in SJNNV and SGNNV.
The effect of zinc supplementation on pregnancy outcomes: a double-blind, randomised controlled trial, Egypt

The present randomised controlled trial (RCT) was conducted to evaluate the effect of two regimens of Zn supplementation on pregnancy outcomes in Alexandria, Egypt. Healthy pregnant women aged 20–45 years and having low serum Zn level below the estimated median for the gestational age were eligible to participate in the trial. Of 1055 pregnant women assessed for the eligibility of low serum Zn level, 675 were eligible. These women were randomly assigned to one of the three groups: the Zn alone group (n 225) received a daily dose of 30 mg ZnSO4, the combined group (n 227) received 30 mg ZnSO4 plus multivitamins (B1, B6, D3, C and E) and the control group (n 223) received placebo (270 mg lactose). They were followed up from the time of recruitment till 1 week after delivery. Overall, there was no detectable difference in the mean birth weight between the three groups (mean 2929·12 (sd 330·28), 2922·22 (sd 324·05) and 2938·48 (sd 317·39) g for the placebo, Zn and Zn plus multivitamin groups, respectively, P= 0·88). Both the single and the combined Zn supplements were almost equally effective in reducing second- and third-stage complications (relative risk (RR) 0·43, 95 % CI 0·31, 0·60 for the Zn group and RR 0·54, 95 % CI 0·40, 0·73 for the combined group). Stillbirth and preterm delivery were significantly lower among the two supplemented groups than the placebo group (P= 0·001). Early neonatal morbidity was also significantly lower in the supplemented groups (RR 0·23, 95 % CI 0·15, 0·35 for the Zn group and RR 0·25, 95 % CI 0·16, 0·37 for the combined group). Collectively, Zn supplementation was effective in reducing pregnancy complications and early neonatal infection among the Zn-deficient women of the present trial.
How Does the Source of Rejection Perceive Innocent Victims?

ABSTRACT Prior studies have consistently revealed a strong positive association between general just-world beliefs and victim blaming. The present research aims to extend the literature by testing whether an act of social rejection overrides the influence of general just-world beliefs on victim blaming. Building upon the theory of moral compensation that people are more prosocial after behaving undesirably, we predicted that people should be less likely to blame an innocent victim after rejecting another person and that general just-world beliefs were not associated with victim blaming among the sources of rejection. To test these predictions, participants first completed a measure of general just-world beliefs and then recalled a past incident in which they rejected or accepted another person. They then read a scenario about school bullying and made attributions for the victim’s suffering. The results supported our predictions and the implications of the study are discussed.
Fracture Toughness of Advanced Ceramics at Room Temperature

This report presents the results obtained by the five U.S. participating laboratories in the Versailles Advanced Materials and Standards (VAMAS) round-robin for fracture toughness of advanced ceramics. Three test methods were used: indentation fracture, indentation strength, and single-edge pre-cracked beam. Two materials were tested: a gas-pressure sintered silicon nitride and a zirconia toughened alumina. Consistent results were obtained with the latter two test methods. Interpretation of fracture toughness in the zirconia alumina composite was complicated by R-curve and environmentally-assisted crack growth phenomena.
Federal Reserve Bank of Minneapolis Research Department Staff Report 417 Sluggish Responses of Prices and Inflation to Monetary Shocks in an Inventory Model of Money Demand *

We examine the responses of prices and inflation to monetary shocks in an inventory-theoretic model of money demand. We show that the price level responds sluggishly to an exogenous increase in the money stock because the dynamics of households' money inventories leads to a partially offsetting endogenous reduction in velocity. We also show that inflation responds sluggishly to an exogenous increase in the nominal interest rate because changes in monetary policy affect the real interest rate. In a quantitative example, we show that this nominal sluggishness is substantial and persistent if inventories in the model are calibrated to match U.S. households' holdings of M2. * A previous draft of this paper circulated under the title " Can a Baumol-Tobin model account for the short-run behavior of velocity? " We would like to thank and several anonymous referees for helpful comments. For financial support, Alvarez thanks the NSF and the Templeton Foundation and Atkeson thanks the NSF. The views expressed herein are those of the authors and not necessarily those of the Federal Reserve Bank of Minneapolis or the Federal Reserve System.
TOXICITY TO TOPICAL DIMETHYL SULFOXIDE IN A PEDIATRIC PATIENT WITH ANTHRACYCLINE EXTRAVASATION

Accidental extravasation of vesicant chemotherapy may cause important tissue injuries. Nowadays, the majority of authors propose topical dimethyl sulfoxide (DMSO), with or without local cooling, as the treatment of choice for anthracyclines extravasation. No significant toxicity has been reported when DMSO is used as topical treatment. In this report, we describe a case of local toxicity consisting of severe pain after its use in a pediatric patient. Illustration shows extravasation area.
Alendronate Does Not Inhibit Early Bone Apposition to Hydroxyapatite-Coated Total Joint Implants: A Preliminary Study

Background: Alendronate is a pyrophosphate analogue of bisphosphonate that has been shown to inhibit osteoclastic bone resorption. Bone formation and remodeling are necessary to establish initial fixation of uncemented implants, especially those coated with a bioactive surface such as hydroxyapatite. Because the process of bone-remodeling that culminates in new-bone formation is thought to be initiated by osteoclastic bone resorption, it is appropriate to test the influence of osteoclast-inhibiting medications on bone apposition to hydroxyapatite-coated implants.Methods: Twelve dogs underwent staged bilateral total hip arthroplasty, with twenty weeks between the first and second operations, with use of a titanium-alloy femoral stem that had a proximal macrotextured surface and a plasma-sprayed hydroxyapatite coating. Six of the dogs received oral alendronate therapy from the time of the surgery until they were killed; the other six dogs were untreated controls. The animals were killed four weeks after the second operation. Sections from matched implant sites (proximal, middle, and distal) were histologically analyzed. The linear extent of bone apposition, the linear extent and the thickness of the hydroxyapatite coating, and the total amount of cortical and trabecular bone were measured with the use of an interactive image analysis system.Results: There were no significant differences in radiographic or histologic findings between the two groups at either four or twenty-four weeks. Although the extent of the hydroxyapatite coating decreased significantly with time in both groups (p < 0.01), we identified no significant influence of alendronate on the extent of bone apposition, the extent or thickness of the hydroxyapatite coating, or the cortical or trabecular bone area around the implants.Conclusions: Many patients who are receiving alendronate for osteoporosis or other disorders may also be candidates for cementless total joint arthroplasty. Although bone formation is generally thought to be initiated by and coupled with bone resorption, our results suggest that alendronate has no discernible effect on the initial fixation of or the short-term bone-remodeling around hydroxyapatite-coated femoral total joint implants.