Miracle-dz/UniFAR-FTUs huggingface dataset:
Temperature‐dependent structural and functional features of a hyperthermostable enzyme using elastic neutron scattering

The dynamic behavior of an endoglucanase from the hyperthermophilic microorganism Pyrococcus furiosus was investigated using elastic neutron scattering. The temperature dependence of the atomic motions was correlated with conformational and functional characteristics of the enzyme. The onset of biological function at temperatures higher than approximately 25°C (the hyperthermostable enzyme is essentially inactive at room temperature) was associated with a dynamical transition in the anharmonic motions domain. This transition from the nonactive to the enzymatically active conformation involved structurally similar conformational substates in the energy landscape. From the mean‐square displacement of the protein atoms, the molecular flexibility and the effective force constants were calculated at different temperature zones. The results showed that the activity increases at higher temperatures where the intramolecular bonds are weakened and the overall rigidity of the protein is decreased. Further temperature increase resulted in significantly increased atomic fluctuations featuring heat denaturation of the protein. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Diffraction contrast from spherically symmetrical coherency strains

Abstract The properties of images formed by diffraction contrast in thin metal foils viewed by transmission electron microscopy are studied by means of the dynamical theory of diffraction, including absorption. It is shown how quantitative information regarding the state of strain in the matrix surrounding a spherical inclusion can be obtained from the micrographs. The theory is exemplified by the case of Cu—2% (wt) Co, and measurements of strain made in this system are in good agreement with the expected value.
Morphologically Docked Synaptic Vesicles Are Reduced insynaptotagmin Mutants of Drosophila

Nerve terminal specializations include mechanisms for maintaining a subpopulation of vesicles in a docked, fusion-ready state. We have investigated the relationship between synaptotagmin and the number of morphologically docked vesicles by an electron microscopic analysis ofDrosophila synaptotagmin (syt) mutants. The overall number of synaptic vesicles in a terminal was reduced, although each active zone continued to have a cluster of vesicles in its vicinity. In addition, there was an increase in the number of large vesicles near synapses. Examining the clusters, we found that the pool of synaptic vesicles immediately adjacent to the presynaptic membrane, the pool that includes the docked population, was reduced to 24 ± 5% (means ± SEM) of control in thesytnull mutation. To separate contributions of overall vesicle depletion and increased spontaneous release from direct effects of synaptotagmin on morphological docking, we examined syt mutants in an altered genetic background. Recombining syt alleles onto a second chromosome bearing an as yet uncharacterized mutation resulted in the expected decrease in evoked release but suppressed the increase in spontaneous release frequency. Motor nerve terminals in this genotype contained more synaptic vesicles than control, yet the number of vesicles immediately adjacent to the presynaptic membrane near active zones was still reduced (33 ± 4% of control). Our findings demonstrate that there is a decrease in the number of morphologically docked vesicles seen in syt mutants. The decreases in docking and evoked release are independent of the increase in spontaneous release. These results support the hypothesis that synaptotagmin stabilizes the docked state.
How Does a Pedagogical Agent Look at a Learner when Providing Evaluation Feedback?

We present in this paper a computational model for controling the gaze direction of a pedagogical agent. We are using a methodogical approach based on digital video corpora. A video corpus was collected. A subset of this corpus was annotated. Rules allowing for controling gaze direction of an agent were then obtained through statistical analysis on the annotations.
ATTENUATION OF REPERFUSION LUNG INJURY AND APOPTOSIS BY A2A ADENOSINE RECEPTOR ACTIVATION IS ASSOCIATED WITH MODULATION OF Bcl-2 AND Bax EXPRESSION AND ACTIVATION OF EXTRACELLULAR SIGNAL-REGULATED KINASES

Adenosine receptors (AR) and extracellular signal-regulated kinases (ERK) have been implicated in tissue protection and apoptosis regulation during ischemia/reperfusion (I/R) injury. This study tests the hypothesis that reduction of reperfusion lung injury after A2AAR activation is associated with attenuation of apoptosis, modulation of ERK activation, and alterations in antiapoptotic and proapoptotic protein expression (Bcl-2 and Bax, respectively). Experiments were performed in intact-chest, spontaneously breathing cats in which the arterial branch of the left lower lung lobe was occluded for 2 h and reperfused for 3 h (I/R group). Animals were treated with the selective A2AAR agonist ATL313 given 5 min before reperfusion alone or in combination with the selective A2AAR antagonist ZM241385. Western blot analysis showed significant reduction in expression of Bcl-2 and increase in expression of Bax after reperfusion, compared with control lungs. Phosphorylated ERK1/2 levels were also increased after reperfusion. Compared with the I/R group, ATL313 markedly (P < 0.01) attenuated indices of injury and apoptosis including the percentage of injured alveoli, wet-dry weight ratio, myeloperoxidase activity, in situ terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end-labeling-positive cells, and caspase 3 activity and expression. Furthermore, compared with reperfused lungs, in ATL313-pretreated lungs, Western blot analysis demonstrated substantial ERK1/2 activation, increased expression of Bcl-2, and attenuated expression of Bax. The protective effects of ATL313 were blocked by pretreatment with ZM241385. In summary, the present study shows that in vivo activation of A2AAR confers protection against reperfusion lung injury. This protection is associated with decreased apoptosis and involves ERK1/2 activation and alterations in antiapoptotic Bcl-2 and proapoptotic Bax proteins.
Analysis of Haptoglobin and Hemoglobin-Haptoglobin Interactions with the Neisseria meningitidis TonB-Dependent Receptor HpuAB by Flow Cytometry

ABSTRACT Neisseria meningitidis expresses a two-component TonB-dependent receptor, HpuAB, which mediates heme-iron (Hm-Fe) acquisition from hemoglobin and hemoglobin-haptoglobin complexes. Due to genetic polymorphisms in the human haptoglobin gene, haptoglobin (and hemoglobin-haptoglobin) exists as three structurally distinct phenotypes. In this study, we examined the influence of the haptoglobin phenotype on the interactions of HpuAB with apo-haptoglobin and hemoglobin-haptoglobin. Growth assays confirmed that HpuAB utilizes hemoglobin-haptoglobin more efficiently than hemoglobin as an Fe source and revealed a preference for human-specific, polymeric 2-2 or 2-1 hemoglobin-haptoglobin complexes. We developed a flow cytometry-based assay to measure the binding kinetics of fluorescein-labeled ligands to HpuAB on live, intact meningococci. The binding affinity of HpuAB for hemoglobin-haptoglobin phenotypes correlated well with the ability of each ligand to support Neisseria meningitidis growth, with higher affinities exhibited for types 2-2 and 2-1 hemoglobin-haptoglobin. Saturable binding of Hb and apo-haptoglobin suggested that HpuAB-mediated utilization of hemoglobin-haptoglobin involves specific interactions with both components. In contrast to previous studies, we detected binding of HpuB expressed alone to hemoglobin, apo-haptoglobin, and hemoglobon-haptoglobin of all three phenotypes. However, in the absence of HpuA, the binding capacity and/or affinity of the receptor was reduced and the dissociation of hemoglobin was impaired. We did not detect binding of HpuA alone to hemoglobin, apo-haptoglobin, or hemoglobin-haptoglobin; however, the lipoprotein is crucial for optimal recognition and use of ligands by the receptor. Finally, this study confirmed the integral role of TonB and the proton motive force in the binding and dissociation of Hb and hemoglobin-haptoglobin from HpuAB.
Interframe Coding of Feature Descriptors for Mobile Augmented Reality

Streaming mobile augmented reality applications require both real-time recognition and tracking of objects of interest in a video sequence. Typically, local features are calculated from the gradients of a canonical patch around a keypoint in individual video frames. In this paper, we propose a temporally coherent keypoint detector and design efficient interframe predictive coding techniques for canonical patches, feature descriptors, and keypoint locations. In the proposed system, we strive to transmit each patch or its equivalent feature descriptor with as few bits as possible by modifying a previously transmitted patch or descriptor. Our solution enables server-based mobile augmented reality where a continuous stream of salient information, sufficient for image-based retrieval, and object localization, is sent at a bit-rate that is practical for today's wireless links and less than one-tenth of the bit-rate needed to stream the compressed video to the server.
Antibacterial activity of finafloxacin under different pH conditions against isogenic strains of Escherichia coli expressing combinations of defined mechanisms of fluoroquinolone resistance.

OBJECTIVES Finafloxacin is an investigational fluoroquinolone exhibiting broad-spectrum activity that is enhanced under slightly acidic conditions (pH 5.0-6.5). The impact of individual and combinations of chromosomal mutations (gyrA, parC and marR) and the plasmid-mediated fluoroquinolone resistance mechanisms QepA1, QnrA1, QnrB1, QnrS1 and AAC(6')-Ib-cr were investigated. METHODS The MICs of finafloxacin, compared with those of ciprofloxacin, levofloxacin and moxifloxacin, were determined at pH 5.8 and 7.2. RESULTS MICs of finafloxacin compared with other fluoroquinolones at pH 5.8 were lower by a factor of 2-256. MICs of finafloxacin were unaffected by QepA1. Moreover, finafloxacin appeared not to be a substrate for AAC(6')-Ib-cr. CONCLUSIONS Compared with ciprofloxacin, levofloxacin and moxifloxacin, finafloxacin shows higher activity especially at pH 5.8 against Escherichia coli mutants expressing known fluoroquinolone resistance determinants alone and in combinations.
Transjugular intrahepatic portosystemic stent-shunt and its effects on orthotopic liver transplantation

Background It has been reported that preoperative transjugular intrahepatic portosystemic stent-shunt (TIPSS) reduces peri-operative transfusion requirements during orthotopic liver transplant, and may result in fewer episodes of poor, early graft function by reducing portosystemic shunting, thus improving portal blood supply to the graft. Objective To test the hypotheses that TIPSS improves early graft function and reduces transfusion requirements. Methods A retrospective review of 82 liver transplant recipients between 1993 and 1999 was performed. The subgroups comprised 29 patients who had TIPSS prior to first orthotopic liver transplant and 53 matched controls without TIPSS. Results There was no significant difference in the early graft function in the two groups. The prothrombin time before an orthotopic liver transplant was independently predictive of initial poor function. Transfusion requirements and total operating times were similar for both groups, although transfusion requirements were greater in those patients where TIPSS led to technical difficulties during the operation (n = 6). The TIPSS patients required a longer hospital stay than the non-TIPSS patients (41 ± 8 vs 26 ± 4 days, P < 0.05). There were significantly more patients needing dialysis in the TIPSS group (41.3% vs 9.4%, P < 0.001). Pulmonary infection was less common in the TIPSS group (P < 0.05), with a trend to reduced wound infections. The 12 month patient and graft survival were similar in both groups. Serum albumin levels assessed before orthotopic liver transplant independently predicted 12 month graft survival. Conclusions TIPSS does not improve early graft function, nor reduce blood transfusion requirements perioperatively. The longer post-operative hospital stay in the TIPSS group is worthy of further study. TIPSS prior to transplantation, despite having the potential for technical operative complications, has no detrimental effects on patient and graft survival, and if required should be undertaken.
Posttraumatic Stress Symptoms and Work-Related Accomplishment as Predictors of General Health and Medical Utilization Among Special Operations Forces Personnel

Abstract Research has established clear links among posttraumatic stress disorder (PTSD), somatic symptoms, and general health among conventional force military personnel. It is possible that the same relationships exist among Special Operations Force (SOF) personnel, but there are very few, if any, studies that examine these relationships. This study investigated correlates of general health and medical visits among SOF personnel and found that the interaction of somatic and PTSD symptoms was associated with worse health and more frequent medical visits. Follow-up analyses indicated that the interaction of avoidance symptoms with somatic symptoms was significantly associated with worse health, whereas the interaction of emotional numbing with somatic symptoms significantly contributed to increased medical visits. In addition, the results suggest that a sense of accomplishment among SOF personnel may serve as a protective factor against poor health. The results suggest developing interactions among SOF personnel that promote a sense of achievement to ultimately improve the health of the force.
Mechanical, electrical and microstructural characterisation of multifunctional structural power composites

Multifunctional composites which can fulfil more than one role within a system have attracted considerable interest. This work focusses on structural supercapacitors which simultaneously carry mechanical load whilst storing/delivering electrical energy. Critical mechanical properties (in-plane shear and in-plane compression performance) of two monofunctional and four multifunctional materials were characterised, which gave an insight into the relationships between these properties, the microstructures and fracture processes. The reinforcements included baseline T300 fabric, which was then either grafted or sized with carbon nanotubes, whilst the baseline matrix was MTM57, which was blended with ionic liquid and lithium salt (two concentrations) to imbue multifunctionality. The resulting composites exhibited a high degree of matrix heterogeneity, with the ionic liquid phase preferentially forming at the fibres, resulting in poor matrix-dominated properties. However, fibre-dominated properties were not depressed. Thus, it was demonstrated that these materials can now offer weight savings over conventional monofunctional systems when under modest loading.
Transplacental induction of lymphomas in Swiss mice by carbendazim and sodium nitrite

Swiss mice at different stages of pregnancy were treated intragastrically with the pesticide Carbendazim (MBC., BCM, methyl‐2‐benzimidazole carbamate) together with sodium nitrite. Lymphomas developed in 33.3% of young mice whose mothers were treated in the first week of pregnancy, in 53.3 % of those whose mothers were treated during the second week, and in 38.8% of those born of mothers treated during the third week. Treatment during the whole period of pregnancy yielded on an average 70.0% malignancy in offspring. However, administration of Carbendazim by itself did not produce lymphomas in the first generation. In lymphomas induced by in vivo‐formed N‐nitroso compounds, A‐ and C‐type oncornavirus particles were observed with the electron microscope.
Nanostructuring surfaces with conjugated silica colloids deposited using silicon-based microcantilevers

In this paper, the assembly and stability of locally spotted spherical nanoparticles onto various substrates are studied. Arrays of silicon-based microcantilevers, combined with an automated three-stage spotter, are used to deposit picolitre droplets containing 300 nm diameter polyethylene glycol and 150 nm diameter amino conjugated silica nanospheres onto silicon, allylamine and acrylic acid surfaces. Matrices of colloid spots ranging from 10 to 100 µm in diameter have been successfully patterned. SEM characterizations of the nanoparticles’ geometry and spatial distribution within the spots were carried out, showing the colloid aggregation at the droplet’s rim and the selective stability of the printed patterns. The expected substrate functionalization was assessed by XPS characterizations of the nanoparticles’ surfaces. Finally, polyethylene glycol–SiO2 nanoparticle conjugates were used as masks during a selective reactive ion etching of the silicon substrate, and silicon nanopillars have been obtained. This work opens up possibilities of high spatial resolution nanopatterning with nanoparticle conjugates.
Antimicrobial prophylaxis for urinary tract infection in persons with spinal cord dysfunction.

Searching MEDLINE from 1966 to January 1998, and EMBASE from 1974 to January 1998, were searched using the following search terms: 'urinary tract', 'urinary tract infections', 'bacteriuria', 'paraplegia', 'quadriplegia', 'spinal cord injuries', 'multiple sclerosis', 'neurogenic bladder' and 'neuropathic bladder' (free text term). Case reports and studies of animals were excluded. CINAHL was also searched from 1982 to July 1998 using analogous terms. No language restrictions were applied in any search and 'grey' literature, such as letters and conference abstracts, was not excluded. Additional articles were identified by contacting experts and by reviewing the reference lists of articles obtained from the searches. The authors also queried experts about possible unpublished studies, but none were identified.
Early exit optimizations for additive machine learned ranking systems

Some commercial web search engines rely on sophisticated machine learning systems for ranking web documents. Due to very large collection sizes and tight constraints on query response times, online efficiency of these learning systems forms a bottleneck. An important problem in such systems is to speedup the ranking process without sacrificing much from the quality of results. In this paper, we propose optimization strategies that allow short-circuiting score computations in additive learning systems. The strategies are evaluated over a state-of-the-art machine learning system and a large, real-life query log, obtained from Yahoo! By the proposed strategies, we are able to speedup the score computations by more than four times with almost no loss in result quality.
A biodegradabilidade da blenda de poli(β-Hidroxibutirato-co-Valerato)/amido anfótero na presença de microrganismos

The increasing consumption of plastics has generated environmental problems because it takes more than a hundred years for a discarded polymer to degrade. The ideal plastic should present desirable industrial properties and be degradable within a satisfactory time period. Researches is conducted to plastics with good properties for packaging, but that are biodegradable when discarded to the environment. In this work we evaluated the biodegradation of the blend of the copolymer poly(hydroxybutyrate-hydroxyvalerate, PHB-HV, which is a natural, biodegradable and biocompatible thermoplastic, and of the starch amphiprotic, in the proportion of 75 and 25% m/m, respectively. The results were obtained through the Sturm test, a methodology for the evaluation of biodegradation in the presence of a mixed culture of Phanerochaete chrysosporium and Talaromyces wortmannii fungi. The results pointed to biodegradation of the blend as a function of the time, with the appearance of terminal carboxylic groups. In addition, a new crystalline symmetry was observed in the polymeric structure.
A Permeability Study of O2 and the Trace Amine p-Tyramine through Model Phosphatidylcholine Bilayers

We study here the permeability of the hydrophobic O2 molecule through a model DPPC bilayer at 323K and 350K, and of the trace amine p-tyramine through PC bilayers at 310K. The tyramine results are compared to previous experimental work at 298K. Nonequilibrium work methods were used in conjunction to simultaneously obtain both the potential of mean force (PMF) and the position dependent transmembrane diffusion coefficient, D(z), from the simulations. These in turn were used to calculate the permeability coefficient, P, through the inhomogeneous solubility-diffusion model. The results for O2 are consistent with previous simulations, and agree with experimentally measured P values for PC bilayers. A temperature dependence in the permeability of O2 through DPPC was obtained, with P decreasing at higher temperatures. Two relevant species of p-tyramine were simulated, from which the PMF and D(z) were calculated. The charged species had a large energetic barrier to crossing the bilayer of ~ 21 kcal/mol, while the uncharged, deprotonated species had a much lower barrier of ~ 7 kcal/mol. The effective in silico permeability for p-tyramine was calculated by applying three approximations, all of which gave nearly identical results (presented here as a function of the pKa). As the permeability value calculated from simulation was highly dependent on the pKa of the amine group, a further pKa study was performed that also varied the fraction of the uncharged and zwitterionic p-tyramine species. Using the experimental P value together with the simulated results, we were able to label the phenolic group as responsible for the pKa1 and the amine for the pKa2, that together represent all of the experimentally measured pKa values for p-tyramine. This agrees with older experimental results, in contrast to more recent work that has suggested there is a strong ambiguity in the pKa values.
Learning in Wubble World

Why do children master language so quickly and thoroughly, whereas gigabytes of text and enormously sophisticated learning algorithms produce at best shallow semantics in machines? Because children have help from competent speakers who relate language to what's happening in the child's environment. To facilitate the task of machine word learning, we developed a simulated environment, called "Wubble World," and populated it with entities called wubbles. Children interact with the wubbles using natural language, and act as teachers when the wubble needs help. This paper presents our word learning algorithms and provides some empirical results.