Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular analysis of the soluble butane monooxygenase from 'Pseudomonas butanovora'.

'Pseudomonas butanovora' is capable of growth with butane via the oxidation of butane to 1-butanol, which is catalysed by a soluble butane monooxygenase (sBMO). In vitro oxidation of ethylene (an alternative substrate for sBMO) was reconstituted in the soluble portion of cell extracts and was NADH-dependent. Butane monooxygenase was separated into three components which were obligately required for substrate oxidation. The N-terminal sequences of the peptides associated with butane monooxygenase led to the cloning and sequencing of the 5797 nucleotide bmo gene cluster. Comparisons of the deduced amino acid sequences with other multicomponent monooxygenases suggest that sBMO is a multimeric hydroxylase with 61, 45 and 19 kDa subunits encoded by bmoXYZ, a 40 kDa oxidoreductase encoded by bmoC, and a 15 kDa regulatory protein encoded by bmoB. A sixth structural gene (bmoD) encodes a 9.6 kDa protein with similarity exclusively to mmoD (orfY), a putative metal centre assembly protein of the soluble methane monooxygenases. Insertional inactivation of bmoX resulted in a mutant 'P. butanovora' strain incapable of growth with butane. A putative promoter element characteristic of promoters associated with sigma(54)-dependent transcription initiation was located upstream of the bmo genes. Expression of all six genes was detected in butane-induced cells. Butane monooxygenase from 'P. butanovora' aligns most closely with non-haem carboxylate-bridged diiron monooxygenases and, moreover, contains the characteristic iron-binding motif. The structural and mechanistic implications of the high sequence identity (up to 64%) between the peptides of butane monooxygenase and methane monooxygenases are discussed.
Effects of storage on efficacy of red cell transfusion: When is it not safe?

ObjectiveTo review the literature on red blood cell storage and its relationship to the efficacy of transfusion. ResultsWell-documented changes occur to the red blood cell product during ex vivo storage. These changes include a reduction in red blood cell deformability, altered red blood cell adhesiveness and aggregability, and a reduction in 2,3-diphosphoglycerate and ATP. Bioactive compounds with proinflammatory effects also accumulate in the storage medium. These changes reduce posttransfusion viability of red blood cells. The clinical effects beyond posttransfusion viability are uncertain, but a growing body of evidence suggests that the storage lesion may reduce tissue oxygen availability, have proinflammatory and immunomodulatory effects, and influence morbidity and mortality. There are no published randomized, control trials examining the effect of storage duration on morbidity and mortality. Leukoreduction improves the quality of stored red blood cell products and in some studies has been shown to reduce morbidity and mortality. ConclusionAlthough storage duration influences the quality of red blood cell product, there is currently insufficient evidence to advocate shorter storage periods for red blood cell products.
Ciliary muscle morphologic changes with accommodation and axial ametropia.

Sheppard et al. studied ciliary muscle morphology during accommodation. However, in the Methods section, they specified that the morphologic measurements were judged from the ciliary muscle–sclera boundary to the pigmented ciliary epithelium, which anatomically is the ciliary body. The ciliary muscle is only part of the ciliary body, which also comprises connective tissue, a complex vascular network, and neuronal tissue—components that are clearly defined separately in any histologic preparation. Imaging methods have limited tissuespecific ability, as can be seen in a paper by Silverman et al. The distinction between the ciliary muscle and the ciliary body is not a semantic issue. Functionally, the ciliary muscle counteracts with the connective tissue around it, and the net effect defines the ciliary body’s morphologic changes, the zonular tension, and the crystalline lens position and curvature. The paper therefore provides data on the morphologic changes in the ciliary body during accommodation, whereas the changes in its subcomponents cannot be analyzed on the basis of the acquired data. Joshua Ben-nun
Randomized phase II study of two gemcitabine schedules for patients with impaired performance status (Karnofsky performance status </= 70) and advanced non-small-cell lung cancer.

PURPOSE This randomized phase II study compared two treatment schedules of gemcitabine in patients with non-small-cell lung cancer (NSCLC) and impaired Karnofsky performance status (KP). Primary objectives were to record changes from baseline KP and to assess symptom palliation. Secondary objectives were overall survival, tumor response, and toxicity. PATIENTS AND METHODS Patients with stage IIIb and IV NSCLC and KP </= 70 were randomly assigned to receive gemcitabine 1,000 mg/m(2) on days 1, 8, and 15 of each 28-day cycle (3w4) or gemcitabine 1,500 mg/m(2) on days 1 and 8 of each 21-day cycle (2w3), both for up to six cycles. KP, toxicity, and SS14 lung cancer specific questions were recorded before each cycle of treatment. Response was evaluated 4 weeks after the last cycle. RESULTS One hundred seventy-four patients were enrolled. There was significant early attrition due to disease progression; only 61.5% of patients were alive at 2 months. There was a significant improvement in KP from baseline to pre-cycle 3 in both arms, with a trend in favor of the 3w4 regimen for duration and faster onset of improvement. Eight of the 17 quality-of-life (QOL) variables assessed showed an improvement of more than 10% between baseline and the start of the third cycle of treatment. Response rate, survival, and duration were similar in both arms. CONCLUSION There was no significant difference between the two schedules examined in terms of improvement in KP or QOL, but there seemed to be a trend in favor of the 3w4 schedule.
Multiple intracellular signaling pathways of the neuropeptide substance P receptor

The rat substance P (SP) receptor cDNA has been transfected into cultured rat KNRK cells, and a stable cell line expressing functional SP receptors established. Upon stimulation with SP, these cells responded by simultaneously activating two signaling pathways: the mobilization of intracellular Ca2+ and the raising of cyclic adenosine triphosphate (cAMP) levels. Both Ca2+ and cAMP responses were elicited in a similar dose‐dependent manner with half maximal concentrations of approximately 5 × 10−10 M. Following ionomycin treatment SP‐dependent Ca2+ responses were abolished, whereas cAMP responses were preserved. Forskolin eliminated the SP‐dependent cAMP elevation, however, the SP‐induced Ca2+ mobilization remained unchanged. Furthermore, treatment with phorbol esters had no significant effect on either of the two SP‐induced responses. Thus it appears that the SP receptor is capable of independently activating Ca2+ mobilization and cAMP pathways. These results may provide new insights for further understanding the diverse activities of SP in various systems in vitro and in vivo. © 1992 Wiley‐Liss, Inc.
MADS-box transcription factors adopt alternative mechanisms for bending DNA.

Transcription factor-induced DNA bending is important in determining local promoter architecture and it is thought to be a key determinant of their function. The human MADS-box transcription factors serum response factor and MEF2A exhibit different propensities to bend their binding sites. Here, we have investigated the ability of several family members from different species to bend DNA and the molecular mechanisms underlying this process. Differential DNA bending is observed in yeast and plant MADS-box proteins. Like MEF2A, the yeast proteins Rlm1 and Smp1 exhibit low DNA bending propensities. A comparison of serum response factor and SQUA reveals that the basic mechanisms of DNA bending appear to be conserved between these proteins, although several key differences do exist. In contrast to serum response factor, SQUA bends DNA in a DNA sequence-dependent manner. In both proteins, protein-DNA contacts made between residues in the beta-loop and the N-terminal end of the recognition helices in the MADS-box are the major determinants of DNA bending. However, although residues which are involved in DNA bending are predicted to be located in similar positions in their tertiary structures, different residues dictate bending by each protein. Further complexities are uncovered in the links between the DNA bending propensity and the binding specificity. In combination with structural studies, our results provide a model to explain how differential bending by MADS-box proteins is achieved at the molecular level and provide insights into how this might affect their biological function.
Regional grey and white matter volumetric changes in myalgic encephalomyelitis (chronic fatigue syndrome): a voxel-based morphometry 3 T MRI study.

OBJECTIVE It is not established whether myalgic encephalomyelitis/chronic fatigue syndrome (CFS) is associated with structural brain changes. The aim of this study was to investigate this by conducting the largest voxel-based morphometry study to date in CFS. METHODS High-resolution structural 3 T cerebral MRI scanning was carried out in 26 patients with CFS and 26 age- and gender-matched healthy volunteers. Voxel-wise generalised linear modelling was applied to the processed MR data using permutation-based non-parametric testing, forming clusters at t>2.3 and testing clusters for significance at p<0.05, corrected for multiple comparisons across space. RESULTS Significant voxels (p<0.05, corrected for multiple comparisons) depicting reduced grey matter volume in the CFS group were noted in the occipital lobes (right and left occipital poles; left lateral occipital cortex, superior division; and left supracalcrine cortex), the right angular gyrus and the posterior division of the left parahippocampal gyrus. Significant voxels (p<0.05, corrected for multiple comparisons) depicting reduced white matter volume in the CFS group were also noted in the left occipital lobe. CONCLUSION These data support the hypothesis that significant neuroanatomical changes occur in CFS, and are consistent with the complaint of impaired memory that is common in this illness; they also suggest that subtle abnormalities in visual processing, and discrepancies between intended actions and consequent movements, may occur in CFS.
An agent-based modeling for housing prices with bounded rationality

This study proposes an agent-based model to investigate major stakeholders’ behaviors in the housing market. The proposed model mimics the heterogeneous behaviors of individual buyers and sellers in a housing market considering bounded rationality. The simulation results of case study in Shanghai are robust and reproduce stylized facts including as volatility clustering, absence of autocorrelations, heavy tail, loss asymmetry, and aggregational gaussianity on the absolute return.
Analytical performance specifications for changes in assay bias (Δbias) for data with logarithmic distributions as assessed by effects on reference change values

Background The distributions of within-subject biological variation are usually described as coefficients of variation, as are analytical performance specifications for bias, imprecision and other characteristics. Estimation of specifications required for reference change values is traditionally done using relationship between the batch-related changes during routine performance, described as Δbias, and the coefficients of variation for analytical imprecision (CVA): the original theory is based on standard deviations or coefficients of variation calculated as if distributions were Gaussian. Methods The distribution of between-subject biological variation can generally be described as log-Gaussian. Moreover, recent analyses of within-subject biological variation suggest that many measurands have log-Gaussian distributions. In consequence, we generated a model for the estimation of analytical performance specifications for reference change value, with combination of Δbias and CVA based on log-Gaussian distributions of CVI as natural logarithms. The model was tested using plasma prolactin and glucose as examples. Results Analytical performance specifications for reference change value generated using the new model based on log-Gaussian distributions were practically identical with the traditional model based on Gaussian distributions. Conclusion The traditional and simple to apply model used to generate analytical performance specifications for reference change value, based on the use of coefficients of variation and assuming Gaussian distributions for both CVI and CVA, is generally useful.
Maladaptive enlargement of the brachial artery in severe obesity is reversed with weight loss

Maladaptive peripheral arterial remodeling, which leads to large arteries with low shear stress, may be associated with increased cardiovascular risk. We tested the hypothesis that arterial enlargement in severe obesity represents maladaptive remodeling and that weight reduction would reverse this process. We evaluated brachial arterial diameter and flow using ultrasound in 244 severely obese patients (age 44 ± 11 years, 80% female, body mass index (BMI) 46 ± 9 kg/m) at baseline and in a group of 67 subjects who experienced weight loss at 1 year. Higher BMI was associated with larger brachial artery diameter (p = 0.01) and lower shear stress (p = 0.008), indicating maladaptive remodeling. Significant (≥ 10%) weight reduction was associated with a decrease in resting arterial diameter (—0.19 ± 0.47 mm, p = 0.02) along with a trend toward increased shear stress. Decreased systemic inflammation was associated with weight loss-induced reverse remodeling of the brachial artery. Our findings demonstrate the presence of maladaptive arterial remodeling in advanced obesity that was ameliorated by significant weight loss.
β-Amyloid Causes Depletion of Synaptic Vesicles Leading to Neurotransmission Failure*

Alzheimer disease is a progressive neurodegenerative brain disorder that leads to major debilitating cognitive deficits. It is believed that the alterations capable of causing brain circuitry dysfunctions have a slow onset and that the full blown disease may take several years to develop. Therefore, it is important to understand the early, asymptomatic, and possible reversible states of the disease with the aim of proposing preventive and disease-modifying therapeutic strategies. It is largely unknown how amyloid β-peptide (Aβ), a principal agent in Alzheimer disease, affects synapses in brain neurons. In this study, we found that similar to other pore-forming neurotoxins, Aβ induced a rapid increase in intracellular calcium and miniature currents, indicating an enhancement in vesicular transmitter release. Significantly, blockade of these effects by low extracellular calcium and a peptide known to act as an inhibitor of the Aβ-induced pore prevented the delayed failure, indicating that Aβ blocks neurotransmission by causing vesicular depletion. This new mechanism for Aβ synaptic toxicity should provide an alternative pathway to search for small molecules that can antagonize these effects of Aβ.
Explaining tourism competitiveness in small and medium destinations: the Italian case

The aim of the paper is to provide evidence of causal relationships between attributes of competitiveness and tourism destination competitiveness (TDC) in small and medium destinations (SMDs). A model of destination competitiveness has been developed and integrated with attributes of competitiveness, and then applied to a unique dataset of 370 outstanding Italian SMDs. A principal component analysis and a partial least square regression have been performed to test the model. The use of economic and financial measures as dependent variables, in addition to standard measures of destination performance, allows to investigate the concept of TDC from a wider economic point of view. Empirical evidence reveals that the multidimensionality and relativity of the concept of TDC influence the relationships among predictors and dependent variables. Managerial capabilities, quality of services, and policies aimed at fostering local empowerment are found to be key determinants of the competitiveness of Italian outstanding SMDs.
[Associations between hepatitis B virus x gene mutations and hepatocellular carcinoma].

OBJECTIVE To investigate the association of mutations in the hepatitis B virus (HBV) X gene (HBX, encoding the HBx protein) and development of hepatocellular carcinoma (HCC). METHODS Forty-four patients with HBV-related HCC participated in the study, along with 76 patients with chronic HBV infection who assessed as controls. All patients had serum HBV DNA levels that were higher than 10(3) copies/ml. Extracted HBV DNA was subjected to nested PCR to amplify the HBX gene, followed by direct sequencing. All sequencing data were compared to the consensus HBV sequence to identify mutations. The sequencing data were analyzed by Chromas and SeqMan software. RESULTS Mutations of G1467C, G/C1479A, C1485T and C1653T in the X region were found, but did not show any significant difference in occurrence between the HCC group and the chronic HBV infection group (P>0.05). The T1674C mutation in the X region, however, occurred more frequently in the HCC group (29.27% vs.6.67%, P<0.05). Prevalence of the T1753C mutation and the A1762T/G1764A double mutation in the BCP region was significantly higher in the HCC group than in the chronic HBV infection group (P<0.05) and in the group of patients with hepatitis B e antigen (HBeAg)-negative status compared to the patients with HBeAg-positive status (P<0.05). CONCLUSION Incidence of the T1674C mutation in the X region and of the T1753C mutation and the A1762T/G1764A double mutation in the BCP region was higher for patients with HBV-related HCC; the T1753C mutation and the A1762T/G1764A double mutation may inhibit the formation of HBeAg.
Expression of Receptors for Complement Anaphylatoxins C3a and C5a Following Permanent Focal Cerebral Ischemia in the Mouse

In the present study, we have examined the expression of anaphylatoxin C3a and C5a receptors (C3aR and C5aR) at the mRNA and protein levels in ischemic brain tissues following permanent middle cerebral artery (MCA) occlusion in the mouse. C3aR and C5aR mRNAs were both detected by semiquantitative reverse transcription and polymerase chain reaction (RT-PCR) and the cellular distribution of each receptor was analyzed by immunohistochemistry. Significant increases in the expression of C3aR and C5aR mRNAs in the ischemic cortex were observed; the expression of both reached a peak at 2 days after MCA occlusion (4.3- and 3.4-fold increases, respectively, compared with nonoperated control cortical samples; P < 0.00625 with Bonferroni's correction, n = 3). C3aR and C5aR stainings were found constitutively on neurons and astrocytes. In ischemic tissues, we observed that C3aR and C5aR were expressed de novo on endothelial cells of blood vessels, at 6 h and 2 days after MCA occlusion, respectively. C3aR and C5aR immunostaining was increased in macrophage-like cells and reactive astrocytes 7 days postocclusion. C3a and C5a may play an important role in promoting inflammatory and/or repair processes in the ischemic brain by regulating glial cell activation and chemotaxis.
Adrenal function in pediatric critical illness*

Objectives Adrenal dysfunction has been documented in critically ill adult populations and in children with septic shock and may have serious consequences if undiagnosed. However, there is no information available on adrenal function in critically ill children with various underlying conditions. Design A prospective, descriptive study was carried out to investigate the occurrence of adrenal dysfunction in pediatric critical illness. Patients Thirteen patients were consecutively recruited from a pediatric critical care unit with Pediatric Risk of Mortality Scores (PRISM; illness severity scores) ≥10 and hemodynamic instability as defined by the need for inotropes and/or >20 mL/kg fluid in a 24-hr period. Interventions Baseline cortisol and adrenocorticotropic hormone (ACTH) levels were measured followed by post-ACTH stimulation test cortisol levels to determine adrenal reserve. Measurements and Main Results Baseline cortisol levels ranged from 0.10 to 37.4 &mgr;g/dL (mean, 12.2 ± 9.6). Adrenal dysfunction as defined by a baseline cortisol level of <7 &mgr;g/dL (am cortisol) or a post-ACTH stimulation level of <18 &mgr;g/dL was observed in four of the 13 patients (31%; 95% confidence interval, 5.7%,55.9%). All three of the patients with baseline cortisol levels of <7 &mgr;g/dL had low-normal ACTH levels. There was no difference in baseline PRISM scores (14.7 ± 4.11, 12.7 ± 2.65;p = .37) or admitting diagnoses for those with and without adrenal dysfunction. Conclusions We conclude that some critically ill children do no mount adequate basal cortisol levels in the face of severe physiologic stress but do respond to external ACTH stimulation to better delineate the hypothalamic-pituitary-adrenal axis in critically ill children and to determine the clinical consequences of these biochemical abnormalities.
Age‐Dependent Impairment of Mitochondrial Function in Primate Brain

Abstract: It has been hypothesized that some of the functional impairments associated with aging are the result of increasing oxidative damage to mitochondrial DNA that produces defects in oxidative phosphorylation. To test this hypothesis, we examined the enzymes that catalyze oxidative phosphorylation in crude mitochondrial preparations from frontoparietal cortex of 20 rhesus monkeys (5‐34 years old). Samples were assayed for complex I, complex II‐III, complex IV, complex V, and citrate synthase activities. When enzyme activities were corrected for citrate synthase activities (to account for variable degrees of mitochondrial enrichment), linear regression analysis demonstrated a significant negative correlation of the activities of complex I (p < 0.002) and complex IV (p < 0.03) with age but no significant change in complex II‐III or complex V activities. Relative to animals 6.9 ± 0.9 years old (n = 7), the citrate synthase‐corrected activity of complex I was reduced by 17% in animals 22.5 ± 0.9 years old (n = 6) (p < 0.05) and by 22% in animals 30.7 ± 0.9 years old (n = 7) (p < 0.01). Similar age‐related reductions in the activities of complexes I and IV were obtained when enzyme activities were corrected for complex II‐III activity. These findings show an age‐associated progressive impairment of mitochondrial complex I and complex IV activities in cerebral cortices of primates.