Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of dapB, a gene required by Pseudomonas syringae pv. tabaci BR2.024 for lysine and tabtoxinine-beta-lactam biosynthesis

The dapB gene, which encodes L-2,3-dihydrodipicolinate reductase, the second enzyme of the lysine branch of the aspartic amino acid family, was cloned and sequenced from a tabtoxin-producing bacterium, Pseudomonas syringae pv. tabaci BR2.024. The deduced amino acid sequence shared 60 to 90% identity to known dapB gene products from gram-negative bacteria and 19 to 21% identity to the dapB products from gram-positive bacteria. The consensus sequence for the NAD(P)H binding site [(V/I)(A/G)(V/I)XGXXGXXG)] and the proposed substrate binding site (HHRHK) were conserved in the polypeptide. A BR2.024 dapB mutant is a diaminopimelate auxotroph and tabtoxin negative. The addition of a mixture of L-,L-, D,D-, and meso-diaminopimelate to defined media restored growth but not tabtoxin production. Cloned DNA fragments containing the parental dapB gene restored the ability to grow in defined media and tabtoxin production to the dapB mutant. These results indicate that the dapB gene is required for both lysine and tabtoxin biosynthesis, thus providing the first genetic evidence that the biosynthesis of tabtoxin proceeds in part along the lysine biosynthetic pathway. These data also suggest that L-2,3,4,5-tetrahydrodipicolinate is a common intermediate for both lysine and tabtoxin biosynthesis.
What Causes Financial Crisis in Asian Countries?

In this paper, we investigate the indicators of financial crisis in Asian countries, focusing more on the impact of corporate governance. Unlike the previous studies such as Johnson et al. (2000) and Acemoglu et al. (2003) that use some fixed measures of corporate governance based on the law in force in a specific year—such as the anti-director right index (ADRI) or the anti-self dealing index (ASDI)—we employ the annual Worldwide Governance Index (WGIs) and the Quality of Governance Index. The regression results, which use the data of 19 Asian countries from 1996 to 2015, and control for country fixed effect and the business cycle, show that the macroeconomic factors appear to have no effect, or a minor effect, on currency depreciation. However, better corporate governance reduces the decline in currency value.
Obesity, acute kidney injury and mortality in patients with sepsis: a cohort analysis

Abstract Although the prognostic effect of obesity has been studied in critically ill patients its impact on outcomes of septic patients and its role as a risk factor for acute kidney injury (AKI) is not consensual. We aimed to analyze the impact of obesity on the occurrence of AKI and on in-hospital mortality in a cohort of critically ill septic patients. This study is retrospective including 456 adult patients with sepsis admitted to the Division of Intensive Medicine of the Centro Hospitalar Lisboa Norte (Lisbon, Portugal) between January 2008 and December 2014. Obesity was defined as a body mass index of 30 kg/m2 or higher. The Kidney Disease Improving Global Outcomes classification was used to diagnose and classify patients developing AKI. AKI occurred in 87.5% of patients (19.5% with stage 1, 22.6% with stage 2 and 45.4% with stage 3). Obese patients developed AKI more frequently than non-obese patients (92.8% versus 85.5%, p = .035; unadjusted OR 2.2 (95% CI: 1.04–4.6), p = . 039; adjusted OR 2.31 (95% CI: 1.07–5.02), p = . 034). The percentage of obese patients, however, did not differ between AKI stages (stage 1, 25.1%; stage 2, 28.6%; stage 3, 15.4%; p = .145). There was no association between obesity and mortality (p = .739). Of note, when comparing AKI patients with or without obesity in terms of in-hospital mortality there were also no significant differences between those groups (38.4% versus 38.4%, p = .998). Obesity was associated with the occurrence of AKI in critically ill patients with sepsis; however, it was not associated with in-hospital mortality.
A novel mean-shift architecture for scalable multiprocessor implementation

Organizing data into its natural grouping based on intrinsic characteristics is the most sensible thing to do with unlabeled data. Mean shift is a non-parametric mode seeking algorithm widely used for data clustering, image segmentation and object tracking, but its use in real time applications is limited because of its high computational cost. In this paper we propose a hybrid, sequentially unfolded, model for the implementation of mean shift clustering algorithm targeting Hardware Platforms. The proposed model uses multiple processors working in parallel on independent data allowing faster convergence of the algorithm. The model also supports scalability with respect to total number of working processors. Experimentation has yielded that computational cost decreases exponentially in each iteration. The proposed model can be implemented on any hardware which can support parallel architecture. Finally, it is also shown that hardware implementation will give same results as its software implementation.
Self-mutilation in personality disorders: psychological and biological correlates.

OBJECTIVE The goal of this study was to determine whether self-mutilators with personality disorders differ from nonmutilators with personality disorders in impulsivity, aggression, and other psychopathology and whether serotonergic dysfunction contributes to self-mutilation. METHOD Twenty-six self-mutilators with personality disorders were matched to 26 control subjects with personality disorders for gender, age, education, axis I diagnosis of affective disorder, and axis II diagnosis of personality disorder. Numerous indexes of psychopathology as well as CSF 5-hydroxyindoleacetic acid (5-HIAA) levels and platelet imipramine binding sites (Bmax) and affinity (Kd) were determined. RESULTS Self-mutilators had significantly more severe character pathology, had greater lifetime aggression, and were more antisocial than the control subjects. The self-mutilators scored higher on the Hamilton Rating Scale for Depression but not on the Beck Depression Inventory or the Beck Hopelessness Scale. The two groups did not differ on the Buss-Durkee Hostility and Guilt Inventory or on the Sensation Seeking Scale. The degree of self-mutilation was significantly correlated with impulsivity, chronic anger, and somatic anxiety. Both self-mutilation and impulsivity showed significant negative correlations with Bmax, although the two groups did not differ in CSF 5-HIAA levels or in platelet imipramine binding. CONCLUSIONS The results demonstrate the contribution of severe character pathology, aggression, impulsivity, anxiety, and anger to self-mutilation and provide preliminary support for the hypothesis of underlying serotonergic dysfunction facilitating self-mutilation.
Meningeal transient receptor potential channel M8 activation causes cutaneous facial and hindpaw allodynia in a preclinical rodent model of headache

Background Migraine headache is a neurological disorder affecting millions worldwide. However, little is known about the mechanisms contributing to migraine. Recent genome-wide association studies have found single nucleotide polymorphisms in the gene encoding transient receptor potential channel M8. Transient receptor potential channel M8 is generally known as a cold receptor but it has been implicated in pain signaling and may play a role in migraine pain. Methods In order to investigate whether transient receptor potential channel M8 may contribute to the pain of migraine, the transient receptor potential channel M8 activator icilin was applied to the dura mater using a rat behavioral model of headache. Cutaneous allodynia was measured for 5 hours using Von Frey filaments. Results : Dural application of icilin produced cutaneous facial and hind paw allodynia that was attenuated by systemic pretreatment with the transient receptor potential channel M8-selective antagonist AMG1161 (10 mg/kg p.o.). Further, the anti-migraine agent sumatriptan (0.6 mg/kg s.c.) or the non-selective NOS inhibitor L-NAME (20 mg/kg i.p.) also attenuated allodynia when given as a pretreatment. Conclusions These data indicate that transient receptor potential channel M8 activation in the meninges produces behaviors in rats that are consistent with migraine and that are sensitive to pharmacological mechanisms known to have efficacy for migraine in humans. The findings suggest that activation of meningeal transient receptor potential channel M8 may contribute to the pain of migraine.
Oil Bodies and Oleosins in Physcomitrella Possess Characteristics Representative of Early Trends in Evolution1[W][OA]

Searches of sequenced genomes of diverse organisms revealed that the moss Physcomitrella patens is the most primitive organism possessing oleosin genes. Microscopy examination of Physcomitrella revealed that oil bodies (OBs) were abundant in the photosynthetic vegetative gametophyte and the reproductive spore. Chromatography illustrated the neutral lipids in OBs isolated from the gametophyte to be largely steryl esters and triacylglycerols, and SDS-PAGE showed the major proteins to be oleosins. Reverse transcription-PCR revealed the expression of all three oleosin genes to be tissue specific. This tissue specificity was greatly altered via alternative splicing, a control mechanism of oleosin gene expression unknown in higher plants. During the production of sex organs at the tips of gametophyte branches, the number of OBs in the top gametophyte tissue decreased concomitant with increases in the number of peroxisomes and level of transcripts encoding the glyoxylate cycle enzymes; thus, the OBs are food reserves for gluconeogenesis. In spores during germination, peroxisomes adjacent to OBs, along with transcripts encoding the glyoxylate cycle enzymes, appeared; thus, the spore OBs are food reserves for gluconeogenesis and equivalent to seed OBs. The one-cell-layer gametophyte could be observed easily with confocal microscopy for the subcellular OBs and other structures. Transient expression of various gene constructs transformed into gametophyte cells revealed that all OBs were linked to the endoplasmic reticulum (ER), that oleosins were synthesized in extended regions of the ER, and that two different oleosins were colocated in all OBs.
Addressing the "problem" of temporal correlations in MVPA analysis

The use of multivariate pattern analysis (MVPA) has grown substantially over the past few years. Many studies using MVPA estimate the response of individual trial activity and perform hypothesis testing using a non-parametric approach. Here we show that the default auto regression model of order 1 used for temporal whitening of BOLD data is problematic in that it leads to biased permutation tests. We show that the correlation of activity estimates across trials can cause extreme bias in non-parametric hypothesis testing so that the proportion of type I or type II errors are inflated. Crucially for MVPA, this inflation increases with sphere size. The error magnitude is such that in our data set, strong univariate effects are completely missed. By whitening the data with a more general auto regression (AR) model, one can correct the bias in permutation testing for better signal detection. Applying higher order AR models is already implemented in many neuroimaging software packages as a non-default option. The use of more aggressive temporal whitening may also prove crucial for valid MVPA inference in fast event related designs.
Cluster analysis of diffusion tensor magnetic resonance images in human head injury.

OBJECTIVE Issues surrounding the nature of the edema associated with traumatic brain injury in humans, and its evolution in the acute phase, remain unresolved. This study aimed to characterize the topographical nature of the pathophysiological changes in human traumatic brain injury with diffusion tensor magnetic resonance imaging. METHODS Multislice diffusion-weighted magnetic resonance imaging data were acquired from five patients undergoing elective ventilation for management of traumatic focal contusion or hematomas. The diffusion tensor and the T2-weighted intensity were then computed for every voxel in the image data set for each patient. The topographical distribution of abnormalities in the trace of the diffusion tensor and T2-weighted images were characterized by cluster analysis. RESULTS In four patients with technically satisfactory data, a narrow band of tissue was observed in the periphery of focal lesions, which was characterized by selective reduction in the trace of the diffusion tensor, without any associated increase in the T2-weighted signal intensity. CONCLUSION This change is interpreted as indicating either a partial redistribution of water from the extra- to intracellular compartment, or a reduction in the diffusivity of water in the intracellular or cytosolic environment. These diffusion and T2-weighted characteristics are also found in early ischemic change, hence, such regions may represent potentially salvageable tissue at risk of permanent damage. The study illustrates the advantage of using information contained within the diffusion tensor in addition to more conventional imaging sequences.
Gains from Trade with Variable Trade Elasticities

We measure gains from trade in multisector economies with nonhomothetic preferences where changes in trade costs generate reallocation of expenditure across sectors. We show how to measure the trade elasticity and how it relates to welfare. In this environment, the trade elasticity now varies both across countries and with levels of trade costs. In an application, we find that the trade elasticity varies substantially across countries and that the gains from moving from autarky to observed trade are on average between 24% and 28% greater than in a model where the trade elasticity is constant.
Whole sediment toxicity identification evaluation tools for pyrethroid insecticides: III. Temperature manipulation

Since the toxicity of pyrethroid insecticides is known to increase at low temperatures, the use of temperature manipulation was explored as a whole‐sediment toxicity identification evaluation (TIE) tool to help identify sediment samples in which pyrethroid insecticides are responsible for observed toxicity. The amphipod Hyalella azteca is commonly used for toxicity testing of sediments at a 23°C test temperature. However, a temperature reduction to 18°C doubled the toxicity of pyrethroids, and a further reduction to 13°C tripled their toxicity. A similar response, though less dramatic, was found for 1,1‐bis(p‐chlorophenyl)‐2,2,2‐trichloroethane (DDT), and dissimilar temperature responses were seen for cadmium and the insecticide chlorpyrifos. Tests with field‐collected sediments containing pyrethroids and/or chlorpyrifos showed the expected thermal dependency in nearly all instances. The inverse relationship between temperature and toxicity provides a simple approach to help establish when pyrethroids are the principal toxicant in a sediment sample that could be used as a supplemental tool in concert with chemical analysis or other TIE manipulations. The phenomenon appears to be, in part, a consequence of a reduced ability to biotransform the toxic parent compound at cooler temperatures. The strong dependence of pyrethroid toxicity on temperature has important ramifications for predicting their environmental effects, and the standard test temperature of 23°C dramatically underestimates risk to resident fauna during the cooler months.
Age affects the adjustment of cognitive control after a conflict: evidence from the bivalency effect

Age affects cognitive control. When facing a conflict, older adults are less able to activate goal-relevant information and inhibit irrelevant information. However, cognitive control also affects the events after a conflict. The purpose of this study was to determine whether age affects the adjustment of cognitive control following a conflict. To this end, we investigated the bivalency effect, that is, the performance slowing occurring after the conflict induced by bivalent stimuli (i.e., stimuli with features for two tasks). In two experiments, we tested young adults (aged 20–30) and older adults (aged 65–85) in a paradigm requiring alternations between three tasks, with bivalent stimuli occasionally occurring on one task. The young adults showed a slowing for all trials following bivalent stimuli. This indicates a widespread and long-lasting bivalency effect, replicating previous findings. In contrast, the older adults showed a more specific and shorter-lived slowing. Thus, age affects the adjustment of cognitive control following a conflict.
Mucoadhesive liposomes as ocular delivery system: physical, microbiological, and in vivo assessment

Background: Mucoadhesive drug delivery is a promising strategy to overcome ocular biopharmaceutical constraints. Objective and methods: Ciprofloxacin HCl-loaded reverse phase evaporation liposomes were coated with different concentrations and molecular weights of mucoadhesive biocompatible chitosan polymer to form chitosomes. This colloidal mucoadhesive system was evaluated in vitro and in vivo with respect to deliver the antibiotic to ocular surface. Results and conclusion: The results obtained pointed out that liposome coating process resulted in entrapment efficiency reduction and higher chitosan concentration, and molecular weight showed a more pronounced effect. No morphological differences between coated and uncoated liposomes were observed. Diffusion was the drug release mechanism from chitosomes. Concerning rheological behavior, pseudoplastic flow was characteristic to the prepared chitosomal dispersions. In addition, chitosan coating improved the ocular permeation of ciprofloxacin HCl. Microbiologically; this formulated system enhanced antimicrobial activity of ciprofloxacin HCl against both Gram-positive and Gram-negative bacteria. Moreover, this mucoadhesive system was able to inhibit the growth of Pseudomonas aeruginosa in rabbits' eyes for 24 hours when compared to the marketed preparation. In vivo bacterial conjunctivitis model elucidated that symptoms were controlled by the prolonged release formulation such as that done by the marketed product.
Modeling the lift DC-DC converter in the state space discrete time

The lift technique has been widely described in the literature by Luo et al. They focus on the steady state operation of the power cells mainly. On the other side, a complete dynamic characterisation is missing up to now. This paper provides the dynamic models of the lift power cells and converters. Capacitive switching characterizes their operation and modeling can be obtained with high accuracy adopting the same procedures that are well suited for describing the dynamic behaviours of other switched capacitor circuits, f.i. the Cockcroft-Walton multipliers. The approach is the state space discrete time protocol with some additional tricks for the precise evaluation of the sampled data values and of the matrices A, B, C and D. The paper describes how to derive the coefficients of the state space matrices of the Luo lift converter and makes reference to a software tool for the automatic analysis. The transfer function matrix of the power cell provides six transfer functions that are plotted versus frequency. After assigning a suitable feedback network, the converter is characterized by four closed loop transfer functions. Forecasts of the frequency responses are compared with experimental results
PART OF A SPECIAL ISSUE ON FUNCTIONAL -STRUCTURAL PLANT MODELLING Quantitative assessment of automatic reconstructions of branching systems obtained from laser scanning

† Background and Aims Automatic acquisition of plant architecture is a major challenge for the construction of quantitative models of plant development. Recently, 3-D laser scanners have made it possible to acquire 3-D images representing a sampling of an object’s surface. A number of specific methods have been proposed to reconstruct plausible branching structures from this new type of data, but critical questions remain regarding their suitability and accuracy before they can be fully exploited for use in biological applications. † Methods In this paper, an evaluation framework to assess the accuracy of tree reconstructions is presented. The use of this framework is illustrated on a selection of laser scans of trees. Scanned data were manipulated by experienced researchers to produce reference tree reconstructions against which comparisons could be made. The evaluation framework is given two tree structures and compares both their elements and their topological organization. Similar elements are identified based on geometric criteria using an optimization algorithm. The organization of these elements is then compared and their similarity quantified. From these analyses, two indices of geometrical and structural similarities are defined, and the automatic reconstructions can thus be compared with the reference structures in order to assess their accuracy. † Key Results The evaluation framework that was developed was successful at capturing the variation in similarities between two structures as different levels of noise were introduced. The framework was used to compare three different reconstruction methods taken from the literature, and allowed sensitive parameters of each one to be determined. The framework was also generalized for the evaluation of root reconstruction from 2-D images and demonstrated its sensitivity to higher architectural complexity of structure which was not detected with a global evaluation criterion. † Conclusions The evaluation framework presented quantifies geometric and structural similarities between two structures. It can be applied to the characterization and comparison of automatic reconstructions of plant structures from laser scanner data and 2-D images. As such, it can be used as a reference test for comparing and assessing reconstruction procedures.
Increased Cyclooxygenase-2 Expression in Duodenal Compared with Colonic Tissues in Familial Adenomatous Polyposis and Relationship to the −765G → C COX-2 Polymorphism

Background: Colorectal cancers arising in patients with familial adenomatous polyposis (FAP) can be largely prevented by polyp surveillance and prophylactic colectomy. As a result, duodenal adenocarcinoma has become a leading cause of death in patients with FAP. Cyclooxygenase 2 (COX-2) inhibition is effective against colorectal polyposis in FAP, but is less effective in treating duodenal polyps. We compared the expression of COX-2 in duodenal and colorectal adenomas from patients with FAP and from patients with sporadic neoplasms and correlated expression to a COX-2 promoter polymorphism (−765G/→C) that is reported to influence COX-2 expression. Methods: The study population included 36 FAP patients with colonic adenomas, 22 FAP patients with duodenal adenomas, 22 patients with sporadic duodenal adenomas, and 17 patients with sporadic duodenal adenocarcinoma. Neoplastic and corresponding normal tissue COX-2 expressions were determined using immunohistochemistry on tissue microarrays. The prevalence and ethnic distribution of a polymorphism in the COX-2 promoter that influences COX-2 expression (−765G → C) were determined in DNA from 274 individuals by real-time quantitative PCR. Results: Among patients with FAP, histologically normal duodenal mucosa showed higher COX-2 expression than normal colonic mucosa (P < 0.02), and duodenal adenomas had higher COX-2 expression than colonic adenomas (P ≤ 0.01). In addition, the normal duodenum of patients with FAP showed higher COX-2 expression than the normal duodenal mucosa of patients with sporadic adenomas (P < 0.05). COX-2 expression was significantly higher in the normal-appearing (P < 0.01) mucosa of patients with FAP carrying the −765GG genotype compared with those carrying the −765GC or −765CC genotypes. The −765C genotype was more common in African Americans than in Caucasians (52% versus 33%, P < 0.01). Conclusions: High COX-2 expression in the normal and adenomatous duodenal mucosa of patients with FAP may explain the poorer response of these neoplasms to chemoprevention with COX-2 inhibitors.