bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of the para-nitrophenol catabolic pathway, and characterization of three enzymes involved in the hydroquinone pathway, in pseudomonas sp. 1-7
Authors: Zhang Shuangyu , Sun Wen , Xu Li , Zheng Xiaomei , Chu Xiaoyu , Tian Jian , Wu Ningfeng , Fan Yunliu 
Published: March 2012

Abstract

Background

para-Nitrophenol (PNP), a priority environmental pollutant, is hazardous to humans and animals. However, the information relating to the PNP degradation pathways and their enzymes remain limited.

Results

Pseudomonas sp.1-7 was isolated from methyl parathion (MP)-polluted activated sludge and was shown to degrade PNP. Two different intermediates, hydroquinone (HQ) and 4-nitrocatechol (4-NC) were detected in the catabolism of PNP. This indicated that Pseudomonas sp.1-7 degraded PNP by two different pathways, namely the HQ pathway, and the hydroxyquinol (BT) pathway (also referred to as the 4-NC pathway). A gene cluster (pdcEDGFCBA) was identified in a 10.6 kb DNA fragment of a fosmid library, which cluster encoded the following enzymes involved in PNP degradation: PNP 4-monooxygenase (PdcA), p-benzoquinone (BQ) reductase (PdcB), hydroxyquinol (BT) 1,2-dioxygenase (PdcC), maleylacetate (MA) reductase (PdcF), 4-hydroxymuconic semialdehyde (4-HS) dehydrogenase (PdcG), and hydroquinone (HQ) 1,2-dioxygenase (PdcDE). Four genes (pdcDEFG) were expressed in E. coli and the purified pdcDE, pdcG and pdcF gene products were shown to convert HQ to 4-HS, 4-HS to MA and MA to β-ketoadipate respectively by in vitro activity assays.

Conclusions
The cloning, sequencing, and characterization of these genes along with the functional PNP degradation studies identified 4-NC, HQ, 4-HS, and MA as intermediates in the degradation pathway of PNP by Pseudomonas sp.1-7. This is the first conclusive report for both 4-NC and HQ- mediated degradation of PNP by one microorganism.
Sural nerve involvement in experimental hypertension: morphology and morphometry in male and female normotensive Wistar-Kyoto (WKY) and spontaneously hypertensive rats (SHR)
Authors: Sanada Luciana Sayuri , da Rocha Kalil Andréa Lurdes , Tavares Marcelo Rodrigo , Neubern Milena Cardoso Maia , Salgado Helio Cesar , Fazan Valéria Paula Sassoli 
Published: March 2012

Abstract

Background
The sural nerve has been widely investigated in experimental models of neuropathies but information about its involvement in hypertension was not yet explored. The aim of the present study was to compare the morphological and morphometric aspects of different segments of the sural nerve in male and female spontaneously hypertensive (SHR) and normotensive Wistar-Kyoto (WKY) rats. Rats aged 20 weeks (N = 6 in each group) were investigated. After arterial pressure and heart rate recordings in anesthetized animals, right and left sural nerves were removed and prepared for epoxy resin embedding and light microscopy. Morphometric analysis was performed with the aid of computer software, and took into consideration the fascicle area and diameter, as well as myelinated fiber number, density, area and diameter.

Results
Significant differences were observed for the myelinated fiber number and density, comparing different genders of WKY and SHR. Also, significant differences for the morphological (thickening of the endoneural blood vessel walls and lumen reduction) and morphometric (myelinated fibers diameter and G ratio) parameters of myelinated fibers were identified. Morphological exam of the myelinated fibers suggested the presence of a neuropathy due to hypertension in both SHR genders.

Conclusions
These results indicate that hypertension altered important morphometric parameters related to nerve conduction of sural nerve in hypertensive animals. Moreover the comparison between males and females of WKY and SHR allows the conclusion that the morphological and morphometric parameters of sural nerve are not gender related. The morphometric approach confirmed the presence of neuropathy, mainly associated to the small myelinated fibers. In conclusion, the present study collected evidences that the high blood pressure in SHR is affecting the sural nerve myelinated fibers.
Automated systems to identify relevant documents in product risk management
Authors: Wee Xue Ting , Koh Yvonne , Yap Chun Wei 
Published: March 2012

Abstract

Background
Product risk management involves critical assessment of the risks and benefits of health products circulating in the market. One of the important sources of safety information is the primary literature, especially for newer products which regulatory authorities have relatively little experience with. Although the primary literature provides vast and diverse information, only a small proportion of which is useful for product risk assessment work. Hence, the aim of this study is to explore the possibility of using text mining to automate the identification of useful articles, which will reduce the time taken for literature search and hence improving work efficiency. In this study, term-frequency inverse document-frequency values were computed for predictors extracted from the titles and abstracts of articles related to three tumour necrosis factors-alpha blockers. A general automated system was developed using only general predictors and was tested for its generalizability using articles related to four other drug classes. Several specific automated systems were developed using both general and specific predictors and training sets of different sizes in order to determine the minimum number of articles required for developing such systems.

Results
The general automated system had an area under the curve value of 0.731 and was able to rank 34.6% and 46.2% of the total number of 'useful' articles among the first 10% and 20% of the articles presented to the evaluators when tested on the generalizability set. However, its use may be limited by the subjective definition of useful articles. For the specific automated system, it was found that only 20 articles were required to develop a specific automated system with a prediction performance (AUC 0.748) that was better than that of general automated system.

Conclusions
Specific automated systems can be developed rapidly and avoid problems caused by subjective definition of useful articles. Thus the efficiency of product risk management can be improved with the use of specific automated systems.
One-step of tryptophan attenuator inactivation and promoter swapping to improve the production of L-tryptophan in Escherichia coli
Authors: Gu Pengfei , Yang Fan , Kang Junhua , Wang Qian , Qi Qingsheng 
Published: March 2012

Abstract

Background
L-tryptophan is an aromatic amino acid widely used in the food, chemical and pharmaceutical industries. In Escherichia coli, L-tryptophan is synthesized from phosphoenolpyruvate and erythrose 4-phosphate by enzymes in the shikimate pathway and L-tryptophan branch pathway, while L-serine and phosphoribosylpyrophosphate are also involved in L-tryptophan synthesis. In order to construct a microbial strain for efficient L-tryptophan production from glucose, we developed a one step tryptophan attenuator inactivation and promoter swapping strategy for metabolic flux optimization after a base strain was obtained by overexpressing the tktA, mutated trpE and aroG genes and inactivating a series of competitive steps.

Results
The engineered E. coli GPT1002 with tryptophan attenuator inactivation and tryptophan operon promoter substitution exhibited 1.67 ~ 9.29 times higher transcription of tryptophan operon genes than the control GPT1001. In addition, this strain accumulated 1.70 g l-1 L-tryptophan after 36 h batch cultivation in 300-mL shake flask. Bioreactor fermentation experiments showed that GPT1002 could produce 10.15 g l-1 L-tryptophan in 48 h.

Conclusions
The one step inactivating and promoter swapping is an efficient method for metabolic engineering. This method can also be applied in other bacteria.
The emerging role of microRNA in regulation of endotoxin tolerance
Authors: Quinn Edel M , Wang JiangHuai , Redmond Henry P 
Published: March 2012

ABSTRACT
Endotoxin tolerance is a phenomenon where cells show reduced responsiveness toward repeated endotoxin stimulation. Regulation of tolerance occurs at multiple levels of the cell signaling cascade, and many of these levels are potentially regulated by miRNA, which are a class of small RNA that bind to mRNA to down-regulate gene expression at the post-transcriptional level. Roles have been identified for miR-146a, miR-221, miR-579, miR-125b, miR-155, let-7e, and miR-98 in regulating the TLR4 signaling pathway during the development of endotoxin tolerance at receptor, signaling pathway, and gene transcription and translational levels. miRNA represent exciting, new potential targets in attempts to exogenously modulate development of endotoxin tolerance.
Determining the role of mononuclear phagocytes in prion neuroinvasion from the skin
Authors: Wathne Gwennaelle J , Kissenpfennig Adrien , Malissen Bernard , Zurzolo Chiara , Mabbott Neil A 
Published: March 2012

ABSTRACT
Many prion diseases are acquired by peripheral exposure, and skin lesions are an effective route of transmission. Following exposure, early prion replication, upon FDCs in the draining LN is obligatory for the spread of disease to the brain. However, the mechanism by which prions are conveyed to the draining LN is uncertain. Here, transgenic mice were used, in which langerin+ cells, including epidermal LCs and langerin+ classical DCs, were specifically depleted. These were used in parallel with transgenic mice, in which nonepidermal CD11c+ cells were specifically depleted. Our data show that prion pathogenesis, following exposure via skin scarification, occurred independently of LC and other langerin+ cells. However, the depletion of nonepidermal CD11c+ cells impaired the early accumulation of prions in the draining LN, implying a role for these cells in the propagation of prions from the skin. Therefore, together, these data suggest that the propagation of prions from the skin to the draining LN occurs via dermal classical DCs, independently of langerin+ cells.
mRNA-Selective Translation Induced by FSH in Primary Sertoli Cells
Authors: Musnier Astrid , León Kelly , Morales Julia , Reiter Eric , Boulo Thomas , Costache Vlad , Vourc'h Patrick , Heitzler Domitille , Oulhen Nathalie , Poupon Anne , Boulben Sandrine , Cormier Patrick , Crépieux Pascale 
Published: March 2012

AbstractFSH is a key hormonal regulator of Sertoli cell secretory activity, required to optimize sperm production. To fulfil its biological function, FSH binds a G protein-coupled receptor, the FSH-R. The FSH-R-transduced signaling network ultimately leads to the transcription or down-regulation of numerous genes. In addition, recent evidence has suggested that FSH might also regulate protein translation. However, this point has never been demonstrated conclusively yet. Here we have addressed this issue in primary rat Sertoli cells endogenously expressing physiological levels of FSH-R. We observed that, within 90 min of stimulation, FSH not only enhanced overall protein synthesis in a mammalian target of rapamycin-dependent manner but also increased the recruitment of mRNA to polysomes. m7GTP pull-down experiments revealed the functional recruitment of mammalian target of rapamycin and p70 S6 kinase to the 5′cap, further supported by the enhanced phosphorylation of one of p70 S6 kinase targets, the eukaryotic initiation factor 4B. Importantly, the scaffolding eukaryotic initiation factor 4G was also recruited, whereas eukaryotic initiation factor 4E-binding protein, the eukaryotic initiation factor 4E generic inhibitor, appeared to play a minor role in translational regulations induced by FSH, in contrast to what is generally observed in response to anabolic factors. This particular regulation of the translational machinery by FSH stimulation might support mRNA-selective translation, as shown here by quantitative RT-PCR amplification of the c-fos and vascular endothelial growth factor mRNA but not of all FSH target mRNA, in polysomal fractions. These findings add a new level of complexity to FSH biological roles in its natural target cells, which has been underappreciated so far.
One step beyond: Different step-to-step transitions exist during continuous contact brachiation in siamangs
Authors: Michilsens Fana , D'Août Kristiaan , Vereecke Evie E. , Aerts Peter 
Published: March 2012

Summary
In brachiation, two main gaits are distinguished, ricochetal brachiation and continuous contact brachiation. During ricochetal brachiation, a flight phase exists and the body centre of mass (bCOM) describes a parabolic trajectory. For continuous contact brachiation, where at least one hand is always in contact with the substrate, we showed in an earlier paper that four step-to-step transition types occur. We referred to these as a ‘point’, a ‘loop’, a ‘backward pendulum’ and a ‘parabolic’ transition. Only the first two transition types have previously been mentioned in the existing literature on gibbon brachiation. In the current study, we used three-dimensional video and force analysis to describe and characterize these four step-to-step transition types. Results show that, although individual preference occurs, the brachiation strides characterized by each transition type are mainly associated with speed. Yet, these four transitions seem to form a continuum rather than four distinct types. Energy recovery and collision fraction are used as estimators of mechanical efficiency of brachiation and, remarkably, these parameters do not differ between strides with different transition types. All strides show high energy recoveries (mean  = 70±11.4%) and low collision fractions (mean  = 0.2±0.13), regardless of the step-to-step transition type used. We conclude that siamangs have efficient means of modifying locomotor speed during continuous contact brachiation by choosing particular step-to-step transition types, which all minimize collision fraction and enhance energy recovery.
High-fat diet exposure induces IgG accumulation in hypothalamic microglia
Authors: Yi Chun-Xia , Tschöp Matthias H. , Woods Stephen C. , Hofmann Susanna M. 
Published: March 2012

Summary
The medio-basal hypothalamic arcuate nucleus (ARC), with its relatively "leaky" blood brain barrier that allows more circulating molecules to enter the brain, has emerged as a key sensor of blood-borne signals. In both the ARC and white adipose tissue (WAT), consumption of a high-fat diet (HFD) rapidly induces infiltration of microglia (ARC) or macrophages (WAT). Animals with HFD-induced obesity (DIO) and insulin resistance additionally accumulate B-lymphocytes in WAT, increasing local production of pathogenic antibodies. We therefore asked whether DIO mice or genetically obese ob/ob mice have increased IgG in the ARC, analogous to the recent observations in WAT. Following 16 weeks exposure to a HFD, WT mice had significantly increased IgG-ir signaling that was specific to the ARC and is exclusively concentrated in microglia. In contrast, IgG-ir of age-matched obese ob/ob mice fed standard chow had ARC IgG levels comparable to those in chow-fed WT control mice. However, following 2 weeks of HFD exposure, ob/ob mice also had a significant increase of IgG-ir in the ARC. In summary, our findings reveal a novel pathophysiological phenomenon specific for the hypothalamic ARC, which is induced by exposure to a HFD and can be enhanced, but not caused, by genetic obesity.
Local Cutaneous Necrosis Secondary to a Prolonged Peripheral Infusion of Methylene Blue in Vasodilatory Shock
Authors: Dumbarton Tristan Charles , Gorman Sean K , Minor Samuel , Loubani Osama , White Fletcher , Green Robert 
Published: March 2012

Objective: To report a case of methylene blue extravasation and subsequent tissue necrosis in a patient with refractory septic shock. Case Summary: A 47-year-old female presented with febrile neutropenia secondary to chemotherapy. The patient quickly decompensated to refractory septic shock in the critical care unit despite implementation of early goal-directed therapy as well as intravenous norepinephrine and vasopressin to stabilize her hemodynamic status. She received a 16-hour infusion of 1% methylene blue 0.25 mg·kg−1 ·h−1, titrated up to 0.5 mg ·kg−1 ·h−1, via a peripheral intravenous catheter. Ten hours after the start ot the methylene blue infusion, she experienced a local extravasation injury, which led to distal digital necrosis. While her hemodynamic status improved dramatically, allowing discharge from the intensive care unit and eventually to home, the extravasation site became necrotic and required debridement and skin graft. Discussion: Methylene blue is a vasoactive chemical that has been shown to provide hemodynamic stability in the treatment of refractory septic shock. Methylene blue administration is not considered standard of practice in the treatment of refractory septic shock and many aspects of its dosing, route, duration, and adverse effects are poorly described. As such, there is little guidance for its administration. We postulate that, in our patient, in the presence of systemic vasopressin and norepinephrine, methylene blue caused extensive vasoconstriction at the site of extravasation, resulting in tissue ischemia and necrosis. Tissue necrosis secondary to peripheral intravenous extravasation has not been previously described and is not listed as an adverse outcome on the drug monograph. The Naranjo probability scale indicates that the tissue necrosis was probably caused by the methylene blue extravasation. Conclusions: To mitigate future risk to limb and skin, we recommend that methylene blue infusions be delivered via central venous catheter. Extra care should be given to patients with risk factors for extravasation, such as sedation, presence of systemic disease, proximal intravenous puncture sites, and improperly placed catheters.
Structural Materials: Understanding Atomic-Scale Microstructures
Authors: Marquis Emmanuelle A. , Miller Michael K. , Blavette Didier , Ringer Simon P. , Sudbrack Chantal K. , Smith George D.W. 
Published: March 2012

AbstractWith the ability to locate and identify atoms in three dimensions, atom-probe tomography (APT) has revolutionized our understanding of structure-property relationships in materials used for structural applications. The atomic-scale details of clusters, second phases, and microstructural defects that control alloy properties have been investigated, providing an unprecedented level of detail on the origins of aging behavior, strength, creep, fracture toughness, corrosion, and irradiation resistance. Moreover, atomic-scale microscopy combined with atomistic simulation and theoretical modeling of material behavior can guide new alloy design. In this article, selected examples highlight how APT has led to a deeper understanding of materials structures and therefore properties, starting with the phase transformations controlling the aging and strengthening behavior of complex Al-, Fe-, and Ni-based alloys systems. The chemistry of interfaces and structural defects that play a crucial role in high-temperature strengthening, fracture, and corrosion resistance are also discussed, with particular reference to Zr- and Al-alloys and FeAl intermetallics.
Atom-Probe Tomography of Semiconductor Materials and Device Structures
Authors: Lauhon Lincoln J. , Adusumilli Praneet , Ronsheim Paul , Flaitz Philip L. , Lawrence Dan 
Published: March 2012

AbstractThe development of laser-assisted atom-probe tomography (APT) analysis and new sample preparation approaches have led to significant advances in the characterization of semiconductor materials and device structures by APT. The high chemical sensitivity and three-dimensional spatial resolution of APT makes it uniquely capable of addressing challenges resulting from the continued shrinking of semiconductor device dimensions, the integration of new materials and interfaces, and the optimization of evolving fabrication processes. Particularly pressing concerns include the variability in device performance due to discrete impurity atom distributions, the phase and interface stability in contacts and gate dielectrics, and the validation of simulations of impurity diffusion. This overview of APT of semiconductors features research on metal-silicide contact formation and phase control, silicon field-effect transistors, and silicon and germanium nanowires. Work on silicide contacts to silicon is reviewed to demonstrate impurity characterization in small volumes and indicate how APT can facilitate defect mitigation and process optimization. Impurity contour analysis of a pFET semiconductor demonstrates the site-specificity that is achievable with current APTs and highlights complex device challenges that can be uniquely addressed. Finally, research on semiconducting nanowires and nanowire heterostructures demonstrates the potential for analysis of materials derived from bottom-up synthesis methods.
Prospects for Nanobiology with Atom-Probe Tomography
Authors: Kelly Thomas F. , Nishikawa Osamu , Panitz J.A. , Prosa Ty J. 
Published: March 2012

AbstractThe merits of atom-probe tomography (APT) of inorganic materials are well established, as described in this volume. However, one of the long-held aspirations of atom-probe scientists, structural and chemical characterization of organic and biological materials at near-atomic resolution, has yet to be fully realized. A few proof-of-concept type investigations have shown that APT of organic materials is feasible, but a number of challenges still exist with regard to specimen preparation and conversion of raw time-of-flight mass spectrometry data into a three-dimensional map of ions containing structural and chemical information at an acceptable resolution. Recent research aided by hardware improvements and specimen preparation advances has made some progress toward this goal. This article reviews the historical developments in this field, presents some recent results, and considers what life science researchers might expect from this technology.
Manipulation of Photons by Photonic Crystals
Authors: Noda Susumu 
Published: March 2012

AbstractPhotonic crystals, in which the refractive index changes periodically, provide an exciting new tool for the manipulation of photons and have received keen interest from a variety of fields. This article reviews recent progress in the manipulation of photons by photonic crystals. First, the article covers spontaneous emission, a fundamental phenomenon associated with all photonic devices that emit light, which now can be successfully controlled. Light emission is suppressed in areas where the photonic crystal is complete, while strong emission occurs in the areas where there are artificial defects. Next, it is shown that a very strong confinement of photons in a small volume on the scale of cubic wavelengths becomes possible by using photonic crystals, where nanocavities with ultrahigh-Q values of more than 2 million have been successfully demonstrated. Finally, photonic crystals promise to realize unprecedented types of lasers, which can produce tailored beams on demand, while keeping stable single longitudinal and lateral modes.