julilili42/papers huggingface dataset:
IRON IN MICROBIAL METABOLISMS
2011-04-01

Research Article| April 01, 2011 IRON IN MICROBIAL METABOLISMS Kurt O. Konhauser; Kurt O. Konhauser 1Department of Earth and Atmospheric Sciences University of Alberta Edmonton, Alberta T6G 2E3, Canada E-mail: kurtk@ualberta.ca Search for other works by this author on: GSW Google Scholar Andreas Kappler; Andreas Kappler 2Geomicrobiology, Center for Applied Geosciences University of Tübingen Sigwartstrasse 10, 72076 Tübingen, Germany Search for other works by this author on: GSW Google Scholar Eric E. Roden Eric E. Roden 3Department of Geosciences, University of Wisconsin–Madison Madison, WI 53706, USA Search for other works by this author on: GSW Google Scholar Elements (2011) 7 (2): 89–93. https://doi.org/10.2113/gselements.7.2.89 Article history first online: 09 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Search Site Citation Kurt O. Konhauser, Andreas Kappler, Eric E. Roden; IRON IN MICROBIAL METABOLISMS. Elements 2011;; 7 (2): 89–93. doi: https://doi.org/10.2113/gselements.7.2.89 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyElements Search Advanced Search Abstract Microbes are intimately involved in the iron cycle. First, acquisition of iron by microorganisms for biochemical requirements is a key process in the iron cycle in oxygenated, circumneutral pH environments, where the solubility of Fe(III) (oxyhydr)oxides is extremely low. Second, a number of aerobic (using O2) and anaerobic (living in the absence of O2) autotrophic bacteria gain energy for growth from the oxidation of dissolved and solid-phase Fe(II) compounds to Fe(III) (oxyhydr)oxides. Third, heterotrophic Fe(III)-reducing bacteria close the chemical loop by reducing solid-phase Fe(III) minerals back to dissolved and solid-phase Fe(II). Together these metabolic processes control the partitioning of the Earth's fourth most abundant crustal element, and they are additionally tied to the cycling of several major nutrients (e.g. carbon, oxygen, nitrogen, sulfur) and trace elements (e.g. phosphorus, nickel) in modern and ancient environments. You do not have access to this content, please speak to your institutional administrator if you feel you should have access.
Biosynthetic Gene Cluster of the Non-ribosomally Synthesized Cyclodepsipeptide Skyllamycin: Deciphering Unprecedented Ways of Unusual Hydroxylation Reactions
2011-04-01

The cyclic depsipeptide skyllamycin A is a potent inhibitor of the platelet-derived growth factor (PDGF) signaling pathway by inhibiting binding of homodimeric PDGF BB to the PDGF β-receptor. Its structure contains a cinnamoyl side chain and shows a high amount of β-hydroxylated amino acids as well as an unusual α-hydroxyglycine moiety as a rare structural modification. The skyllamycin biosynthetic gene cluster was cloned and sequenced from Streptomyces sp. Acta 2897. Its analysis revealed the presence of open reading frames encoding proteins for fatty acid precursor biosynthesis, non-ribosomal peptide synthetases, regulators, and transporters along with other modifying enzymes. Specific in-frame mutagenesis of these tailoring enzymes resulted in the production of novel skyllamycin derivatives revealing that β-hydroxy groups in skyllamycin A are introduced by a promiscuous cytochrome P450 monooxygenase, whereas a two-component flavin-dependent monooxygenase is involved in α-hydroxylation.
Apoptosis of regulatory T lymphocytes is increased in chronic inflammatory bowel disease and reversed by anti-TNFα treatment
2011-04-01

Background and aims Inappropriate immune responses contribute to the continuous stimulation of the intestinal immune system in chronic inflammatory bowel disease (IBD). Among several pathogenic factors, a numerical deficiency of regulatory T (Treg) cells has been suggested to lead to an insufficient compensation of chronically activated T lymphocytes. This study was conducted to investigate whether increased apoptosis contributes to Treg cell deficiency in IBD and whether successful treatment with antitumour necrosis factor α (TNFα) is achieved by reducing of Treg cell apoptosis. Methods Apoptosis of CD4 + Foxp3 + Treg cells in tissue sections of patients with active IBD was analysed by immunohistochemistry and TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labelling) staining. Apoptosis of peripheral blood CD4 + CD25 + Foxp3 + Treg cells was investigated by flow cytometry and annexin-V staining. In addition, caspase activity and apoptosis were measured in sera of patients with IBD treated with anti-TNFα by a luminometric caspase enzyme assay. Results It is demonstrated that patients with active IBD revealed increased apoptosis of local CD4 + Foxp3 + Treg cells in the inflamed mucosa compared with non-inflamed control colon tissue. Moreover, in peripheral blood a reduced frequency and increased apoptosis of Treg cells were found and accompanied by elevated caspase activity in the serum. During anti-TNFα treatment, Treg cell apoptosis declined in close correlation with elevated peripheral Treg cell numbers and a decrease of caspase activation and disease activity. Conclusions These data suggest that increased apoptosis of Treg cells plays a potentially important role in the pathogenesis of IBD and can be reversed by anti-TNFα treatment. Measurement of Treg cell apoptosis and serum caspase activity might therefore represent promising tools for monitoring disease activity and treatment response in patients with IBD.
Computer‐Suggested Facial Makeup
2011-04-01

Abstract Finding the best makeup for a given human face is an art in its own right. Experienced makeup artists train for years to be skilled enough to propose a best‐fit makeup for an individual. In this work we propose a system that automates this task. We acquired the appearance of 56 human faces, both without and with professional makeup. To this end, we use a controlled‐light setup, which allows to capture detailed facial appearance information, such as diffuse reflectance, normals, subsurface‐scattering, specularity, or glossiness. A 3D morphable face model is used to obtain 3D positional information and to register all faces into a common parameterization. We then define makeup to be the change of facial appearance and use the acquired database to find a mapping from the space of human facial appearance to makeup. Our main application is to use this mapping to suggest the best‐fit makeup for novel faces that are not in the database. Further applications are makeup transfer, automatic rating of makeup, makeup‐training, or makeup‐exaggeration. As our makeup representation captures a change in reflectance and scattering, it allows us to synthesize faces with makeup in novel 3D views and novel lighting with high realism. The effectiveness of our approach is further validated in a user‐study.
Accounting for Individual Differences in Bradley-Terry Models by Means of Recursive Partitioning
2011-04-01

The preference scaling of a group of subjects may not be homogeneous, but different groups of subjects with certain characteristics may show different preference scalings, each of which can be derived from paired comparisons by means of the Bradley-Terry model. Usually, either different models are fit in predefined subsets of the sample or the effects of subject covariates are explicitly specified in a parametric model. In both cases, categorical covariates can be employed directly to distinguish between the different groups, while numeric covariates are typically discretized prior to modeling. Here, a semiparametric approach for recursive partitioning of Bradley-Terry models is introduced as a means for identifying groups of subjects with homogeneous preference scalings in a data-driven way. In this approach, the covariates that—in main effects or interactions—distinguish between groups of subjects with different preference orderings, are detected automatically from the set of candidate covariates. One main advantage of this approach is that sensible partitions in numeric covariates are also detected automatically.
The Bipedal Stem CrocodilianPoposaurus gracilis: Inferring Function in Fossils and Innovation in Archosaur Locomotion
2011-04-01

We introduce a spectacular new specimen of a Late Triassic stem crocodilian identified as Poposaurus gracilis. It is part of a poorly known group, Poposauroidea, that, because of its striking similarities with contemporaneous stem avians ("dinosaurs"), has long puzzled archosaur paleontologists. Observed vertebrate locomotor behaviors, together with exceptional preservation of distinctive anatomical clues in this fossil, enable us to examine locomotor evolution in light of new advances in phylogenetic relationships among Triassic archosaurs. Because this stem crocodilian is unambiguously an archosaur, a diapsid, a tetrapod and a choanate sarcopterygian, we can safely infer major components of its locomotor behavior. These inferences, together with form-function constraints, suggest that P. gracilis was a fleet-footed, obligately erect-postured, striding biped. That behavior seems to have been superimposed on the ancestral archosaur's innovative locomotor repertoire, which includes the capacity to "high walk." These novelties persist in a recognizable form in archosaurs for at least 245 million years and are widely distributed across Earth's surface in diverse ecological settings. They thus qualify as evolutionary innovations regardless of significant differences in diversification rates among extant diapsid reptiles.
How does neuromodulation work
2011-04-01

Abstract Although sacral neuromodulation (SNM) is approved and successfully used for different urological and proctologic functional diseases for the long‐term treatment, less is known about the working mechanisms underlying SNM. This review highlights SNM clinical application, the current data of LUT neuroanatomy and neurophysiology, SNM techniques and its prospective working mechanisms. Functional imaging techniques have facilitated a more detailed insight into the neural network between the central nervous system (CNS) and the lower urinary tract (LUT). In addition to the well‐known factors of the spinal micturition pathway, several pontine (e.g. pontine micturition centre) and suprapontine (e.g. cingulate cortex) regions and their interactions have been identified. An attribution of CNS activity levels to different LUT conditions is possible for the first time. Based on this information, different SNM actions could also have been allocated to different ascending/descending pathways and supraspinal regions, whereas acute SNM especially affects regions of learning activity, chronic SNM might result in CNS plasticity even though clinical effectiveness fades after SNM deactivation. Studies to treat fecal incontinence or to prevent detrusor overactivity in complete spinal cord injured patients support the importance of sympathetic pathways for the action of SNM. Despite increasing knowledge about SNM influence on the CNS, the complexity of its underlying working mechanisms is not understood at all. Further investigations with improved functional imaging techniques will enhance our SNM background. Neurourol. Urodynam. Neurourol. Urodynam. 30:762–765, 2011. © 2011 Wiley‐Liss, Inc.
How Valid Is Negotiation Research Based on Student Sample Groups? New Insights into a Long-Standing Controversy
2011-04-01

Abstract Although a considerable amount of research has examined the impact of experience on negotiation behavior and performance, we still know very little about the usefulness of student samples in negotiation research because most studies have compared the performance of inexperienced students with those who had received some kind of extensive negotiation training or with experienced professional negotiators(s). Against this background, we investigate whether the results obtained from trained student samples are generally similar to those of professional negotiators. Generally, our data confirm our hypotheses that students with some negotiation training and experience perform better than untrained student negotiators and that they are not significantly outperformed by professional negotiators. From this, we conclude that many questions in the field of negotiation research can be effectively tested by using trained students as experimental subjects.
Grid-based visual terrain classification for outdoor robots using local features
2011-04-01

In this paper we present a comparison of multiple approaches to visual terrain classification for outdoor mobile robots based on local features. We compare the more traditional texture classification approaches, such as Local Binary Patterns, Local Ternary Patterns and a newer extension Local Adaptive Ternary Patterns, and also modify and test three non-traditional approaches called SURF, DAISY and CCH. We drove our robot under different weather and ground conditions and captured images of five different terrain types for our experiments. We did not filter out blurred images which are due to robot motion and other artifacts caused by rain, etc.We used Random Forests for classification, and cross-validation for the verification of our results. The results show that most of the approaches work well for terrain classification in a fast moving mobile robot, despite image blur and other artifacts induced due to extremely variant weather conditions.
rhKGF stimulates lung surfactant production in neonatal rats in vivo
2011-04-01

Abstract Surfactant deficiency and bronchopulmonary dysplasia (BPD), major obstacles in preterm infants, are addressed with pre‐ and postnatal glucocorticoids which also evoke harmful catabolic side‐effects. Keratinocyte growth factor (KGF) accelerates surfactant production in fetal type II pneumocytes (PN‐II), protects epithelia from injury and is deficient in lungs developing BPD, highlighting its potential efficacy in neonates. Neonatal rats were treated with recombinant human (rh)KGF, betamethasone, or their combination for 48 hr prior to sacrifice after which body weight, surfactant, and tissue phosphatidylcholines (PC) were investigated at postnatal d3, d7, d15, and d21. Pneumocyte proliferation, surfactant protein (SP) expression and SP‐B/C in lung lavage fluid (LLF) were also determined at d7 and d21 to identify broader surfactant changes occurring at the beginning and end of the initial alveolarization phase. While all treatments increased secreted surfactant PC, BM compromised animal growth whereas rhKGF did not. At d3 rhKGF was more effective in male compared to female rats. Single treatments became less effective towards d21. Neither treatment altered PC composition in LLF. BM inhibited PN‐II proliferation and increased surfactant PCs at the expense of tissue PCs. rhKGF however increased surfactant PCs without decreasing other PC species. Whereas SP‐B/C gene expression was induced by all treatments, the changes in secreted SP‐B/C mirrored those observed for surfactant PC. Our results encourage investigation of the mechanisms by which rhKGF improves surfactant homoeostasis, and detailed examination of its efficacy in neonatal lung injury models with a view to implementing it as a non‐catabolic surfactant‐increasing therapeutic in neonatal intensive care. Pediatr. Pulmonol. 2011; 46:883–895. © 2011 Wiley‐Liss, Inc.
Caveolin 1 mRNA is Overexpressed in Malignant Renal Tissue and Might Serve as a Novel Diagnostic Marker For Renal Cancer
2011-04-01

To our knowledge, this is the first study to show that CAV1 mRNA expression, using quantitative real-time PCR, is significantly higher in RCC compared with normal renal tissue and increases with tumor stage. CAV1 mRNA expression might serve as a candidate biomarker for objective prognosis indicating RCC aggressiveness. Our data encourage further investigations to determine the role of CAV1 in RCC.
Internet use among patients with psychosomatic disorders: What are the health-related demands and needs?
2011-04-01

While Internet-based health-related offers for various disorders are increasing, little is known about the way patients with psychosomatic disorders use the Internet. We conducted a questionnaire survey in outpatient clinics at two university hospitals’ Departments of Psychosomatic Medicine. Seventy-four percent of N = 274 patients had Internet home access and 60 percent of those patients reported health-related Internet use. Patients expressed the wish for more professional, evidence-based online information and expert-guided treatment. The survey results support the Internet’s high potential in future treatment strategies for patients with psychosomatic disorders.
Enlarging the NSAIDs Family: Ether, Ester and Acid Derivatives of the 1,5-Diarylpyrrole Scaffold as Novel Anti-Inflammatory and Analgesic Agents
2011-04-01

The development of the coxib family has represented a stimulating approach in the treatment of inflammatory disorders, such as arthritis, and for the management of acute pains, in relation to the well-known traditional Non-Steroidal Anti-inflammatory Drugs (t-NSAIDs). Prompted by the pursuit for new cyclooxygenase-2 (COX-2) inhibitors, endowed with fine tuned selectivity and high potency, in the past years we have identified novel classes of ether, ester and acid molecules characterized by the 1,5-diarylpyrrole scaffold as potentially powerful anti-inflammatory molecules (12-66). All compounds proved to exert an in vitro inhibition profile as good as that shown by reference compounds. Compounds bearing a p-methylsulfonylphenyl substituent at C5 displayed the best issues. In particular, ester derivatives proved to perform the best in vitro profile in terms of selectivity and activity toward COX-2. The cell-based assay data showed that an increase of hindrance at the C3 side chain of compounds could translate to activity enhancement. The human whole blood (HWB) test let to highlight that submitted compounds displayed 5-10 fold higher selectivity for COX-2 vs COX-1 which should translate clinically to an acceptable gastrointestinal safety and mitigate the cardiovascular effects highlighted by highly selective COX-2 inhibitors. Finally, to assess in vivo anti-inflammatory and analgesic activity three different tests (rat paw pressure, rat paw oedema and abdominal constriction) were performed. Results showed good in vivo anti-inflammatory and analgesic activities. The issues gained with these classes of compounds represent, nowadays, a potent stimulus for a further enlargement of the NSAIDs family. In this review we describe the results obtained by our research group on this topic.
Cognitive Relatives yet Moral Strangers?
2011-04-01

Abstract This article provides an empirically based, interdisciplinary approach to the following two questions: Do animals possess behavioral and cognitive characteristics such as culture, language, and a theory of mind? And if so, what are the implications, when long-standing criteria used to justify differences in moral consideration between humans and animals are no longer considered indisputable? One basic implication is that the psychological needs of captive animals should be adequately catered for. However, for species such as great apes and dolphins with whom we share major characteristics of personhood, welfare considerations alone may not suffice, and consideration of basic rights may be morally warranted—as for humans. Although characteristics supporting the status of personhood are present to differing degrees among the diverse array of animal species, this is a barrier to moral consideration only if anthropocentric, exclusive, and monolithic viewpoints about the necessary prerequisites for personhood are applied. We examine the flaws inherent within such positions and argue for inalienable species-appropriate rights.
About a peri-Gondwanan-North African enlarged acceptance of the Caledonian Orogeny
2011-04-01

The notion of “Caledonian Orogeny” is restricted by most authors to the Ordovician-Devonian thermotectonic events associated with the Laurentia-Baltica- Avalonia suturing. However, some views consider an orogeny as the sum of tectonic, metamorphic and magmatic events accompanying an entire supercontinent assembly or Wilson cycle. Following this line of thinking, the Caledonian and Variscan orogenies successively assembled Pangea. During the Ordovician Period, rifting, collision, deformation, metamorphism and magmatism took place within the Gondwana margin. All these events are known today in the basement of the Cadomian terranes from Iberia through the Alps up to the Romanian Carpathians and Balkans. We plead here for an enlargement of the “Caledonian Orogeny” terminology to these events and places, under the name of the “Caledonian North African orogenic event" or "Caledonian North African orogeny"
The Distinctiveness of a Unifying Science: Cybernetics' Way to West Germany
2011-04-01

As it spread into different countries, cybernetics was shaped by the tensions between international networks of scientists and national restrictions set by political, social, and cultural influences. Such extra-scientific factors caused a huge variability in cybernetic applications. This article examines the evolution of cybernetics in West Germany as both a cultural and scientific-technological phenomenon.
A New, Rapid, Standardized Method for Harvesting Split Skin Grafts in Rodents
2011-04-01

Using this new standardized method, grafts of equal size and thickness can be obtained rapidly. It is cheap and highly reproducible and can be carried out by a single surgeon. It provides a rapid healing process with fewer complications and immensely reduced stress for the animals.
A quantum chemical study of the structure and energy of β-diketonates. XVII. Internal rotation of radical substituents in β-diketonate molecules
2011-04-01

A quantum chemical study of the internal rotation of CX3 (X = H, F, CH3) radical substituents in scandium and calcium β-diketonate complexes is performed. Calculations are carried out using the GAUSSIAN-03 program at the HF and DFT/B3LYP levels with relativistic effective core pseudo-potentials and valence double zeta basis sets. Analytical expressions V(φ) are obtained that describe the potential energy variation during the rotation of CX3 groups. The rotation of CH3 and CF3 groups is shown to be described by a simple potential of the form V = V 0/2 + V 3cos(3φ), while for the description of the rotation of tert-butyl groups it is required to use a more complex function V = V 0/2 + V 3cos(3φ) + V 6cos(6φ). Based on the obtained expressions for V(φ), the effective torsion angles φef of the rotation of CX3 groups are calculated for different temperatures. It is shown that φef obtained based on the quantum chemical calculations are close to the values obtained in electron diffraction experiments.