bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series
Authors: Dahmen Tim , Baudoin Jean-Pierre , Lupini Andrew R. , Kübel Christian , Slusallek Philipp , de Jonge Niels 
Published: February 2014

AbstractIn this study, a combined tilt- and focal series is proposed as a new recording scheme for high-angle annular dark-field scanning transmission electron microscopy (STEM) tomography. Three-dimensional (3D) data were acquired by mechanically tilting the specimen, and recording a through-focal series at each tilt direction. The sample was a whole-mount macrophage cell with embedded gold nanoparticles. The tilt–focal algebraic reconstruction technique (TF-ART) is introduced as a new algorithm to reconstruct tomograms from such combined tilt- and focal series. The feasibility of TF-ART was demonstrated by 3D reconstruction of the experimental 3D data. The results were compared with a conventional STEM tilt series of a similar sample. The combined tilt- and focal series led to smaller “missing wedge” artifacts, and a higher axial resolution than obtained for the STEM tilt series, thus improving on one of the main issues of tilt series-based electron tomography.
Conservation agriculture in Southern Africa: Advances in knowledge
Authors: Thierfelder Christian , Rusinamhodzi Leonard , Ngwira Amos R. , Mupangwa Walter , Nyagumbo Isaiah , Kassie Girma T. , Cairns Jill E. 
Published: February 2014

AbstractThe increasing demand for food from limited available land, in light of declining soil fertility and future threats of climate variability and change have increased the need for more sustainable crop management systems. Conservation agriculture (CA) is based on the three principles of minimum soil disturbance, surface crop residue retention and crop rotations, and is one of the available options. In Southern Africa, CA has been intensively promoted for more than a decade to combat declining soil fertility and to stabilize crop yields. The objective of this review is to summarize recent advances in knowledge about the benefits of CA and highlight constraints to its widespread adoption within Southern Africa. Research results from Southern Africa showed that CA generally increased water infiltration, reduced soil erosion and run-off, thereby increasing available soil moisture and deeper drainage. Physical, chemical and biological soil parameters were also improved under CA in the medium to long term. CA increased crop productivity and also reduced on-farm labor, especially when direct seeding techniques and herbicides were used. As with other cropping systems, CA has constraints at both the field and farm level. Challenges to adoption in Southern Africa include the retention of sufficient crop residues, crop rotations, weed control, pest and diseases, farmer perception and economic limitations, including poorly developed markets. It was concluded that CA is not a ‘one-size-fits-all’ solution and often needs significant adaptation and flexibility when implementing it across farming systems. However, CA may potentially reduce future soil fertility decline, the effects of seasonal dry-spells and may have a large impact on food security and farmers’ livelihoods if the challenges can be overcome.
Identification of a conserved branched RNA structure that functions as a factor-independent terminator
Authors: Johnson Christopher M. , Chen Yuqing , Lee Heejin , Ke Ailong , Weaver Keith E. , Dunny Gary M. 
Published: February 2014

Significance
All cells regulate which regions of DNA are transcribed to RNA. Controlling where transcription terminates is an essential part of this regulation. In bacterial cells, RNA structures, referred to as factor-independent terminators, can interact with RNA polymerase to direct termination. These structures are typically inverted sequence repeats that form an RNA hairpin followed by several uridine residues. We identified a branched RNA structure that functions as a factor-independent terminator. The terminated product is a functional small RNA, but termination is inefficient, allowing transcription of downstream genes. Additional branched terminators are encoded in bacterial chromosomes, demonstrating that this unusual terminator is not unique. This work reveals an unappreciated structural diversity of factor-independent terminators and will inform annotation of bacterial genomes.
Osteopontin expression by CD103−dendritic cells drives intestinal inflammation
Authors: Kourepini Evangelia , Aggelakopoulou Maria , Alissafi Themis , Paschalidis Nikolaos , Simoes Davina C. M. , Panoutsakopoulou Vily 
Published: February 2014

SignificanceDendritic cells (DCs) are important for the development of intestinal inflammation in humans with inflammatory bowel disease (IBD) and in mice with experimental colitis. We demonstrate that a subset of DCs, CD103−DCs, isolated from murine mesenteric lymph nodes, is highly pathogenic for murine intestinal inflammation and expresses high levels of the cytokine osteopontin (Opn). This Opn expression by CD103−DCs is crucial for their pathogenicity. We define a specific domain of Opn protein significant for inducing pathogenic properties in CD103−DCs. Blockade of the interaction of this Opn domain with integrin α9 expressed on CD103−DCs abrogated their harmful effects. These findings may open new paths in IBD treatment.
NF-κB signaling mediates homeostatic maturation of new T cells
Authors: Silva Ana , Cornish Georgina , Ley Steven C. , Seddon Benedict 
Published: February 2014

Significance
Interleukin (IL)-7 is critical for the maintenance of the peripheral T-cell compartment of the adaptive immune system. Our study identifies a role for the Nuclear Factor κ-B (NF-κB) signalling pathway in the control of IL-7 receptor expression by T cells. Following thymic selection, new T cells specifically up-regulate IL-7R even as they leave the thymus, and we reveal that this expression is strictly NF-κB dependent. NF-κB signaling was only required transiently, however, and once fully mature, naive T cells did not require NF-κB signaling to maintain IL-7R expression. Therefore, we reveal a developmental role for NF-κB signaling for the normal maturation and function of new T cells.
Scaffold-mediated lentiviral transduction for functional tissue engineering of cartilage
Authors: Brunger Jonathan M. , Huynh Nguyen P. T. , Guenther Caitlin M. , Perez-Pinera Pablo , Moutos Franklin T. , Sanchez-Adams Johannah , Gersbach Charles A. , Guilak Farshid 
Published: February 2014

SignificanceEngineered replacements for musculoskeletal tissues generally require extensive ex vivo manipulation of stem cells to achieve controlled differentiation and phenotypic stability. The ability to control cell differentiation using cell-instructive scaffolds that have biomechanical properties approximating those of native tissue would represent a transformative advance in functional tissue engineering. The goal of this study was to develop a bioactive scaffold capable of mediating cell differentiation and formation of an extracellular matrix with the biochemical composition and mechanical features that mimic native tissue properties. By combining innovative gene delivery strategies with advanced biomaterial design, we demonstrate the feasibility of generating constructs capable of restoring biological and mechanical function.
Vesicle capture, not delivery, scales up neuropeptide storage in neuroendocrine terminals
Authors: Bulgari Dinara , Zhou Chaoming , Hewes Randall S. , Deitcher David L. , Levitan Edwin S. 
Published: February 2014

Significance
Neuropeptides, which affect mood and behavior, are synthesized in the soma and delivered to nerve terminals for storage and release. Yet, among identified neurons, there is great variation in the abundance of neuropeptides in terminals. Demonstrated transcriptional regulation of neuropeptide synthesis supports the view that presynaptic neuropeptide stores are proportional to synthesis-driven delivery of neuropeptide-containing vesicles to terminals. However, we show that nerve terminals with dramatically different neuropeptide stores are supported by identical vesicle delivery and differ instead in efficiency of vesicle capture. Vesicle capture in the terminal is under transcriptional control and influences vesicle distribution and replacement as well as neuropeptide accumulation for release. Thus, vesicle capture is a major determinant of nerve terminal function.
How force unfolding differs from chemical denaturation
Authors: Stirnemann Guillaume , Kang Seung-gu , Zhou Ruhong , Berne Bruce J. 
Published: February 2014

Significance
Proteins can be unfolded either chemically by denaturing agents (such as urea) or by mechanical force (such as optical tweezers). If these two methods produce quite different unfolded structures, the course of the subsequent protein refolding when these agents are removed will be quite different. Our computer simulations show that the respective unfolded states are indeed very different, being fully extended under force, with no contacts, and partially extended in urea with many nonnative contacts. Understanding these differences is crucial because such configurations serve as starting points for different single-molecule experimental studies of protein folding. These differences can affect both the folding mechanism and the kinetics observed, leading to very different interpretations.
Mislocalization of phosphotransferase as a cause of mucolipidosis III αβ
Authors: van Meel Eline , Qian Yi , Kornfeld Stuart A. 
Published: February 2014

Significance
Most disease-causing mutations in genes encoding enzymes impair the folding or catalytic function of the affected protein. Here we report that two missense mutations in the N-terminal cytoplasmic tail of a Golgi-localized enzyme result in the failure of the enzyme to be retained in the Golgi, with subsequent degradation in lysosomes/release from the cells. This mislocalization of catalytically active phosphotransferase represents the basis of the lysosomal storage disorder present in patients with these mutations. In addition, these findings provide a clue to the signals that retain this enzyme, and perhaps other Golgi-resident enzymes, in the Golgi complex.
Direct Aorta Ascending Approach in Transcatheter Aortic Valve Implantation
Authors: Dahle Gry , Rein Kjell-Arne 
Published: February 2014

Objective Direct aorta ascending approach [transaortic approach (TAo)] is a new access way for transcatheter aortic valve implantation (TAVI) to be used in patients with peripheral vascular disease and as an alternative to transapical approach. Methods Both the Edwards SAPIEN and CoreValve systems were used. Depending on the position of the ascending aorta, the relation to the sternum, the brachiocephalic vein, vein grafts, and left and right internal mammary artery grafts from previous heart surgery, either right minithoracotomy or left ministernotomy was selected. Computed tomographic scan with reconstruction was applied for this decision making. A hybrid operating room was used with echocardiographic and fluoroscopy guidance. Results We have done 30 procedures via the aorta ascendens. The mean age of the patients was 80 years, and 18 were men. The mean Logistic EuroSCORE of 33 reflects the comorbidities. More than half of the patients had coronary vessel disease and had undergone coronary artery bypass graft; 20% had abdominal aortic aneurysm. The mean ejection fraction was 41%, and the patients were in New York Heart Association class III to IV. The mean gradient was 50 mm Hg, and the mean valve area was 0.7 cm2. The mean valve size was 28 mm. The use of Edwards SAPIEN versus CoreValve was 50%/50%, and thoracotomy versus sternotomy was 9 versus 21. All procedures were done successfully, but one patient had a periprocedural valve-in-valve implantation. Twenty-two patients were extubated in the operation room. The patients stayed in the intensive care unit for one night. Six patients were reoperated on. One patient had a postoperative balloon aortic valvuloplasty. The overall survival was 81% (follow up, 1–18 months). Conclusions Access design is an important issue in TAVI. When central approach is needed, TAVI-TAo is safe. For patients with low ejection fraction, the TAVI-TAo is preferred to the TAVI-transapical. The cannulation technique of the aorta is well known for cardiothoracic surgeons, and the method is feasible both for the Medtronic CoreValve and the Edwards SAPIEN valve, either via right minithoracotomy or ministernotomy to obtain the best coaxial alignment. It seems easier to position the bigger valves more precisely via this central approach.
Defining the Role of Chest Radiography in Determining Candidacy for Pectus Excavatum Repair
Authors: Poston Patrick M. , Patel Sonali S. , Rajput Maheen , Rossi Nicholas O. , Davis James E. , Turek Joseph W. 
Published: February 2014

Objective The Haller index (HI), derived from computed tomography (CT) of the chest, remains the standard for determining pectus excavatum (PE) severity. The ability to accurately determine PE severity from chest radiography (CXR) may provide substantial benefits. This study proposes to establish data-driven criteria for the use of CXR as a diagnostic modality in the preoperative evaluation of patients with PE. Methods A database of 77 patients with PE receiving preoperative CXR and CT was created. Haller indices were obtained from CT scans. Two cardiothoracic surgeons, blinded to the CT HI scores, independently calculated CXR HIs. Interrater reliability, correlations, sensitivity, specificity, and accuracy were calculated. Results A significant correlation was found between CXR HI estimates of the two observers, r = 0.84. Computed tomography HIs were used as the standard for identifying patients meeting surgical criteria (CT HI ≥3.2). From this, sensitivities, specificities, and accuracies were calculated for the corresponding CXR HIs determined by each observer. Observer CXR HI estimates had a sensitivity of 0.94 and 0.92, specificity of 0.77 and 0.42, and accuracy of 0.88 and 0.75. Conclusions We found a strong correlation between HIs calculated with each modality. In addition, CXR HIs demonstrated good interrater reliability. Although the sensitivity of CXR in diagnosing severe PE (CT HI ≥3.2) was high, specificity was less convincing. However, when using a cutoff of CXR HIs of 3.75 or greater, combined specificity was quite high (0.96). We recommend replacing CT with CXR in the pre-operative evaluation for PE. Computed tomography should be used as a confirmatory test for CXR HIs between 3.2 and 3.75.
Can the Cyanobacterial Carbon-Concentrating Mechanism Increase Photosynthesis in Crop Species? A Theoretical Analysis
Authors: McGrath Justin M. , Long Stephen P. 
Published: February 2014

AbstractExperimental elevation of [CO2] around C3 crops in the field has been shown to increase yields by suppressing the Rubisco oxygenase reaction and, in turn, photorespiration. Bioengineering a cyanobacterial carbon-concentrating mechanism (CCM) into C3 crop species provides a potential means of elevating [CO2] at Rubisco, thereby decreasing photorespiration and increasing photosynthetic efficiency and yield. The cyanobacterial CCM is an attractive alternative relative to other CCMs, because its features do not require anatomical changes to leaf tissue. However, the potential benefits of engineering the entire CCM into a C3 leaf are unexamined. Here, a CO2 and HCO3 − diffusion-reaction model is developed to examine how components of the cyanobacterial CCM affect leaf light-saturated CO2 uptake (A sat) and to determine whether a different Rubisco isoform would perform better in a leaf with a cyanobacterial CCM. The results show that the addition of carboxysomes without other CCM components substantially decreases A sat and that the best first step is the addition of HCO3 − transporters, as a single HCO3 − transporter increased modeled A sat by 9%. Addition of all major CCM components increased A sat from 24 to 38 µmol m−2 s−1. Several Rubisco isoforms were compared in the model, and increasing ribulose bisphosphate regeneration rate will allow for further improvements by using a Rubisco isoform adapted to high [CO2]. Results from field studies that artificially raise [CO2] suggest that this 60% increase in A sat could result in a 36% to 60% increase in yield.
Apyrase Suppression Raises Extracellular ATP Levels and Induces Gene Expression and Cell Wall Changes Characteristic of Stress Responses
Authors: Lim Min Hui , Wu Jian , Yao Jianchao , Gallardo Ignacio F. , Dugger Jason W. , Webb Lauren J. , Huang James , Salmi Mari L. , Song Jawon , Clark Greg , Roux Stanley J. 
Published: February 2014

Abstract
Plant cells release ATP into their extracellular matrix as they grow, and extracellular ATP (eATP) can modulate the rate of cell growth in diverse tissues. Two closely related apyrases (APYs) in Arabidopsis (Arabidopsis thaliana), APY1 and APY2, function, in part, to control the concentration of eATP. The expression of APY1/APY2 can be inhibited by RNA interference, and this suppression leads to an increase in the concentration of eATP in the extracellular medium and severely reduces growth. To clarify how the suppression of APY1 and APY2 is linked to growth inhibition, the gene expression changes that occur in seedlings when apyrase expression is suppressed were assayed by microarray and quantitative real-time-PCR analyses. The most significant gene expression changes induced by APY suppression were in genes involved in biotic stress responses, which include those genes regulating wall composition and extensibility. These expression changes predicted specific chemical changes in the walls of mutant seedlings, and two of these changes, wall lignification and decreased methyl ester bonds, were verified by direct analyses. Taken together, the results are consistent with the hypothesis that APY1, APY2, and eATP play important roles in the signaling steps that link biotic stresses to plant defense responses and growth changes.
Additional Amphivasal Bundles in Pedicel Pith Exacerbate Central Fruit Dominance and Induce Self-Thinning of Lateral Fruitlets in Apple
Authors: Celton Jean-Marc , Dheilly Emmanuelle , Guillou Marie-Charlotte , Simonneau Fabienne , Juchaux Marjorie , Costes Evelyne , Laurens François , Renou Jean-Pierre 
Published: February 2014

AbstractApple (Malus × domestica) trees naturally produce an excess of fruitlets that negatively affect the commercial value of fruits brought to maturity and impact their capacity to develop flower buds the following season. Therefore, chemical thinning has become an important cultural practice, allowing the selective removal of unwanted fruitlets. As the public pressure to limit the use of chemical agents increases, the control of thinning becomes a major issue. Here, we characterized the self-thinning capacity of an apple hybrid genotype from the tree scale to the molecular level. Additional amphivasal vascular bundles were identified in the pith of pedicels supporting the fruitlets with the lowest abscission potential (central fruitlet), indicating that these bundles might have a role in the acquisition of dominance over lateral fruitlets. Sugar content analysis revealed that central fruitlets were better supplied in sorbitol than lateral fruitlets. Transcriptomic profiles allowed us to identify genes potentially involved in the overproduction of vascular tissues in central pedicels. In addition, histological and transcriptomic data permitted a detailed characterization of abscission zone development and the identification of key genes involved in this process. Our data confirm the major role of ethylene, auxin, and cell wall-remodeling enzymes in abscission zone formation. The shedding process in this hybrid appears to be triggered by a naturally exacerbated dominance of central fruitlets over lateral ones, brought about by an increased supply of sugars, possibly through additional amphivasal vascular bundles. The characterization of this genotype opens new perspectives for the selection of elite apple cultivars.
Melatonin and tadalafil treatment improves erectile dysfunction after spinal cord injury in rats
Authors: Tavukçu Hasan Hüseyin , Şener Tarik Emre , Tinay İlker , Akbal Cem , Erşahin Mehmet , Çevik Özge , Çadırcı Selin , Reiter Russel J , Şener Göksel 
Published: February 2014

Summary

Oxidative stress plays an important role both in spinal cord injury (SCI) and erectile dysfunction (ED). The present study investigated the effects of melatonin and tadalafil treatment alone or in combination on SCI‐induced ED.

Male Wistar albino rats (n = 40) were divided into five groups: sham‐operated control and SCI‐injured rats given either vehicle, melatonin (10 mg/kg, i.p.), tadalafil (10 mg/kg, p.o.) or a combination of melatonin and tadalafil. Spinal cord injury was induced using a standard weight‐drop method. On Day 7 after SCI, intracavernosal pressure (ICP) was measured and all rats were decapitated. Cavernosal tissues were obtained to examine caspase 3, nitric oxide synthase (NOS), myeloperoxidase (MPO) and superoxide dismutase (SOD) activities, as well as cGMP, nerve growth factor (NGF), malondialdehyde (MDA) and glutathione (GSH) levels.

Spinal cord injury caused oxidative damage, as evidenced by increases in MDA and cGMP levels. In addition, MPO and caspase 3 activites were increased after SCI, whereas GSH and NGF levels and SOD activity were reduced. Melatonin effectively reversed these oxidative changes. Furthermore, in rats treated with both melatonin and tadalafil, the recoveries were more pronounced than in rats given either melatonin or tadalafil alone. The ICP/mean arterial pressure value in vehicle‐treated SCI rats was significantly higher than in the control group, whereas in the tadalafil‐ and tadalafil + melatonin‐treated groups have returned this value had returned to control levels.

As an individual treatment, and especially when combined with tadalafil, a well‐known agent in the treatment of ED, melatonin prevented SCI‐induced oxidative damage to cavernosal tissues and restored ED, most likely due to its anti‐oxidant effects.
Dual symbiosis with co‐occurring sulfur‐oxidizing symbionts in vestimentiferan tubeworms from a Mediterranean hydrothermal vent
Authors: Zimmermann Judith , Lott Christian , Weber Miriam , Ramette Alban , Bright Monika , Dubilier Nicole , Petersen Jillian M. 
Published: February 2014

SummaryVestimentiferan Tws colonize hydrothermal vents and cold seeps worldwide. They lack a digestive system and gain nutrition from endosymbiotic sulfur‐oxidizing bacteria. It is currently assumed that vestimentiferan Tws harbour only a single endosymbiont type. A few studies found indications for additional symbionts, but conclusive evidence for a multiple symbiosis is still missing. We investigated Tws from Marsili Seamount, a hydrothermal vent in the Mediterranean Sea. Molecular and morphological analyses identified the Tws as Lamellibrachia anaximandri. 16S ribosomal RNA clone libraries revealed two distinct gammaproteobacterial phylotypes that were closely related to sequences from other Lamellibrachia symbionts. Catalysed reporter deposition fluorescence in situ hybridization with specific probes showed that these sequences are from two distinct symbionts. We also found two variants of key genes for sulfur oxidation and carbon fixation, suggesting that both symbiont types are autotrophic sulfur oxidizers. Our results therefore show that vestimentiferans can host multiple co‐occurring symbiont types. Statistical analyses of vestimentiferan symbiont diversity revealed that host genus, habitat type, water depth and geographic region together accounted for 27% of genetic diversity, but only water depth had a significant effect on its own. Phylogenetic analyses showed a clear grouping of sequences according to depth, thus confirming the important role water depth played in shaping vestimentiferan symbiont diversity.