bluuebunny/crossref_metadata_2025 huggingface dataset:
The multiple nucleotide–divalent cation binding modes ofSaccharomyces cerevisiaeCK2α indicate a possible co-substrate hydrolysis product (ADP/GDP) release pathway
Authors: Liu Huihui , Wang Hong , Teng Maikun , Li Xu
Published: January 2014

CK2 is a ubiquitous and conserved protein kinase in eukaryotic organisms and is important in many biological processes. It is unique in maintaining constitutive activity and in using both ATP and GTP as phosphor donors. In this study, crystal structures of recombinantSaccharomyces cerevisiaeCK2α (scCK2α) complexed with GMPPNP, ATP and AMPPN with either Mg2+or Mn2+as the coordinated divalent cation are presented. The overall structure ofscCK2α shows high similarity to its homologous proteins by consisting of two domains with the co-substrate lying in the cleft between them. However, three characteristic features distinguishscCK2α from its homologues. Firstly, the Lys45–Glu53 and Arg48–Glu53 interactions inscCK2α lead Lys50 to adopt a unique conformation that is able to stabilize the γ-phosphate of the co-substrate, which makes the existence of the `essential divalent cation' not so essential. The multiple nucleotide–divalent cation binding modes of the active site ofscCK2α are apparently different from the two-divalent-cation-occupied active site ofZea maysCK2α and human CK2α. Secondly, conformational change of Glu53 inscCK2α–AMPPN breaks its interaction with Lys45 and Arg48; as a result, the co-substrate binding pocket becomes more open. This may suggest a clue to a possible ADP/GDP-release pathway, because the NE1 atom of the Trp in the `DWG motif' of CK2α forms a hydrogen bond to the O atom of Leu212, which seems to make ADP release by means of the `DFG-in flip to DFG-out' model found in most eukaryotic protein kinases impossible. Coincidentally, two sulfate ions which may mimic two phosphate groups were captured by Arg161 and Lys197 around the pocket. Mutagenesis and biochemical experiments on R161A and K197A mutants support the above proposal. Finally,scCK2α is unique in containing an insertion region whose function had not been identified in previous research. It is found that the insertion region contributes to maintaining the constitutively active conformation of thescCK2α catalytic site, but does not participate in interaction with the regulatory subunits.
Structure ofBacillus subtilisγ-glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site-directed glutamate analogue
Authors: Ida Tomoyo , Suzuki Hideyuki , Fukuyama Keiichi , Hiratake Jun , Wada Kei
Published: January 2014

γ-Glutamyltranspeptidase (GGT) is an enzyme that plays a central role in glutathione metabolism, and acivicin is a classical inhibitor of GGT. Here, the structure of acivicin bound toBacillus subtilisGGT determined by X-ray crystallography to 1.8 Å resolution is presented, in which it binds to the active site in a similar manner to that inHelicobacter pyloriGGT, but in a different binding mode to that inEscherichia coliGGT. InB. subtilisGGT, acivicin is bound covalently through its C3 atom withsp2hybridization to Thr403 Oγ, the catalytic nucleophile of the enzyme. The results show that acivicin-binding sites are common, but the binding manners and orientations of its five-membered dihydroisoxazole ring are diverse in the binding pockets of GGTs.
Structure of crenactin, an archaeal actin homologue active at 90°C
Authors: Lindås Ann-Christin , Chruszcz Maksymilian , Bernander Rolf , Valegård Karin
Published: January 2014

The crystal structure of the archaeal actin, crenactin, from the rod-shaped hyperthermophilic (optimal growth at 90°C) crenarchaeonPyrobaculum calidifontisis reported at 3.35 Å resolution. Despite low amino-acid sequence identity, the three-dimensional structure of the protein monomer is highly similar to those of eukaryotic actin and the bacterial MreB protein. Crenactin-specific features are also evident, as well as elements that are shared between crenactin and eukaryotic actin but are not found in MreB. In the crystal, crenactin monomers form right-handed helices, demonstrating that the protein is capable of forming filament-like structures. Monomer interactions in the helix, as well as interactions between crenactin and ADP in the nucleotide-binding pocket, are resolved at the atomic level and compared with those of actin and MreB. The results provide insights into the structural and functional properties of a heat-stable archaeal actin and contribute to the understanding of the evolution of actin-family proteins in the three domains of life.
Peptidoglycan in combination with muramyldipeptide synergistically induces an interleukin‐10‐dependent T helper 2‐dominant immune response
Authors: Matsui Katsuhiko , Ikeda Reiko
Published: January 2014

In this study, peptidoglycan (PEG) from Staphylococcus aureus‐stimulated, but not muramyldipeptide (MDP)‐stimulated, Langerhans cells (LCs) induced a dose‐dependent Th2‐prone immune response. However, when LCs were stimulated with PEG in combination with MDP, the strength of Th2 immune responses was synergistically augmented by MDP. Furthermore, it was found that production of IL‐10, but not of IL‐12 p40, by PEG‐stimulated LCs was also enhanced in the presence of MDP. These results suggest that MDP enhances Th2 cell development through up‐regulation of IL‐10 production from PEG‐stimulated LCs, increase the importance of S. aureus colonization in patients with atopic dermatitis.
Monetary Policy and the Uncovered Interest Rate Parity Puzzle: Theory and Empirical Results for Oceania
Authors: Guender Alfred V.
Published: January 2014

This article offers a theory‐based explanation for why high‐ interest‐rate countries see their currencies appreciate, the so‐called UIP puzzle. The central bank bases its target rule on the lag of the policy instrument and the CPI inflation rate. When combined with a stylised model of an open economy, the endogenous target rule can account for the systematic negative relation between the change in the exchange rate and the lagged interest rate differential. Foreign inflation and the foreign interest rate also affect nominal exchange rate changes. The model‐based behaviour of the exchange rate is tested on New Zealand and Australian data with mixed results.
PKCε Contributes to Chronic Ethanol‐Induced Steatosis in Mice but not Inflammation and Necrosis
Authors: Kaiser J. Phillip , Guo Luping , Beier Juliane I. , Zhang Jun , Bhatnagar Aruni , Arteel Gavin E.
Published: January 2014

Background

Protein kinase C epsilon (PKCε) has been shown to play a role in experimental steatosis by acute alcohol. The “two‐hit” hypothesis implies that preventing steatosis should blunt more advanced liver damage (e.g., inflammation and necrosis). However, the role of PKCε in these pathologies is not yet known. The goal of this current work was to address this question in a model of chronic alcohol exposure using antisense oligonucleotides (ASO) against PKCε.

Methods

Accordingly, PKCε ASO‐ and saline‐treated mice were fed high‐fat control or ethanol (EtOH)‐containing enteral diets for 4 weeks.

Results

Chronic EtOH exposure significantly elevated hepatic lipid pools as well as activated PKCε. The PKCε ASO partially blunted the increases in hepatic lipids caused by EtOH. Administration of PKCε ASO also completely prevented the increase in the expression of fatty acid synthase, and tumor necrosis factor α caused by EtOH. Despite these protective effects, the PKCε ASO was unable to prevent the increases in inflammation and necrosis caused by chronic EtOH. These latter results correlated with an inability of the PKCε ASO to blunt the up‐regulation of plasminogen activator inhibitor‐1 (PAI‐1) and the accumulation of fibrin. Importantly, PAI‐1 has been previously shown to more robustly mediate inflammation and necrosis (vs. steatosis) after chronic EtOH exposure.

Conclusions

This study identifies a novel potential mechanism where EtOH, independent of steatosis, can contribute to liver damage. These results also suggest that PAI‐1 and fibrin accumulation may be at the center of this PKCε‐independent pathway.
Identification of anti‐CD98 antibody mimotopes for inducing antibodies with antitumor activity by mimotope immunization
Authors: Saito Misa , Kondo Masahiro , Ohshima Motohiro , Deguchi Kazuki , Hayashi Hideki , Inoue Kazuyuki , Tsuji Daiki , Masuko Takashi , Itoh Kunihiko
Published: January 2014

A mimotope is an antibody‐epitope‐mimicking peptide retrieved from a phage display random peptide library. Immunization with antitumor antibody‐derived mimotopes is promising for inducing antitumor immunity in hosts. In this study, we isolated linear and constrained mimotopes from HBJ127, a tumor‐suppressing anti‐CD98 heavy chain mAb, and determined their abilities for induction of antitumor activity equal to that of the parent antibody. We detected elevated levels of antipeptide responses, but failed to detect reactivity against native CD98‐expressing HeLa cells in sera of immunized mice. Phage display panning and selection of mimotope‐immunized mouse spleen‐derived antibody Fab library showed that HeLa cell‐reactive Fabs were successfully retrieved from the library. This finding indicates that native antigen‐reactive Fab clones represented an undetectable minor population in mimotope‐induced antibody repertoire. Functional and structural analysis of retrieved Fab clones revealed that they were almost identical to the parent antibody. From these results, we confirmed that mimotope immunization was promising for retrieving antitumor antibodies equivalent to the parent antibody, although the co‐administration of adjuvant compounds such as T‐cell epitope peptides and Toll‐like receptor 4 agonist peptides is likely to be necessary for inducing stronger antitumor immunity than mimotope injection alone.
Targeting DNA damage response in cancer therapy
Authors: Hosoya Noriko , Miyagawa Kiyoshi
Published: January 2014

Cancer chemotherapy and radiotherapy are designed to kill cancer cells mostly by inducing DNA damage. DNA damage is normally recognized and repaired by the intrinsic DNA damage response machinery. If the damaged lesions are successfully repaired, the cells will survive. In order to specifically and effectively kill cancer cells by therapies that induce DNA damage, it is important to take advantage of specific abnormalities in the DNA damage response machinery that are present in cancer cells but not in normal cells. Such properties of cancer cells can provide biomarkers or targets for sensitization. For example, defects or upregulation of the specific pathways that recognize or repair specific types of DNA damage can serve as biomarkers of favorable or poor response to therapies that induce such types of DNA damage. Inhibition of a DNA damage response pathway may enhance the therapeutic effects in combination with the DNA‐damaging agents. Moreover, it may also be useful as a monotherapy when it achieves synthetic lethality, in which inhibition of a complementary DNA damage response pathway selectively kills cancer cells that have a defect in a particular DNA repair pathway. The most striking application of this strategy is the treatment of cancers deficient in homologous recombination by poly(ADP‐ribose) polymerase inhibitors. In this review, we describe the impact of targeting the cancer‐specific aberrations in the DNA damage response by explaining how these treatment strategies are currently being evaluated in preclinical or clinical trials.
Micafungin as antifungal prophylaxis in recipients of allogeneic hematopoietic stem cell transplantation: results of different dosage levels in clinical practice
Authors: Langebrake Claudia , Rohde Holger , Lellek Heinrich , Wolschke Christine , Kröger Nicolaus M.
Published: January 2014

Micafungin has been approved for the prophylaxis of Candida infections in patients undergoing allogeneic hematopoietic stem cell transplantation (allo‐HSCT). Here, we report a single‐center experience of three different dose levels regarding efficacy, toxicity, and colonization with Candida ssp. in clinical practice. In total, 150 consecutive adult patients who underwent allo‐HSCT received micafungin at a dosage of 50, 100, or 150 mg once daily for primary antifungal prophylaxis. Of those patients receiving more than six d of micafungin prophylaxis, 12/46 (26%), 6/44 (14%), and 9/46 (20%) were switched to empiric antifungal treatment. The frequency of invasive fungal infections (IFIs) according to EORTC criteria did not differ significantly (7/46; 15% vs. 5/44; 11% vs. 5/46; 11%) across the different dosage groups. In the 50‐mg group, there was one case of candidemia with C. parapsilosis after 12 d of micafungin prophylaxis. In all three groups, micafungin prophylaxis was well tolerated without any case of toxicity‐related treatment discontinuation. Renal function was not significantly altered, while increase of bilirubin was mainly due to concomitant ATG application. The incidence of IFIs is similar irrespective of the micafungin dosage while there was a trend toward more frequent change to empiric antifungal treatment as well as oropharyngeal colonization with candida in the lowest dosage group.
Increased cortical extracellular adenosine correlates with seizure termination
Authors: Van Gompel Jamie J. , Bower Mark R. , Worrell Gregory A. , Stead Matt , Chang Su‐Youne , Goerss Stephan J. , Kim Inyong , Bennet Kevin E. , Meyer Fredric B. , Marsh W. Richard , Blaha Charles D. , Lee Kendall H.
Published: January 2014

Objective

Seizures are currently defined by their electrographic features. However, neuronal networks are intrinsically dependent on neurotransmitters of which little is known regarding their periictal dynamics. Evidence supports adenosine as having a prominent role in seizure termination, as its administration can terminate and reduce seizures in animal models. Furthermore, microdialysis studies in humans suggest that adenosine is elevated periictally, but the relationship to the seizure is obscured by its temporal measurement limitations. Because electrochemical techniques can provide vastly superior temporal resolution, we test the hypothesis that extracellular adenosine concentrations rise during seizure termination in an animal model and humans using electrochemistry.

Methods

White farm swine (n = 45) were used in an acute cortical model of epilepsy, and 10 human epilepsy patients were studied during intraoperative electrocorticography (ECoG). Wireless Instantaneous Neurotransmitter Concentration Sensor (WINCS)–based fast scan cyclic voltammetry (FSCV) and fixed potential amperometry were obtained utilizing an adenosine‐specific triangular waveform or biosensors, respectively.

Results

Simultaneous ECoG and electrochemistry demonstrated an average adenosine increase of 260% compared to baseline, at 7.5 ± 16.9 s with amperometry (n = 75 events) and 2.6 ± 11.2 s with FSCV (n = 15 events) prior to electrographic seizure termination. In agreement with these animal data, adenosine elevation prior to seizure termination in a human patient utilizing FSCV was also seen.

Significance

Simultaneous ECoG and electrochemical recording supports the hypothesis that adenosine rises prior to seizure termination, suggesting that adenosine itself may be responsible for seizure termination. Future work using intraoperative WINCS–based FSCV recording may help to elucidate the precise relationship between adenosine and seizure termination.
Glucose metabolism transporters and epilepsy: Only GLUT1 has an established role
Authors: Hildebrand Michael S. , Damiano John A. , Mullen Saul A. , Bellows Susannah T. , Oliver Karen L. , Dahl Hans‐Henrik M. , Scheffer Ingrid E. , Berkovic Samuel F.
Published: January 2014

The availability of glucose, and its glycolytic product lactate, for cerebral energy metabolism is regulated by specific brain transporters. Inadequate energy delivery leads to neurologic impairment. Haploinsufficiency of the glucose transporter GLUT1 causes a characteristic early onset encephalopathy, and has recently emerged as an important cause of a variety of childhood or later‐onset generalized epilepsies and paroxysmal exercise‐induced dyskinesia. We explored whether mutations in the genes encoding the other major glucose (GLUT3) or lactate (MCT1/2/3/4) transporters involved in cerebral energy metabolism also cause generalized epilepsies. A cohort of 119 cases with myoclonic astatic epilepsy or early onset absence epilepsy was screened for nucleotide variants in these five candidate genes. No epilepsy‐causing mutations were identified, indicating that of the major energetic fuel transporters in the brain, only GLUT1 is clearly associated with generalized epilepsy.
Napsin A is a useful marker for metastatic adenocarcinomas of pulmonary origin
Authors: Kim Moon‐Young , Go Heounjeong , Koh Jaemoon , Lee Kyoungbun , Min Hye‐Sook , Kim Min‐A , Jeon Yoon Kyung , Lee Hye‐Seung , Moon Kyung‐Chul , Park So Yeon , Kim Woo‐Ho , Chung Doo Hyun
Published: January 2014

Aims

To address whether napsin A is useful for identifying metastatic adenocarcinomas of pulmonary origin.

Methods and results

Fifty‐four cases of adenocarcinoma that metastasized from the lungs to various sites and 1762 cases of carcinoma from various organs were immunostained for napsin A, TTF‐1, CK7, CK20 and CDX2 using tissue microarray. The expression patterns of napsin A and TTF‐1 in metastatic pulmonary adenocarcinomas were compared with matched primary lung tumours. Napsin A and TTF‐1 were expressed in 87.0% and 81.5% of the metastatic pulmonary adenocarcinomas, respectively. Although there was no significant difference in the positivity of napsin A and TTF‐1 as a single marker in metastatic pulmonary adenocarcinomas, the expression scores for napsin A were much higher than those for TTF‐1 (P < 0.001). Moreover, the positivity and expression scores of napsin A in primary pulmonary adenocarcinomas were maintained in metastatic adenocarcinomas better than TTF‐1. Most non‐pulmonary adenocarcinomas were negative for napsin A, except for renal cell carcinomas (13.4%), ovarian adenocarcinomas (7.1%) and uterine endometrial adenocarcinomas (14.5%). In particular, clear cell adenocarcinomas of ovary (68.8%) and uterus (66.7%) frequently expressed napsin A.

Conclusions

These data suggest that napsin A may be a useful marker for identifying metastatic adenocarcinomas of pulmonary origin in combination with TTF‐1.
Assessment of Postoperative Pain in Cats After Ovariectomy by Laparoscopy, Median Celiotomy, or Flank Laparotomy
Authors: Gauthier Olivier , Holopherne‐Doran Delphine , Gendarme Thalia , Chebroux Alexandre , Thorin Chantal , Tainturier Daniel , Bencharif Djemil
Published: January 2014

Objective

To compare postoperative pain, duration of surgery, and duration of anesthesia for 3 methods of ovariectomy in cats: (1) conventional ventral median open approach (Midline), (2) right flank approach (Flank), and (3) median 2‐portal laparoscopic procedure (Lap).

Study Design

Randomized, prospective clinical trial.

Animals

Healthy, sexually intact female cats (n = 60).

Methods

Cats were randomly assigned to 1 of 3 groups: Midline (n = 20), Flank (20), and Lap (20) were evaluated 1, 2, 4, 6, and 12 hours after endotracheal extubation. Postoperative pain was scored using the 4A‐vet pain scale that combines a subjective numerical pain rating and objective scoring of physiologic and behavioral variables including the response to stimulation of the surgical site. Pain scores (PS) were compared between groups.

Results

There was a significant difference in the PS between groups. PS for Midline and Flank were not significantly different but were both significantly higher compared with Lap. Depending on time, 5–20% of the cats had intense postoperative pain in both Midline and Flank groups. None of the Lap cats had intense postoperative pain.

Conclusions

Laparoscopic ovariectomy, although slower, appeared less painful compared with conventional ventral midline and flank ovariectomy. Postoperative pain did not differ significantly between midline and flank groups.
Using levels of evidence to compare clinical impact from research
Authors: Ahmad Tashfeen , Chinoy Muhammad Amin , Tayyab Muhammad
Published: January 2014

Objectives

Impact of medical institutions on clinical decision‐making globally might be estimated by the level of evidence of their research articles. The aim of this study was to compare levels of evidence of articles for Pakistan.

Methods

We compared levels of evidence of articles from Pakistan, Nigeria, Japan, and the United States (U.S.).

Results

Majority (73%) of articles in U.S. general medical journals were high levels (1–2), while majority (66% to 95%) in Japanese, Nigerian, Pakistani, and sub‐specialty U.S. journals were lower levels (3–4) (P < 0.001). The number of articles from various regions of Pakistan did not correspond to their population or number of medical colleges/universities, mainly due to the skewing effect of one institution from Karachi which contributed 38% of all high‐level articles.

Conclusions

A comparison of levels of evidence of articles across institutions might reflect relative potential of clinical impact, and might be useful for institutions, policy makers, and health research planners for priority setting.
An exploration of the effects of introducing a telemonitoring system for continence assessment in a nursing home
Authors: Yu Ping , Hailey David , Fleming Richard , Traynor Victoria
Published: January 2014

Aims and objectives

To explore the effects of introducing a telemonitoring and care planning system for urinary continence assessment in a nursing home and adherence by care staff to urinary continence care plans.

Background

Only a few studies have explored the effect of introducing telemonitoring system on urinary continence care, none for older people in nursing homes.

Design

Pre‐ and postintervention repeated measures design.

Methods

Data for the study were collected from August–October 2011. Care staff were trained in the use of a telemonitoring system for continence assessment. Voiding events for each older person were recorded using the system during a 72‐hour urinary continence assessment, and the data were used to prepare an individualised care plan. After two weeks of using the new care plan, a second assessment was carried out for each older person, using the telemonitoring system.

Results

The participants were on average 81 years old and assessed as having high care needs. The statistically significant outcomes were as follows: reduced volume of urine voided into continence aids, reduced number of prescribed toileting visits, increased number of actual toilet visits, increased number of successful toileting events and increased adherence to urinary continence care plans by staff.

Conclusions

During a 12‐week trial, urinary continence assessment and management of older people were improved. This suggests that the introduction of a suitably designed telemonitoring system combined with staff training can improve urinary continence care.

Relevance to clinical practice

The results suggest that nursing homes can improve continence assessment and management practices by adopting an appropriately designed mobile, wireless telemonitoring system for continence assessment and providing the associated staff training programmes.
Evaluation of an individualised programme to promote self‐care in sleep‐activity in patients with coronary artery disease – a randomised intervention study
Authors: Johansson Anna , Adamson Anita , Ejdebäck Jan , Edéll‐Gustafsson Ulla
Published: January 2014

Aims and objectives

To evaluate the effectiveness of an individualised programme to promote self‐care in sleep‐activity in patients with coronary artery disease.

Background

Recent scientific findings have shown that low physical exercise and stress interfere with coronary artery disease patients' sleep quality and sleep efficiency independent of gender, age and co‐morbidity.

Design

A randomised pretest–post‐test control design.

Methods

Forty‐seven patients who had undergone a coronary revascularisation procedure and/or pharmacological treatment three to seven weeks earlier at a general hospital were randomised to either an intervention group or a control group. Data collection was carried out by questionnaires, a study‐specific sleep diary and actigraphy registration for 10 consecutive 24‐hour periods, with a follow‐up after three to four months. The intervention group underwent a nurse‐led individualised education programme to promote self‐care of sleep‐activity. Sleep habits and sleep‐related lifestyle together formed the basis for setting up individual goals together with the nurse. Individual advice on physical training, relaxation exercise and a CD‐based relaxation programme was provided by a physiotherapist. Both groups received a brochure about sleep and stress.

Results

At a three‐ to four‐month follow‐up, the main improvements were seen in the intervention group regarding sleep quality, sleep duration and sleep efficiency in the sleep diary and sleep efficiency in actigraphy. Statistical improvements in health‐related quality of life were revealed. This was not so obvious in the control group.

Conclusions

An individualised intervention programme to promote self‐care of sleep‐activity including relaxation in patients with coronary artery disease led by a nurse may improve sleep quality. However, a longitudinal study to promote self‐care in sleep‐activity should be performed using a larger sample and multiple sites with continuous follow‐ups to determine whether any positive effects remain stable over time.

Relevance to clinical practice

Implementation of a multiprofessional individualised programme to promote self‐care of sleep‐activity including relaxation based on patients' needs, supported by a healthcare team and led by nurses, is important in clinical practice.
Exenatide dosing in alpacas
Authors: Cebra C. K. , Smith C. C. , Stang B. V. , Tornquist S. J.
Published: January 2014

In order to investigate whether exenatide could be used to stimulate glucose clearance and insulin secretion in alpacas without causing colic signs, six healthy adult alpacas were injected once a day with increasing subcutaneous doses. A follow‐up intravenous glucose injection was given to induce hyperglycemia, and serial blood samples were collected to measure plasma concentrations of glucose, insulin, triglycerides, beta‐hydroxybutyrate, and nonesterified fatty acids. The exenatide doses used were saline control (no drug), and 0.02, 0.05, or 0.1 mcg/kg injected subcutaneously. Alpacas had significantly lower plasma glucose concentrations and higher insulin concentrations on all treatment days compared with the control day, but the increase in insulin was significantly greater and lasted significantly longer when the alpacas received the two higher dosages. Two of the alpacas developed mild colic signs at the 0.05 mcg/kg dose and were not evaluated at the highest dose. Based on these findings, the 0.05 mcg/kg dose appears to offer the greatest stimulation of insulin secretion and glucose clearance without excessive risk or severity of complications.
Modeling within field variation of the compaction layer in a paddy rice field using a proximal soil sensing system
Authors: Islam M. M. , Saey T. , De Smedt P. , Van De Vijver E. , Delefortrie S. , Van Meirvenne M.
Published: January 2014

A key characteristic of flooded paddy fields is the plough pan. This is a sub‐soil layer of greater compaction and bulk density, which restricts water losses through percolation. However, the thickness of this compacted layer can be inconsistent, with consequences such as variable percolation and leaching losses of nutrients, which therefore requires precision management of soil water. Our objective was to evaluate a methodology to model the thickness of the compacted soil layer using a non‐invasive electromagnetic induction sensor (EM38‐MK2). A 2.7 ha alluvial non‐saline paddy rice field was measured with a proximal soil sensing system using theEM38‐MK2 and the apparent electrical conductivity (ECa) of the wet paddy soil was recorded at a high‐resolution (1.0 × 0.5 m). Soil bulk density (n = 10) was measured using undisturbed soil cores, which covered locations with large and smallECavalues. At the same locations (within 1 m2) the depth of the different soil layers was determined by penetrometer. Then a fitting procedure was used to model theECa– depth response functions of theEM38‐MK2, which involved solving a system of non‐linear equations and aR2value of 0.89 was found. These predictions were evaluated using independent observations (n = 18) where aPearson correlation coefficient of 0.87 with anRMSEEvalue of 0.03 m was found. TheECameasurements allowed the detail estimation of the compacted layer thickness. The link between water percolation losses and thickness of the compacted layer was confirmed by independent observations with an inverse relationship having aPearson correlation coefficient of 0.89. This rapid, non‐invasive and cost‐effective technique offers new opportunities to measure differences in the thickness of compacted layers in water‐saturated soils. This has potential for site‐specific soil management in paddy rice fields.
Visual Evaluation of Soil Structure Under Grassland management
Authors: Cui J. , Askari M. S. , Holden N. M.
Published: January 2014

Twenty sites representing the typical range of grass‐based beef and dairy production management intensity in Ireland were used to assess soil structural quality with the Visual Evaluation of Soil Structure (VESS) method combined with laboratory analysis. The results showed that VESS was suitable for assessing soil structural quality for grassland productivity. According to the threshold values proposed by Ball [Soil Use and Management (2007), 23, 329–337] for management intervention, all fields except one in this study were between Sq 1 and Sq 3, indicating that the typical range of management intensity does not cause undue soil damage and can be regarded as sustainable for soil structure. There was an indication that as intensification increases, temperate maritime grassland soils showed signs of degradation with respect to soil structure for maintaining grass productivity. While reseeding might solve some problems, it causes others due to the release of soil carbon. This raises the prospect that ‘sustainable intensification’ of livestock production may be limited by the health of the soil resource that supports it. Significant negative correlations between Sq and soil C content (P < 0.01) and between Sq and soil N content (P < 0.05) were observed, indicating a close relationship between soil structure and soil carbon and nitrogen.
First Complete Genome Sequence of Escherichia albertii Strain KF1, a New Potential Human Enteric Pathogen
Authors: Fiedoruk Krzysztof , Daniluk Tamara , Swiecicka Izabela , Murawska Emilia , Sciepuk Malgorzata , Leszczynska Katarzyna
Published: January 2014

Escherichia albertii
has been recently recognized as an emerging human and bird enteric pathogen. Here, we report the first complete chromosome nucleotide sequence of a clinical isolate of
E. albertii
strain KF1, which may provide information about the pathogenic potential of this new species and the mechanisms of evolution of enteropathogenic
Escherichia
spp.
Complete Genome Sequence of Mycoplasma ovis Strain Michigan, a Hemoplasma of Sheep with Two Distinct 16S rRNA Genes
Authors: Deshuillers Pierre L. , Santos Andrea P. , do Nascimento Naíla C. , Hampel Joseph A. , Bergin Ingrid L. , Dyson Melissa C. , Messick Joanne B.
Published: January 2014

We report the complete genome sequence of
Mycoplasma ovis
strain Michigan. Its single circular chromosome has 702,511 bp and contains 2 copies of the 16S rRNA gene, one corresponding to
M. ovis
and the other to “
Candidatus
Mycoplasma haemovis.” All housekeeping genes and the 5S-23S rRNA genes are present in single copies.
Whole-Genome Sequence Characterization of a Beak and Feather Disease Virus in a Wild Regent Parrot (
Polytelis anthopeplus monarchoides
)
Authors: Sarker Subir , Forwood Jade K. , Ghorashi Seyed A. , McLelland David , Peters Andrew , Raidal Shane R.
Published: January 2014

The whole-genome sequence of beak and feather disease virus (BFDV) from a wild Australian regent parrot (
Polytelis anthopeplus monarchoides
) was characterized. The genome consists of 1,993 bp and has a typical stem-loop structure between open reading frame 1 (ORF1) and ORF2. This is the first evidence of BFDV infection as well as the complete genome sequence for this host species, globally.
Complete Genome Sequence of a Porcine Parvovirus Strain Isolated in Central China
Authors: Wang Lin-Qing , Wang Yan , Chen Long-Biao , Fu Peng-Fei , Chen Hong-Ying , Cui Bao-An
Published: January 2014

We report here the complete genome sequence of the porcine parvovirus (PPV) strain J-PPV, isolated from central China. Our data, together with sequence data for PPV isolates from other regions of China, will help in understanding the epidemiology and molecular characteristics of PPV field isolates in China.
Draft Genome Sequence of Bacillus thuringiensis Strain BrMgv02-JM63, a Chitinolytic Bacterium Isolated from Oil-Contaminated Mangrove Soil in Brazil
Authors: Marcon Joelma , Taketani Rodrigo Gouvêa , Dini-Andreote Francisco , Mazzero Giulia Inocêncio , Soares Fabio Lino , Melo Itamar Soares , Azevedo João Lúcio , Andreote Fernando Dini
Published: January 2014

Here, we report the draft genome sequence and the automatic annotation of
Bacillus thuringiensis
strain BrMgv02-JM63. This genome comprises a set of genes involved in the metabolism of chitin and
N
-acetylglucosamine utilization, thus suggesting the possible role of this strain in the cycling of organic matter in mangrove soils.
Draft Genome Sequence of the Aquatic Phosphorus-Solubilizing and -Mineralizing Bacterium
Bacillus
sp. Strain CPSM8
Authors: Maitra Nilanjan , Whitman William B. , Ayyampalayam Saravanaraj , Samanta Srikanta , Sarkar Keka , Bandopadhyay Chinmay , Aftabuddin M. , Sharma Anil P. , Manna Sanjib K.
Published: January 2014

Bacillus
sp. strain CPSM8 is an efficient solubilizer and mineralizer of phosphorus. Here, we present the 4.39-Mb draft genome sequence of the strain, providing insight into the phosphorus-releasing genes related to productivity in aquatic habitats.
Clown nose: a case of disfiguring nodular squamous cell carcinoma of the face
Authors: Colletti Giacomo , Allevi Fabiana , Moneghini Laura , Palvarini Marina
Published: January 2014

‘Clown nose’ (CN) is the common medical term referring to a reddish-brown bulge involving the tip of the nose, reminding of a clown's fake red nose. Reports about these tumours are scarce. Most reports refer to metastatic skin manifestation of systemic malignancies: this condition has been rarely described as a primary skin neoplasm. We report a case of a 31-year-old patient with a giant cutaneous squamous cell carcinoma of the nose which evolved into a CN. After ruling out genetic or immune risk factors, the patient was treated with surgical excision of the lesion and local reconstruction with good aesthetic outcome and no recurrence over a 2-year follow-up.
Leucoerythroblastosis and thrombocytopenia as clues to metastatic malignancy
Authors: Mahdi E J , Mahdi A J
Published: January 2014

The association of metastatic breast cancer presenting as thrombocytopenia and anaemia is demonstrated in the following case of a 79-year-old woman. Her main symptoms were abdominal pain, altered bowel habit and weight loss. Without a clear causative pathology, she underwent a CT scan which demonstrated multiple sclerotic bone lesions. With a raised CA15-3 and strong oestrogen receptor positivity on immunohistochemistry on a trephine bone marrow biopsy, a diagnosis of metastatic lobular breast cancer was made. Interestingly, only a small breast mass was noted on mammography. The patient was managed conservatively and initiated on supportive therapy. This case report summarises the varying presentation of bone marrow suppression secondary to metastatic infiltration, especially in the absence of classical symptoms associated with primary solid tumour. Accurate bone marrow analysis is also vital in establishing the final diagnosis.
Light microscopy survey of extant gymnosperm root protophloem and comparison with basal angiosperms
Authors: Pesacreta Thomas C. , Purpera Michael A.
Published: January 2014

Gymnosperm root protophloem is not well understood. There is a question as to whether root protophloem cells mature as phloem parenchyma, or as sieve elements, or if within the protophloem there is an anatomical and evolutionary gradient having characteristics of both cell types. This question is relevant to understanding anatomical and physiological mechanisms that supply nutrients to the root tip. Anatomical data from a broad range of species show that gymnosperms have one to three layers of parenchymatous protophloem cells located at the vascular cylinder periphery between the pericyle and the metaphloem. In some species, these cells are associated with secretory idioblasts. Near the root apex, protophloem cells develop a large central vacuole and, in transverse sections, their radial walls tend to be radially elongated. When mature, these cells are highly longitudinally elongated. Only these cells exhibit surging toward the root apex during chemical fixation. These data indicate that protophloem of gymnosperm roots lacks sieve elements. Because of its distinctive anatomical characteristics and the absence of sieve elements, gymnosperm root protophloem is a vegetative synapomorphy among extant species. The restriction of this tissue type to gymnosperms supports the hypothesis that it originated in a progenitor of that clade.
Effect of GUP on the Kepler problem and a variable minimal length
Authors: Ahmadi Fatemeh , Khodagholizadeh Jafar
Published: January 2014

Various approaches to quantum gravity, such as string theory, predict a minimal measurable length and a modification of the Heisenberg uncertainty principle near the Plank scale, known as the generalized uncertainty principle (GUP). Here we study the effects of GUP, which preserves the rotational symmetry of the space–time, on the Kepler problem. By comparing the value of the perihelion shift of the planet Mercury in Schwarzschild – de Sitter space–time with the resultant value of GUP, we find a relation between the minimal measurable length and the cosmological constant of the space–time. Now, if the cosmological constant varies with time, we have a variable minimal length in the space–time. Finally, we investigate the effects of GUP on the stability of circular orbits.
Deposit temperature of pyroclastic density currents emplaced during the El Chichón 1982 and Colima 1913 eruptions
Authors: Sulpizio Roberto , Zanella Elena , Macías José Luis , Saucedo Ricardo
Published: January 2014

New data on the pyroclastic density current (PDC) deposit temperature (
T
dep
) are provided for two prominent eruptions of Mexican volcanoes of the twentieth century: the 1982 eruption of El Chichón and the 1913 eruption of Colima. In spite of similar lithofacies, magma composition and pre-eruptive conditions, the
T
dep
of the PDCs from the 1982 (El Chichón) and 1913 (Colima) eruptions differ significantly, with intervals of
T
dep
of 360–420 °C and 250–330 °C, respectively. These new data emphasize that a full understanding of the physical mechanisms responsible for equilibrium temperature attainment within a pyroclastic deposit has not yet been realized. The
T
dep
measured for El Chichón PDC deposits confirm the preliminary data published elsewhere, while Colima magnetic temperatures provide different values to those published previously.

supplementary-material:

T
dep
measurements for the different sites at El Chichon volcano and Colima volcano are available at:
http://www.geolsoc.org.uk/SUP18695
.
Magma flow and palaeo-stress deduced from magnetic fabric analysis of the Álftafjörður dyke swarm: implications for shallow crustal magma transport in Icelandic volcanic systems
Authors: Eriksson P. I. , Riishuus M. S. , Elming S.-Å.
Published: January 2014

Neogene regional mafic dykes extending north of the Álftafjörður central volcano in east Iceland are studied to test models of dyke swarm emplacement at spreading ridges. This is accomplished by using anisotropy of magnetic susceptibility to define fossilized magma flow regimes. The imbrication of the foliation plane, defined by the minor susceptibility axis, is used as an indicator of the flow direction. Contemporaneous shear resolved on the dyke walls may modify a pure flow-induced fabric and such shear regimes are therefore retracted. The magma flow and palaeo-stress resolved on the dykes are determined in 13 of 24 dykes. The magma flow is interpreted as subhorizontal and northwards directed away from the central volcano for nine dykes, and found to be vertical in three cases. The preferentially subhorizontal magma flow in the Álftafjörður swarm suggests that dyke propagation in this type of Icelandic volcanic system originates in shallow crustal magma chambers. The regional tectonic palaeo-stress field is deduced to cause oblique spreading across the Álftafjörður dyke swarm and govern a subhorizontal dextral shear component on the dyke planes during propagation. This interpretation is not in conflict with the left-stepping en echelon trend distribution of individual dykes relative to the trend of the swarm.
The hydrostatic pressure indifference point underestimates orthostatic redistribution of blood in humans
Authors: Petersen L. G. , Carlsen J. F. , Nielsen M. B. , Damgaard M. , Secher N. H.
Published: January 2014

The hydrostatic indifference point (HIP; where venous pressure is unaffected by posture) is located at the level of the diaphragm and is believed to indicate the orthostatic redistribution of blood, but it remains unknown whether HIP coincides with the indifference point for blood volume (VIP). During graded (± 20°) head-up (HUT) and head-down tilt (HDT) in 12 male volunteers, we determined HIP from central venous pressure and VIP from redistribution of both blood, using ultrasound imaging of the inferior caval vein (VIPui), and fluid volume, by regional electrical admittance (VIPadm). Furthermore, we evaluated whether inflation of medical antishock trousers (to 70 mmHg) affected HIP and VIP. Leaving cardiovascular variables unaffected by tilt, HIP was located 7 ± 4 cm (mean ± SD) below the 4th intercostal space (IC-4) during HUT and was similar (7 ± 3 cm) during HDT and higher ( P < 0.0001) than both VIPui (HUT: 22 ± 16 cm; HDT: 13 ± 7 cm) and VIPadm (HUT: 29 ± 9 cm; HDT: 20 ± 9 cm below IC-4). During HUT antishock trousers elevated both HIP and VIPui [to 3 ± 5 cm ( P = 0.028) and 17 ± 7 cm below IC-4 ( P = 0.051), respectively], while VIPadm remained unaffected. By simultaneous recording of pressure and filling of the inferior caval vein as well as fluid distribution, we found HIP located corresponding to the diaphragm while VIP was placed low in the abdomen, and that medical antishock trousers elevated both HIP and VIP. The low indifference point for volume shows that the gravitational influence on distribution of blood is more profound than indicated by the indifference point for venous pressure.
Identification of Immune Factors Regulating Antitumor Immunity Using Polymeric Vaccines with Multiple Adjuvants
Authors: Ali Omar A. , Verbeke Catia , Johnson Chris , Sands R. Warren , Lewin Sarah A. , White Des , Doherty Edward , Dranoff Glenn , Mooney David J.
Published: January 2014

The innate cellular and molecular components required to mediate effective vaccination against weak tumor-associated antigens remain unclear. In this study, we used polymeric cancer vaccines incorporating different classes of adjuvants to induce tumor protection, to identify dendritic cell (DC) subsets and cytokines critical to this efficacy. Three-dimensional, porous polymer matrices loaded with tumor lysates and presenting distinct combinations of granulocyte macrophage colony-stimulating factor (GM-CSF) and various Toll-like receptor (TLR) agonists affected 70% to 90% prophylactic tumor protection in B16-F10 melanoma models. In aggressive, therapeutic B16 models, the vaccine systems incorporating GM-CSF in combination with P(I:C) or CpG-ODN induced the complete regression of solid tumors (≤40 mm2), resulting in 33% long-term survival. Regression analysis revealed that the numbers of vaccine-resident CD8(+) DCs, plasmacytoid DCs (pDC), along with local interleukin (IL)-12, and granulocyte colony-stimulating factor (G-CSF) concentrations correlated strongly to vaccine efficacy regardless of adjuvant type. Furthermore, vaccine studies in Batf3−/− mice revealed that CD8(+) DCs are required to affect tumor protection, as vaccines in these mice were deficient in cytotoxic T lymphocytes priming and IL-12 induction in comparison with wild-type. These studies broadly demonstrate that three-dimensional polymeric vaccines provide a potent platform for prophylactic and therapeutic protection, and can be used as a tool to identify critical components of a desired immune response. Specifically, these results suggest that CD8(+) DCs, pDCs, IL-12, and G-CSF play important roles in priming effective antitumor responses with these vaccines. Cancer Res; 74(6); 1670–81. ©2014 AACR.
Exposure to a Histone Deacetylase Inhibitor Has Detrimental Effects on Human Lymphocyte Viability and Function
Authors: Wong Deborah J.L. , Rao Amol , Avramis Earl , Matsunaga Douglas R. , Komatsubara Kimberly M. , Atefi Mohammad S. , Escuin-Ordinas Helena , Chodon Thinle , Koya Richard C. , Ribas Antoni , Comin-Anduix Begoña
Published: January 2014

Histone deacetylase inhibitors (HDACi) have been reported to increase tumor antigen expression, and have been successfully tested as adjuvants for melanoma immunotherapy in mouse models. In this work, we tested the effects of a pan-HDACi on human lymphocytes and melanoma cell lines. Effects of the pan-HDACi panobinostat (LBH589) on cell viability, cell cycle, apoptosis, and DNA damage were determined in peripheral blood mononuclear cells (PBMC) from 2 healthy donors, 13 patients with metastatic melanoma, 2 bone marrow samples from patients with different malignances, and 12 human melanoma cell lines. Intracellular signaling in lymphocytes, with or without cytokine stimulation, was analyzed by phospho-flow cytometry in one of each type. The IC50 in PBMCs was <20 nmol/L compared with >600 nmol/L in melanoma cell lines; >40% apoptotic cell death in PBMCs versus <10% in melanoma cell lines was seen at the same concentration. Phospho-histone variant H2A.X (pH2A.X) increased 2-fold in healthy donor PBMCs at 1 nmol/L, whereas the same effect in the melanoma cell line M229 required 10 nmol/L. pH2A.X was inhibited slightly in the PBMCs of 3 patients with metastatic melanoma at 1 nmol/L and in the melanoma cell line M370 at 10 nmol/L. Panobinostat inhibited phospho-STAT1/3/5/6, -p38, -ERK, -p53, -cyclin D3, and -histone H3 in flow cytometry–gated healthy donor B and T cells, whereas it induced up to 6-fold activation in patients with metastatic melanoma and bone marrow samples. In human lymphocytes, panobinostat alters key lymphocyte activation signaling pathways and is cytotoxic at concentrations much lower than those required for melanoma antitumor activity, resulting in an adverse therapeutic window. Cancer Immunol Res; 2(5); 459–68. ©2014 AACR.