bluuebunny/crossref_metadata_2025 huggingface dataset:
Inflammatory biomarkers and prediction for intensive care unit admission in severe community-acquired pneumonia*
Authors: Ramírez Paula , Ferrer Miquel , Martí Verónica , Reyes Soledad , Martínez Raquel , Menéndez Rosario , Ewig Santiago , Torres Antoni
Published: June 2011

Objective:

Increased inflammatory response is related to severity and outcome in community-acquired pneumonia, but the role of inflammatory biomarkers in deciding intensive care unit admission is unknown. We assessed the relationship between inflammatory response, prediction for intensive care unit admission, delayed intensive care unit admission, and outcome in patients with community-acquired pneumonia.

Design:

Prospective clinical study.

Setting:

Intensive care units of two university hospitals.

Patients:

We included 627 ward and 58 intensive care unit patients with community-acquired pneumonia, 36 with direct and 22 with delayed intensive care unit admission.

Interventions:

Serum levels of C-reactive protein, procalcitonin, tumor necrosis factor-α, interleukin-1, interleukin-6, interleukin-8, and interleukin-10 at admission.

Measurements and Main Results:

We assessed the prediction for intensive care unit admission of biomarkers and the Infectious Diseases Society of America/American Thoracic Society guidelines minor criteria for severe community-acquired pneumonia. Procalcitonin (p = .001), C-reactive protein (p = .005), tumor necrosis factor-α (p = .042), and interleukin-6 (p = .003) levels were higher in intensive care unit-admitted patients; however, the Infectious Diseases Society of America/American Thoracic Society guidelines minor severity criteria predicted better intensive care unit admission (odds ratio, 12.03; 95% confidence interval, 5.13–28.20; p < .001). No patient with severe community-acquired pneumonia by three or more minor severity criteria and procalcitonin levels below the optimal cutoff (0.35 ng/mL) needed intensive care unit admission compared with 14 (23%) with levels above the cutoff (p = .032). In patients initially admitted to wards, procalcitonin (p = .012) and C-reactive protein (p = .039) were higher in those 22 patients subsequently transferred to the intensive care unit after adjusting for age, comorbidities, and Pneumonia Severity Index risk class. Despite initially admitted to wards, 14 (64%) patients with delayed intensive care unit admission had already criteria for severe community-acquired pneumonia at admission compared with 73 (12%) ward patients (p < .001).

Conclusion:

Inflammatory biomarkers identified patients needing intensive care unit admission, including those with delayed intensive care unit admission. Patients with severe community-acquired pneumonia by minor criteria and low levels of procalcitonin may be safely admitted to wards. Correctly applying the Infectious Diseases Society of America/American Thoracic Society guidelines would reduce substantially delayed intensive care unit admission.
Neptuniibacter halophilus sp. nov., isolated from a salt pan, and emended description of the genus

Neptuniibacter
Authors: Chen Ming-Hui , Sheu Shih-Yi , Chiu Tzu-Fang , Chen Wen-Ming
Published: June 2011

A bacterial strain designated antisso-13T was isolated from a salt pan in southern Taiwan and characterized using a polyphasic taxonomic approach. Strain antisso-13T was Gram-negative, aerobic, creamy white in colour, rod-shaped and motile by single monopolar flagellum. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain antisso-13T belonged to the genus

Neptuniibacter

and its closest neighbour was

Neptuniibacter caesariensis

MED92T, with 96.7 % sequence similarity. Phylogenetic analyses based on rpoB and recA gene sequences and deduced amino acid sequences also revealed that the novel strain and

N. caesariensis

MED92T formed a distinct phylogenetic cluster. Strain antisso-13T exhibited optimal growth at 25–30 °C, with 2.0–4.0 % NaCl and at pH 7.0. Cellular fatty acids were C16 : 1ω7c (39.8 %), C18 : 1ω7c (29.4 %), C16 : 0 (15.5 %), C10 : 0 3-OH (7.5 %), anteiso-C11 : 0 (1.8 %), C18 : 0 (1.8 %), C11 : 0 2-OH (1.6 %), iso-C10 : 0 (1.2 %) and C14 : 0 (1.1 %). The major respiratory quinone was ubiquinone Q-8. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine and several uncharacterized polar lipids and the DNA G+C content was 54.2 mol%. The results of physiological and biochemical tests allowed clear phenotypic differentiation of this isolate from previously described members of the genus

Neptuniibacter

. It is evident from the genotypic and phenotypic data that strain antisso-13T should be classified as a representative of a novel species in the genus

Neptuniibacter

. The name proposed for this taxon is Neptuniibacter halophilus sp. nov.; the type strain is antisso-13T ( = LMG 25378T = BCRC 80079T). An emended description of the genus

Neptuniibacter

is provided.
Actinomadura sediminis sp. nov., a marine actinomycete isolated from mangrove sediment
Authors: He Jie , Xu Ying , Sahu Maloy Kumar , Tian Xin-Peng , Nie Guo-Xing , Xie Qiong , Zhang Si , Sivakumar Kannan , Li Wen-Jun
Published: June 2011

In this study, the taxonomic position of an actinobacterium, strain YIM M 10931T, which was isolated from a mangrove sediment sample collected in Dugong Creek, Little Andaman, India, was determined by a polyphasic approach. This Gram-positive, aerobic strain produced branched substrate mycelium and aerial hyphae, which differentiated into short, hooked or spiral spore chains. The organism contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole cell sugars consisted of mannose, ribose, glucose, galactose and madurose. The cellular fatty acid profile mainly consisted of iso-C16 : 0, 10-methyl C18 : 0 and C16 : 0. The quinone system was predominantly composed of MK-9(H8) (45.5 %) and MK-9(H6) (39 %). The phospholipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol and two unknown phospholipids. The organism showed a combination of morphological and chemotaxonomic properties typical of members of the genus

Actinomadura

. Moreover, phylogenetic analysis based on a 16S rRNA gene sequence generated from the strain identified its closest relatives as

Actinomadura cremea

DSM 43676T (98.4 % sequence similarity),

Actinomadura rifamycini

DSM 43936T (97.4 %) and

Actinomadura apis

IM17-1T (96.9 %). It was obvious from the resulting phylogenetic trees that strain YIM M 10931T belongs to a distinct subclade within the evolutionary radiation of the genus

Actinomadura

. DNA–DNA hybridizations of strain YIM M 10931T with

A. cremea

DSM 43676T and

A. rifamycini

DSM 43936T were performed and further confirmed that the isolate represents a separate genomic species. Based on the phenotypic and genotypic characteristics presented, it is proposed that strain YIM M 10931T represents a novel species within the genus

Actinomadura

, for which the name Actinomadura sediminis sp. nov. is proposed; the type strain is YIM M 10931T ( = CCTCC AA 2010009T = DSM 45500T).
Kribbella amoyensis sp. nov., isolated from rhizosphere soil of a pharmaceutical plant, Typhonium giganteum Engl.
Authors: Xu Zhen , Xu Qingyan , Zheng Zhonghui , Huang Yaojian
Published: June 2011

An actinomycete, designated XMU 198T, was isolated from the rhizosphere soil of a pharmaceutical plant, Typhonium giganteum Engl., collected in Xiamen City, China. 16S rRNA gene sequence analysis showed that the isolate exhibited highest sequence similarities with

Kribbella flavida

KACC 20148T,

K. karoonensis

Q41T and

K. alba

YIM 31975T (98.7, 98.4 and 98.2 %, respectively). The chemotaxonomic characteristics further supported the assignment of strain XMU 198T to the genus

Kribbella

: ll-diaminopimelic acid in the cell-wall peptidoglycan; glucose and galactose with minor amounts of ribose as the whole-cell sugars; polar lipids comprising phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and unidentified phospholipids; a fatty acid profile characterized by the predominance of iso-C16 : 0, iso-C14 : 0 and anteiso-C15 : 0; and MK-9(H4) as the main menaquinone. Gyrase subunit B gene (gyrB) sequence analysis showed that the genetic distances between strain XMU 198T and all other members of the genus

Kribbella

were greater than 0.014, the value used as the threshold for species delineation within this genus. A wide range of genotypic and phenotypic characteristics, as well as DNA–DNA relatedness between strain XMU 198T and

K. flavida

DSM 17836T (41.18 %),

K. karoonensis

Q41T (38.02 %) and

K. alba

DSM 15500T (50.58 %), distinguished the isolate from its closest phylogenetic neighbours. On the basis of the above data, a novel species of the genus

Kribbella

, Kribbella amoyensis sp. nov., is proposed. The type strain is XMU 198T ( = DSM 24683T = NBRC 107914T).
High-throughput mapping of the promoters of the mouse olfactory receptor genes reveals a new type of mammalian promoter and provides insight into olfactory receptor gene regulation
Authors: Clowney E. Josephine , Magklara Angeliki , Colquitt Bradley M. , Pathak Nidhi , Lane Robert P. , Lomvardas Stavros
Published: June 2011

The olfactory receptor (OR) genes are the largest mammalian gene family and are expressed in a monogenic and monoallelic fashion in olfactory neurons. Using a high-throughput approach, we mapped the transcription start sites of 1085 of the 1400 murine OR genes and performed computational analysis that revealed potential transcription factor binding sites shared by the majority of these promoters. Our analysis produced a hierarchical model for OR promoter recognition in which unusually high AT content, a unique epigenetic signature, and a stereotypically positioned O/E site distinguish OR promoters from the rest of the murine promoters. Our computations revealed an intriguing correlation between promoter AT content and evolutionary plasticity, as the most AT-rich promoters regulate rapidly evolving gene families. Within the AT-rich promoter category the position of the TATA-box does not correlate with the transcription start site. Instead, a spike in GC composition might define the exact location of the TSS, introducing the concept of “genomic contrast” in transcriptional regulation. Finally, our experiments show that genomic neighborhood rather than promoter sequence correlates with the probability of different OR genes to be expressed in the same olfactory cell.
TheCOP1OrthologPPSRegulates the Juvenile–Adult and Vegetative–Reproductive Phase Changes in Rice
Authors: Tanaka Nobuhiro , Itoh Hironori , Sentoku Naoki , Kojima Mikiko , Sakakibara Hitoshi , Izawa Takeshi , Itoh Jun-Ichi , Nagato Yasuo
Published: June 2011

Because plant reproductive development occurs only in adult plants, the juvenile-to-adult phase change is an indispensable part of the plant life cycle. We identified two allelic mutants, peter pan syndrome-1 (pps-1) and pps-2, that prolong the juvenile phase in rice (Oryza sativa) and showed that rice PPS is an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC1. The pps-1 mutant exhibits delayed expression of miR156 and miR172 and the suppression of GA biosynthetic genes, reducing the GA3 content in this mutant. In spite of its prolonged juvenile phase, the pps-1 mutant flowers early, and this is associated with derepression of RAP1B expression in pps-1 plants independently of the Hd1-Hd3a/RFT1 photoperiodic pathway. PPS is strongly expressed in the fourth and fifth leaves, suggesting that it regulates the onset of the adult phase downstream of MORI1 and upstream of miR156 and miR172. Its ability to regulate the vegetative phase change and the time of flowering suggests that rice PPS acquired novel functions during the evolution of rice/monocots.
Defective Pollen WallIs Required for Anther and Microspore Development in Rice and Encodes a Fatty Acyl Carrier Protein Reductase
Authors: Shi Jing , Tan Hexin , Yu Xiao-Hong , Liu Yuanyun , Liang Wanqi , Ranathunge Kosala , Franke Rochus Benni , Schreiber Lukas , Wang Yujiong , Kai Guoying , Shanklin John , Ma Hong , Zhang Dabing
Published: June 2011

Aliphatic alcohols naturally exist in many organisms as important cellular components; however, their roles in extracellular polymer biosynthesis are poorly defined. We report here the isolation and characterization of a rice (Oryza sativa) male-sterile mutant, defective pollen wall (dpw), which displays defective anther development and degenerated pollen grains with an irregular exine. Chemical analysis revealed that dpw anthers had a dramatic reduction in cutin monomers and an altered composition of cuticular wax, as well as soluble fatty acids and alcohols. Using map-based cloning, we identified the DPW gene, which is expressed in both tapetal cells and microspores during anther development. Biochemical analysis of the recombinant DPW enzyme shows that it is a novel fatty acid reductase that produces 1-hexadecanol and exhibits >270-fold higher specificity for palmiltoyl-acyl carrier protein than for C16:0 CoA substrates. DPW was predominantly targeted to plastids mediated by its N-terminal transit peptide. Moreover, we demonstrate that the monocot DPW from rice complements the dicot Arabidopsis thaliana male sterile2 (ms2) mutant and is the probable ortholog of MS2. These data suggest that DPWs participate in a conserved step in primary fatty alcohol synthesis for anther cuticle and pollen sporopollenin biosynthesis in monocots and dicots.
Clinical experience with Optivate®, high‐purity factor VIII (FVIII) product with von Willebrand factor (VWF) in young children with haemophilia A
Authors: MATYSIAK M. , BOBROWSKA H. , BALWIERZ W. , CHYBICKA A. , KOWALCZYK J. R. , SHAIKH‐ZAIDI R. , GILLANDERS K. , DASH C. H.
Published: June 2011

Summary.  Optivate® is a high‐purity FVIII/VWF product. Its safety, tolerability and efficacy in subjects ≥12 years have been demonstrated. This study was undertaken to assess Optivate® in children with haemophilia A. Twenty‐five children, including one PUP (previously untreated patient), aged 1–6 years (mean 4.67 years) were treated with Optivate® for 26 weeks. Inhibitors were assessed every 3 months and viral status at the study start and end. Prophylaxis was used by five boys and on demand by twenty. The mean number of bleeds in the study was lower compared to the same period pre‐study (12.0/child vs. 16.2/child), with fewer bleeds (P < 0.05) in the prophylactic subgroup (8.0/child) compared with the on‐demand sub‐group (13.4/child). Fourteen major bleeds were reported, all by the on‐demand sub‐group. Children on prophylaxis were administered a mean of 59.4 infusions; on‐demand group 35.1 infusions. A total of 998 infusions were used with a mean dose of 29.1 IU kg−1, and a mean of 38.6 exposure days (ED). Children <4 years used higher doses, and reported fewer bleeds than older children. Children’s Parents/Guardians rated Optivate® as helpful or very helpful in controlling 97.5% of bleeds by the prophylactic group, and in 98.5% of the bleeds in the on‐demand group. Only 5 of 101 ADRs were treatment‐related events (5%), all were mild and non‐serious. There were no clinically significant changes in vital signs, viral transmissions or inhibitors. In young children Optivate® was well tolerated, safe and efficacious.
Host translational control of a polydnavirus, Cotesia plutellae bracovirus, by sequestering host eIF4A to prevent formation of a translation initiation complex
Authors: Surakasi V. P. , Nalini M. , Kim Y.
Published: June 2011

Host translational control is a viral strategy to exploit host cellular resources. Parasitization by some endoparasitoids containing polydnaviruses inhibits the synthesis of specific host proteins at post‐transcriptional level. Two host translation inhibitory factors (HTIFs) have been proposed in Cotesia plutellae bracovirus (CpBV). Parasitization by C. plutellae inhibited storage protein 1 (SP1) synthesis of Plutella xylostella at post‐transcriptional level. One HTIF, CpBV15β, inhibited the translation of SP1 mRNA in an in vitro translation assay using rabbit reticulocyte lysate, but did not inhibit its own mRNA. To further analyse the discrimination of target and nontarget mRNAs of the inhibitory effect of HTIF, 5′ untranslated regions (UTRs) of SP1 and CpBV15β mRNA were reciprocally exchanged. In the presence of HTIFs, the chimeric CpBV15β mRNA that contained SP1 5′ UTR was not translated, whereas the chimeric SP1 mRNA that contained CpBV15β 5′ UTR was translated. There was a difference in the 5′ UTR secondary structures between target (SP1) and nontarget (CpBV15α and CpBV15β) mRNAs in terms of thermal stability. Different mutant 5′ UTRs of SP1 mRNA were prepared by point mutations to modify their secondary structures. The constructs containing 5′ UTRs of high thermal stability in their secondary structures were inhibited by HTIF, but those of low thermal stability were not. Immunoprecipitation with CpBV15β antibody coprecipitated eIF4A, which would be required for unwinding the secondary structure of the 5′ UTR. These results indicate that the viral HTIF discriminates between host mRNAs according to their dependency on eIF4A to form a functional initiation complex for translation.
DNA methylation in insects: on the brink of the epigenomic era
Authors: Glastad K. M. , Hunt B. G. , Yi S. V. , Goodisman M. A. D.
Published: June 2011

DNA methylation plays an important role in gene regulation in animals. However, the evolution and function of DNA methylation has only recently emerged as the subject of widespread study in insects. In this review we profile the known distribution of DNA methylation systems across insect taxa and synthesize functional inferences from studies of DNA methylation in insects and vertebrates. Unlike vertebrate genomes, which tend to be globally methylated, DNA methylation is primarily targeted to genes in insects. Nevertheless, mounting evidence suggests that a specialized role exists for genic methylation in the regulation of transcription, and possibly mRNA splicing, in both insects and mammals. Investigations in several insect taxa further reveal that DNA methylation is preferentially targeted to ubiquitously expressed genes and may play a key role in the regulation of phenotypic plasticity. We suggest that insects are particularly amenable to advancing our understanding of the biological functions of DNA methylation, because insects are evolutionarily diverse, display several lineage‐specific losses of DNA methylation and possess tractable patterns of DNA methylation in moderately sized genomes.
Contact sensitization pattern in 172 atopic subjects
Authors: Landeck Lilla , Schalock Peter , Baden Lynn , González Ernesto
Published: June 2011

Background  Some authors have claimed a decreased cell‐mediated immunity among atopic individuals, which would lead to observations of decreased rates of allergic contact dermatitis (ACD).

Objectives  The purpose of our study was to investigate contact sensitization patterns in atopic subjects compared with non‐atopic subjects.

Methods  Patch test data for 1247 patients undergoing patch testing at Massachusetts General Hospital between 1990 and 2006 were reviewed. Using accepted criteria, 172 subjects were classified as atopic individuals (AIs), and 1075 were classified as non‐atopic individuals (NAIs). Sensitization rates were compared between these two groups.

Results  Sensitization rates (65.0% and 57.4% in the AI and NAI groups, respectively) and average numbers of positive responses (1.5 and 1.2 in the AI and NAI groups, respectively) were higher in AIs. Leading allergens observed were similar for both groups. Sensitization to potassium dichromate and phenylmercuric acetate was significantly greater in the AI group. The most frequent diagnosis in both groups was ACD (41.9% and 45.5% in the AI and NAI groups, respectively). In addition, more NAIs who were employed in occupations with exposure to wet and/or irritant conditions had hand eczema (P < 0.005).

Conclusions  Atopic individuals were shown to be at least as likely to have ACD as NAIs. The most common sensitizers were similar in both groups, suggesting common sources of sensitization.
Egg allergy in patients over 14 years old suffering from atopic eczema
Authors: Čelakovská Jarmila , Ettlerová Květuše , Ettler Karel , Vaněčková Jaroslava
Published: June 2011

Objective  The aim of this study was to evaluate the occurrence of egg allergy in patients over 14 years old suffering from atopic eczema and especially to evaluate if egg allergy can deteriorate the course of atopic eczema in this group of patients.

Materials and methods  Altogether 179 patients suffering from atopic eczema were included in the study: 51 men and 128 women, with an average age of 26.2 years (SD 9.5 years), with median SCORAD 31.6 (SD 13.3) points. A complete allergological and dermatological examination was performed on all patients, including diagnostic work‐up of food allergy to egg [skin prick tests, atopy patch tests (APTs), measurement of specific IgE level to egg yolks or whites]. Open exposure test (OET) with egg was performed in patients with positive results in some of these diagnostic methods. Food allergy to egg was determined according to positive results in the OET or according to sufficient anamnestical data about the severe allergic reaction after the ingestion of an egg.

Results  An allergy to egg was confirmed in 11 patients out of 179 (6%). Of these patients, only six (3.3%) had a clear improvement in the SCORAD after the elimination of egg. Other triggering factors may cause exacerbation of the atopic eczema in the patients enrolled in the study. Twenty‐eight percent of patients were only sensitized to egg without clinical symptoms. ATPs were a useful tool in the diagnosis of food allergy to egg in patients without IgE reactivity.

Conclusion  Egg allergy may play an important role in the worsening of atopic eczema acting as a triggering–exacerbating factor in a minority of patients. The diagnostic work‐up may comprise the challenge tests to confirm the food allergy to egg.
Barrier function of intact and impaired skin: percutaneous penetration of caffeine and salicylic acid
Authors: Rubio Laia , Alonso Cristina , López Olga , Rodríguez Gelen , Coderch Luisa , Notario Jaime , de la Maza Alfonso , Parra José L.
Published: June 2011

Background  Normally, percutaneous absorption tests are carried out using skin biopsies for an apparent and acceptable physiological condition. However, under different pathological conditions, the stratum corneum (SC) barrier function is impaired.

Methods  The barrier function of the SC was assessed by correlation between the number of repeated applications of tape strips on the skin and its transepidermal water loss (TEWL), as well as by in vitro percutaneous absorption studies of different compounds, using Franz diffusion cells and porcine skin previously stripped.

Results  A progressive diminution of the skin barrier function has been detected by TEWL both in vitro and in vivo as the number of skin tape strips increases. On the other hand, the percutaneous absorption of the compounds tested increases in a different way as the number of strips increases. Salicylic acid increases linearly depending on the barrier disturbance. However, percutaneous absorption of caffeine exponentially increased with barrier disturbance. Our results indicate that the barrier impairment of skin always increases the penetration behavior of a given compound; however, the hydrophilic–lipophilic balance of the compounds or formulations used could greatly modify its penetration profile, especially when a modified skin is used.

Conclusions  This in vitro protocol may be useful to simulate the percutaneous absorption profile of some drugs applied onto skin with an impaired SC barrier function and could be used to avoid, to some extent, the use of in vivo experimental animal models in the dermopharmaceutical field.
PROCEEDINGS OF A PRELIMINARY WORKSHOP AT GASTRO 2009 – NARROW BANDING IMAGING IN DIGESTIVE ENDOSCOPY: CLINICAL OUTCOME OF CLASSIFICATION (OMED‐JGES EDUCATIONAL MEETING HELD ON 22 NOVEMBER, 2009)
Authors: REY JEAN‐FRANCOIS , LAMBERT RENE , AABAKKEN LARS , DEKKER EVELIEN , EAST JAMES E. , KALTENBACH TONYA , KATO MOTOTSUGU , SHARMA PRATEEK , TANAKA SHINJI
Published: June 2011

This publication reports the proceedings of the preliminary meeting of the working party that met at Gastro 2009 during the World Congress in London. The purpose of the preliminary meeting was to consider the areas that require attention, to discuss some of the findings that have already been published and to agree on the way forward. Our reason for publishing these proceedings is to stimulate interest in this venture and to provide the opportunity for input from the endoscopy community worldwide. The next meeting of the working party will be at the JGES Society meeting in Aomori in April 2011 when we hope to prepare a preliminary classification. This will be presented for general discussion and debate at the International Congress of Endoscopy (ICE) in Los Angeles in September 2011.
GASTRIC ADENOCARCINOMA OF FUNDIC GLAND TYPE (CHIEF CELL PREDOMINANT TYPE) TREATED WITH ENDOSCOPIC ASPIRATION MUCOSECTOMY
Authors: FUKATSU HIROTOSHI , MIYOSHI HARUKA , ISHIKI KUNIHARU , TAMURA MAIKO , YAO TAKASHI
Published: June 2011

Upper endoscopy screening in an asymptomatic 56‐year‐old man showed a small, yellowish elevated lesion with a central depression on the posterior wall in the gastric cardia. Biopsy specimens from this lesion were suspicious of carcinoid tumor. We suspected this lesion to be a sporadic gastric carcinoid tumor with a diameter of 5 mm, limited to the mucosal layer. We then performed an endoscopic aspiration mucosectomy with a cap‐fitted endoscope. Microscopically, the lesion obtained from the resected specimen was minimally invasive to the submucosa and showed highly differentiated columnar cells in irregularly anastomosing glands. Immunohistology was positive for pepsinogen‐I, and MUC6, partially positive for H+/K+‐ATPase, and negative for MUC5AC. In addition, it was positive for synaptophysin and CD56, and negative for chromogranin A. We finally diagnosed the patient as having gastric adenocarcinoma of fundic gland type (chief cell predominant type) with minimal invasion (100 µm) to the submucosa. Surveillance endoscopy with biopsy specimens and abdominal computed tomography at 1 year revealed no evidence of tumor recurrence. We herein report this rare case of gastric adenocarcinoma of fundic gland type (chief cell predominant type).
BRIDGING TRADE THEORY AND LABOUR ECONOMETRICS: THE EFFECTS OF INTERNATIONAL MIGRATION*
Authors: Gaston Noel , Nelson Douglas R.
Published: June 2011

AbstractThis paper surveys current theoretical and empirical research on international migration with a particular emphasis on the links between trade theory and labour empirics.
Correlation Analysis of Quantitative Diffusion Parameters in Ipsilateral Cerebral Peduncle during Wallerian Degeneration with Motor Function Outcome after Cerebral Ischemic Stroke
Authors: Liu Xiang , Tian Wei , Qiu Xing , Li Juntao , Thomson Scott , Li Lilin , Wang Henry Z.
Published: June 2011

BACKGROUND AND PURPOSE

To evaluate the time periods of Wallerian degeneration (WD) in which the diffusion parameters of ipsilateral corticalspinal tract (CST) can be used to predict the motor function outcome after brain infarction.

METHODS

This retrospective study classified 48 diffusion tensor imaging patients with WD along CST into four groups based on the following time points after stroke onset, Group 1: within the first 2 weeks; Group 2: from 3 to 4 weeks; Group 3: from 5 to 14 weeks; Group 4: after 14 weeks. The apparent diffusion coefficient (ADC), fractional anisotropy (FA), and their ratios (=ipsilateral diffusion value/contralateral value) of cerebral peduncle were evaluated. The correlation between imaging parameters in each group and the motor function scores appraised at 8 months after stroke onset were assessed.

RESULTS

There was no evident correlation of FA ratio (rFA) in Group 1 with motor function score (P= .05). The rFA and FA correlated with motor function score in other groups (P < .001 in each group). The ADC ratio and ipsilateral ADC value only showed significant correlation of with motor function score in Group 4 (P= .016 and .029, respectively).

CONCLUSIONS

The rFA and ipsilateral FA values after 2 weeks of stroke onset correlate with the motor function outcome.
CONTRAST HARMONIC ULTRASOUND APPEARANCE OF CONSECUTIVE PERCUTANEOUS RENAL BIOPSIES IN DOGS
Authors: HAERS HENDRIK , SMETS PASCALE , PEY PASCALINE , PIRON KOEN , DAMINET SYLVIE , SAUNDERS JIMMY H.
Published: June 2011

Ultrasound‐guided percutaneous renal biopsy may be associated with complications, especially when using larger needles. Contrast harmonic ultrasound increases blood pool echo intensity, enhancing parenchymal lesions. Therefore, contrast harmonic ultrasound is a potential alternative screening method for postbiopsy renal lesions. Renal biopsies were performed using 14 G needles in 11 healthy Beagles, at three occasions: 0 (“Baseline Biopsy”; BB), 4 (“Biopsy 2”; B2), and 6 months (“Biopsy 3”; B3). Ultrasound and contrast harmonic ultrasound of biopsied kidneys were performed approximately 30 min after biopsy (week 0) at BB and B2, and repeated once every week (weeks 1–3) until normal appearance. At B3, only contrast harmonic ultrasound was performed, both immediately and 30‐min postbiopsy. Contrast harmonic ultrasound images were reviewed using subjective and semiquantitative methods to describe lesions including number, shape, size, sharpness, echogenicity, and evolution. More renal lesions were detected with contrast harmonic ultrasound (22/22) compared with conventional ultrasound (14/22). The majority appeared at week 0 as hypoechoic tract(s) (27/33), the other (6/33) as ill‐defined areas or area/tract combination, all having variable size, shape, and echogenicity. Seven tracts had a small subcapsular hematoma. In most kidneys, similar or gradual decrease of size and sharpness, and increased echogenicity was observed until normal appearance occurred at week 1 (1/22), week 2 (18/22), or week 3 (22/22). Two Beagles developed complications. At B3, immediately postbiopsy, tracts were hyperechoic in 9/11 kidneys, becoming hypoechoic again 30 min later. Contrast harmonic ultrasound is a valuable method to evaluate postbiopsy renal lesions in dogs.
COMPARISON OF RADIOGRAPHIC AND SCINTIGRAPHIC FINDINGS OF THE SPINOUS PROCESSES IN THE EQUINE THORACOLUMBAR REGION
Authors: ZIMMERMAN MARIEKE , DYSON SUE , MURRAY RACHEL
Published: June 2011

Back pain is common in horses, but there has been no large‐scale in‐depth study describing radiographic changes of the spinous processes, the relationship between radiographic and scintigraphic findings, and the effect of size, age, breed, or discipline. The objectives were to investigate the frequency of occurrence in horses with perceived back pain of: (1) radiographic alteration of the spinous process structure; (2) increased radiopharmaceutical uptake (IRU) in the spinous processes; and (3) to compare radiographic and scintigraphic findings; and to determine if there was breed, gender, age, bodyweight, height, or work discipline predisposition for close, impinging, or overriding spinous processes. Radiographic and scintigraphic images of the thoracolumbar spine of 604 horses were graded. A radiographic grade for each spinous process (T8–L6) was assigned (0–7). The maximum radiographic grade for each horse was defined as the highest grade assigned to any spinous process; the total radiographic grade was the sum of all grades for each horse. A scintigraphic grade for each spinous process was determined (0–3). The maximum scintigraphic grade for each horse was defined as the highest grade assigned to any spinous process; the total scintigraphic grade was the sum of all grades for each horse. Associations between radiology and scintigraphy and age, gender, breed, height, weight, and discipline were analyzed statistically. The severity of radiographic lesions of the spinous processes was associated with the severity of scintigraphic abnormalities. The caudal thoracic spine (T14–T17) was most frequently affected. There was a significant breed and age effect, with Thoroughbreds and older horses having higher total and maximum radiographic grades. The severity of the lesions of the spinous processes was significantly associated with the presence of osteoarthritis of the articular process joints. It was concluded that there is a wide range of radiographic abnormalities of the spinous processes seen in horses with or without back pain. There is an association between radiographic and scintigraphic grades of the spinous processes.
Lithium: Still a Major Option in the Management of Bipolar Disorder
Authors: Licht Rasmus W.
Published: June 2011

Still after more than 50 years, lithium is a major treatment of bipolar disorder, even though it has not been promoted by the pharmaceutical industry over the last decades. In recent years the evidence base on lithium for bipolar disorder has substantially increased due to results from a number of trials. Therefore, a review of this evidence is timely. The efficacy of lithium as an acute treatment and as a maintenance treatment of bipolar disorder was evaluated through a review of the evidence, focusing on modern, randomized, parallel‐group designed trials. Additionally, the evidence was sought translated into the proper use of lithium in clinical practice. Lithium's antimanic efficacy has been convincingly demonstrated. However, as blood monitoring due to the risk of toxicity is required and due to an insufficient response in highly agitated patients, lithium monotherapy has a limited place in the acute treatment of severe manic states. For acute bipolar depression, results are conflicting. Recent maintenance trials have added substantially to the documentation of lithium's long‐term stabilizing properties in bipolar disorder, and these properties have been demonstrated independently of any acute response to lithium. Finally, it is now beyond doubt that not only does lithium prevent mania, but also depression in bipolar disorder. Lithium is still to be considered a major if not the most important mood‐ stabilizer, at least for maintaining long‐term stability in patients with bipolar disorder. The potential risks of lithium should be weighed up against its benefits and the fact that serious adverse effects are usually avoidable.
OPTIMAL HARVEST FEEDBACK RULE ACCOUNTING FOR THE FISHING‐UP EFFECT AND SIZE‐DEPENDENT PRICING
Authors: ZIMMERMANN FABIAN , STEINSHAMN STEIN IVAR , HEINO MIKKO
Published: June 2011

Abstract Fishing leads to truncation of a population's age and size structure. However, large‐sized fish are usually more valuable per unit weight than small ones. Nevertheless, these size‐related factors have mostly been ignored in bioeconomic modeling. Here, we present a simple extension to the Gordon–Schaefer model that accounts for variations in mean individual catch weight, and derive the feedback rule for optimal harvest in this setting. As the Gordon–Schaefer model has no population structure, size effects have to be accounted for indirectly. Here we assume a simple negative relationship between fishing effort and mean individual weight, and a positive relationship between mean catch weight and price. The aim is to emulate alterations of size structure in fish populations due to fishing and the influence of size on price per weight unit and eventually, net revenues. This demonstrates, on a general level, how such size‐dependent effects change the patterns of optimal harvest paths and sustainable revenue in single fish stocks. The model shows clear shifts toward lower levels of optimal effort and yield compared to classical models without size effects. This suggests that ignoring body size could lead to misleading assumptions and policies, potentially causing rent dissipation and suboptimal utilization of renewable resources.
Computational Experiments for Science Education
Authors: Xie Charles , Tinker Robert , Tinker Barbara , Pallant Amy , Damelin Daniel , Berenfeld Boris
Published: June 2011

Computational experiments based on solving fundamental physics equations bring authentic science to the classroom.
Inducing Sleep by Remote Control Facilitates Memory Consolidation in
Drosophila
Authors: Donlea Jeffrey M. , Thimgan Matthew S. , Suzuki Yasuko , Gottschalk Laura , Shaw Paul J.
Published: June 2011

Inducing sleep in flies reverses deficits in long-term memory caused by social enrichment.
Scale for the Phase Diagram of Quantum Chromodynamics
Authors: Gupta Sourendu , Luo Xiaofeng , Mohanty Bedangadas , Ritter Hans Georg , Xu Nu
Published: June 2011

The temperature scale for the breakdown of protons and neutrons can be determined from high-energy ion collisions and calculations.
A Cell Cycle Phosphoproteome of the Yeast Centrosome
Authors: Keck Jamie M. , Jones Michele H. , Wong Catherine C. L. , Binkley Jonathan , Chen Daici , Jaspersen Sue L. , Holinger Eric P. , Xu Tao , Niepel Mario , Rout Michael P. , Vogel Jackie , Sidow Arend , Yates John R. , Winey Mark
Published: June 2011

Phosphorylation of the yeast centrosome reveals sites of regulation and predicts complex regulation of mammalian centrosomes.
Apollo Physicist Launches Noisy Dustup Over Old Moon Data
Authors: Laursen Lucas
Published: June 2011

The floating dust believed to explain the lunar horizon glow may have been interference from heaters on nearby instruments, according to a new analysis.
Short- and Long-Term Adaptation to Ethanol Stress and Its Cross-Protective Consequences in Lactobacillus plantarum
Authors: van Bokhorst-van de Veen Hermien , Abee Tjakko , Tempelaars Marcel , Bron Peter A. , Kleerebezem Michiel , Marco Maria L.
Published: June 2011

This paper describes the molecular responses of
Lactobacillus plantarum
WCFS1 toward ethanol exposure. Global transcriptome profiling using DNA microarrays demonstrated adaptation of the microorganism to the presence of 8% ethanol over short (10-min and 30-min) and long (24-h) time intervals. A total of 57 genes were differentially expressed at all time points. Expression levels of an additional 859 and 873 genes were modulated after 30 min and 24 h of exposure to the solvent, respectively. Ethanol exposure led to induced expression of genes involved in citrate metabolism and cell envelope architecture, as well as canonical stress response pathways controlled by the central stress regulators HrcA and CtsR. Correspondingly, cells grown for 24 h in medium containing 8% ethanol exhibited higher levels of citrate consumption and modified cell membrane fatty acid composition and showed invaginating septa compared with cells grown in liquid medium without ethanol. In addition, these physiological changes resulted in cross-protection against high temperatures but not against several other stresses tested. To evaluate the role of HrcA and CtsR in ethanol tolerance,
ctsR
and
hrcA
gene deletion mutants were constructed. The growth rate of the
L. plantarum
Δ
ctsR
::
cat
strain was impaired in de Man-Rogosa-Sharpe (MRS) medium containing 8% ethanol, whereas growth of the
L. plantarum
Δ
hrcA
::
cat
and Δ
ctsR
Δ
hrcA
::
cat
mutants was indistinguishable from that of wild-type cells. Overall, these results suggest that the induction of CtsR class III stress responses provides cross-protection against heat stress.
Concentration and Diversity of Noroviruses Detected in Luxembourg Wastewaters in 2008-2009
Authors: Skraber Sylvain , Langlet Jérémie , Kremer Jacques R. , Mossong Joël , De Landtsheer Sébastien , Even Jos , Muller Claude P. , Hoffmann Lucien , Cauchie Henry-Michel
Published: June 2011

Noroviruses (NoV) in 78 wastewater samples from Luxembourg were quantified, cloned, and sequenced in 2008-2009. The concentrations of NoV genogroup II and the relative occurrences of certain genotypes changed significantly during the winter season. NoV genogroup I was frequently detected by real-time reverse transcription-PCR (RT-PCR), albeit at 30-fold lower concentrations than for genogroup II, hampering attempts to assess overall genetic diversity by the cloning/sequencing approach.
Differences in the Rumen Methanogen Populations of Lactating Jersey and Holstein Dairy Cows under the Same Diet Regimen
Authors: King Erin E. , Smith Rachel P. , St-Pierre Benoit , Wright André-Denis G.
Published: June 2011

In the dairy cattle industry, Holstein and Jersey are the breeds most commonly used for production. They differ in performance by various traits, such as body size, milk production, and milk composition. With increased concerns about the impact of agriculture on climate change, potential differences in other traits, such as methane emission, also need to be characterized further. Since methane is produced in the rumen by methanogenic archaea, we investigated whether the population structure of methanogen communities would differ between Holsteins and Jerseys. Breed-specific rumen methanogen 16S rRNA gene clone libraries were constructed from pooled PCR products obtained from lactating Holstein and Jersey cows, generating 180 and 185 clones, respectively. The combined 365 sequences were assigned to 55 species-level operational taxonomic units (OTUs). Twenty OTUs, representing 85% of the combined library sequences, were common to both breeds, while 23 OTUs (36 sequences) were found only in the Holstein library and 12 OTUs (18 sequences) were found only in the Jersey library, highlighting increased diversity in the Holstein library. Other differences included the observation that sequences with species-like sequence identity to
Methanobrevibacter millerae
were represented more highly in the Jersey breed, while
Methanosphaera
-related sequences and novel uncultured methanogen clones were more frequent in the Holstein library. In contrast, OTU sequences with species-level sequence identity to
Methanobrevibacter ruminantium
were represented similarly in both libraries. Since the sampled animals were from a single herd consisting of two breeds which were fed the same diet and maintained under the same environmental conditions, the differences we observed may be due to differences in host breed genetics.
Endosomal Localization of the Serum Resistance-Associated Protein in African Trypanosomes Confers Human Infectivity
Authors: Stephens Natalie A. , Hajduk Stephen L.
Published: June 2011

Trypanosoma brucei rhodesiense
is the causative agent of human African sleeping sickness. While the closely related subspecies
T. brucei brucei
is highly susceptible to lysis by a subclass of human high-density lipoproteins (HDL) called trypanosome lytic factor (TLF),
T. brucei rhodesiense
is resistant and therefore able to establish acute and fatal infections in humans. This resistance is due to expression of the serum resistance-associated (SRA) gene, a member of the variant surface glycoprotein (VSG) gene family. Although much has been done to establish the role of SRA in human serum resistance, the specific molecular mechanism of SRA-mediated resistance remains a mystery. Thus, we report the trafficking and steady-state localization of SRA in order to provide more insight into the mechanism of SRA-mediated resistance. We show that SRA traffics to the flagellar pocket of bloodstream-form
T. brucei
organisms, where it localizes transiently before being endocytosed to its steady-state localization in endosomes, and we demonstrate that the critical point of colocalization between SRA and TLF occurs intracellularly.
Quorum Sensing and Silencing in Vibrio parahaemolyticus
Authors: Gode-Potratz Cindy J. , McCarter Linda L.
Published: June 2011

The quorum regulatory cascade is poorly characterized in
Vibrio parahaemolyticus
, in part because swarming and virulence factors—the hallmarks of the organism—are repressed by this scheme of gene control, and quorum sensing seems to be silenced in many isolates. In these studies, we examine a swarming-proficient, virulent strain and identify an altered-function allele of the quorum regulator
luxO
that is demonstrated to produce a constitutively active mimic of LuxO∼P. We find that LuxO* affects the expression of three small regulatory RNAs (Qrrs) and the activity of a translational fusion in
opaR
, the output regulator. Tests for epistasis showed that
luxO
* is dominant over
luxO
and that
opaR
is dominant over
luxO
. Thus, information flow through the central elements of the
V. parahaemolyticus
quorum pathway is proven for the first time. Quorum-sensing output was explored using microarray profiling: the OpaR regulon encompasses ∼5.2% of the genome. OpaR represses the surface-sensing and type III secretion system 1 (T3SS1) regulons. One novel discovery is that OpaR strongly and oppositely regulates two type VI secretion systems (T6SS). New functional consequences of OpaR control were demonstrated: OpaR increases the cellular cyclic di-GMP (c-di-GMP) level, positively controls chitin-induced DNA competency, and profoundly blocks cytotoxicity toward host cells. In expanding the previously known quorum effects beyond the induction of the capsule and the repression of swarming to elucidate the global scope of genes in the OpaR regulon, this study yields many clues to distinguishing traits of this
Vibrio
species; it underscores the profoundly divergent survival strategies of the quorum On/Off phase variants.
Genome of the Cyanobacterium Microcoleus vaginatusFGP-2, a Photosynthetic Ecosystem Engineer of Arid Land Soil Biocrusts Worldwide
Authors: Starkenburg Shawn R. , Reitenga Krista G. , Freitas Tracey , Johnson Shannon , Chain Patrick S. G. , Garcia-Pichel Ferran , Kuske Cheryl R.
Published: June 2011

The filamentous cyanobacterium
Microcoleus vaginatus
is found in arid land soils worldwide. The genome of
M. vaginatus
strain FGP-2 allows exploration of genes involved in photosynthesis, desiccation tolerance, alkane production, and other features contributing to this organism's ability to function as a major component of biological soil crusts in arid lands.
Genome Sequence of Helicobacter bizzozeroniiStrain CIII-1, an Isolate from Human Gastric Mucosa
Authors: Schott Thomas , Rossi Mirko , Hänninen Marja-Liisa
Published: June 2011

The canine-adaptedHelicobacter bizzozeroniiis the only nonpyloriHelicobacterspecies isolated from human gastric biopsy tissue. Here we present the genome sequence of strain CIII-1, isolated from a 45-year-old female patient with severe gastric symptoms. This is the first genome sequence of nonpylori gastricHelicobacterisolated from human gastritis.
Genome Sequences of Eight Morphologically Diverse Alphaproteobacteria
Authors: Brown Pamela J. B. , Kysela David T. , Buechlein Aaron , Hemmerich Chris , Brun Yves V.
Published: June 2011

The
Alphaproteobacteria
comprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera
Asticcacaulis
,
Hirschia
,
Hyphomicrobium
, and
Rhodomicrobium
.
Genome Sequence of Salinisphaera shabanensis, a Gammaproteobacterium from the Harsh, Variable Environment of the Brine-Seawater Interface of the Shaban Deep in the Red Sea
Authors: Antunes André , Alam Intikhab , Bajic Vladimir B. , Stingl Ulrich
Published: June 2011

We present the genome of
Salinisphaera shabanensis
, isolated from a brine-seawater interface and representing a new order within the
Gammaproteobacteria
. Its adaptations to physicochemical and nutrient availability fluctuations include six genes encoding heavy metal-translocating P-type ATPases and multiple genes involved in iron uptake, siderophore production, and poly-β-hydroxybutyrate synthesis.
Genome Sequence of Halorhabdus tiamatea, the First Archaeon Isolated from a Deep-Sea Anoxic Brine Lake
Authors: Antunes André , Alam Intikhab , Bajic Vladimir B. , Stingl Ulrich
Published: June 2011

We present the draft genome of
Halorhabdus tiamatea
, the first member of the
Archaea
ever isolated from a deep-sea anoxic brine. Genome comparison with
Halorhabdus utahensis
revealed some striking differences, including a marked increase in genes associated with transmembrane transport and putative genes for a trehalose synthase and a lactate dehydrogenase.