bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competing intermolecular interactions in some `bridge-flipped' isomeric phenylhydrazones
Authors: Ojala William H. , Arola Trina M. , Brigino Ann M. , Leavell Jeremy D. , Ojala Charles R. 
Published: June 2012

To examine the roles of competing intermolecular interactions in differentiating the molecular packing arrangements of some isomeric phenylhydrazones from each other, the crystal structures of five nitrile–halogen substituted phenylhydrazones and two nitro–halogen substituted phenylhydrazones have been determined and are described here: (E)-4-cyanobenzaldehyde 4-chlorophenylhydrazone, C14H10ClN3, (Ia); (E)-4-cyanobenzaldehyde 4-bromophenylhydrazone, C14H10BrN3, (Ib); (E)-4-cyanobenzaldehyde 4-iodophenylhydrazone, C14H10IN3, (Ic); (E)-4-bromobenzaldehyde 4-cyanophenylhydrazone, C14H10BrN3, (IIb); (E)-4-iodobenzaldehyde 4-cyanophenylhydrazone, C14H10IN3, (IIc); (E)-4-chlorobenzaldehyde 4-nitrophenylhydrazone, C13H10ClN3O2, (III); and (E)-4-nitrobenzaldehyde 4-chlorophenylhydrazone, C13H10ClN3O2, (IV). Both (Ia) and (Ib) are disordered (less than 7% of the molecules have the minor orientation in each structure). Pairs (Ia)/(Ib) and (IIb)/(IIc), related by a halogen exchange, are isomorphous, but none of the `bridge-flipped' isomeric pairs,viz.(Ib)/(IIb), (Ic)/(IIc) or (III)/(IV), is isomorphous. In the nitrile–halogen structures (Ia)–(Ic) and (IIb)–(IIc), only the bridge N—H group and not the bridge C—H group acts as a hydrogen-bond donor to the nitrile group, but in the nitro–halogen structures (III) (withZ′ = 2) and (IV), both the bridge N—H group and the bridge C—H group interact with the nitro group as hydrogen-bond donors, albeitviadifferent motifs. The occurrence here of the bridge C—H contact with a hydrogen-bond acceptor suggests the possibility that other pairs of `bridge-flipped' isomeric phenylhydrazones may prove to be isomorphous, regardless of the change from isomer to isomer in the position of the N—H group within the bridge.
Amplification of all 11 RNA segments of group A rotaviruses based on reverse transcription polymerase chain reaction
Authors: Fujii Yoshiki , Shimoike Takashi , Takagi Hirotaka , Murakami Kosuke , Todaka‐Takai Reiko , Park YoungBin , Katayama Kazuhiko 
Published: June 2012

ABSTRACTGroup A rotaviruses (RVA) are a major cause of acute infantile gastroenteritis. The viral genome comprises 11 double‐stranded RNA segments and the respective gene segments are classified into more than eight genotypes, according to the nucleotide sequence similarities. So far, it has been difficult to amplify full‐length sequences of long RNA segments of rotaviruses by one‐time only RT‐PCR (especially in the genes for the viral proteins VP1, VP2, VP3 and VP4). In this study, a set of universal primers to amplify all 11 segments of RVA was designed by aligning the nucleotide sequences of the typical rotavirus strains. Using these primers and a high‐fidelity and rapid DNA polymerase in a one‐step reverse transcription polymerase chain reaction, almost the entire length of all 11 segments of the seven rotavirus strains Wa, DS‐1, Hochi, 69M, WI61, M37 and SA11‐S1 were accurately and rapidly amplified. In addition, all 11 segments of rotavirus obtained from a fecal specimen were successfully amplified. In conclusion, the method described here will be useful as an RVA detection system and protocol for complete analysis of the 11 genome sequences.
An attenuated mutant of avian pathogenic Escherichia coli serovar O78: a possible live vaccine strain for prevention of avian colibacillosis
Authors: Nagano Tetsuji , Kitahara Rie , Nagai Shinya 
Published: June 2012

ABSTRACTHere construction of an attenuated mutant of an avian pathogenic Escherichia coli serovar O78 using an allelic exchange procedure is described. The mutant AESN1331, which carries a deletion in the crp gene, lost tryptophan deaminase activity and therefore lacked the ability to produce indole. The mutant strain additionally lacked the ability to adsorb Congo red, no longer fermented sugars other than glucose and L‐arabinose, did not harbor four known virulence‐associated genes (iss, tsh, cvaA, papC), and was susceptible to many antimicrobials, with the exception of nalidixic acid. The lethal dose (LD50 value) of the mutant strain on intravenous challenge in chickens was approximately 10‐fold higher than that of the parent strain. Additionally, the mutant strain was rapidly eliminated from chickens, being detected in the respiratory tract only on the first day post‐inoculation by fine spray. Administration of the mutant strain via various routes such as spray and eye drop for chickens, as well as in ovo inoculation for embryonated egg, evoked an effective immune response that protected against a virulent wild‐type E. coli O78 strain. Specifically, after immunization with the mutant strain, chickens challenged intravenously with an E. coli O78 strain exhibited decreases in mortality, clinical scores, organ lesion scores, and recovery of the challenge strain from organs compared to non‐immunized chickens. These findings suggest that AESN1331 is a suitable candidate for a live vaccine strain to protect chickens from colibacillosis caused by avian E. coli O78.
Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae
Authors: Yadav Mukesh Kumar , Kwon Seong Keun , Cho Chang Gun , Park Seok‐Won , Chae Sung‐Won , Song Jae‐Jun 
Published: June 2012

ABSTRACTIn this study, the gene expression profile of early in vitro Streptococcus pneumoniae biofilm with respect to planktonic cells in cDNA microarray analysis is reported. Microarray analysis with respect to planktonic cells was performed on total RNA extracted from biofilms grown in 24‐well microtiter plates. To validate the microarray results, real‐time RT‐PCR was performed on 13 differentially expressed genes and one constitutively expressed gene. The cDNA‐microarray analyses identified 89 genes that were significantly differentially expressed in biofilm and planktonic cells. Genes involved in isoprenoid biosynthesis, cell wall biosynthesis, translation and purine and pyrimidine nucleotide metabolic pathways were exclusively expressed in the biofilms, whereas transcription regulator genes were exclusively expressed in planktonic cells. The real‐time RT‐PCR results of 13 differentially regulated genes were completely in agreement with the microarray data. The exclusive up regulation in biofilms of genes involved in the mevalonate pathway, cell wall biosynthesis, translation and purine and pyrimidine nucleotide metabolic pathways suggests that expression of these genes may be required for initial biofilm formation, and growth and survival of bacteria in biofilms. The up regulation of related genes suggests that cells in biofilms may be under stress conditions and possibly actively involved in the protein synthesis required to adapt to a new environment.
Role of JC virus agnoprotein in virion formation
Authors: Suzuki Tadaki , Semba Shingo , Sunden Yuji , Orba Yasuko , Kobayashi Shintaro , Nagashima Kazuo , Kimura Takashi , Hasegawa Hideki , Sawa Hirofumi 
Published: June 2012

ABSTRACTJC virus (JCV) belongs to the polyomavirus family of double‐stranded DNA viruses and causes progressive multifocal leukoencephalopathy in humans. JCV encodes early proteins (large T antigen, small T antigen, and T′ antigen) and four late proteins (agnoprotein, and three viral capsid proteins, VP1, VP2, and VP3). In the current study, a novel function for JCV agnoprotein in the morphogenesis of JC virion particles was identified. It was found that mature virions of agnoprotein‐negative JCV are irregularly shaped. Sucrose gradient sedimentation and cesium chloride gradient ultracentrifugation analyses revealed that the particles of virus lacking agnoprotein assemble into irregularly sized virions, and that agnoprotein alters the efficiency of formation of VP1 virus‐like particles. An in vitro binding assay and immunocytochemistry revealed that agnoprotein binds to glutathione S‐transferase fusion proteins of VP1 and that some fractions of agnoprotein colocalize with VP1 in the nucleus. In addition, gel filtration analysis of formation of VP1‐pentamers revealed that agnoprotein enhances formation of these pentamers by interacting with VP1. The present findings suggest that JCV agnoprotein plays a role, similar to that of SV40 agnoprotein, in facilitating virion assembly.
A multicentre observational study of intra‐operative ventilatory management during general anaesthesia: tidal volumes and relation to body weight
Authors: Jaber S. , Coisel Y. , Chanques G. , Futier E. , Constantin J.‐M. , Michelet P. , Beaussier M. , Lefrant J.‐Y. , Allaouchiche B. , Capdevila X. , Marret E. 
Published: June 2012

SummaryWe conducted an observational prospective multicenter study to describe the practices of mechanical ventilation, to determine the incidence of use of large intra‐operative tidal volumes (≥ 10 ml.kg−1 of ideal body weight) and to identify patient factors associated with this practice. Of the 2960 patients studied in 97 anaesthesia units from 49 hospitals, volume controlled mode was the most commonly used (85%). The mean (SD) tidal volume was 533 (82) ml; 7.7 (1.3) ml.kg−1 (actual weight) and 8.8 (1.4) ml.kg−1 (ideal body weight)). The lungs of 381 (18%) patients were ventilated with a tidal volume > 10 ml.kg−1 ideal body weight. Being female (OR 5.58 (95% CI 4.20–7.43)) and by logistic regression, underweight (OR 0.06 (95% CI 0.01–0.45)), overweight (OR 1.98 (95% CI 1.49–2.65)), obese (OR 5.02 (95% CI 3.51–7.16)), severely obese (OR 10.12 (95% CI 5.79–17.68)) and morbidly obese (OR 14.49 (95% CI 6.99–30.03)) were the significant (p ≤ 0.005) independent factors for the use of large tidal volumes during anaesthesia.
Psychological adjustment among left‐behind children in rural China: the role of parental migration and parent–child communication
Authors: Su S. , Li X. , Lin D. , Xu X. , Zhu M. 
Published: June 2012

AbstractBackgroundLeft‐behind children refer to those rural children who are under 18 years of age and are left at home when both or one of their parents migrate to urban area for work. Recent findings showed that left‐behind children were disadvantaged by developmental, emotional and social problems.MethodA sample of 1165 rural children and adolescents were recruited to examine the characteristics of left‐behind children and explore the differences in psychological adjustment (including satisfaction, loneliness and happiness) by patterns of parental migration (i.e. no parent migrating, one parent migrating or two parents migrating) and the level of parent–child communication in rural China.Results(1) Compared with children with one parent migrating, children with two parents migrating were separated from their parents at younger ages, for longer periods, and saw their migrant parents less frequently. (2) Children with two parents migrating reported the lowest level of satisfaction among the three groups of rural children. Both groups of children with one or two parents migrating experienced more loneliness compared with children with no parent migrating. There were no significant differences in school satisfaction and happiness among the three groups. (3) The children who reported a higher level of parent–child communication also reported a higher level of life and school satisfaction and happiness, and no differences in loneliness were found by levels of parent–child communication.ConclusionsThese results indicate that loneliness was the most common and important experience of left‐behind children. Parent–child communication is important for the development of all rural children, including those who were left behind by their migrant parents.
Dispersal and upstream migration of an amphidromous neritid snail: implications for restoring migratory pathways in tropical streams
Authors: GORBACH KATHLEEN R. , BENBOW M. ERIC , McINTOSH MOLLIE D. , BURKY ALBERT J. 
Published: June 2012

Summary1. The amphidromous life cycle of several species of neritid snails, shrimp and gobies throughout the tropics includes juveniles that migrate from the ocean to breed in fresh water. In many Hawaiian streams, the decline of Neritina granosa, an endemic gastropod, has been associated with habitat degradation and water withdrawal, which are common factors affecting tropical rivers around the world.2. We investigated the effects of water withdrawal and density on dispersal and upstream migration of N. granosa using three experimental treatments: (i) reduced flow (RF) owing to a stream diversion, (ii) natural flow (NF) and (iii) natural flow with artificially increased snail density. For each treatment, snails were differentially tagged and released in a stream without a natural, extant population of N. granosa.3. Capture rates ranged from 17 to 65% over a 63‐day period following release. Captures on 2–6 days after release measured initial dispersal and migration, whereas longer‐term migration rates were calculated from snails captured 16–63 days after release. Snails under NF displayed positive rheotactic behaviour, with only 3–12% demonstrating initial downstream movement. Under RF, 22–77% of snails moved downstream or showed no bias either way.4. Initial mean upstream migration rate (UMR) was 0.25, 0.66 and 1.16 m day−1 under RF, NF and natural flow with increased snail density, respectively. Longer‐term migration rates did not differ significantly between treatments, and the overall mean was 0.62 m day−1.5. Principal component analysis and generalised linear models were used to identify habitat characteristics important to UMR, with habitat and reach‐scale hydraulics as the most important factors. The relationship between discharge and UMR suggested it would take 11–35 years for snails to migrate past the most upstream water diversion. However, rates from published studies of neritid snail species migrating en masse or in long lines under natural situations suggested that N. granosa could migrate above stream diversions within 72 days–2.5 years (when in an aggregation) and 29 days–1.1 years (when following in long lines of individuals).6. An understanding of upstream neritid snail migration can be used for the management and conservation of this and other migratory species in tropical streams.
Sea anemones may thrive in a high CO2 world
Authors: Suggett David J. , Hall‐Spencer Jason M. , Rodolfo‐Metalpa Riccardo , Boatman Toby G. , Payton Ross , Tye Pettay D. , Johnson Vivienne R. , Warner Mark E. , Lawson Tracy 
Published: June 2012

AbstractIncreased seawater pCO2, and in turn ‘ocean acidification’ (OA), is predicted to profoundly impact marine ecosystem diversity and function this century. Much research has already focussed on calcifying reef‐forming corals (Class: Anthozoa) that appear particularly susceptible to OA via reduced net calcification. However, here we show that OA‐like conditions can simultaneously enhance the ecological success of non‐calcifying anthozoans, which not only play key ecological and biogeochemical roles in present day benthic ecosystems but also represent a model organism should calcifying anthozoans exist as less calcified (soft‐bodied) forms in future oceans. Increased growth (abundance and size) of the sea anemone (Anemonia viridis) population was observed along a natural CO2 gradient at Vulcano, Italy. Both gross photosynthesis (PG) and respiration (R) increased with pCO2 indicating that the increased growth was, at least in part, fuelled by bottom up (CO2 stimulation) of metabolism. The increase of PG outweighed that of R and the genetic identity of the symbiotic microalgae (Symbiodinium spp.) remained unchanged (type A19) suggesting proximity to the vent site relieved CO2 limitation of the anemones' symbiotic microalgal population. Our observations of enhanced productivity with pCO2, which are consistent with previous reports for some calcifying corals, convey an increase in fitness that may enable non‐calcifying anthozoans to thrive in future environments, i.e. higher seawater pCO2. Understanding how CO2‐enhanced productivity of non‐ (and less‐) calcifying anthozoans applies more widely to tropical ecosystems is a priority where such organisms can dominate benthic ecosystems, in particular following localized anthropogenic stress.
Benign mesenchymal tumours and tumour‐like lesions in end‐stage renal disease
Authors: Büttner Maike , Kufer Verena , Brunner Kathrin , Hartmann Arndt , Amann Kerstin , Agaimy Abbas 
Published: June 2012

Aims:  Mesenchymal neoplasms of the kidney are rare, and most represent sporadic angiomyolipomas. A few haemangiomas have been reported in end‐stage renal disease (ESRD) but, to date, no study has focused on the frequency and morphological spectrum of mesenchymal lesions in ESRD.Methods and results:  We evaluated retrospectively 90 nephrectomy specimens with ESRD. Haemangiomas were detected in eight cases (8.8%; six males and two females; mean age: 55 years); four were multifocal and four had concurrent renal epithelial neoplasms. Lesions involved the medulla (three), cortex (two) or both (three), and the size range was 1–25 mm (mean 4.8 mm). Histologically, all were capillary haemangiomas with an at least focally detectable spleen‐like anastomosing pattern. All tumours stained positively for CD31 and FLI‐1, but none expressed pankeratin (KL‐1), podoplanin/D2‐40, HHV8 or GLUT‐1. Minute angiomyolipomas (mean size 2.3 mm) were detected in four patients (mean age 49.5 years). Tumour‐like smooth muscle proliferations were seen surrounding muscular arteries (eight), occasionally admixed with fat extending from the renal sinus mimicking angiomyolipoma. No similar tumours were found in 105 control kidneys.Conclusions:  Benign haemangiomas are not uncommon in ESRD, but may be under‐recognized. They display distinctive morphology and should be distinguished from angiosarcomas and capillary‐rich renal cell carcinomas.
Does the proliferation fraction help identify mature B cell lymphomas with double‐ and triple‐hit translocations?
Authors: Mationg‐Kalaw Emarene , Tan Leonard H C , Tay Kevin , Lim Soon Thye , Tang Tiffany , Lee Yvonne Y L , Tan Soo Yong 
Published: June 2012

Mationg‐Kalaw E, Tan L H C, Tay K, Lim S T, Tang T, Lee Y Y L & Tan S Y  (2012) Histopathology Does the proliferation fraction help identify mature B cell lymphomas with double‐ and triple‐hit translocations?Aims:  The entity ‘B cell lymphoma, unclassifiable, with features intermediate between diffuse large B cell lymphoma (DLBCL) and Burkitt lymphoma (BL)’ refers to B cell neoplasms that share overlapping characteristics of BL and DLBCL. A subset of these ‘grey‐zone lymphomas’ possesses C‐MYC and IGH translocations but, in addition, contains additional rearrangements of BCL2 and/or BCL6 genes. The aim of this study was to investigate if the proliferation fraction by Ki67 immunostaining can be used to identify such double‐/triple‐hit lymphomas.Methods and results:  We studied 492 cases of mature aggressive B cell neoplasms by histology, immunohistochemistry and interphase fluorescence in‐situ hybridization (FISH) using break‐apart probes against C‐MYC, BCL2, BCL6, IGH, MALT1, PAX5 and CCND1. Forty Burkitt lymphomas and 28 cases of MYC+ double‐/triple‐hit lymphomas were identified. Of the latter, 77% and 54% displayed proliferation fractions exceeding 75% and 90%, respectively. With a cut‐off of >75% by Ki67 immunostaining, the sensitivity and specificity for detection of MYC+ double/triple translocations was 0.77 and 0.36. Raising the proliferation fraction criterion to >90% improved the specificity to 0.62 at the expense of a low sensitivity of 0.54.Conclusions:  Immunostaining for Ki67 is not a useful approach to prescreen B cell lymphomas for MYC+ double/triple translocations.
Effect of tick saliva on signalling pathways activated by TLR‐2 ligand and Borrelia afzelii in dendritic cells
Authors: LIESKOVSKA J. , KOPECKY J. 
Published: June 2012

SummaryDendritic cells are a sentinel in defending against pathogens and tick saliva facilitates transmission of tick‐borne pathogens by modulating the host immune response. The maturation of dendritic cells is inhibited by tick saliva. To elucidate the mechanism of this inhibition, we tested the impact of Ixodes ricinus tick saliva on signalling pathways activated by Toll‐like receptor (TLR‐2) ligand and Borrelia afzelii in spleen dendritic cells. The activation of nuclear factor‐κB (NF‐κB) p65 and phosphatidylinositol‐3 kinase (PI3K)/Akt pathways was decreased by tick saliva upon both TLR‐2 and Borrelia stimulation. Among the mitogen‐activated protein kinases (MAPK), the activation of extracellular matrix‐regulated kinase (Erk1/2) was suppressed by tick saliva, but not p38. In response to spirochaetes, the amount of TNF‐α decreased in the presence of tick saliva which was mediated by selective suppression of Erk1/2, NF‐κB and Akt as tick saliva mimicked the effect of their specific inhibitors, UO126, IKK‐IV and LY294002, respectively. Saliva‐induced enhancement of IL‐10 was not observed in the presence of specific inhibitor of Protein Kinase A (PKA), H‐89, suggesting the involvement of PKA pathway in IL‐10 production. Our cumulative data show that tick saliva interferes with several signalling pathways, thus modulating the immune functions of dendritic cells.
SUB1A‐dependent and ‐independent mechanisms are involved in the flooding tolerance of wild rice species
Authors: Niroula Raj Kumar , Pucciariello Chiara , Ho Viet The , Novi Giacomo , Fukao Takeshi , Perata Pierdomenico 
Published: June 2012

SummaryCrop tolerance to flooding is an important agronomic trait. Although rice (Oryza sativa) is considered a flood‐tolerant crop, only limited cultivars display tolerance to prolonged submergence, which is largely attributed to the presence of the SUB1A gene. Wild Oryza species have the potential to unveil adaptive mechanisms and shed light on the basis of submergence tolerance traits. In this study, we screened 109 Oryza genotypes belonging to different rice genome groups for flooding tolerance. Oryza nivara and Oryza rufipogon accessions, belonging to the A‐genome group, together with Oryza sativa, showed a wide range of submergence responses, and the tolerance‐related SUB1A‐1 and the intolerance‐related SUB1A‐2 alleles were found in tolerant and sensitive accessions, respectively. Flooding‐tolerant accessions of Oryza rhizomatis and Oryza eichingeri, belonging to the C‐genome group, were also identified. Interestingly, SUB1A was absent in these species, which possess a SUB1 orthologue with high similarity to O. sativa SUB1C. The expression patterns of submergence‐induced genes in these rice genotypes indicated limited induction of anaerobic genes, with classical anaerobic proteins poorly induced in O. rhizomatis under submergence. The results indicated that SUB1A‐1 is not essential to confer submergence tolerance in the wild rice genotypes belonging to the C‐genome group, which show instead a SUB1A‐independent response to submergence.