bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flow cytometry‐based enrichment for cell shape mutants identifies multiple genes that influence Helicobacter pylori morphology
Authors: Sycuro Laura K. , Rule Chelsea S. , Petersen Timothy W. , Wyckoff Timna J. , Sessler Tate , Nagarkar Dilip B. , Khalid Fakhra , Pincus Zachary , Biboy Jacoby , Vollmer Waldemar , Salama Nina R. 
Published: October 2013

SummaryThe helical cell shape of Helicobacter pylori is highly conserved and contributes to its ability to swim through and colonize the viscous gastric mucus layer. A multi‐faceted peptidoglycan (PG) modification programme involving four recently characterized peptidases and two accessory proteins is essential for maintaining H. pylori's helicity. To expedite identification of additional shape‐determining genes, we employed flow cytometry with fluorescence‐activated cell sorting (FACS) to enrich a transposon library for bacterial cells with altered light scattering profiles that correlate with perturbed cell morphology. After a single round of sorting, 15% of our clones exhibited a stable cell shape defect, reflecting 37‐fold enrichment. Sorted clones with straight rod morphology contained insertions in known PG peptidases, as well as an insertion in csd6, which we demonstrated has ld‐carboxypeptidase activity and cleaves monomeric tetrapeptides in the PG sacculus, yielding tripeptides. Other mutants had only slight changes in helicity due to insertions in genes encoding MviN/MurJ, a protein possibly involved in initiating PG synthesis, and the hypothetical protein HPG27_782. Our findings demonstrate FACS robustly detects perturbations of bacterial cell shape and identify additional PG peptide modifications associated with helical cell shape in H. pylori.
Clinical and radiological correlation in patients with vertebrobasilar artery occlusion
Authors: Ogata Toshiyasu , Takemoto Koichiro , Okawa Masakazu , Hamada Omi , Abe Hiroshi , Iwaasa Mitsutoshi , Higashi Toshio , Takano Koichi , Tsuboi Yoshio , Kitazono Takanari , Inoue Tooru 
Published: October 2013

AbstractAimAlthough ischemic stroke in posterior stroke induces approximately one‐fifth of all strokes, basilar artery occlusion (BAO) and bilateral intracranial vertebral artery occlusion (BIVAO) are relatively rare. The present study was carried out to clarify the differences in clinical features between patients with ischemic stroke caused by BAO and BIVAO.MethodsWe retrospectively investigated 17 patients with ischemic stroke caused by either BAO or BIVAO who were transferred to our emergency ward within 24 hours of onset. Intravenous and intra‐arterial thrombolysis, stenting, and medications were given according to the patient's age, underlying diseases, time from onset, stroke etiology, and degree of neurological symptoms. Patient background, underlying diseases, findings on admission, prior history of stroke, prior antithrombotic treatment, sites of infarction, treatment, and outcome at discharge were compared between patients with BAO and BIVAO.ResultsA total of 10 patients had BAO and seven had BIVAO. The stroke etiology was significantly different between the two groups; 60% of patients with BAO had cardioembolic stroke, whereas more than 70% of cases of BIVAO were induced by large artery atherosclerosis (P = 0.039). Although initial neurological deficits as evaluated by the National Institute of Health and Stroke Scale score differed (P = 0.005), the median modified Rankin Scale became similar at discharge (P = 0.42).ConclusionsIschemic stroke caused by BIVAO was frequently induced by large artery atherosclerosis, whereas that caused by BAO was categorized as cardioembolic stroke. Although patients with BIVAO had less severe disease than those with BAO on admission, both groups showed poor functional outcomes at discharge.
Pistillate flowers experience more pollen limitation and less geitonogamy than perfect flowers in a gynomonoecious herb
Authors: Mamut Jannathan , Xiong Ying‐Ze , Tan Dun‐Yan , Huang Shuang‐Quan 
Published: October 2013

Summary

Gynomonoecy, a sexual system in which plants have both pistillate (female) flowers and perfect (hermaphroditic) flowers, occurs in at least 15 families, but the differential reproductive strategies of the two flower morphs within one individual remain unclear.

Racemes of Eremurus anisopterus (Xanthorrhoeaceae) have basal pistillate and distal perfect flowers. To compare sex allocation and reproductive success between the two flower morphs, we measured floral traits, pollinator preferences, and pollen movement in the field.

Pollen limitation was more severe in pistillate flowers; bee pollinators preferred to visit perfect flowers, which were also capable of partial self‐fertilization. Pollen‐staining experiments indicated that perfect flowers received a higher proportion of intra‐plant pollen (geitonogamy) than pistillate flowers. Plants with greater numbers of pistillate flowers received more outcross pollen. The differential reproductive success conformed with differential floral sex allocation, in which pistillate flowers produce fewer but larger ovules, resulting in outcrossed seeds.

Our flower manipulations in these nectarless gynomonoecious plants demonstrated that perfect flowers promote seed quantity in that they are more attractive to pollinators, while pistillate flowers compensate for the loss of male function through better seed quality. These results are consistent with the outcrossing‐benefit hypothesis for gynomonoecy.
Development and characterization of single‐nucleotide polymorphism markers from 454 transcriptome sequences in oil palm (Elaeis guineensis)
Authors: Pootakham Wirulda , Uthaipaisanwong Pichahpuk , Sangsrakru Duangjai , Yoocha Thippawan , Tragoonrung Somvong , Tangphatsornruang Sithichoke 
Published: October 2013

AbstractOil palm (Elaeis guineensis) has recently emerged as the world's most important economic crop, with the world production of palm oil surpassing that of soybean. The utilization of palm oil as a feedstock in biodiesel production has triggered a dramatic rise in its global demand. In recent years, marker‐assisted selections have played a pivotal role in oil palm breeding programmes as they have several advantages over traditional breeding approaches. We have explored the possibility of developing single‐nucleotide polymorphism (SNP) markers in Elaeis guineensis using the 454‐derived transcriptomic sequence data. We have identified 823 putative SNP positions in silico using a set of highly stringent criteria. Forty‐six bi‐allelic SNP positions were validated by the traditional Sanger sequencing method. The polymorphism information contents (PICs) and the observed heterozygosity (HO) ranged from 0.066 to 0.375 and 0 to 0.928, respectively. These SNP markers will be useful for the construction of high‐density genetic maps (allowing the identification of commercially desirable quantitative trait loci), genetic variation studies and the population structure analyses in E. guineensis.
Methylene tetrahydrofolate reductase polymorphisms and homocysteine level in heart defects
Authors: Sahiner Umit M , Alanay Yasemin , Alehan Dursun , Tuncbilek Ergul , Alikasifoglu Mehmet 
Published: October 2013

AbstractBackgroundWhile several single nucleotide polymorphisms are known to influence the metabolism of folate, the methylene tetrahydrofolate reductase (MTHFR) gene has been the most extensively studied. The aim of this study was to investigate the relationship between the MTHFR polymorphisms 1298A>C and 677C>T and congenital heart disease. In addition, the relationship between these gene polymorphisms and homocysteine level was determined in Turkish subjects.MethodsPatients with non‐syndromic congenital heart defects who were admitted to the Pediatric Cardiology Unit at Hacettepe University Ihsan Dogramaci Children's Hospital, Ankara, Turkey between June 2002 and June 2003 were recruited for the study. A total of 163 children with congenital heart defects (mean age, 7.63 ± 6.03 years; M/F, 93/70) and 93 healthy controls were analyzed.ResultsWhen evaluated either separately or together, there were no differences in the frequency of MTHFR 677C>T or 1298A>C polymorphisms between the children with congenital heart defects and the control group. The results were the same when considering only conotruncal defects. Those with the 677C>T polymorphism had significantly lower homocysteine level (P = 0.004), but the 1298A>C polymorphism was not related to homocysteine level.ConclusionNo relationship was found between congenital heart defects and 1298A>C or 677C>T polymorphisms. The 677C>T polymorphism was related to low homocysteine level. Because there is often much heterogeneity between populations, this study should be conducted in different populations and with larger numbers of participants.
Morality and a Scaffolding of Facts
Authors: Carter Drew 
Published: October 2013

AbstractIn reply to Michael Campbell, I reformulate my questions of Raimond Gaita, avoiding the expression “form of life”. I examine what might remove the need for my questions, before taking up Campbell's line of thought about what he calls the “inwardness” of moral concepts. Campbell helps to clarify the picture of moral concepts advanced by Wittgensteinian moral philosophers. But at a general level, the picture remains unclear where a grammar meets its scaffolding of facts. Some may find this unproblematic, and indeed unavoidable. But I remain unsure of this, and hope to provide at least a useful caution.
Seedling development in buckwheat and the discovery of the photomorphogenic shade‐avoidance response
Authors: Kutschera U. , Briggs W. R. 
Published: October 2013

AbstractNumerous botanists of the early 19th century investigated the effect of sunlight on plant development, but no clear picture developed. One hundred and fifty years ago, Julius Sachs (1863) systematically analysed the light–plant relationships, using developing garden nasturtium (Tropaeolum majus) and seedlings of buckwheat (Fagopyron esculentum) as experimental material. From these studies, Sachs elucidated the phenomenon of photomorphogenesis (plant development under the influence of daylight) and the associated ‘shade‐avoidance response’. We have reproduced the classical buckwheat experiments of Sachs (1863) and document the original shade‐avoidance syndrome with reference to hypocotyl elongation and cotyledon development in darkness (skotomorphogenesis), white light and shade induced by a canopy of green leaves. In subsequent publications, Sachs elaborated his concepts of 1863 and postulated the occurrence of ‘flower‐inducing substances’. In addition, he argued that the shade‐avoidance response in cereals, such as wheat and maize, is responsible for lodging in crowded plant communities. We discuss these processes with respect to the red‐ to far‐red light/phytochrome B relationships. Finally, we summarise the phytochrome B–phytohormone (auxin, brassinosteroids) connection within the cells of shaded Arabidopsis plants, and present a simple model to illustrate the shade‐avoidance syndrome. In addition, we address the relationship between plant density and health of the corresponding population, a topic that was raised for the first time by Sachs (1863) in his seminal paper and elaborated in his textbooks.
The Expression and Significance of TIPE2 in Peripheral Blood Mononuclear Cells from Asthmatic Children
Authors: Ma Y. , Liu X. , Wei Z. , Wang X. , Wang Z. , Zhong W. , Li Y. , Zhu F. , Guo C. , Zhang L. , Wang X. 
Published: October 2013

AbstractTumour necrosis factor‐α‐induced protein‐8 like‐2 (TIPE2) is a newly identified immune negative regulator. The abnormal expression of TIPE2 has been found in several human inflammatory diseases. However, the expression level and clinical significance of TIPE2 in childhood asthma remain unclear. In this study, we detected TIPE2 expression in peripheral blood mononuclear cells (PBMC) from 42 children with asthma and 39 healthy controls by RT‐PCR, qRT‐PCR and Western blot. We also detected the levels of serum total immunoglobulin E (IgE), eosinophil (EO), interleukin‐4 (IL‐4) and interferon‐γ (IFN‐γ) and analysed the correlations of TIPE2 expression with IgE, EO, IL‐4 and IFN‐γ. The results showed that TIPE2 mRNA and protein expression were decreased in children with asthma compared with healthy controls. The levels of IgE, EO and IL‐4 in the children with asthma were obviously higher than those in normal controls, while the level of IFN‐γ in patients with asthma was significantly lower than that in healthy subjects. Furthermore, the expression level of TIPE2 mRNA was negatively correlated with IgE, EO and IL‐4. However, no statistically significant correlation was found between TIPE2 mRNA expression and serum IFN‐γ level. In conclusion, our data suggest that reduced TIPE2 expression may contribute to the pathogenesis of childhood asthma.
Association of Disease Severity with IL‐1 levels in Methotrexate‐treated Psoriasis Patients
Authors: Tamilselvi E. , Haripriya D. , Hemamalini M. , Pushpa G. , Swapna S. 
Published: October 2013

AbstractInterleukin‐1 plays a key role in inflammation and keratinocyte activation. It is an important mediator in the initiation and maintenance of psoriatic plaques and may represent an attractive therapeutic target. The aim of this study is to evaluate the effect of Methotrexate (MTX) on IL‐1 α and IL‐1 β levels in both plasma and skin biopsy of patients with psoriasis and to investigate their association with clinical disease activity. Forty‐five control subjects and 58 patients with psoriasis were recruited for this study. The patients were treated with 7.5 mg of MTX per week for 12 weeks. Folic acid was given at 5 mg once daily except on the day of MTX for 12 weeks. Blood samples and lesional skin biopsy were taken. Disease severity was assessed by Psoriasis Area Severity Index (PASI) score. IL‐1 levels in plasma and skin biopsy were analysed using ELISA. PASI score declined significantly (P < 0.001) from day 0 to 12 weeks of MTX treatment. IL‐1 α level in plasma and skin biopsy was reduced at day 0 sample and elevated significantly (P < 0.001) after MTX treatment. IL‐1β level in plasma and skin biopsy was higher at day 0 sample and reduced significantly (P < 0.001) after MTX treatment. IL‐1α levels and PASI score showed inverse correlation score before and after treatment with MTX. Whereas IL‐1β levels showed positive correlation before and after treatment with MTX. Decreasing IL‐1β levels by MTXs in psoriasis may block the Th17 differentiation. This shows the therapeutic effect of MTX in controlling the immunopathogenesis of psoriasis.
Assessment of Digital Image Correlation Measurement Accuracy in the Ultimate Error Regime: Main Results of a Collaborative Benchmark
Authors: Amiot F. , Bornert M. , Doumalin P. , Dupré J. ‐C. , Fazzini M. , Orteu J. ‐J. , Poilâne C. , Robert L. , Rotinat R. , Toussaint E. , Wattrisse B. , Wienin J. S. 
Published: October 2013

ABSTRACTWe report on the main results of a collaborative work devoted to the study of the uncertainties associated with Digital image correlation techniques (DIC). More specifically, the dependence of displacement measurement uncertainties with both image characteristics and DIC parameters is emphasised. A previous work [Bornert et al. (2009) Assessment of digital image correlation measurement errors: methodology and results. Exp. Mech. 49, 353–370] dedicated to situations with spatially fluctuating displacement fields demonstrated the existence of an ‘ultimate error’ regime, insensitive to the mismatch between the shape function and the real displacement field. The present work is focused on this ultimate error. To ensure that there is no mismatch error, synthetic images of in‐plane rigid body translation have been analysed. Several DIC softwares developed by or in use in the French community have been used to explore the effects of a large number of settings. The discrepancies between DIC evaluated displacements and prescribed ones have been statistically analysed in terms of random errors and systematic bias, in correlation with the fractional part τ of the displacement component expressed in pixels. Main results are as follows: (i) bias amplitude is almost always insensitive to subset size, (ii) standard deviation of random error increases with noise level and decreases with subset size and (iii) DIC formulations can be split up into two main families regarding bias sensitivity to noise. For the first one, bias amplitude increases with noise while it remains nearly constant for the second one. In addition, for the first family, a strong dependence of random error with τ is observed for noisy images.
Morphometric evaluation of the fetal rat liver after maternal dexamethasone treatment: effect on the maturation of erythroid and megakaryocytic cells
Authors: Neves Flávia Macedo de Oliveira , Paccola Camila Cicconi , Miraglia Sandra Maria , Cipriano Ivone 
Published: October 2013

BackgroundDuring pregnancy, glucocorticoids are frequently used to accelerate fetal lung maturation in preterm delivery. However, prenatal administration of glucocorticoids has been shown to affect organs such as fetal liver, an important hematopoietic organ during fetal development.ObjectiveThe aim of this study was to document the qualitative and quantitative changes in erythroid and megakaryocytic cell populations found in fetal livers as well as the hematology profile in neonates after maternal glucocorticoid treatment in rats.MethodsPregnant female Wistar rats were treated with dexamethasone 21‐phosphate from days 13 to 16 of gestation. On the 17th day of pregnancy, the fetuses were collected and their livers processed for light and transmission electron microscopy. Glycol methacrylate‐embedded sections were stained with PAS to determine the erythroblast and megakaryocytic cell frequencies. Fetal liver pieces embedded in Spurr resin were analyzed by transmission electron microscopy for morphologic changes. A standard hematology profile was evaluated in neonatal rats.ResultsIn the fetuses from treated dams, the total cell number of erythroid cells in livers was significantly reduced compared to control fetuses (P < .001), but erythroblasts did not present ultrastructural abnormalities. The degree of maturation in the megakaryocyte series tended to be increased. In neonates, there were elevated numbers of nucleated RBCs (P = .002), along with a higher HCT and HGB (P = .02). In addition, the platelet concentration was also significantly increased (P < .007).ConclusionThese results suggest that maternal dexamethasone treatment has quantitative effects on erythroid and megakaryocytic cells in fetal liver and the neonatal hematology profile in rats.
Potential roles of ATP and local neurons in the monitoring of blood O2 content by rat aortic bodies
Authors: Piskuric N. A. , Zhang M. , Vollmer C. , Nurse C. A. 
Published: October 2013

New Findings
What is the central question of this study?How do aortic bodies monitor blood O2 content? We investigated whether ATP, known to be released from red blood cells during hypoxia, could contribute via interactions with local neurons.
What is the main finding and its importance?In dissociated aortic body cultures from the vagus and recurrent laryngeal nerves, some local neurons expressed functional P2X2/3 purinoceptors and were electrically coupled; there was also the potential for cholinergic neurotransmission. Large molecules, such as Evans Blue, had easy access to local neurons via the circulation. We hypothesize that sensing of low blood O2 content may involve ATP release from red blood cells, leading to stimulation of local ‘sensory’ aortic body neurons.
Aortic bodies are arterial chemoreceptors presumed to monitor blood O2 content by unknown mechanisms, in contrast to their well‐studied carotid body counterparts, which monitor and /pH. We recently showed that rat aortic body chemoreceptors (type I cells), located at the left vagus–recurrent laryngeal nerve bifurcation, responded to and /pH in a manner similar to carotid body type I cells. These aortic bodies are uniquely associated with a group of local neurons, which are also sensitive to these stimuli. Here, we hypothesized that these local neurons may contribute to monitoring blood O2 content. During perforated patch recordings, ATP, known to be released from (carotid body) type I cells and red blood cells during hypoxia, induced inward currents and excited ∼45% of local neurons (EC50∼1 μm), mainly via heteromeric P2X2/3 purinoceptors. While ATP also induced a rise in intracellular [Ca2+] in a subpopulation of these neurons, almost all of them responded to nicotinic cholinergic agonists. During paired recordings, several juxtaposed neurons showed strong bidirectional electrical coupling, suggesting a local co‐ordination of electrical activity. Perfusion with Evans Blue dye resulted in labelling of aortic body paraganglia, suggesting they have ready access to circulatory factors, e.g. ATP released from red blood cells during hypoxia. When combined with confocal immunofluorescence, the dye‐labelled regions coincided with areas containing tyrosine hydroxylase‐positive type I cell clusters and P2X2‐positive nerve endings. We propose a working model whereby local neurons, red blood cells, ATP signalling and low blood flow contribute to the unique ability of the aortic body to monitor blood O2 content.
The Effect of Reynolds Number on Transonic Compressor Blade Rotor Section
Authors: Farahani A. Shahrabi , Amiri H. Beheshti , Khazaei H. , Madadi A. , Fathi A. 
Published: October 2013

To achieve at a more precise designing procedure in axial-compressors as well as a higher pressure ratio value, a comprehensive understanding on the flow aerodynamics and the governing phenomena is required. Existence of these complicated phenomena e.g., simultaneous production of supersonic and subsonic flows, shock-boundary layer interaction, unique incidence phenomenon, etc, makes it difficult to analyze the flow in the transonic compressors. One of the methods which is useful in the modeling of the phenomena occur in the compressors is investigating the flow in the blade to blade passage.
In this paper, employing the simultaneous solution of the full Navier-Stokes equations (using the Roe-FDS numerical method) and turbulence equations (using the K–w (SST) model) the flow has been simulated in the blade to blade passage of a transonic compressor. In the following, in order to comparison the predicted results with experimental data, required adjustments and conditions have been taken into account.
After passing through the first transonic compressor stages, the flow becomes remarkably compressed. In such conditions, the Reynolds number considerably changes compared to the inflow Reynolds number. In the present work, it is intended to numerically investigate the effects of the inflow Reynolds number on the unique incidence, flow losses, deviation angle, and also shock position changes, in three different important states of “Minimum loss” and “Choked flow” in started conditions and “Stall operation” in unstarted conditions.