bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colorful microdiversity of Synechococcus strains (picocyanobacteria) isolated from the Baltic Sea
Authors: Haverkamp Thomas H A , Schouten Daphne , Doeleman Marije , Wollenzien Ute , Huisman Jef , Stal Lucas J 
Published: December 2008

Abstract
Synechococcus is a cosmopolitan genus of picocyanobacteria living in the photic zone of freshwater and marine ecosystems. Here, we describe the isolation of 46 closely related picocyanobacterial strains from the Baltic Sea. The isolates showed considerable variation in their cell size and pigmentation phenotypes, yielding a colorful variety of red, pink and blue-green strains. These pigmentation phenotypes could not be differentiated on the basis of their 16S rRNA-internal transcribed spacer (ITS) sequences. Thirty-nine strains, designated BSea, possessed 16S rRNA-ITS sequences almost identical with Synechococcus strain WH5701. Despite their similar 16S rRNA-ITS sequences, the BSea strains separated into several different clusters when comparing the phycocyanin (cpcBA) operon. This separation was largely consistent with the phycobiliprotein composition of the different BSea strains. The majority of phycocyanin (PC)-rich Bsea strains clustered with WH5701. Remarkably, the phycoerythrin (PE)-rich strains of BSea formed an as yet unidentified cluster within the cpcBA phylogeny, distantly related to other PE-rich groups. Detailed analysis of the cpcBA operon using neighbour-net analysis indicated that the PE-rich BSea strains are probably endemic for the Baltic Sea. Comparison of the phylogenies obtained by the 16S rRNA-ITS, the cpcBA, and the concatenated 16S rRNA-ITS and cpcBA operon sequences revealed possible events of horizontal gene transfer among different Synechococcus lineages. Our results show that microdiversity is important in Synechococcus populations and that it can reflect extensive diversification of different pigmentation phenotypes into different ecological niches.
Cross-Modal Interactions of Auditory and Somatic Inputs in the Brainstem and Midbrain and Their Imbalance in Tinnitus and Deafness
Authors: Dehmel S. , Cui Y. L. , Shore S. E. 
Published: December 2008

Purpose
This review outlines the anatomical and functional bases of somatosensory influences on auditory processing in the normal brainstem and midbrain. It then explores how interactions between the auditory and somatosensory system are modified through deafness, and their impact on tinnitus is discussed.

Method
Literature review, tract tracing, immunohistochemistry, and in vivo electrophysiological recordings were used.

Results
Somatosensory input originates in the dorsal root ganglia and trigeminal ganglia, and is transmitted directly and indirectly through 2nd-order nuclei to the ventral cochlear nucleus, dorsal cochlear nucleus (DCN), and inferior colliculus. The glutamatergic somatosensory afferents can be segregated from auditory nerve inputs by the type of vesicular glutamate transporters present in their terminals. Electrical stimulation of the somatosensory input results in a complex combination of excitation and inhibition, and alters the rate and timing of responses to acoustic stimulation. Deafness increases the spontaneous rates of those neurons that receive excitatory somatosensory input and results in a greater sensitivity of DCN neurons to trigeminal stimulation.

Conclusions
Auditory-somatosensory bimodal integration is already present in 1st-order auditory nuclei. The balance of excitation and inhibition elicited by somatosensory input is altered following deafness. The increase in somatosensory influence on auditory neurons when their auditory input is diminished could be due to cross-modal reinnervation or increased synaptic strength, and may contribute to mechanisms underlying somatic tinnitus.
Symptomatic partial rotator cuff tears: Diagnostic performance of ultrasound and magnetic resonance imaging with surgical correlation
Authors: Vlychou M. , Dailiana Z. , Fotiadou A. , Papanagiotou M. , Fezoulidis I.V. , Malizos K. 
Published: December 2008

Background: The painful shoulder is a relatively common clinical entity that may be attributed to a variety of pathologies, including partial rotator cuff tears. Conservative treatment or surgical intervention may be offered, depending on the extent of the partial tear and the degree of patient discomfort. Purpose: To apply ultrasound (US) imaging in order to evaluate the prevalence of partial rotator cuff tears in patients with painful shoulders. Material and Methods: Fifty-six patients (17 men, 39 women; mean age 53.7 years) were included in the study, with symptomatic impingement syndrome of the shoulder after having failed to respond to conservative treatment. All patients underwent US and magnetic resonance imaging (MRI) scans prior to surgical intervention. Results: Arthroscopy or mini-open surgery revealed 53 cases with partial tears of the rotator cuff and three with extensive tendinopathy. Both imaging modalities detected successfully 44 cases of partial tears of the supraspinatus tendon. US imaging yielded a sensitivity of 95.6%, a specificity of 70%, an accuracy of 91%, and a positive predictive accuracy of 93.6%. The corresponding values for MRI were 97.7%, 63.6%, 91%, and 91.7%, respectively. Conclusion: US imaging can be considered almost equally effective in detecting partial tears of the rotator cuff compared to MRI, particularly located in the area of the supraspinatus tendon. MRI may be reserved for doubtful or complex cases, in which delineation of adjacent structures is mandatory prior to surgical intervention.
Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila
Authors: Myasnikova Ekaterina , Surkova Svetlana , Panok Lena , Samsonova Maria , Reinitz John 
Published: December 2008

Abstract
Motivation: Currently the confocal scanning microscopy of fluorescently tagged molecules is extensively employed to acquire quantitative data on gene expression at cellular resolution. Following this approach, we generated a large dataset on the expression of segmentation genes in the Drosophila blastoderm, that is widely used in systems biology studies. As data accuracy is of critical importance for the success of studies in this field, we took a shot to evaluate possible errors introduced in the data by acquisition and processing methods. This article deals with errors introduced by confocal microscope.
Results: In confocal imaging, the inevitable photon noise is commonly reduced by the averaging of multiple frames. The averaging may introduce errors into the data, if single frames are clipped by microscope hardware. A method based on censoring technique is used to estimate and correct this type of errors. Additional source of errors is the quantification of blurred images. To estimate and correct these errors, the Richardson–Lucy deconvolution method was modified to provide the higher accuracy of data read off from blurred images of the Drosophila blastoderm. We have found that the sizes of errors introduced by confocal imaging make up ∼5–7% of the mean intensity values and do not disguise the dynamic behavior and characteristic features of gene expression patterns. We also defined a range of microscope parameters for the acquisition of sufficiently accurate data.
Availability: http://urchin.spbcas.ru/downloads/step/step.htm
Contact: myasnikova@spbcas.ru
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Pepper veinal mottle virus in Tomato and Pepper in Taiwan
Authors: Cheng Y. H. , Wang R. Y. , Chen C. C. , Chang C. A. , Jan F.-J. 
Published: December 2008

In May of 2006, samples from tomato plants (Solanum lycopersicum cv. Known-you 301) exhibiting necrotic symptoms on stems, petioles, and leaves were collected from Chiayi County, Taiwan. Double-antibody sandwich-ELISAs were performed using Cucumber mosaic virus, Tomato mosaic virus, Potato virus Y, Watermelon silver mottle virus, and Chilli veinal mottle virus (ChiVMV) polyclonal antibodies. Three of eight samples reacted with antibodies against ChiVMV but not with the others. Using the potyvirus degenerate primers (Hrp 5/Pot 1) (2), an expected 1.5-kb DNA fragment including the 3′-end of the NIb gene, the complete coat protein (CP) gene, and the 3′-nontranslatable region of the virus was amplified from total RNA isolated from these three samples by reverse transcription (RT)-PCR. A homology search in GenBank indicated that the new tomato-infecting virus in Taiwan belongs to Pepper veinal mottle virus (PVMV) since they shared >90% amino acid identity in the CP gene. A virus culture (Tom1) isolated from one of the diseased tomatoes was then established in Chenopodium quinoa and Nicotiana benthamiana and the CP gene was amplified and sequenced (GenBank Accession No. EU719647). Comparisons of the 807-nt CP gene with those of five PVMV isolates available in GenBank showed 81.5 to 93.1% nucleotide and 90.0 to 97.8% amino acid identity. Tom1 induced irregular necrotic lesions on stems, petioles, and leaves of tomato while inducing only mild mottle symptoms on pepper. Serological cross reaction between ChiVMV and PVMV has been observed previously (1,3) and also found in this study. To differentiate these two potyviruses by RT-PCR, primer pair CPVMVup/dw (5′-TATTC(T/C)TCAGTGTGG(A/T/C)T(T/C)CCACCAT and 5′-(T/C)C(A/T)C(A/T)(A/T/G)(A/T)AA(A/G)CCATAA(A/C)(A/C)ATA(A/G)T(T/C)T) was designed on the basis of the comparison of the CP gene and the 3′-nontranslatable region of the PVMV and ChiVMV. DNA fragments of 171 and 259 bp are expected to be amplified from ChiVMV and PVMV, respectively, by RT-PCR with primers CPVMVup/dw. In a field survey done in 2006, samples from diseased peppers (Capsicum annuum) that reacted with the polyclonal antibodies against ChiVMV were further identified by RT-PCR with primers CPVMVup/dw, indicating that both ChiVMV and PVMV infected pepper crops (Capsicum spp.) in Taiwan. A pepper isolate (Pep1) of PVMV was obtained from Nantou County through three times of single lesion passages on C. quinoa and then propagated on N. benthamiana. The CP gene of Pep1 was amplified and sequenced (GenBank Accession No. EU719646) and found to share 99.1% nucleotide and 100% amino acid identity with that of Tom1. Pep1 caused mild mottle symptoms on leaves of both tomato and pepper. To our knowledge, this is the first report of the presence of PVMV in Taiwan as well as in East Asia. References: (1) B. Moury et al. Phytopathology 95:227, 2005. (2) S. S. Pappu et al. Plant Dis. 82:1121, 1998. (3) W. S. Tsai et al. Plant Pathol. 58:408, 2008.
Wheat Cryptochromes: Subcellular Localization and Involvement in Photomorphogenesis and Osmotic Stress Responses
Authors: Xu Pei , Xiang Yang , Zhu Huilan , Xu Haibin , Zhang Zhengzhi , Zhang Caiqin , Zhang Lixia , Ma Zhengqiang 
Published: December 2008

AbstractCryptochromes (CRYs) are blue light receptors important for plant growth and development. Comprehensive information on monocot CRYs is currently only available for rice (Oryza sativa). We report here the molecular and functional characterization of two CRY genes, TaCRY1a and TaCRY2, from the monocot wheat (Triticum aestivum). The expression of TaCRY1a was most abundant in seedling leaves and barely detected in roots and germinating embryos under normal growth conditions. The expression of TaCRY2 in germinating embryos was equivalent to that in leaves and much higher than the TaCRY1a counterpart. Transition from dark to light slightly affected the expression of TaCRY1a and TaCRY2 in leaves, and red light produced a stronger induction of TaCRY1a. Treatment of seedlings with high salt, polyethylene glycol, and abscisic acid (ABA) up-regulated TaCRY2 in roots and germinating embryos. TaCRY1a displays a light-responsive nucleocytoplasmic shuttling pattern similar to that of Arabidopsis (Arabidopsis thaliana) CRY1, contains nuclear localization domains in both the N and C termini, and includes information for nuclear export in its N-terminal domain. TaCRY2 was localized to the nucleus in the dark. Expression of TaCRY1a-green fluorescent protein or TaCRY2-green fluorescent protein in Arabidopsis conferred a shorter hypocotyl phenotype under blue light. These transgenic Arabidopsis plants showed higher sensitivity to high-salt, osmotic stress, and ABA treatment during germination and postgermination development, and they displayed altered expression of stress/ABA-responsive genes. The primary root growth in transgenic seedlings was less tolerant of ABA. These observations indicate that TaCRY1 and TaCRY2 might be involved in the ABA signaling pathway in addition to their role in primary blue light signal transduction.
The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome
Authors: Wagner Stefanie , Sorg Isabel , Degiacomi Matteo , Journet Laure , Peraro Matteo Dal , Cornelis Guy R. 
Published: December 2008

SummaryThe length of the Yersinia injectisome needle is determined by the protein YscP, which could act as a molecular ruler. The analysis of the correlation between the size of YscP and the needle length in seven wild‐type strains of Yersinia enterocolitica reinforced this hypothesis but hinted that the secondary structure of YscP might influence needle length. Hence, 11 variants of YscP515 were generated by multiple Pro or Gly substitutions. The needle length changed in inverse function of the helical content, indicating that not only the number of residues but also their structure controls length. Taking the secondary motifs into account, Pro/Gly‐variants were subjected to in silico modelling to simulate the extension of YscP upon needle growth. The calculated lengths when the helical content is preserved correlated strikingly with the measured needle length, with a constant difference of ∼29 nm, which corresponds approximately to the size of the basal body. These data support the ruler model and show that the functional ruler has a helical structure.
The Arabidopsis glutathione transferase gene family displays complex stress regulation and co‐silencing multiple genes results in altered metabolic sensitivity to oxidative stress
Authors: Sappl Pia G. , Carroll Adam J. , Clifton Rachael , Lister Ryan , Whelan James , Harvey Millar A. , Singh Karam B. 
Published: December 2008

SummaryPlant glutathione transferases (GSTs) are induced by diverse biotic and abiotic stimuli, and are important for protecting plants against oxidative damage. We have studied the primary transcriptional stress response of the entire Arabidopsis GST family to seven stresses, including both biotic and abiotic stimuli, with a focus on early changes in gene expression. Our results indicate that individual GST genes are highly specific in their induction patterns. Furthermore, we have been able to link individual GSTs to particular stress stimuli. Using RNAi, we successfully co‐silenced a group of four phi GSTs that represent some of the most highly expressed GST genes. Despite a marked reduction in total phi GST protein levels, the transgenic plants showed no reduction in GST activity as measured using the model substrate 1‐chloro‐2,4‐dinitrobenzene (CDNB), and appeared to have surprisingly robust physical phenotypes during stress. However, analysis of metabolite pools showed oxidation of the glutathione pool in the RNAi lines, and we observed alterations in carbon and nitrogen compounds following salicylic acid and hydrogen peroxide stress treatments, indicative of oxidative modification of primary metabolism. Thus, there appears to be a high degree of functional redundancy within the Arabidopsis GST family, with extensive disruption being required to reveal the roles of phi GSTs in protection against oxidative stress.
CRYOSURGICAL PROSTATECTOMY
Authors: Ortved W. E. , O'Kelly F. M. , Todd I. A. D. , Maxwell J. B. , Sutton M.R. 
Published: December 2008

SUMMARYThis paper discusses the background and effect of the use of intense cold to destroy and ablate unwanted tissue in the obstructive prostate. The equipment and methods so far adopted are explained. A review of the first 100 cases done by our Canadian group from January to August 1966 is tabulated. Our experience to date indicates that in selected cases this new modality offers a further tool in treating prostate gland disease, and thereby broadens the range of safety in surgery of the prostate.
AN EVALUATION OF ROUTINE CYTOLOGICAL EXAMINATION OF THE URINE
Authors: Cullen T. H. , Popham R. R. , Voss H. J. 
Published: December 2008

SUMMARYThe results of cytological examination of the urine in a series which includes malignant and benign lesions of the uro‐epithelium are reported.The technique used is described and the cytological findings compared with the histology.It is concluded that routine cytological examination of the urine, particularly in patients who have had hæmaturia, is a valuable additional diagnostic aid. Earlier diagnosis may be made in cases of malignant disease of the renal pelvis, ureter and bladder diverticulum.Less success has been obtained in the detection of recurrence in the follow‐up of treated cases of malignant disease of the bladder in this series.
A better estimate of the internal consistency reliability of frontal EEG asymmetry scores
Authors: Towers David N. , Allen John J.B. 
Published: December 2008

AbstractFrontal alpha asymmetry is typically computed using alpha power averaged across many overlapping epochs. Previous reports have estimated the internal consistency reliability of asymmetry by dividing resting EEG sessions into segments of equal duration (e.g., 1 min) and treating asymmetry scores for each segment as “items” to estimate internal consistency reliability using Cronbach's alpha. Cronbach's alpha partly depends on the number of items, such that this approach may underestimate reliability by using less than the number of distinct items available. Reliability estimates for resting EEG data in the present study (204 subjects, 8 sessions) were obtained using mean split‐half correlations with epoch alpha power as treated as separate items. Estimates at all scalp sites and reference schemes approached .90 with as few as 100 epochs, suggesting the internal consistency of frontal asymmetry is greater than that previously reported.
Comparing Direct Abiotic Amelioration and Facilitation as Tools for Restoration of Semiarid Grasslands
Authors: Pueyo Yolanda , Alados Concepción L. , García‐Ávila Beatriz , Kéfi Sonia , Maestro Melchor , Rietkerk Max 
Published: December 2008

Abstract Desertification can be an irreversible process due to positive feedback among degraded plant and soil dynamics. The recovery of semiarid degraded ecosystems may need human intervention. In restoration practices, the abiotic conditions often need to be improved to overcome the positive plant–soil feedback loops. Using nurse‐plants to improve abiotic conditions for introduced individuals (facilitation) has been suggested as an alternative to direct abiotic amelioration. Here, we compared direct abiotic amelioration and facilitation as tools for restoration of semiarid grasslands in Spain. Seedlings and seeds of Lygeum spartum and Salsola vermiculata were planted and sown in a stably degraded semiarid area in Northeast Spain. Two levels of direct abiotic amelioration (ploughing and damming) and indirect abiotic amelioration through facilitation by Suaeda vera nurse shrubs were compared with a control with no amelioration treatment. The control treatment showed low plant establishment, confirming the practical irreversibility of the degraded state. Plant establishment was significantly higher in the three treatments with interventions than in the control treatment. The best treatment depended on the plant trait considered, but damming was in most cases better than plant facilitation. However, facilitation maintained the nutrient‐rich topsoil layer. Given the relative success of facilitation, revegetation using the facilitative effect of nurse‐plants would, in principle, be recommended for restoring semiarid grasslands. Direct abiotic amelioration would be needed under extreme degradation or harsh climatic conditions.
Interleukin‐10 is associated with resistance to febrile seizures: Genetic association and experimental animal studies
Authors: Ishizaki Yoshito , Kira Ryutaro , Fukuda Mitsumasa , Torisu Hiroyuki , Sakai Yasunari , Sanefuji Masafumi , Yukaya Naoko , Hara Toshiro 
Published: December 2008

SummaryPurpose:  Febrile seizures (FS) are the most common form of childhood convulsions. Many reports have shown that a proinflammatory cytokine, interleukin‐1 (IL‐1) β, may have a facilitatory effect on the development of FS. We have previously shown that the IL1B ‐511C/T single nucleotide polymorphism (SNP) is associated with simple FS of sporadic occurrence. The balance between pro‐ and antiinflammatory cytokines influences the regulation of infections and could, therefore, play a role in the pathogenesis of FS. Here, to determine whether pro‐ and antiinflammatory cytokine genes are responsible for the susceptibility to FS, we have performed an association study on functional SNPs of cytokine genes in FS patients and controls.Methods:  The promoter SNPs of four inflammatory cytokine genes (IL6 ‐572C/G, IL8 ‐251A/T, IL10 ‐592A/C and TNFA ‐1037C/T) were examined in 249 patients with FS (186 simple and 63 complex FS) and 225 controls. Because the IL10 ‐592 SNP showed a positive association with FS, two additional SNPs (IL10 ‐1082A/G and ‐819T/C) were subjected to haplotype analysis. Furthermore, we examined the in vivo role of IL‐10 in hyperthermia‐induced seizures using immature animal models.Results:  The frequencies of the IL10 ‐592C allele and ‐1082A/‐819C/‐592C haplotype were significantly decreased in FS as compared with in controls (p = 0.014 and 0.013, respectively). The seizure threshold temperature in the IL‐10–administered rats was significantly higher than that in the saline‐treated control ones (p = 0.027).Conclusions:  The present study suggests that IL‐10 is genetically associated with FS and, contrary to IL‐1β, confers resistance to FS.
Localized transmeningeal muscimol prevents neocortical seizures in rats and nonhuman primates: Therapeutic implications
Authors: Ludvig Nandor , Baptiste Shirn L. , Tang Hai M. , Medveczky Geza , Von Gizycki Hans , Charchaflieh Jean , Devinsky Orrin , Kuzniecky Ruben I. 
Published: December 2008

SummaryPurpose: To determine whether muscimol delivered epidurally or into the subarachnoid space can prevent and/or terminate acetylcholine (Ach)–induced focal neocortical seizures at concentrations not affecting behavior and background electroencephalography (EEG) activity.Methods: Rats (n = 12) and squirrel monkeys (n = 3) were chronically implanted with an epidural or subarachnoid drug delivery device, respectively, over the right frontal/parietal cortex, with adjacent EEG electrodes. Recordings were performed in behaving rats and chaired monkeys. Via the implants, either a control solution (artificial cerebrospinal fluid, ACSF) or muscimol (0.25–12.5 mm) was delivered locally as a “pretreatment,” followed by the similar delivery of a seizure‐inducing concentration of Ach. In five additional rats, the quantities of food‐pellets consumed during epidural ACSF and muscimol (2.5 mm) exposures were measured. In a last group of four rats, muscimol (0.8–2.5 mm) was delivered epidurally during the ongoing, Ach‐induced EEG seizure.Results: In contrast to ACSF pretreatments, epidural muscimol pretreatment in rats completely prevented the seizures at and above 2.5 mm. In the monkeys, subarachnoid muscimol pretreatments at 2.5 mmcompletely prevented the focal‐seizure–inducing effect of Ach, whereas similar deliveries of ACSF did not affect the seizures. Furthermore, 2.5 mmepidural muscimol left the eating behavior of rats intact and caused only slight changes in the EEG power spectra. Finally, muscimol delivery during Ach‐induced EEG seizures terminated the seizure activity within 1–3 min.Conclusions: The results of this study suggest that muscimol is a viable candidate for the transmeningeal pharmacotherapy of intractable focal epilepsy.