bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular subdivision of the marine diatom Thalassiosira rotulain relation to geographic distribution, genome size, and physiology
Authors: Whittaker Kerry A , Rignanese Dayna R , Olson Robert J , Rynearson Tatiana A 
Published: October 2012

Abstract

Background
Marine phytoplankton drift passively with currents, have high dispersal potentials and can be comprised of morphologically cryptic species. To examine molecular subdivision in the marine diatom Thalassiosira rotula, variations in rDNA sequence, genome size, and growth rate were examined among isolates collected from the Atlantic and Pacific Ocean basins. Analyses of rDNA included T. gravida because morphological studies have argued that T. rotula and T. gravida are conspecific.

Results
Culture collection isolates of T. gravida and T. rotula diverged by 7.0 ± 0.3% at the ITS1 and by 0.8 ± 0.03% at the 28S. Within T. rotula, field and culture collection isolates were subdivided into three lineages that diverged by 0.6 ± 0.3% at the ITS1 and 0% at the 28S. The predicted ITS1 secondary structure revealed no compensatory base pair changes among lineages. Differences in genome size were observed among isolates, but were not correlated with ITS1 lineages. Maximum acclimated growth rates of isolates revealed genotype by environment effects, but these were also not correlated with ITS1 lineages. In contrast, intra-individual variation in the multi-copy ITS1 revealed no evidence of recombination amongst lineages, and molecular clock estimates indicated that lineages diverged 0.68 Mya. The three lineages exhibited different geographic distributions and, with one exception, each field sample was dominated by a single lineage.

Conclusions
The degree of inter- and intra-specific divergence between T. gravida and T. rotula suggests they should continue to be treated as separate species. The phylogenetic distinction of the three closely-related T. rotula lineages was unclear. On the one hand, the lineages showed no physiological differences, no consistent genome size differences and no significant changes in the ITS1 secondary structure, suggesting there are no barriers to interbreeding among lineages. In contrast, analysis of intra-individual variation in the multicopy ITS1 as well as molecular clock estimates of divergence suggest these lineages have not interbred for significant periods of time. Given the current data, these lineages should be considered a single species. Furthermore, these T. rotula lineages may be ecologically relevant, given their differential abundance over large spatial scales.
Pathway Distiller - multisource biological pathway consolidation
Authors: Doderer Mark S , Anguiano Zachry , Suresh Uthra , Dashnamoorthy Ravi , Bishop Alexander JR , Chen Yidong 
Published: October 2012

Abstract

Background
One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally describe the set of genes, much effort has been made to collect curated biological pathways into publicly accessible databases. When combining disparate databases, highly related or redundant pathways exist, making their consolidation into pathway concepts essential. This will facilitate unbiased, comprehensive yet streamlined analysis of experiments that result in large gene sets.

Methods
After gene set enrichment finds representative pathways for large gene sets, pathways are consolidated into representative pathway concepts. Three complementary, but different methods of pathway consolidation are explored. Enrichment Consolidation combines the set of the pathways enriched for the signature gene list through iterative combining of enriched pathways with other pathways with similar signature gene sets; Weighted Consolidation utilizes a Protein-Protein Interaction network based gene-weighting approach that finds clusters of both enriched and non-enriched pathways limited to the experiments' resultant gene list; and finally the de novo Consolidation method uses several measurements of pathway similarity, that finds static pathway clusters independent of any given experiment.

Results
We demonstrate that the three consolidation methods provide unified yet different functional insights of a resultant gene set derived from a genome-wide profiling experiment. Results from the methods are presented, demonstrating their applications in biological studies and comparing with a pathway web-based framework that also combines several pathway databases. Additionally a web-based consolidation framework that encompasses all three methods discussed in this paper, Pathway Distiller (http://cbbiweb.uthscsa.edu/PathwayDistiller), is established to allow researchers access to the methods and example microarray data described in this manuscript, and the ability to analyze their own gene list by using our unique consolidation methods.

Conclusions
By combining several pathway systems, implementing different, but complementary pathway consolidation methods, and providing a user-friendly web-accessible tool, we have enabled users the ability to extract functional explanations of their genome wide experiments.
Prognostic value of semi-quantitative bacteruria counts in the diagnosis of group B streptococcus urinary tract infection: a 4-year retrospective study in adult patients
Authors: Tan Chee K , Ulett Kimberly B , Steele Michael , Benjamin William H , Ulett Glen C 
Published: October 2012

Abstract

Background
Semi-quantitative bacteruria counts (s-QBC) are important in the diagnosis of urinary tract infection (UTI) due to most uropathogens. The prognostic value of s-QBC for diagnosis of UTI due to group B streptococcus (GBS) is unknown. In this study, we assessed the value of s-QBC for differentiating acute GBS UTI from asymptomatic bacteruria (ABU), independent of other potential prognostic indicators.

Methods
Medical record review and urinalysis (UA) values for 1593 patients who had urinary GBS isolated (103 to ≥105 CFU/ml) during a four-year period were analyzed using binary logistic regression to determine the predictive values of s-QBC, age, and gender for infection category (acute UTI, ABU) based on the clinical diagnosis.

Results
s-QBC alone had a strong predictive value for infection category but only for ABU. Multivariate logistic regression showed similar predictive power of s-QBC for infection category using age as a co-predictor, which was also independently associated with infection category. Typical s-QBC cut-off values that are commonly used in diagnostic settings had no significant power in predicting infection category. Among other UA measures, proteinuria and hematuria were significantly associated with acute infection.

Conclusions
Together, these data show that s-QBC is not useful in the differential diagnosis of GBS UTI. Among the patients in this study, age was an equally effective prognostic indicator compared to s-QBC for identifying high- and low-risk patients for acute GBS UTI. Collectively, these findings indicate that age-based associations may be equally as useful as s-QBC for predicting infection category in the setting of adult patients with GBS-positive urine cultures.
Effects of ginsenoside Re on LPS-induced inflammatory mediators in BV2 microglial cells
Authors: Lee Kang-Woo , Jung So Young , Choi Sun-Mi , Yang Eun Jin 
Published: October 2012

Abstract

Background
Microglial activation plays an important role in neurodegenerative diseases by producing several pro-inflammatory enzymes and pro-inflammatory cytokines. Lipopolysaccharide (LPS)-induced inflammation leads to the activation of microglial cells in the central nervous system (CNS) and is associated with the pathological mechanisms of neurodegenerative diseases, including PD, AD, and ALS. Ginseng is a natural antioxidant used in herbal medicine and contains ginsenosides (Rb1, Rg1, Rg3, Re, and Rd), which have anti-neoplastic and anti-stress properties.
This study demonstrates the involvement of the anti-inflammatory signaling pathway, ginsenoside-Re (G-Re), which is one of the ginsenosides mediated by LPS-induced neuroinflammation in BV2 microglial cells.

Methods
BV2 microglial cells were pretreated with 2 μg/ml G-Re and stimulated with 1 μg/ml LPS to induce neuroinflammation. To investigate the effect of G-Re on LPS-induced cell signaling, we performed western blotting and immunofluorescence using specific antibodies, such as phospho-p38, COX2, and iNOS.

Results
Pretreatment with 2 μg/ml G-Re was neuroprotective against 1 μg/ml LPS-treated microglial cells. The neuroprotective events induced by G-Re treatment in neuroinflammation occurred via the phospho-p38, iNOS, and COX2 signaling pathways in BV2 cells.

Conclusion
Taken together, we suggest that G-Re exerts a beneficial effect on neuroinflammatory events in neurodegenerative diseases.
Isotope Coded Protein Labeling analysis of plasma specimens from acute severe dengue fever patients
Authors: Fragnoud Romain , Yugueros-Marcos Javier , Pachot Alexandre , Bedin Frederic 
Published: October 2012

AbstractBackgroundDengue fever is the most important arthropod born viral disease of public health significance. Although most patients suffer only from flu-like symptoms, a small group of patient experiences more severe forms of the disease. To contribute to a better understanding of its pathogenesis this study aims to identify proteins differentially expressed in a pool of five viremic plasma from severe dengue patients relative to a pool of five non-severe dengue patients.ResultsThe use of Isotope Coded Protein Labeling (ICPLTM) to analyze plasma depleted of twenty high-abundance proteins allowed for the identification of 51 differentially expressed proteins, which were characterized by mass spectrometry. Using quantitative ELISA, three of these proteins (Leucine-rich glycoprotein 1, Vitamin D binding-protein and Ferritin) were confirmed as having an increased expression in a panel of severe dengue plasma. The proteins identified as overexpressed by ICPLTMin severe dengue plasma involve in clear up action after cell injury, tissue coherence and immune defense.ConclusionThis ICPLTMstudy evaluating differences between acute severe dengue plasmas and acute non-severe dengue plasmas suggests that the three proteins identified are overexpressed early in the course of the disease. Their possible use as biomarkers for the prognostic of disease severity is discussed.
Dendritic cell CNS recruitment correlates with disease severity in EAE via CCL2 chemotaxis at the blood–brain barrier through paracellular transmigration and ERK activation
Authors: Sagar Divya , Lamontagne Anne , Foss Catherine A , Khan Zafar K , Pomper Martin G , Jain Pooja 
Published: October 2012

AbstractBackgroundTransmigration of circulating dendritic cells (DCs) into the central nervous system (CNS) across the blood–brain barrier (BBB) has not thus far been investigated. An increase in immune cell infiltration across the BBB, uncontrolled activation and antigen presentation are influenced by chemokines. Chemokine ligand 2 (CCL2) is a potent chemoattractant known to be secreted by the BBB but has not been implicated in the recruitment of DCs specifically at the BBB.MethodsExperimental autoimmune encephalomyelitis (EAE) was induced in C57BL/6 mice by injection of MOG35–55peptide and pertussis toxin intraperitoneally. Animals with increasing degree of EAE score were sacrificed and subjected to near-infrared and fluorescence imaging analysis to detect and localize the accumulation of CD11c+-labeled DCs with respect to CCL2 expression. To further characterize the direct effect of CCL2 in DC trafficking at the BBB, we utilized anin vitroBBB model consisting of human brain microvascular endothelial cells to compare migratory patterns of monocyte-derived dendritic cells, CD4+and CD8+T cells. Further, this model was used to image transmigration using fluorescence microcopy and to assess specific molecular signaling pathways involved in transmigration.ResultsNear-infrared imaging of DC transmigration correlated with the severity of inflammation during EAE.Ex vivohistology confirmed the presence of CCL2 in EAE lesions, with DCs emerging from perivascular spaces. DCs exhibited more efficient transmigration than T cells in BBB model studies. These observations correlated with transwell imaging, which indicated a paracellular versus transcellular pattern of migration by DCs and T cells. Moreover, at the molecular level, CCL2 seems to facilitate DC transmigration in an ERK1/2-dependent manner.ConclusionCNS recruitment of DCs correlates with disease severity in EAE via CCL2 chemotaxis and paracellular transmigration across the BBB, which is facilitated by ERK activation. Overall, these comprehensive studies provide a state-of-the-art view of DCs within the CNS, elucidate their path across the BBB, and highlight potential mechanisms involved in CCL2-mediated DC trafficking.
Polyoxovanadate–Surfactant Hybrid Layered Crystal Containing One-Dimensional Hydrogen-Bonded Cluster Chain
Authors: Ito Takeru , Taira Minako , Fukumoto Kazuhiro , Yamamoto Kazuhiro , Naruke Haruo , Tomita Koji 
Published: October 2012

Abstract
A polyoxovanadate–surfactant hybrid layered crystal was synthesized by using decyltrimethylammonium (C10) cation. The hybrid crystal with a formula of (C10)4[H2V10O28]·8H2O (C10–V10) contained diprotonated decavanadate anions, which were connected to each other to form hydrogen-bonded cluster chains. Conductivity and photoreactivity of C10–V10 were also investigated.
Molecular Dynamics of Octyl Urea Crystals Analyzed by Solid-state NMR
Authors: Ohashi Ryutaro , Wakabayashi Gou , Mizuno Motohiro , Soeta Takahiro , Hashimoto Masao , Yamamura Kimiaki 
Published: October 2012

Abstract
Octyl urea has one solid–solid phase transition at the temperature of 353.2 K. The solid–solid phase transition of octyl urea has a large entropy, that is comparable to its melting entropy. In this study, octyl urea was examined by solid-state NMR in order to investigate the sources of the large transition entropy. The NMR results indicate that conformational exchange and molecular motion in the octyl urea are the sources of the large entropy of the solid–solid transition.
Enantioselective Recognition of Tartaric Acid on Magnetoelectrodeposited Copper Film Electrodes
Authors: Mogi Iwao , Watanabe Kazuo 
Published: October 2012

Abstract
Cu films were electrodeposited under a magnetic field of 5 T, and cyclic voltammograms (CVs) of the enantiomers of tartaric acid were investigated on the Cu film electrodes. The chiral behavior of the CVs was observed as the peak current difference between the enantiomers. The dependence of the chiral behavior on the potential sweep rate indicates that the enantioselective recognition is performed as the difference in the electron-transfer rate of the enantiomers at the chiral sites on the film surfaces.
Evaluation of a Pharmacist-Managed Anticoagulation Clinic
Authors: Graham Maqual R. , Fish Kristin , Schaefer R. Spencer , Galyean Rick , Hardinger Karen L. 
Published: October 2012

Background Anticoagulation therapy is important in the prevention and treatment of cardioembolic events. Warfarin is frequently used but requires continual monitoring to ensure safety and efficacy. The target time in therapeutic range (TTR) is not always achieved. Objectives The objectives for this study were to determine the TTR for a pharmacist-managed anticoagulation clinic and identify reasons for sub- and supratherapeutic international normalized ratio (INR) values. Methods Medical records for subjects prescribed warfarin were reviewed. Demographic and relevant clinical information was assessed. INR measurements were extracted for subjects enrolled. The TTR was calculated, and the cause for sub- or supratherapeutic values was determined when possible. Results One hundred twenty-six subjects were included in this retrospective study. The calculated TTR was 51%. The cause for more than 65% of the sub- and supratherapeutic INR values could not be determined. One subject incurred a clot and 6 subjects suffered a bleed. No deaths occurred. Age was the only factor that correlated with a supratherapeutic INR value ( r = −0.179, P = .045). Conclusion Pharmacists in the anticoagulation clinic are effectively managing patients who are taking warfarin by frequently maintaining INR values near or within the recommended therapeutic range. Very few negative outcomes occurred during the time of study.
The Central American Epidemic of CKD
Authors: Weiner Daniel E. , McClean Michael D. , Kaufman James S. , Brooks Daniel R. 
Published: October 2012

Summary
Recent reports have described an apparent epidemic of CKD along the Pacific coast of Central America, such that CKD is a leading cause of death among working-age men in lower-altitude agricultural communities in this region. Given the limited availability of kidney replacement therapies in this region, CKD often is a terminal diagnosis, lending greater urgency to the identification of a modifiable cause. This article discusses the epidemiology of CKD in this region, reviews the clinical features of this CKD outbreak, discusses potential causes and the evidence supporting these hypotheses, and highlights the wider implications of this epidemic of CKD.
Navigated transcranial magnetic stimulation for preoperative language mapping in a patient with a left frontoopercular glioblastoma
Authors: Sollmann Nico , Picht Thomas , Mäkelä Jyrki P. , Meyer Bernhard , Ringel Florian , Krieg Sandro M. 
Published: October 2012

Up to now, navigated transcranial magnetic stimulation (nTMS) has been used for motor mapping in the vicinity of rolandic brain lesions. Recently, nTMS has also been suggested to be useful in mapping human language areas.
The authors describe the case of a left-handed patient with a left-side glioblastoma within the opercular inferior frontal gyrus who presented with severe motor aphasia. Preoperative functional MRI (fMRI) indicated speech dominance of the right hemisphere and did not show any language-related activation in the vicinity of the tumor. Navigated TMS, however, showed a significantly higher rate of induced speech arrests for the left than for the right. Left-side direct cortical stimulation induced clear speech arrests during awake surgery.
This case suggests that nTMS may be useful for preoperative speech mapping in tumors affecting the anatomy, vasculature, and brain oxygen levels and therefore impairing fMRI reliability.
Relationship between hospital surgical volume, lobectomy rates, and adverse perioperative events at US epilepsy centers
Authors: Englot Dario J. , Ouyang David , Wang Doris D. , Rolston John D. , Garcia Paul A. , Chang Edward F. 
Published: October 2012

Object
Epilepsy surgery remains significantly underutilized. The authors recently reported that the number of lobectomies for localized intractable epilepsy in the US has not changed despite the implementation of clear evidence-based guidelines 10 years ago supporting early referral for surgery. To better understand why epilepsy surgery continues to be underused, the authors' objective was to carefully examine hospital-related factors related to the following: 1) where patients are being admitted for the evaluation of epilepsy, 2) rates of utilization for surgery across hospitals, and 3) perioperative morbidity between hospitals with low versus high volumes of epilepsy surgery.

Methods
The authors performed a population-based cohort study of US hospitals between 1990 and 2008 using the Nationwide Inpatient Sample (NIS), stratifying epilepsy surgery rates and trends as well as perioperative morbidity rates by hospital surgical volume.

Results
The number of lobectomies for epilepsy performed at high-volume centers (> 15 lobectomies/year) significantly decreased between 1990 and 2008 (F = 20.4, p < 0.001), while significantly more procedures were performed at middle-volume hospitals (5–15 lobectomies/year) over time (F = 16.1, p < 0.001). No time trend was observed for hospitals performing fewer than 5 procedures per year. However, patients admitted to high-volume centers were significantly more likely to receive lobectomy than those at low-volume hospitals (relative risk 1.05, 95% CI 1.03–1.08, p < 0.001). Also, the incidence of perioperative adverse events was significantly higher at low-volume hospitals (12.9%) than at high-volume centers (6.1%) (relative risk 1.08, 95% CI 1.03–1.07, p < 0.001).

Conclusions
Hospital volume is an important predictor of epilepsy surgery utilization and perioperative morbidity. Patients with medically refractory epilepsy should be referred to a comprehensive epilepsy treatment center for surgical evaluation by an experienced clinical team.
Improvement of sagittal balance and lumbar lordosis following less invasive adult spinal deformity surgery with expandable cages and percutaneous instrumentation
Authors: Wang Michael Y. 
Published: October 2012

Object
The treatment of adult spinal deformity (ASD) remains a challenge for the spine surgeon. While minimally invasive surgery (MIS) has many favorable attributes that would be of great benefit for the ASD population, improvements in lordosis and sagittal balance have remained elusive in cases involving the MIS approach. This report describes the evolution of an MIS method for treating ASD with attention to sagittal correction.

Methods
Over an 18-month period 25 patients with thoracolumbar scoliosis were treated surgically. The mean patient age was 72 years, and 68% of the population was female. Patients were treated with multilevel facet osteotomies and interbody fusion in which expandable cages (mean 3.2 levels) were placed and percutaneous screw fixation (mean 5.3 levels) was performed. Seven patients underwent supplemental percutaneous iliac fixation.

Results
All patients underwent MIS without conversion to a traditional open procedure. The mean operative time was 273 mins and the mean blood loss was 416 ml. There were no intraoperative complications. The Cobb angle over the scoliotic deformity improved from a mean of 29.2° to that of 9.0° (p < 0.001). Lumbar lordosis between L-1 and S-1 improved from a mean of 27.8° to one of 42.6° (p < 0.001). Sagittal vertical axis improved from 7.4 cm to 4.3 cm (p = 0.001). Numeric pain scale scores improved as well, an average of 3.3 and 4.2 for the leg and back, respectively. A mean improvement of 20.8 points on the Oswestry Disability Index was seen at 12 months. Complications included: two cases requiring hardware repositioning, one case of screw pullout, one asymptomatic pedicle screw breach, prolonged hospitalization from constipation, and one acute coronary syndrome developing 3 days after surgery without myocardial damage.

Conclusions
An expanding body of evidence suggests that sagittal balance remains a keystone for good outcomes after ASD surgery. Minimally invasive surgery that involves a combination of osteotomies, interbody height restoration, and advanced fixation techniques may achieve this goal in patients with less severe deformities. While feasibility will have to be proven with larger series and improved surgical methods, the present technique holds promise as a means of reducing the significant morbidity associated with surgery in the ASD population.