bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and phylogenetic characterization of the sieve element occlusion gene family in Fabaceae and non-Fabaceaeplants
Authors: Rüping Boris , Ernst Antonia M , Jekat Stephan B , Nordzieke Steffen , Reineke Anna R , Müller Boje , Bornberg-Bauer Erich , Prüfer Dirk , Noll Gundula A 
Published: October 2010

Abstract

Background
The phloem of dicotyledonous plants contains specialized P-proteins (phloem proteins) that accumulate during sieve element differentiation and remain parietally associated with the cisternae of the endoplasmic reticulum in mature sieve elements. Wounding causes P-protein filaments to accumulate at the sieve plates and block the translocation of photosynthate. Specialized, spindle-shaped P-proteins known as forisomes that undergo reversible calcium-dependent conformational changes have evolved exclusively in the Fabaceae. Recently, the molecular characterization of three genes encoding forisome components in the model legume Medicago truncatula (MtSEO1, MtSEO2 and MtSEO3; SEO = sieve element occlusion) was reported, but little is known about the molecular characteristics of P-proteins in non-Fabaceae.

Results
We performed a comprehensive genome-wide comparative analysis by screening the M. truncatula, Glycine max, Arabidopsis thaliana, Vitis vinifera and Solanum phureja genomes, and a Malus domestica EST library for homologs of MtSEO1, MtSEO2 and MtSEO3 and identified numerous novel SEO genes in Fabaceae and even non-Fabaceae plants, which do not possess forisomes. Even in Fabaceae some SEO genes appear to not encode forisome components. All SEO genes have a similar exon-intron structure and are expressed predominantly in the phloem. Phylogenetic analysis revealed the presence of several subgroups with Fabaceae-specific subgroups containing all of the known as well as newly identified forisome component proteins. We constructed Hidden Markov Models that identified three conserved protein domains, which characterize SEO proteins when present in combination. In addition, one common and three subgroup specific protein motifs were found in the amino acid sequences of SEO proteins. SEO genes are organized in genomic clusters and the conserved synteny allowed us to identify several M. truncatula vs G. max orthologs as well as paralogs within the G. max genome.

Conclusions
The unexpected occurrence of forisome-like genes in non-Fabaceae plants may indicate that these proteins encode species-specific P-proteins, which is backed up by the phloem-specific expression profiles. The conservation of gene structure, the presence of specific motifs and domains and the genomic synteny argue for a common phylogenetic origin of forisomes and other P-proteins.
The course of untreated anxiety and depression, and determinants of poor one-year outcome: a one-year cohort study
Authors: van Beljouw Ilse MJ , Verhaak Peter FM , Cuijpers Pim , van Marwijk Harm WJ , Penninx Brenda WJH 
Published: October 2010

Abstract

Background
Little is known about the course and outcome of untreated anxiety and depression in patients with and without a self-perceived need for care. The aim of the present study was to examine the one-year course of untreated anxiety and depression, and to determine predictors of a poor outcome.

Method
Baseline and one-year follow-up data were used of 594 primary care patients with current anxiety or depressive disorders at baseline (established by the Composite Interview Diagnostic Instrument (CIDI)), from the Netherlands Study of Depression and Anxiety (NESDA). Receipt of and need for care were assessed by the Perceived Need for Care Questionnaire (PNCQ).

Results
In depression, treated and untreated patients with a perceived treatment need showed more rapid symptom decline but greater symptom severity at follow-up than untreated patients without a self-perceived mental problem or treatment need. A lower education level, lower income, unemployment, loneliness, less social support, perceived need for care, number of somatic disorders, a comorbid anxiety and depressive disorder and symptom severity at baseline predicted a poorer outcome in both anxiety and depression. When all variables were considered at the same time, only baseline symptom severity appeared to predict a poorer outcome in anxiety. In depression, a poorer outcome was also predicted by more loneliness and a comorbid anxiety and depressive disorder.

Conclusion
In clinical practice, special attention should be paid to exploring the need for care among possible risk groups (e.g. low social economic status, low social support), and support them in making an informed decision on whether or not to seek treatment.
Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors
Authors: Ribeiro Cristina , Togawa Roberto C , Neshich Izabella AP , Mazoni Ivan , Mancini Adauto L , Minardi Raquel C de Melo , da Silveira Carlos H , Jardine José G , Santoro Marcelo M , Neshich Goran 
Published: October 2010

Abstract

Background
Enzymes belonging to the same super family of proteins in general operate on variety of substrates and are inhibited by wide selection of inhibitors. In this work our main objective was to expand the scope of studies that consider only the catalytic and binding pocket amino acids while analyzing enzyme specificity and instead, include a wider category which we have named the Interface Forming Residues (IFR). We were motivated to identify those amino acids with decreased accessibility to solvent after docking of different types of inhibitors to sub classes of serine proteases and then create a table (matrix) of all amino acid positions at the interface as well as their respective occupancies. Our goal is to establish a platform for analysis of the relationship between IFR characteristics and binding properties/specificity for bi-molecular complexes.

Results
We propose a novel method for describing binding properties and delineating serine proteases specificity by compiling an exhaustive table of interface forming residues (IFR) for serine proteases and their inhibitors. Currently, the Protein Data Bank (PDB) does not contain all the data that our analysis would require. Therefore, an in silico approach was designed for building corresponding complexes
The IFRs are obtained by "rigid body docking" among 70 structurally aligned, sequence wise non-redundant, serine protease structures with 3 inhibitors: bovine pancreatic trypsin inhibitor (BPTI), ecotine and ovomucoid third domain inhibitor. The table (matrix) of all amino acid positions at the interface and their respective occupancy is created. We also developed a new computational protocol for predicting IFRs for those complexes which were not deciphered experimentally so far, achieving accuracy of at least 0.97.

Conclusions
The serine proteases interfaces prefer polar (including glycine) residues (with some exceptions). Charged residues were found to be uniquely prevalent at the interfaces between the "miscellaneous-virus" subfamily and the three inhibitors. This prompts speculation about how important this difference in IFR characteristics is for maintaining virulence of those organisms.
Our work here provides a unique tool for both structure/function relationship analysis as well as a compilation of indicators detailing how the specificity of various serine proteases may have been achieved and/or could be altered. It also indicates that the interface forming residues which also determine specificity of serine protease subfamily can not be presented in a canonical way but rather as a matrix of alternative populations of amino acids occupying variety of IFR positions.
Imported malaria in an area in southern Madrid, 2005-2008
Authors: Rey Sonia , Zuza Inés , Martínez-Mondéjar Belén , Rubio José M , Merino Francisco J 
Published: October 2010

Abstract

Background
In Spain, malaria cases are mostly due to migrants and travellers returning from endemic areas. The objective of this work was to describe the malaria cases diagnosed at the Severo Ochoa University Hospital (HUSO) in Leganés in the south of the Madrid Region from 2005 to 2008.

Methods
Descriptive retrospective study performed at HUSO. Data sources are registries from the Microbiology Department and malaria cases notified to the Preventive Medicine Department. Analysed parameters were: administrative, demographical, related to the stay at the endemic country, clinical, microbiological diagnosis method, pregnancy, treatment and prophylaxis, co-infections, and days of hospital stay.

Results
Fifty-seven patients diagnosed with malaria were studied. Case distribution per year was 13 in 2005, 15 in 2006, 15 in 2007 and 14 in 2008. Thirty-three patients were female (57.9%) and 24 male (42.1%). Mean age was 27.8 years. Most of the malaria cases were acquired in Nigeria (49.1%) and Equatorial Guinea (32.7%). 29.1% of the patients were immigrants who had arrived recently, and 61.8% acquired malaria when travelling to their countries of origin to visit friends and relatives (VFR). Majority of cases were diagnosed between June and September. Microscopy was positive in 39 cases (68.4%) immunochromatography in 42 (73.7%) and PCR in the 55 cases where performed. Plasmodium falciparum was responsible for 94.7% of the cases. The more frequent symptoms were fever (77.2%), followed by headache and gastrointestinal symptoms (33.3%). Nine cases needed hospital admittance, a pregnant woman, three children, four VFR and an African tourist, but all evolved favourably. Chemoprophylaxis data was known from 55 patients. It was taken correctly in one case (1.8%), in five (9.1%) the prophylaxis was improper while the others 49 (89.1%) cases had not followed any anti-malarial prophylaxis.

Conclusions
Children, pregnant women and the VFR have the highest risk to present severe malaria and to need hospital admittance. Another important risk factor for acquiring malaria is incorrect prophylaxis. The first place for malaria acquisition was Nigeria and the main species causing malaria was P. falciparum.
Review for the generalist: The antinuclear antibody test in children - When to use it and what to do with a positive titer
Authors: Malleson Peter N , Mackinnon Murray J , Sailer-Hoeck Michaela , Spencer Charles H 
Published: October 2010

AbstractThe antinuclear antibody test (ANA) is a much overused test in pediatrics. The ANA does have a role in serologic testing but it should be a very limited one. It is often ordered as a screening test for rheumatic illnesses in a primary care setting. However, since it has low specificity and sensitivity for most rheumatic and musculoskeletal illnesses in children, it should not be ordered as a screening test for non-specific complaints such as musculoskeletal pain. It should only be used as a diagnostic test for children with probable Systemic Lupus Erythematosus (SLE) or Mixed Connective Tissue Disease, (MCTD) and other possible overlap-like illnesses. Such children should have developed definite signs and symptoms of a disease before the ANA is ordered. This review presents data supporting these conclusions and a review of the ANA literature in adults and children.By limiting ANA testing, primary care providers can avoid needless venipuncture pain, unnecessary referrals, extra medical expenses, and most importantly, significant parental anxieties. It is best not to do the ANA test in most children but if it ordered and is positive in a low titer (<1:640), the results can be ignored if the child is otherwise well and does not have other features of a systemic illness.
Genetic diversity and C2-like subgenogroup strains of enterovirus 71, Taiwan, 2008
Authors: Huang Yuan-Pin , Lin Tsuey-Li , Hsu Li-Ching , Chen Yu-Ju , Tseng Yin-Hsin , Hsu Chiu-Chu , Fan Wen-Bin , Yang Jyh-Yuan , Chang Feng-Yee , Wu Ho-Sheng 
Published: October 2010

Abstract

Background
Human enterovirus 71 (EV-71) is known of having caused numerous outbreaks of hand-foot-mouth disease, and other clinical manifestations globally. In 2008, 989 EV-71 strains were isolated in Taiwan.

Results
In this study, the genetic and antigenic properties of these strains were analyzed and the genetic diversity of EV-71 subgenogroups surfacing in Taiwan was depicted, which includes 3 previously reported subgenogroups of C5, B5, and C4, and one C2-like subgenogroup. Based on the phylogenetic analyses using their complete genome nucleotide sequences and neutralization tests, the C2-like subgenogroup forms a genetically distinct cluster from other subgenogroups, and the antisera show a maximum of 128-fold decrease of neutralization titer against this subgenogroup. In addition, the subgenogroup C4 isolates of 2008 were found quite similar genetically to the Chinese strains that caused outbreaks in recent years and thus they should be carefully watched.

Conclusions
Other than to be the first report describing the existence of C2-like subgenogroup of EV-71 in Taiwan, this article also foresees a potential of subgenogroup C4 outbreaks in Taiwan in the near future.
Lung abscess predicts the surgical outcome in patients with pleural empyema
Authors: Huang Hung-Che , Chen Heng-Chung , Fang Hsin-Yuan , Lin Yi-Chieh , Wu Chin-Yen , Cheng Ching-Yuan 
Published: October 2010

Abstract

Objectives
Most cases of pleural empyema are caused by pulmonary infections, which are usually combined with pneumonia or lung abscess. The mortality of patients with pleural empyema remains high (up to 20%). It also contributes to higher hospital costs and longer hospital stays. We studied pleural empyema with combined lung abscess to determine if abscess was associated with mortality.

Methods
From January 2004 to December 2006, we retrospectively reviewed 259 patients diagnosed with pleural empyema who received thoracscopic decortications of the pleura in a single medical center. We evaluated their clinical data and analyzed their chest computed tomography scans. Outcomes of pleural empyema were compared between groups with and without lung abscess.

Results
Twenty-two pleural empyema patients had lung abscesses. Clinical data showed significantly higher incidences in the lung abscess group of pre-operative leukocytosis, need for an intensive care unit stay and mortality.

Conclusion
Patients with pleural empyema and lung abscess have higher intensive care unit admission rate, higher mortality during 30 days and overall mortality than patients with pleural empyema. The odds ratio of lung abscess is 4.685. Physician shall pay more attention on high risk patient of lung abscess for early detection and management.
“Substitutable” Polymer Brushes: Reactive Poly(methacrylate) Brushes with Exchangeable Alkoxyamine Units in the Side Chain
Authors: Sato Tomoya , Amamoto Yoshifumi , Yamaguchi Hiroki , Otsuka Hideyuki , Takahara Atsushi 
Published: October 2010

Abstract
A reactive polymer brush containing alkoxyamine units in the side chains, when heated with an alkoxyamine-terminated fluorinated nongrafted polymer, gave a grafted copolymer brush by a radical crossover reaction of alkoxyamine units. The fluorinated grafted copolymer brush could be converted back to the parent polymer brush upon treatment with an excess of low-molecular alkoxyamine. The reversible change in the surface properties of the brush was confirmed by X-ray photoelectron spectroscopy and contact angle measurements.
Aggregation of l-Cysteinato Tricobaltate(III) Anions by Lanthanide(III) Cations into Dimensional Structures That are Controlled by Diastereoisomerism and Ionic Size
Authors: Yuan Hou Qun , Igashira-Kamiyama Asako , Konno Takumi 
Published: October 2010

Abstract
Treatment of the ΛLLLΛLLL and ΔLLLΔLLL isomers of K3[Co{Co(l-cys-N,S)3}2] (K3[1], l-cys: l-cysteinate) with Ln(NO3)3 (Ln = La and Yb) in water gave coordination polymers, ΛLLLΛLLL-Ln[1] and ΔLLLΔLLL-Ln[1], respectively, in which [1]3− binds to Ln3+ through carboxylate groups in a 1:1 ratio. It was found that the dimensional structures of Ln[1] are controlled not only by the diastereoisomerism of [1]3− (ΛLLLΛLLL vs. ΔLLLΔLLL) but also by the ionic size of Ln3+ (La3+ vs. Yb3+).
Novel Phenanthroline Derivatives for Electron Transport in Organic Light-emitting Diodes
Authors: Kathirgamanathan Poopathy , Surendrakumar Sivagnanasundram , Ravichandran Seenivasagam , Vanga Raghava Reddy , Antipan-Lara Juan , Ganeshamurugan Subramaniam , Kumaravel Muttulingham , Paramaswara Gnanamoly , Arkley Vincent 
Published: October 2010

Abstract
A series of novel arylvinyl-substituted phenanthroline derivatives have been synthesized and their applications as electron-transporting materials in organic light-emitting diodes (OLED’s) have been investigated. One particular derivative, namely, 2,9-bis(2-thiophen-2-ylvinyl)[1,10]phenanthroline shows significantly lower operating voltage than tris(8-quinolinolato)aluminum(III) (Alq3) and substantially higher lifetime than bathophenanthroline (BPhen).
Validation and Implementation of an Algorithm for Reporting the Automated Absolute Neutrophil Count From Selected Flagged Specimens
Authors: Sireci Anthony N. , Herlitz Leal , Lee Keagan , Bautista Jessica L. , Kratz Alexander 
Published: October 2010

Abstract
Samples that are flagged by automated cell counters and, therefore, require a time-consuming microscopic review cause unacceptable wait times for patients in hematology/oncology clinics. We used a set of 518 samples to validate that 5 flags on Sysmex XE/XT instruments (Sysmex, Kobe, Japan) could safely be ignored when the absolute neutrophil count (ANC) was the primary clinical question. The R2 between automated and manual ANCs was 96.9% for samples triggering non-ANC flags, with 1 clinically significant discrepant sample out of 296 (0.3%). A new test code allowing clinicians to specify “ANC-only” was implemented, and these non-ANC specific flags were disregarded. The new order set was used in 16.3% of patients. Automated reporting of the ANC in selected flagged samples reduced the review rate by 60% and decreased the turnaround time by 100 minutes. This approach to automatically report the ANC in selected flagged specimens in which the ANC is the primary clinical interest safely decreases the turnaround time for many ANC samples.
The Specificity of Immunophenotypic Alterations in Blasts in Nonacute Myeloid Disorders
Authors: Harrington Alexandra , Olteanu Horatiu , Kroft Steven 
Published: October 2010

Abstract
Data regarding flow cytometry (FC) in nonacute myeloid disorders is confounded by variable gating strategies and controls limited to normal bone marrow (BM) samples. Blasts in diagnostic BM samples of myelodysplastic syndromes (MDSs), myeloproliferative neoplasms (MPNs), and chronic myelomonocytic leukemias (CMMLs) were compared with 20 nonneoplastic cytopenias/cytoses (CCs) and negative staging BM samples using 4-color FC. Blasts in 10 of 20 CCs showed immunophenotypic differences vs control samples. Immunophenotypic alterations were identified in 18 of 21 MDSs, 11 of 14 MPNs, and 7 of 7 CMMLs vs control samples and 13 (62%) of 21 MDSs, 7 (50%) of 14 MPNs, and 3 (43%) of 7 CMMLs vs CCs. Neoplastic-specific blast immunophenotypic changes included expression of CD7, CD11b, CD15, CD36, and CD56; CD34 overexpression; HLA-DR variability; lack of CD13 and CD33; underexpression of CD13, CD33, CD45, and HLA-DR; and partial loss of CD13, CD33, CD38, and CD117. In all cases, blasts were CD34+. Several blast immunophenotypic alterations are shared in neoplastic and nonneoplastic BM samples. Approximately 40% to 60% of neoplastic BM samples exhibited aberrancies not seen in reactive BM samples.
Cerebrospinal Fluid Penetration of High-Dose Daptomycin in Suspected Staphylococcus aureus Meningitis
Authors: Riser M Shawn , Bland Christopher M , Rudisill Celeste N , Bookstaver P Brandon 
Published: October 2010

Objective: To report a case of methicillin-sensitive Staphylococcus aureus (MSSA) bacteremia with suspected MSSA meningitis treated with high-dose daptomycin assessed with concurrent serum and cerebrospinal fluid (CSF) concentrations. Case Summary: A 54-year-old male presented to the emergency department with generalized weakness and presumed health-care–associated pneumonia shown on chest radiograph. Treatment was empirically initiated with vancomycin, levofloxacin, and piperacillin/tazobactam. Blood cultures revealed S. aureus susceptible to oxacillin. Empiric antibiotic treatment was narrowed to nafcillin on day 4. On day 8, the patient developed acute renal failure (serum creatinine 1.9 mg/dL, increased from 1.2 mg/dL the previous day and 0.8 mg/dL on admission). The patient's Glasgow Coma Score was 3, with normal findings shown on computed tomography scan of the head 72 hours following an episode of cardiac arrest on day 10. The patient experienced relapsing MSSA bacteremia on day 9, increasing the suspicion for a central nervous system (CNS) infection. Nafcillin was discontinued and daptomycin 9 mg/kg daily was initiated for suspected meningitis and was continued until the patient's death on day 16. Daptomycin serum and CSF trough concentrations were 11.21 μg/mL and 0.52 μg/mL, respectively, prior to the third dose. Lumbar puncture results were inconclusive and no further blood cultures were positive for MSSA. Creatine kinase levels were normal prior to daptomycin therapy and were not reassessed. Discussion: Daptomycin was initiated in our patient secondary to possible nafcillin-induced acute interstitial nephritis and relapsing bacteremia. At a dose of 9 mg/kg, resultant penetration of 5% was higher than in previous reports, more consistent with inflamed meninges. Conclusions: High-dose daptomycin may be an alternative option for MSSA bacteremia with or without a CNS source in patients who have failed or cannot tolerate standard therapy. Further clinical evaluation in patients with confirmed meningitis is warranted.
Fatty acid composition of serum phospholipids in cystic fibrosis (CF) patients with or without CF related liver disease
Authors: Van Biervliet Stephanie , Van Biervliet Jean-Pierre , Robberecht Eddy , Christophe Armand 
Published: October 2010

Abstract

Background: In cystic fibrosis (CF), changes in fatty acid (FA) composition of serum phospholipids (PL) and cell membranes can account, in part, for the inflammatory state of the disease. The severity of the genotype is known to correlate with the degree of FA changes. Liver diseases, such as cholestasis and cirrhosis are also known to influence FA status. Until now, there is no data on the influence of CF related liver disease (CFRLD) on the FA status of CF patients. The aim of this study was to evaluate, whether the presence of CFRLD influences FA status.

Methods: A fasting blood sample for the determination of serum vitamin E and PL-FA composition was collected from 79 CF patients with stable pulmonary disease and under good control in our CF centre. Patients with CFRLD (n=13) were compared to CF patients with the same severity of genotype (n=66) but without CFRLD.

Results: The CF patients with CFRLD had lower docosahexaenoic acid (DHA, 22:6n-3) and increased docosatetraenoic acid (22:4n-6). There were no significant differences in the precursors of these FAs.

Conclusions: DHA concentration in patients with CFRLD is decreased more substantially compared with their genotype controls. The presence of CFRLD should be taken into account in future FA studies in CF patients.
Clin Chem Lab Med 2010;48:1751–5.