bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ribosomal RNA gene fragments from fossilized cyanobacteria identified in primary gypsum from the late Miocene, Italy
Authors: PANIERI G. , LUGLI S. , MANZI V. , ROVERI M. , SCHREIBER B. C. , PALINSKA K. A. 
Published: January 2010

AbstractEarth scientists have searched for signs of microscopic life in ancient samples of permafrost, ice, deep‐sea sediments, amber, salt and chert. Until now, evidence of cyanobacteria has not been reported in any studies of ancient DNA older than a few thousand years. Here, we investigate morphologically, biochemically and genetically primary evaporites depositedin situduring the late Miocene (Messinian) Salinity Crisis from the north‐eastern Apennines of Italy. The evaporites contain fossilized bacterial structures having identical morphological forms as modern microbes. We successfully extracted and amplified genetic material belonging to ancient cyanobacteria from gypsum crystals dating back to 5.910–5.816 Ma, when the Mediterranean became a giant hypersaline brine pool. This finding represents the oldest ancient cyanobacterial DNA to date. Our clone library and its phylogenetic comparison with present cyanobacterial populations point to a marine origin for the depositional basin. This investigation opens the possibility of including fossil cyanobacterial DNA into the palaeo‐reconstruction of various environments and could also be used to quantify the ecological importance of cyanobacteria through geological time. These genetic markers serve as biosignatures providing important clues about ancient life and begin a new discussion concerning the debate on the origin of late Miocene evaporites in the Mediterranean.
Comparison of Health Outcomes for Male Seniors in the Veterans Health Administration and Medicare Advantage Plans
Authors: Selim Alfredo J. , Berlowitz Dan , Kazis Lewis E. , Rogers William , Wright Steven M. , Qian Shirley X. , Rothendler James A. , Spiro III Avron , Miller Donald , Selim Bernardo J. , Fincke Benjamin G. 
Published: December 2009

Objectives. To compare the Veterans Health Administration (VHA) with the Medicare Advantage (MA) plans with regard to health outcomes.Data Sources. The Medicare Health Outcome Survey, the 1999 Large Health Survey of Veteran Enrollees, and the Ambulatory Care Survey of Healthcare Experiences of Patients (Fiscal Years 2002 and 2003).Study Design. A retrospective study.Extraction Methods. Men 65+ receiving care in MA (N=198,421) or in VHA (N=360,316). We compared the risk‐adjusted probability of being alive with the same or better physical (PCS) and mental (MCS) health at 2‐years follow‐up. We computed hazard ratio (HR) for 2‐year mortality.Principal Findings. Veterans had a higher adjusted probability of being alive with the same or better PCS compared with MA participants (VHA 69.2 versus MA 63.6 percent, p<.001). VHA patients had a higher adjusted probability than MA patients of being alive with the same or better MCS (76.1 versus 69.6 percent, p<.001). The HRs for mortality in the MA were higher than in the VHA (HR, 1.26 [95 percent CI 1.23–1.29]).Conclusions. Our findings indicate that the VHA has better patient outcomes than the private managed care plans in Medicare. The VHA's performance offers encouragement that the public sector can both finance and provide exemplary health care.
Use and practice of patient diaries in Swedish intensive care units: a national survey
Authors: Åkerman Eva , Granberg‐Axéll Anetth , Ersson Anders , Fridlund Bengt , Bergbom Ingegerd 
Published: January 2010

Aims and objectives: To describe and compare the extent and application of patients' diaries in Sweden. Background: Since 1991, patient diaries have been used in intensive care unit (ICU) follow‐up in Sweden. There is paucity of relevant data evaluating the effect of this tool and also on what premises patients are enrolled. Likewise, data are sparse on the diaries' design, content structure and the use of photographs. Design: Descriptive explorative design by a semi‐structured telephone interview. Methods: The interview results were analysed with descriptive statistics and differences between the ICU levels were explored by χ2 analysis. Qualitative manifest content analysis was performed to explore the purpose of diary writing. Results: Of all ICUs (n = 85), 99% responded and 75% used diaries. The source of inspiration was collegial rather than from scientific data. The main reason for keeping a diary was to help the patient to recapitulate the ICU stay. Discrepancies between the different levels of ICUs were detected in patient selection, dedicated staff for follow‐up and the use of photographs. Comparison between the χ2 analysis and the content analysis outcome displayed incongruence between the set unit‐goals and the activities for achievement but did not explain the procedural differences detected. Conclusion: The uses of diaries in post ICU follow up were found to be common in Sweden. A majority used defined goals and content structure. However, there were differences in practice and patient recruitment among the levels of ICUs. These discrepancies seemed not to be based on evidence‐based data nor on ongoing research or evaluation but merely on professional judgement. As ICU follow‐up is resource intense and time consuming, it is paramount that solid criteria for patient selection and guidelines for the structure and use of diaries in post‐ICU follow‐up are defined.
Sensitivity of Bedside Ultrasound and Supine Anteroposterior Chest Radiographs for the Identification of Pneumothorax After Blunt Trauma
Authors: Gentry Wilkerson R. , Stone Michael B. 
Published: January 2010

AbstractObjectives:  Supine anteroposterior (AP) chest radiographs in patients with blunt trauma have poor sensitivity for the identification of pneumothorax. Ultrasound (US) has been proposed as an alternative screening test for pneumothorax in this population. The authors conducted an evidence‐based review of the medical literature to compare sensitivity of bedside US and AP chest radiographs in identifying pneumothorax after blunt trauma.Methods:  MEDLINE and EMBASE databases were searched for trials from 1965 through June 2009 using a search strategy derived from the following PICO formulation of our clinical question: patients included adult (18 +  years) emergency department (ED) patients in whom pneumothorax was suspected after blunt trauma. The intervention was thoracic ultrasonography for the detection of pneumothorax. The comparator was the supine AP chest radiograph during the initial evaluation of the patient. The outcome was the diagnostic performance of US in identifying the presence of pneumothorax in the study population. The criterion standard for the presence or absence of pneumothorax was computed tomography (CT) of the chest or a rush of air during thoracostomy tube placement (in unstable patients). Prospective, observational trials of emergency physician (EP)‐performed thoracic US were included. Trials in which the exams were performed by radiologists or surgeons, or trials that investigated patients suffering penetrating trauma or with spontaneous or iatrogenic pneumothoraces, were excluded. The methodologic quality of the studies was assessed. Qualitative methods were used to summarize the study results. Data analysis consisted of test performance (sensitivity and specificity, with 95% confidence intervals [CIs]) of thoracic US and supine AP chest radiography.Results:  Four prospective observational studies were identified, with a total of 606 subjects who met the inclusion and exclusion criteria. The sensitivity and specificity of US for the detection of pneumothorax ranged from 86% to 98% and 97% to 100%, respectively. The sensitivity of supine AP chest radiographs for the detection of pneumothorax ranged from 28% to 75%. The specificity of supine AP chest radiographs was 100% in all included studies.Conclusions:  This evidence‐based review suggests that bedside thoracic US is a more sensitive screening test than supine AP chest radiography for the detection of pneumothorax in adult patients with blunt chest trauma.ACADEMIC EMERGENCY MEDICINE 2010; 17:11–17 © 2010 by the Society for Academic Emergency Medicine
High efficacy and minimal peptide required for the anti‐angiogenic and anti‐hepatocarcinoma activities of plasminogen K5
Authors: Yang Xia , Cai Weibin , Xu Zumin , Chen Jing , Li Chaoyang , Liu Shaojun , Yang Zhonghan , Pan Qiuhui , Li Mingtao , Ma Jianxing , Gao Guoquan 
Published: December 2009

AbstractKringle 5(K5) is the fifth kringle domain of human plasminogen and its anti‐angiogenic activity is more potent than angiostatin that includes the first four kringle fragment of plasminogen. Our recent study demonstrated that K5 suppressed hepatocarcinoma growth by anti‐angiogenesis. To find high efficacy and minimal peptide sequence required for the anti‐angiogenic and anti‐tumour activities of K5, two deletion mutants of K5 were generated. The amino acid residues outside kringle domain of intact K5 (Pro452‐Ala542) were deleted to form K5mut1(Cys462‐Cys541). The residue Cys462 was deleted again to form K5mut2(Met463‐Cys541). K5mut1 specifically inhibited proliferation, migration and induced apoptosis of endothelial cells, with an apparent two‐fold enhanced activity than K5. Intraperitoneal injection of K5mut1 resulted in more potent tumour growth inhibition and microvessel density reduction than K5 both in HepA‐grafted and Bel7402‐xenografted hepatocarcinoma mouse models. These results suggested that K5mut1 has more potent anti‐angiogenic activity than intact K5. K5mut2, which lacks only the amino terminal cysteine of K5mut1, completely lost the activity, suggesting that the kringle domain is essential for the activity of K5. The activity was enhanced to K5mut1 level when five acidic amino acids of K5 in NH2 terminal outside kringle domain were replaced by five serine residues (K5mut3). The shielding effect of acidic amino acids may explain why K5mut1 has higher activity. K5, K5mut1 and K5mut3 held characteristic β‐sheet spectrum while K5mut2 adopted random coil structure. These results suggest that K5mut1 with high efficacy is the minimal active peptide sequence of K5 and may have therapeutic potential in liver cancer.
ORIGINAL ARTICLE: No Association Between the GSTP1 Exon 5 Polymorphism and Susceptibility to Advanced Stage Endometriosis in the Korean Population
Authors: Jeon Myung Jae , Choi Young Min , Hong Min A , Lee Gyoung Hoon , Ku Seung Yup , Kim Seok Hyun , Kim Jung Gu , Moon Shin Yong 
Published: December 2009

CitationJeon MJ, Choi YM, Hong MA, Lee GH, Ku SY, Kim SH, Kim JG, Moon SY. No Association between the GSTP1 exon 5 polymorphism and susceptibility to advanced stage endometriosis in the Korean population. Am J Reprod Immunol 2010; 63: 222–226Problem  To investigate whether the glutathione‐S‐transferase P1 (GSTP1) exon 5 polymorphism is associated with susceptibility to advanced stage endometriosis in Korean women.Method of study  Case–control study in a collective of 260 patients and 164 controls. Genotyping of the GSTP1 exon 5 polymorphism was performed by using real‐time TaqMan PCR assay.Results  The genotype distribution of the GSTP1 exon 5 polymorphism in the endometriosis group was not significantly different from that of the control group (AA/AG/GG rates were 64.2%/32.7%/3.1% and 65.2%/31.7%/3.0% for the endometriosis and control groups, respectively, P = 0.977). Further subgroup analysis according to either stage or bilaterality of ovarian endometrioma also found no significant difference in the genotype distribution between any of the endometriosis subgroups and the control group.Conclusion  These findings suggest that the GSTP1 exon 5 polymorphism is not a major determinant of the development of advanced stage endometriosis in the Korean population.
ORIGINAL ARTICLE: Transforming Growth Factor‐Beta1 Gene Polymorphisms in Korean Patients with Pre‐eclampsia
Authors: Kim Shin Young , Lim Ji Hyae , Park So Yeon , Yang Jae Hyug , Kim Moon Young , Kim Min Hyoung , Ryu Hyun Mee 
Published: January 2010

Citation Kim SY, Lim JH, Park SY, Yang JH, Kim MY, Kim MH, Ryu HM. Transforming growth factor‐beta1 (TGF‐β1) gene polymorphisms in Korean patients with pre‐eclampsia. Am J Reprod Immunol 2010; 63: 291–298Problem  The aim of this study was to investigate whether c.869T>C (Leu10Pro) and c.915G>C (Arg25Pro) polymorphisms in exon1 of the transforming growth factor‐beta1 (TGF‐β1) gene are associated with development of pre‐eclampsia (PE) in Korean women.Method of study  We analyzed blood samples from 164 patients with PE and 182 healthy pregnant women using the polymerase chain reaction and DNA sequencing.Results  The frequencies of the 869CC and combined TC/CC genotypes were higher in patients with PE than in healthy controls. In the PE with intrauterine growth restriction (IUGR), the frequencies of these genotypes were also higher than that in controls. Furthermore, the 869C allele frequency was significantly higher in both PE and IUGR‐complicated PE than in controls. Multivariate analysis showed that the 869TC, CC, and combined TC/CC genotypes were associated with an increased risk of PE compared with the 869TT genotype. In addition, the 869TC, CC, and combined TC/CC genotypes were significantly associated with an increased risk of IUGR‐complicated PE compared with the 869TT genotype. The TGF‐β1 c.915G>C polymorphism was not detected in our population.Conclusion  Our findings indicate that the TGF‐β1 c.869T>C polymorphism may be a genetic risk factor for PE and IUGR‐complicated PE.
Cross‐species divergence of the major recognition pathways of ubiquitylated substrates for ubiquitin/26S proteasome‐mediated proteolysis
Authors: Fatimababy Antony S. , Lin Ya‐Ling , Usharani Raju , Radjacommare Ramalingam , Wang Hsing‐Ting , Tsai Hwang‐Long , Lee Yenfen , Fu Hongyong 
Published: January 2010

The recognition of ubiquitylated substrates is an essential element of ubiquitin/26S proteasome‐mediated proteolysis (UPP), which is mediated directly by the proteasome subunit RPN10 and/or RPN13, or indirectly by ubiquitin receptors containing ubiquitin‐like and ubiquitin‐associated domains. By pull‐down and mutagenesis assays, we detected cross‐species divergence of the major recognition pathways. RPN10 plays a major role in direct recognition in Arabidopsis and yeast based on the strong affinity for the long and K48‐linked ubiquitin chains. In contrast, both the RPN10 and RPN13 homologs play major roles in humans. For indirect recognition, the RAD23 and DSK2 homologs (except for the human DSK2 homolog) are major receptors. The human RAD23 homolog is targeted to the 26S proteasome by the RPN10 and RPN13 homologs. In comparison, Arabidopsis uses UIM1 and UIM3 of RPN10 to bind DSK2 and RAD23, respectively. Yeast uses UIM in RPN10 and LRR in RPN1. Overall, multiple proteasome subunits are responsible for the direct and/or indirect recognition of ubiquitylated substrates in yeast and humans. In contrast, a single proteasome subunit, RPN10, is critical for both the direct and indirect recognition pathways in Arabidopsis. In agreement with these results, the accumulation of ubiquitylated substrates and severe pleiotropic phenotypes of vegetative and reproductive growth are associated with the loss of RPN10 function in an Arabidopsis T‐DNA insertion mutant. This implies that the targeting and proteolysis of the critical regulators involved are affected. These results support a cross‐species mechanistic and functional divergence of the major recognition pathways for ubiquitylated substrates of UPP.Structured digital abstract
A list of the large number of protein‐protein interactions described in this article is available via the MINT article ID MINT‐7307429
Mechanical heating of protostellar discs
Authors: Lubow S. H. , Pringle J. E. 
Published: December 2009

Abstract
The magnetic field structure of a protostar truncates the accretion disc at some magnetospheric radius greater than the stellar radius. If the stellar rotation axis is not aligned with the disc rotation then the magnetic stresses at this radius transfer misaligned angular momentum and so lead to a tilt in the inner disc. If the configuration and/or strength of the stellar field changes with time then the degree of induced tilt also changes. Under appropriate circumstances such m= 1 tilting motions of the disc can propagate outward through the disc as warp waves. These waves must damp as they approach the corotation radius where their frequency matches the local Keplerian frequency. If the waves propagate sufficiently far, then the disc heating that results from the wave damping can provide a dominant contribution to a local disc heating, and so cause a disc flaring. This flaring can in turn cause changes in the disc spectral energy distribution.
A PCR‐RFLP assay for gender assignment in the three‐toed sloths (Bradypus, Pilosa, Bradypodidae)
Authors: MARTINELLI ARTURO B. , DE MORAES‐BARROS NADIA , ALVARENGA CLARA S. , CHAVES PAULO B. , SANTOS LUIZ A. D. , FAGUNDES VALÉRIA 
Published: December 2009

AbstractThe three‐toed sloths (Bradypus) are slow‐moving arboreal neotropical mammals. Understanding demographic variables (such as sex ratio) of populations is a key for conservation purposes. Nevertheless, gender assignment of Bradypus is particularly challenging because of the lack of sexual dimorphism in infants and in adults, particularly B. torquatus, the most endangered of the three‐toed sloths, in which sex is attributed by visual observation of the reproductively active males. Here, we standardized a method for sexing Bradypus individuals using PCR‐RFLP of sex‐linked genes ZFX/ZFY. This assay was validated with known‐gender animals and proved accurate to assign gender on three Bradypus species.
Rapid and reliable high‐throughput methods of DNA extraction for use in barcoding and molecular systematics of mushrooms
Authors: DENTINGER BRYN T. M. , MARGARITESCU SIMONA , MONCALVO JEAN‐MARC 
Published: December 2009

AbstractWe present two methods for DNA extraction from fresh and dried mushrooms that are adaptable to high‐throughput sequencing initiatives, such as DNA barcoding. Our results show that these protocols yield ∼85% sequencing success from recently collected materials. Tests with both recent (<2 year) and older (>100 years) specimens reveal that older collections have low success rates and may be an inefficient resource for populating a barcode database. However, our method of extracting DNA from herbarium samples using small amount of tissue is reliable and could be used for important historical specimens. The application of these protocols greatly reduces time, and therefore cost, of generating DNA sequences from mushrooms and other fungi vs. traditional extraction methods. The efficiency of these methods illustrates that standardization and streamlining of sample processing should be shifted from the laboratory to the field.
Hematologic and biochemical reference intervals for Norwegian crossbreed grower pigs
Authors: Klem Thea Blystad , Bleken Elisabeth , Morberg Hanne , Thoresen Stein Istre , Framstad Tore 
Published: December 2009

Background: Hematologic and biochemical reference intervals depend on many factors, including environment and age. Reference intervals for Norwegian grower pigs are lacking, and previously published reference intervals for similar pigs from other countries are now outdated due to significant changes in management and breeding on the pig farms.Objectives: The aim of this study was to determine updated reference intervals for hematologic and biochemical analytes in healthy crossbred grower pigs, and to compare the results among 3 different farms.Methods: Blood samples were collected from 104 clinically healthy pigs of the most common Norwegian crossbreed (Landrace Yorkshire sow × Landrace Duroc boar). The pigs were 12–16 weeks old, weighed 30–50 kg, of both sexes, and lived on 3 farms in eastern Norway. Automated hematologic and biochemical analysis were performed using ADVIA 2120 and ADVIA 1650 analyzers.Results: Five samples were excluded because of hemolysis (1) or outliers (4). Reference intervals were calculated using parametric or nonparametric methods, depending on data distribution. Mean, median, minimum, and maximum values were tabulated.Conclusions: The reference intervals calculated in this study will be useful for the diagnosis and monitoring of disease in this widespread crossbreed pig. Compared with previously published reference values, reference intervals for total WBC count, creatine kinase and alanine aminotransferase activities, and albumin, bilirubin, and urea concentrations in this study differed notably.
Automated counting of nucleated cells in equine synovial fluid without and with hyaluronidase pretreatment
Authors: Ekmann Anita , Rigdal Marie‐Louise , Gröndahl Gittan 
Published: December 2009

Background: Microscopy is usually used to obtain manual total and differential cell counts in equine synovial fluid. A faster, more precise method is desirable.Objectives: The objectives were to compare an automated impedance method with a manual method for obtaining total and differential cell counts in equine synovial fluid and to evaluate the effect of pretreatment with hyaluronidase on automated results.Methods: Synovial fluid samples (n=48) were collected into EDTA and analyzed within 48 hours. Automated total and differential cell counts were evaluated using a Medonic CA620‐VET hematology analyzer before and after pretreatment for 5–30 minutes with hyaluronidase (final concentration 0.01 mg/mL). A hemacytometer count and microscopic evaluation of a direct smear were used as the reference method. Intra‐assay coefficients of variation (CV) were determined.Results: Thirty‐one of 46 untreated samples and 0/46 hyaluronidase‐treated samples were error‐flagged by the analyzer. Correlation between automated (ANCC) and manual (MNCC) nucleated cell counts in untreated samples (n=15; R2=0.93) and pretreated samples (n=46; R2=0.94) was high, and pseudomedian difference was low. Intra‐assay CVs for samples with medium and high cellularity were significantly lower for ANCC (1.5–2.7%) compared with MNCC (6.1–15.7%) (P<.01). Valid automated differential cell counts were not obtained.Conclusions: Automated total cell counts obtained on the Medonic analyzer correlate well with manual counts in equine synovial fluid; however, pretreatment with hyaluronidase is required to minimize error flags. Automated differential counts are not accurate for synovial fluid.
ON A BASIS FOR THE FRAMED LINK VECTOR SPACE SPANNED BY CHORD DIAGRAMS
Authors: BISCHOF BRYAN , KOGAN ROMAN , YETTER DAVID N. 
Published: December 2009

In view of the result of Kontsevich, now often called "the fundamental theorem of Vassiliev theory", identifying the graded dual of the associated graded vector space to the space of Vassiliev invariants filtered by degree with the linear span of chord diagrams modulo the "4T-relation" (and in the unframed case, originally considered by Vassiliev, the "1T-" or "isolated chord relation"), it is a problem of some interest to provide a basis for the space of chord diagrams modulo the 4T-relation. We construct the basis for the vector space spanned by chord diagrams with n chords and m link components, modulo 4T relations for n ≤ 5.