bluuebunny/crossref_metadata_2025_split huggingface dataset:
Agreement Assessment of Tigecycline Susceptibilities Determined by the Disk Diffusion and Broth Microdilution Methods among Commonly Encountered Resistant Bacterial Isolates: Results from the TigecyclineIn VitroSurveillance in Taiwan (TIST) Study, 2008 to 2010
Authors: Liu Jien-Wei , Ko Wen-Chien , Huang Cheng-Hua , Liao Chun-Hsing , Lu Chin-Te , Chuang Yin-Ching , Tsao Shih-Ming , Chen Yao-Shen , Liu Yung-Ching , Chen Wei-Yu , Jang Tsrang-Neng , Lin Hsiu-Chen , Chen Chih-Ming , Shi Zhi-Yuan , Pan Sung-Ching , Yang Jia-Ling , Kung Hsiang-Chi , Liu Chun-Eng , Cheng Yu-Jen , Chen Yen-Hsu , Lu Po-Liang , Sun Wu , Wang Lih-Shinn , Yu Kwok-Woon , Chiang Ping-Cherng , Lee Ming-Hsun , Lee Chun-Ming , Hsu Gwo-Jong , Hsueh Po-Ren 
Published: December 2011

ABSTRACTThe TigecyclineIn VitroSurveillance in Taiwan (TIST) study, initiated in 2006, is a nationwide surveillance program designed to longitudinally monitor thein vitroactivity of tigecycline against commonly encountered drug-resistant bacteria. This study compared thein vitroactivity of tigecycline against 3,014 isolates of clinically important drug-resistant bacteria using the standard broth microdilution and disk diffusion methods. Species studied included methicillin-resistantStaphylococcus aureus(MRSA;n= 759), vancomycin-resistantEnterococcus faecium(VRE;n= 191), extended-spectrum β-lactamase (ESBL)-producingEscherichia coli(n= 602), ESBL-producingKlebsiella pneumoniae(n= 736), andAcinetobacter baumannii(n= 726) that had been collected from patients treated between 2008 and 2010 at 20 hospitals in Taiwan. MICs and inhibition zone diameters were interpreted according to the currently recommended U.S. Food and Drug Administration (FDA) criteria and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. The MIC90values of tigecycline against MRSA, VRE, ESBL-producingE. coli, ESBL-producingK. pneumoniae, andA. baumanniiwere 0.5, 0.125, 0.5, 2, and 8 μg/ml, respectively. The total error rates between the two methods using the FDA criteria were high: 38.4% for ESBL-producingK. pneumoniaeand 33.8% forA. baumannii. Using the EUCAST criteria, the total error rate was also high (54.6%) forA. baumanniiisolates. The total error rates between these two methods were <5% for MRSA, VRE, and ESBL-producingE. coli. For routine susceptibility testing of ESBL-producingK. pneumoniaeandA. baumanniiagainst tigecycline, the broth microdilution method should be used because of the poor correlation of results between these two methods.
Oseltamivir Inhibits H7 Influenza Virus Replication in Mice Inoculated by the Ocular Route
Authors: Belser Jessica A. , Sleeman Katrina , Pearce Melissa B. , Katz Jacqueline M. , Gubareva Larisa V. , Tumpey Terrence M. 
Published: December 2011

ABSTRACT
The majority of human infections associated with H7 influenza viruses have resulted in ocular and not respiratory disease. While oseltamivir has been prescribed to individuals presenting with conjunctivitis following H7 virus exposure, it is unknown if oseltamivir inhibits virus replication in ocular tissue. We demonstrate that H7 viruses possess sensitivity to neuraminidase inhibitors and that administration of oseltamivir before ocular virus challenge in mice inhibits H7N7 and H7N3 virus replication in ocular and respiratory tissues.
Unidentified Chronic Fatigue Syndrome/myalgic encephalomyelitis (CFS/ME) is a major cause of school absence: surveillance outcomes from school-based clinics
Authors: Crawley Esther M , Emond Alan M , Sterne Jonathan A C 
Published: December 2011

ObjectiveTo investigate the feasibility of conducting clinics for chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) in schools.DesignSchool-based clinical project.ParticipantsChildren aged 11–16 years were enrolled in three state secondary schools in England.Main outcome measuresNumber of children newly diagnosed as having CFS/ME.MethodsAttendance officers identified children missing ≥20% of school in a 6-week term without a known cause, excluding those with a single episode off school, a known medical illness explaining the absence or known to be truanting. Children with fatigue were referred to a specialist CFS/ME service for further assessment. The authors compared children with CFS/ME identified through school-based clinics with those referred via health services. Outcomes of CFS/ME were evaluated at 6 weeks and 6 months.Results461 of the 2855 enrolled children had missed ≥20% school over a 6-week period. In 315, of whom three had CFS/ME, the reason for absence was known. 112 of the 146 children with unexplained absence attended clinical review at school; two had been previously diagnosed as having CFS/ME and 42 were referred on to a specialist clinic, where 23 were newly diagnosed as having CFS/ME. Therefore, 28 of the 2855 (1.0%) children had CFS/ME. Children with CFS/ME identified through surveillance had been ill for an amount of time comparable to those referred via health services but had less fatigue (mean difference 4.4, 95% CI 2.2 to 6.6), less disability (mean difference −5.7, 95% CI −7.9 to −3.5) and fewer symptoms (mean difference 1.86, 95% CI 0.8 to 2.93). Of 19 children followed up, six had fully recovered at 6 weeks and a further six at 6 months.ConclusionsChronic fatigue is an important cause of unexplained absence from school. Children diagnosed through school-based clinics are less severely affected than those referred to specialist services and appear to make rapid progress when they access treatment.
Transmission of HIV-1 drug resistance in Benin could jeopardise future treatment options
Authors: Chamberland Annie , Diabaté Souleymane , Sylla Mohamed , Anagounou Séverin , Geraldo Nassirou , Zannou Djimon Marcel , Labbé Annie-Claude , Worobey Michael , Alary Michel , Tremblay Cécile 
Published: December 2011

ObjectivesAs access to antiretrovirals (ARV) increases in developing countries, the identification of optimal therapeutic regimens and prevention strategies requires the identification of resistance pathways in non-B subtypes as well as the surveillance of drug mutation resistance (SDMR) including the trafficking of viral strains between high-risk groups such as commercial sex workers (CSW) and the general population (GP). In this study, the authors evaluated the rate of primary resistance mutations and the epidemiological link between isolates from GP and CSW from Bénin.MethodsPlasma samples were obtained from 129 HIV-1-infected treatment-naïve individuals. Drug resistance mutations were identified using SDMR list and compared with other resistance algorithms.ResultsNo nucleoside reverse transcriptase inhibitor resistance mutations were found. Four patients had non-nucleoside reverse transcriptase inhibitor resistance (K103N, G190A). One patient exhibited protease inhibitors resistance mutation, F53Y. Using the SDMR list, the authors obtained a rate of 3.9% of primary resistance. Nevertheless, the authors observed several mutations not on SDMR list but included in others resistance database, taking those mutations into account, the authors obtained a rate of 15.5%.ConclusionsAlthough our results show a low rate of SDMR, this algorithm may underestimate resistance mutations that may impact treatment options in developing countries. Primary resistance rates were similar in CSW and in the GP. Our phylogenetic analysis confirmed the genetic exchange between groups.
Quantifying the deep-sea rock and fossil record bias using coccolithophores
Authors: Lloyd Graeme T. , Smith Andrew B. , Young Jeremy R. 
Published: December 2011

Abstract
While many studies show a correlation between observed taxonomic richness and various measures of geological sampling, all have been based on the same record of terrestrial and marine sediments collected from the land. Here we present the first analyses of how rock and fossil records vary in the deep-sea. We have developed a novel database of species occurrences of coccolithophores sampled during major drilling programs of the North Atlantic, including the Mediterranean and Caribbean. Our sampling proxy, the number of deep-sea sites sampled – perhaps the most direct measure of sampling used so far – shows an exponential rise towards the Recent. Over the same period species-richness has grown in an approximately linear fashion, but genus-level richness shows a sharp initial increase followed by a much slower decline. However, correlations between both richness measures and sampling are extremely strong and a model assuming true diversity to be constant accurately predicts much of observed richness. We conclude that the deep-sea fossil record, like its land-based counterpart, bears a rock record bias.
Skeletal mineralogy and biodiversity of marine invertebrates: size matters more than seawater chemistry
Authors: Cherns Lesley , Wright V. Paul 
Published: December 2011

Abstract
It is now well established that seawater chemistry, as well as influencing non-skeletal marine precipitation (‘calcite’ and ‘aragonite seas’), has affected skeletal mineral secretion in some algal and marine invertebrate groups. Skeletal mineralogy has had a yet more profound consequence on fossil preservation. The realization that the fossil record of marine organisms with an aragonite shell is widely depleted in some shelf settings through early, effectively syn-depositional, dissolution (‘missing molluscs’ effect) has led to a re-evaluation of the composition, diversity, ecological and trophic structure of marine benthic communities. Comparisons of molluscan lagerstätten from ‘calcite’ and ‘aragonite seas’ show a similar pattern of skeletal mineralogical loss, that is, no differences are discernibly linked to changed seawater geochemistry. It is notable that the rare mollusc-rich skeletal lagerstätten faunas in the fossil record include many small individuals. Micromolluscs are quantitatively important among modern shell assemblages, yet small size is a major source of taphonomic and biodiversity loss in the fossil record. In skeletal lagerstätten faunas, micromolluscs contribute variably to mollusc biodiversity but appear particularly significant through at least to Triassic times. They highlight a further ‘missing molluscs’ effect of taphonomic loss through early dissolution.
Variation in stratigraphic congruence (GER) through the Phanerozoic and across higher taxa is partially determined by sources of bias
Authors: O'Connor Anne , Moncrieff Clive , Wills Matthew A. 
Published: December 2011

Abstract

Many published cladograms report measures of stratigraphic congruence. Strong congruence between cladistic branching order and the order of first fossil occurrences is taken to support both the accuracy of cladograms and the fidelity of the record. Poor congruence may reflect inaccurate trees, a misleading fossil record, or both. However, it has been demonstrated that most congruence indices are logically or empirically biased by parameters that are not uniformly distributed across taxa or through time. These include tree size and balance, mean ghost range duration (gap size) and the range and distribution of origination dates. This study used 650 published cladograms to investigate the influence of these variables on the Gap Excess Ratio (GER). In a range of multivariate models, factors other than congruence
per se
explained up to 74.5% of the observed variance in GER amongst trees. Arthropods typically have poorer GER values than other groups, but the residual differences from our models are much less striking. The models also show no clear residual trend in GER through the Phanerozoic. Because the GER is strongly influenced by parameters related to cladogram size, balance and duration, comparisons across trees should be made with caution.

Supplementary material:

Data legends are available at
http://www.geolsoc.org.uk/SUP18484
Impact of outcrop area on estimates of Phanerozoic terrestrial biodiversity trends
Authors: Wall P. D. , Ivany L. C. , Wilkinson B. H. 
Published: December 2011

Abstract
Studies of biodiversity through time have primarily focused on the marine realm which is generally considered to have a more complete record than terrestrial environments. Recently, this assumption has been challenged, and it has been argued that the record of life on land is comparable or even more robust than that of the shallow oceans. Moreover, it has been claimed that terrestrial successions preserve an exponential rise in diversity, even when corrected for sampling biases such as changes in continental rock volume through time. We evaluate relations between terrestrial diversity and exposed areas of terrestrial sediments using our compiled data on areas of global continental outcrops and generic diversity from the Paleobiology Database. Terrestrial global generic diversity and terrestrial outcrop area are highly correlated following a linear relation. No significant correlation is observed between habitat area and either outcrop area or biodiversity, suggesting that the observed relation between diversity and outcrop area is not driven by a common cause, such as eustasy. We do find evidence for a small residual increase in diversity through time after removing the effect of outcrop area, but caution that this may be driven by an increased proportion of terrestrial fauna with high preservation potential.
Macrostratigraphy and macroevolution in marine environments: testing the common-cause hypothesis
Authors: Peters Shanan E. , Heim Noel A. 
Published: December 2011

Abstract
Quantitative patterns in the sedimentary rock record predict many different macroevolutionary patterns in the fossil record, but the reasons for this predictability remain uncertain. There are two competing, but non-mutually exclusive, hypotheses: (1) similarities reflect a sampling bias imposed by variable and incomplete sampling of fossils, and (2) similarities reflect environmental perturbations that influence both the patterns of sedimentation and macroevolution (i.e., common-cause). Macrostratigraphy, which is based on the quantitative analysis of hiatus-bound rock packages, permits variation in the rock record to be expressed in terms of rock quantity and, more importantly, spatiotemporal continuity. In combination with spatially-explicit fossil occurrence data in the Paleobiology Database, it is now possible to more rigorously test alternative hypotheses for similarities in the rock and fossil records and to start distinguishing between geologically-controlled sampling bias and the common-cause hypothesis. Here we summarize results from measuring the intersection of Macrostrat and the Paleobiology Database. Our results suggest that patterns in the fossil record are not dominated by large-scale stratigraphic biases. Instead, they suggest that linkages between multiple Earth systems are driving both spatiotemporal patterns of sedimentation and macroevolution.
The fossil record and spatial structuring of environments and biodiversity in the Cenozoic of New Zealand
Authors: Crampton James S. , Foote Michael , Cooper Roger A. , Beu Alan G. , Peters Shanan E. 
Published: December 2011

Abstract
There is increasing evidence to suggest that drivers of bias in the fossil record have also affected actual biodiversity history, so that controls of artefact and true pattern are confounded. Here we examine the role of spatial structuring of the environment as one component of this common cause hypothesis. Our results are based on sampling standardized analyses of the post-Middle Eocene record of shelf molluscs from New Zealand. We find that spatial structuring of the environment directly influenced the quality of the fossil record. Contrary to our expectations, however, we find no evidence to suggest that spatial structuring of the environment was a strong or direct driver of taxic rates, net diversity, or spatial structuring in mollusc faunas at the scale of analysis. Stage-to-stage variation in sampling standardized diversity over the past 40 Ma exhibits two superficially independent dynamics: (a) changes in net diversity were associated primarily with changes in origination rate; and (b) an unknown common cause related extinction rate to the quality of the fossil record and, indirectly, to spatial structuring of the environment. We suggest that tectonic drivers, manifest as second-order sequence stratigraphic cycles, are likely to have been a key element of this common cause.
Modeling a Lethal Prostate Cancer Variant with Small-Cell Carcinoma Features
Authors: Tzelepi Vassiliki , Zhang Jiexin , Lu Jing-Fang , Kleb Brittany , Wu Guanglin , Wan Xinhai , Hoang Anh , Efstathiou Eleni , Sircar Kanishka , Navone Nora M. , Troncoso Patricia , Liang Shoudan , Logothetis Christopher J. , Maity Sankar N. , Aparicio Ana M. 
Published: December 2011

Abstract
Purpose: Small-cell prostate carcinoma (SCPC) morphology predicts for a distinct clinical behavior, resistance to androgen ablation, and frequent but short responses to chemotherapy. We sought to develop model systems that reflect human SCPC and can improve our understanding of its biology.
Experimental Design: We developed a set of castration-resistant prostate carcinomas xenografts and examined their fidelity to their human tumors of origin. We compared the expression and genomic profiles of SCPC and large-cell neuroendocrine carcinoma (LCNEC) xenografts to those of typical prostate adenocarcinoma xenografts. Results were validated immunohistochemically in a panel of 60 human tumors.
Results: The reported SCPC and LCNEC xenografts retain high fidelity to their human tumors of origin and are characterized by a marked upregulation of UBE2C and other mitotic genes in the absence of androgen receptor (AR), retinoblastoma (RB1), and cyclin D1 (CCND1) expression. We confirmed these findings in a panel of samples of CRPC patients. In addition, array comparative genomic hybridization of the xenografts showed that the SCPC/LCNEC tumors display more copy number variations than the adenocarcinoma counterparts. Amplification of the UBE2C locus and microdeletions of RB1 were present in a subset, but none displayed AR nor CCND1 deletions. The AR, RB1, and CCND1 promoters showed no CpG methylation in the SCPC xenografts.
Conclusion: Modeling human prostate carcinoma with xenografts allows in-depth and detailed studies of its underlying biology. The detailed clinical annotation of the donor tumors enables associations of anticipated relevance to be made. Future studies in the xenografts will address the functional significance of the findings. Clin Cancer Res; 18(3); 666–77. ©2011 AACR.
Preparation and characterization of poly(imide siloxane) block copolymers based on diphenylthioether dianhydride isomer mixtures
Authors: Pei Xueliang , Chen Guofei , Fang Xingzhong 
Published: December 2011

A series of poly(imide siloxane) block copolymers were prepared based on diphenylthioether dianhydride isomer mixtures (m-TDPA), 4,4′-oxydianiline (ODA) and bis(γ-aminopropyl)polydimethylsiloxane (APPS). The ODA and m-TDPA composed the hard segment, while the APPS and m-TDPA composed the soft segment. The hard segment length was kept constant, while the soft segment lengths were varied with varying the APPS contents. The copolymers had inherent viscosities range from 0.37 to 0.51 dL g−1, and their weight-average molecular weights and number-average molecular weights were in the range of 45 000–52 600 and 21 300–27 000, respectively. All copolymers were readily soluble in many organic solvents, and could afford flexible films via solution casting. The cast films exhibited mechanical properties with tensile strengths at break of 26.7–86.2 MPa, elongations at break of 9.9–112.2%, and tensile moduli of 0.12–2.15 GPa, depending on the soft segment length. The films also exhibited low water uptakes in the range of 0.18–0.68 wt.%. Furthermore, the copolymers showed high glass transition temperatures derived from the hard segments in the range of 196–225 °C, and good thermal stability with almost no weight loss up to 350 °C under nitrogen atmosphere and 335 °C under air atmosphere.
Risk of complications during hematopoietic stem cell collection in pediatric sibling donors: a prospective European Group for Blood and Marrow Transplantation Pediatric Diseases Working Party study
Authors: Styczynski Jan , Balduzzi Adriana , Gil Lidia , Labopin Myriam , Hamladji Rose-Marie , Marktel Sarah , Yesilipek M. Akif , Fagioli Franca , Ehlert Karoline , Matulova Martina , Dalle Jean-Hugues , Wachowiak Jacek , Miano Maurizio , Messina Chiara , Diaz Miguel Angel , Vermylen Christiane , Eyrich Matthias , Badell Isabel , Dreger Peter , Gozdzik Jolanta , Hutt Daphna , Rascon Jelena , Dini Giorgio , Peters Christina 
Published: December 2011

Abstract
We investigated prospectively factors influencing the safety of hematopoietic stem cell (HSC) collection in 453 pediatric donors. The children in the study donated either BM or peripheral blood stem cells (PBSCs) according to center policy. A large variability in approach to donor issues was observed between the participating centers. Significant differences were observed between BM and PBSC donors regarding pain, blood allotransfusion, duration of hospital stay, and iron supplementation; however, differences between the groups undergoing BM vs PBSC donation preclude direct risk comparisons between the 2 procedures. The most common adverse event was pain, reported mainly by older children after BM harvest, but also observed after central venous catheter (CVC) placement for PBSC collection. With regard to severe adverse events, one patient (0.7%) developed a pneumothorax with hydrothorax after CVC placement for PBSC collection. The risk of allotransfusion after BM harvest was associated with a donor age of < 4 years and a BM harvest volume of > 20 mL/kg. Children < 4 years were at higher risk than older children for allotransfusion after BM harvest and there was a higher risk of complications from CVC placement before apheresis. We conclude that PBSC and BM collection are safe procedures in children.
Assessment and prognostic value of the European LeukemiaNet criteria for clinicohematologic response, resistance, and intolerance to hydroxyurea in polycythemia vera
Authors: Alvarez-Larrán Alberto , Pereira Arturo , Cervantes Francisco , Arellano-Rodrigo Eduardo , Hernández-Boluda Juan-Carlos , Ferrer-Marín Francisca , Angona Anna , Gómez Montse , Muiña Begoña , Guillén Helga , Teruel Anabel , Bellosillo Beatriz , Burgaleta Carmen , Vicente Vicente , Besses Carles 
Published: December 2011

Abstract
Criteria of response and definition of resistance and intolerance to hydroxyurea (HU) in polycythemia vera (PV) were proposed by the European LeukemiaNet (ELN). Such criteria were evaluated in 261 PV patients (median follow-up, 7.2 years) treated with HU for a median of 4.4 years. Complete response, partial response, and no response were observed in 24%, 66%, and 10% of patients, respectively. Achieving ELN response (complete or partial) or hematocrit response did not result in better survival or less thrombosis and bleeding. On the contrary, having no response in leukocyte count was associated with higher risk of death (HR, 2.7; 95% confidence interval [CI], 1.3%-5.4%; P = .007), whereas lack of response in platelet count involved a higher risk of thrombosis and bleeding. Resistance and intolerance to HU was registered in 11% and 13% of patients, respectively. Resistance to HU was associated with higher risk of death (HR, 5.6; 95% CI, 2.7%-11.9%; P < .001) and transformation (HR, 6.8; 95% CI, 3.0%-15.4%; P < .001). In summary, fulfilling the ELN definition for response to HU was not associated with a benefit in the clinical outcome in PV, whereas response in platelet and white blood cell counts were predictive of less thrombohemorrhagic complications and better prognosis, respectively. Resistance to HU was an adverse prognostic factor.