bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is local anaesthesia superior to general anaesthesia in endovascular repair of abdominal aortic aneurysm?
Authors: Harky Amer , Grafton-Clarke Ciaran , Chan Jeremy 
Published: May 2019

Summary
A best evidence topic in cardiovascular surgery was written in accordance to a structured protocol. The question addressed was: in patients undergoing endovascular repair of abdominal aortic aneurysm (EVAR), is local anaesthetic (LA) superior to general anaesthetic in terms of perioperative outcomes? Altogether, 630 publications were found using the reported search protocol, of which 3 represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type and primary outcomes were tabulated. The 3 included studies are systematic reviews with meta-analyses, with no randomized trials identified. Within the studies, there is a degree of heterogeneity in terms of surgical case-mix (elective or emergency EVAR or both) and anaesthetic technique (LA, regional anaesthetic, local-regional anaesthetic and general anaesthetic). With 1 study not providing pooled estimates, the second study demonstrated statistical significance in favour of local-regional anaesthetic within the elective setting in terms of mortality [pooled odds ratio (OR) 0.70, 95% confidence interval (CI) 0.52–0.95; P = 0.02], morbidity (pooled OR 0.73, 95% CI 0.55–0.96; P = 0.0006) and total length of hospital admission (pooled mean difference: −1.53, 95% CI −2.53 to −0.53; P = 0.00001). The third study failed to demonstrate a statistically significant mortality benefit with LA (pooled OR 0.54, 95% CI 0.21–1.41; P = 0.211). While the results of these studies fail to provide a clear answer to a complex surgical problem, it would be appropriate, in the light of current evidence, to recommend LA as non-inferior to general anaesthetic in both emergency and elective settings.
The Politics of Method: Taming the New, Making Data Official
Authors: Ruppert Evelyn , Scheel Stephan 
Published: May 2019

AbstractStatisticians are under pressure to innovate, partly due to shrinking budgets and the call to do more with less, but also due to technological advances and the emergence of new actors promising to produce more accurate and timely statistics with what has come to be known as “big data.” This raises the question, how do new forms of data and methods become legitimate and official? We approach this question by conceiving of official statistics as part of a transnational field in which different factions of actors compete and struggle over the authority to innovate the data and methods that are legitimated to produce official statistics. We consider these struggles as a politics of method that is not reducible to a competition between ideas and words. They are also material insofar as they feature competing digital devices mobilized to demonstrate the validity of new data and methods. Through two empirical examples, we identify the strategy of reassembling methods to capture how statisticians tame and contain innovations based on big data, especially those introduced by data scientists, by integrating and simultaneously subordinating them to existing methods. By doing so, we suggest that reassembling is an innovation strategy that secures the relative position of national and international statisticians within the transnational field of statistics.
Antifungal activity and killing kinetics of anidulafungin, caspofungin and amphotericin B against Candida auris
Authors: Dudiuk Catiana , Berrio Indira , Leonardelli Florencia , Morales-Lopez Soraya , Theill Laura , Macedo Daiana , Yesid-Rodriguez José , Salcedo Soraya , Marin Adriana , Gamarra Soledad , Garcia-Effron Guillermo 
Published: May 2019

AbstractBackgroundCandida auris is an emerging MDR pathogen. It shows reduced susceptibility to azole drugs and, in some strains, high amphotericin B MICs have been described. For these reasons, echinocandins were proposed as first-line treatment for C. auris infections. However, information on how echinocandins and amphotericin B act against this species is lacking.ObjectivesOur aim was to establish the killing kinetics of anidulafungin, caspofungin and amphotericin B against C. auris by time–kill methodology and to determine if these antifungals behave as fungicidal or fungistatic agents against this species.MethodsThe susceptibility of 50 C. auris strains was studied. Nine strains were selected (based on echinocandin MICs) to be further studied. Minimal fungicidal concentrations, in vitro dose–response and time–kill patterns were determined.ResultsEchinocandins showed lower MIC values than amphotericin B (geometric mean of 0.12 and 0.94 mg/L, respectively). Anidulafungin and caspofungin showed no fungicidal activity at any concentration (maximum log decreases in cfu/mL between 1.34 and 2.22). On the other hand, amphotericin B showed fungicidal activity, but at high concentrations (≥2.00 mg/L). In addition, the tested polyene was faster than echinocandins at killing 50% of the initial inoculum (0.92 versus >8.00 h, respectively).ConclusionsAmphotericin B was the only agent regarded as fungicidal against C. auris. Moreover, C. auris should be considered tolerant to caspofungin and anidulafungin considering that their MFC:MIC ratios were mostly ≥32 and that after 6 h of incubation the starting inoculum was not reduced in >90%.
Safety and efficacy of rifabutin among HIV/TB-coinfected children on lopinavir/ritonavir-based ART
Authors: Rawizza Holly E , Darin Kristin M , Oladokun Regina , Brown Biobele , Ogunbosi Babatunde , David Nkiruka , Akanmu Sulaimon , Olaitan Oluremi , Chang Charlotte , Scarsi Kimberly K , Okonkwo Prosper , Kanki Phyllis J 
Published: May 2019

Abstract

Background
TB is the leading cause of death among HIV-infected children, yet treatment options for those who require PI-based ART are suboptimal. Rifabutin is the preferred rifamycin for adults on PI-based ART; only one study has evaluated its use among children on PIs and two of six children developed treatment-limiting neutropenia.

Methods
Since 2009, rifabutin has been available for HIV/TB-coinfected children requiring PI-based ART in the Harvard/APIN programme in Nigeria. We retrospectively analysed laboratory and clinical toxicities at baseline and during rifabutin therapy, and examined HIV/TB outcomes.

Results
Between 2009 and 2015, 48 children received rifabutin-containing TB therapy with PI (lopinavir/ritonavir)-based ART: 50% were female with a median (IQR) baseline age of 1.7 (0.9–5.0) years and a median (IQR) CD4+ cell percentage of 15% (9%–25%); 52% were ART experienced. Eighty-five percent completed the 6 month rifabutin course with resolution of TB symptoms and 79% were retained in care at 12 months. Adverse events (grade 1–4) were more common at baseline (27%) than during rifabutin treatment (15%) (P = 0.006). Absolute neutrophil count was lower during rifabutin compared with baseline (median = 1762 versus 2976 cells/mm3, respectively), but only one instance (2%) of grade 3 neutropenia occurred during rifabutin treatment.

Conclusions
With clinical and laboratory monitoring, our data suggest that rifabutin is a safe option for TB therapy among children on PI-based ART. By contrast with the only other study of this combination in children, severe neutropenia was rare. Furthermore, outcomes from this cohort suggest that rifabutin is effective, and a novel option for children who require PI-based ART. Additional study of rifabutin plus PIs in children is urgently needed.
Toll-like receptor 7 regulates osteoclastogenesis in rheumatoid arthritis
Authors: Kim Kyoung-Woon , Kim Bo-Mi , Won Ji-Yeon , Lee Kyung-Ann , Kim Hae-Rim , Lee Sang-Heon 
Published: May 2019

AbstractThis study aimed to determine the regulatory role of toll-like receptor 7 (TLR7) in receptor activator of nuclear factor kappa-B ligand (RANKL) production and osteoclast differentiation in rheumatoid arthritis (RA). In confocal microscopy, the co-expression of TLR7, CD55 and RANKL was determined in RA synovial fibroblasts. After RA synovial fibroblasts were treated with imiquimod, the RANKL gene expression and protein production were determined by real-time polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA). Osteoclastogenesis from peripheral blood CD14+ monocytes which were cultured with imiquimod was assessed by determining the numbers of tartrate-resistant acid phosphatase (TRAP)-positive multinucleated cells. The signal pathways mediating the TLR7-induced RANKL expression and osteoclastogenesis were analysed after inhibition of intracellular signal molecules and their phosphorylation. Imiquimod stimulated the expression of TLR7 and RANKL and production of RANKL in RA synovial fibroblasts, increasing the phosphorylation of TRAF6, IRF7, mitogen-activated protein kinases (MAPK), c-Jun and NFATc1. When CD14+ monocytes were cultured with imiquimod or co-cultured with imiquimod-pre-treated RA synovial fibroblasts, they were differentiated into TRAP+ multinucleated osteoclasts in the absence of RANKL. TLR7 activation-induced osteoclastogenesis in RA through direct induction of osteoclast differentiation from its precursors and up-regulation of RANKL production in RA synovial fibroblasts. Thus, the blockage of TLR7 pathway could be a promising therapeutic strategy for preventing bone destruction in RA.
Effects of Two Cultivated Brassica spp. on the Development and Performance of Diadegma semiclausum (Hymenoptera: Ichneumonidae) and Cotesia vestalis (Hymenoptera: Braconidae) Parasitizing Plutella xylostella (Lepidoptera: Plutellidae) in Kenya
Authors: Kahuthia-Gathu Ruth , Othim Stephen T O 
Published: May 2019

AbstractThe diamondback moth (DBM), Plutella xylostella L., is the most destructive pest affecting vegetable production in Kenya and around the world. Parasitoids have shown promising results in lowering the pest populations and damage caused by DBM. However, variations in host plant quality have been reported to have bottom-up effects up to the third and fourth trophic levels. We assessed the effects of two cultivated Brassica varieties (cabbage, Brassica oleracea var. capitata L. cultivar ‘Gloria F1’ and kale, B. oleracea var. acephala L. cultivar ‘Thousand headed’) on the development and performance of the specialist pest P. xylostella and two exotic parasitoids Diadegma semiclausum (Hellen) and Cotesia vestalis (Haliday). The exposed larval period of DBM took about 1.5 d longer on kale than cabbage and the total immature development time of both females and males was significantly longer on kale than cabbage. Higher pupal weight and higher fecundity were recorded on DBM fed on kale. Development time of D. semiclausum and C. vestalis was not affected by the host crop as was the parasitism rate of D. semiclausum. Heavier male pupae and larger adults of D. semiclausum, as well as more fecund adults of C. vestalis, were obtained from hosts fed on cabbage. Larger adults of C. vestalis were obtained from herbivores fed on kale. These results show potentially positive effects of host plant allelochemicals that are detrimental to herbivores while promoting parasitoid development and performance, which can be harnessed for the control of DBM.
Developing a Quality of Cancer Survivorship Care Framework: Implications for Clinical Care, Research, and Policy
Authors: Nekhlyudov Larissa , Mollica Michelle A , Jacobsen Paul B , Mayer Deborah K , Shulman Lawrence N , Geiger Ann M 
Published: May 2019

Abstract
There are now close to 17 million cancer survivors in the United States, and this number is expected to continue to grow. One decade ago the Institute of Medicine report, From Cancer Patient to Cancer Survivor: Lost in Transition, outlined 10 recommendations aiming to provide coordinated, comprehensive care for cancer survivors. Although there has been noteworthy progress made since the release of the report, gaps remain in research, clinical practice, and policy. Specifically, the recommendation calling for the development of quality measures in cancer survivorship care has yet to be fulfilled. In this commentary, we describe the development of a comprehensive, evidence-based cancer survivorship care quality framework and propose the next steps to systematically apply it in clinical settings, research, and policy.
Contrasting Epidemiology and Clinicopathology of Female Breast Cancer in Asians vs the US Population
Authors: Lin Ching-Hung , Yap Yoon Sim , Lee Kyung-Hun , Im Seock-Ah , Naito Yoichi , Yeo Winnie , Ueno Takayuki , Kwong Ava , Li Huiping , Huang Shu-Min , Leung Roland , Han Wonshik , Tan Benita , Hu Fu-Chang , Huang Chiun-Sheng , Cheng Ann-Lii , Lu Yen-Shen ,   The Asian Breast Cancer Cooperative Group
Published: May 2019

AbstractBackgroundThe incidence of breast cancer among younger East Asian women has been increasing rapidly over recent decades. This international collaborative study systemically compared the differences in age-specific incidences and pathological characteristics of breast cancer in East Asian women and women of predominantly European ancestry.MethodsWe excerpted analytic data from six national cancer registries (979 675 cases) and eight hospitals (18 008 cases) in East Asian countries and/or regions and, for comparisons, from the US Surveillance, Epidemiology, and End Results program database. Linear regression analyses of age-specific incidences of female breast cancer and logistic regression analyses of age-specific pathological characteristics of breast cancer were performed. All statistical tests were two-sided.ResultsUnlike female colorectal cancer, the age-specific incidences of breast cancer among East Asian women aged 59 years and younger increased disproportionally over recent decades relative to rates in US contemporaries. For years 2010–2014, the estimated age-specific probability of estrogen receptor positivity increased with age in American patients, whereas that of triple-negative breast cancer (TNBC) declined with age. No similar trends were evident in East Asian patients; their probability of estrogen receptor positivity at age 40–49 years was statistically significantly higher (odd ratio [OR] = 1.50, 95% confidence interval [CI] = 1.36 to 1.67, P &lt; .001) and of TNBC was statistically significantly lower (OR = 0.79, 95% CI = 0.71 to 0.88, P &lt; .001), whereas the probability of ER positivity at age 50–59 years was statistically significantly lower (OR = 0.88, 95% CI = 0.828 to 0.95, P &lt; .001). Subgroup analyses of US Surveillance, Epidemiology, and End Results data showed similarly distinct patterns between East Asian American and white American patients.ConclusionsContrasting age-specific incidences and pathological characteristics of breast cancer between East Asian and American women, as well as between East Asian Americans and white Americans, suggests racial differences in the biology.
Multiple intestinal intussusceptions caused by highly impaired gastrointestinal motility in a patient with chronic cannabis consumption
Authors: Prokopchuk Olga , Neumann Philipp-Alexander , Hüser Norbert , Friess Helmut , Wilhelm Dirk 
Published: May 2019

Abstract
Since the therapeutic use of cannabis and its derivatives is currently rising, the adverse effects of cannabis and cannabinoids are of special interest. However little is known about the possible effects of long-term use of cannabis on the gastrointestinal motility. Herewith we describe the case of a patient with a rare severe form of intestinal intussusception following long-term cannabis consumption. The case shall raise awareness of possible life threatening complications of the use of cannabis and its derivates.
Response of Sulfolobus solfataricus Dpo4 polymerase in vitro to a DNA G-quadruplex
Authors: Berroyer Alexandra , Alvarado Gloria , Larson Erik D 
Published: May 2019

Abstract
Repetitive DNA sequences support the formation of structures that can interrupt replication and repair, leading to breaks and mutagenesis. One particularly stable structure is G-quadruplex (G4) DNA, which is four-stranded and formed from tandemly repetitive guanine bases. When folded within a template, G4 interferes with DNA synthesis. Similar to non-duplex structures, DNA base lesions can also halt an advancing replication fork, but the Y-family polymerases solve this problem by bypassing the damage. In order to better understand how guanine-rich DNA is replicated, we have investigated the activity of the model Y-family polymerase, Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4), on guanine-rich templates in vitro. We find that Dpo4 progression on templates containing either a single GC-rich hairpin or a G4 DNA structure is greatly reduced and synthesis stalls at the structure. Human polymerase eta (hPol eta) showed the same pattern of stalling at G4; however, and in contrast to Klenow, hPol eta and Dpo4 partially synthesise into the guanine repeat. Substitution of the nucleotide selectivity residue in Dpo4 with alanine permitted ribonucleotide incorporation on unstructured templates, but this further reduced the ability of Dpo4 to synthesise across from the guanine repeats. The advancement of Dpo4 on G4 templates was highest when the reaction was supplied with only deoxycytidine triphosphate, suggesting that high-fidelity synthesis is favoured over misincorporation. Our results are consistent with a model where the Y-family polymerases pause upon encountering G4 structures but have an ability to negotiate some synthesis through tetrad-associated guanines. This suggests that the Y-family polymerases reduce mutagenesis by catalysing the accurate replication of repetitive DNA sequences, but most likely in concert with additional replication and structure resolution activities.
Chromatin condensation fluctuations rather than steady-state predict chromatin accessibility
Authors: Audugé Nicolas , Padilla-Parra Sergi , Tramier Marc , Borghi Nicolas , Coppey-Moisan Maïté 
Published: May 2019

AbstractChromatin accessibility to protein factors is critical for genome activities. However, the dynamic properties of chromatin higher-order structures that regulate its accessibility are poorly understood. Here, we took advantage of the microenvironment sensitivity of the fluorescence lifetime of EGFP-H4 histone incorporated in chromatin to map in the nucleus of live cells the dynamics of chromatin condensation and its direct interaction with a tail acetylation recognition domain (the double bromodomain module of human TAFII250, dBD). We reveal chromatin condensation fluctuations supported by mechanisms fundamentally distinct from that of condensation. Fluctuations are spontaneous, yet their amplitudes are affected by their sub-nuclear localization and by distinct and competing mechanisms dependent on histone acetylation, ATP and both. Moreover, we show that accessibility of acetylated histone H4 to dBD is not restricted by chromatin condensation nor predicted by acetylation, rather, it is predicted by chromatin condensation fluctuations.
EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies
Authors: Krainer Julie , Weinhäusel Andreas , Hanak Karel , Pulverer Walter , Özen Seza , Vierlinger Klemens , Pabinger Stephan 
Published: May 2019

Abstract
DNA methylation is one of the major epigenetic modifications and has frequently demonstrated its suitability as diagnostic and prognostic biomarker. In addition to chip and sequencing based epigenome wide methylation profiling methods, targeted bisulfite sequencing (TBS) has been established as a cost-effective approach for routine diagnostics and target validation applications. Yet, an easy-to-use tool for the analysis of TBS data in combination with array-based methylation results has been missing. Consequently, we have developed EPIC-TABSAT, a user-friendly web-based application for the analysis of targeted sequencing data that additionally allows the integration of array-based methylation results. The tool can handle multiple targets as well as multiple sequencing files in parallel and covers the complete data analysis workflow from calculation of quality metrics to methylation calling and interactive result presentation. The graphical user interface offers an unprecedented way to interpret TBS data alone or in combination with array-based methylation studies. Together with the computation of target-specific epialleles it is useful in validation, research, and routine diagnostic environments. EPIC-TABSAT is freely accessible to all users at https://tabsat.ait.ac.at/.
NAPS update: network analysis of molecular dynamics data and protein–nucleic acid complexes
Authors: Chakrabarty Broto , Naganathan Varun , Garg Kanak , Agarwal Yash , Parekh Nita 
Published: May 2019

AbstractNetwork theory is now a method of choice to gain insights in understanding protein structure, folding and function. In combination with molecular dynamics (MD) simulations, it is an invaluable tool with widespread applications such as analyzing subtle conformational changes and flexibility regions in proteins, dynamic correlation analysis across distant regions for allosteric communications, in drug design to reveal alternative binding pockets for drugs, etc. Updated version of NAPS now facilitates network analysis of the complete repertoire of these biomolecules, i.e., proteins, protein–protein/nucleic acid complexes, MD trajectories, and RNA. Various options provided for analysis of MD trajectories include individual network construction and analysis of intermediate time-steps, comparative analysis of these networks, construction and analysis of average network of the ensemble of trajectories and dynamic cross-correlations. For protein–nucleic acid complexes, networks of the whole complex as well as that of the interface can be constructed and analyzed. For analysis of proteins, protein–protein complexes and MD trajectories, network construction based on inter-residue interaction energies with realistic edge-weights obtained from standard force fields is provided to capture the atomistic details. Updated version of NAPS also provides improved visualization features, interactive plots and bulk execution. URL: http://bioinf.iiit.ac.in/NAPS/
DaReUS-Loop: a web server to model multiple loops in homology models
Authors: Karami Yasaman , Rey Julien , Postic Guillaume , Murail Samuel , Tufféry Pierre , de Vries Sjoerd J 
Published: May 2019

AbstractLoop regions in protein structures often have crucial roles, and they are much more variable in sequence and structure than other regions. In homology modeling, this leads to larger deviations from the homologous templates, and loop modeling of homology models remains an open problem. To address this issue, we have previously developed the DaReUS-Loop protocol, leading to significant improvement over existing methods. Here, a DaReUS-Loop web server is presented, providing an automated platform for modeling or remodeling loops in the context of homology models. This is the first web server accepting a protein with up to 20 loop regions, and modeling them all in parallel. It also provides a prediction confidence level that corresponds to the expected accuracy of the loops. DaReUS-Loop facilitates the analysis of the results through its interactive graphical interface and is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/DaReUS-Loop/.