bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying homomorphic sex chromosomes from wild‐caught adults with limited genomic resources
Authors: Brelsford Alan , Lavanchy Guillaume , Sermier Roberto , Rausch Anna , Perrin Nicolas 
Published: November 2016

AbstractWe demonstrate a genotyping‐by‐sequencing approach to identify homomorphic sex chromosomes and their homolog in a distantly related reference genome, based on noninvasive sampling of wild‐caught individuals, in the moor frog Rana arvalis. Double‐digest RADseq libraries were generated using buccal swabs from 30 males and 21 females from the same population. Search for sex‐limited markers from the unfiltered data set (411 446 RAD tags) was more successful than searches from a filtered data set (33 073 RAD tags) for markers showing sex differences in heterozygosity or in allele frequencies. Altogether, we obtained 292 putatively sex‐linked RAD loci, 98% of which point to male heterogamety. We could map 15 of them to the Xenopus tropicalis genome, all but one on chromosome pair 1, which seems regularly co‐opted for sex determination among amphibians. The most efficient mapping strategy was a three‐step hierarchical approach, where R. arvalis reads were first mapped to a low‐coverage genome of Rana temporaria (17 My divergence), then the R. temporaria scaffolds to the Nanorana parkeri genome (90 My divergence), and finally the N. parkeri scaffolds to the X. tropicalis genome (210 My). We validated our conclusions with PCR primers amplifying part of Dmrt1, a candidate sex determination gene mapping to chromosome 1: a sex‐diagnostic allele was present in all 30 males but in none of the 21 females. Our approach is likely to be productive in many situations where biological samples and/or genomic resources are limited.
Compliance of post‐radiation therapy head and neck cancer patients with caries preventive protocols
Authors: Frydrych AM , Slack‐Smith LM , Parsons R 
Published: November 2016

AbstractBackgroundCaries prevention is paramount in safeguarding the life quality of head and neck cancer patients and is dependent on patient compliance with caries preventive protocols. The purpose of this study was to examine this compliance.MethodsAll records of patients referred to one public oral medicine clinic servicing a head and neck oncology unit of one major Western Australian hospital, between January 2005 and December 2011, were examined. Data extracted included patient and cancer characteristics and compliance with dietary advice, dental care, oral hygiene instruction and fluoride use over a follow‐up period of at least 12 months. Compliance was assessed against various oral health outcomes and patient characteristics.ResultsOf the 116 participants, 75.9% complied with all caries preventive measures over a mean follow‐up period of 45 months. Non‐compliance with regular dental attendance (P = 0.004), oral hygiene instruction (P = 0.009), dietary advice (P = 0.034) and daily fluoride use (P = 0.018) were associated with the development of dental caries post‐treatment. The presence of dental caries at the time of cancer diagnosis was predictive of poorer compliance.ConclusionsHigh compliance with caries preventive measures is attainable in the head and neck cancer patient group. Factors other than fluoride use seem important in caries prevention.
Effect of ketoconazole, a strong CYP3A inhibitor, on the pharmacokinetics of venetoclax, a BCL‐2 inhibitor, in patients with non‐Hodgkin lymphoma
Authors: Agarwal Suresh K. , Salem Ahmed Hamed , Danilov Alexey V. , Hu Beibei , Puvvada Soham , Gutierrez Martin , Chien David , Lewis Lionel D. , Wong Shekman L. 
Published: November 2016

AimsTo examine the effect of a strong cytochrome P450 (CYP) 3A inhibitor, ketoconazole, on the pharmacokinetics, safety and tolerability of venetoclax.MethodsTwelve patients with non‐Hodgkin lymphoma (NHL) were enrolled in this Phase 1, open‐label, fixed‐sequence study. Patients received a single 50 mg dose of venetoclax orally on Day 1 and Day 8, and a 400 mg once daily dose of ketoconazole on Days 5–11. Blood samples were collected predose and up to 96 h after each venetoclax dose on Day 1 and Day 8.ResultsEleven patients had evaluable pharmacokinetic data and were therefore included in the statistical analyses. Compared to administration of a single 50 mg dose of venetoclax alone, ketoconazole increased the venetoclax mean maximum observed plasma concentration (Cmax) and area under the plasma concentration–time curve from time 0 to infinity (AUC∞) by 2.3‐fold (90% confidence interval [CI]: 2.0–2.7) and 6.4‐fold (90% CI: 4.5–9.2; range: 2‐ to 12‐fold), respectively.ConclusionsCoadministration of venetoclax with multiple doses of ketoconazole resulted in a significant increase of venetoclax exposures, strongly suggesting that CYP3A plays a major role in elimination of venetoclax in patients. These results suggest the need to avoid concomitant use with strong and moderate inhibitors or inducers of CYP3A during the venetoclax ramp‐up phase in chronic lymphocytic leukaemia (CLL) patients. For patients who have completed the ramp‐up phase, a modification in venetoclax dose for use with strong and moderate inhibitors or inducers of CYP3A is recommended.
Statistical reporting in the BJH: some dos and don'ts
Authors: Hills Robert K. 
Published: November 2016

SummaryStatistics provides an important tool to enable large amounts of data from an experiment to be summarised and conclusions drawn. To be informative statistics need to serve the experimenter appropriately and give clear and understandable answers. It is important that the reader can clearly understand the methodology used, and that that methodology is appropriate to the situation. We present here some issues to be considered when writing for publication in the British Journal of Haematology (BJH).
Deficits in oral health behavior and oral health status in patients after lung transplantation
Authors: Marcinkowski Anna , Ziebolz Dirk , Kleibrink Bjoern E. , Weinreich Gerhard , Kamler Markus , Teschler Helmut , Sommerwerck Urte 
Published: November 2016

AbstractBackgroundDental status has been implicated in several systemic inflammatory diseases and is a potential focus for systemic infections. Therefore, most lung‐transplant centers have recommendations regarding pre‐transplant dental care and follow‐up, but there are no official clinical guidelines. To date there is little information on oral health status in lung transplant (LTx) recipients. The aim of this study was to systematically assess oral health status in LTx recipients.ObjectivesThe aim of this study was to assess oral health status, including periodontal disease, oral health behavior, and awareness of the need for good oral health after LTx.MethodsLTx recipients were recruited during follow‐up outpatient visits at a university clinic transplant unit. Oral health status was quantified using the count of Decayed, Missing, and Filled Teeth (DMF‐T) and the grade of periodontal disease was measured by probing depth. Patients' oral health behavior was assessed using a questionnaire.ResultsSeventy‐three patients were included at 5.8 ± 3.4 years after lung transplantation. The mean DMF‐T was 21.9 ± 5.5. Patients with cystic fibrosis as the indication for transplantation had a significantly lower DMF‐T than patients with chronic obstructive pulmonary disease as the transplant indication. Of the 66 patients with teeth, 97% had moderate or severe periodontal disease. The prevalence of moderate or severe periodontal disease was significantly higher in LTx recipients (mean age 55.9 years) compared with older individuals (age 65‐74 years) from the German general population (P < .005).ConclusionsThis single center study shows deficits in oral health and oral health behavior in patients after LTx. There is a strong need for interdisciplinary collaboration and clinical guidelines to foster better oral health education of the transplant recipient and better oral health.
Tracheobronchial foreign body removal in infants who had very small airways: A prospective clinical trial
Authors: Woo Seung Hoon , Park Jung Je , Kwon Minsu , Ryu Jun Sun , Kim Jin Pyeong 
Published: November 2016

AbstractBackground and AimsTracheobronchial foreign body aspiration is a life‐threatening emergency. Using a rigid bronchoscope with optical forceps is the most effective method for foreign body removal. However, occasionally for some infants these instruments could not be used, as they may be too large for their small airways. Here, they present the apnea technique with only an optical forceps for foreign body removal in infants with very small airways.MethodsForeign bodies were removed using only an optical forceps for infants who had very small diameter airways. After general anesthesia, the suspension laryngoscope was set just above the vocal cord, and the inserted ventilation tube was pulled out, followed by a new one being inserted through the suspension laryngoscope and placed at the trachea. With the oxygen saturation at 100%, we pulled out the ventilation tube and inserted the optical forceps with an endoscope. After that, the foreign body was removed by the optical forceps.ResultsThe foreign body removal using only an optical forceps is technically feasible for an infant. The mean operation time was 40.33 ± 8.06 min, and the hospital stay was 2.25 ± 0.62 days. When we pulled out the ventilation tube, the O2 saturation mean time (apnea time) was 106.25 ± 14.30 sec. In 12 infants, the foreign body was removed completely without a need for a second procedure.ConclusionsThe apnea technique for the removal of foreign body from the airway, using only an optical forceps with an endoscope, is useful in infants who had very small airways.
An exponential change decline function to estimate soil organic carbon stocks and their changes from topsoil measurements
Authors: Ottoy S. , Elsen A. , Van De Vreken P. , Gobin A. , Merckx R. , Hermy M. , Van Orshoven J. 
Published: November 2016

Soil organic carbon (SOC) stocks and their changes are important indicators in ecosystem service assessments. Routine soil inventories are often limited to the topsoil, even though a non‐negligible fraction of SOC is known to be stored in deeper horizons. To assess SOC stocks and their changes in the upper metre of the soil profile, vertical extrapolation of topsoil SOC measurements is necessary. The commonly used exponential decline function is not valid, however, for soil types in which subsurface horizons with a larger SOC content (‘anomalies’) occur. Here, we propose an exponential change decline function to account for these profile anomalies. Therefore, we applied the exponential decline function to the difference between the recent (2008–11) and historical (1947–74) SOC contents in the topsoil and compared the results with those derived by the original method. We applied the exponential change decline function to 54 041 agricultural land units (7159 km2) in Flanders (Belgium) and were able to model specific profile characteristics such as spodic horizons, plaggic topsoil and peat substrates. For these particular land units, the exponential decline function underestimated SOC stocks; therefore, it compromised an in‐depth assessment of changes in SOC stocks over time. This study shows that the exponential change decline function is promising for certain soil types and will contribute to the more accurate assessment of ecosystem service indicators. In addition, we emphasize the need for more detailed descriptions of subsoil reference profiles, sampled by pedogenetic horizon rather than by fixed depth interval to optimize calibration of the decline functions.HighlightsWhen recent soil sampling is limited to the topsoil, extrapolation is needed to assess subsoil SOC stocks.
We modified the exponential decline function to model SOC‐rich subsurface horizons with the integration of legacy data.
An appropriate extrapolation approach is essential for in‐depth SOC assessments.
Detailed subsoil data are needed to optimize the calibration of the decline functions.
Level of evidence in endodontics: what does it mean?
Authors: Haapasalo Markus 
Published: November 2016

This review is a short summary of how the level of evidence in endodontics and endodontic research in particular is defined. The goal of this review is to help dentists and endodontists to become familiar with the evidence pyramid and thereby better evaluate the reliability of evidence on daily practices and choices in patient care. All medical treatment, including endodontic treatment, should be based on the best available evidence. In this review, the definition of evidence is presented and the different levels in the evidence pyramid are discussed with a special focus on endodontics. Much of the presently published endodontic research is done in vitro, which is regarded as the lowest level of evidence. However, it is important to understand that a low level of evidence does not mean that the research in itself is of poor quality or somehow unreliable. Instead, it means that one cannot draw conclusions from in vitro studies to clinical events with a high probability of accuracy. The in vitro results may be true, and often are, but more evidence from different types of studies such as case‐control and cohort studies and even randomized controlled trials is needed to increase the probability that the results obtained in research do in fact correctly reflect the real events, e.g. level of probability of healing after a specific type of treatment for a specific disease. This review also discusses why the highest level of evidence may be difficult to obtain for a variety of practical and ethical reasons, and why not all endodontic treatment needs to be based on information from randomized controlled trials and systematic reviews.
Associative effects between fresh perennial ryegrass and white clover on dynamics of intake and digestion in sheep
Authors: Niderkorn V. , Martin C. , Le Morvan A. , Rochette Y. , Awad M. , Baumont R. 
Published: November 2016

AbstractThe aim of this study was to determine the associative effects between fresh perennial ryegrass and fresh white clover on intake and digestion in sheep. Five proportions of ryegrass and white clover, ranging from 0 to 1 in 0·25 increments (DM basis), were allocated to two groups of five sheep according to a replicated 5 × 5 Latin square design, and intake behaviour and digestive parameters including methane (CH4) emissions were measured. Feeding behaviour was affected through increased forage intake when the proportion of white clover was increased, and there were positive associative effects on intake, eating time and eating rate during the main meals consumed immediately after feed was given. These effects seemed to be related to a greater motivation to eat, rather to more efficient digestion, as no difference on DM digestibility (average 766 g kg−1) was detected. There were no differences in CH4 yield (average 18·1 g kg−1 DM intake) among the treatments. The optimal proportion of white clover fed with ryegrass to optimize intake and digestion was between 0·25 and 0·50. These results indicate that mixing perennial ryegrass and white clover positively affects forage intake in sheep and their motivation to eat.
The impact of physicians' communication styles on evaluation of physicians and information processing: A randomized study with simulated video consultations on contraception with an intrauterine device
Authors: Bientzle Martina , Fissler Tim , Cress Ulrike , Kimmerle Joachim 
Published: November 2016

AbstractObjectiveThis study aimed at examining the impact of different types of physicians' communication styles on people's subsequent evaluation of physician attributes as well as on their information processing, attitude and decision making.MethodIn a between‐group experiment, 80 participants watched one of three videos in which a gynaecologist displayed a particular communication style in a consultation situation on contraception with an intrauterine device. We compared doctor‐centred communication (DCC) vs patient‐centred communication (PCC) vs patient‐centred communication with need‐orientation (PCC‐N).ResultsIn the PCC condition, participants perceived the physician to be more empathetic and more competent than in the DCC condition. In the DCC condition, participants showed less attitude change compared to the other conditions. In the PCC‐N condition, the physician was perceived as more empathetic and more socially competent than in the other conditions. However, participants acquired less knowledge in the PCC‐N condition.ConclusionWe conclude that appropriate application of particular communication styles depends on specific consultation goals. Our results suggest that patients' needs should be addressed if the main goal is to build a good relationship, whereas a traditional PCC style appears to be more effective in communicating factual information.
A novel spontaneous mutation in the TAP2 gene unravels its role in macrophage survival
Authors: Lapenna Antonio , Omar Ibrahim , Berger Michael 
Published: November 2016

SummaryWe report a new mouse strain with a single point mutation in the type 2 transporter associated with antigen processing (TAP2). This strain randomly arose in one of our C57BL/6J mouse colonies and was initially discovered because of the lack of CD8+ T cells in the periphery. Following our observation, we subsequently revealed a lack of cell surface MHC‐I expression, derived from TAP2 protein deficiency. Our strain, named eightless, has a C to T substitution in exon 5 resulting in a glutamine to stop codon substitution at position 285 in the TAP2 protein. Interestingly, in addition to the expected lack of CD8+ T cell phenotype, eightless mice have a diminished number of macrophages in their peritoneum. Moreover, following peritoneal inflammation, elicited eightless macrophages showed impaired survival both in vivo and ex vivo. Our study describes the first ever TAP2 complete knockout mouse strain and provides a possible explanation for why patients with TAP2 deficiency syndrome present clinical manifestations that would suggest a phagocyte defect rather than a lack of CD8+ T cells.
Commentary: Mapping the young, resilient brain – reflections on Burt et al. (2016)
Authors: Shaw Philip 
Published: November 2016

The resilience of many children in the face of adversity has long been a research focus. The study by Burt et al. delineates the neuroanatomy of resilience, using in vivo magnetic resonance images acquired on 1,800 youth. They find that resilient youth had a larger right lateral prefrontal cortex compared to youth who either lacked resilience or did not experience adversity. The size of the right lateral prefrontal cortex was further associated with a likelihood of a maladaptive problem of alcohol use. These findings implicate high‐order regulatory processes supported by the right lateral prefrontal cortex as pivotal in resilience. The study also sets the stage for exploring how neuroimaging data, combined with behavioral and genomic information might be used to assess treatment efficacy and identify children who need therapeutic interventions to boost their resilience.
Local adaptation of reproductive performance during thermal stress
Authors: Porcelli D. , Gaston K. J. , Butlin R. K. , Snook R. R. 
Published: November 2016

AbstractConsiderable evidence exists for local adaptation of critical thermal limits in ectotherms following adult temperature stress, but fewer studies have tested for local adaptation of sublethal heat stress effects across life‐history stages. In organisms with complex life cycles, such as holometabolous insects, heat stress during juvenile stages may severely impact gametogenesis, having downstream consequences on reproductive performance that may be mediated by local adaptation, although this is rarely studied. Here, we tested how exposure to either benign or heat stress temperature during juvenile and adult stages, either independently or combined, influences egg‐to‐adult viability, adult sperm motility and fertility in high‐ and low‐latitude populations ofDrosophila subobscura. We found both population‐ and temperature‐specific effects on survival and sperm motility; juvenile heat stress decreased survival and subsequent sperm motility and each trait was lower in the northern population. We found an interaction between population and temperature on fertility following application of juvenile heat stress; although fertility was negatively impacted in both populations, the southern population was less affected. When the adult stage was also subject to heat stress, the southern population exhibited positive carry‐over effects whereas the northern population's fertility remained low. Thus, the northern population is more susceptible to sublethal reproductive consequences following exposure to juvenile heat stress. This may be common in other organisms with complex life cycles and current models predicting population responses to climate change, which do not take into account the impact of juvenile heat stress on reproductive performance, may be too conservative.
Assessment of self‐produced PCR methods for the detection of Toxoplasma gondii DNA in meat
Authors: Jiang Shoufu , He Yanyan , Zhang Yaoguang , Zhang Xiaoping , Jiang Li , Wang Zhenyu , Zhu Qian , Ma Xiaojiang 
Published: November 2016

AbstractThe objective was to develop a highly sensitive and specific polymerase chain reaction (PCR) method for the detection of Toxoplasma gondii DNA in meat. To increase the capacity for the processing of meat samples by improving DNA extraction, four PCR assays were developed and compared using the B1 gene as the target gene for the detection of T. gondii DNA in meat. The results show high specificity and reproducibility for all four PCR assays in clearly detecting DNA samples from four strains of T. gondii while producing no amplification signal for ten other parasites or in healthy meat. Three real‐time quantitative PCR assays were 10‐fold more sensitive than the conventional PCR assay, with a detection limit of 4.5 × 101 copies of T. gondii DNA being equivalent to 1.3 bradyzoites. The most sensitive method was SYBR Green I qPCR because it uses special fluorescent dyes directly binding to the amplified double‐stranded DNA sequences and the fluorescence signal is proportional to the amount of PCR products that observed by nearly 1,000‐fold increase in fluorescence intensity. This assay has another advantages over other PCR assays, including less expense (without probe), ease of operation and quicker operation of the test.Practical applicationsThe traditional method for detecting T. gondii in meat samples involves the use of a bioassay that is laborious, time‐consuming and not sensitive. The SYBR Green I qPCR assay developed in this study provides a rapid, sensitive, and specific technique and is applicable to surveillance measures for foodborne toxoplasmosis pathogens in meat or meat products as an alternative detection method.