bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans
Authors: Steinrücken Matthias , Spence Jeffrey P. , Kamm John A. , Wieczorek Emilia , Song Yun S. 
Published: December 2017

AbstractGenetic evidence has revealed that the ancestors of modern human populations outside of Africa and their hominin sister groups, notably the Neanderthals, exchanged genetic material in the past. The distribution of these introgressed sequence-tracts along modern-day human genomes provides insight into the ancient structure and migration patterns of these archaic populations. Furthermore, it facilitates studying the selective processes that lead to the accumulation or depletion of introgressed genetic variation. Recent studies have developed methods to localize these introgressed regions, reporting long regions that are depleted of Neanderthal introgression and enriched in genes, suggesting negative selection against the Neanderthal variants. On the other hand, enriched Neanderthal ancestry in hair- and skin-related genes suggests that some introgressed variants facilitated adaptation to new environments. Here, we present a model-based method calleddiCal-admixand apply it to detect tracts of Neanderthal introgression in modern humans. We demonstrate its efficiency and accuracy through extensive simulations. We use our method to detect introgressed regions in modern human individuals from the 1000 Genomes Project, using a high coverage genome from a Neanderthal individual from the Altai mountains as reference. Our introgression detection results and findings concerning their functional implications are largely concordant with previous studies, and are consistent with weak selection against Neanderthal ancestry. We find some evidence that selection against Neanderthal ancestry was due to higher genetic load in Neanderthals, resulting from small effective population size, rather than Dobzhansky-Müller incompatibilities. Finally, we investigate the role of the X-chromosome in the divergence between Neanderthals and modern humans.
Experimental and computational framework for a dynamic protein atlas of human cell division
Authors: Cai Yin , Hossain M. Julius , Hériché Jean-Karim , Politi Antonio Z. , Walther Nike , Koch Birgit , Wachsmuth Malte , Nijmeijer Bianca , Kueblbeck Moritz , Kavur Marina Martinic , Ladurner Rene , Alexander Stephanie , Peters Jan-Michael , Ellenberg Jan 
Published: December 2017

SUMMARYEssential biological functions, such as mitosis, require tight coordination of hundreds of proteins in space and time. Localization, timing of interactions and changes in cellular structure are all crucial to ensure correct assembly, function and regulation of protein complexes1-4. Live cell imaging can reveal protein distributions and dynamics but experimental and theoretical challenges prevented its use to produce quantitative data and a model of mitosis that comprehensively integrates information and enables analysis of the dynamic interactions between the molecular parts of the mitotic machinery within changing cellular boundaries.To address this, we generated a 4D image data-driven, canonical model of the morphological changes during mitotic progression of human cells. We used this model to integrate dynamic 3D concentration data of many fluorescently knocked-in mitotic proteins, imaged by fluorescence correlation spectroscopy-calibrated microscopy5. The approach taken here in the context of the MitoSys consortium to generate a dynamic protein atlas of human cell division is generic. It can be applied to systematically map and mine dynamic protein localization networks that drive cell division in different cell types and can be conceptually transferred to other cellular functions.
Whatever Happened to Overloaded Government?
Authors: Moran Michael 
Published: December 2017

AbstractAnthony King was, among other things, an outstandingly acute public intellectual. His work on overload and policy fiasco exemplifies this. His original diagnosis in his famous paper of 1975 was deeply pessimistic in character, but subsequent adaptations by government solved many of the original problems arising from dependency relations. These adaptations amounted to the creation of a Madisonian system of regulation that insulated policy makers from democratic pressures. But these adaptations in turn created new difficulties that lie at the root of the analysis in King and Crewe's The Blunders of our Governments, published nearly four decades after King's original classic paper.
GRAPHITE: A graphical environment for scalable in situ video tracking of moving insects
Authors: Rossetti Blair J. , Dynes Travis , Brosi Berry , de Roode Jacobus C. , Kong Jun 
Published: December 2017

Abstract

Methods for measuring animal movement are critical for understanding numerous ecological and evolutionary processes. However, few methods are available for small organisms, and even fewer methods offer consistent individual‐level resolution while remaining affordable, scalable and operable in the field.

We describe a low‐cost animal movement tracking method with a user‐friendly graphical interface, called GRAPHITE. Our automated software can quantify motions of insects by offline video analysis of inexpensive and lightweight human‐readable tags attached to individual insects. The integrated graphical editor provides a full‐featured environment for users to review the generated tracking data and make individual‐ or group‐level edits.

GRAPHITE is a novel video analysis and graphical editing software (Matlab v.9.0.0+) that identifies tags in image frames with a minimal false negative rate, links sequences of corresponding tags into “tracks” for each individual insect, infers the tag identifier, and provides a user‐friendly graphical environment for editing tracking data. Users can either batch process raw video data using the full analysis pipeline or execute GRAPHITE modules independently for a tailored analysis.

We demonstrate the efficacy of the developed software with a specific application to the movement of honey bees at the entrance of hives. However, this system can be easily modified to track individually marked insects of 3 mm and larger. A notable advantage of this method is its ability to provide easy access to individual‐level tracking data using human‐readable tags.
Reintroduction or natural colonization? Using cost‐distance analysis to inform decisions about Rodrigues Island Fody and Warbler reintroductions
Authors: Davies O. A. M. , Huggins A. E. , Begue J. A. , Groombridge J. J. , Jones C. , Norfolk D. , Steward P. , Tatayah V. , Zuël N. , Ewen J. G. 
Published: December 2017

AbstractWhen making decisions about reintroducing a species, practitioners need to consider whether the release site contains habitat suitable for those species, whether past extinction drivers have been remedied and whether reintroduction is the best option for the species to recolonize the release site. These concerns are captured within two paradigms; the habitat and metapopulation paradigms. We use cost‐distance analysis to assess the need for reintroduction of two bird species, Rodrigues Fody and Rodrigues Warbler, to Anse Quitor reserve on Rodrigues Island, testing hypotheses based on these underlying paradigms. Given a lack of detailed field studies of dispersal across the landscape on either species we rely on expert judgment. Our results show that experts believe Rodrigues Fody will naturally colonize Anse Quitor but that Rodrigues Warbler may not, at least within a time frame of 10 years. This information and treatment of expert judgment allows greater justification in reintroduction planning. Our method shows one way to assist in reintroduction decision making in poorly studied systems.
Decidual CD68+HLA‐DR+CD163− M1 macrophages increase in miscarriages with normal fetal chromosome
Authors: Shimada Shigeki , Ebina Yasuhiko , Iijima Norifumi , Deguchi Masashi , Yamada Hideto 
Published: December 2017

ProblemIs an abnormal increase or decrease of M1/M2 macrophages observed in the deciduae of miscarriages with normal fetal chromosome (MN)?Methods of studyDeciduae of 18 MN and 26 miscarriages with abnormal fetal chromosome (MA) were obtained. Additionally, deciduae from 15 women whose pregnancies ended in induced abortions (IA) and endometriums at the mid‐luteal phase from 19 non‐pregnant women endomeriums of mid‐luteal phases (EM) were obtained. Macrophages were analyzed by flow cytometry using monoclonal antibodies for CD68, HLA‐DR, and CD163.ResultsM1 macrophages, defined as CD68+HLA‐DR+CD163− cells, increased in MN compared with MA or IA. M2 macrophages, defined as CD68+HLA‐DR−CD163+ cells, increased in the deciduae of MA and IA compared with EM. However, this increase was not observed in the deciduae of MN.ConclusionOur findings of phenotypic characters of decidual macrophages in MN provide additional evidence that M2 polarization is favorable for the maintenance of early stages of pregnancy.
Postoperative outcomes following cardiac surgery in non‐anaemic iron‐replete and iron‐deficient patients – an exploratory study
Authors: Miles L. F. , Kunz S. A. , Na L. H. , Braat S. , Burbury K. , Story D. A. 
Published: December 2017

SummaryIron deficiency anaemia is strongly associated with poor outcomes after cardiac surgery. However, pre‐operative non‐anaemic iron deficiency (a probable anaemia precursor) has not been comprehensively examined in patients undergoing cardiac surgery, despite biological plausibility and evidence from other patient populations of negative effect on outcome. This exploratory retrospective cohort study aimed to compare an iron‐deficient group of patients undergoing cardiac surgery with an iron‐replete group. Consecutive non‐anaemic patients undergoing elective coronary artery bypass grafting or single valve replacement in our institution between January 2013 and December 2015 were considered for inclusion. Data from a total of 277 patients were analysed, and were categorised by iron status and blood haemoglobin concentration into iron‐deficient (n = 109) and iron‐replete (n = 168) groups. Compared with the iron‐replete group, patients in the iron‐deficient group were more likely to be female (43% vs. 12%, iron‐replete, respectively); older, mean (SD) age 64.4 (9.7) vs. 63.2 (10.3) years; and to have a higher pre‐operative EuroSCORE (median IQR [range]) 3 (2–5 [0–10]) vs. 3 (2–4 [0–9]), with a lower preoperative haemoglobin of 141.6 (11.6) vs. 148.3 (11.7) g.l−1. Univariate analysis suggested that iron‐deficient patients had a longer hospital length of stay (7 (6–9 [2–40]) vs. 7 (5–8 [4–23]) days; p = 0.013) and fewer days alive and out of hospital at postoperative day 90 (83 (80–84 [0–87]) vs. 83 (81–85 [34–86]), p = 0.009). There was no evidence of an association between iron deficiency and either lower nadir haemoglobin or higher requirement for blood products during inpatient stay. After adjusting the model for pre‐operative age, sex, renal function, EuroSCORE and haemoglobin, the mean increase in hospital length of stay in the iron‐deficient group relative to the iron‐replete group was 0.86 days (bootstrapped 95%CI −0.37 to 2.22, p = 0.098). This exploratory study suggests there is weak evidence of an association between non‐anaemic iron deficiency and outcome after cardiac surgery after controlling for potentially confounding variables.
Determination of the optimal programmed intermittent epidural bolus volume of bupivacaine 0.0625% with fentanyl 2 μg.ml−1 at a fixed interval of forty minutes: a biased coin up‐and‐down sequential allocation trial
Authors: Zakus P. , Arzola C. , Bittencourt R. , Downey K. , Ye X. Y. , Carvalho J. C. 
Published: December 2017

SummaryThe optimum time interval for 10 ml boluses of bupivacaine 0.0625% + fentanyl 2 μg.ml−1 as part of a programmed intermittent epidural bolus regimen has been found to be 40 min. This regimen was shown to be effective without the use of supplementary patient‐controlled epidural analgesia boluses in 90% of women during the first stage of labour, although with a rate of sensory block to ice above T6 in 34% of women. We aimed to determine the optimum programmed intermittent epidural bolus volume at a 40 min interval to provide effective analgesia in 90% of women (EV90) during the first stage of labour, without the use of patient‐controlled epidural analgesia. We performed a prospective double‐blind dose‐finding study using the biased coin up‐and‐down sequential allocation method in 40 women. The estimated EV90 was 11.0 (95%CI 10.0–11.7) ml with the isotonic regression method and 10.7 (95%CI 10.3–11.0) ml with the truncated Dixon and Mood method. Overall, 18 women had a sensory block above T6, and 37 women exhibited no motor block. No women required treatment for hypotension. In conclusion, it is not possible to reduce the programmed intermittent epidural bolus volume from 10 ml, used in our current regimen, without compromising the quality of analgesia. Using this regimen, a high proportion of women will develop a sensory block above T6.
Is myocardial repolarization duration associated with repolarization heterogeneity?
Authors: Marill Keith A. , Dorsey Pat , Holmes Anthony , Muthal Ketaki , Miller Emily S. , Xue Joel 
Published: December 2017

BackgroundDispersion of repolarization is theorized as one mechanism by which myocardial repolarization prolongation causes lethal torsades de pointes, (TdP). Our primary purpose was to determine whether prolongation of myocardial repolarization as measured by the heart rate‐corrected J‐to‐T peak interval (JTpkc), is associated with repolarization heterogeneity as measured by transmural dispersion, defined as the median duration from the peak to the end of the T wave (TpTe).MethodsA retrospective cohort study was performed at a single urban tertiary ED from July 2011–September 2012. Inclusion criteria included all consecutive ED patients with ECG based on QTc and QRS intervals. Automated measurements of all intervals were performed. The association of JTpkc with the dependent variable TpTe was assessed after adjustment for QRS and RR interval durations with a multiple linear regression model. A secondary analysis included a similar adjusted assessment of the association of JTpkc with QT dispersion, QTd. Finally, we constructed two multiple regression models to assess the association of clinical causative factors of TdP with TpTe and JTpkc.ResultsEight hundred seventy‐four cases were included: 186 with QTc <500 ms, 118 with QTc ≥500 and QRS ≥120 ms, and 570 with QTc ≥500 and QRS <120 ms. The coefficient for association of JTpkc with TpTe was −0.10 (95%CI −0.15 to −0.05), and for JTpkc with QTd was 0.03 (95% CI −0.01 to 0.06). Clinical causative TdP factors were associated more with JTpkc than TpTe.ConclusionRepolarization duration as measured by JTpkc is not positively associated with dispersion of repolarization as measured by TpTe or QTd. Dispersion of repolarization may not be a critical mechanistic link between QTc prolongation and TdP.
Application of the ISNT rules on retinal nerve fibre layer thickness and neuroretinal rim area in healthy myopic eyes
Authors: Qiu Kunliang , Wang Geng , Lu Xuehui , Zhang Riping , Sun Lixia , Zhang Mingzhi 
Published: December 2017

AbstractPurposeWe determined the applicability of inferior > superior > nasal > temporal (ISNT) rules on retinal nerve fibre layer (RNFL) thickness and rim area and evaluated the impact of various ocular factors on the performance of the ISNT rules in healthy myopic eyes.MethodsA total of 138 eyes from 138 healthy myopic subjects were included in this cross‐sectional observational study. The peripapillary RNFL and optic disc in each eye were imaged with Cirrus HD optical coherence tomography (OCT) and Heidelberg Retina Tomograph II (HRT2), respectively. The performance of the inferior > superior (IS), inferior > superior > nasal > temporal (IST) and ISNT rules on RNFL thickness and rim area was determined and compared between low‐to‐moderate myopia and high myopia. The effects of ocular factors [including axial length, disc area, disc tilt, disc torsion, disc‐fovea angle (DFA) and retina artery angle] on the performance of ISNT rules were evaluated with logistic regression analysis.ResultsThe mean axial length and refractive error were 25.57 ± 1.09 mm (range, 22.52–28.77 mm) and −5.12 ± 2.30 D [range, −9.63 to −0.50 dioptres (D)], respectively. Sixty‐three per cent of the healthy eyes were compliant with the ISNT rule on rim area, while ISNT rule on RNFL thickness was followed in only 11.6% of the included eyes. For rim area, smaller disc area was significantly associated with increased compliance of the IS rule (odds ratio: 0.46, p = 0.039), IST rule (odds ratio: 0.46, p = 0.037) and ISNT rule (odds ratio: 0.44, p = 0.030). For RNFL thickness, greater DFA was significantly associated with increased compliance of the IS and IST rules (odds ratio: 1.30, p < 0.001; odds ratio: 1.19, p = 0.006, respectively).ConclusionIn healthy myopic subjects, 88.4% and 37% of eyes did not comply with the ISNT rule on RNFL thickness and rim area, respectively. Due to significant low compliance in healthy eyes, the ISNT rule and its variants have limited potential utility in diagnosing glaucoma in myopic subjects.
The treatment of postoperative endophthalmitis: should we still follow the endophthalmitis vitrectomy study more than two decades after its publication?
Authors: Grzybowski Andrzej , Turczynowska Magdalena , Kuhn Ferenc 
Published: December 2017

AbstractConducted in the early 1990s Endophthalmitis Vitrectomy Study (EVS) have helped in establishing reasonable guidelines for the management of infectious postoperative endophthalmitis. However at present, more than 20 years after its publication, tremendous progress has been introduced in vitrectomy technology, which now permits the vitreoretinal surgeon to perform surgery more safely, and with better outcomes. Moerover, performing a complete vitreous removal, along with the moving up of the surgical intervention to as early as possible allows the prevention of complications that would limit the functional improvement postoperatively. Thus, it is now highly needed to re‐evaluate the conclusions of the EVS study.
Evaluation of a computerized cognitive behavioural therapy programme, MindWise (2.0), for adults with mild‐to‐moderate depression and anxiety
Authors: Collins Sarah , Byrne Michael , Hawe James , O'Reilly Gary 
Published: December 2017

ObjectivesTo investigate the acceptability and utility of a newly developed computerized cognitive behavioural therapy (cCBT) programme, MindWise (2.0), for adults attending Irish primary care psychology services.MethodAdult primary care psychology service users across four rural locations in Ireland were invited to participate in this study. A total of 60 service users participated in the MindWise (2.0) treatment group and compared to 22 people in a comparison waiting list control group. Participants completed pre‐ and post‐intervention outcome measures of anxiety, depression, and work/social functioning.ResultsAt post‐intervention, 25 of 60 people in the MindWise (2.0) condition had fully completed the programme and 19 of 22 people in the waiting list condition provided time 2 data. Relative to those in the control group, the MindWise (2.0) participants reported significantly reduced symptoms of anxiety and no change in depression or work/social functioning.ConclusionsThe newly developed cCBT programme, MindWise (2.0), resulted in significant improvements on a measure of anxiety and may address some barriers to accessing more traditional face‐to‐face mental health services for adults in a primary care setting. Further programme development and related research appears both warranted and needed to lower programme drop‐out, establish if gains in anxiety management are maintained over time, and support people in a primary care context with depression.Practitioner points

There is a growing evidence base that computerized self‐help programmes can assist in a stepped‐care approach to adult mental health service provision.

These programmes require further development to address issues such as high dropout, the development of equally effective transdiagnostic content, and greater effectiveness in the country of origin.

This study evaluated the acceptability and utility of a brief online CBT programme for adults referred due to anxiety or low mood to primary care psychology services in the national health service in Ireland.

Results indicate that 42% of people completed the programme and experienced a significant reduction in anxiety but not depression and no improvement in work or social adjustment compared to similar adults on a waiting list for services.

This study suggests the programme warrants further development and research and may in time become a useful and suitable intervention within the national health service in Ireland.
Induction of mast cell accumulation by chymase via an enzymatic activity‐ and intercellular adhesion molecule‐1‐dependent mechanism
Authors: Zhang Huiyun , Wang Junling , Wang Ling , Zhan Mengmeng , Li Shigang , Fang Zeman , Xu Ciyan , Zheng Yanshan , He Shaoheng 
Published: December 2017

Background and PurposeChymase is a unique, abundant secretory product of mast cells and a potent chemoattractant for eosinophils, monocytes and neutrophils, but little is known of its influence on mast cell accumulation.Experimental ApproachA mouse peritoneal inflammation model, cell migration assay and flowcytometry analysis, were used to investigate the role of chymase in recruiting mast cells.Key ResultsChymase increased, by up to 5.4‐fold, mast cell numbers in mouse peritoneum. Inhibitors of chymase, heat‐inactivation of the enzyme, sodium cromoglycate and terfenadine, and pretreatment of mice with anti‐intercellular adhesion molecule 1, anti‐L‐selectin, anti‐CD11a and anti‐CD18 antibodies dramatically diminished the chymase‐induced increase in mast cell accumulation. These findings indicate that this effect of chymase is dependent on its enzymatic activity and activation of adhesion molecules. In addition, chymase provoked a significant increase in 5‐HT and eotaxin release (up to 1.8‐ and 2.2‐fold, respectively) in mouse peritoneum. Since 5‐HT, eotaxin and RANTES can induce marked mast cell accumulation, these indirect mechanisms may also contribute to chymase‐induced mast cell accumulation. Moreover, chymase increased the trans‐endothelium migration of mast cells in vitro indicating it also acts as a chemoattractant.Conclusion and ImplicationsThe finding that mast cells accumulate in response to chymase implies further that chymase is a major pro‐inflammatory mediator of mast cells. This effect of chymase, a major product of mast cell granules, suggests a novel self‐amplification mechanism for mast cell accumulation in allergic inflammation. Mast cell stabilizers and inhibitors of chymase may have potential as a treatment of allergic disorders.