bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of incidental colorectal pathology on positron emission tomography/computed tomography
Authors: Mui Milton , Akhurst Timothy , Warrier Satish K. , Lynch A. Craig , Heriot Alexander G.
Published: September 2016

Background

Positron emission tomography/computed tomography (PET/CT) is an important modality in cancer imaging. With its increasing availability and use, it is not uncommon to detect incidental focal colorectal
18F‐FDG uptake which poses a diagnostic challenge, as they may be associated with malignant or pre‐malignant colorectal lesions. The aim of our study is to determine the proportion of these findings which represents true pathology.

Methods

Patients with incidental focal colorectal
18F‐FDG uptake on PET/CT who subsequently underwent colonoscopy between January 2002 to September 2013 were identified from a prospective database in a tertiary referral centre. PET/CT results were correlated with colonoscopy and pathology results in these patients. Positive predictive values (PPVs) and 95% confidence intervals (CIs) of PET/CT in the detection of incidental colorectal pathology were calculated.

Results

A total of 148 patients (92 men and 56 women), with a mean age 73 years (range of 36 to 93 years) were included in the study. A total of 170 foci of colorectal
18F‐FDG uptake were detected on PET/CT. Of these, 101 foci corresponded to a malignant or pre‐malignant lesion (PPV 59%; 95% CI: 52–67%). On a per‐patient analysis, 93 patients had at least one focus of colorectal
18F‐FDG uptake which corresponded to a pre‐malignant or malignant lesion (PPV 63%; 95% CI: 54–71%).

Conclusion

Focal colorectal
18F‐FDG uptake on PET/CT is associated with a significant proportion of malignant or pre‐malignant lesions. Further evaluation with colonoscopy is recommended.
Transition zone pull‐through in Hirschsprung's disease: a tertiary hospital experience
Authors: Ghosh Dhruva N. , Liu Yingrui , Cass Daniel T. , Soundappan Soundappan S. V.
Published: September 2016

Background

Pull‐through of ganglionic bowel is essential for successful treatment of Hirschsprung's disease. We studied the incidence of transition zone pull‐through in our institution and compared its outcome with ganglionic bowel pull‐through.

Methods

Children who underwent Soave's pull‐through for Hirschsprung's disease from January 2005 to November 2012 were studied. Patients were divided into two groups: ganglionic bowel pull‐throughs (Group 1) and transition zone pull‐throughs (Group 2). Demographics, presentations, surgical procedure, post‐operative results and complications including redo procedures were recorded and reviewed along with histopathology reports.

Results

Fifty patients underwent Soave's pull‐through for Hirschsprung's disease in our group. The median age at surgery was 13.5 days in Group 1 and 22.5 days in Group 2. Transition zone pull‐through occurred in eight children (16%). Transition zone pull‐through was attributed to errors in histologic interpretation (n = 5), sampling (n = 2) and surgical technique (n = 1). The transition zone was significantly longer in Group 2 (P = 0.002). Constipation and enterocolitis were the main complications needing therapy. One child in Group 2 required surgery for adhesive intestinal obstruction.

Conclusions

The length of the transition zone in children with transition zone pull‐through was significantly longer. Though our children with transition zone pull‐through did not require redo surgery the possibility of redo surgery remains. Transition zone pull‐through should still be considered an error and should be prevented.
Pilot manikin study showed that a supraglottic airway device improved simulated neonatal ventilation in a low‐resource setting
Authors: Pejovic Nicolas J. , Trevisanuto Daniele , Nankunda Jolly , Tylleskär Thorkild
Published: September 2016

Aim

We compared the performance of personnel in a low‐resource setting when they used the I‐gel cuffless neonatal laryngeal mask or a face mask on a neonatal airway management manikin.

Methods

At Mulago Hospital, Uganda, 25 doctors, nurses and midwives involved in neonatal resuscitation were given brief training with the I‐gel and face mask. Then, every participant was observed positioning both devices on three consecutive occasions. The success rate and insertion times leading to effective positive pressure ventilation (PPV) were recorded. Participants rated the perceived efficiency of the devices using a five‐point Likert scale.

Results

The I‐gel achieved a 100% success rate on all three occasions, but the face mask was significantly less effective in achieving effective PPV and the failure rates at the first, second and third attempts were 28%, 8% and 20%, respectively. The perceived efficiency of the devices was significantly superior for the I‐gel (4.7 ± 0.4) than the face mask (3.3 ± 0.8).

Conclusion

The I‐gel was more effective than the face mask in establishing PPV in the manikin, and user satisfaction was higher. These encouraging manikin data could be a stepping stone for clinical research on the use of the I‐gel for neonatal resuscitation in low‐resource settings.
Development of somatosensory‐evoked potentials in foetal sheep: effects of betamethasone
Authors: Anegroaie P. , Frasch M. G. , Rupprecht S. , Antonow‐Schlorke I. , Müller T. , Schubert H. , Witte O. W. , Schwab M.
Published: September 2016

Aim

Antenatal glucocorticoids are used to accelerate foetal lung maturation in babies threatened with premature labour. We examined the influence of glucocorticoids on functional and structural maturation of the central somatosensory pathway in foetal sheep. Somatosensory‐evoked potentials (SEP) reflect processing of somatosensory stimuli. SEP latencies are determined by afferent stimuli transmission while SEP amplitudes reveal cerebral processing.

Methods

After chronic instrumentation of foetal sheep, mothers received saline (n = 9) or three courses of betamethasone (human equivalent dose of 2 × 110 μg kg−1 betamethasone i.m. 24 h apart, n = 12) at 0.7, 0.75 and 0.8 of gestational age. Trigeminal SEP were evoked prior to, 4 and 24 h after each injection and at 0.8 of gestational age before brains were histologically processed.

Results

Somatosensory‐evoked potentials were already detectable at 0.7 of gestation age. The early and late responses N20 and N200 were the only reproducible peaks over the entire study period. With advancing gestational age, SEP latencies decreased but amplitudes remained unchanged. Acutely, betamethasone did not affect SEP latencies and amplitudes 4 and 24 h following administration. Chronically, betamethasone delayed developmental decrease in the N200 but not N20 latency by 2 weeks without affecting amplitudes. In parallel, betamethasone decreased subcortical white matter myelination but did not affect network formation and synaptic density in the somatosensory cortex.

Conclusion

Somatosensory stimuli are already processed by the foetal cerebral cortex at the beginning of the third trimester. Subsequent developmental decrease in SEP latencies suggests ongoing maturation of afferent sensory transmission. Antenatal glucocorticoids affect structural and functional development of the somatosensory system with specific effects at subcortical level.
The fundamental role of ecological feedback mechanisms for the adaptive management of seagrass ecosystems – a review
Authors: Maxwell Paul S. , Eklöf Johan S. , van Katwijk Marieke M. , O'Brien Katherine R. , de la Torre‐Castro Maricela , Boström Christoffer , Bouma Tjeerd J. , Krause‐Jensen Dorte , Unsworth Richard K. F. , van Tussenbroek Brigitta I. , van der Heide Tjisse
Published: September 2016

Seagrass meadows are vital ecosystems in coastal zones worldwide, but are also under global threat. One of the major hurdles restricting the success of seagrass conservation and restoration is our limited understanding of ecological feedback mechanisms. In these ecosystems, multiple, self‐reinforcing feedbacks can undermine conservation efforts by masking environmental impacts until the decline is precipitous, or alternatively they can inhibit seagrass recovery in spite of restoration efforts. However, no clear framework yet exists for identifying or dealing with feedbacks to improve the management of seagrass ecosystems. Here we review the causes and consequences of multiple feedbacks between seagrass and biotic and/or abiotic processes. We demonstrate how feedbacks have the potential to impose or reinforce regimes of either seagrass dominance or unvegetated substrate, and how the strength and importance of these feedbacks vary across environmental gradients. Although a myriad of feedbacks have now been identified, the co‐occurrence and likely interaction among feedbacks has largely been overlooked to date due to difficulties in analysis and detection. Here we take a fundamental step forward by modelling the interactions among two distinct above‐ and belowground feedbacks to demonstrate that interacting feedbacks are likely to be important for ecosystem resilience. On this basis, we propose a five‐step adaptive management plan to address feedback dynamics for effective conservation and restoration strategies. The management plan provides guidance to aid in the identification and prioritisation of likely feedbacks in different seagrass ecosystems.
Upregulation of programmed cell death ligand 1 promotes resistance response in non‐small‐cell lung cancer patients treated with neo‐adjuvant chemotherapy
Authors: Zhang Panpan , Ma Yuanyuan , Lv Chao , Huang Miao , Li Mingzhen , Dong Bin , Liu Xijuan , An Guo , Zhang Wenlong , Zhang Jianzhi , Zhang Liyi , Zhang Shanyuan , Yang Yue
Published: September 2016

To assess the association of the programmed cell death ligand 1 (PD‐L1) with cisplatin‐based neo‐adjuvant chemotherapy (NAC) response, we investigated the level of PD‐L1 and found increased PD‐L1 expression in chemo‐resistant tumors compared with chemo‐sensitive tumors according to RNA‐Seq analysis. In a cohort of 92 patients with NAC, the positive staining of PD‐L1 was correlated with TNM stage, lower sensitive‐response rates and shorter overall survival rates. In another 30 paired tumor specimens pre‐ and post‐chemotherapy, the patients with high PD‐L1 expression post‐chemotherapy had a worse outcome and higher stable disease rate. CD8+ tumor‐infiltrating lymphocytes were found to be related to chemosensitive response and better prognosis and negative PD‐L1 expression. Furthermore, in two patient‐derived xenograft models and cell lines A549 and PC‐9, cisplatin upregulated PD‐L1 expression, and the enhancement of PD‐L1 in cancer cell lines was in a drug dose‐dependent manner. Moreover, the depletion of PD‐L1 significantly reduced cisplatin resistance. When phosphatidylinositol 3‐kinase/protein kinase B signaling was inhibited by corresponding inhibitors, PD‐L1 expression was downregulated and apoptosis was upregulated in the cisplatin‐treated cancer cells. These results suggest that the upregulation of PD‐L1 promotes a resistance response in lung cancer cells that might be through activation of the phosphatidylinositol 3‐kinase/protein kinase B pathway and suppression of tumor‐infiltrating lymphocytes. The high expression of PD‐L1 after NAC could be an indication of therapeutic resistance and poor prognosis in patients with non‐small‐cell lung cancer.
Adverse effects of voriconazole: Over a decade of use
Authors: Levine Miriam T. , Chandrasekar Pranatharthi H.
Published: September 2016

Voriconazole use has increased since the drug's introduction in 2002, and new and unique adverse effects are emerging as patients undergo prolonged therapy. Most concerning is the increased risk of cutaneous malignancies, primarily squamous cell carcinoma (SCC); this risk is duration dependent and the associated malignancies tend to be more aggressive and multifocal. Voriconazole is also associated with phototoxicity (which may be a precursor to malignancy), periostitis, hallucinations and encephalopathy, peripheral neuropathy, alopecia, nail changes, hyponatremia, and other adverse effects. Some toxicities (neuropsychiatric and gastrointestinal including hepatic) are seen in clear association with supratherapeutic serum voriconazole levels; thus, careful monitoring of voriconazole levels is a critical component of safe drug use. Guidelines for screening for adverse effects after long‐term voriconazole use may be beneficial and need to be established.
Carbon sources and trophic structure in a macrophyte‐dominated polyculture pond assessed by stable‐isotope analysis
Authors: Mao Zhi G. , Gu Xiao H. , Zeng Qing F. , Chen Hui H.
Published: September 2016

Freshwater polyculture systems should efficiently utilise natural food resources and pond habitats with the consequent effects of reducing costs and increasing productivity. However, understanding of the primary carbon sources and food web within polyculture ponds, and especially macrophyte‐dominated ponds, remains limited.

Stable‐isotope analysis was used to identify the main carbon sources and describe the trophic patterns of freshwater fauna in a polyculture pond around Lake Gucheng, China. An isotope mixing model (SIAR) was also used to estimate the relative contribution of four basal sources (suspended particulate organic matter [SPOM], sedimentary organic matter [SOM], macrophytes and epiphytes) to invertebrates and different fish trophic groups.

Basal resources showed distinct δ13C values, ranging from −24.3 to −20.5‰, which allowed for a powerful discrimination of carbon sources. Consumers were also well separated in δ13C (−24.0 to −20.0‰ for invertebrates and −24.4 to −18.9‰ for fish), suggesting considerable differences in ultimate sources of carbon. Results from the SIAR model indicated that epiphytes were the most important carbon sources for crustaceans, herbivorous fish, omnivorous fish and piscivorous fish, while SPOM made the highest contribution to zooplankton, chironomids, molluscs, annelids, planktivorous fish and benthivorous fish.

Mean δ15N values, combined with calculated food source contributions, were used to elucidate the food‐web structure of this polyculture pond, which suggested that carbon fixed by primary producers could be transported up the food chain to piscivorous fish through four main trophic pathways: one based mainly on SPOM, one on both SPOM and SOM, one on SPOM, SOM, macrophytes and epiphytes, and one based on both macrophytes and epiphytes.

Our results emphasised the trophic importance of epiphytes on submerged macrophytes, a key component in the polyculture ponds, for the main culture species: Chinese mitten crab (Eriocheir sinensis: Varunidae), freshwater shrimp (Macrobrachium nipponense: Palaemonidae), and high‐value piscivorous fish. This study also revealed the high level of complexity of polyculture pond food webs, and suggests that a diversity of major trophic pathways may be a characteristic of macrophyte‐dominated aquatic ecosystems.
Strategic Renewal: Past Research, Theoretical Tensions and Future Challenges
Authors: Schmitt Achim , Raisch Sebastian , Volberda Henk W.
Published: September 2016

Strategic renewal has become a prominent theme in a variety of organization and management research domains in recent years. It refers to the process that allows organizations to alter their path dependence by transforming their strategic intent and capabilities. With contributions from an increasing range of theoretical perspectives and research contexts, the strategic renewal literature has become fragmented and lacks common definitions and conceptual clarity, which prevent cross‐fertilization and harm further development. This study systematically reviews the various literature streams on strategic renewal to provide a more integrative perspective. The authors identify three key theoretical tensions at the heart of strategic renewal research, namely learning vs. resource, induced vs. autonomous, and co‐alignment vs. co‐creation. By exploring these key tensions, the authors define strategic renewal's conceptual core, identify gaps in the past literature, and provide guidance for future research.
Purchases, Penalties, and Power: The Relationship Between Earnings and Housework
Authors: Carlson Daniel L. , Lynch Jamie L.
Published: September 2016

Studies examining the association of housework with earnings have not tested for causal directionality despite competing theories about causal ordering. Autonomy theory and the relative resources, gender display, and gender deviance neutralization hypotheses suggest personal and relative earnings affect time in housework, whereas human capital theory implies the opposite. Using data from N = 3,719 continuously married couples in Waves 1 and 2 of the National Survey of Families and Households and structural equation modeling, the authors found that wives' personal earnings and housework are reciprocally related; her earnings have a stronger effect on housework than vice versa. For husbands, time in routine housework affects earnings only. The authors observed little evidence that relative earnings affect husbands' or wives' housework time; rather, they identified a significant effect of housework on one's share of couples' earnings. These results support autonomy theory for wives and a human capital perspective for both spouses.
What we use is not what we know: environmental predictors in plant distribution models
Authors: Mod Heidi K. , Scherrer Daniel , Luoto Miska , Guisan Antoine
Published: September 2016

Aims

The choice of environmental predictor variables in correlative models of plant species distributions (hereafter SDMs) is crucial to ensure predictive accuracy and model realism, as highlighted in multiple earlier studies. Because variable selection is directly related to a model's capacity to capture important species' environmental requirements, one would expect an explicit prior consideration of all ecophysiologically meaningful variables. For plants, these include temperature, water, soil nutrients, light, and in some cases, disturbances and biotic interactions. However, the set of predictors used in published correlative plant SDM studies varies considerably. No comprehensive review exists of what environmental predictors are meaningful, available (or missing) and used in practice to predict plant distributions. Contributing to answer these questions is the aim of this review.

Methods

We carried out an extensive, systematic review of recently published plant SDM studies (years 2010–2015; n = 200) to determine the predictors used (and not used) in the models. We additionally conducted an in‐depth review of SDM studies in selected journals to identify temporal trends in the use of predictors (years 2000–2015; n = 40).

Results

A large majority of plant SDM studies neglected several ecophysiologically meaningful environmental variables, and the number of relevant predictors used in models has stagnated or even declined over the last 15 yr.

Conclusions

Neglecting ecophysiologically meaningful predictors can result in incomplete niche quantification and can thus limit the predictive power of plant SDMs. Some of these missing predictors are already available spatially or may soon become available (e.g. soil moisture). However, others are not yet easily obtainable across whole study extents (e.g. soil pH and nutrients), and their development should receive increased attention. We conclude that more effort should be made to build ecologically more sound plant SDMs. This requires a more thorough rationale for the choice of environmental predictors needed to meet the study goal, and the development of missing ones. The latter calls for increased collaborative effort between ecological and geo‐environmental sciences.
Preservice teachers' in‐the‐moment teaching decisions in reading
Authors: Griffith Robin
Published: September 2016

This study examines the types of in‐the‐moment teaching decisions 97 preservice teachers made while teaching reading and how their growing bodies of teacher knowledge influenced their abilities to think, know, feel and act like a teacher (Feiman‐Nemser,). Findings indicated that the teacher educator's use of “metacognitive decision‐making” to promote a culture of identifying, drawing attention to, reflecting on and evaluating teaching decisions influenced the preservice teachers' abilities to think, know, feel and act like a teacher. These findings have implications for teacher education and for those who support novice teachers.
Minimal cytosolic iron‐sulfur cluster assembly machinery of Giardia intestinalis is partially associated with mitosomes
Authors: Pyrih Jan , Pyrihová Eva , Kolísko Martin , Stojanovová Darja , Basu Somsuvro , Harant Karel , Haindrich Alexander C. , Doležal Pavel , Lukeš Julius , Roger Andrew , Tachezy Jan
Published: September 2016

Iron‐sulfur (Fe‐S) clusters are essential cofactors that enable proteins to transport electrons, sense signals, or catalyze chemical reactions. The maturation of dozens of Fe‐S proteins in various compartments of every eukaryotic cell is driven by several assembly pathways. The ubiquitous cytosolic Fe‐S cluster assembly (CIA) pathway, typically composed of eight highly conserved proteins, depends on mitochondrial Fe‐S cluster assembly (ISC) machinery. Giardia intestinalis contains one of the smallest eukaryotic genomes and the mitosome, an extremely reduced mitochondrion. Because the only pathway known to be retained within this organelle is the synthesis of Fe‐S clusters mediated by ISC machinery, a likely function of the mitosome is to cooperate with the CIA pathway. We investigated the cellular localization of CIA components in G. intestinalis and the origin and distribution of CIA‐related components and Tah18‐like proteins in other Metamonada. We show that orthologs of Tah18 and Dre2 are missing in these eukaryotes. In Giardia, all CIA components are exclusively cytosolic, with the important exception of Cia2 and two Nbp35 paralogs, which are present in the mitosomes. We propose that the dual localization of Cia2 and Nbp35 proteins in Giardia might represent a novel connection between the ISC and the CIA pathways.
Estimating resource preferences of a native bumblebee: the effects of availability and use–availability models on preference estimates
Authors: Harmon‐Threatt Alexandra N. , de Valpine Perry , Kremen Claire
Published: September 2016

Identifying resource preference is considered essential for developing targeted conservation plans but, for many species, questions remain about the best way to estimate preference. Resource preferences for bees are particularly difficult to determine as the resources they collect, nectar and pollen, are challenging to estimate availability and collection. Resources are traditionally measured at the flower or inflorescence level, but these measures of availability do not correspond to the resources actually used by bees. Additionally, it is unclear as to whether common models including availability are appropriate for bees which may target resources regardless of available quantities. Here we first compare two common hypotheses of resource use – the ‘random use hypothesis’ and the ‘linear preferences hypothesis’ – using three different measures of availability (pollen, flower and inflorescence) – to determine if one measure of availability was better for understanding bee pollen use. Next, the superior model using availability was compared to a novel model of bee pollen use the ‘target use hypothesis’. This model assumes that bees target some resources regardless of how much of each resource is available (but assuming resources are present at a site), and thus models preference without availability data. Of the models including availability, the linear preference model using inflorescence availability best explained the pollen use data. This suggests that bumblebee pollen use is non‐random and that cues to identify and locate resources (i.e. display size and quantity) may be more important than the quantity of the resource available (i.e. pollen availability). Additionally, in most cases the target use model explained the data equal to or better than the other models suggesting bee resource use may be better modeled without measured availability data compared to linear models. These results could be important for expanding resource use analysis of bees that are difficult to quantify availability.
The priority of prediction in ecological understanding
Authors: Houlahan Jeff E. , McKinney Shawn T. , Anderson T. Michael , McGill Brian J.
Published: September 2016

The objective of science is to understand the natural world; we argue that prediction is the only way to demonstrate scientific understanding, implying that prediction should be a fundamental aspect of all scientific disciplines. Reproducibility is an essential requirement of good science and arises from the ability to develop models that make accurate predictions on new data. Ecology, however, with a few exceptions, has abandoned prediction as a central focus and faces its own crisis of reproducibility. Models are where ecological understanding is stored and they are the source of all predictions – no prediction is possible without a model of the world. Models can be improved in three ways: model variables, functional relationships among dependent and independent variables, and in parameter estimates. Ecologists rarely test to assess whether new models have made advances by identifying new and important variables, elucidating functional relationships, or improving parameter estimates. Without these tests it is difficult to know if we understand more today than we did yesterday. A new commitment to prediction in ecology would lead to, among other things, more mature (i.e. quantitative) hypotheses, prioritization of modeling techniques that are more appropriate for prediction (e.g. using continuous independent variables rather than categorical) and, ultimately, advancement towards a more general understanding of the natural world.

Synthesis

Ecology, with a few exceptions, has abandoned prediction and therefore the ability to demonstrate understanding. Here we address how this has inhibited progress in ecology and explore how a renewed focus on prediction would benefit ecologists. The lack of emphasis on prediction has resulted in a discipline that tests qualitative, imprecise hypotheses with little concern for whether the results are generalizable beyond where and when the data were collected. A renewed commitment to prediction would allow ecologists to address critical questions about the generalizability of our results and the progress we are making towards understanding the natural world.
The effect of coloured overlays and lenses on reading: a systematic review of the literature
Authors: Griffiths Philip G. , Taylor Robert H. , Henderson Lisa M. , Barrett Brendan T.
Published: September 2016

Purpose

There are many anecdotal claims and research reports that coloured lenses and overlays improve reading performance. Here we present the results of a systematic review of this literature and examine the quality of the evidence.

Methods

We systematically reviewed the literature concerning the effect of coloured lenses or overlays on reading performance by searching the PsychInfo, Medline and Embase databases. This revealed 51 published items (containing 54 data sets). Given that different systems are in use for issuing coloured overlays or lenses, we reviewed the evidence under four separate system headings (Intuitive, Irlen, Harris/Chromagen and Other), classifying each published item using the Cochrane Risk of Bias tool.

Results

Although the different colour systems have been subjected to different amounts of scientific scrutiny, the results do not differ according to the system type, or whether the sample under investigation was classified as having visual stress (or a similarly defined condition), reading difficulty, or both. The majority of studies are subject to ‘high’ or ‘uncertain’ risk of bias in one or more key aspects of study design or outcome, with studies at lower risk from bias providing less support for the benefit of coloured lenses/overlays on reading ability. While many studies report improvements with coloured lenses, the effect size is generally small and/or similar to the improvement found with a placebo condition. We discuss the strengths and shortcomings of the published literature and, whilst acknowledging the difficulties associated with conducting trials of this type, offer some suggestions about how future trials might be conducted.

Conclusions

Consistent with previous reviews and advice from several professional bodies, we conclude that the use of coloured lenses or overlays to ameliorate reading difficulties cannot be endorsed and that any benefits reported by individuals in clinical settings are likely to be the result of placebo, practice or Hawthorne effects.
Identification of quantitative trait loci controlling soybean seed weight in recombinant inbred lines derived from PI 483463 (Glycine soja) × ‘Hutcheson’ (G. max)
Authors: Kulkarni Krishnanand P. , Kim Minsu , Shannon J. Grover , Lee Jeong‐Dong
Published: September 2016

The objective of this study was to identify quantitative trait loci (QTLs) controlling 100‐seed weight in soybean using 188 recombinant inbred lines (RIL) derived from a cross of PI 483463 and ‘Hutcheson’. The parents and RILs were grown for 4 years (2010–2013), and mature, dry seeds were used for 100‐seed weight measurement. The variance components of genotype (a), environment (e) and a × e interactions for seed weight were highly significant. The QTL analysis identified 14 QTLs explaining 3.83–12.23% of the total phenotypic variation. One of the QTLs, qSW17‐2, was found to be the stable QTL, being identified in all the environments with high phenotypic variation as compared to the other QTLs. Of the 14 QTLs, 10 QTLs showed colocalization with the seed weight QTLs identified in earlier reports, and four QTLs, qSW5‐1, qSW14‐1, qSW15‐1 and qSW15‐2, found to be the novel QTLs. A two‐dimensional genome scan revealed 11 pairs of epistatic QTLs across 11 chromosomes. The QTLs identified in this study may be useful in genetic improvement of soybean seed weight.
An Accuracy Based Approach to Higher Order Evidence
Authors: Schoenfield Miriam
Published: September 2016

The aim of this paper is to apply the accuracy based approach to epistemology to the case of higher order evidence: evidence that bears on the rationality of one's beliefs. I proceed in two stages. First, I show that the accuracy based framework that is standardly used to motivate rational requirements supports steadfastness—a position according to which higher order evidence should have no impact on one's doxastic attitudes towards first order propositions. The argument for this will require a generalization of an important result by Greaves and Wallace for the claim that conditionalization maximizes expected accuracy. The generalization I provide will, among other things, allow us to apply the result to cases of self‐locating evidence. In the second stage, I develop an alternative framework. Very roughly, what distinguishes the traditional approach from the alternative one is that, on the traditional picture, we're interested in evaluating the expected accuracy of conforming to an update procedure. On the alternative picture that I develop, instead of considering how good an update procedure is as a plan to conform to, we consider how good it is as a plan to make. I show how, given the use of strictly proper scoring rules, the alternative picture vindicates calibrationism: a view according to which higher order evidence should have a significant impact on our beliefs. I conclude with some thoughts about why higher order evidence poses a serious challenge for standard ways of thinking about rationality.
Estimating Whole-Brain Dynamics by Using Spectral Clustering
Authors: Cribben Ivor , Yu Yi
Published: September 2016

The estimation of time varying networks for functional magnetic resonance imaging data sets is of increasing importance and interest. We formulate the problem in a high dimensional time series framework and introduce a data-driven method, namely network change points detection, which detects change points in the network structure of a multivariate time series, with each component of the time series represented by a node in the network. Network change points detection is applied to various simulated data and a resting state functional magnetic resonance imaging data set. This new methodology also allows us to identify common functional states within and across subjects. Finally, network change points detection promises to offer a deep insight into the large-scale characterizations and dynamics of the brain.
Bayesian Modelling of Dupuytren Disease by Using Gaussian Copula Graphical Models
Authors: Mohammadi Abdolreza , Abegaz Fentaw , Heuvel Edwin , Wit Ernst C.
Published: September 2016

Dupuytren disease is a fibroproliferative disorder with unknown aetiology that often progresses and eventually can cause permanent contractures of the fingers affected. We provide a computationally efficient Bayesian framework to discover potential risk factors and investigate which fingers are jointly affected. Our Bayesian approach is based on Gaussian copula graphical models, which provide a way to discover the underlying conditional independence structure of variables in multivariate data of mixed types. In particular, we combine the semiparametric Gaussian copula with extended rank likelihood to analyse multivariate data of mixed types with arbitrary marginal distributions. For structural learning, we construct a computationally efficient search algorithm by using a transdimensional Markov chain Monte Carlo algorithm based on a birth–death process. In addition, to make our statistical method easily accessible to other researchers, we have implemented our method in C++ and provide an interface with R software as an R package BDgraph, which is freely available from http://CRAN.R-project.org/package=BDgraph.
A Semi‐parametric Transformation Frailty Model for Semi‐competing Risks Survival Data
Authors: Jiang Fei , Haneuse Sebastien
Published: August 2016

In the analysis of semi‐competing risks data interest lies in estimation and inference with respect to a so‐called non‐terminal event, the observation of which is subject to a terminal event. Multi‐state models are commonly used to analyse such data, with covariate effects on the transition/intensity functions typically specified via the Cox model and dependence between the non‐terminal and terminal events specified, in part, by a unit‐specific shared frailty term. To ensure identifiability, the frailties are typically assumed to arise from a parametric distribution, specifically a Gamma distribution with mean 1.0 and variance, say, σ2. When the frailty distribution is misspecified, however, the resulting estimator is not guaranteed to be consistent, with the extent of asymptotic bias depending on the discrepancy between the assumed and true frailty distributions. In this paper, we propose a novel class of transformation models for semi‐competing risks analysis that permit the non‐parametric specification of the frailty distribution. To ensure identifiability, the class restricts to parametric specifications of the transformation and the error distribution; the latter are flexible, however, and cover a broad range of possible specifications. We also derive the semi‐parametric efficient score under the complete data setting and propose a non‐parametric score imputation method to handle right censoring; consistency and asymptotic normality of the resulting estimators is derived and small‐sample operating characteristics evaluated via simulation. Although the proposed semi‐parametric transformation model and non‐parametric score imputation method are motivated by the analysis of semi‐competing risks data, they are broadly applicable to any analysis of multivariate time‐to‐event outcomes in which a unit‐specific shared frailty is used to account for correlation. Finally, the proposed model and estimation procedures are applied to a study of hospital readmission among patients diagnosed with pancreatic cancer.
HLA‐B*15:388, a novel variant of HLA‐B*15, discovered in a Taiwanese individual
Authors: Yang K. L. , Lin P. Y.
Published: September 2016

One nucleotide replacement at residue 47 of HLA‐B*15:18:01:01 results in a new allele, HLA‐B*15:388.
Assessing the impact of defining a global priority research agenda to address HIV‐associated tuberculosis
Authors: Odone Anna , Matteelli Alberto , Chiesa Valentina , Cella Paola , Ferrari Antonio , Pezzetti Federica , Signorelli Carlo , Getahun Haileyesus
Published: September 2016

Objectives

In 2010, the WHO issued 77 priority research questions (PRQs) to address HIV‐associated TB. Objective of the this study was to assess the impact of defining the research agenda in stimulating and directing research around priority research questions.

Methods

We used number and type of scientific publications as a proxy to quantitatively assess the impact of research agenda setting. We conducted 77 single systematic reviews – one for every PRQ – building 77 different search strategies using PRQs’ keywords. Multivariate logistic regression models were applied to assess the quantity and quality of research produced over time and accounting for selected covariates.

Results

In 2009–2015, PRQs were addressed by 1631 publications (median: 11 studies published per PRQ, range 1–96). The most published area was ‘Intensified TB case finding’ (median: 23 studies/PRQ, range: 2–74). The majority (62.1%, n = 1013) were published as original studies, and more than half (58%, n = 585) were conducted in the African region. Original studies’ publication increased over the study period (P trend = <0.001). They focused more on the ‘Intensified TB case finding’ (OR = 2.17, 95% CI: 1.56–2.93) and ‘Drug‐resistant TB and HIV infection’ (OR = 2.12, 95% CI: 1.47–3.06) areas than non‐original studies. Original studies were published in journals of lower impact factor and received a smaller number of citations than non‐original studies (OR = 0.54, 95% CI: 0.42‐0.69).

Conclusion

The generation of evidence to address PRQs has increased over time particularly in selected fields. Setting a priority research agenda for HIV‐associated TB might have positively influenced the direction and the conduct of research and contributed to the global response to such a major threat to health.
Analysis of exome sequencing data sets reveals structural variation in the coding region of ABO in individuals of African ancestry
Authors: Fox Keolu , Johnsen Jill M. , Coe Bradley P. , Frazar Chris D. , Reiner Alexander P. ,   NHLBI Exome Sequencing Project, Minority Health‐GRID Network, Eichler Evan E. , Nickerson Deborah A.
Published: September 2016

BACKGROUND

ABO is a blood group system of high clinical significance due to the prevalence of ABO variation that can cause major, potentially life‐threatening, transfusion reactions.

STUDY DESIGN AND METHODS

Using multiple large‐scale next‐generation sequence data sets, we demonstrate the application of read‐depth approaches to discover previously unsuspected structural variation (SV) in the ABO gene in individuals of African ancestry.

RESULTS

Our analysis of SV in the ABO gene across 6432 exomes reveals a partial deletion in the ABO gene in 32 individuals of African ancestry that predicts a novel O allele.

CONCLUSION

Our study demonstrates the power that analyses of large‐scale sequencing data, particularly data sets containing underrepresented populations, can provide in identifying novel SVs.
Outcome Following Partial Unilateral Hysterectomy by Standing Flank Approach in Dairy Cattle
Authors: Marchionatti Emma , Nichols Sylvain , Babkine Marie , Lardé Hélène , Lefebvre Réjean , Desrochers André
Published: September 2016

Objective

To describe the clinical findings, surgical treatment, and long‐term outcome of dairy cattle undergoing partial hysterectomy with or without unilateral ovariectomy.

Study Design

Retrospective case series.

Animals

Dairy cattle (n = 7).

Methods

Medical records (June 2007–June 2014) of dairy cattle that had partial hysterectomy with or without ipsilateral ovariectomy were reviewed. Follow‐up data were obtained by telephone interviews with owners and referring veterinarians between 6 months and 7 years following discharge.

Results

Seven dairy cattle met the inclusion criteria. Diagnoses made intra‐ or postoperatively were ovarian abscess with multiorgan adhesions (4 cows), segmental aplasia of the uterus (2 cows), and uterine lymphosarcoma (1 cow). Partial hysterectomy with or without unilateral ovariectomy was performed without surgical complications by standing flank approach. All cows were successfully discharged from the hospital (short‐term prognosis). Five cows became pregnant, and 4 delivered live calves and had a satisfactory productive life without long‐term complications.

Conclusion

Partial hysterectomy by standing flank approach should be considered as a viable treatment option for unilateral ovarian or uterine problems in dairy cattle. Cattle undergoing partial hysterectomy with or without ipsilateral ovariectomy are capable of satisfactory reproduction and milk production after surgery with no short‐ or long‐term complications.
Multi‐Center Retrospective Evaluation of Screw and Polymethylmethacrylate Constructs for Atlantoaxial Fixation in Dogs
Authors: Stout Steele Megan W. , Hodshon Amy W. , Hopkins Andrew L. , Tracy Gaemia M. , Cohen Noah D. , Kerwin Sharon C. , Boudreau C. Elizabeth , Thomas William B. , Mankin Joseph M. , Levine Jonathan M.
Published: September 2016

Objective

To evaluate outcome and adverse events following ventral stabilization of the atlantoaxial (AA) joint in dogs with clinical AA subluxation using screw/polymethymethacrylate (PMMA) constructs in a retrospective, multi‐center cohort study.

Study Design

Historical cohort study.

Animals

35 client‐owned dogs.

Methods

Medical records from 3 institutions were reviewed to identify dogs with AA subluxation treated with ventral screw and PMMA constructs. Data on signalment, pre‐ and postoperative neurologic status, imaging performed, and adverse events were retrieved. Neurologic examination data were abstracted to generate a modified Frankel score at admission, discharge, and re‐examination. Telephone interview of owners >180 days postoperative was conducted.

Results

Thirty‐five dogs with AA subluxation treated with ventral screw/PMMA constructs were included. Most dogs were young (median age 1 year), small breed dogs with acute onset of neurologic signs (median duration 22.5 hours). Most dogs were non‐ambulatory at the time of admission (median modified Frankel score 3). Adverse events were identified in 15/35 dogs including 9 dogs with major adverse events. Four dogs required a second surgery due to vertebral canal violation (n = 2) or implant failure (n = 2). Re‐examination at 4–6 weeks postoperative reported 15/28 dogs with improved neurologic status and 19/28 dogs were ambulatory. Telephone follow‐up was available for 23/35 dogs with 23/23 reported as ambulatory (median follow‐up 390 days).

Conclusions

Ventral application of screw and PMMA constructs for AA subluxation, as described here, is associated with clinical improvement in the majority of dog. Major adverse events are infrequent and the technique is considered relatively safe.
Problemáticas en torno a la gestión de bienes patrimoniales. El caso del patrimonio ferroviario de la localidad de Sundblad (Argentina)
Authors: Pinassi Andrés
Published: September 2016

La localidad de Sundblad, pequeño poblado de la provincia de Buenos Aires (Argentina), surge asociada al ferrocarril, como gran parte de las aglomeraciones del país. En la actualidad, resultado de disímiles procesos económicos y sociales, se evidencia un deterioro de su patrimonio ferroviario. En este contexto, el presente artículo analiza las problemáticas en torno a dichos bienes patrimoniales, su gestión y los actores clave implicados. Como aporte, a modo de reflexión, se presentan determinados lineamientos, contribuyentes a la puesta en valor del sector a escala local.
COLONIALIDAD TERRITORIAL Y EVOLUCIÓN URBANA EN LA HABANA.
Authors: Farrés Delgado Yasser
Published: September 2016

La colonialidad refiere a un conjunto de patrones de poder de larga duración que emergieron con el colonialismo en las Américas pero que se mantienen vivos más allá de los estrictos límites de las administraciones coloniales. Estos patrones se han reflejado en la evolución urbano-arquitectónica de las ciudades poscoloniales del “Sur Global”, que
reproducen modelos arquitectónicos, urbanos y territoriales promovidos desde los países del “Norte Global”. Esto justifica hablar de la existencia de la “colonialidad territorial”, concepto que sirve para replantear la historia urbana. En ese sentido, el artículo mostrará cómo ha ocurrido esta en el caso de La Habana (Cuba) a lo largo de su historia
Aspectos de sostenibilidad de productos no maderables del bosque con uso curativo en el oeste de Pará, Brasil
Authors: May Thomas
Published: September 2016

Se analiza la sostenibilidad de los doce productos no maderables de los bosques amazónicos usados con fines curativos y más vendidos en el mercado local del oeste del estado de Pará, Brasil, en base a observaciones de campo e informaciones bibliográficas, tomando como hilo conductor los factores que inciden, de origen externo versus origen interno, y de impactos en la disponibilidad del recurso versus impactos en los aspectos económicos y sociales. Se concluye que 1) de la destrucción y degradación de los bosques cabe esperar un impacto negativo, a mediano y largo plazo, si bien a corto plazo ayuda a aumentar la oferta de ciertos productos, 2) la venta en el el mercado nacional e internacional les pone ciertas dificultades a los productores extractivistas, que no existen en el mercado local, que además parece ser relativamente estable, 3) las informaciones sobre las características biológicas de las especies indican que ellas en la mayoría de los casos permiten una utilización sostenible de los recursos no maderables por vía extractivista, y 4) en especies con características favorables de reproducción, crecimiento y desarrollo hasta la madurez reproductiva, la plantación a escala local es una estrategia promisora para la reducción de la disponibilidad del recurso, aumentando la productividad de la mano de obra local.  
Conocimiento Ecológico Tradicional de la Biodiversidad de Bosques en una comunidad Matlatzinca, México
Authors: Millán-Rojas Laura , Arteaga-Reyes Tizbe T. , Moctezuma-Pérez Sergio , Velasco-Orozco Juan Jesús , Arzate-Salvador José Concepción
Published: September 2016

La inclusión del conocimiento ecológico tradicional sobre la biodiversidad en la toma de decisiones, es prioritaria para garantizar el respeto de los conocimientos tradicionales y conjuntarlo con los conocimientos científicos para la protección y conservación de los recursos naturales. El objetivo del presente estudio fue documentar el conocimiento ecológico tradicional que posee un grupo indígena del altiplano central de México. Se emplearon metodologías cualitativas destacando observación directa, entrevistas y un taller participativo. Los resultados obtenidos demuestran que hay una continuidad del conocimiento ecológico tradicional basada en aspectos culturales. Este conocimiento junto con las creencias y prácticas de los habitantes influye en los valores doméstico, económico, medicinal, ritual y ontológico otorgados a la flora y fauna de sus bosques.
Transformaciones y conflictos socioambientales en la jach´a puna del sur peruano
Authors: Varas Castrillo Maria Nilda
Published: September 2016

Se estudian las transformaciones y los conflictos socioambientales en la jach ´a puna, en el sur peruano. Los resultados muestran cambios institucionales y ecosistémicos que se aceleraron hace cinco décadas por la intervención del Estado y la incursión de las empresas mineras transnacionales, las cuales utilizan intensivamente el agua, lo que ha provocado que los territorios y las relaciones humanas se complejicen y reconfiguren creando situaciones que podrían tener graves consecuencias para la crianza de camélidos andinos y el aprovisionamiento de agua en las cuencas. Esto genera impactos en la hidrobiodiversidad y en las organizaciones tradicionales de la región.