bluuebunny/crossref_metadata_2025 huggingface dataset:
The first five years of single-cell cancer genomics and beyond
Authors: Navin Nicholas E.
Published: October 2015

Single-cell sequencing (SCS) is a powerful new tool for investigating evolution and diversity in cancer and understanding the role of rare cells in tumor progression. These methods have begun to unravel key questions in cancer biology that have been difficult to address with bulk tumor measurements. Over the past five years, there has been extraordinary progress in technological developments and research applications, but these efforts represent only the tip of the iceberg. In the coming years, SCS will greatly improve our understanding of invasion, metastasis, and therapy resistance during cancer progression. These tools will also have direct translational applications in the clinic, in areas such as early detection, noninvasive monitoring, and guiding targeted therapy. In this perspective, I discuss the progress that has been made and the myriad of unexplored applications that still lie ahead in cancer research and medicine.
The intersection of microbiome and host at the skin interface: genomic- and metagenomic-based insights
Authors: Grice Elizabeth A.
Published: October 2015

The past two decades have been marked by a surge in research to understand the microbial communities that live in association with the human body, in part stimulated by affordable, high-throughput DNA sequencing technology. In the context of the skin, this Perspective focuses on the current state of genomic- and metagenomic-based host–microbe research and future challenges and opportunities to move the field forward. These include elucidating nonbacterial components of the skin microbiome (i.e., viruses); systematic studies to address common perturbations to the skin microbiome (e.g., antimicrobial drugs, topical cosmetic/hygienic products); improved approaches for identifying potential microbial triggers for skin diseases, including species- and strain-level resolution; and improved, clinically relevant models for studying the functional and mechanistic roles of the skin microbiome. In the next 20 years, we can realistically expect that our knowledge of the skin microbiome will inform the clinical management and treatment of skin disorders through diagnostic tests to stratify patient subsets and predict best treatment modality and outcomes and through treatment strategies such as targeted manipulation or reconstitution of microbial communities.
A vision for ubiquitous sequencing
Authors: Erlich Yaniv
Published: October 2015

Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors—miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors.
Captive Care, Raising, and Breeding of the Veiled Chameleon (Chamaeleo calyptratus)
Authors: Diaz Raul E. , Anderson Christopher V. , Baumann Diana P. , Kupronis Richard , Jewell David , Piraquive Christina , Kupronis Jill , Winter Kristy , Greek Thomas J. , Trainor Paul A.
Published: October 2015

Squamate reptiles comprise approximately one-third of all living amniotes. In most of these species, it is difficult to study gastrulation and neurulation because the embryos are at a late stage of development at the time of oviposition. This is not the case, however, in veiled chameleons (Chamaeleo calyptratus), which are increasingly being used as a model organism to study these and other developmental and evolutionary phenomena. Originating from the Arabian Peninsula, veiled chameleons are arboreal specialists that possess extensive morphological specializations for climbing. They naturally inhabit semitropical habitats, but they also have an almost 30-yr history of being bred in captivity. Veiled chameleons breed readily and do not require a period of cooling to induce the reproductive cycle, and females can produce ∼45–90 eggs multiple times per year. Thus, compared with other reptiles, relatively few animals are needed to maintain a productive breeding colony. Herein, we present the conditions, equipment, and techniques required for proper husbandry and breeding of veiled chameleons within a laboratory environment.
The competitive growth of cubic domains in Ti1–xAlxN films studied by diffraction anomalous near-edge structure spectroscopy
Authors: Pinot Y. , Tuilier M.-H. , Pac M.-J. , Rousselot C. , Thiaudière D.
Published: October 2015

Titanium and aluminium nitride films deposited by magnetron sputtering generally grow as columnar domains made of oriented nanocrystallites with cubic or hexagonal symmetry depending on Al content, which are embedded in more disordered grain boundaries. The substitution of Al atoms for Ti in the cubic lattice of the films improves their resistance to wear and oxidation, allowing their use as protective coatings. TiK-edge X-ray absorption spectroscopy, which probes both crystallized and more disordered grain boundaries, and X-ray diffraction anomalous fine structure, which is sensitive to short- and long-range order within a given crystallized domain, are carried out on a set of Ti1–xAlxN films deposited by magnetron sputtering on Si substrates. Attention is paid to the shape of the pre-edge region, which is sensitive to the symmetry of the site occupied by Ti atoms, either octahedral in face-centred-cubic Ti-rich (TiN, Ti0.54Al0.46N) samples or tetrahedral in hexagonal-close-packed Al-rich (Ti0.32Al0.68N) films. In order to obain information on the titanium environment in the well crystallized areas, subtraction of the smooth part of the energy-dependent structure factor for the Bragg reflections is applied to the pre-edge region of the diffraction anomalous data in order to restore their spectroscopic appearance. A flat pre-edge is related to the typical octahedral environment of Ti atoms for cubic reflections. The difference observed between pre-edge spectra associated with face-centred-cubic 200 and 111 Bragg reflections of Ti0.54Al0.46N is assigned to Ti enrichment of 111 large well ordered domains compared with the more disordered 200 ones. The sharp peak observed in the spectrum recorded from the hexagonal 002 peak of Ti0.32Al0.68N can be regarded as a standard for the pure tetrahedral Ti environment in hexagonal-close-packed nitride.
Comprehensive derivation of bond-valence parameters for ion pairs involving oxygen
Authors: Gagné Olivier Charles , Hawthorne Frank Christopher
Published: October 2015

Published two-body bond-valence parameters for cation–oxygen bonds have been evaluatedviathe root mean-square deviation (RMSD) from the valence-sum rule for 128 cations, using 180 194 filtered bond lengths from 31 489 coordination polyhedra. Values of the RMSD range from 0.033–2.451 v.u. (1.1–40.9% per unit of charge) with a weighted mean of 0.174 v.u. (7.34% per unit of charge). The set of best published parameters has been determined for 128 ions and used as a benchmark for the determination of new bond-valence parameters in this paper. Two common methods for the derivation of bond-valence parameters have been evaluated: (1) fixingBand solving forRo; (2) the graphical method. On a subset of 90 ions observed in more than one coordination, fixingBat 0.37 Å leads to a mean weighted-RMSD of 0.139 v.u. (6.7% per unit of charge), while graphical derivation gives 0.161 v.u. (8.0% per unit of charge). The advantages and disadvantages of these (and other) methods of derivation have been considered, leading to the conclusion that current methods of derivation of bond-valence parameters are not satisfactory. A new method of derivation is introduced, the GRG (generalized reduced gradient) method, which leads to a mean weighted-RMSD of 0.128 v.u. (6.1% per unit of charge) over the same sample of 90 multiple-coordination ions. The evaluation of 19 two-parameter equations and 7 three-parameter equations to model the bond-valence–bond-length relation indicates that: (1) many equations can adequately describe the relation; (2) a plateau has been reached in the fit for two-parameter equations; (3) the equation of Brown & Altermatt (1985) is sufficiently good that use of any of the other equations tested is not warranted. Improved bond-valence parameters have been derived for 135 ions for the equation of Brown & Altermatt (1985) in terms of both the cation and anion bond-valence sums using the GRG method and our complete data set.
Human resources – strength and weakness in protection of intellectual capital
Authors: Olander Heidi , Hurmelinna-Laukkanen Pia , Heilmann Pia
Published: October 2015

Purpose

– Human resources in knowledge intensive industries create the basis for continuing innovation and subsequent firm performance. At the same time, they pose risks for the competitiveness of the firm: unwanted leaking of knowledge and intellectual capital to outsiders exposes firm-critical knowledge, and knowledge leaving with a departing key employee may jeopardise the firm’s projects. The purpose of this paper is to examine how human resource management can serve as a protection mechanism to diminish knowledge leaking and leaving via employees.

Design/methodology/approach

– The authors approach these issues through a case study utilising interview data from 22 interviews within two large research and development intensive firms.

Findings

– Human resources could be seen both as a strength and weakness of a firm with respect to knowledge protection. The findings indicate that there are numerous practices related to commitment, trust, motivation, and sense of responsibility available to deploy to strengthen loyalty and to improve preservation of intellectual capital.

Originality/value

– While human resources management aspects have been widely discussed with regard job profitability and efficiency in generating intellectual capital, their connection to knowledge protection has often been overlooked. This study aims to contribute to this area.
Vatted dreams: neurophilosophy and the politics of phenomenal internalism
Authors: Langlitz Nicolas
Published: October 2015

Despite much social‐scientific work on the neurosciences, little ethnographic and historical attention has been paid to the field of neurophilosophy. Yet anthropologists studying brain research occasionally critique neurophilosophers for reducing the mind to the brain while affirmatively citing philosophers of mind who present the mind as emerging from interactions between brain, body, and environment. This article examines the ostracized camp of so‐called ‘phenomenal internalists’ – neurophilosophers who believe that consciousness can supervene on the brain alone. This ontological commitment is driven by certain existential and political experiences from false awakenings to disenchantment with the counterculture of the 1970s. But it also draws from neuroscientific research on the dreaming brain. The inquiry concludes with a plea to anthropologists to attend to relations of detachment, both social and neural, and to reconsider their own ontological commitment to externalism in the light of dream research.
The artist Carl Abrahams and the cosmopolitan work of centring and peripheralizing the self⋆
Authors: Wardle Huon
Published: October 2015

The article looks at the work and life of Jamaican artist and ‘citizen of the world’ Carl Abrahams. Responding to Gell's argument that art should be thought of as a ‘technology of enchantment’, and to a wider approach that seeks to explain art by reference to cultural context, the article takes Abrahams's ownWeltkenntnis, or world‐knowledge, as its focus. TheWeltkenntnisof an artist, or indeed any person, is often at odds both with their surrounding cultural situation and the technical means they have to express themselves. It is never entirely possible to reduce a particular form of self‐expression either to the wider worldview or to a particular set of technical effects. The article explores the conceptual tensions involved in Abrahams's claims to be a cosmopolitan artist and his work of centring and peripheralizing himself in colonial and postcolonial Jamaica.
Characteristics of the Psidium cattleianum invasion of secondary rainforests
Authors: Tng David Y. P. , Goosem Miriam W. , Paz Claudia P. , Preece Noel D. , Goosem Stephen , Fensham Roderick J. , Laurance Susan G. W.
Published: October 2015

Strawberry guava (Psidium cattleianum) is a shade‐tolerant shrub or small tree invader in tropical and subtropical regions and is considered among the world's top 100 worst invasive species. Studies from affected regions report deleterious effects of strawberry guava invasion on native vegetation. Here we examine the life history demographics and environmental determinants of strawberry guava invasions to inform effective weed management in affected rainforest regions. We surveyed the vegetation of 8 mature rainforest and 33 successional sites at various stages of regeneration in the Australian Wet Tropics and found that strawberry guava invasion was largely restricted to successional forests. Strawberry guava exhibited high stem and seedling densities, represented approximately 8% of all individual stems recorded and 20% of all seedlings recorded. The species also had the highest basal area among all the non‐native woody species measured. We compared environmental and community level effects between strawberry guava‐invaded and non‐invaded sites, and modelled how the species basal area and recruitment patterns respond to these effects. Invaded sites differed from non‐invaded sites in several environmental features such as aspect, distance from intact forest blocks, as well as supported higher grass and herb stem densities. Our analysis showed that invasion is currently ongoing in secondary forests, and also that strawberry guava is able to establish and persist under closed canopies. If left unchecked, strawberry guava invasion will have deleterious consequences for native regenerating forest in the Australian Wet Tropics.
Equine Embryo Sexing and Ultrasonographic Foetal Sexing – Interests and Applicability
Authors: Crișan M. I. , Damian A. , Morar I. , Páll E. , Peștean C. , Groza I. Șt.
Published: October 2015

The ability to choose the sex of the offspring is of upmost economic importance for horse breeders. Unlike other species, horses present several reproductive peculiarities that interfere with assisted reproductive technologies used in other large animals (such as bovine) and make them difficult to apply. Thus, there is a great interest to determine the sex of the offspring as soon as possible. This has led to the development of several technologies to serve this purpose, which can be classified into two categories. One is equine embryo sexing by either non‐invasive biotechnological methods, such as monitoring of X‐linked enzymes before X chromosome inactivation and detection of sex‐specific antigen, or by invasive biotechnological methods, such as cytogenetic analysis and polymerase chain reaction (PCR). The other one is equine foetus sexing using ultrasound scanning in different stages of its development (early, mid or late), by different approaches (transrectally or transabdominally). This can be performed with classic B‐mode ultrasound machines or using 3D‐mode and Doppler‐mode scanners. This review article offers a comprehensive overview of the current status of these procedures as well as an assessment of their interests and applicability.
Botulinum toxin therapy for chronic anal fissures: where are we at currently?
Authors: Dat Anthony , Chin Martin , Skinner Stewart , Farmer Chip , Wale Roger , Carne Peter , Bell Stephen , Warrier Satish K.
Published: October 2015

Background

Botulinum toxin (Botox) injection for chronic anal fissure (CAF) is commonly performed, yet there remains no consensus on optimal dosage or frequency of injections required to achieve complete resolution of anal fissure. The aim of this study was to determine the effectiveness of Botox and side‐effect profile in the management of CAF.

Methods

A retrospective clinical study of patients between 2010 and 2014 who underwent a Botox injection for CAF at a tertiary centre was performed. The effectiveness of Botox was measured using standardized outcomes including overall healing rate, presence of anal pain, recurrence and need for repeat botulinum injection. Binary outcomes were assessed using logistic regression model. The analysis was performed using Stata version 13 (StataCorp, College Station, TX, USA).

Results

One hundred and one patients underwent 126 Botox injections within the study period. The mean first post‐operative visit was at 1 month. The overall recurrence rate was 32%. The majority of patients were given 33 U. No statistically significant relationship between dose and recurrence was identified. The presence of pain at the first post‐operative visit was a predictor of future recurrence (odds ratio 3.92, confidence interval 1.58–9.74, P = 0.003).

Conclusion

Botox is an effective strategy for CAF. Low doses can be given with good efficacy as highlighted by our audit and has the potential for great cost saving. The best predictor of recurrence is the presence of pain at the first post‐procedure visit.
The Viable Violinist
Authors: Hawking Michael
Published: October 2015

In the aftermath of the Kermit Gosnell trial and Giubilini and Minerva's article ‘After‐birth abortion’, abortion‐rights advocates have been pressured to provide an account of the moral difference between abortion, particularly late‐term abortion, and infanticide. In response, some scholars have defended a moral distinction by appealing to an argument developed by Judith Jarvis Thomson in A defense of abortion. However, once Thomson's analogy is refined to account for the morally relevant features of late‐term pregnancy, rather than distinguishing between late‐term abortion and infanticide, it reinforces their moral similarity. This is because late‐term abortion requires more than detachment – it requires an act of feticide to ensure the death of the viable fetus. As such, a Thomsonian account cannot be deployed successfully as a response to Giubilini and Minerva. Those wishing to defend late‐term abortion while rejecting the permissibility of infanticide will need to provide an alternative account of the difference, or else accept Giubilini and Minerva's conclusion.
Opportunities in Reform: Bioethics and Mental Health Ethics
Authors: Williams Arthur Robin
Published: October 2015

Last year marks the first year of implementation for both the Patient Protection and Affordable Care Act and the Mental Health Parity and Addiction Equity Act in the United States. As a result, healthcare reform is moving in the direction of integrating care for physical and mental illness, nudging clinicians to consider medical and psychiatric comorbidity as the expectation rather than the exception. Understanding the intersections of physical and mental illness with autonomy and self‐determination in a system realigning its values so fundamentally therefore becomes a top priority for clinicians. Yet Bioethics has missed opportunities to help guide clinicians through one of medicine's most ethically rich and challenging fields.

Bioethics' distancing from mental illness is perhaps best explained by two overarching themes: 1) An intrinsic opposition between approaches to personhood rooted in Bioethics' early efforts to protect the competent individual from abuses in the research setting; and 2) Structural forces, such as deinstitutionalization, the Patient Rights Movement, and managed care. These two themes help explain Bioethics' relationship to mental health ethics and may also guide opportunities for rapprochement. The potential role for Bioethics may have the greatest implications for international human rights if bioethicists can re‐energize an understanding of autonomy as not only free from abusive intrusions but also with rights to treatment and other fundamental necessities for restoring freedom of choice and self‐determination. Bioethics thus has a great opportunity amid healthcare reform to strengthen the important role of the virtuous and humanistic care provider.
Sedimentary evidence for late Messinian uplift of theSEmargin of the Central Anatolian Plateau: Adana Basin, southern Turkey
Authors: Radeff Giuditta , Schildgen Taylor F. , Cosentino Domenico , Strecker Manfred R. , Cipollari Paola , Darbaş Güldemin , Gürbüz Kemal
Published: October 2015

The Adana Basin of southern Turkey, located at theSEmargin of the Central Anatolian Plateau in the vicinity of the Arabia‐Eurasia collision zone, is ideally suited to record Neogene and Quaternary topographic and tectonic changes in the easternmost Mediterranean realm. On the basis of our correlation of 34 seismic reflection profiles with corresponding exposed units along the margins of the Adana Basin, we identify and characterize the seismic facies that corresponds to the upper part of the Messinian Handere Formation (ca. 5.45 to 5.33 Ma), which consists mainly of fluvial conglomerates and marls. The seismic reflection profiles indicate thatca. 1100 km3of the Handere Formation upper sub‐unit is distributed overca. 3000 km2, reflecting local sedimentation rates of up to 12.5 mm year−1. This indicates a major increase in both sediment supply and subsidence rates atca. 5.45 Ma. Our provenance analysis of the Handere Formation upper sub‐unit based on clast counting and palaeocurrent measurements reveals that most of the sediment is derived from the Taurus Mountains at theSEmargin of the Central Anatolian Plateau and regions farther north. A comparison of these results with the composition of recent fluvial conglomerates and the present‐day drainage basins indicates major changes between late Messinian and present‐day source areas. We suggest that these changes in drainage patterns and lithological characteristics result from uplift and ensuing erosion of theSEmargin of the plateau. We interpret the tectonic evolution of the southern flank of the Anatolian Plateau and the coeval subsidence and sedimentation in the Adana Basin to be related to deep lithospheric processes, particularly lithospheric delamination and slab break‐off.
basin%Ro: A vitrinite reflectance model derived from basin and laboratory data
Authors: Nielsen S. B. , Clausen O. R. , McGregor E.
Published: October 2015

The combination of vitrinite reflectance, apatite fission track and present‐day borehole temperature data is very useful when performing tectonic and thermal reconstructions in sedimentary basins which, in turn, are essential for assessing risk in hydrocarbon exploration and for testing hypotheses of basin evolution. Releasing the full potential of the combined data set requires that the predictive models are accurate in themselves. Here, we calibrate a new kinetic vitrinite reflectance model ‘basin%Ro’ using borehole data from a number of sedimentary basins and vitrinite reflectance data from laboratory maturation experiments. The entire data set is inverted for the kinetic parameters of the reflectance model under consideration of uncertainty in the temperature histories of the calibration samples. The method is not sensitive to inconsistent calibration data, which are revealed by significant corrections to the temperature histories. The performance of the model is tested on independent well data from the East China Sea and the Nova Scotian Shelf. The widely used easy%Ro‐model overestimates vitrinite reflectance in the interval 0.5–1.7% Ro by up to 0.35%. Delimiting of oil generating intervals by prediction of vitrinite reflectance may lead to significant underestimation of the generative potential, which may call for a revision of some petroleum systems. The overestimation by easy%Ro may have fuelled the idea of pressure retardation of vitrinite reflectance evolution under sedimentary basin conditions, where pressures in fact are too low for this to be important.
Retinol binding protein and vitamin D associations with serum antibody isotypes, serum influenza virus-specific neutralizing activities and airway cytokine profiles
Authors: Jones B G , Oshansky C M , Bajracharya R , Tang L , Sun Y , Wong S S , Webby R , Thomas P G , Hurwitz J L
Published: October 2015

Vitamin A supports the induction of immunoglobulin (Ig)A responses at mucosal surfaces in mice, but much less is known about the influence of vitamins on antibody isotype expression in humans. To address this knowledge gap, we examined 46 residual blood samples from adults and children, some of whom were experiencing influenza virus infections of the respiratory tract. Assays were performed for retinol binding protein (RBP, a surrogate for vitamin A), vitamin D (a related vitamin) and antibody isotypes. Results showed that all but two tested samples exhibited RBP and/or vitamin D insufficiencies or deficiencies. Vitamin D correlated with blood IgM and IgG3, while RBP correlated with IgG4 and IgA. RBP also correlated positively with age and with influenza virus-specific antibody neutralization titres. Individuals with low blood RBP levels exhibited the highest frequencies of over-expressed cytokines and growth factors in nasal wash samples, an indication of inflamed mucosal tissues. While cause–effect relationships were not discerned, results support a hypothesis that vitamins directly influence B cell isotype expression in humans, and by so doing may help protect mucosal surfaces from respiratory viral disease.
Barrier function and natural moisturizing factor levels after cumulative exposure to a fruit‐derived organic acid and a detergent: different outcomes in atopic and healthy skin and relevance for occupational contact dermatitis in the food industry
Authors: Angelova‐Fischer Irena , Hoek Anne‐Karin , Dapic Irena , Jakasa Ivone , Kezic Sanja , Fischer Tobias W. , Zillikens Detlef
Published: October 2015

Background

Fruit‐derived organic compounds and detergents are relevant exposure factors for occupational contact dermatitis in the food industry. Although individuals with atopic dermatitis (AD) are at risk for development of occupational contact dermatitis, there have been no controlled studies on the effects of repeated exposure to multiple irritants, relevant for the food industry, in atopic skin.

Objectives

The aim of the study was to investigate the outcomes of repeated exposure to a fruit‐derived organic acid and a detergent in AD compared to healthy volunteers.

Methods

The volunteers were exposed to 2.0% acetic acid (AcA) and/or 0.5% sodium lauryl sulfate (SLS) in controlled tandem repeated irritation test. The outcomes were assessed by measurements of erythema, transepidermal water loss (TEWL) and natural moisturizing factor (NMF) levels.

Results

In the AD volunteers, repeated AcA exposure led to barrier disruption and significant TEWL increase; no significant differences after the same exposure in the healthy controls were found. Repeated exposure to SLS and the irritant tandems enhanced the reactions and resulted in a significantly higher increase in TEWL in the AD compared to the control group. Cumulative irritant exposure reduced the NMF levels in both groups.

Conclusions

Differences in the severity of irritant‐induced barrier impairment in atopic individuals contribute to the risk for occupational contact dermatitis in result of multiple exposures to food‐derived irritants and detergents.
Anomalous Evidence, Confidence Change, and Theory Change
Authors: Hemmerich Joshua A. , Van Voorhis Kellie , Wiley Jennifer
Published: October 2015

A novel experimental paradigm that measured theory change and confidence in participants' theories was used in three experiments to test the effects of anomalous evidence. Experiment 1 varied the amount of anomalous evidence to see if “dose size” made incremental changes in confidence toward theory change. Experiment 2 varied whether anomalous evidence was convergent (of multiple types) or replicating (similar finding repeated). Experiment 3 varied whether participants were provided with an alternative theory that explained the anomalous evidence. All experiments showed that participants' confidence changes were commensurate with the amount of anomalous evidence presented, and that larger decreases in confidence predicted theory changes. Convergent evidence and the presentation of an alternative theory led to larger confidence change. Convergent evidence also caused more theory changes. Even when people do not change theories, factors pertinent to the evidence and alternative theories decrease their confidence in their current theory and move them incrementally closer to theory change.
Indolent CD8‐positive lymphoid proliferation of acral sites: three further cases of a rare entity and an update on a unique patient
Authors: Kluk Justine , Kai Anneke , Koch Dimitra , Taibjee Saleem M. , O'Connor Simon , Persic Mojca , Morris Stephen , Whittaker Sean , Cerroni Lorenzo , Kempf Werner , Petrella Tony , Robson Alistair
Published: October 2015

Background

Primary cutaneous indolent CD8‐positive lymphoid proliferation is an emerging entity characterized by slowly enlarging papules and nodules that are pathologically comprised of clonal nonepidermotropic medium‐sized atypical CD8(+) T‐cells. Although the majority of lesions are solitary and located on the ears, bilateral symmetrical presentations have been described and lesions may arise at other peripheral or ‘acral’ sites. Patients follow a benign clinical course and systemic involvement has not yet been observed. Despite this, some medical practitioners classify such lesions as peripheral T‐cell lymphoma, NOS, a category implying aggressive disease.

Objectives

We present three cases seen in our institutions and provide an update on a previously reported unique patient who continues to develop recurrent and multifocal skin lesions.

Results

Systemic disease progression has not been observed, even in the presence of recurrent and multifocal cutaneous disease.

Conclusions

Indolent CD8‐positive lymphoid proliferation of acral sites is a distinctive and readily identifiable entity and should be included in the next consensus revision of cutaneous lymphoma classification. Although cases described thus far have followed an indolent clinical course, dermatologists should remain guarded about the prognosis and full staging and longitudinal observation are recommended until this condition is better understood.
Examining the locations of medical marijuana dispensaries in Los Angeles
Authors: Thomas Crystal , Freisthler Bridget
Published: October 2015

Introduction and Aims

Little is known about the spatial distribution of medical marijuana dispensaries, particularly whether or not sites are disproportionately located in minority or communities with younger populations. This paper will assess if there is a relationship between medical marijuana dispensaries and neighbourhood characteristics.

Design and Methods

This study used an ecological, cross‐sectional design of 1000 census tracts from Los Angeles city in 2012 to explore the relationship between neighbourhood sociodemographics, structural features of neighbourhoods and density of medical marijuana dispensaries. Locations of dispensaries were obtained through a premise survey of all listed dispensaries. Data on neighbourhood characteristics were obtained from Geolytics. The study used Bayesian conditionally autoregressive models that include controls for spatial heterogeneity to analyse the data.

Results

Findings show that dispensaries are located in areas that allow for commercial establishments. Results indicate a positive relationship between dispensaries and percent commercially zoned, areas with highway ramp access, density of on‐ and off‐premise alcohol outlets and percent Hispanic residents.

Discussion and Conclusions

In sum, the findings suggest that, likely because of zoning regulations, dispensaries were located in primarily commercially zoned areas with greater road access (as measured by the presence of highway ramps). Given that areas with higher densities of dispensaries also have higher densities of alcohol outlets, future work should examine how this co‐location affects neighbourhood problems such as crime and violence. [Thomas C, Freisthler B. Examining the locations of medical marijuana dispensaries in Los Angeles. Drug Alcohol Rev 2016;35:334–337]
Investigating the impact of pain, age, Gross Motor Function Classification System, and sex on health‐related quality of life in children with cerebral palsy
Authors: Findlay Briar , Switzer Lauren , Narayanan Unni , Chen Shiyi , Fehlings Darcy
Published: October 2015

Aim

To explore whether health‐related quality of life (HRQOL) can be predicted by pain, age, Gross Motor Function Classification System (GMFCS) level, and sex in children with cerebral palsy (CP) and whether different pain etiologies have varying effects on HRQOL.

Methods

Children with CP aged 3 to 19 years and their caregivers were consecutively recruited. Caregivers reported their child's pain (Health Utilities Index 3 [HUI3] pain subset) and HRQOL (DISABKIDS questionnaires). Physicians identified pain etiologies. A multiple linear regression model determined whether pain, GMFCS level, sex, and age predicted HRQOL. An ANOVA evaluated the effects of pain etiologies on HRQOL.

Results

Three hundred and forty‐four participants were approached and 87% (n=300) participated. Sufficient data were available on 248 (72% of total sample). Sixty‐six participants (27%) formed the pain group with HUI3 pain scores of at least 3. The presence of pain and increasing age significantly negatively predicted HRQOL (p<0.001, R2=0.141), while GMFCS and sex did not. Musculoskeletal deformity (24%) and hypertonia (18%) were the most frequent pain causes. HRQOL statistically differed depending on the pain etiology (p=0.028) with musculoskeletal deformity showing the lowest mean HRQOL.

Interpretation

The presence of pain and increasing age negatively predict HRQOL in CP. musculoskeletal deformity has the greatest negative impact on HRQOL.
Gastric emptying and disease activity in inflammatory bowel disease
Authors: Keller Jutta , Binnewies Ulrich , Rösch Marie , Juul Holst Jens , Beglinger Christoph , Andresen Viola , Layer Peter
Published: October 2015

Background

Gastric emptying (GE) is delayed in a subset of patients with inflammatory bowel disease (IBD). We have shown before that altered release of gastrointestinal hormones may contribute to GE disturbances, but overall effects of disease activity remain unclear. Thus, we aimed to evaluate GE in patients with IBD during active disease and following therapy.

Design

A total of 20 healthy subjects (HC) and 26 patients with IBD hospitalized because of an acute episode of their disease (Crohn's disease (CD) n = 13, ulcerative colitis (UC) n = 13) underwent a standardized 13C‐octanoic acid GE breath test (baseline test). Plasma glucose, cholecystokinin (CCK), peptide YY (PYY) and glucagon‐like peptide‐1 (GLP‐1) were measured periodically throughout the test. A total of 16 patients underwent a second GE test after 3–4 months of therapy.

Results

At baseline, nine patients with IBD had pathologically delayed GE half‐time (T½ > 150 min) (P = 0·028 vs. HC). Moreover, T½ was significantly longer in the total group of patients with IBD than in HC (129 ± 12 min vs. 96 ± 7, P = 0·030). Postprandial GLP‐1 responses were elevated in IBD (P = 0·002 vs. HC) and correlated with T½ (P = 0·05). Following therapy clinical activity indices and T½ were decreased in IBD (P ≤ 0·01 vs. baseline), and T½ no longer differed from HC (P > 0·5). Moreover, GLP‐1 plasma levels decreased significantly (P = 0·031).

Conclusions

Higher disease activity in IBD is associated with prolonged GE and increased release of GLP‐1. Following effective therapy, GE is accelerated and GLP‐1 release decreases significantly. Thus, increased release of GLP‐1 from the inflamed mucosa might contribute to GE disturbances in IBD.
Blackmania gen. nov. and the related genus Acaudella (Hemiptera: Aphididae: Aphidinae)
Authors: Kanturski Mariusz , Wieczorek Karina
Published: October 2015

The aphid genus Blackmania gen. nov. is described. In the genus, B. eastopi sp. nov. associated with Polygonum equisetiforme (Polygonaceae) from Israel and Cyprus is described and illustrated. Morphologically, the new genus is similar to the genus Acaudella in respect to the lack of a cauda. Acaudella puchovi, associated with Atraphaxis caucasica (=A. buxifolia) and A. spinosa (Polygonaceae) from Uzbekistan and Israel, is re‐described and the apterous viviparous female is figured for the first time. The lectotype and paralectotypes of A. puchovi are also designated. An identification key to known species of the tribe Macrosiphini without cauda is provided. The morphological separation of B. eastopi gen. nov., sp. nov. from A. puchovi is visualized using principal component analysis.
Expanding population edges: theories, traits, and trade‐offs
Authors: Chuang Angela , Peterson Christopher R.
Published: October 2015

Recent patterns of global change have highlighted the importance of understanding the dynamics and mechanisms of species range shifts and expansions. Unique demographic features, spatial processes, and selective pressures can result in the accumulation and evolution of distinctive phenotypic traits at the leading edges of expansions. We review the characteristics of expanding range margins and highlight possible mechanisms for the appearance of phenotypic differences between individuals at the leading edge and core of the range. The development of life history traits that increase dispersal or reproductive ability is predicted by theory and supported with extensive empirical evidence. Many examples of rapid phenotypic change are associated with trade‐offs that may influence the persistence of the trait once expansion ends. Accounting for the effects of edge phenotypes and related trade‐offs could be critical for predicting the spread of invasive species and population responses to climate change.
Fluid mapping in deeply buried Ordovician paleokarst reservoirs in the Tarim Basin, western China
Authors: Zhang Y. Y. , Sun Z. D. , Han J. F. , Wang H. Y. , Fan C. Y.
Published: October 2015

The storage spaces within deeply buried Ordovician paleokarst reservoirs in the Tarim Basin are mostly secondary and characterized by strong heterogeneity and some degree of anisotropy. The types of fluids that fill the spaces within these reservoirs are of great importance for hydrocarbon exploration and exploitation. However, fluid identification from seismic data is often controversial in this area because the seismic velocity for this particular reservoir could be significantly influenced by many factors, including pore shapes, porosity, fluid types, and mineral contents. In this study, we employ the differential effective medium‐Gassmann rock physics model to interpret and discuss the characteristics of conventional karstic carbonate reservoirs in the Tarim Basin that are filled with different fluids (oil, gas, and water) using logging data and thus objectively build corresponding fluid identification criteria. These criteria are subsequently evaluated by amplitude versus offset (AVO) forward analysis based on typical logging data and further applied to ascertain the reservoir fluid types in two different areas in the Tarim Basin based on prestack inversion results. For conventional carbonate reservoirs, gas can be distinguished from heavy oil and water, but heavy oil and water are broadly similar on seismic data. For condensate carbonate reservoirs, water can be differentiated from light oil (i.e., condensates) and gas, but light oil and gas demonstrate substantial similarities in terms of their seismic responses. The predicted fluid results are in good agreement with the results of drilling and oil testing. In particular, modeling the seismically resolvable reservoirs in the carbonate strata in the Tarim Basin, which have needle‐ and sphere‐shaped storage spaces (pore aspect ratio > 0.3) and clay content that is lower than 5%, indicates that fluid properties could be properly evaluated if the porosity is larger than 5% for conventional carbonate reservoirs and >7% for condensate carbonate reservoirs.
Does lymphopenia or macrocytosis reflect 6‐thioguanine levels in patients with inflammatory bowel disease treated with azathioprine or 6‐mercaptopurine?
Authors: Heerasing N. M. , Ng J. F. , Dowling D.
Published: October 2015

Background

The thiopurine drugs, 6‐mercaptopurine and azathioprine, remain the mainstay of immunomodulator therapy for inflammatory bowel disease (IBD). Optimal management depends on achieving therapeutic levels of 6‐thioguanine (6‐TGN), but measuring thiopurine metabolites is associated with significant cost. Thiopurines cause lymphopenia and an increase in mean corpuscular volume (MCV). It is unclear whether any clinically useful correlation exists between 6‐TGN levels and lymphocyte count or MCV.

Aims

The aim of this study is to investigate the correlation between 6‐TGN levels and lymphocyte count and MCV in thiopurine‐treated patients with IBD.

Methods

We analysed a prospectively acquired database of 67 patients with IBD treated with thiopurine therapy. The data were analysed looking at the relationship between 6‐TGN levels and both lymphocyte count and MCV by using the Spearman's rank correlation coefficient.

Results

Twenty‐seven (40%) patients had therapeutic 6‐TGN levels. Thirty‐three (49%) patients had sub‐therapeutic 6‐TGN levels. A weak positive correlation between 6‐TGN levels and lymphocyte count was demonstrated, but this was not statistically significant (Spearman's R = 0.14, P = 0.23). Spearman's rank correlation coefficient between 6‐TGN levels and MCV was statistically significant (R = 0.42, P = 0.0005). MCV >101 fL excluded a subtherapeutic 6‐TGN level with positive predictive value of 92%.

Conclusions

There is no specific lymphopenia that can be assumed to indicate a therapeutic 6‐TGN level. The relationship between 6‐TGN levels and MCV is likely to be clinically relevant. If MCV is elevated, 6‐TGN is unlikely to be sub‐therapeutic. MCV is a potential surrogate marker which can rule out sub‐therapeutic thiopurine metabolites in patients with IBD treated with azathioprine or 6‐mercaptopurine.
FASD Prevalence among Schoolchildren in Poland
Authors: Okulicz‐Kozaryn Katarzyna , Borkowska Magdalena , Brzózka Krzysztof
Published: October 2015

Background

Prenatal Alcohol Exposure is a major cause of brain damage and developmental delay, known as Fetal Alcohol Spectrum Disorders (FASD) but in Poland is rarely diagnosed and the scale of problem is not known.

Methods

An active case ascertainment approach was applied to estimate the prevalence of FASD among 7–9 years olds. Pre‐screening was conducted in 113 randomly selected regular and special schools. In the screening phase participated 280 children (54% from the risk group, 60% boys). The entire number of eligible students (N = 2500) was taken as a denominator.

Results

The prevalence of FASD is not lower than 2%, including 0.4% of Fetal Alcohol Syndrome.

Conclusions

Neurodevelopmental disorders associated with PAE are a serious challenge for the public health system. Development of procedures and services to diagnose and to support individuals affected by PAE and their families is an urgent need in Poland.
Rates of inbreeding and genetic adaptation for populations managed as herds in zoos with a rotational mating system or with optimized contribution of parents
Authors: Mucha S. , Komen H.
Published: October 2015

This study compares two genetic management scenarios for species kept in herds, such as deer. The simulations were designed so that their results can be extended to a wide range of zoo populations. In the first scenario, the simulated populations of size 3 × 20, 6 × 40 or 20 × 60 (herds × animals in herd) were managed with a rotational mating (RM) scheme in which 10%, 20% or 50% of males were selected for breeding and moved between herds in a circular fashion. The second scenario was based on optimal contribution theory (OC). OC requires an accurate pedigree to calculate kinship; males were selected and assigned numbers of offspring to minimize kinship in the next generation. RM was efficient in restriction of inbreeding and produced results comparable with OC. However, RM can result in genetic adaptation of the population to the zoo environment, in particular when 20% or less males are selected for rotation and selection of animals is not random. Lowest rates of inbreeding were obtained by combining OC with rotation of males as in the RM scheme. RM is easy to implement in practice and does not require pedigree data. When full pedigree is available, OC management is preferable.
Statistical modeling of nitrogen‐dependent modulation of root system architecture in Arabidopsis thaliana
Authors: Araya Takao , Kubo Takuya , von Wirén Nicolaus , Takahashi Hideki
Published: October 2015

Plant root development is strongly affected by nutrient availability. Despite the importance of structure and function of roots in nutrient acquisition, statistical modeling approaches to evaluate dynamic and temporal modulations of root system architecture in response to nutrient availability have remained as widely open and exploratory areas in root biology. In this study, we developed a statistical modeling approach to investigate modulations of root system architecture in response to nitrogen availability. Mathematical models were designed for quantitative assessment of root growth and root branching phenotypes and their dynamic relationships based on hierarchical configuration of primary and lateral roots formulating the fishbone‐shaped root system architecture in Arabidopsis thaliana. Time‐series datasets reporting dynamic changes in root developmental traits on different nitrate or ammonium concentrations were generated for statistical analyses. Regression analyses unraveled key parameters associated with: (i) inhibition of primary root growth under nitrogen limitation or on ammonium; (ii) rapid progression of lateral root emergence in response to ammonium; and (iii) inhibition of lateral root elongation in the presence of excess nitrate or ammonium. This study provides a statistical framework for interpreting dynamic modulation of root system architecture, supported by meta‐analysis of datasets displaying morphological responses of roots to diverse nitrogen supplies.