bluuebunny/crossref_metadata_2025 huggingface dataset:
Different hydrogen-bonded chains in the crystal structures of three alkylN-[(E)-1-(2-benzylidene-1-methylhydrazinyl)-3-hydroxy-1-oxopropan-2-yl]carbamates
Authors: Noguiera Thais C. M. , Pinheiro Alessandra C. , Wardell James L. , Souza Marcus V. N. de , Abberley Jordan P. , Harrison William T. A.
Published: June 2015

The crystal structures of three methylated hydrazine carbamate derivatives prepared by multi-step syntheses from L-serine are presented, namely benzylN-{(E)-1-[2-(4-cyanobenzylidene)-1-methylhydrazinyl]-3-hydroxy-1-oxopropan-2-yl}carbamate, C20H20N4O4,tert-butylN-{(E)-1-[2-(4-cyanobenzylidene)-1-methylhydrazinyl]-3-hydroxy-1-oxopropan-2-yl}carbamate, C17H22N4O4, andtert-butylN-[(E)-1-(2-benzylidene-1-methylhydrazinyl)-3-hydroxy-1-oxopropan-2-yl]carbamate, C16H23N3O4. One of them shows that an unexpected racemization has occurred during the mild-condition methylation reaction. In each crystal structure, the molecules are linked into chains by O—H...O hydrogen bonds, but with significant differences between them.
Crystal structure of (1R,4R)-tert-butyl 3-oxo-2-oxa-5-azabicyclo[2.2.2]octane-5-carboxylate
Authors: Krishnamurthy Suvratha , Jalli Venkataprasad , Vagvala Tarun Chand , Moriguchi Tetsuji , Tsuge Akihiko
Published: June 2015

In the title compound, C11H17NO4, commonly known asN-tert-butoxycarbonyl-5-hydroxy-D-pipecolic acid lactone, the absolute configuration is (1R,4R) due to the enantiomeric purity of the starting material which remains unchanged during the course of the reaction. In the crystal there no intermolecular hydrogen bonds.
Crystal structure of 6-amino-4-(3-bromo-4-methoxyphenyl)-3-methyl-2,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile dimethyl sulfoxide monosolvate
Authors: Yousuf Sammer , Bano Huma , Muhammad Munira Taj , Khan Khalid Mohammed
Published: June 2015

In the pyrazole molecule of the title solvate, C15H13BrN4O2·C2H6OS, the dihedral angle between the benzene ring and the mean plane of the dihydropyrano[2,3-c]pyrazole ring system [r.m.s deviation = 0.031 (2) Å] is 86.71 (14)°. In the crystal, the pyrazole molecules are linked by N—H...N hydrogen bonds, forming a layer parallel to (10-1). The pyrazole and dimethyl sulfoxide molecules are connected by an N—H...O hydrogen bond.
Innovative technologies for autism: critical reflections on digital bubbles
Authors: Parsons Sarah , Yuill Nicola , Brosnan Mark , Good Judith
Published: June 2015

Purpose

– There is increasing interest from researchers, teachers and other professionals, individuals with autism, and families about the potential for innovative technologies to transform learning experiences and facilitate friendships and social networks. Media accounts have highlighted both the apparently miraculous impacts of technology on supporting communication and learning for people with autism, as well as significant concerns about whether technology use is healthy, safe and socially appropriate for children and young people. Rarely, however, is any evidence reported to support either set of claims. The paper aims to discuss these issues.

Design/methodology/approach

– This short paper reports on an Economic and Social Research Council-funded seminar series in the UK that is critically reviewing and discussing the field with respect to the research evidence base but also the assumptions that are made about where, how and whether innovative technologies may be useful for people with autism and their families.

Findings

– The first seminar in the series focused on whether technologies create a social bubble for people with autism and presented research demonstrating that technology use can be positive, supportive and rewarding.

Originality/value

– This paper offers an up-to-date insight into some of key debates about the benefits and limitations of social technologies for people with autism. Its value lies in raising questions about, and discussing evidence that challenges, some of the negative assumptions that are often perpetuated by the media about the potentially harmful effects of technologies.
Conceptual and operational perspectives on ecosystem restoration options in the European Union and elsewhere
Authors: Kotiaho Janne S. , Moilanen Atte
Published: June 2015

Egoh et al. (2014) prioritized areas for ecological restoration in the European Union (EU) so that Europe could cost‐efficiently meet the globally agreed 15% restoration target.

We identify three major deficiencies in their analysis, one conceptual and two operational, which compromise the conclusions of the prioritization.

The conceptual flaw is neglect of both the magnitude of degradation and the magnitude of improvement of the ecosystem condition expected due to restoration.

The first operational flaw is inclusion of inappropriately measured restoration costs into the analyses. The second is use of spatial units that are so large (10 × 10 km) that only a fraction of each unit could realistically be restored, thereby overestimating restoration gains.

Synthesis and applications. The prioritization suggested by Egoh et al. (2014) runs a risk of focusing restoration efforts towards areas where the ecological improvement of restoration is the smallest. Thus, in this article, we propose that the recommendations by Egoh et al. (2014) will not help to achieve the high‐level target of the Convention on Biological Diversity and EU of halting the loss of biodiversity and the degradation of ecosystem services, but instead may actually compromise progress towards the target. More detailed analyses are needed before well‐informed decisions about restoration prioritization can be made across the EU and elsewhere.
Ark or park: the need to predict relative effectiveness of ex situ and in situ conservation before attempting captive breeding
Authors: Dolman Paul M. , Collar Nigel J. , Scotland Keith M. , Burnside Robert. J.
Published: June 2015

When species face extinction, captive breeding may be appropriate. However, captive breeding may be unsuccessful, while reducing motivation and resources for in situ conservation and impacting wild source populations. Despite such risks, decisions are generally taken without rigorous evaluation. We develop an individual‐based, stochastic population model to evaluate the potential effectiveness of captive‐breeding and release programmes, illustrated by the critically endangered Ardeotis nigriceps Vigors great Indian bustard.

The model was parameterized from a comprehensive review of captive breeding and wild demography of large bustards. To handle uncertainty in the standards of captive‐breeding performance that may be achieved, we explored four scenarios of programme quality: ‘full range’ (parameters sampled across the observed range), ‘below average’, ‘above average’ and ‘best possible’ (performance observed in exemplary breeding programmes). Results are evaluated examining: (i) the probability of captive population extirpation within 50 years and (ii) numbers of adult females subsequently established in the wild following release, compared to an alternative strategy of in situ conservation without attempting captive breeding.

Successful implementation of captive breeding, involving permanent retention of 20 breeding females and release of surplus juveniles, required collection of many wild eggs and consistent ‘best possible’ performance across all aspects of the programme. Under ‘full‐range’ and ‘above‐average’ scenarios, captive population extirpation probabilities were 73–88% and 23–51% respectively, depending on egg collection rates.

Although most (73–92%) ‘best possible’ programmes supported releases, re‐establishment of free‐living adults also required effective in situ conservation. Incremental implementation of effective conservation measures over the initial 10 years resulted in more free‐living adults within 35 years if eggs were left in the wild without attempting captive breeding.

Synthesis and applications. For the great Indian bustard Ardeotis nigriceps, rapid implementation of in situ conservation offers a better chance to avoid extinction than captive breeding. Demographic modelling of threatened species should be used to examine whether captive breeding will bring net benefits to conservation programmes.
Using an ‘Interpretative Model’ for Contextual Design of Heritage Landscape Databases: The Case of St Helena Island National Park in Queensland, Australia
Authors: YANG CHEN
Published: June 2015

Due to the increasing speed of landscape changes and the massive development of computer technologies, the methods of representing heritage landscapes using digital tools have become a worldwide concern in conservation research. The aim of this paper is to demonstrate how an ‘interpretative model’ can be used for contextual design of heritage landscape information systems. This approach is explored through building a geographic information system database for St Helena Island national park in Moreton Bay, South East Queensland, Australia. Stakeholders' interpretations of this landscape were collected through interviews, and then used as a framework for designing the database. The designed database is a digital inventory providing contextual descriptions of the historic infrastructure remnants on St Helena Island. It also reveals the priorities of different sites in terms of historic research, landscape restoration, and tourism development. Additionally, this database produces thematic maps of the intangible heritage values, which could be used for landscape interpretation. This approach is different from the existing methods because building a heritage information system is deemed as an interpretative activity, rather than a value‐free replication of the physical environment. This approach also shows how a cultural landscape methodology can be used to create a flexible information system for heritage conservation. The conclusion is that an ‘interpretative model’ of database design facilitates a more explicit focus on information support, and is a potentially effective approach to user‐centred design of geographic information systems.
Just Noticeable Differences and Weber Fraction of Oral Thickness Perception of Model Beverages
Authors: Camacho Sara , Dop Mathilde , de Graaf Cees , Stieger Markus
Published: June 2015

Rheological properties of beverages contribute considerably to texture perception. When developing new beverages, it is important to have knowledge on the smallest differences of viscosity which a consumer can discriminate. Thickness is the sensory attribute most commonly used to describe the viscosity of beverages. The aim of this study was to determine the Just Noticeable Differences (JNDs) of oral thickness perception and the Weber fraction (K) of Newtonian model stimuli (maltodextrin solutions). JNDs were determined using the method of constant stimuli with 5 reference stimuli ranging in viscosity from 10 to 100 mPa⋅s. JNDs increased with increasing viscosity of the reference stimulus. The Weber fraction (K) for oral thickness perception of model beverages was K = 0.26 for the studied viscosity range. The Weber fraction for oral thickness perception is comparable to Weber fractions reported in literature for perception of kinesthetic food firmness and spreadability, creaminess, sourness, and bitterness perception. This demonstrates that the human sensitivity towards oral discrimination of thickness of liquid stimuli is comparable to the human sensitivity towards discrimination of specific texture properties and specific taste stimuli.
Molecular prey identification in Central European piscivores
Authors: Thalinger Bettina , Oehm Johannes , Mayr Hannes , Obwexer Armin , Zeisler Christiane , Traugott Michael
Published: June 2015

Diet analysis is an important aspect when investigating the ecology of fish‐eating animals and essential for assessing their functional role in food webs across aquatic and terrestrial ecosystems. The identification of fish remains in dietary samples, however, can be time‐consuming and unsatisfying using conventional morphological analysis of prey remains. Here, we present a two‐step multiplexPCRsystem, comprised of six assays, allowing for rapid, sensitive and specific detection of fishDNAin dietary samples. This approach encompasses 78 fish and lamprey species native to Central European freshwaters and enables the identification of 31 species, six genera, two families, two orders and two fish family clusters. All targeted taxa were successfully amplified from 25 template molecules, and each assay was specific when tested against a wide range of invertebrates and vertebrates inhabiting aquatic environments. The applicability of the multiplexPCRsystem was evaluated in a feeding trial, wherein it outperformed morphological prey analysis regarding species‐specific prey identification in faeces of Eurasian otters. Additionally, a wide spectrum of fish species was detected in field‐collected faecal samples and regurgitated pellets of Common Kingfishers and Great Cormorants, demonstrating the broad applicability of the approach. In conclusion, this multiplexPCRsystem provides an efficient, easy to use and cost‐effective tool for assessing the trophic ecology of piscivores in Central Europe. Furthermore, the multiplexPCRs and the primers described therein will be applicable whereverDNAof the targeted fish species needs to be detected at high sensitivity and specificity.
The use of ‘mother and baby gifts’ (MBGs) to increase uptake of supervised births in the Milne Bay Province of Papua New Guinea
Authors: Kirby Barry , Mola Glen , Case Colin , Robson Stephen J.
Published: June 2015

Improving access to supervised birth reduces mortality in developing countries. In the Milne Bay Province of Papua New Guinea, many women do not deliver at local health centres (HCs) because they feel ‘shy’ at presenting in an impoverished state and not having baby's clothes, and the state of facilities associated with HCs was poor. To overcome this, women were offered ‘mother and baby gifts’ (MBGs) at the time of delivery. We found subsequent increases in the rate of supervised birth in all HCs surveyed.
Acute colonic pseudo‐obstruction in pregnancy
Authors: Reeves Michael , Frizelle Frank , Wakeman Christopher , Parker Catherine
Published: June 2015

Background

Acute colonic pseudo‐obstruction is an uncommon but potentially morbid complication of pregnancy. The aim of the study was to review a single institution's experience with acute colonic pseudo‐obstruction in post‐partum patients and develop an algorithm for management based on a literature review.

Methods

This is a retrospective study where patients were identified over a 2‐year period (1 December 2012 to 31 November 2014) by checking all deliveries in Christchurch Women's Hospital against diagnosis codes for bowel obstruction and ileus. Clinical records and radiology were then reviewed to identify those with acute colonic pseudo‐obstruction and the management of these patients was reviewed.

Results

Over the study period, seven patients were identified from 10 240 deliveries. Two patients required laparotomy and the rest resolved without surgical intervention. One patient was treated with neostigmine and three with erythromycin. One patient had an unsuccessful attempt at endoscopic decompression, however, symptoms resolved without further intervention following this. A management algorithm was developed based on the literature review.

Conclusions

Acute colonic pseudo‐obstruction occurs in post‐partum patients more frequently than suspected (one in 1500 deliveries). The management needs to be active with early correction of electrolyte abnormalities, avoidance of narcotic pain relief and early mobilization. Timely administration of neostigmine or endoscopic decompression can reduce the incidence of colonic ischaemia and perforation and the need for surgical intervention.
Metastases to the kidney: a comprehensive analysis of 151 patients from a tertiary referral centre
Authors: Zhou Cathy , Urbauer Diana L. , Fellman Bryan M. , Tamboli Pheroze , Zhang Miao , Matin Surena F. , Wood Christopher G. , Karam Jose A.
Published: June 2015

Objective

To describe the presentation, treatment and outcomes of patients with metastatic tumours to the kidney treated at a tertiary referral centre.

Patients and Methods

We retrospectively identified 151 patients diagnosed with a primary non‐renal malignancy with renal metastasis. Clinical, radiographic and pathological characteristics were assessed. Overall survival (OS) was calculated using Kaplan–Meier methods.

Results

The median patient age was 56.7 years. The most common presenting symptoms were flank pain (30%), haematuria (16%) and weight loss (12%). Most primary cancers were carcinomas (80.8%). The most common primary tumour sites were lung (43.7%), colorectal (10.6%), head and neck (6%), breast (5.3%), soft tissue (5.3%) and thyroid (5.3%). Renal metastases were typically solitary (77.5%). Concordance between radiologist and clinician imaging assessment was 54.0%. Three ablations and 48 nephrectomies were performed. For non‐surgical patients, renal metastasis diagnosis was made with fine‐needle aspiration or biopsy. The median OS from primary tumour diagnosis was 3.08 years and the median OS from time of metastatic diagnosis was 1.13 years. For patients treated with surgery, median OS from primary tumour diagnosis was 4.81 years, and OS from metastatic diagnosis was 2.24 years.

Conclusions

Metastases to the kidney are a rare entity. Survival appears to be longer in patients who are candidates for and are treated with surgery. Surgical intervention in carefully selected patients with oligometastatic disease and good performance status should be considered. A multidisciplinary approach with input from urologists, oncologists, radiologists and pathologists is needed to achieve the optimum outcomes for this specific patient population.
Smoking and survival after breast cancer diagnosis in Japanese women: A prospective cohort study
Authors: Kakugawa Yoichiro , Kawai Masaaki , Nishino Yoshikazu , Fukamachi Kayoko , Ishida Takanori , Ohuchi Noriaki , Minami Yuko
Published: June 2015

The results of previous studies investigating whether there is an association between active smoking and risk of death among breast cancer patients have been inconsistent. We investigated the association between active and passive smoking and risk of all‐cause and breast cancer‐specific death among female breast cancer patients in relation to menopausal and tumor estrogen/progesterone receptor (ER/PR) status. The present study included 848 patients admitted to a single hospital in Japan from 1997 to 2007. Active or passive smoking status was assessed using a self‐administered questionnaire. The patients were followed until 31 December 2010. We used a Cox proportional‐hazard model to estimate hazard ratios (HR). During a median follow‐up period of 6.7 years, 170 all‐cause and 132 breast cancer‐specific deaths were observed. Among premenopausal patients, current smokers showed a non‐significant higher risk of all‐cause and breast cancer‐specific death. A duration of smoking >21.5 years was positively associated with all‐cause (HR = 3.09, 95% confidence interval [CI], 1.17–8.20) and breast cancer‐specific death (HR = 3.35, 95%CI: 1.22–9.23,Ptrend = 0.035) among premenopausal patients. In premenopausal patients withER+ orPR+ tumors, there was some suggestion that a longer duration of smoking was associated with higher risk of all‐cause and breast cancer‐specific death. Passive smoking demonstrated no significant risk. Our results suggest that a longer duration of active smoking is associated with an increased risk of all‐cause and breast cancer‐specific death among premenopausal patients, possibly with hormonal receptor‐positive tumors. Breast cancer patients should be informed about the importance of smoking cessation.
Oriental Flânerie: Fürst Pückler‐Muskau's Aus Mehemed Alis Reich
Authors: Richter Daniela
Published: June 2015

In this article, I examine the Oriental travel writing by Fürst Hermann von Pückler‐Muskau as flânerie, in terms of literary historians' depictions of the nineteenth‐century French flâneur and Walter Benjamin's writings. Pückler's narrator, who is placed at the center of the travel text in question, Aus Mehemed Alis Reich, bears resemblance to the flâneur in several respects, including the position he assumes within the scenarios that he depicts, his relative detachment from the events, and the anecdotal and entertaining nature of the narrative. This narrative style provided the readers of the mid‐nineteenth century with both a new type of travel text and an unusual narrator, who, through his particular social status, was able to access different social spheres and enjoy different travel experiences than the majority of travel writers, who were mostly from the middle class.
Caregiver daily impression could reflect illness latency and severity in frail elderly residents in long‐term care facilities: A pilot study
Authors: Ae Ryusuke , Kojo Takao , Okayama Masanobu , Tsuboi Satoshi , Makino Nobuko , Kotani Kazuhiko , Aoyama Yasuko , Nakamura Yosikazu
Published: June 2015

Aims

To propose a caregiver daily impression (CDI) rating instrument for personal caregivers of residents living in long‐term care facilities (LTCF) to comprehensively evaluate residents' daily health condition, and to investigate whether the CDI reflects illness latency and severity in residents transferred emergently.

Methods

We carried out a retrospective review of facility care records from 20 LTCF in Hyogo, Japan. The participants were 169 LTCF residents with episodes of transfer to emergency hospitalization facilities during a 3‐month period. We determined specific CDI variables by interviewing experienced LTCF caregivers, and then carried out a principal component analysis to determine the major parameter set. The generated components were incorporated into a regression model to investigate the association with hospitalization.

Results

The mean age was 87.9 ± 6.5 years, 68% were women and 28% of transfers resulted in hospitalization. The interview procedure identified 12 specific CDI variables, and the principal component analysis generated five distinct components: “change in feeding,” “change in emotion,” “disengaged or listless gaze,” “decrease in eye reactivity” and “change in movement.” By multivariate logistic regression, hospitalization was associated with “decrease in eye reactivity” (adjusted OR 1.78, 95% CI 1.07–2.97) and poor vital signs (adjusted OR 2.84, 95% CI 1.15–6.98), but not with body temperature (adjusted OR 1.29, 95% CI 0.52–3.21).

Conclusions

The CDI might reflect underlying illness severity beyond quantitative physical findings. Once the CDI can be appropriately validated, quantified and linked to physical findings, it could be used by caregivers for daily resident assessments and as a practical triage tool in emergency situations. Geriatr Gerontol Int 2016; 16: 612–617.
Intra‐ and trans‐generational effects of larval diet on susceptibility to an entomopathogenic fungus, Beauveria bassiana, in the greater wax moth, Galleria mellonella
Authors: Kangassalo K. , Valtonen T. M. , Roff D. , Pölkki M. , Dubovskiy I. M. , Sorvari J. , Rantala M. J.
Published: June 2015

In addition to nutritional conditions experienced by individuals themselves, those experienced by their parents can affect their immune function. Here, we studied the intra‐ and trans‐generational effects of larval diet on susceptibility to an entomopathogenic fungus, Beauveria bassiana, in the greater wax moth, Galleria mellonella. In the first part of the study, a split‐brood design was used to compare the susceptibility of full sibs raised either on low‐ or on high‐nutrition larval diet. In the second part of the study, a similar experimental design was employed to investigate the effects of maternal and paternal diet as well as their interaction on offspring's susceptibility. In the first part of the study, we found that individuals fed with high‐nutrition diet had higher mortality from infection than individuals fed with low‐nutrition diet. However, diet did not affect post‐infection survival time. Conversely, in the second part of the study, maternal diet was found to have no significant effect on final mortality rate of offspring, but it affected survival time: larvae with high‐nutrition maternal diet survived fewer days after infection than larvae with low‐nutrition maternal diet. Paternal diet had no significant effect on offspring's susceptibility to the fungus, indicating that paternal effects are not as important as maternal effects in influencing immune function in this species. Our findings provide further indication that maternal nutrition affects immune function in insects, and suggest that the direct effects of nutrition on immunity may be different, yet parallel, to those caused by parental nutrition.
Biological characterization of the skin of shortfin mako sharkIsurus oxyrinchusand preliminary study of the hydrodynamic behaviour through computational fluid dynamics
Authors: Díez G. , Soto M. , Blanco J. M.
Published: June 2015

This study characterized the morphology, density and orientation of the dermal denticles along the body of a shortfin mako sharkIsurus oxyrinchusand identified the hydrodynamic parameters of its body through a computational fluid‐dynamics model. The study showed a great variability in the morphology, size, shape, orientation and density of dermal denticles along the body ofI. oxyrinchus. There was a significant higher density in dorsal and ventral areas of the body and their highest angular deviations were found in the lower part of the mouth and in the areas between the pre‐caudal pit and the second dorsal and pelvic fins. A detailed three‐dimensional geometry from a scanned body of a shark was carried out to evaluate the hydrodynamic properties such as drag coefficient, lift coefficient and superficial (skin) friction coefficient of the skin together with flow velocity field, according to different roughness coefficients simulating the effect of the dermal denticles. This preliminary approach contributed to detailed information of the denticle interactions. As the height of the denticles was increased, flow velocity and the effect of lift decreased whereas drag increased. The highest peaks of skin friction coefficient were observed around the pectoral fins.
Empirical gradient threshold technique for automated segmentation across image modalities and cell lines
Authors: CHALFOUN J. , MAJURSKI M. , PESKIN A. , BREEN C. , BAJCSY P. , BRADY M.
Published: June 2015

New microscopy technologies are enabling image acquisition of terabyte‐sized data sets consisting of hundreds of thousands of images. In order to retrieve and analyze the biological information in these large data sets, segmentation is needed to detect the regions containing cells or cell colonies. Our work with hundreds of large images (each 21 000×21 000 pixels) requires a segmentation method that: (1) yields high segmentation accuracy, (2) is applicable to multiple cell lines with various densities of cells and cell colonies, and several imaging modalities, (3) can process large data sets in a timely manner, (4) has a low memory footprint and (5) has a small number of user‐set parameters that do not require adjustment during the segmentation of large image sets. None of the currently available segmentation methods meet all these requirements. Segmentation based on image gradient thresholding is fast and has a low memory footprint. However, existing techniques that automate the selection of the gradient image threshold do not work across image modalities, multiple cell lines, and a wide range of foreground/background densities (requirement 2) and all failed the requirement for robust parameters that do not require re‐adjustment with time (requirement 5).

We present a novel and empirically derived image gradient threshold selection method for separating foreground and background pixels in an image that meets all the requirements listed above. We quantify the difference between our approach and existing ones in terms of accuracy, execution speed, memory usage and number of adjustable parameters on a reference data set. This reference data set consists of 501 validation images with manually determined segmentations and image sizes ranging from 0.36 Megapixels to 850 Megapixels. It includes four different cell lines and two image modalities: phase contrast and fluorescent. Our new technique, called Empirical Gradient Threshold (EGT), is derived from this reference data set with a 10‐fold cross‐validation method. EGT segments cells or colonies with resulting Dice accuracy index measurements above 0.92 for all cross‐validation data sets. EGT results has also been visually verified on a much larger data set that includes bright field and Differential Interference Contrast (DIC) images, 16 cell lines and 61 time‐sequence data sets, for a total of 17 479 images. This method is implemented as an open‐source plugin to ImageJ as well as a standalone executable that can be downloaded from the following link:https://isg.nist.gov/.
Programmed death 1 and its ligands do not limit experimental foreign antigen‐induced immune complex glomerulonephritis
Authors: Ooi Joshua D , Li Ming , Kourkoutzelos Katerina , Yagita Hideo , Azuma Miyuki , Holdsworth Stephen R , Kitching A Richard
Published: June 2015

Aim

Interactions between the co‐stimulatory molecule programmed death 1 (PD‐1) and its ligands, PD‐L1 and PD‐L2, constrain T‐cell responses and help maintain peripheral tolerance. Glomerulonephritis can result from a variety of antigens, both self and foreign, and from humoural and cellular effector responses. These studies aimed to define the role of PD1 and its ligands in circulating immune complex glomerulonephritis induced by immunity to a foreign antigen.

Methods

Immune complex glomerulonephritis was initiated by injecting BALB/c mice with horse spleen apoferritin intraperitoneally daily for 14 days. Inhibitory anti‐mouse PD‐1, anti‐PD‐L1 or anti‐PD‐L2 antibodies were administered every other day. Renal disease and immune responses were studied.

Results

Daily injection of horse spleen apoferritin‐induced proliferative immune complex glomerulonephritis in control antibody‐treated mice, but inhibiting PD‐1 did not augment renal injury. Specifically, blocking PD‐1 did not increase serum antigen‐specific antibodies or increase glomerular immunoglobulin G deposition, the hallmark of injury in this model. Furthermore, C3 deposition was unaffected and glomerular macrophages were reduced after anti‐PD‐1 antibodies. However, anti‐PD‐1 administration did increase splenocyte proliferation and cytokine production including interferon‐γ, interleukin (IL)‐4, and IL‐17, but not IL‐10. Neutralizing either PD‐L1 or PD‐L2 alone did not result in major alterations in renal injury.

Conclusion

The endogenous PD‐1/PD‐L pathway does not limit acute experimental foreign antigen‐induced circulating immune complex glomerulonephritis.
Recently evolved diversity and convergent radiations of rainforest mahoganies (Meliaceae) shed new light on the origins of rainforest hyperdiversity
Authors: Koenen Erik J. M. , Clarkson James J. , Pennington Terence D. , Chatrou Lars W.
Published: June 2015

Tropical rainforest hyperdiversity is often suggested to have evolved over a long time‐span (the ‘museum’ model), but there is also evidence for recent rainforest radiations. The mahoganies (Meliaceae) are a prominent plant group in lowland tropical rainforests world‐wide but also occur in all other tropical ecosystems. We investigated whether rainforest diversity in Meliaceae has accumulated over a long time or has more recently evolved.

We inferred the largest time‐calibrated phylogeny for the family to date, reconstructed ancestral states for habitat and deciduousness, estimated diversification rates and modeled potential shifts in macro‐evolutionary processes using a recently developed Bayesian method.

The ancestral Meliaceae is reconstructed as a deciduous species that inhabited seasonal habitats. Rainforest clades have diversified from the Late Oligocene or Early Miocene onwards. Two contemporaneous Amazonian clades have converged on similar ecologies and high speciation rates.

Most species‐level diversity of Meliaceae in rainforest is recent. Other studies have found steady accumulation of lineages, but the large majority of plant species diversity in rainforests is recent, suggesting (episodic) species turnover. Rainforest hyperdiversity may best be explained by recent radiations from a large stock of higher level taxa.
Plant contributions to our understanding of sex chromosome evolution
Authors: Charlesworth Deborah
Published: June 2015

A minority of angiosperms have male and female flowers separated in distinct individuals (dioecy), and most dioecious plants do not have cytologically different (heteromorphic) sex chromosomes. Plants nevertheless have several advantages for the study of sex chromosome evolution, as genetic sex determination has evolved repeatedly and is often absent in close relatives. I review sex‐determining regions in non‐model plant species, which may help us to understand when and how (and, potentially, test hypotheses about why) recombination suppression evolves within young sex chromosomes. I emphasize high‐throughput sequencing approaches that are increasingly being applied to plants to test for non‐recombining regions. These data are particularly illuminating when combined with sequence data that allow phylogenetic analyses, and estimates of when these regions evolved. Together with comparative genetic mapping, this has revealed that sex‐determining loci and sex‐linked regions evolved independently in many plant lineages, sometimes in closely related dioecious species, and often within the past few million years. In reviewing recent progress, I suggest areas for future work, such as the use of phylogenies to allow the informed choice of outgroup species suitable for inferring the directions of changes, including testing whether Y chromosome‐like regions are undergoing genetic degeneration, a predicted consequence of losing recombination.

Contents

Summary
52

I.
Introduction: advantages of plants for the study of sex chromosome evolution
53

II.
Sex chromosomes and estimation of their ages from sequence divergence
53

III.
Which plants have sex chromosomes?
54

IV.
Haploid plants
55

V.
Plants with very small, or no, non‐recombining regions
55

VI.
Comparative genetic mapping
56

VII.
Why does suppressed recombination evolve?
57

VIII.
Recombination suppression: mechanisms
58

IX.
Old established sex chromosome systems
59

X.
Genetic degeneration: the need for empirical data in a phylogenetic setting
59

XI.
Plant sex‐determining loci
61

XII.
Conclusions
62

Acknowledgements
62

References
62
Outcrossing potential between 11 important genetically modified crops and the Chilean vascular flora
Authors: Sánchez Miguel A. , Cid Pablo , Navarrete Humberto , Aguirre Carlos , Chacón Gustavo , Salazar Erika , Prieto Humberto
Published: June 2015

The potential impact of genetically modified (GM) crops on biodiversity is one of the main concerns in an environmental risk assessment (ERA). The likelihood of outcrossing and pollen‐mediated gene flow from GM crops and non‐GM crops are explained by the same principles and depend primarily on the biology of the species. We conducted a national‐scale study of the likelihood of outcrossing between 11 GM crops and vascular plants in Chile by use of a systematized database that included cultivated, introduced and native plant species in Chile. The database included geographical distributions and key biological and agronomical characteristics for 3505 introduced, 4993 native and 257 cultivated (of which 11 were native and 246 were introduced) plant species. Out of the considered GM crops (cotton, soya bean, maize, grape, wheat, rice, sugar beet, alfalfa, canola, tomato and potato), only potato and tomato presented native relatives (66 species total). Introduced relative species showed that three GM groups were formed having: a) up to one introduced relative (cotton and soya bean), b) up to two (rice, grape, maize and wheat) and c) from two to seven (sugar beet, alfalfa, canola, tomato and potato). In particular, GM crops presenting introduced noncultivated relative species were canola (1 relative species), alfalfa (up to 4), rice (1), tomato (up to 2) and potato (up to 2). The outcrossing potential between species [OP; scaled from ‘very low’ (1) to ‘very high’ (5)] was developed, showing medium OPs (3) for GM–native relative interactions when they occurred, low (2) for GMs and introduced noncultivated and high (4) for the grape‐Vitis vinifera GM–introduced cultivated interaction. This analytical tool might be useful for future ERA for unconfined GM crop release in Chile.
Taste dysfunction in patients undergoing hematopoietic stem cell transplantation: Clinical evaluation in children
Authors: Majorana Alessandra , Amadori Francesca , Bardellini Elena , Campus Guglielmo , Conti Giulio , Strohmenger Laura , Schumacher Richard Fabian , Polimeni Antonella
Published: June 2015

The aim of this study was to determine the variability of TD in children undergoing HSCT. Cases were identified as consecutively enrolled children in the period January 2011–January 2013 among patients attending the Paediatric Department of Spedali Civili of Brescia and all candidates to HSCT. The TST was conducted in two phases: identification of threshold values and identification of perceived stimulus intensity. Sixteen sapid solutions with four flavors (sucrose, sodium chloride, citric acid, and quinine hydrochloride) at four different concentrations were administered in a random sequence. The same protocol was administered at different time intervals: before starting the conditioning therapy (T0), during the conditioning therapy (T1) (two times), and every three months (two times) after engraftment post‐HSCT (T2). A p‐value < 0.05 was considered statistically significant. Fifty‐one children (29 female and 22 male, mean age 5.2 ± 0.7 yr) were enrolled. Threshold value means for the four flavors increased during HSCT conditioning therapy (T1) (p < 0.01); intensity of perceived stimulus decreased during HSCT conditioning therapy (p < 0.01). At six months after engraftment (T2), both parameters had returned to starting values (T0). Changes in taste perception in children undergoing HSCT seem to occur especially during the conditioning therapy and resolve in about six months after engraftment post‐HSCT.
Vaccination‐Related Side Effects, Humoral Immunity, and Adverse Events during the Civilian Smallpox Vaccination Campaign, Arkansas, 2003
Authors: Haselow Dirk
Published: June 2015

Objective

Smallpox vaccination has been associated with notable side effects and adverse events. This study assessed the frequency of each among public health workers immunized during the 2003 Arkansas civilian smallpox vaccination campaign to allow individuals and policymakers to make informed decisions whether repeat vaccination, as recommended in 10‐year intervals, should be considered.

Design and Sample

This descriptive study summarizes postvaccination surveillance data for all civilians receiving smallpox vaccine (Dryvax) in Arkansas in 2003.

Measures

Rates of side effects and adverse events were determined. Vaccinia‐specific antibody titers among a subset of public health response team members were also assessed.

Results

Of the 1,124 vaccine recipients, 87% had a major take response. Substantial symptomatology, a 2% adverse event rate, a 0.5% hospitalization rate, and zero inadvertent transmission following vaccination were observed. Vaccinia‐specific antibody titers increased on average 9‐fold from 2.21*102 to 2.16*103 one month after vaccination. We found no association of age, sex, or racial subgroups with adverse events, hospitalizations, a lower take response rate, or lower postvaccination antibody titers.

Conclusions

Prominent side effect profiles and adverse events among study participants seem to support individual and institutional reluctance to vaccinate civilians in the absence of smallpox reemergence.
Gestational Weight Gain Trend and Population Attributable Risks of Adverse Fetal Growth Outcomes in Ohio
Authors: Chen Aimin , Xu Fan , Xie Changchun , Wu Tianying , Vuong Ann M. , Miao Maohua , Yuan Wei , DeFranco Emily A.
Published: June 2015

Background

The trend of gestational weight gain (GWG) in relation to the Institute of Medicine (IOM) guidelines and the population attributable risks (PARs) of GWG on fetal growth outcomes remain unclear.

Methods

We analysed Ohio birth certificates from 2006 to 2012 to examine GWG trend by prepregnancy body mass index, to calculate the risk of small‐ and large‐for‐gestational age (SGA and LGA), and macrosomia (birthweight >4000 g or >4500 g) infants, and to estimate the PARs of GWG below or above the guidelines.

Results

Of 869 531 women who delivered singleton live births at 22–44 weeks of gestation, 4.5% were underweight, 48.9% were normal weight, 23.9% were overweight, and 22.7% were obese before pregnancy. About 36.5% of underweight, 52.6% of normal weight, 72.5% of overweight, and 62.4% of obese women gained weight above the guidelines, with only slight changes from 2006 to 2012. Also, 34.9% of underweight, 20.1% of normal weight, 16.3% of overweight, and 27.0% of obese women gained weight below the guidelines. The PAR of GWG below or above the guidelines was −13% for SGA, 32.6% for LGA, 28.1% for macrosomia >4000 g, and 48.3% for macrosomia >4500 g, mostly driven by currently GWG above the guidelines in normal weight, overweight, and obese women.

Conclusions

A high percentage of pregnant women gained weight outside of the current IOM GWG guidelines; however, changes from 2006 to 2012 were small. GWG above the IOM guidelines significantly contributed to a large proportion of LGA and macrosomic infants in the general population.
Environmental Protection as an Exception to the Freedom of Establishment and the Freedom to Provide Services in the European Union
Authors: Casado Casado Lucia
Published: June 2015

This article examines the tensions between European Union policy on environmental protection and the safeguarding of Community freedoms, focusing particularly on the freedom of establishment and the freedom to provide services. It offers an analysis of the scope of environmental protection as a justification for exceptions from Community freedoms in the case law of the European Court of Justice. It also examines the specific provisions on environmental protection set out in Directive 2006/123 on services in the internal market. In particular, it determines the scope of the environmental exception under the provisions of this Directive, according to which protection of the environment justifies specific derogations from the regulatory framework governing the freedom of establishment and freedom to provide services.
A Proportional Hazards Regression Model for the Subdistribution with Covariates‐adjusted Censoring Weight for Competing Risks Data
Authors: He Peng , Eriksson Frank , Scheike Thomas H. , Zhang Mei‐Jie
Published: June 2015

With competing risks data, one often needs to assess the treatment and covariate effects on the cumulative incidence function. Fine and Gray proposed a proportional hazards regression model for the subdistribution of a competing risk with the assumption that the censoring distribution and the covariates are independent. Covariate‐dependent censoring sometimes occurs in medical studies. In this paper, we study the proportional hazards regression model for the subdistribution of a competing risk with proper adjustments for covariate‐dependent censoring. We consider a covariate‐adjusted weight function by fitting the Cox model for the censoring distribution and using the predictive probability for each individual. Our simulation study shows that the covariate‐adjusted weight estimator is basically unbiased when the censoring time depends on the covariates, and the covariate‐adjusted weight approach works well for the variance estimator as well. We illustrate our methods with bone marrow transplant data from the Center for International Blood and Marrow Transplant Research. Here, cancer relapse and death in complete remission are two competing risks.
The Coupler Surface of the RSRS Mechanism
Authors: Rojas Nicolas , Dollar Aaron M.
Published: June 2015

Two degree-of-freedom (2-DOF) closed spatial linkages can be useful in the design of robotic devices for spatial rigid-body guidance or manipulation. One of the simplest linkages of this type, without any passive DOF on its links, is the revolute-spherical-revolute-spherical (RSRS) four-bar spatial linkage. Although the RSRS topology has been used in some robotics applications, the kinematics study of this basic linkage has unexpectedly received little attention in the literature over the years. Counteracting this historical tendency, this work presents the derivation of the general implicit equation of the surface generated by a point on the coupler link of the general RSRS spatial mechanism. Since the derived surface equation expresses the Cartesian coordinates of the coupler point as a function only of known geometric parameters of the linkage, the equation can be useful, for instance, in the process of synthesizing new devices. The steps for generating the coupler surface, which is computed from a distance-based parametrization of the mechanism and is algebraic of order twelve, are detailed and a web link where the interested reader can download the full equation for further study is provided. It is also shown how the celebrated sextic curve of the planar four-bar linkage is obtained from this RSRS dodecic.
Prevalence of Antimicrobial Resistance and Transfer of Tetracycline Resistance Genes in Escherichia coli Isolates from Beef Cattle
Authors: Shin Seung Won , Shin Min Kyoung , Jung Myunghwan , Belaynehe Kuastros Mekonnen , Yoo Han Sang
Published: June 2015

The aim of this study was to investigate the prevalence and transferability of resistance in tetracycline-resistant
Escherichia coli
isolates recovered from beef cattle in South Korea. A total of 155
E. coli
isolates were collected from feces in South Korea, and 146 were confirmed to be resistant to tetracycline. The tetracycline resistance gene
tet
(A) (46.5%) was the most prevalent, followed by
tet
(B) (45.1%) and
tet
(C) (5.8%). Strains carrying
tet
(A) plus
tet
(B) and
tet
(B) plus
tet
(C) were detected in two isolates each. In terms of phylogenetic grouping, 101 (65.2%) isolates were classified as phylogenetic group B1, followed in decreasing order by D (17.4%), A (14.2%), and B2 (3.2%). Ninety-one (62.3%) isolates were determined to be multidrug resistant by the disk diffusion method. MIC testing using the principal tetracyclines, namely, tetracycline, chlortetracycline, oxytetracycline, doxycycline, and minocycline, revealed that isolates carrying
tet
(B) had higher MIC values than isolates carrying
tet
(A). Conjugation assays showed that 121 (82.9%) isolates could transfer a tetracycline resistance gene to a recipient via the IncFIB replicon (65.1%). This study suggests that the high prevalence of tetracycline-resistant
E. coli
isolates in beef cattle is due to the transferability of tetracycline resistance genes between
E. coli
populations which have survived the selective pressure caused by the use of antimicrobial agents.
Genome Sequence of Photobacterium halotolerans MELD1, with Mercury Reductase (
merA
), Isolated from
Phragmites australis
Authors: Mathew Dony Chacko , Mathew Gincy Marina , Gicana Ronnie Gicaraya , Huang Chieh-Chen
Published: June 2015

Here, we present the whole-genome sequence of
Photobacterium halotolerans
strain, MELD1, isolated from the roots of a terrestrial plant
Phragmites australis
grown in soil heavily contaminated with mercury and dioxin. The genome provides further insight into the adaptation of bacteria to the toxic environment from where it was isolated.
Complete Genome Sequence of Agrobacterium tumefaciens Ach5
Authors: Huang Ya-Yi , Cho Shu-Ting , Lo Wen-Sui , Wang Yi-Chieh , Lai Erh-Min , Kuo Chih-Horng
Published: June 2015

Agrobacterium tumefaciens
is a phytopathogenic bacterium that causes crown gall disease. The strain Ach5 was isolated from yarrow (
Achillea ptarmica
L.) and is the wild-type progenitor of other derived strains widely used for plant transformation. Here, we report the complete genome sequence of this bacterium.