bluuebunny/crossref_metadata_2025_split huggingface dataset:
“In-silico studies of facilitated VEGF(s) – VEGFR(s) bindings for assessment of Lysine as an indirect Low-Mol-Wt angiogen: Experimental validation of a potential synthetic Low-Mol-Wt angiogen”
Authors: Verma Priyanshu , Bir Aritri , Banerjee Anindita , Basu Joy , Kar Sujoy , Samanta Sujoy Kumar , Datta Debatosh 
Published: September 2016

AbstractIn-vivo angiogenesis process is highly conserved and is mediated through a family of peptides having VEGF-A as the lead member. A respective receptor family comprising of members VEGFR-1, 2, 3 gets expressed on the endothelial cell membrane of the vascular bed in ischemic zone along with parallel expressions of VEGF-A, B, C, D and PlGF. Degree of ischaemia is the main regulator of these coupled expressions of angiogenic peptides/factors (AFs) and respective receptor(s) for a paracrine angiogenic process to take place. Physiological angiogenesis in intrauterine growth phase is the lead process in foetal growth, organogenesis and cellular specialization. Post birth and with aging, this process gets gradually inefficient and slow. In the present in-silico study, all angiogenic factors and receptor species are examined as for their binding stability in basal unaided condition and in presence of a possible Low-Mol-Wt linkage molecule–Lysine. Also a Lysine analogue 1,6-diaminohexanoic acid has been examined for its angiogenic potential both in dry docking experiment and in cell culture assay.
Using palaeoecology to determine baseline ecological requirements and interaction networks for de‐extinction candidate species
Authors: Wood Jamie R. , Perry George L. W. , Wilmshurst Janet M. 
Published: September 2016

SummaryA key rationale for pursuing de‐extinction is the potential to restore lost processes and function to modern ecosystems. However, understanding and providing for the ecological requirements of the candidate species will also play a key role in determining the ultimate success of a de‐extinction. This assessment is challenging for prehistoric extinct species, where empirical studies or observations on their ecology are not available or are incomplete.A healthy, stable and self‐sustaining population of a resurrected species needs to be embedded in an ecological interaction network that consists not only of interactions between a resurrected species and its external environment (e.g. habitat, diet), but also those where the resurrected species is the environment (e.g. microbiota and parasites). Palaeoecology can provide information on all of these interactions for extinct species, and this information can help guide and inform the selection of suitable de‐extinction candidates or traits for resurrection.Ecological interaction network analyses offer a complementary tool to existing frameworks for determining the suitability of de‐extinction candidates, allowing palaeoecological information to be used to identify and quantify the potential implications of removing or adding resurrected species/functions to an ecosystem.Although palaeoecological data and understanding clearly have an important role in informing and modelling the potential ecological functions provided by extinct species, they can only ever provide an incomplete picture and therefore would only complement, rather than replace, observational or experimental data on the resurrected organisms themselves.Alay summaryis available for this article.
Changing odour landscapes: the effect of anthropogenic volatile pollutants on plant–pollinator olfactory communication
Authors: Jürgens Andreas , Bischoff Mascha 
Published: September 2016

Summary

Olfactory signals, often in synergy with visual signals, mediate the interactions between plants and animals. However, urbanization and agricultural practices are both sources of volatile organic compounds (VOCs) and reactive oxygen species (ROS) that have the potential to interfere with plant–animal communication and to disrupt mutualistic interactions. In this review, we explore how anthropogenic airborne pollutants may disrupt chemical information transfer between flowering plants and flower visitors.

The emission of anthropogenic volatile pollutants (AVPs) including VOCs and formation of ROS, for example from traffic or industries, and non‐natural biogenic VOCs, for example from introduced crops, may have a number of effects: (i) changes in plant signalling as a consequence of plants experiencing physiological stress; (ii) chemical interference (chemical degradation/transformation of infochemicals); (iii) increased levels of background noise impeding signal detection; and (iv) changes in pollinator signal perception and behaviour. All of the above in turn could have consequences for the biological fitness of plants and animals that rely on olfactory information as pivotal functional signals.

The study of anthropogenic airborne pollutants and their effects on plant signalling is just emerging and the impacts of this aspect of anthropogenic emissions are barely understood. Volatiles emitted from anthropogenically changed landscapes could, however, have far‐reaching consequences for ecosystem functioning in adjacent natural zones, particularly in fragmented landscapes. In response to the wide gap in our knowledge on the mechanisms that govern interference of anthropogenic VOCs with olfactory information, future research directions are proposed with the aim to inspire research to help elucidate the risks of anthropogenic VOCs for plant–pollinator communities and improve risk assessment strategies.

A lay summary is available for this article.
The Institution of a Standardized Investigation Protocol for Sudden Infant Death in the Eastern Metropole, Cape Town, South Africa,,
Authors: Dempers Johan J. , Coldrey Jean , Burger Elsie H. , Thompson Vonita , Wadee Shabbir A. , Odendaal Hein J. , Sens Mary Ann , Randall Brad B. , Folkerth Rebecca D. , Kinney Hannah C. ,   the PASS Network
Published: September 2016

AbstractThe rate for the sudden infant death syndrome (SIDS) in Cape Town, South Africa, is estimated to be among the highest in the world (3.41/1000 live births). In several of these areas, including those of extreme poverty, only sporadic, nonstandardized infant autopsy, and death scene investigation (DSI) occurred. In this report, we detail a feasibility project comprising 18 autopsied infants with sudden and unexpected death whose causes of death were adjudicated according to the 1991NICHDdefinitions (SIDS,n= 7; known cause of death,n= 7; and unclassified,n= 4). We instituted a standardized autopsy and infantDSIthrough a collaborative effort of local forensic pathology officers and clinical providers. The high standard of forensic investigation met international standards, identified preventable disease, and allowed for incorporation of research. We conclude that an effective infant autopsy andDSIprotocol can be established in areas with both high sudden unexpected infant death, and elsewhere. (SUID)/SIDSrisk and infrastructure challenges.
Frances Burney's Methods of Narrating the Court Experience
Authors: Clark Lorna J. 
Published: September 2016

AbstractFrances Burney's journals were once read as realistic representations of life in the Georgian period, based on a censored and doctored text. The current edition of Court Journals prints many passages previously unavailable, and reveals that some of the journal entries were not kept daily but written up long afterwards. This paper explores the implications of these discoveries on our understanding of the text, examining the selection of material, restriction of focus, and self‐presentation that help Burney create her effects. As she practises her craft, she lays the groundwork for her most creative period of writing, following retirement from court.
Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology
Authors: Briskine Roman V. , Paape Timothy , Shimizu‐Inatsugi Rie , Nishiyama Tomoaki , Akama Satoru , Sese Jun , Shimizu Kentaro K. 
Published: September 2016

AbstractThe self‐incompatible species Arabidopsis halleri is a close relative of the self‐compatible model plant Arabidopsis thaliana. The broad European and Asian distribution and heavy metal hyperaccumulation ability make A. halleri a useful model for ecological genomics studies. We used long‐insert mate‐pair libraries to improve the genome assembly of the A. halleri ssp. gemmifera Tada mine genotype (W302) collected from a site with high contamination by heavy metals in Japan. After five rounds of forced selfing, heterozygosity was reduced to 0.04%, which facilitated subsequent genome assembly. Our assembly now covers 196 Mb or 78% of the estimated genome size and achieved scaffold N50 length of 712 kb. To validate assembly and annotation, we used synteny of A. halleri Tada mine with a previously published high‐quality reference assembly of a closely related species, Arabidopsis lyrata. Further validation of the assembly quality comes from synteny and phylogenetic analysis of the HEAVY METAL ATPASE4 (HMA4) and METAL TOLERANCE PROTEIN1 (MTP1) regions using published sequences from European A. halleri for comparison. Three tandemly duplicated copies of HMA4, key gene involved in cadmium and zinc hyperaccumulation, were assembled on a single scaffold. The assembly will enhance the genomewide studies of A. halleri as well as the allopolyploid Arabidopsis kamchatica derived from A. lyrata and A. halleri.
Regulation of development of rat stem and progenitor Leydig cells by activin
Authors: Li L. , Wang Y. , Li X. , Liu S. , Wang G. , Lin H. , Zhu Q. , Guo J. , Chen H. , Ge H.‐S. , Ge R.‐S. 
Published: September 2016

SummaryStem Leydig cells have been demonstrated to differentiate into adult Leydig cells via intermediate stages of progenitor and immature Leydig cells. However, the exact regulatory mechanisms are unclear. We hypothesized that the development of stem or progenitor Leydig cells depends upon locally produced growth factors. Microarray analysis revealed that the expression levels of activin type I receptor (Acvr1) and activin A receptor type II‐like 1 (Acvrl1) were stem > progenitor = immature = adult Leydig cells. This indicates that their ligand activin might play an important role in stem and progenitor Leydig cell proliferation and differentiation. When seminiferous tubules were incubated with 1 or 10 ng/mL activin A for 3 days, it concentration‐dependently increased EdU incorporation into stem Leydig cells by up to 20‐fold. When progenitor Leydig cells were incubated with 1 or 10 ng/mL activin A for 2 days, it concentration‐dependently increased 3H‐thymidine incorporation into progenitor Leydig cells by up to 200%. Real‐time PCR analysis showed that activin A primarily increased Pcna expression but reduced Star, Hsd3b1, and Cyp17a1 expression levels. Activin A also significantly inhibited the basal and luteinizing hormone‐stimulated androgen production. In conclusion, activin A primarily stimulates the proliferation of stem and progenitor Leydig cells, but inhibits the differentiation of stem and progenitor Leydig cells into the Leydig cell lineage in rat testis.
Procedural and shunt‐related complications and mortality of the transjugular intrahepatic portosystemic shunt (TIPSS)
Authors: Bettinger D. , Schultheiss M. , Boettler T. , Muljono M. , Thimme R. , Rössle M. 
Published: September 2016

SummaryBackgroundThe implantation of a transjugular intrahepatic portosystemic shunt (TIPSS) is a complex angiographic procedure performed in patients with end‐stage liver disease. Numerous case reports and narrative reviews have been published so far; however, studies systematically investigating procedural and shunt‐related complications are lacking.AimTo systematically investigate complications and mortality occurring during the index hospital stay and the early (4‐week) period after TIPSS implantation.MethodsThe study includes 389 patients who received a TIPSS implantation between 2004 and 2014. Data were obtained from the clinical records and technical reports of the TIPSS implantation.ResultsDuring the index hospital stay, procedure‐related complications occurred in 42 patients (10.8%) with intraperitoneal bleeding in 8 patients (2.1%) and infections in 14 patients (3.6%). Shunt‐ and disease‐related complications consisted of hepatic encephalopathy (1‐year incidence 29%), non‐procedural infections (8.7%) and acute hepatic decompensation (4.1%). Nine patients (2.3%) died during the index hospital stay from procedure‐related (two patients, 0.5%), shunt‐related (four patients, 1%) or disease‐related causes (three patients, 0.8%). 23 patients (5.9%) died during 4 weeks after TIPSS implantation. The 1‐year probability of survival was 67.7% and was negatively associated with severe hepatic encephalopathy and acute hepatic decompensation.ConclusionsExcept hepatic encephalopathy, severe procedure‐ and shunt‐related complications are rare and early mortality is low.
Stabilisation of periarticular fractures and osteotomies with a notched head locking T‐plate
Authors: Tan CJ , Johnson KA 
Published: September 2016

ObjectiveTo report the clinical outcomes and complications of small animals that had articular or periarticular fractures or osteotomies stabilised with a notched head locking T‐plate.MethodsMedical records were searched retrospectively to identify animals that had a notched head locking T‐plate used to stabilise a small articular or periarticular bone fragment.ResultsNine dogs and two cats had an articular or periarticular bone fragment stabilised with a 2.0‐ or 2.4‐mm notched head locking T‐plate (12 procedures). The median body weight was 4.7 kg. The plate was modified by removing holes in 10/12 procedures and a combination of locking and non‐locking screws were used in 7/12 procedures. All fractures or osteotomies progressed to clinical union. There were two intraoperative complications (intra‐articular screw placement and overlong screw) and two postoperative complications (skin necrosis and stress protection)ConclusionsThis study reports the successful use of a 2.0‐ or 2.4‐mm notched head locking T‐plate for articular or periarticular fractures or osteotomies in a variety of small‐breed dogs and cats. Care must be taken to prevent inadvertent penetration of the articular surface, particularly in regions such as the proximal tibia. The ability to modify the plate dimensions intraoperatively proved beneficial in most cases.
Adjuvant chemotherapy may improve disease‐free survival in patients with rectal cancer positive for MRI‐detected extramural venous invasion following chemoradiation
Authors: Chand M. , Rasheed S. , Heald R. , Swift I. , West N. , Rao S. , Tekkis P. , Brown G. 
Published: September 2016

AbstractAimMRI‐detected extramural venous invasion (mrEMVI) is a poor prognostic factor in rectal cancer. Preoperative chemoradiotherapy (CRT) can cause regression in the severity of EMVI and subsequently improve survival whereas mrEMVI persisting after CRT confers an increased risk of recurrence. The effect of adjuvant chemotherapy (AC) following CRT on survival in rectal cancer remains unclear. The aim of this study was to determine whether there is a survival advantage for AC given to patients with mrEMVI persisting after CRT.MethodA prospective analysis was conducted of consecutive patients with locally advanced rectal cancer between 2006 and 2013. All patients underwent CRT followed by surgery. AC was given to selected patients based on the presence of specific ‘high‐risk’ features. Comparison was made between patients offered AC with observation alone. The primary outcome was 3‐year disease‐free survival (DFS).ResultsOf 631 patients, 227 (36.0%) demonstrated persistent mrEMVI following CRT. Patients were grouped on the basis of AC or observation and were matched for age, performance status and final histopathological staging. Three‐year DFS in the AC group was 74.6% compared with 53.7% in the observation only group. AC had a survival benefit on multivariate analysis (hazard ratio 0.458; 95% CI: 0.271–0.775, P = 0.004).ConclusionPatients with persistent mrEMVI following CRT who receive AC may have a decreased risk of recurrence and an improved 3‐year DFS compared with patients not receiving AC, irrespective of age and performance status.
Identifying, Characterising and Assessing New Practices in Doctoral Education
Authors: Baschung Lukas 
Published: September 2016

AbstractTraditionally, European doctoral education has principally taken place within the binary relationship of professors and their doctoral students according to the apprenticeship model. However, in the last one to two decades, this model has been questioned. Governments and higher education institutions (HEIs) reform doctoral education by establishing and running structured doctoral programmes or Doctoral Schools. Inspired by American Graduate Schools, various forms of Doctoral Schools have been increasingly emerging in many European HEIs. This article identifies, characterises and critically assesses the principal changes in doctoral education practices introduced through Doctoral Schools on the basis of eight case studies carried out in Swiss and Norwegian HEIs. The empirical analysis results in the identification of six types of changes which concern doctoral students’ recruitment, curricular component, supervision, scientific exchange, tracking and their career. These changes lead to four kind of trends – which vary according to the case study – consisting of a structuring, standardisation and opening of doctoral education, whereas its academic character is maintained. If greater competitiveness, better scientific quality and higher graduating rates may be achieved, problems in terms of ‘brain drain’, workload, supervision, innovation and careers may even be reinforced or at least not completely solved.
Riparian management: A restoration tool for New Zealand streams
Authors: McKergow Lucy A. , Matheson Fleur E. , Quinn John M. 
Published: September 2016

SummaryMany New Zealanders are planning and implementing riparian management, and riparian fencing and planting are now standard best practice tools for water quality and habitat restoration. New Zealand has a long history of action, with the first catchment riparian schemes and science dating back to the 1970s. As a result of this, there is now solid scientific evidence that demonstrates the value of a range of management actions including the following: riparian zones and buffers for livestock exclusion (fencing with or without planting), nutrient processing, shading small streams for temperature control, providing leaf and wood input to stream ecosystems, and enhancing fish and invertebrate habitat. In the last decade or so, on‐ground action has accelerated significantly with the introduction of dairy industry and government agreed targets. In 2015, 96% of dairy cows had been excluded from waterways >1 m wide and >30 cm deep on land that cows graze during the milking season providing impetus for on‐ground action to spread into other pastoral industries. Tools for planning, managing and implementing successful riparian restoration have proliferated, informed by on‐ground successes and failures. Despite this, there remain challenges for individuals or communities planning riparian restoration. Careful case‐by‐case assessment is recommended to ensure that plans match design to local landscape constraints and can realistically contribute to improved water quality or habitat outcomes.
The effect of targeted high‐threat weed control on wet forest understorey vegetation in the Central Highlands region, Victoria
Authors: Wills Timothy J. , Kutt Alex S. 
Published: September 2016

SummaryThe effective control of highly invasive weeds in Australia is an important conservation management action. In this study, we monitored the outcome of herbicide control on high‐threat weeds in the wet forests of the Central Highlands of Victoria. Twenty‐two control (no weed control) and 32 treatment (weed control) plots were surveyed annually over 24 months. Initial results show that weed cover and frequency decreased substantially in response to weed control; however, it is too early to determine the response of native species. We recommend that herbicide control and the associated monitoring programme be continued, and depending on the outcomes, data should be used to develop a more integrated management strategy.
Global changes in soil stocks of carbon, nitrogen, phosphorus, and sulphur as influenced by long‐term agricultural production
Authors: Kopittke Peter M. , Dalal Ram C. , Finn Damien , Menzies Neal W. 
Published: September 2016

AbstractQuantifying changes in stocks of C, N, P, and S in agricultural soils is important not only for managing these soils sustainably as required to feed a growing human population, but for C and N, they are also important for understanding fluxes of greenhouse gases from the soil environment. In a global meta‐analysis, 102 studies were examined to investigate changes in soil stocks of organic C, total N, total P, and total S associated with long‐term land‐use changes. Conversion of native vegetation to cropping resulted in substantial losses of C (−1.6 kg m−2, −43%), N (−0.15 kg m−2, −42%), P (−0.029 kg m−2, −27%), and S (−0.015 kg m−2, −33%). The subsequent conversion of conventional cropping systems to no‐till, organic agriculture, or organic amendment systems subsequently increased stocks, but the magnitude of this increase (average of +0.47 kg m−2 for C and +0.051 kg m−2 for N) was small relative to the initial decrease. We also examined the conversion of native vegetation to pasture, with changes in C (−11%), N (+4.1%), and P (+25%) generally being modest relative to changes caused by conversion to cropping. The C:N ratio remained relatively constant irrespective of changes in land use, whilst in contrast, the C:S ratio decreased by 21% in soils converted to cropping – this suggesting that biochemical mineralization is of importance for S. The data presented here will assist in the assessment of different agricultural production systems on soil stocks of C, N, P, and S – this information assisting not only in quantifying the effects of existing agricultural production on these stocks, but also allowing for informed decision‐making regarding the potential effects of future land‐use changes.