bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species assignment from trace DNA sequences: an in silico assessment of the test used to survey for foxes in Tasmania
Authors: MacDonald Anna J. , Sarre Stephen D. 
Published: July 2015

Summary

Diagnostic DNA tests have become important for species detection from environmental samples and are increasingly applied to the analysis of ecological systems and in wildlife management. The availability of reference DNA sequences from many taxa enables the development of diagnostic PCR primers.

Where there is a high risk of false‐positive PCR amplification, or where even a low rate of false positives has serious management implications, DNA sequencing is crucial for accurate specimen identification. The ability of DNA sequencing to discriminate among target and non‐target species must be explored for each system.

The red fox Vulpes vulpes is an invasive pest in Australia. A fox‐specific PCR and sequencing test has been applied to a systematic survey of scats collected in Tasmania, where the management of a recent fox incursion remains controversial.

We investigated the risk that DNA sequences obtained using this test might be mistakenly assigned to fox in cases of non‐specific amplification, or mistakenly assigned to another species when fox DNA was correctly amplified. We conducted an analysis of barcoding efficacy using cytochrome b sequences from 74 vertebrates.

In our analysis, no non‐fox sequences were identified as fox (false positives) and no genuine fox sequences were misidentified (false negatives). This two‐stage DNA test, including PCR screening and sequencing steps, can reliably discriminate fox DNA from that of other Australian species.

Synthesis and applications. DNA tests are attractive to wildlife managers interested in detecting species that are cryptic or difficult to identify. When DNA data directly influence management decisions, it is important to understand the limitations of the genetic markers and the likely causes of failed identifications or erroneous species assignments. We show that short cytochrome b sequences can provide high specificity for vertebrate species assignment. We highlight the importance of developing appropriate reference sequence data bases for each study system, and of evaluating the potential for misidentification of different taxa.
Regulate Yourself
Authors: Lloyd John 
Published: July 2015

AbstractThe Leveson Inquiry recommended that a new press regulator be created, with a statutory backing—which the government and opposition agreed should be a Royal Charter. Presently, a Press Recognition Panel, backed by the Charter, has been created, but has attracted no requests for recognition. Only one regulator has been set up—IPSO: it has a membership of most of the newspaper and magazine groups in the UK, but will not ask for recognition, since it does not wish to have any formal link with the state. Though the campaign against the Royal Charter has been grossly overblown, the press is right to refuse to join an institution which is guaranteed by the state. State‐backed regulation, in any form, will not in the UK lead to tyranny, censorship or any more than occasional meddling. But a link to the state is a bad idea for an independent press. Not only does this set a bad precedent, opening up a temptation for behind‐the‐scenes pressure, but more importantly it misses the point. Bad and abusive journalism is not improved by regulation. It is improved by journalists understanding the main task of journalism is to report and analyse accurately and neutrally. This complements robust debate and opinion and contributes greatly to a well‐informed citizenry.
Injectable Progestin‐Only Contraception is Associated With Increased Levels of Pro‐Inflammatory Cytokines in the Female Genital Tract
Authors: Deese Jennifer , Masson Lindi , Miller William , Cohen Myron , Morrison Charles , Wang Meng , Ahmed Khatija , Agot Kawango , Crucitti Tania , Abdellati Saïd , Van Damme Lut 
Published: July 2015

ProblemGenital inflammatory changes may be a mechanism of increased HIV risk among injectable progestin‐only contraception (IPC) users.Method of StudyWe conducted a cross‐sectional analysis of 376 Kenyan and South African women. Genital cytokines and secretory leukocyte peptidase inhibitor concentrations in a reference population were compared to IPC users and women with reproductive tract infections.ResultsNo significant variability in marker concentrations was observed by age or site. Depot medroxyprogesterone acetate (DMPA) users had significantly higher MIP‐1α, MIP‐1β, IL‐6, IL‐8, IP‐10, and RANTES concentrations. Norethisterone oenanthate users had significantly higher IL‐6, IL‐8, and RANTES concentrations. Women with sexually transmitted infections had variable inflammation, and women with bacterial vaginosis exhibited a mixed profile of up and downregulation.ConclusionThe finding of substantial mucosal inflammation among DMPA users provides evidence which, combined with the results of prior studies, suggests that DMPA may create an immune environment conducive to HIV target cell recruitment and inhibitory for antiviral activity.
Tear film proteins deposited on high water content contact lenses identified with two‐dimensional gel electrophoresis and mass spectrometry
Authors: Nielsen Kim , Vorum Henrik , Ehlers Niels , Aagaard Nicolaj , Hjortdal Jesper , Honoré Bent 
Published: July 2015

AbstractPurposeTear film proteins adhere to the surface of contact lenses (CLs). While the proteins in the tears have been extensively studied with various proteomic techniques, adhered proteins to CLs are less studied. In this pilot study, we have separated proteins with 2D gel electrophoresis prior to the conventional mass spectrometry (MS) in order to analyse the deposited proteins on hydrogel CLs from myopic patients.MethodspHEMA and PVA hydrogel CLs worn by 3 patients for different time lengths were analysed. After wear, the CLs were frozen at −20°C. Proteins were extracted in lysis buffer, separated on 12% polyacrylamide gels and silver‐stained. Protein spots were excised and identified with liquid chromatography – tandem MS.ResultsDeposited proteins were extracted with a yield of 26–66 μg and separated by 2D gel electrophoresis. The silver‐stained gels showed similar protein patterns independent of the patient, hydrogel type and wear time. Seventy‐two spots were analysed with MS, representing at least 12 different tear film proteins or protein fragments.ConclusionsDeposited tear film proteins from a single set of CLs worn for 1 day can successfully be analysed first with 2D gel electrophoresis and subsequently with MS, thus making examination of individual patients possible. The protein composition appeared homogeneous between the test persons which is a necessity for additional comparison analysis. The molecular masses of the identified proteins indicate that protein degradation occurs only as a minor event. Myopic patients were investigated in this pilot study, but the combined techniques can easily be applied to other eye diseases.
Molecular Analysis of Pediatric Oligodendrogliomas Highlights Genetic Differences with Adult Counterparts and Other Pediatric Gliomas
Authors: Nauen David , Haley Lisa , Lin Ming‐Tseh , Perry Arie , Giannini Caterina , Burger Peter C. , Rodriguez Fausto J. 
Published: July 2015

AbstractOligodendroglioma represents a distinctive neoplasm in adults but similar neoplasms occur rarely in children. We studied 20 cases of pediatric oligodendroglioma by SNP array (median age 9 years, range 1–19; 15 grade II and 5 grade III). Cytogenetic abnormalities were present in 8 (53%) grade II and all five anaplastic oligodendrogliomas. Most changes were in the form of deletion and copy neutral loss of heterozygosity (LOH). The most common abnormality was 1p deletion (n = 5). Whole arm 1p19q co‐deletion was present in three cases from adolescent patients and 9p loss in 3, including one low‐grade oligodendroglioma with CDKN2A homozygous deletion. Common losses were largely limited to the anaplastic subset (n = 5) and included 3q29 (n = 3), 11p (n = 3), 17q (n = 3), 4q (n = 2), 6p (n = 2), 13q (n = 2), 14q (n = 2), 17p (n = 2) and whole Ch 18 loss (n = 2). Gains were non‐recurrent except for whole Ch 7 (n = 2) and gain on 12q (n = 2) including the MDM2 locus. Possible germ line LOH (or uniparental disomy) was present in seven cases (35%), with one focal abnormality (22q13.1‐13.2) in two. BRAF‐KIAA1549 fusions and BRAF p.V600E mutations were absent (n = 13 and 8). In summary, cytogenetic alterations in pediatric oligodendrogliomas are characterized mostly by genomic losses, particularly in anaplastic tumors.
Exploring the oral health experiences of homeless people: a deconstruction–reconstruction formulation
Authors: Coles Emma , Freeman Ruth 
Published: July 2015

AbstractObjectiveTo explore qualitatively, using a grounded theory approach, homeless people's awareness of their oral health needs and how they access dental services using a deconstruction–reconstruction formulation, and provide recommendations for service designers and dental professionals who work with people experiencing homelessness.MethodsA qualitative study using grounded theory methodology was conducted. A purposive sample of homeless people was recruited from health facilities and organizations serving homeless populations in four Scottish cities and towns. Participants were interviewed about their oral health within the wider context of their experiences of homelessness. Initial research questions were open and focused on social processes such as oral health practices and interaction with dental services. Data collection and analysis were carried out simultaneously and iteratively, with emerging findings informing subsequent cycles. Data analysis was guided by Glaser and Strauss's grounded theory methodology and involved constant comparison, coding of transcripts and detailed memo‐writing.ResultsThirty‐four homeless people took part. Participant experiences were conceptualized as a journey into and through the stages of homelessness, towards ‘reclaiming life’. Oral health experiences were mapped as a parallel 3‐stage journey from the deconstruction of self‐care, to the construction and maintenance of the neglected dentine, and finally to the reclamation of oral health resulting in a reconstructed functioning dentition.ConclusionsThis qualitative exploration using a deconstruction–reconstruction formulation has added to the understanding of homeless people's oral health awareness and dental treatment access while permitting an examination of the wider socioeconomic and psychosocial issues that disrupt their intentions to attend for treatment. These findings provide service designers and dental professionals with recommendations for the provision of responsive, acceptable and appropriate dental health services for those experiencing homelessness.
Diesel exhaust particles exacerbate allergic rhinitis in mice by disrupting the nasal epithelial barrier
Authors: Fukuoka A. , Matsushita K. , Morikawa T. , Takano H. , Yoshimoto T. 
Published: July 2015

SummaryBackgroundDiesel exhaust particles (DEP), traffic‐related air pollutants, are considered environmental factors that affect allergic diseases adversely. However, the exact effect of DEP on allergic rhinitis (AR) is unclear.ObjectiveWe thought to investigate the effect of DEP on seasonal AR using a mouse model.MethodsRagweed‐pollen‐sensitized mice were nasally challenged with ragweed pollen in the presence or absence of DEP. The frequency of sneezing was evaluated immediately after each nasal challenge. The expression of a tight junction (TJ) protein, zonula occludens‐1 (ZO‐1), was examined by immunohistochemistry in AR mice. RPMI 2650 cells were used for in vitro examination of paracellular permeability.ResultsMice challenged with ragweed pollen plus DEP showed increased frequency of sneezing compared with mice challenged with pollen alone. Interestingly, intranasal DEP pretreatment before ragweed pollen challenge increased ragweed‐pollen‐induced sneezing to levels comparable with the co‐administration group. In vitro examination revealed that DEP reduced ZO‐1 expression in RPMI 2650 cells. In addition, intranasal administration of DEP, but not ragweed pollen, disrupted nasal mucosal TJs in vivo. The effect of a single DEP treatment on ragweed‐induced sneezing and ZO‐1 expression persisted for at least 4 days and was inversely correlated. Finally, an antioxidant substance, N‐acetyl‐L‐cysteine, inhibited DEP‐mediated TJ disruption and exacerbation of sneezing in AR.Conclusions and Clinical RelevanceDEP disrupts TJs by a reactive oxygen species‐mediated pathway, leading to the increased permeability of nasal epithelial cells. This may result in the promotion of allergen delivery into subepithelial tissues contributing to the exacerbation of immediate allergic responses.
Nonalcoholic fatty pancreas disease and Nonalcoholic fatty liver disease: more than ectopic fat
Authors: Della Corte C. , Mosca A. , Majo F. , Lucidi V. , Panera N. , Giglioni E. , Monti L. , Stronati L. , Alisi A. , Nobili V. 
Published: July 2015

SummaryObjectiveThe aim of this study was to evaluate the metabolic effects of fatty pancreas (nonalcoholic fatty pancreas disease – NAFPD) in a group of obese paediatric patients with nonalcoholic fatty liver disease (NAFLD).MethodsWe included 121 consecutive children with echographic evidence of hepatic steatosis. All patients underwent to abdominal ultrasound to evaluate pancreatic echogenic pattern. We divided the patients into two groups on the basis of the presence of fatty pancreas. In all patients liver function tests, lipid and gluco‐insulinemic profile were evaluated. A selected subset of patients (67) underwent to liver biopsy.ResultsOf these 121 patients, 58 showed NAFPD and 63 patients exhibited a normal pancreatic echogenic pattern. No differences were found in age, transaminases serum levels, lipid profile and pancreatic enzymes between the two groups. The patients with NAFPD had a significantly higher z‐BMI, fasting insulin, insulin resistance (HOMA‐IR) and lower ISI respect to the group without fatty pancreas. The patients with fatty pancreas showed a more advanced form of liver disease, with higher values of fibrosis, ballooning and NAS score with respect to the group without NAFPD.ConclusionsOur study demonstrated that NAFPD is a frequent condition in obese paediatric patients affected by NAFLD. Our data suggest that pancreatic fat should not be considered an inert accumulation of fat, but as an additional factor able to affect glucose metabolism and severity of liver disease, increasing the risk of develop metabolic syndrome.
Are All Non‐Family Managers (NFMs) Equal? The Impact of NFM Characteristics and Diversity on Family Firm Performance
Authors: Binacci Martina , Peruffo Enzo , Oriani Raffaele , Minichilli Alessandro 
Published: July 2015

AbstractManuscript TypeEmpiricalResearch Question/IssueAlthough non‐family managers (NFMs) can be expected to influence firm performance, this issue is largely under‐investigated. In this study, we examine how diversity inside the non‐family component of the top management team (non‐family team, or NFT) influences family firm performance. More specifically, we investigate the performance effects of three specific sources of NFT diversity (NFT size; NFT tenure diversity; and NFT dominant functional diversity).Research Findings/InsightsThe analysis of 584 survey responses by top managers representing 97 complete NFTs (and the related top management teams, TMTs) out of the top 500 family‐controlled firms in the Italian furniture industry indicates that (1) NFT‐dominant functional diversity improves firm performance; (2) a U‐shaped relationship exists between NFT tenure diversity and family firm performance; (3) an inverted U‐shaped relationship exists between NFT size and family firm performance. Additionally, we show that the relation between non‐family manager characteristics and firm performance is moderated by family dominance in the entire TMT, that is, the proportion of family to non‐family managers.Theoretical/Academic ImplicationsOur results call for further exploration regarding the demographic characteristics of non‐family managers and their effect on the performance of family firms. In this way, they have several implications for the family business literature, contributing to the growing debate on the socio‐emotional wealth (SEW) perspective of family firms’ behaviors. Moreover, our results highlight the importance of better contextualizing research on strategic leadership and strategic leaders.Practitioner/Policy ImplicationsOur study suggests that the choice of outsiders should take into account not only their “market value” and reputation, but also the attributes of other NFMs among the company's executives, providing guidance to family owners in their decisions about professionalization.
Changing the paradigm of organ utilization from PHS increased‐risk donors: an opportunity whose time has come?
Authors: Sibulesky Lena , Javed Imran , Reyes Jorge D. , Limaye Ajit P. 
Published: July 2015

AbstractApproximately 8–11% of all organ donors are classified by Public Health Service (PHS) as increased‐risk. The proportion of PHS increased‐risk donors is on the rise. At the University of Washington Medical Center, in 2014, the proportion of transplants from PHS increased‐risk donors was 28% of liver transplants and 23% of kidney transplants. Nationally, transplant providers have been reluctant to use organs from PHS increased‐risk donors because of concern for transmission of HIV, HCV, or HBV. There is also patient apprehension when these organs are being offered, and thus the discard rate of these otherwise good quality organs is high. Because of the organ shortage, preventing underutilization of such organs is essential. We provide data and considerations that should be used to guide the use of organs from PHS increased‐risk donors.
Inter‐ and intraspecific variation in susceptibility to dothistroma needle blight in Britain. How susceptible are Pinus sylvestris and Pinus contorta?
Authors: Fraser S. , Woodward S. , Brown A.V. 
Published: July 2015

SummaryDothistroma needle blight (DNB), caused by Dothistroma septosporum, is a serious disease in British pine plantations. Natural infection (NI) and artificial inoculation (AI) experiments were conducted to evaluate the susceptibility of Pinus sylvestris and Pinus contorta to DNB, relative to Pinus mugo, Pinus muricata, Pinus nigra ssp. laricio, Pinus nigra ssp. nigra and Pinus ponderosa. A range of P. sylvestris and P. contorta provenances were included in experiments to simultaneously investigate intraspecific variation within these host species. In NI experiments, 20–30 12‐month‐old seedlings of each species/provenance were planted adjacent to infected mature trees at two Scottish sites. In the AI experiment, eighteen 16‐month‐old seedlings of each species/provenance were inoculated with a D. septosporum conidial suspension and maintained under optimum conditions for D. septosporum infection and development. In the NI experiments, the most DNB‐susceptible species were P. muricata and P. ponderosa, while the least susceptible species were P. contorta and P. sylvestris. Pinus nigra spp. nigra and P. nigra spp. laricio had intermediate DNB susceptibility. In the AI experiment, there was no evidence for interspecific variation in DNB susceptibility. Intraspecific variation in DNB susceptibility within P. sylvestris was seen in the NI experiment, but not the AI experiment. Intraspecific variation in DNB susceptibility within P. contorta was not observed in either experiment. In a further AI experiment with 24‐month‐old P. sylvestris and P. contorta seedlings, the virulence of three Scottish D. septosporum isolates (haplotypes) was examined. There was no significant interaction between isolate and relative susceptibility of pine species/provenances. Furthermore, no between‐isolate variation in virulence was observed.
A newly identified mouse hypothalamic area having bidirectional neural connections with the lateral septum: the perifornical area of the anterior hypothalamus rich in chondroitin sulfate proteoglycans
Authors: Horii‐Hayashi Noriko , Sasagawa Takayo , Hashimoto Takashi , Kaneko Takeshi , Takeuchi Kosei , Nishi Mayumi 
Published: July 2015

AbstractWhile previous studies and brain atlases divide the hypothalamus into many nuclei and areas, uncharacterised regions remain. Here, we report a new region in the mouse anterior hypothalamus (AH), a triangular‐shaped perifornical area of the anterior hypothalamus (PeFAH) between the paraventricular hypothalamic nucleus and fornix, that abundantly expresses chondroitin sulfate proteoglycans (CSPGs). The PeFAH strongly stained with markers for chondroitin sulfate/CSPGs such as Wisteria floribunda agglutinin and antibodies against aggrecan and chondroitin 6 sulfate. Nissl‐stained sections of the PeFAH clearly distinguished it as a region of comparatively low density compared to neighboring regions, the paraventricular nucleus and central division of the anterior hypothalamic area. Immunohistochemical and DNA microarray analyses suggested that PeFAH contains sparsely distributed calretinin‐positive neurons and a compact cluster of enkephalinergic neurons. Neuronal tract tracing revealed that both enkephalin‐ and calretinin‐positive neurons project to the lateral septum (LS), while the PeFAH receives input from calbindin‐positive LS neurons. These results suggest bidirectional connections between the PeFAH and LS. Considering neuronal subtype and projection, part of PeFAH that includes a cluster of enkephalinergic neurons is similar to the rat perifornical nucleus and guinea pig magnocellular dorsal nucleus. Finally, we examined c‐Fos expression after several types of stimuli and found that PeFAH neuronal activity was increased by psychological but not homeostatic stressors. These findings suggest that the PeFAH is a source of enkephalin peptides in the LS and indicate that bidirectional neural connections between these regions may participate in controlling responses to psychological stressors.
Probing the role of highly conserved residues in triosephosphate isomerase – analysis of site specific mutants at positions 64 and 75 in the Plasmodial enzyme
Authors: Bandyopadhyay Debarati , Murthy Mathur R. N. , Balaram Hemalatha , Balaram Padmanabhan 
Published: July 2015

Highly conserved residues in enzymes are often found to be clustered close to active sites, suggesting that functional constraints dictate the nature of amino acid residues accommodated at these sites. Using the Plasmodium falciparum triosephosphate isomerase (PfTIM) enzyme (EC 5.3.1.1) as a template, we have examined the effects of mutations at positions 64 and 75, which are not directly involved in the proton transfer cycle. Thr (T) occurring at position 75 is completely conserved, whereas only Gln (Q) and Glu (E) are accommodated at position 64. Biophysical and kinetic data are reported for four T75 (T75S/V/C/N) and two Q64 (Q64N/E) mutants. The dimeric structure is weakened in the Q64E and Q64N mutants, whereas dimer integrity is unimpaired in all four T75 mutants. Measurement of the concentration dependence of enzyme activity permits an estimate of Kd values for dimer dissociation (Q64N = 73.7 ± 9.2 nm and Q64E = 44.6 ± 8.4 nm). The T75S/V/C mutants have activities comparable to the wild‐type enzyme, whereas a fourfold drop is observed for T75N. All four T75 mutants show a dramatic fall in activity between 35 °C and 45 °C. Crystal structure determination of the T75S/V/N mutants provides insights into the variations in local interactions, with the T75N mutant showing the largest changes. Hydrogen‐bond interactions determine dimer stability restricting the choice of residues at position 64 to Gln (Q) and Glu (E). At position 75, the overwhelming preference for Thr (T) may be dictated by the imperative of maintaining temperature stability of enzyme activity.DatabaseStructural data have been deposited in the Protein Data Bank under accession numbers 4ZZ9, 5BMW, 5BMX, 5BNK and 5BRB.