bluuebunny/crossref_metadata_2025_split huggingface dataset:
The immunomodulatory CEA cell adhesion molecule 6 (CEACAM6/CD66c) is a candidate receptor for the influenza A virus
Authors: Rahman Shah Kamranur , Ansari Mairaj Ahmed , Gaur Pratibha , Ahmad Imtiyaz , Chakravarty Chandrani , Verma Dileep Kumar , Chhibber Sanjay , Nehal Naila , Sellathanby Shanmugaapriya , Wirth Dagmar , Waris Gulam , Lal Sunil K. 
Published: January 2017

AbstractTo establish a productive infection in host cells, viruses often use one or multiple host membrane glycoprotein as their receptors. For Influenza A virus (IAV) such a glycoprotein receptor has not been described, to date. Here we show that IAV is using the host membrane glycoprotein CD66c as a receptor for entry into human epithelial lung cells. Neuraminidase (NA), a viral spike protein binds to CD66c on the cell surface during IAV entry into the host cells. Lung cells overexpressing CD66c showed an increase in virus binding and subsequent entry into the cell. Upon comparison, CD66c demonstrated higher binding capacity than other membrane glycoproteins (EGFR and DC-SIGN) reported earlier to facilitate IAV entry into host cells. siRNA mediated knockdown of CD66c from lung cells inhibited virus binding on cell surface and entry into cells. Blocking CD66c by antibody on the cell surface resulted in decreased virus entry. We found CD66c is a specific glycoprotein receptor for influenza A virus that did not affect entry of non-IAV RNA virus (Hepatitis C virus). Finally, IAV pre-incubated with recombinant CD66c protein when administered intranasally in mice showed decreased cytopathic effects in mice lungs. This publication is the first to report CD66c (CEACAM6) as a glycoprotein receptor for Influenza A virus.Significance StatementCells are enclosed by a semipermeable membrane that allows selective exchange of biomolecules between cells and their surroundings. A set of specialized proteins in this semipermeable membrane, work like gatekeepers to the cell and regulate entry of these biomolecules. One class of such surface proteins is termed as receptors. Viruses bind to one or more of these receptors and manipulate gatekeepers for their own successful entry into host-cells. A membrane protein that influenza A virus (Flu virus) uses for entry into the cells was not discovered till date. This study reports for the first time, a receptor for influenza A virus, that was sought after by researchers for decades. The viral receptor is a promising target that can be used to inhibit virus entry into host cells.
Allele Frequency Spectrum in a Cancer Cell Population
Authors: Ohtsuki H. , Innan H. 
Published: January 2017

ABSTRACTA cancer grows from a single cell, thereby constituting a large cell population. In this work, we are interested in how mutations accumulate in a cancer cell population. We provided a theoretical framework of the stochastic process in a cancer cell population and obtained near exact expressions of allele frequency spectrum or AFS (only continuous approximation is involved) from both forward and backward treatments under a simple setting; all cells undergo cell division and die at constant rates,bandd, respectively, such that the entire population grows exponentially. This setting means that once a parental cancer cell is established, in the following growth phase, all mutations are assumed to have no effect onbord(i.e., neutral or passengers). Our theoretical results show that the difference from organismal population genetics is mainly in the coalescent time scale, and the mutation rate is defined per cell division, not per time unit (e.g., generation). Except for these two factors, the basic logic are very similar between organismal and cancer population genetics, indicating that a number of well established theories of organismal population genetics could be translated to cancer population genetics with simple modifications.
The differential spatiotemporal expression pattern of shelterin genes throughout lifespan
Authors: Wagner Kay-Dietrich , Ying Yilin , Leong Waiian , Jiang Jie , Hu Xuefei , Chen Yi , Michiels Jean-François , Lu Yiming , Gilson Eric , Wagner Nicole , Ye Jing 
Published: January 2017

AbstractShelterin forms the core complex of telomere proteins and plays critical roles in protecting telomeres against unwanted activation of the DNA damage response and in maintaining telomere length homeostasis. Although shelterin expression is believed to be ubiquitous for stabilization of chromosomal ends, some evidence suggests that some shelterin subunits have tissue-specific functions. However, very little is known regarding how shelterin subunit gene expression is regulated during development and aging. Using two different animal models, the mouse and zebrafish, we reveal herein that shelterin subunits exhibit distinct spatial and temporal expression patterns that do not correlate with the proliferative status of the organ systems examined. Together, this work shows that the shelterin subunits exhibit distinct spatiotemporal expression patterns, suggesting important tissue-specific functions during development throughout the lifespan.
Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions
Authors: Martins André L. , Walavalkar Ninad M. , Anderson Warren D. , Zang Chongzhi , Guertin Michael J. 
Published: January 2017

AbstractCoupling molecular biology to high throughput sequencing has revolutionized the study of biology. Molecular genomics techniques are continually refined to provide higher resolution mapping of nucleic acid interactions and structure. Sequence preferences of enzymes can interfere with the accurate interpretation of these data. We developedseqOutBiasto characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymatic sequence biases.SeqOutBiasefficiently corrects DNase-seq, TACh-seq, ATAC-seq, MNase-seq, and PRO-seq data. We show thatseqOutBiascorrection facilitates identification of true molecular signatures resulting from transcription factors and RNA polymerase interacting with DNA.
The eBethArké Syriac digital library: a case study
Authors: Beard Isaiah 
Published: January 2017

Purpose
The purpose of this paper is to review and describe the teamwork, collaboration and learning experiences involved in meeting the unique challenges of establishing a new digital library for Syriac collections. The eBetharké Syriac Digital Library Portal is a collaborative effort between the libraries at Rutgers, The State University of New Jersey, and the Beth Mardutho Syriac Institute, a traditional library of texts, to create a specialized digital library collection online. This digital library features content in and relating to Syriac, an Aramaic dialect spoken in the first century A.D. and for which a great deal of historically significant documents was written during the period.

Design/methodology/approach
This task required effort and research on multiple fronts, including software development; collaboration on technical, interpersonal and policy-based levels; and in overcoming challenges related to the predominant computing platforms installed and in use by potential users of this digital library.

Findings
This collaboration provided significant new challenges and learning experiences among the staff who worked on this project and provides a base upon which our digital library platforms can diversify and be more culturally aware.

Social implications
There have been increasing calls within the academic community for better support in the technological space for this and other contemporary languages of the region. Creation of such a platform and expanding it significantly would benefit scholars of Middle Eastern texts in much the same way digital repositories have revolutionized online text access for the Western world.

Originality/value
The project is unique in that it is believed to the first production-level, digital preservation-specific Syriac digital library of its kind. It supports the display of metadata and descriptive details for digital library objects not just in English, but in Arabic and Syriac languages as well, where appropriate
The devil is in the detail: Bourdieu and teachers’ early career learning
Authors: Kirkby Jane , Moss Julianne , Godinho Sally 
Published: January 2017

Purpose
The purpose of this paper is to present how the social learning theory of Bourdieu (1990; Bourdieu and Passeron, 1990) can be a valuable tool to investigate mentoring relationships of beginning teachers with their more experienced colleagues. Bourdieu’s work provides a lens to magnify the social exchanges that occur during the mentoring relationship, so that what tends to be hidden in the “logic of practice” (Bourdieu, 1990) is drawn into view. The paper shows how the mentor is ascribed power that enables domination, and how this tends to result in cultural reproduction. A case study is used to identify aspects of social and cultural learning that demonstrate this process.

Design/methodology/approach
The paper draws on a year-long narrative inquiry of beginning secondary teachers’ mentoring experiences in the state of Victoria, Australia. The data were generated through in-depth interviews and participants’ diary entries to answer the research question “What personal, professional knowledge is developed through beginning teachers’ early experiences with induction and mentoring?”

Findings
The researcher found that attention to minutiae of mentor/mentee interactions can suggest how symbolic violence shapes personal, professional knowledge.

Research limitations/implications
This small-scale study has some limitations. However, as an illustration of organisational learning, with strong connections to Bourdieu’s theoretical work, it can provide some illuminating insights into how policy can be enacted at the micro-level. In particular, there are implications for how mentor teachers engage in their roles and understand the potential impact of their interactions with beginning teachers.

Originality/value
This study applies Bourdieu’s framework of cultural reproduction as an analysis tool for a qualitative study of the mentoring of beginning teachers.
An Analysis of Turkey's and BRICS’ Voting Cohesion in the UN General Assembly during 2002–2014
Authors: Kurşun Ali Murat , Parlar Dal Emel 
Published: January 2017

AbstractThis paper attempts to analyze the voting behavior of Turkey in the UN General Assembly between 2002 and 2014 in comparison with those of the Brazil, Russia, India, China and South Africa (BRICS) countries by using selected reference groups of India, Brazil, South Africa (IBSA), EU, permanent members of the UN Security Council (P5) and the Western group of P5 (USA, UK, France) with the help of a two layered methodology. In doing so, this paper, with a two‐layered quantitative and qualitative methodological model, empirically tests Turkey's voting alignments and cohesion scores in the UN General Assembly to provide a comparative perspective on the degree of foreign policy cohesion among Turkey and its BRICS peers by comparing the group and pair‐wise ‘cohesion’ results. Finally, this paper will qualitatively analyze and discuss Turkey's exceptional voting behaviors and alignments with both the Western group of P5 and the BRICS to understand the nature of the international issues leading to convergences or divisions between Turkey and the BRICS and to demonstrate Turkey's in‐between and dual foreign policy role in international affairs.
Effect of selective laser trabeculoplasty on ocular haemodynamics in primary open‐angle glaucoma
Authors: Pillunat Karin R. , Spoerl Eberhard , Terai Naim , Pillunat Lutz E. 
Published: January 2017

AbstractPurposeSelective laser trabeculoplasty (SLT) is known to reduce intraocular pressure (IOP) effectively. The aim of this study, however, was to evaluate the effect ofSLTon ocular haemodynamics.MethodsA total of 69 eyes of 69 patients (age 67.8 ± 9.9 years) with already treated primary open‐angle glaucoma who were assigned forSLTfor furtherIOPreduction were consecutively enrolled in this prospective interventional case series. Intraocular pressure, the ocular pulse amplitude (OPA), ocular pulse volume (OPV) and pulsatile ocular blood flow (pOBF) were assessed with the Ocular Blood Flow Analyzer prior to and 3 months afterSLT.ResultsIntraocular pressure was statistically significantly reduced from 16.0 ± 5.4 mmHg to 12.8 ± 4.0 mmHg (p = 0.001). TheOPAdid not change (p = 0.783) afterIOPreduction followingSLT.OPVandpOBFincreased statistically significantly.OPVincreased from 7.33 ± 3.05 to 8.59 ± 3.35 μl (17.2%; p = 0.001) andpOBFfrom 17.11 ± 5.42 to 19.74 ± 6.59 μl/s (15.4%; p = 0.002).ConclusionSelective laser trabeculoplasty probably does not induce any pharmacological changes effecting systemic blood pressure or ocular blood flow as topicalIOP‐lowering medication might do, nor does it change biomechanical properties of the eye as surgery could. Therefore, an increase in ocular blood flow followingSLTcan only be explained by the reduction inIOPand might be a sign of dysfunctional autoregulation in glaucoma patients.
Sequential high‐ and low‐dose systemic corticosteroid therapy for severe childhood alopecia areata
Authors: Jahn‐Bassler Karin , Bauer Wolfgang Michael , Karlhofer Franz , Vossen Matthias G. , Stingl Georg 
Published: January 2017

SummaryBackgroundGiven the limited number of therapeutic options, severe childhood alopecia areata (AA) poses a clinical challenge. The best and most rapid response rates can be achieved with high‐dose systemic corticosteroids, however, relapse following treatment discontinuation is inevitable. Due to systemic side effects, long‐term high‐dose corticosteroid regimens are not feasible. Following initial pulse therapy, continuation of corticosteroid therapy at a dose below the Cushing threshold might be able to suppress disease activity without causing severe side effects.Patients and methodsThirteen children with severe AA were enrolled in our open observational study. Seven had alopecia totalis or universalis; the remaining six children had multifocal alopecia affecting more than 50 % of the scalp. The treatment regimen consisted of initial pulse therapy with prednisolone 2 mg/kg PO, which was subsequently tapered to a maintenance dose below the individual Cushing threshold within nine weeks. Children were followed‐up for one to three years.ResultsSixty‐two percent of individuals showed complete hair regrowth. The mean time to response was 6.6 weeks. Said response was sustained with maintenance therapy for the entire follow‐up period. Noticeable side effects included weight gain (1–3 kg), which was observed in all children, and mild steroid acne in 23 % of cases.ConclusionsSequential high‐ and low‐dose prednisolone therapy is an effective and safe therapeutic option for childhood AA.
Therapieoptionen beim Pyoderma gangraenosum
Authors: Quist Sven R. , Kraas Luise 
Published: January 2017

ZusammenfassungDas Pyoderma gangraenosum (PG) gehört zu den orphan diseases, deren Erforschung sich lediglich auf einzelne, randomisierte, multizentrische sowie retrospektive Studien stützen kann und überwiegend auf Fallserien an kleinen Patientenkollektiven beruht. Die Therapie basiert neben topischen und lokal intraläsionalen Therapieoptionen, bei initialem und leichtem Krankheitsverlauf, insbesondere auf der Gabe von Systemtherapeutika. Diese beinhaltet neben den systemischen Glukokortikosteroiden und Ciclosporin A (CsA) auch Biologika wie intravenöses Immunglobulin G (IVIG), die TNFα‐Inhibitoren Infliximab, Adalimumab und Etanercept, den IL‐12/23‐Antikörper Ustekinumab, den Interleukin‐1‐Rezeptorantagonist Anakinra und den Interleukin‐1β‐Antikörper Canakinumab. Die besten evidenzbasierten Studienergebnisse liegen zu CsA, Prednisolon und Infliximab vor, letzteres insbesondere bei gleichzeitigem Vorliegen einer Colitis ulcerosa oder eines Morbus Crohn. Kleinere Fallserien liegen für ein Ansprechen auf IVIG und Canakinumab vor. Obwohl die Erstbeschreibung durch Brocq fast 100 Jahren zurückliegt und die Behandlungsnotwendigkeit des PG früh erkannt wurde, bleibt die Therapie des PG bis heute eine klinische Herausforderung. Weitere klinische Studien, insbesondere an dringend erforderlichen größeren Patientenkollektiven, ein besseres Verständnis der Ätiopathogenese, der Einsatz moderner zielgerichteter Therapien mit höherer Effektivität und geringerer Nebenwirkungsrate als die konventionellen Immunsuppressiva Prednisolon und CsA lassen trotz des seltenen aber schwerwiegenden Krankheitsbildes eine Verbesserung der Therapieoptionen in Zukunft erwarten.
Echocardiographic characteristics of pulmonary artery involvement in Takayasu arteritis
Authors: Jiang Wei , Yang Yuanhua , Lv Xiuzhang , Li Yidan , Ma Zhanhong , Li Jifeng 
Published: January 2017

BackgroundUp to 50% patients with Takayasu arteritis have pulmonary artery involvement. Hence, the early identification of pulmonary artery involvement to facilitate prompt treatment is required.MethodsThis retrospective study was performed in patients diagnosed with Takayasu arteritis between January 2009 and January 2016. Pulmonary artery involvement was confirmed with computed tomographic pulmonary angiography. Images from transthoracic echocardiography in three windows (suprasternal right pulmonary artery long‐axis view, parasternal aortic short‐axis view, and subxiphoid view) were documented and analyzed.ResultsA total of 27 patients had Takayasu arteritis and pulmonary artery involvement. Characteristic changes identified by echocardiography included luminal medium‐to‐high echogenic signals, stenosis, and occlusion, as well as intimal thickening. Left pulmonary artery involvement was revealed in the parasternal aortic short‐axis view. Right pulmonary artery involvement was best observed in the suprasternal right pulmonary artery long‐axis view, with complementary views from the parasternal aortic short‐axis and subxiphoid angles. Pulmonary trunk involvement was not observed in all three windows.ConclusionsTransthoracic echocardiography could be a useful noninvasive test to detect pulmonary artery involvement in patients with Takayasu arteritis.
Disturbance maintains native and exotic plant species richness in invaded grassy woodlands
Authors: Driscoll Don A. 
Published: January 2017

AbstractQuestionCommunity invasion and dominance by exotic species can be abetted by disturbance and elevated nutrient levels. However, impacts of exotics on native species are often manifest through competition, suggesting disturbance or nutrient management could benefit native species. I therefore asked: does nutrient reduction through carbon addition, or disturbance to reduce biomass, contribute to restoration by increasing occurrence and richness of native plant species?LocationSE Australia.MethodsUsing a field experiment spanning 4 yrs, this study assessed the potential for carbon addition, three types of disturbance (burn, crop, slash) and their interaction with native herbivore grazing to reduce exotic, and increase native, plant species in a critically endangered grassy woodland in SE Australia.ResultsAdding carbon reduced occurrence of one native and three exotic species, while increasing one exotic and one native species. The value of adding carbon for restoration was therefore ambiguous. Fencing to exclude the high‐density kangaroo population had temporary beneficial effects, suggesting that grazing reduced the number of native and exotic plant species by up to 56% and 21%, respectively. Species richness declined by year 3 in fenced areas, likely through competitive exclusion. Burn, slash and crop treatments also provided disturbance that maintained species richness and occurrence of many species, both native and exotic. Most grazing interactions reflected the benefit of alternative disturbance in the absence of grazing. However, there was also evidence that two species declined when crop and grazing acted in combination.ConclusionsVery high grazing by native herbivores reduced plant species richness in this study. However, grazing or other forms of disturbance appeared critical for preventing a small number of exotic species from driving down occurrence and richness of many other native and exotic plant species. Although increased exotic species richness is undesirable, disturbance led to a better outcome for conservation than the low‐disturbance alternatives.
Evidence of extinction debt through the survival and colonization of each species in semi‐natural grasslands
Authors: Otsu Chiaki , Iijima Hayato , Nagaike Takuo , Hoshino Yoshinobu 
Published: January 2017

AbstractAimsThere is a time lag between loss of semi‐natural grassland and a reduction of population size that leads to the extinction of grassland plant specialists; thus, current species richness in the grassland may include an ‘extinction debt’. However, previous studies have not tried to detect the presence of an extinction debt from individual species loss and colonization rates in an assemblage of plant species. In addition, few researchers have studied extinction debt using factors other than landscape changes [e.g. the impacts of management (mowing or burning), habitat use by large herbivores or climate factors]. In the present study, we examined an extinction debt for vascular plant species by monitoring their survival and colonization dynamics.LocationAbandoned and managed semi‐natural grasslands, central Japan, where the area of grasslands has decreased considerably.MethodsWe re‐surveyed species compositions in the 2000s in plots that had been surveyed in the 1980s, and estimated the impacts of the past (1910s) and recent (1980s–2000s) proportion of the total grassland area and the abovementioned factors on species dynamics during the past 20 yrs using hierarchical Bayesian models.ResultsIn abandoned grasslands, the past grassland proportion was significantly positively associated with the probabilities of survival of 96% of the grassland specialists and of colonization by 21% of these specialists. The effects of the past grassland proportion on the specialists were much stronger than those of recent grassland proportion and the other factors studied (i.e. herbivores, climate). In managed grasslands, however, the past grassland proportion had little effect on survival of and colonization by specialists from the result that few specialists were significantly affected by past grassland proportion.ConclusionsWe found higher probabilities of both survival of and colonization by grassland specialists at sites with larger past habitat areas, which suggests that there is a time lag after habitat loss before the loss of specialists. In addition, we found that continuous management inhibits payment of the extinction debt created by the habitat loss.