bluuebunny/crossref_metadata_2025_split huggingface dataset:
PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq
Authors: Wen Bo , Xu Shaohang , Zhou Ruo , Zhang Bing , Wang Xiaojing , Liu Xin , Xu Xun , Liu Siqi 
Published: June 2016

Abstract
Background
Peptide identification based upon mass spectrometry (MS) is generally achieved by comparison of the experimental mass spectra with the theoretically digested peptides derived from a reference protein database. Obviously, this strategy could not identify peptide and protein sequences that are absent from a reference database. A customized protein database on the basis of RNA-Seq data is thus proposed to assist with and improve the identification of novel peptides. Correspondingly, development of a comprehensive pipeline, which provides an end-to-end solution for novel peptide detection with the customized protein database, is necessary.

Results
A pipeline with an R package, assigned as a PGA utility, was developed that enables automated treatment to the tandem mass spectrometry (MS/MS) data acquired from different MS platforms and construction of customized protein databases based on RNA-Seq data with or without a reference genome guide. Hence, PGA can identify novel peptides and generate an HTML-based report with a visualized interface. On the basis of a published dataset, PGA was employed to identify peptides, resulting in 636 novel peptides, including 510 single amino acid polymorphism (SAP) peptides, 2 INDEL peptides, 49 splice junction peptides, and 75 novel transcript-derived peptides. The software is freely available from http://bioconductor.org/packages/PGA/, and the example reports are available at http://wenbostar.github.io/PGA/.

Conclusions
The pipeline of PGA, aimed at being platform-independent and easy-to-use, was successfully developed and shown to be capable of identifying novel peptides by searching the customized protein database derived from RNA-Seq data.
Detection of disseminated tumor cells in lymph nodes from patients with early stage non-small cell lung cancer
Authors: Kongsgaard Ane , Boye Kjetil , Fodstad Øystein , Juell Siri , Jørgensen Lars H. , Solberg Steinar , Helland Åslaug , Brustugun Odd Terje , Mælandsmo Gunhild Mari 
Published: June 2016

Abstract
Background
The regional lymph node involvement is a major prognostic factor in patients with non-small cell lung cancer (NSCLC) undergoing surgical resection. Disease relapse is common, suggesting that early disseminated disease is already present in the regional lymph nodes at the time of surgery, and that the current nodal staging classification might be suboptimal. Early detection of disseminated tumor cells (DTCs) in lymph nodes could potentially enable identification of subcategories of patients with high risk of disease relapse.

Method
Lymph node samples were collected from 128 NSCLC patients at the time of surgery and the presence of DTCs determined by immunomagnetic selection (IMS) using the MOC31 antibody recognizing EpCAM. Results obtained with IMS were compared to the pathological staging obtained by histopathology. Associations between the presence of DTCs and clinicopathological variables and patient outcome were investigated.

Results
DTCs were detected in 40 % of the lymph node samples by IMS. Their presence was significantly associated with pN status as assessed by histopathology, and samples from 83 % of the patients with lymph node metastases (pN1-2) had detectable DTCs. In the group of patients who were negative for lymph node metastases by standard histopathology (pN0) DTCs were detected in 32 %. The presence of DTCs was not associated with any other clinicopathological variables. Patients with IMS-positive samples showed decreased relapse free survival compared to patients with IMS-negative samples, but the difference was not statistically significant. The pN status was significantly associated with both relapse free and overall survival, but the presence of DTCs had no prognostic impact in the subcategory of patients with pN0 status.

Conclusion
Our findings do not support further development of lymph node DTC detection for clinical use in early stage NSCLC.
CD68 on rat macrophages binds tightly to S100A8 and S100A9 and helps to regulate the cells’ immune functions
Authors: Okada Kohki , Arai Satoshi , Itoh Hiroshi , Adachi Souichi , Hayashida Masahiko , Nakase Hiroshi , Ikemoto Masaki 
Published: June 2016

Abstract
S100A8 and S100A9 (S100 proteins) are regulators of immune cells of myeloid origin. Whereas S100 proteins are found at high concentrations in such cells, their immunologic roles remain unclear. We focused on cluster of differentiation 68 (CD68). The aim of this study is to investigate whether CD68 binds to extracellular S100A8 and/or S100A9 and subsequently participates in the regulation of the cells’ immune functions. ELISA and affinity chromatography showed that both recombinant rat S100A8 (r-S100A8) and r-S100A9 bound to r-CD68, but not to r-CD14. Flow cytometry clearly showed evidences supporting above the 2 results. As analyzed by flow cytometry, a less amount of r-S100A8 or r-S100A9 bound to the macrophages treated with some deglycosylation enzymes. In an in vitro assay, the expression levels of S100A8 and S100A9 were significantly suppressed after the macrophages had been treated with an anti-CD68 antibody (ED1). As stimulated macrophages with r-S100A9, the expression of IL-1β mRNA in macrophages, which were treated with anti-TLR4 or -RAGE antibodies, was significantly suppressed. r-S100A8 up-regulated IL-6 and IL-10 mRNAs, while r-S100A9 did TNF-α and IL-6 mRNAs, although these regulations were not statistically significant. Small interfering CD68 also significantly suppressed activation of macrophages through an autocrine pathway by r-S100A8 or r-S100A9. In macrophages stimulated with LPS, fluorescent immunologic staining showed that most CD68 colocalized with S100A8 or S100A9 and that the levels of all 3 molecules were markedly increased. In conclusion, CD68 on macrophages binds to S100A8 and S100A9 and thereby, plays a role in the regulation of the cells’ immune functions.
Nicotine induces neutrophil extracellular traps
Authors: Hosseinzadeh Ava , Thompson Paul R , Segal Brahm H , Urban Constantin F 
Published: June 2016

Abstract
NETs serve to ensnare and kill microbial pathogens. However, NETs can at the same time contribute to tissue damage and excessive inflammation. Nicotine is a major toxic agent and has been associated with exacerbated inflammatory diseases. The current study aimed at investigating the role of nicotine, the addictive component of tobacco and electronic cigarettes, on triggering NET formation. We report that nicotine induces neutrophils to release NETs in a dose-dependent manner. Nicotine-induced NET formation is mediated via nicotine acetylcholine receptors, depends on Akt and PAD4 activation, but is Nox2-independent, as demonstrated by pharmacological inhibition of Nox2 and by use of Nox2-deficient mouse neutrophils. These findings demonstrate that nicotine induces NETs, which may in turn contribute to smoking-related diseases.
An organelle K+ channel is required for osmoregulation in Chlamydomonas reinhardtii
Authors: Xu Feifei , Wu Xiaoan , Jiang Lin-Hua , Zhao Hucheng , Pan Junmin 
Published: June 2016

ABSTRACT
Fresh water protozoa and algae face hypotonic challenges in their living environment. Many of them employ a contractile vacuole system to uptake excessive water from the cytoplasm and expel it to the environment to achieve cellular homeostasis. K+, a major osmolyte in contractile vacuole, is predicted to create higher osmolarity for water influx. Molecular mechanisms for K+ permeation through the plasma membrane have been well studied. However, how K+ permeates organelles such as the contractile vacuole is not clear. Here, we show that the six-transmembrane K+ channel KCN11 in Chlamydomonas is exclusively localized to contractile vacuole. Ectopic expression of KCN11 in HEK293T cells results in voltage-gated K+ channel activity. Disruption of the gene or mutation of key residues for K+ permeability of the channel leads to dysfunction of cell osmoregulation in very hypotonic conditions. The contractile cycle is inhibited in the mutant cells with a slower rate of contractile vacuole swelling, leading to cell death. These data demonstrate a new role for six-transmembrane K+ channels in contractile vacuole functioning and provide further insights into osmoregulation mediated by the contractile vacuole.
In vivo regulation of integrin turnover by outside-in activation
Authors: López-Ceballos Pablo , Herrera-Reyes Alejandra Donají , Coombs Daniel , Tanentzapf Guy 
Published: June 2016

ABSTRACT
The development of three-dimensional tissue architecture requires precise control over the attachment of cells to the extracellular matrix (ECM). Integrins, the main ECM-binding receptors in animals, are regulated in multiple ways to modulate cell–ECM adhesion. One example is the conformational activation of integrins by extracellular signals (‘outside-in activation’) or by intracellular signals (‘inside-out activation’), whereas another is the modulation of integrin turnover. We demonstrate that outside-in activation regulates integrin turnover to stabilize tissue architecture in vivo. Treating Drosophila embryos with Mg2+ and Mn2+, known to induce outside-in activation, resulted in decreased integrin turnover. Mathematical modeling combined with mutational analysis provides mechanistic insight into the stabilization of integrins at the membrane. We show that as tissues mature, outside-in activation is crucial for regulating the stabilization of integrin-mediated adhesions. This data identifies a new in vivo role for outside-in activation and sheds light on the key transition between tissue morphogenesis and maintenance.
Προσδοκίες και οφέλη γυναικών από τη φοίτησή τους στο ΕΑΠ
Authors: Βασάλα Παρασκευή , Κονταρίδου Ειρήνη 
Published: June 2016

Η ευελιξία και η μορφωτική αυτονομία των εκπαιδευομένων καθιστά την ΑεξΑΕ ιδιαίτερα φιλική στις ενήλικες γυναίκες, με τους ποικίλους και συχνά συγκρουόμενους ρόλους εντός των στερεοτυπικά και πατριαρχικά διαμορφωμένων κοινωνικών δομών. Αντικείμενο της έρευνας αποτέλεσαν οι προσδοκίες και τα οφέλη που εξασφάλισαν από τη φοίτησή τους οι μεταπτυχιακές φοιτήτριες του Ελληνικού Ανοικτού Πανεπιστημίου (ΕΑΠ) που είχαν κάνει προπτυχιακές σπουδές στο ίδρυμα. Η έρευνα διεξήχθη το 2012 με ημι-δομημένη συνέντευξη και το δείγμα αποτέλεσαν 17 φοιτήτριες. Τα αποτελέσματα ανέδειξαν πως η δυναμική συμμετοχή των γυναικών στο ΕΑΠ αντικατοπτρίζει την ανάγκη για κοινωνική εξέλιξη και ενεργοποίηση, αλλά και την αγωνία τους να μην παραγκωνισθούν στην ασταθή και κρίσιμη οικονομική – κοινωνική συγκυρία. Η εκπαιδευτική διεργασία τις βοήθησε να καλλιεργήσουν στάσεις, γνώσεις και δεξιότητες που προήγαγαν την κατάρτιση και την προσωπική τους καλλιέργεια και ενδυνάμωση. Τέλος, η «φωνή» των γυναικών – συμβάλλοντας στην κατανόηση του νοήματος που οι ίδιες δίνουν στις σπουδές τους – εμπλουτίζει την ακαδημαϊκή συζήτηση και αναδεικνύει πεδία για μελλοντικές σχετικές έρευνες.
Διδασκαλία ως φαινόμενο χωροχρονικής αποπλαισίωσης και ο ρόλος των νέων και ψηφιακών Μέσων για το σχεδιασμό της
Authors: Αλιβίζος Σοφός (Λοΐζος) 
Published: June 2016

Το άρθρο επικεντρώνεται στις διαφοροποιήσεις που λαμβάνουν χώρα στο φαινόμενο της διδασκαλίας και επηρεάζουν προφανώς την διευθέτηση της εκπαιδευτικής διαδικασίας, τόσο στη δια ζώσης όσο και σε μικτές μορφές εκπαίδευσης. Η ανάλυση εστιάζει στη σχέση που υπάρχει μεταξύ Διδασκαλίας, Μέσων και Κοινωνίας η οποία τεκμηριώνεται σε τρεις ενότητες. Η πρώτη παρουσιάζει τέσσερα στάδια εξέλιξης της διδασκαλίας σε κοινωνίες με διαφορετικό τρόπο οργάνωσης και πολιτισμικά τεχνουργήματα. Η δεύτερη σκιαγραφεί τη χωροχρονική αποπλαισίωση των περιβαλλόντων μάθησης κάνοντας αναφορά στο μετρικό και στο ψηφιακό χώρο καθώς επίσης και σε μορφές ηλεκτρονικής και διαδικτυακής μάθησης. Η τρίτη εστιάζει στη σημασία της ολιστικής παιδαγωγική θεώρησης των ηλεκτρονικών περιβαλλόντων. Στο τέλος διατυπώνονται συμπεράσματα για την παιδαγωγικά τεκμηριωμένη ένταξη ψηφιακών μέσων στην εκπαιδευτική διαδικασία.
Η πρωτοβουλία αριστείας στα γερμανικά πανεπιστήμια: το πανεπιστημιακό όραμα του μέλλοντος μεταξύ παγκόσμιου ακαδημαϊκού ανταγωνισμού και Νέας Δημόσιας Διοίκησης
Authors: Γιαννακόπουλος Άγγελος , Μάρας Κώστας 
Published: June 2016

<p>Το άρθρο αναλύει τον θεσμό αριστείας που εισήχθη το 2006 στην ανώτατη εκπαίδευση στη Γερμανία με γνώμονα τέσσερις κυρίως άξονες. Κατά πρώτον, περιγράφεται η γενικότερα προβληματική κατάσταση όσον αφορά δυνατότητες έρευνας που παρέχονται στους μεταδιδακτορικούς επιστήμονες οι οποίοι αποτελούν την πολυπληθέστερη ομάδα επιστημόνων που εργάζεται στα γερμανικά πανεπιστήμια. Ακολούθως, σημειώνεται πως τα κριτήρια αξιολόγησης της αριστείας καθ' εαυτής είναι όχι μόνον ρευστά αλλά έχουν να κάνουν πολύ περισσότερο με όρους που ελάχιστα συγγενεύουν με την εξέχουσα επιστημονική απόδοση. Διαπιστώνεται πως η αριστεία είναι περισσότερο προϋπόθεση και συγχρόνως αποτέλεσμα της κατοχής κοινωνυχού κεφαλαίου, παρά προϊόν αντικειμενικής κριτηριολογίας, τυποποιημένων διαβαθμίσεων και ποσοτικών σταθμίσεων. Κατά τρίτον, η πρωτοβουλία αριστείας στα γερμανιχά πανεπιστήμια καθιστά φανερό το γεγονός μιας σημαντικής στροφής στη γενικότερη εκπαιδευτική 'φιλοσοφία' που στοχεύει στην αντικατάσταση της παραδοσιακής ιδέας του πανεπιστημίου με τις επιταγές της Νέας Δημόσιας Διοίκησης, δηλαδή την οικονομική αξιοποίηση των αποτελεσμάτων της έρευνας, την περιστολή των δαπανών λειτουργίας και διαχείρισης και την ορθολογικοποίηση της τρέχουσας λειτουργίας των ακαδημαϊκών θεσμών με γνώμονα τις αρχές οργάνωσης και διοίκησης επιχειρήσεων. Ενώ προκύπτουν έτσι σοβαρά ερωτήματα πάνω στο όραμα του πανεπιστημίου του μέλλοντος, το άρθρο αποτιμά, κατά τέταρτον, τις θεσμικές αλλαγές στο πανεπιστήμιο αριστείας της Konstanz, όπου επιβεβαιώνεται με τον καλύτερο τρόπο και σε όλα τα επίπεδα η προαναφερθείσα κριτική στον θεσμό.</p>
Selected Medication Safety Risks to Manage in 2016—Part II Methylergonovine Errors in Obstetrics
Authors: Cohen Michael R. , Smetzer Judy L. 
Published: June 2016

These medication errors have occurred in health care facilities at least once. They will happen again—perhaps where you work. Through education and alertness of personnel and procedural safeguards, they can be avoided. You should consider publishing accounts of errors in your newsletters and/or presenting them at your inservice training programs. Your assistance is required to continue this feature. The reports described here were received through the Institute for Safe Medication Practices (ISMP) Medication Errors Reporting Program. Any reports published by ISMP will be anonymous. Comments are also invited; the writers' names will be published if desired. ISMP may be contacted at the address shown below. Errors, close calls, or hazardous conditions may be reported directly to ISMP through the ISMP Web site ( www.ismp.org ), by calling 800-FAIL-SAFE, or via e-mail at ismpinfo@ismp.org . ISMP guarantees the confidentiality and security of the information received and respects reporters' wishes as to the level of detail included in publications.
Reducing Readmission at an Academic Medical Center: Results of a Pharmacy-Facilitated Discharge Counseling and Medication Reconciliation Program
Authors: Zemaitis Christopher T. , Morris Ginger , Cabie Maribeth , Abdelghany Osama , Lee Lorraine 
Published: June 2016

Background Hospital readmission has been identified as a key quality indicator and a target for reducing health care spending. Objective To evaluate the impact of a pharmacy-facilitated medication reconciliation and patient education model with post discharge follow-up on 30-day readmissions. Methods This prospective, historical control study included all patients admitted during a 6-month period to a general medicine unit with the highest 30-day readmission rate at Yale-New Haven Hospital. Patients were excluded if they expired prior to discharge, transferred, left against medical advice, were discharged to hospice, or were previously enrolled in the study. Upon admission, pharmacy technicians compiled the medication reconciliation information. Interventions were made by the pharmacist communicating with the patient's primary team. Medication and disease state counseling and final medication reconciliation were performed by the pharmacist before discharge. The primary outcome measure was 30-day readmission rates during the intervention period compared to the preceding 6 months and the same time period the previous year. Secondary outcomes included the total number of pharmacist-identified medication reconciliation interventions, total pharmacy resource utilization, and identification of patients at high risk for readmission. Results Study outcomes showed a 27% reduction in readmission during the intervention period. The pharmacist made a total of 546 medication interventions. The average pharmacist and pharmacy technician time per patient were 28.9 and 23.7 minutes, respectively. Conclusions Pharmacy-facilitated medication reconciliation and patient education of medicine patients decreased 30-day readmission rates.
Estudo de adaptação e validação de uma escala de perceção de liderança ética para líderes portugueses
Authors: Neves Maria de Lurdes Gomes , Jordão Filomena , Pina e Cunha Miguel , Vieira Diana Aguiar , Coimbra Joaquim Luís 
Published: June 2016

Os líderes influenciam o comportamento individual e organizacional, incluindo a dimensão ética, sendo igualmente influenciados pela suas expetativas, interpretações e interações com os outros (Glynn & Jamerson, 2006; Kellerman, 2004).Frequentemente intervêm em diferentes contextos éticos, o que torna difícil para as pessoas "boas" tomarem boas decisões em situações más" (Glynn & Jamerson, 2006, p. 154).A liderança ética pode ser considerada como a "demonstração de conduta normativamente adequada através de ações pessoais e das relações interpessoais, assim como a promoção de tal conduta para os liderados através de uma comunicação bidireccional, reforço e tomada de decisão" (Brown, Trevino & Harrison, 2005, 9.120).O estudo aqui apresentado teve como objetivo desenvolver uma escala de liderança ética (Hanges & Dickson, 2004) para líderes portugueses com base na adaptação e validação da escala realizada por De Hoog e Den Hartog (2008).Os resultados obtidos evidenciam qualidades psicométicas adequadas, com um valor elevado de consistência interna. As análises fatoriais exploratórias revelam uma estrutura que aponta para a existência de dois fatores para a escala definidos como Liderança Ètica e Liderança Despótica que integram as respetivas dimensões.Importa, futuramente realizar uma análise da estabilidade das escalas com outra amostra por forma a verificar-se a consistência do s valores obtidos.
Adaptação da Escala de Empatia com Animais (EEA) para a população portuguesa
Authors: Emauz Ana , Gaspar Augusta , Esteves Francisco , Carvalhosa Susana Fonseca 
Published: June 2016

O interesse pelo estudo das relações entre humanos e animais tem vindo a crescer nos últimos anos, mas a empatia para com animais é um tema ainda recente na literatura, levando a uma maior necessidade de desenvolver instrumentos adequados para a medir. A Escala de Empatia para com Animais (EEA, Paul, 2000) é o instrumento mais utilizado, tendo por isso sido escolhido para o presente estudo. Através de uma análise exploratória e confirmatória obteve-se um modelo estrutural com dois componentes, denominados de Desvinculação Emocional (DE) e Preocupação Empática com os Animais (PEA). A estrutura final reporta um modelo bem ajustado, com um bom nível de consistência interna, tanto da escala global, como das suas subescalas. Foi encontrada uma correlação positiva entre a EEA e outra escala de empatia traço dirigida a humanos (IRI), o que veio reforçar a validade de construto deste instrumento para a sua utilização no panorama nacional.
The Number of Pain Sites and Other Non‐pain Symptoms are Important Clues for Diagnosis: A Cross‐sectional Study of Outpatients with Multiple Somatic Complaints
Authors: Kita Keiichiro , Nagatsuma Masahiro , Wakaguri Akira , Sekijima Azusa , Watanabe Fumiko , Kuroiwa Maiko , Miura Taro , Koura Tomoyuki , Yoshida Kiichiro , Kuroiwa Shota , Yamashiro Seiji 
Published: June 2016

Background: In general practice, a wide variety of patients often present with various complaints. Some of them have multiple somatic symptoms, and it is possible for a general practitioner to miss an organic disease. In this cross‐sectional study, we retrospectively examined the correlation between the number of complaints and the prevalence of diseases in order to elucidate clues to help detect organic diseases in patients with multiple somatic complaints.Method: We evaluated 386 new walk‐in outpatients who presented to the department of general medicine at the Toyama University Hospital between January 2014 and December 2014 with pain symptoms. Symptoms were classified by the number of pain sites (NPS) and the number of other non‐pain complaints (NOC). Then we examined the association between these two variables and the final diagnosis.Results: The prevalence of organic diseases in the four and more NPS group was significantly higher than that of the three or less NPS group (66.7% and 27.5%, respectively). Psychiatric diseases were more prevalent in the group who had three and more NOC than in the patient population with two or less NOC (36.4% and 4.4%, respectively).Conclusion: Counting NPS and NOC could contribute to proper management of patients with multiple somatic complaints.
Economising, Strategising and the Vertical Boundaries of the firm
Authors: Leahy Dermot , Montagna Catia 
Published: June 2016

AbstractWe bridge the organisational economics and industrial economics literatures on the vertical boundaries of the firm by contextualising the transaction cost approach to the make-or-buy decision within an oligopolistic market structure. Firms invest in the quality of the intermediate resulting in the endogenous determination of the price of the intermediate and marginal production cost of the final good. We highlight new strategic incentives to outsource and/or vertically integrate and show how these incentives can result in asymmetric-mode-of-operations, investment and costs. We apply our model to a number of different international trading setups.
A Marxist Argumentative Scheme on Basic Income and Wage Share in an Anti-capitalist Agenda
Authors: Manjarin Edgar , Szlinder Maciej 
Published: June 2016

AbstractIn this article, we present an anti-capitalist argument for basic income based on its predicted effects on the wage share dynamics and its relation with the working class’ bargaining power. Our considerations are located in the Marxist tradition and based mainly on contributions to the Marxist analytical framework made by Rosa Luxemburg and Michał Kalecki. We argue that basic income should lead to a rise of the share of wages in the GDP, by significantly improving workers’ bargaining position in various ways: through increasing the effective demand and investments by redistributing income to the advantage of the poorer groups of the society; through guaranteeing the realisation of basic needs outside the labour market; through positive influence on the collective bargaining power, especially during a strike; and through enhancing engagement in alternative relations of production as well as in political struggle for a better situation of working people. We also distinguish some necessary conditions in a realistic historical scenario where the positive, anti-capitalist dynamic launched by basic income could be set into motion.