bluuebunny/crossref_metadata_2025_split huggingface dataset:
MAbTope: A Method for Improved Epitope Mapping
Authors: Bourquard Thomas , Musnier Astrid , Puard Vincent , Tahir Shifa , Ayoub Mohammed Akli , Jullian Yann , Boulo Thomas , Gallay Nathalie , Watier Hervé , Bruneau Gilles , Reiter Eric , Crépieux Pascale , Poupon Anne 
Published: October 2018

Abstract
Abs are very efficient drugs, ∼70 of them are already approved for medical use, over 500 are in clinical development, and many more are in preclinical development. One important step in the characterization and protection of a therapeutic Ab is the determination of its cognate epitope. The gold standard is the three-dimensional structure of the Ab/Ag complex by crystallography or nuclear magnetic resonance spectroscopy. However, it remains a tedious task, and its outcome is uncertain. We have developed MAbTope, a docking-based prediction method of the epitope associated with straightforward experimental validation procedures. We show that MAbTope predicts the correct epitope for each of 129 tested examples of Ab/Ag complexes of known structure. We further validated this method through the successful determination, and experimental validation (using human embryonic kidney cells 293), of the epitopes recognized by two therapeutic Abs targeting TNF-α: certolizumab and golimumab.
GM-CSF Culture Revisited: Preparation of Bulk Populations of Highly Pure Dendritic Cells from Mouse Bone Marrow
Authors: Jin Dongbin , Sprent Jonathan 
Published: October 2018

Abstract
Dendritic cells (DC) loaded with specific peptides are strongly immunogenic for T cells and can be used for cancer immunotherapy. For immunogenic tumors such as melanoma, injection of autologous DC loaded with tumor cell extracts or peptides can induce tumor regression but in only a small proportion of patients. Nevertheless, recent studies on the efficacy of checkpoint blockade for boosting antitumor immunity plus advances in defining tumor neoantigens are stimulating renewed interest in DC immunotherapy. Despite intensive investigation, however, preparation of bulk populations of mature DC has proved difficult, and most preparations contain a significant proportion of potentially tolerogenic immature DC. In this study, we have modified the well-established GM-CSF culture system to prepare substantial quantities of highly pure (&gt;95%) mature DC from mouse bone marrow cells and defined their progenitors. We show that obtaining high yields and purity of DC are heavily dependent on cell density in the cultures and the tempo of addition of growth and maturation stimuli. When loaded with specific peptide, the DC are strongly immunogenic for CD4 and CD8 T cells in vivo and elicit effective antitumor immunity.
Correlation study of thyroid nodule cytopathology and histopathology at two institutions in Jordan
Authors: Abdullah Niveen , Hajeer Manar , Abudalu Loay , Sughayer Maher 
Published: October 2018

Background:
Fine-needle aspiration (FNA) plays a fundamental role in determining the appropriate management for patients presenting with thyroid nodules.

Aims:
The aims of this study are to evaluate thyroid FNA test performance parameters through a cytohistological correlation.

Materials and Methods:
A retrospective analysis of all thyroid FNAs received over a period of 18 months was carried out. The findings were compared to their subsequent definite diagnoses on surgical specimens as well as to their follow-up repeat FNA results. A total of 499 thyroid FNAs were collected and reviewed against The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC). The percentage of each diagnostic category was calculated, and the implied risk of malignancy was determined by comparing the cytology results to their definite diagnoses obtained on the resection specimens. Analytical procedures were performed using Microsoft Excel.

Results:
Out of 499 thyroid FNAs, a benign interpretation was found in 273 patients (54.7%), atypia of undetermined significance in 81 (16.2%), follicular neoplasm in 20 (4%), suspicious for malignancy in 36 (7.2%), malignant in 32 (6.4%) and were nondiagnostic in 57 patients (11.4%). Only 101 patients (20.2%) underwent surgical resection and 47 (9.4%) underwent a follow-up FNA. After cytohistological correlation, FNA test performance, calculated by excluding the inadequate and undetermined categories revealed test sensitivity, specificity, and diagnostic accuracy of 95.6%, 54.8%, and 78.9%, respectively. The positive predictive value was 75.4%, and the negative predictive value was 89.5%.

Conclusions:
Our results are comparable to those previously published figures. The rate of atypia of undetermined significance/follicular lesion of undetermined significance is higher than what is currently recommended in TBSRTC.
Retour d’expérience : programme de sélection d’équipements et infrastructures de gestion des déchets adaptés au contexte des villes secondaires d’Afrique de l’Ouest
Authors: Dabire James , Gango Abdoulaye 
Published: October 2018

With the support of CEAS Suisse, Ingénieurs sans frontières (ISF Belgium), and NGO Autre Terre (Belgium), CEAS Burkina is implementing since 2008 a Project which aim to support municipal solid wastes management in seven secondary towns in Burkina Faso. Municipal solid wastes management are indeed one of the major challenge municipalities of Burkina Faso which always do not have the human, technical and financial resources to correctly ensure this public service, transferred to them within the framework of decentralisation. CEAS Burkina’s challenges in supporting these five collectivities is to help set up and implement a waste management system that can be technically and financially assumed by the communes. In this process, the issue of equipments and infrastructures emerged as a preliminary.This article presents the challenges and the results reached by research/design of infrastructures and equipment adapted to secondary cities context. It highlights some difficulties, draws lessons learned from the implementation of the research activities and concludes with recommendations for wide diffusion of the innovations.
Avec l’appui de ses partenaires techniques et financiers, que sont le CEAS (Suisse), Ingénieurs sans frontières (ISF Belgique), l'ONG Autre Terre (Belgique), l'Association Centre écologique Albert Schweitzer du Burkina Faso (CEAS Burkina) met en œuvre depuis 2008 un Projet d’appui à la gestion des déchets municipaux dans sept villes secondaires du Burkina. La gestion des déchets solides municipaux est en effet un des défis majeurs pour les municipalités des pays en développement qui ne disposent pas toujours des moyens organisationnels, humains, techniques et financiers nécessaires pour assurer correctement ce service public qui leur a été transféré. L’enjeu pour le développement durable de ces collectivités est donc de mettre en place un système de gestion des déchets adapté qui puisse être techniquement et financièrement assumé par les communes. La question des équipements et infrastructures s’avère majeure dans ce processus de recherche/développement.Cet article présente quelques innovations en matière d’équipements et infrastructures pour la gestion des déchets municipaux qui ont été développées suite aux travaux de recherche/conception réalisés par le CEAS Burkina. Il en analyse les principales forces et faiblesses avant de conclure par des recommandations spécifiques pour la diffusion de ces innovations.
Two Men in a Trickbag: White, Black, and the Operation of Schopenhauerian Ethics in Cormac McCarthy'sThe Sunset Limited
Authors: Hillier Russell M. 
Published: October 2018

AbstractThe operation of Schopenhauerian ethics is perhaps nowhere more painstakingly expounded in McCarthy's oeuvre than in The Sunset Limited. When set within Schopenhauer's ethical system, the respective positions of Black and White readily yield to evaluation. On the one hand, White, who appears to be a classic embodiment of Schopenhauer's pessimism, is lacking according to Schopenhauer's standard of ethical excellence. White's egoistic standpoint on the world is devoid of substance and credibility and his disdain for and willful isolation from others betrays an unhealthy, narcissistic, and other-denying egoism. On the other hand, Black's ethical conduct not only satisfies the criteria of Schopenhauer's virtuous man, his way of life is also depicted as making significant progress on the path toward Schopenhauerian sainthood. Once an egoist himself and now a devoted altruist, Black has awoken from his “beggar's dream” to recognize a human fellowship of pain, the presence of his “innermost self” in all others, and the need to obey a moral imperative to be compassionate. Considered against the backdrop of Schopenhauer's ethical framework, The Sunset Limited plays out a fierce opposition between the troubled egoism of White, “a professor of darkness,” and the saintly altruism of Black, “an emissary of Jesus.”
A Relationship Between the One-Way MANOVA Test Statistic and the Hotelling Lawley Trace Test Statistic
Authors: Arachchige Don Hasthika S. Rupasinghe 
Published: October 2018

The One-Way MANOVA model is a special case of the multivariate linear model, and this paper shows that the One-Way
MANOVA test statistic and the Hotelling Lawley trace test statistic are equivalent if the design matrix is carefully chosen.
Het hoger beroep inzake het schietincident in Alphen aan den Rijn: hoe gerechtigheid zegevierde, en de geest in de fles bleef
Authors: Maes K.L. 
Published: October 2018

Het hoger beroep inzake het schietincident in Alphen aan den Rijn: hoe gerechtigheid zegevierde, en de geest in de fles bleef
Op 27 maart 2018 is de politie door het Gerechtshof Den Haag aansprakelijk gehouden voor de door de slachtoffers en nabestaanden geleden letsel- en overlijdensschade vanwege het ten onrechte verstrekken van de wapenvergunning aan Tristan van der V., nadat deze aansprakelijkheid eerder op relativiteitsgronden strandde bij de Rechtbank Den Haag. In het onderhavige artikel worden beide uitspraken besproken en de afwijkende oordelen tegen elkaar afgezet. De kritieken waarmee met name het vonnis is ontvangen, geven bovendien aanleiding om de daarmee verweven secundaire aansprakelijkheidsproblematiek nader onder de loep te nemen. Want waarom hield de rechtbank de aansprakelijkheidsdeur zo krampachtig dicht, en zet het hof deze desondanks (meer) open?
U vraagt, wij draaien iets anders
Authors: van Dijck G. 
Published: October 2018

U vraagt, wij draaien iets anders. Een empirische studie naar wat benadeelden zoeken en krijgen in zaken over seksueel misbruik door de rooms-katholieke kerk
De wereldwijde belangstelling die het seksueel misbruik door de rooms-katholieke kerk heeft gekregen, heeft in Nederland geresulteerd in een procedure voor slachtoffers van dit seksueel misbruik in Nederland. Deze bijdrage doet verslag van een onderzoek waarin is geanalyseerd (1) of benadeelden kregen wat zij zochten, en (2) wat daarnaast verklaarde waarom de geschilbeslechters overgingen tot het toekennen van niet-financiële compensatie zoals excuses, erkenning van het leed en erkenning van het seksueel misbruik.
Evaluation of Carabelli’s trait in a group of Turkish patients
Authors: KAZAK Mağrur 
Published: October 2018

Objectives: Dental
morphological characteristics are useful for providing information in phylogenic
and genetic studies and also for understanding variations within and among
species. Carabelli cusp is expressed in several degrees and in different
frequencies among humans; thus, it is helpful in comparing and characterizing
populations. The objective of this retrospective study was to evaluate
Carabelli’s trait (CT) in a group of Turkish patients. Materials and Methods: In this study, 213
patients between age of 14-65 (mean age 29.99 ± 10.04) were analyzed
retrospectively according to presence or absence of CT on permanent maxillary
first and second molars. All data were statistically analyzed using the IBM
SPSS version 22 program (IBM SPSS, Turkey) and the chi-squared test; p &lt; 0.05 was considered as
statistically significant. Results: Prevalence of CT was found to be 47.9% in the
selected Turkish group. Incidence of CT in any of the teeth on #16/26 was 46.9%
and 4.2% on #17/27. Incidence was detected more on #26 (43.2%) than on #16
(40.4%). Bilateral presence of CT on #16/26 was detected in 78%. CT was seen in
50.7% of females and in 42.9% of males. There was no statistically significant
difference between genders (p &gt; 0.05). Conclusions: Expression of CT can be placed in moderate prevalence group. There was no
sexual dimorphism in its occurrence in the studied group. CT can be a valuable criterion to determine differences
among various populations and a significant insight into the migratory patterns
in a selected geographical area.
Number of File Usage on Dentinal Defect Incidence of WaveOne GOLD and Reciproc NiTi Instruments
Authors: YILMAZ Koray , ÖZYÜREK Taha , USLU Gülşah 
Published: October 2018

AbstractObjectives:To compare the incidences of dentinal defects caused by Reciproc and WaveOne GOLD NiTi files during root canal preparation and to exam the effect of number of file usage on the incidence of dentinal defect. Materials and Methods:Two hundred seventy mandibular incisor teeth were randomly divided into 3 different groups as follows: negative control (no preparation performed) (n: 30), Reciproc (n: 120) and WaveOne GOLD (n: 120) groups. The specimens were sliced at 3, 6 and 9 mm from the apex. Microscopic pictures of the specimens were taken with the aid of light emitting diode and the dentinal defects were examined. Results:There was no statistically difference among the WaveOne GOLD, Reciproc and control groups in terms of dentinal defect formation. The number of dentinal defects occurred in apical region in Reciproc group following 4thuse was found to be statistically higher than 1st, 2nd, and 3rduse in WaveOne GOLD group (P&lt; .05).Conclusion:All the NiTi files tested in present study were found to cause defect in root canal dentin but there were not significant difference among the WaveOne GOLD, Reciproc and control groups in term of total dentinal defect formation
Human Osteoblast Hücre Hattı Üzerinde Qmix, Etilen Diamintetraasetik Asit ve Klorhheksidin’in Sitotoksisitesinin Değerlendirilmesi
Authors: UĞUR AYDIN Zeliha , AKPINAR Kerem Engin , HEPOKUR Ceylan , ALTUNBAŞ Demet 
Published: October 2018

Amaç:
Bu çalışmada, QMix ™, etilendiamintetraasetik asit ve klorheksidin irrigasyon
solüsyonlarının human osteoblast hücreleri hattı üzerindeki zamana bağlı toksik
etkisi değerlendirdi.

Materyal ve metod: Human
osteoblast hücreleri, % 5 CO2 ve% 100 bağıl nem içeren bir ortamda 37ºC'de
tek tabakalı olacak şekilde kültüre edildi. Hücreler 4 saat ve 24 saat boyunca etilendiamintetraasetik
asit (EDTA), klorheksidin (CHX) ve QMix ™ 'e maruz bırakıldı. Hücre canlılığı
2,3-bis (2-metoksi-4-nitro-5-sülfenil) -5 - [(fenilamino) karbonil] -2H-tetrazolyum
hidroksit kiti (XTT) ile değerlendirildi. Human osteoblast hücrelerinin
ortalama yaşayabilirliğindeki farklılıklar istatistiksel olarak
değerlendirildi.

Bulgular:
Deney solüsyonlarındaki ve kontrol grubundaki canlı hücrelerin ortalama yüzdesi
arasında hem 4 saatlik (p˂0,001) hem de
24 saatlik (p =0,004) uygulamanın
sonrasında istatistiksel olarak anlamlı
fark görüldü. Canlı hücrelerin ortalama yüzdesi, EDTA, CHX ve QMixTM
grubunda uygulama süresinin artması ile istatistiksel olarak anlamlı derecede
azaldı (p˂0,05). 4 saat süresince uygulamanın ardından CHX ‘e göre EDTA ve Qmix
istatistiksel olarak anlamı derecede daha az toksik etki gösterdi
(p˂0,05). 24 saat süresince uygulamanın
ardından ise irrigasyon solüsyonlarının toksisitesi arasında istatistiksel
olarak anlamlı fark bulunmadı (p&gt;0,05).

Sonuç: Bu
çalışmada kullanılan irrigasyon solüsyonları human osteoblast hücre hattı
üzerinde çeşitli derecede toksik etki gösterdi. Uygulama süresinin artması kullanılan
irrigasyon solüsyonlarının human
osteoblast hücre hattı üzerindeki toksisitesini de arttırdı.
Flexible piecewise linear model for investigating dose-response relationship in meta-analysis: methodology, examples, and comparison
Authors: Xu Chang , Thabane Lehana , Liu Tong-Zu , Li Ling , Borhan Sayem , Sun Xin 
Published: October 2018

Objectives: Dose-response meta-analysis (DRMA) is widely employed to establishing the potential dose-response relationship between continuous exposures and disease outcomes. However, no method is readily available for exploring the relation between a discrete exposure and a binary or continuous outcome. We proposed a piecewise linear (PL) DRMA model as a solution to this issue.
Methods: We illustrated the methodology of PL model in both one-stage DRMA approach and two-stage DRMA approach. The method by testing the equality of slopes of each piecewise was employed to judge if there is “piecewise effect” against simple linear trend. We then used sleep (continuous exposure) and parity (discrete exposure) data as examples to illustrate how to apply PL model in DRMA using the Stata code attached. We also empirically compared the slopes of PL model with simple linear as well as restricted cubic spline (RCS) model.
Results: Both one-stage and two-stage PL DRMA model fitted well in our examples, and the results were similar. Obvious “piecewise effects” were detected in both the two examples by the method we used. In our example, the PL model showed better fitting effect and practical reliable results compared to simple linear model, while similar results for to RCS model.
Conclusion: Piecewise linear function is a simple and valid method for DRMA and can be used for discrete exposures. It also represents a superior model to linear model in DRMA and may be an alternative model to non-linear model.
Landscape dynamics of Paspalum quadrifarium grasslands analyzed by Morphological Spatial Pattern Analysis (MSPA)
Authors: Gandini Marcelo L , Lara Bruno D , Moreno Laura Beatriz , Cañibano Maria A , Gandini Patricia A 
Published: October 2018

Background. Despite its wide distribution worldwide, only 4.6% of temperate grasslands are included within systems of protected areas. In Argentina, this situation is even more alarming: only 1.05% is protected. The study area (central area of the southern Salado River basin) has a large extent of grasslands of Paspalum quadrifarium (Pq) which has been target since the last century of a variety of agricultural management practices including fire burning for cattle grazing.
Methods. Binary images of presence-absence data of Pq from a 42-year (1974-2016) land cover change study were used as base data. MSPA (Morphological Spatial Pattern Analysis) and Network Analysis were performed to the data using Guidos Toolbox for the estimation of habitat and connectivity dynamics of the Pq patches (fragments).
Results. A loss of the coverage area and habitat nuclei of this grassland was observed between the beginning and the end of the study period. A drastic reduction in connectivity was also evident in resulting maps. The number of large Pq grassland fragments (> 50 ha) decreased during the study period, and fragmentation measured as number of components (patches) was higher at the end of study period. The Pq pajonal nuclei had their minimum representativeness in 2000, and recovered slightly in 2011, but with a significant percentage increase of the small patches (=islets) and linear elements as bridges and branches. Large corridors (mainly edge of roads) could be observed at the end of study period, while the total connectivity of the landscape pattern drops abruptly.
Discussion. The habitat reduction could have an impact on the ecosystem functioning and the mobility of some species of native fauna. The connecting elements of the landscape were maintained and/or recovered in percentage in 2011 and 2016. This fact, although favoring the dispersion of the present diversity in the habitat nuclei could cause degradation by an edge effect. On the methodological side, the use of a proved tool as Guidos Toolbox for evaluating forest fragmentation could also be useful for monitoring dynamics of a grassland-habitat fragmentation.
Long-Term Blood Pressure Variability and Visual Field Progression in Glaucoma
Authors: Pham Vincent Q. , Nishida Takashi , Moghimi Sasan , Girkin Christopher A. , Fazio Massimo A. , Liebmann Jeffrey M. , Zangwill Linda M. , Weinreb Robert N. 
Published: November 2024

ImportanceLong-term variability of blood pressure may be associated with visual field (VF) progression in patients with glaucoma.ObjectivesTo investigate the association between blood pressure parameters and VF progression over time in patients with glaucoma.Design, Setting, and ParticipantsThis retrospective cohort study of longitudinal data included patients with suspected or confirmed glaucoma who were selected from the Diagnostic Innovations in Glaucoma Study and the African Descent and Glaucoma Evaluation Study. Patients underwent blood pressure and VF testing from November 2000 to December 2022, and data were analyzed in October 2023.ExposureSuspected or confirmed glaucoma.Main Outcomes and MeasuresMean and SD values of blood pressure variables were calculated for systolic and diastolic arterial pressures. These parameters were incorporated into multivariable mixed-effect models to investigate the association between blood pressure parameters and mean intraocular pressure with rates of VF mean deviation loss. Interaction terms between blood pressure parameters and mean intraocular pressure were also included in the models.ResultsA total of 1674 eyes from 985 patients were assessed (mean [SD] age, 61.2 [0.4] years; 563 female [57.2%]). The mean rate of VF mean deviation change was −0.13 (95% CI, −0.16 to −0.10) dB/y over a mean follow-up of 8.0 (95% CI, 7.7-8.2) years. The interaction terms of higher mean blood pressure and higher SD of blood pressure were associated with faster annual mean deviation changes for both mean arterial pressure (0.02 [95% CI, 0.01-0.04] dB/y per 1-mm Hg higher; P = .001) and diastolic arterial pressure (0.02 [95% CI, 0.01-0.03] dB/y per 1-mm Hg higher; P &amp;lt; .001). The interaction term of higher SD of blood pressure and higher mean intraocular pressure was associated with faster annual mean deviation changes for both mean arterial pressure (0.01 [95% CI, 0.00-0.02] μm per 1-mm Hg higher; P = .003) and diastolic arterial pressure (0.01 [95% CI, 0.00-0.01] μm per 1-mm Hg higher; P = .001).Conclusions and RelevanceIn this cohort study, higher mean blood pressure and higher SD of blood pressure were associated with faster VF progression. These findings suggest that long-term variability of blood pressure may be a modifier of the association between intraocular pressure and VF progression in glaucoma.