bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytogenetic complexity in chronic lymphocytic leukemia: definitions, associations, and clinical impact
Authors: Baliakas Panagiotis , Jeromin Sabine , Iskas Michalis , Puiggros Anna , Plevova Karla , Nguyen-Khac Florence , Davis Zadie , Rigolin Gian Matteo , Visentin Andrea , Xochelli Aliki , Delgado Julio , Baran-Marszak Fanny , Stalika Evangelia , Abrisqueta Pau , Durechova Kristina , Papaioannou George , Eclache Virginie , Dimou Maria , Iliakis Theodoros , Collado Rosa , Doubek Michael , Calasanz M. Jose , Ruiz-Xiville Neus , Moreno Carolina , Jarosova Marie , Leeksma Alexander C. , Panayiotidis Panayiotis , Podgornik Helena , Cymbalista Florence , Anagnostopoulos Achilles , Trentin Livio , Stavroyianni Niki , Davi Fred , Ghia Paolo , Kater Arnon P. , Cuneo Antonio , Pospisilova Sarka , Espinet Blanca , Athanasiadou Anastasia , Oscier David , Haferlach Claudia , Stamatopoulos Kostas 
Published: January 2019

AbstractRecent evidence suggests that complex karyotype (CK) defined by the presence of ≥3 chromosomal aberrations (structural and/or numerical) identified by using chromosome-banding analysis (CBA) may be relevant for treatment decision-making in chronic lymphocytic leukemia (CLL). However, many challenges toward the routine clinical application of CBA remain. In a retrospective study of 5290 patients with available CBA data, we explored both clinicobiological associations and the clinical impact of CK in CLL. We found that patients with ≥5 abnormalities, defined as high-CK, exhibit uniformly dismal clinical outcomes, independently of clinical stage, TP53 aberrations (deletion of chromosome 17p and/or TP53 mutations [TP53abs]), and the expression of somatically hypermutated (M-CLL) or unmutated immunoglobulin heavy variable genes. Thus, they contrasted with CK cases with 3 or 4 aberrations (low-CK and intermediate-CK, respectively) who followed aggressive disease courses only in the presence of TP53abs. At the other end of the spectrum, patients with CK and +12,+19 displayed an exceptionally indolent profile. Building upon CK, TP53abs, and immunoglobulin heavy variable gene somatic hypermutation status, we propose a novel hierarchical model in which patients with high-CK exhibit the worst prognosis, whereas those with mutated CLL lacking CK or TP53abs, as well as CK with +12,+19, show the longest overall survival. Thus, CK should not be axiomatically considered unfavorable in CLL, representing a heterogeneous group with variable clinical behavior. High-CK with ≥5 chromosomal aberrations emerges as prognostically adverse, independent of other biomarkers. Prospective clinical validation is warranted before ultimately incorporating high-CK in risk stratification of CLL.
Clinical features of Sjögren's syndrome patients with autoantibodies against interferons
Authors: Burbelo Peter D. , Browne Sarah , Holland Steve M. , Iadarola Michael J. , Alevizos Ilias 
Published: January 2019

AbstractBackgroundSjögren's syndrome (SS) is an autoimmune disease characterized by immune attack on the salivary and lacrimal glands. Given the known cytokine activation and type I interferon gene expression signature found in SS, we hypothesized that anticytokine autoantibodies might be detectable by Luciferase immunoprecipitation systems in some SS patients and correlate with clinical symptoms.ResultsLuciferase immunoprecipitation systems was used to screen for serum anti‐cytokine autoantibodies in 57 primary SS patients and 25 healthy volunteers. Autoantibodies were detected against GMCSF, interferon‐γ, ‐α and, ‐ω in one, two, two and six patients with SS, respectively. None of the healthy volunteers showed anticytokine autoantibodies and none of the SS or control subjects showed autoantibodies against interferon‐λ. One 51‐year old female SS subject with the highest anti‐interferon‐α and ‐ω autoantibody levels had stable autoantibody levels over the course of a year. In vitro functional testing of serum autoantibodies from this subject demonstrated partially neutralizing activity for interferon‐α signaling. Clinical information on this individual revealed a low focus score and high levels of unstimulated salivary flow, suggesting the possibility that interferon‐α autoantibody neutralizing activity may have contributed to the milder sicca symptoms.ConclusionOverall, these findings demonstrate that a subset of SS patients (16%) harbor autoantibodies against GMCSF, interferon‐γ, interferon‐ω, and interferon‐α. These data support the observation that high levels of interferon‐α autoantibodies may attenuate disease symptoms in SS.
Objective knowledge, subjective knowledge, and prior experience of organic cotton apparel
Authors: Han Tae-Im 
Published: January 2019

AbstractThe purpose of this research is to examine the relationships between objective knowledge, subjective knowledge, and prior experience of organic cotton apparel and their effects on purchase behaviors. The sample of the present study consisted of Millennial consumers living in the United States. Multiple regression and cluster analysis were used to assess the relationship among variables. Objective and subjective knowledge related to organic cotton apparel had a weak relationship suggesting they are distinct measures of knowledge. Direct experience, indirect experience, and education level were significant predictors of subjective knowledge, however, they had insignificant effects on objective knowledge. Furthermore, consumers who are willing to pay more for organic cotton and willing to search actively for organic cotton apparel displayed a higher level of subjective knowledge and had more experience with the product. Objective knowledge was found to have a limited relationship with pro-environmental behaviors. The current study examined distinct types of knowledge associated with organic cotton apparel and their relationship to pro-environmental behaviors which provides a sound basis for better understanding consumers’ organic apparel purchase. It is widely accepted that product knowledge affects consumer behaviors, however, how product knowledge is measured varies extensively across consumer research. The findings offer a valid explanation for the contradictory findings in previous research in terms of the effect of product knowledge on purchase behaviors.
The Transcoding of the Codex Xolotl in Don Fernando de Alva Ixtlilxochitl’s Historia de la nación chichimeca
Authors: García Loaeza Pablo 
Published: January 2019

Abstract
This article considers the interplay among interpretation, intent, and ingenuity involved in don Fernando de Alva Ixtlilxochitl’s transcoding of the Codex Xolotl in the first part of his definitive work, the Historia de la nación chichimeca, by way of his earlier Sumaria relación de todas las cosas de la Nueva España. Scholars tend to focus on Alva Ixtlilxochitl’s role as a more or less reliable intermediary through whom the Codex Xolotl’s information has been transmitted. However, in order to better understand his contribution to Mexican ethnohistory, it is important to acknowledge him as a diligent researcher who was also an exceptional writer and storyteller.
Between theLofand the Liberators: Mapuche Authority in Chile’s Guerra a Muerte(1819–1825)
Authors: Zarley Jesse 
Published: January 2019

AbstractThis article examines the actions of Francisco Mariluán and Venancio Coñuepan, two rival caciques of the Mapuche indigenous people, during Chile’s independence wars to understand how indigenous leaders defended their sovereignty and shaped the transition from colony to nation in Spanish South America. Between 1819 and 1825, lands in southern Chile and western Río de la Plata that were controlled by the Mapuche became the stage for a civil war between Spanish royalists and Chilean patriots known as the guerra a muerte (war to the death). Mariluán and Coñuepan supported different sides in the conflict, but they expressed their support through diplomatic practices rooted in material and ritual reciprocities of negotiation, letter writing, and gift giving. By centering how Mariluán and Coñuepan imposed interethnic ritual negotiations (parlamentos) and diplomatic protocols on Chilean leaders, the article argues for the importance of indigenous practices of reciprocity and definitions of authority on the former frontiers of the Spanish Empire. These reciprocities governed interethnic encounters and changed the character of the conflict into a Mapuche war.
An Ishihara-style test of animal colour vision
Authors: Cheney Karen L. , Green Naomi F. , Vibert Alexander P. , Vorobyev Misha , Marshall N. Justin , Osorio Daniel C. , Endler John A. 
Published: January 2019

ABSTRACT
Colour vision mediates ecologically relevant tasks for many animals, such as mate choice, foraging and predator avoidance. However, our understanding of animal colour perception is largely derived from human psychophysics, and behavioural tests of non-human animals are required to understand how colour signals are perceived. Here, we introduce a novel test of colour vision in animals inspired by the Ishihara colour charts, which are widely used to identify human colour deficiencies. In our method, distractor dots have a fixed chromaticity (hue and saturation) but vary in luminance. Animals can be trained to find single target dots that differ from distractor dots in chromaticity. We provide MATLAB code for creating these stimuli, which can be modified for use with different animals. We demonstrate the success of this method with triggerfish, Rhinecanthus aculeatus, which quickly learnt to select target dots that differed from distractor dots, and highlight behavioural parameters that can be measured, including success of finding the target dot, time to detection and error rate. We calculated discrimination thresholds by testing whether target colours that were of increasing colour distances (ΔS) from distractor dots could be detected, and calculated discrimination thresholds in different directions of colour space. At least for some colours, thresholds indicated better discrimination than expected from the receptor noise limited (RNL) model assuming 5% Weber fraction for the long-wavelength cone. This methodology could be used with other animals to address questions such as luminance thresholds, sensory bias, effects of sensory noise, colour categorization and saliency.
Identifying stroke therapeutics from preclinical models: A protocol for a novel application of network meta-analysis
Authors: Lalu Manoj M. , Fergusson Dean A. , Cheng Wei , Avey Marc T. , Corbett Dale , Dowlatshahi Dar , Macleod Malcolm R. , Sena Emily S. , Moher David , Shorr Risa , McCann Sarah K. , Gray Laura J. , Hill Michael D. , O'Connor Annette , Thayer Kristina , Haggar Fatima , Dobriyal Aditi , Chung Hee Sahng , Welton Nicky J. , Hutton Brian 
Published: January 2019

Introduction: Globally, stroke is the second leading cause of death. Despite the burden of illness and death, few acute interventions are available to patients with ischemic stroke. Over 1,000 potential neuroprotective therapeutics have been evaluated in preclinical models. It is important to use robust evidence synthesis methods to appropriately assess which therapies should be translated to the clinical setting for evaluation in human studies. This protocol details planned methods to conduct a systematic review to identify and appraise eligible studies and to use a network meta-analysis to synthesize available evidence to answer the following questions: in preclinical in vivo models of focal ischemic stroke, what are the relative benefits of competing therapies tested in combination with the gold standard treatment alteplase in (i) reducing cerebral infarction size, and (ii) improving neurobehavioural outcomes? Methods: We will search Ovid Medline and Embase for articles on the effects of combination therapies with alteplase. Controlled comparison studies of preclinical in vivo models of experimentally induced focal ischemia testing the efficacy of therapies with alteplase versus alteplase alone will be identified. Outcomes to be extracted include infarct size (primary outcome) and neurobehavioural measures. Risk of bias and construct validity will be assessed using tools appropriate for preclinical studies. Here we describe steps undertaken to perform preclinical network meta-analysis to synthesise all evidence for each outcome and obtain a comprehensive ranking of all treatments. This will be a novel use of this evidence synthesis approach in stroke medicine to assess pre-clinical therapeutics. Combining all evidence to simultaneously compare mutliple therapuetics tested preclinically may provide a rationale for the clinical translation of therapeutics for patients with ischemic stroke. Dissemination: Review findings will be submitted to a peer-reviewed journal and presented at relevant scientific meetings to promote knowledge transfer. Registration: PROSPERO number to be submitted following peer review.
Studies on Biological Test of Formulated Diets Supplementation of Vitamin E for the Broodstock of Females Blue Swimming Crab, Portunus pelagicus (Linnaeus, 1758)
Authors: Efrizal Efrizal , Zakaria Indra Junaidi , Rusnam Rusnam , Suryati Suryati , Yolanda Nofa 
Published: January 2019

Background: Currently, great progress in the artificial propagation of commercially important portunid crabs of the genus Portunus has been achieved, and various methods have been adopted in mass-scale hatchery activities. This study analyzed the biological testing of formulated diets with different dose supplementations of vitamin E for the broodstock of female blue swimming crabs, P. pelagicus (Linnaeus, 1758) Methods: Female crab samples were collected from the coastal region of Padang, West Sumatra. The method used in this study was completely randomized design, with four treatment regimens (n=5 crabs each) of dietary vitamin E (0, 300, 600, and 900 IU/kg formulated diets). Results: The results show that the supplementation of vitamin E in the formulated diet had a significant effect (P <0.05) on the absolute weight growth, carapace length and carapace width. Conclusions: Supplementation of vitamin E on in formulated diet causes broodstock blue swimming crab molting, with a percentage value of 40–80% on day 20 and 20% on day 30, with a 100% survival rate.
Selection and regeneration of purple sweet potato calli against drought stress simulated by polyethylene glycol
Authors: Sunaryo Widi , Darnaningsih Darnaningsih , Nurhasanah Nurhasanah 
Published: January 2019

Background: Water shortage due to natural and/or technical drought stress, widespread throughout Sumatra, Java, Sulawesi and Kalimantan islands, significantly reduces crop production. The development of varieties tolerant to drought stress is important since it is more effective rather than improving irrigation infrastructure to increase the sweet potato productivity. Methods: Selection and regeneration experiments assessing purple sweet potato callus tolerance of drought stress, simulated by polyethylene glycol (PEG), were conducted to generate new variant plants tolerant of drought stress. Sterile explants (leaf and petiole) generated from previous in vitro culture were inoculated to the Murishage and Skoog (MS) medium containing plant growth regulator combination as treatments to induce calli. The calli were then transferred to half-MS medium containing 0, 5, 10, 15 and 20% PEG as selection agent for drought tolerance. The surviving calli were regenerated in the MS medium containing 0, 0.5, 1 or 1.5 mg l-1 6-benzylaminopurine (BAP). The callus formation, growth and survivability during in vitro culture were measured. Results: Calli were successfully formed in almost all media containing 2,4-Dichlorophenoxyacetic acid (2,4-D ) with the concentration of 1, 2, 3 and 4 mg l-1 and BAP (concentration: 0.5 and 1 mg l-1), but the medium of MS + 2 mg l-1 2,4-D + 0.5 mg l-1 BAP resulted in the highest number of induced calli per treatment (mean=11.36), with the percentage of responsive explants standing at around 96%. The higher the concentration of PEG, the lower the number of surviving calli. At 20% PEG, only 54.42% calli survived. There were five plants successfully regenerated from the survived calli at 20% PEG, using MS medium containing 1.5 mg l-1 BAP. Conclusions: The experiment has successfully produced putative drought-tolerant plants by callus screening using PEG as drought-tolerance-selecting agent in purple sweet potato.
Economic valuation from direct use of mangrove forest restoration in Balikpapan Bay, East Kalimantan, Indonesia
Authors: Lahjie Abubakar M. , Nouval Bagus , Lahjie Annisa Abubakar , Ruslim Yosep , Kristiningrum Rochadi 
Published: January 2019

Background: The mangrove forests in Balikpapan Bay, Indonesia, have been used as a source of livelihood for local community more than 150 years. Since the natural products of the mangrove forest, such as wood and seafood, are not able to meet the economic needs of the local community, some areas have been converted into brackish water ponds with traditional aquaculture systems. The growth of brackish water ponds over the last five decades has been identified as the main cause of ecosystem destruction. However, the mangrove ecosystem has been restored naturally through tidal action and seeds falling from mangrove trees. Methods: This study focused on the mangrove tree species Rhizophora apiculata, with ages ranging from 3 to 40 years. Initially, the study site (area, 1 ha) was plotted. The study sample size included 30% of the local population, chosen by systematic random sampling. The data collection was undertaken as follows: 1) measurement of the diameter and height of mangrove trees; 2) observation of local fish auctions; and 3) interviewing of fishers and local communities regarding the direct use of the natural products of the mangrove ecosystem. Results: It is suggested that the total income from wood production is IDR 742,425,000 year-1 or US $0.933 person-1 day-1. Furthermore, the total income from fishing is IDR 1,019,056,640 year-1 or US $1.28 person-1 day-1. Pre-thinning income level for wood harvesting is still low. The income difference between wood production and fishing resulted in the rate of overfishing reaching 37.3%. The highest observed wood production was reached at the age of 25 years, and the highest value of mean annual increment (MAI) is 5.39 m3 ha-1 at the age of 40 years. Conclusions: This study showed that tree thinning, ranging from 90 to 350 trees ha-1, can increase the value of MAI by around 24.5%.
The prevalence of dental caries among Egyptian children and adolescences and its association with age, socioeconomic status, dietary habits and other risk factors. A cross-sectional study
Authors: Abbass Marwa M.S. , Mahmoud Sara Ahmed , El Moshy Sara , Rady Dina , AbuBakr Nermeen , Radwan Israa Ahmed , Ahmed Attera , Abdou Ahmed , Al Jawaldeh Ayoub 
Published: January 2019

Background: Dental caries is a chronic, multifactorial disease, with limited data available for the Egyptian population. The aim of this study is to assess the prevalence of dental caries among Egyptian children and adolescents in correlation with age, gender, body mass index, socioeconomic status, parental education, biological risk factors and dietary habits. Methods: A total number of 369 Egyptian children and adolescents (age ranges from 3-18 years) were examined over the period from 15th November 2017 to 13th January 2018. Socio-demographic data, oral hygiene measures and dietary habits for children were recorded. Dental status was analyzed using decayed, missing and filled tooth index (dmft) for deciduous dentition and (DMFT) index for permanent dentition. For mixed dentition (deft) index was used, d (decayed tooth indicated for filling), e (decayed tooth indicated for extraction) and f (filled tooth). Results: 74% of the children had dental caries with mean dmft: 3.23±4.07; deft: 4.21±3.21; DMFT: 1.04±1.56. In primary dentition, dmft of the children was positively correlated with age, beans, candies, crackers, chocolates and inversely correlated with gender, socio-economic status (SES), parental education, brushing frequency of the parent, brushing frequency of the parent to the child teeth, brushing frequency of the child and consumption of eggs, fruits/vegetables, milk and milk products. In mixed dentition, deft was positively correlated with candies, crackers, citric juices, while negatively correlated with age, SES, parental education, brushing frequency of the parent to the child, brushing frequency of the child, fruits/vegetables. In permanent dentition, DMFT in children was positively correlated with age and chocolates while not correlated with any of the remaining risk factors. Conclusion: The present study clarifies the significant risk factors associated with dental caries amongst Egyptian children. This will help in planning strategies to prevent and treat such disease.
Robust and efficient identification of biomarkers from RNA-Seq data using median control chart
Authors: Shahjaman Md , Akter Habiba , Rashid Md. Mamunur , Asifuzzaman Md. Ibnul , Hossen Md. Bipul , Rahman Md. Rezanur 
Published: January 2019

Background: One of the main goals of RNA-seq data analysis is identification of biomarkers that are differentially expressed (DE) across two or more experimental conditions. RNA-seq uses next generation sequencing technology and it has many advantages over microarrays. Numerous statistical methods have already been developed for identification the biomarkers from RNA-seq data. Most of these methods were based on either Poisson distribution or negative binomial distribution. However, efficient biomarker identification from discrete RNA-seq data is hampered by existing methods when the datasets contain outliers or extreme observations. Specially, the performance of these methods becomes more severe when the data come from a small number of samples in the presence of outliers. Therefore, in this study, an attempt is made to propose an outlier detection and modification approach for RNA-seq data to overcome the aforesaid problems of traditional methods. We make our proposed method facilitate in RNA-seq data by transforming the read count data into continuous data. Methods: We use median control chart to detect and modify the outlying observation in a log-transformed RNA-seq dataset. To investigate the performance of the proposed method in absence and presence of outliers, we employ the five popular biomarker selection methods (edgeR, edgeR_robust, DEseq, DEseq2 and limma) both in simulated and real datasets. Results: The simulation results strongly suggest that the performance of the proposed method improved in the presence of outliers. The proposed method also detected an additional 18 outlying DE genes from a real mouse RNA-seq dataset that were not detected by traditional methods. Using the KEGG pathway and gene ontology analysis results we reveal that these genes may be biomarkers, which require validation in a wet lab. Conclusions: Our proposal is to apply the proposed method for biomarker identification from other RNA-seq data.