bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying Chagas disease vectors using Elliptic Fourier Descriptors of body contour: A case for the cryptic dimidiata complex
Authors: Flores Daryl David Cruz , Arenas Elizabeth Arellano , Ávila Dennis Denis , Ibarra-Cerdeña Carlos N. 
Published: April 2020

Abstract
Background Triatoma dimidiata (Reduviidae: Triatominae) is an important vector of Chagas disease in various countries in the Americas. Phylogenetic studies using sequences from the cyt b, ND4, and 16S rRNA genes, have defined three lineages in Mexico and part of Central America, indicated between 6% and 14% divergence among haplogroups. While there is a marked genetic differentiation, methods for identifying them using morphometric analyses with landmarks have not yet been fully resolutive. Elliptical Fourier Descriptors (EFDs), which mathematically describe the shape of any closed two-dimensional contours, could be a potentially useful alternative method. Our objective was to validate the use of EFDs for the identification of three lineages of this species complex. Method 84 dorsal view images of individuals of the three lineages were used. Body contours were described with EFDs using between 5 and 30 harmonics. The number of obtained coefficients was reduced by a Principal Components Analysis and the first axis scores were used as shape variables. Before performing the discrimination of haplogroups, we compared statistically the first five principal components among them. A linear discriminant function analysis and an Ordination plot of the Discriminant Analysis were performed using the shape variables. Finally, a confusion matrix of the Ordination plot of the Discriminant Analysis was obtained to estimate the classification errors. Results When comparing the first five PC scores, significant differences were found among at least two haplogroups for all principal components except for PC3. The first principal component explained 50% of the variability, regardless the number of harmonics used. The results of Discriminant Analysis get improved by increasing the number of harmonics and components considered. With 25 harmonics and 8 components, the identification of haplogroups was achieved with an overall efficiency greater than 97%. The ordering diagram shown the correct discrimination of haplogroups, with only one error of discrimination corroborated by the confusion matrix. Conclusions The use of EFD is a simple and useful method for the identification of the main lineages of Triatoma dimidiata , with high values ​​of correct identification.
106Ruthenium eye plaque brachytherapy in the management of medium sized uveal melanoma
Authors: Jiang Ping , Purtskhvanidze Konstantine , Kandzia Gerit , Neumann Dirk , Luetzen Ulf , Siebert Frank-André , Roider Johann , Dunst Juergen 
Published: April 2020

Abstract
Background: To evaluate 106Ruthenium Brachytherapy in management of medium sized uveal melanoma, with emphasis on 5-year outcome and toxicity.Methods: From 2007 to 2015, 39 patients were treated with 106 Ru eye plaques brachytherapy. At the time of diagnosis, the median tumor depth was 3.0 mm (CI: 1.6-8.9 mm). Median dose at the apex of the tumor was 145 Gy (± SD: 12.1Gy). The median sclera dose was 444.0Gy (±SD: 257.3 Gy). Results: Median follow-up was 61.5 months (CI: 8.1-138 mon.). 34 patients (87.1%) remained free of recurrence. In 26 (66.7%) patients a total regression was achieved after a median period of 12 months (CI: 3-60 mon.). By the final examination, the visual acuity of 26 (66.7%) patients was better than 20/200. 12 (30.7%) patients had a visual acuity better than 20/40.Retinopathy was detected in 11 (28.2%) patients. After treatments only 1 (5.1%) patients had active vascular changes by the last examination. Moderate optic neuropathy was observed in 4 (10.3%) patients. Cataract development was diagnosed in 21 (53.8%) patients, although 16 (41%) of them had bilateral cataract development.Special emphasis was made on patients with larger tumors. Twelve out of the 39 patients had a tumor with a depth of 5mm or more. There was no significant difference neither in local control (75 % in tumors ≥5mm versus 92.6 % in tumors <5mm) nor in side effects between both groups. Conclusions: Our study proved 106 Ru -brachytherapy to be an excellent treatment option with regard to tumor control and preservation of the visual acuity in well-selected patients. The data suggest that this treatment is also suitable for tumors with a depth of more than 5mm.
Preliminary Validation of Infant Sucking Measurement System with Healthy Term Infants
Authors: Park Jinhee , D’Imperio Luke A. , Rose Aaron H. , Parrillo Elaina , Thoyre Suzanne M. , Naughton Michael J. 
Published: April 2020

Abstract
Background: Although various methods have been used to objectively evaluate an infant’s sucking behavior during breast- and bottle-feeding, variations in instruments and technologies currently employed make it difficult to compare findings across breast and bottle-feeding conditions. Therefore, we developed a new method, the Infant Sucking Measurement System (ISMS) that provides a consistent assessment of sucking across breast and bottle-feeding. The purpose of this study was to present preliminary findings of the feasibility and validity of the ISMS.Methods: In Phase 1, we examined the ability of the ISMS to differentiate different levels of negative pressure generated by an artificial sucking condition using a breast pump. In Phase 2, we tested the feasibility and validity of the ISMS with data obtained from four mothers and their healthy full-term infants (two bottle-feedings and two breastfeedings). Intraoral pressures were measured using the ISMS along with a video camera simultaneously recording the infant’s cheek movements. Mothers provided feedback for improvement of the ISMS design. Following each observation, the team reviewed the findings and refined the system; refinements were trialed with the next study. To test the validity of the ISMS, a one-minute period with the highest quality ISMS signal was selected from each feeding to examine the synchrony between ISMS intraoral pressure measurements and coded cheek movements.Results: The ISMS differential pressures when low, medium, and high suction pressures were applied by a breast pump were 18.8, 29.6, and 40.3 kPa, respectively. The agreement between direct observation of sucking and ISMS data was high (mean: 90.6%, range: 84.6-100%). With a series of modifications, we found that the ISMS was a feasible method of reliably measuring intraoral pressure during breast-feeding; however, further testing is necessary to optimize methods of securing the catheter to the bottle nipple.Conclusions: Preliminary data support the validity of the ISMS for identifying sucks and quantifying intraoral pressure generated by sucks in both breast and bottle-feeding. Although further modifications are needed to improve the attachment of the device to the bottle nipple, our initial results support further investigation of the ISMS for use in high-risk infants to evaluate sucking behaviors.
Recovery and Maintenance of NESTIN Expression in Umbilical Cord-MSC Using a Novel Culture Medium
Authors: Liu Yuncheng , Xiao Feidi , Hu Xiang , Tang Zan , Fu Zeqin , Liang Xiao , Zeng Guifang , Zeng Weijie , Liao Yan , Ren Yuan , Liu Zhiyu , Peng Hao , Mei Qiuhong , Liu Muyun 
Published: April 2020

Abstract
Mesenchymal stem cells (MSC) are a popular candidate in cellular therapy for many diseases. It is well known by its feature of self-renewal and differentiation potential. NESTIN is a cytoskeletal protein that expresses in MSC and plays an important role in cell proliferation and differentiation. Here, we demonstrated that adding UltraGRO, which is a medium supplement, could maintain and partially recover the expression of NESTIN in human umbilical cord derived MSCs (UC-MSCs). Furthermore, the UC-MSCs cultured with UltraGRO showed a better immunomodulation ability in colitis mouse model compared with that cultured in other mediums. This indicates that the use of novel culture medium benefits to the maintenance of NESTIN expression and NESTIN may be one of the vital factors that regulate the performances of MSC.
Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat (Avena sativa L.)
Authors: Yang Zheng , Wang Kai , Zhao Cuizhu , Zhang Meng 
Published: April 2020

Abstract
Background: Oat (Avena sativa L.), a hexaploid crop with unknown genome, has valuable nutritional, medicinal and pharmaceutical uses. However, none of suitable RGs (reference genes) for qPCR (quantitative real-time PCR) has been documented in oat yet. Single-copy gene is often selected as RG, which is challengeable or impactable in unexplored polyploids.Results: In this study, eleven candidate RGs, including four duplicated genes, were selected from oat transcriptome. The stability and the optimal combination of these candidate RGs were assessed in 18 oat samples by using four statistical algorithms including the ΔCt method, geNorm, NormFinder and BestKeeper. The most stable RGs for all samples, shoots and roots of seedlings, developing seeds and developing endosperms were EIF4A (Eukaryotic initiation factor 4A-3), UBC21 (Ubiquitin-Conjugating Enzyme 21), EP (Expressed protein) and EIF4A respectively, among which UBC21 was a four-copy duplicated gene. The reliability was validated by the expression pattern of AsPKP1 (Plastidial Pyruvate Kinase 1) normalized to the most and the least stable RGs in developing oat seeds and endosperms.Conclusions: These results provide a proof of concept that the duplicated RG is feasible for qPCR in polyploids. To our knowledge, this study is the first systematic research on the optimal RGs for accurate qPCR normalization of gene expression in different organs and tissues of oat.
Interconnectivity between molecular subtypes and tumor stage in colorectal cancer
Authors: Braak R.R.J. Coebergh van den , Hoorn Sanne ten , Sieuwerts A.M. , Tuynman J.B. , Smid M. , Wilting S. , Martens J.W.M. , Punt C.J.A. , Foekens J.A. , Medema J.P. , IJzermans J.N.M. , Vermeulen Louis 
Published: April 2020

Abstract
Background There are profound individual differences in clinical outcome between colorectal cancers (CRCs) presenting with identical stage of disease. Molecular stratification, in conjunction with the traditional TNM staging, is a promising way to predict patient outcomes. We investigated the interconnectivity between tumor stage and tumor biology reflected by the Consensus Molecular Subtypes (CMSs) in CRC, and explored the possible value of these insights in patients with stage II colon cancer. Methods We performed a retrospective analysis using clinical records and gene expression profiling in a meta-cohort of 1040 CRC patients. The interconnectivity of tumor biology and disease stage was assessed by investigating the association between CMSs and TNM classification. In order to validate the clinical applicability of our findings we employed a meta-cohort of 197 stage II colon cancers. Results CMS4 was significantly more prevalent in advanced stages of disease (III-IV). The observed differential gene expression between cancer stages is predominantly explained by the biological differences as reflected by CMS subtypes. Gene signatures for stage III-IV and CMS4 were highly correlated. CMS4 cancers showed an increased progression rate to more advanced stages. Indeed, determining CMSs was a relevant addition to TNM classification in identifying stage II colon cancer patients with high-risk of disease recurrence. Conclusions Considerable interconnectivity between tumor biology and tumor stage in CRC exists. This implies that the TNM stage, in addition to the stage of progression, also reflects distinct biological disease entities. These insights can be utilized to optimize identification of high-risk stage II colon cancers.
Phenotypic and molecular analysis of insecticide resistance in Aedes albopictus populations from Greece
Authors: Balaska Sofia , Fotakis Emmanouil Alexandros , Kioulos Ilias , Grigoraki Linda , Mpellou Spyridoula , Chaskopoulou Alexandra , Vontas John 
Published: April 2020

Abstract
Background: Aedes albopictus has a well-established presence in southern European countries, associated with recent disease outbreaks (e.g. Chikungunya). Development of insecticide resistance in the vector is a major concern as it’s control mainly relies on the use of biocides. Data on the specie’s resistance status is essential for efficient and sustainable control. Methods: We investigated the insecticide resistance status of several Ae. albopictus populations from Greece. Bioassays were performed against diflubenzuron (DFB), B. thuringiensis var. israelensis (Bti), deltamethrin and malathion. Molecular analysis of known insecticide resistance loci was performed, i.e. voltage-gated sodium channel (VGSC) mutations associated with pyrethroid resistance; presence and frequency of carboxylesterases 3 (CCEae3a) and 6 (CCEae6a) gene amplification associated with organophosphate (OP) resistance and; chitin synthase-1 (CHS-1) for the possible presence of DFB resistance mutations. Results: Bioassays showed full susceptibility to DFB, Bti and deltamethrin, but resistance against the OP malathion. VGSC analysis revealed a widespread distribution of mutations F1534C (in all populations, with allelic frequencies between 6.6% - 68.3%), and I1532T (in 6 populations), but absence of V1016G. CCE gene amplifications were recorded in 8 out of 11 populations. Co-presence of mutation F1534C and CCEae3a amplification was reported in a subgroup of samples. No mutations at the CHS locus I1043 were detected. Conclusions: The results indicate: (i) the suitability of larvicides DFB and Bti for Ae. albopictus control in Greece, (ii) a possible incipient pyrethroid resistance due to the presence of kdr mutations and (iii) a possible reduced efficacy of OPs, in a scenario of re-introducing them for vector control. The study highlights the need for systematic resistance monitoring for developing and implementing appropriate evidence-based control programs. Key words: diagnostic, arbovirus, mosquito tiger, insecticide resistance, vector control, Europe
Theoretical Molecular Docking Study of the Structural Disruption of the Viral 3CL-Protease of COVID19 Induced by Binding of Capsaicin, Piperine and Curcumin Part 1: A Comparative Study with Chloroquine and Hydrochloroquine Two Antimalaric Drugs
Authors: Gonzalez-Paz Lenin A. , Lossada Carla A. , Moncayo Luis S. , Romero Freddy , Paz J. L. , Vera-Villalobos Joan , Pérez Aleivi E. , San-Blas Ernesto , Alvarado Ysaias J. 
Published: April 2020

Abstract
The global pandemic caused by infections of the new coronavirus (COVID-19) makes it necessary to find possible less toxic and easily accessible therapeutic agents. In this study, we used strategies docking and molecular dynamics to analyze phytochemical compounds against FDA-approved antimalarial drugs recommended for the treatment of COVID-19. The evaluation was performed with the docking scores MolDock Score and Rerank Score calculated by Molegro Molecular. The DockThor server was used to generate the complexes and myPresto for the dynamic studies. Preliminary results suggested that piperine, capsaicin, and curcumin have the best docking scores and that they are capable of promoting structural changes in the viral protease by inducing folding of the enzyme. Curcumin and capsaicin bring the enzyme to a more compact conformational state compared to the native state, compared to chloroquine. Even though, it is unknown if these induced changes in protease are related to any inhibitory effect observed both in vitro and in vivo for any of these compounds. Further studies on the mechanisms of action of these compounds of interest are required, as well as experimental demonstrations. However, these results are interesting because they can serve as a starting point for subsequent experimental or/and in silico studies based on chemical structure-activity relationships taking these small molecules and their possible derivatives.
From sequence data to patient result: a solution for HIV drug resistance genotyping with Exatype, end to end software for Pol-HIV-1 Sanger based Sequence analysis and patient HIV drug resistance result generation
Authors: Kingwara Leonard , Karanja Muthoni , Ngugi Catherine , Kangogo Geoffrey , Bera Kipkerich , Kimani Maureen , Bowen Nancy , Abuya Dorcus , Oramisi Violet , Mukui Irene 
Published: April 2020

Abstract
Introduction: With the rapid scale-up of antiretroviral therapy (ART) to treat HIV infection, there are ongoing concerns regarding probable emergence and transmission of HIV drug resistance (HIVDR) mutations. This scale-up has to lead to an increased need for routine HIVDR testing to inform the clinical decision on a regimen switch. Although the majority of wet laboratory processes are standardized, slow, labor-intensive data transfer and subjective manual sequence interpretation steps are still required to finalize and release patient results. We thus set out to validate the applicability of a software package to generate HIVDR patient results from raw sequence data independently.Methods: We assessed the performance characteristics of Hyrax Bioscience's Exatype (a sequence data to patient result, fully automated sequence analysis software, which consolidates RECall, MEGA X and the Stanford HIV database) against the standard method (RECall and Stanford database). Exatype is a web-based HIV Drug resistance bioinformatic pipeline available at sanger.exatype.com. To validate the exatype, we used a test set of 135 remnant HIV viral load samples at the National HIV Reference Laboratory (NHRL).Result: We analyzed, and successfully generated results of 126 sequences out of 135 specimens by both standard and Exatype software. Result production using Exatype required minimal hands-on time in comparison to the standard (6 computation-hours using the standard method versus 1.5 Exatype computation-hours). Concordance between the two systems was 99.8% for 311,227 bases compared. 99.7 % of the 0.2% discordant bases, were attributed to nucleotide mixtures as a result of the sequence editing in Recall. Both methods identified similar (99.1%) critical antiretroviral resistance-associated mutations resulting in a 99.2% concordance of resistance susceptibility interpretations. Base calling comparison between the two methods had Cohen's kappa (0.97 to 0.99) implying an almost perfect agreement with minimal base calling variation. On a predefined dataset, RECall editing displayed the highest probability to score mixtures accurately one vs. 0.71 and the lowest chance to inaccurately assign mixtures to pure nucleotides (0.002–0.0008). This advantage is attributable to the manual sequence editing in RECall.Conclusion: The reduction in hands-on time needed is a benefit when using the Exatype HIV DR sequence analysis platform and result generation tool. There is a minimal difference in base calling between Exatype and standard methods. Although the discrepancy has minimal impact on drug resistance interpretation, allowance of sequence editing in Exatype as RECall can significantly improve its performance.
Analysis of clinical characteristics of SARS-CoV-2 infected cases: a retrospective study of medical records
Authors: Zhang Han , Lu Lian , Hu Wei , Zhang Jian , Zhu Wei , He Qi-Qiang , Sun Cheng-Cao , Li De-Jia 
Published: April 2020

Abstract
In order to identify the clinical characteristics of patients with Corona Virus Disease 2019 (COVID-19) and find out the characteristic effects of 2019 New Coronavirus (SARS-CoV-2) infection on changes in clinical and laboratory data, we analyzed the medical records of 80 suspected cases who admitted in the national designated hospital due to the relevant clinical manifestations of SARS-CoV-2 infection from January 22 to February 13, 2020. 62 (77.5%) confirmed cases and 18 (22.5%) negative cases were confirmed by SARS-CoV-2 nucleic acid test. Epidemiological investigation and statistical analysis were carried out on the clinical and laboratory data of all suspected cases of COVID-19, the specific indicators were found, and the clinical characteristics of COVID-19 were described. Compared with the patients with negative nucleic acid test, the patients with positive nucleic acid test showed shorter time of onset of symptoms, higher plasma CO2 level, lower eosinophil ratio, lower platelet count and hematocrit, lower serum sodium level, higher serum creatinine, higher blood urea and plasma albumin levels (all P<0.05). Our results might provide some suggestions in diagnosis, clinical treatment and prevention for COVID-19.
The Fröhlich-Morchio-Strocchi mechanism and quantum gravity
Authors: Maas Axel 
Published: April 2020

Taking manifest invariance under both gauge symmetry and
diffeomorphisms as a guiding principle physical objects are constructed
for Yang-Mills-Higgs theory coupled to quantum gravity. These objects
are entirely classified by quantum numbers defined in the tangent space.
Applying the Fröhlich-Morchio-Strocchi mechanism to these objects
reveals that they coincide with ordinary correlation functions in
quantum-field theory, if quantum fluctuations of gravity and curvature
become small. Taking these descriptions literally exhibits how quantum
gravity fields need to dress quantum fields to create physical objects,
i. e. giving a graviton component to ordinary observed particles. The
same mechanism provides access to the physical spectrum of pure
gravitational degrees of freedom.
Formulation and Evaluation of a Novel Itraconazole-Clotrimazole Topical Emulgel for the Treatment of Sporotrichosis
Authors: Noronha Letícia L. , Ferreira Patricia G. , G.S. Lima Carolina , Borba-Santos Luana P. , Rozental Sonia , de Moraes Marcela , Silva Fernando C. da , Ferreira Vitor F. , Futuro Débora O. 
Published: April 2020

:
In recent years, the development of new pharmaceutical formulations for the treatment of sporotrichosis
has become a relevant research field. In this work, we aimed to develop an emulgel containing itraconazole
and clotrimazole to ensure therapeutic effectiveness against Sporothrix brasiliensis. The topical use of a formulation
that combines both drugs represents an interesting option for the complementary treatment of sporotrichosis.
The emulgel formulation was prepared and evaluated for its zeta potential, viscosity, in vitro antifungal activity
and stability at different storage conditions. The results showed that the newly developed emulgel displayed
promising physicochemical characteristics, as well as a good in vitro inhibitory activity against S. brasiliensis
yeasts. The results obtained in this work suggest that the emulgel containing itraconazole and clotrimazole might
highly be efficient and a complementary therapy to oral administration in the treatment of sporotrichosis.