bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypertrophic cardiomyopathy genetic test reports: A qualitative study of patient understanding of uninformative genetic test results
Authors: Nightingale Brooke M. , Hovick Shelly R. , Brock Pamela , Callahan Emily , Jordan Elizabeth , Roggenbuck Jennifer , Sturm Amy C. , Morales Ana 
Published: August 2019

AbstractStudies have shown that patients with hypertrophic cardiomyopathy (HCM) may misinterpret the meaning of uninformative genetic testing results to mean that a genetic etiology and family members’ risk is ruled out. We hypothesized that poor comprehension of the laboratory genetic test report may contribute to this misunderstanding. We conducted a qualitative study to examine patient understanding of uninformative laboratory results and reports and elicit suggestions for an improved report. Fifteen participants with HCM were interviewed after undergoing genetic testing and receiving their report. While all patients read the report, most participants reported only partially reading it. Most reported not understanding the report at all or only partially understanding it because a provider explained it to them. Some participants said that the report was helpful for understanding their result, but there was evidence of misunderstanding; most participants stated that specific aspects of the report were unhelpful. While most of our participants communicated risk with relatives, none said that the report helped with the communication. Most participants did not recall or find the accompanying physician‐directed result letter useful for their understanding or familial communication. Many participants expressed need for a supplemental report that illustrates a personalized clinical ‘action plan’ that could summarize clinical and familial implications of the result for the patient and their family. We conclude that laboratory reports and physician‐directed result letters did not help participants understand their results or their familial implications. Our results suggest opportunities for research to explore the utility of a patient‐directed result supplement to improve patient comprehension of genetic test results and outline clinical recommendations via a patient action plan.
TMPRSS3 regulates cell viability and apoptosis processes of HEI‐OC1 cells via regulation of the circ‐Slc4a2, miR‐182 and Akt cascade
Authors: Zhang Zhi‐Wen , Pang Bo , Chen Yi‐Chao , Peng An‐Quan 
Published: August 2019

AbstractBackgroundThe present study aimed to investigate the functions and regulation mechanism of the transmembrane protease, serine 3 (TMPRSS3), which plays an important role in sensorineural hearing loss.MethodsHouse Ear Institute‐Organ of Corti 1 (HEI‐OC1) cells, comprising auditory‐related cells, were used in the present study. An overexpression vector and small hairpin RNA target on TMPRSS3 were designed and transfected into HEI‐OC1 cells. Circular RNA (circRNA) sequencing was conducted and expression profiles were obtained. The circular structure of circRNAs was validated with a polymerase chain reaction and Sanger sequencing using convergent and divergent primers.ResultsOverexpression of TMPRSS3 increased cell viability, whereas suppression of TMPRSS3 increased the percentage of apoptotic cells and decreased cell viability, compared to the control group. circRNA sequencing provided expression profiles indicating that the overexpression of TMPRSS3 increased the expression level of 195 circRNAs. Results of GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) studies indicated that the circRNAs are focused on the RAS signaling pathway. The pathway, circ‐Slc41a2 (chr10: 82744115|82767120), miR‐182 and Akt, might comprise one of the key cascades of TMPRSS3.ConclusionsTMPRSS3 is an important molecule in the regulation of cell viability and cell apoptosis of HEI‐OC1 cells. Its functions are dependent on the circ‐Slc41a2, miR‐182 and Akt cascade.
Is papillary thyroid microcarcinoma a biologically different disease? A propensity score‐matched analysis
Authors: Hsu Yi‐Chiung , Lee Jie‐Jen , Chien Ming‐Nan , Chen Ming‐Jen , Leung Ching‐Hsiang , Cheng Shih‐Ping 
Published: August 2019

AbstractBackgroundPapillary thyroid microcarcinoma exhibits an indolent clinical course and could be a candidate for active surveillance in the appropriate setting. It remains unknown whether papillary microcarcinoma is biologically different from larger papillary carcinoma >1 cm.MethodsWe analyzed clinicopathological information and transcriptome data of papillary thyroid cancer samples from The Cancer Genome Atlas. Propensity‐score matching was used to construct a matched cohort consisting of 29 microcarcinomas and 58 carcinomas. Principal component analysis and unsupervised hierarchical cluster analysis were carried out to investigate the similarity of gene expression profiles.ResultsAfter adjustment for differences in baseline clinicopathological and genetic factors, transcriptome could be grouped mainly on the basis of tumor class (BRAF‐like vs RAS‐like) and tumor size (microcarcinoma vs carcinoma). The gene set enrichment analysis showed that extracellular matrix‐associated pathways were enriched in the MSigDB database.ConclusionPapillary thyroid microcarcinomas display a distinct gene expression pattern different from the corresponding carcinomas. We hypothesize that tumor microenvironment may play a role in the microcarcinoma/carcinoma phenotypic divergence.
Performance evaluation of computed tomography systems: Summary of AAPM Task Group 233
Authors: Samei Ehsan , Bakalyar Donovan , Boedeker Kirsten L. , Brady Samuel , Fan Jiahua , Leng Shuai , Myers Kyle J. , Popescu Lucretiu M. , Ramirez Giraldo Juan Carlos , Ranallo Frank , Solomon Justin , Vaishnav Jay , Wang Jia 
Published: August 2019

BackgroundThe rapid development and complexity of new x‐ray computed tomography (CT) technologies and the need for evidence‐based optimization of image quality with respect to radiation and contrast media dose call for an updated approach towards CT performance evaluation.AimsThis report offers updated testing guidelines for testing CT systems with an enhanced focus on the operational performance including iterative reconstructions and automatic exposure control (AEC) techniques.Materials and MethodsThe report was developed based on a comprehensive review of best methods and practices in the scientific literature. The detailed methods include the assessment of 1) CT noise (magnitude, texture, nonuniformity, inhomogeneity), 2) resolution (task transfer function under varying conditions and its scalar reflections), 3) task‐based performance (detectability, estimability), and 4) AEC performance (spatial, noise, and mA concordance of attenuation and exposure modulation). The methods include varying reconstruction and tube current modulation conditions, standardized testing protocols, and standardized quantities and metrology to facilitate tracking, benchmarking, and quantitative comparisons.ResultsThe methods, implemented in cited publications, are robust to provide a representative reflection of CT system performance as used operationally in a clinical facility. The methods include recommendations for phantoms and phantom image analysis.DiscussionIn line with the current professional trajectory of the field toward quantitation and operational engagement, the stated methods offer quantitation that is more predictive of clinical performance than specification‐based approaches. They can pave the way to approach performance testing of new CT systems not only in terms of acceptance testing (i.e., verifying a device meets predefined specifications), but also system commissioning (i.e., determining how the system can be used most effectively in clinical practice).ConclusionWe offer a set of common testing procedures that can be utilized towards the optimal clinical utilization of CT imaging devices, benchmarking across varying systems and times, and a basis to develop future performance‐based criteria for CT imaging.
The negative growth of a brief depressive spell among U.S. adolescents
Authors: Quinlan Paul , Vanderziel Alyssa , Gregoire Villisha , Anthony James C. 
Published: August 2019

AbstractObjectiveStudying adolescent‐onset brief depressive spells, we saw a chance to adapt a cross‐cohort approach for successive cross‐sectionally gathered epidemiological estimates on birth cohorts.MethodsThe United States (US) study population estimates are for noninstitutionalized community‐dwelling 17‐ to 18‐year‐olds, sampled, recruited, and assessed using audio computer assisted self‐interviews for the National Surveys on Drug Use and Health each year, 2008–2016. Estimated age and year‐specific lifetime history cumulative incidence proportions are presented, with 95% confidence intervals, as well as age‐specific meta‐analysis summary estimates.ResultsOccurrence of a brief depressive spell (BDS) among the 2008 U.S. 17‐year‐olds showed a surprising difference with the 2009 statistically independent sample of that same “birth cohort” assessed at age 18 years. “Negative growth” was seen instead of an expected increase in those affected. Independent replication estimates of this BDS negative growth difference were seen in multiple successive birth cohorts.ConclusionsThis well‐replicated difference in BDS estimates offers a fascinating puzzle to be solved with focused inquiry. The puzzle's solution is important because National Surveys on Drug Use and Health does not assess Major Depression unless a BDS lifetime history is ascertained.
Effect of oocyte vitrification on DNA damage in metaphase II oocytes and the resulting preimplantation embryos
Authors: Chang Haoya , Chen Huanhuan , Zhang Lei , Wang Yile , Xie Xiaogang , Zhang Yong , Quan Fusheng 
Published: August 2019

AbstractAs an assisted reproduction technology, vitrification has been widely used for oocyte and embryo cryopreservation. Many studies have indicated that vitrification affects ultrastructure, gene expression, and epigenetic status. However, it is still controversial whether oocyte vitrification could induce DNA damage in metaphase II (MII) oocytes and the resulting early embryos. This study determined whether mouse oocytes vitrification induce DNA damage in MII oocytes and the resulting preimplantation embryos, and causes for vitrification‐induced DNA damage. The effects of oocyte vitrification on reactive oxygen species (ROS) levels, γ‐H2AX accumulation, apoptosis, early embryonic development, and the expression of DNA damage‐related genes in early embryos derived by in vitro fertilization were examined. The results indicated that vitrification significantly increased the number of γ‐H2AX foci in zygotes and two‐cell embryos. Trp53bp1 was upregulated in zygotes, two‐cell embryos and four‐cell embryos in the vitrified group, and Brca1 was increased in two‐cell embryos after vitrification. Vitrification also increased the ROS levels in MII oocytes, zygotes, and two‐cell embryos and the apoptotic rate in blastocysts. Resveratrol (3,5,4′‐trihydroxystilbene) treatment decreased the ROS levels and the accumulation of γ‐H2AX foci in zygotes and two‐cell embryos and the apoptotic rate in blastocysts after vitrification. Overall, vitrification‐induced abnormal ROS generation, γ‐H2AX accumulation, an increase in the apoptotic rate and the disruption of early embryonic development. Resveratrol treatment could decrease ROS levels, γ‐H2AX accumulation, and the apoptotic rate and improve early embryonic development. Vitrification‐associated γ‐H2AX accumulation is at least partially due to abnormal ROS generation.
The translational functions of embryonic poly(A)‐binding protein during gametogenesis and early embryo development
Authors: Ozturk Saffet 
Published: August 2019

AbstractEmbryonic poly(A)‐binding protein (EPAB) is an RNA‐binding protein that binds to the poly(A) tails and AU‐rich element at the 3′ ends of messenger RNA (mRNAs). The main functions of EPAB are to protect stored mRNAs from undergoing deadenylation and subsequent degradation and to be involved in their translational regulation during spermatogenesis, oogenesis, and early embryogenesis. Following the first characterization of Epab in the Xenopus oocytes and early embryos, spatial and temporal expression and potential roles of the Epab gene have been determined in the vertebrate germ cells and early embryos. In this review, we have comprehensively evaluated all studies in this field and discussed the particular functions of EPAB in the spermatogenic cells, oocytes, early embryos, and somatic cells in vertebrates.
Unexpected Secondary Nucleation in Poly(Vinyl acetate) Nanoparticle Synthesis by Ab Initio Batch Emulsion Polymerization Using Poly(Vinyl alcohol) as Surfactant
Authors: Rocha‐Botello Gabriela , Olvera‐Guillen Roberto , Herrera‐Ordonez Jorge , Cruz‐Soto Martha , Victoria‐Valenzuela David 
Published: August 2019

AbstractKinetic aspects of the vinyl acetate ab initio batch emulsion polymerization using poly(vinyl alcohol) to produce polymer nanoparticles are studied. The initial nucleation step is followed by limited coagulation and then by the generation of new particles. It seems that this is the first report of secondary nucleation phenomenon occurring in the system under study in batch mode. To explain this phenomenon, a mathematical model that allows to determine whether certain polymerization conditions and the presence/absence of a steric barrier, can lead or not to significant secondary nucleation is developed. It is deduced that the effect of such steric barrier on the free‐radical entry process plays a key role on the observed phenomenon.
Effects of a group‐based physical activity program for pediatric patients with cancer on physical activity and symptom experience: A quasi‐experimental study
Authors: Ouyang Na , Cai Ruiqing , Zhou Xuezhen , Huang Haiying , Qiu Xing , Liu Ke 
Published: August 2019

AbstractAimsTo examine the effects of a group‐based physical activity intervention on improvement in physical activity and mitigation of symptom distress among pediatric patients with cancer.MethodsBased on convenience sampling, 57 pediatric patients with cancer admitted to the cancer center were included in the intervention group. The control group included 57 pediatric patients with cancer from two other hospitals matched to the patients in the intervention group by age, sex, and diagnosis. A group‐based physical activity program was implemented among the children in the intervention group, whereas the children in the control group received standard care. Physical activity and symptoms were measured using the Children's Leisure Time Activities Study Survey‐Chinese and using the Memorial Symptom Assessment Scale 10–18 at baseline and after the 12th exercise session in both the intervention and control groups.ResultsThe repeated‐measures analysis of variance showed that the main intervention effects on the decrease in light‐intensity physical activity and increase in moderate‐to‐vigorous physical activity were significant between the two groups (P < .001). The group‐based physical activity intervention could decrease the scores of psychological symptoms (P < .001), Global Distress Index (P < .001), and physical symptoms (P = .01) when comparing the difference between the two groups before and after the intervention. There was no significant difference in the number of symptoms or the total symptom experience score between the two groups.ConclusionThese findings suggest that a group‐based physical activity intervention can promote physical activity and relieve psychological and physical symptom distress among pediatric patients with cancer.
A versatile method for cyclic polymers from conjugated and unconjugated vinyl monomers
Authors: Liu Xueping , Chen Ji‐Qiang , Zhang Minghui , Wu Ying , Yang Miao , Zhang Ke 
Published: August 2019

ABSTRACTA versatile method was introduced to prepare cyclic polymers from both conjugated and unconjugated vinyl monomers. It was developed on the combination of the RAFT polymerization and the self‐accelerating double strain‐promoted azide‐alkyne click (DSPAAC) reaction. In this approach, a switchable chain transfer agent 1 was designed to have hydroxyl terminals and a functional pyridinyl group. The protonation and deprotonation of pyridinyl group endowed the chain transfer agent 1 with a switchable control capability to RAFT polymerization of both conjugated and unconjugated vinyl monomers. Based on this, RAFT polymerization and the following hydroxyl end group modification were used to prepare various azide‐terminated linear polymers including polystyrene, poly(N‐vinylcarbazole), and polystyrene‐block‐poly(N‐vinylcarbazole). Using sym‐dibenzo‐1,5‐cyclooctadiene‐3,7‐diyne (DBA) as small linkers, the corresponding cyclic polymers were then prepared via the DSPAAC reaction between DBA and azide terminals of the linear precursors. Due to the self‐accelerating property of DSPAAC reaction, this bimolecular ring‐closing reaction could efficiently produce the pure cyclic polymers using excess molar amounts of DBA to linear polymer precursors. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 1811–1820
Ensembling multiple raw coevolutionary features with deep residual neural networks for contact‐map prediction in CASP13
Authors: Li Yang , Zhang Chengxin , Bell Eric W. , Yu Dong‐Jun , Zhang Yang 
Published: August 2019

AbstractWe report the results of residue‐residue contact prediction of a new pipeline built purely on the learning of coevolutionary features in the CASP13 experiment. For a query sequence, the pipeline starts with the collection of multiple sequence alignments (MSAs) from multiple genome and metagenome sequence databases using two complementary Hidden Markov Model (HMM)‐based searching tools. Three profile matrices, built on covariance, precision, and pseudolikelihood maximization respectively, are then created from the MSAs, which are used as the input features of a deep residual convolutional neural network architecture for contact‐map training and prediction. Two ensembling strategies have been proposed to integrate the matrix features through end‐to‐end training and stacking, resulting in two complementary programs called TripletRes and ResTriplet, respectively. For the 31 free‐modeling domains that do not have homologous templates in the PDB, TripletRes and ResTriplet generated comparable results with an average accuracy of 0.640 and 0.646, respectively, for the top L/5 long‐range predictions, where 71% and 74% of the cases have an accuracy above 0.5. Detailed data analyses showed that the strength of the pipeline is due to the sensitive MSA construction and the advanced strategies for coevolutionary feature ensembling. Domain splitting was also found to help enhance the contact prediction performance. Nevertheless, contact models for tail regions, which often involve a high number of alignment gaps, and for targets with few homologous sequences are still suboptimal. Development of new approaches where the model is specifically trained on these regions and targets might help address these problems.
Pharmacodynamics, safety, and immunogenicity of Pelmeg®, a pegfilgrastim biosimilar in healthy subjects
Authors: Wessels Hendrik , Lehnick Dirk , Höfler Josef , Jankowsky Ruediger , Chamberlain Paul , Roth Karsten 
Published: August 2019

AbstractA pharmacodynamics (PD) and immunogenicity study was conducted to investigate biosimilarity of Pelmeg®, a pegfilgrastim biosimilar to EU‐authorized Neulasta®. The multiple‐dose, randomized, double‐blind, two‐sequence, and three‐period cross‐over study comprised 96 healthy male subjects, receiving Pelmeg (Test [T]) and Neulasta (Reference [R]) in a sequential manner (T‐T‐R vs R‐R‐T). Subjects were dosed with 3 mg pegfilgrastim, as this dose was previously shown to be in the ascending part of the dose‐response curve for PD. The primary PD endpoint was the area under the effect curve (AUEC0‐last) for absolute neutrophil count (ANC). The primary immunogenicity endpoint was proportion of anti‐drug antibody (ADA)‐positive subjects at the end of Period 2 (ie, after administration of two doses of the same study drug). Comparability was demonstrated for the PD endpoint, with the geometric mean ratio (T/R) of AUEC0‐last being 101.59%, with a corresponding 95% CI of [99.58; 103.63]. Of note, when using tighter acceptance limits (90.00%‐111.00%), comparability between test and reference was shown as well. Only two confirmed ADA positive samples were detected, one after treatment with Pelmeg and one after Neulasta. These had a low ADA titer, no filgrastim reactivity, and no neutralizing capacity. No clinically meaningful differences in safety between Pelmeg and Neulasta were observed. Overall, the results from this study confirmed the biosimilarity of Pelmeg and Neulasta for PD and immunogenicity, as shown already at the bioanalytical level and in the pivotal PK/PD study with Pelmeg.
Using a genetic algorithm to generate D‐optimal designs for mixture‐process variable experiments
Authors: Pradubsri Wasinee , Chomtee Boonorm , Borkowski John J. 
Published: August 2019

AbstractThis article presents and develops a genetic algorithm (GA) to generate D‐efficient designs for mixture‐process variable experiments. It is assumed the levels of a process variable are controlled during the process. The GA approach searches design points from a set of possible points over a continuous region and works without having a finite user‐defined candidate set. We compare the performance of designs generated by the GA with designs generated by two exchange algorithms (DETMAX and k‐exchange) in terms of D‐efficiencies and fraction of design space (FDS) plots which are used to evaluate a design's prediction variance properties. To illustrate the methodology, examples involving three and four mixture components and one process variable are proposed for creating the optimal designs. The results show that GA designs have superior prediction variance properties in comparison with the DETMAX and k‐exchange algorithm designs when the design space is the simplex or is a highly‐constrained subspace of the simplex.
Extended Kalman filters for fractional‐order nonlinear continuous‐time systems containing unknown parameters with correlated colored noises
Authors: Huang Xiaomin , Gao Zhe , Ma Ruicheng , Chen Xiaojiao 
Published: August 2019

SummaryBy using the Grünwald‐Letnikov (G‐L) difference method and the Tustin generating function method, this study presents extended Kalman filters to achieve satisfactory state estimation for fractional‐order nonlinear continuous‐time systems that containing some unknown parameters with the correlated fractional‐order colored noises. Based on the G‐L difference method and the Tustin generating function method, the difference equations corresponding to fractional‐order nonlinear continuous‐time systems are constructed respectively. The first‐order Taylor expansion is used to linearize the nonlinear functions in the estimated system, which provides the system model for extended Kalman filters. Using the augmented vector method, the unknown parameters are regarded as new state vectors, and the augmented difference equation is constructed. Based on the augmented difference equation, extended Kalman filters are designed to estimate the state of fractional‐order nonlinear systems with process noise as fractional‐order colored noise or measurement noise as fractional‐order colored noise. Meanwhile, the extended Kalman filters proposed in this paper can also estimate the unknown parameters effectively. Finally, the effectiveness of the proposed extended Kalman filters is validated in simulation with two examples.