bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and Transcriptomic Analyses of Breast Cancer Primaries and Matched Metastases in AURORA, the Breast International Group (BIG) Molecular Screening Initiative
Authors: Aftimos Philippe , Oliveira Mafalda , Irrthum Alexandre , Fumagalli Debora , Sotiriou Christos , Gal-Yam Einav Nili , Robson Mark E. , Ndozeng Justin , Di Leo Angelo , Ciruelos Eva M. , de Azambuja Evandro , Viale Giuseppe , Scheepers Elsemieke D. , Curigliano Giuseppe , Bliss Judith M. , Reis-Filho Jorge S. , Colleoni Marco , Balic Marija , Cardoso Fatima , Albanell Joan , Duhem Caroline , Marreaud Sandrine , Romagnoli Dario , Rojas Beatriz , Gombos Andrea , Wildiers Hans , Guerrero-Zotano Angel , Hall Peter , Bonetti Andrea , Larsson Karolina Fs , Degiorgis Martina , Khodaverdi Silvia , Greil Richard , Sverrisdóttir Ásgerdur , Paoli Marta , Seyll Ethel , Loibl Sibylle , Linderholm Barbro , Zoppoli Gabriele , Davidson Nancy E. , Johannsson Oskar Th , Bedard Philippe L. , Loi Sherene , Knox Susan , Cameron David A. , Harbeck Nadia , Montoya Maite Lasa , Brandão Mariana , Vingiani Andrea , Caballero Carmela , Hilbers Florentine S. , Yates Lucy R. , Benelli Matteo , Venet David , Piccart Martine J. 
Published: June 2021

Abstract

AURORA aims to study the processes of relapse in metastatic breast cancer (MBC) by performing multi-omics profiling on paired primary tumors and early-course metastases. Among 381 patients (primary tumor and metastasis pairs: 252 targeted gene sequencing, 152 RNA sequencing, 67 single nucleotide polymorphism arrays), we found a driver role for GATA1 and MEN1 somatic mutations. Metastases were enriched in ESR1, PTEN, CDH1, PIK3CA, and RB1 mutations; MDM4 and MYC amplifications; and ARID1A deletions. An increase in clonality was observed in driver genes such as ERBB2 and RB1. Intrinsic subtype switching occurred in 36% of cases. Luminal A/B to HER2-enriched switching was associated with TP53 and/or PIK3CA mutations. Metastases had lower immune score and increased immune-permissive cells. High tumor mutational burden correlated to shorter time to relapse in HR+/HER2− cancers. ESCAT tier I/II alterations were detected in 51% of patients and matched therapy was used in 7%. Integration of multi-omics analyses in clinical practice could affect treatment strategies in MBC.

Significance:
The AURORA program, through the genomic and transcriptomic analyses of matched primary and metastatic samples from 381 patients with breast cancer, coupled with prospectively collected clinical data, identified genomic alterations enriched in metastases and prognostic biomarkers. ESCAT tier I/II alterations were detected in more than half of the patients.
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Impact of High-Deductible Health Plans on Emergency Department Patients With Nonspecific Chest Pain and Their Subsequent Care
Authors: Chou Shih-Chuan , Hong Arthur S. , Weiner Scott G. , Wharam J. Frank 
Published: June 2021

Background:
Timely evaluation of acute chest pain is necessary, although most evaluations will not find significant coronary disease. With employers increasingly adopting high-deductible health plans (HDHP), how HDHPs impact subsequent care after an emergency department (ED) diagnosis of nonspecific chest pain is unclear.

Methods:
Using a commercial and Medicare Advantage claims database, we identified members 19 to 63 years old whose employers exclusively offered low-deductible (≤$500) plans in 1 year, then, at an index date, mandated enrollment in HDHPs (≥$1000) for a subsequent year. We matched them with contemporaneous members whose employers only offered low-deductible plans. Primary outcomes included population rates of index ED visits with a principal diagnosis of nonspecific chest pain, admission during index ED visits, and index ED visits followed by noninvasive cardiac testing within 3 and 30 days, coronary revascularization, and acute myocardial infarction hospitalization within 30 days. We performed a cumulative interrupted time-series analysis, comparing changes in annual outcomes between the HDHP and control groups before and after the index date using aggregate-level segmented regression. Members from higher-poverty neighborhoods were a subgroup of interest.

Results:
After matching, we included 557 501 members in the HDHP group and 5 861 990 in the control group, with mean ages of 42.0 years, 48% to 49% female, and 67% to 68% non-Hispanic White individuals. Employer-mandated HDHP switches were associated with a relative decrease of 4.3% (95% CI, –5.9 to –2.7; absolute change, –4.5 [95% CI, –6.3 to –2.8] per 10 000 person-years) in nonspecific chest pain ED visits and 11.3% (95% CI, –14.0 to –8.6) decrease (absolute change, –1.7 per 10 000 person-years [95% CI, –2.1 to –1.2]) in visits leading to hospitalization. There was no significant decrease in subsequent noninvasive testing or revascularization procedures. An increase in 30-day acute myocardial infarction admissions was not statistically significant (15.9% [95% CI, –1.0 to 32.7]; absolute change, 0.3 per 10 000 person-years [95% CI, –0.01 to 0.5]) but was significant among members from higher-poverty neighborhoods.

Conclusions:
Employer-mandated HDHP switches were associated with decreased nonspecific chest pain ED visits and hospitalization from these ED visits, but no significant change in post-ED cardiac testing. However, HDHP enrollment was associated with increased 30-day acute myocardial infarction admission after ED diagnosis of nonspecific chest pain among members from higher-poverty neighborhoods.
Fatigue Following Pediatric Arterial Ischemic Stroke
Authors: Greenham Mardee , Gordon Anne L. , Cooper Anna , Hearps Stephen , Ditchfield Michael , Coleman Lee , Hunt Rod W. , Mackay Mark T. , Monagle Paul , Anderson Vicki 
Published: June 2021

Background and Purpose:
The aims of this study were to assess the prevalence of multidimensional fatigue symptoms 5 years after pediatric arterial ischemic stroke and identify factors associated with fatigue.

Methods:
Thirty-one children (19 males) with pediatric arterial ischemic stroke, participating in a larger prospective, longitudinal study, were recruited to this study at 5 years poststroke. Parent- and self-rated PedsQL Multidimensional Fatigue Scale scores were compared with published normative data. Associations between parent-rated PedsQL Multidimensional Fatigue Scale, demographics, stroke characteristics, and concurrent outcomes were examined.

Results:
Parent-rated total, general and cognitive fatigue were significantly poorer than population norms, with more than half of all parents reporting fatigue symptoms in their children. One-third of children also reported experiencing fatigue symptoms, but their ratings did not differ significantly from normative expectations, as such, all further analyses were on parent ratings of fatigue. Older age at stroke and larger lesion size predicted greater general fatigue; older age, female sex, and higher social risk predicted more sleep/rest fatigue. No significant predictors of cognitive fatigue were identified and only older age at stroke predicted total fatigue. Greater fatigue was associated with poorer adaptive functioning, motor skills, participation, quality of life, and behavior problems but not attention.

Conclusions:
Fatigue is a common problem following pediatric arterial ischemic stroke and is associated with the functional difficulties often seen in this population. This study highlights the importance of long-term monitoring following pediatric arterial ischemic stroke and the need for effective interventions to treat fatigue in children.
Observations of Diurnal Variability under the Cirrus Canopy of Typhoon Kong-rey (2018)
Authors: Trabing Benjamin C. , Bell Michael M. 
Published: June 2021

AbstractA growing body of work has documented the existence of diurnal oscillations in the tropical cyclone outflow layer. These diurnal pulses have been examined primarily using satellites or numerical models, and detailed full tropospheric observations or case study analyses of diurnal pulses are lacking. Questions remain on the vertical extent of diurnal pulses and whether diurnal pulses are coupled to convective bands or constrained to the outflow layer. During the Propagation of Intraseasonal Tropical Oscillations (PISTON) field campaign, diurnal oscillations in the upper-level clouds were observed during Typhoon Kong-rey’s (2018) rapid intensification. Over a 3.5 day period where a broad distribution of cold upper-level clouds was overhead, detailed observations of Typhoon Kong-rey’s rainbands show that convection had reduced echo tops but enhanced reflectivity and differential reflectivity aloft compared to other observations during PISTON. Shortwave heating in the upper-levels increased the stability profile in an overall favorable thermodynamic environment for convection during the day, which could help to explain the diurnal differences in convective structure. Under the cirrus canopy, nocturnal convection was deeper and daytime convection shallower in contrast to the rest of the PISTON dataset. Diurnal oscillations in the brightness temperatures were found to be coupled to radially outward propagating convective rainbands that were preceded ~6 hours by outflow jets. The cooling pulses occurred earlier than found in previous studies. The pulses were asymmetric spatially which is likely due to a combination of the vertical wind shear and storm intensity.
Effects of Trade Wind Strength on Airflow and Cloudiness over O‘ahu
Authors: Hsiao Feng , Chen Yi-Leng , Van Nguyen Hiep , Hitzl David Eugene , Ballard Robert 
Published: June 2021

AbstractSatellite observations and high-resolution modeling during July–August 2013 are used to study the effects of trade wind strength on island wake circulations and cloudiness over O‘ahu, Hawai‘i. O‘ahu is composed of two northwest–southeast orientated mountain ranges: the Wai‘anae Range (~1227 m) along the western leeside coast and the Ko‘olau Range (~944 m) along the eastern windward coast. At night, the flow deceleration of the incoming northeasterly trade winds on the eastern windward side is more significant when trades are stronger.In the afternoon hours, effective albedo and simulated cloud water are greater over the Ko‘olau Range when trades are stronger, and clouds are advected downstream by the trade winds aloft. Over the Wai‘anae Range, orographic clouds are more significant when trades are weaker due to less moisture removal by orographic precipitation over the Ko‘olau Range and the development of both upslope flow on the eastern slope and upslope/sea-breeze flow along the western coast, the latter of which brings in warm, moist air from the ocean. When trades are weaker, cloudiness off the western leeside coast is more extensive and originates from orographic cloud development over the Wai‘anae Range, which drifts downstream due to a combination of trade winds and the easterly return flow aloft. The latter is associated with the low-level sea-breeze/upslope flow.
Dr. Answer AI for Prostate Cancer: Predicting Biochemical Recurrence Following Radical Prostatectomy
Authors: Park Jihwan , Rho Mi Jung , Moon Hyong Woo , Kim Jaewon , Lee Chanjung , Kim Dongbum , Kim Choung-Soo , Jeon Seong Soo , Kang Minyong , Lee Ji Youl 
Published: June 2021

Objectives: To develop a model to predict biochemical recurrence (BCR) after radical prostatectomy (RP), using artificial intelligence (AI) techniques. Patients and Methods: This study collected data from 7,128 patients with prostate cancer (PCa) who received RP at 3 tertiary hospitals. After preprocessing, we used the data of 6,755 cases to generate the BCR prediction model. There were 16 input variables with BCR as the outcome variable. We used a random forest to develop the model. Several sampling techniques were used to address class imbalances. Results: We achieved good performance using a random forest with synthetic minority oversampling technique (SMOTE) using Tomek links, edited nearest neighbors (ENN), and random oversampling: accuracy = 96.59%, recall = 95.49%, precision = 97.66%, F1 score = 96.59%, and ROC AUC = 98.83%. Conclusion: We developed a BCR prediction model for RP. The Dr. Answer AI project, which was developed based on our BCR prediction model, helps physicians and patients to make treatment decisions in the clinical follow-up process as a clinical decision support system.
Analysis of Geometric and Dosimetric Effects of Bra Application to Support Large or Pendulous Breasts During Radiotherapy Planning: A Retrospective Single-Center Study
Authors: Park So Hyun , Choi Jinhyun 
Published: June 2021

Purpose: To evaluate geometric and dosimetric effects of bra application during radiotherapy planning for breast cancer patients with large and pendulous breasts. Materials and Methods: Twenty patients with chest sizes >38 inches between April 2019 and July 2019 underwent radiotherapy planning with and without a radiation bra (Chabner XRT®). Geometric and dosimetric parameters included the breast volume, superior-inferior (SI) distance, separation (S) as the distance of the longest diameter of the clinical target volume (CTV), conformity number (CN), and homogeneity index (HI) of CTV. The organs at risk (OARs) were defined as the lungs, heart, and liver. Results: The use of the radiation bra provided mean changes of −0.51 cm for S, −1.45 cm for SI, and −61.18 cc for breast volume (all P < 0.05). Breast volume was correlated with bra-related changes in cross diameter (r = 0.641, P = 0.002) and volume (r = 0.680, P = 0.001). Significant dose reductions were observed for the lungs (mean V10: 19.58 cc, V20: 17.13 cc, Dmean: 86.24 cGy) and heart (Dmean: 170.23 cGy). No significant differences were observed for CN (0.62-0.67) and HI (0.19-0.20) of the CTV. Conclusion: The application of a radiation bra was associated with better geometric and dosimetric planning parameters, with a smaller CTV and lower doses to the OARs (lungs and heart) in the radiotherapy field. In addition, we expect that bra use during radiotherapy would provide emotional benefits.
Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction
Authors: Liu Siyuan , Wang Tong , Xu Qijiang , Shao Bin , Yin Jian , Liu Tie-Yan 
Published: June 2021

AbstractBackgroundFragment libraries play a key role in fragment-assembly based protein structure prediction, where protein fragments are assembled to form a complete three-dimensional structure. Rich and accurate structural information embedded in fragment libraries has not been systematically extracted and used beyond fragment assembly.MethodsTo better leverage the valuable structural information for protein structure prediction, we extracted seven types of structural information from fragment libraries. We broadened the usage of such structural information by transforming fragment libraries into protein-specific potentials for gradient-descent based protein folding and encoding fragment libraries as structural features for protein property prediction.ResultsFragment libraires improved the accuracy of protein folding and outperformed state-of-the-art algorithms with respect to predicted properties, such as torsion angles and inter-residue distances.ConclusionOur work implies that the rich structural information extracted from fragment libraries can complement sequence-derived features to help protein structure prediction.
How well do genetic markers inform about responses to intraspecific admixture? A comparative analysis of microsatellites and RADseq
Authors: Yıldırım Yeşerin , Forsman Anders , Sunde Johanna 
Published: June 2021

AbstractBackgroundFitness consequences of intraspecific genetic admixture can vary from positive to negative depending on the genetic composition of the populations and environmental conditions. Because admixture has potential to influence the success of management and conservation efforts, genetic similarity has been suggested to be used as a proxy to predict the outcome. Studies utilizing microsatellites (a neutral marker) to investigate associations between genetic distance and admixture effects show conflicting results. Marker types that yield information on genome-wide and/or adaptive variation might be more useful for predicting responses to inter-population hybridization. In this study we utilized published data for three populations of pike (Esox lucius) to investigate associations between offspring performance (hatching success) and parental genetic similarity in experimentally purebred and admixed families, based on neutral (microsatellites), genome-wide neutral (RADseq SNPs), and adaptive (SNPs under selection) markers.ResultsEstimated similarity varied among the markers, likely reflecting differences in their inherent properties, but was consistently higher in purebred than admixed families. A significant interaction between marker type and admixture treatment reflected that neutral SNPs yielded higher estimates than adaptive SNPs for admixed families whereas no difference was found for purebred families, which indicates that neutral similarity was not reflective of adaptive similarity. When all samples were pooled, no association between similarity and performance was found for any marker. For microsatellites, similarity was positively correlated with hatching success in purebred families, whereas no association was found in admixed families; however, the direction of the effect differed between the population combinations.ConclusionsThe results strengthen the notion that, as of today, there is no proxy that can reliably predicted the outcome of admixture. This emphasizes the need of further studies to advance knowledge that can shed light on how to safeguard against negative consequences of admixture, and thereby inform management and promote conservation of biological diversity.
Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae)
Authors: Maren Nathan , Zhao Fangzhou , Aryal Rishi , Touchell Darren , Liu Wusheng , Ranney Thomas , Ashrafi Hamid 
Published: June 2021

AbstractBackgroundTripidium ravennaeis a cold-hardy, diploid species in the sugarcane complex (PoaceaesubtribeSaccharinae) with considerable potential as a genetic resource for developing improved bioenergy and ornamental grasses. An improved understanding of the genetic regulation of reproductive processes (e.g., floral induction, inflorescence development, and seed development) will enable future applications of precision breeding and gene editing of floral and seed development. In particular, the ability to silence reproductive processes would allow for developing seedless forms of valuable but potentially invasive plants. The objective of this research was to characterize the gene expression environment of reproductive development inT. ravennae.ResultsDuring the early phases of inflorescence development, multiple key canonical floral integrators and pathways were identified. Annotations of type II subfamily of MADS-box transcription factors, in particular, were over-represented in the GO enrichment analyses and tests for differential expression (FDRp-value < 0.05). The differential expression of floral integrators observed in the early phases of inflorescence development diminished prior to inflorescence determinacy regulation. Differential expression analysis did not identify many unique genes at mid-inflorescence development stages, though typical biological processes involved in plant growth and development expressed abundantly. The increase in inflorescence determinacy regulatory elements and putative homeotic floral development unigenes at mid-inflorescence development coincided with the expression of multiple meiosis annotations and multicellular organism developmental processes. Analysis of seed development identified multiple unigenes involved in oxidative-reductive processes.ConclusionReproduction in grasses is a dynamic system involving the sequential coordination of complex gene regulatory networks and developmental processes. This research identified differentially expressed transcripts associated with floral induction, inflorescence development, and seed development inT. ravennae. These results provide insights into the molecular regulation of reproductive development and provide a foundation for future investigations and analyses, including genome annotation, functional genomics characterization, gene family evolutionary studies, comparative genomics, and precision breeding.
A newly developed paper embedded microchip based on LAMP for rapid multiple detections of foodborne pathogens
Authors: Zhang Mimi , Liu Jinfeng , Shen Zhiqiang , Liu Yongxin , Song Yang , Liang Yu , Li Zhende , Nie Lingmei , Fang Yanjun , Zhao Youquan 
Published: June 2021

Abstract
Background
Microfluidic chip detection technology is considered a potent tool for many bioanalytic applications. Rapid detection of foodborne pathogens in the early stages is imperative to prevent the outbreak of foodborne diseases, known as a severe threat to human health. Conventional bacterial culture methods for detecting foodborne pathogens are time-consuming, laborious, and lacking in pathogen diagnosis. To overcome this problem, we have created an embedded paper-based microchip based on isothermal loop amplification (LAMP), which can rapidly and sensitively detect foodborne pathogens.

Results
We embed paper impregnated with LAMP reagent and specific primers in multiple reaction chambers of the microchip. The solution containing the target pathogen was injected into the center chamber and uniformly distributed into the reaction chamber by centrifugal force. The purified DNA of Escherichia coli O157:H7, Salmonella spp., Staphylococcus aureus, and Vibrio parahaemolyticus has been successfully amplified and directly detected on the microchip. The E. coli O157:H7 DNA was identified as low as 0.0134 ng μL− 1. Besides, the potential of this microchip in point-of-care testing was further tested by combining the on-chip sample purification module and using milk spiked with Salmonella spp.. The pyrolyzed milk sample was filtered through a polydopamine-coated paper embedded in the inside of the sample chamber. It was transported to the reaction chamber by centrifugal force for LAMP amplification. Then direct chip detection was performed in the reaction chamber embedded with calcein-soaked paper. The detection limit of Salmonella spp. in the sample measured by the microchip was approximately 12 CFU mL− 1.

Conclusion
The paper embedded LAMP microchip offers inexpensive, user-friendly, and highly selective pathogen detection capabilities. It is expected to have great potential as a quick, efficient, and cost-effective solution for future foodborne pathogen detection.
In vivo oxygen measurement in cerebrospinal fluid of pigs to determine physiologic and pathophysiologic oxygen values during CNS infections
Authors: de Buhr Nicole , Martens Alexander , Meurer Marita , Bonilla Marta C. , Söbbeler Franz , Twele Lara , Neudeck Stephan , Wendt Michael , Beineke Andreas , Kästner Sabine , von Köckritz-Blickwede Maren 
Published: June 2021

AbstractDuring infection and inflammation, a reduced oxygen level clearly affects cellular functions. Oxygen levels during CNS infections are unknown. Here we established and evaluated an in vivo measurement system to characterize the oxygen level in parallel with bacterial numbers (CFU/mL), the cell number and pH level inside the CSF of healthy compared to Streptococcus suis-infected pigs. The animals were anesthetized over a seven-hour period with isoflurane in air/oxygen at physiologic arterial partial pressure of oxygen. Oxygen levels in CSF of anesthetized pigs were compared to euthanized pigs. The detected partial pressure of oxygen in the CSF remained constant in a range of 47–63 mmHg, independent of the infection status (bacterial or cell number). In contrast, the pH value showed a slight drop during infection, which correlated with cell and bacterial number in CSF. We present physiologic oxygen and pH values in CSF during the onset of bacterial meningitis.