bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the Enlightenment of Wright’s Organic Thought to Chinese Contemporary Architecture
Authors: Lu Wang 
Published: May 2021

Abstract
Frank Lloyd Wright is one of the most important architects in the United States in the 20th century. His idea of organic architecture has a great influence on the modern architecture of the world. The contents of “nature”, “organic” and “unity of nature and man” in organic architecture have been recognized and paid more and more attention all over the world. By analyzing the relationship between Lai’s unique machine architecture thought and Chinese classical philosophy, the application value of organic thought to Chinese contemporary architecture has been found.
Study on landscape design of urban riverside green space based on environmental behavior——Take the small garden of Nanchuan East Road in Xining City as an example
Authors: Zhiman Zhang , Xianyu Zhang 
Published: May 2021

Abstract
Urban riverside green space is not only an important part of urban ecosystem, but also an important carrier of urban civilization, but also a green space for people to travel and relax every day. This paper summarizes the connotation of urban riverside green space and environmental behavior, discusses the interaction between landscape design and visitor psychology and behavior from the perspective of environmental behavior, and designs the landscape design of Nanchuan East Road Park in Xining City with functional zoning as the starting point.
Vibration response law of high-rise building to tunnel blasting
Authors: Ding Xinyu , Ji Xinyu , Gao Shang , Sun Zhongbo , Wang Hailiang 
Published: May 2021

Abstract
In order to study the propagation and attenuation process of blasting seismic waves on high-rise buildings, taking the blasting construction of the entrance A of Xizhen Station of Qingdao Metro Line 1 as an example, the vibration velocity of the 33-story frame structure under the blasting construction condition were analyzed. The results show that: under the action of blasting seismic waves, the vertical vibration velocity of the building structure is greater than the horizontal direction; the vibration velocity of the underground structure of the building presents an oscillation trend, the vibration velocity of the above-ground structure decays rapidly, and there is an elevation amplification effect on the top floor; the research results have certain reference significance for urban blasting construction, monitoring, and seismic protection measures of high-rise buildings.
The Effect of Orchestra Pit Diffusion on the Auditorium Acoustics of Opera House
Authors: Yian Chen , Yuezhe Zhao 
Published: May 2021

Abstract
A scale model of the Zhuhai Opera House, with 7 kinds of simulated orchestra pits, was made and analyzed in an experiment. The pulse response of the auditorium of the opera house was measured and analyzed. The results show that diffusion treatments for the orchestra pit can affect the sound transmission of stage source, increasing C80 and D50 in the rear part of the auditorium and can also affect the sound transmission of pit source, making the average value of G in the auditorium rise. As well, no significant changes were found on EDT and T20 under the diffusion treatment of the orchestra pit.
Evaluation of BioPlex 2200 tTG-IgA Diagnostic Performance for Serology-Based Diagnosis of Celiac Disease
Authors: Pacheco M Cristina , Lee Dale , Dickerson Jane 
Published: May 2021

Abstract

Objectives
Forgoing biopsy for the diagnosis of celiac disease in children with tissue transglutaminase immunoglobulin A (tTG-IgA) levels greater than or equal to 10 times the upper limit of normal (≥10×ULN) has been advocated by the European Society of Paediatric Gastroenterology, Hepatology and Nutrition.

Methods
Our retrospective study tested the specificity and positive predictive value (PPV) of the BioPlex 2200 assay (Bio-Rad Laboratories) in diagnosing celiac disease at the ≥10×ULN tTG-IgA threshold, which is ≥150 U/mL (negative &lt;15 U/mL). We used the tTG-IgA and duodenal biopsy results within 6 months following tTG-IgA measurements from 542 patients who had any number of duodenal biopsy fragments, of whom 165 patients had 5 or more tissue fragments. Sensitivity and specificity of the test were calculated using histology as the gold standard for Marsh class 2 and above.

Results
For histopathologic findings in the duodenum with Marsh 2 and higher, the specificity and PPV of the BioPlex 2200 at ≥10×ULN tTG-IgA were 99.5% and 95.4% using all biopsies and 97.9% and 94.9% for biopsies with 5 or more tissue fragments.

Conclusions
Should clinical considerations preclude endoscopy, the BioPlex 2200 assay at ≥10×ULN TTG-IgA could be considered highly suggestive of disease.
Interspecific aggression in sympatry between congeneric tropical birds
Authors: Drucker Jacob R , Senner Nathan R , Gomez Juan Pablo 
Published: May 2021

AbstractInterspecific aggression may shape species distributions through competitive exclusion, resulting in spatial segregation, or facilitate sympatry as an adaptive mechanism for resource partitioning. Competitive exclusion results from asymmetric aggression of one species towards another, but if the aggressive relationship between species is symmetric, they may persist in sympatry. Interspecific aggression is widely cited as a mechanism for maintaining the distributional limits of tropical birds, but how it shapes the spatial dynamics of competing species that are sympatric over larger geographic areas is less clear. To address this issue, we conducted reciprocal playback experiments on two congeneric Antbirds — Thamnophilus atrinucha and T. doliatus — that occur in sympatry across a habitat matrix in Colombia to characterize their relationship as symmetrically or asymmetrically aggressive and analyzed point count data to assess the degree to which they occur sympatrically. We found weak evidence for competitive exclusion, with the larger T. doliatus responding asymmetrically to T. atrinucha, and the two species having a low co-detection rate during point counts. However, despite their 22% difference in body size, T. atrinucha still responded to T. doliatus playback in over half of our trials, and the two species co-occurred on nearly 25% of point counts, indicating that interspecific aggression does not drive complete spatial segregation. Our findings highlight how the degree to which one species can competitively exclude another may vary, especially across a dynamic landscape.
Sparse allele vectors and the savvy software suite
Authors: LeFaive Jonathon , Smith Albert V , Kang Hyun Min , Abecasis Gonçalo 
Published: May 2021

Abstract

Summary
The sparse allele vectors file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput association analysis by leveraging techniques for fast deserialization of data into computer memory. A command line interface has been developed to complement the storage format and supports basic features like importing, exporting and subsetting. Additionally, a C++ programming API is available allowing for easy integration into analysis software.

Availability and implementation
https://github.com/statgen/savvy.

Supplementary information
Supplementary data are available at Bioinformatics online.
Biochemical markers for pregnancy in the spent culture medium of in vitro produced bovine embryos
Authors: de Oliveira Fernandes Gabriela , Milazzotto Marcella Pecora , Fidelis Andrei Antonioni Guedes , Kawamoto Taynan Stonoga , de Oliveira Leme Ligiane , de Lima Camila Bruna , Franco Maurício Machaim , Dode Margot Alves Nunes 
Published: May 2021

Abstract
The present study aimed to identify biomarkers to assess the quality of in vitro produced (IVP) bovine embryos in the culture media. IVP embryos on Day (D) 5 of development were transferred to individual drops, where they were maintained for the last 48 h of culture. Thereafter, the medium was collected and the embryos were transferred to the recipients. After pregnancy diagnosis, the media were grouped into the pregnant and nonpregnant groups. The metabolic profiles of the media were analyzed via electrospray ionization mass spectrometry, and the concentrations of pyruvate, lactate, and glutamate were assessed using fluorimetry. The spectrometric profile revealed that the media from embryos from the pregnant group presented a higher signal intensity compared to that of the nonpregnant group; the ions 156.13 Da [M + H]+, 444.33 Da [M + H]+, and 305.97 Da [M + H]+ were identified as biomarkers. Spent culture medium from expanded blastocysts (Bx) that established pregnancy had a greater concentration of pyruvate (p = 0.0174) and lesser concentration of lactate (p = 0.042) than spent culture medium from Bx that did not establish pregnancy. Moreover, pyruvate in the culture media of Bx can predict pregnancy with 90.9% sensitivity and 75% specificity. In conclusion, we identified markers in the culture media that helped in assessing the most viable IVP embryos with a greater potential to establish pregnancy.
Within-patient randomized clinical trial comparing incisional negative-pressure wound therapy with suction drains in gender-affirming mastectomies
Authors: Timmermans F W , Mokken S E , Smit J M , Zwanenburg P R , van Hout N , Bouman M B , Middelkoop E , Mullender M G 
Published: May 2021

Abstract

Background
Incisional negative-pressure wound therapy (iNPWT) is widely adopted by different disciplines for multiple indications. Questions about the most appropriate uses and value of iNPWT have been raised.

Methods
An open-label within-patient RCT was conducted in transgender men undergoing gender-affirming mastectomies. The objective was to determine the effect of iNPWT as a substitute for standard dressing and suction drains on wound healing complications. One chest side was randomized to receive the iNPWT intervention, and the other to standard dressing with suction drain. The primary endpoints were wound healing complications (haematoma, seroma, infection, and dehiscence) after three months. Additional outcomes were pain according to a numerical rating scale and patient satisfaction one week after surgery.

Results
Eighty-five patients were included, of whom 81 received both the iNPWT and standard treatment. Drain removal criteria were met within 24 h in 95 per cent of the patients. No significant decrease in wound healing complications was registered on the iNPWT side, but the seroma rate was significantly increased. In contrast, patients experienced both significantly less pain and increased comfort on the iNPWT side. No medical device-related adverse events were registered.

Conclusion
Substituting short-term suction drains with iNPWT in gender-affirming mastectomies increased the seroma rates and did not decrease the amount of wound healing complications. Registration number: NTR7412 (Netherlands Trial Register).
Butyrate-containing structured lipids act on HDAC4, HDAC6, DNA damage and telomerase activity during promotion of experimental hepatocarcinogenesis
Authors: Ortega Juliana Festa , Heidor Renato , Auriemo Ana Paula , Marques Affonso Juliana , Pereira D’ Amico Thais , Herz Corinna , de Conti Aline , Ract Juliana , Gioieli Luiz Antônio , Purgatto Eduardo , Lamy Evelyn , P. Pogribny Igor , Salvador Moreno Fernando 
Published: May 2021

Abstract
Hepatocellular carcinoma (HCC) presents with a high treatment resistance and poor prognosis. Early diagnosis and preventive approaches such as chemoprevention are essential for the HCC control. Therefore, we evaluated the chemopreventive effects of butyrate-containing structured lipids (STLs) administered during the promotion stage of hepatocarcinogenesis in rats submitted to the ‘resistant hepatocyte’ (RH) model. Administration of butyrate-containing STLs inhibited the incidence and mean number of visible hepatic nodules per rat and reduced the number and area of glutathione S-transferase placental form-positive (GST-P+) preneoplastic focal lesions in the livers. This was accompanied by the induction of apoptosis and an increased level of hepatic butyric acid. Treatment with butyrate-containing STLs resulted in increased histone H3 lysine 9 (H3K9) acetylation, reduction of total histone deacetylase (HDAC) activity, and lower levels of HDAC4 and HDAC6 proteins. The chemopreventive effect of butyrate-containing STLs was also associated with the increased nuclear compartmentalization of p53 protein and reduced expression of the Bcl-2 protein. In addition, rats treated with butyrate-containing STLs showed decreased DNA damage and telomerase activity in the livers. These results demonstrate that the suppressive activity of butyrate-containing STLs is associated with inhibition of elevated during hepatocarcinogenesis chromatin-modifying proteins HDAC4 and HDAC6, subcellular redistribution of the p53 protein, and decreased DNA damage and telomerase activity.
Cognition-Related Functional Topographies in Parkinson’s Disease: Localized Loss of the Ventral Default Mode Network
Authors: Schindlbeck Katharina A , Vo An , Mattis Paul J , Villringer Kersten , Marzinzik Frank , Fiebach Jochen B , Eidelberg David 
Published: May 2021

Abstract
Cognitive dysfunction in Parkinson’s disease (PD) is associated with increased expression of the PD cognition-related pattern (PDCP), which overlaps with the normal default mode network (DMN). Here, we sought to determine the degree to which the former network represents loss of the latter as a manifestation of the disease process. To address this, we first analyzed metabolic images (fluorodeoxyglucose positron emission tomography [PET]) from a large PD sample with varying cognitive performance. Cognitive impairment in these patients correlated with increased PDCP expression as well as DMN loss. We next determined the spatial relationship of the 2 topographies at the subnetwork level. To this end, we analyzed resting-state functional magnetic resonance imaging (rs-fMRI) data from an independent population. This approach uncovered a significant PD cognition-related network that resembled previously identified PET- and rs-fMRI-based PDCP topographies. Further analysis revealed selective loss of the ventral DMN subnetwork (precuneus and posterior cingulate cortex) in PD, whereas the anterior and posterior components were not affected by the disease. Importantly, the PDCP also included a number of non-DMN regions such as the dorsolateral prefrontal and medial temporal cortex. The findings show that the PDCP is a reproducible cognition-related network that is topographically distinct from the normal DMN.
Current Paradigms of Combination Therapy in Methicillin-Resistant Staphylococcus aureus (MRSA) Bacteremia: Does it Work, Which Combination, and For Which Patients?
Authors: Rose Warren , Fantl Michael , Geriak Matthew , Nizet Victor , Sakoulas George 
Published: May 2021

Abstract
The last several years have seen an emergence of literature documenting the utility of combination antimicrobial therapy, particularly in the salvage of refractory methicillin-resistant Staphylococcus aureus (MRSA) bacteremia. Recent clinical data are shaping conundrums of which regimens may be more beneficial, which can be potentially harmful, and which subset of patients stand to benefit from more aggressive treatment regimens than called for by current standards. In addition, the incorporation of combination therapy for MRSA bacteremia should be accompanied by the reminder that antimicrobial therapy does not need to be uniform for the entire duration, with an early intensive phase in high inoculum infections (eg, with combination therapy), followed by a consolidation phase (ie, monotherapy). This review and perspective consolidates the recent data on this subject and directs future goals in filling the knowledge gaps to methodically move forward towards improving patient outcomes.
Risk Factors for Respiratory Syncytial Virus–Associated Community Deaths in Zambian Infants
Authors: Murphy Caitriona , MacLeod William B , Forman Leah S , Mwananyanda Lawrence , Kwenda Geoffrey , Pieciak Rachel C , Mupila Zachariah , Thea Donald , Chikoti Chilufya , Yankonde Baron , Ngoma Bernard , Chimoga Charles , Gill Christopher J 
Published: May 2021

AbstractBackgroundRespiratory syncytial virus (RSV) is a major cause of infant deaths. Its epidemiology in low- and middle-income countries is poorly understood. Risk factors associated with RSV-associated infant deaths that occur in community settings are incompletely known.MethodsCommunity deaths for infants aged 4 days to 6 months were identified during a 3-year postmortem RSV prevalence study at the main city morgue in Lusaka, Zambia, where 80% of deaths are registered. This analysis focuses on the subset of deaths for which an abbreviated verbal autopsy was available and intended to sort deaths into respiratory or nonrespiratory causes by clinical adjudication. Posterior nasopharyngeal swab samples were collected within 48 hours of death and tested for RSV using quantitative reverse-transcription polymerase chain reaction. Associations between potential risk factors were determined as relative risks with 95% confidence intervals (CIs).ResultsWe prospectively enrolled 798 community infant deaths with verbal autopsies and RSV laboratory results, of which 62 results were positive. The mean age of the infants was 10 weeks, and 41.4% of them were male. Of all deaths, 44% were attributed to respiratory causes. RSV was detected in 7.8% of the community infants and was significantly associated with respiratory deaths (risk ratio, 4.0 [95% CI, 2.2–7.1]). Compared with older infants, those aged 0–8 weeks had a 2.83 (95% CI, 1.30–6.15) increased risk of dying with RSV. The risk of RSV for the 0–8-week age group increased to 5.24 (1.56–33.14) with adjustment for demographics, parental education, and geography. RSV deaths were increased with domiciliary overcrowding and were concentrated in poor and dense neighborhoods in Lusaka (risk ratio, 2.00 [95% CI, 1.22–3.27]).ConclusionRSV is a significant contributor to community respiratory deaths in this population, particularly in the first 3 months of life and in the more poor and dense parts of Lusaka.
Regional Spread of blaNDM-1-Containing Klebsiella pneumoniae ST147 in Post-Acute Care Facilities
Authors: Lapp Zena , Crawford Ryan , Miles-Jay Arianna , Pirani Ali , Trick William E , Weinstein Robert A , Hayden Mary K , Snitkin Evan S , Lin Michael Y 
Published: May 2021

Abstract

Background
Carbapenem-resistant Enterobacterales (CRE) harboring blaKPC have been endemic in Chicago-area healthcare networks for more than a decade. During 2016–2019, a series of regional point-prevalence surveys identified increasing prevalence of blaNDM-containing CRE in multiple long-term acute care hospitals (LTACHs) and ventilator-capable skilled nursing facilities (vSNFs). We performed a genomic epidemiology investigation of blaNDM-producing CRE to understand their regional emergence and spread.

Methods
We performed whole-genome sequencing on New Delhi metallo-beta-lactamase (NDM)+ CRE isolates from 4 point-prevalence surveys across 35 facilities (LTACHs, vSNFs, and acute care hospital medical intensive care units) in the Chicago area and investigated the genomic relatedness and transmission dynamics of these isolates over time.

Results
Genomic analyses revealed that the rise of NDM+ CRE was due to the clonal dissemination of an sequence type (ST) 147 Klebsiella pneumoniae strain harboring blaNDM-1 on an IncF plasmid. Dated phylogenetic reconstructions indicated that ST147 was introduced into the region around 2013 and likely acquired NDM around 2015. Analyzing the relatedness of strains within and between facilities supported initial increases in prevalence due to intrafacility transmission in certain vSNFs, with evidence of subsequent interfacility spread among LTACHs and vSNFs connected by patient transfer.

Conclusions
We identified a regional outbreak of blaNDM-1 ST147 that began in and disseminated across Chicago area post-acute care facilities. Our findings highlight the importance of performing genomic surveillance at post-acute care facilities to identify emerging threats.
Gender gap in authorship within published orthodontic research. An observational study on evidence and time-trends over a decade
Authors: Schumacher Caterina , Eliades Theodore , Koletsi Despina 
Published: May 2021

Summary

Aim
To assess the representation of female authors in senior and leading positions in orthodontic research publications, as well as the fraction of women participating in the publication reports, for over a decade. In addition, association of women representation in orthodontic research and characteristics such as journal of publication, year, study design/topic, and others, were sought.

Materials and methods
Electronic search was performed within three major orthodontic journals, namely the European Journal of Orthodontics (EJO), the American Journal of Orthodontics and Dentofacial Orthopedics (AJODO), and the Angle Orthodontist (ANGLE) to identify all types of research articles published within two distinct year cohorts, the 2008–10 and the 2018–20. The outcomes of interest pertained to proportion of women in senior (last) and leading (first) position, and fraction of overall participation in the author list.

Results
A total of 2539 articles were eligible for inclusion, with an overall number of contributing authors being 11 608, of which 34.4% were female. For seniority in authorship, 30.1% (312/1038) of the publications within 2018–20 were attributed to female authors, while 25.8% (388/1501) was identified in 2008–10. Publication timeline, geographic region, and thematic topic of publication were determined as significant predictors. For leading (first) authorship, the respective percentages were 44.7% (464/1038) within 2018–20, and 34.7% (521/1501) in 2008–10. Dissemination timeline, geographic region and journal of publication were identified by the multivariable analysis, as revealing evidence of association with female leading publication authorship. Overall, the median proportion of female authors within the author list was 33.0%.

Conclusions
A gender gap related to Orthodontic research publications is persistent, with participation of women either as senior, or as leading authors, being suboptimal. Consistent efforts should be set in place, to facilitate more equal representation of women in research publishing, being supported by academia.
Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie
Authors: Varabyou Ales , Pockrandt Christopher , Salzberg Steven L , Pertea Mihaela 
Published: May 2021

Abstract
The ability to detect recombination in pathogen genomes is crucial to the accuracy of phylogenetic analysis and consequently to forecasting the spread of infectious diseases and to developing therapeutics and public health policies. However, in case of the SARS-CoV-2, the low divergence of near-identical genomes sequenced over a short period of time makes conventional analysis infeasible. Using a novel method, we identified 225 anomalous SARS-CoV-2 genomes of likely recombinant origins out of the first 87,695 genomes to be released, several of which have persisted in the population. Bolotie is specifically designed to perform a rapid search for inter-clade recombination events over extremely large datasets, facilitating analysis of novel isolates in seconds. In cases where raw sequencing data were available, we were able to rule out the possibility that these samples represented co-infections by analyzing the underlying sequence reads. The Bolotie software and other data from our study are available at https://github.com/salzberg-lab/bolotie.