bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of maternal age & birth order on the development of unilateral and bilateral retinoblastoma: a multicentre study
Authors: Lloyd Philippa , Westcott Mark , Kaliki Swathi , Ji Xunda , Zou Yihua , Rashid Riffat , Sultana Sadia , Sherief Sadik Taju , Cassoux Nathalie , Diaz Coronado Rosdali Yesenia , Garcia Leon Juan Luis , López Arturo Manuel Zapata , Polyakov Vladimir G. , Ushakova Tatiana L. , Roy Soma Rani , Ahmad Alia , Harby Lamis Al , Berry Jesse L. , Kim Jonathan , Polski Ashley , Astbury Nicholas J. , Bascaran Covadonga , Blum Sharon , Bowman Richard , Burton Matthew J. , Foster Allen , Gomel Nir , Keren-Froim Naama , Madgar Shiran , Stacey Andrew W. , Mohamed Ashik , Zondervan Marcia , Sagoo Mandeep S. , Fabian Ido Didi , Reddy M. Ashwin 
Published: March 2022

Abstract
Background/Objectives
Retinoblastoma is a common childhood intraocular malignancy, the bilateral form of which most commonly results from a de novo germline pathogenic variant in the RB1 gene. Both advanced maternal age and decreasing birth order are known to increase the risk of de novo germline pathogenic variants, while the influence of national wealth is understudied. This cohort study aimed to retrospectively observe whether these factors influence the ratio of bilateral retinoblastoma cases compared to unilateral retinoblastoma, thereby inferring an influence on the development of de novo germline pathogenic variants in RB1.

Subjects/Methods
Data from 688 patients from 11 centres in 10 countries were analysed using a series of statistical methods.

Results
No associations were found between advanced maternal age, birth order or GDP per capita and the ratio of bilateral to unilateral retinoblastoma cases (p values = 0.534, 0.201, 0.067, respectively), indicating that these factors do not contribute to the development of a de novo pathogenic variant.

Conclusions
Despite a lack of a definitive control group and genetic testing, this study demonstrates that advanced maternal age, birth order or GDP per capita do not influence the risk of developing a bilateral retinoblastoma.
Additional findings of tibial dysplasia in a male with orofaciodigital syndrome type XVI
Authors: Chinen Yasutsugu , Nakamura Sadao , Yanagi Kumiko , Kaneshi Takuya , Goya Hideki , Yoshida Tomohide , Satou Kazuhito , Kaname Tadashi , Naritomi Kenji , Nakanishi Koichi 
Published: March 2022

AbstractWe describe the case of a male patient with orofaciodigital (OFD) syndrome type XVI with a homozygous variant of TMEM107 (p.Phe106del) and the additional findings of tibial dysplasia, which is a pivotal finding of OFD syndrome type IV. His family history included two fetuses with anencephaly with or without cleft lip/palate and polydactyly with no genetic information. Careful attention should be given to the interpretation of this rare pattern.
Effects of cryo-EM cooling on structural ensembles
Authors: Bock Lars V. , Grubmüller Helmut 
Published: March 2022

AbstractStructure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed during cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be overcome, which is expected to reduce B-factors in ensembles imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures.
On-surface synthesis of triangulene trimers via dehydration reaction
Authors: Cheng Suqin , Xue Zhijie , Li Can , Liu Yufeng , Xiang Longjun , Ke Youqi , Yan Kaking , Wang Shiyong , Yu Ping 
Published: March 2022

AbstractTriangulene and its homologues are of considerable interest for molecular spintronics due to their high-spin ground states as well as the potential for constructing high spin frameworks. Realizing triangulene-based high-spin system on surface is challenging but of particular importance for understanding π-electron magnetism. Here, we report two approaches to generate triangulene trimers on Au(111) by using surface-assisted dehydration and alkyne trimerization, respectively. We find that the developed dehydration reaction shows much higher chemoselectivity thus resulting in significant promotion of product yield compared to that using alkyne trimerization approach, through cutting the side reaction path. Combined with spin-polarized density functional theory calculations, scanning tunneling spectroscopy measurements identify the septuple (S = 3) high-spin ground state and quantify the collective ferromagnetic interaction among three triangulene units. Our results demonstrate the approaches to fabricate high-quality triangulene-based high spin systems and understand their magnetic interactions, which are essential for realizing carbon-based spintronic devices.
Updating global urbanization projections under the Shared Socioeconomic Pathways
Authors: Chen Shiyin , Huang Qingxu , Muttarak Raya , Fang Jiayi , Liu Tao , He Chunyang , Liu Ziwen , Zhu Lei 
Published: March 2022

AbstractUrbanization level is an important indicator of socioeconomic development, and projecting its dynamics is fundamental for studies related to global socioeconomic and climate change. This paper aims to update the projections of global urbanization from 2015 to 2100 under the Shared Socioeconomic Pathways by using the logistic fitting model and iteratively identifying reference countries. Based on historical urbanization level database from the World Urbanization Prospects, projected urbanization levels and uncertainties are provided for 204 countries and areas every five years. The 2010–2100 year-by-year projected urbanization levels and uncertainties based on the annual historical data from the World Bank (WB) for 188 of countries and areas are also provided. The projections based on the two datasets were compared and the latter were validated using the historical values of the WB for the years 2010–2018. The updated dataset of urbanization level is relevant for understanding future socioeconomic development, its implications for climate change and policy planning.
SINBAD, structural, experimental and clinical characterization of STAT inhibitors and their potential applications
Authors: Plens-Gałąska Martyna , Woźniak Tomasz , Wesoły Joanna , Bluyssen Hans A. R. 
Published: March 2022

AbstractThe abnormal activation of signal transducer and activator of transcription (STAT) protein family is recognized as cause or driving force behind multiple diseases progression. Therefore, searching for potential treatment strategy is pursued by multiple scientific groups. We consider that providing comprehensive, integrated and unified dataset for STAT inhibitory compounds may serve as important tool for other researchers. We developed SINBAD (STAT INhbitor Biology And Drug-ability) in response to our experience with inhibitory compound research, knowing that gathering detailed information is crucial for effective experiment design and also for finding potential solutions in case of obtaining inconclusive results. SINBAD is a curated database of STAT inhibitors which have been published and described in scientific articles providing prove of their inhibitory properties. It is a tool allowing easy analysis of experimental conditions and provides detailed information about known STAT inhibitory compounds.
High resolution optical mapping of cardiac electrophysiology in pre-clinical models
Authors: O’Shea Christopher , Winter James , Kabir S. Nashitha , O’Reilly Molly , Wells Simon P , Baines Olivia , Sommerfeld Laura C. , Correia Joao , Lei Ming , Kirchhof Paulus , Holmes Andrew P. , Fabritz Larissa , Rajpoot Kashif , Pavlovic Davor 
Published: March 2022

AbstractOptical mapping of animal models is a widely used technique in pre-clinical cardiac research. It has several advantages over other methods, including higher spatial resolution, contactless recording and direct visualisation of action potentials and calcium transients. Optical mapping enables simultaneous study of action potential and calcium transient morphology, conduction dynamics, regional heterogeneity, restitution and arrhythmogenesis. In this dataset, we have optically mapped Langendorff perfused isolated whole hearts (mouse and guinea pig) and superfused isolated atria (mouse). Raw datasets (consisting of over 400 files) can be combined with open-source software for processing and analysis. We have generated a comprehensive post-processed dataset characterising the baseline cardiac electrophysiology in these widely used pre-clinical models. This dataset also provides reference information detailing the effect of heart rate, clinically used anti-arrhythmic drugs, ischaemia-reperfusion and sympathetic nervous stimulation on cardiac electrophysiology. The effects of these interventions can be studied in a global or regional manner, enabling new insights into the prevention and initiation of arrhythmia.
Identification of a novel gene signature in second-trimester amniotic fluid for the prediction of preterm birth
Authors: Kim Min-A , Lee Eun-Ju , Yang Wookyeom , Shin Ha-Yeon , Kim Young-Han , Kim Jae-Hoon 
Published: March 2022

AbstractPreterm birth affects approximately 5% to 7% of live births worldwide and is the leading cause of neonatal morbidity and mortality. Amniotic fluid supernatant (AFS) contains abundant cell-free nucleic acids (cfNAs) that can provide genetic information associated with pregnancy complications. In the current study, cfNAs of AFS in the early second-trimester before the onset of symptoms of preterm birth were analyzed, and we compared gene expression levels between spontaneous preterm birth (n = 5) and term birth (n = 5) groups using sequencing analysis. Differential expression analyses detected 24 genes with increased and 6 genes with decreased expression in the preterm birth group compared to term birth. Upregulated expressions of RDH14, ZNF572, VOPP1, SERPINA12, and TCF15 were validated in an extended AFS sample by quantitative PCR (preterm birth group, n = 21; term birth group, n = 40). Five candidate genes displayed a significant increase in mRNA expression in immortalized trophoblast HTR-8/SVneo cell with H2O2 treatment. Moreover, the expression of five candidate genes was increased to more than twofold by pretreatment with lipopolysaccharide in HTR-8/SVneo cells. Changes in gene expression between preterm birth and term birth is strongly correlated with oxidative stress and infection during pregnancy. Specific expression patterns of genes could be used as potential markers for the early identification of women at risk of having a spontaneous preterm birth.
Exercise suppresses tumor growth independent of high fat food intake and associated immune dysfunction
Authors: Hojman Pernille , Stagaard Rikke , Adachi-Fernandez Emi , Deshmukh Atul S. , Mund Andreas , Olsen Caroline H. , Keller Lena , Pedersen Bente K. , Gehl Julie 
Published: March 2022

AbstractEpidemiological data suggest that exercise training protects from cancer independent of BMI. Here, we aimed to elucidate mechanisms involved in voluntary wheel running-dependent control of tumor growth across chow and high-fat diets. Access to running wheels decreased tumor growth in B16F10 tumor-bearing on chow (− 50%) or high-fat diets (− 75%, p < 0.001), however, tumor growth was augmented in high-fat fed mice (+ 53%, p < 0.001). Tumor growth correlated with serum glucose (p < 0.01), leptin (p < 0.01), and ghrelin levels (p < 0.01), but not with serum insulin levels. Voluntary wheel running increased immune recognition of tumors as determined by microarray analysis and gene expression analysis of markers of macrophages, NK and T cells, but the induction of markers of macrophages and NK cells was attenuated with high-fat feeding. Moreover, we found that the regulator of innate immunity, ZBP1, was induced by wheel running, attenuated by high-fat feeding and associated with innate immune recognition in the B16F10 tumors. We observed no effects of ZBP1 on cell cycle arrest, or exercise-regulated necrosis in the tumors of running mice. Taken together, our data support epidemiological findings showing that exercise suppresses tumor growth independent of BMI, however, our data suggest that high-fat feeding attenuates exercise-mediated immune recognition of tumors.
Molecular evidence for natural hybridization between Rumex crispus and R. obtusifolius (Polygonaceae) in Korea
Authors: Bhandari Gauri Shankar , Park Chong-Wook 
Published: March 2022

AbstractInterspecific hybridization has been suggested to occur frequently inRumex(Polygonaceae). Several hypothesized combinations of parental species of hybrids based on their intermediate morphology have been suggested in the genus, but few of them have been phylogenetically tested. We analyzed nuclear and chloroplast DNA sequence data of a putative natural hybrid betweenRumex crispusandRumex obtusifoliusfrom Korea to confirm its hybrid status and to determine the maternal parent. Analysis of the nuclear DNApgiCregion revealed thatR. crispusandR. obtusifoliushave contributed to the nuclear genome of the putative hybrids. The haplotype distribution pattern inferred from the combined sequence data set of five chloroplast DNA regions (matK, rbcL-accDIGS, trnK-rps16IGS, ycf6-psbMIGS andpsbA-trnHIGS) indicated bidirectional hybridization events betweenR. crispusandR. obtusifolius. This paper provides the first molecular evidence for interspecific hybridization betweenR. crispusandR. obtusifolius. In addition, our findings strongly suggested that Korean populations ofRumex japonicushave a hybrid origin, andR. crispusmay represent one of the parental taxa.
Collateral responses to classical cytotoxic chemotherapies are heterogeneous and sensitivities are sparse
Authors: Dalin Simona , Grauman-Boss Beatrice , Lauffenburger Douglas A. , Hemann Michael T. 
Published: March 2022

AbstractChemotherapy resistance is a major obstacle to curing cancer patients. Combination drug regimens have shown promise as a method to overcome resistance; however, to date only some cancers have been cured with this method. Collateral sensitivity—the phenomenon whereby resistance to one drug is co-occurrent with sensitivity to a second drug—has been gaining traction as a promising new concept to guide rational design of combination regimens. Here we evolved over 100 subclones of the Eµ-Myc; p19ARF−/− cell line to be resistant to one of four classical chemotherapy agents: doxorubicin, vincristine, paclitaxel, and cisplatin. We then surveyed collateral responses to acquisition of resistance to these agents. Although numerous collateral sensitivities have been documented for antibiotics and targeted cancer therapies, we observed only one collateral sensitivity: half of cell lines that acquired resistance to paclitaxel also acquired a collateral sensitivity to verapamil. However, we found that the mechanism of this collateral sensitivity was unrelated to the mechanism of paclitaxel resistance. Interestingly, we observed heterogeneity in the phenotypic response to acquisition of resistance to most of the drugs we tested, most notably for paclitaxel, suggesting the existence of multiple different states of resistance. Surprisingly, this phenotypic heterogeneity in paclitaxel resistant cell lines was unrelated to transcriptomic heterogeneity among those cell lines. These features of phenotypic and transcriptomic heterogeneity must be taken into account in future studies of treated tumor subclones and in design of chemotherapy combinations.
A mathematical-adapted model to analyze the characteristics for the mortality of COVID-19
Authors: Hao Baobing , Liu Chengyou , Wang Yuhe , Zhu Ninjun , Ding Yong , Wu Jing , Wang Yu , Sun Fang , Chen Lixun 
Published: March 2022

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China, has led to the rapid development of Coronavirus disease 2019 (COVID-19) pandemic. COVID-19 represents a fatal disease with a great global public health importance. This study aims to develop a three-parameter Weibull mathematical model using continuous functions to represent discrete COVID-19 data. Subsequently, the model was applied to quantitatively analyze the characteristics for the mortality of COVID-19, including the age, sex, the length of symptom time to hospitalization time (SH), hospitalization date to death time (HD) and symptom time to death time time (SD) and others. A three-parameter mathematical model was developed by combining the reported cases in the Data Repository from the Center for Systems Science and Engineering at Johns Hopkins University and applied to estimate and analyze the characteristics for mortality of COVID-19. We found that the scale parameters of males and females were 5.85 and 5.45, respectively. Probability density functions in both males and females were negative skewness. 5% of male patients died under the age of 43.28 (44.37 for females), 50% died under 69.55 (73.25 for females), and 95% died under 86.59 (92.78 for females). The peak age of male death was 67.45 years, while that of female death was 71.10 years. The peak and median values of SH, HD and SD in male death were correspondingly 1.17, 5.18 and 10.30 days, and 4.29, 11.36 and 16.33 days, while those in female death were 1.19, 5.80 and 12.08 days, and 4.60, 12.44 and 17.67 days, respectively. The peak age of probability density in male and female deaths was 69.55 and 73.25 years, while the high point age of their mortality risk was 77.51 and 81.73 years, respectively. The mathematical model can fit and simulate the impact of various factors on IFR. From the simulation results of the model, we can intuitively find the IFR, peak age, average age and other information of each age. In terms of time factors, the mortality rate of the most susceptible population is not the highest, and the distribution of male patients is different from the distribution of females. This means that Self-protection and self-recovery in females against SARS-CoV-2 virus might be better than those of males. Males were more likely to be infected, more likely to be admitted to the ICU and more likely to die of COVID-19. Moreover, the infection fatality ration (IFR) of COVID-19 population was intrinsically linked to the infection age. Public health measures to protect vulnerable sex and age groups might be a simple and effective way to reduce IFR.
Sedimentary and diagenetic characteristics of the Z21 field in the Huizhou depression, Pearl River Mouth basin, South China Sea
Authors: Liu Longlong , Dong Hongzhi , Wu Yinjiao , Fan Ronghua , Sun Zhongqiang , Huang Rihui , Zhang Jinliang 
Published: March 2022

AbstractThe Huizhou Depression in the Pearl River Mouth basin has prospective hydrocarbon potential, with Miocene sandstones as its main oil and gas-bearing reservoir. The sandstones in Miocene formation of the Z21 offshore oil–gas field composed of medium-grained, moderately sorted subarkose and lithic arkose. In this study, a total of six depositional lithofacies, namely Massive fine- to medium-grained sandstone (Sm), ripple cross-laminated fine-grained sandstone (Sr), parallel-laminated siltstone and claystone (Fl), lenticular siltstone (Sl), parallel-bedded fine-grained sandstone (Sp), wavy laminated siltstone (Sw), and two depositional systems, namely nearshore sand bar (SB) and sand sheet (SS) were identified based on core observations and seismic study. Distributions of the porosity (13.9%) and permeability (35.8 mD) reveal that the Miocene sandstones have characteristics of low porosity and low permeability, with high heterogeneity. The sedimentary system, primary texture and diagenesis jointly control the reservoir quality. Sandstones with sand bars as well coarse-grained tend to exhibit a higher quality. Mechanical compaction and calcite (average 6.81%) cementation are the major determinants to reductions in porosity and permeability. The total clay minerals (average 5.27%) generally lead to reduction of porosity, whereas chlorite coatings and illite within a certain content range may enhance the preservation of porosity in eodiagenesis. Dissolution of feldspar and debris contribute significantly to improving the reservoir quality.
BMP1 is not required for lung fibrosis in mice
Authors: Ma Hsiao-Yen , N’Diaye Elsa-Noah , Caplazi Patrick , Huang Zhiyu , Arlantico Alexander , Jeet Surinder , Wong Aaron , Brightbill Hans D. , Li Qingling , Wong Weng Ruth , Sandoval Wendy , Tam Lucinda , Newman Robert , Roose-Girma Merone , Ding Ning 
Published: March 2022

AbstractBone morphogenetic protein 1 (BMP1) belongs to the astacin/BMP1/tolloid-like family of zinc metalloproteinases, which play a fundamental role in the development and formation of extracellular matrix (ECM). BMP1 mediates the cleavage of carboxyl terminal (C-term) propeptides from procollagens, a crucial step in fibrillar collagen fiber formation. Blocking BMP1 by small molecule or antibody inhibitors has been linked to anti-fibrotic activity in the preclinical models of skin, kidney and liver fibrosis. Therefore, we reason that BMP1 may be important for the pathogenesis of lung fibrosis and BMP1 could be a potential therapeutic target for progressive fibrotic disease such as idiopathic pulmonary fibrosis (IPF). Here, we observed the increased expression of BMP1 in both human IPF lungs and mouse fibrotic lungs induced by bleomycin. Furthermore, we developed an inducible Bmp1 conditional knockout (cKO) mouse strain. We found that Bmp1 deletion does not protect mice from lung fibrosis triggered by bleomycin. Moreover, we found no significant impact of BMP1 deficiency upon C-term propeptide of type I procollagen (CICP) production in the fibrotic mouse lungs. Based on these results, we propose that BMP1 is not required for lung fibrosis in mice and BMP1 may not be considered a candidate therapeutic target for IPF.