bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends in social inequalities in breastfeeding and infant formulas in Latin American countries between the 1990 and 2010 decades
Authors: Ferreira Camila S , Azeredo Catarina M , Rinaldi Ana Elisa M 
Published: January 2021

AbstractObjective:To analyse trends of social inequality in breastfeeding and infant formula (IF) use in Latin America between 1990 and 2010 decades.Design:Time-series cross-sectional study with data from Demographic and Health Surveys. We described the prevalence of exclusive breastfeeding (EBF), breastfeeding between 6 and 12 months (BF6-12) and IF for infants under 6 months (IF < 6) and between 6 and 12 months (IF6-12). Social inequalities were assessed using the slope index of inequality (SII) and concentration index (CIX). Trends in the prevalence of breastfeeding, IF and index of social inequality were analysed by a linear regression model with weighted least squares variance.Setting:Bolivia, Colombia, Dominican Republic, Guatemala, Haiti and Peru.Participants:51·358 alive infants younger than 12 months.Results:Five countries showed an increasing trend for EBF and BF6-12, four increased for IF < 6 and six for IF6-12. Simultaneous decrease in IF < 6 (Colombia: −0·3/year; Haiti: −0·02/year) and increase in EBF (Colombia: +2·0/year; Haiti: +1·9/year) were observed only in two countries. EBF prevalence was high in the lowest income quintiles in five countries, and IF prevalence was high in the highest income quintiles in all countries and over the decades. For BF6-12, a decrease in inequality (prevalence increased in the highest quintile) was observed in Guatemala (SII1995 = −0·42; SII2015 = −0·28) and the Dominican Republic (SII1996 = −0·54; SII2013 = −0·26). Guatemala was the only country showing a decrease in inequality for BF (SII = −0·005; CIX = −0·0035) and an increase for IF (SII = 0·022; CIX = 0·01).Conclusions:The inequality in BF and IF remained over time. However, inequality in IF < 6 has decreased because low-income infants have increased use and high-income infants have decreased.
The Impact of the COVID-19 outbreak on climate change and air quality: four country case studies
Authors: Samani Pouya , García-Velásquez Carlos , Fleury Perine , van der Meer Yvonne 
Published: January 2021

Non-technical summaryTo decrease the negative impacts of the coronavirus outbreak on human health, governments have implemented wide-ranging control measures. Moreover, they were urged to tackle a new challenge in energy policies to supply a new form of demand derived from new lifestyles of citizens and different energy consumption patterns. This article investigates the impacts of these changes on climate change and human health (due to air pollution) as a challenge for both citizens and governments in four countries: Colombia, France, the Netherlands, and Portugal.Technical summaryThe emergence of coronavirus disease 2019 (COVID-19) pandemic has been associated with global challenges in both energy supply and demand. Numerous articles have discussed the potential benefits of COVID-19 for our planet to mitigate greenhouse gas (GHG) emissions and air pollutants. By bringing the emissions from the energy production together with the air quality indicators, this article studies the impact on climate change and human health due to the COVID-19 pandemic, and the consequent changes in energy policies of governments as well as lifestyles in different societies. This study shows that in spite of having a reduction, the GHG emissions might go back to previous or higher levels if governments do not see this pandemic as an opportunity to promote the use of renewable energies, which are becoming cheaper than non-renewables. Additionally, lower energy demand and less anthropogenic activities do not necessarily result in lower GHG emissions from energy production. Our results highlight the need for revising the policies and decisions of both governments and citizens, as temporary reductions in the levels of energy demand and air pollutants can easily be counterbalanced by adverse effects, known as the ‘rebound effect.’Social media summaryHow did the changes in energy consumption and production due to COVID-19 affect climate change and human health in different countries?
Circadian Rhythm of Dune‐Field Activity
Authors: Gunn A. , Wanker M. , Lancaster N. , Edmonds D. A. , Ewing R. C. , Jerolmack D. J. 
Published: January 2021

AbstractWind‐blown sand dunes are both a consequence and a driver of climate dynamics; they arise under persistently dry and windy conditions, and are sometimes a source for airborne dust. Dune fields experience extreme daily changes in temperature, yet the role of atmospheric stability in driving sand transport and dust emission has not been established. Here, we report on an unprecedented multiscale field experiment at the White Sands Dune Field (New Mexico, USA), where by measuring wind, humidity and temperature profiles in the atmosphere concurrently with sediment transport, we demonstrate that a daily rhythm of sand and dust transport arises from nonequilibrium atmospheric boundary layer convection. A global analysis of 45 dune fields confirms the connection found in situ between surface wind speed and diurnal temperature cycles, revealing an unrecognized climate feedback that may contribute to the growth of deserts on Earth and dune activity on Mars.
Negative Unjacketed Pore Modulus in Limestones? Critical Examination of a Peculiar Laboratory Observation
Authors: Tan Wenhui , Müller Tobias M. , Ba Jing 
Published: January 2021

AbstractThere is recent experimental evidence that the effective pressure coefficient for pore volume exceeds unity in limestones with dual porosity structure. Within the realm of linear poroelastcity, this means that the unjacketed pore modulus is negative. This would be a rather unusual rock behavior since it implies that the pore volume increases for a positive pressure increment during hydrostatic compression. Generally, any deviation of the unjacketed pore modulus from strictly positive mineral bulk modulus means that the deformation is inhomogeneous. We critically examine these observations by attempting to reconcile them with the poroelastic constitutive equations of micro‐inhomogeneous rocks that encompass inhomogeneous deformations. Consistency checks among measured poroelastic constants reveal that the measurement accuracy of pore volume changes concurring with the deformation experiments is not as high as desired. However, assigning moderate variations to the measured pore volume changes either due to random or systematic measurement errors, we show that the experimental observations are indeed reconcilable with the constitutive poroelastic equations. Hence, the negative unjacketed pore modulus observed is deemed plausible though overestimated. Within the poroelasticity framework for micro‐inhomogeneous rocks, a negative unjacketed pore modulus is the result of a partial localization of elastic strain energy in the fluid space. This in turn could be caused by dissolved calcite particles that block thin pore throats and thus generate temporary fluid pressure compartmentalization. A far‐reaching consequence of a negative unjacketed pore modulus is that description of the undrained bulk modulus in rocks with dual porosity structure is more complicated than previously thought.
A Metasurface Based Gain Enhanced Dual Band Patch Antenna Using SRRs With Defected Ground Structure
Authors: Samantaray Diptiranjan , Bhattacharyya Somak 
Published: January 2021

AbstractThis study proposes a metasurface (MS) based high performance antenna in which the radiating patch is embedded with split ring resonators in its square slots. The slotted corner cut rectangular patch antenna with defected ground plane and the MS are placed together in the same plane. The designed prototype operates over dual frequencies with impedance bandwidths (S11 < −10 dB) of 4.02% and 28.24% at 9.20 and 11.65 GHz respectively. The antenna possesses a maximum return loss of 42 dB at 11.65 GHz over 11.23–14.5 GHz band while the measured realized gain of 10.66 dBi has been obtained at 14.44 GHz. The antenna exhibits unidirectional far‐field radiation characteristics and the radiation efficiency of 67% has been achieved at 14.44 GHz. The antenna prototype has been fabricated on FR4 dielectric substrate, having an electrical size of 1.16λ0 × 1.82λ0 × 0.06λ0, where λ0 is the free‐space wavelength at 11.65 GHz. This makes the proposed antenna single‐layer, broad impedance bandwidth, high gain and ease of fabrication in nature. The measured results are in good agreement with the simulated ones. The designed antenna can be applicable in defense and military, satellite communication, medical analysis for determination of radio waves and numerous communication fields.
Musashi 2 influences chronic lymphocytic leukemia cell survival and growth making it a potential therapeutic target
Authors: Palacios Florencia , Yan Xiao-Jie , Ferrer Gerardo , Chen Shih-Shih , Vergani Stefano , Yang Xuejing , Gardner Jeffrey , Barrientos Jaqueline C. , Rock Philip , Burack Richard , Kolitz Jonathan E. , Allen Steven L. , Kharas Michael G. , Abdel-Wahab Omar , Rai Kanti R. , Chiorazzi Nicholas 
Published: January 2021

AbstractProgression of chronic lymphocytic leukemia (CLL) results from the expansion of a small fraction of proliferating leukemic B cells. When comparing the global gene expression of recently divided CLL cells with that of previously divided cells, we found higher levels of genes involved in regulating gene expression. One of these was the oncogene Musashi 2 (MSI2), an RNA-binding protein that induces or represses translation. While there is an established role for MSI2 in normal and malignant stem cells, much less is known about its expression and role in CLL. Here we report for the first time ex vivo and in vitro experiments that MSI2 protein levels are higher in dividing and recently divided leukemic cells and that downregulating MSI2 expression or blocking its function eliminates primary human and murine CLL and mature myeloid cells. Notably, mature T cells and hematopoietic stem and progenitor cells are not affected. We also confirm that higher MSI2 levels correlate with poor outcome markers, shorter time-to-first-treatment, and overall survival. Thus, our data highlight an important role for MSI2 in CLL-cell survival and proliferation and associate MSI2 with poor prognosis in CLL patients. Collectively, these findings pinpoint MSI2 as a potentially valuable therapeutic target in CLL.
Tumor-associated antigen Prame targets tumor suppressor p14/ARF for degradation as the receptor protein of CRL2Prame complex
Authors: Zhang Wenjuan , Li Lihui , Cai Lili , Liang Yupei , Xu Junfeng , Liu Yue , Zhou Lisha , Ding Chen , Zhang Yanmei , Zhao Hu , Qin Jun , Shao Zhimin , Wei Wenyi , Jia Lijun 
Published: January 2021

AbstractProtein Preferentially Expressed Antigen in Melanoma (Prame), a tumor-associated antigen, has been found to frequently overexpress in various cancers, which indicates advanced cancer stages and poor clinical prognosis. Moreover, previous reports noted that Prame functions as a substrate recognizing receptor protein of Cullin RING E3 ligases (CRLs) to mediate potential substrates degradation through Ubiquitin Proteasome System (UPS). However, none of the Prame specific substrate has been identified so far. In this study, proteomic analysis of RBX1-interacting proteins revealed p14/ARF, a well-known tumor suppressor, as a novel ubiquitin target of RBX1. Subsequently, immunoprecipitation and in vivo ubiquitination assay determined Cullin2-RBX1-Transcription Elongation Factor B Subunit 2 (EloB) assembled CRL2 E3 ligase complex to regulate the ubiquitination and subsequent degradation of p14/ARF. Finally, through siRNA screening, Prame was identified as the specific receptor protein responsible for recognizing p14/ARF to be degraded. Additionally, via bioinformatics analysis of TCGA database and clinical samples, Prame was determined to overexpress in tumor tissues vs. paired adjacent tissues and associated with poor prognosis of cancer patients. As such, downregulation of Prame expression significantly restrained cancer cell growth by inducing G2/M phase cell cycle arrest, which could be rescued by simultaneously knocking down of p14/ARF. Altogether, targeting overexpressed Prame in cancer cells inactivated RBX1-Cullin2-EloB-Prame E3 ligase (CRL2Prame) and halted p14/ARF degradation to restrain tumor growth by inducing G2/M phase cell cycle arrest.
Cdk5rap3 is essential for intestinal Paneth cell development and maintenance
Authors: Quintero Michaela , Liu Siyang , Xia Yanhua , Huang Yonghong , Zou Yi , Li Ge , Hu Ling , Singh Nagendra , Blumberg Richard , Cai Yafei , Xu Hong , Li Honglin 
Published: January 2021

AbstractIntestinal Paneth cells are professional exocrine cells that play crucial roles in maintenance of homeostatic microbiome, modulation of mucosal immunity, and support for stem cell self-renewal. Dysfunction of these cells may lead to the pathogenesis of human diseases such as inflammatory bowel disease (IBD). Cdk5 activator binding protein Cdk5rap3 (also known as C53 and LZAP) was originally identified as a binding protein of Cdk5 activator p35. Although previous studies have indicated its involvement in a wide range of signaling pathways, the physiological function of Cdk5rap3 remains largely undefined. In this study, we found that Cdk5rap3 deficiency resulted in very early embryonic lethality, indicating its indispensable role in embryogenesis. To further investigate its function in the adult tissues and organs, we generated intestinal epithelial cell (IEC)-specific knockout mouse model to examine its role in intestinal development and tissue homeostasis. IEC-specific deletion of Cdk5rap3 led to nearly complete loss of Paneth cells and increased susceptibility to experimentally induced colitis. Interestingly, Cdk5rap3 deficiency resulted in downregulation of key transcription factors Gfi1 and Sox9, indicating its crucial role in Paneth cell fate specification. Furthermore, Cdk5rap3 is highly expressed in mature Paneth cells. Paneth cell-specific knockout of Cdk5rap3 caused partial loss of Paneth cells, while inducible acute deletion of Cdk5rap3 resulted in disassembly of the rough endoplasmic reticulum (RER) and abnormal zymogen granules in the mature Paneth cells, as well as loss of Paneth cells. Together, our results provide definitive evidence for the essential role of Cdk5rap3 in Paneth cell development and maintenance.
Complete sequences of Schizosaccharomyces pombe subtelomeres reveal multiple patterns of genome variation
Authors: Oizumi Yusuke , Kaji Takuto , Tashiro Sanki , Takeshita Yumiko , Date Yuko , Kanoh Junko 
Published: January 2021

AbstractGenome sequences have been determined for many model organisms; however, repetitive regions such as centromeres, telomeres, and subtelomeres have not yet been sequenced completely. Here, we report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe. We overcame technical difficulties to obtain subtelomeric repetitive sequences by constructing strains that possess single SH regions of a standard laboratory strain. In addition, some natural isolates of S. pombe were analyzed using previous sequencing data. Whole sequences of SH regions revealed that each SH region consists of two distinct parts with mosaics of multiple common segments or blocks showing high variation among subtelomeres and strains. Subtelomere regions show relatively high frequency of nucleotide variations among strains compared with the other chromosomal regions. Furthermore, we identified subtelomeric RecQ-type helicase genes, tlh3 and tlh4, which add to the already known tlh1 and tlh2, and found that the tlh1–4 genes show high sequence variation with missense mutations, insertions, and deletions but no severe effects on their RNA expression. Our results indicate that SH sequences are highly polymorphic and hot spots for genome variation. These features of subtelomeres may have contributed to genome diversity and, conversely, various diseases.
Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics
Authors: Pillon Monica C. , Frazier Meredith N. , Dillard Lucas B. , Williams Jason G. , Kocaman Seda , Krahn Juno M. , Perera Lalith , Hayne Cassandra K. , Gordon Jacob , Stewart Zachary D. , Sobhany Mack , Deterding Leesa J. , Hsu Allen L. , Dandey Venkata P. , Borgnia Mario J. , Stanley Robin E. 
Published: January 2021

AbstractNsp15, a uridine specific endoribonuclease conserved across coronaviruses, processes viral RNA to evade detection by host defense systems. Crystal structures of Nsp15 from different coronaviruses have shown a common hexameric assembly, yet how the enzyme recognizes and processes RNA remains poorly understood. Here we report a series of cryo-EM reconstructions of SARS-CoV-2 Nsp15, in both apo and UTP-bound states. The cryo-EM reconstructions, combined with biochemistry, mass spectrometry, and molecular dynamics, expose molecular details of how critical active site residues recognize uridine and facilitate catalysis of the phosphodiester bond. Mass spectrometry revealed the accumulation of cyclic phosphate cleavage products, while analysis of the apo and UTP-bound datasets revealed conformational dynamics not observed by crystal structures that are likely important to facilitate substrate recognition and regulate nuclease activity. Collectively, these findings advance understanding of how Nsp15 processes viral RNA and provide a structural framework for the development of new therapeutics.
TALEN outperforms Cas9 in editing heterochromatin target sites
Authors: Jain Surbhi , Shukla Saurabh , Yang Che , Zhang Meng , Fatma Zia , Lingamaneni Manasi , Abesteh Shireen , Lane Stephan Thomas , Xiong Xiong , Wang Yuchuan , Schroeder Charles M. , Selvin Paul R. , Zhao Huimin 
Published: January 2021

AbstractGenome editing critically relies on selective recognition of target sites. However, despite recent progress, the underlying search mechanism of genome-editing proteins is not fully understood in the context of cellular chromatin environments. Here, we use single-molecule imaging in live cells to directly study the behavior of CRISPR/Cas9 and TALEN. Our single-molecule imaging of genome-editing proteins reveals that Cas9 is less efficient in heterochromatin than TALEN because Cas9 becomes encumbered by local searches on non-specific sites in these regions. We find up to a fivefold increase in editing efficiency for TALEN compared to Cas9 in heterochromatin regions. Overall, our results show that Cas9 and TALEN use a combination of 3-D and local searches to identify target sites, and the nanoscopic granularity of local search determines the editing outcomes of the genome-editing proteins. Taken together, our results suggest that TALEN is a more efficient gene-editing tool than Cas9 for applications in heterochromatin.
Niche derived netrin-1 regulates hematopoietic stem cell dormancy via its receptor neogenin-1
Authors: Renders Simon , Svendsen Arthur Flohr , Panten Jasper , Rama Nicolas , Maryanovich Maria , Sommerkamp Pia , Ladel Luisa , Redavid Anna Rita , Gibert Benjamin , Lazare Seka , Ducarouge Benjamin , Schönberger Katharina , Narr Andreas , Tourbez Manon , Dethmers-Ausema Bertien , Zwart Erik , Hotz-Wagenblatt Agnes , Zhang Dachuan , Korn Claudia , Zeisberger Petra , Przybylla Adriana , Sohn Markus , Mendez-Ferrer Simon , Heikenwälder Mathias , Brune Maik , Klimmeck Daniel , Bystrykh Leonid , Frenette Paul S. , Mehlen Patrick , de Haan Gerald , Cabezas-Wallscheid Nina , Trumpp Andreas 
Published: January 2021

AbstractHaematopoietic stem cells (HSCs) are characterized by their self-renewal potential associated to dormancy. Here we identify the cell surface receptor neogenin-1 as specifically expressed in dormant HSCs. Loss of neogenin-1 initially leads to increased HSC expansion but subsequently to loss of self-renewal and premature exhaustion in vivo. Its ligand netrin-1 induces Egr1 expression and maintains quiescence and function of cultured HSCs in a Neo1 dependent manner. Produced by arteriolar endothelial and periarteriolar stromal cells, conditional netrin-1 deletion in the bone marrow niche reduces HSC numbers, quiescence and self-renewal, while overexpression increases quiescence in vivo. Ageing associated bone marrow remodelling leads to the decline of netrin-1 expression in niches and a compensatory but reversible upregulation of neogenin-1 on HSCs. Our study suggests that niche produced netrin-1 preserves HSC quiescence and self-renewal via neogenin-1 function. Decline of netrin-1 production during ageing leads to the gradual decrease of Neo1 mediated HSC self-renewal.
APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling
Authors: Liu Tung-Chang , Lin Chun-Ting , Chang Kai-Cheng , Guo Kai-Wei , Wang Shuying , Chu Jhih-Wei , Hsiao Yu-Yuan 
Published: January 2021

AbstractThe exonuclease activity of Apurinic/apyrimidinic endonuclease 1 (APE1) is responsible for processing matched/mismatched terminus in various DNA repair pathways and for removing nucleoside analogs associated with drug resistance. To fill in the gap of structural basis for exonucleolytic cleavage, we determine the APE1-dsDNA complex structures displaying end-binding. As an exonuclease, APE1 does not show base preference but can distinguish dsDNAs with different structural features. Integration with assaying enzyme activity and binding affinity for a variety of substrates reveals for the first time that both endonucleolytic and exonucleolytic cleavage can be understood by an induced space-filling model. Binding dsDNA induces RM (Arg176 and Met269) bridge that defines a long and narrow product pocket for exquisite machinery of substrate selection. Our study paves the way to comprehend end-processing of dsDNA in the cell and the drug resistance relating to APE1.
LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate
Authors: Jin Run , Klasfeld Samantha , Zhu Yang , Fernandez Garcia Meilin , Xiao Jun , Han Soon-Ki , Konkol Adam , Wagner Doris 
Published: January 2021

AbstractMaster transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer transcription factors have prominent roles in this process because of their ability to contact their cognate binding motifs in closed chromatin. Reprogramming is pervasive in plants, whose development is plastic and tuned by the environment, yet little is known about pioneer transcription factors in this kingdom. Here, we show that the master transcription factor LEAFY (LFY), which promotes floral fate through upregulation of the floral commitment factor APETALA1 (AP1), is a pioneer transcription factor. In vitro, LFY binds to the endogenous AP1 target locus DNA assembled into a nucleosome. In vivo, LFY associates with nucleosome occupied binding sites at the majority of its target loci, including AP1. Upon binding, LFY ‘unlocks’ chromatin locally by displacing the H1 linker histone and by recruiting SWI/SNF chromatin remodelers, but broad changes in chromatin accessibility occur later. Our study provides a mechanistic framework for patterning of inflorescence architecture and uncovers striking similarities between LFY and animal pioneer transcription factor.