bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of decayed, missing, filled teeth index between thalassemia major patients and control group in Iran: a systematic review and meta-analysis
Authors: Moosazadeh Mahmood , Gorji Nadia Elyassi , Nasiri Pegah , Shafaroudi Ali Malekzadeh 
Published: November 2020

Abstract
Introduction
Scientific evidence of the association between Decayed, Missing, and Filled Teeth (DMFT) and thalassemia are conflicting and difficult to establish conclusions. Therefore, this study aimed to determine the relationship between dental caries (using the DMFT index) and thalassemia major using meta-analysis.

Methods
Databases were searched using such keywords as “Thalassemia,” “Caries,” “decay,” “DMFT,” “Iran,” and OR operators, AND, and NOT. After the elimination of duplicate documentation, the articles which met the inclusion criteria were selected. Quality assessment was performed based on the Newcastle-Ottawa Quality Checklist. Thereafter, the standardized mean difference of the DMFT index was estimated.

Results
In eight studies, the mean DMFT was compared between patients with thalassemia major and the control group. In six studies, the mean of this index was higher in patients with thalassemia major than in the control group and in all six of the studies, the differences were statistically significant. The mean standardized difference of DMFT, D, M, and F were reported as 1.36 (0.41, 2.30), 2.63 (0.42, 4.84), 1.65 (−0.14, 3.45), and 0.02 (−1.67, 1.72), respectively.

Conclusion
The results of this meta-analysis indicated that DMFT index was more inappropriate in patients with thalassemia, as compared to the control group which represents the higher incidence of dental caries among patients with thalassemia compared to the control group.
Accuracy and stability of electronic apex locator length measurements in root canals with wide apical foramen: an ex vivo study
Authors: Shacham Maayan , Levin Avi , Shemesh Avi , Lvovsky Alex , Ben Itzhak Joe , Solomonov Michael 
Published: November 2020

AbstractThe aim of the current study was to determine the accuracy of electronic apex locator (EAL) measurements when using files of different sizes in roots with wide apical foramina while considering a new parameter ofstabilityof EAL reading. Ten teeth with straight roots were subjected to a sequential widening of the apical foramen to 0.6, 0.7, and 0.8 mm. The roots were embedded after each enlargement stage in an alginate mold and subjected to EAL readings. Measurements were done using sequential K-file sizes and the self-adjusting file (SAF). Measurement stability was introduced as a new additional parameter. As the difference between the file size used and the apical diameter of the canal decreases, the results obtained were more accurate and stable. The stability and accuracy of the measurements coincided with each other in a statistically significant manner. Within the limitations of the present ex vivo study, it may be concluded that in straight canals with wide apical foramina of 0.6–0.8 mm, both SS K-files which fit snugly to the walls of apical foramen and the SAF file may offer both accurate and stable EAL measurements.
Exosomes and breast cancer drug resistance
Authors: Dong Xingli , Bai Xupeng , Ni Jie , Zhang Hao , Duan Wei , Graham Peter , Li Yong 
Published: November 2020

AbstractDrug resistance is a daunting challenge in the treatment of breast cancer (BC). Exosomes, as intercellular communicative vectors in the tumor microenvironment, play an important role in BC progression. With the in-depth understanding of tumor heterogeneity, an emerging role of exosomes in drug resistance has attracted extensive attention. The functional proteins or non-coding RNAs contained in exosomes secreted from tumor and stromal cells mediate drug resistance by regulating drug efflux and metabolism, pro-survival signaling, epithelial–mesenchymal transition, stem-like property, and tumor microenvironmental remodeling. In this review, we summarize the underlying associations between exosomes and drug resistance of BC and discuss the unique biogenesis of exosomes, the change of exosome cargo, and the pattern of release by BC cells in response to drug treatment. Moreover, we propose exosome as a candidate biomarker in predicting and monitoring the therapeutic drug response of BC and as a potential target or carrier to reverse the drug resistance of BC.
Multi-year incubation experiments boost confidence in model projections of long-term soil carbon dynamics
Authors: Jian Siyang , Li Jianwei , Wang Gangsheng , Kluber Laurel A. , Schadt Christopher W. , Liang Junyi , Mayes Melanie A. 
Published: November 2020

AbstractGlobal soil organic carbon (SOC) stocks may decline with a warmer climate. However, model projections of changes in SOC due to climate warming depend on microbially-driven processes that are usually parameterized based on laboratory incubations. To assess how lab-scale incubation datasets inform model projections over decades, we optimized five microbially-relevant parameters in the Microbial-ENzyme Decomposition (MEND) model using 16 short-term glucose (6-day), 16 short-term cellulose (30-day) and 16 long-term cellulose (729-day) incubation datasets with soils from forests and grasslands across contrasting soil types. Our analysis identified consistently higher parameter estimates given the short-term versus long-term datasets. Implementing the short-term and long-term parameters, respectively, resulted in SOC loss (–8.2 ± 5.1% or –3.9 ± 2.8%), and minor SOC gain (1.8 ± 1.0%) in response to 5 °C warming, while only the latter is consistent with a meta-analysis of 149 field warming observations (1.6 ± 4.0%). Comparing multiple subsets of cellulose incubations (i.e., 6, 30, 90, 180, 360, 480 and 729-day) revealed comparable projections to the observed long-term SOC changes under warming only on 480- and 729-day. Integrating multi-year datasets of soil incubations (e.g., > 1.5 years) with microbial models can thus achieve more reasonable parameterization of key microbial processes and subsequently boost the accuracy and confidence of long-term SOC projections.
Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury
Authors: Floriddia Elisa M. , Lourenço Tânia , Zhang Shupei , van Bruggen David , Hilscher Markus M. , Kukanja Petra , Gonçalves dos Santos João P. , Altınkök Müge , Yokota Chika , Llorens-Bobadilla Enric , Mulinyawe Sara B. , Grãos Mário , Sun Lu O. , Frisén Jonas , Nilsson Mats , Castelo-Branco Gonçalo 
Published: November 2020

AbstractMature oligodendrocytes (MOLs) show transcriptional heterogeneity, the functional consequences of which are unclear. MOL heterogeneity might correlate with the local environment or their interactions with different neuron types. Here, we show that distinct MOL populations have spatial preference in the mammalian central nervous system (CNS). We found that MOL type 2 (MOL2) is enriched in the spinal cord when compared to the brain, while MOL types 5 and 6 (MOL5/6) increase their contribution to the OL lineage with age in all analyzed regions. MOL2 and MOL5/6 also have distinct spatial preference in the spinal cord regions where motor and sensory tracts run. OL progenitor cells (OPCs) are not specified into distinct MOL populations during development, excluding a major contribution of OPC intrinsic mechanisms determining MOL heterogeneity. In disease, MOL2 and MOL5/6 present different susceptibility during the chronic phase following traumatic spinal cord injury. Our results demonstrate that the distinct MOL populations have different spatial preference and different responses to disease.
Impacts of irrigated agriculture on food–energy–water–CO2 nexus across metacoupled systems
Authors: Xu Zhenci , Chen Xiuzhi , Liu Jianguo , Zhang Yu , Chau Sophia , Bhattarai Nishan , Wang Ye , Li Yingjie , Connor Thomas , Li Yunkai 
Published: November 2020

AbstractIrrigated agriculture has important implications for achieving the United Nations Sustainable Development Goals. However, there is a lack of systematic and quantitative analyses of its impacts on food–energy–water–CO2 nexus. Here we studied impacts of irrigated agriculture on food–energy–water–CO2 nexus across food sending systems (the North China Plain (NCP)), food receiving systems (the rest of China) and spillover systems (Hubei Province, affected by interactions between sending and receiving systems), using life cycle assessment, model scenarios, and the framework of metacoupling (socioeconomic-environmental interactions within and across borders). Results indicated that food supply from the NCP promoted food sustainability in the rest of China, but the NCP consumed over four times more water than its total annual renewable water, with large variations in food–energy–water–CO2 nexus across counties. Although Hubei Province was seldom directly involved in the food trade, it experienced substantial losses in water and land due to the construction of the South-to-North Water Transfer Project which aims to alleviate water shortages in the NCP. This study suggests the need to understand impacts of agriculture on food–energy–water–CO2 nexus in other parts of the world to achieve global sustainability.
Self-attenuation of extreme events in Navier–Stokes turbulence
Authors: Buaria Dhawal , Pumir Alain , Bodenschatz Eberhard 
Published: November 2020

AbstractTurbulent fluid flows are ubiquitous in nature and technology, and are mathematically described by the incompressible Navier-Stokes equations. A hallmark of turbulence is spontaneous generation of intense whirls, resulting from amplification of the fluid rotation-rate (vorticity) by its deformation-rate (strain). This interaction, encoded in the non-linearity of Navier-Stokes equations, is non-local, i.e., depends on the entire state of the flow, constituting a serious hindrance in turbulence theory and even establishing regularity of the equations. Here, we unveil a novel aspect of this interaction, by separating strain into local and non-local contributions utilizing the Biot-Savart integral of vorticity in a sphere of radius R. Analyzing highly-resolved numerical turbulent solutions to Navier-Stokes equations, we find that when vorticity becomes very large, the local strain over small R surprisingly counteracts further amplification. This uncovered self-attenuation mechanism is further shown to be connected to local Beltramization of the flow, and could provide a direction in establishing the regularity of Navier-Stokes equations.
Computationally predicting clinical drug combination efficacy with cancer cell line screens and independent drug action
Authors: Ling Alexander , Huang R. Stephanie 
Published: November 2020

AbstractEvidence has recently emerged that many clinical cancer drug combinations may derive their efficacy from independent drug action (IDA), where patients only receive benefit from the single most effective drug in a drug combination. Here we present IDACombo, an IDA based method to predict the efficacy of drug combinations using monotherapy data from high-throughput cancer cell line screens. We show that IDACombo predictions closely agree with measured drug combination efficacies both in vitro (Pearson’s correlation = 0.93 when comparing predicted efficacies to measured efficacies for >5000 combinations) and in a systematically selected set of clinical trials (accuracy > 84% for predicting statistically significant improvements in patient outcomes for 26 first line therapy trials). Finally, we demonstrate how IDACombo can be used to systematically prioritize combinations for development in specific cancer settings, providing a framework for quickly translating existing monotherapy cell line data into clinically meaningful predictions of drug combination efficacy.
Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses
Authors: Mick Eran , Kamm Jack , Pisco Angela Oliveira , Ratnasiri Kalani , Babik Jennifer M. , Castañeda Gloria , DeRisi Joseph L. , Detweiler Angela M. , Hao Samantha L. , Kangelaris Kirsten N. , Kumar G. Renuka , Li Lucy M. , Mann Sabrina A. , Neff Norma , Prasad Priya A. , Serpa Paula Hayakawa , Shah Sachin J. , Spottiswoode Natasha , Tan Michelle , Calfee Carolyn S. , Christenson Stephanie A. , Kistler Amy , Langelier Charles 
Published: November 2020

AbstractSARS-CoV-2 infection is characterized by peak viral load in the upper airway prior to or at the time of symptom onset, an unusual feature that has enabled widespread transmission of the virus and precipitated a global pandemic. How SARS-CoV-2 is able to achieve high titer in the absence of symptoms remains unclear. Here, we examine the upper airway host transcriptional response in patients with COVID-19 (n = 93), other viral (n = 41) or non-viral (n = 100) acute respiratory illnesses (ARIs). Compared with other viral ARIs, COVID-19 is characterized by a pronounced interferon response but attenuated activation of other innate immune pathways, including toll-like receptor, interleukin and chemokine signaling. The IL-1 and NLRP3 inflammasome pathways are markedly less responsive to SARS-CoV-2, commensurate with a signature of diminished neutrophil and macrophage recruitment. This pattern resembles previously described distinctions between symptomatic and asymptomatic viral infections and may partly explain the propensity for pre-symptomatic transmission in COVID-19. We further use machine learning to build 27-, 10- and 3-gene classifiers that differentiate COVID-19 from other ARIs with AUROCs of 0.981, 0.954 and 0.885, respectively. Classifier performance is stable across a wide range of viral load, suggesting utility in mitigating false positive or false negative results of direct SARS-CoV-2 tests.
XPC deficiency increases risk of hematologic malignancies through mutator phenotype and characteristic mutational signature
Authors: Yurchenko Andrey A. , Padioleau Ismael , Matkarimov Bakhyt T. , Soulier Jean , Sarasin Alain , Nikolaev Sergey 
Published: November 2020

AbstractRecent studies demonstrated a dramatically increased risk of leukemia in patients with a rare genetic disorder, Xeroderma Pigmentosum group C (XP-C), characterized by constitutive deficiency of global genome nucleotide excision repair (GG-NER). The genetic mechanisms of non-skin cancers in XP-C patients remain unexplored. In this study, we analyze a unique collection of internal XP-C tumor genomes including 6 leukemias and 2 sarcomas. We observe a specific mutational pattern and an average of 25-fold increase of mutation rates in XP-C versus sporadic leukemia which we presume leads to its elevated incidence and early appearance. We describe a strong mutational asymmetry with respect to transcription and the direction of replication in XP-C tumors suggesting association of mutagenesis with bulky purine DNA lesions of probably endogenous origin. These findings suggest existence of a balance between formation and repair of bulky DNA lesions by GG-NER in human body cells which is disrupted in XP-C patients.
Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep
Authors: Dong Xiyang , Rattray Jayne E. , Campbell D. Calvin , Webb Jamie , Chakraborty Anirban , Adebayo Oyeboade , Matthews Stuart , Li Carmen , Fowler Martin , Morrison Natasha M. , MacDonald Adam , Groves Ryan A. , Lewis Ian A. , Wang Scott H. , Mayumi Daisuke , Greening Chris , Hubert Casey R. J. 
Published: November 2020

AbstractAt marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. Here we combined geophysical, geochemical, metagenomic and metabolomic measurements to profile microbial activities at a newly discovered cold seep in the deep sea. Metagenomic profiling revealed compositional and functional differentiation between near-surface sediments and deeper subsurface layers. In both sulfate-rich and sulfate-depleted depths, various archaeal and bacterial community members are actively oxidizing thermogenic hydrocarbons anaerobically. Depth distributions of hydrocarbon-oxidizing archaea revealed that they are not necessarily associated with sulfate reduction, which is especially surprising for anaerobic ethane and butane oxidizers. Overall, these findings link subseafloor microbiomes to various biochemical mechanisms for the anaerobic degradation of deeply-sourced thermogenic hydrocarbons.
Vaccine elicitation of HIV broadly neutralizing antibodies from engineered B cells
Authors: Huang Deli , Tran Jenny Tuyet , Olson Alex , Vollbrecht Thomas , Tenuta Mary , Guryleva Mariia V. , Fuller Roberta P. , Schiffner Torben , Abadejos Justin R. , Couvrette Lauren , Blane Tanya R. , Saye Karen , Li Wenjuan , Landais Elise , Gonzalez-Martin Alicia , Schief William , Murrell Ben , Burton Dennis R. , Nemazee David , Voss James E. 
Published: November 2020

AbstractHIV broadly neutralizing antibodies (bnAbs) can suppress viremia and protect against HIV infection. However, their elicitation is made difficult by low frequencies of appropriate precursor B cell receptors and the complex maturation pathways required to generate bnAbs from these precursors. Antibody genes can be engineered into B cells for expression as both a functional antigen receptor on cell surfaces and as secreted antibody. Here, we show that HIV bnAb-engineered primary mouse B cells can be adoptively transferred and vaccinated in immunocompetent mice resulting in the expansion of durable bnAb memory and long-lived plasma cells. Somatic hypermutation after immunization indicates that engineered cells have the capacity to respond to an evolving pathogen. These results encourage further exploration of engineered B cell vaccines as a strategy for durable elicitation of HIV bnAbs to protect against infection and as a contributor to a functional HIV cure.
FIS1 encodes a GA2-oxidase that regulates fruit firmness in tomato
Authors: Li Ren , Sun Shuai , Wang Haijing , Wang Ketao , Yu Hong , Zhou Zhen , Xin Peiyong , Chu Jinfang , Zhao Tongmin , Wang Huanzhong , Li Jiayang , Cui Xia 
Published: November 2020

AbstractFruit firmness is a target trait in tomato breeding because it facilitates transportation and storage. However, it is also a complex trait and uncovering the molecular genetic mechanisms controlling fruit firmness has proven challenging. Here, we report the map-based cloning and functional characterization of qFIRM SKIN 1 (qFIS1), a major quantitative trait locus that partially determines the difference in compression resistance between cultivated and wild tomato accessions. FIS1 encodes a GA2-oxidase, and its mutation leads to increased bioactive gibberellin content, enhanced cutin and wax biosynthesis, and increased fruit firmness and shelf life. Importantly, FIS1 has no unfavorable effect on fruit weight or taste, making it an ideal target for breeders. Our study demonstrates that FIS1 mediates gibberellin catabolism and regulates fruit firmness, and it offers a potential strategy for tomato breeders to produce firmer fruit.
d-Orbital steered active sites through ligand editing on heterometal imidazole frameworks for rechargeable zinc-air battery
Authors: Jiang Yi , Deng Ya-Ping , Liang Ruilin , Fu Jing , Gao Rui , Luo Dan , Bai Zhengyu , Hu Yongfeng , Yu Aiping , Chen Zhongwei 
Published: November 2020

AbstractThe implementation of pristine metal-organic frameworks as air electrode may spark fresh vitality to rechargeable zinc-air batteries, but successful employment is rare due to the challenges in regulating their electronic states and structural porosity. Here we conquer these issues by incorporating ligand vacancies and hierarchical pores into cobalt-zinc heterometal imidazole frameworks. Systematic characterization and theoretical modeling disclose that the ligand editing eases surmountable energy barrier for *OH deprotonation by its efficacy to steer metal d-orbital electron occupancy. As a stride forward, the selected cobalt-zinc heterometallic alliance lifts the energy level of unsaturated d-orbitals and optimizes their adsorption/desorption process with oxygenated intermediates. With these merits, cobalt-zinc heterometal imidazole frameworks, as a conceptually unique electrode, empowers zinc-air battery with a discharge-charge voltage gap of 0.8 V and a cyclability of 1250 h at 15 mA cm–2, outperforming the noble-metal benchmarks.
Highly accurate long-read HiFi sequencing data for five complex genomes
Authors: Hon Ting , Mars Kristin , Young Greg , Tsai Yu-Chih , Karalius Joseph W. , Landolin Jane M. , Maurer Nicholas , Kudrna David , Hardigan Michael A. , Steiner Cynthia C. , Knapp Steven J. , Ware Doreen , Shapiro Beth , Peluso Paul , Rank David R. 
Published: November 2020

AbstractThe PacBio®HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10–25 kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes. Currently, there is a need for sample data sets to both evaluate the benefits of these long accurate reads as well as for development of bioinformatic tools including genome assemblers, variant callers, and haplotyping algorithms. We present deep coverage HiFi datasets for five complex samples including the two inbred model genomesMus musculusandZea mays, as well as two complex genomes, octoploidFragaria × ananassaand the diploid anuranRana muscosa. Additionally, we release sequence data from a mock metagenome community. The datasets reported here can be used without restriction to develop new algorithms and explore complex genome structure and evolution. Data were generated on the PacBio Sequel II System.
Ecological drivers of genetic connectivity for African malaria vectors Anopheles gambiae and An. arabiensis
Authors: Hemming-Schroeder Elizabeth , Zhong Daibin , Machani Maxwell , Nguyen Hoan , Thong Sarah , Kahindi Samuel , Mbogo Charles , Atieli Harrysone , Githeko Andrew , Lehmann Tovi , Kazura James W. , Yan Guiyun 
Published: November 2020

AbstractAnopheles gambiaeandAn. arabiensisare major malaria vectors in sub-Saharan Africa. Knowledge of how geographical factors drive the dispersal and gene flow of malaria vectors can help in combatting insecticide resistance spread and planning new vector control interventions. Here, we used a landscape genetics approach to investigate population relatedness and genetic connectivity ofAn. gambiaeandAn. arabiensisacross Kenya and determined the changes in mosquito population genetic diversity after 20 years of intensive malaria control efforts. We found a significant reduction in genetic diversity inAn. gambiae, but not inAn. arabiensisas compared to prior to the 20-year period in western Kenya. Significant population structure among populations was found for both species. The most important ecological driver for dispersal and gene flow ofAn. gambiaeandAn. arabiensiswas tree cover and cropland, respectively. These findings highlight that human induced environmental modifications may enhance genetic connectivity of malaria vectors.