bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative neuroanatomy of ctenophores: Neural and muscular systems in Euplokamis dunlapae and related species
Authors: Norekian Tigran P. , Moroz Leonid L. 
Published: September 2019

AbstractCtenophora is an early‐branching basal metazoan lineage, which may have evolved neurons and muscles independently from other animals. However, despite the profound diversity among ctenophores, basal neuroanatomical data are limited to representatives of two genera. Here, we describe the organization of neuromuscular systems in eight ctenophore species focusing on Euplokamis dunlapae—the representative of the lineage sister to all other ctenophores. Cydippids (Hormiphora hormiphora and Dryodora glandiformis) and lobates (Bolinopsis infundibulum and Mnemiopsis leidyi) were used as reference platforms to cover both morphological and ecological diversity within the phylum. We show that even with substantial environmental differences, the basal organization of neural systems is conserved among ctenophores. In all species, we detected two distributed neuronal subsystems: the subepithelial polygonal network and the mesogleal elements. Nevertheless, each species developed specific innovations in neural, muscular, and receptor systems. Most notable Euplokamis‐specific features are the following: (a) Comb nerves with giant axons. These nerves directly coordinate the rapid escape response bypassing the central integrative structure known as the aboral sensory organ. (b) Neural processes in tentacles along the rows of “boxes” providing structural support and located under striated muscles. (c) Radial muscles that cross the mesoglea and connect the outer wall to the aboral canal. (d) Flat muscles, encircling each meridional canal. Also, we detected a structurally different rectangular neural network in the feeding lobes of Lobata (Mnemiopsis/Bolinopsis) but not in other species. The described lineage‐specific innovations can be used for future single‐cell atlases of ctenophores and analyses of neuronal evolution in basal metazoans.
An improved join‐free snowflake schema for ETL and OLAP of data warehouse
Authors: Jianmin Wang , Wenbin Zhao , Tongrang Fan , Shilong Yang , Hongwei Lv 
Published: September 2019

SummaryThe emergence of big data makes more and more enterprise change data management strategy, from simple data storage to OLAP query analysis; meanwhile, NoSQL‐based data warehouse receive more increasing attention than traditional SQL‐based database. By improving the JFSS model for ETL, this paper proposes the uniform distribution code (UDC), model identification code (MIC), standard dimension code (SDC), and attribute dimensional code (ADC); defines the data storage format of <Rowkey Compound Code, Sec (Value)>; and identifies the extraction, transformation, and loading strategies of data warehouse. Several experiments are carried out to analyze single record and range record queries as typical OLAP based on Hadoop database (HBase). The results show the proposed scheme can provide lower overhead than the traditional SQL‐based database while facilitating the scope and flexibility of data warehouse services.
STARR‐seq and UMI‐STARR‐seq: Assessing Enhancer Activities for Genome‐Wide‐, High‐, and Low‐Complexity Candidate Libraries
Authors: Neumayr Christoph , Pagani Michaela , Stark Alexander , Arnold Cosmas D. 
Published: September 2019

AbstractThe identification of transcriptional enhancers and the quantitative assessment of enhancer activities is essential to understanding how regulatory information for gene expression is encoded in animal and human genomes. Further, it is key to understanding how sequence variants affect enhancer function. STARR‐seq enables the direct and quantitative assessment of enhancer activity for millions of candidate sequences of arbitrary length and origin in parallel, allowing the screening of entire genomes and the establishment of genome‐wide enhancer activity maps.In STARR‐seq, the candidate sequences are cloned downstream of the core promoter into a reporter gene's transcription unit (i.e., the 3′ UTR). Candidates that function as active enhancers lead to the transcription of reporter mRNAs that harbor the candidates’ sequences. This direct coupling of enhancer sequence and enhancer activity in cis enables the straightforward and efficient cloning of complex candidate libraries and the assessment of enhancer activities of millions of candidates in parallel by quantifying the reporter mRNAs by deep sequencing. This article describes how to create focused and genome‐wide human STARR‐seq libraries and how to perform STARR‐seq screens in mammalian cells, and also describes a novel STARR‐seq variant (UMI‐STARR‐seq) that allows the accurate counting of reporter mRNAs for STARR‐seq libraries of low complexity. © 2019 The Authors.Basic Protocol 1: STARR‐seq plasmid library cloningBasic Protocol 2: Mammalian STARR‐seq screening protocolAlternate Protocol: UMI‐STARR‐seq screening protocol—unique molecular identifier integrationSupport Protocol: Transfection of human cells using the MaxCyte STX scalable transfection system
100 yr of primary succession highlights stochasticity and competition driving community establishment and stability
Authors: Buma B. , Bisbing S. M. , Wiles G. , Bidlack A. L. 
Published: September 2019

AbstractThe study of community succession is one of the oldest pursuits in ecology. Challenges remain in terms of evaluating the predictability of succession and the reliability of the chronosequence methods typically used to study community development. The research of William S. Cooper in Glacier Bay National Park is an early and well‐known example of successional ecology that provides a long‐term observational data set to test hypotheses derived from space‐for‐time substitutions. It also provides a unique opportunity to explore the importance of historical contingencies and as an example of a revitalized historical study system. We test the textbook successional trajectory in Glacier Bay and evaluate long‐term plant community development via primary succession through extensive fieldwork, remote sensing, dendrochronological methods, and newly discovered data that fills in data gaps (1940s to late 1980s) in continuous measurement over 100+ years. To date, Cooper's quadrats do not support the classic facilitation model of succession in which a sequence of species interacts to form predictable successional trajectories. Rather, stochastic early community assembly and subsequent inhibition have dominated; most species arrived shortly after deglaciation and have remained stable for 50+ years. Chronosequence studies assuming prior composition are thus questionable, as no predictable species sequence or timeline was observed. This underscores the significance of assumptions about early conditions in chronosequences and the need to defend such assumptions. Furthermore, this work brings a classic study system in ecology up to date via a plot size expansion, new baseline biogeochemical data, and spatial mapping for future researchers for its second century of observation.
Influence of Dissolved Organic Carbon on the Acute Toxicity of Copper and Zinc to White Sturgeon (Acipenser transmontanus) and a Cladoceran (Ceriodaphnia dubia)
Authors: Ivey Christopher D. , Besser John M. , Steevens Jeffrey A. , Walther Michael J. , Melton Vanessa D. 
Published: September 2019

Abstract
We conducted acute lethality tests with white sturgeon (Acipenser transmontanus) and Ceriodaphnia dubia exposed to copper and zinc at dissolved organic carbon concentrations ranging from 0.5 to 5.5 mg/L. Dissolved organic carbon had minimal effects on zinc toxicity but did have a protective effect on acute copper toxicity, which was equal to that predicted by the copper biotic ligand model (BLM). The BLM-adjusted copper median effect concentrations for A. transmontanus ranged from 2.4 to 8.2 mg/L. Environ Toxicol Chem 2019;38:2682–2687. Published 2019 Wiley Periodicals, Inc. on behalf of SETAC. This article is a US government work, and as such, is in the public domain in the United States of America.
Measuring global economic activity
Authors: Hamilton James D. 
Published: September 2019

SummaryA number of economic studies have used a proxy for world real economic activity derived from shipping costs. This measure turns out to depend on a normalization that has substantive consequences, of which users of the index had been unaware prior to this paper. This paper further evaluates this and alternative measures in terms of treatment of trends, coherence with world output, and correlation with commodity prices. I conclude that measures derived from world industrial production offer a better indicator of global real economic activity.
Multivariate dynamic intensity peaks‐over‐threshold models
Authors: Hautsch Nikolaus , Herrera Rodrigo 
Published: September 2019

SummaryWe propose a multivariate dynamic intensity peaks‐over‐threshold model to capture extremes in multivariate return processes. The random occurrence of extremes is modeled by a multivariate dynamic intensity model, while temporal clustering of their size is captured by an autoregressive multiplicative error model. Applying the model to daily returns of three major stock indexes yields strong empirical support for a temporal clustering of both the occurrence and the size of extremes. Backtesting value‐at‐risk and expected shortfall forecasts shows that the consideration of clustering effects and of feedback between the magnitudes and the intensity of extremes results in better forecasts of risk.
Effects of a 12-Month Supervised, Community-Based, Multimodal Exercise Program Followed by a 6-Month Research-to-Practice Transition on Bone Mineral Density, Trabecular Microarchitecture, and Physical Function in Older Adults: A Randomized Controlled Trial
Authors: Daly Robin M , Gianoudis Jenny , Kersh Mariana E , Bailey Christine A , Ebeling Peter R , Krug Roland , Nowson Caryl A , Hill Keith , Sanders Kerrie M 
Published: September 2019

ABSTRACTMulticomponent exercise programs are recommended to reduce fracture risk; however, their effectiveness in real-world community settings remain uncertain. This 18-month randomized controlled trial investigated the effects of a 12-month, community-based, supervised multicomponent exercise program followed by a 6-month “research-to-practice” transition on areal bone mineral density (BMD), trabecular bone microarchitecture, functional performance, and falls in older adults at increased fracture risk. One-hundred and sixty-two adults aged ≥60 years with osteopenia or at increased falls risk were randomized to the Osteo-cise: Strong Bones for Life multicomponent exercise program (n = 81) or a control group (n = 81). Exercise consisted of progressive resistance, weight-bearing impact, and balance training (3-days/week) performed at community leisure centers. Overall 148 (91%) participants completed the trial, and mean exercise adherence was 59% after 12 months and 45% during the final 6 months. After 12 months, there were significant net beneficial effects of exercise on lumbar spine and femoral neck BMD (1.0% to 1.1%, p &lt; 0.05), muscle strength (10% to 13%, p &lt; 0.05), and physical function (timed stair climb 5%; four-square step test 6%; sit-to-stand 16%, p ranging &lt;0.05 to &lt;0.001), which persisted after the 6-month transition. There were no significant effects of the 18-month intervention on distal femur or proximal tibia trabecular bone microarchitecture or falls incidence, but per protocol analysis (≥66% exercise adherence) revealed there was a significant net benefit of exercise (mean [95% confidence interval] 2.8% [0.2, 5,4]) on proximal tibia trabecular bone volume fraction (Osteo-cise 1.5% [−1.2, 4.2]; controls −1.3% [−2.6, 0.1]) after 18 months due to changes in trabecular number (Osteo-cise 1.7% [−0.9, 4.3]; controls −1.1% [−2.4, 0.2]) but not trabecular thickness (Osteo-cise − 0.2% [−0.5, 0.2]; controls −0.2% [−0.4, 0.0]). In conclusion, this study supports the effectiveness of the Osteo-cise: Strong Bones for Life program as a real-world, pragmatic, evidence-based community exercise program to improve multiple musculoskeletal health outcomes in older adults at increased fracture risk. © 2019 American Society for Bone and Mineral Research.
Murine Placental-Fetal Phosphate Dyshomeostasis Caused by an Xpr1 Deficiency Accelerates Placental Calcification and Restricts Fetal Growth in Late Gestation
Authors: Xu Xuan , Li Xiunan , Sun Hao , Cao Zhijian , Gao Ruixi , Niu Tingting , Wang Yanli , Ma Tingbin , Chen Rui , Wang Cheng , Yang Zhengang , Liu Jing Yu 
Published: September 2019

ABSTRACT
Phosphorus is a necessary component of all living organisms. This nutrient is mainly transported from the maternal blood to the fetus via the placenta, and insufficient phosphorus availability via the placenta disturbs the normal development of the fetus, especially fetal bone formation in late gestation. Key proteins (phosphate transporters and exporters) that are responsible for the maintenance of placental-fetal phosphorus homeostasis have been identified. A deficiency in the phosphate transporter Pit2 has been shown to result in placental calcification and the retardation of fetal development in mice. What roles does XPR1 (the only known phosphate exporter) play in maintaining placental-fetal phosphorus homeostasis? In this study, we found that Xpr1 expression is strong in the murine placenta and increases with age during gestation. We generated a global Xpr1 knockout mouse and found that heterozygous (Xpr1+/−) and homozygous (Xpr1−/−) fetuses have lower inorganic phosphate (Pi) levels in amniotic fluid and serum and a decreased skeletal mineral content. Xpr1-deficient placentas show abnormal Pi exchange during gestation. Therefore, Xpr1 deficiency in the placenta disrupts placental-fetal Pi homeostasis. We also discovered that the placentas of the Xpr1+/− and Xpr1−/− embryos are severely calcified. Mendelian inheritance statistics for offspring outcomes indicated that Xpr1-deficient embryos are significantly reduced in late gestation. In addition, Xpr1−/− mice die perinatally and a small proportion of Xpr1+/− mice die neonatally. RNA sequence (RNA-Seq) analysis of placental mRNA revealed that many of the transcripts are significantly differentially expressed due to Xpr1 deficiency and are linked to dysfunction of the placenta. This study is the first to reveal that XPR1 plays an important role in maintaining placental-fetal Pi homeostasis, disruption of which causes severe placental calcification, delays normal placental function, and restricts fetal growth. © 2019 American Society for Bone and Mineral Research.
High-Impact Exercise Increased Femoral Neck Bone Density With No Adverse Effects on Imaging Markers of Knee Osteoarthritis in Postmenopausal Women
Authors: Hartley Chris , Folland Jonathan P , Kerslake Robert , Brooke-Wavell Katherine 
Published: September 2019

ABSTRACT
High-impact exercise can improve femoral neck bone mass but findings in postmenopausal women have been inconsistent and there may be concern at the effects of high-impact exercise on joint health. We investigated the effects of a high-impact exercise intervention on bone mineral density (BMD), bone mineral content (BMC), and section modulus (Z) as well as imaging biomarkers of osteoarthritis (OA) in healthy postmenopausal women. Forty-two women aged 55 to 70 years who were at least 12 months postmenopausal were recruited. The 6-month intervention consisted of progressive, unilateral, high-impact exercise incorporating multidirectional hops on one randomly assigned exercise leg (EL) for comparison with the contralateral control leg (CL). Dual-energy X-ray absorptiometry (DXA) was used to measure BMD, BMC, and Z of the femoral neck. Magnetic resonance imaging (MRI) of the knee joint was used to analyze the biochemical composition of articular cartilage using T2 relaxometry and to analyze joint pathology associated with OA using semiquantitative analysis. Thirty-five participants (61.7 ± 4.3 years) completed the intervention with a mean adherence of 76.8% ± 22.5%. Femoral neck BMD, BMC, and Z all increased in the EL (+0.81%, +0.69%, and +3.18%, respectively) compared to decreases in the CL (−0.57%, −0.71%, and −0.75%: all interaction effects p &lt; 0.05). There was a significant increase in mean T2 relaxation times (main effect of time p = 0.011) but this did not differ between the EL and CL, indicating no global effect. Semiquantitative analysis showed high prevalence of bone marrow lesions (BML) and cartilage defects, especially in the patellofemoral joint (PFJ), with no indication that the intervention caused pathology progression. In conclusion, a high-impact exercise intervention that requires little time, cost, or specialist equipment improved femoral neck BMD with no negative effects on knee OA imaging biomarkers. Unilateral high-impact exercise is a feasible intervention to reduce hip fracture risk in healthy postmenopausal women. © 2019 American Society for Bone and Mineral Research.
Sex-Specific Muscular Mediation of the Relationship Between Physical Activity and Cortical Bone in Young Adults
Authors: Higgins Simon , Sokolowski Chester M , Vishwanathan Megha , Schmidt Michael D , Evans Ellen M , Lewis Richard D 
Published: September 2019

ABSTRACT
Muscle mass is a commonly cited mediator of the relationship between physical activity (PA) and bone, representing the mechanical forces generated during PA. However, neuromuscular properties (eg, peak force) also account for unique portions of variance in skeletal outcomes. We used serial multiple mediation to explore the intermediary role of muscle mass and force in the relationships between cortical bone and moderate-to-vigorous intensity PA (MVPA). In a cross-sectional sample of young adults (n = 147, 19.7 ± 0.7 years old, 52.4% female) cortical diaphyseal bone was assessed via peripheral quantitative computed tomography at the mid-tibia. Peak isokinetic torque in knee extension was assessed via Biodex dynamometer. Thigh fat-free soft tissue (FFST) mass, assessed via dual-energy X-ray absorptiometry, represented the muscular aspect of tibial mechanical forces. Habitual MVPA was assessed objectively over 7 days using Actigraph GT3X+ accelerometers. Participants exceeded MVPA guidelines (89.14 ± 27.29 min/day), with males performing 44.5% more vigorous-intensity activity relative to females (p &lt; 0.05). Males had greater knee extension torque and thigh FFST mass compared to females (55.3%, and 34.2%, respectively, all p &lt; 0.05). In combined-sex models, controlling for tibia length and age, MVPA was associated with strength strain index (pSSI) through two indirect pathways: (i) thigh FFST mass (b = 1.11 ± 0.37; 95% CI, 0.47 to 1.93), and (i) thigh FFST mass and knee extensor torque in sequence (b = 0.30 ± 0.16; 95% CI, 0.09 to 0.73). However, in sex-specific models MVPA was associated with pSSI indirectly through its relationship with knee extensor torque in males (b = 0.78 ± 0.48; 95% CI, 0.04 to 2.02) and thigh FFST mass in females (b = 1.12 ± 0.50; 95% CI, 0.37 to 2.46). Bootstrapped CIs confirmed these mediation pathways. The relationship between MVPA and cortical structure appears to be mediated by muscle in young adults, with potential sex-differences in the muscular pathway. If confirmed, these findings may highlight novel avenues for the promotion of bone strength in young adults. © 2019 American Society for Bone and Mineral Research.
Potential of circulating pro‐angiogenic microRNA expressions as biomarkers for rapid angiographic stenotic progression and restenosis risks in coronary artery disease patients underwent percutaneous coronary intervention
Authors: Dai Rui , Liu Yijue , Zhou Yi , Xiong Xiaoju , Zhou Wei , Li Weijuan , Zhou Wenping , Chen Manhua 
Published: September 2019

AbstractBackgroundThis study aimed to investigate the correlation of pro‐angiogenic microRNA (miRNA) expressions with rapid angiographic stenotic progression (RASP) and restenosis risks in coronary artery disease (CAD) patients underwent percutaneous coronary intervention (PCI) with drug‐eluting stents (DES).MethodsA total of 286 CAD patients underwent PCI with DES were consecutively recruited in this study. Plasma samples were collected before PCI operation, and 14 pro‐angiogenic miRNAs were measured by real‐time quantitative reverse transcription‐polymerase chain reaction. Rapid angiographic stenotic progression at nontarget lesions and restenosis at stented lesions were evaluated by quantitative coronary angiography at 12 months after PCI operation.ResultsThe occurrence rates of RASP and restenosis were 39.5% and 22.4%, respectively. Let‐7f, miR‐19a, miR‐19b‐1, miR‐92a, miR‐126, miR‐210, and miR‐296 were decreased in RASP patients than non‐RASP patients, among which let‐7f, miR‐19a, miR‐126, miR‐210, and miR‐296 independently correlated with lower RASP occurrence by multivariate analysis, followed by receiver‐operating characteristic (ROC) curve exhibited that these five miRNAs showed great value in predicting RASP risk with area under curve (AUC) 0.879 (95% CI: 0.841‐0.917). Besides, let‐7f, miR‐19a, miR‐92a, miR‐126, miR‐130a, and miR‐210 were reduced in restenosis patients than non‐restenosis patients, among them miR‐19a, miR‐126, miR‐210, and miR‐378 independently correlated with lower restenosis occurrence by multivariate analysis, followed by ROC curve disclosed that these four miRNAs had good value in predicting restenosis risk with AUC 0.776 (95% CI: 0.722‐0.831).ConclusionsCirculating let‐7f, miR‐19a, miR‐126, miR‐210, and miR‐296 independently correlate with reduced RASP risk, while miR‐19a, miR‐126, miR‐210, and miR‐378 independently correlate with decreased restenosis risk in CAD patients underwent PCI with DES.
How Candida antarctica lipase B can be activated in natural deep eutectic solvents: experimental and molecular dynamics studies
Authors: Nian Binbin , Cao Chen , Liu Yuanfa 
Published: September 2019

AbstractBACKGROUNDNatural deep eutectic solvents (NADESs), a class of green solvents which completely accords to 12 principles of green chemistry, have proven to have great potential applications in enzymatic reactions. Despite strong interest, the role of NADESs in these processes, and the molecular interaction between enzymes and NADESs, still remain ambiguous. In the present study, the stability and activity of Candida Antarctica lipase B (CALB) were studied, and the mechanism by which CALB was activated in NADESs was explored systematically from both molecular‐ and macroscopic‐scale perspectives.RESULTSThe results suggested that the activity of CALB in all NADESs was significantly higher than that of the control (ethanol). Moreover, the stability of CALB increased to 115.48 ± 1.36% and 108.54 ± 1.26% in betaine‐glycerin (B‐Gly) and choline chloride‐glycerol (C‐Gly), but decreased to 91.69 ± 3.26% and 92.31 ± 3.36% in betaine‐xylitol (B‐X) and choline chloride‐xylitol (C‐X), respectively. The results of circular dichroism (CD), fluorescence spectroscopy and molecular dynamics studies (MD) indicated that there was no significant change in the secondary structure of CALB. Furthermore, the results of MD provide some information supporting that CALB was stabilized by the hydrogen(H)‐bonding interaction between surface amino residues of CALB and NADESs and was activated via the H‐bonding interaction between substrate and NADESs in the acyl‐binding pocket.CONCLUSIONThe mechanism by which CALB was activated and stabilized via the H‐bonding interactions in NADESs was revealed in the present study. This provides a scientific basis from which to further explore the potential application of NADESs in enzymatic reactions in food engineering and health‐related fields. © 2019 Society of Chemical Industry