bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are cannabis users less likely to gain weight? Results from a national 3-year prospective study
Authors: Alshaarawy Omayma , Anthony James C 
Published: March 2019

Abstract

Background
Pre-clinical studies indicate increased food intake and weight gain as cannabinoid effects. Cross-sectional epidemiological studies, however, indicate lower prevalence of obesity among cannabis users. Here, we aim to study the weight-gain research question in the prospectively conducted National Epidemiologic Survey on Alcohol and Related Conditions (NESARC).

Methods
NESARC was designed to produce nationally representative estimates for the US population. Participants (aged 18+) completed computer-assisted personal interviews on cannabis use, body weight and height at Waves 1 (W1, 2001–02) and 2 (W2, 2004–05). General linear modelling yields estimates for change in body mass index (BMI) regressed on cannabis-use status, with covariate adjustment based on a conceptual model for BMI determinants (n = 33 000).

Results
At W2, 77% of the participants never used cannabis, 18% had discontinued use (‘quit’), 3% were initiates and 2% were persistent users. Estimated W1-to-W2 BMI change shows an increase for all subgroups. Compared with never-users (reference), inverse slope estimates and attenuated change (%) in BMI between W1 and W2 are seen for cannabis-use subgroups: quitters [β = –0.81; 95% confidence interval (CI) = –1.01, –0.60], initiates (β = –0.97; 95% CI = –1.36, –0.57) and persistent users (β = –1.26; 95% CI = –1.81, –0.72).

Conclusion
This new prospective study builds from anecdotes, pre-clinical studies and cross-sectional evidence on inverse associations linking cannabis use and obesity and shows an inverse cannabis–BMI increase association. Confirmatory studies with rigorous cannabis and BMI assays will be needed.
Predicting extragalactic distance errors using Bayesian inference in multimeasurement catalogues
Authors: Chaparro-Molano Germán , Cuervo Juan Carlos , Restrepo Gaitán Oscar Alberto , Torres Arzayús Sergio 
Published: March 2019

ABSTRACT
We propose the use of robust, Bayesian methods for estimating extragalactic distance errors in multimeasurement catalogues. We seek to improve upon the more commonly used frequentist propagation-of-error methods, as they fail to explain both the scatter between different measurements and the effects of skewness in the metric distance probability distribution. For individual galaxies, the most transparent way to assess the variance of redshift independent distances is to directly sample the posterior probability distribution obtained from the mixture of reported measurements. However, sampling the posterior can be cumbersome for catalogue-wide precision cosmology applications. We compare the performance of frequentist methods versus our proposed measures for estimating the true variance of the metric distance probability distribution. We provide pre-computed distance error data tables for galaxies in three catalogues: NED-D, HyperLEDA, and Cosmicflows-3. Additionally, we develop a Bayesian model that considers systematic and random effects in the estimation of errors for Tully–Fisher (TF) relation derived distances in NED-D. We validate this model with a Bayesian p-value computed using the Freeman–Tukey discrepancy measure as a posterior predictive check. We are then able to predict distance errors for 884 galaxies in the NED-D catalogue and 203 galaxies in the HyperLEDA catalogue that do not report TF distance modulus errors. Our goal is that our estimated and predicted errors are used in catalogue-wide applications that require acknowledging the true variance of extragalactic distance measurements.
Improving diagnosis and monitoring of treatment response in pulmonary tuberculosis using the molecular bacterial load assay (MBLA)
Authors: Sabiiti Wilber , Azam Khalide , Kuchaka Davis , Mtafya Bariki , Bowness Ruth , Oravcova Katarina , Farmer Eoghan C W , Honeyborne Isobella , Evangelopoulos Dimitrios , McHugh Timothy D , Xiao Han , Khosa Celso , Rachow Andrea , Heinrich Norbert , Kampira Elizabeth , Davies Gerry , Bhatt Nilesh , Ntinginya Nyanda Elias , Viegas Sofia , Jani Ilesh , Kamdolozi Mercy , Mdolo Aaron , Khonga Margaret , Boeree Martin J , Philips Patrick PJ , Sloan Derek J , Hoelscher Michael , Kibiki Gibson Sammy , Gillespie Stephen H 
Published: March 2019

AbstractObjectivesBetter outcomes in tuberculosis require new diagnostic and treatment monitoring tools. In this paper we evaluated the utility of a marker ofM. tuberculosisviable count, the Molecular Bacterial Load assay (MBLA) for diagnosis and treatment monitoring of tuberculosis in a high burden setting.MethodsPatients with smear positive pulmonary tuberculosis from two sites in Tanzania and one each in Malawi and Mozambique. Sputum samples were taken weekly for the first 12 weeks of treatment and evaluated by MBLA and mycobacterial growth indicator tube method (MGIT).ResultsThe results of high and low positive control samples confirmed inter site reproducibility. Over the 12 weeks of treatment there was a steady decline in the viable bacterial load as measured by the MBLA that corresponds to rise in time to a positive result (TTP) in the Mycobacterial Growth Indicator Tube. Both MBLA and MGIT provided similar time to test negativity. Importantly, as treatment progressed samples in MGIT were increasingly likely to be contaminated, which compromised the acquisition of results but did not affect MBLA samples.ConclusionsMBLA produces a reproducible measure ofMtbviable count comparable to that of MGIT that is not compromised by contamination in a real-world setting. As a molecular test, the results can be available in as little as four hours and could allow health care professionals to identify rapidly patients who are failing therapy.
Distinct YFV lineages co-circulated in the Central-Western and Southeastern Brazilian regions from 2015 to 2018
Authors: Delatorre Edson , de Abreu Filipe Vieira Santos , Ribeiro Ieda Pereira , Gómez Mariela Martínez , dos Santos Alexandre Araújo Cunha , Ferreira-de-Brito Anielly , Santos Neves Maycon Sebastião Alberto , Bonelly Iule , de Miranda Rafaella Moraes , Furtado Nathália Dias , Souza Raphael Lidiane Menezes , de Fátima Fernandes da Silva Lucileis , de Castro Márcia Gonçalves , Ramos Daniel Gaskauskas , Martins Romano Alessandro Pecêgo , Kallás Esper Georges , Paulo Vicente Ana Carolina , Bello Gonzalo , Lourenço-de-Oliveira Ricardo , Bonaldo Myrna Cristina 
Published: March 2019

AbstractThe current outbreak of yellow fever virus (YFV) that is afflicting Brazil since the end of 2016 probably originated from a re-introduction of YFV from endemic areas into the non-endemic Southeastern Brazil. However, the lack of genomic sequences from endemic regions hinders the tracking of YFV’s dissemination routes. We assessed the origin and spread of the ongoing YFV Brazilian outbreak analyzing a new set of YFV strains infecting humans, non-human primates (NHP) and mosquitoes sampled across five Brazilian states from endemic and non-endemic regions between 2015 and 2018. We found two YFV sub-clade 1E lineages circulating in NHP from Goiás state (GO), resulting from independent viral introductions into the Araguaia tributary river basin: while the strain from 2017 clustered intermingled with Venezuelan YFV strains from 2000, the YFV strain sampled in 2015 clustered with sequences of the current YFV outbreak in the Brazilian Southeastern region (named YFV2015-2018 lineage), displaying the same molecular signature associated to the current YFV outbreak. After its introduction in GO at around mid-2014, the YFV2015-2018 lineage followed two paths of dissemination outside GO, originating two major YFV sub-lineages: 1) the YFVMG/ES/RJ sub-lineage spread sequentially from the eastern area of Minas Gerais state to Espírito Santo and then to Rio de Janeiro states, following the Southeast Atlantic basin; 2) the YFVMG/SP sub-lineage spread from the southwestern area of Minas Gerais to the metropolitan region of São Paulo state, following the Paraná basin. These results indicate the ongoing YFV outbreak in Southeastern Brazil originated from a dissemination event from GO almost two years before its recognition at the end of 2016. From GO this lineage was introduced in Minas Gerais state at least two times, originating two sub-lineages that followed different routes towards densely populated areas. The spread of YFV outside endemic regions for at least four years stresses the imperative importance of the continuous monitoring of YFV to aid decision-making for effective control policies aiming the increase of vaccination coverage to avoid the YFV transmission in densely populated urban centers.
Programmable bacteria induce durable tumor regression and systemic antitumor immunity
Authors: Chowdhury Sreyan , Hinchliffe Taylor E. , Castro Samuel , Coker Courtney , Arpaia Nicholas , Danino Tal 
Published: March 2019

SUMMARY PARAGRAPHSynthetic biology is driving a new era of medicine through the genetic programming of living cells1,2. This transformative approach allows for the creation of engineered systems that intelligently sense and respond to diverse environments, ultimately adding specificity and efficacy that extends beyond the capabilities of molecular-based therapeutics3–5. One particular focus area has been the engineering of bacteria as therapeutic delivery systems to selectively release therapeutic payloads in vivo6–8. Here, we engineered a non-pathogenic E. coli to specifically lyse within the tumor microenvironment and release an encoded nanobody antagonist of CD47 (CD47nb)9, an anti-phagocytic receptor commonly overexpressed in several human cancers10,11. We show that intratumoral delivery of CD47nb by tumor-colonizing bacteria increases activation of tumor-infiltrating T cells, stimulates rapid tumor regression, prevents metastasis, and leads to long-term survival in a syngeneic tumor model. Moreover, we report that local injection of CD47nb bacteria stimulates systemic antitumor immune responses that reduce the growth of untreated tumors – providing, to the best of our knowledge, the first demonstration of an abscopal effect induced by a bacteria cancer therapy. Thus, engineered bacteria may be used for safe and local delivery of immunotherapeutic payloads leading to systemic antitumor immunity.
Role of Rare and Low Frequency Variants in Gene-Alcohol Interactions on Plasma Lipid Levels
Authors: Wang Zhe , Chen Han , Bartz Traci M. , Bielak Lawrence F. , Chasman Daniel I. , Feitosa Mary F. , Franceschini Nora , Guo Xiuqing , Lim Elise , Noordam Raymond , Richard Melissa A. , Wang Heming , Cade Brian , Adrienne Cupples L. , de Vries Paul S. , Giulanini Franco , Lee Jiwon , Lemaitre Rozenn N. , Martin Lisa W. , Reiner Alex P. , Rich Stephen S. , Schreiner Pamela J. , Sidney Stephen , Sitlani Colleen M. , Smith Jennifer A. , van Dijk Ko Willems , Yao Jie , Zhao Wei , Fornage Myriam , Kardia Sharon L.R. , Kooperberg Charles , Liu Ching-Ti , Mook-Kanamori Dennis O , Province Michael A. , Psaty Bruce M. , Redline Susan , Ridker Paul M. , Rotter Jerome I. , Boerwinkle Eric , Morrison Alanna C. 
Published: March 2019

AbstractBackgroundAlcohol intake influences plasma lipid levels and such effects may be modulated by genetic variants.ObjectiveWe aimed to characterize the role of aggregated rare and low-frequency variants in gene by alcohol consumption interactions associated with fasting plasma lipid levels.DesignIn the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium, fasting plasma triglycerides (TG), and high- and low-density lipoprotein cholesterol (HDL-c and LDL-c) were measured in 34,153 European Americans from five discovery studies and 32,275 individuals from six replication studies. Rare and low-frequency protein coding variants (minor allele frequency ≤ 5%) measured by an exome array were aggregated by genes and evaluated by a gene-environment interaction (GxE) test and a joint test of genetic main and GxE interaction effects. Two dichotomous self-reported alcohol consumption variables, current drinker, defined as any recurrent drinking behavior, and regular drinker, defined as the subset of current drinkers who consume at least two drinks per week, were considered.ResultsWe discovered and replicated 21 gene-lipid associations at 13 known lipid loci through the joint test. Eight loci (PCSK9, LPA, LPL, LIPG, ANGPTL4, APOB, APOC3 and CD300LG) remained significant after conditioning on the common index single nucleotide polymorphism (SNP) identified by previous genome-wide association studies, suggesting an independent role for rare and low-frequency variants at these loci. One significant gene-alcohol interaction on TG was discovered at a Bonferroni corrected significance level (p-value <5×10−5) and replicated (p-value <0.013 for the interaction test) inSMC5.ConclusionsIn conclusion, this study applied new gene-based statistical approaches to uncover the role of rare and low-frequency variants in gene-alcohol consumption interactions on lipid levels.
A spatial cell culture model for predicting chemotherapy dosing strategies
Authors: Zhu Shu , Deb Dhruba , Danino Tal 
Published: March 2019

AbstractPredicting patient responses to chemotherapy regimens is a major challenge in cancer treatment. To do this requires quantitative mathematical models to predict optimal dose and frequency for a particular drug, and experimental model systems such as three-dimensional organoids that accurately recapitulate the tumor microenvironment and heterogeneity. However, tracking the spatial dynamics of multiple cell types in three-dimensions can be a significant challenge in terms of time and throughput. Here we develop a two-dimensional system that allows for simple tracking of cell populations via fluorescence microscopy for modeling spatial dynamics in tumors. We first develop multiple 4T1 breast cancer cell lines resistant to varying concentrations of doxorubicin, and demonstrate how well mixed and spatially heterogeneous populations expand in a two-dimensional colony. We subject cell populations to varied dose and frequency of chemotherapy and measure colony growth radius and populations. We then build a mathematical model to describe the dynamics of both chemosensitive and chemoresistant populations, where we determine which number of doses can produce the smallest tumor size based on parameters in the system. In the future, this system can be adapted to quickly optimize dosing strategies in the setting of heterogeneous cell types or patient derived cells with varied chemoresistance.
Monarch butterfly declines reported in Boyle et al. (2019) are biased by unexamined changes in museum collections over time
Authors: Wepprich Tyson 
Published: March 2019

AbstractMuseum records provide an underutilized source of information for documenting long-term changes in phenology, species interactions, and trait evolution. However, non-systematic collection data must be treated carefully if they are to approximate abundance, as trends may be confounded with spatial or temporal changes in sampling effort. Boyle et al. (2019b) argue that the relative abundance of Eastern North American Monarch butterflies (Danaus plexippus) has been in a long-term decline since the mid-20th century, following a similar decline in milkweed (Asclepias spp.) herbarium records. I demonstrate that this reported abundance trend is biased by the choice to standardize Monarch records as a proportion of all Lepidoptera collected. The sampling of Lepidoptera has changed systematically over time to favor moths, causing the apparent trend in Monarch records. With the data standardized more appropriately, I show that the trend in Monarch records shows no mid-century decline and increases over recent decades. As the trend in Monarch museum specimens contradicts the recent trend in Monarch abundance documented from systematic population monitoring, I argue that these records are unreliable for abundance estimates. The conclusion in Boyle et al. (2019b) that Monarch declines started in the mid-20th century is unwarranted both because the trend is biased by sampling changes in museum records and because the trend in Monarch records, when corrected, does not correspond with real-world population abundance.
The laminar profile of sleep spindles in humans
Authors: Ujma Péter P. , Hajnal Boglárka , Bódizs Róbert , Gombos Ferenc , Erőss Loránd , Wittner Lucia , Halgren Eric , Cash Sydney , Ulbert István , Fabó Dániel 
Published: March 2019

AbstractSleep spindles are generated in thalamocortical, corticothalamic and possibly cortico-cortical circuits. Previous hypotheses suggested that slow and fast spindles or spindles with various spatial extent may be generated in different circuits with various cortical laminar innervation patterns. We used NREM sleep EEG data recorded from four human epileptic patients undergoing presurgical electrophysiological monitoring with subdural electrocorticographic grids (ECoG) and implanted laminar microelectrodes penetrating the cortex (IME). The position of IME electrodes within cortical layers was confirmed using postsurgical histological reconstructions. Many micro-domain spindles detected on the IME occurred only in one layer and were absent from the ECoG, but with increasing amplitude simultaneous detection in other layers and on the ECoG became more likely. Macro-domain spindles sufficiently large to be detected on the ECoG were in contrast usually accompanied by IME spindles. Neither micro-domain nor macro-domain spindle cortical profiles were strongly associated with sleep spindle frequency or globality. Multiple-unit and single-unit activity during spindles, however, was heterogeneous across spindle types, but also across layers and subjects. Our results indicate that extremely local spindles may occur in any cortical layer, but co-occurrence at other locations becomes likelier with increasing amplitude and the relatively large spindles detected on ECoG channels have a stereotypical laminar profile. We found no compelling evidence that different spindle types are associated with different laminar profiles, suggesting that they are generated in cortical and thalamic circuits with similar cortical innervation patterns. Local neuronal activity is a stronger candidate mechanism for driving functional differences between spindles subtypes.
Dietary restriction induces post-transcriptional regulation of longevity genes
Authors: Rollins Jarod A. , Snow Santina S. , Kapahi Pankaj , Rogers Aric N. 
Published: March 2019

AbstractDietary restriction increases lifespan through adaptive changes in gene expression. To understand more about these changes, we analyzed the transcriptome and translatome ofC. eleganssubjected to dietary restriction. Transcription of muscle regulatory and structural genes increased, while increased expression of amino acid metabolism and neuropeptide signaling genes was controlled at the level of translation. Evaluation of post-transcriptional regulation identified putative roles for RNA binding proteins, RNA editing, microRNA, alternative splicing, and nonsense mediated decay in response to nutrient limitation. Using RNA interference, we discovered several differentially expressed genes that regulate lifespan. We also found a compensatory role for translational regulation, which offsets dampened expression of a large subset of transcriptionally downregulated genes. Furthermore, 3’ UTR editing and intron retention increase under dietary restriction and correlate with diminished translation, while trans-spliced genes are refractory to reduced translation efficiency compared to messages with the native 5’ UTR. Finally, we find thatsmg-6andsmg-7, which are genes governing selection and turnover of nonsense mediated decay targets, are required for increased lifespan under dietary restriction.
Identification of RBPMS as a smooth muscle master splicing regulator via proximity of its gene with super-enhancers
Authors: Nakagaki-Silva Erick E. , Gooding Clare , Llorian Miriam , Jacob Aishwarya Griselda , Richards Frederick , Buckroyd Adrian , Sinha Sanjay , Smith Christopher W.J. 
Published: March 2019

AbstractAlternative splicing (AS) programs are primarily controlled by regulatory RNA binding proteins (RBPs). It has been proposed that a small number of master splicing regulators might control cell-specific splicing networks and that these RBPs could be identified by proximity of their genes to transcriptional super-enhancers. Using this approach we identified RBPMS as a critical splicing regulator in differentiated vascular smooth muscle cells (SMCs). RBPMS is highly down-regulated during phenotypic switching of SMCs from a contractile to a motile and proliferative phenotype and is responsible for 20% of the AS changes during this transition. RBPMS directly regulates AS of numerous components of the actin cytoskeleton and focal adhesion machineries whose activity is critical for SMC function in both phenotypes. RBPMS also regulates splicing of other splicing, post-transcriptional and transcription regulators including the key SMC transcription factor Myocardin, thereby matching many of the criteria of a master regulator of AS in SMCs.
Noninvasive prenatal diagnosis for Hemophilia A by haplotype-based approach using cell-free fetal DNA in maternal plasma
Authors: He Zhihui , Chen Chao , Guo Fengyu , Jiang Lu , Zhu Yaping , Li Dan , Wu Renhua , Lu Rong , Zhao Mei , Chen Fang , Ni Peixiang , Sun Jun , Peng Zhiyu 
Published: March 2019

AbstractObjectivesThis study was used to demonstrate the feasibility of haplotype-based noninvasive prenatal diagnosis for Hemophilia A.MethodsTwo families affected by Hemophilia A participated in our study. Maternal haplotypes associated with pathogenic mutation was built using targeted region genotypes of mother and the proband. Combined with maternal pathogenic haplotype, a Hidden Markov Model was constructed to deduce fetal haplotype using high-coverage targeted sequencing of maternal plasma. The presence of pathogenic haplotype in male indicated affected fetus, in female indicated carrier. Prenatal diagnosis was confirmed with amniocentesis by long distance PCR.ResultsThe haplotype-based noninvasive prenatal diagnosis was successfully performed in Hemophilia A. One fetus was identified to be normal, another fetus was identified as carrier, and the results were confirmed by amniocentesis .ConclusionOur research demonstrated the feasibility of noninvasive prenatal diagnosis for Hemophilia A by haplotype-based approach.