bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dapagliflozin Attenuates Cardiac Remodeling in Mice Model of Cardiac Pressure Overload
Authors: Shi Lin , Zhu Diqi , Wang Shoubao , Jiang Aixia , Li Fen 
Published: January 2019

Abstract

BACKGROUND
Dapagliflozin (DAPA) is an inhibitor of sodium-glucose cotransporter 2 prescribed for type 2 diabetes mellitus. DAPA plays a protective role against cardiovascular diseases. Nevertheless, the effect and mechanism of DAPA on pressure-overload-induced cardiac remodeling has not been determined.

METHODS
We used a transverse aortic constriction (TAC) induced cardiac remodeling model to evaluate the effect of DAPA. Twenty-four C57BL/6J mice were divided into 3 groups: Sham, TAC, and TAC + DAPA groups (n = 8, each). DAPA was administered by gavage (1.0 mg/kg/day) for 4 weeks in the TAC + DAPA group, and then the myocardial hypertrophy, cardiac systolic function, myocardial fibrosis, and cardiomyocyte apoptosis were evaluated.

RESULTS
Mice in TAC group showed increased heart weight/body weight, left ventricular (LV) diameter, LV posterior wall thickness, and decreased LV ejection fraction and LV fractional shortening. The collagen volume fraction and perivascular collagen area/luminal area ratio were significantly greater in the TAC group; the TUNEL-positive cell number and PARP level were also increased. We found that DAPA treatment reduced myocardial hypertrophy, myocardial interstitial and perivascular fibrosis, and cardiomyocyte apoptosis. Furthermore, DAPA administration inhibited phosphorylation of P38 and JNK in TAC group. In addition, the inhibited phosphorylation of FoxO1 in the TAC mice was upregulated by DAPA administration.

CONCLUSION
DAPA administration had a cardioprotective effect by improving cardiac systolic function, inhibiting myocardial fibrosis and cardiomyocyte apoptosis in a TAC mouse model, indicating that it could serve as a new therapy to prevent pathological cardiac remodeling in nondiabetics.
A comparison of deterministic and stochastic approaches for sensitivity analysis in computational systems biology
Authors: Simoni Giulia , Vo Hong Thanh , Priami Corrado , Marchetti Luca 
Published: January 2019

AbstractWith the recent rising application of mathematical models in the field of computational systems biology, the interest in sensitivity analysis methods had increased. The stochastic approach, based on chemical master equations, and the deterministic approach, based on ordinary differential equations (ODEs), are the two main approaches for analyzing mathematical models of biochemical systems. In this work, the performance of these approaches to compute sensitivity coefficients is explored in situations where stochastic and deterministic simulation can potentially provide different results (systems with unstable steady states, oscillators with population extinction and bistable systems). We consider two methods in the deterministic approach, namely the direct differential method and the finite difference method, and five methods in the stochastic approach, namely the Girsanov transformation, the independent random number method, the common random number method, the coupled finite difference method and the rejection-based finite difference method. The reviewed methods are compared in terms of sensitivity values and computational time to identify differences in outcome that can highlight conditions in which one approach performs better than the other.
CMEP: a database for circulating microRNA expression profiling
Authors: Li Jian-Rong , Tong Chun-Yip , Sung Tsai-Jung , Kang Ting-Yu , Zhou Xianghong Jasmine , Liu Chun-Chi 
Published: January 2019

AbstractMotivationIn recent years, several experimental studies have revealed that the microRNAs (miRNAs) in serum, plasma, exosome and whole blood are dysregulated in various types of diseases, indicating that the circulating miRNAs may serve as potential noninvasive biomarkers for disease diagnosis and prognosis. However, no database has been constructed to integrate the large-scale circulating miRNA profiles, explore the functional pathways involved and predict the potential biomarkers using feature selection between the disease conditions. Although there have been several studies attempting to generate a circulating miRNA database, they have not yet integrated the large-scale circulating miRNA profiles or provided the biomarker-selection function using machine learning methods.ResultsTo fill this gap, we constructed the Circulating MicroRNA Expression Profiling (CMEP) database for integrating, analyzing and visualizing the large-scale expression profiles of phenotype-specific circulating miRNAs. The CMEP database contains massive datasets that were manually curated from NCBI GEO and the exRNA Atlas, including 66 datasets, 228 subsets and 10 419 samples. The CMEP provides the differential expression circulating miRNAs analysis and the KEGG functional pathway enrichment analysis. Furthermore, to provide the function of noninvasive biomarker discovery, we implemented several feature-selection methods, including ridge regression, lasso regression, support vector machine and random forests. Finally, we implemented a user-friendly web interface to improve the user experience and to visualize the data and results of CMEP.Availability and implementationCMEP is accessible at http://syslab5.nchu.edu.tw/CMEP.
Medical Assistance in Death as a Unique Opportunity to Advance Human Immunodeficiency Virus Cure Research
Authors: Sandstrom Teslin S , Burke Schinkel Stephanie C , Angel Jonathan B 
Published: January 2019

AbstractThe inability to sample deep-tissue reservoirs in individuals living with human immunodeficiency virus (HIV) has greatly hindered accurate estimates of viral reservoir size and distribution. Animal models and collection of tissues during autopsies of HIV-positive individuals are 2 proposed solutions to this problem. Each, however, has its limitations. In this Viewpoint, we argue that tissue donation following medical assistance in death (MAiD) will form an invaluable resource for the characterization of the viral reservoir in the context of current HIV cure research. In support, we discuss a recent instance in which an individual living with HIV chose to donate their body/tissues to HIV research prior to undergoing MAiD at our institution. Going forward, we hope this will help provide support to individuals in their decisions around tissue donation following MAiD, while highlighting how healthcare providers, by complying with such wishes, can affect patient satisfaction in the last days of life.
Nearly complete deletion of BubR1 causes microcephaly through shortened mitosis and massive cell death
Authors: Simmons Ambrosia J , Park Raehee , Sterling Noelle A , Jang Mi-Hyeon , van Deursen Jan M A , Yen Timothy J , Cho Seo-Hee , Kim Seonhee 
Published: January 2019

Abstract
BUB-related 1 (BubR1) encoded by Budding Uninhibited by Benzimidazole 1B (BUB1B) is a crucial mitotic checkpoint protein ensuring proper segregation of chromosomes during mitosis. Mutations of BUB1B are responsible for mosaic variegated aneuploidy (MVA), a human congenital disorder characterized by extensive abnormalities in chromosome number. Although microcephaly is a prominent feature of MVA carrying the BUB1B mutation, how BubR1 deficiency disturbs neural progenitor proliferation and neuronal output and leads to microcephaly is unknown. Here we show that conditional loss of BubR1 in mouse cerebral cortex recapitulates microcephaly. BubR1-deficient cortex includes a strikingly reduced number of late-born, but not of early-born, neurons, although BubR1 expression is substantially reduced from an early stage. Importantly, absence of BubR1 decreases the proportion of neural progenitors in mitosis, specifically in metaphase, suggesting shortened mitosis owing to premature chromosome segregation. In the BubR1 mutant, massive apoptotic cell death, which is likely due to the compromised genomic integrity that results from aberrant mitosis, depletes progenitors and neurons during neurogenesis. There is no apparent alteration in centrosome number, spindle formation or primary cilia, suggesting that the major effect of BubR1 deficiency on neural progenitors is to impair the mitotic checkpoint. This finding highlights the importance of the mitotic checkpoint in the pathogenesis of microcephaly. Furthermore, the ependymal cell layer does not form in the conditional knockout, revealing an unrecognized role of BubR1 in assuring the integrity of the ventricular system, which may account for the presence of hydrocephalus in some patients.
A case study in text mining: Textual analysis of the Territorial Papers
Authors: Ledolter Johannes , VanderVelde Lea 
Published: January 2019

Abstract
The Territorial Papers of the United States are a valuable and underused resource containing almost 10,000 documents written between 1789 and 1848 about the formation of new sovereign states from US territory. These communications between the federal government and frontier settlers comprise the actual discourse of the nation’s expansion over six decades. Digitizing the Territorial Papers permits the possibility of analyzing the entire corpus globally. Text mining and topic modeling methods give us a lens on the language patterns through which new state governments and the expanding nation were formed. An initial statistical analysis of the textual information provides a visualization of content, helps discern how ideals about governance emerged, and lays the foundation for developing more sophisticated hypotheses and theoretical constructs.
Evolution of the cold gas properties of simulated post-starburst galaxies
Authors: Davis Timothy A , van de Voort Freeke , Rowlands Kate , McAlpine Stuart , Wild Vivienne , Crain Robert A 
Published: January 2019

Abstract
Post-starburst galaxies are typically considered to be a transition population, en route to the red sequence after a recent quenching event. Despite this, recent observations have shown that these objects typically have large reservoirs of cold molecular gas. In this paper we study the star-forming gas properties of a large sample of post-starburst galaxies selected from the cosmological, hydrodynamical EAGLE simulations. These objects resemble observed high-mass post-starburst galaxies both spectroscopically and in terms of their space density, stellar mass distribution, and sizes. We find that the vast majority of simulated post-starburst galaxies have significant gas reservoirs, with star-forming gas masses ≈109 M⊙, in good agreement with those seen in observational samples. The simulation reproduces the observed time evolution of the gas fraction of the post-starburst galaxy population, with the average galaxy losing ≈90 per cent of its star-forming interstellar medium in only ≈600 Myr. A variety of gas consumption/loss processes are responsible for this rapid evolution, including mergers and environmental effects, while active galactic nuclei play only a secondary role. The fast evolution in the gas fraction of post-starburst galaxies is accompanied by a clear decrease in the efficiency of star formation due to a decrease in the dense gas fraction. We predict that forthcoming ALMA observations of the gas reservoirs of low-redshift post-starburst galaxies will show that the molecular gas is typically compact and has disturbed kinematics, reflecting the disruptive nature of many of the evolutionary pathways that build up the post-starburst galaxy population.
Three candidate globular clusters discovered in the Galactic bulge
Authors: Camargo D , Minniti D 
Published: January 2019

ABSTRACT
This work reports the discovery of three new globular clusters (GCs) towards the Galactic bulge – Camargo 1107, 1108, and 1109. The discovery was made using the WISE, 2MASS, VVV, and Gaia-DR2 photometry. The new findings are old (12.0−13.5 Gyr) and metal-poor GCs ([Fe/H] &lt; −1.5 dex) located in the bulge area close to the Milky Way (MW) mid-plane. Although the old ages and low metallicities suggest that the newly discovered GCs are likely associated with the inner halo, the possibility of these clusters being part of a primordial bulge GC subpopulation cannot be ruled out. Camargo 1107, for instance, presents a metallicity of [Fe/H] = −2.2 ± 0.4 dex and an age of 13.5 ± 2 Gyr, which may suggest that this cluster formed just after the big bang in the very early Universe. The discovery of GCs such as the new findings is crucial to built a coherent picture of the inner Galaxy. It is likely that at least a few more dozens of GCs are still to be discovered in the bulge.
Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Authors: Fedosov Alexander E , Malcolm Gavin , Terryn Yves , Gorson Juliette , Modica Maria Vittoria , Holford Mandë , Puillandre Nicolas 
Published: January 2019

ABSTRACTThe conoidean family Terebridae is an intriguing lineage of marine gastropods, which are of considerable interest due to their varied anatomy and complex venoms. Terebrids are abundant, easily recognizable and widely distributed in tropical and subtropical waters, but our findings have demonstrated that their systematics requires revision. Here we elaborate the classification of Terebridae based on a recently published molecular phylogeny of 154 species, plus characters of the shell and anterior alimentary system. The 407 living species of the family, including seven species described herein, are assigned to three subfamilies: Pellifroniinae new subfamily, Pervicaciinae and Terebrinae. The Pellifroniinae comprises five deep-water species in two genera, Pellifronia and Bathyterebra n. gen. Pellifroniinae possess a radula of duplex marginal teeth, well-developed proboscis and venom gland, and a very small rhynchodeal introvert. The Pervicaciinae includes c. 50 species in the predominantly Indo-Pacific genera Duplicaria and Partecosta. Pervicaciinae possess salivary glands, a radula of solid recurved marginal teeth and a weakly developed rhynchodeal introvert, but lack proboscis and venom gland. The remaining Terebridae species are classified into 15 genera in the subfamily Terebrinae (including four genera described herein); nine genera are defined on the basis of phylogenetic data and six solely on shell morphology. The Indo-Pacific genera Profunditerebra n. gen., Maculauger n. gen. and Myurellopsis n. gen. each include about a dozen species. The first is restricted to the deep waters of the Indo-West Pacific, while the latter two range widely in both geographic and bathymetric distribution. Neoterebra n. gen. encompasses about 65 species from a range of localities in the eastern Pacific, Caribbean, and Atlantic, and from varying depths. To characterize the highly diversified genera Terebra, Punctoterebra, Myurella and Duplicaria, each of which comprise several morphological clusters, we propose the use of DNA-based diagnoses. These diagnoses are combined with more informative descriptions to define most of the supraspecific taxa of Terebridae, to provide a comprehensive revision of the group.
Variability of Antibiotic Prescribing in a Large Healthcare Network Despite Adjusting for Patient-Mix: Reconsidering Targets for Improved Prescribing
Authors: Jung Sophia , Sexton Mary Elizabeth , Owens Sallie , Spell Nathan , Fridkin Scott 
Published: January 2019

Abstract

Background
In the outpatient setting, the majority of antibiotic prescriptions are for acute respiratory infections (ARIs), but most of these infections are viral and antibiotics are unnecessary. We analyzed provider-specific antibiotic prescribing in a group of outpatient clinics affiliated with an academic medical center to inform future interventions to minimize unnecessary antibiotic use.

Methods
We conducted a cross-sectional study of patients who presented with an ARI to any of 15 The Emory Clinic (TEC) primary care clinic sites between October 2015 and September 2017. We performed multivariable logistic regression analysis to examine the impact of patient, provider, and clinic characteristics on antibiotic prescribing. We also compared provider-specific prescribing rates within and between clinic sites.

Results
A total of 53.4% of the 9600 patient encounters with a diagnosis of ARI resulted in an antibiotic prescription. The odds of an encounter resulting in an antibiotic prescription were independently associated with patient characteristics of white race (adjusted odds ratio [aOR] = 1.59; 95% confidence interval [CI], 1.47–1.73), older age (aOR = 1.32, 95% CI = 1.20–1.46 for patients 51 to 64 years; aOR = 1.32, 95% CI = 1.20–1.46 for patients ≥65 years), and comorbid condition presence (aOR = 1.19; 95% CI, 1.09–1.30). Of the 109 providers, 13 (12%) had a rate significantly higher than predicted by modeling.

Conclusions
Antibiotic prescribing for ARIs within TEC outpatient settings is higher than expected based on prescribing guidelines, with substantial variation in prescribing rates by site and provider. These data lay the foundation for quality improvement interventions to reduce unnecessary antibiotic prescribing.
Evaluating equine feeding behavior utilizing GrowSafe Systems: a pilot study1
Authors: Dickson Emily C , Kayser William C , Latham Christine M , Leatherwood Jessica L , Daigle Courtney L , White Sarah H 
Published: January 2019

Abstract
Equine research and management is limited to single-housing systems if individual animal intake is to be precisely recorded. Even then, dry forage intake is difficult to quantify accurately due to stomping or mixing hay with fecal matter and bedding. In cattle management, GrowSafe Systems (GrowSafe) is a commonly used tool to closely monitor individual animal feeding data using radio frequency identification (RFID) tag technology. Animals are equipped with a unique RFID tag that is read by the feed bunks each time the animal lowers its head into the bunk to consume feed. The objectives of this pilot study were 1) to test the feasibility of use of the GrowSafe system with horses by measuring intake of dry hay and 2) to characterize feeding behaviors of horses in an individually housed (without competition) or group-housed (with competition) setting. To test the hypothesis that horses would consume more hay when individually (NOCOMP) compared to group-housed (COMP), 10 mature Quarter Horses (14 ± 1.5 yr) were placed in one of four pens containing GrowSafe feed bunks in a 4-wk crossover design consisting of two 2-wk treatment periods. Pen 1 contained five horses with access to two GrowSafe bunks (Period 1: n = 4 mares, n = 1 gelding; Period 2: n = 5 geldings); pens 2, 3, and 4 contained one horse each with access to one bunk. Horses were individually fed 0.25% body weight (BW; dry matter [DM] basis) of a commercial concentrate once per day and were allowed Coastal bermudagrass hay in the GrowSafe bunks ad libitum. Although five horses were used in the group-housed (COMP) pen to more closely mimic a true group environment, only data from horses that experienced both housing systems (n = 3 mares and n = 3 geldings) were used for statistical analyses. Hourly (P = 0.008) and daily (P = 0.003) durations of hay feeding were higher for NOCOMP compared to COMP horses, and total daily intake (g DM/kg BW) of NOCOMP horses tended to be greater (P = 0.09) than COMP horses. Conversely, eating rate (g DM/kg BW/min) was greater (P = 0.04) for COMP compared to NOCOMP mares but was unaffected by housing in geldings. The GrowSafe system may provide an opportunity for efficient and effective monitoring of individual horse feed intake and feeding behavior in group-housing situations in horses.
Environmental and epigenetic regulation ofRiderretrotransposons in tomato
Authors: Benoit Matthias , Drost Hajk-Georg , Catoni Marco , Gouil Quentin , Lopez-Gomollon Sara , Baulcombe David , Paszkowski Jerzy 
Published: January 2019

ABSTRACTTransposable elements in crop plants are the powerful drivers of phenotypic variation that has been selected during domestication and breeding programs. In tomato, transpositions of the LTR (long terminal repeat) retrotransposon familyRiderhave contributed to various phenotypes of agronomical interest, such as fruit shape and colour. However, the mechanisms regulatingRideractivity are largely unknown. We have developed a bioinformatics pipeline for the functional annotation of retrotransposons containing LTRs and defined all full-lengthRiderelements in the tomato genome. Subsequently, we showed that accumulation ofRidertranscripts and transposition intermediates in the form of extrachromosomal DNA is triggered by drought stress and relies on abscisic acid signalling. We provide evidence that residual activity ofRideris controlled by epigenetic mechanisms involving siRNAs and the RNA-dependent DNA methylation pathway. Finally, we demonstrate the broad distribution ofRider-likeelements in other plant species, including crops. Thus our work identifiesRideras an environment-responsive element and a potential source of genetic and epigenetic variation in plants.
Ethanol-induced conditioned place preference and aversion differentially alter plasticity in the bed nucleus of stria terminalis
Authors: Pati Dipanwita , Pina Melanie M. , Kash Thomas L. 
Published: January 2019

AbstractContextual cues associated with drugs of abuse, such as ethanol, can trigger craving and drug seeking behavior. Pavlovian procedures, such as place conditioning, have been widely used to study the rewarding/aversive properties of drugs and the association between environmental cues and drug seeking. Previous research has shown that ethanol as an unconditioned stimulus can induce a strong conditioned place preference (CPP) or aversion (CPA) in rodents. However, the neural mechanisms underlying ethanol induced reward and aversion have not been thoroughly investigated. The bed nucleus of the stria terminalis (BNST), an integral part of the extended amygdala, is engaged by both rewarding and aversive stimuli and plays a role in ethanol seeking behavior. Here, we used ex-vivo slice physiology to probe learning-induced synaptic plasticity in the BNST following ethanol-induced CPP and CPA. Male DBA/2J mice (2-3 months old) were conditioned using previously reported ethanol-induced CPP/CPA procedures. Ethanol-induced CPP was associated with increased neuronal excitability in the ventral BNST (vBNST). Conversely, ethanol-induced CPA resulted in a significant decrease in spontaneous glutamatergic transmission without alterations in GABAergic signaling. Ethanol-CPA also led to significant increase in paired pulse ratio at excitatory synapses, suggestive of a decrease in presynaptic glutamate release. Collectively, these data demonstrate that the vBNST is involved in the modulation of contextual learning associated with both the rewarding and the aversive properties of ethanol in mice.
Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP)
Authors: Tandon Kshitij , Chiang Pei-Wen , Lu Chih-Ying , Wada Naohisa , Yang Shan-Hua , Chan Ya-Fan , Chen Ping-Yun , Chang Hsiao-Yu , Chou Ming-Shean , Chen Wen-Ming , Tang Sen-Lin 
Published: January 2019

AbstractDominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral-sulfur cycle by metabolizing Dimethylsulfoniopropionate (DMSP) into Dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) genomes of strains of a recently added species Endozoicomonas acroporae (Acr-14T, Acr-1 and Acr-5) isolated from the coral Acropora muricata and performed comparative genomic analysis on genus Endozoicomonas. We identified the first DMSP CoA-transferase/lyase—a dddD gene homolog found in all E. acroporae strains—and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as the sole carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.