bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative visualization of alternative exon expression from RNA-seq data
Authors: Katz Yarden , Wang Eric T. , Silterra Jacob , Schwartz Schraga , Wong Bang , Thorvaldsdóttir Helga , Robinson James T. , Mesirov Jill P. , Airoldi Edoardo M. , Burge Christopher B. 
Published: January 2015

Abstract
Motivation: Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples.
Results: To help address this problem, we present Sashimi plots, a quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer or with a stand-alone command line program.
Availability and implementation: Software code and documentation freely available here: http://miso.readthedocs.org/en/fastmiso/sashimi.html
Contact: mesirov@broadinstitute.org, airoldi@fas.harvard.edu or cburge@mit.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Whartonia (Fascutonia) natsumei (Acari: Trombiculidae): A New Bat Chigger Collected from Plecotus auritus (Chiroptera: Vespertilionidae) in Japan, with Host and Distribution Records of the Genus Whartonia
Authors: Takahashi Mamoru , Takahashi Hisae , Kikuchi Hirosato 
Published: January 2015

Abstract
We describe and illustrate a new bat chigger, Whartonia (Fascutonia) natsumei Takahashi, Takahashi & Kikuchi n. sp., ex. Plecotus auritus (Linnaeus, 1758), from Japan, and summarize the host and distribution records of the chiggers of the genus Whartonia . With the description of a new species here, the number of Whartonia species increases to 40 composed of 22 species from Asia, 14 from North and South America in addition to Central America, and four from Africa.
Effects of Larval Competitors and Predators on Oviposition Site Selection of Anopheles gambiae Sensu Stricto
Authors: Munga Stephen , Minakawa Noboru , Zhou Guofa , Barrack Okeyo-Owuor J. , Githeko Andrew K. , Yan Guiyun 
Published: January 2015

Abstract
We examined whether predators and competitors influence selection of oviposition sites by Anopheles gambiae Giles. Mosquitoes in cages laid significantly fewer eggs in rainwater conditioned with a predator (backswimmers, Notonecta sp.) than in unconditioned rainwater. Rainwater conditioned with a putative competitor (tadpoles, Xenopus sp.) also had fewer eggs than unconditioned rainwater. Similarly, mosquitoes laid significantly fewer eggs in rainwater conditioned with five and 50 An. gambiae larvae than in unconditioned rainwater. When larvae were present, significantly more eggs were laid in containers with five larvae than in containers with higher densities, but the differences in number of eggs laid were not significant among the densities of 40, 70, and 100 larvae. This study demonstrated that caged An. gambiae females avoid oviposition in habitats with supposed competitors and predators.
Occurrence of Serotonin Immunoreactivity in the Central Nervous System and Midgut of Adult Female Tabanus nigrovittatus (Diptera: Tabanidae)
Authors: Haselton Aaron T. , Yin Chih-Ming , Stoffolano John G. 
Published: January 2015

Abstract
Serotonin is an important neuromessenger used in a variety of signaling pathways throughout the animal kingdom. In insects, serotonin has been demonstrated to mediate feeding and feeding-related behaviors. In this study, serotonin antibody was localized in cells and processes throughout the central nervous system (CNS) and midgut of female horse fly Tabanus nigrovittatus Macquart. In the CNS, immunoreactivity was localized in cells and processes throughout the brain and ventral nerve cord. In the midgut, a fine network of immunoreactive processes was observed running along the outer surface of the midgut, with a decrease in innervation toward the posterior region of the midgut.
Evidence That Scabies Mites (Acari: Sarcoptidae) Influence Production of Interleukin-10 and the Function of T-Regulatory Cells (Tr1) in Humans
Authors: Arlian Larry G. , Morgan Marjorie S. , Paul Cassandra C. 
Published: January 2015

Abstract
We performed experiments to determine whether an extract of Sarcoptes scabiei (De Geer) influenced cytokine expression by human T-lymphocytes. Peripheral blood mononuclear cells from five sensitized donors and four donors without sensitization to scabies mites were challenged with a T-cell mitogen alone, with scabies extract (SS) alone, or with mitogen and SS together. Supernatants were analyzed for the cytokines interferon-γ (IFNγ), interleukin (IL)-2, IL-4, and IL-10. No IL-2 or IL-4 was produced in response to scabies extract. Cells from both naïve and sensitized donors produced large amounts of IFNγ and IL-10. The lack of IL-4 but high levels of IL-10 suggests that IL-10 was likely secreted by type 1 T-regulatory cells, which were activated by something in the scabies extract. IL-10 has anti-inflammatory and immune-suppressive effects. It may play a key role in depressing the inflammatory and immune responses in humans so that clinical symptoms are not seen until 4–6 wk after a person becomes infested with scabies mites.
Laboratory Transmission of Japanese Encephalitis and West Nile Viruses by Molestus Form of Culex pipiens (Diptera: Culicidae) Collected in Uzbekistan in 2004
Authors: Turell M. J. , Mores C. N. , Dohm D. J. , Komilov N. , Paragas J. , Lee J. S. , Shermuhemedova D. , Endy T. P. , Kodirov A. , Khodjaev S. 
Published: January 2015

Abstract
We evaluated the molestus form of Culex pipiens pipiens (L.) (hereafter referred to as "molestus") captured near Tashkent, Uzbekistan, for their ability to transmit Japanese encephalitis (family Flaviviridae, genus Flavivirus, JEV) and West Nile (family Flaviviridae, genus Flavivirus, WNV) viruses under laboratory conditions. These molestus were highly competent laboratory vectors of WNV, with infection and dissemination rates of 96 and 81%, respectively. Approximately 75% of female molestus that fed after development of a disseminated infection transmitted virus by bite. Therefore, ≈60% of those molestus taking a second bloodmeal between 16 and 25 d after an infectious bloodmeal would be expected to transmit WNV by bite. In contrast, these molestus were less efficient vectors of JEV, with infection and dissemination rates of 51 and 25%, respectively. In addition, only 33% of individuals with a disseminated infection transmitted JEV by bite, indicating a significant salivary gland barrier. Therefore, only ≈8% of orally exposed individuals would be expected to transmit JEV by bite if they took a second bloodmeal 16–25 d later. These data indicate that the molestus form of Cx. p. pipiens should be considered a potentially important vector of WNV in Uzbekistan and may become involved in the transmission of JEV, should this virus be introduced into Uzbekistan.
Characterizing Population Dynamics of Aedes sollicitans (Diptera: Culicidae) Using Meteorological Data
Authors: Shone Scott M. , Curriero Frank C. , Lesser Cyrus R. , Glass Gregory E. 
Published: January 2015

Abstract
Numerous studies have investigated the role of weather on insect species. For mosquitoes, these studies have yielded mixed results. Although it is clear that weather impacts mosquito population dynamics, these investigations have failed to accurately characterize their fluctuations. We use a novel graphical method to examine large numbers of meteorological aggregations of varying lengths and lags simultaneously to establish relationships between these summary variables and mosquito counts, to gain a better understanding of the weather effects. Poisson regression models were developed to characterize the population dynamics of Aedes sollicitans (Walker) by using meteorological data and a 34-yr set of daily mosquito count data. The models accurately characterize mosquito dynamics over time and space. The aggregated meteorological variables included in the model were lowest minimum tides between days 27 and 14 before trapping, total precipitation between days 22 and 9, total precipitation on day 1 and the day of trapping, cooling degree-days on day 0, average minimum relative humidity between days 28 and 9, lowest stream flow from day 11 to day 0, and lowest minimum temperature between days 28 and 13.
Investigation of Ground Level and Remote-Sensed Data for Habitat Classification and Prediction of Survival of Ixodes scapularis in Habitats of Southeastern Canada
Authors: Ogden N. H. , Barker I. K. , Beauchamp G. , Brazeau S. , Charron D. F. , Maarouf A. , Morshed M. G. , O’Callaghan C. J. , Thompson R. A. , Waltner-Toews D. , Waltner-Toews M. , Lindsay L. R. 
Published: January 2015

Abstract
In southeastern Canada, most populations of Ixodes scapularis Say, the Lyme disease vector, occur in Carolinian forests. Climate change projections suggest a northward range expansion of I. scapularis this century, but it is unclear whether more northerly habitats are suitable for I. scapularis survival. In this study, we assessed the suitability of woodlands of the Lower Great Lakes/St. Lawrence Plain region for I. scapularis by comparing tick egg survival in four different woodlands. Woodlands where I. scapularis are established, and sand dune where I. scapularis do not survive, served as positive and negative control sites, respectively. At two woodland sites, egg survival was the same as at the positive control site, but at two of the sites survival was significantly less than either the positive control site, or one of the other test sites. Egg survival in all woodland sites was significantly higher than in the sand dune site. Ground level habitat classification discriminated among woodlands in which tick survival differed. The likelihood that I. scapularis populations could persist in the different habitats, as deduced using a population model of I. scapularis, was significantly associated with variations in Landsat 7 ETM+ data (normalized difference vegetation index [NDVI] and Tasselled Cap indices). The NDVI index predicted habitat suitability at Long Point, Ontario, with high sensitivity but moderate specificity. Our study suggests that I. scapularis populations could establish in more northerly woodland types than those in which they currently exist. Suitable habitats may be detected by ground-level habitat classification, and remote-sensed data may assist this process.
Effects of Prior Infestation on Host Choice of Bat Flies (Diptera: Streblidae)
Authors: Dick Carl W. , Dick Sonya C. 
Published: January 2015

Abstract
Experimental approaches provide insight into the dynamics of species competition and coexistence, but studies of ectoparasitic arthropods are rare. Host choice experiments were undertaken in Amazonian Peru, by using obligate bat fly parasites of Seba’s short-tailed bat, Carollia perspicillata (L.). The fly species Trichobius joblingi Wenzel strongly preferred clean hosts to those previously infested with individuals of T. joblingi. Abundance thresholds may limit conspecific parasites on host individuals, and similar morphologies and habitat use may increase intraspecific competition among individuals of T. joblingi. T. joblingi did not distinguish between clean hosts and those previously infested with flies of another species, Speiseria ambigua Kessel. Results suggest that the presence of a morphologically dissimilar species does not preclude subsequent colonization. Differential microhabitat selection, aided by adaptive morphology, may facilitate species coexistence among ectoparasitic bat fly species.
Detection of Anaplasma phagocytophilum and Babesia odocoilei DNA in Ixodes scapularis (Acari: Ixodidae) Collected in Indiana
Authors: Steiner Fresia E. , Pinger Robert R. , Vann Carolyn N. , Abley Melanie J. , Sullivan Bridget , Grindle Nate , Clay Keith , Fuqua Clay 
Published: January 2015

Abstract
The blacklegged tick, Ixodes scapularis Say, first reported in Indiana in 1987, has now been detected in more than half of Indiana’s counties. The first case of human granulocytic ehrlichiosis (human anaplasmosis) in Indiana was reported in 2002. We now report the detection of Anaplasma phagocytophilum and Babesia odocoilei in I. scapularis ticks collected in northern Indiana. Using polymerase chain reaction analysis, 41 of 193 adult ticks (21.2%) collected from deer were positive for A. phagocytophylum, and 22 (11.4%) were positive for Babesia sp. Restriction fragment analysis of 12, and sequencing of another five of the amplified products identified these parasites as B. odocoilei. Five ticks (2.6%) were coinfected. Eight of 68 questing adult ticks (11.8%) were positive for A. phagocytophilum; seven (10.3%) were positive for Babesia sp. Six of the latter seven positive samples were determined to be B. odocoilei by restriction fragment analysis and sequencing of two samples. None of 39 pools of nymphs was positive for Babesia sp. Three of 15 ticks (20%) collected from a dog were positive for A. phagocytophilum and three ticks (20%) were positive for Babesia sp. One was confirmed as B. odocoilei. One tick was coinfected. This is the first report of the presence of these two agents in ticks in Indiana.
Genomic Characterization Reveals Insights Into Patulin Biosynthesis and Pathogenicity in Penicillium Species
Authors: Li Boqiang , Zong Yuanyuan , Du Zhenglin , Chen Yong , Zhang Zhanquan , Qin Guozheng , Zhao Wenming , Tian Shiping 
Published: January 2015

Penicillium species are fungal pathogens that infect crop plants worldwide. P. expansum differs from P. italicum and P. digitatum, all major postharvest pathogens of pome and citrus, in that the former is able to produce the mycotoxin patulin and has a broader host range. The molecular basis of host-specificity of fungal pathogens has now become the focus of recent research. The present report provides the whole genome sequence of P. expansum (33.52 Mb) and P. italicum (28.99 Mb) and identifies differences in genome structure, important pathogenic characters, and secondary metabolite (SM) gene clusters in Penicillium species. We identified a total of 55 gene clusters potentially related to secondary metabolism, including a cluster of 15 genes (named PePatA to PePatO), that may be involved in patulin biosynthesis in P. expansum. Functional studies confirmed that PePatL and PePatK play crucial roles in the biosynthesis of patulin and that patulin production is not related to virulence of P. expansum. Collectively, P. expansum contains more pathogenic genes and SM gene clusters, in particular, an intact patulin cluster, than P. italicum or P. digitatum. These findings provide important information relevant to understanding the molecular network of patulin biosynthesis and mechanisms of host-specificity in Penicillium species. Ballester et al. ( MPMI-09-14-0261-FI ) reported similar results and conclusions in MPMI's March 2015 Focus Issue.
Using Cardiac Magnetic Resonance Imaging to Evaluate Cardiac Function and Predict Outcomes in Patients with Valvular Heart Disease
Authors: Emerson Dominic A. , Amdur Richard L. , Morrissette Jason R. , Mordini Federico E. , Nagy Christian D. , Greenberg Michael D. , Trachiotis Gregory D. 
Published: January 2015

Objective In valvular heart disease, elevated left atrial and pulmonary pressures contribute to right ventricular strain and, ultimately, right ventricle failure. Elevated pulmonary artery (PAP) and left ventricular end diastolic pressures are used as markers of right ventricle dysfunction and correlate with poor outcomes. Using cardiac magnetic resonance imaging (CMR), it is possible to directly quantify both left and right ventricular ejection function (LVEF and RVEF), and here, we compare CMR with traditional markers as outcome predictors. Methods A retrospective review of prospectively collected data was performed for patients from January 2004 to February 2008 at a single center (n = 103). Patients were divided into those receiving CMR (n = 56) and those receiving only catheterization (n = 47). Univariate and multivariate logistic regression models were applied to determine predictors of mortality. Finally, predictive models for mortality using PAP, mean PAP, and left ventricular end diastolic pressure were compared to models using LVEF and RVEF obtained from CMR. Results Preoperative average CMR LVEF and RVEF were 57% and 46%, respectively. Only age emerged as an isolated predictor of mortality ( P = 0.01) within the univariate models. Stepwise regression models were created using the catheterization or CMR data. When compared, the CMR model has a slightly better R2, c (prediction accuracy), and sensitivity/specificity (0.22 vs 0.28, 0.77 vs 0.82, and 0.63/0.62 vs 0.69/0.64, respectively). Conclusions Within our population, LVEF and RVEF predict mortality as least as well as traditional catheterization values. Additionally, CMR may identify of elevated PAPs caused by right ventricle dysfunction and those due to other causes, allowing these other causes to be addressed preoperatively.
A Geometric Model of the Normal Human Aortic Root and Design of a Fully Anatomic Aortic Root Graft
Authors: Crooke Philip S. , Beavan L. Alan , Griffin Charles D. , Mazzitelli Domenico , Rankin J. Scott 
Published: January 2015

Objective Available aortic root grafts generally flare outward in the sinus region, and this feature improves procedural ease. However, no current device is based on normal aortic root geometry, and a fully anatomic aortic root graft could further facilitate valve-sparing root operations. Methods To develop a model of the normal human aortic root, high-resolution computed tomographic angiogram images from 11 normal human aortas generated high-density x, y, z coordinates of valve and root structures in Mathematica. Three-dimensional least-squares regression analyses assessed geometry of the aortic valve and root. Shapes and dimensions were quantified, and minor variations in geometry were simplified during graft design. Results Normal aortic valve and root geometry was represented as three leaflet-sinus general ellipsoids nested within a cylindrical aorta. Sinotubular junction diameter was 5 mm larger than the valve base—with a slight funnel-shaped outward commissural flare but cylindrical geometry above the midvalve. The valve base was elliptical, but the midvalve and the sinotubular junction were circular above the midvalve level. Commissural locations on the base circumference were equidistant. On the basis of average three-dimensional geometry, a root graft was designed for root remodeling procedures—to be used with an internal geometric annuloplasty ring of the same design. Conclusions An aortic root graft was designed on the basis of mathematical analyses of computed tomographic angiogram images. The design incorporated three anatomic sinuses, commissural symmetry, and compatibility with geometric ring annuloplasty. The anatomic graft may prove useful for restoring aortic root geometry toward normal during aortic valve and root surgery.
Fatal Cardiac Arrest in 2 Children
Authors: Brenner Scott M. , Boucher Jenny 
Published: January 2015

Introduction
Ondansetron is commonly used to treat vomiting in gastroenteritis, but has a United States Food and Drug Administration black box warning for risk of Q wave to T wave time interval (QT) prolongation. We report 2 pediatric cases of fatal refractory cardiac arrest after administration of ondansetron.

Cases
A 10-year-old previously healthy boy presented to the emergency room with gastroenteritis symptoms. After intravenous fluids, morphine, antibiotics, and 2 doses of ondansetron, the patient became unresponsive with agonal respirations and a wide complex tachycardia consistent with ventricular tachycardia. In a second case, an 86-day-old infant with previously unidentified congenital cardiomyopathy presented to our emergency department with gastroenteritis symptoms. The patient received ondansetron and subsequently experienced repeated bouts of supraventricular tachycardia which progressed to ventricular fibrillation. Resuscitation efforts failed in each case, and both patients expired.

Discussion
Ondansetron can cause dose-dependent QT prolongation effects, which are more clinically relevant when other proarrhythmic elements are present. There is very limited published experience on use of ondansetron in children younger than 2 years. Our 2 cases join 2 previous case reports of death after ondansetron administration for gastroenteritis. The pharmacology of ondansetron's cardiac effects and drug-induced QT prolongation is discussed.

Conclusions
Patients may have hidden risk factors that, together with ondansetron, could result in a proarrhythmic state that could lead to adverse effects, such as arrhythmias. Administration of ondansetron should be individualized and used cautiously in patients with risk factors for arrhythmia.
Live Imaging of Inorganic Phosphate in Plants with Cellular and Subcellular Resolution
Authors: Mukherjee Pallavi , Banerjee Swayoma , Wheeler Amanda , Ratliff Lyndsay A. , Irigoyen Sonia , Garcia L. Rene , Lockless Steve W. , Versaw Wayne K. 
Published: January 2015

Abstract
Despite variable and often scarce supplies of inorganic phosphate (Pi) from soils, plants must distribute appropriate amounts of Pi to each cell and subcellular compartment to sustain essential metabolic activities. The ability to monitor Pi dynamics with subcellular resolution in live plants is, therefore, critical for understanding how this essential nutrient is acquired, mobilized, recycled, and stored. Fluorescence indicator protein for inorganic phosphate (FLIPPi) sensors are genetically encoded fluorescence resonance energy transfer-based sensors that have been used to monitor Pi dynamics in cultured animal cells. Here, we present a series of Pi sensors optimized for use in plants. Substitution of the enhanced yellow fluorescent protein component of a FLIPPi sensor with a circularly permuted version of Venus enhanced sensor dynamic range nearly 2.5-fold. The resulting circularly permuted FLIPPi sensor was subjected to a high-efficiency mutagenesis strategy that relied on statistical coupling analysis to identify regions of the protein likely to influence Pi affinity. A series of affinity mutants was selected with dissociation constant values of 0.08 to 11 mm, which span the range for most plant cell compartments. The sensors were expressed in Arabidopsis (Arabidopsis thaliana), and ratiometric imaging was used to monitor cytosolic Pi dynamics in root cells in response to Pi deprivation and resupply. Moreover, plastid-targeted versions of the sensors expressed in the wild type and a mutant lacking the PHOSPHATE TRANSPORT4;2 plastidic Pi transporter confirmed a physiological role for this transporter in Pi export from root plastids. These circularly permuted FLIPPi sensors, therefore, enable detailed analysis of Pi dynamics with subcellular resolution in live plants.