bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes
Authors: Beisser Daniela , Graupner Nadine , Bock Christina , Wodniok Sabina , Grossmann Lars , Vos Matthijs , Sures Bernd , Rahmann Sven , Boenigk Jens 
Published: January 2017

BackgroundChrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes.ResultsWe sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae.ConclusionsOur study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.
Henricia djakonovisp. nov. (Echinodermata, Echinasteridae): a new sea star species from the Sea of Japan
Authors: Chichvarkhin Anton 
Published: January 2017

A new sea star species,H. djakonovisp.n., was discovered in Rudnaya Bay in the Sea of Japan. This is a sympatric species of the well-known and common speciesHenricia pseudoleviusculaDjakonov, 1958. Both species are similar in body size and proportions, shape of skeletal plates, and life coloration, which distinguishes them from the otherHenriciaspecies inhabiting the Sea of Japan. Nevertheless, these species can be distinguished by their abactinal spines: in both species, they are short and barrel-like, but the new species is the onlyHenriciaspecies in Russian waters of the Pacific that possesses such spines with a massive, smooth, bullet-like tip. The spines inH. pseudoleviusculaare crowned with a variable number of well-developed thorns. About half (<50%) of the abactinal pseudopaxillae in the new species are oval, not crescent-shaped as inH. pseudoleviuscula.
The fishing and natural mortality of large, piscivorous Bull Trout and Rainbow Trout in Kootenay Lake, British Columbia (2008–2013)
Authors: Thorley Joseph L. , Andrusak Greg F. 
Published: January 2017

BackgroundEstimates of fishing and natural mortality are important for understanding, and ultimately managing, commercial and recreational fisheries. High reward tags with fixed station acoustic telemetry provides a promising approach to monitoring mortality rates in large lake recreational fisheries. Kootenay Lake is a large lake which supports an important recreational fishery for large Bull Trout and Rainbow Trout.MethodsBetween 2008 and 2013, 88 large (≥500 mm) Bull Trout and 149 large (≥500 mm) Rainbow Trout were marked with an acoustic transmitter and/or high reward ($100) anchor tags in Kootenay Lake. The subsequent detections and angler recaptures were analysed using a Bayesian individual state-space Cormack–Jolly–Seber (CJS) survival model with indicator variable selection.ResultsThe final CJS survival model estimated that the annual interval probability of being recaptured by an angler was 0.17 (95% CRI [0.11–0.23]) for Bull Trout and 0.14 (95% CRI [0.09–0.19]) for Rainbow Trout. The annual interval survival probability for Bull Trout was estimated to have declined from 0.91 (95% CRI [0.76–0.97]) in 2009 to just 0.46 (95% CRI [0.24–0.76]) in 2013. Rainbow Trout survival was most strongly affected by spawning. The annual interval survival probability was 0.77 (95% CRI [0.68–0.85]) for a non-spawning Rainbow Trout compared to 0.41 (95% CRI [0.30–0.53]) for a spawner. The probability of spawning increased with the fork length for both species and decreased over the course of the study for Rainbow Trout.DiscussionFishing mortality was relatively low and constant while natural mortality was relatively high and variable. The results indicate that angler effort is not the primary driver of short-term population fluctations in the Rainbow Trout abundance. Variation in the probability of Rainbow Trout spawning suggests that the spring escapement at the outflow of Trout Lake may be a less reliable index of abundance than previously assumed. Multi-species stock assessment models need to account for the fact that large Bull Trout are more abundant than large Rainbow Trout in Kootenay Lake.
Are maternal and sonographic factors associated with the detection of a fetal echogenic cardiac focus?
Authors: Ehrenberg H M , Fischer R L , Hediger M L , Hansen C , Stine D 
Published: January 2017

To evaluate the influence of maternal weight and the orientation of the fetal 4‐chamber heart view on the detection of a fetal echogenic cardiac focus.In this nested case‐control study, 103 women undergoing anatomic surveys at 15 to 22 weeks between January 1, 1997, and June 15, 1999, were identified as having an echogenic cardiac focus via our computerized database. A control group was selected from among the same group of patients. Data were collected from the sonography reports, prenatal records, and sonographic images of 4‐chamber heart views; maternal characteristics and sonographic details were recorded, including the orientation of the 4‐chamber view (apical, basilar, and right and left lateral).Gravidas in the echogenic cardiac focus group were more likely to be of lower weight (68.0 +/‐ 14.4 versus 72.9 +/‐ 18.3 kg; P = .04), of lower body mass index (25.5 +/‐ 5.3 versus 27.3 +/‐ 6.2 kg/m2; P = .03), of younger age (24.4 +/‐ 6.5 versus 26.9 +/‐ 6.9 years; P = .01), and African American or Asian (37.9% versus 27.2% and 9.7% versus 2%; P = .01). Cases were scanned at earlier gestational ages (18.9 +/‐ 1.6 versus 19.5 +/‐ 1.7 weeks; P = .01). The focus group was more likely to have had an apical view of the fetal heart taken (80.8% versus 51.4%; P = .0001). Controls were more likely to have had a right lateral view taken (44.6% versus 20.8%; P = .002). No significant difference was found between groups in terms of any other maternal or sonographic variable studied.The echogenic cardiac focus group was more likely to have a lower body mass index and to be scanned with the apical fetal heart view. The orientation of the fetal 4‐chamber heart view exerted the most statistically significant influence on detection rates for the echogenic cardiac focus, implying that the more technically facile the sonographic study, the more likely an echogenic cardiac focus will be found.
Hydatid liver cyst: an 11‐year experience of treatment with percutaneous aspiration and ethanol injection.
Authors: Giorgio A , Tarantino L , de Stefano G , Francica G , Mariniello N , Farella N , Perrotta A , Aloisio V , Esposito F 
Published: January 2017

To report an 11‐year experience of treatment of hydatid liver cysts with double percutaneous aspiration and injection of alcohol.Of the 129 patients with 174 hydatid liver cysts admitted to our department between January 1988 and January 1999, 79 patients with 119 vital hydatid liver cysts were selected for double percutaneous aspiration and injection of alcohol. Under ultrasonographic guidance, cystic cavities were first drained through fine needles, and then 95% sterile ethanol was injected and left in situ. The same procedure was repeated 3 days later without reaspiration of the injected alcohol. General anesthesia without endotracheal intubation was performed in 21 selected cases.Double percutaneous aspiration and injection of alcohol was completed in 78 patients with 118 hydatid liver cysts. In 1 case the procedure could not be accomplished because of an intracystic hemorrhage. A total of 254 punctures were performed, and the ethanol injected per session ranged between 12 and 250 mL. The mean hospital stay was 2.9 days (range, 2‐7 days). The overall median follow‐up was 48 months (range, 6‐122 months). At the last ultrasonographic examination, 45.8% of the treated hydatid liver cysts had a solid pattern, 47.4% were no longer appreciable, and 6.8% had a minimal liquid component. Intracystic relapse occurred in 5% of the patients. In no case were any new cysts observed either in different hepatic segments or in any extrahepatic location. The morbidity rate was 9%, and 1 death occurred (mortality rate, 1.3%).Over a long period, double percutaneous aspiration and injection of alcohol proved to be a substantially safe, effective, and low‐cost procedure for hydatid liver cyst treatment.
Significance of the solid component in predicting malignancy in ovarian cystic teratomas: diagnostic considerations.
Authors: Mlikotic A , McPhaul L , Hansen G C , Sinow R M 
Published: January 2017

To determine whether gray scale characteristics of the solid components of cystic ovarian teratomas exist that could differentiate more common benign forms from malignant variants.We retrospectively reviewed the sonographic images of 188 ovarian teratomas that contain at least a 25% cystic component and correlated the images with the final diagnosis. Features of the solid component assessed included its echo texture, overall appearance, shape, size, and internal homogeneity.One‐hundred seventy‐seven teratomas were benign, and 11 were malignant; among the malignant masses, 7 were high grade. Of the benign forms, 155 solid components (88%) were hyperechoic, 168 (95%) were focal in appearance, 105 (59%) were nodular in shape, and 123 (69%) were uniformly solid. Of the malignant types, 9 solid components (82%) were isoechoic, 6 (55%) had branching, 6 (55%) were irregular in shape, and 8 (73%) were uniformly solid. Five malignant teratomas (45% overall and 71% of high‐grade subtypes) had branching isoechoic components. Only 2 benign teratomas (1%) had isoechoic components that branched.The presence of a branching isoechoic component in a cystic ovarian teratoma may suggest malignancy.
Fourteen‐gauge ultrasonographically guided large‐core needle biopsy of breast masses.
Authors: Schoonjans J M , Brem R F 
Published: January 2017

Large‐core needle biopsy of the breast can be performed with stereotactic or ultrasonographic guidance. However, ultrasonographically guided large‐core needle biopsy has notable advantages, including the absence of ionizing radiation, increased patient comfort, and greater cost‐effectiveness. The purpose of this study was to evaluate the accuracy of ultrasonographically guided large‐core needle biopsy for the diagnosis of breast cancer in palpable and nonpalpable breast masses.The study was a retrospective review of consecutive ultrasonographically guided large‐core needle biopsies for indeterminate breast masses. A total 424 ultrasonographically guided core biopsies were performed in 367 patients with 1 or more breast masses. Ultrasonographically guided core biopsy was performed with a 14‐gauge spring‐loaded needle and a freehand technique. Correlation of ultrasonographically guided core biopsy pathologic findings with subsequent surgical pathologic findings or long‐term imaging follow‐up was performed.Of 424 indeterminate breast lesions for which histopathologic findings were obtained by ultrasonographically guided core biopsy, 234 cancers were diagnosed. Twenty‐eight additional lesions had either questionable but not definitively malignant pathologic features (n = 11) or radiologic‐pathologic discordance (n = 17) and were surgically excised. Of these, 8 additional cancers were diagnosed. Patients or surgeons chose excision of 41 additional lesions that were benign on ultrasonographically guided core biopsy No cancer was found in these surgical specimens. One additional cancer was diagnosed at a 6‐month imaging follow‐up because of interval growth. On the basis of surgical and long‐term imaging follow‐up, the sensitivity of ultrasonographically guided core biopsy for the diagnosis of breast carcinoma was 99.2% (95% confidence interval, 95.6%‐99.9%) in 173 palpable breast masses and 93.2% (95% confidence interval, 87.1%‐97%) in 251 nonpalpable masses. In cancers diagnosed on the basis of immediate surgical excision as a result of ultrasonographically guided core biopsy that showed either questionable pathologic features or radiologic‐pathologic discordance, the sensitivity of ultrasonographically guided core biopsy for the diagnosis of breast cancer was 99.2%.Ultrasonographically guided large‐core needle biopsy is a sensitive percutaneous biopsy method for the diagnosis of breast cancer in palpable and nonpalpable breast masses.
Identification of the Fetal Hippocampus and Fornix and Role of 3‐Dimensional Sonography
Authors: Gindes Liat , Weissmann-Brenner Alina , Weisz Boaz , Zajicek Michal , Geffen Keren Tzadikevitch , Achiron Reuven 
Published: January 2017

ObjectivesThe purposes of this study were to identify the fetal hippocampus and fornix using 3‐dimensional sonography, to measure their curved length during pregnancy, and to describe a systematic method for volume data set analysis of the fetal hippocampus and fornix.MethodsThree‐dimensional volumes of the fetal brain were acquired prospectively in 34 patients between 14 and 37 weeks' gestation. Volumes were acquired with trans‐abdominal and transvaginal transducers. All volumes were analyzed offline by 2 examiners separately. The feasibility of identifying the fetal hippocampus and fornix was analyzed. The curved length of the hippocampus‐fornix structure was measured on the right and left hemispheres.ResultsThe fetal hippocampus and fornix were identified bilaterally in 32 of 34 fetuses (94%) at gestational ages of 14 weeks 5 days to 37 weeks 1 day (mean, 23 weeks 3 days). In 1 fetus (3%), only one side was shown, and in another fetus (3%), both sides were obscured by acoustic shadows. A systematic approach for identification of the fetal hippocampus is described. Linear growth of the fetal hippocampus and fornix was shown during pregnancy and was correlated with both the gestational week and the head circumference (R = 0.71 and 0.74, respectively; P = .01). The length of the hippocampus and fornix did not differ between the left and the right hemispheres (P = .598).ConclusionsThe fetal hippocampus and fornix can be identified by a systematic analysis of 3‐dimensional data set volumes. The normal hippocampus and fornix show linear growth throughout pregnancy.
First‐Trimester Visualization of the Fourth Ventricle in Fetuses With and Without Spina Bifida
Authors: Solt Ido , Acuna Joann G. , Adeniji Beni A. , Mirocha James , Kim Matthew J. , Rotmensch Siegfried 
Published: January 2017

ObjectivesThe purpose of this study was to examine the efficacy of nonvisualization of the fourth ventricle for first‐trimester detection of spina bifida.MethodsA total of 250 digitally stored sonographic examinations at gestational ages of 11 weeks to 13 weeks 6 days (245 normal and 5 randomly interspersed spina bifida cases) were retrospectively analyzed by 4 blinded reviewers for the presence or absence of the fourth ventricle followed by an anteroposterior ventricular dimension measurement. The ventricle size was related to the crown‐rump length and gestational age by linear regression analysis and Pearson correlation.ResultsThe fourth ventricle was identified in 971 of 1000 image readings (97.1%). False‐negative and false‐positive readings occurred in 11 of 20 (55.0%) and 20 of 980 (2.0%) cases, respectively (sensitivity, 0.45; specificity, 0.98.). False‐negative and false‐positive readings were evenly distributed throughout the gestational age range. When the ventricular size was measurable, its mean dimensions increased linearly with gestational age and were below the fifth percentile in 10 of 245 (4.0%) normal and 0 of 4 spina bifida cases, respectively. Intraclass correlation coefficient estimates were calculated based on the 2‐way analysis of variance model and found to be 0.30 for a single rater and 0.64 for the mean of 4 raters.ConclusionsNonvisualization of the first‐trimester fourth ventricle is a less robust screening parameter for spina bifida than previously published.
Color‐Coded Duplex Sonography Compared to Multidetector Computed Tomography for the Diagnosis of Crohn Disease Relapse and Complications
Authors: Gaitini Diana , Kreitenberg Adam J. , Fischer Doron , Maza Itay , Chowers Yehuda 
Published: January 2017

ObjectivesThe purpose of this study was to evaluate the accuracy of color‐coded duplex sonography for the diagnosis of Crohn disease relapse and complications compared to multidetector computed tomography (CT).MethodsThe Institutional Ethics Committee approved the protocol research, and written consent forms were obtained. Patients with a diagnosis of Crohn disease presenting with symptoms of relapse or complications (54 patients; 27 female; ages 9–80 years; mean, 34.6 years) were enrolled. Patients underwent color‐coded duplex sonography and multidetector CT examinations within 2 weeks of each other. Multidetector CT was the reference standard. The location and extent of diseased bowel, wall thickness, stenosis, hyperemia, mesenteric fat thickening, lymphadenopathy, abscesses, fistulas, peritoneal fluid, and signs of hepatobiliary disease were searched for.ResultsAbout of 80% of the patients had terminal ileal involvement, and 55% had disease confined to the ileum. A significant correlation between the two modalities was found regarding wall thickness, abscesses, and fistulas (P < .05). Color‐coded duplex sonography had sensitivity and specificity of 88% and 53%, respectively, for diagnosis of luminal stenosis. Hyperemia was more commonly diagnosed on color‐coded duplex sonography. Color‐coded duplex sonography had sensitivity and specificity of 84% and 83% for diagnosis of mesenteric fat thickening and lymphadenopathy and 66% and 86% for peritoneal fluid. Fatty liver was found in 18% and gallstone disease in 6%.ConclusionsColor‐coded duplex sonography was accurate in diagnosing the disease location, wall thickness, and extraintestinal inflammatory findings associated with Crohn disease, potentially placing it as the first‐line imaging modality for the diagnosis of Crohn disease relapse and complications.
Varicocele and Epididymitis in Behçet Disease
Authors: Yilmaz Omer , Yilmaz Sedat , Kisacik Bunyamin , Aydogdu Mehmet , Bozkurt Yalcin , Erdem Hakan , Pay Salih , Saglam Mutlu , Dinc Ayhan 
Published: January 2017

Objective—Behçet disease is a systemic disease with protean manifestations. Vasculitis is a hallmark of the disease and may involve arteries, veins, and capillaries. Varicocele is dilatation of the pampiniform plexus veins. We aimed to investigate the incidence of varicocele in patients with Behçet disease.MethodsThe study included 47 male patients with Behçet disease and 31 healthy control participants. All underwent a clinical evaluation including a medical history and systemic and scrotal examinations. Subsequently, 2 investigators blinded to the clinical data performed sonographic examinations and measured pampiniform plexus vein diameters.ResultsThe mean age of the patients ± SD was 23.4 ± 3.2 years; disease durations ranged from 3 to 120 months (46 ± 31 months). Scrotal pain or a palpable mass was detected by clinical examination in 24 patients with Behçet disease (51.1%) and 5 healthy participants (16.1%; P = .002). By color Doppler examination, left varicocele was diagnosed in 26 patients with Behçet disease (55.3%) and 9 healthy participants (29%; P = .02). All patients with right varicocele also had left varicocele; that condition was detected in 10.6% (5 patients) of the Behçet disease group and 6.4% (2 patients) of the control group (P > .05). Eight patients with Behçet disease (17%) had epididymitis, whereas none of the healthy participants did (P = .019, Fisher exact test). Genital ulcers and erythema nodosum lesions were more common among patients with varicocele (P = .034 and .058, respectively). There were no differences in smoking, epididymitis, arthritis, uveitis, or other clinical parameters for distinguishing varicocele in patients with Behçet disease.ConclusionsThe incidence of varicocele was increased in Behçet disease. Whether varicocele confers fertility problems in patients with Behçet disease and the underlying mechanism for a possible association are yet to be determined.
Early Visualization and Measurement of the Pericallosal Artery
Authors: Pati Mariangela , Cani Carlotta , Bertucci Emma , Re Claudia , Latella Silvia , D'Amico Roberto , Mazza Vincenzo 
Published: January 2017

ObjectivesThe purpose of this study was to evaluate the feasibility of visualization and measurement of the pericallosal artery during early stages of gestation.MethodsThe study group comprised 80 pregnant women between 12 and 21 weeks' gestation who attended our ultrasound unit. Transabdominal or transvaginal sonography was performed to obtain the optimal angle of a midsagittal section. High‐definition flow power Doppler imaging was used to visualize the pericallosal artery. In a sagittal plane, the lengths of the pericallosal artery were measured using a straight line to connect the most anterior and posterior points. All patients were reexamined at a later stage of pregnancy to verify the existence of the corpus callosum and pericallosal artery.ResultsVisualization of the pericallosal artery was evident in 71 fetuses, in all of whom the biparietal diameter was greater than 20 mm. We were able to verify normal anatomy and the existence of the pericallosal artery in these fetuses between 30 and 32 weeks' gestation. A positive linear association was found between the length of the pericallosal artery and the gestational age (R2 = 0.95) and the biparietal diameter at each gestational age (R2 = 0.99).ConclusionsOur data show that it is feasible to visualize and measure the pericallosal artery from an early stage of gestation, and this measurement could be an indirect indication of normal corpus callosum development.