bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genes2WordCloud: a quick way to identify biological themes from gene lists and free text
Authors: Baroukh Caroline , Jenkins Sherry L , Dannenfelser Ruth , Ma'ayan Avi 
Published: November 2011

Abstract

Background
Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications.

Results
Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice.

Methods
Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W.

Conclusions
Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications.
Decreased levels of serum glutathione peroxidase 3 are associated with papillary serous ovarian cancer and disease progression
Authors: Agnani Deep , Camacho-Vanegas Olga , Camacho Catalina , Lele Shashi , Odunsi Kunle , Cohen Samantha , Dottino Peter , Martignetti John A 
Published: November 2011

Abstract

Background
Glutathione peroxidase 3 (GPX3) is a selenocysteine-containing antioxidant enzyme that reacts with hydrogen peroxide and soluble fatty acid hydroperoxides, thereby helping to maintain redox balance within cells. Serum levels of GPX3 have been found to be reduced in various cancers including prostrate, thyroid, colorectal, breast and gastric cancers. Intriguingly, GPX3 has been reported to be upregulated in clear cell ovarian cancer tissues and thus may have implications in chemotherapeutic resistance. Since clear cell and serous subtypes of ovarian cancer represent two distinct disease entities, the aim of this study was to determine GPX3 levels in serous ovarian cancer patients and establish its potential as a biomarker for detection and/or surveillance of papillary serous ovarian cancer, the most frequent form of ovarian tumors in women.

Patients and Methods
Serum was obtained from 66 patients (median age: 62 years, range: 22-89) prior to surgery and 65 controls with a comparable age-range (median age: 53 years, range: 25-83). ELISA was used to determine the levels of serum GPX3. The Mann Whitney U test was performed to determine statistical significance between the levels of serum GPX3 in patients and controls.

Results
Serum levels of GPX3 were found to be significantly lower in patients than controls (p = 1 × 10-2). Furthermore, this was found to be dependent on the stage of disease. While levels in early stage (I/II) patients showed no significant difference when compared to controls, there was a significant reduction in late stage (III/IV, p = 9 × 10-4) and recurrent (p = 1 × 10-2) patients. There was a statistically significant reduction in levels of GPX3 between early and late stage (p = 5 × 10-4) as well as early and recurrent (p = 1 × 10-2) patients. Comparison of women and controls stratified to include only women at or above 50 years of age shows that the same trends were maintained and the differences became more statistically significant.

Conclusions
Serum GPX3 levels are decreased in women with papillary serous ovarian cancer in a stage-dependent manner and also decreased in women with disease recurrence. Whether this decrease represents a general feature in response to the disease or a link to the progression of the cancer is unknown. Understanding this relationship may have clinical and therapeutic consequences for women with papillary serous adenocarcinoma.
Rapid contrast gain reduction following motion adaptation
Authors: Nordström Karin , de Miguel Irene Moyer , O'Carroll David C. 
Published: November 2011

SUMMARY
Neural and sensory systems adapt to prolonged stimulation to allow signaling across broader input ranges than otherwise possible with the limited bandwidth of single neurons and receptors. In the visual system, adaptation takes place at every stage of processing, from the photoreceptors that adapt to prevailing luminance conditions, to higher-order motion-sensitive neurons that adapt to prolonged exposure to motion. Recent experiments using dynamic, fluctuating visual stimuli indicate that adaptation operates on a time scale similar to that of the response itself. Further work from our own laboratory has highlighted the role for rapid motion adaptation in reliable encoding of natural image motion. Physiologically, motion adaptation can be broken down into four separate components. It is not clear from the previous studies which of these motion adaptation components are involved in the fast and dynamic response changes. To investigate the adapted response in more detail, we therefore analyzed the effect of motion adaptation using a test–adapt–test protocol with adapting durations ranging from 20 ms to 20 s. Our results underscore the very rapid rate of motion adaptation, suggesting that under free flight, visual motion-sensitive neurons continuously adapt to the changing scenery. This might help explain recent observations of strong invariance in the response to natural scenes with highly variable contrast and image structure.
Divergent transcriptomic responses to repeated and single cold exposures in Drosophila melanogaster
Authors: Zhang Jian , Marshall Katie E. , Westwood J. Timothy , Clark Melody S. , Sinclair Brent J. 
Published: November 2011

SUMMARY
Insects in the field are exposed to multiple bouts of cold, and there is increasing evidence that the fitness consequences of repeated cold exposure differ from the impacts of a single cold exposure. We tested the hypothesis that different kinds of cold exposure (in this case, single short, prolonged and repeated cold exposure) would result in differential gene expression. We exposed 3 day old adult female wild-type Drosophila melanogaster (Diptera: Drosophilidae) to –0.5°C for a single 2 h exposure, a single 10 h exposure, or five 2 h exposures on consecutive days, and extracted RNA after 6 h of recovery. Global gene expression was quantified using an oligonucleotide microarray and validated with real-time PCR using different biological replicates. We identified 76 genes upregulated in response to multiple cold exposure, 69 in response to prolonged cold exposure and 20 genes upregulated in response to a single short cold exposure, with a small amount of overlap between treatments. Three genes – Turandot A, Hephaestus and CG11374 – were upregulated in response to all three cold exposure treatments. Key functional groups upregulated include genes associated with muscle structure and function, the immune response, stress response, carbohydrate metabolism and egg production. We conclude that cold exposure has wide-ranging effects on gene expression in D. melanogaster and that increased duration or frequency of cold exposure has impacts different to those of a single short cold exposure. This has important implications for extrapolating laboratory studies of insect overwintering that are based on only a single cold exposure.
Hydrogen sulfide (H2S) and hypoxia inhibit salmonid gastrointestinal motility: evidence for H2S as an oxygen sensor
Authors: Dombkowski Ryan A. , Naylor Marie G. , Shoemaker Emma , Smith Michelle , DeLeon Eric R. , Stoy Gilbrian F. , Gao Yan , Olson Kenneth R. 
Published: November 2011

SUMMARYHydrogen sulfide (H2S) has been shown to affect gastrointestinal (GI) motility and signaling in mammals and O2-dependent H2S metabolism has been proposed to serve as an O2 ‘sensor’ that couples hypoxic stimuli to effector responses in a variety of other O2-sensing tissues. The low PO2 values and high H2S concentrations routinely encountered in the GI tract suggest that H2S might also be involved in hypoxic responses in these tissues. In the present study we examined the effect of H2S on stomach, esophagus, gallbladder and intestinal motility in the rainbow trout (Oncorhynchus mykiss) and coho salmon (Oncorhynchus kisutch) and we evaluated the potential for H2S in oxygen sensing by examining GI responses to hypoxia in the presence of known inhibitors of H2S biosynthesis and by adding the sulfide donor cysteine (Cys). We also measured H2S production by intestinal tissue in real time and in the presence and absence of oxygen. In tissues exhibiting spontaneous contractions, H2S inhibited contraction magnitude (area under the curve and amplitude) and frequency, and in all tissues it reduced baseline tension in a concentration-dependent relationship. Longitudinal intestinal smooth muscle was significantly more sensitive to H2S than other tissues, exhibiting significant inhibitory responses at 1–10 μmol l–1 H2S. The effects of hypoxia were essentially identical to those of H2S in longitudinal and circular intestinal smooth muscle; of special note was a unique transient stimulatory effect upon application of both hypoxia and H2S. Inhibitors of enzymes implicated in H2S biosynthesis (cystathionine β-synthase and cystathionine γ-lyase) partially inhibited the effects of hypoxia whereas the hypoxic effects were augmented by the sulfide donor Cys. Furthermore, tissue production of H2S was inversely related to O2; addition of Cys to intestinal tissue homogenate stimulated H2S production when the tissue was gassed with 100% nitrogen (∼0% O2), whereas addition of oxygen (∼10% O2) reversed this to net H2S consumption. This study shows that the inhibitory effects of H2S on the GI tract of a non-mammalian vertebrate are identical to those reported in mammals and they provide further evidence that H2S is a key mediator of the hypoxic response in a variety of O2-sensitive tissues.
Black wildebeest skeletal muscle exhibits high oxidative capacity and a high proportion of type IIx fibres
Authors: Kohn Tertius Abraham , Curry Jennifer Wendy , Noakes Timothy David 
Published: November 2011

SUMMARY
The aim of the study was to investigate the skeletal muscle characteristics of black wildebeest (Connochaetes gnou) in terms of fibre type and metabolism. Samples were obtained post mortem from the vastus lateralis and longissimus lumborum muscles and analysed for myosin heavy chain (MHC) content. Citrate synthase (CS), 3-hydroxyacyl co A dehydrogenase (3HAD), phosphofructokinase (PFK), lactate dehydrogenase (LDH) and creatine kinase (CK) activities were measured spectrophotometrically to represent the major metabolic pathways in these muscles. Both muscles had less than 20% MHC I, whereas MHC IIa and MHC IIx were expressed in excess of 50% in the vastus lateralis and longissimus lumborum muscles, respectively. Overall fibre size was 2675±1034 μm2, which is small compared with other species. Oxidative capacity (CS and 3HAD) in both muscles was high and did not differ from one another, but the longissimus lumborum had significantly (P&lt;0.05) higher PFK, LDH and CK activities. No relationships were observed between fibre type and the oxidative and oxygen-independent metabolic capacity as measured by specific enzyme activities. This study confirms the presence of both fast-twitch fibres and high oxidative capacity in black wildebeest, indicating an animal that can run very fast but is also fatigue resistant.
Locomotor activity during the frenzy swim: analysing early swimming behaviour in hatchling sea turtles
Authors: Pereira Carla M. , Booth David T. , Limpus Colin J. 
Published: November 2011

SUMMARYSwimming effort of hatchling sea turtles varies across species. In this study we analysed how swim thrust is produced in terms of power stroke rate, mean maximum thrust per power stroke and percentage of time spent power stroking throughout the first 18 h of swimming after entering the water, in both loggerhead and flatback turtle hatchlings and compared this with previous data from green turtle hatchlings. Loggerhead and green turtle hatchlings had similar power stroke rates and percentage of time spent power stroking throughout the trial, although mean maximum thrust was always significantly higher in green hatchlings, making them the most vigorous swimmers in our three-species comparison. Flatback hatchlings, however, were different from the other two species, with overall lower values in all three swimming variables. Their swimming effort dropped significantly during the first 2 h and kept decreasing significantly until the end of the trial at 18 h. These results support the hypothesis that ecological factors mould the swimming behaviour of hatchling sea turtles, with predator pressure being important in determining the strategy used to swim offshore. Loggerhead and green turtle hatchlings seem to adopt an intensely vigorous and energetically costly frenzy swim that would quickly take them offshore into the open ocean in order to reduce their exposure to near-shore aquatic predators. Flatback hatchlings, however, are restricted in geographic distribution and remain within the continental shelf region where predator pressure is probably relatively constant. For this reason, flatback hatchlings might use only part of their energy reserves during a less vigorous frenzy phase, with lower overall energy expenditure during the first day compared with loggerhead and green turtle hatchlings.
Kingfisher feathers – colouration by pigments, spongy nanostructures and thin films
Authors: Stavenga Doekele G. , Tinbergen Jan , Leertouwer Hein L. , Wilts Bodo D. 
Published: November 2011

SUMMARYThe colours of the common kingfisher, Alcedo atthis, reside in the barbs of the three main types of feather: the orange breast feathers, the cyan back feathers and the blue tail feathers. Scanning electron microscopy showed that the orange barbs contain small pigment granules. The cyan and blue barbs contain spongy nanostructures with slightly different dimensions, causing different reflectance spectra. Imaging scatterometry showed that the pigmented barbs create a diffuse orange scattering and the spongy barb structures create iridescence. The extent of the angle-dependent light scattering increases with decreasing wavelength. All barbs have a cortical envelope with a thickness of a few micrometres. The reflectance spectra of the cortex of the barbs show oscillations when measured from small areas, but when measured from larger areas the spectra become wavelength independent. This can be directly understood with thin film modelling, assuming a somewhat variable cortex thickness. The cortex reflectance appears to be small but not negligible with respect to the pigmentary and structural barb reflectance.
The recruiter's excitement – features of thoracic vibrations during the honey bee's waggle dance related to food source profitability
Authors: Hrncir Michael , Maia-Silva Camila , Mc Cabe Sofia I. , Farina Walter M. 
Published: November 2011

SUMMARYThe honey bee's waggle dance constitutes a remarkable example of an efficient code allowing social exploitation of available feeding sites. In addition to indicating the position (distance, direction) of a food patch, both the occurrence and frequency of the dances depend on the profitability of the exploited resource (sugar concentration, solution flow rate). During the waggle dance, successful foragers generate pulsed thoracic vibrations that putatively serve as a source of different kinds of information for hive bees, who cannot visually decode dances in the darkness of the hive. In the present study, we asked whether these vibrations are a reliable estimator of the excitement of the dancer when food profitability changes in terms of both sugar concentration and solution flow rate. The probability of producing thoracic vibrations as well as several features related to their intensity during the waggle phase (pulse duration, velocity amplitude, duty cycle) increased with both these profitability variables. The number of vibratory pulses, however, was independent of sugar concentration and reward rate exploited. Thus, pulse number could indeed be used by dance followers as reliable information about food source distance, as suggested in previous studies. The variability of the dancer's thoracic vibrations in relation to changes in food profitability suggests their role as an indicator of the recruiter's motivational state. Hence, the vibrations could make an important contribution to forager reactivation and, consequently, to the organisation of collective foraging processes in honey bees.
Pharmacological characterisation of apical Na+ and Cl– transport mechanisms of the anal papillae in the larval mosquitoAedes aegypti
Authors: Duca Olimpia Del , Nasirian Azadeh , Galperin Vladimir , Donini Andrew 
Published: November 2011

SUMMARYThe anal papillae of freshwater mosquito larvae are important sites of NaCl uptake, thereby acting to offset the dilution of the hemolymph by the dilute habitat. The ion-transport mechanisms in the anal papillae are not well understood. In this study, the scanning ion-selective electrode technique (SIET) was utilized to measure ion fluxes at the anal papillae, and pharmacological inhibitors of ion transport were utilized to identify ion-transport mechanisms. Na+ uptake by the anal papillae was inhibited by bafilomycin and phenamil but not by HMA. Cl– uptake was inhibited by methazolamide, SITS and DIDS but not by bafilomycin. H+ secretion was inhibited by bafilomycin and methazolamide. Ouabain and bumetanide had no effect on NaCl uptake or H+ secretion. Together, the results suggest that Na+ uptake at the apical membrane occurs through a Na+ channel that is driven by a V-type H+-ATPase and that Cl– uptake occurs through a Cl–/HCO3– exchanger, with carbonic anhydrase providing H+ and HCO3– to the V-type H+-ATPase and exchanger, respectively.
Insights into Uranyl Ion Binding to Ubiquitin from Molecular Modeling and Dynamics Simulations
Authors: Lin Ying-Wu , Nie Chang-Ming , Liao Li-Fu 
Published: November 2011

Abstract
Uranium is toxic to the human body with mechanisms not fully understood. The interaction between uranyl ion (UO22+) and ubiquitin (Ub) was predicted by molecular modeling, molecular dynamics (MD) simulation, and steered molecular dynamics (SMD) simulation. The structural and dynamics consequences, as well as protein unfolding behavior, upon uranyl binding to two surface residues of Ub, Glu18 and Asp21, were revealed at an atomic level. This in silico study exhibits a possibility of UO22+ binding to Ub, providing a possible mechanism of uranyl toxicity in vivo.
Stent-graft placement for urgent treatment or prevention of bleeding
Authors: Semiz-Oysu Aslihan , Keussen Inger , Cwikiel Wojciech 
Published: November 2011

Background Stent-graft treatment of the patients with ongoing bleeding may be beneficial in specific situations, especially when preservation of blood flow to the distant organs is important. Purpose To present the results of stent-graft placement for urgent treatment or prevention of the bleeding. Material and Methods Stent-graft placement was performed urgently for the treatment of active bleeding and/or pseudoaneurysm/aneurysm in 17 patients. Diagnoses were based on clinical findings and/or imaging studies. The etiology was previous major surgery and/or percutaneous intervention in 13, malignancy in one, pancreatitis and pseudocyst in one, multitrauma due to traffic accident in one and unknown cause in one patient. Results A total of 23 stent-grafts were placed. Angiograms obtained after placement revealed patent stent-graft with no further active extravasation or filling of pseudoaneurysm in 14 patients. Due to persistent bleeding, embolization was performed in two patients. In three patients, the stent-grafts were found to be thrombosed either immediately after placement ( n = 1) or at follow-up ( n = 2). Stent-grafts were patent in six of nine patients that could be followed (between 3 months and 6 years). Conclusion Urgent stent-graft placement may be an alternative to endovascular embolization or surgery. It may be preferred when embolization is technically difficult or impossible and/or when preservation of blood supply to distal organs is essential such as in liver transplant grafts or extremity salvage.
FDG-PET/CT in the diagnosis of recurrent breast cancer
Authors: Murakami Ryusuke , Kumita Shin-ichiro , Yoshida Tamiko , Ishihara Keiichi , Kiriyama Tomonari , Hakozaki Kenta , Yanagihara Keiko , Iida Shinya , Tsuchiya Shin-ichi 
Published: November 2011

Background An advantage of PET/CT has been demonstrated for diagnosis of several tumor entities. In patients with breast cancer, early diagnosis and accurate restaging of recurrence after surgery is important for selection of the most appropriate therapeutic strategy. Purpose To evaluate the accuracy of integrated positron emission tomography and computed tomography (PET/CT) using 18F-fluorodeoxyglucose (FDG), for follow-up of patients with suspected recurrent breast cancer. Material and Methods Forty-seven patients with suspected recurrent breast cancer underwent PET/CT. The PET and PET/CT images were interpreted without knowledge of the results of other diagnostic modalities, and compared with each other with reference to the final diagnosis. Results Twenty-five (53%) patients suffered tumor recurrence. The overall sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of PET/CT were 96%, 91%, 92%, 95%, and 94%, respectively. In comparison with PET, PET/CT had a higher sensitivity and accuracy (96% vs. 80% and 94% vs. 81%, respectively). The difference in diagnostic accuracy between PET/CT and PET was significant ( P < 0.05). Conclusion The present findings indicate that PET/CT is an accurate, sensitive and reliable modality for screening and detection of breast cancer recurrence. PET/CT appears to be an effective surveillance tool, as it is able to cover the whole body in a single procedure and shows good performance.