bluuebunny/crossref_metadata_2025_split huggingface dataset:
Myelodysplasia followed by Good's Syndrome: A unique manifestation associated with thymoma
Authors: Chen Ling‐Ping , Tsai Jui‐Shan , Lai Wei‐Ming , Yen Ling‐Jung , Yu Ming‐Sun , Lin Shyh‐Jer 
Published: February 2012

AbstractGood's syndrome, also known as thymoma with combined immunodeficiency, is rare. The immunodeficiency may precede, arise concurrently with or follow the diagnosis of thymoma. In addition to myasthenia gravis and Good's syndrome, paraneoplastic syndromes associated with thymoma can also be manifested with hematological disorders, such as pure red cell aplasia, aplastic anemia, agranulocytosis, hemolytic anemia, pernicious anemia, and paroxysmal nocturnal hemoglobinuria. Myelodysplastic syndrome is a group of clonal hematopoietic stem cell diseases characterized by cytopenia(s), dysplasia in one or more lineages, ineffective hematopoiesis, and potential precursors of acute leukemia. One proposed pathogenesis of myelodysplasia is autoantibodies that directly reject against hematopoietic cells, but this situation is rare in thymoma. Herein, we report a thymoma patient with unique paraneoplastic syndromes who developed myelodysplasia prior to Good's syndrome. Early and accurate diagnosis of myelodysplastic syndrome is important for disease management, especially in patients whose myelodysplastic syndrome is possibly derived from autoimmunity. For thymoma patients with recurrent infections, comprehensive immunologic studies to exclude the possibility of Good's syndrome and prophylactic intravenous immunoglobulin infusion in suitable candidates are warranted.
Comparison of novel and existing tools for studying drug sensitivity against the hookworm Ancylostoma ceylanicum in vitro
Authors: TRITTEN LUCIENNE , BRAISSANT OLIVIER , KEISER JENNIFER 
Published: February 2012

SUMMARYThe motility assay is the current gold standard for evaluating drug effects on hookworm larvae and adults, however, among other drawbacks the assay is time consuming, and prone to individual subjectivity. We evaluated six alternative in vitro assays, namely the feeding inhibition assay, the colourimetric AlamarBlue®, MTT formazan and acid phosphatase activity assays, as well as isothermal calorimetry and the xCELLigence System using Ancylostoma ceylanicum third-stage larvae, stimulated third-stage larvae and adults. The performances of the assays were compared to the motility assay using three standard drugs: albendazole, levamisole and ivermectin (100–1 μg/ml). None of the assays investigated offered an advantage over the motility assay, because they were all inapplicable to third-stage larvae, which were presumably metabolically and physically too inactive. Among all assays tested the xCELLigence System performed best on adult worms as the test was accurate, simple, required a minimal number of worms and offered the possibility for conducting a medium-throughput screening.
Surface energy partitioning over four dominant vegetation types across the United States in a coupled regional climate model (Weather Research and Forecasting Model 3–Community Land Model 3.5)
Authors: Lu Yaqiong , Kueppers Lara M. 
Published: February 2012

Accurate representation of surface energy partitioning is crucial for studying land surface processes and the climatic influence of land cover and land use change using coupled climate‐land surface models. A critical question for these models, especially for newly coupled ones, is whether they can adequately distinguish differences in surface energy partitioning among different vegetation types. We evaluated 3 years (2004–2006) of surface energy partitioning and surface climate over four dominant vegetation types (cropland, grassland, needleleaf evergreen forest, and broadleaf deciduous forest) across the United States in a recently coupled regional climate model, Weather Research and Forecasting Model 3–Community Land Model 3.5 (WRF3‐CLM3.5), by comparing model output to observations (AmeriFlux, Clouds and the Earth's Radiant Energy System (CERES), and Parameter‐elevation Regressions on Independent Slopes Model (PRISM) data) and to standard WRF model output. We found that WRF3‐CLM3.5 can capture the seasonal pattern in energy partitioning for needleleaf evergreen forest but needs improvements in cropland, grassland, and broadleaf deciduous forest. Correcting the leaf area index representation for cropland and grassland could immediately improve the simulation of latent heat flux and hence the energy partitioning. Adding an irrigation scheme is especially important for cropland in the Midwest, where the strongly coupled soil moisture and precipitation can form a positive feedback that reduces latent heat flux and increases the warm bias. For deciduous forest, the simulated excess latent heat flux before leaf emergence is mainly from soil evaporation, requiring further improvement in the soil evaporation scheme. Finally, the domain‐wide overestimated net radiation contributes to positive biases in sensible, latent, and ground heat flux, as well as surface temperature. The standard WRF simulation has a similar warm bias, implicating errors in modules other than the land surface code. A sensitivity test suggests that improved simulation of downward solar radiation could reduce the energy flux and temperature biases. After adding irrigation process and correcting the leaf area index, WRF3‐CLM3.5 appears reliable for studying conversions between natural grassland and irrigated cropland and between needleleaf evergreen forest and grassland.
Medullary Thyroid Nodules by Measurement of Calcitonin (Ct) in Aspiration Needle Washout in Patients with Multinodular Goiter and Moderately Elevated Serum Ct
Authors: Trimboli P. , Nigri G. , Romanelli F. , Cicciarella Modica D. , Crescenzi A. , Valabrega S. , Giovanella L. 
Published: February 2012

AbstractThe accuracy of fine needle aspiration cytology (FNAC) is low in medullary thyroid carcinomas (MTC). Recently, a few papers analyzed the measurement of calcitonin (Ct) in washout of the needle after aspiration (WO-Ct) suggesting that this approach may be useful in patients with high serum Ct.Here we reported, for the first time in our best knowledge, 3 patients with multinodular goiter, moderately elevated serum Ct, high value of WO-Ct, and medullary outcome. These findings suggest that in presence of high serum Ct, FNAC should be performed in all nodules, and it should be combined with WO-Ct in all cases.
Treatment of Diabetic Ketoacidosis (DKA) with 2 Different Regimens Regarding Fluid Substitution and Insulin Dosage (0.025 vs. 0.1 units/kg/h)
Authors: Kapellen T. , Vogel C. , Telleis D. , Siekmeyer M. , Kiess W. 
Published: February 2012

AbstractDiabetic ketoacidosis (DKA) is still the most dangerous acute complication in type 1 diabetes. The aim of this study was to compare treatment of DKA with a regimen of a low insulin dose (0.025 units/kg/h) vs. a standard insulin dose (0.1 units/kg/h).We retrospectively analysed all cases of children and adolescents (age 0–18 years) with type 1 diabetes and DKA who needed treatment in the ICU in the time period of 1998–2005 in 2 pediatric diabetes centers. In a chart review of the first 48 h after onset of DKA the following parameters where evaluated: pH, blood glucose, sodium, potassium, and ketones in urine. Consciousness, neurological status and complications such as cerebral edema, hypoglycaemia or hypokalemia were also recorded.23 children were treated in center A (low insulin dose) whereas 41 where treated in center B (standard insulin dose). Mean age of the patients was 8.9 (range 1.58–17.7) and 13.5 years (1.25–17.7) respectively (p=0.134). Mean pH was 7.1 and HCO3 was 9.05 and 7.79 respectively (p=0.122). Initial blood glucose was 26 mmol/l (no difference between the 2 centres). Treatment with the standard insulin dose resulted in a slightly shorter duration of acidosis (8 h in center A, 6.5 h in center B) and a significantly faster normalization of blood glucose (18 h in A, vs. 10.5 h in B) (p<0.005). During the first day we found similar and very low rates of hypoglycaemia. In center B one case of suspected cerebral edema and cerebral infarction occurred.Low dose insulin substitution is as safe as the recommended standard dose in respect to the occurrence of acute complications. Acidosis is broken slightly earlier with the standard dose. Implications of this earlier normalisation of pH remain unclear.
A 10-year Retrospective Study of Primary Hyperparathyroidism in Children
Authors: Li C.-C. , Yang C. , Wang S. , Zhang J. , Kong X.-R. , Ouyang J. 
Published: February 2012

AbstractPrimary hyperparathyroidism (PHPT) in children is thought to be extremely rare. The exact incidence is unknown and little is known of the characteristics of the disease. We reviewed our experience with PHPT to better characterize these patients.We carried out a retrospective study in 12 patients (age 9–16 years) who had surgical treatment between 2001 and 2011 in a single institution.There were 5 male subjects and 7 female subjects. The diagnosis of PHPT in pediatric patients is frequently delayed with an average time of 41 months. The main signs of PHPT were urinary and bone disorders, as well as non-specific signs. All patients had preoperative localization studies prior to operation. Combined using of neck sonography, MIBI-scintigraphy and CT and/or MRI, our patients had a positive predictive value of 100%. After operation, all patients were confirmed to have parathyroid adenoma. 1 patient had 2 adenomas, 1 of which was an ectopic adenoma located in the mediastinum. 9 patients experienced symptomatic hypocalcemia postoperatively. No patients had any serious long-term effects from parathyroidectomy at our institution. All patients were cured after removal of the parathyroid adenoma. No permanent complication was observed for all patients.PHPT in children is rare, the commonest signs are urinary and bone tissue impairment, as well as non-specific signs. Evaluation of serum calcium and PTH levels is diagnostic in suspected patients. Preoperative localization is essential. Surgery is without significant complications. Surgical treatment of PHPT is curative and definitive.
Influence of Adrenal Subclinical Hypercortisolism on Hypertension in Patients with Adrenal Incidentaloma
Authors: Oki K. , Yamane K. , Nakanishi S. , Shiwa T. , Kohno N. 
Published: February 2012

AbstractThe purpose of our study was to clarify whether subtle cortisol-producing tumors, such as not only subclinical Cushing’s syndrome (SubCS) but also subclinical hypercortisolism (SH), influence the prevalence of hypertension, since numerous basic research studies have noted that glucocorticoid excess influences blood pressure.80 patients with adrenocortical adenomas (39 women and 41 men; mean age 62.1 years) were enrolled. SubCS was diagnosed using a diagnostic criteria, and SH was diagnosed as the presence of a serum cortisol level greater than 50 nmol/L following 1-mg dexamethasone suppression test (DST).SubCS, SH, or non-functioning adrenocortical adenoma (NF) was diagnosed in 14, 13, or 53 patients, respectively. The prevalence of hypertension differed significantly among the diagnoses (SubCS, 78.6%; SH, 84.6%; NF, 39.6%; P=0.002), whereas no differences in other clinical characteristics such as age, sex, or waist girth were observed. The patients with SH had an 11.7-fold increased risk (95% confidence interval: 1.9–72.7, P=0.009) and those with SubCS had a 9.5-fold increased risk (95% confidence interval: 1.9–48.3, P=0.007) for hypertension compared to those with NF using a multivariate analysis.We demonstrated that subtle cortisol-producing tumors, such as SH as well as SubCS, were an independent risk factor for hypertension. The cut-off value of the 1-mg DST would be appropriate to predict the development of hypertension.
Quantifying the hurricane risk to offshore wind turbines
Authors: Rose Stephen , Jaramillo Paulina , Small Mitchell J. , Grossmann Iris , Apt Jay 
Published: February 2012

The U.S. Department of Energy has estimated that if the United States is to generate 20% of its electricity from wind, over 50 GW will be required from shallow offshore turbines. Hurricanes are a potential risk to these turbines. Turbine tower buckling has been observed in typhoons, but no offshore wind turbines have yet been built in the United States. We present a probabilistic model to estimate the number of turbines that would be destroyed by hurricanes in an offshore wind farm. We apply this model to estimate the risk to offshore wind farms in four representative locations in the Atlantic and Gulf Coastal waters of the United States. In the most vulnerable areas now being actively considered by developers, nearly half the turbines in a farm are likely to be destroyed in a 20-y period. Reasonable mitigation measures—increasing the design reference wind load, ensuring that the nacelle can be turned into rapidly changing winds, and building most wind plants in the areas with lower risk—can greatly enhance the probability that offshore wind can help to meet the United States’ electricity needs.
Two-dimensional IR spectroscopy and segmental
13
C labeling reveals the domain structure of human γD-crystallin amyloid fibrils
Authors: Moran Sean D. , Woys Ann Marie , Buchanan Lauren E. , Bixby Eli , Decatur Sean M. , Zanni Martin T. 
Published: February 2012

The structural eye lens protein γD-crystallin is a major component of cataracts, but its conformation when aggregated is unknown. Using expressed protein ligation, we uniformly
13
C labeled one of the two Greek key domains so that they are individually resolved in two-dimensional (2D) IR spectra for structural and kinetic analysis. Upon acid-induced amyloid fibril formation, the 2D IR spectra reveal that the C-terminal domain forms amyloid β-sheets, whereas the N-terminal domain becomes extremely disordered but lies in close proximity to the β-sheets. Two-dimensional IR kinetics experiments show that fibril nucleation and extension occur exclusively in the C-terminal domain. These results are unexpected because the N-terminal domain is less stable in the monomer form. Isotope dilution experiments reveal that each C-terminal domain contributes two or fewer adjacent β-strands to each β-sheet. From these observations, we propose an initial structural model for γD-crystallin amyloid fibrils. Because only 1 μg of protein is required for a 2D IR spectrum, even poorly expressing proteins can be studied under many conditions using this approach. Thus, we believe that 2D IR and protein ligation will be useful for structural and kinetic studies of many protein systems for which IR spectroscopy can be straightforwardly applied, such as membrane and amyloidogenic proteins.
The identification of short linear motif-mediated interfaces within the human interactome
Authors: Weatheritt R. J. , Luck K. , Petsalaki E. , Davey N. E. , Gibson T. J. 
Published: February 2012

Abstract
Motivation: Eukaryotic proteins are highly modular, containing multiple interaction interfaces that mediate binding to a network of regulators and effectors. Recent advances in high-throughput proteomics have rapidly expanded the number of known protein–protein interactions (PPIs); however, the molecular basis for the majority of these interactions remains to be elucidated. There has been a growing appreciation of the importance of a subset of these PPIs, namely those mediated by short linear motifs (SLiMs), particularly the canonical and ubiquitous SH2, SH3 and PDZ domain-binding motifs. However, these motif classes represent only a small fraction of known SLiMs and outside these examples little effort has been made, either bioinformatically or experimentally, to discover the full complement of motif instances.
Results: In this article, interaction data are analysed to identify and characterize an important subset of PPIs, those involving SLiMs binding to globular domains. To do this, we introduce iELM, a method to identify interactions mediated by SLiMs and add molecular details of the interaction interfaces to both interacting proteins. The method identifies SLiM-mediated interfaces from PPI data by searching for known SLiM–domain pairs. This approach was applied to the human interactome to identify a set of high-confidence putative SLiM-mediated PPIs.
Availability: iELM is freely available at http://elmint.embl.de
Contact: toby.gibson@embl.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Spliceman—a computational web server that predicts sequence variations in pre-mRNA splicing
Authors: Lim Kian Huat , Fairbrother William Guy 
Published: February 2012

Abstract
Summary: It was previously demonstrated that splicing elements are positional dependent. We exploited this relationship between location and function by comparing positional distributions between all possible 4096 hexamers around a database of human splice sites. The distance measure used in this study found point mutations that produced higher distances disrupted splicing, whereas point mutations with smaller distances generally had no effect on splicing. Reasoning the idea that functional splicing elements have signature positional distributions around constitutively spliced exons, we introduce Spliceman—an online tool that predicts how likely distant mutations around annotated splice sites were to disrupt splicing. Spliceman takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation included the analyses of 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish.
Availability: Freely available on the web at http://fairbrother.biomed.brown.edu/spliceman/
Contact: fairbrother@brown.edu
Susceptibility of the human pathways graphs to fragmentation by small sets of microRNAs
Authors: Naamati Guy , Friedman Yitzhak , Balaga Ohad , Linial Michal 
Published: February 2012

Abstract
Motivation: MicroRNAs (miRNAs) are short sequences that negatively regulate gene expression. The current understanding of miRNA and their corresponding mRNA targets is primarily based on prediction programs. This study addresses the potential of a coordinated action of miRNAs to manipulate the human pathways. Specifically, we investigate the effectiveness of disrupting the topology of human pathway graphs through a regulation by miRNAs.
Results: From a set of miRNA candidates that is associated with a pathway, an exhaustive search for all possible doubles and triplets (coined miR-Duo, miR-Trios) is performed. The impact of each miR-combination on the connectivity of the pathway graph was quantified. About 170 human pathways were tested, and the miR-Duos and miR-Trios were scored for their ability to disrupt these pathway graphs. We show that 75% of all pathways are effectively disconnected by a small number of pathway-specific miR-Trios. Only 15% of the human pathways are resistant to fragmentation by miR-Duos or miR-Trios. Significantly, the combination of the most effective miR-Trios is unique. Thus, a specific regulation of a pathway within the cell is guaranteed. The impact of the selected miR-Duo/Trios on various diseases is discussed.
Conclusions: The methodology presented shows that the synthesis of the topology of a network with a detailed understanding of the miRNAs' regulation is useful in exposing critical nodes of the network. We propose the miR-Trio approach as a basis for rationally designed perturbation experiments.
Contact: michall@cc.huji.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics
Authors: Bonnal Raoul J.P. , Aerts Jan , Githinji George , Goto Naohisa , MacLean Dan , Miller Chase A. , Mishima Hiroyuki , Pagani Massimiliano , Ramirez-Gonzalez Ricardo , Smant Geert , Strozzi Francesco , Syme Rob , Vos Rutger , Wennblom Trevor J. , Woodcroft Ben J. , Katayama Toshiaki , Prins Pjotr 
Published: February 2012

Abstract
Summary: Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices.
Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics.
Availability: Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html
Contact: bonnal@ingm.org
Buddhist Art and Architecture in Nepal
Authors: Lo Bue Erberto 
Published: February 2012

The earliest evidence of the presence of Buddhism in the Nepal Valley belongs to the 5th century. According to inscriptions of the Licchavi dynasty, the Buddhist ruler Vrsadeva (fl. c. 400 ce) founded a monastery at Svayambhu. Most Licchavi foundations have disappeared, but a few, such as the Gum monastery near Sankhu, have survived. The Buddhist pantheon in Nepal is obviously related to the Indian tradition, in which Buddhism and Hinduism coexisted and influenced each other through many centuries. Although the sophisticated artistic production in the Nepal Valley represents to some extent the continuation of the aesthetics prevailing in India under the Gupta, Pâla, and Sena dynasties, the art and architecture of its original inhabitants, the Newars, developed in a unique way. Even after their Buddhist tradition was cut off from its sources following the destruction of all Indian monastic universities by the 13th century, Newar artists continued to produce images for Buddhists not only in Nepal, but also in other countries, particularly Tibet. At least two Buddhist traditions and related styles may be distinguished in Nepal: the Newar ones of the Nepal Valley, where Buddhism followed its own local development; and the Tibetan ones, in areas inhabited by people of Tibetan stock and language, such as Lo (Mustang) and Dölpo, and in the Nepal Valley itself, where the number of Tibetan monasteries has increased significantly since the 1960s. That accounts for iconographic and stylistic differences in images produced even by the same artist, who traditionally can adapt easily to the requests of his client. The traditional style of architecture characterizing most of the 363 monasteries in the Nepal Valley, the earliest ones dating to the Licchavi dynasty, may be traced to Buddhist monastic structures such as those found at Sanchi, Ajanta, and Ellora, representing stone versions of now-lost Indian wooden architecture, but at the same time prototypes of the brick and wood monasteries of the Nepal Valley. Newar monasteries are characterized by three essential elements: the main shrine, a small stupa in the middle of the courtyard, and a tantric temple above the shrine. Their courtyards are surrounded by rooms that do not necessarily conform in their function to their Indian models, since, following the decline of Buddhism in the Nepal Valley, they have sometimes turned into residential buildings. Another feature deriving from Indian architecture is the tòrana, originally a decorated arch leading to a shrine, which in the Nepal Valley turned into a semicircular panel placed above the doors of shrines or gates.