bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Gastrectomy in Patients With Delayed Gastric Emptying After Antireflux Surgery or Large Hiatal Hernia Repair
Authors: Gerritsen Arja , Furnée Edgar J. B. , Gooszen Hein G. , Wondergem Maurits , Hazebroek Eric J. 
Published: February 2013

AbstractBackgroundRevision antireflux surgery and large hiatal hernia repair require extensive dissection at the gastroesophageal junction. This may lead to troublesome symptoms due to delayed gastric emptying, eventually requiring gastrectomy. The aim of this study was to evaluate the outcome of gastrectomy for severely delayed gastric emptying after large hiatal hernia repair or redo antireflux surgery.MethodsEleven patients were treated between 1995 and 2010 and entered in the study. Preoperative and operative data were retrospectively collected. Standardized questionnaires were sent to all of the patients to evaluate symptomatic outcome.ResultsThe primary intervention was Nissen fundoplication in nine patients, Toupet fundoplication in one, and cruroplasty in another. The repairs were for refractory gastroesophageal reflux disease in five patients and a symptomatic large hiatal hernia in six. Subsequent gastrectomy was partial in four patients, subtotal in six, and total in one. There was one minor postoperative complication. After a mean (±SD) duration of 102 ± 59 months, nine patients were available for symptomatic follow‐up. Eight patients experienced daily symptoms related to dumping. Daily symptoms indicative of delayed gastric emptying were present in seven patients at follow‐up. Mean general quality of life was increased from 3.8 ± 2.2 before gastrectomy to 5.4 ± 1.8 at follow‐up. Eight patients reported gastrectomy as worthwhile.ConclusionGastrectomy after previous antireflux surgery or large hiatal hernia repair is safe with the potential to improve quality of life. Although upper gastrointestinal symptoms tend to persist, gastrectomy can be considered a reasonable, last‐resort surgical option for alleviating upper gastrointestinal symptoms after this kind of surgery.
Parametrically excited inverted double pendulum and efficient bipedal walking with an upper body
Authors: Honjo Toyoyuki , Nagano Akinori , Luo Zhi-Wei 
Published: February 2013

SUMMARYWalking locomotion involves complex movement of total center of mass. Not only the lower body behavior but also the upper body behavior affects the walking characteristics. Therefore, in this paper we derive the principle of parametrically excited inverted double pendulum to consider both lower body and upper body dynamics. We propose one approach to utilize the upper body behavior of the robot for energy efficient bipedal locomotion. In addition, we analyze the property of parametrically excited inverted double pendulum.
The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields
Authors: Indio Valentina , Martelli Pier Luigi , Savojardo Castrense , Fariselli Piero , Casadio Rita 
Published: February 2013

Abstract
Motivation: Targeting peptides are the most important signal controlling the import of nuclear encoded proteins into mitochondria and plastids. In the lack of experimental information, their prediction is an essential step when proteomes are annotated for inferring both the localization and the sequence of mature proteins.
Results: We developed TPpred a new predictor of organelle-targeting peptides based on Grammatical-Restrained Hidden Conditional Random Fields. TPpred is trained on a non-redundant dataset of proteins where the presence of a target peptide was experimentally validated, comprising 297 sequences. When tested on the 297 positive and some other 8010 negative examples, TPpred outperformed available methods in both accuracy and Matthews correlation index (96% and 0.58, respectively). Given its very low–false-positive rate (3.0%), TPpred is, therefore, well suited for large-scale analyses at the proteome level. We predicted that from ∼4 to 9% of the sequences of human, Arabidopsis thaliana and yeast proteomes contain targeting peptides and are, therefore, likely to be localized in mitochondria and plastids. TPpred predictions correlate to a good extent with the experimental annotation of the subcellular localization, when available. TPpred was also trained and tested to predict the cleavage site of the organelle-targeting peptide: on this task, the average error of TPpred on mitochondrial and plastidic proteins is 7 and 15 residues, respectively. This value is lower than the error reported by other methods currently available.
Availability: The TPpred datasets are available at http://biocomp.unibo.it/∼valentina/TPpred/. TPpred is available on request from the authors.
Contact: gigi@biocomp.unibo.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Making automated multiple alignments of very large numbers of protein sequences
Authors: Sievers Fabian , Dineen David , Wilm Andreas , Higgins Desmond G. 
Published: February 2013

Abstract
Motivation: Recent developments in sequence alignment software have made possible multiple sequence alignments (MSAs) of &gt;100000 sequences in reasonable times. At present, there are no systematic analyses concerning the scalability of the alignment quality as the number of aligned sequences is increased.
Results: We benchmarked a wide range of widely used MSA packages using a selection of protein families with some known structures and found that the accuracy of such alignments decreases markedly as the number of sequences grows. This is more or less true of all packages and protein families. The phenomenon is mostly due to the accumulation of alignment errors, rather than problems in guide-tree construction. This is partly alleviated by using iterative refinement or selectively adding sequences. The average accuracy of progressive methods by comparison with structure-based benchmarks can be improved by incorporating information derived from high-quality structural alignments of sequences with solved structures. This suggests that the availability of high quality curated alignments will have to complement algorithmic and/or software developments in the long-term.
Availability and implementation: Benchmark data used in this study are available at http://www.clustal.org/omega/homfam-20110613-25.tar.gz and http://www.clustal.org/omega/bali3fam-26.tar.gz.
Contact: fabian.sievers@ucd.ie
Supplementary information: Supplementary data are available at Bioinformatics online.
Rotavirus Vaccination in Central Europe
Authors: Mészner Zsófia , Anca Ioana , André Francis , Chlibek Roman , Čižman Milan , Grzesiowski Paweł , Mangarov Atanas , Pokorn Marko , Prymula Roman , Richter Darko , Salman Nuran , Šimurka Pavol , Tamm Eda , Tešović Goran , Urbancikova Ingrid , Usonis Vytautas , Zavadska Dace ,   Central European Vaccine Awareness Group (CEVAG)
Published: February 2013

ABSTRACTEach year, rotavirus (RV) infection is the leading cause of acute gastroenteritis requiring hospitalisation and of nosocomially transmitted diseases in children younger than 5 years across Central European Vaccination Awareness Group (CEVAG) countries; however, inadequate surveillance systems and lack of routine RV testing still exist in most CEVAG countries, making it difficult to accurately assess the present burden of acute RV gastroenteritis in the younger population. Furthermore, routine immunisation of infants with RV vaccines has not been implemented, and no official and uniform recommendations exist in most of the countries in these territories. The present study provides CEVAG country‐specific estimates of the disease burden of RV gastroenteritis among the youngest population and presents evidence‐based advice on the use of RV vaccines in the region, while providing a framework for vaccination at the national level.
Pediatric Celiac Disease, Cryptogenic Hypertransaminasemia, and Autoimmune Hepatitis
Authors: Vajro Pietro , Paolella Giulia , Maggiore Giuseppe , Giordano Giuseppe 
Published: February 2013

ABSTRACTObjective:The association between celiac disease (CD) and liver disease in pediatrics is widely recognized, but its prevalence is unknown. This study aims to conduct a systematic review and meta‐analysis to evaluate the prevalence of CD in children with cryptogenic persistent hypertransaminasemia (HTS) or autoimmune hepatitis (AIH), and vice versa.Methods:We searched MEDLINE/PubMed, the Cochrane Library, Web of Science, and MD Consult from 1977 to May 2012 for studies reporting either CD and HTS or AIH. Pooled prevalences with 95% confidence intervals (CI) and relative risk (RR) were calculated.Results:Nine studies (2046 patients) were identified. Pooled prevalences of CD in children with mild, nonspecific cryptogenic persistent HTS and vice versa were 12.0% (95% CI 4.17–29.96) and 36.0% (95% CI 32.15–40.11), respectively. A gluten‐free diet normalized transaminase levels in 77% to 100% of patients with CD within 4 to 8 months. Pooled prevalences of CD in children with AIH and vice versa were 6.3% (95% CI 3.87–11.73) and 1.4% (95% CI 0.84–2.15), respectively. The RR of HTS in children with CD versus the general population, and of CD in children with HTS was 6.55 (95% CI 5.65–7.60) and 11.59 (95% CI 3.80–35.33), respectively. The corresponding RR of AIH in children with CD was 188.54 (95% CI 92.23–385.43). The RR of CD in children with AIH was 6.63 (95% CI 3.86–11.40).Conclusions:CD is associated with elevated transaminase levels in about one‐third of newly diagnosed children. Cryptogenic persistent HTS may signal gluten‐dependent nonspecific mild hepatitis (12.0% of cases) or more rarely (6.3%) severe CD‐related autoimmune hepatopathy. RRs confirm these trends in the considered associations.
Physical Modeling of Fold‐and‐Thrust Belt Evolution and Triangle Zone Development: Dabashan Foreland Belt (Northeast Sichuan basin, China) as an Example
Authors: Ruirui WANG , Yueqiao ZHANG , Guoai XIE 
Published: February 2013

AbstractTriangle zones, generally found in foreland fold‐and‐thrust belts, serve as favorable objects of petroleum exploration. Taking the Dabashan foreland belt as an example, we studied the formation and development of triangle zones, and investigated the effect of décollements and the mechanical contrast of lithology by employing the method of physical modeling. Four experimental models were conducted in the work. The results showed that ‘sand wedges’ grew episodically, recorded by deformational length, height and slope angle. The height versus shortening rate presented an S‐shape curve, and uplifting occurred successively in the direction of the foreland belt. During the formation of the triangle zone, layer‐parallel shortening took place at the outset; deformation decoupling then occurred between the upper and lower brittle layers, divided by a middle‐embedded silicone polymers layer. The upper brittle layers deformed mainly by folding, while the lower sand layers by thrusting. As shortening continued, the geometry of a triangle zone was altered. We consider that the triangle zone in the Dabashan foreland belt was modified from an early one based on available seismic profiles and the experimental results. In addition, décollements and mechanical contrast impose significant influence on structural development, which can directly give rise to structural discrepancies. More décollements and obvious mechanical contrast between brittle layers can promote the coupling between the upper and lower brittle layers. Basal décollement controls the whole deformation and decreases the slope angle of the wedge, while roof décollement determines whether a triangle zone can be formed.
Groundwater Flow Simulation and its Application in Groundwater Resource Evaluation in the North China Plain, China
Authors: Jingli SHAO , Ling LI , Yali CUI , Zhaoji ZHANG 
Published: February 2013

AbstractThe purpose of this study is to establish a 3D groundwater flow modelling for evaluating groundwater resources of the North China Plain. First, the North China Plain was divided into three aquifers vertically through a characterization of hydrogeological conditions. Groundwater model software GMS was used for modeling to divide the area of simulation into a regular network of 164 rows and 148 lines. This model was verified through fitting of the observed and the simulated groundwater flow Gelds at deep and shallow layers and comparison between the observed and simulated hydrographs at 64 typical observation wells. Furthermore, water budget analysis was also performed during the simulation period (2002–2003). Results of the established groundwater flow model showed that the average annual groundwater recharge of the North China Plain during 1991 to 2003 was 256.68×108 m3/yr with safe yield of groundwater resources up to 213.49×108 m3/yr, in which safe yield of shallow groundwater and that of deep groundwater was up to 191.65×108 m3/yr and 22.64×108 m3/yr respectively. Finally, this model was integrated with proposal for groundwater withdrawal in the study area after commencement of water supply by South‐North Water Transfer Project, aiming to predict the changing trend of groundwater regime. As indicated by prediction results, South‐North Water Transfer Project, which is favorable for effective control of expansion and intensification of existing depression cone, would play a positive role in alleviation of short supply of groundwater in the North China Plain as well as maintenance and protection of groundwater.
Application of the Engineering‐Geological Conditions in Land‐Use Plans in the Petrvald Region (Czech Republic)
Authors: MARSCHALKO Marian , YILMAZ Işık , BEDNARIK Martin , KUBEČKA Karel , BOUCHAL Tomáš 
Published: February 2013

AbstractThe objective of this paper is to demonstrate necessity to inform relevant parties about engineering‐geological conditions for various practical purposes, especially including appropriate land‐use planning. However, the relationship between relevant geological information and the geological environment is vital for foundation engineering purposes, especially where demanding structures are involved. This information is most conveniently structured when accumulated information concerning engineering‐geological zones is utilized. This necessarily includes knowledge of rock workability and also of the pre‐Quaternary bedrock, and these characteristics were then related to the current built‐up area and future development according to the land‐use plans in a case study are from the Petrvald Region (Czech Republic). The geological environment of area has been severely influenced by anthropogenic effects of deep black coal mining. Results of this research showed that future development should be founded on spoil banks, dumps, and settling basins. According to the land‐use plan, this zone occupies 44.9% of the area of interest, and its materials predominantly emanate from mining in the Ostrava–Karvina Coal District. For future foundation structures planned there, it is imperative to consult detailed engineering‐geological study. However, attention to and reliance on this necessity is not reflected in the existing land‐use plan.
Avoiding fishy growth curves
Authors: Pardo Sebastián A. , Cooper Andrew B. , Dulvy Nicholas K. 
Published: February 2013

SummarySomatic growth is a fundamental property of living organisms, and is of particular importance for species with indeterminate growth that can change in size continuously throughout their life. For example, fishes can increase in size by 2–6 orders of magnitude during their lifetime, resulting in changes in production, consumption and function at the ecosystem scale. Within species, growth rates are traded off against other life‐history parameters, hence an accurate description of growth is essential to understand the comparative demography, productivity, fisheries yield and extinction risk of populations and species.The growth trajectory of indeterminate growing sharks and rays (elasmobranchs) and bony fishes (teleosts) is usually modelled using a three‐parameter logarithmic function, the von Bertalanffy growth function (VBGF), to describe the total length of the average individual at any given age. Recently, however, a two‐parameter form has gained popularity. Rather than being estimated in the model fitting process, the third y‐intercept parameter (L0) of theVBGFhas been interpreted as being biologically equivalent to, and thus fixed as, the empirically estimated size at birth.We tested the equivalence assumption thatL0is the same or similar to size at birth by comparing empirical estimates of size at birth available from the literature with estimates ofL0from published data from elasmobranchs, and found that even though there is an overlap of values, there is a high degree of variability between them.We calculate the bias in the growth coefficient (k) of theVBGFby comparison between the two‐ and three‐parameter estimation methods. We show that slight deviations in fixedL0can cause considerable bias in growth estimates in the two‐parameterVBGFwhile providing no benefit even whenL0matches the true value. We show that the effect of this biased growth estimate has profound consequences for fisheries stock status.We strongly recommend the use of the three‐parameterVBGFand discourage use of the two‐parameterVBGFbecause it results in substantially biased growth estimates even with slight variations in the value of fixedL0.
High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities
Authors: Zhan Aibin , Hulák Martin , Sylvester Francisco , Huang Xiaoting , Adebayo Abisola A. , Abbott Cathryn L. , Adamowicz Sarah J. , Heath Daniel D. , Cristescu Melania E. , MacIsaac Hugh J. 
Published: February 2013

Summary

Concerns regarding the rapid loss of endemic biodiversity, and introduction and spread of non‐indigenous species, have focused attention on the need and ability to detect species present in communities at low abundance. However, detection of rare species poses immense technical challenges, especially for morphologically cryptic species, microscopic taxa and those beneath the water surface in aquatic ecosystems.
Next‐generation sequencing technology provides a robust tool to assess biodiversity, especially for detection of rare species. Here, we assess the sensitivity of 454 pyrosequencing for detection of rare species using known indicator species spiked into existing complex plankton samples. In addition, we develop universal small subunit ribosomal DNA primers for amplification of a wide range of taxa for detailed description of biodiversity in complex communities.
A universality test of newly designed primers for the hypervariable V4 region of the nuclear small subunit ribosomal DNA (V4‐nSSU) using a plankton sample collected from Hamilton Harbor showed that 454 pyrosequencing based on this universal primer pair can recover a wide range of taxa, including animals, plants (algae), fungi, blue‐green algae and protists.
A sensitivity test showed that 454 pyrosequencing based on newly designed universal V4‐nSSU primers was extremely sensitive for detection of very rare species. Pyrosequencing was able to recover spiked indicator species with biomass percentage as low as approximately 2·3 × 10−5% when 24 artificially assembled samples were tagged and sequenced in one PicoTiter plate (i.e. sequencing depth of an equivalent of 1/24 PicoTiter plate). In addition, spiked rare species were sometimes recovered as singletons (i.e. Operational Taxonomic Units represented by a single sequence), suggesting that at least some singletons are informative for recovering unique lineages in ‘rare biospheres’.
The method established here allows biologists to better investigate the composition of aquatic communities, especially for detection of rare taxa. Despite a small‐scale pyrosequencing effort, we demonstrate the extreme sensitivity of pyrosequencing using rare species spiked into plankton samples. We propose that the method is a powerful tool for detection of rare native and/or alien species.
Differential protease activity augments polyphagy in Helicoverpa armigera
Authors: Chikate Y. R. , Tamhane V. A. , Joshi R. S. , Gupta V. S. , Giri A. P. 
Published: February 2013

AbstractHelicoverpa armigera (Lepidoptera: Noctuidae) and other polyphagous agricultural pests are extending their plant host range and emerging as serious agents in restraining crop productivity. Dynamic regulation, coupled with a diversity of digestive and detoxifying enzymes, play a crucial role in the adaptation of polyphagous insects. To investigate the functional intricacy of serine proteases in the development and polyphagy of H. armigera, we profiled the expression of eight trypsin‐like and four chymotrypsin‐like phylogenetically diverse mRNAs from different life stages of H. armigera reared on nutritionally distinct host plants. These analyses revealed diet‐ and stage‐specific protease expression patterns. The trypsins expressed showed structural variations, which might result in differential substrate specificity and interaction with inhibitors. Protease profiles in the presence of inhibitors and their mass spectrometric analyses revealed insight into their differential activity. These findings emphasize the differential expression of serine proteases and their consequences for digestive physiology in promoting polyphagy in H. armigera.
Significance of hepatitis B virus core‐related antigen and covalently closed circular DNA levels as markers of hepatitis B virus re‐infection after liver transplantation
Authors: Matsuzaki Toshihisa , Tatsuki Ichikawa , Otani Masashi , Akiyama Motohisa , Ozawa Eisuke , Miuma Satoshi , Miyaaki Hisamitsu , Taura Naota , Hayashi Tomayoshi , Okudaira Sadayuki , Takatsuki Mitsuhisa , Isomoto Hajime , Takeshima Fuminao , Eguchi Susumu , Nakao Kazuhiko 
Published: February 2013

AbstractBackground and AimCurrently, hepatitis B virus (HBV) re‐infection after liver transplantation (LT) can be almost completely suppressed by the administration of HBV reverse transcriptase inhibitors and hepatitis B immunoglobulins. However, after transplantation, there is no indicator of HBV replication because tests for the serum hepatitis B surface antigen and HBV‐DNA are both negative. Therefore, the criteria for reducing and discontinuing these precautions are unclear. In this study, we examined the serum HBV core‐related antigen (HBcrAg) and intrahepatic covalently closed circular DNA (cccDNA) in order to determine if these could be useful markers for HBV re‐infection.MethodsThirty‐one patients underwent LT for HBV‐related liver disease at Nagasaki University Hospital from 2001 to 2010. Of these, 20 cases were followed up for more than 1 year (median follow‐up period, 903 days). We measured serum HBcrAg and intrahepatic cccDNA levels in liver tissue. In addition, in nine cases, we assessed the serial changes of HBcrAg and intrahepatic cccDNA levels from preoperative periods to stable periods.ResultsWe examined serum HBcrAg and intrahepatic cccDNA levels in 20 patients (35 samples). HBcrAg and cccDNA levels were significantly correlated with each other (r = 0.616, P < 0.001). From a clinical aspect, the fibrosis stage was significantly lower in both HBcrAg‐ and cccDNA‐negative patients than in HBcrAg‐ or cccDNA‐positive patients.ConclusionsHBcrAg and cccDNA were useful as HBV re‐infection markers after LT. Keeping patients' HBcrAg and cccDNA negative after LT might contribute to long‐term graft survival.