bluuebunny/crossref_metadata_2025_split huggingface dataset:
A generic complete dynamic logic for reasoning about purity and effects
Authors: Mossakowski Till , Schröder Lutz , Goncharov Sergey 
Published: April 2010

Abstract
For a number of programming languages, among them Eiffel, C, Java, and Ruby, Hoare-style logics and dynamic logics have been developed. In these logics, pre- and postconditions are typically formulated using potentially effectful programs. In order to ensure that these pre- and postconditions behave like logical formulae (that is, enjoy some kind of referential transparency), a notion of purity is needed. Here, we introduce a generic framework for reasoning about purity and effects. Effects are modelled abstractly and axiomatically, using Moggi’s idea of encapsulation of effects as monads. We introduce a dynamic logic (from which, as usual, a Hoare logic can be derived) whose logical formulae are pure programs in a strong sense. We formulate a set of proof rules for this logic, and prove it to be complete with respect to a categorical semantics. Using dynamic logic, we then develop a relaxed notion of purity which allows for observationally neutral effects such writing on newly allocated memory.
Has the Accuracy of Preoperative Diagnosis Improved in Cases of Early‐stage Gastric Cancer?
Authors: Tsujimoto Hironori , Sugasawa Hidekazu , Ono Satoshi , Ichikura Takashi , Yamamoto Junji , Hase Kazuo 
Published: April 2010

AbstractBackgroundAdequate preoperative evaluation for gastric cancer staging is essential to develop an individualized treatment strategy involving surgery with reduced lymphadenectomy and laparoscopic gastrectomy.MethodsA total of 509 gastric cancer patients with clinical Stage IA or IB disease were divided into two groups: 304 patients were admitted in 2000 or earlier (Group A), and 205 patients were admitted in 2001, when multidetector computed tomography (MD‐CT) was available, or later (Group B). We evaluated the accuracy of the preoperative diagnoses of tumor depth, lymph node involvement, and tumor stage.ResultsWith respect to tumor depth, 94.5 and 52.8% of patients were staged correctly in cT1 and cT2 patients, respectively. Among both cT1 and cT2 patients, the underestimated rates were lower in Group B than in Group A. For nodal metastasis, 83.2 and 30.0% of patients were staged correctly in cN0 and cN1 patients, respectively. Among the cN0 patients, 82.1 and 84.7% of Group A and Group B patients, respectively, were staged correctly. Among the cN1 patients, none of the patients in Group B was underestimated, while 9.7% of Group A patients were underestimated. There was a significant increase in the percentage of correctly staged patients and a decrease in the percentage of underestimated patients in Group B in comparison to Group A in both cStage IA and cStage IB patients.ConclusionsRemarkable advances have been observed in the accuracy of preoperative staging in the early stage of gastric cancer. However, it is necessary to continue to develop accurate preoperative and intraoperative diagnostic systems.
Impact of the Introduction of Laparoscopic Wedge Resection as a Surgical Option for Suspected Small/Medium‐Sized Gastrointestinal Stromal Tumors of the Stomach on Perioperative and Oncologic Outcomes
Authors: Goh Brian K. P. , Chow Pierce K. H. , Chok Aik‐Yong , Chan Weng‐Hoong , Chung Yaw‐Fui A. , Ong Hock‐Soo , Wong Wai‐Keong 
Published: April 2010

AbstractBackgroundThe present study is designed to determine the feasibility and impact of the introduction of laparoscopic wedge resection as a surgical option for the treatment of suspected small/medium‐sized (<7 cm) gastric gastrointestinal stromal tumors (GISTs).MethodsThe study involved a retrospective review of 53 consecutive patients who underwent laparoscopic or open wedge resection of a suspected gastric GIST. It was divided into two consecutive time periods wherein laparoscopic resection was a surgical option only in the latter period. Comparisons were made between the outcomes of patients who underwent laparoscopic versus open wedge resection and the outcomes of patients treated during the two consecutive time periods (to determine the impact of the introduction of laparoscopic wedge resection),ResultsFourteen patients (26%) underwent laparoscopic wedge resection with 1 conversion. The pathological exam showed that 41 patients (77%) had a GIST. Laparoscopic resection was significantly associated with a longer operative time, an earlier return of bowel function, earlier resumption of liquid and solid diet, decreased duration of parenteral or epidural analgesia use, and shorter postoperative hospitalization compared to open resection. There was no statistical difference in the rate of R1 resection and actuarial recurrence‐free survival for the two approaches. Comparison between the two time periods demonstrated that the introduction of the laparoscopic approach in the latter period resulted in an earlier return of bowel function, earlier resumption of liquid and solid diet, and decreased duration of parenteral or epidural analgesia.ConclusionsLaparoscopic wedge resection for gastric GIST can be safely adopted. It is associated with a more favorable perioperative outcome than the open approach. Its introduction as a surgical option has resulted in an improvement in perioperative outcomes without compromising oncologic safety at our institution.
Comparing Hepatic Resection and Transarterial Chemoembolization for Barcelona Clinic Liver Cancer (BCLC) Stage B Hepatocellular Carcinoma: Change for Treatment of Choice?
Authors: Lin Chin‐Ta , Hsu Kuo‐Feng , Chen Teng‐Wei , Yu Jyh‐Cherng , Chan De‐Chuan , Yu Chih‐Yung , Hsieh Tsai‐Yuan , Fan Hsiu‐Lung , Kuo Shih‐Ming , Chung Kuo‐Piao , Hsieh Chung‐Bao 
Published: April 2010

AbstractBackgroundCompared to transarterial chemoembolization (TACE) for patients with hepatocellular carcinoma (HCC), stage B in the Barcelona Clinic Liver Cancer (BCLC) classification, the role of hepatic resection remains unclear. The present study compared the long‐term outcome of hepatic resection with TACE in the treatment of BCLC stage B HCC.MethodsA total of 171 patients with BCLC stage B, Child’s classification A (Child A), HCC were included in this retrospective study. Of these, 93 patients underwent hepatic resection (group I) and 73 patients received TACE (group II). We evaluated the long‐term outcome and therapy‐related mortality in both groups. The risk factors of mortality were assessed. The survival curve was analyzed by the Kaplan–Meier method.ResultsThe 1‐, 2‐, and 3‐year overall survival rates for the two groups after hepatic resection and TACE were 83%, 62%, 49% and 39%, 5%, 2%, respectively (P < 0.0001). We did not observe significant differences in the therapy‐related mortality between the two groups (P = 0.78). Treatment modality and serum albumin level were independent risk factors for survival by Cox regression analysis.ConclusionsOur study demonstrated that hepatic resection for BCLC stage B, Child A HCC patients had better survival rates than TACE group. Thus, hepatic resection is indicated in selected patients with BCLC stage B.
How to measure the urban‐wildland ecotone: redefining ‘peri‐urban’ areas
Authors: MacGregor‐Fors Ian 
Published: April 2010

AbstractThe array of definitions regarding ‘peri‐urban’ areas do not allow the precise measurement of its boundaries in a city. In this study, I developed an easy‐to‐use method to calculate the area where urban and adjacent non‐urban systems intermingle. To validate that such areas were ecologically meaningful, I compared bird community species‐richness, abundance, and composition from ‘intra‐’ and ‘peri‐urban’ areas in a medium‐sized neotropical city. Results show that ‘peri‐urban’ areas represent an important ecological interaction area for birds, and differ greatly from ‘intra‐urban’ areas. The proposed method is robust and useful for a great variety of amoeboid‐growing cities.
A senescence accelerated mouse model to study aging in the larynx
Authors: Kolachala Vasantha L. , Torres‐Gonzalez Edilson , Mwangi Simon , Kelly Patricia , Brigham Kenneth L. , Pavlath Grace K. , Rojas Mauricio , Johns Michael M. 
Published: April 2010

ObjectiveAge‐related changes in the larynx lead to significant voice impairment and reduced quality of life. There is a need for aged animal models that have practical generation times to study the fundamental changes and new therapeutics for the aging voice. The senescence accelerated prone mouse strain (SAMP) animals experience rapid aging without any experimental manipulation. The main objective of this study was to demonstrate the use of senescence accelerated mice to study aging in the larynx.Study DesignMurine model.SettingDepartment of Animal Resources, Emory University.Subjects and MethodsLarynges from five senescence accelerated prone mice, five normal aging senescence resistant mice, and five C57BL/6 mice were harvested and processed for paraffin sections. Histomorphometry was performed for assessment of collagen and hyaluronic acid distribution. In addition, frozen laryngeal tissue was harvested for transcriptional and translational assessment of collagen‐1, using real‐time polymerase chain reaction with specific primers and Western blots. Myofibroblast assessment was performed by immunostaining for the presence of α‐smooth muscle actin.ResultsThe deposition of collagen increased at six months of age in the SAMP vocal fold, and the level of collagen‐1 mRNA increased with age. The myofibroblast protein α‐smooth muscle actin was also found at a higher concentration in the SAMP vocal tissue. In contrast, the levels of hyaluronic acid in the vocal folds of SAMP mice decreased with age when compared to age‐matched C57BL/6 mice.ConclusionSAMP mice show accelerated, age‐related changes in the vocal fold that were evident at as early as six months of age. The use of senescence accelerated mice offers promise as a model to study age‐related laryngeal changes.
Drest in a little brief authority: Controls in residential work with adolescents
Authors: Lampen John 
Published: April 2010

SummaryI have suggested that in residential work with adolescents anxiety about controls is sometimes excessive, but given a pseudo‐justification by invoking parental models. A clearer understanding of the variety of parental tasks might help to reduce this anxiety. In the residential setting, however, the adults have other tasks, which include removing the obstacles to the emergence of a healthy moral consensus, the explicit and implicit expression of this consensus to which both they and the youngsters can contribute, the embodiment of a caring philosophy with which the youngsters can identify; and the encouragement of eventual independence, self‐control, and responsibility for others.
A new genus of Phyllobothriidae (Cestoda: Tetraphyllidea) in carcharhiniform sharks from Iran and Australia
Authors: Caira J.N. , Malek M. , Ruhnke T. 
Published: April 2010

AbstractThe collection of cestodes from the carcharhiniform shark Carcharhinus cf. dussumieri in the Persian Gulf off Iran resulted in the discovery of the new genus and species of tetraphyllidean tapeworm, Doliobothrium haselii n. gen. n. sp. Collections from the carcharhiniform shark Rhizoprionodon acutus in the Timor Sea off northern Australia resulted in material that is consistent with a species originally described as Pithophorus musculosus from this host species in India, but that appears to represent a second species in the new genus. This second species is redescribed and transferred to Doliobothrium n. gen. The two species differ from one another in total length, testis number and total number of proglottids, with the latter species generally being smaller in overall size than the former species. Histological sections and scanning electron microscopy confirm that this new genus differs from all other phyllobothriid genera in the possession of bothridia that both lack apical suckers and are tubular in form, bearing proximal and distal apertures. Despite differences in scolex morphology, the proglottids of the new genus are remarkably similar to those seen in Orectolobicestus, Paraorygmatobothrium and Ruhnkecestus, all of which also parasitize sharks. These four genera also share the presence of serrate gladiate spinitriches on their proximal bothridial surfaces. This is only the second report of a cestode from an elasmobranch from the Persian Gulf. Limited available data suggest that the fauna of this region resembles that of other regions of the Indo-Pacific. Furthermore, owing to the paucity of available information and specimens, it is recommended that Pithophorus and three of its remaining described species (i.e. P. pakistanensis, P. trygoni, P. yamagutii) be considered as a genus inquirendum and species inquirenda, respectively.
Comparison between cartilage–perichondrium composite ‘ring’ graft and temporalis fascia in type one tympanoplasty in children
Authors: Albirmawy O A 
Published: April 2010

AbstractObjective:This study aimed to evaluate the anatomical and audiological outcomes of primary type one tympanoplasty performed with a modified cartilage–perichondrium composite ‘ring’ graft, and to compare them with results for primary type one tympanoplasty performed with temporalis fascia, in children.Study design:Retrospective clinical study.Setting:Otolaryngology department, Tanta University Hospital, Egypt.Patients and methods:Records were evaluated for 82 children with dry tympanic membrane perforation (any size) and intact ossicular chain, and with no history of previous ear surgery except for tympanostomy. Patients of similar age and middle-ear pathology were selected to make the two groups as homogeneous as possible. An underlay type one tympanoplasty, using either a ring graft or temporalis fascia, was performed: 40 children were included in the ring graft group and 42 in the temporalis fascia group. All procedures were performed by the same surgeon. A successful anatomical outcome was considered to comprise full, intact healing of the graft without perforation, retraction, lateralisation or blunting, for at least one year post-operatively. Patients' post-operative pure tone average air–bone gap and speech reception threshold were compared with pre-operative levels, within and between the two groups.Results:Type one tympanoplasty using a ring graft technique resulted in a significantly greater graft acceptance rate (95 per cent) compared with the temporalis fascia technique (76.2 per cent;p < 0.01). Pure tone average air–bone gap and speech reception threshold levels improved significantly in both the ring graft and fascia groups (p < 0.001). There was no significant difference in audiometric results between the two groups (p > 0.05), although there was a trend towards better post-operative results in the ring group.Conclusion:In our paediatric patients, type one tympanoplasty with a modified cartilage–perichondrium composite ring graft yielded good anatomical and functional results. The anatomical results obtained using this graft (with its unique appearance and stability during and after surgery) were superior to those for temporalis fascia. The ring graft group had equivalent, if not better, post-operative audiometric results, compared with the temporalis fascia group. Thus, the ring graft is believed to be effective in enabling both tympanic membrane closure and rapid hearing improvement, in the paediatric population.
Influence of substratum colour on the recruitment of macrofouling communities
Authors: Satheesh S. , Wesley S. Godwin 
Published: April 2010

Settlement of the fouling community is generally influenced by the physical, chemical and biological properties of the settling surface. The colour of the substratum may also exert an influence on larval settlement. In the present study, the influence of surface colour on the recruitment of fouling communities was investigated by suspending acrylic panels (red, green, blue, white and yellow) in coastal waters. Results showed that the colour of the substratum plays an important role in the recruitment of sessile species. Recruitment was comparatively high on red and blue coloured surfaces. Barnacle and tubeworm recruitment showed significant variation (Tukey test, P < 0.05) between different coloured surfaces. The significant conclusion of this study is that the colour of the artificial substrata should be taken into consideration when interpreting results from short-term biofouling studies.
CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data
Authors: Ivakhno Sergii , Tavaré Simon 
Published: April 2010

AbstractMotivation: The current generation of single nucleotide polymorphism (SNP) arrays allows measurement of copy number aberrations (CNAs) in cancer at more than one million locations in the genome in hundreds of tumour samples. Most research has focused on single-sample CNA discovery, the so-called segmentation problem. The availability of high-density, large sample-size SNP array datasets makes the identification of recurrent copy number changes in cancer, an important issue that can be addressed using the cross-sample information.Results: We present a novel approach for finding regions of recurrent copy number aberrations, called CNAnova, from Affymetrix SNP 6.0 array data. The method derives its statistical properties from a control dataset composed of normal samples and, in contrast to previous methods, does not require segmentation and permutation steps. For rigorous testing of the algorithm and comparison to existing methods, we developed a simulation scheme that uses the noise distribution present in Affymetrix arrays. Application of the method to 128 acute lymphoblastic leukaemia samples shows that CNAnova achieves lower error rate than a popular alternative approach. We also describe an extension of the CNAnova framework to identify recurrent CNA regions with intra-tumour heterogeneity, present in either primary or relapsed samples from the same patients.Availability: The CNAnova package and synthetic datasets are available at http://www.compbio.group.cam.ac.uk/software.htmlContact: sergii.ivakhno@cancer.org.ukSupplementary information: Supplementary data are available at Bioinformatics online.
Proteomic Analysis of Biopsied Human Colonic Mucosa
Authors: Gourley Glenn R , Yang Libang , Higgins LeeAnn , Riviere Michael A , David Larry L 
Published: April 2010

ABSTRACTBackground and Objectives:Pediatric gastroenterologists have a unique opportunity to study the proteins in the gastrointestinal tract. To assess the power of proteomic studies we compared 2 methods for analysis of proteins in normal human colonic mucosa: 2‐dimensional gel electrophoresis (2DE) and 2‐dimensional liquid chromatography (2DLC) in conjunction with mass spectrometry. We used Ingenuity Pathway Analysis to examine these proteins regarding function, location, and relation to disease.Results:2DLC identified 550 proteins, whereas 2DE identified 107 proteins, 18 of which were not observed with 2DLC. The function associated with the largest number of proteins for both methods was cancer (236 proteins with 2DLC, 61 proteins with 2DE). The largest group of proteins was from the cytoplasm (49.3% from 2DE and 49.1% from 2DLC). Two hundred seventy of the total 568 proteins were related to 26 different categories of human disease and 200 of these 270 were described in large intestine, 227 were described in blood, and 149 were described in serum or plasma.Conclusions:These methods are complementary, although many more proteins were identified with 2DLC. This suggests that 2DLC should have greater utility in examining changes in the proteome of the colonic mucosa during disease than 2DE. However, some proteins found were unique to 2DE, and thus the methods chosen for a given analysis must be matched with the proteins to be studied. When pediatric gastroenterologists use proteomic methods, there is a new opportunity to increase our understanding of the gastrointestinal tract in health and disease.
Quality of Life in Children With Crohn Disease
Authors: Hill RJ , Lewindon PJ , Muir R , Grangé I , Connor FL , Ee LC , Withers GD , Cleghorn GJ , Davies PSW 
Published: April 2010

ABSTRACTObjectives:Quality of life (QOL) is reportedly poor in children with Crohn disease (CD) but improves with increasing disease duration. This article aims to detail QOL in a cohort of Australian children with CD in relation to disease duration, disease activity, and treatment.Materials and Methods:QOL, assessed using the IMPACT‐III questionnaire, and disease activity measures, assessed using the Pediatric Crohn's Disease Activity Index (PCDAI), were available in 41 children with CD. For this cohort, a total of 186 measurements of both parameters were available.Results:QOL was found to be significantly lower, and disease activity significantly higher (F = 31.1, P = 0.00), in patients within 6 months of their diagnosis compared with those up to 2.5 years, up to 5 years, and beyond 5 years since diagnosis. Higher disease activity was associated with poorer QOL (r = −0.51, P = 0.00). Total QOL was highest in children on nil medications and lowest in children on enteral nutrition. The PCDAI (t = −6.0, P = 0.00) was a significant predictor of QOL, with the clinical history (t = −6.9, P = 0.00) and examination (t = −2.9, P = 0.01) sections of the PCDAI significantly predicting QOL. Disease duration, age, or sex was neither related to nor significant predictors of QOL, but height z score and type of treatment approached significance.Conclusions:Children with CD within 6 months of their diagnosis have impaired QOL compared with those diagnosed beyond 6 months. These patients, along with those with growth impairment, ongoing elevated disease activity with abdominal pain, diarrhoea and/or perirectal and extraintestinal complications, may benefit from regular assessments of QOL as part of their clinical treatment.
Structure of theMethanothermobacter thermautotrophicusexosome RNase PH ring
Authors: Ng C. Leong , Waterman David G. , Antson Alfred A. , Ortiz-Lombardía Miguel 
Published: April 2010

The core of the exosome, a versatile multisubunit RNA-processing enzyme found in archaea and eukaryotes, includes a ring of six RNase PH subunits. This basic architecture is homologous to those of the bacterial and archaeal RNase PHs and the bacterial polynucleotide phosphorylase (PNPase). While all six RNase PH monomers are catalytically active in the homohexameric RNase PH, only half of them are functional in the bacterial PNPase and in the archaeal exosome core and none are functional in the yeast and human exosome cores. Here, the crystal structure of the RNase PH ring from the exosome of the anaerobic methanogenic archaeonMethanothermobacter thermautotrophicusis described at 2.65 Å resolution. Free phosphate anions were found for the first time in the active sites of the RNase PH subunits of an exosome structure and provide structural snapshots of a critical intermediate in the phosphorolytic degradation of RNA by the exosome. Furthermore, the present structure highlights the plasticity of the surfaces delineating the polar regions of the RNase PH ring of the exosome, a feature that can facilitate both interaction with the many cofactors involved in exosome function and the processive activity of this enzyme.