bluuebunny/crossref_metadata_2025_split huggingface dataset:
Building developmental gene regulatory networks
Authors: Li Enhu , Davidson Eric H. 
Published: June 2009

AbstractAnimal development is an elaborate process programmed by genomic regulatory instructions. Regulatory genes encode transcription factors and signal molecules, and their expression is under the control of cis‐regulatory modules that define the logic of transcriptional responses to the inputs of other regulatory genes. The functional linkages among regulatory genes constitute the gene regulatory networks (GRNs) that govern cell specification and patterning in development. Constructing such networks requires identification of the regulatory genes involved and characterization of their temporal and spatial expression patterns. Interactions (activation/repression) among transcription factors or signals can be investigated by large‐scale perturbation analysis, in which the function of each gene is specifically blocked. Resultant expression changes are then integrated to identify direct linkages, and to reveal the structure of the GRN. Predicted GRN linkages can be tested and verified by cis‐regulatory analysis. The explanatory power of the GRN was shown in the lineage specification of sea urchin endomesoderm. Acquiring such networks is essential for a systematic and mechanistic understanding of the developmental process. Birth Defects Research (Part C) 87:123–130, 2009. © 2009 Wiley‐Liss, Inc.
Apprehending multicellularity: Regulatory networks, genomics, and evolution
Authors: Aravind L. , Anantharaman Vivek , Venancio Thiago M. 
Published: June 2009

AbstractThe genomic revolution has provided the first glimpses of the architecture of regulatory networks. Combined with evolutionary information, the “network view” of life processes leads to remarkable insights into how biological systems have been shaped by various forces. This understanding is critical because biological systems, including regulatory networks, are not products of engineering but of historical contingencies. In this light, we attempt a synthetic overview of the natural history of regulatory networks operating in the development and differentiation of multicellular organisms. We first introduce regulatory networks and their organizational principles as can be deduced using ideas from the graph theory. We then discuss findings from comparative genomics to illustrate the effects of lineage‐specific expansions, gene‐loss, and nonprotein‐coding DNA on the architecture of networks. We consider the interaction between expansions of transcription factors, and cis regulatory and more general chromatin state stabilizing elements in the emergence of morphological complexity. Finally, we consider a case study of the Notch subnetwork, which is present throughout Metazoa, to examine how such a regulatory system has been pieced together in evolution from new innovations and pre‐existing components that were originally functionally distinct. Birth Defects Research (Part C) 87:143–164, 2009. © 2009 Wiley‐Liss, Inc.
The utilization of glycogen accumulating organisms for mixed culture production of polyhydroxyalkanoates
Authors: Bengtsson Simon 
Published: June 2009

AbstractProduction of polyhydroxyalkanoates (PHAs) by an open mixed culture enriched in glycogen accumulating organisms (GAOs) under alternating anaerobic–aerobic conditions with acetate as carbon source was investigated. The culture exhibited a stable enrichment performance over the 450‐day operating period with regards to phenotypic behavior and microbial community structure. Candidatus Competibacter phosphatis dominated the culture at between 54% and 70% of the bacterial biomass throughout the study, as determined by fluorescence in situ hybridization. In batch experiments under anaerobic conditions, PHA containing 3‐hydroxybutyrate (3HB) and 27 mol‐% 3‐hydroxyvalerate (3HV) was accumulated up to 49% of cell dry weight utilizing the glycogen pool stored in the SBR cycle. Under aerobic and ammonia limited conditions, PHA comprising only 3HB was accumulated to 60% of cell dry weight. Glycogen was consumed during aerobic PHA accumulation as well as under anaerobic conditions, but with different stoichiometry. Under aerobic conditions 0.31 C‐mol glycogen was consumed per consumed C‐mol acetate compared to 0.99 under anaerobic conditions. Both the PHA biomass content and the specific PHA production rate obtained were similar to what is typically obtained using the more commonly applied aerobic dynamic feeding strategy. Biotechnol. Bioeng. 2009; 104: 698–708 © 2009 Wiley Periodicals, Inc.
Forequarter amputation for malignancy
Authors: Rickelt J , Hoekstra H , van Coevorden F , de Vreeze R , Verhoef C , van Geel A N 
Published: June 2009

Abstract

Background
Forequarter amputation (FQA) is an important treatment for malignant disease of the shoulder girdle. The aim of this study was to elucidate its role in surgical oncology.

Methods
This retrospective study analysed 40 patients who had an FQA. In nine, the chest wall was resected. The most frequent diagnoses were soft-tissue sarcoma (28 patients) and recurrent breast cancer (five).

Results
Median follow-up was 16 (range 1–184) months. The 1-year, 2-year and 5-year overall survival for patients with malignant disease was 71, 59 and 38 per cent respectively. The median time to local recurrence (eight patients) was 4 (range 1–19) months. Thirty-two patients had curative FQA with a 1-year, 2-year and 5-year overall survival of 90, 75 and 48 per cent respectively, and a median overall survival of 51 months. The 5-year overall and disease-free survival for soft-tissue sarcoma was 41 and 26 per cent respectively. Eight patients had a palliative FQA with a median survival of 5 (range 1–12) months.

Conclusion
In locoregional disease such as sarcoma, FQA may offer the only possibility of cure. However, in patients with axillary metastasis, FQA has no impact on survival, although local control may improve the patient's quality of life.
Socioeconomic deprivation adversely affects survival of patients with rectal cancer
Authors: Harris A R , Bowley D M , Stannard A , Kurrimboccus S , Geh J I , Karandikar S 
Published: June 2009

Abstract

Background
The aim was to examine the influence of socioeconomic deprivation on stage at presentation, perioperative mortality, permanent stoma rates and overall survival in patients with rectal cancer.

Methods
Data on patient demographics, mode and stage of presentation, and short- and longer-term outcomes were extracted from a database of patients with rectal cancer. Comparisons were made after stratification into quintiles of socioeconomic deprivation.

Results
In total 486 patients were identified. Fewer patients from the most deprived group than from the least deprived group underwent resectional surgery (79·2 versus 93 per cent; P = 0·005). Permanent stoma rates among patients who had surgery were 40·8 and 30 per cent respectively (P = 0·110). The overall 5-year survival rate was 32·8 per cent for the most deprived compared with 64·0 per cent for the least deprived patients (P &lt; 0·001). Respective rates for those who underwent resectional surgery were 49·9 and 72 per cent (P = 0·030).

Conclusion
In rectal cancer, socioeconomic deprivation appears to be associated with poorer outcomes and survival. This has important implications for healthcare planning.
Systematic review and meta-analysis of prophylactic gastroenterostomy for unresectable advanced pancreatic cancer
Authors: Hüser N , Michalski C W , Schuster T , Friess H , Kleeff J 
Published: June 2009

Abstract

Background
The value of prophylactic gastroenterostomy (usually combined with a biliary bypass) in patients with unresectable cancer of the pancreatic head is controversial.

Methods
A systematic review of retrospective and prospective studies, and a meta-analysis of prospective studies, on the use of prophylactic gastroenterostomy for unresectable pancreatic cancer were performed.

Results
Analysis of retrospective studies did not reveal any advantage or disadvantage of prophylactic gastroenterostomy. Three prospective studies comparing prophylactic gastroenterostomy plus biliodigestive anastomosis with no bypass or a biliodigestive anastomosis alone were identified (altogether 218 patients). For patients who had prophylactic gastroenterostomy, the chance of gastric outlet obstruction during follow-up was significantly lower (odds ratio (OR) 0·06 (95 per cent confidence interval (c.i.) 0·02 to 0·21); P &lt; 0·001). The rates of postoperative delayed gastric emptying were similar in both groups (OR 1·93 (95 per cent c.i. 0·57 to 6·53); P = 0·290), as were morbidity and mortality. The estimated duration of hospital stay after prophylactic gastroenterostomy was 3 days longer than for patients without bypass (weighted mean difference 3·1 (95 per cent c.i. 0·7 to 5·5); P = 0·010).

Conclusion
Prophylactic gastroenterostomy should be performed during surgical exploration of patients with unresectable pancreatic head tumours because it reduces the incidence of long-term gastroduodenal obstruction without impairing short-term outcome.
Two-week target for laparoscopic cholecystectomy following gallstone pancreatitis is achievable and cost neutral
Authors: Monkhouse S J W , Court E L , Dash I , Coombs N J 
Published: June 2009

Abstract

Background
The British Society of Gastroenterology recommends that all patients with gallstone pancreatitis should undergo cholecystectomy within 2 weeks. This study assessed whether these guidelines are feasible and cost-effective.

Methods
Admissions for gallstone pancreatitis between January 2006 and January 2008 were reviewed. Readmissions for subsequent pancreatitis or biliary pathology were noted together with additional investigations, severity scores, hospital stay and time to cholecystectomy. The costs of readmission and theoretical costs of developing a dedicated operating list were provided by independent accountants.

Results
During the 2 years, 153 patients were admitted. Twenty-one patients (13·7 per cent) had further attacks requiring 40 readmissions. There were no deaths. Additional hospital costs related to readmissions were £172 170, including bed occupancy (£67 860), investigations (£12 510) and 153 cholecystectomies on an existing theatre list (£91 800). The estimated cost of staffing a half-day theatre list every fortnight, performing 153 cholecystectomies, was £170 391.

Conclusion
Instigating a dedicated theatre for cholecystectomy after biliary pancreatitis has many potential benefits. The costs of readmissions and ad hoc operating are balanced by those of a dedicated theatre list in the long term. Implementation of the guidelines would save approximately £900 annually and be cost neutral.
A new efficient mixture screening design for optimization of media
Authors: Rispoli Fred , Shah Vishal 
Published: June 2009

AbstractScreening ingredients for the optimization of media is an important first step to reduce the many potential ingredients down to the vital few components. In this study, we propose a new method of screening for mixture experiments called the centroid screening design. Comparison of the proposed design with Plackett‐Burman, fractional factorial, simplex lattice design, and modified mixture design shows that the centroid screening design is the most efficient of all the designs in terms of the small number of experimental runs needed and for detecting high‐order interaction among ingredients. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009
Cost of care of patients with personality disorders in forensic psychiatric hospitals in the Netherlands
Authors: Avramenko Aleksandr , Evers Silvia , Philipse Martien , Chakhssi Farid , Ament Andre 
Published: June 2009

AbstractBackground Ter beschikking stelling (TBS) clinics form the mainstay of forensic psychiatric services in the Netherlands. Their costs are rising, but little is known about how these costs are distributed.Aim To determine the distribution of service costs for patients with personality disorders in TBS medium security units in the Netherlands.Method Data on service use were extracted retrospectively from the case files of 55 people with personality disorder who are residents in six medium security units within two TBS centres during 2006 (De Rooyse Wissel and Pompestichting). Standard unit costs were obtained for each service, and multiplied by frequency of service use to obtain the total cost of service per patient. A modified version of the Secure Facilities Service Use Schedule was completed.Results The average daily cost of a bed in a TBS hospital in 2006 was 388 Euros (402 (SD 37) Euros in De Rooyse Wissel; 375 (SD 48) Euros in the Pompestichting). Over half of this was spent on non‐treatment fixed costs (overheads). There was considerable difference between patients and between unit variations in the other costs, but about one‐third went on costs of staying in department (sociotherapists), and less than 10% each on specific therapeutic interventions or daily activities. About 3% of the budget overall was spent on other costs, but, as these included escorted leaves, at times these costs accounted for a much higher proportion of the per patient expenditure.Conclusion Our results may provide a baseline measurement, with which future costs of TBS treatment can be compared as the services expand and develop. More attention to costs in this way may help to contain budget increases. New studies could examine more specific aspects of treatment or other specific patient groups. Copyright © 2009 John Wiley & Sons, Ltd.
Gender differences in jail inmates' symptoms of mental illness, treatment history and treatment seeking
Authors: Drapalski Amy L. , Youman Kerstin , Stuewig Jeff , Tangney June 
Published: June 2009

AbstractBackground Rates of mental illness among prisoners are substantial, but little is known about the unique mental health needs of women in jail, those under pre‐trial custodial remand or serving short sentences.Aims To compare male and female jail inmates along a wide range of symptoms of mental illness using identical assessment methods, and to examine gender differences in treatment seeking before and during incarceration.Methods Soon after incarceration in a county jail, 360 male and 154 female pre‐trial and post‐trial inmates completed the Personality Assessment Inventory, a wide‐ranging measure of psychiatric symptoms. Treatment seeking information was taken from official jail records.Results Women were more likely to report clinically significant symptoms of anxiety, borderline personality features, somatic concerns and trauma‐related symptoms; however, trauma‐related symptoms and borderline features were also common among male inmates. Although both men and women reported high rates of drug‐related problems, alcohol‐related problems were twice as prevalent among male inmates. Female inmates were more likely to seek and be enrolled in jail‐based treatment; there were no differences in reported help seeking prior to incarceration.Conclusions Female jail inmates are especially in need of mental health services. Effective interventions for post‐traumatic stress disorder and borderline personality disorder are needed in jail settings for both male and female inmates during incarceration and upon release. Copyright © 2009 John Wiley & Sons, Ltd.
Relief of severe immediate postoperative superior vena cava stenosis with covered stent: Case report with midterm follow up
Authors: Rossi F. Raul I. , Manica João Luiz L. 
Published: June 2009

AbstractSinus venous atrial septal defects are commonly associated with abnormal pulmonary venous connection. Numerous surgical techniques have been proposed with excellent short‐ and long‐term outcomes. Pulmonary and superior vena cava obstructions, as well as rhythm disturbances, are the most common problems seen during follow up. However, acute postoperative superior vena cava obstruction with successful percutaneous covered‐stent implantation has not been reported in the literature. The objective of this study is to report a unique case of acute obstruction of the superior vena cava on the first postoperative day after sinus venous atrial septal defect repair in an infant who was successfully relieved by a percutaneous angioplasty with covered‐stent implantation, and the midterm follow up after this intervention. © 2009 Wiley‐Liss, Inc.
Conducting Polymer Networks Cross‐Linked by “Isolated” Functional Dyes: Design, Synthesis, and Electrochemical Polymerization of Doubly Strapped Light‐Harvesting Porphyrin/Oligothiophene Monomers
Authors: Sugiyasu Kazunori , Takeuchi Masayuki 
Published: June 2009

AbstractDye‐functionalized conducting polymers: A new concept in the design of monomers gives bithiophene‐based monomers as “isolated” functional dyes, thus yielding electroactive films through anodic electrochemical polymerization (see picture).magnified imageWe have synthesized doubly strapped porphyrin derivatives with four bithiophene segments that diverge from the porphyrin core, namely, Por(BT)4 and PorZn(BT)4. These molecules are designed as electrochemically polymerizable monomers that will yield the highly cross‐linked conducting polymeric networks poly[Por(BT)4] and poly[PorZn(BT)4], respectively, through an oxidative coupling reaction among the bithiophene moieties. Selective synthesis of the distal doubly strapped porphyrin derivatives was successful from the bis(formylphenyl) and bis(dipyrrolylmethylphenyl) straps under Lindsey conditions. Slow kinetics observed for the zinc insertion reaction toward the doubly strapped porphyrin derivative revealed that both faces of the porphyrin plane are overlaid with alkyl chain straps. To probe this “isolation” effect, photophysical properties of the monomers and their model components were investigated by UV/Vis and fluorescence spectroscopic analysis. An absorption spectral comparison between the diluted solution and the thin solid film of Por(BT)4 demonstrated that the porphyrin molecule is shielded by the double strap and self‐aggregation is prevented. It is noteworthy that the fluorescence of the spin‐coated film of the doubly strapped porphyrin monomer was twice as strong as that of an unstrapped porphyrin, thus indicating that the double strap can suppress undesired deactivation processes from the photoexcited state. In addition, fluorescence spectral measurements revealed that quantitative energy transfer from the oligothiophene segments to the porphyrin molecule takes place, which demonstrates an effective electronic interaction between these two chromophores. Electrochemical polymerization of the monomers Por(BT)4 and PorZn(BT)4 gave robust films that showed stable electrochemistry. Absorption spectral measurements and electrochemical characterization of the obtained films showed that the doubly strapped porphyrins are incorporated into the conducting polymer networks without any decomposition and protonation. Given all these observations above, our new monomer design based on functional dyes shielded by the double strap will lead to new organic optoelectronic materials in which functional molecules are spatially incorporated and isolated and yet show an effective electronic interactions with the conducting polymer backbones.
A Gadolinium‐Binding Cyclodecapeptide with a Large High‐Field Relaxivity Involving Second‐Sphere Water
Authors: Bonnet Célia S. , Fries Pascal H. , Crouzy Serge , Sénèque Olivier , Cisnetti Federico , Boturyn Didier , Dumy Pascal , Delangle Pascale 
Published: June 2009

AbstractA new cyclodecapeptide incorporating two prolylglycine sequences as β‐turn inducers and bearing four side chains with acidic carboxyl groups for cation complexation has been prepared. Structural analysis in water by 1H NMR spectroscopy and CD shows that this template adopts a conformation suitable for the complexation of lanthanide ions Ln3+, with its carboxyl groups oriented on the same face of the peptide scaffold. Luminescence titrations show that mononuclear Ln–PA complexes are formed with apparent stability constants of log β110≈6.5 (pH 7). The high‐field water relaxivity values arising from the Gd–PA complex at 200–500 MHz have been interpreted with molecular parameters determined independently. The experimentally determined water relaxivities are undoubtedly 30 % higher than the expected values for this complex with two inner‐sphere (IS) water molecules and a medium‐range rotational correlation time (τR=386 ps (±10 %)). This led us to propose the existence of a large second‐sphere (2S) contribution to the relaxivity caused by the interaction of water molecules with the hydrophilic peptide ligand by hydrogen‐bonding.
A Stereodivergent Strategy to Both Product Enantiomers from the Same Enantiomer of a Stereoinducing Catalyst: Agelastatin A
Authors: Trost Barry M. , Dong Guangbin 
Published: June 2009

AbstractIn this article, we report a full account of our recent development of pyrroles and N‐alkoxyamides as new classes of nucleophiles for palladium‐catalyzed AAA reactions, along with application of these methodologies in the total synthesis of agelastatin A, a marine natural product with exceptional anticancer activity and other biological properties. Our method allows for access to either regioisomer of the pyrrolopiperazinones (6 and 19) with high efficiency and enantioselectivity. Note that isomer 19 was obtained via a cascade reaction through a double allylic alkylation pathway. From regioisomer 6, the total synthesis of (+)‐agelastatin A was completed in a very short fashion (four steps from 6), during the course of which we developed a new copper catalyst for aziridination and an In(OTf)3/DMSO system to oxidatively open an N‐tosyl aziridine. Starting with the other pyrrolopiperazinone 19, a five‐step sequence has been developed to furnish a formal total synthesis of (−)‐agelastatin A. A unique feature of our syntheses is the use of two rather different strategies for the total syntheses of both enantiomers of agelastatin A using the same enantiomer of a chiral palladium catalyst.
ChemInform Abstract: Crystal Structures and Magnetic Properties of Fluorite‐Related Oxides Ln3NbO7 (Ln = Lanthanides).
Authors: Doi Yoshihiro , Harada Yuka , Hinatsu Yukio 
Published: June 2009

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Networks of Icosahedra in the Sodium—Zinc—Stannides Na16Zn13.54Sn13.46(5) (I), Na22Zn20Sn19(1) (II), and Na34Zn66Sn38(1) (III).
Authors: Kim Sung‐Jin , Faessler Thomas F. 
Published: June 2009

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Increase in Magnetoresistivity in Ba2CoS3 via Zn2+/Co2+ Substitution.
Authors: Harrison Mark R. , Hardy Vincent , Maignan Antoine , Francesconi M. Grazia 
Published: June 2009

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Phase Equilibria in Systems Ce—M—Sb (M: Si, Ge, Sn) and Superstructure Ce12Ge9‐xSb23+x (x = 3.8 .+‐. 0.1).
Authors: Nasir Navida , Grytsiv Andriy , Rogl Peter , Saccone Adriana , Giester Gerald 
Published: June 2009

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.