bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunoglobulin heavy chain gene regulation through polyadenylation and splicing competition
Authors: Peterson Martha L. 
Published: July 2010

AbstractThe immunoglobulin heavy chain (IgH) genes, which encode one of the two chains of antibody molecules, were the first cellular genes shown to undergo developmentally regulated alternative RNA processing. These genes produce two different mRNAs from a single primary transcript. One mRNA is cleaved and polyadenylated at an upstream poly(A) signal while the other mRNA removes this poly(A) signal by RNA splicing and is cleaved and polyadenylated at a downstream poly(A) site. A broad range of studies have been performed to understand the mechanism of IgH RNA processing regulation during B lymphocyte development. The model that has emerged is much more complex than envisioned by the earliest view of regulation through poly(A) signal choice. Regulation requires that the IgH gene contain competing splice and cleavage–polyadenylation reactions with balanced efficiencies. Because non‐IgH genes with these structural features also can be regulated, IgH gene‐specific sequence elements are not required for regulation. Changes in cleavage–polyadenylation and RNA splicing, as well as pol II elongation, all contribute to IgH developmental RNA processing regulation. Multiple factors are likely involved in the regulation during B lymphocyte maturation. Additional biologically relevant factors that contribute to IgH regulation remain to be identified and incorporated into a mechanistic model for regulation. Much of the work to date confirms the complex nature of IgH mRNA regulation and suggests that a thorough understanding of this control will remain a challenge. However, it is also likely that such understanding will help elucidate novel mechanisms of RNA processing regulation. WIREs RNA 2011 2 92–105 DOI: 10.1002/wrna.36This article is categorized under:

RNA Processing > Splicing Regulation/Alternative Splicing
RNA Processing > 3' End Processing
RNA in Disease and Development > RNA in Development
Recent Advances in Lanthanide‐Containing Polyoxotungstates
Authors: Bassil Bassem S. , Kortz Ulrich 
Published: July 2010

AbstractThe area of lanthanide‐containing polyoxometalates has been a field of large interest for several years due to the interesting structural and physicochemical properties of such compounds. This chemistry is dominated by tungsten based POMs, as a large number of vacant (lacunary) polytungstate precursors is known (as opposed to vanadium or molybdenum based POMs). The main subclasses in this field are lanthanide‐containing iso‐ and hetero‐polytungstates. The number of examples in the latter class is significantly larger than the former, probably because more lacunary hetero‐ than iso‐polytungstates are known. Here we report on recent examples of lanthanide‐containing iso‐ and hetero‐polytungstates with a focus on synthetic and in particular structural aspects. The compounds discussed include discrete molecular species as well as 1‐, 2‐ and 3‐D solid‐state assemblies.
A model checking-based approach for security policy verification of mobile systems
Authors: Braghin Chiara , Sharygina Natasha , Barone-Adesi Katerina 
Published: July 2010

AbstractThis article describes an approach for the automated verification of mobile systems. Mobile systems are characterized by the explicit notion oflocation(e.g., sites where they run) and the ability to execute at different locations, yielding a number of security issues. To this aim, we formalize mobile systems as Labeled Kripke Structures, encapsulating the notion oflocation netthat describes the hierarchical nesting of the threads constituting the system. Then, we formalize a genericsecurity-policy specification languagethat includes rules for expressing and manipulating the code location. In contrast to many other approaches, our technique supports both access control and information flow specification. We developed a prototype framework for model checking of mobile systems. It works directly on the program code (in contrast to most traditional process-algebraic approaches that can model only limited details of mobile systems) and uses abstraction-refinement techniques, based also on location abstractions, to manage the program state space. We experimented with a number of mobile code benchmarks by verifying various security policies. The experimental results demonstrate the validity of the proposed mobile system modeling and policy specification formalisms and highlight the advantages of the model checking-based approach, which combines the validation of security properties with other checks, such as the validation of buffer overflows.
Pancreaticojejunal Bridge‐Anastomosis: A Novel Option for Surgeon to Preserve Pancreatic Body and Tail in Urgent Reoperation for Intra‐abdominal Massive Hemorrhage after Pancreaticoduodenectomy
Authors: Xu Jin , Dai Xianwei , Bu Xianmin , Gao Feng , Zhang Xiaobo 
Published: July 2010

AbstractBackgroundPostoperative intra‐abdominal massive bleeding is a rare and life‐threatening complication associated with pancreaticoduodenectomy. Completion pancreatectomy (CP) was usually performed during reexploration for the complication. The management could decrease the complications, such as the pancreatic leakage or intraluminal infection after reexploration, but could increase mortality during the perioperative period. It also could result in loss of pancreatic function forever. This study evaluated an alternative surgical management for intra‐abdominal massive hemorrhage to prevent pancreas function, simplify the surgical processes, and decrease the mortality of relaparotomy.MethodsOutcome after pancreaticojejunal bridge‐anastomosis (PJBA) performed between January 2006 and June 2009 was compared with that after CP performed between February 1984 and December 2005.ResultsBetween February 1984 and June 2009, 963 patients underwent the Whipple procedure (PD) or pylorus‐preserving pancreaticoduodectomy (PPPD). Pancreatic leakage occurred in 103 patients (10.7%); 22 cases (21.4%) developed into intra‐abdominal massive bleeding. Nonsurgical procedures of transarterial embolization (TAE) were performed in ten (45.45%) patients, of whom one died (10%). Twelve (54.55%) underwent reoperation. Five had CP with one death (20%). Pancreatic remnant was preserved by pancreaticojejunal bridge‐anastomosis (PJBA) in seven patients with no deaths. The reexploration time was 340 ± 48.2 min vs. 247.9 ± 40.8 min (P < 0.01) for CP and PJBA group and the blood loss was 2,180 ± 526.3 ml vs. 1,628.6 ± 325.1 ml (P < 0.05). In‐hospital time for CP was less than that for PJBA (P < 0.05). All patients with CP still developed endocrine insufficiency (“brittle” diabetes) and diarrhea (exocrine insufficiency). There were no evidences of exocrine and endocrine insufficiency in patients with PJBA.ConclusionsPancreaticojejunal bridge‐anastomosis is an easy, simple, and safe procedure for intra‐abdominal massive hemorrhage associated with pancreaticoduodenectomy. It could decrease the mortality of reoperation and preserve the pancreatic function.
RP‐HPLC/MS‐APCI Analysis of Branched Chain TAG Prepared by Precursor‐Directed Biosynthesis with Rhodococcuserythropolis
Authors: Schreiberová Olga , Krulikovská Tereza , Sigler Karel , Čejková Alena , Řezanka Tomáš 
Published: July 2010

AbstractReversed phase liquid chromatography–atmospheric pressure chemical ionization mass spectrometry (RP‐HPLC/MS‐APCI) was used to analyze both synthetic triacylglycerols (TAG) having 1–3 branched fatty acids (FA) in the molecule, and natural TAG prepared by precursor directed biosynthesis from valine, leucine and isoleucine and the corresponding branched short‐chain acids in cultivations of Rhodococcus erythropolis. The technique made it possible to identify and quantify TAG differing in a single branched‐chain FA. Altogether 11 TAG were synthesized, out of which 8 were synthesized stereospecifically. Branched‐ and straight‐chain‐TAG were separated and identified while TAG differing only in iso or anteiso FA could not be separated. The APCI mass spectra of iso‐, anteiso‐ and straight‐chain TAG were completely identical. The natural material was found to contain 19 TAG having at least one branched FA. Cultivation on six different substrates showed, apart from the presumed and common incorporation of precursors to iso‐even, iso‐odd and anteiso FA, also some unusual features such as an increase in the content of odd‐FA after the addition of Val (attributed to catabolism of Val to propionate) or the appearance of branched monounsaturated FA. The two‐sample paired t test, when applied to the TAG, showed that only the pair Val and isobutyrate differ in incorporation into FA—see, e.g. proportions of M/M/O and brM/brM/O (1.2:1.2 and 1.9:1.2, respectively). Also, incorporation of Val (isobutyrate) yielded only TAG having two branched FA in the molecule, whereas Leu and Ile (isovalerate and 2‐methyl‐butyrate) gave only TAG with a single branched FA in the molecule.
Enzymatic Synthesis of Feruloylated Lipids: Comparison of the Efficiency of Vinyl Ferulate and Ethyl Ferulate as Substrates
Authors: Yu Yang , Zheng Yan , Quan Jing , Wu Cheng‐Yao , Wang Ya‐Juan , Branford‐White Christopher , Zhu Li‐Min 
Published: July 2010

AbstractA facile and efficient enzymatic synthesis approach to synthesize feruloylated lipids, which are composed of 1(3)‐feruloyl‐monooleyl‐glycerol and 1(3)‐feruloyl‐dioleyl‐glycerol, through lipase‐catalyzed transesterification using vinyl ferulate (VF) and ethyl ferulate (EF) as substrate, respectively, with triolein was developed. When VF was used as substrate, a maximum of conversion yield of 91.1% was obtained at 55 °C, 20 mg/mL enzyme content, water activity (aw) = 0.07, 62 h. This was greater than that when EF was used as substrate (69.6%, 50 °C, 33.3 mg/mL enzyme content, aw = 0.07, 96 h). Candida antarctica lipase (Novozym 435) can be reused for 13 runs without evident loss in activity and stability when VF was used as substrate. The results demonstrate that VF has greater synthetic efficiency and it provides another effective approach to prepare feruloylated lipids under normal pressure, making industry application feasible.
Unlimited shelf space in Internet supply chains: Treasure trove or wasteland?
Authors: Rabinovich Elliot , Sinha Rajiv , Laseter Timothy 
Published: July 2010

AbstractInternet retailing offers merchants limitless shelf space. This has led experts to highlight the existence of a “long tail” of offerings on the web and assert that the future of online business is “selling less of more.” However, it is difficult for Internet retailers of physical goods to sell a large scope of products without having to handle potentially large amounts of product returns from customers. This is due to the fact that customers can and do get overwhelmed by excessive product variety and often make erroneous purchasing decisions. We shed light on this issue through an assessment of theoretical predictions based on data from sales and returns of almost 7000 products in a particular product category. While retailers can benefit from expanding the scope of their inventories to generate Internet sales, the success of this strategy will depend on the control of unjustified product returns by consumers and the management of recurrent execution errors and product fit failures in transactions with customers. Furthermore, from our results, the gains that this strategy will bring to retailers will be bound by the amount of time products have been available on the Internet retailer's site, as well as by other attributes such as product price and size.
Primitive origins of prostate cancer: In vivo evidence for prostate‐regenerating cells and prostate cancer‐initiating cells
Authors: Goldstein Andrew S. , Stoyanova Tanya , Witte Owen N. 
Published: July 2010

AbstractTissue stem cells have been linked to cancers of epithelial origin including the prostate. There are three relevant issues concerning stem cells and cancer that rely solely on functional studies: 1. Are there tissue‐regenerating stem cells in the adult organ? 2. Can tissue‐regenerating cells serve as targets for transformation? 3. Do primary tumors contain tumor‐propagating (cancer stem) cells? We will review the recent literature with respect to these critical issues to provide a direct link between primitive cells and prostate cancer.
COMMENT ON CYRUS SCHAYEGH, “‘SEEING LIKE A STATE’: AN ESSAY ON THE HISTORIOGRAPHY OF MODERN IRAN” (IJMES42 [2010]: 37–61)
Authors: Keddie Nikki R. 
Published: July 2010

Cyrus Schayegh's “‘Seeing Like a State’: An Essay on the Historiography of Modern Iran” tries to show how historians of the Pahlavi era “have been gripped by the image of an omnipotent, completely autonomous state and how, each one . . . turned this image into what I call methodological statism” (p. 38). He discusses critically several works by historians and political scientists while mentioning more favorably a few works by anthropologists and sociologists and then indicates what he considers a better approach to Pahlavi history. Although I agree with some of his criticisms and am glad to see a serious discussion of historiography, I think he overstates the sins of historians and fails to distinguish between historians and political scientists, whose discipline leads them to emphasize the state.
Memory monitoring failure in confabulation: Evidence from the semantic illusion paradigm
Authors: KAN IRENE P. , LAROCQUE KAREN F. , LAFLECHE GINETTE , COSLETT H. BRANCH , VERFAELLIE MIEKE 
Published: July 2010

AbstractSeveral prominent models of confabulation characterize the syndrome as a failure in controlled aspects of memory retrieval, such as pre-retrieval cue specification and post-retrieval monitoring. These models have been generated primarily in the context of studies of autobiographical memory retrieval. Less research has focused on the existence and mechanisms of semantic confabulation. We examined whether confabulation extends to the semantic domain, and if so, whether it could be understood as a monitoring failure. We focus on post-retrieval monitoring by using a verification task that minimizes cue specification demands. We used the semantic illusion paradigm that elicits erroneous endorsement of misleading statements (e.g., “Two animals of each kind were brought onto the Ark by Moses before the great flood”) even in controls, despite their knowing the correct answer (e.g., Noah). Monitoring demands were manipulated by varying semantic overlap between target and foils, ranging from high semantic overlap to unrelated. We found that semantic overlap modulated the magnitude of semantic illusion in all groups. Compared to controls, both confabulators and non-confabulators had greater difficulty monitoring semantically related foils; however, elevated endorsement of unrelated foils was unique to confabulators. We interpret our findings in the context of a two-process model of post-retrieval monitoring. (JINS, 2010, 16, 1006–1017.)
Confabulation in schizophrenia: A neuropsychological study
Authors: LORENTE-ROVIRA E. , SANTOS-GÓMEZ J.L. , MORO M. , VILLAGRÁN J.M. , MCKENNA P.J. 
Published: July 2010

AbstractConfabulation has been documented in schizophrenia, but its neuropsychological correlates appear to be different from those of confabulation in neurological disease states. Forty-five schizophrenic patients and 37 controls were administered a task requiring them to recall fables. They also underwent testing with a range of memory and executive tasks. The patients with schizophrenia produced significantly more confabulations than the controls. After correcting for multiple comparisons, confabulation was not significantly associated with memory impairment, and was associated with impairment on only one of eight executive measures, the Brixton Test. Confabulation scores were also associated with impairment on two semantic memory tests. Confabulation was correlated with intrusion errors in recall, but not false positive errors in a recognition task. The findings suggest that confabulation in schizophrenia is unrelated to the episodic memory impairment seen in the disorder. However, the association with a circumscribed deficit in executive function could be consistent with a defective strategic retrieval account of confabulation similar to that of Moscovitch and co-workers, interacting with defective semantic memory. (JINS, 2010,16, 1018–1026.)
The impact of the water rights system on smallholder irrigators' willingness to pay for water in Limpopo province, South Africa
Authors: SPEELMAN STIJN , FAROLFI STEFANO , FRIJA AYMEN , D'HAESE MARIJKE , D'HAESE LUC 
Published: July 2010

ABSTRACTWater rights are currently receiving increased attention from scholars and policymakers due to the growing understanding that ill-defined water rights impair efficient use. In South Africa, smallholder irrigation faces problems of low water use efficiency and cost recovery of government investments. This study uses contingent ranking to analyse the willingness to pay (WTP) of smallholder irrigators for changes in the water rights system. The results indicate that smallholders are prepared to pay considerably higher water prices if these are connected to improvements in the water rights system. By segmenting the population it was also shown that the importance attached to water rights dimensions varies in each segment. While lower institutional trust and lower income levels lead to a lower WTP for transferability, experiencing water shortage increases this WTP. Such information is valuable in guiding policy makers in the future design of water rights.
RACE DOESN'T MATTER, RACE MATTERS
Authors: Simon Bryant 
Published: July 2010

AbstractThis enthographically-based essay uses the case of Starbucks and the company's diversity policies and relationship with Magic Johnson to explore the desire for postracialism in post Civil Rights—post Martin Luther King, Jr. and post protest—mainstream America. Where did this desire come from and how did corporate America package this desire? What is the relationship between the selling of postracialism and voting for Barack Obama? What are the implications of these marketing moves? What do they tell us about business and about ourselves?
Liberal Religion, Artistic Autonomy, and the Culture of Secular Choral Societies
Authors: VINSON DUNCAN 
Published: July 2010

AbstractU.S. choral societies typically formalize themselves as secular organizations analogous to symphony orchestras and opera companies. Yet choral societies differ from symphonic or operatic organizations because almost all choruses depend on volunteer singers. Part of what attracts singers into choruses is a sometimes unacknowledged affinity between the religious traditions of liberal Christians and Jews and the culture of choral singing as practiced in formally secular choral societies. The liberal tradition in religion encourages a habitus toward music that might be called a “sense of liturgy”: The interpretation of musical works historically and collectively, rather than as didactic works addressed to an individual. Although many canonical choral works are Christian in content, liberal religion encourages distancing mechanisms that allow people from other faith traditions, or none at all, to engage with these works. In short, the posture of artistic autonomy often found within formally secular choral societies, in which there is no overt religious test for membership, owes part of its genesis to the religious habits of liberal Christians and Jews. The present article explores this affinity by drawing on ethnomusicological fieldwork among choral singers in New England, as well as published accounts of a 1996 controversy over the performance of religious music by a public school choir in Utah.
Microbial community structure across the tree of life in the extreme Río Tinto
Authors: Amaral-Zettler Linda A , Zettler Erik R , Theroux Susanna M , Palacios Carmen , Aguilera Angeles , Amils Ricardo 
Published: July 2010

Abstract
Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Río Tinto (RT) in southwestern Spain provides a rare opportunity to conduct an ecosystem-wide biodiversity inventory at the level of all three domains of life, because diversity there is low and almost exclusively microbial. Despite improvements in high-throughput DNA sequencing, environmental biodiversity studies that use molecular metrics and consider entire ecosystems are rare. These studies can be prohibitively expensive if domains are considered separately, and differences in copy number of eukaryotic ribosomal RNA genes can bias estimates of relative abundances of phylotypes recovered. In this study we have overcome these barriers (1) by targeting all three domains in a single polymerase chain reaction amplification and (2) by using a replicated sampling design that allows for incidence-based methods to extract measures of richness and carry out downstream analyses that address community structuring effects. Our work showed that combined bacterial and archaeal richness is an order of magnitude higher than eukaryotic richness. We also found that eukaryotic richness was highest at the most extreme sites, whereas combined bacterial and archaeal richness was highest at less extreme sites. Quantitative community phylogenetics showed abiotic forces to be primarily responsible for shaping the RT community structure. Canonical correspondence analysis revealed co-occurrence of obligate symbionts and their putative hosts that may contribute to biotic forces shaping community structure and may further provide a possible mechanism for persistence of certain low-abundance bacteria encountered in the RT.
Alternative pathways for phosphonate metabolism in thermophilic cyanobacteria from microbial mats
Authors: Gomez-Garcia Maria R , Davison Michelle , Blain-Hartnung Matthew , Grossman Arthur R , Bhaya Devaki 
Published: July 2010

Abstract
Synechococcus sp. represents an ecologically diverse group of cyanobacteria found in numerous environments, including hot-spring microbial mats, where they are spatially distributed along thermal, light and oxygen gradients. These thermophiles engage in photosynthesis and aerobic respiration during the day, but switch to fermentative metabolism and nitrogen fixation at night. The genome of Synechococcus OS-B′, isolated from Octopus Spring (Yellowstone National Park) contains a phn gene cluster encoding a phosphonate (Phn) transporter and a C–P lyase. A closely related isolate, Synechococcus OS-A, lacks this cluster, but contains genes encoding putative phosphonatases (Phnases) that appear to be active only in the presence of the Phn substrate. Both isolates grow well on several different Phns as a sole phosphorus (P) source. Interestingly, Synechococcus OS-B′ can use the organic carbon backbones of Phns for heterotrophic growth in the dark, whereas in the light this strain releases organic carbon from Phn as ethane or methane (depending on the specific Phn available); Synechococcus OS-A has neither of these capabilities. These differences in metabolic strategies for assimilating the P and C of Phn by two closely related Synechococcus spp. are suggestive of niche-specific constraints in the evolution of nutrient assimilation pathways and syntrophic relationships among the microbial populations of the hot-spring mats. Thus, it is critical to evaluate levels of various P sources, including Phn, in thermally active habitats and the potential importance of these compounds in the biogeochemical cycling of P and C (some Phn compounds also contain N) in diverse terrestrial environments.