bluuebunny/crossref_metadata_2025_split huggingface dataset:
De Moivre's Poisson Approximation to the Binomial
Authors: Bellhouse David R. , Davison Matt 
Published: October 2009

Summary In his first work on probability, written in 1711, Abraham De Moivre looked at the problem of finding the number of trials required in a binomial experiment to achieve a probability of 1/2 of finding at least some given number of successes. He looked at two cases: when the probability of success p = 1/2 and when p is small but n, the number of trials, is large. In the latter case, unlike other problems that he solved in probability, De Moivre never revealed his method of solution. We explore the solution that De Moivre originally suggests and find that his method does not work. We explore other numerical solutions and put forward the suggestion that De Moivre relied on a very cumbersome and tedious method of solution based on his earlier work on series in the 1690s. Since his method was neither quick nor mathematically elegant, he never revealed the method that he used to obtain his numerical solutions.
Water Resources Modeling of the Ganges‐Brahmaputra‐Meghna River Basins Using Satellite Remote Sensing Data1
Authors: Nishat Bushra , Rahman S.M. Mahbubur 
Published: October 2009

Nishat, Bushra and S.M. Mahbubur Rahman, 2009. Water Resources Modeling of the Ganges‐Brahmaputra‐Meghna River Basins Using Satellite Remote Sensing Data. Journal of the American Water Resources Association (JAWRA) 45(6):1313‐1327.Abstract:  Large‐scale water resources modeling can provide useful insights on future water availability scenarios for downstream nations in anticipation of proposed upstream water resources projects in large international river basins (IRBs). However, model set up can be challenging due to the large amounts of data requirement on both static states (soils, vegetation, topography, drainage network, etc.) and dynamic variables (rainfall, streamflow, soil moisture, evapotranspiration, etc.) over the basin from multiple nations and data collection agencies. Under such circumstances, satellite remote sensing provides a more pragmatic and convenient alternative because of the vantage of space and easy availability from a single data platform. In this paper, we demonstrate a modeling effort to set up a water resources management model, MIKE BASIN, over the Ganges, Brahmaputra, and Meghna (GBM) river basins. The model is set up with the objective of providing Bangladesh, the lowermost riparian nation in the GBM basins, a framework for assessing proposed water diversion scenarios in the upstream transboundary regions of India and deriving quantitative impacts on water availability. Using an array of satellite remote sensing data on topography, vegetation, and rainfall from the transboundary regions, we demonstrate that it is possible to calibrate MIKE BASIN to a satisfactory level and predict streamflow in the Ganges and Brahmaputra rivers at the entry points of Bangladesh at relevant scales of water resources management. Simulated runoff for the Ganges and Brahmaputra rivers follow the trends in the rated discharge for the calibration period. However, monthly flow volume differs from the actual rated flow by (−) 8% to (+) 20% in the Ganges basin, by (−) 15 to (+) 12% in the Brahmaputra basin, and by (−) 15 to (+) 19% in the Meghna basin. Our large‐scale modeling initiative is generic enough for other downstream nations in IRBs to adopt for their own modeling needs.
Groundwater Banking in Aquifers that Interact With Surface Water: Aquifer Response Functions and Double‐Entry Accounting1
Authors: Contor Bryce A. 
Published: October 2009

Contor, Bryce A., 2009. Groundwater Banking in Aquifers That Interact With Surface Water: Aquifer Response Functions and Double‐Entry Accounting. Journal of the American Water Resources Association (JAWRA) 45(6):1465‐1474.Abstract:  Increasing worldwide demands for water call for mechanisms to facilitate storage of seasonal supplies and mechanisms to facilitate reallocation of water. Markets are economically efficient reallocation and incentive mechanisms when market conditions prevail, but special hydrologic and administrative conditions of water use and allocation interfere with required market conditions. Water banking in general can bring market forces to bear on water storage and reallocation, improving economic efficiency and therefore the welfare of society as a whole. Groundwater banking can utilize advantages of aquifers as storage vessels with vast capacity, low construction cost, and protection of stored water. For groundwater banking in aquifers that interact with surface water, an accounting system is needed that addresses the depletion of stored volumes of water as water migrates to surface water. Constructing such a system requires integration of hydrologic, economic, and legal principles with principles of financial accounting. Simple mass‐balance accounting, even with allowances for depletion, is not adequate in these aquifers. Aquifer response functions are mathematical descriptions of the impact that aquifer pumping or recharge events have upon hydraulically connected surface water bodies. Double‐entry accounting is a financial accounting methodology for tracking asset inventories and ownership claims upon assets. The powerful innovation of linking aquifer response functions with double‐entry accounting technologies allows application of groundwater banking to aquifers where deposits can be depleted by migration to hydraulically connected surface water. It honors the hydrologic realities of groundwater/surface water interaction, the legal requirements of prior appropriation water law, and the economic requirements for equitable and efficient allocation of resources.
Development and Analytical Validation of an Immunoassay for Quantifying Serum Anti-Pertussis Toxin Antibodies Resulting from
Bordetella pertussis
Infection
Authors: Menzies Sandra L. , Kadwad Vijay , Pawloski Lucia C. , Lin Tsai-Lien , Baughman Andrew L. , Martin Monte , Tondella Maria Lucia C. , Meade Bruce D. 
Published: October 2009

ABSTRACT

Adequately sensitive and specific methods to diagnose pertussis in adolescents and adults are not widely available. Currently, no Food and Drug Administration-approved diagnostic assays are available for the serodiagnosis of
Bordetella pertussis
. Since concentrations of
B. pertussis
-specific antibodies tend to be high during the later phases of disease, a simple, rapid, easily transferable serodiagnostic test was developed. This article describes test development, initial evaluation of a prototype kit enzyme-linked immunosorbent assay (ELISA) in an interlaboratory collaborative study, and analytical validation. The data presented here demonstrate that the kit met all prespecified criteria for precision, linearity, and accuracy for samples with anti-pertussis toxin (PT) immunoglobulin G (IgG) antibody concentrations in the range of 50 to 150 ELISA units (EU)/ml, the range believed to be most relevant for serodiagnosis. The assay met the precision and linearity criteria for a wider range, namely, from 50 to 200 EU/ml; however, the accuracy criterion was not met at 200 EU/ml. When the newly adopted World Health Organization International Standard for pertussis antiserum (human) reference reagent was used to evaluate accuracy, the accuracy criteria were met from 50 to 200 international units/ml. In conclusion, the IgG anti-PT ELISA met all assay validation parameters within the range considered most relevant for serodiagnosis. This ELISA was developed and analytically validated as a user-friendly kit that can be used in both qualitative and quantitative formats. The technology for producing the kit is transferable to public health laboratories.
Rapid Detection of
Mycobacterium tuberculosis
and Rifampin Resistance by Use of On-Demand, Near-Patient Technology
Authors: Helb Danica , Jones Martin , Story Elizabeth , Boehme Catharina , Wallace Ellen , Ho Ken , Kop JoAnn , Owens Michelle R. , Rodgers Richard , Banada Padmapriya , Safi Hassan , Blakemore Robert , Lan N. T. Ngoc , Jones-López Edward C. , Levi Michael , Burday Michele , Ayakaka Irene , Mugerwa Roy D. , McMillan Bill , Winn-Deen Emily , Christel Lee , Dailey Peter , Perkins Mark D. , Persing David H. , Alland David 
Published: October 2009

ABSTRACT

Current nucleic acid amplification methods to detect
Mycobacterium tuberculosis
are complex, labor-intensive, and technically challenging. We developed and performed the first analysis of the Cepheid Gene Xpert System's MTB/RIF assay, an integrated hands-free sputum-processing and real-time PCR system with rapid on-demand, near-patient technology, to simultaneously detect
M. tuberculosis
and rifampin resistance. Analytic tests of
M. tuberculosis
DNA demonstrated a limit of detection (LOD) of 4.5 genomes per reaction. Studies using sputum spiked with known numbers of
M. tuberculosis
CFU predicted a clinical LOD of 131 CFU/ml. Killing studies showed that the assay's buffer decreased
M. tuberculosis
viability by at least 8 logs, substantially reducing biohazards. Tests of 23 different commonly occurring rifampin resistance mutations demonstrated that all 23 (100%) would be identified as rifampin resistant. An analysis of 20 nontuberculosis mycobacteria species confirmed high assay specificity. A small clinical validation study of 107 clinical sputum samples from suspected tuberculosis cases in Vietnam detected 29/29 (100%) smear-positive culture-positive cases and 33/39 (84.6%) or 38/53 (71.7%) smear-negative culture-positive cases, as determined by growth on solid medium or on both solid and liquid media, respectively.
M. tuberculosis
was not detected in 25/25 (100%) of the culture-negative samples. A study of 64 smear-positive culture-positive sputa from retreatment tuberculosis cases in Uganda detected 63/64 (98.4%) culture-positive cases and 9/9 (100%) cases of rifampin resistance. Rifampin resistance was excluded in 54/55 (98.2%) susceptible cases. Specificity rose to 100% after correcting for a conventional susceptibility test error. In conclusion, this highly sensitive and simple-to-use system can detect
M. tuberculosis
directly from sputum in less than 2 h.
Adherence Factors in Atypical Enteropathogenic
Escherichia coli
Strains Expressing the Localized Adherence-Like Pattern in HEp-2 Cells
Authors: Scaletsky Isabel C. A. , Aranda Katia R. S. , Souza Tamara B. , Silva Neusa P. 
Published: October 2009

ABSTRACT

Although atypical enteropathogenic
Escherichia coli
(aEPEC) strains are frequently implicated in childhood diarrhea in developing countries, not much is known about their adherence properties. The phenotypic and genotypic characterization of 29 aEPEC strains expressing the localized adherence-like pattern points toward the involvement of
E. coli
common pilus (ECP), intimins, and other known
E. coli
adhesins in this pattern.
The Oncolytic Activity of Newcastle Disease Virus NDV-HUJ on Chemoresistant Primary Melanoma Cells Is Dependent on the Proapoptotic Activity of the Inhibitor of Apoptosis Protein Livin
Authors: Lazar Itay , Yaacov Barak , Shiloach Tamar , Eliahoo Elad , Kadouri Luna , Lotem Michal , Perlman Riki , Zakay-Rones Zichria , Panet Amos , Ben-Yehuda Dina 
Published: October 2009

ABSTRACT
Patients with advanced melanoma usually do not benefit from conventional chemotherapy treatment. There is therefore a true need for a new kind of therapy for melanoma. One factor responsible for the poor prognosis of melanoma is the inhibitor of apoptosis protein (IAP) family member Livin. In this study, we applied a novel approach for the treatment of melanoma, using a unique strain of the oncolytic Newcastle disease virus (NDV-HUJ). We found that, unlike chemotherapeutic drugs, NDV-HUJ, a one-cycle replicating virus, overcomes the resistance to apoptosis of melanoma primary cultures that over express the Livin protein. In contrast, melanoma tumor cells that do not express Livin are relatively resistant to NDV-HUJ treatment. Furthermore, we show that NDV-HUJ-induced oncolysis is attributed to the dual function of Livin: although Livin inhibits apoptosis through the inhibition of caspases, under the robust apoptotic stimulation of NDV-HUJ, caspases can cleave Livin to create a truncated protein with a paradoxical proapoptotic activity. Thus, NDV-HUJ is a potent inducer of apoptosis that can overcome the antiapoptotic effect of Livin and allow cleavage of Livin into the proapoptotic tLivin protein. Moreover, the results indicate that the interferon system, which is functional in melanoma, is not involved in NDV-induced oncolysis. Taken together, our data offer the possibility of a new viral oncolytic treatment for chemoresistant melanoma.
A
trans
-Complementing Recombination Trap Demonstrates a Low Propensity of Flaviviruses for Intermolecular Recombination
Authors: Taucher Christian , Berger Angelika , Mandl Christian W. 
Published: October 2009

ABSTRACT

Intermolecular recombination between the genomes of closely related RNA viruses can result in the emergence of novel strains with altered pathogenic potential and antigenicity. Although recombination between flavivirus genomes has never been demonstrated experimentally, the potential risk of generating undesirable recombinants has nevertheless been a matter of concern and controversy with respect to the development of live flavivirus vaccines. As an experimental system for investigating the ability of flavivirus genomes to recombine, we developed a “recombination trap,” which was designed to allow the products of rare recombination events to be selected and amplified. To do this, we established reciprocal packaging systems consisting of pairs of self-replicating subgenomic RNAs (replicons) derived from tick-borne encephalitis virus (TBEV), West Nile virus (WNV), and Japanese encephalitis virus (JEV) that could complement each other in
trans
and thus be propagated together in cell culture over multiple passages. Any infectious viruses with intact, full-length genomes that were generated by recombination of the two replicons would be selected and enriched by end point dilution passage, as was demonstrated in a spiking experiment in which a small amount of wild-type virus was mixed with the packaged replicons. Using the recombination trap and the JEV system, we detected two aberrant recombination events, both of which yielded unnatural genomes containing duplications. Infectious clones of both of these genomes yielded viruses with impaired growth properties. Despite the fact that the replicon pairs shared approximately 600 nucleotides of identical sequence where a precise homologous crossover event would have yielded a wild-type genome, this was not observed in any of these systems, and the TBEV and WNV systems did not yield any viable recombinant genomes at all. Our results show that intergenomic recombination can occur in the structural region of flaviviruses but that its frequency appears to be very low and that therefore it probably does not represent a major risk in the use of live, attenuated flavivirus vaccines.
Hepatitis B and Hepatitis C Virus Replication Upregulates Serine Protease Inhibitor Kazal, Resulting in Cellular Resistance to Serine Protease-Dependent Apoptosis
Authors: Lamontagne Jason , Pinkerton Mark , Block Timothy M. , Lu Xuanyong 
Published: October 2009

ABSTRACT
Hepatitis B and C viruses (HBV and HCV, respectively) are different and distinct viruses, but there are striking similarities in their disease potential. Infection by either virus can cause chronic hepatitis, liver cirrhosis, and ultimately, liver cancer, despite the fact that no pathogenetic mechanisms are known which are shared by the two viruses. Our recent studies have suggested that replication of either of these viruses upregulates a cellular protein called serine protease inhibitor Kazal (SPIK). Furthermore, the data have shown that cells containing HBV and HCV are more resistant to serine protease-dependent apoptotic death. Since our previous studies have shown that SPIK is an inhibitor of serine protease-dependent apoptosis, it is hypothesized that the upregulation of SPIK caused by HBV and HCV replication leads to cell resistance to apoptosis. The evasion of apoptotic death by infected cells results in persistent viral replication and constant liver inflammation, which leads to gradual accumulation of genetic changes and eventual development of cancer. These findings suggest a possibility by which HBV and HCV, two very different viruses, can share a common mechanism in provoking liver disease and cancer.
Late Domain-Independent Rescue of a Release-Deficient Moloney Murine Leukemia Virus by the Ubiquitin Ligase Itch
Authors: Jadwin Joshua A. , Rudd Victoria , Sette Paola , Challa Swathi , Bouamr Fadila 
Published: October 2009

ABSTRACT
Moloney murine leukemia virus (MoMLV) Gag utilizes its late (L) domain motif PPPY to bind members of the Nedd4-like ubiquitin ligase family. These interactions recruit components of the cell's budding machinery that are critical for virus release. MoMLV Gag contains two additional L domains, PSAP and LYPAL, that are believed to drive residual MoMLV release via interactions with cellular proteins Tsg101 and Alix, respectively. We found that overexpression of Tsg101 or Alix failed to rescue the release of PPPY-deficient MoMLV via these other L domains. However, low-level expression of the ubiquitin ligase Itch potently rescued the release and infectivity of MoMLV lacking PPPY function. In contrast, other ubiquitin ligases such as WWP1, Nedd4.1, Nedd4.2, and Nedd4.2s did not rescue this release-deficient virus. Efficient rescue required the ubiquitin ligase activity of Itch and an intact C2 domain but not presence of the endophilin-binding site. Additionally, we found Itch to immunoprecipitate with MoMLV Gag lacking the PPPY motif and to be incorporated into rescued MoMLV particles. The PSAP and LYPAL motifs were dispensable for Itch-mediated virus rescue, and their absence did not affect the incorporation of Itch into the rescued particles. Itch-mediated rescue of release-defective MoMLV was sensitive to inhibition by dominant-negative versions of ESCRT-III components and the VPS4 AAA ATPase, indicating that Itch-mediated correction of MoMLV release defects requires the integrity of the host vacuolar sorting protein pathway. RNA interference knockdown of Itch suppressed the residual release of the MoMLV lacking the PPPY motif. Interestingly, Itch stimulation of the PPPY-deficient MoMLV release was accompanied by the enhancement of Gag ubiquitination and the appearance of new ubiquitinated Gag proteins in virions. Together, these results suggest that Itch can facilitate MoMLV release in an L domain-independent manner via a mechanism that requires the host budding machinery and involves Gag ubiquitination.
Conserved Residues in the UL24 Protein of Herpes Simplex Virus 1 Are Important for Dispersal of the Nucleolar Protein Nucleolin
Authors: Bertrand Luc , Leiva-Torres Gabriel André , Hyjazie Huda , Pearson Angela 
Published: October 2009

ABSTRACT
The UL24 family of proteins is widely conserved among herpesviruses. We demonstrated previously that UL24 of herpes simplex virus 1 (HSV-1) is important for the dispersal of nucleolin from nucleolar foci throughout the nuclei of infected cells. Furthermore, the N-terminal portion of UL24 localizes to nuclei and can disperse nucleolin in the absence of any other viral proteins. In this study, we tested the hypothesis that highly conserved residues in UL24 are important for the ability of the protein to modify the nuclear distribution of nucleolin. We constructed a panel of substitution mutations in UL24 and tested their effects on nucleolin staining patterns. We found that modified UL24 proteins exhibited a range of subcellular distributions. Mutations associated with a wild-type localization pattern for UL24 correlated with high levels of nucleolin dispersal. Interestingly, mutations targeting two regions, namely, within the first homology domain and overlapping or near the previously identified PD-(D/E)XK endonuclease motif, caused the most altered UL24 localization pattern and the most drastic reduction in its ability to disperse nucleolin. Viral mutants corresponding to the substitutions G121A and E99A/K101A both exhibited a syncytial plaque phenotype at 39°C. vUL24-E99A/K101A replicated to lower titers than did vUL24-G121A or KOS. Furthermore, the E99A/K101A mutation caused the greatest impairment of HSV-1-induced dispersal of nucleolin. Our results identified residues in UL24 that are critical for the ability of UL24 to alter nucleoli and further support the notion that the endonuclease motif is important for the function of UL24 during infection.
A U
L
47 Gene Deletion Mutant of Bovine Herpesvirus Type 1 Exhibits Impaired Growth in Cell Culture and Lack of Virulence in Cattle
Authors: Lobanov Vladislav A. , Maher-Sturgess Sheryl L. , Snider Marlene G. , Lawman Zoe , Babiuk Lorne A. , van Drunen Littel-van den Hurk Sylvia 
Published: October 2009

ABSTRACT

Tegument protein VP8 encoded by the U
L
47 gene of bovine herpesvirus type 1 (BHV-1) is the most abundant constituent of mature virions. In the present report, we describe the characterization of U
L
47 gene-deleted BHV-1 in cultured cells and its natural host. The U
L
47 deletion mutant exhibited reduced plaque size and more than 100-fold decrease in intracellular and extracellular viral titers in cultured cells. Ultrastructural observations of infected cells showed normal maturation of BHV-1 virions in the absence of VP8. There was no evidence for a change in immediate-early gene activator function of VP16 in the U
L
47 deletion mutant virus-infected cells, since bovine ICP4 mRNA and protein levels were similar to those in the wild-type and revertant virus-infected cells throughout the course of infection. Whereas VP16, glycoprotein C (gC), gB, and VP5 were expressed to wild-type levels in the U
L
47 deletion mutant-infected cells, the gD and VP22 protein levels were significantly reduced. The reduction in gD protein was associated with increased turnover of the protein. Furthermore, some of the analyzed early and late proteins were expressed with earlier kinetics in the absence of VP8. Extracellular virions of the U
L
47 deletion mutant contained reduced amounts of gD, gB, gC, and VP22 but similar amounts of VP16 compared to those of wild-type or revertant virus particles. In addition, the U
L
47 gene product was indispensable for BHV-1 replication in vivo, since no clinical manifestations or viral shedding were detected in the U
L
47 deletion mutant-infected calves, and the virus failed to induce significant levels of humoral and cellular immunity.