bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harvest‐based Bayesian estimation of sika deer populations using state‐space models
Authors: Yamamura Kohji , Matsuda Hiroyuki , Yokomizo Hiroyuki , Kaji Koichi , Uno Hiroyuki , Tamada Katsumi , Kurumada Toshio , Saitoh Takashi , Hirakawa Hirofumi 
Published: December 2007

AbstractWe have estimated the number of sika deer,Cervus nippon, in Hokkaido, Japan, with the aim of developing a management program that will reduce the level of agricultural damage caused by these deer. A population index that is defined by the population divided by the population of 1993 is first estimated from the data obtained during a spotlight survey. A generalized linear mixed model (GLMM) with corner point constraints is used in this estimation. We then estimate the population from the index by evaluating the response of index to the known amount of harvest, including hunting. A stage‐structured model is used in this harvest‐based estimation. It is well‐known that estimates of indices suffer from large observation errors when the probability of the observation fluctuates widely; therefore, we apply state‐space modeling to the harvest‐based estimation to remove the observation errors. We propose the use of Bayesian estimation with uniform prior‐distributions as an approximation of the maximum likelihood estimation, without permitting an arbitrary assumption that the parameters fluctuate following prior‐distributions. We are able to demonstrate that the harvest‐based Bayesian estimation is effective in reducing the observation errors in sika deer populations, but the stage‐structured model requires many demographic parameters to be known prior to running the analyses. These parameters cannot be estimated from the observed time‐series of the index if there is insufficient data. We then construct a univariate model by simplifying the stage‐structured model and show that the simplified model yields estimates that are nearly identical to those obtained from the stage‐structured model. This simplification of the model simultaneously clarifies which parameter is important in estimating the population.
A novel member of the ligand-gated chloride channel gene family from Haemonchus contortus
Authors: FORRESTER S. G. , SIDDIQUI S. Z. 
Published: December 2007

SUMMARYLigand-gated chloride channels (LGCCs) are key components of the nervous system of parasitic nematodes and important targets for anthelmintics. Here, we describe the isolation and characterization of a novel member of the LGCC gene family (HcLGCC1) from the parasitic nematode Haemonchus contortus. Sequence analysis revealed that the channel subunit encoded by HcLGCC1 is anion selective and a member of a group of channels characterized as having two Cys-loops in the N-terminal ligand-binding domain†. Although the overall function of HcLGCC1 is presently unknown, the gene may play a key role in the early developmental stages of the parasite. Further investigations into the function of LGCCs, such as HcLGCC1, in parasitic nematodes should have implications for the discovery of new anthelmintic targets.
Salvage of Long-Term Central Venous Catheters During an Outbreak ofPseudomonas putidaandStenotrophomonas maltophiliaInfections Associated With Contaminated Heparin Catheter-Lock Solution
Authors: Dias M. Beatriz Souza , Habert Alina Bernardes , Borrasca Vera , Stempliuk Valeska , Ciolli Aina , Araújo M. Rita E. , Costa Silvia F. , Levin Anna S. 
Published: December 2007

Objective.To describe the management of patients with long-term central venous catheters (CVCs) during an outbreak of infection due toPseudomonas putidaandStenotrophomonas maltophiliaassociated with contaminated heparin catheter-lock solution.Design.Descriptive study.Setting.Private, 250-bed tertiary-care hospital.Methods.In March 2003, we identified 2 febrile cancer patients withP. putidabacteremia. Over 2 days, 7 cases of bacteremia were identified; lots of syringes prefilled with heparin catheter-lock solution, supplied by a compounding pharmacy, were recalled and samples were cultured. More cases of bacteremia appeared during the following days, and any patient who had had a catheter lock infused with the suspect solution was asked to provide blood samples for culture, even if the patient was asymptomatic. Isolates that were recovered from culture were typed by pulsed-field gel electrophoresis. Antimicrobial salvage treatment of long-term CVCs was attempted.Results.A total of 154 patients had had their catheter lock infused with solution from the lots that were suspected of being contaminated. Only 48 of these patients had CVCs. By day 7 of the outbreak, 18 of these patients had become symptomatic. Twenty-six of the remaining 30 asymptomatic patients then also provided blood samples for culture, 10 of whom developed fever shortly after samples were collected. Thirty-two patients were identified who hadP. putidabacteremia; 9 also had infection due toS. maltophilia. Samples from 1 of the 3 lots of prefilled syringes in use at the time of the outbreak also grewP. putidaon culture. Molecular typing identified 3 different clones ofP. putidafrom patients and heparin catheter-lock solution, and 1 clone ofS. maltophilia. A total of 27 patients received antimicrobial therapy regimens, some of which included decontamination of the catheter lock with anti-infective lock solution. Of 27 patients, 19 (70%) retained their long-term CVC during the 6-month follow-up period.Conclusions.To our knowledge, this is one of the largest prospective experiences in the management of bloodstream infection associated with long-term CVCs. The infections were caused by gram-negative bacilli and were managed without catheter removal, with a high response rate. We emphasize the risks of using intravenous formulations of medications supplied by compounding pharmacies that produce large quantities of drugs.
Optimization of a Type III Secretion System-Based
Pseudomonas aeruginosa
Live Vector for Antigen Delivery
Authors: Epaulard Olivier , Derouazi Madiha , Margerit Carole , Marlu Raphaël , Filopon Didier , Polack Benoît , Toussaint Bertrand 
Published: December 2007

ABSTRACT

During the last few years, the use of type III secretion system-based bacterial vectors for immunotherapy purposes has been assessed in various applications. We showed that a type III secretion-based
Pseudomonas aeruginosa
vector delivering the ovalbumin (OVA) antigen induced an efficient specific CD8
+
T-lymphocyte immune response against OVA-expressing cells. Because of the intrinsic toxicity of the vector, further virulence attenuation was needed. Therefore, we explored the effects of the deletion of quorum-sensing genes and the
aroA
gene toward toxicity and efficiency of the vector strain. The
aroA
mutation in our strain (making the strain auxotrophic for aromatic amino acids) conferred a strikingly reduced toxicity, with the bacterial lethal dose being more than 100 times higher than that of the parental strain. The quorum-sensing gene mutation alone was associated with a slightly reduced toxicity. In a prophylactic OVA-expressing melanoma mouse model, an OVA-delivering
aroA
-deficient mutant was the most efficient at a low dose (10
5
), but dose enhancement was not associated with a greater immune response. The quorum-sensing-deficient strain was the most efficient at a mild dose (10
6
), but this dose was close to the toxic dose. Combination of both mutations conferred the highest efficiency at an elevated dose (10
7
), in agreement with the known negative effects of quorum-sensing molecules upon T-cell activation. In conclusion, we have obtained a promising immunotherapy vector regarding toxicity and efficiency for further developments in both antitumor and anti-infectious strategies.
Production of Recombinant Antigens of
Ureaplasma parvum
Serotypes 3 and 6 for Development of a Serological Assay
Authors: Vancutsem E. , Echahidi F. , Van Geel K. , Muyldermans G. , Soetens O. , Naessens A. 
Published: December 2007

ABSTRACT

Recombinant antigens of
Ureaplasma parvum
serotypes 3 and 6 were produced in order to develop a serological assay for
Ureaplasma
antibody detection. The genes of the multiple banded antigen (MBA) were amplified by PCR and cloned in a pTrcHis TOPO plasmid. Purified recombinant proteins were evaluated in Western blotting and enzyme-linked immunosorbent assay (ELISA) with monoclonal antibodies and human sera. Our approach was successful in the production of the recombinant MBAs (rMBAs) for serotypes 3 and 6. The antigens tested positive with serotype-specific monoclonal antibodies in Western blotting and in ELISA. Prominent reactions were detected with the rMBAs and their homologous monoclonal antibodies. Strong cross-reactions were visible in ELISA between rMBA 3 and the monoclonal antibodies from the other
U. parvum
serotypes. A weak cross-reaction was seen with rMBA 3 and the monoclonal antibody from serotype 4. rMBA 6 showed cross-reaction only with the monoclonal antibody from
U. parvum
serotype 1. Fifty-one percent of the sera obtained from culture-positive women reacted with one or both rMBAs. Only three (15%) of the sera from culture-negative women reacted with the rMBA. The positive reactions were observed only with rMBA 6. These preliminary tests showed the potential usefulness of the rMBAs produced for detecting an antibody response against
Ureaplasma
antigens.
Brain Abscess Caused by
Streptomyces
Infection following Penetration Trauma: Case Report and Results of Susceptibility Analysis of 92 Isolates of
Streptomyces
Species Submitted to the CDC from 2000 to 2004
Authors: Rose Charles E. , Brown June M. , Fisher John F. 
Published: December 2007

ABSTRACT

The case of a patient who presented with a brain abscess caused by
Streptomyces
infection following penetrating cerebral trauma with a soil-contaminated object generated an interest in optimizing antimicrobial therapy. Collaboration with the Centers for Disease Control and Prevention led to the analysis of susceptibility data for
Streptomyces
isolates that suggested that amikacin (100% susceptibility for 92 isolates tested) and linezolid, an oxazolidinone (100% susceptibility for 41 isolates tested), offer reliable activity against all isolates.
Isolation and Characterization of
Bartonella bacilliformis
from an Expatriate Ecuadorian
Authors: Lydy Shari L. , Eremeeva Marina E. , Asnis Deborah , Paddock Christopher D. , Nicholson William L. , Silverman David J. , Dasch Gregory A. 
Published: December 2007

ABSTRACT

Carrion's disease is typically biphasic with acute febrile illness characterized by bacteremia and severe hemolytic anemia (Oroya fever), followed by benign, chronic cutaneous lesions (verruga peruana). The causative agent,
Bartonella bacilliformis
, is endemic in specific regions of Peru and Ecuador. We describe atypical infection in an expatriate patient who presented with acute splenomegaly and anemia 3 years after visiting Ecuador. Initial serology and PCR of the patient's blood and serum were negative for
Bartonella henselae
,
Bartonella quintana
, and
B. bacilliformis
. Histology of splenic biopsy was suggestive of bacillary angiomatosis, but immunohistochemistry ruled out
B. henselae
and
B. quintana
. Bacilli (isolate EC-01) were subsequently cultured from the patient's blood and analyzed using multilocus sequence typing, protein gel electrophoresis with Western blotting, and an immunofluorescence assay (IFA) against a panel of sera from patients with Oroya fever in Peru. The EC-01 nucleotide sequences (
gltA
and internal transcribed spacer) and protein band banding pattern were most similar to a subset of
B. bacilliformis
isolates from the region of Caraz, Ancash, in Peru, where
B. bacilliformis
is endemic. By IFA, the patient's serum reacted strongly to two out of the three Peruvian
B. bacilliformis
isolates tested, and EC-01 antigen reacted with 13/20 Oroya fever sera. Bacilliary angiomatosis-like lesions were also detected in the spleen of the patient, who was inapparently infected with
B. bacilliformis
and who presumably acquired infection in a region of Ecuador where
B. bacilliformis
was not thought to be endemic. This study suggests that the range of
B. bacilliformis
may be expanding from areas of endemicity in Ecuador and that infection may present as atypical clinical disease.
Multiplex Detection of Human Herpesviruses from Archival Specimens by Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Authors: Sjöholm Malin I. L. , Dillner Joakim , Carlson Joyce 
Published: December 2007

ABSTRACT
The human herpesviruses are involved in a variety of diseases. Large-scale evaluation of the clinical and epidemiological importance of different herpesviruses requires high-throughput methods. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a method that has a multiplex capacity enabling simultaneous detection of several viruses in a single sample. PCR-based methods for the multiplex detection of all known human herpesviruses were developed on the MALDI-TOF MS system. A variety of 882 archival samples, including bronchoalveolar lavage, conjunctival fluid, sore secretion, blister material, plasma, serum, and urine, analyzed for herpesviruses using PCR-based reference methods, were used to evaluate the MALDI-TOF MS method. The overall concordance rate between the MALDI-TOF MS method and the reference methods was 95.6% (κ = 0.90). In summary, the MALDI-TOF MS method is well suited for large-scale detection of all known human herpesviruses in a wide variety of archival biological specimens.
Early Impairment of Gut Function and Gut Flora Supporting a Role for Alteration of Gastrointestinal Mucosa in Human Immunodeficiency Virus Pathogenesis
Authors: Gori Andrea , Tincati Camilla , Rizzardini Giuliano , Torti Carlo , Quirino Tiziana , Haarman Monique , Ben Amor Kaouther , van Schaik Jacqueline , Vriesema Aldwin , Knol Jan , Marchetti Giulia , Welling Gjalt , Clerici Mario 
Published: December 2007

ABSTRACT
Our results show that impairment of the gastrointestinal tracts in human immunodeficiency virus (HIV)-positive patients is present in the early phases of HIV disease. This impairment is associated with alterations in gut microbiota and intestinal inflammatory parameters. These findings support the hypothesis that alterations at the gastrointestinal-tract level are a key factor in HIV pathogenesis.
Visualization of Double-Stranded RNA in Cells Supporting Hepatitis C Virus RNA Replication
Authors: Targett-Adams Paul , Boulant Steeve , McLauchlan John 
Published: December 2007

ABSTRACT
The mechanisms involved in hepatitis C virus (HCV) RNA replication are unknown, and this aspect of the virus life cycle is not understood. It is thought that virus-encoded nonstructural proteins and RNA genomes interact on rearranged endoplasmic reticulum (ER) membranes to form replication complexes, which are believed to be sites of RNA synthesis. We report that, through the use of an antibody specific for double-stranded RNA (dsRNA), dsRNA is readily detectable in Huh-7 cells that contain replicating HCV JFH-1 genomes but is absent in control cells. Therefore, as that of other RNA virus genomes, the replication of the HCV genome may involve the generation of a dsRNA replicative intermediate. In Huh-7 cells supporting HCV RNA replication, dsRNA was observed as discrete foci, associated with virus-encoded NS5A and core proteins and identical in morphology and distribution to structures containing HCV RNA visualized by fluorescence-based hybridization methods. Three-dimensional reconstruction of deconvolved z-stack images of virus-infected cells provided detailed insight into the relationship among dsRNA foci, NS5A, the ER, and lipid droplets (LDs). This analysis revealed that dsRNA foci were located on the surface of the ER and often surrounded, partially or wholly, by a network of ER-bound NS5A protein. Additionally, virus-induced dsRNA foci were juxtaposed to LDs, attached to the ER. Thus, we report the visualization of HCV-induced dsRNA foci, the likely sites of virus RNA replication, and propose that HCV genome synthesis occurs at LD-associated sites attached to the ER in virus-infected cells.
Jaagsiekte Sheep Retrovirus Utilizes a pH-Dependent Endocytosis Pathway for Entry
Authors: Bertrand Pascale , Côté Marceline , Zheng Yi-Min , Albritton Lorraine M. , Liu Shan-Lu 
Published: December 2007

ABSTRACT
Using Moloney murine leukemia virus pseudovirions bearing the envelope protein of Jaagsiekte sheep retrovirus (JSRV), we report here that entry was weakly inhibited by lysosomotropic agents but was profoundly blocked by bafilomycin A1 (BafA1). Kinetics studies revealed that JSRV entry is a slow process and was substantially blocked by a dominant-negative mutant of dynamin. Interestingly, a low-pH pulse overcame the BafA1 block to JSRV infection, although this occurred only if virus-bound cells were preincubated at 37°C, consistent with a very early entry event such as endocytosis being required before the low-pH-dependent step occurs. Moreover, JSRV pseudovirions were resistant to low-pH inactivation. Altogether, this study reveals that JSRV utilizes a pH-dependent, dynamin-associated endocytosis pathway for entry that differs from the classical pH-dependent entry pathway of vesicular stomatitis virus.
Vaccinia Virus A34 Glycoprotein Determines the Protein Composition of the Extracellular Virus Envelope
Authors: Perdiguero Beatriz , Lorenzo María M. , Blasco Rafael 
Published: December 2007

ABSTRACT

The outer envelope of the extracellular form of vaccinia virus contains five virus-encoded proteins, F13, A33, A34, A56, and B5, that, with the exception of A56, are implicated in virus egress or infectivity. A34, a type II transmembrane glycoprotein, is involved in the induction of actin tails, the release of enveloped virus from the surfaces of infected cells, and the disruption of the virus envelope after ligand binding prior to virus entry. To investigate interactions between A34 and other envelope proteins, a recombinant vaccinia virus (vA34R
HA
) expressing an epitope-tagged version of A34 (A34
HA
) was constructed by appending an epitope from influenza virus hemagglutinin to the C terminus of A34. Complexes of A34
HA
with B5 and A36, but not with A33 or F13, were detected in vA34R
HA
-infected cells. A series of vaccinia viruses expressing mutated versions of the B5 protein was used to investigate the domain(s) of B5 required for interaction with A34. Both the cytoplasmic and the transmembrane domains of B5 were dispensable for binding to A34. Most of the extracellular domain of B5, which contains four short consensus repeats homologous to complement control proteins, was sufficient for A34 interaction, indicating that both proteins interact through their ectodomains. Immunofluorescence experiments on cells infected with A34-deficient virus indicated that A34 is required for efficient targeting of B5, A36, and A33 into wrapped virions. Consistent with this observation, the envelope of A34-deficient virus contained normal amounts of F13 but decreased amounts of A33 and B5 with respect to the parental WR virus. These results point to A34 as a major determinant in the protein composition of the vaccinia virus envelope.
Evidence for Differential Roles for NKG2D Receptor Signaling in Innate Host Defense against Coronavirus-Induced Neurological and Liver Disease
Authors: Walsh Kevin B. , Lodoen Melissa B. , Edwards Robert A. , Lanier Lewis L. , Lane Thomas E. 
Published: December 2007

ABSTRACTInfection of SCID mice with a recombinant murine coronavirus (mouse hepatitis virus [MHV]) expressing the T-cell chemoattractant CXC chemokine ligand 10 (CXCL10) resulted in increased survival and reduced viral burden within the brain and liver compared to those of mice infected with an isogenic control virus (MHV), supporting an important role for CXCL10 in innate immune responses following viral infection. Enhanced protection in MHV-CXCL10-infected mice correlated with increased gamma interferon (IFN-γ) production by infiltrating natural killer (NK) cells within the brain and reduced liver pathology. To explore the underlying mechanisms associated with protection from disease in MHV-CXCL10-infected mice, the functional contributions of the NK cell-activating receptor NKG2D in host defense were examined. The administration of an NKG2D-blocking antibody to MHV-CXCL10-infected mice did not reduce survival, dampen IFN-γ production in the brain, or affect liver pathology. However, NKG2D neutralization increased viral titers within the liver, suggesting a protective role for NKG2D signaling in this organ. These data indicate that (i) CXCL10 enhances innate immune responses, resulting in protection from MHV-induced neurological and liver disease; (ii) elevated NK cell IFN-γ expression in the brain of MHV-CXCL10-infected mice occurs independently of NKG2D; and (iii) NKG2D signaling promotes antiviral activity within the livers of MHV-infected mice that is not dependent on IFN-γ and tumor necrosis factor alpha secretion.
4E10-Resistant Variants in a Human Immunodeficiency Virus Type 1 Subtype C-Infected Individual with an Anti-Membrane-Proximal External Region-Neutralizing Antibody Response
Authors: Gray Elin S. , Moore Penny L. , Bibollet-Ruche Frederic , Li Hui , Decker Julie M. , Meyers Tammy , Shaw George M. , Morris Lynn 
Published: December 2007

ABSTRACT

The broadly neutralizing monoclonal antibody (MAb) 4E10 recognizes a linear epitope in the C terminus of the membrane-proximal external region (MPER) of gp41. This epitope is particularly attractive for vaccine design because it is highly conserved among human immunodeficiency virus type 1 (HIV-1) strains and neutralization escape in vivo has not been observed. Multiple
env
genes were cloned from an HIV-1 subtype C virus isolated from a 7-year-old perinatally infected child who had anti-MPER neutralizing antibodies. One clone (TM20.13) was resistant to 4E10 neutralization as a result of an F673L substitution in the MPER. Frequency analysis showed that F673L was present in 33% of the viral variants and in all cases was linked to the presence of an intact 2F5 epitope. Two other envelope clones were sensitive to 4E10 neutralization, but TM20.5 was 10-fold less sensitive than TM20.6. Substitutions at positions 674 and 677 within the MPER rendered TM20.5 more sensitive to 4E10 but had no effect on TM20.6. Using chimeric and mutant constructs of these two variants, we further demonstrated that the lentivirus lytic peptide-2 domain in the cytoplasmic tail affected the accessibility of the 4E10 epitope, as well as virus infectivity. Collectively, these genetic changes in the face of a neutralizing antibody response to the MPER strongly suggested immune escape from antibody responses targeting this region.
The geological results of seismic refraction surveys in the Bristol Channel, 1970-1973
Authors: BROOKS MICHAEL , JAMES DAVID GARETH 
Published: December 2007

Results are presented of eighteen refraction traverses in the Bristol Channel. Estimates based on refraction and CSP surveys indicate a Mesozoic sequence about 2000 m thick in the Bristol Channel syncline north of Devon. The Central Bristol Channel fault zone in the northern limb of the syncline has an overall southerly downthrow of over 1000 m. Up to 270 m of Mesozoic strata occur in the outer part of Swansea Bay and the Helwick syncline contains about 700 m of Mesozoic strata SW of Gower. There is evidence for an igneous intrusion at shallow depth west of Lundy in the vicinity of a positive Bouguer anomaly. The Tertiary basin E. of the Sticklepath fault in Barnstaple Bay is at least 340 m thick. A high velocity refractor 2500 m below Carmarthen Bay is interpreted as lower Palaeozoic or Precambrian volcanic rocks.
The surveys suggest that Cenozoic, Mesozoic and upper Palaeozoic strata can normally be differentiated on the basis of velocity but the results are of limited use in mapping upper Palaeozoic rocks and, in particular, provide no evidence for the major thrust postulated to subcrop beneath the Mesozoic strata of the Bristol Channel syncline.