bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of Near-Wellbore Alteration and Formation Stress Parameters From Borehole Sonic Data
Authors: Sinha Bikash , Bratton Tom , Cryer Jesse , Nieting Steve , Ugueto Gustavo , Bakulin Andrey , Hauser Matt 
Published: July 2008

Summary
Highly depleted reservoirs exhibit sharply lower pore pressures and horizontal stress magnitudes than does the overlying shaly formation. Drilling through such depleted reservoirs can cause severe fluid loss and drilling-induced wellbore instability. Accurate and reliable estimates of horizontal stresses can provide an early warning of impending drilling problems that may be mitigated by appropriate drilling fluid design and drilling practices. We have developed a new multifrequency inversion algorithm for the estimation of maximum and minimum horizontal stress magnitudes using cross-dipole dispersions. Borehole sonic data for the case study presented in this paper was acquired by a cross-dipole sonic tool in a deepwater well, offshore Louisiana in the Gulf of Mexico (GOM). The logged interval spans 1,000 ft below the casing shoe. In addition, the Modular Dynamic Tester (MDT) (©Schlumberger) minifrac tests were performed at three depths in shale, thus yielding two minimum horizontal stress magnitudes. The borehole sonic data were suitable for the inversion of crossdipole dispersions at three depths in shale, as well as at a depth in a highly depleted sand reservoir. There was one depth in shale above the depleted sand where we could estimate the minimum horizontal stress magnitude with both the MDT minifrac tests and inversion of borehole sonic data. The results of the two techniques are consistent, providing encouragement for further validation of the multifrequency inversion of cross-dipole dispersions to estimate horizontal stresses. Even though the overburden stress is expected to increase with depth, both the maximum (SHmax) and minimum (Shmin) horizontal stresses obtained from the inversion of borehole sonic data are significantly smaller in the depleted sand than in the overburden shale. However, both the horizontal stress magnitudes increase again in the shale below the depleted sand. Such rapid variations in horizontal stress magnitudes cause large fluctuations in the safe mud-weight window. This challenge in drilling through the depleted sand was successfully handled by using special drilling fluid to mitigate seepage losses and the differential sticking in the depleted sand and overlying shale. We have also performed dipole radial profiling (DRP) of formation shear slownesses using the measured cross-dipole dispersions at three depths in shale and one in highly depleted sand. Analysis of radial profiles in the two orthogonal directions indicates plastic yielding or stiffening of rock in the near-wellbore region. While plastic yielding increases the shear slowness, stiffening would reduce the shear slowness.
Afghanistan's Kuchi Pastoralists: Change and Adaptation
Authors: De Weijer Frauke 
Published: July 2008

Abstract
Afghanistan's nomadic peoples are now either migratory and livestockdependent pastoralists or recently settled but formerly migratory pastoralists, who still hold on to the cultural identity and refer to themselves as kuchi. Radical changes in both summer and winter pastures have taken place over the last centuries, and currently the pastoralists' access to the summer pastures in the central highlands is compromised. Customary mechanisms had come into existence over the last century, and still function in certain areas. However, in large areas, and in particular those where issues of grazing rights have become heavily politicized and strongly associated with ethnic identity, there is a high level of conflict over these user's rights, which have often proven to be inflammable. There are large differences in migration patterns and livelihood strategies between the pastoralists of the different regions. Income derived from livestock production is often supplemented by other income sources, like harvesting and casual labour, but also through the purchase of agricultural land. In recent years, an increased diversification of household income and a move towards a more semi-migratory lifestyle has taken place. Pastoralists still do make an important contribution to Afghanistan's national economy, as they did in the past (35 per cent of all exports were from livestock products). Recent estimates indicate that there around 2.5 million kuchi, of which 1.5 million are still migratory pastoralists and one million are currently not migratory and are former pastoralists. The drought of 1999 to 2004 severely affected pastoralist livelihoods and livestock numbers plummeted. Estimates on livestock numbers indicate that in the north they started reaching their pre-war levels, whereas the south and the east are still lagging behind. It has been estimated that kuchi own around 30 to 50 per cent of the national herd.
Acute heart failure in patients with acute myocardial infarction treated with primary percutaneous coronary intervention☆
Authors: Santoro Giovanni M. , Carrabba Nazario , Migliorini Angela , Parodi Guido , Valenti Renato 
Published: July 2008

AbstractBackground:Scanty data exist about the relation between acute heart failure (HF) and acute myocardial infarction (AMI).Aim:To assess the impact of HF on outcome in AMI patients treated with primary percutaneous coronary intervention (PCI).Methods and results:Out of 2089 AMI patients, 82% did not present HF, 17% presented HF on admission and 1% developed HF after hospitalisation. Predictors of HF on admission were age, diabetes, prior MI, time delay to admission, anterior location, and TIMI grade 0–1 in the culprit vessel. Predictors of HF during hospitalisation were age and peak creatine kinase. The 1‐ and 6‐month mortalities were 1.1% and 2.2%, 8% and 12%, 26% and 33% in patients without HF, with HF on admission and after hospitalisation, respectively. The risk of death was higher in patients with HF than in patients without HF (HR 3.47), as well as in patients with HF after admission (HR 5.19) than in patients with HF on admission (HR 2.44).Conclusions:In a primary PCI setting, the incidence of HF on hospital admission remains high, but mortality is lower when compared with historical patient series. Primary PCI may prevent the development of HF during hospitalisation; however, when HF develops, the prognosis remains severe.
Crystal structure of RimI from Salmonella typhimurium LT2, the GNAT responsible for Nα‐acetylation of ribosomal protein S18
Authors: Vetting Matthew W. , Bareich David C. , Yu Michael , Blanchard John S. 
Published: July 2008

AbstractThe three ribosomal proteins L7, S5, and S18 are included in the rare subset of prokaryotic proteins that are known to be Nα‐acetylated. The GCN5‐related N‐acetyltransferase (GNAT) protein RimI, responsible for the Nα‐acetylation of the ribosomal protein S18, was cloned from Salmonella typhimurium LT2 (RimIST), overexpressed, and purified to homogeneity. Steady‐state kinetic parameters for RimIST were determined for AcCoA and a peptide substrate consisting of the first six amino acids of the target protein S18. The crystal structure of RimIST was determined in complex with CoA, AcCoA, and a CoA‐S‐acetyl‐ARYFRR bisubstrate inhibitor. The structures are consistent with a direct nucleophilic addition–elimination mechanism with Glu103 and Tyr115 acting as the catalytic base and acid, respectively. The RimIST‐bisubstrate complex suggests that several residues change conformation upon interacting with the N terminus of S18, including Glu103, the proposed active site base, facilitating proton exchange and catalysis.
Differential ubiquitin binding of the UBA domains from human c‐Cbl and Cbl‐b: NMR structural and biochemical insights
Authors: Zhou Zi‐Ren , Gao Hong‐Chang , Zhou Chen‐Jie , Chang Yong‐Gang , Hong Jing , Song Ai‐Xin , Lin Dong‐Hai , Hu Hong‐Yu 
Published: July 2008

AbstractThe Cbl proteins, RING‐type E3 ubiquitin ligases, are responsible for ubiquitinating the activated tyrosine kinases and targeting them for degradation. Both c‐Cbl and Cbl‐b have a UBA (ubiquitin‐associated) domain at their C‐terminal ends, and these two UBA domains share a high sequence similarity (75%). However, only the UBA from Cbl‐b, but not from c‐Cbl, can bind ubiquitin (Ub). To understand the mechanism by which the UBA domains specifically interact with Ub with different affinities, we determined the solution NMR structures of these two UBA domains, cUBA from human c‐Cbl and UBAb from Cbl‐b. Their structures show that these two UBA domains share the same fold, a compact three‐helix bundle, highly resembling the typical UBA fold. Chemical shift perturbation experiments reveal that the helix‐1 and loop‐1 of UBAb form a predominately hydrophobic surface for Ub binding. By comparing the Ub‐interacting surface on UBAb and its counterpart on cUBA, we find that the hydrophobic patch on cUBA is interrupted by a negatively charged residue Glu12. Fluorescence titration data show that the Ala12Glu mutant of UBAb completely loses the ability to bind Ub, whereas the mutation disrupting the dimerization has no significant effect on Ub binding. This study provides structural and biochemical insights into the Ub binding specificities of the Cbl UBA domains, in which the hydrophobic surface distribution on the first helix plays crucial roles in their differential affinities for Ub binding. That is, the amino acid residue diversity in the helix‐1 region, but not the dimerization, determines the abilities of various UBA domains binding with Ub.
Cross-Reactivity between Immune Responses to
Helicobacter bilis
and
Helicobacter pylori
in a Population in Thailand at High Risk of Developing Cholangiocarcinoma
Authors: Pisani Paola , Whary Mark T. , Nilsson Ingrid , Sriamporn Supannee , Wadström Torkel , Fox James G. , Ljungh Åsa , Forman David 
Published: July 2008

ABSTRACT

Helicobacter bilis
DNA has been detected in human tissue and is a candidate for etiologic investigations on the causes of hepatic and biliary tract diseases, but reliable serologic tests need to be developed in order to pursue such investigations. The scope of this study was to assess the specificity of two assays for
H. bilis
immune response allowing for
H. pylori
, and their cross-reactivity in a population in Thailand at high risk for cholangiocarcinoma. Plasma samples from 92 Thai volunteers were independently tested in two laboratories (Massachusetts Institute of Technology [MIT] and Lund). MIT performed three analyses of
H. pylori
and
H. bilis
based either on (i) outer membrane protein (OMP) with no preabsorption or on antigens derived from whole-cell sonicate before (ii) or after (iii) preabsorption with
H. pylori
sonicate protein. Lund used cell surface proteins from
H. pylori
and
H. bilis
as antigens. Testing for
H. bilis
was preabsorbed with a whole-cell lysate of
H. pylori
. More than 80% of the samples were positive for
H. pylori
in both laboratories. As tested by MIT, 58.7% (95% confidence interval, 47.9 to 68.9%) were positive for
H. bilis
by OMP and 44.5% (34.1 to 55.3%) were positive for
H. bilis
sonicate protein, but only 15.2% (8.6 to 24.2%) remained positive after preabsorption with
H. pylori
sonicate protein. Lund found 34.5% of the samples positive for
H. bilis
(22.0 to 41.0%), which was statistically compatible with all three MIT results. Serologic responses to OMPs of the two bacteria coincided in 66 and 45% of the samples in the MIT and Lund assays, respectively. We found high cross-reactivity between the immune responses to
H. pylori
and
H. bilis
antigens. More-specific
H. bilis
antigens need to be isolated to develop serologic tests suitable for epidemiological studies.
Identification of Enteroviruses in Naturally Infected Captive Primates
Authors: Nix W. Allan , Jiang Baoming , Maher Kaija , Strobert Elizabeth , Oberste M. Steven 
Published: July 2008

ABSTRACT
In a recent study, we investigated cases of diarrheal disease among monkeys at a U.S. primate center. In that study, enteroviruses were detected in a high proportion of the fecal specimens tested. To determine whether the enterovirus detections represented the circulation of one or more simian enteroviruses within the colony or the transmission of human enteroviruses from animal handlers, we determined in the present study the serotype identity of each virus by reverse transcription-PCR and sequencing of a portion of the VP1 gene, a region whose sequence corresponds to antigenic type. Enteroviruses were identified in 37 of 56 specimens (66%), 30 of 40 rhesus macaques, 5 of 11 pigtail macaques, 2 of 4 sooty mangabeys, and 0 of 1 chimpanzee. No previously known human viruses were detected. Three previously known simian enterovirus serotypes—SV6, SV19, and SV46—were among the viruses identified, but more than half of the identified viruses were previously unknown; these have been assigned as new types: EV92 and EV103.
Associations between the Genotypes of
Staphylococcus aureus
Bloodstream Isolates and Clinical Characteristics and Outcomes of Bacteremic Patients
Authors: Lalani Tahaniyat , Federspiel Jerome J. , Boucher Helen W. , Rude Thomas H. , Bae In-Gyu , Rybak Michael J. , Tonthat Giang T. , Corey G. Ralph , Stryjewski Martin E. , Sakoulas George , Chu Vivian H. , Alder Jeff , Steenbergen Judith N. , Luperchio Steven A. , Campion Marilyn , Woods Christopher W. , Fowler Vance G. 
Published: July 2008

ABSTRACT

We investigated associations between the genotypic and phenotypic features of
Staphylococcus aureus
bloodstream isolates and the clinical characteristics of bacteremic patients enrolled in a phase III trial of
S. aureus
bacteremia and endocarditis. Isolates underwent pulsed-field gel electrophoresis, PCR for 33 putative virulence genes, and screening for heteroresistant glycopeptide intermediate
S. aureus
(hGISA). A total of 230 isolates (141 methicillin-susceptible
S. aureus
and 89 methicillin-resistant
S. aureus
[MRSA]) were analyzed. North American and European
S. aureus
isolates differed in their genotypic characteristics. Overall, 26% of the MRSA bloodstream isolates were USA 300 strains. Patients with USA 300 MRSA bacteremia were more likely to be injection drug users (61% versus 15%;
P
< 0.001), to have right-sided endocarditis (39% versus 9%;
P
= 0.002), and to be cured of right-sided endocarditis (100% versus 33%;
P
= 0.01) than patients with non-USA 300 MRSA bacteremia. Patients with persistent bacteremia were less likely to be infected with Panton-Valentine leukocidin gene (
pvl
)-constitutive MRSA (19% versus 56%;
P
= 0.005). Although 7 of 89 MRSA isolates (8%) exhibited the hGISA phenotype, no association with persistent bacteremia, daptomycin resistance, or bacterial genotype was observed. This study suggests that the virulence gene profiles of
S. aureus
bloodstream isolates from North America and Europe differ significantly. In this study of bloodstream isolates collected as part of a multinational randomized clinical trial, USA 300 and
pvl
-constitutive MRSA strains were associated with better clinical outcomes.
Clinical Impact of
Mycobacterium tuberculosis
W-Beijing Genotype Strain Infection on Aged Patients in Taiwan
Authors: Feng Jia-Yih , Su Wei-Juin , Tsai Cheng-Chien , Chang Shi-Chuan 
Published: July 2008

ABSTRACT

The impact of W-Beijing genotype
Mycobacterium tuberculosis
on treatment outcome was evaluated in 249 newly diagnosed tuberculosis patients. No significant difference in the treatment outcome was found between the W-Beijing and non-W-Beijing groups. However, a poor outcome was more common in the elderly patients (≥65 years) infected with the W-Beijing strain.
Human T-Cell Leukemia Virus Type 1 Infection Leads to Arrest in the G
1
Phase of the Cell Cycle
Authors: Liu Meihong , Yang Liangpeng , Zhang Ling , Liu Baoying , Merling Randall , Xia Zheng , Giam Chou-Zen 
Published: July 2008

ABSTRACT

Infection by the human T-cell leukemia virus type 1 (HTLV-1) is thought to cause dysregulated T-cell proliferation, which in turn leads to adult T-cell leukemia/lymphoma. Early cellular changes after HTLV-1 infection have been difficult to study due to the poorly infectious nature of HTLV-1 and the need for cell-to-cell contact for HTLV-1 transmission. Using a series of reporter systems, we show that HeLa cells cease proliferation within one or two division cycles after infection by HTLV-1 or transduction of the HTLV-1
tax
gene. HTLV-1-infected HeLa cells, like their
tax
-transduced counterparts, expressed high levels of p21

CIP1
/
WAF1

and p27

KIP1

, developed mitotic abnormalities, and became arrested in G
1
in senescence. In contrast, cells of a human osteosarcoma lineage (HOS) continued to divide after HTLV-1 infection or Tax expression, albeit at a reduced growth rate and with mitotic aberrations. Unique to HOS cells is the dramatic reduction of p21

CIP1
/
WAF1

and p27

KIP1

expression, which is in part associated with the constitutive activation of the phosphatidylinositol-3-kinase (PI3K)-protein kinase B (Akt) pathway. The loss of p21

CIP1
/
WAF1

and p27

KIP1

in HOS cells apparently allows HTLV-1- and Tax-induced G
1
arrest to be bypassed. Finally, HTLV-1 infection and Tax expression also cause human SupT1 T cells to arrest in the G
1
phase of the cell cycle. These results suggest that productive HTLV-1 infection ordinarily leads to Tax-mediated G
1
arrest. However, T cells containing somatic mutations that inactivate p21

CIP1
/
WAF1

and p27

KIP1

may continue to proliferate after HTLV-1 infection and Tax expression. These infected cells can expand clonally, accumulate additional chromosomal abnormalities, and progress to cancer.
Human Immunodeficiency Virus Type 1 Vif Induces Cell Cycle Delay via Recruitment of the Same E3 Ubiquitin Ligase Complex That Targets APOBEC3 Proteins for Degradation
Authors: DeHart Jason L. , Bosque Alberto , Harris Reuben S. , Planelles Vicente 
Published: July 2008

ABSTRACTHuman immunodeficiency virus type 1 (HIV-1) Vif recruits a Cullin 5 ubiquitin ligase that targets APOBEC3 proteins for degradation. Recently, Vif has also been shown to induce cell cycle disturbance in G2. We show that in contrast to the expression of Vpr, the expression of Vif does not preclude cell division, and therefore, Vif causes delay and not arrest in G2. We also demonstrate that the interaction of Vif with the ubiquitin ligase is required for cell cycle disruption, as was previously shown for HIV-1 Vpr. The presence of APOBEC3 D/E, F, and G had no influence on Vif-induced alteration of the cell cycle. We conclude that cell cycle delay by Vif is a result of ubiquitination and degradation of a cellular protein that is different from the known APOBEC3 family members.
Temporal and Spatial Dynamics of Human Immunodeficiency Virus Type 1 Circulating Recombinant Forms 08_BC and 07_BC in Asia
Authors: Tee Kok Keng , Pybus Oliver G. , Li Xiao-Jie , Han Xiaoxu , Shang Hong , Kamarulzaman Adeeba , Takebe Yutaka 
Published: July 2008

ABSTRACT
Human immunodeficiency virus type 1 (HIV-1) CRF08_BC and CRF07_BC are two major recombinants descended from subtypes B′ and C. Despite their massive epidemic impact in China, their migration patterns and divergence times remain unknown. Phylogenetic and population genetic analyses were performed on 228 HIV-1 sequences representing CRF08_BC, CRF07_BC, and subtype C strains from different locations across China, India, and Myanmar. Genome-specific rates of evolution and divergence times were estimated using a Bayesian Markov chain Monte Carlo framework under various evolutionary models. CRF08_BC originated in 1990.3 (95% credible region [CR], 1988.6 to 1991.9) in Yunnan province before spreading to Guangxi (south) and Liaoning (northeast) around 1995. Inside Guangxi region, the eastward expansion of CRF08_BC continued from Baise city (west) to Binyang (central) between 1997 and 1998 and later spread into Pingxiang around 1999 in the south, mainly through injecting drug users. Additionally, CRF07_BC diverged from its common ancestor in 1993.3 (95% CR, 1991.2 to 1995.2) before crossing the border into southern Taiwan in late 1990s. Phylogenetic analysis indicates that both CRF08_BC and CRF07_BC can trace their origins to Yunnan. The parental Indian subtype C lineage likely entered China around 1981.2 (95% CR, 1976.7 to 1985.9). Using a multiple unlinked locus model, we also showed that the dates of divergence calculated in this study may not be significantly affected by intrasubtype recombination among different lineages. This is the first phylodynamic study depicting the spatiotemporal dynamics of HIV/AIDS in East Asia.
Changes in Population Dynamics during Long-Term Evolution of Sabin Type 1 Poliovirus in an Immunodeficient Patient
Authors: Odoom John K. , Yunus Zaira , Dunn Glynis , Minor Philip D. , Martín Javier 
Published: July 2008

ABSTRACT
The evolution of the Sabin strain of type 1 poliovirus in a hypogammaglobulinemia patient for a period of 649 days is described. Twelve poliovirus isolates from sequential stool samples encompassing days 21 to 649 after vaccination with Sabin 1 were characterized in terms of their antigenic properties, virulence in transgenic mice, sensitivity for growth at high temperatures, and differences in nucleotide sequence from the Sabin 1 strain. Poliovirus isolates from the immunodeficient patient evolved gradually toward non-temperature-sensitive and neurovirulent phenotypes, accumulating mutations at key nucleotide positions that correlated with the observed reversion to biological properties typical of wild polioviruses. Analysis of plaque-purified viruses from stool samples revealed complex genetic and evolutionary relationships between the poliovirus strains. The generation of various coevolving genetic lineages incorporating different mutations was observed at early stages of virus excretion. The main driving force for genetic diversity appeared to be the selection of mutations at attenuation sites, particularly in the 5′ noncoding region and the VP1 BC loop. Recombination between virus strains from the two main lineages was observed between days 63 and 88. Genetic heterogeneity among plaque-purified viruses at each time point seemed to decrease with time, and only viruses belonging to a unique genotypic lineage were seen from day 105 after vaccination. The relevance of vaccine-derived poliovirus strains for disease surveillance and future polio immunization policies is discussed in the context of the Global Polio Eradication Initiative.