bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unequal Evolutionary Rates in the Human Immunodeficiency Virus Type 1 (HIV-1) Pandemic: the Evolutionary Rate of HIV-1 Slows Down When the Epidemic Rate Increases
Authors: Berry Irina Maljkovic , Ribeiro Ruy , Kothari Moulik , Athreya Gayathri , Daniels Marcus , Lee Ha Youn , Bruno William , Leitner Thomas 
Published: July 2007

ABSTRACT

HIV-1 sequences in intravenous drug user (IDU) networks are highly homogenous even after several years, while this is not observed in most sexual epidemics. To address this disparity, we examined the human immunodeficiency virus type 1 (HIV-1) evolutionary rate on the population level for IDU and heterosexual transmissions. All available HIV-1
env
V3 sequences from IDU outbreaks and heterosexual epidemics with known sampling dates were collected from the Los Alamos HIV sequence database. Evolutionary rates were calculated using phylogenetic trees with a
t
test root optimization of dated samples. The evolutionary rate of HIV-1 subtype A1 was found to be 8.4 times lower in fast spread among IDUs in the former Soviet Union (FSU) than in slow spread among heterosexual individuals in Africa. Mixed epidemics (IDU and heterosexual) showed intermediate evolutionary rates, indicating a combination of fast- and slow-spread patterns. Hence, if transmissions occur repeatedly during the initial stage of host infection, before selective pressures of the immune system have much impact, the rate of HIV-1 evolution on the population level will decrease. Conversely, in slow spread, where HIV-1 evolves under the pressure of the immune system before a donor infects a recipient, the virus evolution at the population level will increase. Epidemiological modeling confirmed that the evolutionary rate of HIV-1 depends on the rate of spread and predicted that the HIV-1 evolutionary rate in a fast-spreading epidemic, e.g., for IDUs in the FSU, will increase as the population becomes saturated with infections and the virus starts to spread to other risk groups.
Role of Env in Resistance of Feline Immunodeficiency Virus (FIV)-Infected Cats to Superinfection by a Second FIV Strain as Determined by Using a Chimeric Virus
Authors: Giannecchini Simone , Pistello Mauro , Isola Patrizia , Matteucci Donatella , Mazzetti Paola , Freer Giulia , Bendinelli Mauro 
Published: July 2007

ABSTRACT

A more or less pronounced resistance to superinfection by a second strain of the infecting virus has been observed in many lentivirus-infected hosts. We used a chimeric feline immunodeficiency virus (FIV), designated FIV
χ
, containing a large part of the
env
gene of a clade B virus (strain M2) and all the rest of the genome of a clade A virus (a p34TF10 molecular clone of the Petaluma strain modified to grow in lymphoid cells), to gain insights into such resistance. FIV
χ
was infectious and moderately pathogenic for cats and in vitro exhibited the neutralization specificity of the
env
donor. The experiments performed were bidirectional, in that cats preinfected with either parental virus were challenged with FIV
χ
and vice versa. The preinfected animals were partially or completely protected relative to what was observed in naïve control animals, most likely due, at least in part, to the circumstance that in all the preinfecting/challenge virus combinations examined, the first and the second virus shared significant viral components. Based on the proportions of complete protection observed, the role of a strongly matched viral envelope appeared to be modest and possibly dependent on the time interval between the first and the second infection. Furthermore, complete protection and the presence of measurable neutralizing antibodies capable of blocking the second virus in vitro were not associated.
N-Linked Glycan Modifications in gp120 of Human Immunodeficiency Virus Type 1 Subtype C Render Partial Sensitivity to 2G12 Antibody Neutralization
Authors: Gray Elin S. , Moore Penny L. , Pantophlet Ralph A. , Morris Lynn 
Published: July 2007

ABSTRACT
The monoclonal antibody (MAb) 2G12 recognizes a cluster of high-mannose oligosaccharides on the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp120 and is one of a select group of MAbs with broad neutralizing activity. However, subtype C viruses are generally resistant to 2G12 neutralization. This has been attributed to the absence of a glycosylation site at position 295 in most subtype C gp120s, which instead is typically occupied by a Val residue. Here we show that N-linked glycans in addition to the one at position 295 are important in the formation of the 2G12 epitope in subtype C gp120. Introduction of the glycosylation site at position 295 into three subtype C molecular clones, Du151.2, COT9.6, and COT6.15, did increase 2G12 binding to all three mutagenized gp120s, but at various levels. The COT9-V295N mutant showed the strongest 2G12 binding and was the only mutant to become sensitive to 2G12 neutralization, although very high antibody concentrations were required. Introduction of a glycosylation site at position 448 into mutant COT6-V295N, which occurs naturally in COT9, resulted in a virus that was partially sensitive to 2G12. Interestingly, a glycosylation site at position 442, which is common among subtype C viruses, also contributed to the 2G12 epitope. The addition of this glycan increased virus neutralization sensitivity to 2G12, whereas its deletion conferred resistance. Collectively, our results indicate that the 2G12 binding site cannot readily be reconstituted on the envelopes of subtype C viruses, suggesting structural differences from other HIV subtypes in which the 2G12 epitope is naturally expressed.
Specific Residues of the Influenza A Virus Hemagglutinin Viral RNA Are Important for Efficient Packaging into Budding Virions
Authors: Marsh Glenn A. , Hatami Raheleh , Palese Peter 
Published: July 2007

ABSTRACT
A final step in the influenza virus replication cycle is the assembly of the viral structural proteins and the packaging of the eight segments of viral RNA (vRNA) into a fully infectious virion. The process by which the RNA genome is packaged efficiently remains poorly understood. In an approach to analyze how vRNA is packaged, we rescued a seven-segmented virus lacking the hemagglutinin (HA) vRNA (deltaHA virus). This virus could be passaged in cells constitutively expressing HA protein, but it was attenuated in comparison to wild-type A/WSN/33 virus. Supplementing the deltaHA virus with an artificial segment containing green fluorescent protein (GFP) or red fluorescent protein (RFP) with HA packaging regions (45 3′ and 80 5′ nucleotides) partially restored the growth of this virus to wild-type levels. The absence of the HA vRNA in the deltaHA virus resulted in a 40 to 60% reduction in the packaging of the PA, NP, NA, M, and NS vRNAs, as measured by quantitative PCR (qPCR), and the packaging of these vRNAs was partially restored in the presence of GFP/RFP packaging constructs. To further define nucleotides of the HA coding sequence which are important for vRNA packaging, synonymous mutations were introduced into the full-length HA cDNA of influenza A/WSN/33 and A/Puerto Rico/8/34 viruses, and mutant viruses were rescued. qPCR analysis of vRNAs packaged in these mutant viruses identified a key region of the open reading frame (nucleotides 1659 to 1671) that is critical for the efficient packaging of an influenza virus H1 HA segment.
d-Serine inhibits AMPA receptor-mediated current in rat hippocampal neurons
Authors: Gong Xiang-Qun , Zabek Rebecca L. , Bai Donglin 
Published: July 2007

d-Serine, a recently identified gliotransmitter, serves as an endogenous coagonist binding to the glycine site of N-methyl-d-aspartate (NMDA) receptors. However, it is not clear whether this native ligand is able to bind to and modulate α-amino-3-hydroxyl-5-methyl-4-isoxazolepropionate (AMPA) receptors. In the present study, we showed that d-serine was able to concentration-dependently inhibit kainate-induced AMPA receptor-mediated current in acutely isolated hippocampal neurons. The blocking action of d-serine on AMPA receptors was characterized by a shift in concentration–response curve of kainate-induced current to the right with no change in the maximal response and independent of holding potential in the range of –80 to +60 mV. This is consistent with a model that d-serine is a competitive antagonist on AMPA receptors. In contrast, l-serine did not exert such an inhibitory action. Consistent with this observation, we found that several d-isoforms, but not l-isoforms, of endogenous and exogenous amino acids were able to block AMPA receptors. These results indicate that there is a low affinity and stereo-selective site at the agonist binding pocket of AMPA receptors for these d-amino acids. More importantly, vesicular-released endogenous d-serine from astrocytes could potentially modulate AMPA receptors in synaptic transmission in hippocampus.
Neoadjuvant Docetaxel and Capecitabine and the Use of Thymidine Phosphorylase as a Predictive Biomarker in Breast Cancer
Authors: Layman Rachel M. , Thomas Dafydd G. , Griffith Kent A. , Smerage Jeffrey B. , Helvie Mark A. , Roubidoux Marilyn A. , Diehl Kathleen M. , Newman Lisa A. , Sabel Michael S. , Hayman James A. , Pierce Lori J. , Hayes Daniel F. , Schott Anne F. 
Published: July 2007

Abstract
Purpose: Thymidine phosphorylase (TP) induction by docetaxel is a proposed mechanism for the observed preclinical synergy of docetaxel and capecitabine (DC). We evaluated whether TP protein expression is increased by docetaxel and correlates with pathologic complete response (pCR) in breast cancer patients.
Experimental Design: Women with stage II to III breast cancer were given four cycles of neoadjuvant docetaxel 36 mg/m2 i.v. over 30 min on days 1, 8, and 15 and capecitabine 2,000 mg/d, in two divided doses, on days 5 to 21 of a 28-day cycle. Radiology-directed biopsies of the breast tumors were done at baseline and 5 days after the first dose of docetaxel to evaluate TP expression. Following DC therapy, patients had core breast biopsies, and if residual disease was present, received four cycles of standard dose-dense doxorubin and cyclophosphamide (AC).
Results: The pCR rate was 26.9% (95% confidence interval, 11.6-47.8). Up-regulation of TP expression was not observed by either quantitative immunofluorescence (QIF) or immunohistochemistry. Radiology-directed core biopsy after neoadjuvant chemotherapy accurately predicted pathologic response in 88% (95% confidence interval, 69.8-97.6) of the cases. Neither level of TP expression nor TP up-regulation correlated with pCR. Significant toxicity resulted in therapy discontinuation in 3 of 26 patients.
Conclusions: DC chemotherapy exhibited a similar pCR rate compared with standard taxane regimens, with increased toxicity. TP expression was not up-regulated after docetaxel and did not correlate with therapeutic response. Core breast biopsy after neoadjuvant chemotherapy accurately predicted pathologic response.
Significance of Immunohistochemical Expression of Estrogen Receptors α and β in Squamous Cell Carcinoma of the Esophagus
Authors: Nozoe Tadahiro , Oyama Tsunehiro , Takenoyama Mitsuhiro , Hanagiri Takeshi , Sugio Kenji , Yasumoto Kosei 
Published: July 2007

Abstract
Purpose: Possible significance of sex hormone estrogen as an antitumor therapeutic arm toward esophageal squamous cell carcinoma (ESCC) cells has been suggested. The aim of the current study was to clarify the clinicopathologic significance of an immunohistochemical expression of estrogen receptors α and β (ERα and ERβ) in ESCC.
Experimental Design: Expression of ERα and ERβ were examined using an immunohistochemical methods in 73 paraffin-embedded sections collected from patients with ESCC who had been subjected to esophageal resection and digestive reconstruction without any preoperative induction therapy.
Results: Forty-seven (64.4%) ESCCs had a positive cytoplasmic expression of ERα and 21 (28.8%) ESCCs had a positive nuclear expression of ERβ. Univariate analysis showed that both positive ERα expression (P = 0.0001) and negative ERβ expression (P = 0.026) were unfavorable prognostic indicators in ESCC. Moreover, multivariate analysis showed that ERα-positive/ERβ-negative expression (P = 0.003) and progression of tumor stage (P = 0.014) were found to be independent unfavorable prognostic indicators in ESCCs.
Conclusions: Immunohistochemical expression of ERα and ERβ were found to be observed in ESCC. Positive expression of ERα in addition to negative expression of ERβ proved to be an unfavorable independent prognostic indicator in ESCC.
“1D+4DVAR” Assimilation of NCEP Stage-IV Radar and Gauge Hourly Precipitation Data at ECMWF
Authors: Lopez Philippe , Bauer Peter 
Published: July 2007

Abstract
The one- plus four-dimensional variational data assimilation (“1D+4DVAR”) method currently run in operations at ECMWF with rain-affected radiances from the Special Sensor Microwave Imager is used to study the potential impact of assimilating NCEP stage-IV analyses of hourly accumulated surface precipitation over the U.S. mainland. These data are a combination of rain gauge measurements and observations from the high-resolution Doppler Next-Generation Weather Radars. Several 1D+4DVAR experiments have been run over a month in spring 2005. First, the quality of the precipitation forecasts in the control experiment is assessed. Then, it is shown that the impact of the assimilation of the additional rain observations on global scores of dynamical fields and temperature is rather neutral, while precipitation scores are improved for forecast ranges up to 12 h. Additional 1D+4DVAR experiments in which all moisture-affected observations are removed over the United States demonstrate that the NCEP stage-IV precipitation data on their own can clearly be beneficial to the analyses and subsequent forecasts of the moisture field. This result suggests that the potential impact of precipitation observations is overshadowed by the influence of other high-quality humidity observations, in particular, radiosondes. It also confirms that the assimilation of precipitation observations has the ability to improve the quality of moisture analyses and forecasts in data-sparse regions. Finally, the limitations inherent in the current assimilation of precipitation data, their implications for the future, and possible ways of improvement are discussed.
The “Triple Point” on 24 May 2002 during IHOP. Part II: Ground-Radar and In Situ Boundary Layer Analysis of Cumulus Development and Convection Initiation
Authors: Ziegler Conrad L. , Rasmussen Erik N. , Buban Michael S. , Richardson Yvette P. , Miller L. Jay , Rabin Robert M. 
Published: July 2007

Abstract
Cumulus formation and convection initiation are examined near a cold front–dryline “triple point” intersection on 24 May 2002 during the International H2O Project (IHOP). A new Lagrangian objective analysis technique assimilates in situ measurements using time-dependent Doppler-derived 3D wind fields, providing output 3D fields of water vapor mixing ratio, virtual potential temperature, and lifted condensation level (LCL) and water-saturated (i.e., cloud) volumes on a subdomain of the radar analysis grid. The radar and Lagrangian analyses reveal the presence of along-wind (i.e., longitudinal) and cross-wind (i.e., transverse) roll circulations in the boundary layer (BL). A remarkable finding of the evolving radar analyses is the apparent persistence of both transverse rolls and individual updraft, vertical vorticity, and reflectivity cores for periods of up to 30 min or more while moving approximately with the local BL wind. Satellite cloud images and single-camera ground photogrammetry imply that clouds tend to develop either over or on the downwind edge of BL updrafts, with a tendency for clouds to elongate and dissipate in the downwind direction relative to cloud layer winds due to weakening updrafts and mixing with drier overlying air. The Lagrangian and radar wind analyses support a parcel continuity principle for cumulus formation, which requires that rising moist air parcels achieve their LCL before moving laterally out of the updraft. Cumuli form within penetrative updrafts in the elevated residual layer (ERL) overlying the moist BL east of the triple point, but remain capped by a convection inhibition (CIN)-bearing layer above the ERL. Dropsonde data suggest the existence of a convergence line about 80 km east of the triple point where deep lifting of BL moisture and locally reduced CIN together support convection initiation.
Lower-Tropospheric Height Tendencies Associated with the Shearwise and Transverse Components of Quasigeostrophic Vertical Motion
Authors: Martin Jonathan E. 
Published: July 2007

Abstract
The recent suggestion that lower-tropospheric cyclogenesis is predominantly a result of column stretching associated with the updraft portion of the shearwise quasigeostrophic (QG) vertical motion is quantified through direct calculation of 900-hPa height tendencies via the QG vorticity equation. Comparison of the separate lower-tropospheric height tendencies associated with the shearwise and transverse portions of QG omega in a robust cyclogenesis event demonstrates that the shearwise updraft drives the largest part (&gt;80%) of the cyclogenetic height falls at least through the end of the mature stage of the life cycle. The lower-tropospheric height falls and vorticity production near the sea level pressure minimum of the occluded surface cyclone are driven nearly equally by shearwise and transverse updrafts.
Microphysical and Radiative Effects of Ice Clouds on Tropical Equilibrium States: A Two-Dimensional Cloud-Resolving Modeling Study
Authors: Ping Fan , Luo Zhexian , Li Xiaofan 
Published: July 2007

Abstract
The microphysical and radiative effects of ice clouds on tropical equilibrium states are investigated based on three two-dimensional cloud-resolving simulations imposed by zero vertical velocity and time-invariant zonal wind and sea surface temperature. An experiment without ice microphysics (ice microphysical and radiative effects; C00), another experiment without ice radiative effects (CI0), and the control experiment (CIR) are carried out. The model with cyclic lateral boundaries is integrated for 40 days to reach equilibrium states in all experiments. CI0 produces a colder and drier equilibrium state than CIR and C00 do through generating a larger IR cooling, a larger vapor condensation rate, and consuming a larger amount of water vapor. A larger surface rain rate occurs in CI0 than in CIR and C00. The ice radiative effects on thermodynamic equilibrium states are stronger than the ice microphysical effects so that the exclusion of ice microphysics yields a colder and drier equilibrium state in C00 than in CIR. The ice radiative effects and the ice microphysical effects on surface rainfall processes are largely offset, which leads to similar zonal-mean surface rain rates in C00 and CIR.
Electrical and Polarimetric Radar Observations of a Multicell Storm in TELEX
Authors: Bruning Eric C. , Rust W. David , Schuur Terry J. , MacGorman Donald R. , Krehbiel Paul R. , Rison William 
Published: July 2007

Abstract
On 28–29 June 2004 a multicellular thunderstorm west of Oklahoma City, Oklahoma, was probed as part of the Thunderstorm Electrification and Lightning Experiment field program. This study makes use of radar observations from the Norman, Oklahoma, polarimetric Weather Surveillance Radar-1988 Doppler, three-dimensional lightning mapping data from the Oklahoma Lightning Mapping Array (LMA), and balloon-borne vector electric field meter (EFM) measurements. The storm had a low flash rate (30 flashes in 40 min). Four charge regions were inferred from a combination of LMA and EFM data. Lower positive charge near 4 km and midlevel negative charge from 4.5 to 6 km MSL (from 0° to −6.5°C) were generated in and adjacent to a vigorous updraft pulse. Further midlevel negative charge from 4.5 to 6 km MSL and upper positive charge from 6 to 8 km (from −6.5° to −19°C) were generated later in quantity sufficient to initiate lightning as the updraft decayed. A negative screening layer was present near the storm top (8.5 km MSL, −25°C). Initial lightning flashes were between lower positive and midlevel negative charge and started occurring shortly after a cell began lofting hydrometeors into the mixed phase region, where graupel was formed. A leader from the storm’s first flash avoided a region where polarimetric radar suggested wet growth and the resultant absence of noninductive charging of those hydrometeors. Initiation locations of later flashes that propagated into the upper positive charge tracked the descending location of a polarimetric signature of graupel. As the storm decayed, electric fields greater than 160 kV m−1 exceeded the minimum threshold for lightning initiation suggested by the hypothesized runaway breakdown process at 5.5 km MSL, but lightning did not occur. The small spatial extent (≈100 m) of the large electric field may not have been sufficient to allow runaway breakdown to fully develop and initiate lightning.
Winter Lightning and North Atlantic Oscillation
Authors: de Pablo Fernando , Soriano Luis Rivas 
Published: July 2007

Abstract
The relationship between the North Atlantic Oscillation (NAO) and total (in cloud and cloud to ground) lightning activity during the wintertime (December to March) is analyzed. Lightning data from the Optical Transient Detector were used and were studied in the North Atlantic and western European area. The southern half of the area analyzed (latitudes lower than ∼50°N) was observed to have an increased (decreased) lightning flash rate associated with negative (positive) NAO index values. The opposite relationship was found when the northern half (latitudes higher than ∼50°N) was considered. In both cases, the effect of the NAO on the lightning activity was stronger over the eastern area analyzed. Low (clearly &lt;1) absolute values of the NAO index seem to be associated with minimum lightning activity.
The Dryline on 22 May 2002 during IHOP: Ground-Radar and In Situ Data Analyses of the Dryline and Boundary Layer Evolution
Authors: Buban Michael S. , Ziegler Conrad L. , Rasmussen Erik N. , Richardson Yvette P. 
Published: July 2007

Abstract
On the afternoon and evening of 22 May 2002, high-resolution observations of the boundary layer (BL) and a dryline were obtained in the eastern Oklahoma and Texas panhandles during the International H2O Project. Using overdetermined multiple-Doppler radar syntheses in concert with a Lagrangian analysis of water vapor and temperature fields, the 3D kinematic and thermodynamic structure of the dryline and surrounding BL have been analyzed over a nearly 2-h period. The dryline is resolved as a strong (2–4 g kg−1 km−1) gradient of water vapor mixing ratio that resides in a nearly north–south-oriented zone of convergence. Maintained through frontogenesis, the dryline is also located within a gradient of virtual potential temperature, which induces a persistent, solenoidally forced secondary circulation. Initially quasi-stationary, the dryline retrogrades to the west during early evening and displays complicated substructures including small wavelike perturbations that travel from south to north at nearly the speed of the mean BL flow. A second, minor dryline has similar characteristics to the first, but has weaker gradients and circulations. The BL adjacent to the dryline exhibits complicated structures, consisting of combinations of open cells, horizontal convective rolls, and transverse rolls. Strong convergence and vertical motion at the dryline act to lift moisture, and high-based cumulus clouds are observed in the analysis domain. Although the top of the analysis domain is below the lifted condensation level height, vertical extrapolation of the moisture fields generally agrees with cloud locations. Mesoscale vortices that move along the dryline induce a transient eastward dryline motion due to the eastward advection of dry air following misocyclone passage. Refractivity-based moisture and differential reflectivity analyses are used to help interpret the Lagrangian analyses.