bluuebunny/crossref_metadata_2025_split huggingface dataset:
Initial B-Cell Responses to Transmitted Human Immunodeficiency Virus Type 1: Virion-Binding Immunoglobulin M (IgM) and IgG Antibodies Followed by Plasma Anti-gp41 Antibodies with Ineffective Control of Initial Viremia
Authors: Tomaras Georgia D. , Yates Nicole L. , Liu Pinghuang , Qin Li , Fouda Genevieve G. , Chavez Leslie L. , Decamp Allan C. , Parks Robert J. , Ashley Vicki C. , Lucas Judith T. , Cohen Myron , Eron Joseph , Hicks Charles B. , Liao Hua-Xin , Self Steven G. , Landucci Gary , Forthal Donald N. , Weinhold Kent J. , Keele Brandon F. , Hahn Beatrice H. , Greenberg Michael L. , Morris Lynn , Karim Salim S. Abdool , Blattner William A. , Montefiori David C. , Shaw George M. , Perelson Alan S. , Haynes Barton F. 
Published: October 2008

ABSTRACTA window of opportunity for immune responses to extinguish human immunodeficiency virus type 1 (HIV-1) exists from the moment of transmission through establishment of the latent pool of HIV-1-infected cells. A critical time to study the initial immune responses to the transmitted/founder virus is the eclipse phase of HIV-1 infection (time from transmission to the first appearance of plasma virus), but, to date, this period has been logistically difficult to analyze. To probe B-cell responses immediately following HIV-1 transmission, we have determined envelope-specific antibody responses to autologous and consensus Envs in plasma donors from the United States for whom frequent plasma samples were available at time points immediately before, during, and after HIV-1 plasma viral load (VL) ramp-up in acute infection, and we have modeled the antibody effect on the kinetics of plasma viremia. The first detectable B-cell response was in the form of immune complexes 8 days after plasma virus detection, whereas the first free plasma anti-HIV-1 antibody was to gp41 and appeared 13 days after the appearance of plasma virus. In contrast, envelope gp120-specific antibodies were delayed an additional 14 days. Mathematical modeling of the earliest viral dynamics was performed to determine the impact of antibody on HIV replication in vivo as assessed by plasma VL. Including the initial anti-gp41 immunoglobulin G (IgG), IgM, or both responses in the model did not significantly impact the early dynamics of plasma VL. These results demonstrate that the first IgM and IgG antibodies induced by transmitted HIV-1 are capable of binding virions but have little impact on acute-phase viremia at the timing and magnitude that they occur in natural infection.
Sequence Conservation and Differential Expression of Marek's Disease Virus MicroRNAs
Authors: Morgan Robin , Anderson Amy , Bernberg Erin , Kamboj Sachin , Huang Emily , Lagasse Grace , Isaacs Grace , Parcells Mark , Meyers Blake C. , Green Pamela J. , Burnside Joan 
Published: October 2008

ABSTRACT

Marek's disease virus (MDV), a herpesvirus that causes a lymphoproliferative disorder in chickens, encodes a number of microRNAs derived primarily from two locations in the MDV genome. One cluster of microRNA genes flanks the
meq
oncogene, and a second cluster is found within the latency-associated transcript (LAT) region. The sequences of MDV microRNAs from a collection of field and reference strains with various levels of virulence were compared and found to be highly conserved. However, microRNAs from the
meq
cluster were detected at higher levels in lymphomas caused by a form of the virus designated very virulent plus (vv+; strain 615K, also known as T. King) than in those caused by a less virulent (very virulent [vv]) form (RB1B). For example, levels of mdv1-miR-M4, which shares a seed sequence with miR-155, a microRNA implicated in B-cell lymphoma, were threefold higher and levels of mdv1-miR-M2*/3p were more than sixfold higher in vv+ MDV-induced tumors than in vv MDV-induced tumors. In contrast, levels of the microRNAs from the LAT cluster were equivalent in tumors produced by vv and vv+ strains. Additionally, mdv1-miR-M4 is the MDV microRNA most highly expressed in tumors, where it accounts for 72% of all MDV microRNAs, as determined by deep sequencing. These data suggest that the
meq
cluster microRNAs play an important role in the pathogenicity of MDV.
Human Immunodeficiency Virus Type 1 Superinfection Occurs despite Relatively Robust Neutralizing Antibody Responses
Authors: Blish Catherine A. , Dogan Ozge C. , Derby Nina R. , Nguyen Minh-An , Chohan Bhavna , Richardson Barbra A. , Overbaugh Julie 
Published: October 2008

ABSTRACT
Superinfection by a second human immunodeficiency virus type 1 (HIV-1) strain indicates that gaps in protective immunity occur during natural infection. To define the role of HIV-1-specific neutralizing antibodies (NAbs) in this setting, we examined NAb responses in 6 women who became superinfected between ∼1 to 5 years following initial infection compared to 18 women with similar risk factors who did not. Although superinfected individuals had less NAb breadth than matched controls at ∼1 year postinfection, no significant differences in the breadth or potency of NAb responses were observed just prior to the second infection. In fact, four of the six subjects had relatively broad and potent NAb responses prior to infection by the second strain. To more specifically examine the specificity of the NAbs against the superinfecting virus, these variants were cloned from five of the six individuals. The superinfecting variants did not appear to be inherently neutralization resistant, as measured against a pool of plasma from unrelated HIV-infected individuals. Moreover, the superinfected individuals were able to mount autologous NAb responses to these variants following reinfection. In addition, most superinfected individuals had NAbs that could neutralize their second viral strains prior to their reinfection, suggesting that the level of NAbs elicited during natural infection was not sufficient to block infection. These data indicate that preventing infection by vaccination will likely require broader and more potent NAb responses than those found in HIV-1-infected individuals.
VP26 of White Spot Syndrome Virus Functions as a Linker Protein between the Envelope and Nucleocapsid of Virions by Binding with VP51
Authors: Wan Qiang , Xu Limei , Yang Feng 
Published: October 2008

ABSTRACT
The envelopment of the nucleocapsid is an important step in white spot syndrome virus (WSSV) assembly. Previous studies showed that VP26, a major envelope protein of WSSV, can interact with viral nucleocapsid. In this study, using the biotin label transfer technique, we found that the biotin label was transferred from Bio-rVP26 to the viral capsid protein VP51 or from Bio-MBP-VP51 to VP26. Far-Western analyses provided further evidence for direct interaction between VP26 and VP51. Therefore, we conclude that VP26 functions as a matrix-like linker protein between the viral envelope and nucleocapsid, which suggests that VP26 is a key factor in the envelopment of WSSV virion.
4Q372 1 and the Continuation of Joseph's Exile
Authors: Thiessen Matthew 
Published: October 2008

AbstractIt has been argued that the fragment 4Q372 1 contains polemic against the Samaritans and their temple cult at Gerizim. While allusions to Samaritans are found in the text, their presence signifies to the restored southern tribes that their restoration is not yet complete. Since the northern tribes, represented by the person of Joseph, remain in foreign lands, the promised deliverance of Deut 32 remains unfulfilled. In contrast to those in the south who might be tempted to conclude, with Ps 78, that God had rejected Joseph, 4Q372 1 suggests that the south's fate is inextricably intertwined with Joseph's fate.
4QMMT and Paradigms of Second Temple Jewish Nomism
Authors: Hogeterp Albert 
Published: October 2008

AbstractThe article reconsiders 4QMMT's perspective on Torah and justification in view of the recent debate about paradigms of covenantal nomism (E. P. Sanders) and of justification and variegated nomism (D. A. Carson, P. T. O'Brien, M. A. Seifrid). The hortatory part, in particular 4QMMT C 23–32, takes into account divine grace through forgiveness and search for the Torah as normative direction. Human works and divine justification are thereby not conflated in MMT's understanding of Torah. e notion of covenant theology reflected in 4QMMT comes closer to that of the Damascus Document than to the more polarized notion of covenant in the Community Rule.
The Throne Visions of Daniel 7, 1 Enoch 14, and the Qumran Book of Giants (4Q530): An Analysis of Their Literary Relationship
Authors: Stokes Ryan 
Published: October 2008

AbstractIn Dan 7:9–10, the apocalyptic seer narrates his vision of God's heavenly throne. According to most scholars, Daniel's vision account depends literarily on the supposedly more primitive visionary traditions found in 1 Enoch 14 and the Book of Giants of the Dead Sea Scrolls. Certain divergences in these traditions, however, reveal that it is in fact 1 Enoch 14 that depends on a vision account much like that found in Dan 7. The Book of Giants and Daniel, on the other hand, both seem to make use of a common tradition, each adapting it in a different way.
The Problem of Characterizing the 4QReworked Pentateuch Manuscripts: Bible, Rewritten Bible, or None of the Above?
Authors: Zahn Molly 
Published: October 2008

AbstractThis article engages the problem of whether the five manuscripts classified as 4QReworked Pentateuch (4Q158, 4Q364–367) should be considered extrabiblical compositions or simply expansive copies of the Pentateuch. Since similar methods of reworking scripture appear in both types of text, focusing on the ways scripture is reworked in the 4QRP manuscripts cannot solve the problem. Other criteria such as the literary voice, scope, and coverage of a work are more promising. The fragmentary state of the texts, however, precludes a definitive solution and requires that multiple possibilities be considered.
Modeling Soybean Rust Spore Escape from Infected Canopies: Model Description and Preliminary Results
Authors: Andrade David , Pan Zaitao , Dannevik William , Zidek Jeremy 
Published: October 2008

Abstract
Asian soybean rust, caused by Phakopsora pachyrhizi, an airborne fungal pathogen, is an annual threat to U.S. soybean production. The disease is spread during the growing season by fungal spores that are transported from warm southern locations where they overwinter. Current models of long distance spore transport treat spore sources as constant emitters. However, evidence suggests that the spore escape rate depends on 1) the interaction between spores and turbulence within and above an infected canopy and 2) the filtering capacity of the canopy to trap upward-traveling spores. Accordingly, a theoretically motivated yet computationally simple forecast model for escape rate is proposed using a simple turbulence closure method and a parameterization of the canopy porosity. Preliminary escape-rate forecasts were made using the friction velocity, an estimate of initial spore concentrations inside an infected canopy, and the canopy’s leaf area distribution. Sensitivity tests were conducted to determine which biological and meteorological variables and parameters most impact modeled spore escape rates. The spore escape model was integrated with a large-scale spore transport model that was used to forecast spore deposition over U.S. soybean production regions. Preliminary results suggest that varying meteorological conditions significantly impact escape rates and the spread of the disease.
Sudden Nocturnal Warming Events in Mississippi
Authors: White Loren D. 
Published: October 2008

Abstract
Significant episodes of sudden nocturnal warming have been observed by the Mississippi Mesonet. The probable relation of these nocturnal warming events to surface layer regime transitions between a decoupled quiescent surface layer and a more turbulent, less thermodynamically stable surface layer is discussed within the context of four examples with different temporal signatures. In general, the changes in wind speed and inversion strength are consistent with expectations for such regime changes. However, details of individual events indicate a wider variety of event characteristics than has been documented previously. The cases examined are proposed as prototypes for four different types of warming event, based on the evolution of temperature and dewpoint as well as on whether clear forcing from a mesoscale or synoptic frontal passage can be identified. Using this classification system and a subjective evaluation of event magnitude, the frequency of nocturnal warming events is analyzed for four mesonet stations at varying distance inland over the period of record.
Spontaneous Imbalance and Hybrid Vortex–Gravity Structures
Authors: McIntyre Michael E. 
Published: October 2008

AbstractAfter reviewing the background, this article discusses the recently discovered examples of hybrid propagating structures consisting of vortex dipoles and comoving gravity waves undergoing wave capture. It is shown how these examples fall outside the scope of the Lighthill theory of spontaneous imbalance and, concomitantly, outside the scope of shallow-water dynamics. Besides the fact that going from shallow-water to continuous stratification allows disparate vertical scales—small for inertia–gravity waves and large for vortical motion—the key points are 1) that by contrast with cases covered by the Lighthill theory, the wave source feels a substantial radiation reaction when Rossby numbers R ≳ 1, so that the source cannot be prescribed in advance; 2) that examples of this sort may supply exceptions to the general rule that spontaneous imbalance is exponentially small in R; and 3) that unsteady vortical motion in continuous stratification can stay close to balance thanks to three quite separate mechanisms. These are as follows: first, the near-suppression, by the Lighthill mechanism, of large-scale imbalance (inertia–gravity waves of large horizontal scale), where “large” means large relative to a Rossby deformation length LD characterizing the vortical motion; second, the flaccidity, and hence near-steadiness, of LD-wide jets that meander and form loops, Gulf-Stream-like, on streamwise scales ≫ LD; and third, the dissipation of small-scale imbalance by wave capture leading to wave breaking, which is generically probable in an environment of random shear and straining. Shallow-water models include the first two mechanisms but exclude the third.
A Coupled GCM Analysis of MJO Activity at the Onset of El Niño
Authors: Marshall A. G. , Alves O. , Hendon H. H. 
Published: October 2008

Abstract
The ocean dynamics of the Madden–Julian oscillation (MJO) and its interaction with El Niño–Southern Oscillation (ENSO) are assessed using a flux-corrected coupled model experiment from the Australian Bureau of Meteorology. The model demonstrates the correct oceanic Kelvin wave response to the MJO-related westerly winds in the western Pacific. Although there may be a role for the MJO in influencing the strength of El Niño, its impact is difficult to separate from that of strong heat content preconditioning of ENSO. Hence, the MJO–ENSO relationship is assessed starting from a background state of low heat content anomalies in the western Pacific that are also characteristic of recent observed El Niño events. The model shows a strong relationship between ENSO and the MJO near the peak of El Niño. At this time, the sea surface temperature (SST) anomaly is largest in the central Pacific, and it is difficult to separate cause and effect. Near the onset of El Niño, however, when Pacific Ocean SST anomalies are near zero, an increase in MJO activity is associated with Kelvin wave activity and stronger subsequent ENSO warming. A significant increase in the number of MJO events, rather than the strength of individual MJO events, leads to stronger eastern Pacific warming; the MJO appears not to be responsible for the occurrence of El Niño itself, but, rather, is important for influencing its development thus. This research supports a role for downwelling oceanic Kelvin waves and subsequent deepening of the thermocline in contributing to eastern Pacific warming during the onset of El Niño.
Observational Evidence of Reemergence in the Extratropical Southern Hemisphere
Authors: Ciasto Laura M. , Thompson David W. J. 
Published: October 2008

Abstract
Observations of subsurface temperatures are used to examine the winter-to-winter “reemergence” of sea surface temperature (SST) anomalies in the extratropical South Pacific Ocean. Reemergence is the mechanism through which SST anomalies formed in the late winter are sequestered beneath the relatively shallow summer mixed layer and then reentrained into the deepening mixed layer during the following autumn/winter. Although several studies have extensively examined reemergence in the Northern Hemisphere (NH), this is the first study to use observations of subsurface temperatures to document reemergence in the extratropical Southern Hemisphere (SH). The SH subsurface data reveal a pronounced reemergence signal in the western extratropical South Pacific. In this region, surface thermal anomalies formed during late SH winter are observed to persist below the summertime mixed layer and reemerge at the surface during the following early winter months. As such, SST anomalies formed during late winter are strongly correlated with SST anomalies during the following early winter but are not significantly correlated with SST anomalies during the intervening summer months. The results based on subsurface data are robust to small changes in the period of analysis and are qualitatively similar to existing evidence of reemergence in the NH. Analyses of independent SST data reveal that reemergence is widespread in the western extratropical South Pacific basin but is less discernible in SST anomalies over the eastern part of the basin.
Turbulence and Wind Shear in Layers of Large Doppler Spectrum Width in Stratiform Precipitation
Authors: Melnikov Valery M. , Doviak Richard J. 
Published: October 2008

Abstract
Weather radar observations of stratiform precipitation often reveal regions having very large measured Doppler spectrum widths, exceeding 7, and sometimes 10, m s−1. These widths are larger than those typically found in thunderstorms; widths larger than 4 m s−1 are associated with moderate or severe turbulence in thunderstorms. In this work, stratiform precipitation has been found to have layers of widths larger than 4 m s−1 in more than 80% of cases studied, wherein the shear of the wind on scales that are large compared to the dimensions of the radar resolution volume is the dominant contributor to spectrum width. Analyzed data show that if width ≤7 m s−1, and if the layers are not wavy or patchy, these layers have weak turbulence. On the other hand, regions having widths &gt;4 m s−1 in patches or in wavelike structures are likely to have moderate to severe turbulence with the potential to be a hazard to safe flight. To separate the contributions to spectrum width from wind shear and turbulence and to evaluate the errors in turbulence estimates, data have been collected with elevation increments much less than a beamwidth. Despite beamwidth limitations, the small elevation increments reveal impressive structures in the fields. For example, the “cat’s eye” structure associated with Kelvin–Helmholtz waves is clearly exhibited in the fields of spectrum width observed at low-elevation angles, but not in the reflectivity or velocity fields. Reflectivity fields in stratiform precipitation are featureless compared to spectrum width fields.
Differential Suture Loading in an Experimental Rotator Cuff Repair
Authors: Howe Christopher , Huber Philippe , Wolf Fredric M. , Matsen Frederick 
Published: October 2008

Background Repairs of large rotator cuff tears often fail to heal. A possible factor in these failures is excessive tension in the repair sutures, causing them to pull through the tendon. Hypothesis Arm positions encountered during early rehabilitation after cuff repair can dramatically increase the relative tension in the different sutures of the cuff repair. Study Design Controlled laboratory study. Methods In a cadaver model, a 4-suture supraspinatus repair was carried out with transosseous sutures. After the repair, the arm was placed in 12 different positions. The tension in each suture was monitored using individual load cells. Results When the arm was externally rotated relative to the plane of the scapula, the tension in the anterior suture was over 10 times that in the posterior suture (P <. 001). When the arm was internally rotated, the tension in the posterior suture was over 10 times that in the anterior suture (P <. 0005). When the arm was in neutral rotation, there was no significant difference in the suture tension. Conclusions This study is the first report of direct suture tension measurement after a model rotator cuff repair. In this model, 30° of either internal or external rotation of the arm in relation to the plane of the scapula created substantial imbalances in the tension between the most anterior and most posterior sutures of a supraspinatus repair, regardless of the position of abduction. Clinical Relevance Avoiding external rotation stretching during the healing of supraspinatus repairs may prevent tension overload in the critical anterior suture.
Multiligamentous Injuries of the Knee and Associated Vascular Injuries
Authors: McDonough E. Barry , Wojtys Edward M. 
Published: October 2008

Background Recently published studies have raised the question of whether arteriography is warranted in the evaluation of multiligamentous injuries of the knee. Purpose The objective is to report the frequency of associated vascular injuries in the multiligament-injured knee and examine the role arteriography plays in the treatment protocol. Study Design Case series; Level of evidence, 4. Methods A retrospective analysis was performed on 71 patients over a 12-year period who had a diagnosis of multiligamentous injury of the knee with a tibial-femoral dislocation documented based on physical examination and magnetic resonance imaging findings. Results Of 72 knee injuries involving multiple ligaments, 12 vascular injuries were identified. Four knees were found to have a vascular injury at initial presentation based on abnormal physical examination and confirmed with arteriography. Eight patients with a vascular injury had normal pulses. Routine arteriography discovered an intimal injury of the popliteal artery in 5 of these patients. Arteriography in the remaining 3 patients was interpreted as normal. Conclusion These findings suggest that physical examination alone is not sufficient in detecting the majority of vascular injuries after a suspected knee dislocation.