Markovian noise modelling and parameter extraction framework for quantum devices

In recent years, Noisy Intermediate Scale Quantum (NISQ) computers have been widely used as a test bed for quantum dynamics. This work provides a new hardware-agnostic framework for modelling the Markovian noise and dynamics of quantum systems in benchmark procedures used to evaluate device performance. As an accessible example, the application and performance of this framework is demonstrated on IBM Quantum computers. This framework serves to extract multiple calibration parameters simultaneously through a simplified process which is more reliable than previously studied calibration experiments and tomographic procedures. Additionally, this method allows for real-time calibration of several hardware parameters of a quantum computer within a comprehensive procedure, providing quantitative insight into the performance of each device to be accounted for in future quantum circuits. The framework proposed here has the additional benefit of highlighting the consistency among qubit pairs when extracting parameters, which leads to a less computationally expensive calibration process than evaluating the entire device at once.

Modeling Acute Chemoradiotherapy (CRT) Diarrhea Severity Using Automatically Contoured Small Bowel

PURPOSE/OBJECTIVE(S)

Acute severe diarrhea is a common toxicity in rectal cancer patients receiving CRT. A better understanding of the radiation tolerance of the small bowel is needed especially for novel radiation drug combinations. We investigate the dose impact by providing auto-contoured small bowel, using data from the ARISTOTLE phase III trial ISRCTN: 09351447.

MATERIALS/METHODS

A subset of participants (n = 93/564) with locally advanced rectal cancer in the ARISTOTLE trial testing the addition of concurrent irinotecan (n = 48) to neoadjuvant capecitabine (n = 45) CRT (45/25 Gy/fx), in an MRI defined high risk of loco-regional failure. CRT was delivered with conformal techniques. Diarrhea was measured using CTCAE v4.0 weekly. We applied an AI-based auto-contouring model to segment the small bowel on planning CT. The small-bowel DVH parameters were combined with the treatment arm, age, sex and MRI-defined tumor stage in a linear regression (LR) model to predict acute diarrhea severity. Explainable Shapley values (conditional marginalized expectation of a machine learning model per feature) were used to quantify the independent and normalized impact of radiation dose vs Irinotecan on the likelihood of severe diarrhea.

RESULTS

The auto-contouring model accuracy was consistent with clinical practice (mean dice coefficient = 0.739) and clinically acceptable when reviewed by clinicians. The treatment arm, MRI-defined T stage and small-bowel mean dose were found to be independently correlated to the diarrhea severity (p<0.001). V30Gy showed the strongest correlation to diarrhea severity in all the DVH parameters. The LR using the three variables yielded mean AUC scores of 0.898 (95% CI: [0.831,0.958]) on predicting Grade 2 and higher diarrhea, and 0.774 (95% CI: [0.678,0.869]) on predicting Grade 3 diarrhea based on 10-fold cross-validation. Shapley values showed that V30Gy>30.56 cm3 increases the likelihood of more severe diarrhea against the average (grade = 1.03) in the cohort. The impact of irradiation will be larger than the usage of Irinotecan within the patients with V30Gy >160.93 cm3.

CONCLUSION

We accurately modelled acute diarrhea (AUC = 0.90) for rectal cancer patients receiving CRT using AI-contoured small-bowel structures. The treatment arm and small-bowel dose were independently correlated to the diarrhea severity. The explainable model allowed us to quantify the impact of radiation dose, usage of irinotecan, and its combination, with a threshold of V30Gy = 160.93 cm3 yielding an equivalent impact. We will be extending the analysis to the whole trial cohort to improve the statistical power.

What Can Proton Beam Therapy Achieve for Patients with Pectus Excavatum Requiring Left Breast, Axilla and Internal Mammary Nodal Radiotherapy?

AIMS

Exposure of the heart to radiation increases the risk of ischaemic heart disease, proportionate to the mean heart dose (MHD). Radiotherapy techniques including proton beam therapy (PBT) can reduce MHD. The aims of this study were to quantify the MHD reduction achievable by PBT compared with volumetric modulated arc therapy in breath hold (VMAT-BH) in patients with pectus excavatum (PEx), to identify an anatomical metric from a computed tomography scan that might indicate which patients will achieve the greatest MHD reductions from PBT.

MATERIALS AND METHODS

Sixteen patients with PEx (Haller Index ≥2.7) were identified from radiotherapy planning computed tomography images. Left breast/chest wall, axilla (I-IV) and internal mammary node (IMN) volumes were delineated. VMAT and PBT plans were prepared, all satisfying target coverage constraints. Signed-rank comparisons of techniques were undertaken for the mean dose to the heart, ipsilateral lung and contralateral breast. Spearman's rho correlations were calculated for anatomical metrics against MHD reduction achieved by PBT.

RESULTS

The mean MHD for VMAT-BH plans was 4.1 Gy compared with 0.7 Gy for PBT plans. PBT reduced MHD by an average of 3.4 Gy (range 2.8-4.4 Gy) compared with VMAT-BH (P < 0.001). PBT significantly reduced the mean dose to the ipsilateral lung (4.7 Gy, P < 0.001) and contralateral breast (2.7 Gy, P < 0.001). The distance (mm) at the most inferomedial extent of IMN volume (IMN to heart distance) negatively correlated with MHD reduction achieved by PBT (Spearman's rho -0.88 (95% confidence interval -0.96 to -0.67, P < 0.001)).

CONCLUSION

For patients with PEx requiring left-sided breast and IMN radiotherapy, a clinically significant MHD reduction is achievable using PBT, compared with the optimal photon technique (VMAT-BH). This is a patient group in whom PBT could have the greatest benefit.

[Appropriate use of psychotropic drugs in institutionalized elderly presenting acute confusional state (delirium)]

Delirium (acute confusion) is a common, morbid, and costly geriatric syndrome that affects onethird of hospitalized older adults. As evidence mounts that delirium may persist for weeks to months, concern about delirium can no longer be restricted to acute hospitals. We present a review about non-pharmacologic and pharmacologic management of delirium in institution.

Inflaming the diseased brain: a role for tainted melanins

Inflammation plays a crucial role in neurodegenerative diseases, but the irritants responsible for this response remain largely unknown. This report addressed the hypothesis that hypochlorous acid reacts with dopamine to produce melanic precipitates that promote cerebral inflammation. Spectrophotometric studies demonstrated that nM amounts of HOCl and dopamine react within seconds. A second-order rate constant for the reaction of HOCl and dopamine of 2.5 × 10(4)M(-1)s(-1) was obtained by measuring loss of dopaminergic fluorescence due to HOCl. Gravimetric measurements, electron microscopy, elemental analysis, and a novel use of flow cytometry confirmed that the major product of this reaction is a precipitate with an average diameter of 1.5 μm. Flow cytometry was also used to demonstrate the preferential reaction of HOCl with dopamine rather than albumin. Engulfment of the chlorodopamine particulates by phagocytes in vitro caused these cells to release TNFα and die. Intrastriatal administration of 10(6) particles also increased the content of TNFα in the brain and led to a 50% loss of the dopaminergic neurons in the nigra. These studies indicate that HOCl and dopamine react quickly and preferentially with each other to produce particles that promote inflammation and neuronal death in the brain.

A shift in the collagen V antigenic epitope leads to T helper phenotype switch and immune response to self-antigen leading to chronic lung allograft rejection

Immune responses to human leucocyte antigen (HLA) and self-antigen collagen V (Col-V) have been proposed in the pathogenesis of chronic rejection (bronchiolitis obliterans syndrome, BOS) following human lung transplantation (LTx). In this study, we defined the role for the shift in immunodominant epitopes of Col-V in inducing T helper phenotype switch leading to immunity to Col-V and BOS. Sera and lavage from BOS(+) LTx recipients with antibodies to Col-V were analysed. Two years prior to BOS, patients developed antibodies to both Col-V,α1(V) and α2(V) chains. However, at clinical diagnosis of BOS, antibodies became restricted to α1(V). Further, lung biopsy from BOS(+) patients bound to antibodies to α1(V), indicating that these epitopes are exposed. Fourteen Col-V peptides [pep1-14, pep1-4 specific to α1(V), pep5-8 to α1,2(V) and pep9-14 to α2(V)] which bind to HLA-DR4 and -DR7, demonstrated that prior to BOS, pep 6, 7, 9, 11 and 14 were immunodominant and induced interleukin (IL)-10. However, at BOS, the response switched to pep1, 4 and 5 and induced interferon (IFN)-γ and IL-17 responses, but not IL-10. The T helper (Th) phenotype switch is accompanied by decreased frequency of regulatory T cells (T(regs) ) in the lavage. LTx recipients with antibodies to α1(V) also demonstrated increased matrix metalloproteinase (MMP) activation with decreased MMP inhibitor, tissue inhibitor of metalloproteinase (TIMP), suggesting that MMP activation may play a role in the exposure of new Col-V antigenic epitopes. We conclude that a shift in immunodominance of self-antigenic determinants of Col-V results in induction of IFN-γ and IL-17 with loss of tolerance leading to autoimmunity to Col-V, which leads to chronic lung allograft rejection.

Conidia production ofBeauveria sp. by solid-state fermentation for biocontrol ofIlex paraguariensis caterpillars

Conidia production of Beauveria sp. strain LAG by solid-state fermentation (SSF) using blends of agro-industrial residues (residual potatoes and sugar-cane bagasse) was optimized with respect to cultivation conditions and the composition of substrate mixture in Erlenmeyer flasks and column-type bioreactor. With a blend of 60 % residual potatoes and 40 % sugar-cane bagasse the optimum conditions achieved were: incubation temperature 26 degrees C, initial substrate pH 6, inoculum concentration 10(7) conidia per g substrate; optimal initial moisture of the substrate was 70 % for Erlenmeyer flasks, in column-type bioreactor (with forced aeration) the optimal initial moisture of the substrate was 65 % with airflow of 60 mL/min. The highest production (1.07 x 10(10) conidia per g dry substrate) was achieved after a 10-d fermentation. The conidia were used in laboratory assays against Thelosia camina and Hylesia sp., caterpillars that are serious pests of mate plants. The mortality of T. camina was >90 % 10 d after spraying caterpillars with 1 mL conidia suspension at a concentration 10(5)-10(8)/mL. For Hylesia sp., the mortality was 70 %, 7 d after immersion in the conidia suspension containing 108 conidia per mL. Therefore, the Beauveria sp. LAG can be considered to be an important biocontrol instrument in the prospect of the Integrated Pest Management for mate plants.

The transmembrane protein of HIV-1 primary isolates modulates cell surface expression of their envelope glycoproteins

We have recently shown that the level of cell surface expression of envelope glycoproteins derived from various human immunodeficiency virus type 1 (HIV-1) primary isolates (PI) was lower than those of envelope glycoproteins derived from T-cell laboratory-adapted (TCLA) HIV-1 (D. Brand et al., 2000, Virology 271, 350-362). We investigated this phenomenon by comparing the cell surface expression of chimeric envelope glycoproteins constructed by swapping the gp120 surface and gp41 transmembrane glycoproteins of the TCLA HIV-1MN and the PI HIV-1(133), HIV-1G365, or HIV-1EFRA. We found that each chimeric envelope construct had a cell surface-specific pattern of expression similar to that of the parental envelope glycoproteins corresponding to the gp41. Thus, the difference in cell surface expression observed between TCLA viruses and various PI is probably due to a signal located in gp41. Identification of this signal may be important for the design of PI envelope-derived immunogens and may increase our understanding of the mechanisms by which HIV-1 escapes from the immune system.

Packed bed column fermenter and kinetic modeling for upgrading the nutritional quality of coffee husk in solid-state fermentation

Studies were carried out to evaluate solid-state fermentation (SSF) for the upgradation of the nutritional quality of coffee husk by degrading the caffeine and tannins present in it. SSF was carried out by Aspergillus niger LPBx in a glass column fermenter using factorial design experiments and surface response methodology to optimize bioprocess parameters such as the substrate pH and moisture content and aeration rate. The first factorial design showed that the moisture content of the substrate and aeration rate were significant factors for the degradation of toxic compounds, which was confirmed by the second factorial design too. The kinetic study showed that the degradation of toxic compounds was related to the development of the mold and its respiration and also to the consumption of the reducing sugars present in coffee husk. From the values obtained experimentally for the oxygen uptake rate and CO(2) evolved, the system determined a biomass yield (Y(x/o)) of 3.811 (g of biomass).(g of consumed O(2))(-1) and a maintenance coefficient (m) of 0.0031 (g of consumed O(2)).(g biomass of biomass)(-1).h(-1). The best results on the degradation of caffeine (90%) and tannins (57%) were achieved when SSF was carried out with a 30 mL.min(-1) aeration rate using coffee husk having a 55% initial moisture content. The inoculation rate did not affect the metabolization of the toxic compounds by the fungal culture. After SSF, the protein content of the husk was increased to 10.6%, which was more than double that of the unfermented husk (5.2%).

Outcomes of patients using a tiered trauma response protocol

OBJECTIVES

This study evaluated processes of care and outcome for injured patients at a Level I trauma center who had been either treated as a full trauma team activation (FULL) or managed with a modified trauma team activation (MOD).

METHODS

A retrospective methodology was used to evaluate all patients entered into the regional trauma system and transported from the scene to a Level I trauma center. Patients treated during a 2-year period of exclusively FULL trauma team protocols were compared with patients managed during a subsequent 2-year period after implementation of a two-tiered response. In the later era, trauma system patients were designated before hospital arrival as either FULL or MOD trauma team responses. An additional case-control analysis was conducted on a subset of MOD trauma team response patients who were undertriaged; that is, in retrospect, they met criteria for a FULL response. The outcomes in the case-control group were compared by chi2 tests and Mann-Whitney U tests. Statistical significance was assumed for p < 0.05.

RESULTS

During the presystem period, 1,740 patients were transported as trauma system entries to Oregon Health Sciences University. During the postsystem period, 2,333 patients were transported to Oregon Health Sciences University as either MOD trauma system entries (1,272 [55%]) or as FULL trauma system entries (1,061 [45%]). Postsystem patients had longer time intervals in the emergency department compared with presystem patients. Death rates for patients who died in the emergency department or before hospital discharge were similar. Among patients who were designated as MOD trauma system entries and were subsequently categorized as meeting FULL trauma team criteria, mortality rate was low.

CONCLUSION

Implementation of the tiered response protocol led to a substantial change in the operational response in the emergency department. Although processes of care were nominally prolonged, adverse consequences were not identified. We concluded from this quality improvement review that implementation of a tiered response protocol was satisfactory and improved efficiency. Further work is required to improve accuracy of the categorization of trauma system patients as either MOD or FULL trauma codes.

Immunogenicity of recombinant envelope glycoproteins derived from T-cell line-adapted isolates or primary HIV isolates: a comparative study using multivalent vaccine approaches

We investigated immunogenic properties of native envelope glycoproteins derived from HIV-1 (subtype B). Our main objective was to assess whether the design of multivalent vaccines affects generation of neutralizing antibodies against primary viruses. Recombinant Semliki Forest virus (SFV) particles producing various HIV-1 envelope glycoproteins were used as vaccine vectors. The following multivalent vaccination approaches were compared: 1) immunization with a mixture of recombinant SFV expressing envelope glycoproteins derived from three HIV-1 primary isolates and two T-cell laboratory-adapted (TCLA) viruses; 2) immunization with a mixture of recombinant SFV expressing only the envelope glycoproteins derived from three HIV-1 primary isolates; 3) sequential immunizations with the recombinant SFV expressing the envelope glycoproteins derived from three HIV-1 primary isolates and two TCLA viruses, respectively. Two monovalent vaccine approaches using SFV expressing envelope glycoproteins derived from a single primary isolate or TCLA virus were also included in the study. The multivalent vaccination strategies based on SFV vaccine vectors did not induce more neutralizing antibodies than the previously tested TCLA envelope immunogens, which gave disappointing results against primary isolates.

A comparison of patient characteristics and survival in two trauma centres located in different countries

INTRODUCTION

The aim of the study was to compare patient characteristics and mortality in severely injured patients in two trauma centres located in different countries, allowing for differences in case-mix. It represents a direct bench-marking exercise between the trauma centres at the North Staffordshire Hospital (NSH), Stoke-on-Trent, UK and the Oregon Health Sciences University (OHSU) Hospital, Portland, Oregon, USA.

METHODS

Patients of all ages admitted to the two hospitals during 1995 and 1996 with an Injury Severity Score >15 were included, except for those who died in the emergency departments. Twenty-three factors were studied, including the Injury Severity Score, Glasgow Coma Score, mechanism of injury and anatomical site of injury. Outcome analysis was based on mortality at discharge.

RESULTS

The pattern of trauma differed significantly between Stoke and Portland. Patients from Stoke tended to be older, presented with a lower conscious level and a lower systolic blood pressure and were intubated less frequently before arriving at hospital. Mortality depended on similar factors in both centres, especially age, highest AIS score, systolic blood pressure and Glasgow Coma Score.The crude analysis of mortality showed a highly significant odds-ratio of 1.64 in Stoke compared with Portland. Single-factor adjustments were made for the above four factors, which had a similar influence on mortality in both centres. Adjusting for the first three factors individually did not alter the odds-ratio, which stayed in the range 1.53-1.59 and remained highly significant. Adjusting for the Glasgow Coma Score reduced the odds-ratio to 0.82 and rendered it non-significant. In a multi-factor logistic regression model incorporating all of the factors shown to influence mortality in either centre, the odds-ratio was 1.7 but was not significant.

CONCLUSION

The analysis illustrates the limitations and pitfalls of making crude outcome comparisons between centres. Highly significant differences in crude mortality were rendered non-significant by case-mix adjustments, supporting the null hypothesis that the two centres were equally effective in terms of this short-term indicator of outcome. To achieve a meaningful comparison between centres, adjustments must be made for the factors which affect mortality.

Identification of the glycoprotein 41(TM) cytoplasmic tail domains of human immunodeficiency virus type 1 that interact with Pr55Gag particles

We investigated the protein/protein interactions that occur during human immunodeficiency virus (HIV-1) budding. We evaluated the binding to Pr55Gag particles of peptides mapping to the cytoplasmic tail of gp41TM and of host-cell proteins, in a cell-free, in vitro assay. Host-cell proteins and irrelevant viral envelope peptides did not bind. Peptides corresponding to a large central domain of the gp41TM cytoplasmic tail (93 residues) bound to Pr55Gag particles. This demonstrates that a Gag/Env interaction is responsible for the specific incorporation of the Env glycoprotein into nascent HIV-1 virions, and defines more accurately the gp41TM domain involved in this interaction.

Biological detoxification of coffee husk by filamentous fungi using a solid state fermentation system

Studies were carried out on detoxification of coffee husk in solid state fermentation using three different strains of Rhizopus, Phanerochaete, and Aspergillus sp. Fungal strains were selected by their ability to grow on a coffee husk extract-agar medium. Using R. arrizus LPB-79, the best results on the degradation of caffeine (87%) and tannins (65%) were obtained with pH 6.0 and moisture 60% in 6 days. When P. chrysosporium BK was used, maximum degradation of caffeine and tannins were 70.8 and 45%, respectively, with coffee husk having 65% moisture and pH 5.5 in 14 days. The Aspergillus strain, isolated from the coffee husk, showed best biomass formation on coffee husk extract-agar medium. Optimization assays were conducted using factorial design, and surface response experiments with Aspergillus sp. The best detoxification rates achieved were 92% for caffeine and 65% for tannins. The results showed good prospects of using these fungal strains, in particular Aspergillus sp., for the detoxification of coffee husk.

Antigenic properties of recombinant envelope glycoproteins derived from T-cell-line-adapted isolates or primary human immunodeficiency virus isolates and their relationship to immunogenicity

The native envelope glycoproteins of primary HIV-1 virions have weaker antigenicity than do T-cell laboratory-adapted (TCLA) viruses. These antigenic properties require further evaluation if recombinant envelope glycoproteins are produced as part of a vaccine strategy. In this study, we compared the antigenicity of recombinant envelope glycoproteins derived from three primary isolates (PI) (HIV-1(BX08), HIV-1(CHA), and HIV-1(133)) and two TCLA viruses (HIV-1(HXB2) and HIV-1(MN)) produced using the Semliki Forest virus (SFV) system. This analysis was performed by radioimmunoprecipitation assays and flow cytometry. The results suggest that the SFV produces envelope glycoproteins with features in common with the envelopes found in naturally occurring virions. In particular, the PI envelopes had weak heterogeneous antigenic properties. However, the cytometric analysis also showed that there was less envelope glycoprotein on the cell surface for the PI envelopes than for those of TCLA viruses, suggesting differences in their intracellular trafficking. The immunogenic properties of the various envelope glycoproteins were evaluated in mice using recombinant SFV particles as vaccine vectors. The PI envelopes were less immunogenic than the TCLA envelopes, probably due to both their low antigenicity and cell surface expression level. Thus, it may be difficult to design an effective vaccine based on native recombinant PI envelopes.

Measuring injury risk factors: question reliability in a statewide sample

BACKGROUND

Recently (1996-98), Colorado added 15 questions pertaining to injury related risks and behaviors to the behavioral risk factor surveillance system (BRFSS). Questions addressed bicycle helmet use, traffic crashes, exposure to violence, suicidal behavior, and gun storage.

OBJECTIVE

To measure the test-retest reliability of these injury related questions.

METHODS

Of 330 BRFSS participants, 229 (69%) were called a second time and reasked nine selected injury questions. Retests were completed 7-28 days after the original interview.

RESULTS

Test-retest agreement was very high (kappa >0.80) for bicycle helmet use, domestic police visits, and gun ownership. All other injury risk questions had substantial agreement (kappa >0.60).

CONCLUSIONS

The injury related questions added to the Colorado BRFSS have high test-retest reliability.

Phase III study of granulocyte-macrophage colony-stimulating factor in advanced HIV disease: effect on infections, CD4 cell counts and HIV suppression. Leukine/HIV Study Group

OBJECTIVE

To evaluate the effect of adjuvant granulocyte-macrophage colony-stimulating factor (GM-CSF) (sargramostim, yeast-derived recombinant human GM-CSF) on incidence and time to opportunistic infection or death, plasma HIV-RNA, and CD4 cell count in patients with advanced HIV disease.

METHODS

This Phase III randomized, double-blind, placebo-controlled trial enrolled subjects with CD4 cell counts < or = 50 x 10(6)/l or < or = 100 x 10(6)/l with a prior AIDS-defining illness on stable antiretroviral therapy. Subjects were stratified by baseline HIV-RNA level (> or = or < 30,000 copies/ml) and randomized to receive subcutaneous injections of GM-CSF 250 microg or placebo three times per week for 24 weeks. Subjects were permitted to continue on blinded drug for up to 20 months. Subjects were evaluated for infections, plasma HIV-RNA, lymphocyte counts, changes in antiretroviral therapy, toxicity, and survival.

RESULTS

Three-hundred and nine subjects received at least one dose of study drug, 70% completed 24 weeks of therapy. Groups were well matched at baseline. Significant increases in CD4 cell and neutrophil counts were observed at 1, 3, and 6 months in the GM-CSF group. GM-CSF significantly reduced the incidence of overall infections (78% placebo versus 67% GM-CSF; P = 0.03) and delayed time to first infection (56 days placebo versus 97 days GM-CSF; P = 0.04). No statistical difference in cumulative opportunistic infections was observed between groups; however, among subjects without an opportunistic infection prior to study, the GM-CSF group demonstrated a trend towards fewer subjects with an opportunistic infection on study (26% placebo versus 8% GM-CSF; P = 0.08). Change in HIV-RNA was not significantly different between groups, but significantly fewer GM-CSF subjects with baseline viral load < 30,000 copies/ml had changes in antiretroviral therapy for increased viral load (42% placebo versus 21% GM-CSF; P = 0.01). In patients with HIV-RNA levels below the limit of detection at baseline, more GM-CSF patients maintained an undetectable viral load at 24 weeks (54% placebo versus 83% GM-CSF; P = 0.02). GM-CSF was well tolerated.

CONCLUSIONS

GM-CSF significantly increased CD4 cell count and decreased virological breakthrough and overall infection rate in subjects with advanced HIV disease.

Age-associated changes in cognitive function in highly educated adults: emerging myths and realities

The effects of education and continued intellectual engagement on age-associated cognitive change were investigated in a sample of 102 members of the professional and college communities in the metro Atlanta Georgia area (ages 30-76). All participants were administered a 60-minute battery that measured different aspects of memory, intelligence and cognitive performance. Age-associated declines in performance were detected on the digit symbol measure of intelligence. Conversely, positive but non-significant trends were detected on the picture completion, arithmetic and similarities subtests. Age effects were also noted on some measures of the Wisconsin Card Sorting Test and both versions of the Trail Making Test. The findings suggest that at least among the highly educated, certain cognitive abilities may receive some degree of amelioration as a consequence of continued intellectual engagement. However, the effects may be associated more with compensation rather than protection against the effects of ageing.

Role of the HIV type 1 glycoprotein 120 V3 loop in determining coreceptor usage

Macrophage (M)-tropic HIV-1 isolates use the beta-chemokine receptor CCR5 as a coreceptor for entry, while T cell line-adapted (TCLA) strains use CXCR4 and dual-tropic strains can use either CCR5 or CXCR4. To investigate the viral determinants involved in choice of coreceptor, we used a fusion assay based on the infection of CD4+ HeLa cells that express one or both coreceptors with Semliki Forest virus (SFV) recombinants expressing the native HIV-1 gp160 of a primary M-tropic isolate (HIV-1BX08), a TCLA isolate (HIV-1LAI), or a dual-tropic strain (HIV-1MN). We examined whether the V3 region of these glycoproteins interacts directly with the corresponding coreceptors by assaying coreceptor-dependent cell-to-cell fusion mediated by the different recombinants in the presence of various synthetic linear peptides. Synthetic peptides corresponding to different V3 loop sequences blocked syncytium formation in a coreceptor-specific manner. Synthetic V2 peptides were also inhibitory for syncytium formation, but showed no apparent coreceptor specificity. A BX08 V3 peptide with a D320 --> R substitution retained no inhibitory capacity for BX08 Env-mediated cell-to-cell fusion, but inhibited LAI Env-mediated fusion as efficiently as the homologous LAI V3 peptide. The same mutation engineered in the BX08 env gene rendered it able to form syncytia on CD4+CXCR4+CCR5-HeLa cells and susceptible to inhibition by SDF-1alpha and MIP-1beta. Other substitutions tested (D320 --> Q/D324 --> N or S306 --> R) exhibited intermediate effects on coreceptor usage. These results underscore the importance of the V3 loop in modulating coreceptor choice and show that single amino acid modifications in V3 can dramatically modify coreceptor usage. Moreover, they provide evidence that linear V3 loop peptides can compete with intact cell surface-expressed gp120/gp41 for CCR5 or CXCR4 interaction.

Generation of monoclonal antibodies to native human immunodeficiency virus type 1 envelope glycoprotein by immunization of mice with naked RNA

The Semliki Forest virus (SFV) vector system is a new approach for in vivo expression of heterologous proteins and can also be used to generate specific immune responses in animal models. HIV-1 envelope glycoprotein produced using the SFV expression system is correctly folded, cleaved, transported to the cell surface and exhibits functional activity. We evaluated a recombinant Semliki Forest virus naked RNA-based immunization protocol for generation of monoclonal antibodies against the HIV-1 envelope glycoprotein. In vitro-transcribed RNA encoding for the SFV replicase complex and Env protein of HIV-1 (HXB2 strain) was injected intramuscularly to mice. This approach elicited an Env-specific antibody response in four mice out of five and a monoclonal antibody, 12H2, directed against gp41 was produced. Our results show that recombinant SFV RNA immunization can potentially be used as a quick and direct method to produce monoclonal antibodies, with the particular advantage that vectored RNA, rather than purified antigen, delivers a complex oligomer produced correctly.

Comparative analysis of humoral immune responses to HIV type 1 envelope glycoproteins in mice immunized with a DNA vaccine, recombinant Semliki Forest virus RNA, or recombinant Semliki Forest virus particles

The Semliki Forest virus (SFV) system seems to be a useful new approach for generating effective immune responses against HIV-1 in animal models. We evaluated this system by comparing the humoral immune responses raised in mice immunized against the HIV-1 envelope with the SFV system, a DNA vaccine, and a recombinant Env glycoprotein. gp160 ELISA antibody titers (204,800) were highest in the sera from mice immunized with recombinant Semliki Forest virus particles. These sera contained antibodies to the CD4-binding site and recognized linear epitopes on gp120 and gp41 that were also recognized by a pool of sera from HIV1-infected individuals. This demonstrates that the HIV-1 envelope produced in vivo by the SFV system does not fold aberrantly. A low level of neutralizing antibodies against the HIV-1LAI strain was also detected in the serum of one mouse immunized with recombinant SFV particles, suggesting that booster injections should be given to achieve a more effective immune response. SFV recombinant particles induced the strongest humoral responses to the HIV-1 envelope of all the potential HIV env vaccines tested.

Interaction between hepatitis delta virus-encoded proteins and hepatitis B virus envelope protein domains

Hepatitis delta virus (HDV) packaging requires prenylation of the HDV large protein (p27), as well as a direct protein-protein interaction between HDV proteins and hepatitis B virus (HBV) envelope protein domains. To investigate this interaction, we have analysed the binding capacity of baculovirus-expressed delta p24 and p27 proteins to synthetic peptides specific for the HBV envelope. Although a higher degree of binding was observed with p27, both p24 and p27 could bind HBV envelope peptides. One such peptide corresponded to residues 56-80 located in the cytosolic loop of the small HBV envelope protein, and another corresponded to 23 carboxy-terminal residues of the pre-S1 specific to the large HBV envelope protein. This indicates that in addition to p27, p24 may contribute to packaging of HDV through a protein-protein interaction with HBV envelope domains, and that an interaction between the pre-S1 polypeptide and delta proteins may play a role in infectivity.

Commentaries on 'Trusting the surgeon: A tornado from Bristol' (editorial)

Commentaries on 'Trusting the surgeon: A tornado from Bristol' by Don Hindle.

Comparison of antibody responses to different forms of HIV-1 core antigens by epitope mapping

The specificity of antibodies to HIV-1 capsid (p24CA) and matrix (p17MA) proteins, produced in mice against unprocessed immature assembled polyprotein (wild-type p55 virus-like particles or chimeric p55 virus-like particles) or against the monomeric mature form (rp24CA/rp17MA), was analyzed by a microplate epitope mapping assay using a panel of synthetic peptides covering the entire p24CA plus p17MA sequences of HIV-1LAI. All immunized mice developed anti-p24CA and anti-p17MA antibodies, although the spectrum of specificity of these antibodies was different. Four p24 CA epitopes (residues 176-192, 201-218, 233-253, 285-304) were recognized by anti-rp24CA/rp17MA antibodies, whereas one p17MA epitope (residues 11-25) and one p24CA epitope (residues 176-192) were constantly recognized by anti-p55 virus-like particle antibodies. These results suggest a different specificity pattern of anti-p24CA and anti-p17MA antibodies depending on whether they are produced against the soluble mature form or the immature assembled form of the gag proteins.

Variability of femoral muscle attachments

Analytical and experimental models of the musculoskeletal system often assume single values rather than ranges for anatomical input parameters. The hypothesis of the present study was that anatomical variability significantly influences the results of biomechanical analyses, specifically regarding the moment arms of the various thigh muscles. Insertions and origins of muscles crossing or attaching to the femur were digitized in six specimens. Muscle volumes were measured; muscle attachment area and centroid location were computed. To demonstrate the influence of inter-individual anatomic variability on a mechanical modeling parameter, the corresponding range of muscle moment arms were calculated. Standard deviations, as a percentage of the mean, were about 70% for attachment area and 80% for muscle volume and attachment centroid location. The resulting moment arms of the m. gluteus maximus and m. rectus femoris were especially sensitive to anatomical variations (SD 65%). The results indicate that sensitivity to anatomical variations should be analyzed in any investigation simulating musculoskeletal interactions. To avoid misinterpretations, investigators should consider using several anatomical configurations rather than relying on a mean data set.

Assembly and immunogenicity of chimeric Gag-Env proteins derived from the human immunodeficiency virus type 1

We evaluated the potential of the precursor Gag protein (Pr55) of the human immunodeficiency virus type 1 (HIV-1) as a carrier for the presentation of envelope epitopes. Recombinant chimeric core-envelope protein-expressing constructs were derived by deletion of regions within the gag gene, especially of regions encoding p24 capsid epitopes. Sequences encoding either the principal neutralization determinant (PND) and/or the CD4-binding domains (CD4BS) were then inserted. Deletion of residues 196-226 within the p24 capsid protein did not prevent self-assembly into virus-like particles (VLPs) whereas deletion of residues 299-328 completely abolished VLP formation. Thus the major homology region (MHR) and proximal sequences are required for capsid assembly. An immunization study in mice showed that assembled chimeric proteins elicited strong anti-Gag, weak anti-envelope, and no neutralizing humoral responses. Nonassembled chimeric proteins were poor immunogens. Mapping of Pr55 antigenic sites using sera from immunized mice and peptides overlapping the entire Gag precursor showed that p24 capsid and p17 matrix epitopes presented to the immune system differed from the mature form (p24 or p17) and the multimeric immature form (Pr55).

Frequency of early in utero HIV-1 infection: a blind DNA polymerase chain reaction study on 100 fetal thymuses

OBJECTIVE

To estimate the prevalence of in utero transmission of HIV-1 through the second trimester.

MATERIAL AND METHODS

One hundred consecutive, unselected, intact fetuses, beyond 15 weeks gestational age (mean, 22.4 weeks) were studied. These were obtained following spontaneous intrauterine deaths (n = 4), miscarriages (n = 4), and elective mid-trimester terminations (n = 92), eight of which were fetuses with malformations from HIV-1-positive pregnancies. Coded DNA extracts from the fetal thymuses were tested blindly by polymerase chain reaction in three laboratories using a total of six different primer pairs.

RESULTS

Two thymuses tested positive [95% confidence interval (Cl), 0.2-7]. Results from the three laboratories were consistent in all 100 cases. The two fetuses with HIV in the thymus both tested positive in other organs, demonstrating systemic HIV infection. The first fetus, whose mother had advanced AIDS, had died in utero and had diffuse toxoplasmosis. The second died following extremely premature delivery in a pregnancy complicated by repeated bleeding. HIV infection was observed in none of the 92 fetuses that resulted from elective mid-trimester terminations (95% Cl, 0-4).

CONCLUSION

The frequency of early in utero HIV infection appears to be low, compared with transmission rates in infants born to HIV-1-infected mothers, suggesting that transmission occurs mostly later in pregnancy and/or at delivery. Specific risk factors may have implications in the occurrence of early as opposed to late transmission.

A simple procedure to generate chimeric Pr55gag virus-like particles expressing the principal neutralization domain of human immunodeficiency virus type 1

The Pr55gag human immunodeficiency virus type 1 (HIV-1) precursor protein that is capable of auto-assembling was used as a carrier for a consensus sequence of the principal neutralization domain (PND) of the HIV-1 envelope. For this purpose, a modified HIV-1 gag gene with deletion of the sequence encoding a previously described p24 epitope (amino acids 196-228 of Pr55gag) was first obtained using PCR with degenerate primers, and then cloned. This deleted gag gene allowed in a second time the insertion of a synthetic oligonucleotide cassette encoding the North American/European consensus PND precisely in place of the p24 epitope. The chimeric gene was then inserted into a baculovirus transfer vector and expressed in insect cells. The construct formed 100-140 nm virus-like particles that were released into the extracellular medium. The use of a serum-free medium that supports growth of insect cells facilitated the downstream purification of the extracellular particles. The chimeric particles were recognized by monoclonal antibodies directed to V3 by Western blot but not by immune electron microscopy, suggesting that, although the inserted sequence was still antigenic it was not exposed at the surface of the particles. The results show the ability of Pr55gag to serve as a carrier for easy insertion, in a precisely defined region, of selected epitopes of gp120 surface envelope protein, and to still auto-assemble in virus-like particles. However, the data indicate that exposed epitopes of the mature p24 protein are not presented similarly in the Pr55 precursor, and therefore that different constructs with various insertions in different places must be generated. Such constructs offer an attractive approach for HIV vaccine development and will need evaluation for both antigenicity and immunogenicity.

Determinants of human immunodeficiency virus type 1 entry in the CDR2 loop of the CD4 glycoprotein

Various roles for the viral receptor, CD4, have been proposed in facilitating human immunodeficiency virus type 1 (HIV-1) entry, including virion binding to the target cell and the induction of conformational changes in the viral envelope glycoproteins required for the membrane fusion reaction. Here, we compare the structural requirements in the CDR2-like loop of CD4 domain 1, the major contact site of the gp120 envelope glycoprotein, for gp120 binding and virus entry. For every CD4 mutant examined, the level of cell surface expression and the gp120 binding affinity were sufficient to explain the relative ability to function as a viral receptor. The decrease in relative infectibility associated with decreased gp120 binding affinity was more pronounced at lower cell surface CD4 concentrations. These results imply that both receptor density and affinity determine the efficiency of HIV-1 entry and that specific structures in the CD4 residues examined are probably not required for HIV-1 entry functions other than gp120 binding.

High antigenic cross-reactivity of the V3 consensus sequences of HIV-1 gp120

The principal neutralization determinant (PND) of the human immunodeficiency virus type 1 (HIV-1) is located within the variable V3 region of the external envelope protein gp120. Although it is recognized that V3 sequences induce antibody response with restricted neutralization activity in vitro, we observed that the V3 consensus sequences representing North American/European and African isolates were highly cross-reactive, binding 94 and 77%, respectively, of sera collected from HIV-1 individuals originating from various parts of the world. Even HIV-1-positive sera from some East African residents, infected by strains whose V3 loop sequences are undoubtedly distinct from the North American/European consensus V3 loop sequence, reacted better to the V3 North American/European consensus peptide than to African-specific V3 sequences. Results indicate that the V3 consensus sequences represent the best candidates for optimal cross-reactivity with a wide variety of strains. Furthermore, using immunoassays for antibodies to prototype-specific V3 sequences, it is shown that HIV-1 strains related to the MN group are prevalent in West Africa, indicating either a West African origin of the MN-related viruses or more probably an introduction of this group of viruses through European/North American contacts.

Enzyme-linked oligosorbent assay for detection of polymerase chain reaction-amplified human immunodeficiency virus type 1

An enzyme-linked oligosorbent assay (ELOSA) was developed for the detection on microtiter plates of polymerase chain reaction (PCR)-amplified human immunodeficiency virus type 1 (HIV-1) DNA. The denatured PCR product was hybridized with a passively adsorbed oligonucleotide capture probe and a horseradish peroxidase-labeled oligonucleotide detection probe. The sensitivity and specificity of the PCR-ELOSA technique depended to some extent on the nucleotide sequences of the oligonucleotide primer and probe quartet used in the amplification and detection. We evaluated five oligonucleotide quartets located in the gag, pol, vpr, env, and nef regions of HIV-1. DNAs from 39 HIV-1-seropositive individuals and 27 healthy HIV-1-seronegative controls were amplified by the PCR procedure, and the products were detected by ELOSA. Ten copies of HIV-1 DNA against a background of 1 microgram of human DNA were specifically detected by PCR-ELOSA. Specificities and sensitivities were, respectively, 100 and 95% for the gag system, 100 and 97% for the pol system, 100 and 85% for the vpr system, 96 and 95% for the env system, and 100 and 95% for the nef system. The simplicity of ELOSA makes it suitable for automation and applicable to genetic testing and detection of viral and bacterial DNAs or RNAs in most routine laboratories.

Prevalence and significance of hepatitis C virus (HCV) viremia in HCV antibody-positive subjects from various populations

Hepatitis C virus (HCV) infection is currently assessed by detection of antibodies to HCV with immunoassays. However, in the absence of an in vitro system to isolate the virus, or an immunoassay to identify HCV antigen in blood, an ongoing acute or chronic HCV infection can be diagnosed only by detection of HCV RNA by polymerase chain reaction. We used a reverse transcription-nested polymerase chain reaction to detect an HCV 5' noncoding viral RNA sequence in serum specimens collected from anti-HCV-positive individuals belonging to different risk groups and compared the results with those obtained with a prototype recombinant immunoblot assay (Chiron HCV SIA prototype recombinant immunoblot assay [RIBA]) containing four different viral peptides (c22, c33c, c100, and NS5). The prevalence of HCV viremia ranged from 25.9% in HCV antibody-positive blood donors to 92% in HCV antibody-positive hemophiliacs. Elevated alanine aminotransferase values in HCV antibody-positive patients were clearly associated with viremia. Ninety-six percent of HCV RNA-positive patients reacted to two viral antigens or more, compared with only 64% of HCV RNA-negative patients. Contrary to previous reports, HCV viremia was not associated with either the presence or the absence of a particular antibody specificity. The newly introduced NS5 peptide did not improve the sensitivity or specificity of the RIBA. Although 20% of the patients in our study whose sera reacted to all of the antigens were HCV RNA negative, the positive predictive value of a RIBA considered positive by the manufacturer (two or more bands), was rather high (78%) and may allow suspicion of viremia in EIA2 enzyme-linked immunosorbent assay-positive patients.

[Value of magnetic resonance imaging in a lipoma of the left ventricle]

A patient with benign left ventricular lipoma was explored pre- and post-operatively with echocardiography, computerized tomography (CT) and magnetic resonance imaging (MRI). With MRI spin-echo sequences the lipoma emitted a bright signal similar to that of normal fatty tissue on the two echoes of the sequence (28 ms and 65 ms). MRI was not better than CT to demonstrate that the tumour was a lipoma, but it proved to be the best technique to obtain information on tumoral spread to the myocardium and pericardium, and it showed the intracavitary extension without the need for contrast medium injection. After surgery, MRI displayed the remains of a septal lipomatous lesion. This case underlines the usefulness of MRI for the evaluation of cardiac tumours, and particularly lipomas.

A chest pain clinic to improve the follow-up of patients released from an urban university teaching hospital emergency department

During a 12-month period, 1,045 of 1,554 patients (67%) over age 30 seen in an urban teaching hospital emergency department with acute chest pain were released based on the clinical judgment of the examining physician. Patients who were released were offered follow-up within 24 to 72 hours in a hospital-based chest pain clinic. Of these 1,045 patients, 772 (74%) returned or were contacted by phone, and 29 were directly admitted; 14 had unstable angina, and eight had new myocardial infarctions. Because of its positive impact on the quality of care at an acceptable cost, the Chest Pain Clinic, which was originally instituted as part of a research protocol, has now become part of the routine spectrum of care provided at the University of Cincinnati Medical Center.