Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data.

High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant-calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller and use of replicate sequencing have the most significant impact on single-nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false-negative rates. When replicates are not available, using a combination of multiple callers with more stringent cutoffs is recommended. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intra-host viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intra-host variation, viral diversity, and viral evolution. IMPORTANCE When viruses replicate inside a host cell, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus nor strongly beneficial can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in the inclusion of false-positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant-calling tools. We used simulated and synthetic data to test their performance against a true set of variants and then used these studies to inform variant identification in data from SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.

Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data.

High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller, and use of replicate sequencing have the most significant impact on single nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false negative rates. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intrahost viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intrahost variation, viral diversity, and viral evolution. IMPORTANCE: When viruses replicate inside a host, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus, nor strongly beneficial, can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in inclusion of false positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant calling tools. We used simulated and synthetic data to test their performance against a true set of variants, and then used these studies to inform variant identification in data from clinical SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.

A high resolution and high detection efficiency depth-encoding detector for brain positron emission tomography based on a 0.75 mm pitch scintillator array.

The quantitative accuracy and precision of brain positron emission tomography (PET) studies can be considerably improved using dedicated brain PET scanners with a uniform high resolution and a high sensitivity across the brain volume. One approach to building such a system is to construct the PET scanner using depth-of-interaction (DOI) encoding detectors with finely segmented and thick crystal arrays. In this paper, the performance of a DOI PET detector based on two 16 × 16 arrays of 2 × 2 mm2 SiPMs coupled to both ends of a 44 × 44 array of 0.69 × 0.69 × 30 mm3 polished LYSO crystals was evaluated at different temperatures (-9°C, 0°C, 10°C, and 20°C) for brain PET applications. The pitch size of the LYSO array is 0.75 mm. The flood histograms show that all the crystal elements in the LYSO array can be resolved except some edge crystals, due to the limited light sharing. The average energy resolution, average DOI resolution, and average timing resolution across crystal elements are 21.1 ± 3.0%, 3.47 ± 0.17 mm, and 1.38 ± 0.09 ns, respectively, which were obtained at a bias voltage of 56.5 V and a temperature of 0°C.

Tomographic imaging with Compton PET modules: ideal case and first implementation.

In our previous studies, we demonstrated that the Compton PET module, a layer structure PET detector with side readout, can provide high performance in terms of spatial/energy/timing resolution, as well as high gamma ray detection efficiency. In this study, we investigate how to translate the high performance of the detector module into good quality reconstructed tomographic images. This study is performed using GATE simulation, as well as with physical experiments. Similar detector geometry is used in the simulation and experiment: two identical 4-layer detector modules are placed with face to face distance of 56 mm. In the simulation study, each layer consists of a 1-mm-pitch pixelated crystal array. In the experimental study, each layer is a monolithic crystal, which is virtually binned into 1 mm2 cells to group single events according to the gamma ray interaction locations. A customized Derenzo phantom was placed between the two detector modules. By rotating the phantom using a motorized rotary stage, data along lines of response (LORs) at different angles were collected for reconstructing the tomographic image. The same reconstruction algorithm was used for both simulation and experimental studies. The results demonstrate that the simulation study could resolve 0.8 mm rods while the experimental study was able to resolve 1.0 mm rods.

Lead-free MCP to improve coincidence time resolution and reduce MCP direct interactions.

Achieving direct imaging of the annihilation position of a positron on an event-by-event basis using an ultrafast detector would have a great impact on the field of nuclear medicine. Cherenkov emission is the most attractive physical phenomenon for realizing such an ultrafast timing performance. Moreover, a microchannel-plate photomultiplier tube (MCP-PMT) is one of the most promising photodetectors for fully exploiting the fast timing properties of Cherenkov emission owing to its excellent single photon time resolution of 25 ps full width at half maximum (FWHM). However, as the MCP structure generally contains a lead compound, the gamma rays frequently and directly interact with the MCP, resulting in the degradation of its timing performance and generation of undesirable side peaks in its coincidence timing histogram. To overcome this problem, we have developed a new MCP-PMT based on an MCP consisting of borosilicate glass, thus drastically reducing the probability of the photoelectric effect occurring in the MCP. To evaluate its insensitivity to gamma rays and its timing performance, a coincidence experiment was performed and showed that the probability of direct interactions was reduced by a factor of 3.4. Moreover, a coincidence time resolution of 35.4 ± 0.4 ps FWHM, which is equivalent to a position resolution of 5.31 mm, was obtained without any pulse height/area cut, improving to 28.7 ± 3.0 ps when selecting on the highest amplitude events by careful optimization of the voltage divider circuit of the new MCP-PMT. The timing performance of this new MCP-PMT presents an important step toward making direct imaging possible.

Ectopic expression of recipient CD47 inhibits mouse macrophage-mediated immune rejection against human stem cell transplants.

Like conventional transplants, immunosuppression is required to facilitate survival and function of human embryonic stem cell (hESC) derivatives after implantation into xenogeneic recipients. We have previously reported that T cells alone are sufficient to reject allogeneic murine ESC derivatives; and strategies that inhibit T-cell activation, including coreceptor and costimulation blockade, prevent hESC derivatives from being rejected. This study aimed to investigate, in addition to T cells, whether macrophages contribute to transplant rejection of hESC xenografts with nonobese diabetic (NOD)/SCID mice that lack functional T and B cells but have macrophages. We show that acute rejection against hESC-derived endothelial cells (hESC-ECs) was mediated, to some degree, by infiltrating macrophages that phagocytosed them. Transgenic expression of murine CD47 on cell surface of hESC-ECs mitigates macrophage-mediated phagocytosis and improves their survival after transplantation. Our results highlight that innate immune cells, such as macrophages, can reject hESC derivatives, raising concern against the use of NOD/SCID as transplant recipients for testing in vivo function of hESC-derived tissues. Augmenting CD47 signaling promotes survival and function of hESC derivatives after xenogeneic transplantation.-Leung, C. S., Li, J., Xu, F., Wong, A. S. L., Lui, K. O. Ectopic expression of recipient CD47 inhibits mouse macrophage-mediated immune rejection against human stem cell transplants.

Single-cell transcriptomics reveal that PD-1 mediates immune tolerance by regulating proliferation of regulatory T cells.

BACKGROUND: We have previously reported an antigen-specific protocol to induce transplant tolerance and linked suppression to human embryonic stem cell (hESC)-derived tissues in immunocompetent mice through coreceptor and costimulation blockade. However, the exact mechanisms of acquired immune tolerance in this model have remained unclear. METHODS: We utilize the NOD.Foxp3hCD2 reporter mouse line and an ablative anti-hCD2 antibody to ask if CD4+FOXP3+ regulatory T cells (Treg) are required for coreceptor and costimulation blockade-induced immune tolerance. We also perform genome-wide single-cell RNA-sequencing to interrogate Treg during immune rejection and tolerance and to indicate possible mechanisms involved in sustaining Treg function. RESULTS: We show that Treg are indispensable for tolerance induced by coreceptor and costimulation blockade as depletion of which with an anti-hCD2 antibody resulted in rejection of hESC-derived pancreatic islets in NOD.Foxp3hCD2 mice. Single-cell transcriptomic profiling of 12,964 intragraft CD4+ T cells derived from rejecting and tolerated grafts reveals that Treg are heterogeneous and functionally distinct in the two outcomes of transplant rejection and tolerance. Treg appear to mainly promote chemotactic and ubiquitin-dependent protein catabolism during transplant rejection while seeming to harness proliferative and immunosuppressive function during tolerance. We also demonstrate that this form of acquired transplant tolerance is associated with increased proliferation and PD-1 expression by Treg. Blocking PD-1 signaling with a neutralizing anti-PD-1 antibody leads to reduced Treg proliferation and graft rejection. CONCLUSIONS: Our results suggest that short-term coreceptor and costimulation blockade mediates immune tolerance to hESC-derived pancreatic islets by promoting Treg proliferation through engagement of PD-1. Our findings could give new insights into clinical development of hESC-derived pancreatic tissues, combined with immunotherapies that expand intragraft Treg, as a potentially sustainable alternative treatment for T1D.

Deciphering the Role of microRNAs in Regulation of Immune Surveillance, Self-Tolerance and Allograft Transplant Outcome.

MicroRNAs are small non-coding RNAs that can modulate gene expression at posttranscriptional level, and they participate in almost all important biological processes. Immune system is elaborately regulated to maintain the equilibrium between immunity and tolerance. Recent studies have revealed significant functions of microRNAs in the maintenance of immune homeostasis using both cell and transgenic mouse models. In collaboration with various transcriptional factors and cytokines, microRNAs constitute an effective and flexible regulatory network governing the development and activation of immune cells; as well as maintenance of immune tolerance. In this review, microRNAs involved in T cell development, proliferation, and lineage differentiation will be summarized. Based on current knowledge, the function of microRNAs in establishing and maintaining immune tolerance will also be discussed in relation to determining the outcome of allograft transplantation.

Increased risk of influenza among vaccinated adults who are obese.

BACKGROUND: Influenza infects 5-15% of the global population each year, and obesity has been shown to be an independent risk factor for increased influenza-related complications including hospitalization and death. However, the risk of developing influenza or influenza-like illness (ILI) in a vaccinated obese adult population has not been addressed. OBJECTIVE: This study evaluated whether obesity was associated with increased risk of influenza and ILI among vaccinated adults. SUBJECTS AND METHODS: During the 2013-2014 and 2014-2015 influenza seasons, we recruited 1042 subjects to a prospective observational study of trivalent inactivated influenza vaccine (IIV3) in adults. A total of 1022 subjects completed the study. Assessments of relative risk for laboratory confirmed influenza and ILI were determined based on body mass index. Seroconversion and seroprotection rates were determined using prevaccination and 26-35 days post vaccination serum samples. Recruitment criteria for this study were adults 18 years of age and older receiving the seasonal trivalent inactivated influenza vaccine (IIV3) for the years 2013-2014 and 2014-2015. Exclusion criteria were immunosuppressive diseases, use of immunomodulatory or immunosuppressive drugs, acute febrile illness, history of Guillain-Barre syndrome, use of theophylline preparations or use of warfarin. RESULTS: Among obese, 9.8% had either confirmed influenza or influenza-like-illness compared with 5.1% of healthy weight participants. Compared with vaccinated healthy weight, obese participants had double the risk of developing influenza or ILI (relative risk=2.01, 95% CI 1.12, 3.60, P=0.020). Seroconversion or seroprotection rates were not different between healthy weight and obese adults with influenza or ILI. CONCLUSIONS: Despite robust serological responses, vaccinated obese adults are twice as likely to develop influenza and ILI compared with healthy weight adults. This finding challenges the current standard for correlates of protection, suggesting use of antibody titers to determine vaccine effectiveness in an obese population may provide misleading information.

Presence of influenza viruses in backyard poultry and swine in El Yali wetland, Chile.

In South America little is known regarding influenza virus circulating in backyard poultry and swine populations. Backyard productive systems (BPS) that breed swine and poultry are widely distributed throughout Chile with high density in the central zone, and several BPS are located within the "El Yali" (EY) ecosystem, which is one of the most important wetlands in South America. Here, 130 different wild bird species have been described, of them, at least 22 species migrate yearly from North America for nesting. For this reason, EY is considered as a high-risk zone for avian influenza virus. This study aims to identify if backyard poultry and swine bred in the EY ecosystem have been exposed to influenza A virus and if so, to identify influenza virus subtypes. A biosecurity and handling survey was applied and samples were collected from BPS in two seasons (spring 2013 and fall 2014) for influenza seroprevalence, and in one season (fall 2014) for virus presence. Seroprevalence at BPS level was 42% (95% CI:22-49) during spring 2013 and 60% (95% CI 43-72) in fall 2014. rRT-PCR for the influenza A matrix gene indicated a viral prevalence of 27% (95% CI:14-39) at BPS level in fall 2014. Eight farms (73% of rRT-PCR positive farms) were also positive to the Elisa test at the same time. One BPS was simultaneously positive (rRT-PCR) in multiple species (poultry, swine and geese) and a H1N2 virus was identified from swine, exemplifying the risk that these BPS may pose for generation of novel influenza viruses.

Isotopic Incorporation and the Effects of Fasting and Dietary Lipid Content on Isotopic Discrimination in Large Carnivorous Mammals.

There has been considerable emphasis on understanding isotopic discrimination for diet estimation in omnivores. However, discrimination may differ for carnivores, particularly species that consume lipid-rich diets. Here, we examined the potential implications of several factors when using stable isotopes to estimate the diets of bears, which can consume lipid-rich diets and, alternatively, fast for weeks to months. We conducted feeding trials with captive brown bears (Ursus arctos) and polar bears (Ursus maritimus). As dietary lipid content increased to ∼90%, we observed increasing differences between blood plasma and diets that had not been lipid extracted (∆(13)Ctissue-bulk diet) and slightly decreasing differences between plasma δ(13)C and lipid-extracted diet. Plasma Δ(15)Ntissue-bulk diet increased with increasing protein content for the four polar bears in this study and data for other mammals from previous studies that were fed purely carnivorous diets. Four adult and four yearling brown bears that fasted 120 d had plasma δ(15)N values that changed by <±2‰. Fasting bears exhibited no trend in plasma δ(13)C. Isotopic incorporation in red blood cells and whole blood was ≥6 mo in subadult and adult bears, which is considerably longer than previously measured in younger and smaller black bears (Ursus americanus). Our results suggest that short-term fasting in carnivores has minimal effects on δ(13)C and δ(15)N discrimination between predators and their prey but that dietary lipid content is an important factor directly affecting δ(13)C discrimination and indirectly affecting δ(15)N discrimination via the inverse relationship with dietary protein content.

Influenza gain-of-function experiments: their role in vaccine virus recommendation and pandemic preparedness.

In recent years, controversy has arisen regarding the risks and benefits of certain types of gain-of-function (GOF) studies involving avian influenza viruses. In this article, we provide specific examples of how different types of data, including information garnered from GOF studies, have helped to shape the influenza vaccine production process-from selection of candidate vaccine viruses (CVVs) to the manufacture and stockpiling of safe, high-yield prepandemic vaccines for the global community. The article is not written to support a specific pro- or anti-GOF stance but rather to inform the scientific community about factors involved in vaccine virus selection and the preparation of prepandemic influenza vaccines and the impact that some GOF information has had on this process.

Community end-of-life care among Chinese older adults living in nursing homes.

AIM: The aim of the present study was to investigate the preference and willingness-to-pay (WTP) of older Chinese adults for community end-of-life care in a nursing home rather than a hospital. METHODS: A total of 1540 older Chinese adults from 140 nursing homes were interviewed. Four hypothetical questions were asked to explore their preferences for end-of-life care. Using a discrete choice approach, specific questions explored acceptable trade-offs between three attributes: availability of doctors onsite, attitude of the care staff and additional cost of care per month. RESULTS: Approximately 35% of respondents preferred end-of-life care in the nursing home, whereas 23% of them would consider it in a better nursing home. A good attitude of staff was the most important attribute of the care site. Respondents were willing to pay an extra cost of US$5 (HK$39) per month for more coverage of doctor's time, and US$49 (HK$379) for a better attitude of staff in the nursing home. The marginal WTP for both more coverage of doctor's time and better attitude of staff amounted to US$54 (HK$418). Respondents on government subsidy valued the cost attribute more highly, as expected, validating the hypothesis that those respondents would be less willing to pay an additional cost for end-of-life care. CONCLUSIONS: Older Chinese adults living in nursing homes are willing to pay an additional fee for community end-of-life care services in nursing homes. Both the availability of the doctor and attitudes of nursing home staff are important, with the most important attribute being the staff attitudes. Geriatr Gerontol Int 2013; 14: 273-284.

Structure of 1-alkyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)amide ionic liquids with linear, branched, and cyclic alkyl groups.

X-ray scattering and molecular dynamics simulations have been carried out to investigate structural differences and similarities in the condensed phase between pyrrolidinium-based ionic liquids paired with the bis(trifluoromethylsulfonyl)amide (NTf2(-)) anion where the cationic tail is linear, branched, or cyclic. This is important in light of the charge and polarity type alternations that have recently been shown to be present in the case of liquids with cations of moderately long linear tails. For this study, we have chosen to use the 1-alkyl-1-methylpyrrolidinium, Pyrr(1,n(+)) with n = 5 or 7, as systems with linear tails, 1-(2-ethylhexyl)-1-methylpyrrolidinium, Pyrr(1,EtHx(+)), as a system with a branched tail, and 1-(cyclohexylmethyl)-1-methylpyrrolidinium, Pyrr(1,ChxMe(+)), as a system with a cyclic tail. We put these results into context by comparing these data with recently published results for the Pyrr(1,n(+))/NTf2(-) ionic liquids with n = 4, 6, 8, and 10.1,2 General methods for interpreting the structure function S(q) in terms of q-dependent natural partitionings are described. This allows for an in-depth analysis of the scattering data based on molecular dynamics (MD) trajectories that highlight the effect of modifying the cationic tail.

How does the ionic liquid organizational landscape change when nonpolar cationic alkyl groups are replaced by polar isoelectronic diethers?

X-ray scattering experiments and molecular dynamics simulations have been performed to investigate the structure of four room temperature ionic liquids (ILs) comprising the bis(trifluoromethylsulfonyl)amide (NTf(2)(-)) anion paired with the triethyloctylammonium (N(2228)(+)) and triethyloctylphosphonium (P(2228)(+)) cations and their isoelectronic diether analogs, the (2-ethoxyethoxy)ethyltriethylammonium (N(222(2O2O2))(+)) and (2-ethoxyethoxy)ethyltriethylphosphonium (P(222(2O2O2))(+)) cations. Agreement between simulations and experiments is good and permits a clear interpretation of the important topological differences between these systems. The first sharp diffraction peak (or prepeak) in the structure function S(q) that is present in the case of the liquids containing the alkyl-substituted cations is absent in the case of the diether substituted analogs. Using different theoretical partitioning schemes for the X-ray structure function, we show that the prepeak present in the alkyl-substituted ILs arises from polarity alternations between charged groups and nonpolar alkyl tails. In the case of the diether substituted ILs, we find considerable curling of tails. Anions can be found with high probability in two different environments: close to the cationic nitrogen (phosphorus) and also close to the two ether groups. For the two diether systems, anions are found in locations from which they are excluded in the alkyl-substituted systems. This removes the longer range (polar/nonpolar) pattern of alternation that gives rise to the prepeak in alkyl-substituted systems.

The addition of pyloroplasty as a new surgical approach to enhance effectiveness of gastric electrical stimulation therapy in patients with gastroparesis.

BACKGROUND: Improvement of gastroparesis (GP) symptoms has been documented in patients treated with gastric electrical stimulation (GES), but acceleration of gastric emptying (GET) is unpredictable. The aim of our study was to evaluate the advantage of adding surgical pyloroplasty (PP) to GES for improvement of GET and control of symptoms in diabetes mellitus (DM), idiopathic (ID), and postvagotomy (P-V) GP. METHODS: A total of 49 (17 - DM, 9 - ID, 23 - P-V) consecutive GP patients: 38 female; mean age 42 (21-73 years); mean weight 158 lbs (102-245), underwent GES implantation, and 26 (53%) additionally received PP. Total Symptoms Score, 4-h GET, adverse events (AEs), and days of hospitalizations were captured at baseline and at the last visit. KEY RESULTS: The mean follow-up was 7 months. Total Symptoms Score in patients who received Enterra and PP or GES alone significantly improved compared to their baseline scores (P < 0.001). GET improved by 64% at 4 h (P < 0.001) in patients with Enterra and PP, compared to 7% observed after GES therapy alone (ns). The most impressive acceleration of GET was seen in the P-V group, who received both therapies (P = 0.004) and 8 (60%) of them normalized GET. No AEs accompanied the addition of PP to the Enterra surgery. CONCLUSIONS & INFERENCES: (i) In drug-refractory GP the addition of PP to GES substantially accelerated GET; (ii) The GET response in P-V group was the most impressive; (iii) Significant symptom reductions were achieved by both procedures; and (iv) PP added to GES may sustain better long-term symptoms control particularly in the P-V setting.

Imaging and Timing Performance of 1cm × 1cm Position-sensitive Solid-state Photomultiplier.

We have designed and built a large-area 1cm × 1cm position-sensitive solid-state photomultiplier (PS-SSPM) for use in detector design for medical imaging applications. Our new large-area PS-SSPM concept implements resistive network between the micro-pixels, which are photodiodes operated in Geiger mode, called Geiger Photodiodes (GPDs), to provide continuous position sensitivity. Here we present imaging and timing performance of the large-area PS-SSPM for different temperatures and operating biases to find the optimum operating parameters for the device in imaging applications. A detector module was built by coupling a polished 8×8 LYSO array, with 1×1×20 mm3 elements, to a 1×1 cm2 PS-SSPM. Flood images recorded at room temperature show good crystal separation as all 64 elements were separated from each other. Cooling the device at 10 °C showed significant improvement. The device optimum bias voltage was ~4.5V over breakdown voltage. The coincidence timing resolution was improved significantly by increasing the operating bias, as well as by lowering the temperature to 0 °C. Results show excellent imaging performance and good timing response with a large-area PS-SSPM device.

Comparing intermediate range order for alkyl- vs. ether-substituted cations in ionic liquids.

X-ray scattering data from four pairs of ionic liquids (ILs) are compared. The alkyl-substituted cations show a first sharp diffraction peak between 3 and 4 nm(-1) that is not observed for ILs having cations with ether- or hydroxy-substitutions. These observations indicate a significant difference in the intermediate range order for these liquids.

Temperature-dependent structure of ionic liquids: X-ray scattering and simulations.

In this article we determine the temperature-dependent structure of the tetradecyltrihexylphosphonium bis(trifluoromethylsulfonyl)amide ionic liquid using a combination of X-ray scattering and molecular dynamics simulations. As in many other room-temperature ionic liquids three characteristic intermolecular peaks can be detected in the structure function S(q). A prepeak or first sharp diffraction peak is observed at about q = 0.42 A(-1). Long range anion-anion correlations are the most important contributors to this peak. In all systems we have studied to date, this prepeak is a signature of solvation asymmetry. The peak in S(q) near q = 0.75 A(-1) is the signature of ionic alternation and arises from the charge ordered separation of ions of the same charge. The most intense diffraction peak near q = 1.37 A(-1) arises from short-range separation between ions of opposite charge combined with a significant contribution from cationic carbon-carbon interactions, indicating that cationic hydrophobic tails have significant contacts.

Optimizing the administration of fixed-dose rate gemcitabine plus capecitabine using an alternating-week schedule: a dose finding and early efficacy study in advanced pancreatic and biliary carcinomas.

OBJECTIVES: This multisite study sought to optimize the dosing, schedule, and administration of fixed-dose rate (FDR) gemcitabine plus capecitabine for advanced pancreatic and biliary tract cancers using an alternating-week dose schedule of both agents. METHODS: Patients with previously untreated advanced pancreatic and biliary tract cancers with Eastern Cooperative Oncology Group performance status of 0 or 1 were eligible. For the dose-finding portion, a standard 3+3 dose-escalation schema was used, with the gemcitabine dose kept at 1000 mg/m(2) administered by FDR (10 mg/m(2)/min) on day 1 of each 14-day cycle, and capecitabine given on days 1 to 7 at doses ranging from 800 to 1500 mg/m(2) twice daily. Primary study objective was determination of maximum tolerated dose (MTD). The cohort at MTD was expanded for further efficacy assessment. RESULTS: A total of 45 patients (median age 61 y; 93% pancreatic/7% biliary; 84% with metastatic disease) were enrolled. Median number of cycles received was 11.5. The MTD using this dose schedule was FDR gemcitabine 1000 mg/m(2) plus capecitabine 1000 mg/m(2) bid, due to a high incidence of late hand-foot syndrome observed at the next higher dose level. Most common nonhematologic adverse events related to treatment included nausea/vomiting (overall rate, 64%; all grade 1/2) and hand-foot syndrome (overall rate, 60%; grade 3, 22%). The incidence of grade 3/4 hematologic adverse events was 24%. Six of 41 evaluable patients (14.6%) had a partial response; 18 of 31 patients (58%) with elevated baseline CA 19-9 level had ≥50% biomarker decline during treatment. Estimated median time to tumor progression and overall survival were 5.5 and 9.8 months, respectively (5.5 and 10.1 mo in the metastatic pancreatic cancer cohort). CONCLUSIONS: This dosing schedule of FDR gemcitabine plus capecitabine is active in patients with advanced pancreatobiliary cancers. Given its favorable toxicity profile and convenience, this regimen represents an appropriate front-line option for this patient population and may serve as the foundation on which new investigational agents are added in future trial design.