Sequence and functional analyses of Haemophilus spp. genomic islands

Comparative analysis of genomic islands of Haemophilus species shows that they are co-evolving as semi-autonomous genomes within the host genome

Exotic foods reveal contact between South Asia and the Near East during the second millennium BCE

Aunque el papel clave del comercio a larga distancia en la transformación de las cocinas en todo el mundo está bien documentado desde al menos la época romana, la prehistoria del comercio de alimentos euroasiático es menos visible. Con el fin de arrojar luz sobre la transformación de las cocinas del Mediterráneo oriental durante la Edad del Bronce y la Edad del Hierro Temprana, analizamos los microrestos y las proteínas conservadas en el cálculo dental de individuos que vivieron durante el segundo milenio a. Nuestros resultados proporcionan evidencia clara del consumo de alimentos básicos esperados, como cereales (Triticeae), sésamo ( Sesamum ) y dátiles ( Phoenix ). Además, informamos evidencia del consumo de soja ( glicina ), probable banano ( Musa ) y cúrcuma (Curcuma ), que hace retroceder la evidencia más antigua de estos alimentos en el Mediterráneo por siglos (cúrcuma) o incluso milenios (soja). Descubrimos que, desde principios del segundo milenio en adelante, al menos algunas personas en el Mediterráneo oriental tuvieron acceso a alimentos de lugares distantes, incluido el sur de Asia, y esos productos probablemente se consumieron en forma de aceites, frutos secos y especias. Estos conocimientos nos obligan a repensar la complejidad y la intensidad del comercio indo-mediterráneo durante la Edad del Bronce, así como el grado de globalización en la cocina del Mediterráneo oriental temprano. Although the key role of long-distance trade in the transformation of cuisines worldwide has been well-documented since at least the Roman era, the prehistory of the Eurasian food trade is less visible. In order to shed light on the transformation of Eastern Mediterranean cuisines during the Bronze Age and Early Iron Age, we analyzed microremains and proteins preserved in the dental calculus of individuals who lived during the second millennium BCE in the Southern Levant. Our results provide clear evidence for the consumption of expected staple foods, such as cereals (Triticeae), sesame (Sesamum), and dates (Phoenix). We additionally report evidence for the consumption of soybean (Glycine), probable banana (Musa), and turmeric (Curcuma), which pushes back the earliest evidence of these foods in the Mediterranean by centuries (turmeric) or even millennia (soybean). We find that, from the early second millennium onwards, at least some people in the Eastern Mediterranean had access to food from distant locations, including South Asia, and such goods were likely consumed as oils, dried fruits, and spices. These insights force us to rethink the complexity and intensity of Indo-Mediterranean trade during the Bronze Age as well as the degree of globalization in early Eastern Mediterranean cuisine

Radio-Frequency Measurements of Coherent Transition and Cherenkov Radiation: Implications for High-Energy Neutrino Detection

We report on measurements of 11-18 cm wavelength radio emission from interactions of 15.2 MeV pulsed electron bunches at the Argonne Wakefield Accelerator. The electrons were observed both in a configuration where they produced primarily transition radiation from an aluminum foil, and in a configuration designed for the electrons to produce Cherenkov radiation in a silica sand target. Our aim was to emulate the large electron excess expected to develop during an electromagnetic cascade initiated by an ultra high-energy particle. Such charge asymmetries are predicted to produce strong coherent radio pulses, which are the basis for several experiments to detect high-energy neutrinos from the showers they induce in Antarctic ice and in the lunar regolith. We detected coherent emission which we attribute both to transition and possibly Cherenkov radiation at different levels depending on the experimental conditions. We discuss implications for experiments relying on radio emission for detection of electromagnetic cascades produced by ultra high-energy neutrinos.Comment: updated figure 10; fixed typo in equation 2.2; accepted by PR

Factors in AIDS Dementia Complex Trial Design: Results and Lessons from the Abacavir Trial

OBJECTIVES: To determine the efficacy of adding abacavir (Ziagen, ABC) to optimal stable background antiretroviral therapy (SBG) to AIDS dementia complex (ADC) patients and address trial design. DESIGN: Phase III randomized, double-blind placebo-controlled trial. SETTING: Tertiary outpatient clinics. PARTICIPANTS: ADC patients on SBG for ≥8 wk. INTERVENTIONS: Participants were randomized to ABC or matched placebo for 12 wk. OUTCOME MEASURES: The primary outcome measure was the change in the summary neuropsychological Z score (NPZ). Secondary measures were HIV RNA and the immune activation markers β-2 microglobulin, soluble tumor necrosis factor (TNF) receptor 2, and quinolinic acid. RESULTS: 105 participants were enrolled. The median change in NPZ at week 12 was +0.76 for the ABC + SBG and +0.63 for the SBG groups (p = 0.735). The lack of efficacy was unlikely related to possible limited antiviral efficacy of ABC: at week 12 more ABC than placebo participants had plasma HIV RNA ≤400 copies/mL (p = 0.002). There were, however, other factors. Two thirds of patients were subsequently found to have had baseline resistance to ABC. Second, there was an unanticipated beneficial effect of SBG that extended beyond 8 wk to 5 mo, thereby rendering some of the patients at baseline unstable. Third, there was an unexpectedly large variability in neuropsychological performance that underpowered the study. Fourth, there was a relative lack of activity of ADC: 56% of all patients had baseline cerebrospinal fluid (CSF) HIV-1 RNA <100 copies/mL and 83% had CSF β-2 microglobulin <3 nmol/L at baseline. CONCLUSIONS: The addition of ABC to SBG for ADC patients was not efficacious, possibly because of the inefficacy of ABC per se, baseline drug resistance, prolonged benefit from existing therapy, difficulties with sample size calculations, and lack of disease activity. Assessment of these trial design factors is critical in the design of future ADC trials

ASCR/HEP Exascale Requirements Review Report

This draft report summarizes and details the findings, results, and recommendations derived from the ASCR/HEP Exascale Requirements Review meeting held in June, 2015. The main conclusions are as follows. 1) Larger, more capable computing and data facilities are needed to support HEP science goals in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of the demand at the 2025 timescale is at least two orders of magnitude -- and in some cases greater -- than that available currently. 2) The growth rate of data produced by simulations is overwhelming the current ability, of both facilities and researchers, to store and analyze it. Additional resources and new techniques for data analysis are urgently needed. 3) Data rates and volumes from HEP experimental facilities are also straining the ability to store and analyze large and complex data volumes. Appropriately configured leadership-class facilities can play a transformational role in enabling scientific discovery from these datasets. 4) A close integration of HPC simulation and data analysis will aid greatly in interpreting results from HEP experiments. Such an integration will minimize data movement and facilitate interdependent workflows. 5) Long-range planning between HEP and ASCR will be required to meet HEP's research needs. To best use ASCR HPC resources the experimental HEP program needs a) an established long-term plan for access to ASCR computational and data resources, b) an ability to map workflows onto HPC resources, c) the ability for ASCR facilities to accommodate workflows run by collaborations that can have thousands of individual members, d) to transition codes to the next-generation HPC platforms that will be available at ASCR facilities, e) to build up and train a workforce capable of developing and using simulations and analysis to support HEP scientific research on next-generation systems.Comment: 77 pages, 13 Figures; draft report, subject to further revisio

Sarcopenia and post-operative morbidity and mortality in patients with gastric cancer

Purpose: Surgical resection for gastric adenocarcinoma is associated with significant post-operative morbidity and mortality. The aim of this study was to assess the prognostic significance of sarcopenia in patients undergoing resection for gastric adenocarcinoma with respect to post-operative morbidity and survival. Materials and Methods: A retrospective analysis was conducted on a cohort of consecutive patients who underwent surgical resection for gastric adenocarcinoma between 2008 and 2014. Patient demographics, radiological parameters, and pathological data were collected. OsiriX software (Pixmeo) was used to measure skeletal muscle area, which was normalized for height to calculate skeletal muscle index. Results: A total of 56 patients (41 male, 15 female; mean age, 68.4 ± 11.9 years) met the inclusion criteria. Of these, 36% (20 of 56) of the patients were sarcopenic pre-operatively. Both sarcopenic and non-sarcopenic patient groups were equally matched with the exception of weight and body mass index (P=0.036 and 0.001, respectively). Sarcopenia was associated with a decreased overall survival (log-rank P=0.003) and was an adverse prognostic predictor of overall survival in multivariate analysis (hazard ratio, 10.915; P=0.001). Sarcopenia was a predictor of serious in-hospital complications in multivariate analysis (odds ratio, 3.508; P=0.042). Conclusions: In patients undergoing curative resection for gastric cancer, there was a statistically significant association between sarcopenia and both decreased overall survival and serious post-operative complications. The measurement and reporting of skeletal muscle index on pre-operative computed tomography should be considered

Raltegravir Cerebrospinal Fluid Concentrations in HIV-1 Infection

Raltegravir is an HIV-1 integrase inhibitor currently used in treatment-experienced HIV-1-infected patients resistant to other drug classes. In order to assess its central nervous system penetration, we measured raltegravir concentrations in cerebrospinal fluid (CSF) and plasma in subjects receiving antiretroviral treatment regimens containing this drug.Raltegravir concentrations were determined by liquid chromatography tandem mass spectrometry in 25 paired CSF and plasma samples from 16 HIV-1-infected individuals. The lower limit of quantitation was 2.0 ng/ml for CSF and 10 ng/ml for plasma.Twenty-four of the 25 CSF samples had detectable raltegravir concentrations with a median raltegravir concentration of 18.4 ng/ml (range, <2.0-126.0). The median plasma raltegravir concentration was 448 ng/ml (range, 37-5180). CSF raltegravir concentrations correlated with CSF:plasma albumin ratios and CSF albumin concentrations.Approximately 50% of the CSF specimens exceeded the IC(95) levels reported to inhibit HIV-1 strains without resistance to integrase inhibitors. In addition to contributing to control of systemic HIV-1 infection, raltegravir achieves local inhibitory concentrations in CSF in most, but not all, patients. Blood-brain and blood-CSF barriers likely restrict drug entry, while enhanced permeability of these barriers enhances drug entry

A population genetic analysis of the Critically Endangered Madagascar big-headed turtle, Erymnochelys madagascariensis across captive and wild populations

Erymnochelys madagascariensis is a Critically Endangered turtle endemic to Madagascar. Anthropogenic activity has depleted the wild population by 70% in the last century, and effective conservation management is essential to ensuring its persistence. Captive breeding was implemented to augment depleted populations in the southern part of Ankarafantsika National Park (ANP), when no genetic data were available for E. madagascariensis. It is unknown how much of the natural population’s diversity is encapsulated in captivity. We used eight microsatellite loci and fragments of two mitochondrial genes to identify the genetic structure of E. madagascariensis in the wild. Captive bred turtles were compared with wild populations in order to assess the representativeness of this ex situ conservation strategy for ANP. Six microsatellite clusters, ten cytochrome b, and nine COI haplotypes were identified across wild populations, with high genetic divergence found between populations in two groups of watersheds. Captive bred individuals represent three out of six sampled microsatellite clusters found in the wild and just one mitochondrial haplotype, possibly due to genetic drift. To improve genetic representation, the strategy of frequent interchange between captive and wild breeders within ANP should be revitalised and, as originally planned, hatchlings or juveniles should not be released beyond ANP