bluuebunny/crossref_metadata_2025 huggingface dataset:
A Compound Risk Indicator for Subject-Specific Prediction of Hip Fracture in Sideways Falls
Authors: Nasiri Sarvi Masoud , Luo Yunhua
Published: January 2016

Low-trauma hip fracture, usually caused by fall from standing height, has become a main source of morbidity and mortality among the elderly. However, the hip fracture risk is subject-dependent as it is related to the subject’s anthropometric parameters, the kinematic/kinetic variables in fall, and the hip anatomy. A compound fracture risk indicator is proposed in this study to define the correlation between the hip fracture risk and subject’s parameters such as anthropometric parameters, bone mineral density (BMD), height of body mass center (HMC), and hip soft tissue thickness (STT). In this study, a two-level, subject-specific biomechanical model composed of a whole-body dynamics model and a proximal femur finite element model was used to predict the hip fracture risk for 80 subjects. The required information was obtained from the subject’s whole body and hip DXA (dual energy X-ray absorptiometry) images. Then, multivariate nonlinear least-square fits of power functions were used to investigate the effect of parameters on hip fracture risk. Results indicated that although BMD is the dominant parameter affecting the hip fracture risk, other parameters such as hip soft tissue thickness and anthropometric parameters also have considerable effects. This finding suggests that the hip fracture risk cannot be accurately predicted by the currently available single factor predictors as they do not consider all multifactorial parameters. However, the proposed function can properly predict the risk of hip fracture in the absence of any computational simulation and biomechanical model. It also quantifies the effect of musculoskeletal-, and organ-level parameters on hip fracture risk and demonstrates which individual is more likely to experience hip fracture.
The Role of Context in Interaction With Virtual Prototypes
Authors: Bordegoni Monica , Cugini Umberto
Published: January 2016

The study of experience in the interaction with goods, both physical and virtual, is consistently affected by the role of the context in which this interaction occurs. The paper analyses the global problem starting from three independent variables: product, people and context, and focuses on the analysis of single couples of independent variables: goods-person, goods-context and person-context. From this analysis it is derived a general framework oriented to the experimenting and validation of the use of Virtual Prototyping to optimize the perceived value of products To-Be.
Rarefaction Wave Propagation in Origami-Based Mechanical Metamaterials
Authors: Yasuda Hiromi , Yang Jinkyu
Published: January 2016

We design origami-based mechanical metamaterials composed of Tachi-Miura Polyhedron (TMP) cells, and we numerically study the propagation of nonlinear waves in them. In order to investigate the dynamics of origami structures, we model these TMP-based metamaterials into a simple multi-bar linkage model. By using this model, we find that these TMP cells exhibit strain softening behavior under compression, which can be tuned by modifying their geometrical configurations or initial conditions. By leveraging such tunable strain softening mechanisms, we verify that the origami-based metamaterials can support the propagation of rarefaction waves. These waves feature tensile wave-fronts despite the application of compressive impact to the system. Such unusual characteristics can be exploited to disintegrate shock waves in a controllable and efficient manner, thereby leading to potential applications in impact mitigation and absorption.
Internal Entrainment Effects on Distributed Combustion
Authors: Khalil Ahmed E. E. , Gupta Ashwani K.
Published: January 2016

Colorless Distributed Combustion (CDC) has been shown to provide ultra-low emissions and enhanced combustion performance of high intensity gas turbine combustors in terms of efficiency and stability. To achieve distributed combustion, the flowfield needs to be carefully tailored for adequate mixing between reactants and hot reactive species from within the combustor to result in high temperature low oxygen concentration environment prior to ignition. Such distributed reactions result in uniform thermal field and also eliminates any hot spots for mitigating NOx emission. Though Distributed Combustion have been extensively studied using a variety of geometries, injection velocities, heat release intensities, and fuels, the role of hot reactive internally recirculated gases requires further examination. In this paper, the impact of internal entrainment of reactive gases on flame structure and behavior is investigated with focus on fostering distributed combustion and providing guidelines for designing high intensity combustors operating in distributed combustion mode. A mixture of nitrogen and carbon dioxide, used to simulate the recirculated gases, is introduced to the air stream prior to mixing with the fuel and subsequent combustion. Increase in the amounts of nitrogen and carbon dioxide (simulating increased entrainment), led to volume distributed reaction over a larger volume in the combustor with enhanced and uniform distribution of the OH* chemiluminescence intensity. At the same time, the bluish flame stabilized by the swirler is replaced with a more uniform almost invisible bluish flame. The increased recirculation also reflected on the pollutants emission, where NO emissions were significantly decreased for the same amount of fuel burned. Lowering oxygen concentration from 21% to 15% (due to increased entrainment) resulted in 80∼90% reduction in NO with no impact on CO emission with sub PPM NO emission achieved at an equivalence ratio of 0.7. The same trend was seen at higher diluents injection temperature as well, with significant pollutants emission reduction down to an oxygen concentration of 10%.
Period-1 Motions in a Two-Degree-of-Freedom Nonlinear Oscillator With Periodic Excitation
Authors: Luo Albert C. J. , Yu Bo
Published: January 2016

In this paper, analytical solutions for period-1 motions in a periodically forced, two-degrees-of-freedom system with a nonlinear spring are developed. The stability and bifurcation of the periodic motions are completed by the eigenvalue analysis. Both symmetric and asymmetric periodic motions are found in the system. Analytical solutions of both stable and unstable period-1 are presented. Finally, numerical simulations of stable and unstable motions in the two degrees of freedom systems are presented. The harmonic amplitude spectrums show the harmonic effects on periodic motions, and the corresponding accuracy of approximate analytical solutions can be observed.
Quantifying the effect of electric current on cell adhesion studied by single-cell force spectroscopy
Authors: Jaatinen Leena , Young Eleanore , Hyttinen Jari , Vörös János , Zambelli Tomaso , Demkó László
Published: January 2016

This study presents the effect of external electric current on the cell adhesive and mechanical properties of the C2C12 mouse myoblast cell line. Changes in cell morphology, viability, cytoskeleton, and focal adhesion structure were studied by standard staining protocols, while single-cell force spectroscopy based on the fluidic force microscopy technology provided a rapid, serial quantification and detailed analysis of cell adhesion and its dynamics. The setup allowed measurements of adhesion forces up to the μN range, and total detachment distances over 40 μm. Force–distance curves have been fitted with a simple elastic model including a cell detachment protocol in order to estimate the Young's modulus of the cells, as well as to reveal changes in the dynamic properties as functions of the applied current dose. While the cell spreading area decreased monotonously with increasing current doses, small current doses resulted only in differences related to cell elasticity. Current doses above 11 As/m2, however, initiated more drastic changes in cell morphology, viability, cellular structure, as well as in properties related to cell adhesion. The observed differences, eventually leading to cell death toward higher doses, might originate from both the decrease in pH and the generation of reactive oxygen species.
A novel perfused Bloch–McConnell simulator for analyzing the accuracy of dynamic hyperpolarized MRS
Authors: Walker Christopher M. , Chen Yunyun , Lai Stephen Y. , Bankson James A.
Published: January 2016

Purpose:

Magnetic resonance spectroscopy of hyperpolarized agents allows real‐time detection of metabolism in vivo. However, the nonrenewable nature of these signals necessitates data acquisitions that differ significantly from conventional magnetic resonance imaging. Signal evolution is permanently altered by the data acquisition scheme, potentially leading to sequence parameter‐dependent bias in quantification. The authors have developed a novel simulation environment to characterize the effects of sequence parameters on magnetic resonance spectroscopy‐based chemical exchange measurements using hyperpolarized pyruvate.

Methods:

Conventional Bloch–McConnell equations were coupled with a pharmacokinetic model for perfusion to allow realistic simulation of in vivo dynamic hyperpolarized signal evolution. In this study, simulations were conducted to explore effects of excitation angle and repetition time on the observed signal and subsequent parametric analysis. Both high and low apparent exchange rates were modeled under assumption of both perfused and closed systems. Bias due to sampling strategy bias was subsequently tested in vivo.

Results:

Simulation of dynamic magnetic resonance spectroscopy studies using hyperpolarized pyruvate demonstrated that for closed systems, accurate measurement of the apparent exchange rate was possible over a wide range of sequence parameters. This was true for both high and low apparent exchange rates, although a low exchange rate was associated with larger errors when excitation angles were high. When effects of perfusion were included to account for pyruvate delivery, a more restricted range of settings led to accurate quantification of exchange rates. Perfusion alleviated some of the errors seen at high excitation angles for low exchange rates. Residuals from parametric analysis did not generally correlate with fit accuracy, implying that the quality of the analysis model was not a major driver of error. Animal studies acquired with sequence parameters that are predicted to impart bias showed a significant under estimation of exchange rates (P < 0.035) compared to parameter combinations that are not expected to bias measurements.

Conclusions:

The authors' results suggest that great care must be taken when measuring dynamic processes by magnetic resonance spectroscopy of hyperpolarized substrates. When comparing apparent exchange rates, choice of sequence parameters will affect the results. Bias introduced by parameters of more advanced acquisition and reconstruction schemes will likely increase compared to the relatively simple dynamic spectroscopy methods tested herein. The modified Bloch–McConnell equations the authors describe will be crucial tools for characterizing and optimizing the performance of these more advanced techniques.
A cybersecurity primer for translational research
Authors: Perakslis Eric D. , Stanley Martin
Published: January 2016

Researchers have responsibilities and liabilities when it comes to the protection of biomedical data from cybersecurity breaches, but the simplest protections are often the most important.
Science Translational Medicine
Podcast: 20 January 2016
Authors: Minikel Eric Vallabh , Vallabh Sonia M. , VanHook Annalisa M.
Published: January 2016

Eric Vallabh Minikel and Sonia Minikel Vallabh explain that genetic variants in the
prion protein
gene differ in how likely they are to cause prion disease.
Novel Genes Related to Ceftriaxone Resistance Found among Ceftriaxone-Resistant Neisseria gonorrhoeae Strains Selected
In Vitro
Authors: Gong Zijian , Lai Wei , Liu Min , Hua Zhengshuang , Sun Yayin , Xu Qingfang , Xia Yue , Zhao Yue , Xie Xiaoyuan
Published: January 2016

The emergence of ceftriaxone-resistant
Neisseria gonorrhoeae
is currently a global public health concern. However, the mechanism of ceftriaxone resistance is not yet fully understood. To investigate the potential genes related to ceftriaxone resistance in
Neisseria gonorrhoeae
, we subcultured six gonococcal strains with increasing concentrations of ceftriaxone and isolated the strains that became resistant. After analyzing several frequently reported genes involved in ceftriaxone resistance, we found only a single mutation in
penA
(A501V). However, differential analysis of the genomes and transcriptomes between pre- and postselection strains revealed many other mutated genes as well as up- and downregulated genes. Transformation of the mutated
penA
gene into nonresistant strains increased the MIC between 2.0- and 5.3-fold, and transformation of mutated
ftsX
increased the MIC between 3.3- and 13.3-fold. Genes encoding the ABC transporters FarB, Tfq, Hfq, and ExbB were overexpressed, while
pilM
,
pilN
, and
pilQ
were downregulated. Furthermore, the resistant strain developed cross-resistance to penicillin and cefuroxime, had an increased biochemical metabolic rate, and presented fitness defects such as prolonged growth time and downregulated PilMNQ. In conclusion, antimicrobial pressure could result in the emergence of ceftriaxone resistance, and the evolution of resistance of
Neisseria gonorrhoeae
to ceftriaxone is a complicated process at both the pretranscriptional and posttranscriptional levels, involving several resistance mechanisms of increased efflux and decreased entry.
Luciferase-Based, High-Throughput Assay for Screening and Profiling Transmission-Blocking Compounds against Plasmodium falciparum Gametocytes
Authors: Lucantoni Leonardo , Fidock David A. , Avery Vicky M.
Published: January 2016

The discovery of new antimalarial drugs able to target both the asexual and gametocyte stages of
Plasmodium falciparum
is critical to the success of the malaria eradication campaign. We have developed and validated a robust, rapid, and cost-effective high-throughput reporter gene assay to identify compounds active against late-stage (stage IV and V) gametocytes. The assay, which is suitable for testing compound activity at incubation times up to 72 h, demonstrates excellent quality and reproducibility, with average
Z
′ values of 0.85 ± 0.01. We used the assay to screen more than 10,000 compounds from three chemically diverse libraries. The screening outcomes highlighted the opportunity to use collections of compounds with known activity against the asexual stages of the parasites as a starting point for gametocytocidal activity detection in order to maximize the chances of identifying gametocytocidal compounds. This assay extends the capabilities of our previously reported luciferase assay, which tested compounds against early-stage gametocytes, and opens possibilities to profile the activities of gametocytocidal compounds over the entire course of gametocytogenesis.
The Nonartemisinin Sesquiterpene Lactones Parthenin and Parthenolide Block Plasmodium falciparum Sexual Stage Transmission
Authors: Balaich Jared N. , Mathias Derrick K. , Torto Baldwyn , Jackson Bryan T. , Tao Dingyin , Ebrahimi Babak , Tarimo Brian B. , Cheseto Xavier , Foster Woodbridge A. , Dinglasan Rhoel R.
Published: January 2016

Parthenin and parthenolide are natural products that are closely related in structure to artemisinin, which is also a sesquiterpene lactone (SQL) and one of the most important antimalarial drugs available. Parthenin, like artemisinin, has an effect onPlasmodiumblood stage development. We extended the evaluation of parthenin as a potential therapeutic for the transmissible stages ofPlasmodium falciparumas it transitions between human and mosquito, with the aim of gaining potential mechanistic insight into the inhibitory activity of this compound. We posited that if parthenin targets different biological pathways in the parasite, this in turn could pave the way for the development of druggable compounds that could prevent the spread of artemisinin-resistant parasites. We examined parthenin's effect on male gamete activation and the ookinete-to-oocyst transition in the mosquito as well as on stage V gametocytes that are present in peripheral blood. Parthenin arrested parasite development for each of the stages tested. The broad inhibitory properties of parthenin on the evaluated parasite stages may suggest different mechanisms of action between parthenin and artemisinin. Parthenin's cytotoxicity notwithstanding, its demonstrated activity in this study suggests that structurally related SQLs with a better safety profile deserve further exploration. We used our battery of assays to test parthenolide, which has a more compelling safety profile. Parthenolide demonstrated activity nearly identical to that of parthenin againstP. falciparum, highlighting its potential as a possible transmission-blocking drug scaffold. We discuss the context of the evidence with respect to the next steps toward expanding the current antimalarial arsenal.
Clinical Utility and Safety of a Model-Based Patient-Tailored Dose of Vancomycin in Neonates
Authors: Leroux Stéphanie , Jacqz-Aigrain Evelyne , Biran Valérie , Lopez Emmanuel , Madeleneau Doriane , Wallon Camille , Zana-Taïeb Elodie , Virlouvet Anne-Laure , Rioualen Stéphane , Zhao Wei
Published: January 2016

Pharmacokinetic modeling has often been applied to evaluate vancomycin pharmacokinetics in neonates. However, clinical application of the model-based personalized vancomycin therapy is still limited. The objective of the present study was to evaluate the clinical utility and safety of a model-based patient-tailored dose of vancomycin in neonates. A model-based vancomycin dosing calculator, developed from a population pharmacokinetic study, has been integrated into the routine clinical care in 3 neonatal intensive care units (Robert Debré, Cochin Port Royal, and Clocheville hospitals) between 2012 and 2014. The target attainment rate, defined as the percentage of patients with a first therapeutic drug monitoring serum vancomycin concentration achieving the target window of 15 to 25 mg/liter, was selected as an endpoint for evaluating the clinical utility. The safety evaluation was focused on nephrotoxicity. The clinical application of the model-based patient-tailored dose of vancomycin has been demonstrated in 190 neonates. The mean (standard deviation) gestational and postnatal ages of the study population were 31.1 (4.9) weeks and 16.7 (21.7) days, respectively. The target attainment rate increased from 41% to 72% without any case of vancomycin-related nephrotoxicity. This proof-of-concept study provides evidence for integrating model-based antimicrobial therapy in neonatal routine care.
Selective Conditions for a Multidrug Resistance Plasmid Depend on the Sociality of Antibiotic Resistance
Authors: Bottery Michael J. , Wood A. Jamie , Brockhurst Michael A.
Published: January 2016

Multidrug resistance (MDR) plasmids frequently carry antibiotic resistance genes conferring qualitatively different mechanisms of resistance. We show here that the antibiotic concentrations selecting for the RK2 plasmid in
Escherichia coli
depend upon the sociality of the drug resistance: the selection for selfish drug resistance (efflux pump) occurred at very low drug concentrations, just 1.3% of the MIC of the plasmid-free antibiotic-sensitive strain, whereas selection for cooperative drug resistance (modifying enzyme) occurred at drug concentrations exceeding the MIC of the plasmid-free strain.
The Hemagglutinin Stem-Binding Monoclonal Antibody VIS410 Controls Influenza Virus-Induced Acute Respiratory Distress Syndrome
Authors: Baranovich Tatiana , Jones Jeremy C. , Russier Marion , Vogel Peter , Szretter Kristy J. , Sloan Susan E. , Seiler Patrick , Trevejo Jose M. , Webby Richard J. , Govorkova Elena A.
Published: January 2016

Most cases of severe influenza are associated with pulmonary complications, such as acute respiratory distress syndrome (ARDS), and no antiviral drugs of proven value for treating such complications are currently available. The use of monoclonal antibodies targeting the stem of the influenza virus surface hemagglutinin (HA) is a rapidly developing strategy for the control of viruses of multiple HA subtypes. However, the mechanisms of action of these antibodies are not fully understood, and their ability to mitigate severe complications of influenza has been poorly studied. We evaluated the effect of treatment with VIS410, a human monoclonal antibody targeting the HA stem region, on the development of ARDS in BALB/c mice after infection with influenza A(H7N9) viruses. Prophylactic administration of VIS410 resulted in the complete protection of mice against lethal A(H7N9) virus challenge. A single therapeutic dose of VIS410 given 24 h after virus inoculation resulted in dose-dependent protection of up to 100% of mice inoculated with neuraminidase inhibitor-susceptible or -resistant A(H7N9) viruses. Compared to the outcomes in mock-treated controls, a single administration of VIS410 improved viral clearance from the lungs, reduced virus spread in lungs in a dose-dependent manner, resulting in a lower lung injury score, reduced the extent of the alteration in lung vascular permeability and protein accumulation in bronchoalveolar lavage fluid, and improved lung physiologic function. Thus, antibodies targeting the HA stem can reduce the severity of ARDS and show promise as agents for controlling pulmonary complications in influenza.
Activity of Bisnaphthalimidopropyl Derivatives against Trypanosoma brucei
Authors: Graça Nuno A. G. , Gaspar Luis , Costa David M. , Loureiro Inês , Thoo-Lin Paul Kong , Ramos Isbaal , Roura Meritxell , Pruvost Alain , Pemberton Ian K. , Loukil Hadjer , MacDougall Jane , Tavares Joana , Cordeiro-da-Silva Anabela
Published: January 2016

Current treatments for African trypanosomiasis are either toxic, costly, difficult to administer, or prone to elicit resistance. This study evaluated the activity of bisnaphthalimidopropyl (BNIP) derivatives against
Trypanosoma brucei
. BNIPDiaminobutane (BNIPDabut), the most active of these compounds, showed
in vitro
inhibition in the single-unit nanomolar range, similar to the activity in the reference drug pentamidine, and presented low toxicity and adequate metabolic stability. Additionally, using a murine model of acute infection and live imaging, a significant decrease in parasite load in BNIPDabut-treated mice was observed. However, cure was not achieved. BNIPDabut constitutes a new scaffold for antitrypanosomal drugs that deserves further consideration.
Impact of Surotomycin on the Gut Microbiota of Healthy Volunteers in a Phase 1 Clinical Trial
Authors: Citron Diane M. , Tyrrell Kerin L. , Dale Suzanne E. , Chesnel Laurent , Goldstein Ellie J. C.
Published: January 2016

Clostridium difficile
-associated diarrhea has been associated with disruption of the normal intestinal microbiota, particularly the
Bacteroides fragilis
group and
Prevotella
species. Surotomycin is a bactericidal cyclic lipopeptide in development for treatment of
Clostridium difficile
-associated diarrhea that has selective and potent activity against
C. difficile
and other Gram-positive bacteria and a minimal impact on intestinal Gram-negative organisms. The impacts of ascending doses of surotomycin on major organism groups in the gut microbiota of healthy volunteers were evaluated during a randomized, double-blind, placebo-controlled, multiple-dose phase 1 study. Thirty volunteers were randomized into 3 cohorts, using a 4:1 ratio, to receive 250 mg, 500 mg, or 1,000 mg of surotomycin, or placebo, twice daily for 14 days. Stool samples collected at baseline (days 0 and 1) and at the end of treatment (days 13 to 15) were cultured quantitatively. The
B. fragilis
group, the
Bacteroides
/
Prevotella
group, and
Enterobacteriaceae
were also quantified by quantitative real-time PCR. Baseline and end-of-treatment stool samples showed 1- to 2-log
10
CFU/g reductions in total bacterial counts for most volunteers. Various decreases in clostridial,
Lactobacillus-Bifidobacterium
group, and enterococcus-streptococcus group counts occurred while patients were receiving surotomycin, whereas the enterobacteria and the
B. fragilis
group persisted at the end of treatment. There was no change in enterococcus MICs of surotomycin, nor was vancomycin-resistant
Enterococcus
detected after exposure. Surotomycin at doses of up to 1,000 mg twice daily had only modest disruptive effects on the gut microbiota. The potential sparing of the gut microbiota by surotomycin may decrease the risk of disease recurrence.
Synthetic α-Hydroxytropolones Inhibit Replication of Wild-Type and Acyclovir-Resistant Herpes Simplex Viruses
Authors: Ireland Peter J. , Tavis John E. , D'Erasmo Michael P. , Hirsch Danielle R. , Murelli Ryan P. , Cadiz Mark M. , Patel Bindi S. , Gupta Ankit K. , Edwards Tiffany C. , Korom Maria , Moran Eileen A. , Morrison Lynda A.
Published: January 2016

Herpes simplex virus 1 (HSV-1) and HSV-2 remain major human pathogens despite the development of anti-HSV therapeutics as some of the first antiviral drugs. Current therapies are incompletely effective and frequently drive the evolution of drug-resistant mutants. We recently determined that certain natural troponoid compounds such as β-thujaplicinol readily suppress HSV-1 and HSV-2 replication. Here, we screened 26 synthetic α-hydroxytropolones with the goals of determining a preliminary structure-activity relationship for the α-hydroxytropolone pharmacophore and providing a starting point for future optimization studies. Twenty-five compounds inhibited HSV-1 and HSV-2 replication at 50 μM, and 10 compounds inhibited HSV-1 and HSV-2 at 5 μM, with similar inhibition patterns and potencies against both viruses being observed. The two most powerful inhibitors shared a common biphenyl side chain, were capable of inhibiting HSV-1 and HSV-2 with a 50% effective concentration (EC
50
) of 81 to 210 nM, and also strongly inhibited acyclovir-resistant mutants. Moderate to low cytotoxicity was observed for all compounds (50% cytotoxic concentration [CC
50
] of 50 to >100 μM). Therapeutic indexes ranged from >170 to >1,200. These data indicate that troponoids and specifically α-hydroxytropolones are a promising lead scaffold for development as anti-HSV drugs provided that toxicity can be further minimized. Troponoid drugs are envisioned to be employed alone or in combination with existing nucleos(t)ide analogs to suppress HSV replication far enough to prevent viral shedding and to limit the development of or treat nucleos(t)ide analog-resistant mutants.
Pharmacokinetics-Pharmacodynamics of Tazobactam in Combination with Piperacillin in an
In Vitro
Infection Model
Authors: Nicasio Anthony M. , VanScoy Brian D. , Mendes Rodrigo E. , Castanheira Mariana , Bulik Catharine C. , Okusanya Olanrewaju O. , Bhavnani Sujata M. , Forrest Alan , Jones Ronald N. , Friedrich Lawrence V. , Steenbergen Judith N. , Ambrose Paul G.
Published: January 2016

We have previously demonstrated the pharmacokinetic-pharmacodynamic (PK-PD) index best associated with the efficacy of tazobactam when used in combination with ceftolozane to be the percentage of the dosing interval during which tazobactam concentrations remained above a threshold value (%time>threshold). Using an
in vitro
infection model and the same isogenic CTX-M-15-producing
Escherichia coli
triplet set genetically engineered to transcribe different levels of
bla
CTX-M-15
, herein we describe dose fractionation studies designed to evaluate the PK-PD index associated with tazobactam efficacy, when given in combination with piperacillin, and the impact of the presence of a different β-lactam agent, or different
bla
CTX-M-15
transcription levels, on the magnitude of the tazobactam PK-PD index necessary for efficacy. The recombinant strains demonstrated piperacillin MIC values of 128, >256, and >256 μg/ml for the low-, moderate-, and high-level CTX-M-15-producing
E. coli
strains, respectively. The MIC value for piperacillin in the presence of 4 μg/ml of tazobactam was 2 μg/ml for all three strains. The PK-PD index associated with tazobactam efficacy was confirmed to be %time>threshold, regardless of β-lactamase transcription (
r
2
= 0.839). The tazobactam concentration thresholds, however, changed with the CTX-M-15 transcription level and were 0.25, 0.5, and 2 μg/ml for the low-, moderate-, and high-level CTX-M-15-producing strains, respectively (
r
2
= 0.921, 0.773, and 0.875, respectively). The %time>threshold values for tazobactam necessary for net bacterial stasis and a 1- and 2-log
10
-unit CFU/ml decrease from baseline at 24 h were 44.9, 62.9, and 84.9%, respectively. In addition to verifying our previous study results, these results also demonstrated that the magnitude of bacterial-cell killing associated with a β-lactam–β-lactamase inhibitor combination is dependent on the amount of β-lactamase produced. These data provide important information for the development of β-lactam–β-lactamase inhibitor combination agents.
Genomic Characterization of Enterobacter cloacae Isolates from China That Coproduce KPC-3 and NDM-1 Carbapenemases
Authors: Du Hong , Chen Liang , Chavda Kalyan D. , Pandey Ruchi , Zhang Haifang , Xie Xiaofang , Tang Yi-Wei , Kreiswirth Barry N.
Published: January 2016

Here, we report two
Enterobacter cloacae
sequence type 231 isolates coproducing KPC-3 and NDM-1 that have caused lethal infections in a tertiary hospital in China. The
bla
NDM-1
-harboring plasmids carry IncA/C
2
and IncR replicons, showing a mosaic plasmid structure, and the
bla
NDM-1
is harbored on a novel class I integron-like element.
bla
KPC-3
is located on a Tn
3
-Δ
bla
TEM-1
-
bla
KPC-3
-ΔTn
1722
element, flanked by two 9-bp direct-repeat sequences and harbored on an IncX6 plasmid.
Targets and Mechanisms Associated with Protection from Severe Plasmodium falciparum Malaria in Kenyan Children
Authors: Murungi Linda M. , Sondén Klara , Llewellyn David , Rono Josea , Guleid Fatuma , Williams Andrew R. , Ogada Edna , Thairu Amos , Färnert Anna , Marsh Kevin , Draper Simon J. , Osier Faith H. A.
Published: January 2016

Severe malaria (SM) is a life-threatening complication of infection with
Plasmodium falciparum
. Epidemiological observations have long indicated that immunity against SM is acquired relatively rapidly, but prospective studies to investigate its immunological basis are logistically challenging and have rarely been undertaken. We investigated the merozoite targets and antibody-mediated mechanisms associated with protection against SM in Kenyan children aged 0 to 2 years. We designed a unique prospective matched case-control study of well-characterized SM clinical phenotypes nested within a longitudinal birth cohort of children (
n
= 5,949) monitored over the first 2 years of life. We quantified immunological parameters in sera collected before the SM event in cases and their individually matched controls to evaluate the prospective odds of developing SM in the first 2 years of life. Anti-AMA1 antibodies were associated with a significant reduction in the odds of developing SM (odds ratio [OR] = 0.37; 95% confidence interval [CI] = 0.15 to 0.90;
P
= 0.029) after adjustment for responses to all other merozoite antigens tested, while those against MSP-2, MSP-3,
Plasmodium falciparum
Rh2 [
Pf
Rh2], MSP-1
19
, and the infected red blood cell surface antigens were not. The combined ability of total IgG to inhibit parasite growth and mediate the release of reactive oxygen species from neutrophils was associated with a marked reduction in the odds of developing SM (OR = 0.07; 95% CI = 0.006 to 0.82;
P
= 0.03). Assays of these two functional mechanisms were poorly correlated (Spearman rank correlation coefficient [

r
s

] = 0.12;
P
= 0.07). Our data provide epidemiological evidence that multiple antibody-dependent mechanisms contribute to protective immunity via distinct targets whose identification could accelerate the development of vaccines to protect against SM.
Biological Activities of Uric Acid in Infection Due to Enteropathogenic and Shiga-Toxigenic Escherichia coli
Authors: Crane John K. , Broome Jacqueline E. , Lis Agnieszka
Published: January 2016

In previous work, we identified xanthine oxidase (XO) as an important enzyme in the interaction between the host and enteropathogenic
Escherichia coli
(EPEC) and Shiga-toxigenic
E. coli
(STEC). Many of the biological effects of XO were due to the hydrogen peroxide produced by the enzyme. We wondered, however, if uric acid generated by XO also had biological effects in the gastrointestinal tract. Uric acid triggered inflammatory responses in the gut, including increased submucosal edema and release of extracellular DNA from host cells. While uric acid alone was unable to trigger a chloride secretory response in intestinal monolayers, it did potentiate the secretory response to cyclic AMP agonists. Uric acid crystals were formed
in vivo
in the lumen of the gut in response to EPEC and STEC infections. While trying to visualize uric acid crystals formed during EPEC and STEC infections, we noticed that uric acid crystals became enmeshed in the neutrophilic extracellular traps (NETs) produced from host cells in response to bacteria in cultured cell systems and in the intestine
in vivo
. Uric acid levels in the gut lumen increased in response to exogenous DNA, and these increases were enhanced by the actions of DNase I. Interestingly, addition of DNase I reduced the numbers of EPEC bacteria recovered after a 20-h infection and protected against EPEC-induced histologic damage.
Primary Role for Toll-Like Receptor-Driven Tumor Necrosis Factor Rather than Cytosolic Immune Detection in Restricting Coxiella burnetii Phase II Replication within Mouse Macrophages
Authors: Bradley William P. , Boyer Mark A. , Nguyen Hieu T. , Birdwell L. Dillon , Yu Janet , Ribeiro Juliana M. , Weiss Susan R. , Zamboni Dario S. , Roy Craig R. , Shin Sunny
Published: January 2016

Coxiella burnetiireplicates within permissive host cells by employing a Dot/Icm type IV secretion system (T4SS) to translocate effector proteins that direct the formation of a parasitophorous vacuole. C57BL/6 mouse macrophages restrict the intracellular replication of theC. burnetiiNine Mile phase II (NMII) strain. However, eliminating Toll-like receptor 2 (TLR2) permits bacterial replication, indicating that the restriction of bacterial replication is immune mediated. Here, we examined whether additional innate immune pathways are employed by C57BL/6 macrophages to sense and restrict NMII replication. In addition to the known role of TLR2 in detecting and restricting NMII infection, we found that TLR4 also contributes to cytokine responses but is not required to restrict bacterial replication. Furthermore, the TLR signaling adaptors MyD88 and Trif are required for cytokine responses and restricting bacterial replication. TheC. burnetiiNMII T4SS translocates bacterial products into C57BL/6 macrophages. However, there was little evidence of cytosolic immune sensing of NMII, as there was a lack of inflammasome activation, T4SS-dependent cytokine responses, and robust type I interferon (IFN) production, and these pathways were not required to restrict bacterial replication. Instead, endogenous tumor necrosis factor (TNF) produced upon TLR sensing ofC. burnetiiNMII was required to control bacterial replication. Therefore, our findings indicate a primary role for TNF produced upon immune detection ofC. burnetiiNMII by TLRs, rather than cytosolic PRRs, in enabling C57BL/6 macrophages to restrict bacterial replication.
ROSET Model of TonB Action in Gram-Negative Bacterial Iron Acquisition
Authors: Klebba Phillip E.
Published: January 2016

Therotationalsurveillance andenergytransfer (ROSET) model of TonB action suggests a mechanism by which the electrochemical proton gradient across the Gram-negative bacterial inner membrane (IM) promotes the transport of iron through ligand-gated porins (LGP) in the outer membrane (OM). TonB associates with the IM by an N-terminal hydrophobic helix that forms a complex with ExbBD. It also contains a central extended length of rigid polypeptide that spans the periplasm and a dimericC-terminal-ββαβ-domain (CTD) with LysM motifs that binds the peptidoglycan (PG) layer beneath the OM bilayer. The TonB CTD forms a dimer with affinity for both PG- and TonB-independent OM proteins (e.g., OmpA), localizing it near the periplasmic interface of the OM bilayer. Porins and other OM proteins associate with PG, and this general affinity allows the TonB CTD dimer to survey the periplasmic surface of the OM bilayer. Energized rotational motion of the TonB N terminus in the fluid IM bilayer promotes the lateral movement of the TonB-ExbBD complex in the IM and of the TonB CTD dimer across the inner surface of the OM. When it encounters an accessible TonB box of a (ligand-bound) LGP, the monomeric form of the CTD binds and recruits it into a 4-stranded β-sheet. Because the CTD is rotating, this binding reaction transfers kinetic energy, created by the electrochemical proton gradient across the IM, through the periplasm to the OM protein. The equilibration of the TonB C terminus between the dimeric and monomeric forms that engage in different binding reactions allows the identification of iron-loaded LGP and then the internalization of iron through their trans-outer membrane β-barrels. Hence, the ROSET model postulates a mechanism for the transfer of energy from the IM to the OM, triggering iron uptake.
Ethylene Glycol Metabolism in the Acetogen Acetobacterium woodii
Authors: Trifunović Dragan , Schuchmann Kai , Müller Volker
Published: January 2016

The acetogenic bacterium
Acetobacterium woodii
is able to grow by the oxidation of diols, such as 1,2-propanediol, 2,3-butanediol, or ethylene glycol. Recent analyses demonstrated fundamentally different ways for oxidation of 1,2-propanediol and 2,3-butanediol. Here, we analyzed the metabolism of ethylene glycol. Our data demonstrate that ethylene glycol is dehydrated to acetaldehyde, which is then disproportionated to ethanol and acetyl coenzyme A (acetyl-CoA). The latter is further converted to acetate, and this pathway is coupled to ATP formation by substrate-level phosphorylation. Apparently, the product ethanol is in part further oxidized and the reducing equivalents are recycled by reduction of CO
2
to acetate in the Wood-Ljungdahl pathway. Biochemical data as well as the results of protein synthesis analysis are consistent with the hypothesis that the propane diol dehydratase (PduCDE) and CoA-dependent propionaldehyde dehydrogenase (PduP) proteins, encoded by the
pdu
gene cluster, also catalyze ethylene glycol dehydration to acetaldehyde and its CoA-dependent oxidation to acetyl-CoA. Moreover, genes encoding bacterial microcompartments as part of the
pdu
gene cluster are also expressed during growth on ethylene glycol, arguing for a dual function of the Pdu microcompartment system.

IMPORTANCE
Acetogenic bacteria are characterized by their ability to use CO
2
as a terminal electron acceptor by a specific pathway, the Wood-Ljungdahl pathway, enabling in most acetogens chemolithoautotrophic growth with H
2
and CO
2
. However, acetogens are very versatile and can use a wide variety of different substrates for growth. Here we report on the elucidation of the pathway for utilization of ethylene glycol by the model acetogen
Acetobacterium woodii
. This diol is degraded by dehydration to acetaldehyde followed by a disproportionation to acetate and ethanol. We present evidence that this pathway is catalyzed by the same enzyme system recently described for the utilization of 1,2-propanediol. The enzymes for ethylene glycol utilization seem to be encapsulated in protein compartments, known as bacterial microcompartments.
Gene Deletion by Fluorescence-Reported Allelic Exchange Mutagenesis in Chlamydia trachomatis
Authors: Mueller Konrad E. , Wolf Katerina , Fields Kenneth A.
Published: January 2016

Although progress in
Chlamydia
genetics has been rapid, genomic modification has previously been limited to point mutations and group II intron insertions which truncate protein products. The bacterium has thus far been intractable to gene deletion or more-complex genomic integrations such as allelic exchange. Herein, we present a novel suicide vector dependent on inducible expression of a chlamydial gene that renders
Chlamydia trachomatis
fully genetically tractable and permits rapid reverse genetics by fluorescence-reported allelic exchange mutagenesis (FRAEM). We describe the first available system of targeting chlamydial genes for deletion or allelic exchange as well as curing plasmids from
C. trachomatis
serovar L2. Furthermore, this approach permits the monitoring of mutagenesis by fluorescence microscopy without disturbing bacterial growth, a significant asset when manipulating obligate intracellular organisms. As proof of principle,
trpA
was successfully deleted and replaced with a sequence encoding both green fluorescent protein (GFP) and β-lactamase. The
trpA
-deficient strain was unable to grow in indole-containing medium, and this phenotype was reversed by complementation with
trpA
expressed in
trans
. To assess reproducibility at alternate sites, FRAEM was repeated for genes encoding type III secretion effectors CTL0063, CTL0064, and CTL0065. In all four cases, stable mutants were recovered one passage after the observation of transformants, and allelic exchange was limited to the specific target gene, as confirmed by whole-genome sequencing. Deleted sequences were not detected by quantitative real-time PCR (qPCR) from isogenic mutant populations. We demonstrate that utilization of the chlamydial suicide vector with FRAEM renders
C. trachomatis
highly amenable to versatile and efficient genetic manipulation.

IMPORTANCE
The obligate intracellular nature of a variety of infectious bacteria presents a significant obstacle to the development of molecular genetic tools for dissecting pathogenicity. Although progress in chlamydial genetics has been rapid, genomic modification has previously been limited to point mutations and group II intron insertions which truncate protein products. The bacterium has thus far been intractable to gene deletion or more-complex genomic integrations such as allelic exchange. Here, we present a novel suicide vector dependent on inducible expression of a chlamydial gene that renders
Chlamydia trachomatis
fully genetically tractable and permits rapid reverse genetics by fluorescence-reported allelic exchange mutagenesis (FRAEM). We describe the first available system of targeting chlamydial genes for deletion or allelic exchange as well as curing plasmids from
C. trachomatis
L2. Furthermore, this approach permits monitoring of mutagenesis by fluorescence microscopy without disturbing bacterial growth, a significant asset when manipulating obligate intracellular organisms.
Consideration of Epstein-Barr Virus-Encoded Noncoding RNAs EBER1 and EBER2 as a Functional Backup of Viral Oncoprotein Latent Membrane Protein 1
Authors: Herbert Kristina M. , Pimienta Genaro
Published: January 2016

The Epstein-Barr virus (EBV)-encoded noncoding RNAs EBER1 and EBER2 are highly abundant through all four latency stages of EBV infection (III-II-I-0) and have been associated with an oncogenic phenotype when expressed in cell lines cultured
in vitro
.
In vivo
, EBV-infected B cells derived from freshly isolated lymphocytes show that EBER1/2 deletion does not impair viral latency. Based on published quantitative proteomics data from BJAB cells expressing EBER1 and EBER2, we propose that the EBERs, through their activation of AKT in a B-cell-specific manner, are a functionally redundant backup of latent membrane protein 1 (LMP1)—an essential oncoprotein in EBV-associated malignancies, with a main role in AKT activation. Our proposed model may explain the lack of effect on viral latency establishment in EBER-minus EBV infection.
The Stealthy Superbug: the Role of Asymptomatic Enteric Carriage in Maintaining a Long-Term Hospital Outbreak of ST228 Methicillin-Resistant Staphylococcus aureus
Authors: Senn Laurence , Clerc Olivier , Zanetti Giorgio , Basset Patrick , Prod’hom Guy , Gordon Nicola C. , Sheppard Anna E. , Crook Derrick W. , James Richard , Thorpe Harry A. , Feil Edward J. , Blanc Dominique S.
Published: January 2016

Whole-genome sequencing (WGS) of 228 isolates was used to elucidate the origin and dynamics of a long-term outbreak of methicillin-resistant
Staphylococcus aureus
(MRSA) sequence type 228 (ST228) SCC
mec
I that involved 1,600 patients in a tertiary care hospital between 2008 and 2012. Combining of the sequence data with detailed metadata on patient admission and movement confirmed that the outbreak was due to the transmission of a single clonal variant of ST228, rather than repeated introductions of this clone into the hospital. We note that this clone is significantly more frequently recovered from groin and rectal swabs than other clones (
P
< 0.0001) and is also significantly more transmissible between roommates (
P
< 0.01). Unrecognized MRSA carriers, together with movements of patients within the hospital, also seem to have played a major role. These atypical colonization and transmission dynamics can help explain how the outbreak was maintained over the long term. This “stealthy” asymptomatic colonization of the gut, combined with heightened transmissibility (potentially reflecting a role for environmental reservoirs), means the dynamics of this outbreak share some properties with enteric pathogens such as vancomycin-resistant enterococci or
Clostridium difficile
.

IMPORTANCE
Using whole-genome sequencing, we showed that a large and prolonged outbreak of methicillin-resistant
Staphylococcus aureus
was due to the clonal spread of a specific strain with genetic elements adapted to the hospital environment. Unrecognized MRSA carriers, the movement of patients within the hospital, and the low detection with clinical specimens were also factors that played a role in this occurrence. The atypical colonization of the gut means the dynamics of this outbreak may share some properties with enteric pathogens.
Growth data of underprivileged children living in rural areas of Chin State, Burma/Myanmar, compared to the WHO reference growth standards: an observational study
Authors: Prenkert Malin , Ehnfors Margareta
Published: January 2016

Objectives

To explore growth data (height-for-age, weight-for-age and BMI-for-age) of children living in poor socioeconomic conditions in rural areas of Chin State, Burma/Myanmar; and to compare these data with the growth and development z-score (GDZ) values for school-aged children and adolescents, provided by the WHO.

Setting

A support and educational programme, run by the Swedish association Chin Development and Research Society (CDRS), was carried out among underprivileged school-aged children, unable to attend school without economic and practical support, living in villages and remote areas in Chin State.

Participants

Community leaders who were well familiar with the citizens in the community identified children in need of this support. Other community members could also suggest or apply for this. The sample includes all participating children in the CDRS programme at the time of the data collection in six townships. The children were placed in host families, close to a suitable school. Two samples with a total of 639 children from 144 villages and remote areas were obtained:

1. Children in the CDRS Chin Programme (CCP) (2007–2010) comprised 558 children: 50% girls and boys.

2. Children in the Chin Society (CCS) (2010) comprised 81 children: 44% girls and 56% boys.

Primary outcome measures

Growth data.

Results

All growth data from both groups deviated significantly from the WHO standard references (p≤0.001). The prevalence of stunting (height-for-age ≤–2SD) was 52% among girls and 68% among boys. High levels of wasting (weight-for-age ≤–2SD) were found among girls 29% and boys 36% aged 5–10 years. In addition, severe thinness (BMI-for-age ≤–2SD) was found among girls 31% and boys 44%, all results to be compared to the expected 2.27%.

Conclusions

Many more than expected—according to the WHO reference values—in CCP and CCS suffered from stunting, wasting and thinness.