bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase 1 Study of the Safety, Tolerability, and Pharmacokinetics of the β-Lactamase Inhibitor Vaborbactam (RPX7009) in Healthy Adult Subjects
Authors: Griffith David C. , Loutit Jeffery S. , Morgan Elizabeth E. , Durso Stephanie , Dudley Michael N. 
Published: August 2016

ABSTRACT

Vaborbactam (formerly RPX7009) is a member of a new class of β-lactamase inhibitor with pharmacokinetic properties similar to those of many β-lactams, including carbapenems. The pharmacokinetics and safety of vaborbactam were evaluated in 80 healthy adult subjects in a first-in-human randomized, placebo-controlled, double-blind, sequential single- and multiple-ascending-dose study. A total of 10 dose cohorts were enrolled in the study, with 6 subjects randomized to receive 250 to 2,000 mg of vaborbactam and 2 subjects randomized to receive placebo in each cohort. Maximum concentrations for vaborbactam were achieved at the end of the 3-h infusion. Vaborbactam exposure (
C
max
and area under the concentration-time curve [AUC]) increased in a dose-proportional manner following multiple doses. There was no evidence of accumulation with multiple doses, consistent with the terminal half-life of ∼2 h. Both the volume of distribution (
V
ss
) and plasma clearance were independent of dose. For the 2,000-mg dose, the plasma clearance was 0.17 ± 0.03 liters/h, the AUC from 0 h to infinity (AUC
0–∞
) was 144.00 ± 13.90 mg · h/liter, and the
V
ss
was 21.80 ± 2.26 mg · h/liter. Urinary recovery was 80% or greater over 48 h across all dose groups. No subjects discontinued the study due to adverse events (AEs), and no serious AEs (SAEs) were observed. All AEs were mild to moderate and similar among the vaborbactam- and placebo-treated subjects, with mild lethargy as the only unique AE reported with the high dose of vaborbactam. Overall, this study revealed the safety, tolerability, and pharmacokinetic profile of vaborbactam and formed the basis for advancement into patient studies in combination with meropenem, including treatment of patients with carbapenem-resistant
Enterobacteriaceae
(CRE) infections. (This study is registered at ClinicalTrials.gov under identifier NCT01751269.)
A Novel RNase 3/ECP Peptide for Pseudomonas aeruginosa Biofilm Eradication That Combines Antimicrobial, Lipopolysaccharide Binding, and Cell-Agglutinating Activities
Authors: Pulido David , Prats-Ejarque Guillem , Villalba Clara , Albacar Marcel , González-López Juan J. , Torrent Marc , Moussaoui Mohammed , Boix Ester 
Published: August 2016

ABSTRACT

Eradication of established biofilm communities of pathogenic Gram-negative species is one of the pending challenges for the development of new antimicrobial agents. In particular,
Pseudomonas aeruginosa
is one of the main dreaded nosocomial species, with a tendency to form organized microbial communities that offer an enhanced resistance to conventional antibiotics. We describe here an engineered antimicrobial peptide (AMP) which combines bactericidal activity with a high bacterial cell agglutination and lipopolysaccharide (LPS) affinity. The RN3(5-17P22-36) peptide is a 30-mer derived from the eosinophil cationic protein (ECP), a host defense RNase secreted by eosinophils upon infection, with a wide spectrum of antipathogen activity. The protein displays high biofilm eradication activity that is not dependent on its RNase catalytic activity, as evaluated by using an active site-defective mutant. On the other hand, the peptide encompasses both the LPS-binding and aggregation-prone regions from the parental protein, which provide the appropriate structural features for the peptide's attachment to the bacterial exopolysaccharide layer and further improved removal of established biofilms. Moreover, the peptide's high cationicity and amphipathicity promote the cell membrane destabilization action. The results are also compared side by side with other reported AMPs effective against either planktonic and/or biofilm forms of
Pseudomonas aeruginosa
strain PAO1. The ECP and its derived peptide are unique in combining high bactericidal potency and cell agglutination activity, achieving effective biofilm eradication at a low micromolar range. We conclude that the designed RN3(5-17P22-36) peptide is a promising lead candidate against Gram-negative biofilms.
Disease Progression and Resolution in Rodent Models of Clostridium difficile Infection and Impact of Antitoxin Antibodies and Vancomycin
Authors: Warn Peter , Thommes Pia , Sattar Abdul , Corbett David , Flattery Amy , Zhang Zuo , Black Todd , Hernandez Lorraine D. , Therien Alex G. 
Published: August 2016

ABSTRACT

Clostridium difficile
causes infections of the colon in susceptible patients. Specifically, gut dysbiosis induced by treatment with broad-spectrum antibiotics facilitates germination of ingested
C. difficile
spores, expansion of vegetative cells, and production of symptom-causing toxins TcdA and TcdB. The current standard of care for
C. difficile
infections (CDI) consists of administration of antibiotics such as vancomycin that target the bacterium but also perpetuate gut dysbiosis, often leading to disease recurrence. The monoclonal antitoxin antibodies actoxumab (anti-TcdA) and bezlotoxumab (anti-TcdB) are currently in development for the prevention of recurrent CDI. In this study, the effects of vancomycin or actoxumab/bezlotoxumab treatment on progression and resolution of CDI were assessed in mice and hamsters. Rodent models of CDI are characterized by an early severe phase of symptomatic disease, associated with high rates of morbidity and mortality; high intestinal
C. difficile
burden; and a disrupted intestinal microbiota. This is followed in surviving animals by gradual recovery of the gut microbiota, associated with clearance of
C. difficile
and resolution of disease symptoms over time. Treatment with vancomycin prevents disease initially by inhibiting outgrowth of
C. difficile
but also delays microbiota recovery, leading to disease relapse following discontinuation of therapy. In contrast, actoxumab/bezlotoxumab treatment does not impact the
C. difficile
burden but rather prevents the appearance of toxin-dependent symptoms during the early severe phase of disease, effectively preventing disease until the microbiota (the body's natural defense against
C. difficile
) has fully recovered. These data provide insight into the mechanism of recurrence following vancomycin administration and into the mechanism of recurrence prevention observed clinically with actoxumab/bezlotoxumab.
Correlation of Checkerboard Synergy Testing with Time-Kill Analysis and Clinical Outcomes of Extensively Drug-Resistant Acinetobacter baumannii Respiratory Infections
Authors: Bremmer Derek N. , Bauer Karri A. , Pouch Stephanie M. , Thomas Keelie , Smith Debra , Goff Debra A. , Pancholi Preeti , Balada-Llasat Joan-Miquel 
Published: August 2016

ABSTRACT

We tested 76 extensively drug-resistant (XDR)
Acinetobacter baumannii
isolates by the checkerboard method using only wells containing serum-achievable concentrations (SACs) of drugs. Checkerboard results were correlated by time-kill assay and clinical outcomes. Minocycline-colistin was the best combination
in vitro
, as it inhibited growth in one or more SAC wells in all isolates. Patients who received a combination that inhibited growth in one or more SAC wells demonstrated better microbiological clearance than those who did not (88% versus 30%;
P
= 0.025). The checkerboard platform may have clinical utility for XDR
A. baumannii
infections.
Lipopolysaccharide Domains Modulate Urovirulence
Authors: Aguiniga Lizath M. , Yaggie Ryan E. , Schaeffer Anthony J. , Klumpp David J. 
Published: August 2016

ABSTRACT

Uropathogenic
Escherichia coli
(UPEC) accounts for 80 to 90% of urinary tract infections (UTI), and the increasing rate of antibiotic resistance among UPEC isolates reinforces the need for vaccines to prevent UTIs and recurrent infections. Previous studies have shown that UPEC isolate NU14 suppresses proinflammatory NF-κB-dependent cytokines (D. J. Klumpp, A. C. Weiser, S. Sengupta, S. G. Forrestal, R. A. Batler, and A. J. Schaeffer, Infect Immun 69:6689–6695, 2001,
http://dx.doi.org/10.1128/IAI.69.11.6689-6695.2001
; B. K. Billips, A. J. Schaeffer, and D. J. Klumpp, Infect Immun 76:3891–3900, 2008,
http://dx.doi.org/10.1128/IAI.00069-08
). However, modification of lipopolysaccharide (LPS) structure by deleting the O-antigen ligase gene (
waaL
) enhanced proinflammatory cytokine secretion. Vaccination with the Δ
waaL
mutant diminished NU14 reservoirs and protected against subsequent infections. Therefore, we hypothesized that LPS structural determinants shape immune responses. We evaluated the contribution of LPS domains to urovirulence corresponding to the inner core (
waaP
,
waaY
, and
rfaQ
), outer core (
rfaG
), and O-antigen (
waaL
,
wzzE
, and
wzyE
). Deletion of
waaP
,
waaY
, and
rfaG
attenuated adherence to urothelial cells
in vitro
. In a murine UTI model, the Δ
rfaG
mutant had the most severe defect in colonization. The mutation of
rfaG
,
waaL
,
wzzE
, and
wzyE
resulted in an inability to form reservoirs in mouse bladders. Infection with the LPS mutant panel resulted in various levels of urinary myeloperoxidase. Since the Δ
waaL
mutant promoted Th
1
-associated adaptive responses in previous studies (B. K. Billips, R. E. Yaggie, J. P. Cashy, A. J. Schaeffer, and D. J. Klumpp, J Infect Dis 200:263–272, 2009,
http://dx.doi.org/10.1086/599839
), we assessed NU14 for Th
2
-associated cytokines. We found NU14 infection stimulated TLR4-dependent bladder interleukin-33 (IL-33) production. Inoculation with
rfaG
,
waaL
,
wzzE
, and
wzyE
mutants showed decreased IL-33 production. We quantified antigen-specific antibodies after infection and found significantly increased IgE and IgG1 in Δ
waaP
mutant-infected mice. Our studies show LPS structural constituents mediate multiple aspects of the UPEC life cycle, including the ability to acutely colonize bladders, form reservoirs, and evoke innate and adaptive immune responses.
Inhibition of P2X Receptors Protects Human Monocytes against Damage by Leukotoxin from Aggregatibacter actinomycetemcomitans and α-Hemolysin from Escherichia coli
Authors: Fagerberg Steen K. , Jakobsen Martin R. , Skals Marianne , Praetorius Helle A. 
Published: August 2016

ABSTRACT

α-Hemolysin (HlyA) from
Escherichia coli
and leukotoxin A (LtxA) from
Aggregatibacter actinomycetemcomitans
are important virulence factors in ascending urinary tract infections and aggressive periodontitis, respectively. The extracellular signaling molecule ATP is released immediately after insertion of the toxins into plasma membranes and, via P2X receptors, is essential for the erythrocyte damage inflicted by these toxins. Moreover, ATP signaling is required for the ensuing recognition and phagocytosis of damaged erythrocytes by the monocytic cell line THP-1. Here, we investigate how these toxins affect THP-1 monocyte function. We demonstrate that both toxins trigger early ATP release and a following increase in the intracellular Ca
2+
concentration ([Ca
2+
]
i
) in THP-1 monocytes. The HlyA- and LtxA-induced [Ca
2+
]
i
response is diminished by the P2 receptor antagonist in a pattern that fits the functional P2 receptor expression in these cells. Both toxins are capable of lysing THP-1 cells, with LtxA being more aggressive. Either desensitization or blockage of P2X
1
, P2X
4
, or P2X
7
receptors markedly reduces toxin-induced cytolysis. This pattern is paralleled in freshly isolated human monocytes from healthy volunteers. Interestingly, only a minor fraction of the toxin-damaged THP-1 monocytes eventually lyse. P2X
7
receptor inhibition generally prevents cell damage, except from a distinct cell shrinkage that prevails in response to the toxins. Moreover, we find that preexposure to HlyA preserves the capacity of THP-1 monocytes to phagocytose damaged erythrocytes and may induce readiness to discriminate between damaged and healthy erythrocytes. These findings suggest a new pharmacological target for protecting monocytes during exposure to pore-forming cytolysins during infection or injury.
Pseudomonas aeruginosa Condensins Support Opposite Differentiation States
Authors: Zhao Hang , Clevenger April L. , Ritchey Jerry W. , Zgurskaya Helen I. , Rybenkov Valentin V. 
Published: August 2016

ABSTRACT

Condensins play a key role in global chromosome packing.
Pseudomonas aeruginosa
encodes two condensins, SMC-ScpAB and MksBEF. We report here that the two proteins are involved in the differentiation of the bacterium and impose opposite physiological states. The inactivation of SMC induced a state characterized by increased adhesion to surfaces as well as defects in competitive growth and colony formation. In contrast, MksB-deficient cells were impaired in biofilm formation with no obvious defects during planktonic growth. The phenotype of the double mutant was dominated by the absence of MksB, indicating that the observed growth defects are regulatory in their nature rather than structural. ATPase mutations recapitulated many of the phenotypes of the condensins, indicating their requirement for a functional protein. Additionally, inactivation of condensins dramatically reduced the virulence of the bacterium in a murine model of lung infection. These data demonstrate that condensins are involved in the differentiation of
P. aeruginosa
and reveal their importance for pathogenicity.

IMPORTANCE
Adaptation and differentiation play key roles in bacterial pathogenicity. In
Pseudomonas aeruginosa
, an opportunistic human pathogen, these processes are mediated by the activity of an intricate regulatory network. We describe here novel members of this network, condensins. We show that the two
P. aeruginosa
condensins specialize in the establishment of the sessile and planktonic states of the bacterium. Whereas condensins have well-established roles in global chromosome organization, their roles in regulating bacterial physiology have remained unknown. Our data indicate that the two programs may be linked. We further show that condensins are essential for the pathogenicity of
P. aeruginosa
.
Depletion of Undecaprenyl Pyrophosphate Phosphatases Disrupts Cell Envelope Biogenesis in Bacillus subtilis
Authors: Zhao Heng , Sun Yingjie , Peters Jason M. , Gross Carol A. , Garner Ethan C. , Helmann John D. 
Published: August 2016

ABSTRACT

The integrity of the bacterial cell envelope is essential to sustain life by countering the high turgor pressure of the cell and providing a barrier against chemical insults. In
Bacillus subtilis
, synthesis of both peptidoglycan and wall teichoic acids requires a common C
55
lipid carrier, undecaprenyl-pyrophosphate (UPP), to ferry precursors across the cytoplasmic membrane. The synthesis and recycling of UPP requires a phosphatase to generate the monophosphate form Und-P, which is the substrate for peptidoglycan and wall teichoic acid synthases. Using an optimized
c
lustered
r
egularly
i
nterspaced
s
hort
p
alindromic
r
epeat (CRISPR) system with catalytically inactive (“
d
ead”)
C
RISPR-
as
sociated protein
9
(dCas9)-based transcriptional repression system (CRISPR interference [CRISPRi]), we demonstrate that
B. subtilis
requires either of two UPP phosphatases, UppP or BcrC, for viability. We show that a third predicted lipid phosphatase (YodM), with homology to diacylglycerol pyrophosphatases, can also support growth when overexpressed. Depletion of UPP phosphatase activity leads to morphological defects consistent with a failure of cell envelope synthesis and strongly activates the σ
M
-dependent cell envelope stress response, including
bcrC
, which encodes one of the two UPP phosphatases. These results highlight the utility of an optimized CRISPRi system for the investigation of synthetic lethal gene pairs, clarify the nature of the
B. subtilis
UPP-Pase enzymes, and provide further evidence linking the σ
M
regulon to cell envelope homeostasis pathways.

IMPORTANCE
The emergence of antibiotic resistance among bacterial pathogens is of critical concern and motivates efforts to develop new therapeutics and increase the utility of those already in use. The lipid II cycle is one of the most frequently targeted processes for antibiotics and has been intensively studied. Despite these efforts, some steps have remained poorly defined, partly due to genetic redundancy. CRISPRi provides a powerful tool to investigate the functions of essential genes and sets of genes. Here, we used an optimized CRISPRi system to demonstrate functional redundancy of two UPP phosphatases that are required for the conversion of the initially synthesized UPP lipid carrier to Und-P, the substrate for the synthesis of the initial lipid-linked precursors in peptidoglycan and wall teichoic acid synthesis.
Season and region of birth as risk factors for coeliac disease a key to the aetiology?
Authors: Namatovu Fredinah , Lindkvist Marie , Olsson Cecilia , Ivarsson Anneli , Sandström Olof 
Published: August 2016

BackgroundCoeliac disease (CD) incidence has increased in recent decades, characterised by variations according to sex, age at diagnosis, year of birth, month of birth and region of birth. Genetic susceptibility and exposure to gluten are the necessary factors in CD aetiology, although several environmental factors are considered.MethodsA nationwide prospective cohort longitudinal study was conducted consisting of 1 912 204 children aged 0–14.9 years born in Sweden from 1991 to 2009. A total of 6569 children were diagnosed with biopsy-verified CD from 47 paediatric departments. Using Cox regression, we examined the association between CD diagnosis and season of birth, region of birth and year of birth.ResultsOverall, CD risk was higher for children born during spring, summer and autumn as compared with children born during winter: adjusted HR for spring 1.08 (95% CI 1.01 to 1.16), summer 1.10 (95% CI 1.03 to 1.18) and autumn 1.10 (95% CI 1.02 to 1.18). Increased CD risk was highest if born in the south, followed by central Sweden when compared with children born in northern Sweden. Children diagnosed at <2 years had an increased CD risk if born in spring while those diagnosed at 2–14.9 years the risk was increased for summer and autumn births. The birth cohort of 1991–1996 had increased CD risk if born during spring, for the 1997–2002 birth cohort the risk increased for summer and autumn births, while for the birth cohort of 2003–2009 the risk was increased if born during autumn.ConclusionsSeason of birth and region of birth are independently and jointly associated with increased risk of developing CD during the first 15 years of life. Seasonal variation in infectious load is the likely explanation.
Barriers to becoming a female surgeon and the influence of female surgical role models
Authors: Kerr Hui-Ling , Armstrong Lesley Ann , Cade Jennifer Ellen 
Published: August 2016

AbstractObjectivesWe aim to investigate the reasons that medical students and junior doctors who are women are less likely to pursue a career in surgery compared with their male counterparts.MethodsAn anonymous questionnaire was distributed to female final year medical students and female junior doctors in two UK hospitals between August and September 2012. Topics included career choice, attitudes to surgery, recognition of female surgical role models and perceived sexual discrimination.Results50 medical students and 50 junior doctors were given our survey. We received a 96% response rate; 46 medical students and 50 junior doctors. 6/50 (12%) junior doctors planned a career in surgery compared with 14/46 (30%) medical students. ‘Work-life balance’ was the main reason cited for not wishing to pursue surgery (29/46 (63%) medical students and 25/50 (50%) junior doctors). 28/46 (61%) medical students and 28/50 (56%) junior doctors had encountered a female surgical role model; only five students and two junior doctors felt that these were influential in their career decision. Of those who had not, approximately 40% in each group felt that if they had, they may have considered surgery. Approximately 30% in each group had encountered female surgeons that had dissuaded them from a surgical career.ConclusionsWork-life balance is still cited by female junior doctors as being the main deterrent to a surgical career. The paucity of female role models and some perceived sexual discrimination may cause female doctors to discount surgery as a career.
Prediction and Predictability for Search Query Acceleration
Authors: Hwang Seung-Won , Kim Saehoon , He Yuxiong , Elnikety Sameh , Choi Seungjin 
Published: August 2016

A commercial web search engine shards its index among many servers, and therefore the response time of a search query is dominated by the slowest server that processes the query. Prior approaches target improving responsiveness by reducing the
tail latency
, or high-percentile response time, of an individual search server. They predict query execution time, and if a query is predicted to be long-running, it runs in parallel; otherwise, it runs sequentially. These approaches are, however, not accurate enough for reducing a high tail latency when responses are aggregated from many servers because this requires each server to reduce a substantially higher tail latency (e.g., the 99.99th percentile), which we call extreme tail latency.

To address tighter requirements of
extreme
tail latency, we propose a new
design space
for the problem, subsuming existing work and also proposing a new solution space. Existing work makes a prediction using features available at indexing time and focuses on optimizing prediction features for accelerating tail queries. In contrast, we identify “when to predict?” as another key optimization question. This opens up a new solution of delaying a prediction by a short duration to allow many short-running queries to complete without parallelization and, at the same time, to allow the predictor to collect a set of dynamic features using runtime information. This new question expands a solution space in two meaningful ways. First, we see a significant reduction of tail latency by leveraging “dynamic” features collected at runtime that estimate query execution time with higher accuracy. Second, we can ask whether to override prediction when the “predictability” is low. We show that considering predictability accelerates the query by achieving a higher recall.

With this prediction, we propose to accelerate the queries that are predicted to be long-running. In our preliminary work, we focused on parallelization as an acceleration scenario. We extend to consider heterogeneous multicore hardware for acceleration. This hardware combines processor cores with different microarchitectures such as energy-efficient little cores and high-performance big cores, and accelerating web search using this hardware has remained an open problem.
We evaluate the proposed prediction framework in two scenarios: (1) query parallelization on a multicore processor and (2) query scheduling on a heterogeneous processor. Our extensive evaluation results show that, for both scenarios of query acceleration using parallelization and heterogeneous cores, the proposed framework is effective in reducing the extreme tail latency compared to a start-of-the-art predictor because of its higher recall, and it improves server throughput by more than 70% because of its improved precision.