bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasonic Nakagami‐parameter characterization of parotid‐gland injury following head‐and‐neck radiotherapy: A feasibility study of late toxicity
Authors: Yang Xiaofeng , Tridandapani Srini , Beitler Jonathan J. , Yu David S. , Wu Ning , Wang Yuefeng , Bruner Deborah W. , Curran Walter J. , Liu Tian 
Published: January 2014

Purpose:The study aims to investigate whether Nakagami parameters—estimated from the statistical distribution of the backscattered ultrasound radio‐frequency (RF) signals—could provide a means for quantitative characterization of parotid‐gland injury resulting from head‐and‐neck radiotherapy.Methods:A preliminary clinical study was conducted with 12 postradiotherapy patients and 12 healthy volunteers. Each participant underwent one ultrasound study in which ultrasound scans were performed in the longitudinal, i.e., vertical orientation on the bilateral parotids. For the 12 patients, the mean radiation dose to the parotid glands was 37.7 ± 9.5 Gy, and the mean follow‐up time was 16.3 ± 4.8 months. All enrolled patients experienced grade 1 or 2 late salivary‐gland toxicity (RTOG/EORTC morbidity scale). The normal parotid glands served as the control group. The Nakagami‐scaling and Nakagami‐shape parameters were computed from the RF data to quantify radiation‐induced parotid‐gland changes.Results:Significant differences in Nakagami parameters were observed between the normal and postradiotherapy parotid glands. Compared with the control group, the Nakagami‐scaling parameter of the postradiotherapy group decreased by 25.8% (p < 0.001), and the Nakagami‐shape parameter decreased by 31.3% (p < 0.001). The area under the receiver operating characteristic curve was 0.85 for the Nakagami‐scaling parameter and was 0.95 for the Nakagami‐shape parameter, which further demonstrated the diagnostic efficiency of the Nakagami parameters.Conclusions:Nakagami parameters could be used to quantitatively measure parotid‐gland injury following head‐and‐neck radiotherapy. Moreover, the clinical feasibility was demonstrated and this study provides meaningful preliminary data for future clinical investigation.
Efficacy of an Abbreviated Induction Regimen of Amphotericin B Deoxycholate for Cryptococcal Meningoencephalitis: 3 Days of Therapy Is Equivalent to 14 Days
Authors: Livermore Joanne , Howard Susan J. , Sharp Andrew D. , Goodwin Joanne , Gregson Lea , Felton Timothy , Schwartz Julie A. , Walker Catherine , Moser Bill , Müller Werner , Harrison Thomas S. , Perfect John R. , Hope William W. 
Published: January 2014

ABSTRACTCryptococcal meningoencephalitis is an urgent global health problem. Induction regimens using 14 days of amphotericin B deoxycholate (dAmB) are considered the standard of care but may not be suitable for resource-poor settings. We investigated the efficacy of conventional and abbreviated regimens of dAmB for cryptococcal meningoencephalitis in both murine and rabbit models of cryptococcal meningoencephalitis. We examined the extent to which immunological effectors contribute to the antifungal effect. We bridged the results to humans as a first critical step to define regimens suitable for further study in clinical trials. There were significant differences in the murine plasma-versus-cerebrum dAmB concentration-time profiles. dAmB was detectable in the cerebrum throughout the experimental period, even following the administration of only three doses of 3 mg/kg. dAmB induced a fungistatic effect in the cerebrum with a 2- to 3-log10CFU/g reduction compared with controls. The effect of 3 days of therapy was the same as that of daily therapy for 14 days. There was no evidence of increased numbers of CD3+CD4+or CD3+CD8+cells in treated mice to account for the persistent antifungal effect of an abbreviated regimen. The administration of dAmB at 1 mg/kg/day for 3 days was the same as daily therapy in rabbits. The bridging studies suggested that a human regimen of 0.7 mg/kg/day for 3 days resulted in nearly maximal antifungal activity in both the cerebrum and cerebrospinal fluid. An abbreviated regimen (3 days of therapy) of dAmB appears to be just as effective as conventional induction therapy for cryptococcal meningoencephalitis.IMPORTANCECryptococcal meningitis is a significant and neglected infection that is associated with excessive morbidity and mortality. In well-resourced health care settings, induction therapy with at least 2 weeks of amphotericin B deoxycholate (dAmB) is advocated. Multiple clinical studies suggest that dAmB is the drug of choice for cryptococcal meningitis. In many parts of the world where the burden of cryptococcal meningitis is highest, it is infeasible to administer dAmB for prolonged periods. This paper provides the experimental basis for the efficacy of abbreviated regimens of dAmB for cryptococcal meningitis. The concept was explored in two well-validated laboratory animal models of cryptococcal meningitis, and the results were bridged to humans by using a range of mathematical modeling techniques. A 3-day regimen is as effective as the standard 14-day course. An abbreviated regimen is significantly more feasible and may enable better antifungal therapy to be administered to many patients with this frequently lethal disease.
Live-Cell Imaging of Phosphoinositide Dynamics and Membrane Architecture during
Legionella
Infection
Authors: Weber Stephen , Wagner Maria , Hilbi Hubert 
Published: January 2014

ABSTRACT

The causative agent of Legionnaires’ disease,
Legionella pneumophila
, replicates in amoebae and macrophages in a distinct membrane-bound compartment, the
Legionella
-containing vacuole (LCV). LCV formation is governed by the bacterial Icm/Dot type IV secretion system that translocates ~300 different “effector” proteins into host cells. Some of the translocated effectors anchor to the LCV membrane via phosphoinositide (PI) lipids. Here, we use the soil amoeba
Dictyostelium discoideum
, producing fluorescent PI probes, to analyze the LCV PI dynamics by live-cell imaging. Upon uptake of wild-type or Icm/Dot-deficient
L. pneumophila
, PtdIns(3,4,5)
P
3
transiently accumulated for an average of 40 s on early phagosomes, which acquired PtdIns(3)
P
within 1 min after uptake. Whereas phagosomes containing Δ
icmT
mutant bacteria remained decorated with PtdIns(3)
P
, more than 80% of wild-type LCVs gradually lost this PI within 2 h. The process was accompanied by a major rearrangement of PtdIns(3)
P
-positive membranes condensing to the cell center. PtdIns(4)
P
transiently localized to early phagosomes harboring wild-type or Δ
icmT L. pneumophila
and was cleared within minutes after uptake. During the following 2 h, PtdIns(4)
P
steadily accumulated only on wild-type LCVs, which maintained a discrete PtdIns(4)
P
identity spatially separated from calnexin-positive endoplasmic reticulum (ER) for at least 8 h. The separation of PtdIns(4)
P
-positive and ER membranes was even more pronounced for LCVs harboring Δ
sidC
-
sdcA
mutant bacteria defective for ER recruitment, without affecting initial bacterial replication in the pathogen vacuole. These findings elucidate the temporal and spatial dynamics of PI lipids implicated in LCV formation and provide insight into host cell membrane and effector protein interactions.

IMPORTANCE
The environmental bacterium
Legionella pneumophila
is the causative agent of Legionnaires’ pneumonia. The bacteria form in free-living amoebae and mammalian immune cells a replication-permissive compartment, the
Legionella
-containing vacuole (LCV). To subvert host cell processes, the bacteria secrete the amazing number of ~300 different proteins into host cells. Some of these proteins bind phosphoinositide (PI) lipids to decorate the LCV. PI lipids are crucial factors involved in host cell membrane dynamics and LCV formation. Using
Dictyostelium
amoebae producing one or two distinct fluorescent probes, we elucidated the dynamic LCV PI pattern in high temporal and spatial resolution. Notably, the endocytic PI lipid PtdIns(3)
P
was slowly cleared from LCVs, thus incapacitating the host cell’s digestive machinery, while PtdIns(4)
P
gradually accumulated on the LCV, enabling critical interactions with host organelles. The LCV PI pattern underlies the spatiotemporal configuration of bacterial effector proteins and therefore represents a crucial aspect of LCV formation.
Comprehensive Functional Analysis of N-Linked Glycans on Ebola Virus GP1
Authors: Lennemann Nicholas J. , Rhein Bethany A. , Ndungo Esther , Chandran Kartik , Qiu Xiangguo , Maury Wendy 
Published: January 2014

ABSTRACT

Ebola virus (EBOV) entry requires the virion surface-associated glycoprotein (GP) that is composed of a trimer of heterodimers (GP1/GP2). The GP1 subunit contains two heavily glycosylated domains, the glycan cap and the mucin-like domain (MLD). The glycan cap contains only N-linked glycans, whereas the MLD contains both N- and O-linked glycans. Site-directed mutagenesis was performed on EBOV GP1 to systematically disrupt N-linked glycan sites to gain an understanding of their role in GP structure and function. All 15 N-glycosylation sites of EBOV GP1 could be removed without compromising the expression of GP. The loss of these 15 glycosylation sites significantly enhanced pseudovirion transduction in Vero cells, which correlated with an increase in protease sensitivity. Interestingly, exposing the receptor-binding domain (RBD) by removing the glycan shield did not allow interaction with the endosomal receptor, NPC1, indicating that the glycan cap/MLD domains mask RBD residues required for binding. The effects of the loss of GP1 N-linked glycans on Ca
2+
-dependent (C-type) lectin (CLEC)-dependent transduction were complex, and the effect was unique for each of the CLECs tested. Surprisingly, EBOV entry into murine peritoneal macrophages was independent of GP1 N-glycans, suggesting that CLEC-GP1 N-glycan interactions are not required for entry into this important primary cell. Finally, the removal of all GP1 N-glycans outside the MLD enhanced antiserum and antibody sensitivity. In total, our results provide evidence that the conserved N-linked glycans on the EBOV GP1 core protect GP from antibody neutralization despite the negative impact the glycans have on viral entry efficiency.

IMPORTANCE
Filovirus outbreaks occur sporadically throughout central Africa, causing high fatality rates among the general public and health care workers. These unpredictable hemorrhagic fever outbreaks are caused by multiple species of Ebola viruses, as well as Marburg virus. While filovirus vaccines and therapeutics are being developed, there are no licensed products. The sole viral envelope glycoprotein, which is a principal immunogenic target, contains a heavy shield of glycans surrounding the conserved receptor-binding domain. We find that disruption of this shield through targeted mutagenesis leads to an increase in cell entry, protease sensitivity, and antiserum/antibody sensitivity but is not sufficient to allow virion binding to the intracellular receptor NPC1. Therefore, our studies provide evidence that filoviruses maintain glycoprotein glycosylation to protect against proteases and antibody neutralization at the expense of efficient entry. Our results unveil interesting insights into the unique entry process of filoviruses and potential immune evasion tactics of the virus.
Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems
Authors: Gomaa Ahmed A. , Klumpe Heidi E. , Luo Michelle L. , Selle Kurt , Barrangou Rodolphe , Beisel Chase L. 
Published: January 2014

ABSTRACT

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems in bacteria and archaea employ CRISPR RNAs to specifically recognize the complementary DNA of foreign invaders, leading to sequence-specific cleavage or degradation of the target DNA. Recent work has shown that the accidental or intentional targeting of the bacterial genome is cytotoxic and can lead to cell death. Here, we have demonstrated that genome targeting with CRISPR-Cas systems can be employed for the sequence-specific and titratable removal of individual bacterial strains and species. Using the type I-E CRISPR-Cas system in
Escherichia coli
as a model, we found that this effect could be elicited using native or imported systems and was similarly potent regardless of the genomic location, strand, or transcriptional activity of the target sequence. Furthermore, the specificity of targeting with CRISPR RNAs could readily distinguish between even highly similar strains in pure or mixed cultures. Finally, varying the collection of delivered CRISPR RNAs could quantitatively control the relative number of individual strains within a mixed culture. Critically, the observed selectivity and programmability of bacterial removal would be virtually impossible with traditional antibiotics, bacteriophages, selectable markers, or tailored growth conditions. Once delivery challenges are addressed, we envision that this approach could offer a novel means to quantitatively control the composition of environmental and industrial microbial consortia and may open new avenues for the development of “smart” antibiotics that circumvent multidrug resistance and differentiate between pathogenic and beneficial microorganisms.

IMPORTANCE
Controlling the composition of microbial populations is a critical aspect in medicine, biotechnology, and environmental cycles. While different antimicrobial strategies, such as antibiotics, antimicrobial peptides, and lytic bacteriophages, offer partial solutions, what remains elusive is a generalized and programmable strategy that can distinguish between even closely related microorganisms and that allows for fine control over the composition of a microbial population. This study demonstrates that RNA-directed immune systems in bacteria and archaea called CRISPR-Cas systems can provide such a strategy. These systems can be employed to selectively and quantitatively remove individual bacterial strains based purely on sequence information, creating opportunities in the treatment of multidrug-resistant infections, the control of industrial fermentations, and the study of microbial consortia.
Postinduction serum infliximab trough level and decrease of C-reactive protein level are associated with durable sustained response to infliximab: a retrospective analysis of the ACCENT I trial
Authors: Cornillie Freddy , Hanauer Stephen B , Diamond Robert H , Wang Jianping , Tang Kezhen L , Xu Zhenhua , Rutgeerts Paul , Vermeire Séverine 
Published: January 2014

BackgroundSerum infliximab trough levels correlate with efficacy; dose escalation is often beneficial in patients with Crohn's disease who stop responding to infliximab treatment.ObjectiveTo carry out a post hoc analysis of A Crohn's Disease Clinical Trial Evaluating Infliximab in a New Long-term Treatment Regimen I (ACCENT I) to evaluate the association between serum infliximab trough levels and C-reactive protein (CRP) after 14 weeks of induction treatment with durable sustained long-term response (Crohn's Disease Activity Index decrease ≥70 points and reduction ≥25% from baseline).DesignACCENT I was a multicentre, randomised, placebo-controlled study. Week 14 trough levels and CRP percentage decrease from baseline to week 14 were compared between patients with and without durable sustained response through week 54. Sensitivity and specificity were determined to predict durable sustained response. Receiver operating characteristic (ROC) curves identified optimal cut-off points; logistic regression determined ORs.ResultsAfter induction with 5 mg/kg infliximab, 25% (37/147) and 33% (47/144) of patients sustained week 14 response to infliximab 5 or 10 mg/kg, respectively, administered every 8 weeks without dose escalation, through week 54. Median week 14 trough levels of patients with and without durable sustained response to infliximab 5 mg/kg were 4.0 and 1.9 μg/mL, respectively (p=0.0331). Optimal predictors of durable sustained response to maintenance infliximab 5 mg/kg were week 14 trough level ≥3.5 µg/mL and ≥60% CRP decrease (ORs (95% CI), 3.5 (1.1 to 11.4) and 7.3 (1.4 to 36.7)), respectively, in patients with raised baseline CRP (>8.0 mg/L); area under the ROC curve was 0.75 for both predictors. A ≥3.5 µg/mL week 14 infliximab serum level did not predict durable sustained response to 10 mg/kg maintenance infliximab.ConclusionsPatients with durable sustained response to maintenance infliximab 5 mg/kg had higher postinduction trough levels than patients without durable sustained response. Serum infliximab trough levels ≥3.5 µg/mL and ≥60% CRP decrease were significantly associated with durable sustained response.
p16INK4a Impairs Homologous Recombination–Mediated DNA Repair in Human Papillomavirus–Positive Head and Neck Tumors
Authors: Dok Rüveyda , Kalev Peter , Van Limbergen Evert Jan , Asbagh Layka Abbasi , Vázquez Iria , Hauben Esther , Sablina Anna , Nuyts Sandra 
Published: January 2014

Abstract
The p16INK4a protein is a principal cyclin-dependent kinase inhibitor that decelerates the cell cycle. Abnormally high levels of p16INK4a are commonly observed in human papillomavirus (HPV)–positive head and neck squamous cell carcinomas (HNSCC). We and others found that p16INK4a overexpression is associated with improved therapy response and survival of patients with HNSCC treated with radiotherapy. However, the functional role of p16INK4a in HNSCC remains unexplored. Our results implicate p16INK4a in regulation of homologous recombination–mediated DNA damage response independently from its role in control of the cell cycle. We found that expression of p16INK4a dramatically affects radiation sensitivity of HNSCC cells. p16INK4a overexpression impairs the recruitment of RAD51 to the site of DNA damage in HPV-positive cells by downregulating of cyclin D1 protein expression. Consistent with the in vitro findings, immunostaining of HNSCC patient samples revealed that high levels p16INK4a expression significantly correlated with decreased cyclin D1 expression. In summary, these findings reveal an unexpected function of p16INK4a in homologous recombination–mediated DNA repair response and imply p16INK4a status as an independent marker to predict response of patients with HNSCC to radiotherapy. Cancer Res; 74(6); 1739–51. ©2014 AACR.
Effect of Transcatheter Aortic Valve Replacement on the Mitral Valve Apparatus and Mitral Regurgitation
Authors: Shibayama Kentaro , Harada Kenji , Berdejo Javier , Mihara Hirotsugu , Tanaka Jun , Gurudevan Swaminatha V. , Siegel Robert , Jilaihawi Hasan , Makkar Raj R. , Shiota Takahiro 
Published: January 2014

Background—
The effect of transcatheter aortic valve replacement (TAVR) on the mitral valve apparatus and factors influencing the reduction of mitral regurgitation with or without mitral leaflet tethering after TAVR are poorly understood. The present 3-dimensional (3D) transesophageal echocardiography study aimed to elucidate early changes further in the structure and function of the mitral valve apparatus after TAVR.

Methods and Results—

We analyzed 90 patients (nontenting group, 56 patients and tenting group, 34 patients) who underwent TAVR using the Edwards SAPIEN and had intraprocedural 3D transesophageal echocardiography evaluation of the mitral valve. Of all patients, mitral regurgitation improved in 54%, remained the same in 38%, and worsened in 8% 1 day after TAVR. There were no statistically significant differences in mitral annular 3D parameters before and after TAVR in both groups. In the tenting group, tenting area (
P
<0.01) and tenting height (
P
<0.01) were decreased, and coaptation length was increased (
P
<0.05) after TAVR. In a multivariable analysis, the predictors of improved mitral regurgitation were the decrease of tenting area (odds ratio, 8.15; 95% confidence interval, 1.31–50.7;
P
<0.05) and the decrease of valvuloarterial impedance (odds ratio, 7.57; 95% confidence interval, 1.15–49.9;
P
<0.05) in the tenting group and the decrease of valvuloarterial impedance (odds ratio, 6.96; 95% confidence interval, 1.24–39.2;
P
<0.05) in the nontenting group.

Conclusions—
Mitral leaflet tethering was improved immediately by TAVR in patients with mitral leaflet tenting regardless of mitral annular geometry. Acute improvement in mitral regurgitation after TAVR is predominantly related to global left ventricular hemodynamics and mitral leaflet tethering change.
Aldose Reductase–Mediated Phosphorylation of p53 Leads to Mitochondrial Dysfunction and Damage in Diabetic Platelets
Authors: Tang Wai Ho , Stitham Jeremiah , Jin Yu , Liu Renjing , Lee Seung Hee , Du Jing , Atteya Gourg , Gleim Scott , Spollett Geralyn , Martin Kathleen , Hwa John 
Published: January 2014

Background—
Platelet abnormalities are well-recognized complications of diabetes mellitus. Mitochondria play a central role in platelet metabolism and activation. Mitochondrial dysfunction is evident in diabetes mellitus. The molecular pathway for hyperglycemia-induced mitochondrial dysfunction in platelets in diabetes mellitus is unknown.

Methods and Results—

Using both human and humanized mouse models, we report that hyperglycemia-induced aldose reductase activation and subsequent reactive oxygen species production lead to increased p53 phosphorylation (Ser15), which promotes mitochondrial dysfunction, damage, and rupture by sequestration of the antiapoptotic protein Bcl-x
L
. In a glucose dose–dependent manner, severe mitochondrial damage leads to loss of mitochondrial membrane potential and platelet apoptosis (cytochrome c release, caspase 3 activation, and phosphatidylserine exposure). Although platelet hyperactivation, mitochondrial dysfunction, aldose reductase activation, reactive oxygen species production, and p53 phosphorylation are all induced by hyperglycemia, we demonstrate that platelet apoptosis and hyperactivation are 2 distinct states that depend on the severity of the hyperglycemia and mitochondrial damage. Combined, both lead to increased thrombus formation in a mouse blood stasis model.

Conclusions—
Aldose reductase contributes to diabetes-mediated mitochondrial dysfunction and damage through the activation of p53. The degree of mitochondrial dysfunction and damage determines whether hyperactivity (mild damage) or apoptosis (severe damage) will ensue. These signaling components provide novel therapeutic targets for thrombotic complications in diabetes mellitus.