bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased Antifungal Drug Resistance in Clinical Isolates of Cryptococcus neoformans in Uganda
Authors: Smith Kyle D. , Achan Beatrice , Hullsiek Kathy Huppler , McDonald Tami R. , Okagaki Laura H. , Alhadab Ali A. , Akampurira Andrew , Rhein Joshua R. , Meya David B. , Boulware David R. , Nielsen Kirsten , Musubire Abdu , Nabeta Henry W. , Williams Darlisha A. , Morawski Bozena , Rolfes Melissa A. , Ndyetukira Jane Francis , Ahimbisibwe Cynthia , Kugonza Florence , Sadiq Alisat , Dyal Jonathan , Neborak Julie M. , King Alexa M. , Yueh Nathan , Velamakanni Sruti S. , Namudde Alice , Kandole Tadeo Kiiza , Eva Laker Julian Kaboggoza , Luggya Tony , Tugume Liliane , Abassi Mahsa , Birkenkamp Kate , Butler Elissa K. , Fujita A. Wendy , Halupnick Ryan , Strain Anna K. , Vedula Priya , Rajasingham Radha , Kambugu Andrew , Bohjanen Paul R. 
Published: September 2015

ABSTRACT

Cryptococcal antigen screening is recommended among people living with AIDS when entering HIV care with a CD4 count of <100 cells/μl, and preemptive fluconazole monotherapy treatment is recommended for those with subclinical cryptococcal antigenemia. Yet, knowledge is limited of current antimicrobial resistance in Africa. We examined antifungal drug susceptibility in 198 clinical isolates collected from Kampala, Uganda, between 2010 and 2014 using the CLSI broth microdilution assay. In comparison with two previous studies from 1998 to 1999 that reported an MIC
50
of 4 μg/ml and an MIC
90
of 8 μg/ml prior to widespread human fluconazole and agricultural azole fungicide usage, we report an upward shift in the fluconazole MIC
50
to 8 μg/ml and an MIC
90
value of 32 μg/ml, with 31% of isolates with a fluconazole MIC of ≥16 μg/ml. We observed an amphotericin B MIC
50
of 0.5 μg/ml and an MIC
90
of 1 μg/ml, of which 99.5% of isolates (197 of 198 isolates) were still susceptible. No correlation between MIC and clinical outcome was observed in the context of amphotericin B and fluconazole combination induction therapy. We also analyzed
Cryptococcus
susceptibility to sertraline, with an MIC
50
of 4 μg/ml, suggesting that sertraline is a promising oral, low-cost, available, novel medication and a possible alternative to fluconazole. Although the CLSI broth microdilution assay is ideal to standardize results, limit human bias, and increase assay capacity, such assays are often inaccessible in low-income countries. Thus, we also developed and validated an assay that could easily be implemented in a resource-limited setting, with similar susceptibility results (
P
= 0.52).
Stepwise Decrease in Daptomycin Susceptibility in Clinical Staphylococcus aureus Isolates Associated with an Initial Mutation in
rpoB
and a Compensatory Inactivation of the
clpX
Gene
Authors: Bæk Kristoffer T. , Thøgersen Louise , Mogenssen René G. , Mellergaard Maiken , Thomsen Line E. , Petersen Andreas , Skov Søren , Cameron David R. , Peleg Anton Y. , Frees Dorte 
Published: September 2015

ABSTRACT

Daptomycin is a lipopeptide antibiotic used clinically for the treatment of methicillin-resistant
Staphylococcus aureus
(MRSA) infections. The emergence of daptomycin-nonsusceptible
S. aureus
isolates during therapy is often associated with multiple genetic changes; however, the relative contributions of these changes to resistance and other phenotypic changes usually remain unclear. The present study was undertaken to investigate this issue using a genetically characterized series of four isogenic clinical MRSA strains derived from a patient with bacteremia before and during daptomycin treatment. The first strain obtained after daptomycin therapy carried a single-nucleotide polymorphism (SNP) in
rpoB
(RpoB A
477
D) that decreased susceptibility not only to daptomycin but also to vancomycin, β-lactams, and rifampin. Furthermore, the
rpoB
mutant exhibited pleiotropic phenotypes, including increased cell wall thickness, reduced expression of virulence traits, induced expression of the stress-associated transcriptional regulator Spx, and slow growth. A subsequently acquired loss-of-function mutation in
clpX
partly alleviated the growth defect conferred by the
rpoB
mutation without changing antibiotic susceptibility. The final isolate acquired three additional mutations, including an SNP in
mprF
(MprF S
295
L) known to confer daptomycin nonsusceptibility, and accordingly, this isolate was the only daptomycin-nonsusceptible strain of this series. Interestingly, in this isolate, the cell wall had regained the same thickness as that of the parental strain, while the level of transcription of the
vraSR
(cell wall stress regulator) was increased. In conclusion, this study illustrates how serial genetic changes selected
in vivo
contribute to daptomycin nonsusceptibility, growth fitness, and virulence traits.
Ribosome Hibernation Facilitates Tolerance of Stationary-Phase Bacteria to Aminoglycosides
Authors: McKay Susannah L. , Portnoy Daniel A. 
Published: September 2015

ABSTRACTUpon entry into stationary phase, bacteria dimerize 70S ribosomes into translationally inactive 100S particles by a process called ribosome hibernation. Previously, we reported that the hibernation-promoting factor (HPF) ofListeria monocytogenesis required for 100S particle formation and facilitates adaptation to a number of stresses. Here, we demonstrate that HPF is required for the high tolerance of stationary-phase cultures to aminoglycosides but not to beta-lactam or quinolone antibiotics. The sensitivity of a Δhpfmutant to gentamicin was suppressed by the bacteriostatic antibiotics chloramphenicol and rifampin, which inhibit translation and transcription, respectively. Disruption of the proton motive force by the ionophore carbonyl cyanidem-chlorophenylhydrazone or mutation of genes involved in respiration also suppressed the sensitivity of the Δhpfmutant. Accordingly, Δhpfmutants had aberrantly high levels of ATP and reducing equivalents during prolonged stationary phase. Analysis of bacterial uptake of fluorescently labeled gentamicin demonstrated that the Δhpfmutant harbored increased intracellular levels of the drug. Finally, deletion of the main ribosome hibernation factor ofEscherichia coli, ribosome modulation factor (rmf), rendered these bacteria susceptible to gentamicin. Taken together, these data suggest that HPF-mediated ribosome hibernation results in repression of the metabolic activity that underlies aminoglycoside tolerance. HPF is conserved in nearly every bacterial pathogen, and the role of ribosome hibernation in antibiotic tolerance may have clinical implications.
Inhibitors of Methionyl-tRNA Synthetase Have Potent Activity against Giardia intestinalis Trophozoites
Authors: Ranade Ranae M. , Zhang Zhongsheng , Gillespie J. Robert , Shibata Sayaka , Verlinde Christophe L. M. J. , Hol Wim G. J. , Fan Erkang , Buckner Frederick S. 
Published: September 2015

ABSTRACT

The methionyl-tRNA synthetase (MetRS) is a novel drug target for the protozoan pathogen
Giardia intestinalis
. This protist contains a single MetRS that is distinct from the human cytoplasmic MetRS. A panel of MetRS inhibitors was tested against recombinant
Giardia
MetRS,
Giardia
trophozoites, and mammalian cell lines. The best compounds inhibited trophozoite growth at 500 nM (metronidazole did so at ∼5,000 nM) and had low cytotoxicity against mammalian cells, indicating excellent potential for further development as anti-
Giardia
drugs.
Analysis of the Zidovudine Resistance Mutations T215Y, M41L, and L210W in HIV-1 Reverse Transcriptase
Authors: Boyer Paul L. , Das Kalyan , Arnold Eddy , Hughes Stephen H. 
Published: September 2015

ABSTRACT
Although anti-human immunodeficiency virus type 1 (HIV-1) therapies have become more sophisticated and more effective, drug resistance continues to be a major problem. Zidovudine (azidothymidine; AZT) was the first nucleoside reverse transcriptase (RT) inhibitor (NRTI) approved for the treatment of HIV-1 infections and is still being used, particularly in the developing world. This drug targets the conversion of single-stranded RNA to double-stranded DNA by HIV-1 RT. However, resistance to the drug quickly appeared both in viruses replicating in cells in culture and in patients undergoing AZT monotherapy. The primary resistance pathway selects for mutations of T215 that change the threonine to either a tyrosine or a phenylalanine (T215Y/F); this resistance pathway involves an ATP-dependent excision mechanism. The pseudo-sugar ring of AZT lacks a 3′ OH; RT incorporates AZT monophosphate (AZTMP), which blocks the end of the viral DNA primer. AZT-resistant forms of HIV-1 RT use ATP in an excision reaction to unblock the 3′ end of the primer strand, allowing its extension by RT. The T215Y AZT resistance mutation is often accompanied by two other mutations, M41L and L210W. In this study, the roles of these mutations, in combination with T215Y, were examined to determine whether they affect polymerization and excision by HIV-1 RT. The M41L mutation appears to help restore the DNA polymerization activity of RT containing the T215Y mutation and also enhances AZTMP excision. The L210W mutation plays a similar role, but it enhances excision by RTs that carry the T215Y mutation when ATP is present at a low concentration.
Analysis of Bacterial Communities during Clostridium difficile Infection in the Mouse
Authors: Semenyuk Ekaterina G. , Poroyko Valeriy A. , Johnston Pehga F. , Jones Sara E. , Knight Katherine L. , Gerding Dale N. , Driks Adam 
Published: September 2015

ABSTRACT

Clostridium difficile
infection (CDI) is a major cause of health care-associated disease. CDI initiates with ingestion of
C. difficile
spores, germination in the gastrointestinal (GI) tract, and then colonization of the large intestine. The interactions between
C. difficile
cells and other bacteria and with host mucosa during CDI remain poorly understood. Here, we addressed the hypothesis that, in a mouse model of CDI,
C. difficile
resides in multicellular communities (biofilms) in association with host mucosa. To do this, we paraffin embedded and then sectioned the GI tracts of infected mice at various days postinfection (p.i.). We then used fluorescent
in situ
hybridization (FISH) with 16S rRNA probes targeting most bacteria as well as
C. difficile
specifically. The results revealed that
C. difficile
is present as a minority member of communities in the outer (loose) mucus layer, in the cecum and colon, starting at day 1 p.i. To generate FISH probes that identify bacteria within mucus-associated communities harboring
C. difficile
, we characterized bacterial populations in the infected mouse GI tract using 16S rRNA gene sequence analysis of bacterial DNA prepared from intestinal content. This analysis revealed the presence of genera of several families belonging to
Bacteroidetes
and
Firmicutes
. These data suggest that formation of multispecies communities associated with the mucus of the cecum and colon is an important early step in GI tract colonization. They raise the possibility that other bacterial species in these communities modulate the ability of
C. difficile
to successfully colonize and, thereby, cause disease.
Application of Synthetic Peptide Arrays To Uncover Cyclic Di-GMP Binding Motifs
Authors: Düvel Juliane , Bense Sarina , Möller Stefan , Bertinetti Daniela , Schwede Frank , Morr Michael , Eckweiler Denitsa , Genieser Hans-Gottfried , Jänsch Lothar , Herberg Friedrich W. , Frank Ronald , Häussler Susanne 
Published: September 2015

ABSTRACT

High levels of the universal bacterial second messenger cyclic di-GMP (c-di-GMP) promote the establishment of surface-attached growth in many bacteria. Not only can c-di-GMP bind to nucleic acids and directly control gene expression, but it also binds to a diverse array of proteins of specialized functions and orchestrates their activity. Since its development in the early 1990s, the synthetic peptide array technique has become a powerful tool for high-throughput approaches and was successfully applied to investigate the binding specificity of protein-ligand interactions. In this study, we used peptide arrays to uncover the c-di-GMP binding site of a
Pseudomonas aeruginosa
protein (PA3740) that was isolated in a chemical proteomics approach. PA3740 was shown to bind c-di-GMP with a high affinity, and peptide arrays uncovered LKKALKKQTNLR to be a putative c-di-GMP binding motif. Most interestingly, different from the previously identified c-di-GMP binding motif of the PilZ domain (RXXXR) or the I site of diguanylate cyclases (RXXD), two leucine residues and a glutamine residue and not the charged amino acids provided the key residues of the binding sequence. Those three amino acids are highly conserved across PA3740 homologs, and their singular exchange to alanine reduced c-di-GMP binding within the full-length protein.

IMPORTANCE
In many bacterial pathogens the universal bacterial second messenger c-di-GMP governs the switch from the planktonic, motile mode of growth to the sessile, biofilm mode of growth. Bacteria adapt their intracellular c-di-GMP levels to a variety of environmental challenges. Several classes of c-di-GMP binding proteins have been structurally characterized, and diverse c-di-GMP binding domains have been identified. Nevertheless, for several c-di-GMP receptors, the binding motif remains to be determined. Here we show that the use of a synthetic peptide array allowed the identification of a c-di-GMP binding motif of a putative c-di-GMP receptor protein in the opportunistic pathogen
P. aeruginosa
. The application of synthetic peptide arrays will facilitate the search for additional c-di-GMP receptor proteins and aid in the characterization of c-di-GMP binding motifs.
Long non-coding RNA chromogenic in situ hybridisation signal pattern correlation with breast tumour pathology
Authors: Zhang Zhouwei , Weaver Donald L , Olsen Daniel , deKay James , Peng Zhihua , Ashikaga Takamaru , Evans Mark F 
Published: September 2015

AimLong non-coding RNAs (lncRNAs) are potential biomarkers for breast cancer risk stratification. LncRNA expression has been investigated primarily by RNA sequencing, quantitative reverse transcription PCR or microarray techniques. In this study, six breast cancer-implicated lncRNAs were investigated by chromogenic in situ hybridisation (CISH).MethodsInvasive breast carcinoma (IBC), ductal carcinoma in situ (DCIS) and normal adjacent (NA) breast tissues from 52 patients were screened by CISH. Staining was graded by modified Allred scoring.ResultsHOTAIR,H19andKCNQ1OT1had significantly higher expression levels in IBC and DCIS than NA (p<0.05), andHOTAIRandH19were expressed more strongly in IBC than in DCIS tissues (p<0.05).HOTAIRandKCNQ101Twere expressed in tumour cells;H19andMEG3were expressed in stromal microenvironment cells;MALAT1was expressed in all cells strongly andZFAS1was negative or weakly expressed in all specimens.ConclusionThese data corroborate the involvement of three lncRNAs (HOTAIR,H19andKCNQ1OT1) in breast tumourigenesis and support lncRNA CISH as a potential clinical assay. Importantly, CISH allows identification of the tissue compartment expressing lncRNA.
Initial hospital management of patients with emergent large vessel occlusion (ELVO): report of the standards and guidelines committee of the Society of NeuroInterventional Surgery
Authors: McTaggart Ryan A , Ansari Sameer A , Goyal Mayank , Abruzzo Todd A , Albani Barb , Arthur Adam J , Alexander Michael J , Albuquerque Felipe C , Baxter Blaise , Bulsara Ketan R , Chen Michael , Almandoz Josser E Delgado , Fraser Justin F , Frei Donald , Gandhi Chirag D , Heck Don V , Hetts Steven W , Hussain M Shazam , Kelly Michael , Klucznik Richard , Lee Seon-Kyu , Leslie-Mawzi Thabele , Meyers Philip M , Prestigiacomo Charles J , Pride G Lee , Patsalides Athos , Starke Robert M , Sunenshine Peter , Rasmussen Peter A , Jayaraman Mahesh V 
Published: September 2015

ObjectiveTo summarize the current literature regarding the initial hospital management of patients with acute ischemic stroke (AIS) secondary to emergent large vessel occlusion (ELVO), and to offer recommendations designed to decrease the time to endovascular treatment (EVT) for appropriately selected patients with stroke.MethodsUsing guidelines for evidenced-based medicine proposed by the Stroke Council of the American Heart Association, a critical review of all available medical literature supporting best initial medical management of patients with AIS secondary to ELVO was performed. The purpose was to identify processes of care that most expeditiously determine the eligibility of a patient with an acute stroke for interventions including intravenous fibrinolysis with recombinant tissue plasminogen activator (IV tPA) and EVT using mechanical embolectomy.ResultsThis review identifies four elements that are required to achieve timely revascularization in ELVO. (1) In addition to non-contrast CT (NCCT) brain scan, CT angiography should be performed in all patients who meet an institutional threshold for clinical stroke severity. The use of any advanced imaging beyond NCCT should not delay the administration of IV tPA in eligible patients. (2) Activation of the neurointerventional team should occur as soon as possible, based on either confirmation of large vessel occlusion or a prespecified clinical severity threshold. (3) Additional imaging techniques, particularly those intended to physiologically select patients for EVT (CT perfusion and diffusion–perfusion mismatch imaging), may provide additional value, but should not delay EVT. (4) Routine use of general anesthesia during EVT procedures, should be avoided if possible. These workflow recommendations apply to both primary and comprehensive stroke centers and should be tailored to meet the needs of individual institutions.ConclusionsPatients with ELVO are at risk for severe neurologic morbidity and mortality. To achieve the best possible clinical outcomes stroke centers must optimize their triage strategies. Strategies that provide patients with ELVO with the fastest access to reperfusion depend upon detail-oriented process improvement.
Presymmetry in the Standard Model with adulterated Dirac neutrinos
Authors: Matute Ernesto A. 
Published: August 2015

Recently we proposed a model for light Dirac neutrinos in which two right-handed (RH) neutrinos per generation are added to the particles of the Standard Model (SM), implemented with the symmetry of fermionic contents. The ordinary one is decoupled via the high scale type-I seesaw mechanism, while the extra pairs off with its left-handed (LH) partner. The symmetry of lepton and quark contents was merely used as a guideline to the choice of parameters because it is not a proper symmetry. Here we argue that the underlying symmetry to take for this correspondence is presymmetry, the hidden electroweak symmetry of the SM extended with RH neutrinos defined by transformations which exchange lepton and quark bare states with the same electroweak charges and no Majorana mass terms in the underlying Lagrangian. It gives a topological character to fractional charges, relates the number of families to the number of quark colors, and now guarantees the great disparity between the couplings of the two RH neutrinos. Thus, Dirac neutrinos with extremely small masses appear as natural predictions of presymmetry, satisfying the ’t Hooft’s naturalness conditions in the extended seesaw where the extra RH neutrinos serve to adulterate the mass properties in the low scale effective theory, which retains without extensions the gauge and Higgs sectors of the SM. However, the high energy threshold for the seesaw implies new physics to stabilize the quantum corrections to the Higgs boson mass in agreement with the naturalness requirement.
STM/STS studies for interplane disorder effects on the electronic states of the Cu–O plane in Bi2201
Authors: Kurosawa T. , Hatta G. , Miyazaki H. , Yamaji J. , Yoshikawa K. , Nakagawa Y. , Shibata Y. , Yoshida H. , Oda M. , Ido M. , Takeyama K. , Momono N. 
Published: September 2015

STM/STS experiments have been performed in [Formula: see text] (R-Bi2201) systems with [Formula: see text] and Eu, which are of a nearly optimal doping level [Formula: see text] but have different [Formula: see text] values, 35 K and 20 K, respectively, to examine interplane disorder effects on the superconducting (SC) gap and the pseudogap (PG) that is accompanied by a checkerboard-type charge order (CCO). We report that as interplane disorders are strengthened by replacing La with Eu in optimal Bi2201, the antinodal PG size [Formula: see text] increases from [Formula: see text] to [Formula: see text], which is comparable to the value for an underdoping level [Formula: see text] in La-Bi2201. On the other hand, the period of CCO in optimal Eu-Bi2201 is the same as in optimal La-Bi2201, about five times lattice constant [Formula: see text] along the Cu–O bond directions; it remains unchanged even if the PG develops markedly to the same degree as for [Formula: see text] in La-Bi2201, whose period is [Formula: see text].
Nodal gap behavior of Bi2Sr2−xLnxCuO6+δ (Ln = La, Eu) investigated by specific heat measurements
Authors: Shimizu M. , Moriya Y. , Baar S. , Momono N. , Amakai Y. , Takano H. , Murayama S. , Kurosawa T. , Oda M. , Ido M. 
Published: September 2015

We performed low-temperature specific heat measurements on slightly underdoped samples of monolayer cuprate superconductors [Formula: see text] (Ln = La, Eu, Ln-Bi2201) under magnetic fields [Formula: see text]. In La-Bi2201, the coefficient [Formula: see text] of [Formula: see text]-linear term in the electronic specific heat [Formula: see text] at [Formula: see text] shows [Formula: see text] dependence, as expected in [Formula: see text] -wave superconductors. In Eu-Bi2201, [Formula: see text] shows almost the same [Formula: see text] dependence as that of La-Bi2201 below [Formula: see text] T, while [Formula: see text] is suppressed above [Formula: see text] T and deviates downward from the [Formula: see text] curve of La-Bi2201. This result suggests the the gap and the electronic excitation spectrum near nodes are modified in Eu-Bi2201 except the region of the Fermi surface in the immediate vicinity of nodes.
A magnetic origin of cuprate superconductivity? A MaxEnt-μSR view
Authors: Boekema C. , Owens F. , Love A. , Li Z. , Sakkaris P. , Dawson W. K. 
Published: September 2015

The fundamental physics of cuprate superconductivity is still much deliberated after three decades of research. In contrast to phononic or polaronic roots, some major theories promote a magnetic origin. In this perspective, we review cuprate magnetism, as probed by muon-spin-rotation [Formula: see text] in [Formula: see text] (RBCO), [Formula: see text] (Bi2212) and [Formula: see text] (Tl2223). Site-search RBCO studies show that muons localize and probe in locations away from the superconducting CuO2 planes. Maximum entropy (MaxEnt, ME) analysis of transverse field [Formula: see text] data of [Formula: see text] (GdBCO) indicates that the muon probes in an undisturbed insulating environment, allowing [Formula: see text] to detect (weak) magnetic features in these cuprates. Concerning Varma’s predicted loop currents, MaxEnt has shown weak [Formula: see text] signals for GdBCO in zero field above and below the critical temperature, [Formula: see text]; these are near the predicted [Formula: see text] Oe. Concerning Zhang’s predicted antiferromagnetism (AF) connected to the vortex cores, we have observed Lorentzian relaxation of cuprate vortex signals below half [Formula: see text], consistent with AF-broadening effects. For both Bi2212 and Tl2223, Lorentzians describe the [Formula: see text] vortex signals much better below [Formula: see text] than Gaussians, indicating that extra AF fields occur near and in the vortex cores. In sum, both our MaxEnt-[Formula: see text] (ME-[Formula: see text]) studies point toward magnetic roots of cuprate superconductivity.