bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystal structure and biochemical analyses reveal that the Arabidopsis triphosphate tunnel metalloenzyme AtTTM3 is a tripolyphosphatase involved in root development
Authors: Moeder Wolfgang , Garcia‐Petit Christel , Ung Huoi , Fucile Geoffrey , Samuel Marcus A. , Christendat Dinesh , Yoshioka Keiko
Published: September 2013

The Arabidopsis protein AtTTM3 belongs to the CYTH superfamily named after its two founding members, the CyaB adenylate cyclase from Aeromonas hydrophila and the mammalian thiamine triphosphatase. In this study we report the three‐dimensional structure of a plant CYTH domain protein, AtTTM3, determined at 1.9 Å resolution. The crystal structure revealed the characteristic tunnel architecture of CYTH proteins, which specialize in the binding of nucleotides and other organic phosphates and in phosphoryl transfer reactions. The β barrel is composed of eight antiparallel β strands with a cluster of conserved inwardly facing acidic and basic amino acid residues. Mutagenesis of these residues in the catalytic core led to an almost complete loss of enzymatic activity. We established that AtTTM3 is not an adenylate cyclase. Instead, the enzyme displayed weak NTP phosphatase as well as strong tripolyphosphatase activities similar to the triphosphate tunnel metalloenzyme proteins from Clostridium thermocellum (CthTTM) and Nitrosomonas europaea (NeuTTM). AtTTM3 is most highly expressed in the proximal meristematic zone of the plant root. Furthermore, an AtTTM3 T‐DNA insertion knockout line displayed a delay in root growth as well as reduced length and number of lateral roots, suggesting a role for AtTTM3 in root development.
N‐linked glycan profiling of GGTA1/CMAH knockout pigs identifies new potential carbohydrate xenoantigens
Authors: Burlak Christopher , Bern Marshall , Brito Alejandro E. , Isailovic Dragan , Wang Zheng‐Yu , Estrada Jose L. , Li Ping , Tector A. Joseph
Published: September 2013

Background

The temporary or long‐term xenotransplantation of pig organs into people would save thousands of lives each year if not for the robust human antibody response to pig carbohydrates. Genetically engineered pigs deficient in galactose α1,3 galactose (gene modified: GGTA1) and N‐glycolylneuraminic acid (gene modified: CMAH) have significantly improved cell survival when challenged by human antibody and complement in vitro. There remains, however, a significant portion of human antibody binding.

Methods

To uncover additional xenoantigens, we compared the asparagine‐linked (N‐linked) glycome from serum proteins of humans, domestic pigs, GGTA1 knockout pigs, and GGTA1/CMAH knockout pigs using mass spectrometry. Carbohydrate structures were determined with assistance from GlycoWorkbench, Cartoonist, and SimGlycan software by comparison to existing database entries and collision‐induced dissociation fragmentation data.

Results

Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS) analysis of reduced and solid‐phase permethylated glycans resulted in the detection of high‐mannose, hybrid, and complex type N‐linked glycans in the 1000–4500 m/z ion range. GGTA1/CMAH knockout pig samples had increased relative amounts of high‐mannose, incomplete, and xylosylated N‐linked glycans. All pig samples had significantly higher amounts of core and possibly antennae fucosylation.

Conclusions

We provide for the first time a comparison of the serum protein glycomes of the human, domestic pig, and genetically modified pigs important to xenotransplantation.
Phylogeny of Aphantochilinae and Strophiinae sensu Simon (Araneae; Thomisidae)
Authors: Teixeira Renato A. , Campos Luiz A. , Lise Arno A.
Published: September 2013

This study tests the monophyly of ant‐mimicking Thomisidae (Aphantochilinae and Strophiinae sensu Simon), redefines the composition of these taxa, proposes tribes and discusses aspects of their myrmecomorphy and biogeography. The analysis is based on a matrix composed of 113 morphological characters and 37 terminal taxa (11 Aphantochilinae, 16 Strophiinae and 10 belonging to the out‐group). The 12 most parsimonious trees with 232 steps, obtained with equally weighted characters, support the monophyly of Aphantochilinae sensu Simon. Strophiinae emerges as a paraphyletic group divided into two clades: a basal clade that groups Strophius and Strigoplus (Strophiini new status) and another clade that includes Ceraarachne, Simorcus and Ulocymus (Ceraarachnini new status) as the sister group of Aphantochilus + Bucranium (Aphantochilini new status). Diagnoses are presented for the tribes and genera in this analysis. The synonymy between Bucranium and Aphantochilus is rejected. Majellula and Acracanthostoma are considered junior synonyms of Bucranium, and Synstrophius of Ceraarachne. The monophyly of Synstrophius is not recovered, S. blanci is transferred to Ceraarachne and S. muricatus is transferred to Ulocymus. Ant‐preying behaviour appears to be basal and has been documented for Strophiini and Aphantochilini species. Myrmecomorphy, which was documented for Aphantochilus, is presumably derived. The biogeographical analysis of Aphantochilinae and Strophiinae suggests an ancient relation between Neotropical, Afrotropical and Oriental species, with probable origin after the breakup of Gondwana, that is, in early Paleogene.
Forest refugia and riverine barriers promote diversification in the West African pygmy shrew (Crocidura obscurior complex, Soricomorpha)
Authors: Jacquet François , Nicolas Violaine , Colyn Marc , Kadjo Blaise , Hutterer Rainer , Decher Jan , Akpatou Bertin , Cruaud Corinne , Denys Christiane
Published: September 2013

The Crocidura obscurior or West African pygmy shrew complex is endemic to West African forests from south‐eastern Guinea, eastern Liberia, southern Côte d'Ivoire and south‐western Ghana. We explore the genetic and morphometric diversity of 239 individuals of the C. obscurior complex from 17 localities across its geographical range. Using genetic data from three mitochondrial (16S, cytochrome b and COI) and four nuclear markers (BRCA1, STAT5A, HDAC2 and RIOK3) and skull geometric morphometrics, we show that this complex is composed of two cryptic and sympatric species, C. obscurior and C. eburnea. We then test several hypotheses to infer their evolutionary history. The observed phylogeographical pattern based on cytochrome b and COI sequences fits the forest refuge theory: during arid phases of the Plio‐Pleistocene, around 3.5, 2.1, 1 and 0.5 Mya, a small number of populations survived in isolated forest patches and diverged allopatrically. During wetter climatic periods, forests expanded, leading to secondary contacts between previously isolated populations. Our results also suggest the possible contribution of episodes of isolation in subrefuges. Historical variation of the West African hydrographic network could also have contributed to the observed patterns of genetic differentiation. Rivers such as the Volta and Sassandra may act as past and/or current barriers to gene flow. Although these two species have sympatric distributions, their phylogeographical histories are somewhat dissimilar due to small differences in their dispersal abilities and ecological requirements.
Flow Behavior and Pressure Drop in Porous Disks With Bifurcating Flow Passages
Authors: Calamas David , Baker John , Sharif Muhammad
Published: September 2013

The performance of a porous disk with hierarchical bifurcating flow passages has been examined. The hierarchical bifurcating flow passages in the heat exchanger mimic those seen in the vascular systems of plants and animals. The effect of bifurcation angle, porosity, and pore size on the pressure drop across a porous disk was examined computationally. The pressure drop across the porous disk was found to increase as the pore size decreased. As the bifurcation angle increased the pressure drop also increased. At high porosities the bifurcation angles did not have an impact on the pressure drop across the porous disk due to flow behavior. Similarly, the effect of bifurcation angle on pressure drop decreased as the pore size increased.
Plasma etching: Yesterday, today, and tomorrow
Authors: Donnelly Vincent M. , Kornblit Avinoam
Published: September 2013

The field of plasma etching is reviewed. Plasma etching, a revolutionary extension of the technique of physical sputtering, was introduced to integrated circuit manufacturing as early as the mid 1960s and more widely in the early 1970s, in an effort to reduce liquid waste disposal in manufacturing and achieve selectivities that were difficult to obtain with wet chemistry. Quickly,the ability to anisotropically etch silicon, aluminum, and silicon dioxide in plasmas became the breakthrough that allowed the features in integrated circuits to continue to shrink over the next 40 years. Some of this early history is reviewed, and a discussion of the evolution in plasma reactor design is included. Some basic principles related to plasma etching such as evaporation rates and Langmuir–Hinshelwood adsorption are introduced. Etching mechanisms of selected materials, silicon,silicon dioxide, and low dielectric-constant materials are discussed in detail. A detailed treatment is presented of applications in current silicon integrated circuit fabrication. Finally, some predictions are offered for future needs and advances in plasma etching for silicon and nonsilicon-based devices.
Functionalization of oxide-free silicon surfaces
Authors: DeBenedetti William J. I. , Chabal Yves J.
Published: September 2013

Much of the microelectronic industry and many uses of silicon are based on the stability of silicon oxide and the electrical quality of its interface with the silicon substrate. It is natural therefore to have focused on functionalizing silicon by grafting molecules on its oxide. However, severe issues are associated with organic functionalization of silicon oxide, such as reproducibility in grafting the layers and quality and stability of these layers once grafted. These problems have stimulated recent efforts to prepare and functionalize high quality oxide-free siliconsurfaces. In this review, methods for transforming such oxide-free,hydrogen-terminated siliconsurfaces are presented, including hydrosilylation (the formation of silicon carbon bonds) and direct replacement of hydrogen by reactive leaving groups (halogens, methoxy, and hydroxyl). These efforts are based on a number of complementary characterization methods, such as infrared absorption and x-ray photoelectron spectroscopy, low energy ion scattering, and capacitance/current voltage measurements. In contrast to previous work on the subject, the focus of this review is on controlled defects on Si(111) surfaces with aim to better understand the surface structure of siliconnanoparticles, the smallest Si object with the highest number of defects. To that end, sections on preparation and selective functionalization of stepped siliconsurfaces are included, and the current characterization and understanding of siliconnanoparticles added. The outlook on where the field may be going is presented.
Pediatric radiation dosimetry for positron‐emitting radionuclides using anthropomorphic phantoms
Authors: Xie Tianwu , Bolch Wesley E. , Lee Choonsik , Zaidi Habib
Published: September 2013

Purpose:

Positron emission tomography (PET) plays an important role in the diagnosis, staging, treatment, and surveillance of clinically localized diseases. Combined PET/CT imaging exhibits significantly higher sensitivity, specificity, and accuracy than conventional imaging when it comes to detecting malignant tumors in children. However, the radiation dose from positron‐emitting radionuclide to the pediatric population is a matter of concern since children are at a particularly high risk when exposed to ionizing radiation.

Methods:

The authors evaluate the absorbed fractions and specific absorbed fractions (SAFs) of monoenergy photons/electrons as well asS‐values of 9 positron‐emitting radionuclides (C‐11, N‐13, O‐15, F‐18, Cu‐64, Ga‐68, Rb‐82, Y‐86, and I‐124) in 48 source regions for 10 anthropomorphic pediatric hybrid models, including the reference newborn, 1‐, 5‐, 10‐, and 15‐yr‐old male and female models, using the Monte Carlo N‐Particle eXtended general purpose Monte Carlo transport code.

Results:

The self‐absorbed SAFs andS‐values for most organs were inversely related to the age and body weight, whereas the cross‐dose terms presented less correlation with body weight. For most source/target organ pairs, Rb‐82 and Y‐86 produce the highest self‐absorbed and cross‐absorbed S‐values, respectively, while Cu‐64 produces the lowest S‐values because of the low‐energy and high‐frequency of electron emissions. Most of the total self‐absorbed S‐values are contributed from nonpenetrating particles (electrons and positrons), which have a linear relationship with body weight. The dependence of self‐absorbed S‐values of the two annihilation photons varies to the reciprocal of 0.76 power of the mass, whereas the self‐absorbed S‐values of positrons vary according to the reciprocal mass.

Conclusions:

The producedS‐values for common positron‐emitting radionuclides can be exploited for the assessment of radiation dose delivered to the pediatric population from various PET radiotracers used in clinical and research settings. The mass scaling method for positron‐emitters can be used to derive patient‐specific S‐values from data of reference phantoms.
Topographic Representation of Numerosity in the Human Parietal Cortex
Authors: Harvey B. M. , Klein B. P. , Petridou N. , Dumoulin S. O.
Published: September 2013

Number Sense

Numerosity perception resembles primary sensory perception and, indeed, it has been called the number sense. As all primary senses are organized topographically in the cortex,

Harvey
et al.

(p.
1123
) tested the hypothesis that numerosity is also organized topographically. Applying ultrahighfield functional brain scanning and using custom-designed analysis, they confirmed that a topographical numerosity map occurs in the human parietal cortex, which displays conventional characteristics, such as a systematic relationship between the cortical location's preferred numerosity and cortical magnification and tuning width.
Decades-Long Changes of the Interstellar Wind Through Our Solar System
Authors: Frisch P. C. , Bzowski M. , Livadiotis G. , McComas D. J. , Moebius E. , Mueller H.-R. , Pryor W. R. , Schwadron N. A. , Sokół J. M. , Vallerga J. V. , Ajello J. M.
Published: September 2013

Wind of Change

The flow of interstellar gas and dust through the solar system was thought to be unvarying, but

Frisch
et al.

(p.
1080
) show that there has been a significant variation of the direction of the flow of interstellar helium through the solar system over the past 40 years. The data, collected by 10 different spacecraft over much of the space age, hint of changes rather than constancy in the solar system's galactic environment.
A Causative Link Between Inner Ear Defects and Long-Term Striatal Dysfunction
Authors: Antoine Michelle W. , Hübner Christian A , Arezzo Joseph C. , Hébert Jean M.
Published: September 2013

Deafness and Misbehavior

Behavioral problems accompanied by hyperactivity often occur in children with severe hearing loss and vestibular impairment. Explanations have focused on socioenvironmental factors, but

Antoine
et al.

(p.
1120
) found that inner ear defects can cause dysfunction in the striatum, which leads to abnormal behavior—especially hyperactivity—mediated by dopamine and glutamate signals, in an area of the striatum that is instrumental in controlling motor output. The abnormal behavior can be reversed by injection of an extracellular signal-regulated kinase inhibitor, which provides a novel target pathway for the treatment of behavioral disorders.
Single-Cell DNA-Methylation Analysis Reveals Epigenetic Chimerism in Preimplantation Embryos
Authors: Lorthongpanich Chanchao , Cheow Lih Feng , Balu Sathish , Quake Stephen R. , Knowles Barbara B. , Burkholder William F. , Solter Davor , Messerschmidt Daniel M.
Published: September 2013

Fatal Chimeras

Impaired DNA-methylation maintenance during early embryonic development may cause imprinting-related diseases.

Lorthongpanich
et al.

(p.
1110
) have devised a sensitive assay to probe multiple imprinted gene loci for their DNA-methylation state at the single-cell level. Blastomeres with defective imprinting showed complex, epigenetic chimeras developed with fatal defects. Pronuclear transfer restored normal mouse development, offering a therapeutic strategy to overcome epigenetic defects caused by maternal insufficiencies.
Neuroendocrine Control of
Drosophila
Larval Light Preference
Authors: Yamanaka Naoki , Romero Nuria M. , Martin Francisco A. , Rewitz Kim F. , Sun Mu , O’Connor Michael B. , Léopold Pierre
Published: September 2013

Looking for the Dark

Mature
Drosophila
larvae wander away from food and seek a dark site for pupation. While investigating this phenomenon

Yamanaka
et al.

(p.
1113
) found that four prothoracicotropic hormone (PTTH)–producing neurons mediate light preference in the central brain. PTTH circulates in the hemolymph and signals via its receptor, Torso, to two light sensors, sensitizing them for light detection. The larvae can then transform from wandering larvae into immobile pupae hidden from light and predatory eyes.
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
Authors: Ridaura Vanessa K. , Faith Jeremiah J. , Rey Federico E. , Cheng Jiye , Duncan Alexis E. , Kau Andrew L. , Griffin Nicholas W. , Lombard Vincent , Henrissat Bernard , Bain James R. , Muehlbauer Michael J. , Ilkayeva Olga , Semenkovich Clay F. , Funai Katsuhiko , Hayashi David K. , Lyle Barbara J. , Martini Margaret C. , Ursell Luke K. , Clemente Jose C. , Van Treuren William , Walters William A. , Knight Rob , Newgard Christopher B. , Heath Andrew C. , Gordon Jeffrey I.
Published: September 2013

Transforming Fat to Thin

How much does the microbiota influence the host's phenotype?

Ridaura
et al.

(
1241214
; see the Perspective by

Walker and Parkhill

) obtained uncultured fecal microbiota from twin pairs discordant for body mass and transplanted them into adult germ-free mice. It was discovered that adiposity is transmissible from human to mouse and that it was associated with changes in serum levels of branched-chain amino acids. Moreover, obese-phenotype mice were invaded by members of the Bacteroidales from the lean mice, but, happily, the lean animals resisted invasion by the obese microbiota.
Unraveling Charge Transport in Conjugated Polymers
Authors: Street R. A.
Published: September 2013

New semiconducting polymers reach record mobility despite apparently lower structural order.
Fighting Obesity with Bacteria
Authors: Walker Alan W. , Parkhill Julian
Published: September 2013

Intestinal bacteria from lean humans can confer protection against fat gain in experimental mice.

[Also see Research Article by

Ridaura
et al.

]
As Syria Crisis Mounts, Scientist Looks Back at Last Major Chemical Attack
Authors: Kaiser Jocelyn
Published: September 2013

As the Syrian crisis unfolds, a scientist involved in investigating the last major chemical attack against civilians, in Iraq in 1988, describes his experience.
Seroprevalence and Risk Factors for Toxoplasma gondii Infection among Pregnant Women in Northeast Iran
Authors: Babaie Jalal , Amiri Samira , Mostafavi Ehsan , Hassan Nayereh , Lotfi Peyman , Esmaeili Rastaghi Ahmad Reza , Golkar Majid
Published: September 2013

We report
Toxoplasma
IgG seroprevalence of 34.4% among 419 pregnant women in Mashhad, northeast Iran. Soil contact, living in rural environment, and level of education were associated with infection. The prevalence did not increase with age, suggesting high infection rate during childhood and adolescence.
Anti-Leishmania infantum IgG Antibody Avidity in Visceral Leishmaniasis
Authors: Tiburcio Monique Gomes Salles , Anversa Laís , Kanunfre Kelly Aparecida , Ferreira Antonio Walter , Rodrigues Júnior Virmondes , Silva Luciana de Almeida
Published: September 2013

IgG avidity tests are used to discriminate acute from chronic infections. There are few reports on the IgG avidity profile of patients with visceral leishmaniasis (VL). This study investigated the anti-
Leishmania
IgG avidity in patients with classic VL (
n
= 10), patients showing clinical cure after treatment (
n
= 18), and asymptomatic subjects with at least one positive
Leishmania
test (
n
= 20). All subjects were from areas in Brazil where VL is endemic. Serum samples were collected from each subject on two different occasions. IgG avidity was evaluated by Western blotting. The proportion of high-avidity antibodies was higher in all samples from patients with classic VL. In contrast, low-avidity antibodies predominated in subjects with a history of VL, including 13 cases (72.2%) in the first assessment and 14 (77.8%) in the second. Fifteen (75%) of the asymptomatic subjects presented a predominance of low-avidity antibodies in the first assessment, and the frequency of high-avidity antibodies increased over time in seven subjects (35%) of this group. Antibodies against the 14- and/or 16-kDa antigen fraction were detected in the first assessment in all patients with classic VL, in 10 (55.5%) treated patients, and in 10 (50%) asymptomatic subjects. These were high-avidity antibodies in most cases. In the asymptomatic group, an increase in IgG avidity against the 14- and/or 16-kDa antigen fraction was observed in three cases (15%). The results indicate distinct responses in infected and asymptomatic subjects, probably associated with the length of time after infection. In this respect, IgG avidity tests represent a new approach to better characterize asymptomatic VL.
Invasive and Noninvasive Streptococcus pneumoniae Capsule and Surface Protein Diversity following the Use of a Conjugate Vaccine
Authors: Croney Christina M. , Nahm Moon H. , Juhn Steven K. , Briles David E. , Crain Marilyn J.
Published: September 2013

The 13-valent pneumococcal conjugate vaccine (PCV13) was introduced in the United States in 2010 for the prevention of invasive pneumococcal disease (IPD) and otitis media. While many studies have reported its potential efficacy for IPD, not much is known about the epidemiology of noninvasive disease following its introduction. We characterized the capsular types and surface protein genes of noninvasive pediatric pneumococcal isolates collected between 2002 and 2010 (
n
= 1,058) at Children's of Alabama following the introduction of PCV7 and tested a subset of noninvasive and previously characterized IPD isolates for the presence of the
pspA
,
pspC
, and
rrgC
genes, which encode protection-eliciting proteins. PCV7 serotypes had dramatically decreased by 2010 (
P
< 0.0001), and only 50% of all noninvasive infections were caused by the PCV13 capsular serotypes. Serotype 19A accounted for 32% of the noninvasive isolates, followed by serotypes 35B (9%), 19F (7%), and 6C (6%). After 7 years of PCV7 usage, there were no changes in the frequencies of the
pspA
or
pspC
genes; 96% of the strains were positive for family 1 or 2
pspA
genes, and 81% were also positive for
pspC
. Unexpectedly, more noninvasive than invasive strains were positive for
rrgC
(
P
< 0.0001), and the proportion of
rrgC
-positive strains in 2008 to 2010 was greater than that in 2002 to 2008 (IPD,
P
< 0.02; noninvasive,
P
< 0.001). Serotypes 19F, 19A, and 35B were more frequently
rrgC
positive (
P
< 0.005) than other serotypes. A vaccine containing antigens, such as PspA, PspC, and/or RrgC, can provide coverage against most non-PCV13-type pneumococci. Continued surveillance is critical for optimal future vaccine development.
Comparison of Simplexa HSV 1 & 2 PCR with Culture, Immunofluorescence, and Laboratory-Developed TaqMan PCR for Detection of Herpes Simplex Virus in Swab Specimens
Authors: Gitman Melissa R. , Ferguson David , Landry Marie L.
Published: September 2013

The Simplexa HSV 1 & 2 direct PCR assay was compared with conventional cell culture, cytospin-enhanced direct fluorescent antibody (DFA), and a laboratory-developed real-time TaqMan PCR (LDT HSV PCR) using extracted nucleic acid for the detection of herpes simplex virus (HSV) in dermal, genital, mouth, ocular, and other swab samples. One hundred seventy-one swabs were tested prospectively, and 58 were positive for HSV (34 HSV-1 and 24 HSV-2). Cytospin-DFA detected 50 (86.2%), conventional cell culture 51 (87.9%), Simplexa direct 55 (94.8%), and LDT HSV PCR 57 (98.3%) of 58 true positives. Simplexa direct detected more positives than DFA and culture, but the differences were not significant (
P
= 0.0736 and
P
= 0.3711, respectively, by the McNemar test). Samples that were positive by all methods (
n
= 48) were strong positives (LDT cycle threshold [

C
T

] value, 14.4 to 26.1). One strongly positive sample was falsely negative by LDT HSV PCR due to a failure of TaqMan probe binding. Three samples falsely negative by Simplexa direct had high

C
T

values by LDT HSV PCR (LDT

C
T

, 35.8 to 38.2). Omission of the DNA extraction step by Simplexa direct led to a drop in sensitivity compared to the sensitivity of LDT HSV PCR using extracted samples (94.8% versus 98.3%, respectively), but the difference was not significant (
P
= 0.6171). Simplexa HSV 1 & 2 direct PCR was the most expensive but required the least training of the assays used, had the lowest hands-on time and fastest assay time (75 min, versus 3 h by LDT HSV PCR), and provided the HSV type.
MALDI Biotyper-Based Rapid Resistance Detection by Stable-Isotope Labeling
Authors: Sparbier Katrin , Lange Christoph , Jung Jette , Wieser Andreas , Schubert Sören , Kostrzewa Markus
Published: September 2013

Against the background of increasing numbers of resistant microorganisms, the fast and cost-efficient detection of microbial resistance is an important clinical requirement for optimal therapeutic intervention. Current routine assays take at least 5 h, but in most cases an overnight incubation is necessary to identify resistant isolates. The usage of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) profiling in combination with growth media containing isotopically labeled amino acids facilitates the detection of resistant microorganisms after 3 h or less directly from the profile spectrum. Growing microorganisms incorporate isotopically labeled amino acids, increasing protein masses and thereby leading to mass shifts of their corresponding peaks in the profile spectra. In the presence of antibiotics, only resistant microorganisms are able to grow and to incorporate the labeled amino acids. This leads to a difference in the mass spectra of susceptible and resistant isolates, allowing their differentiation. In the presented study, we demonstrated the applicability of this novel approach for the detection of methicillin-resistant
Staphylococcus aureus
and tested different bioinformatics approaches for automated data interpretation.
First Outbreak of KPC-2-Producing Klebsiella pneumoniae Sequence Type 258 in a Hospital in South Korea
Authors: Hong Sung Kwan , Yong Dongeun , Kim Kyeongmi , Hong Sang Sook , Hong Seong Geun , Khosbayar Tulgaa , Song Wonkeun , Roh Kyoung Ho , Jeong Seok Hoon , Lee Kyungwon , Chong Yunsop
Published: September 2013

In this study, we report the first outbreak of KPC-2-producing
Klebsiella pneumoniae
isolates from three patients admitted to a neurosurgery department in a South Korean teaching hospital. Multilocus sequence typing showed that the isolates were identical to the previous KPC producers in South Korea and other countries, suggesting clonal spread.
Helicobacter pylori Infection in Infants and Toddlers in South America: Concordance between [
13
C]Urea Breath Test and Monoclonal H. pylori Stool Antigen Test
Authors: Queiroz Dulciene Maria Magalhães , Saito Mayuko , Rocha Gifone Aguiar , Rocha Andreia Maria Camargos , Melo Fabrício Freire , Checkley William , Braga Lúcia Libanez Bessa C. , Silva Igor Simões , Gilman Robert H. , Crabtree Jean E.
Published: September 2013

Accurate noninvasive tests for diagnosing
Helicobacter pylori
infection in very young children are strongly required. We investigated the agreement between the [
13
C]urea breath test ([
13
C]UBT) and a monoclonal ELISA (HpSA) for detection of
H. pylori
antigen in stool. From October 2007 to July 2011, we enrolled 414 infants (123 from Brazil and 291 from Peru) of ages 6 to 30 months. Breath and stool samples were obtained at intervals of at least 3 months from Brazilian (
n
= 415) and Peruvian (
n
= 908) infants. [
13
C]UBT and stool test results concurred with each other in 1,255 (94.86%) cases (kappa coefficient = 0.90; 95% confidence interval [CI] = 0.87 to 0.92). In the
H. pylori
-positive group, delta-over-baseline (DOB) and optical density (OD) values were positively correlated (
r
= 0.62;
P
< 0.001). The positivity of the tests was higher (
P
< 0.001; odds ratio [OR] = 6.01; 95% CI = 4.50 to 8.04) in Peru (546/878; 62.2%) than in Brazil (81/377; 21.5%) and increased with increasing age in Brazil (
P
= 0.02), whereas in Peru it decreased with increasing age (
P
< 0.001). The disagreement between the test results was associated with birth in Brazil and female gender but not with age and diarrhea. Our results suggest that both [
13
C]UBT and the stool monoclonal test are reliable for diagnosing
H. pylori
infection in very young children, which will facilitate robust epidemiological studies in infants and toddlers.
“Epidemic Clones” of Listeria monocytogenes Are Widespread and Ancient Clonal Groups
Authors: Cantinelli Thomas , Chenal-Francisque Viviane , Diancourt Laure , Frezal Lise , Leclercq Alexandre , Wirth Thierry , Lecuit Marc , Brisse Sylvain
Published: September 2013

The food-borne pathogen
Listeria monocytogenes
is genetically heterogeneous. Although some clonal groups have been implicated in multiple outbreaks, there is currently no consensus on how “epidemic clones” should be defined. The objectives of this work were to compare the patterns of sequence diversity on two sets of genes that have been widely used to define
L. monocytogenes
clonal groups: multilocus sequence typing (MLST) and multi-virulence-locus sequence typing (MvLST). Further, we evaluated the diversity within clonal groups by pulsed-field gel electrophoresis (PFGE). Based on 125 isolates of diverse temporal, geographical, and source origins, MLST and MvLST genes (i) had similar patterns of sequence polymorphisms, recombination, and selection, (ii) provided concordant phylogenetic clustering, and (iii) had similar discriminatory power, which was not improved when we combined both data sets. Inclusion of representative strains of previous outbreaks demonstrated the correspondence of epidemic clones with previously recognized MLST clonal complexes. PFGE analysis demonstrated heterogeneity within major clones, most of which were isolated decades before their involvement in outbreaks. We conclude that the “epidemic clone” denominations represent a redundant but largely incomplete nomenclature system for MLST-defined clones, which must be regarded as successful genetic groups that are widely distributed across time and space.
Diagnostic Rates Differ on the Basis of the Number of Read Days with the Use of the InPouch Culture System for Trichomonas vaginalis Screening
Authors: Rivers Charles. A. , Muzny Christina A. , Schwebke Jane R.
Published: September 2013

The InPouch
Trichomonas vaginalis
test is the gold standard for clinical culture for
Trichomonas vaginalis
screening. The current package insert recommends an examination period of 3 days. After review of 2,499 InPouch tests spanning 13 years, we observed that examination up to 3 days will detect only 82.8% (95% confidence interval [CI], 79.0% to 86.2%) of positive specimens.
Oncoprotein E7 from Beta Human Papillomavirus 38 Induces Formation of an Inhibitory Complex for a Subset of p53-Regulated Promoters
Authors: Saidj Djamel , Cros Marie-Pierre , Hernandez-Vargas Hector , Guarino Francesca , Sylla Bakary S. , Tommasino Massimo , Accardi Rosita
Published: September 2013

Our previous studies on cutaneous beta human papillomavirus 38 (HPV38) E6 and E7 oncoproteins highlighted a novel activity of IκB kinase beta (IKKβ) in the nucleus of human keratinocytes, where it phosphorylates and stabilizes ΔNp73α, an antagonist of p53/p73 functions. Here, we further characterize the role of the IKKβ nuclear form. We show that IKKβ nuclear translocation and ΔNp73α accumulation are mediated mainly by HPV38 E7 oncoprotein. Chromatin immunoprecipitation (ChIP)/Re-ChIP experiments showed that ΔNp73α and IKKβ are part, together with two epigenetic enzymes DNA methyltransferase 1 (DNMT1) and the enhancer of zeste homolog 2 (EZH2), of a transcriptional regulatory complex that inhibits the expression of some p53-regulated genes, such as
PIG3
. Recruitment to the PIG3 promoter of EZH2 and DNMT1 resulted in trimethylation of histone 3 on lysine 27 and in DNA methylation, respectively, both events associated with gene expression silencing. Decreases in the intracellular levels of HPV38 E7 or ΔNp73α strongly affected the recruitment of the inhibitory transcriptional complex to the PIG3 promoter, with consequent restoration of p53-regulated gene expression. Finally, the ΔNp73α/IKKβ/DNMT1/EZH2 complex appears to bind a subset of p53-regulated promoters. In fact, the complex is efficiently recruited to several promoters of genes encoding proteins involved in DNA repair and apoptosis, whereas it does not influence the expression of the prosurvival factor Survivin. In summary, our data show that HPV38 via E7 protein promotes the formation of a multiprotein complex that negatively regulates the expression of several p53-regulated genes.
Expression of Betapapillomavirus Oncogenes Increases the Number of Keratinocytes with Stem Cell-Like Properties
Authors: Hufbauer Martin , Biddle Adrian , Borgogna Cinzia , Gariglio Marisa , Doorbar John , Storey Alan , Pfister Herbert , Mackenzie Ian , Akgül Baki
Published: September 2013

Human papillomaviruses (HPV) of genus
Betapapillomavirus
(betaPV) are associated with nonmelanoma skin cancer development in epidermodysplasia verruciformis (EV) and immunosuppressed patients. Epidemiological and molecular studies suggest a carcinogenic activity of betaPV during early stages of cancer development. Since viral oncoproteins delay and perturb keratinocyte differentiation, they may have the capacity to either retain or confer a “stem cell-like” state on oncogene-expressing cells. The aim of this study was to determine (i) whether betaPV alters the expression of cell surface markers, such as CD44 and epithelial cell adhesion molecule (EpCAM), that have been associated with epithelial stemness, and (ii) whether this confers functional stem cell-like properties to human cutaneous keratinocytes. Fluorescence-activated cell sorter (FACS) analysis revealed an increase in the number of cells with high CD44 and EpCAM expression in keratinocyte cultures expressing HPV type 8 (HPV8) oncogenes E2, E6, and E7. Particularly through E7 expression, a distinct increase in clonogenicity and in the formation and size of tumor spheres was observed, accompanied by reduction of the epithelial differentiation marker Calgranulin B. These stem cell-like properties could be attributed to the pool of CD44
high
EpCAM
high
cells, which was increased within the E7 cultures of HPV5, -8, and -20. Enhanced EpCAM levels were present in organotypic skin cultures of primary keratinocytes expressing E7 of the oncogenic HPV types HPV5, -8, and -16 and in clinical samples from EV patients. In conclusion, our data show that betaPV may increase the number of stem cell-like cells present during early carcinogenesis and thus enable the persistence and accumulation of DNA damage necessary to generate malignant stem cells.
Hepatitis C Virus Induces Interleukin-1β (IL-1β)/IL-18 in Circulatory and Resident Liver Macrophages
Authors: Shrivastava Shubham , Mukherjee Anupam , Ray Ranjit , Ray Ratna B.
Published: September 2013

Hepatitis C virus (HCV)-mediated chronic liver disease is a global health problem, and inflammation is believed to be an important player in disease pathogenesis. HCV infection often leads to severe fibrosis/cirrhosis and hepatocellular carcinoma, although the mechanisms for advancement of disease are not fully understood. The proinflammatory cytokines interleukin-1β (IL-1β) and IL-18 have critical roles in establishment of inflammation. In this study, we examined induction of IL-1β/IL-18 secretion following HCV infection. Our results demonstrated that monocyte-derived human macrophages (THP-1) incubated with cell culture-grown HCV enhance the secretion of IL-1β/IL-18 into culture supernatants. A similar cytokine release was also observed for peripheral blood mononuclear cell (PBMC)-derived primary human macrophages and Kupffer cells (liver-resident macrophages) upon incubation with HCV. THP-1 cells incubated with HCV led to caspase-1 activation and release of proinflammatory cytokines. Subsequent studies demonstrated that HCV induces pro-IL-1β and pro-IL-18 synthesis via the NF-κB signaling pathway in macrophages. Furthermore, introduction of HCV viroporin p7 RNA into THP-1 cells was sufficient to cause IL-1β secretion. Together, our results suggested that human macrophages exposed to HCV induce IL-1β and IL-18 secretion, which may play a role in hepatic inflammation.
HLA-DPPolymorphisms Affect the Outcomes of Chronic Hepatitis B Virus Infections, Possibly through Interacting with Viral Mutations
Authors: Zhang Qi , Yin Jianhua , Zhang Yuwei , Deng Yang , Ji Xiaowei , Du Yan , Pu Rui , Han Yifang , Zhao Jun , Han Xue , Zhang Hongwei , Cao Guangwen
Published: September 2013

Genetic polymorphisms ofHLA-DPhave been associated with hepatitis B virus (HBV) persistence. We aimed to determine the effect ofHLA-DPpolymorphisms on the generation of HBV mutations and their interactions on the outcomes of HBV infection. rs3077, rs3135021, rs9277535, and rs2281388 were genotyped in 1,342 healthy controls, 327 HBV clearance subjects, and 2,736 HBV-positive subjects, including 1,108 hepatocellular carcinoma (HCC) patients, using quantitative PCR. HBV mutations were determined by sequencing. Multiplicative interactions ofHLA-DPpolymorphisms and viral mutations were assessed by multivariate logistic regression. rs3077 (from subjects with genotype CT combined with those from subjects with genotype TT [CT+TT] versus CC), rs3135021 (GA+AA versus GG), rs9277535 (GA+AA versus GG), and rs2281388 (CC versus CT+TT) significantly decreased HBV persistence. This effect was found only in genotype B HBV-infected subjects compared to HBV clearance subjects.HLA-DPpolymorphisms promoting HBV clearance were associated with a lower prevalence of mutations increasing HCC risk (C1653T, T1674C/G, A1846T, G1896A and pre-S2 mutations and pre-S deletion in genotype C) and a higher prevalence of mutations decreasing HCC risk (G1652A, T1673C, T1674C, G1719T, G1730C, and G1799C in genotype B and A1727T in genotype C). Significant effects of viral mutations on cirrhosis and HCC were selectively evident in those withHLA-DPpolymorphisms promoting HBV persistence. The interactions of C1653T, T1674C/G, and G1896A mutations withHLA-DPpolymorphisms promoting HBV clearance significantly decreased cirrhosis risk. The interaction of rs9277535 AA with the T1674C/G or G1719T mutation in genotype C significantly decreased HCC risk. In conclusion,HLA-DPpolymorphisms affect genotype B HBV clearance, regulate immune selection of viral mutations, and influence cirrhosis and HCC risks contributed by HBV mutations.
Inverse intubation in entrapped trauma casualties: a simulator based, randomised cross-over comparison of direct, indirect and video laryngoscopy
Authors: Schober Patrick , Krage Ralf , van Groeningen Dick , Loer Stephan A , Schwarte Lothar A
Published: September 2013

Background

Airway management in entrapped casualties with restricted access to the head is challenging. If tracheal intubation is required and conventional laryngoscopy is not possible, intubation must be attempted in a face-to-face approach. Traditionally, this is performed with a standard laryngoscope held in the right hand with the blade facing upward. Recently, alternative methods have been developed to facilitate difficult intubations, and we hypothesised that such techniques are also useful for face-to-face intubations.

Methods

24 (trainee) anaesthesiologists attempted tracheal intubation in a patient simulator (SimMan, Laerdal, Norway) using three techniques in random order: (1) direct laryngoscopy (Macintosh blade #3), (2) indirect optical laryngoscopy (Airtraq, Prodol, Spain) and (3) video laryngoscopy (McGrath, Aircraft Medical, UK). The manikin was sitting with the neck immobilised and only accessible from the left anterolateral side. Success rate (percentage (95% CI)) and tube insertion time (median (IQR)) were recorded.

Results

Success rate did not differ significantly (Airtraq and McGrath 100% (84% to 100%), direct laryngoscopy 88% (68% to 96%)). Intubation was faster with Airtraq (25 s (22–34), p<0.001) and direct laryngoscopy (34 s (22–48), p<0.05) compared with the McGrath technique (55 s (37–96)).

Conclusions

All three techniques have a high success rate, but the usefulness of the video laryngoscope is limited due to longer intubation duration. Inverse direct laryngoscopy showed reasonable intubation times and, given the widespread availability of Macintosh laryngoscopes, seems a useful technique. Intubation was always successful and tended to be fastest with the Airtraq device, suggesting that this technique may be a promising alternative.
Identification of small compound biomarkers of pituitary adenoma: a bilateral inferior petrosal sinus sampling study
Authors: Oklu Rahmi , Deipolyi Amy R , Wicky Stephan , Ergul Emel , Deik Amy A , Chen John W , Hirsch Joshua A , Wojtkiewicz Gregory R , Clish Clary B
Published: September 2013

Evaluation of the pathogenic mechanisms underlying Cushing disease (CD) is limited partly by the inaccessibility of the pituitary gland for biopsy. We used bilateral inferior petrosal sinus sampling (BIPSS), the gold standard in diagnosing pituitary sources of CD, to obtain central blood samples for in vivo metabolomic analysis of pathways involved in pituitary adenomas. We evaluated 16 samples from eight patients who underwent BIPSS to measure adrenocorticotropic hormone (ACTH) levels in the inferior petrosal sinus (IPS) bilaterally. Seven patients had CD with concordant BIPSS, surgical, and pathologic findings. Samples from the IPS contralateral to histologically proven lesions were used as controls. BIPSS of the eighth patient revealed no central pituitary ACTH source, and these samples were also included as controls. Plasma samples were profiled using a combination of three liquid chromatography tandem mass spectrometry methods, which assessed 259 metabolites. Following Bonferroni correction for multiple comparisons, three small compound biomarkers of CD (pyridoxate, deoxycholic acid, and 3-methyladipate) were identified to be significantly altered in pituitary adenomas. The pathway most significantly impacted in CD samples is one previously shown to be upregulated in other cancers. Exploiting the BIPSS technique, we showed a complete metabolite and lipid profile of pituitary adenomas in CD. These potential biomarkers of CD may elucidate tumor biology and suggest possible diagnostic molecular imaging probes as well as therapeutic targets in patients with recurrent disease after surgery.
Increasing chlamydia screening tests in general practice: a modified Zelen prospective Cluster Randomised Controlled Trial evaluating a complex intervention based on the Theory of Planned Behaviour
Authors: McNulty Cliodna A M , Hogan Angela H , Ricketts Ellie J , Wallace Louise , Oliver Isabel , Campbell Rona , Kalwij Sebastian , O'Connell Elaine , Charlett Andre
Published: September 2013

Objective

To determine if a structured complex intervention increases opportunistic chlamydia screening testing of patients aged 15–24 years attending English general practitioner (GP) practices.

Methods

A prospective, Cluster Randomised Controlled Trial with a modified Zelen design involving 160 practices in South West England in 2010. The intervention was based on the Theory of Planned Behaviour (TPB). It comprised of practice-based education with up to two additional contacts to increase the importance of screening to GP staff and their confidence to offer tests through skill development (including videos). Practical resources (targets, posters, invitation cards, computer reminders, newsletters including feedback) aimed to actively influence social cognitions of staff, increasing their testing intention.

Results

Data from 76 intervention and 81 control practices were analysed. In intervention practices, chlamydia screening test rates were 2.43/100 15–24-year-olds registered preintervention, 4.34 during intervention and 3.46 postintervention; controls testing rates were 2.61/100 registered patients prior intervention, 3.0 during intervention and 2.82 postintervention. During the intervention period, testing in intervention practices was 1.76 times as great (CI 1.24 to 2.48) as controls; this persisted for 9 months postintervention (1.57 times as great, CI 1.27 to 2.30). Chlamydia infections detected increased in intervention practices from 2.1/1000 registered 15–24-year-olds prior intervention to 2.5 during the intervention compared with 2.0 and 2.3/1000 in controls (Estimated Rate Ratio intervention versus controls 1.4 (CI 1.01 to 1.93).

Conclusions

This complex intervention doubled chlamydia screening tests in fully engaged practices. The modified Zelen design gave realistic measures of practice full engagement (63%) and efficacy of this educational intervention in general practice; it should be used more often.

Trial registration

The trial was registered on the UK Clinical Research Network Study Portfolio database. UKCRN number 9722.
Exercise training induced myosin heavy chain isoform alteration in the infarcted heart
Authors: Wan Wenhan , Xu Xiaohua , Zhao Weiyan , Garza Michael A. , Zhang John Q.
Published: September 2013

The myosin heavy chain isoform MHC-α has 3-fold higher ATPase activity than MHC-β. After myocardial infarction (MI), MHC-α expression is profoundly downregulated and MHC-β expression is reciprocally upregulated. This shift, which is attributed to low thyroid hormone (TH), contributes to myocardial systolic dysfunction. We investigated the effect of post-MI exercise training on MHC isoforms, TH, and cardiac function. MI was surgically induced in 7-week-old rats by ligation of the coronary artery. The survivors were assigned to 3 groups (n = 10/group): Sham (no MI, no exercise), MISed (MI, no exercise), and MIEx (MI, exercise). Treadmill exercise training began 1 week post-MI and lasted for 8 weeks. Echocardiogram measurements were taken on the day prior to initiation of exercise training and at the end of exercise training. Tissue and blood samples were collected at the end of the experiment. MHC isoform gene and protein expression and TH were measured. Our results illustrated that MHC-α gene expression was higher and MHC-β gene expression was lower in the MIEx group than in the MISed group. Resting serum TH concentrations (T3 and T4) were similar between the 2 MI groups. The MIEx group had higher fractional shortening than the MISed group. In conclusion, post-MI exercise training beneficially altered MHC isoforms and improved cardiac function without changing TH.