bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilocus Sequence Typing of Pathogenic Treponemes Isolated from Cloven-Hoofed Animals and Comparison to Treponemes Isolated from Humans
Authors: Clegg Simon R. , Carter Stuart D. , Birtles Richard J. , Brown Jennifer M. , Hart C. Anthony , Evans Nicholas J. 
Published: May 2016

ABSTRACT

Treponema
species are implicated in many diseases of humans and animals. Digital dermatitis (DD) treponemes are reported to cause severe lesions in cattle, sheep, pigs, goats, and wild elk, causing substantial global animal welfare issues and economic losses. The fastidiousness of these spirochetes has previously precluded studies investigating within-phylogroup genetic diversity. An archive of treponemes that we isolated enabled multilocus sequence typing to quantify the diversity and population structure of DD treponemes. Isolates (
n
= 121) were obtained from different animal hosts in nine countries on three continents. The analyses herein of currently isolated DD treponemes at seven housekeeping gene loci confirm the classification of the three previously designated phylogroups: the
Treponema medium
,
Treponema phagedenis
, and
Treponema pedis
phylogroups. Sequence analysis of seven DD treponeme housekeeping genes revealed a generally low level of diversity among the strains within each phylogroup, removing the need for the previously used “-like” suffix. Surprisingly, all isolates within each phylogroup clustered together, regardless of host or geographic origin, suggesting that the same sequence types (STs) can infect different animals. Some STs were derived from multiple animals from the same farm, highlighting probable within-farm transmissions. Several STs infected multiple hosts from similar geographic regions, identifying probable frequent between-host transmissions. Interestingly,
T. pedis
appears to be evolving more quickly than the
T. medium
or
T. phagedenis
DD treponeme phylogroup, by forming two unique ST complexes. The lack of phylogenetic discrimination between treponemes isolated from different hosts or geographic regions substantially contrasts with the data for other clinically relevant spirochetes.

IMPORTANCE
The recent expansion of the host range of digital dermatitis (DD) treponemes from cattle to sheep, goats, pigs, and wild elk, coupled with the high level of 16S rRNA gene sequence similarity across hosts and with human treponemes, suggests that the same bacterial species can cause disease in multiple different hosts. This multilocus sequence typing (MLST) study further demonstrates that these bacteria isolated from different hosts are indeed very similar, raising the potential for cross-species transmission. The study also shows that infection spread occurs frequently, both locally and globally, suggesting transmission by routes other than animal-animal transmission alone. These results indicate that on-farm biosecurity is important for controlling disease spread in domesticated species. Continued surveillance and vigilance are important for ascertaining the evolution and tracking any further host range expansion of these important pathogens.
Novel
P450nor
Gene Detection Assay Used To Characterize the Prevalence and Diversity of Soil Fungal Denitrifiers
Authors: Novinscak Amy , Goyer Claudia , Zebarth Bernie J. , Burton David L. , Chantigny Martin H. , Filion Martin 
Published: May 2016

ABSTRACT

Denitrifying fungi produce nitrous oxide (N
2
O), a potent greenhouse gas, as they generally lack the ability to convert N
2
O to dinitrogen. Contrary to the case for bacterial denitrifiers, the prevalence and diversity of denitrifying fungi found in the environment are not well characterized. In this study, denitrifying fungi were isolated from various soil ecosystems, and novel PCR primers targeting the
P450nor
gene, encoding the enzyme responsible for the conversion of nitric oxide to N
2
O, were developed, validated, and used to study the diversity of cultivable fungal denitrifiers. This PCR assay was also used to detect
P450nor
genes directly from environmental soil samples. Fungal denitrification capabilities were further validated using an N
2
O gas detection assay and a PCR assay targeting the
nirK
gene. A collection of 492 facultative anaerobic fungi was isolated from 15 soil ecosystems and taxonomically identified by sequencing the internal transcribed spacer sequence. Twenty-seven fungal denitrifiers belonging to 10 genera had the
P450nor
and the
nirK
genes and produced N
2
O from nitrite. N
2
O production is reported in strains not commonly known as denitrifiers, such as
Byssochlamys nivea
,
Volutella ciliata
,
Chloridium
spp., and
Trichocladium
spp. The prevalence of fungal denitrifiers did not follow a soil ecosystem distribution; however, a higher diversity was observed in compost and agricultural soils. The phylogenetic trees constructed using partial
P450nor
and
nirK
gene sequences revealed that both genes clustered taxonomically closely related strains together.

IMPORTANCE
A PCR assay targeting the
P450nor
gene involved in fungal denitrification was developed and validated. The newly developed
P450nor
primers were used on fungal DNA extracted from a collection of fungi isolated from various soil environments and on DNA directly extracted from soil. The results indicated that approximatively 25% of all isolated fungi possessed this gene and were able to convert nitrite to N
2
O. All soil samples from which denitrifying fungi were isolated also tested positive for the presence of
P450nor
. The
P450nor
gene detection assay was reliable in detecting a large diversity of fungal denitrifiers. Due to the lack of homology existing between
P450nor
and bacterial denitrification genes, it is expected that this assay will become a tool of choice for studying fungal denitrifiers.
Loss of SigB in Listeria monocytogenes Strains EGD-e and 10403S Confers Hyperresistance to Hydrogen Peroxide in Stationary Phase under Aerobic Conditions
Authors: Boura Marcia , Keating Ciara , Royet Kevin , Paudyal Ranju , O'Donoghue Beth , O'Byrne Conor P. , Karatzas Kimon A. G. 
Published: May 2016

ABSTRACT

SigB is the main stress gene regulator in
Listeria monocytogenes
affecting the expression of more than 150 genes and thus contributing to multiple-stress resistance. Despite its clear role in most stresses, its role in oxidative stress is uncertain, as results accompanying the loss of
sigB
range from hyperresistance to hypersensitivity. Previously, these differences have been attributed to strain variation. In this study, we show conclusively that unlike for all other stresses, loss of
sigB
results in hyperresistance to H
2
O
2
(more than 8 log CFU ml
−1
compared to the wild type) in aerobically grown stationary-phase cultures of
L. monocytogenes
strains 10403S and EGD-e. Furthermore, growth at 30°C resulted in higher resistance to oxidative stress than that at 37°C. Oxidative stress resistance seemed to be higher with higher levels of oxygen. Under anaerobic conditions, the loss of SigB in 10403S did not affect survival against H
2
O
2
, while in EGD-e, it resulted in a sensitive phenotype. During exponential phase, minor differences occurred, and this result was expected due to the absence of
sigB
transcription. Catalase tests were performed under all conditions, and stronger catalase results corresponded well with a higher survival rate, underpinning the important role of catalase in this phenotype. Furthermore, we assessed the catalase activity in protein lysates, which corresponded with the catalase tests and survival. In addition, reverse transcription-PCR (RT-PCR) showed no differences in transcription between the wild type and the Δ
sigB
mutant in various oxidative stress genes. Further investigation of the molecular mechanism behind this phenotype and its possible consequences for the overall phenotype of
L. monocytogenes
are under way.

IMPORTANCE
SigB is the most important stress gene regulator in
L. monocytogenes
and other Gram-positive bacteria. Its increased expression during stationary phase results in resistance to multiple stresses. However, despite its important role in general stress resistance, its expression is detrimental for the cell in the presence of oxidative stress, as it promotes hypersensitivity against hydrogen peroxide. This peculiar phenotype is an important element of the physiology of
L. monocytogenes
, and it might help us explain the behavior of this organism in environments where oxidative stress is present.
Stick-split mechanism for anthropogenic fluid-induced tensile rock failure
Authors: van der Baan Mirko , Eaton David W. , Preisig Giona 
Published: May 2016

Abstract
Fluids play a critical role in natural and human-induced rock failure. It is unclear, however, if propagation of a tensile fracture is inherently an episodic or continuous process. For example, typical average propagation speeds of hydraulic fracture tips on the order of 1–10 m/min suggest continuous crack growth, possibly at subcritical stress intensities. In contrast, using field observations and numerical and mathematical analyses, we show that fracture growth due to anthropogenic hydraulic fracturing is most likely to occur in an episodic fashion, characterized by stick-split behavior that is analogous to stick-slip motion of earthquakes. The stick-split mechanism is regulated by cyclic variations in fluid pressure near the crack tip, in which each successive failure produces a local pressure drop that temporarily halts or slows fracture propagation. A pressure drop results in partial fracture closure, producing noncontinuous fracture propagation through a process that is reminiscent of hand clapping. Rupture speeds for individual failure events are on the order of the shear-wave velocity of the medium; thus, continuous crack growth is not a likely mechanism for anthropogenic hydraulic fracturing treatments despite slow average tip propagation speeds.
‘The nice thing about doctors is that you can sometimes get a day off school’: an action research study to bring lived experiences from children, parents and hospice staff into medical students' preparation for practice
Authors: Spalding Jessica , Yardley Sarah 
Published: May 2016

Patient and public involvement in healthcare is important to ensure services meet their needs and priorities. Increasingly, patient experiences are being used to educate healthcare professionals. The potential contribution to medical education of children and parents using hospice services has not yet been fully explored.Objectives(1) To explore perceptions of what medical students must learn to become ‘good doctors’ among children, parents and staff in a hospice. (2) To collaborate with children/parents and staff to develop educational materials based on their lived experiences for medical students. (3) To assess feasibility of student-led action research in a children's hospice to develop research skills.MethodsProspective ethical approval received. Volunteer children (n=7), parents (n=5) and staff (n=6) were recruited from a children's hospice. Data were generated in audio-recorded semistructured focus groups, individual interviews and/or activity workshops. Participants discussed what newly qualified doctors’ needed to care for children with life-limiting conditions. Audio data were transcribed and combined with visual data for thematic analysis. Findings were refined by participant feedback. This paper presents thematic findings and educational material created from the project.ResultsThematic analysis identified six learning themes: (1) treat children as individuals; (2) act as a person before being a doctor; (3) interpersonal communication; (4) appreciate the clinical environment; (5) learn from children, parents and other staff; (6) how to be a doctor as part of a team. The student researcher successfully developed qualitative research skills, coproducing materials with participants for sharing learning derived from lived experiences.ConclusionsAll participants were willing and able to make valuable contributions, and believed that this was a worthwhile use of time and effort. Further work is required to understand how best to integrate the experiences of children in hospices into medical education.
Chronic vagal nerve stimulation prevents high-salt diet-induced endothelial dysfunction and aortic stiffening in stroke-prone spontaneously hypertensive rats
Authors: Chapleau Mark W. , Rotella Diane L. , Reho John J. , Rahmouni Kamal , Stauss Harald M. 
Published: May 2016

Parasympathetic activity is often reduced in hypertension and can elicit anti-inflammatory mechanisms. Thus we hypothesized that chronic vagal nerve stimulation (VNS) may alleviate cardiovascular end-organ damage in stroke-prone spontaneously hypertensive rats. Vagal nerve stimulators were implanted, a high-salt diet initiated, and the stimulators turned on (VNS, n = 10) or left off (sham, n = 14) for 4 wk. Arterial pressure increased equally in both groups. After 4 wk, endothelial function, assessed by in vivo imaging of the long posterior ciliary artery (LPCA) after stimulation (pilocarpine) and inhibition ( Nω-nitro-l-arginine methyl ester) of endothelial nitric oxide synthase (eNOS), had significantly declined (−2.3 ± 1.2 μm, P < 0.05) in sham, but was maintained (−0.7 ± 0.8 μm, nonsignificant) in VNS. Furthermore, aortic eNOS activation (phosphorylated to total eNOS protein content ratio) was greater in VNS (0.83 ± 0.07) than in sham (0.47 ± 0.08, P < 0.05). After only 3 wk, ultrasound imaging of the aorta demonstrated decreased aortic strain (−9.7 ± 2.2%, P < 0.05) and distensibility (−2.39 ± 0.49 1,000/mmHg, P < 0.05) and increased pulse-wave velocity (+2.4 ± 0.7 m/s, P < 0.05) in sham but not in VNS (−3.8 ± 3.8%, −0.70 ± 1.4 1,000/mmHg, and +0.1 ± 0.7 m/s, all nonsignificant). Interleukin (IL)-6 serum concentrations tended to be higher in VNS than in sham (34.3 ± 8.3 vs. 16.1 ± 4.6 pg/ml, P = 0.06), and positive correlations were found between NO-dependent relaxation of the LPCA and serum levels of IL-6 ( r = +0.70, P < 0.05) and IL-10 (r = +0.56, P < 0.05) and between aortic eNOS activation and IL-10 ( r = +0.48, P < 0.05). In conclusion, chronic VNS prevents hypertension-induced endothelial dysfunction and aortic stiffening in an animal model of severe hypertension. We speculate that anti-inflammatory mechanisms may contribute to these effects. Listen to this article's corresponding podcast at http://ajpheart.podbean.com/e/chronic-vagal-nerve-stimulation-in-stroke-prone-shr/ .
Upregulated Glucose Metabolism Correlates Inversely with CD8+ T-cell Infiltration and Survival in Squamous Cell Carcinoma
Authors: Ottensmeier Christian H. , Perry Kate L. , Harden Elena L. , Stasakova Jana , Jenei Veronika , Fleming Jason , Wood Oliver , Woo Jeongmin , Woelk Christopher H. , Thomas Gareth J. , Thirdborough Stephen M. 
Published: May 2016

Abstract
Antibodies that block T-cell–regulatory checkpoints have recently emerged as a transformative approach to cancer treatment. However, the clinical efficacy of checkpoint blockade depends upon inherent tumor immunogenicity, with variation in infiltrating T cells contributing to differences in objective response rates. Here, we sought to understand the molecular correlates of tumor-infiltrating T lymphocytes (TIL) in squamous cell carcinoma (SCC), using a systems biologic approach to integrate publicly available omics datasets with histopathologic features. We provide evidence that links TIL abundance and therapeutic outcome to the regulation of tumor glycolysis by EGFR and HIF, both of which are attractive molecular targets for use in combination with immunotherapeutics. Cancer Res; 76(14); 4136–48. ©2016 AACR.
Molecular Pathways: Targeting B7-H3 (CD276) for Human Cancer Immunotherapy
Authors: Picarda Elodie , Ohaegbulam Kim C. , Zang Xingxing 
Published: May 2016

Abstract
B7-H3 (CD276) is an important immune checkpoint member of the B7 and CD28 families. Induced on antigen-presenting cells, B7-H3 plays an important role in the inhibition of T-cell function. Importantly, B7-H3 is highly overexpressed on a wide range of human solid cancers and often correlates with both negative prognosis and poor clinical outcome in patients. Challenges remain to identify the receptor(s) of B7-H3 and thus better elucidate the role of the B7-H3 pathway in immune responses and tumor evasion. With a preferential expression on tumor cells, B7-H3 is an attractive target for cancer immunotherapy. Based on the clinical success of inhibitory immune checkpoint blockade (CTLA-4, PD-1, and PD-L1), mAbs against B7-H3 appear to be a promising therapeutic strategy worthy of development. An unconventional mAb against B7-H3 with antibody-dependent cell-mediated cytotoxicity is currently being evaluated in a phase I clinical trial and has shown encouraging preliminary results. Additional therapeutic approaches in targeting B7-H3, such as blocking mAbs, bispecific mAbs, chimeric antigen receptor T cells, small-molecule inhibitors, and combination therapies, should be evaluated, as these technologies have already shown positive results in various cancer settings. A better understanding of the B7-H3 pathway in humans will surely help to further optimize associated cancer immunotherapies. Clin Cancer Res; 22(14); 3425–31. ©2016 AACR.
Current and Emerging Clinical Applications of Multispectral Optoacoustic Tomography (MSOT) in Oncology
Authors: McNally Lacey R. , Mezera Megan , Morgan Desiree E. , Frederick Peter J. , Yang Eddy S. , Eltoum Isam-Eldin , Grizzle William E. 
Published: May 2016

Abstract
Accurate detection and characterization of cancers are key for providing timely intervention and effective treatments. Current imaging technologies are particularly limited when it comes to detecting very small tumors in vivo, i.e., very early cancers or metastases, differentiating viable tumor from surrounding dead tumor tissue, and evaluating tumor metabolism within tissue. Optoacoustic imaging offers potential solutions to these imaging problems because of its ability to image optical absorption properties of both intrinsic tissue chromophores and exogenous contrast agents without the involvement of ionizing radiation. Optoacoustic imaging uses pulsed laser to induce localized thermoelastic expansion that generates acoustic waves detectable by an ultrasound transducer. To date, multispectral optoacoustic tomography (MSOT) has primarily been used in preclinical research; however, its use in translational and clinical research is expanding. This review focuses on current and emerging applications of optoacoustic imaging for molecular imaging of cancer using both exogenous and endogenous contrast agents and sheds light on potential future clinical applications. Clin Cancer Res; 22(14); 3432–9. ©2016 AACR.
Pharmacological Inhibition of the Protein Kinase MRK/ZAK Radiosensitizes Medulloblastoma
Authors: Markowitz Daniel , Powell Caitlin , Tran Nhan L. , Berens Michael E. , Ryken Timothy C. , Vanan Magimairajan , Rosen Lisa , He Mingzhu , Sun Shan , Symons Marc , Al-Abed Yousef , Ruggieri Rosamaria 
Published: May 2016

Abstract
Medulloblastoma is a cerebellar tumor and the most common pediatric brain malignancy. Radiotherapy is part of the standard care for this tumor, but its effectiveness is accompanied by significant neurocognitive sequelae due to the deleterious effects of radiation on the developing brain. We have previously shown that the protein kinase MRK/ZAK protects tumor cells from radiation-induced cell death by regulating cell-cycle arrest after ionizing radiation. Here, we show that siRNA-mediated MRK depletion sensitizes medulloblastoma primary cells to radiation. We have, therefore, designed and tested a specific small molecule inhibitor of MRK, M443, which binds to MRK in an irreversible fashion and inhibits its activity. We found that M443 strongly radiosensitizes UW228 medulloblastoma cells as well as UI226 patient–derived primary cells, whereas it does not affect the response to radiation of normal brain cells. M443 also inhibits radiation-induced activation of both p38 and Chk2, two proteins that act downstream of MRK and are involved in DNA damage–induced cell-cycle arrest. Importantly, in an animal model of medulloblastoma that employs orthotopic implantation of primary patient–derived UI226 cells in nude mice, M443 in combination with radiation achieved a synergistic increase in survival. We hypothesize that combining radiotherapy with M443 will allow us to lower the radiation dose while maintaining therapeutic efficacy, thereby minimizing radiation-induced side effects. Mol Cancer Ther; 15(8); 1799–808. ©2016 AACR.
Derivation and Validation of a Modified Short Form of the Stroke Impact Scale
Authors: MacIsaac Rachael , Ali Myzoon , Peters Michele , English Coralie , Rodgers Helen , Jenkinson Crispin , Lees Kennedy R. , Quinn Terence J. ,   the VISTA Collaboration
Published: May 2016

Background

The Stroke Impact Scale (
SIS
) is a stroke‐specific, quality of life measure recommended for research and clinical practice. Completion rates are suboptimal and could relate to test burden. We derived and validated a short form SIS (SF‐SIS).

Methods and Results

We examined data from the Virtual International Stroke Trial Archive, generating derivation and validation populations. We derived an
SF
‐
SIS
by selecting 1 item per domain of
SIS
, choosing items most highly correlated with total domain score. Our validation described agreement of
SF
‐
SIS
with original
SIS
and the
SIS
‐16 and correlation with Barthel Index, modified Rankin Scale, National Institutes of Health Stroke Scale, and Euro‐QoL 5 dimensions visual analog scales. We assessed discriminative validity (associations between
SF
‐
SIS
and factors known to influence outcome [age, physiological parameters, and comorbidity]). We assessed face validity and acceptability by sharing the
SF
‐
SIS
with a focus group of stroke survivors and multidisciplinary stroke healthcare staff. From 5549 acute study patients (mean age 68.5 [
SD
13] years, mean
SIS
64 [
SD
32]) and 332 rehabilitation patients (mean age 65.7 [
SD
11] years, mean
SIS
61 [
SD
11]), we derived an 8‐item
SF
‐
SIS
that demonstrated good agreement with original
SIS
and good correlation with our chosen functional and quality of life measures (all ρ>0.70,
P
<0.0001). Significant associations were seen with our chosen predictors of stroke outcome in the acute group (
P
<0.0001). The focus group agreed with the choice of items for
SF
‐
SIS
across 7 of 8 domains
.

Conclusions

Using multiple, complementary methods, we have derived an SF‐
SIS
and demonstrated content, convergent, and discriminant validity. This shortened
SIS
should allow collection of robust quality of life data with less associated test burden.