bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved Draft Genome Sequence of a Monoteliosporic Culture of the Karnal Bunt (Tilletia indica) Pathogen of Wheat
Authors: Kumar Anil , Mishra Pallavi , Maurya Ranjeet , Mishra A. K. , Gupta Vijai K. , Ramteke Pramod W. , Marla Soma S. 
Published: May 2018

ABSTRACT

Karnal bunt of wheat is an internationally quarantined fungal pathogen disease caused by
Tilletia indica
and affects the international commercial seed trade of wheat. We announce here the first improved draft genome assembly of a monoteliosporic culture of the
Tilletia indica
fungus, consisting of 787 scaffolds with an approximate total genome size of 31.83 Mbp, which is more accurate and near to complete than the previous version.
Draft Genome Sequences of Two Chemosynthetic Arcobacter Strains Isolated from Hydraulically Fractured Wells in Marcellus and Utica Shales
Authors: Panescu Jenny , Daly Rebecca A. , Wrighton Kelly C. , Mouser Paula J. 
Published: May 2018

ABSTRACT

Genome sequences were obtained for two isolates of the genus
Arcobacter
from saline fluids produced from hydraulically fractured shale gas wells in the Marcellus and Utica formations. These genomes provide insight into microbial sulfur cycles occurring in a high-salt deep terrestrial shale environment.
Microbial Diversity in Commercial Bee Pollen from Europe, Chile, and Mexico, Based on 16S rRNA Gene Amplicon Metagenome Sequencing
Authors: Moreno Andrade Vicente D. , Saldaña Gutiérrez Carlos , Calvillo Medina Rosa P. , Cruz Hérnandez Andrés , Vázquez Cruz Moisés A. , Torres Ruíz Alfonso , Romero Gómez Sergio , Ramos López Miguel A. , Álvarez-Hidalgo Erika , López-Gaytan Silvia B. , Ramírez Natanahel Salvador , Jones George H. , Hernandez-Flores Jose Luis , Campos-Guillén Juan 
Published: May 2018

ABSTRACT
Bee pollen is a highly nutritive natural foodstuff. Because of its use as a comestible, the association of bacteria with bee pollen is commercially and biologically important. We report here the bacterial diversity of seven bee pollen samples (five from Europe, one from Chile, and one from Mexico) based on 16S rRNA gene amplicon metagenome sequencing.
Genome Sequences of 13 Isolates of Salmonella enterica Serovar Typhimurium var. Copenhagen Obtained from Wild Pigeons in Canada
Authors: Xie Bridget , Dupras Andrée Ann , Duceppe Marc-Olivier , Fattahi-Ghazi Nooshin , Goodridge Lawrence , Ogunremi Dele 
Published: May 2018

ABSTRACT

Pigeon-adapted strains of
Salmonella enterica
serovar Typhimurium var. Copenhagen phage types 2 and 99 obtained from the provinces of Alberta, British Columbia, and Ontario, Canada, were analyzed using whole-genome sequencing. All isolates contained the
Salmonella
virulence plasmid despite the low pathogenicity of this lineage in their avian host.
Complete Genome Sequence of Celeribacter baekdonensis Strain LH4, a Thiosulfate-Oxidizing Alphaproteobacterial Isolate from Gulf of Mexico Continental Slope Sediments
Authors: Flood Beverly E. , Leprich Dalton , Bailey Jake V. 
Published: May 2018

ABSTRACT

We report here the closed genome sequences of
Celeribacter baekdonensis
strain LH4 and five unnamed plasmids obtained through PacBio sequencing with 99.99% consensus concordance. The genomes contained several distinctive features not found in other published
Celeribacter
genomes, including the potential to aerobically degrade styrene and other phenolic compounds.
Draft Genome Sequence of New Vancomycin-Resistant Enterococcus faecium Sequence Type 1421
Authors: Leong Kelvin W. C. , Cooley Louise A. , O’Toole Ronan F. 
Published: May 2018

ABSTRACT

The spread of vancomycin-resistant
Enterococcus faecium
(VREfm) has become a challenge to health care infection control worldwide. In 2015, a marked increase in VREfm isolation was detected in acute public hospitals in Tasmania. We report here the draft whole-genome sequence of a newly designated VREfm sequence type, sequence type 1421 (ST1421).
Draft Genome Sequence of Streptococcus suis Strain SsRC-1, a Human Isolate from a Fatal Case of Toxic Shock Syndrome
Authors: Fillo Silvia , Mancini Fabiola , Anselmo Anna , Fortunato Antonella , Rezza Giovanni , Lista Florigio , Ciervo Alessandra 
Published: May 2018

ABSTRACT

Streptococcus suis
is an economically important pathogen in the pig industry and is also an emerging zoonotic agent responsible for severe infections in humans. Here, we report the genome sequence of
S. suis
strain SsRC-1. Specifically, this strain was a serotype 2 and was isolated from a human fatal case of toxic shock syndrome (TSS) in Italy.
End-tidal carbon dioxide output in manual cardiopulmonary resuscitation versus active compression-decompression device during prehospital quality controlled resuscitation: a case series study
Authors: Setälä Piritta Anniina , Virkkunen Ilkka Tapani , Kämäräinen Antti Jaakko , Huhtala Heini Sisko Annamari , Virta Janne Severi , Yli-Hankala Arvi Mikael , Hoppu Sanna Elisa 
Published: May 2018

BackgroundActive compression–decompression (ACD) devices have enhanced end-tidal carbon dioxide (ETCO2) output in experimental cardiopulmonary resuscitation (CPR) studies. However, the results in out-of-hospital cardiac arrest (OHCA) patients have shown inconsistent outcomes, and earlier studies lacked quality control of CPR attempts. We compared manual CPR with ACD-CPR by measuring ETCO2output using an audiovisual feedback defibrillator to ensure continuous high quality resuscitation attempts.Methods10 witnessed OHCAs were resuscitated, rotating a 2 min cycle with manual CPR and a 2 min cycle of ACD-CPR. Patients were intubated and the ventilation rate was held constant during CPR. CPR quality parameters and ETCO2values were collected continuously with the defibrillator. Differences in ETCO2output between manual CPR and ACD-CPR were analysed using a linear mixed model where ETCO2output produced by a summary of the 2 min cycles was included as the dependent variable, the patient as a random factor and method as a fixed effect. These comparisons were made within each OHCA case to minimise confounding factors between the cases.ResultsMean length of the CPR episodes was 37 (SD 8) min. Mean compression depth was 76 (SD 1.3) mm versus 71 (SD1.0) mm, and mean compression rate was 100 per min (SD 6.7) versus 105 per min (SD 4.9) between ACD-CPR and manual CPR, respectively. For ETCO2output, the interaction between the method and the patient was significant (P<0.001). ETCO2output was higher with manual CPR in 6 of the 10 cases.ConclusionsThis study suggests that quality controlled ACD-CPR is not superior to quality controlled manual CPR when ETCO2is used as a quantitative measure of CPR effectiveness.Trial registration numberNCT00951704; Results.
A multicolour flow cytometric assay for c-MYC protein in B-cell lymphoma
Authors: Alayed Khaled , Schweitzer Karen , Awadallah Amad , Shetty Shashirekha , Turakhia Samir , Meyerson Howard 
Published: May 2018

AimDevelop an objective assay to detect c-MYC protein expression using multiparametric flow cytometry (FCM) as an alternative to immunohistochemistry (IHC).Methods57 patient samples and 11 cell line samples were evaluated. Cell suspensions were obtained and c-MYC staining was performed in combination with CD45 and CD19 and, in some samples, CD10. The percentage of c-MYC+ cells by FCM was correlated with the percentage determined by IHC. The relationship between c-MYC protein expression and the presence of ac-MYCgene rearrangement in aggressive and high-grade lymphomas was also assessed.Resultsc-MYC expression by FCM and IHC demonstrated a high degree of correlation in a training set of 33 patient cases, r=0.92, 11 cell line samples, r=0.81 and in a validation set of 24 aggressive and high-grade B-cell lymphomas, r=0.85.c-MYCgene was rearranged by fluorescence in situ hybridisation in 6/9 samples with high c-MYC expression (>40%) by FCM and 6/14 by IHC.ConclusionsWe have developed a reliable multicolour FCM assay to detect c-MYC expression suitable for clinical laboratories that should be helpful to accurately quantify c-MYC expression in B-cell lymphomas.
Deep crustal architecture of the Parnaíba basin of NE Brazil from receiver function analysis: implications for basin subsidence
Authors: Coelho Diogo L. O. , Julià Jordi , Rodríguez-Tribaldos Verónica , White Nicholas 
Published: May 2018

Abstract

We investigated the crustal architecture of the Parnaíba basin of NE Brazil by analysing receiver functions along a
c.
600 km long transect crossing the central portion of the basin. The transect consisted of nine broadband stations interspaced at
c.
70 km distance recording continuously for a period of 15 months, with the goal of improving our understanding of the origin and evolution of this large cratonic basin. Our results show that crustal thickness varies between 39 and 45 km along the transect, gradually thickening towards the depocentre, and that bulk
V
p
/
V
s
ratios vary between 1.70 and 1.78. The crust can be divided into a 2.0–3.5 km thick layer of low-velocity sediments, a 15–20 km thick upper crust (3.5 <
V
s
< 3.6 km s
−1
) and a 18–22 km thick lower crust (3.7 <
V
s
< 3.8 km s
−1
). Near the depocentre, where the crust is thickest, the bottom 10–12 km of the crust are characterized by fast S-velocities (4.0–4.2 km s
−1
). Our findings confirm that stretching of the lithosphere is minimal and compatible with flexural subsidence. However, loading from a thick, high-density layer of mafic intrusive rocks pervading the lower crust – as recently proposed for the basin – is found to be inconsistent with our bulk
V
p
/
V
s
ratios and lower crustal S-velocities. Flexural bending by a deeper load, perhaps related to deep mantle convection, seems more plausible.
Local cortical activity of distant brain areas can phase-lock to the olfactory bulb’s respiratory rhythm in the freely behaving rat
Authors: Rojas-Líbano Daniel , Wimmer del Solar Jonathan , Aguilar-Rivera Marcelo , Montefusco-Siegmund Rodrigo , Maldonado Pedro E. 
Published: May 2018

An important unresolved question about neural processing is the mechanism by which distant brain areas coordinate their activities and relate their local processing to global neural events. A potential candidate for the local-global integration are slow rhythms such as respiration. In this study, we asked if there are modulations of local cortical processing that are phase-locked to (peripheral) sensory-motor exploratory rhythms. We studied rats on an elevated platform where they would spontaneously display exploratory and rest behaviors. Concurrent with behavior, we monitored whisking through electromyography and the respiratory rhythm from the olfactory bulb (OB) local field potential (LFP). We also recorded LFPs from dorsal hippocampus, primary motor cortex, primary somatosensory cortex, and primary visual cortex. We defined exploration as simultaneous whisking and sniffing above 5 Hz and found that this activity peaked at ~8 Hz. We considered rest as the absence of whisking and sniffing, and in this case, respiration occurred at ~3 Hz. We found a consistent shift across all areas toward these rhythm peaks accompanying behavioral changes. We also found, across areas, that LFP gamma (70–100 Hz) amplitude could phase-lock to the animal’s OB respiratory rhythm, a finding indicative of respiration-locked changes in local processing. In a subset of animals, we also recorded the hippocampal theta activity and found that occurred at frequencies overlapped with respiration but was not spectrally coherent with it, suggesting a different oscillator. Our results are consistent with the notion of respiration as a binder or integrator of activity between brain regions. NEW & NOTEWORTHY In freely behaving rats, we found that local cortical activity within distant brain areas can phase-lock to the respiratory rhythm, more prominently during exploratory behavior than during basal respiration conditions. The findings suggest that the respiration rhythm can provide a common neural clock to integrate activity across brain areas. Our methodology also shows that the animal’s internal rhythms can be used as a reference time frame to analyze physiological activity in free behavior conditions.
Distinct mechanisms explain the control of reach speed planning: evidence from a race model framework
Authors: Venkataratamani Prasanna Venkhatesh , Murthy Aditya 
Published: May 2018

Previous studies have investigated the computational architecture underlying the voluntary control of reach movements that demands a change in position or direction of movement planning. Here we used a novel task in which subjects had to either increase or decrease the movement speed according to a change in target color that occurred randomly during a trial. The applicability of different race models to such a speed redirect task was assessed. We found that the predictions of an independent race model that instantiated an abort-and-replan strategy was consistent with all aspects of performance in the fast-to-slow speed condition. The results from modeling indicated a peculiar asymmetry, in that although the fast-to-slow speed change required inhibition, none of the standard race models was able to explain how movements changed from slow to fast speeds. Interestingly, a weighted averaging model that simulated the gradual merging of two kinematic plans explained behavior in the slow-to-fast speed task. In summary, our work shows how a race model framework can provide an understanding of how the brain controls different aspects of reach movement planning and help distinguish between an abort-and-replan strategy and merging of plans.NEW & NOTEWORTHY For the first time, a race model framework was used to understand how reach speeds are modified. We provide evidence that a fast-to-slow speed change required aborting the current plan and a complete respecification of a new plan, while none of the race models was able to explain an instructed increase of hand movement speed, which was instead accomplished by a merging of a new kinematic plan with the existing kinematic plan.
Force feedback delay affects perception of stiffness but not action, and the effect depends on the hand used but not on the handedness
Authors: Leib Raz , Rubin Inbar , Nisky Ilana 
Published: May 2018

Interaction with an object often requires the estimation of its mechanical properties. We examined whether the hand that is used to interact with the object and their handedness affected people’s estimation of these properties using stiffness estimation as a test case. We recorded participants’ responses on a stiffness discrimination of a virtual elastic force field and the grip force applied on the robotic device during the interaction. In half of the trials, the robotic device delayed the participants’ force feedback. Consistent with previous studies, delayed force feedback biased the perceived stiffness of the force field. Interestingly, in both left-handed and right-handed participants, for the delayed force field, there was even less perceived stiffness when participants used their left hand than their right hand. This result supports the idea that haptic processing is affected by laterality in the brain, not by handedness. Consistent with previous studies, participants adjusted their applied grip force according to the correct size and timing of the load force regardless of the hand that was used, the handedness, or the delay. This suggests that in all of these conditions, participants were able to form an accurate internal representation of the anticipated trajectory of the load force (size and timing) and that this representation was used for accurate control of grip force independently of the perceptual bias. Thus these results provide additional evidence for the dissociation between action and perception in the processing of delayed information. NEW & NOTEWORTHY Introducing delay to force feedback during interaction with an elastic force field biases the perceived stiffness of the force field. We show that this bias depends on the hand that was used for probing but not on handedness. At the same time, both left-handed and right-handed participants adjusted their applied grip force while using either their left or right hands in anticipation of the correct magnitude and timing despite the delay in load force.
Cancer-Associated Fibroblasts Drive Glycolysis in a Targetable Signaling Loop Implicated in Head and Neck Squamous Cell Carcinoma Progression
Authors: Kumar Dhruv , New Jacob , Vishwakarma Vikalp , Joshi Radhika , Enders Jonathan , Lin Fangchen , Dasari Sumana , Gutierrez Wade R. , Leef George , Ponnurangam Sivapriya , Chavan Hemantkumar , Ganaden Lydia , Thornton Mackenzie M. , Dai Hongying , Tawfik Ossama , Straub Jeffrey , Shnayder Yelizaveta , Kakarala Kiran , Tsue Terance Ted , Girod Douglas A. , Van Houten Bennett , Anant Shrikant , Krishnamurthy Partha , Thomas Sufi Mary 
Published: May 2018

Abstract
Despite aggressive therapies, head and neck squamous cell carcinoma (HNSCC) is associated with a less than 50% 5-year survival rate. Late-stage HNSCC frequently consists of up to 80% cancer-associated fibroblasts (CAF). We previously reported that CAF-secreted HGF facilitates HNSCC progression; however, very little is known about the role of CAFs in HNSCC metabolism. Here, we demonstrate that CAF-secreted HGF increases extracellular lactate levels in HNSCC via upregulation of glycolysis. CAF-secreted HGF induced basic FGF (bFGF) secretion from HNSCC. CAFs were more efficient than HNSCC in using lactate as a carbon source. HNSCC-secreted bFGF increased mitochondrial oxidative phosphorylation and HGF secretion from CAFs. Combined inhibition of c-Met and FGFR significantly inhibited CAF-induced HNSCC growth in vitro and in vivo (P &lt; 0.001). Our cumulative findings underscore reciprocal signaling between CAF and HNSCC involving bFGF and HGF. This contributes to metabolic symbiosis and a targetable therapeutic axis involving c-Met and FGFR.
Significance: HNSCC cancer cells and CAFs have a metabolic relationship where CAFs secrete HGF to induce a glycolytic switch in HNSCC cells and HNSCC cells secrete bFGF to promote lactate consumption by CAFs. Cancer Res; 78(14); 3769–82. ©2018 AACR.
An In Vivo Screen Identifies PYGO2 as a Driver for Metastatic Prostate Cancer
Authors: Lu Xin , Pan Xiaolu , Wu Chang-Jiun , Zhao Di , Feng Shan , Zang Yong , Lee Rumi , Khadka Sunada , Amin Samirkumar B. , Jin Eun-Jung , Shang Xiaoying , Deng Pingna , Luo Yanting , Morgenlander William R. , Weinrich Jacqueline , Lu Xuemin , Jiang Shan , Chang Qing , Navone Nora M. , Troncoso Patricia , DePinho Ronald A. , Wang Y. Alan 
Published: May 2018

Abstract
Advanced prostate cancer displays conspicuous chromosomal instability and rampant copy number aberrations, yet the identity of functional drivers resident in many amplicons remain elusive. Here, we implemented a functional genomics approach to identify new oncogenes involved in prostate cancer progression. Through integrated analyses of focal amplicons in large prostate cancer genomic and transcriptomic datasets as well as genes upregulated in metastasis, 276 putative oncogenes were enlisted into an in vivo gain-of-function tumorigenesis screen. Among the top positive hits, we conducted an in-depth functional analysis on Pygopus family PHD finger 2 (PYGO2), located in the amplicon at 1q21.3. PYGO2 overexpression enhances primary tumor growth and local invasion to draining lymph nodes. Conversely, PYGO2 depletion inhibits prostate cancer cell invasion in vitro and progression of primary tumor and metastasis in vivo. In clinical samples, PYGO2 upregulation associated with higher Gleason score and metastasis to lymph nodes and bone. Silencing PYGO2 expression in patient-derived xenograft models impairs tumor progression. Finally, PYGO2 is necessary to enhance the transcriptional activation in response to ligand-induced Wnt/β-catenin signaling. Together, our results indicate that PYGO2 functions as a driver oncogene in the 1q21.3 amplicon and may serve as a potential prognostic biomarker and therapeutic target for metastatic prostate cancer.
Significance: Amplification/overexpression of PYGO2 may serve as a biomarker for prostate cancer progression and metastasis. Cancer Res; 78(14); 3823–33. ©2018 AACR.
Metabolic Imaging of the Human Brain with Hyperpolarized 13C Pyruvate Demonstrates 13C Lactate Production in Brain Tumor Patients
Authors: Miloushev Vesselin Z. , Granlund Kristin L. , Boltyanskiy Rostislav , Lyashchenko Serge K. , DeAngelis Lisa M. , Mellinghoff Ingo K. , Brennan Cameron W. , Tabar Vivian , Yang T. Jonathan , Holodny Andrei I. , Sosa Ramon E. , Guo YanWei W. , Chen Albert P. , Tropp James , Robb Fraser , Keshari Kayvan R. 
Published: May 2018

Abstract
Hyperpolarized (HP) MRI using [1-13C] pyruvate is a novel method that can characterize energy metabolism in the human brain and brain tumors. Here, we present the first dynamically acquired human brain HP 13C metabolic spectra and spatial metabolite maps in cases of both untreated and recurrent tumors. In vivo production of HP lactate from HP pyruvate by tumors was indicative of altered cancer metabolism, whereas production of HP lactate in the entire brain was likely due to baseline metabolism. We correlated our results with standard clinical brain MRI, MRI DCE perfusion, and in one case FDG PET/CT. Our results suggest that HP 13C pyruvate-to-lactate conversion may be a viable metabolic biomarker for assessing tumor response.
Significance: Hyperpolarized pyruvate MRI enables metabolic imaging in the brain and can be a quantitative biomarker for active tumors.
Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/78/14/3755/F1.large.jpg. Cancer Res; 78(14); 3755–60. ©2018 AACR.
Tumor-Infiltrating Lymphocytes and Colorectal Cancer Survival in African American and Caucasian Patients
Authors: Wallace Kristin , Lewin David N. , Sun Shaoli , Spiceland Clayton M. , Rockey Don C. , Alekseyenko Alexander V. , Wu Jennifer D. , Baron John A. , Alberg Anthony J. , Hill Elizabeth G. 
Published: May 2018

Abstract
Background: Compared with Caucasian Americans (CAs), African Americans (AAs) with colorectal cancer have poorer survival, especially younger-age patients. A robust lymphocytic reaction within colorectal cancers is strongly associated with better survival, but whether immune response impacts the disparity in colorectal cancer survival is unknown.
Methods: The study population was comprised of 211 histologically confirmed colorectal cancers at the Medical University of South Carolina (Charleston, SC; 159 CAs and 52 AAs) diagnosed between Jan 01, 2000, and June 30, 2013. We constructed a lymphocyte score based on blinded pathologic assessment of the four different types of lymphocytic reactions. Cox proportional hazards regression was used to evaluate the association between the lymphocyte score and risk of death by race.
Results: Colorectal cancers in AAs (vs. CAs) had a stronger lymphocytic reaction at diagnosis. A high lymphocyte score (vs. the lowest) was associated with better survival in AAs [HR 0.19; 95% confidence interval (CI), 0.04–0.99] and CAs (HR 0.47; 95% CI, 0.15–1.45). AAs with no lymphocytic reaction (vs. other categories) had poor survival HR 4.48 (1.58–12.7) whereas no difference was observed in CAs. The risk of death in AAs (vs. CA) was more pronounced in younger patients (HR 2.92; 95% CI, 1.18–7.22) compared with older (HR 1.20; 95% CI, 0.54–2.67), especially those with lymphocytic poor colorectal cancers.
Conclusions: The lymphocytic reaction in tumor impacted the racial disparity in survival.
Impact: Our results confirm the importance of the lymphocytic score on survival and highlight the need to fully characterize the immune environment of colorectal cancers by race. Cancer Epidemiol Biomarkers Prev; 27(7); 755–61. ©2018 AACR.