bluuebunny/crossref_metadata_2025_split huggingface dataset:
RivR Is a Negative Regulator of Virulence Factor Expression in Group A Streptococcus
Authors: Treviño Jeanette , Liu Zhuyun , Cao Tram N. , Ramirez-Peña Esmeralda , Sumby Paul 
Published: November 2012

ABSTRACTThe bacterial pathogen group AStreptococcus(GAS) causes human diseases ranging from self-limiting pharyngitis (also known as strep throat) to severely invasive necrotizing fasciitis (also known as the flesh-eating syndrome). To control virulence factor expression, GAS utilizes both protein- and RNA-based mechanisms of regulation. Here we report that the transcription factor RivR (RofA-like protein IV) negatively regulates the abundance of mRNAs encoding the hyaluronic acid capsule biosynthesis proteins (hasABC; ∼7-fold) and the protein G-related α2-macroglobulin-binding protein (grab; ∼29-fold). Our data differ significantly from those of a previous study of the RivR regulon. Given thatgrabandhasABCare also negatively regulated by the two-component system CovR/S (controlofvirulence), we tested whether RivR functions through CovR/S. A comparison ofrivandcovsingle and double mutant strains showed that RivR requires CovR activity forgrabandhasABCregulation. Analysis of the upstream region ofrivRidentified a novel promoter the deletion of which reducedrivRmRNA abundance by 70%. ArivRmutant strain had a reduced ability to adhere to human keratinocytes relative to that of the parental and complemented strains, a phenotype that was abolished upon GAS pretreatment with hyaluronidase, highlighting the importance of capsule regulation by RivR during colonization. TherivRmutant strain was also attenuated for virulence in a murine model of bacteremia infection. Thus, we identify RivR as an important regulator of GAS virulence and provide new insight into the regulatory networks controlling virulence factor production in this pathogen.
Assessment of knowledge and attitudes regarding automated external defibrillators and cardiopulmonary resuscitation among American University students
Authors: Bogle Brittany , Mehrotra Sanjay , Chiampas George , Aldeen Amer Z 
Published: November 2012

AimWe sought to quantify knowledge and attitudes regarding automated external defibrillators (AEDs) and cardiopulmonary resuscitation (CPR) among university students. We also aimed to determine awareness of the location of an actual AED on campus.MethodsWe performed an online survey of undergraduate and graduate students at a mid-sized, private university that has 37 AEDs located throughout its two campuses.Results267 students responded to the survey. Almost all respondents could identify CPR (98.5%) and an AED (88.4%) from images, but only 46.1% and 18.4%, respectively, could indicate the basic mechanism of CPR and AEDs. About a quarter (28.1%) of respondents were comfortable using an AED without assistance, compared with 65.5% when offered assistance. Of those who did not feel comfortable, 87.7% indicated that they were ‘afraid of doing something wrong.’ One out of 6 (17.6%) respondents knew that a student centre had an AED, and only 2% could recall its precise location within the building. Most (66.3%) respondents indicated they would look for an AED near fire extinguishers, followed by the entrance of a building (19.6%).ConclusionsThis study found that most students at an American university can identify CPR and AEDs, but do not understand their basic mechanisms of action or are willing to perform CPR or use AEDs unassisted. Recent CPR/AED training and 9-1-1 assistance increases comfort. The most common fear reported was incorrect CPR or AED use. Almost all students could not recall where an AED was located in a student centre.
miRNA-34b Inhibits Prostate Cancer through Demethylation, Active Chromatin Modifications, and AKT Pathways
Authors: Majid Shahana , Dar Altaf A. , Saini Sharanjot , Shahryari Varahram , Arora Sumit , Zaman Mohd Saif , Chang Inik , Yamamura Soichiro , Tanaka Yuichiro , Chiyomaru Takeshi , Deng Guoren , Dahiya Rajvir 
Published: November 2012

AbstractPurpose: miRNAs can act as oncomirs or tumor-suppressor miRs in cancer. This study was undertaken to investigate the status and role of miR-34b in prostate cancer.Experimental Design: Profiling of miR-34b was carried out in human prostate cancer cell lines and clinical samples by quantitative real-time PCR and in situ hybridization. Statistical analyses were done to assess diagnostic/prognostic potential. Biological significance was elucidated by carrying out a series of experiments in vitro and in vivo.Results: We report that miR-34b is silenced in human prostate cancer and the mechanism is through CpG hypermethylation. miR-34b directly targeted methyltransferases and deacetylases resulting in a positive feedback loop inducing partial demethylation and active chromatin modifications. miR-34b expression could predict overall and recurrence-free survival such that patients with high miR-34b levels had longer survival. Functionally, miR-34b inhibited cell proliferation, colony formation, migration/invasion, and triggered G0/G1 cell-cycle arrest and apoptosis by directly targeting the Akt and its downstream proliferative genes. miR-34b caused a decline in the mesenchymal markers vimentin, ZO1, N-cadherin, and Snail with an increase in E-cadherin expression, thus inhibiting epithelial-to-mesenchymal transition. Finally we showed the antitumor effect of miR-34b in vivo. MiR-34b caused a dramatic decrease in tumor growth in nude mice compared with cont-miR.Conclusion: These findings offer new insight into the role of miR-34b in the inhibition of prostate cancer through demethylation, active chromatin modification, and Akt pathways and may provide a rationale for the development of new strategies targeting epigenetic regulation of miRNAs for the treatment of prostate cancer. Clin Cancer Res; 19(1); 73–84. ©2012 AACR.
Impact of a High Loading Dose of Atorvastatin on Contrast-Induced Acute Kidney Injury
Authors: Quintavalle Cristina , Fiore Danilo , De Micco Francesca , Visconti Gabriella , Focaccio Amelia , Golia Bruno , Ricciardelli Bruno , Donnarumma Elvira , Bianco Antonio , Zabatta Maria Assunta , Troncone Giancarlo , Colombo Antonio , Briguori Carlo , Condorelli Gerolama 
Published: November 2012

Background—
The role of statins in the prevention of contrast-induced acute kidney injury (CIAKI) is controversial.

Methods and Results—

First, we investigated the in vivo effects of atorvastatin on CIAKI. Patients with chronic kidney disease enrolled in the Novel Approaches for Preventing or Limiting Events (NAPLES) II trial were randomly assigned to (1) the atorvastatin group (80 mg within 24 hours before contrast media [CM] exposure; n=202) or (2) the control group (n=208). All patients received a high dose of
N
-acetylcysteine and sodium bicarbonate solution. Second, we investigated the in vitro effects of atorvastatin pretreatment on CM-mediated modifications of intracellular pathways leading to apoptosis or survival in renal tubular cells. CIAKI (ie, an increase >10% of serum cystatin C concentration within 24 hours after CM exposure) occurred in 9 of 202 patients in the atorvastatin group (4.5%) and in 37 of 208 patients in the control group (17.8%) (
P
=0.005; odds ratio=0.22; 95% confidence interval, 0.07–0.69). CIAKI rate was lower in the atorvastatin group in both diabetics and nondiabetics and in patients with moderate chronic kidney disease (estimated glomerular filtration rate, 31–60 mL/min per 1.73 m
2
). In the in vitro model, pretreatment with atorvastatin (1) prevented CM-induced renal cell apoptosis by reducing stress kinases activation and (2) restored the survival signals (mediated by Akt and ERK pathways).

Conclusions—
A single high loading dose of atorvastatin administered within 24 hours before CM exposure is effective in reducing the rate of CIAKI. This beneficial effect is observed only in patients at low to medium risk.
Parsing Models for Identifying Multiword Expressions
Authors: Green Spence , de Marneffe Marie-Catherine , Manning Christopher D. 
Published: November 2012

Multiword expressions lie at the syntax/semantics interface and have motivated alternative theories of syntax like Construction Grammar. Until now, however, syntactic analysis and multiword expression identification have been modeled separately in natural language processing. We develop two structured prediction models for joint parsing and multiword expression identification. The first is based on context-free grammars and the second uses tree substitution grammars, a formalism that can store larger syntactic fragments. Our experiments show that both models can identify multiword expressions with much higher accuracy than a state-of-the-art system based on word co-occurrence statistics. We experiment with Arabic and French, which both have pervasive multiword expressions. Relative to English, they also have richer morphology, which induces lexical sparsity in finite corpora. To combat this sparsity, we develop a simple factored lexical representation for the context-free parsing model. Morphological analyses are automatically transformed into rich feature tags that are scored jointly with lexical items. This technique, which we call a factored lexicon, improves both standard parsing and multiword expression identification accuracy.
Stochastic Optimal Control as a Theory of Brain-Machine Interface Operation
Authors: Lagang Manuel , Srinivasan Lakshminarayan 
Published: November 2012

The closed-loop operation of brain-machine interfaces (BMI) provides a framework to study the mechanisms behind neural control through a restricted output channel, with emerging clinical applications to stroke, degenerative disease, and trauma. Despite significant empirically driven improvements in closed-loop BMI systems, a fundamental, experimentally validated theory of closed-loop BMI operation is lacking. Here we propose a compact model based on stochastic optimal control to describe the brain in skillfully operating canonical decoding algorithms. The model produces goal-directed BMI movements with sensory feedback and intrinsically noisy neural output signals. Various experimentally validated phenomena emerge naturally from this model, including performance deterioration with bin width, compensation of biased decoders, and shifts in tuning curves between arm control and BMI control. Analysis of the model provides insight into possible mechanisms underlying these behaviors, with testable predictions. Spike binning may erode performance in part from intrinsic control-dependent constraints, regardless of decoding accuracy. In compensating decoder bias, the brain may incur an energetic cost associated with action potential production. Tuning curve shifts, seen after the mastery of a BMI-based skill, may reflect the brain's implementation of a new closed-loop control policy. The direction and magnitude of tuning curve shifts may be altered by decoder structure, ensemble size, and the costs of closed-loop control. Looking forward, the model provides a framework for the design and simulated testing of an emerging class of BMI algorithms that seek to directly exploit the presence of a human in the loop.
Arctic Cloud Characteristics as Derived from MODIS, CALIPSO, and CloudSat
Authors: Chan Mark Aaron , Comiso Josefino C. 
Published: November 2012

Abstract
The Moderate Resolution Imaging Spectroradiometer (MODIS), Cloud–Aerosol Lidar with Orthogonal Polarization (CALIOP), and CloudSat Cloud Profiling Radar (CPR) set of sensors, all in the Afternoon Constellation (A-Train), has been regarded as among the most powerful tools for characterizing the cloud cover. While providing good complementary information, the authors also observed that, at least for the Arctic region, the different sensors provide significantly different statistics about cloud cover characteristics. Data in 2007 and 2010 were analyzed, and the annual averages of cloud cover in the Arctic region were found to be 66.8%, 78.4%, and 63.3% as derived from MODIS, CALIOP, and CPR, respectively. A large disagreement between MODIS and CALIOP over sea ice and Greenland is observed, with a cloud percentage difference of 30.9% and 31.5%, respectively. In the entire Arctic, the average disagreement between MODIS and CALIOP increased from 13.1% during daytime to 26.7% during nighttime. Furthermore, the MODIS cloud mask accuracy has a high seasonal dependence, in that MODIS–CALIOP disagreement is the lowest during summertime at 10.7% and worst during winter at 28.0%. During nighttime the magnitude of the bias is higher because cloud detection is limited to the use of infrared bands. The clouds not detected by MODIS are typically low-level (top height &lt;2 km) and high-level clouds (top height &gt;6 km) and, especially, those that are geometrically thin (&lt;2 km). Geometrically thin clouds (&lt;2 km) accounted for about 95.5% of all clouds that CPR misses. As reported in a similar study, very low and thin clouds (&lt;0.3 km) over sea ice that are detected by MODIS are sometimes not observed by CPR and misclassified by CALIOP.
Improving accuracy for cancer classification with a new algorithm for genes selection
Authors: Zhang Hongyan , Wang Haiyan , Dai Zhijun , Chen Ming-shun , Yuan Zheming 
Published: November 2012

Abstract

Background
Even though the classification of cancer tissue samples based on gene expression data has advanced considerably in recent years, it faces great challenges to improve accuracy. One of the challenges is to establish an effective method that can select a parsimonious set of relevant genes. So far, most methods for gene selection in literature focus on screening individual or pairs of genes without considering the possible interactions among genes. Here we introduce a new computational method named the Binary Matrix Shuffling Filter (BMSF). It not only overcomes the difficulty associated with the search schemes of traditional wrapper methods and overfitting problem in large dimensional search space but also takes potential gene interactions into account during gene selection. This method, coupled with Support Vector Machine (SVM) for implementation, often selects very small number of genes for easy model interpretability.

Results
We applied our method to 9 two-class gene expression datasets involving human cancers. During the gene selection process, the set of genes to be kept in the model was recursively refined and repeatedly updated according to the effect of a given gene on the contributions of other genes in reference to their usefulness in cancer classification. The small number of informative genes selected from each dataset leads to significantly improved leave-one-out (LOOCV) classification accuracy across all 9 datasets for multiple classifiers. Our method also exhibits broad generalization in the genes selected since multiple commonly used classifiers achieved either equivalent or much higher LOOCV accuracy than those reported in literature.

Conclusions
Evaluation of a gene’s contribution to binary cancer classification is better to be considered after adjusting for the joint effect of a large number of other genes. A computationally efficient search scheme was provided to perform effective search in the extensive feature space that includes possible interactions of many genes. Performance of the algorithm applied to 9 datasets suggests that it is possible to improve the accuracy of cancer classification by a big margin when joint effects of many genes are considered.
A method for high throughput determination of viable bacteria cell counts in 96-well plates
Authors: Hazan Ronen , Que Yok-Ai , Maura Damien , Rahme Laurence G 
Published: November 2012

Abstract

Background
There are several methods for quantitating bacterial cells, each with advantages and disadvantages. The most common method is bacterial plating, which has the advantage of allowing live cell assessment through colony forming unit (CFU) counts but is not well suited for high throughput screening (HTS). On the other hand, spectrophotometry is adaptable to HTS applications but does not differentiate between dead and living bacteria and has low sensitivity.

Results
Here, we report a bacterial cell counting method termed Start Growth Time (SGT) that allows rapid and serial quantification of the absolute or relative number of live cells in a bacterial culture in a high throughput manner. We combined the methodology of quantitative polymerase chain reaction (qPCR) calculations with a previously described qualitative method of bacterial growth determination to develop an improved quantitative method. We show that SGT detects only live bacteria and is sensitive enough to differentiate between 40 and 400 cells/mL. SGT is based on the re-growth time required by a growing cell culture to reach a threshold, and the notion that this time is proportional to the number of cells in the initial inoculum. We show several applications of SGT, including assessment of antibiotic effects on cell viability and determination of an antibiotic tolerant subpopulation fraction within a cell population. SGT results do not differ significantly from results obtained by CFU counts.

Conclusion
SGT is a relatively quick, highly sensitive, reproducible and non-laborious method that can be used in HTS settings to longitudinally assess live cells in bacterial cell cultures.
A case report of type VI dual left anterior descending coronary artery anomaly presenting with non-ST-segment elevation myocardial infarction
Authors: Lee Yonggu , Lim Young-Hyo , Shin Jinho , Kim Kyung-Soo 
Published: November 2012

Abstract

Background
Type VI dual left anterior descending artery (LAD) is a rare coronary anomaly, the first case of which has recently been described. This is the first report of type VI dual LAD anomaly in which the patient presented with non-ST-segment elevation myocardial infarction and percutaneous coronary intervention was performed in the anomalously originating LAD.

Case presentation
A 52-year-old man with diabetes, hypertension and hyperlipidemia presented with chest pain without ST elevation on EKG, although the patient’s troponin I level was elevated. Coronary angiography revealed a short LAD originating from the left main coronary artery and a long LAD originating from the proximal portion of the right coronary artery (RCA). Three-dimensional reconstruction of computed tomography of images revealed that the long LAD originated from the proximal RCA and coursed between the right ventricular outflow tract (RVOT) and the aortic root before entering the mid anterior interventricular groove. The high take-off RCA originated underneath the RVOT, pointing downwards and forming an acute angle with the proximal portion of the long LAD. The anomalous long LAD displayed significant stenosis. We performed successful percutaneous coronary intervention (PCI) in the anomalous artery.

Conclusion
With accurate understanding of the coronary anatomy and appropriate hardware selection, successful PCI can be performed in the in the long LAD in patients with type VI dual LAD anomaly.
Acute portal vein thrombosis precipitated by indomethacin in a HCV-positive elderly patient
Authors: Mantarro Stefania , Tuccori Marco , Pasqualetti Giuseppe , Tognini Sara , Montagnani Sabrina , Monzani Fabio , Blandizzi Corrado 
Published: November 2012

Abstract

Background
An increased risk of venous thromboembolism has been reported in patients treated with non-steroidal anti-inflammatory drugs (NSAIDs). We describe a case of acute portal vein thrombosis (PVT) in a hepatitis C virus (HCV)-positive elderly patient following administration of indomethacin.

Case presentation
A 79-year-old HCV-positive man was hospitalized for severe abdominal pain, nausea and vomiting, 15 days after starting indomethacin for back pain. Clinical signs and imaging evaluations disclosed a picture of PVT. Indomethacin was discontinued, and the patient was started on fondaparinux and antithrombin. He was discharged 15 days later due to improvement of his clinical conditions. Thirty days later, a follow-up ultrasound did not show appreciable signs of PVT. The time elapsing between the start of analgesic therapy and PVT onset suggests a role of indomethacin as the triggering agent. Indomethacin could have precipitated PVT by a combination of at least two detrimental mechanisms: 1) direct action on liver vascular endothelium by inhibition of prostacyclin biosynthesis; 2) damage to the intestinal mucosa, followed by inflammatory and pro-coagulant activation of portal endothelium upon exposure to bacterial endotoxins.

Conclusions
This case can be of interest to physicians, who should exert caution when prescribing NSAIDs for inflammatory pain in patients with background inflammatory dysfunctions of the portal vein endothelium.
Autoantibody against transient receptor potential M1 cation channels of retinal ON bipolar cells in paraneoplastic vitelliform retinopathy
Authors: Wang Yujuan , Abu-Asab Mones S , Li Wei , Aronow Mary E , Singh Arun D , Chan Chi-Chao 
Published: November 2012

Abstract

Background
Paraneoplastic retinopathy is caused by the cross-reaction of neoplasm-directed autoantibodies against retinal antigens and results in retinal damage. Paraneoplastic vitelliform retinopathy, a presumed paraneoplastic retinopathy with features of atypical melanoma-associated retinopathy, has recently been reported in patients with metastatic melanoma. Ocular ultrastructure and its autoantibody localization of paraneoplastic vitelliform retinopathy are still indefinable. This is the first report of anti-transient receptor potential M1 antibody directly against human retinal bipolar dendritic tips in a melanoma patient with paraneoplastic vitelliform retinopathy.

Case presentation
We present a pair of postmortem eyes of an 80-year-old male with metastatic cutaneous melanoma, who developed paraneoplastic vitelliform retinopathy. The autopsied eyes were examined with light microscopy, immunohistochemistry, and transmission electron microscopy. Microscopically, the inner nuclear layer and outer plexiform layer were the most affected retinal structures, with local thinning. The lesions extended to the outer nuclear layer, resulting in focal retinal degeneration, edema, and atrophy. No active inflammation or melanoma cells were observed. Immunohistochemistry showed tightly compact bipolar cell nuclei (protein kinase C alpha/calbindin positive) with blur/loss of ON bipolar cell dendritic tips (transient receptor potential M1 positive) in diffusely condensed outer plexiform layer. The metastatic melanoma cells in his lung also showed immunoreactivity against transient receptor potential M1 antibody. Transmission electron microscopy illustrated degenerated inner nuclear layer with disintegration of cells and loss of cytoplasmic organelles. These cells contained many lysosomal and autophagous bodies and damaged mitochondria. Their nuclei appeared pyknotic and fragmentary. The synapses in the outer plexiform layer were extensively degenerated and replaced with empty vacuoles and disintegrated organelles.

Conclusion
This case provides a convincing histological evidence of melanoma-associated autoantibodies directly against transient receptor potential M1 channels that target the ON bipolar cell structures in the inner nuclear and outer plexiform layers in paraneoplastic vitelliform retinopathy.