bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid evolution of fluoroquinolone-resistant Escherichia coli in Nigeria is temporally associated with fluoroquinolone use
Authors: Lamikanra Adebayo , Crowe Jennifer L , Lijek Rebeccah S , Odetoyin Babatunde W , Wain John , Aboderin A Oladipo , Okeke Iruka N 
Published: November 2011

Abstract

Background
Antibiotic resistance has necessitated fluoroquinolone use but little is known about the selective forces and resistance trajectory in malaria-endemic settings, where selection from the antimalarial chloroquine for fluoroquinolone-resistant bacteria has been proposed.

Methods
Antimicrobial resistance was studied in fecal Escherichia coli isolates in a Nigerian community. Quinolone-resistance determining regions of gyrA and parC were sequenced in nalidixic acid resistant strains and horizontally-transmitted quinolone-resistance genes were sought by PCR. Antimicrobial prescription practices were compared with antimicrobial resistance rates over a period spanning three decades.

Results
Before 2005, quinolone resistance was limited to low-level nalixidic acid resistance in fewer than 4% of E. coli isolates. In 2005, the proportion of isolates demonstrating low-level quinolone resistance due to elevated efflux increased and high-level quinolone resistance and resistance to the fluoroquinolones appeared. Fluoroquinolone resistance was attributable to single nucleotide polymorphisms in quinolone target genes gyrA and/or parC. By 2009, 35 (34.5%) of isolates were quinolone non-susceptible with nine carrying gyrA and parC SNPs and six bearing identical qnrS1 alleles. The antimalarial chloroquine was heavily used throughout the entire period but E. coli with quinolone-specific resistance mechanisms were only detected in the final half decade, immediately following the introduction of the fluoroquinolone antibacterial ciprofloxacin.

Conclusions
Fluoroquinolones, and not chloroquine, appear to be the selective force for fluoroquinolone-resistant fecal E. coli in this setting. Rapid evolution to resistance following fluoroquinolone introduction points the need to implement resistant containment strategies when new antibacterials are introduced into resource-poor settings with high infectious disease burdens.
Evaluating a streamlined clinical tool and educational outreach intervention for health care workers in Malawi: the PALM PLUS case study
Authors: Sodhi Sumeet , Banda Hastings , Kathyola Damson , Burciul Barry , Thompson Sandy , Joshua Martias , Bateman Eric , Fairall Lara , Martiniuk Alexandra , Cornick Ruth , Faris Gill , Draper Beverley , Mondiwa Martha , Katengeza Egnat , Sanudi Lifah , Zwarenstein Merrick , Schull Michael J 
Published: November 2011

Abstract

Background
Nearly 3 million people in resource-poor countries receive antiretrovirals for the treatment of HIV/AIDS, yet millions more require treatment. Key barriers to treatment scale up are shortages of trained health care workers, and challenges integrating HIV/AIDS care with primary care.

The research
PALM PLUS (Practical Approach to Lung Health and HIV/AIDS in Malawi) is an intervention designed to simplify and integrate existing Malawian national guidelines into a single, simple, user-friendly guideline for mid-level health care workers. Training utilizes a peer-to-peer educational outreach approach. Research is being undertaken to evaluate this intervention to generate evidence that will guide future decision-making for consideration of roll out in Malawi. The research consists of a cluster randomized trial in 30 public health centres in Zomba District that measures the effect of the intervention on staff satisfaction and retention, quality of patient care, and costs through quantitative, qualitative and health economics methods.

Results and outcomes
In the first phase of qualitative inquiry respondents from intervention sites demonstrated in-depth knowledge of PALM PLUS compared to those from control sites. Participants in intervention sites felt that the PALM PLUS tool empowered them to provide better health services to patients. Interim staff retention data shows that there were, on average, 3 to 4 staff departing from the control and intervention sites per month. Additional qualitative, quantitative and economic analyses are planned.

The partnership
Dignitas International and the Knowledge Translation Unit at the University of Cape Town Lung Institute have led the adaptation and development of the PALM PLUS intervention, using experience gained through the implementation of the South African precursor, PALSA PLUS. The Malawian partners, REACH Trust and the Research Unit at the Ministry of Health, have led the qualitative and economic evaluations. Dignitas and Ministry of Health have facilitated interaction with implementers and policy-makers.

Challenges and successes
This initiative is an example of South-South knowledge translation between South Africa and Malawi, mediated by a Canadian academic-NGO hybrid. Our success in developing and rolling out PALM PLUS in Malawi suggests that it is possible to adapt and implement this intervention for use in other resource-limited settings.
A study on the effect of different chemical routes on functionalization of MWCNTs by various groups (-COOH, -SO3H, -PO3H2)
Authors: Kumar Pawan , Park Jin-Soo , Randhawa Prabhsharan , Sharma Sandeep , Shin Mun-Sik , Sekhon Satpal Singh 
Published: November 2011

Abstract
Pristine multiwall carbon nanotubes [MWCNTs] have been functionalized with various groups (-COOH, -SO3H, -PO3H2) using different single- and double-step chemical routes. Various chemical treatments were given to MWCNTs using hydrochloric, nitric, phosphoric, and sulphuric acids, followed by a microwave treatment. The effect of the various chemical treatments and the dispersion using a surfactant via ultrasonication on the functionalization of MWCNTs has been studied. The results obtained have been compared with pristine MWCNTs. Scanning electron microscopy, energy dispersive X-ray [EDX] spectroscopy, and transmission electron microscopy confirm the dispersion and functionalization of MWCNTs. Their extent of functionalization with -SO3H and -PO3H2 groups from the EDX spectra has been observed to be higher for the samples functionalized with a double-step chemical route and a single-step chemical route, respectively. The I
D/I
G ratio calculated from Raman data shows a maximum defect concentration for the sample functionalized with the single-step chemical treatment using nitric acid. The dispersion of MWCNTs with the surfactant, Triton X-100, via ultrasonication helps in their unbundling, but the extent of functionalization mainly depends on the chemical route followed for their treatment. The functionalized carbon nanotubes can be used in proton conducting membranes for fuel cells.
Effective harvesting, detection, and conversion of IR radiation due to quantum dots with built-in charge
Authors: Sablon Kimberly , Sergeev Andrei , Vagidov Nizami , Antipov Andrei , Little John , Mitin Vladimir 
Published: November 2011

Abstract
We analyze the effect of doping on photoelectron kinetics in quantum dot [QD] structures and find two strong effects of the built-in-dot charge. First, the built-in-dot charge enhances the infrared [IR] transitions in QD structures. This effect significantly increases electron coupling to IR radiation and improves harvesting of the IR power in QD solar cells. Second, the built-in charge creates potential barriers around dots, and these barriers strongly suppress capture processes for photocarriers of the same sign as the built-in-dot charge. The second effect exponentially increases the photoelectron lifetime in unipolar devices, such as IR photodetectors. In bipolar devices, such as solar cells, the solar radiation creates the built-in-dot charge that equates the electron and hole capture rates. By providing additional charge to QDs, the appropriate doping can significantly suppress the capture and recombination processes via QDs. These improvements of IR absorption and photocarrier kinetics radically increase the responsivity of IR photodetectors and photovoltaic efficiency of QD solar cells.
Facile preparation of highly-dispersed cobalt-silicon mixed oxide nanosphere and its catalytic application in cyclohexane selective oxidation
Authors: Zhang Qiaohong , Chen Chen , Wang Min , Cai Jiaying , Xu Jie , Xia Chungu 
Published: November 2011

AbstractHighly dispersed cobalt-silicon mixed oxide [Co-SiO2] nanosphere was successfully prepared with a modified reverse-phase microemulsion method. This material was characterized in detail by X-ray diffraction, transmission electron microscopy, Fourier transform infrared, ultraviolet-visible diffuse reflectance spectra, X-ray absorption spectroscopy near-edge structure, and N2 adsorption-desorption measurements. High valence state cobalt could be easily obtained without calcination, which is fascinating for the catalytic application for its strong oxidation ability. In the selective oxidation of cyclohexane, Co-SiO2 acted as an efficient catalyst, and good activity could be obtained under mild conditions.
Multiple-set split feasibility problems for total asymptotically strict pseudocontractions mappings
Authors: Yang LI , Chang Shih-Sen , Cho Yeol JE , Kim Jong KYU 
Published: November 2011

AbstractThe purpose of this article is to propose and investigate an algorithm for solving the multiple-set split feasibility problems for total asymptotically strict pseu-docontractions mappings in infinite-dimensional Hilbert spaces. The results presented in this article improve and extend some recent results of A. Moudafi, H. K. Xu, Y. Censor, A. Segal, T. Elfving, N. Kopf, T. Bortfeld, X. A. Motova, Q. Yang, A. Gibali, S. Reich and others.2000 AMS Subject Classification: 47J05; 47H09; 49J25.
Efficient and accurate image alignment using TSK-type neuro-fuzzy network with data-mining-based evolutionary learning algorithm
Authors: Hsu Chi-Yao , Cheng Yi-Chang , Lin Sheng-Fuu 
Published: November 2011

Abstract
Image alignment is considered a key problem in visual inspection applications. The main concerns for such tasks are fast image alignment with subpixel accuracy. About this, neural network-based approaches are very popular in visual inspection because of their high accuracy and efficiency of aligning images. However, such methods are difficult to identify the structure and parameters of neural network. In this study, a Takagi-Sugeno-Kang-type neuro-fuzzy network (NFN) with data-mining-based evolutionary learning algorithm (DMELA) is proposed. Compared with traditional learning algorithms, DMELA combines the self-organization algorithm (SOA), data-mining selection method (DMSM), and regularized least square (RLS) method to not only determine a suitable number of fuzzy rules, but also automatically tune the parameters of NFN. Experimental results are shown to demonstrate superior performance of the DMELA constructed image alignment system over other typical learning algorithms and existing alignment systems. Such system is useful to develop accurate and efficient image alignment systems.
Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses
Authors: Subramanian Ravi P , Wildschutte Julia H , Russo Crystal , Coffin John M 
Published: November 2011

Abstract

Background
Integration of retroviral DNA into a germ cell may lead to a provirus that is transmitted vertically to that host's offspring as an endogenous retrovirus (ERV). In humans, ERVs (HERVs) comprise about 8% of the genome, the vast majority of which are truncated and/or highly mutated and no longer encode functional genes. The most recently active retroviruses that integrated into the human germ line are members of the Betaretrovirus-like HERV-K (HML-2) group, many of which contain intact open reading frames (ORFs) in some or all genes, sometimes encoding functional proteins that are expressed in various tissues. Interestingly, this expression is upregulated in many tumors ranging from breast and ovarian tissues to lymphomas and melanomas, as well as schizophrenia, rheumatoid arthritis, and other disorders.

Results
No study to date has characterized all HML-2 elements in the genome, an essential step towards determining a possible functional role of HML-2 expression in disease. We present here the most comprehensive and accurate catalog of all full-length and partial HML-2 proviruses, as well as solo LTR elements, within the published human genome to date. Furthermore, we provide evidence for preferential maintenance of proviruses and solo LTR elements on gene-rich chromosomes of the human genome and in proximity to gene regions.

Conclusions
Our analysis has found and corrected several errors in the annotation of HML-2 elements in the human genome, including mislabeling of a newly identified group called HML-11. HML-elements have been implicated in a wide array of diseases, and characterization of these elements will play a fundamental role to understand the relationship between endogenous retrovirus expression and disease.
Helicobacter pylori interferes with an embryonic stem cell micro RNA cluster to block cell cycle progression
Authors: Belair Cédric , Baud Jessica , Chabas Sandrine , Sharma Cynthia M , Vogel Jörg , Staedel Cathy , Darfeuille Fabien 
Published: November 2011

Abstract

Background
MicroRNAs, post-transcriptional regulators of eukaryotic gene expression, are implicated in host defense against pathogens. Viruses and bacteria have evolved strategies that suppress microRNA functions, resulting in a sustainable infection. In this work we report that Helicobacter pylori, a human stomach-colonizing bacterium responsible for severe gastric inflammatory diseases and gastric cancers, downregulates an embryonic stem cell microRNA cluster in proliferating gastric epithelial cells to achieve cell cycle arrest.

Results
Using a deep sequencing approach in the AGS cell line, a widely used cell culture model to recapitulate early events of H. pylori infection of gastric mucosa, we reveal that hsa-miR-372 is the most abundant microRNA expressed in this cell line, where, together with hsa-miR-373, it promotes cell proliferation by silencing large tumor suppressor homolog 2 (LATS2) gene expression. Shortly after H. pylori infection, miR-372 and miR-373 synthesis is highly inhibited, leading to the post-transcriptional release of LATS2 expression and thus, to a cell cycle arrest at the G1/S transition. This downregulation of a specific cell-cycle-regulating microRNA is dependent on the translocation of the bacterial effector CagA into the host cells, a mechanism highly associated with the development of severe atrophic gastritis and intestinal-type gastric carcinoma.

Conclusions
These data constitute a novel example of host-pathogen interplay involving microRNAs, and unveil the couple LATS2/miR-372 and miR-373 as an unexpected mechanism in infection-induced cell cycle arrest in proliferating gastric cells, which may be relevant in inhibition of gastric epithelium renewal, a major host defense mechanism against bacterial infections.
Astrocyte elevated gene 1: biological functions and molecular mechanism in cancer and beyond
Authors: Ying Zhe , Li Jun , Li Mengfeng 
Published: November 2011

Abstract
Since its discovery, nearly one decade of research on astrocyte elevated gene 1 (AEG-1) has witnessed expanding knowledge of this molecule, ranging from its role in cancer biology to molecular mechanisms underlying the biological functions. As a multifunctional oncoprotein, AEG-1 has been shown to overexpress in multiple types of human cancer, and the elevation of AEG-1 in tumor cells leads to enhanced phenotypes characteristic of malignant aggressiveness, including increased abilities to proliferate robustly, to invade surrounding tissues, to migrate, to induce neovascularization, and to enhance chemoresistance. The multifunctional role of AEG-1 in tumor development and progression has been found to be associated with several signaling cascades, namely, 1) activation of NF-kappa B, partially through direct interaction with p65; 2) PI3K/AKT signaling triggered by AEG-1 indirectly; 3) enhancement of the transcriptional activity of beta-catenin by indirect activation of MAPK and induction of LEF1; 4) regulation of mi/siRNA-mediated gene silencing by interacting with SND1; and 5) promotion of protective autophagy; in addition to possibly unknown mechanisms. Elevated AEG-1 expression is seen in nearly all tumor types, and in most cases AEG-1 positively correlates with tumor progression and poorer patient survival. Taken together, AEG-1 might represent a potential prognostic biomarker and therapeutic target.
The dynamics underlying pseudo-plateau bursting in a pituitary cell model
Authors: Teka Wondimu , Tabak Joël , Vo Theodore , Wechselberger Martin , Bertram Richard 
Published: November 2011

Abstract
Pituitary cells of the anterior pituitary gland secrete hormones in response to patterns of electrical activity. Several types of pituitary cells produce short bursts of electrical activity which are more effective than single spikes in evoking hormone release. These bursts, called pseudo-plateau bursts, are unlike bursts studied mathematically in neurons (plateau bursting) and the standard fast-slow analysis used for plateau bursting is of limited use. Using an alternative fast-slow analysis, with one fast and two slow variables, we show that pseudo-plateau bursting is a canard-induced mixed mode oscillation. Using this technique, it is possible to determine the region of parameter space where bursting occurs as well as salient properties of the burst such as the number of spikes in the burst. The information gained from this one-fast/two-slow decomposition complements the information obtained from a two-fast/one-slow decomposition.
Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems
Authors: Minoche André E , Dohm Juliane C , Himmelbauer Heinz 
Published: November 2011

Abstract
Background
The generation and analysis of high-throughput sequencing data are becoming a major component of many studies in molecular biology and medical research. Illumina's Genome Analyzer (GA) and HiSeq instruments are currently the most widely used sequencing devices. Here, we comprehensively evaluate properties of genomic HiSeq and GAIIx data derived from two plant genomes and one virus, with read lengths of 95 to 150 bases.

Results
We provide quantifications and evidence for GC bias, error rates, error sequence context, effects of quality filtering, and the reliability of quality values. By combining different filtering criteria we reduced error rates 7-fold at the expense of discarding 12.5% of alignable bases. While overall error rates are low in HiSeq data we observed regions of accumulated wrong base calls. Only 3% of all error positions accounted for 24.7% of all substitution errors. Analyzing the forward and reverse strands separately revealed error rates of up to 18.7%. Insertions and deletions occurred at very low rates on average but increased to up to 2% in homopolymers. A positive correlation between read coverage and GC content was found depending on the GC content range.

Conclusions
The errors and biases we report have implications for the use and the interpretation of Illumina sequencing data. GAIIx and HiSeq data sets show slightly different error profiles. Quality filtering is essential to minimize downstream analysis artifacts. Supporting previous recommendations, the strand-specificity provides a criterion to distinguish sequencing errors from low abundance polymorphisms.
Validation Study of a Quantitative Multigene Reverse Transcriptase–Polymerase Chain Reaction Assay for Assessment of Recurrence Risk in Patients With Stage II Colon Cancer
Authors: Gray Richard G. , Quirke Philip , Handley Kelly , Lopatin Margarita , Magill Laura , Baehner Frederick L. , Beaumont Claire , Clark-Langone Kim M. , Yoshizawa Carl N. , Lee Mark , Watson Drew , Shak Steven , Kerr David J. 
Published: November 2011

Purpose We developed quantitative gene expression assays to assess recurrence risk and benefits from chemotherapy in patients with stage II colon cancer. Patients and Methods We sought validation by using RNA extracted from fixed paraffin-embedded primary colon tumor blocks from 1,436 patients with stage II colon cancer in the QUASAR (Quick and Simple and Reliable) study of adjuvant fluoropyrimidine chemotherapy versus surgery alone. A recurrence score (RS) and a treatment score (TS) were calculated from gene expression levels of 13 cancer-related genes (n = 7 recurrence genes and n = 6 treatment benefit genes) and from five reference genes with prespecified algorithms. Cox proportional hazards regression models and log-rank methods were used to analyze the relationship between the RS and risk of recurrence in patients treated with surgery alone and between TS and benefits of chemotherapy. Results Risk of recurrence was significantly associated with RS (hazard ratio [HR] per interquartile range, 1.38; 95% CI, 1.11 to 1.74; P = .004). Recurrence risks at 3 years were 12%, 18%, and 22% for predefined low, intermediate, and high recurrence risk groups, respectively. T stage (HR, 1.94; P < .001) and mismatch repair (MMR) status (HR, 0.31; P < .001) were the strongest histopathologic prognostic factors. The continuous RS was associated with risk of recurrence (P = .006) beyond these and other covariates. There was no trend for increased benefit from chemotherapy at higher TS (P = .95). Conclusion The continuous 12-gene RS has been validated in a prospective study for assessment of recurrence risk in patients with stage II colon cancer after surgery and provides prognostic value that complements T stage and MMR. The TS was not predictive of chemotherapy benefit.
Improvement in Breast Cancer Outcomes Over Time: Are Older Women Missing Out?
Authors: Smith Benjamin D. , Jiang Jing , McLaughlin Sandra S. , Hurria Arti , Smith Grace L. , Giordano Sharon H. , Buchholz Thomas A. 
Published: November 2011

Purpose Women aged ≥ 75 years account for 40,000 breast cancers/yr and are the most rapidly growing demographic. Recent data demonstrated that breast cancer death rates in the US population are declining, but it is not known whether death rates have declined similarly for older and younger women. We examined the following two outcomes: the rate of breast cancer death in the general population and the risk of breast cancer death in newly diagnosed patients, and we compared change over time in these outcomes for older versus younger women. Methods By using data from National Vital Statistics Reports that spanned from 1990 to 2007, the yearly change in the age-specific rate of breast cancer death was characterized with linear regression. With the use of the Surveillance, Epidemiology, and End Results nine-registry cohort that spanned from 1980 to 1997, the yearly change in age-specific risk of breast cancer death was characterized by using competing-risks regression adjusted for race and stage. Results Relative to 1990, the rate of breast cancer death in the general population decreased by 2.5%/yr for women age 20 to 49 years, 2.1%/yr for women age 50 to 64 years, 2.0%/yr for women age 65 to 74 years, and 1.1%/yr for women age ≥ 75 years. From 1980 to 1997, the adjusted risk of breast cancer death in newly diagnosed patients decreased by 3.6%/yr for women age less than 75 years versus 1.3%/yr for women age ≥ 75 years (P < .001). Over this time interval, the 10-year absolute risk of breast cancer death decreased by 15.3% for women age 50 to 64 years (from 31.9% to 16.6%) but by only 7.5% (from 24.8% to 17.4%) for women age ≥ 75 years. Conclusion Breast cancer outcomes have preferentially improved in women age less than 75 years. Focused research is needed to improve outcomes in older women.