bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical and economic considerations in the treatment of acute exacerbations of chronic bronchitis
Authors: Destache Christopher J. , Dewan Naresh , O'Donohue Walter J. , Campbell J. Clayton , Angelillo Vito A. 
Published: July 2002

Abstract
Limited data exist to guide physicians in the cost-effective treatment of acute exacerbation of chronic bronchitis (AECB). Therefore, the main objective of this study was to determine the antimicrobial efficacy and related costs for patients with AECB. A retrospective review of 60 outpatient medical records with a diagnosis of chronic obstructive pulmonary disease (COPD) and chronic bronchitis episodes from a pulmonary clinic of a teaching institution was undertaken. The participating patients had a total of 224 episodes of AECB requiring antibiotic treatment. Before review, empirical antibiotic choices were divided into first-line (amoxycillin, co-trimoxazole, tetracyclines, erythromycin), second-line (cephradine, cefuroxime, cefaclor, cefprozil) and third-line (co-amoxiclav, azithromycin, ciprofloxacin) agents. Patients receiving first-line agents failed significantly more frequently than third-line agents (19% vs 7%, P &lt;0.05). Additionally, patients prescribed first-line agents were hospitalized significantly more often for AECB within 2 weeks of outpatient treatment as compared with patients prescribed third-line agents (18.0% vs 5.3% third-line agents; P &lt;0.02). Time between subsequent AECB episodes requiring treatment was significantly longer for patients receiving third-line agents compared with first-line and second-line agents (P &lt;0.005). Pharmacy costs were lowest with first-line agents (first-line US$10.30 ± 8.76; second-line US$24.45 ± 25.65; third-line US$45.40 ± 11.11; P &lt; 0.0001), but third-line agents showed a trend towards lower mean total costs of AECB treatment (first-line US$942 ± 2173; second-line, US$563 ± 2296; third-line, US$542 ± 1946). The use of third-line antimicrobials, co-amoxiclav, ciprofloxacin or azithromycin, significantly reduced the failure rate and need for hospitalization, prolonged the time between AECB episodes, and showed a lower total cost for the management of AECB. Prospective studies are needed to confirm these findings.
The global epidemiology of resistance to ciprofloxacin and the changing nature of antibiotic resistance: a 10 year perspective
Authors: Thomson Christopher J. 
Published: July 2002

Abstract
Many studies have examined the in-vitro activity of ciprofloxacin. The results are for the most part encouraging but we must guard against complacency. Levels of ciprofloxacin resistance vary geographically, while some predictably difficult-to-treat organisms such as Pseudomonas aeruginosa,Staphylococcus aureus and Acinetobacter baumannii present challenges globally. The emergence of resistance in species previously exquisitely sensitive to ciprofloxacin, such as Neisseria gonorrhoeae, in countries associated with ‘ pirate’ production and indiscriminate use of antimicrobials represents a major challenge. Ciprofloxacin continues to show excellent activity againstHaemophilus influenzae and Moraxella catharralis. In general, ciprofloxacin shows good activity against Enterobacteriaceae although the emergence of reduced susceptibility and, sometimes, quinolone resistance in multi-resistant isolates should be noted.
Intron—exon structures of eukaryotic model organisms
Authors: Long Manyuan , Deutsch Michael 
Published: July 2002

Abstract
To investigate the distribution of intron—exon structures of eukaryotic genes, we have constructed a general exon database comprising all available introncontaining genes and exon databases from 10 eukaryotic model organisms: Homo sapiens, Mus musculus, Gallus gallus, Rattus norvegicus, Arabidopsis thaliana, Zea mays, Schizosaccharomyces pombe, Aspergillus, Caenorhabditis elegans and Drosophila . We purged redundant genes to avoid the possible bias brought about by redundancy in the databases. After discarding those questionable introns that do not contain correct splice sites, the final database contained 17 102 introns, 21 019 exons and 2903 independent or quasi-independent genes. On average, a eukaryotic gene contains 3.7 introns per kb protein coding region. The exon distribution peaks around 30–40 residues and most introns are 40–125 nt long. The variable intron—exon structures of the 10 model organisms reveal two interesting statistical phenomena, which cast light on some previous speculations. (i) Genome size seems to be correlated with total intron length per gene. For example, invertebrate introns are smaller than those of human genes, while yeast introns are shorter than invertebrate introns. However, this correlation is weak, suggesting that other factors besides genome size may also affect intron size. (ii) Introns smaller than 50 nt are significantly less frequent than longer introns, possibly resulting from a minimum intron size requirement for intron splicing.
Finding Genes in the C2C12 Osteogenic Pathway by k-Nearest-Neighbor Classification of Expression Data
Authors: Theilhaber Joachim , Connolly Timothy , Roman-Roman Sergio , Bushnell Steven , Jackson Amanda , Call Kathy , Garcia Teresa , Baron Roland 
Published: July 2002

A supervised classification scheme for analyzing microarray expression data, based on the k-nearest-neighbor method coupled to noise-reduction filters, has been used to find genes involved in the osteogenic pathway of the mouse C2C12 cell line studied here as a model for in vivo osteogenesis. The scheme uses as input a training set embodying expert biological knowledge, and provides internal estimates of its own misclassification errors, which furthermore enables systematic optimization of the classifier parameters. On the basis of the C2C12-generated expression data set with 34,130 expression profiles across 2 time courses, each comprised of 6 points, and a training set containing known members of the osteogenic, myoblastic, and adipocytic pathways, 176 new genes in addition to 28 originally in the training set are selected as relevant to osteogenesis. For this selection, the estimated sensitivity is 42% and the posterior false-positive rate (fraction of candidates that are spurious) is 12%. The corresponding sensitivity and false-positive rate for detection of myoblastic genes are 9% and 31%, respectively, and only 4% and ∼100%, respectively, for adipocytic genes, in accordance with an experimental design that predominantly stimulated the osteogenic pathway. Validation of this selection is provided by examining expression of the genes in an independent biological assay involving mouse calvaria (skull bone) primary cell cultures, in which a large fraction of the 176 genes are seen to be strongly regulated, as well as by case-by-case analysis of the genes on the basis of expert domain knowledge. The methodology should be generalizable to any situation in which enough a priori biological knowledge exists to define a training set.[Online supplementary material available atwww.genome.org]
Dataset S2 from Nitric Oxide Regulates Gene Expression in Cancers by Controlling Histone Posttranslational Modifications
Authors: Vasudevan Divya , Hickok Jason R. , Bovee Rhea C. , Pham Vy , Mantell Lin L. , Bahroos Neil , Kanabar Pinal , Cao Xing-Jun , Maienschein-Cline Mark , Garcia Benjamin A. , Thomas Douglas D. 
Published: April 2023

<p>GO terms associated with upregulated genes bearing new ÃƒÂ¢Ã‹â€ Ã¢â€žÂ¢NO-induced H3K9ac peaks around promoter regions</p>
Data from Comparison of Corticotropin-Releasing Factor, Dexamethasone, and Temozolomide: Treatment Efficacy and Toxicity in U87 and C6 Intracranial Gliomas
Authors: Moroz Maxim A. , Huang Ruimin , Kochetkov Tatiana , Shi Weiji , Thaler Howard , de Stanchina Elisa , Gamez Idoia , Ryan Robert P. , Blasberg Ronald G. 
Published: April 2023

<div>Abstract<p><b>Purpose/Experimental Design:</b> Treatment of cerebral tumors and peritumoral brain edema remains a clinical challenge and is associated with high morbidity and mortality. Dexamethasone is an effective drug for treating brain edema, but it is associated with well-documented side effects. Corticorelin acetate (Xerecept) or human corticotrophin-releasing factor (hCRF) is a comparatively new drug and has been evaluated in two orthotopic glioma models (U87 and C6), by a direct comparison with dexamethasone and temozolomide.</p><p><b>Results:</b><i>In vitro</i> combination therapy and monotherapy showed a variable response in 6 different glioma cell lines. <i>In vivo</i> studies showed a dose-dependent effect of hCRF (0.03 and 0.1 mg/kg q12h) on survival of U87 intracranial xenograft–bearing animals [median survival: control – 41 days (95% CI 25–61); “low-hCRF” 74.5 days (95% CI 41–88); “high-hCRF” >130 days (95% CI not reached)]. Dexamethasone treatment had no effect on survival, but significant toxicity was observed. A survival benefit was observed with temozolomide and temozolomide + hCRF-treated animals but with significant temozolomide toxicity. C6-bearing animals showed no survival benefit, but there were similar treatment toxicities. The difference in hCRF treatment response between U87 and C6 intracranial gliomas can be explained by a difference in receptor expression. RT-PCR identified CRF2r mRNA in U87 xenografts; no CRF receptors were identified in C6 xenografts.</p><p><b>Conclusions:</b> hCRF was more effective than either dexamethasone or temozolomide in the treatment of U87 xenografts, and results included improved prognosis with long-term survivors and only mild toxicity. The therapeutic efficacy of hCRF seems to be dependent on tumor hCRF receptor (CRFr) expression. These results support further clinical assessment of the therapeutic efficacy of hCRF and levels of CRFr expression in different human gliomas. <i>Clin Cancer Res; 17(10); 3282–92. ©2011 AACR</i>.</p></div>
Data from MicroRNA-200c mitigates invasiveness and restores sensitivity to microtubule-targeting chemotherapeutic agents
Authors: Cochrane Dawn R. , Spoelstra Nicole S. , Howe Erin N. , Nordeen Steven K. , Richer Jennifer K. 
Published: April 2023

<div>Abstract<p>The transcription factor ZEB1 is normally not expressed in epithelial cells. When inappropriately expressed in carcinomas, ZEB1 initiates epithelial to mesenchymal transition due to its ability to repress E-cadherin and other genes involved in polarity. Recently, ZEB1 and ZEB2 have been identified as direct targets of the microRNA-200c family. We find that miR-200c levels are high in well-differentiated endometrial, breast, and ovarian cancer cell lines, but extremely low in poorly differentiated cancer cells. Low or absent miR-200c results in aberrant expression of ZEB1 and consequent repression of E-cadherin. Reinstatement of miR-200c to such cells restores E-cadherin and dramatically reduces migration and invasion. Microarray profiling reveals that in addition to ZEB1 and ZEB2, other mesenchymal genes (such as <i>FN1, NTRK2</i>, and <i>QKI</i>), which are also predicted direct targets of miR-200c, are indeed inhibited by addition of exogenous miR-200c. One such gene, class III β-tubulin (<i>TUBB3</i>), which encodes a tubulin isotype normally found only in neuronal cells, is a direct target of miR-200c. This finding is of particular significance because we show that restoration of miR-200c increases sensitivity to microtubule-targeting agents by 85%. Because expression of TUBB3 is a common mechanism of resistance to microtubule-binding chemotherapeutic agents in many types of solid tumors, the ability of miR-200c to restore chemosensitivity to such agents may be explained by its ability to reduce TUBB3. Because miR-200c is crucial for maintenance of epithelial identity, behavior, and sensitivity to chemotherapy, we propose that it warrants further investigation as a therapeutic strategy for aggressive, drug-resistant cancers. [Mol Cancer Ther 2009;8(5):OF1–12]</p></div>
Tyrosinase‐activated Nanocomposites for Double‐Modals Imaging Guided Photodynamic and Photothermal Synergistic Therapy
Authors: Li Shuo , Zhang Guoyang , Peng Yanghan , Chen Peiyu , Li Jiguang , Wang Xuefei , Wang Zhuo 
Published: April 2023

AbstractTyrosinase (TYR) is an important biomarker of melanoma. The exploration of fluorescent pr‐obes‐based composites is beneficial to build an integrative platform for the diagnosis and treatment of melanoma. Herein, a multifunctional nanocomposite IOBOH@BSA activated by TYR is developed for selective imaging and ablation of melanoma. The chemical structure of IOBOH enables the fluorescence (FL) imaging activated by TYR, photoacoustic (PA) imaging, and photodynamic‐photothermal activity by regulating the balance between radiative decay and non‐radiative decay. IOBOH combined with bovine serum albumin (IOBOH@BSA) presents the response to TYR and realizes FL imaging with mitochondria‐targeting in melanoma. Moreover, IOBOH@BSA shows excellent photothermal ability and is applied for PA imaging. After IOBOH@BSA is activated by TYR, the singlet oxygen generation increases obviously. IOBOH@BSA can realize TYR‐activated imaging and photodynamic‐photothermal therapy of melanoma. The development of TYR‐activated multifunctional nanocomposites promotes the precise imaging and improves the therapeutic effect of melanoma.
Fundamentals and Applications of Raman‐Based Techniques for the Design and Development of Active Biomedical Materials
Authors: Fernández‐Galiana Álvaro , Bibikova Olga , Vilms Pedersen Simon , Stevens Molly M. 
Published: April 2023

AbstractRaman spectroscopy is an analytical method based on light–matter interactions that can interrogate the vibrational modes of matter and provide representative molecular fingerprints. Mediated by its label‐free, non‐invasive nature, and high molecular specificity, Raman‐based techniques have become ubiquitous tools for in situ characterization of materials. This review comprehensively describes the theoretical and practical background of Raman spectroscopy and its advanced variants. The numerous facets of material characterization that Raman scattering can reveal, including biomolecular identification, solid‐to‐solid phase transitions, and spatial mapping of biomolecular species in bioactive materials, are highlighted. The review illustrates the potential of these techniques in the context of active biomedical material design and development by highlighting representative studies from the literature. These studies cover the use of Raman spectroscopy for the characterization of both natural and synthetic biomaterials, including engineered tissue constructs, biopolymer systems, ceramics, and nanoparticle formulations, among others. To increase the accessibility and adoption of these techniques, the present review also provides the reader with practical recommendations on the integration of Raman techniques into the experimental laboratory toolbox. Finally, perspectives on how recent developments in plasmon‐ and coherently‐enhanced Raman spectroscopy can propel Raman from underutilized to critical for biomaterial development are provided.
Horizontal and Vertical Coalescent Microrobotic Collectives Using Ferrofluid Droplets
Authors: Sun Mengmeng , Yang Shihao , Jiang Jialin , Zhang Li 
Published: April 2023

AbstractMany artificial miniature robotic collectives have been developed to overcome the inherent limitations of inadequate individual capabilities. However, the basic building blocks of the reported collectives are mainly in the solid state, where the morphological boundaries of internal individuals are clear and cannot genuinely merge. Miniature robotic collectives based on liquid units still need to be explored; such on‐demand mergeable swarm systems are advantageous for adapting to the changing external environment. Here, a strategy to achieve a coalescent collective system we presented that exploits the ferrofluid droplets' splitting and coalescence properties to trigger the formation of horizontal multimodal and vertical gravity‐resistant collectives and unveil pattern‐enabled robotic functionalities. When subjected to a time‐varying magnetic field, the droplet swarm exhibits a variety of morphologies ranging from horizontal collectives, including vortex‐like, chain‐like, and crystal‐like patterns to vertical layer‐upon‐layer patterns. Using experiments and simulations, the formation and transformation of different morphological collectives are shown and their robust environmental adaptability are demonstrated. Potential applications of the multimodal droplet collectives are presented, including exploring an unknown environment, targeted object delivery, and fluid flow filtration in a lab‐on‐a‐chip. This work may facilitate the design of microrobotic swarm systems and expand the range of materials for miniature robots.
Curated collections for educators: Nine key articles and article series for teaching qualitative research methods
Authors: Lin Sophia , Zimmerman Elise , Datta Suchismita , Selby Maurice , Chan Teresa , Fant Abra 
Published: April 2023

AbstractBackgroundQualitative research explains observations, focusing on how and why phenomena and experiences occur. Qualitative methods go beyond quantitative data and provide critical information inaccessible through quantitative methods. However, at all levels of medical education, there is insufficient exposure to qualitative research. As a result, residents and fellows complete training ill‐equipped to appraise and conduct qualitative studies. As a first step to increasing education in qualitative methods, we sought to create a curated collection of papers for faculty to use in teaching qualitative research at the graduate medical education (GME) level.MethodsWe conducted literature searches on the topic of teaching qualitative research to residents and fellows and queried virtual medical education and qualitative research communities for relevant articles. We searched the reference lists of all articles found through the literature searches and online queries for additional articles. We then conducted a three‐round modified Delphi process to select papers most relevant to faculty teaching qualitative research.ResultsWe found no articles describing qualitative research curricula at the GME level. We identified 74 articles on the topic of qualitative research methods. The modified Delphi process identified the top nine articles or article series most relevant for faculty teaching qualitative research. Several articles explain qualitative methods in the context of medical education, clinical care, or emergency care research. Two articles describe standards of high‐quality qualitative studies, and one article discusses how to conduct the individual qualitative interview to collect data for a qualitative study.ConclusionsWhile we identified no articles reporting already existing qualitative research curricula for residents and fellows, we were able to create a collection of papers on qualitative research relevant to faculty seeking to teach qualitative methods. These papers describe key qualitative research concepts important in instructing trainees as they appraise and begin to develop their own qualitative studies.
Ene Reductase Enabled Intramolecular β‐C−H Functionalization of Substituted Cyclohexanones for Efficient Synthesis of Bridged Bicyclic Nitrogen Scaffolds
Authors: Jiang Guangde , Huang Chunshuai , Harrison Wesley , Li Hongxiang , Zhou Megan , Zhao Huimin 
Published: April 2023

AbstractHerein we report that ene reductases (EREDs) can facilitate an unprecedented intramolecular β‐C−H functionalization reaction for the synthesis of bridged bicyclic nitrogen heterocycles containing the 6‐azabicyclo[3.2.1]octane scaffold. To streamline the synthesis of these privileged motifs, we developed a gram‐scale one‐pot chemoenzymatic cascade by combining iridium photocatalysis with EREDs, using readily available N‐phenylglycines and cyclohexenones that can be obtained from biomass. Further derivatization using enzymatic or chemical methods can convert 6‐azabicyclo[3.2.1]octan‐3‐one into 6‐azabicyclo[3.2.1]octan‐3α‐ols, which can be potentially utilized for the synthesis of azaprophen and its analogues for drug discovery. Mechanistic studies revealed the reaction requires oxygen, presumably to produce oxidized flavin, which can selectively dehydrogenate the 3‐substituted cyclohexanone derivatives to form the α,β‐unsaturated ketone, which subsequently undergoes spontaneous intramolecular aza‐Michael addition under basic conditions.
Solution Plasma‐Assisted Multivariate Metal Nanoalloys Encapsulated with Carbon Dots for Efficient Oxygen Evolution Reaction
Authors: Yan Fufeng , Ding Junyi , Hu Lijun , Li Sizhuan , Zhang Shuai , Wang Minghua , He Linghao , Du Miao 
Published: April 2023

AbstractTo accelerate the reaction kinetics of electrocatalytic oxygen evolution reaction (OER), a multicomponent CDs@(PdFeNiCo)Nbx nanohybrid comprising multiple metal nanoalloys and carbon quantum dots (CDs) was in situ generated by treating the mixture of Nb2C quantum dots (Nb2C QDs) and a variety of metal ions (M2+=Pd2+, Fe2+, Co2+, Ni2+) through the solution plasma (SP) modification technique. The CDs@(PdFeNiCo)Nbx catalyst was further explored as an electrocatalyst for OER in alkaline solution. Under nitrogen plasma irradiation with high input power (200 W), diverse bimetallic nanoalloy particles, including NbPd3, FeNb, NbNi3, and CoNbO4 nanoalloys, were generated, accompanied with the decomposition of Nb2C QDs into CDs. In view of the synergic effect between multivariate metal active sites and highly conjugated CD network, the developed CDs@(PdFeNiCo)Nbx electrocatalyst showed a small overpotential of 240 mV for achieving the current density of 10 mA cm−2, together with a very low Tafel slope of 62 mV dec−1, which substantially outperformed those of the state‐of‐the‐art metal electrocatalysts and was competitive with most metal oxides. The CDs@(PdFeNiCo)Nbx electrocatalyst also showed a negligible overpotential change during 30 h chronopotentiometry measurement. The present work can provide a feasible alternative strategy for the development of an excellent OER electrocatalyst using the SP modification method.
Expression of α‐Synuclein in the mouse retina is confined to inhibitory presynaptic elements
Authors: Yang Qingwen , Lin Xin , Xiao Jiayi , Zhong Wenhui , Wang Fenglan , Tan Hang , Rao Bilin , Qu Jia , Zhang Jun 
Published: April 2023

Abstractα‐Synuclein (α‐Syn) is enriched in presynaptic terminals of the central nervous system including the retina and plays a role in the synaptic vesicle cycle and synaptic transmission. Abnormal aggregation of α‐Syn is considered to be the main component of the Lewy bodies that are the pathological hallmarks of Parkinson's disease. Although expression pattern of α‐Syn has been described in the retinas, its precise cellular and subcellular locations are poorly understood. We investigated the precise expression of α‐Syn using light microscopy (LM) and electron microscopy (EM) with antibodies against α‐Syn in the mouse retina. We found that the majority of α‐Syn immunoreactivity (IR) is located in GABAergic, glycinergic, and dopaminergic amacrine cells, and their processes often make a direct synapse to other labeled or unlabeled amacrine profiles, bipolar cell terminals, or ganglion cell dendrites. Further, our LM and immuno‐EM results confirm the absence of α‐Syn in excitatory photoreceptors, bipolar cell bodies, and their ribbon synapses, providing evidence, for the first time, that ribbon synapses do not express α‐Syn. Additionally, α‐Syn IR is located in the ganglion cells, some of which are intrinsically photosensitive retinal ganglion cells. These results reveal a previously unappreciated inhibitory synapse‐specific expression pattern of α‐Syn in the retina, suggesting that α‐Syn may play a distinct role in the modulation and integration of inhibitory synaptic transmission in the retina.