Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial colonization of endotracheal tubes in intubated neonates.

OBJECTIVE To obtain in vivo bacterial colonization profiles on endotracheal tubes at different sites in the neonatal airway in an attempt to better characterize one potential element of chondritis. DESIGN A case series in which cultures were obtained from calculated segments of 33 endotracheal tubes immediately following extubation. This allowed for sampling at specific levels of the airway corresponding to the trachea, the subglottis, and the oropharynx. Data collected included gender, race, duration of intubation, use of antibiotic therapy, comorbidities, gestational age at birth and extubation, crown-rump length, weight, radiographic distance from tube tip to carina, and culture results. SETTING Newborn intensive care unit at a tertiary care medical center. PATIENTS Twenty-nine neonates intubated for longer than 24 hours (range, 24 hours to 15 days). MAIN OUTCOME MEASURES Bacterial and fungal cultures obtained from 3 endotracheal tube segments for each extubation. RESULTS A statistically significant difference (P < .05) was found in colonization rates between patients intubated for less than 4 days and those intubated for longer periods. No significant difference was noted in bacterial profile between the 3 sites. CONCLUSIONS Data demonstrate that bacterial colonization of an indwelling object in the neonatal airway increases with the duration of intubation. Furthermore, 4 days seems to represent a critical period in the formation of such colonization (possibly in the form of a biofilm). These bacteria may contribute to the chondritis known to precede the development of subglottic stenosis. Further studies are indicated to suggest ways to interrupt this process and reduce the incidence of airway injury.
Providing web servers and training in Bioinformatics: 2010 update on the Bioinformatics Links Directory

The Links Directory at Bioinformatics.ca continues its collaboration with Nucleic Acids Research to jointly publish and compile a freely accessible, online collection of tools, databases and resource materials for bioinformatics and molecular biology research. The July 2010 Web Server issue of Nucleic Acids Research adds an additional 115 web server tools and 7 updates to the directory at http://bioinformatics.ca/links_directory/, bringing the total number of servers listed close to an impressive 1500 links. The Bioinformatics Links Directory represents an excellent community resource for locating bioinformatic tools and databases to aid one’s research, and in this context bioinformatic education needs and initiatives are discussed. A complete list of all links featured in this Nucleic Acids Research 2010 Web Server issue can be accessed online at http://bioinformatics.ca/links_directory/narweb2010/. The 2010 update of the Bioinformatics Links Directory, which includes the Web Server list and summaries, is also available online at the Nucleic Acids Research website, http://nar.oxfordjournals. org/.
COMPRESSION AND AFFINE TRANSFORMS RESILIENT WATERMARKING

iii ÖZET . v DEDICATION. vii ACKNOWLEDGEMENTS. viii LIST OF FIGURES . ix LIST OF TABLES . x LIST OF SYMBOLS . xiii LIST OF ABBREVIATIONS . xiv
Nonparametric Estimation of AUC and Partial AUC under Test-Result-Dependent Sampling

The area under a ROC curve (AUC) and partial area under a ROC curve (pAUC) are important summary measures useful in assessing the accuracy of a diagnostic test or a biomarker in discriminating true disease status. We consider nonparametric estimation of AUC and pAUC under a test-result-dependent sampling (TDS) design, which consists of a simple random component and a test-result-dependent component. A TDS design can yield better efficiency and reduced study cost by oversampling or undersampling subjects falling into specified ranges of test results. We obtain a nonparametric empirical likelihood estimate of the test-result distribution under the TDS design. The estimated test-result distribution is then used to construct consistent estimators for AUC and pAUC. We establish asymptotic properties of the proposed estimators. Simulation shows that the proposed estimators have good finite sample properties and that the TDS design is more efficient than a simple random sampling (SRS) design. A data example based on an ongoing lung cancer trial is provided to illustrate the TDS design and the proposed estimators. Biometrics 000, 000–000 DOI: 000 000 0000 Nonparametric Estimation of AUC and Partial AUC under Test-Result-Dependent Sampling Xiaofei Wang1∗, Junling Ma , Stephen L. George Department of Biostatistics and Bioinformatics Duke University Medical Center, DUMC 2717 Durham, N.C. 27710, U.S.A. Research Center of Applied Statistics School of Statistics and Management Shanghai University of Finance and Economics Shanghai 200433, China ∗email: xiaofei.wang@duke.edu Summary: The area under a ROC curve (AUC) and partial area under a ROC curve (pAUC) are important summary measures useful in assessing the accuracy of a diagnostic test or a biomarker in discriminating true disease status. We consider nonparametric estimation of AUC and pAUC under a test-result-dependent sampling (TDS) design, which consists of a simple random component and a test-result-dependent component. A TDS design can yield better efficiency and reduced study cost by oversampling or undersampling subjects falling into specified ranges of test results. We obtain a nonparametric empirical likelihood estimate of the test-result distribution under the TDS design. The estimated test-result distribution is then used to construct consistent estimators for AUC and pAUC. We establish asymptotic properties of the proposed estimators. Simulation shows that the proposed estimators have good finite sample properties and that the TDS design is more efficient than a simple random sampling (SRS) design. A data example based on an ongoing lung cancer trial is provided to illustrate the TDS design and the proposed estimators.
Identification of Structural and Spatial Features that Influence Storm-Related Dune Erosion along a Barrier-Island Ecosystem in the Gulf of Mexico

Abstract Observations of hurricane impacts on coastal communities and predicted increases in tropical storm activity have spurred an interest in protection and restoration of coastal dunes. Dunes are valued for their role in the protection of infrastructure and aesthetic beauty. Past research on dune erosion has focused primarily on laboratory research or mathematical models. We directly assessed impacts of Hurricanes Ivan (2004) and Dennis (2005) on coastal dunes along Santa Rosa Island, a barrier island in the Gulf of Mexico. We recorded dune area for foredunes and secondary dunes, examined the spatial context of each dune, and recorded structural features of each dune before and after each hurricane. Both hurricanes severely impacted foredunes, and removal of foredune protection by Ivan led to severe impacts on secondary dunes from Dennis. Structural features of the dune, such as height and width, influenced resistance against storm-related erosion, but spatial context, such as location with respect to shoreline, also was important. Coastal dunes on this barrier island may be shifting to a state where their formation, recovery, and restoration are influenced heavily by tropical storm activity. The future success of coastal restoration efforts for maintenance of infrastructure or habitat protection should be cognizant of the importance of spatial context in addition to the structural and vegetation characteristics of dunes.
Traffic Offloading Improvements in Mobile Networks

The exponential increase in mobile IP data usage causes a shortage in the mobile bandwidth. Traffic offloading is regarded as a solution to the exploding growth of mobile broadband data traffic in the mobile networks. In this paper, a content aware traffic offload scheme is proposed to implement using multiple access paths simultaneously. Moreover, the process flow based-on the scheme in Long Term Evolution (LTE) and other traffic offloading improvements are also presented. This scheme utilizes Content Centric Networking (CCN) concept and Digital Fountain Codes to handle the multi-path control and reduce the complexity of traffic offload implementation.
An automatic registration method for multitemporal remote sensing images using land cover patches in rural regoins

This paper proposed a stable land cover patches method (SLPM) for automatic registration of multitemporal remote sensing images in rural regions. We defined the stable land cover patches (SLP) as those land cover patches whose area, centroid and shape keep stable as time. And then, a series of steps, including image preprocessing, patches extraction and patches matching, were applied to extract and match SLPs from remote sensing images. In our experiment, a rural region and two HJ images were selected as our study area and data, and finally an accuracy of 0.57 pixel was achieved.
Self-evaluated and close relative-evaluated Epworth Sleepiness Scale vs. multiple sleep latency test in patients with obstructive sleep apnea.

OBJECTIVES The aims of this study were to determine (1) the agreement in Epworth Sleepiness Scale (ESS) evaluated by patients and their close relatives (CRs), and (2) the correlation of objective sleepiness as measured by multiple sleep latency test (MSLT) with self-evaluated and close relative-evaluated ESS. METHODS A total of 85 consecutive patients with obstructive sleep apnea (OSA) (70 males, age 46.7 ± 12.9 years old) with an apnea-hypopnea index (AHI) > 5 events per hour (mean 38.9 ± 26.8/h) were recruited into this study. All participants underwent an overnight polysomnographic assessment (PSG), MSLT, and ESS rated by both patients and their CRs. Mean sleep latency < 8 min on MSLT was considered objective daytime sleepiness. RESULTS Self-evaluated global ESS score (ESSG) was closely correlated with evaluation by CRs (r = 0.79, p < 0.001); the mean ESSG score evaluated by patients did not significantly differ from that evaluated by CRs (p > 0.05). However, Bland- Altman plot showed individual differences between self-evaluated and CR-evaluated ESS scores, with a 95%CI of -9.3 to 7.0. The mean sleep latency on MSLT was significantly associated with CR-evaluated ESSG (r = -0.23, p < 0.05); significance of association with self-evaluated ESSG was marginal (r = -0.21, p = 0.05). CONCLUSIONS CR-evaluated ESS has a good correlation but also significant individual disagreement with self-evaluated ESS in Chinese patients with OSA. CR-evaluated ESS performs as well as, if not better than, self-evaluated ESS in this population when referring to MSLT.
The effects of an open design on trial participant recruitment, compliance and retention – a randomized controlled trial comparison with a blinded, placebo-controlled design

Background In randomized trials there may be no overriding reason whether or not to have a placebo control. Purpose We assessed the effects of an open trial design (no placebo and people know what tablets they are given) compared with a blinded, placebo-controlled design on recruitment, compliance and retention within a randomized trial of secondary osteoporotic fracture prevention. Methods We undertook a randomized controlled comparison nested within a placebo-controlled trial of nutritional supplementation amongst people aged 70 years or over who had previously sustained a fracture, recruited in a UK teaching hospital. Randomization was 2: 1 in favour of the blinded, placebo-controlled trial design. Results From 180 eligible participants randomized to receive information based on the open trial design, 134 (74.4%) consented to take part, compared with 233 (65.1%) of 358 people randomized to the blinded, placebo-controlled design (difference 9.4%, 95% confidence interval 1.3–17.4%). Reluctance to take a placebo and the desire to know tablet allocation were reasons given for not taking part in the blinded, placebo-controlled design. There was no significant difference in tablet compliance. Open trial participants were more likely to remain in the trial for one year (difference 13.9%, 95% confidence interval 3.1–24.6%), mainly reflecting the high retention of the open trial no tablet group compared to the open trial tablet group (difference 23.6%, 95% confidence interval 11.9–35.2%). The odds ratio for reporting an adverse event in the open trial compared to the blinded, placebo-controlled design was 0.64 (95% confidence interval 0.28–1.49), and for reporting a fracture was 0.81 (0.36–1.85). Conclusions We conclude that using an open trial design may enhance participant recruitment and retention and thus improve generalizability and statistical power, but withdrawal rates may differ between the study allocations and may threaten the internal validity of the trial.
Brain-Wide Maps of Synaptic Input to Cortical Interneurons

Cortical inhibition is mediated by diverse inhibitory neuron types that can each play distinct roles in information processing by virtue of differences in their input sources, intrinsic properties, and innervation targets. Previous studies in brain slices have demonstrated considerable cell-type specificity in laminar sources of local inputs. In contrast, little is known about possible differences in distant inputs to different cortical interneuron types. We used the monosynaptic rabies virus system, in conjunction with mice expressing Cre recombinase in either parvalbumin-positive, somatostatin-positive (SST+), or vasoactive intestinal peptide-positive (VIP+) neurons, to map the brain-wide input to the three major nonoverlapping classes of interneurons in mouse somatosensory cortex. We discovered that all three classes of interneurons received considerable input from known cortical and thalamic input sources, as well as from probable cholinergic cells in the basal nucleus of Meynert. Despite their common input sources, these classes differed in the proportion of long-distance cortical inputs originating from deep versus superficial layers. Similar to their laminar differences in local input, VIP+ neurons received inputs predominantly from deep layers while SST+ neurons received mostly superficial inputs. These classes also differed in the amount of input they received. Cortical and thalamic inputs were greatest onto VIP+ interneurons and smallest onto SST+ neurons. SIGNIFICANCE STATEMENT These results indicate that all three major interneuron classes in the barrel cortex integrate both feedforward and feedback information from throughout the brain to modulate the activity of the local cortical circuit. However, differences in laminar sources and magnitude of distant cortical input suggest differential contributions from cortical areas. More input to vasoactive intestinal peptide-positive (VIP+) neurons than to somatostatin-positive (SST+) neurons suggests that disinhibition of the cortex via VIP+ cells, which inhibit SST+ cells, might be a general feature of long-distance corticocortical and thalamocortical circuits.
A Quantitative Study on the Mutual Fund Rating with LDA

In this paper, based on the Morningstar fund rating result in China, a quantitative study on this fund rating with LDA is proposed. And the following conclusions have been drawn from this study. First, quantitative analysis in Morningstar fund rating in China plays an important role and the characters include total return and risk indexes. Second, there is some qualitative analysis concluded in fund rating also. Third, there is a good prediction result for fund data in the same term. But the persistence of the pattern prediction is poor. There are two demonstrations, one is that the patterns got from the data in 2007 are used for 2008 data set and the other is that the pattern got from one term are used for the following five terms in 2007. The results of experiments above show the poor persistence of the pattern predication.
Sclerema Neonatorum Treated Successfully with Parenteral Steroids: An Experience from a Resource Poor Country

Sclerema neonatorum is a form of panniculitides characterized by diffuse hardening of subcutaneous tissue with minimal inflammation. It usually affects ill and preterm neonates. Prognosis is usually poor in many cases despite aggressive management. Various treatment modalities (antibiotics, intravenous immunoglobulin, steroids, and exchange transfusion) have been explained in literature. Steroids due to its easy availability and low cost can prove to be lifesaving in such cases, especially in resource poor countries. Here, we report a case of sclerema neonatorum in a one-week preterm baby treated successfully with parenteral steroids and antibiotics.
Identification of a Human Valacyclovirase

Valacyclovir is the 5′-valyl ester prodrug of acyclovir, an effective anti-herpetic drug. Systemic availability of acyclovir in humans is three to five times higher when administered orally as the prodrug. The increased bioavailability of valacyclovir is attributed to carrier-mediated intestinal absorption, via the hPEPT1 peptide transporter, followed by the rapid and complete conversion to acyclovir. The one or more human enzymes responsible for in vivo activation of the prodrug to the active drug and its conversion sites, however, have not been identified. In this report, we describe the purification, identification, and characterization of a human enzyme that activates valacyclovir to acyclovir. A protein with significant hydrolytic activity toward valacyclovir, the 5′-glycyl ester of acyclovir, and the 5′-valyl ester of zidovudine (AZT), was purified from Caco-2 cells derived from human intestine. Using a non-redundant data base search, the N-terminal 19-amino acid sequence of the purified 27-kDa, basic protein revealed a perfect match within the N terminus of a serine hydrolase, Biphenyl hydrolase-like (BPHL, gi:4757862) protein, previously cloned from human breast carcinoma. Recombinant BPHL exhibited significant hydrolytic activity for both valacyclovir and valganciclovir with specificity constants (kcat/Km), 420 and 53.2 mm–1·s–1, respectively. We conclude that BPHL may be an important enzyme activating valacyclovir and valganciclovir in humans and an important new target for prodrug design.
Recontigurable User Interfaces for Databases

The fixed nature of user interlaces to databases often means that they cannot easily be made to fit the requirements of a particular group of users or tasks. This paper looks at an approach to the interactive reconfiguration of such interfaces. Thus the creation of novel interfaces to the same database can be greatly speeded up and simplified. The paper shows how these concepts can be employed in the representation of schema design and queries to a semantic data model.
Ultraviolet radiation (UVR) activates p38 MAP kinase and induces post‐transcriptional stabilization of the C/EBPδ mRNA in G0 growth arrested mammary epithelial cells

The G0 growth arrest (quiescent) state is highly conserved in evolution to promote survival under adverse environmental conditions. To maintain viability, G0 growth arrested cells limit gene expression to essential growth control and pro‐survival genes. CCAAT enhancer binding proteinδ (C/EBPδ), a member of the C/EBP family of nuclear proteins, is highly expressed in G0 growth arrested mammary epithelial cells (MECs). Although C/EBPδ gene transcription is elevated during G0 growth arrest, C/EBPδ mRNA and protein are relatively short lived, suggesting tight control of the cellular C/EBPδ content in unstressed, quiescent cells. Treatment of G0 growth arrested MECs with ultraviolet radiation (UVR) dramatically increases the C/EBPδ mRNA half‐life (∼4‐fold) and protein content (∼3‐fold). The mRNA stabilizing effects of UVR treatment are mediated by the C/EBPδ mRNA 3′untranslated region, which contains an AU rich element. UVR increased p38 MAP kinase (MAPK) activation and SB203580, a p38 MAPK inhibitor, blocked UVR‐induced C/EBPδ mRNA stabilization. UVR increased the nuclear to cytoplasmic translocation of HuR, an ARE‐binding protein that functions in mRNA stabilization. Finally, HuR siRNA treatment blocked UVR‐induced stabilization of the C/EBPδ and C/EBPβ mRNAs but had no effect on C/EBPζ (CHOP) mRNA stability. In summary, G0 growth arrested MECs respond to UVR treatment by activating p38 MAPK, increasing HuR translocation and HuR/C/EBPδ mRNA binding and stabilizing the C/EBPδ mRNA. These results identify post‐transcriptional stabilization of the C/EBPδ mRNA as a mechanism to increase C/EBPδ levels in the stress response of quiescent cells to UVR. J. Cell. Biochem. 103: 1657–1669, 2008. © 2007 Wiley‐Liss, Inc.
From phenotype to genotype

SUMMARY Advances in the field of genomics have made it possible to decipher the genetic and transcriptional changes that underlie differences among organisms. Here we discuss the merits and drawbacks of these strategies as they relate to evolutionary biology. We suggest that the molecular basis of natural variation can best be interpreted via the intersection of genomic and transcriptome approaches. We outline how this might be accomplished in practice and assemble the components of a method to comprehend the evolutionary interplay between genotype and phenotype.
A Preference Order Dynamic Program for a Stochastic Traveling Salesman Problem

Consider a traveling salesman problem with stochastic travel times. Our objective is to find a tour with maximum probability of completion by a specified time. This paper presents a preference order dynamic program for solving the problem. To facilitate computation, we introduce a branch-and-bound strategy in the solution procedure. Finally, we propose an implicit enumeration algorithm as an alternative approach.
Alignment of Pharmacotherapy Course Assessments With Course Objectives

Objective. To determine whether instructor-prepared classroom examinations for pharmacotherapy courses were aligned with course goals and objectives. Design. Assessment items from examinations in 2 pharmacotherapy courses were evaluated. Four categories of alignment (depth of knowledge, categorical concurrence, range of knowledge, and balance of representation) were used to match course assessments with objectives. Assessment. While assessments met the criteria for acceptable alignment, there were areas for improvement. Goals and objectives were unevenly assessed, with 1 goal aligning with 45% of all assessment items. The assessments covered all content categories and the range of knowledge established by the objectives, but objectives under specific goals were not evenly assessed. Conclusion. This alignment study provided quantitative data useful for review and revision of pharmacotherapy course objectives and assessments and demonstrated the usefulness of alignment assessment as a tool for continuous quality improvement.
The histone acetylranseferase hMOF acetylates Nrf2 and regulates anti‐drug responses in human non‐small cell lung cancer

The histone acetyltransferase MOF is a member of the MYST family. In mammals, MOF plays critical roles by acetylating histone H4 at K16 and non‐histone substrates such as p53. Here we have investigated the role of MOF in human lung cancer and possible new substrates of hMOF.