bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of a portable nitric oxide analyzer for screening in primary ciliary dyskinesias
Authors: Harris Amanda , Bhullar Esther , Gove Kerry , Joslin Rhiannon , Pelling Jennifer , Evans Hazel J , Walker Woolf T , Lucas Jane S 
Published: February 2014

Abstract

Background
Nasal nitric oxide (nNO) levels are very low in primary ciliary dyskinesia (PCD) and it is used as a screening test.

Methods
We assessed the reliability and usability of a hand-held analyser in comparison to a stationary nitric oxide (NO) analyser in 50 participants (15 healthy, 13 PCD, 22 other respiratory diseases; age 6–79 years). Nasal NO was measured using a stationary NO analyser during a breath-holding maneuver, and using a hand-held analyser during tidal breathing, sampling at 2 ml/sec or 5 ml/sec. The three methods were compared for their specificity and sensitivity as a screen for PCD, their success rate in different age groups, within subject repeatability and acceptability. Correlation between methods was assessed.

Results
Valid nNO measurements were obtained in 94% of participants using the stationary analyser, 96% using the hand-held analyser at 5 ml/sec and 76% at 2 ml/sec. The hand-held device at 5 ml/sec had excellent sensitivity and specificity as a screening test for PCD during tidal breathing (cut-off of 30 nL/min,100% sensitivity, >95% specificity). The cut-off using the stationary analyser during breath-hold was 38 nL/min (100% sensitivity, 95% specificity). The stationary and hand-held analyser (5 ml/sec) showed reasonable within-subject repeatability(% coefficient of variation = 15).

Conclusion
The hand-held NO analyser provides a promising screening tool for PCD.
Rheoreversible hydrogels in paper restoration processes: a versatile tool
Authors: Mazzuca Claudia , Micheli Laura , Marini Federico , Bevilacqua Marta , Bocchinfuso Gianfranco , Palleschi Giuseppe , Palleschi Antonio 
Published: February 2014

Abstract

Background
Paper based artworks are probably ones of the most difficult materials to restore, because of their complexity and fragile structure. Cleaning of paper artifacts, one of the process commonly carried out during restoration, usually involves the use of solvents (organic or not), that may cause several troubles, like swelling and dissolution of some components, and may also be harmful to the users.

Results
Innovative procedure for cleaning paper artworks is reported in this paper. It is based on the use of rheoreversible, biocompatible hydrogels containing poly(ethylene oxide) or poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) and α-cyclodextrin. We have studied two types of polymer with different hydrophobic properties in order to obtain two different hydrogels with slightly different cleaning capabilities. Our overall strategy has been to develop innovative systems based on these hydrogels so as to better confront the problems that a restorer faces during the cleaning of paper samples. Rheoreversible hydrogels are intriguing materials because their application and removal is not invasive and does not require a liquid treatment that could induce damage to the paper.

Conclusions
These hydrogels have been applied in the cleaning of both new and aged paper samples and their cleaning efficiency has been established. Moreover, by comparison with traditional methods, the greater efficacy of the proposed procedure has been demonstrated.
To assess the cleaning efficacy of these hydrogels, a multidisciplinary approach, combining non-invasive spectroscopic infrared techniques together with scanning electron microscopy, chromatographic (HPLC) analysis and pH investigations has been used. Near infrared spectroscopy spectra were coupled with a chemometric analysis to achieve a better interpretation of data.
This work constitutes a preliminary step towards focused study in the development of α-cyclodextrin/polymer hydrogel family which will allow cleaning of paper artifacts with peculiar characteristics.
Translational medicine as a new clinical tool and application which improves metabolic diseases: perspectives from 2012 Sino‐American symposium on clinical and translational medicine
Authors: Shi Lin , López Villar Elena , Chen Chengshui 
Published: February 2014

AbstractBecause of the economic growth and changes in lifestyle, metabolic diseases have become a major public health problem, which impose heavy economic burdens on individuals, families and health systems. However, its precise mediators and mechanisms remain to be fully understood. Clinical translational medicine (CTM) is an emerging area comprising multidisciplinary research from basic science to medical applications and as a new tool to improve human health by reducing disease incidence, morbidity and mortality. It can bridge knowledge of metabolic diseases processes, gained by in vitro and experimental animal models, with the disease pathways found in humans, further to identify their susceptibility genes and enable patients to achieve personalized medicament treatment. Thus, we have the reasons to believe that CTM will play even more roles in the development of new diagnostics, therapies, healthcare, and policies and the Sino‐American Symposium on Clinical and Translational Medicine (SAS‐CTM) will become a more and more important platform for exchanging ideas on clinical and translational research and entails a close collaboration among hospital, academia and industry.
Volume and outcome relation in German liver transplant centers: what lessons can be learned?
Authors: Nijboer Annemarie , Ulrich Frank , Bechstein Wolf O , Schnitzbauer Andreas A 
Published: February 2014

Abstract

Background
The volume and outcome relationship for transplant procedures has become one of the major topics during discussions about consequences following the organ transplantation scandal of wait-list manipulations in Germany during the past year. Proponents of reducing the number of centers argue in favor of increasing quality at highly specialized transplant centers while disregarding the wish of patients for regionally available medical service.

Methods
The homepage of the German Organ Procurement Organization (DSO) was screened for the annual reports of transplant programs for the years 2007 to 2010. Results were extracted from these reports. Additionally, an analysis of volume per million people per number of transplant centers for each German federal state was made to give an overview of the density of transplant programs for the years 2009 to 2011.

Results
In-house mortality (R2 = 0.005, P = 0.518), 3-year survival (R2 = 0.068, P = 0.085), and a ROC analysis for in-house mortality (AUC 0.55, CI: 0.41; 0.68, P = 0.53), did not show volume-outcome relation. Definition of a threshold for good centers was impossible. One-year survival indicated better outcome in high volume centers. R2 = 0.106, P = 0.009. Outcome data in Germany, as provided by Institute für angewandte Qualitätsförderung und Forschung im Gesundheitswesen (AQUA) or the DSO, are not risk adapted for the investigated time period. The factor of transplants per year per million people per transplant centers is 0.6 for Germany. Some Federal States (for example, Bavaria and Northrhine Westfalia) have an oversupply of transplant centers, which means that the average number transplanted per center and year is very low.

Discussion and conclusion
We propose a risk-adapted prospective analysis of outcome and definition of a quality catalogue for liver transplant centers. Volume and outcome relation is not conclusive for liver transplantation in Germany. Data should be collected, for example, for a time period of 3 to 5 years, and decisions influencing the regulation of numbers of transplant centers should be based upon the findings, weighing federal state sovereignty and regional medical requirements against an optimal patient supply while respecting a plausible risk adaption for each center.
A multidisciplinary diagnostic approach preliminary to the restoration of the country church “San Maurizio” located in Ittiri (SS), Italy
Authors: Sammartino Maria P , Cau Gavino , Reale Rita , Ronca Sara , Visco Giovanni 
Published: February 2014

Abstract

Background
The knowledge of the structure of an artefact, as well as that of its constituent materials and of the hosting environment surely ensures safe guideline for its restoration. Unfortunately, in most cases, a scientific investigation preliminary to restoration is not accomplished due to its high costs and, as a fact, diagnostics is performed only for very precious artworks.
This paper aims to provide a multidisciplinary diagnostic procedure that, although not exhaustive, is rigorous and relatively low cost. It was employed in view of the restoration works on a country church located in Sardinia. A careful inspection of all the architectural elements was carried out in order to highlight structural damages as well as sources of them. One stone and one plaster samples were analysed. The salt content was determined, in two different areas of the church, using three different sampling procedures while only the normed method was used for the determination along the stratigraphy of the sampled plaster. Microclimate monitoring was also carried out.

Results
Water infiltration through the roof was observed. Natural stones and artificial building materials used in the basic architecture resulted to have local source. Both the preliminary “by eye” inspection and the optical microscopy revealed several finishing layers in the investigated plaster samples. The salt content, with some exception, resulted rather low. Microclimate parameters show significant variations only in few areas of the building.

Conclusions
Damage observed inside the oldest part of the Church seems to be mainly related to water infiltrations through the roof and the lack of an effective drainage of the rainwater due to a previous bad restoration. Masonry from one of the newest rooms, showing a strong biodeterioration, as well as some areas inside the nave, revealed a significantly high sulphate content. Building materials (stone and aggregates of mortars) are of local provenance.
Vitamin D levels in Indian systemic lupus erythematosus patients: association with disease activity index and interferon alpha
Authors: Mandal Manamita , Tripathy Rina , Panda Aditya K , Pattanaik Sarit S , Dakua Simanchal , Pradhan Anjan Kumar , Chakraborty Soumen , Ravindran Balachandran , Das Bidyut K 
Published: February 2014

Abstract
Introduction
Low levels of vitamin D have been associated with several autoimmune disorders including multiple sclerosis, rheumatoid arthritis, type 1 diabetes and systemic lupus erythematosus (SLE). The major source of vitamin D is sunlight but exposure of SLE patients to UV rays has been shown to exacerbate disease pathology. Studies in various populations have shown an association between low vitamin D levels and higher SLE disease activity.

Methods
We enrolled 129 patients who fulfilled American College of Rheumatology criteria in the study. There were 79 treatment-naïve cases and 50 patients who were under treatment for underlying SLE. There were 100 healthy subjects from similar geographical areas included as controls. Plasma 25-OH vitamin D3 and interferon (IFN)-α levels were quantified by enzyme-linked immunosorbent assay (ELISA). The gene expression level of IFN-α was determined by quantitative real-time reverse transcriptase polymerase chain reaction (RT-PCR).

Results
Plasma 25-OH vitamin D3 significantly correlated in an inverse manner with systemic lupus erythematosus disease activity index (SLEDAI) scores (P <0.0001, r = -0.42), anti-dsDNA (P <0.0001, r = -0.39), plasma IFN-α (P <0.0001, r = -0.43) and levels of IFN-α gene expression (P = 0.0009, r = -0.45). Further, plasma levels of IFN-α positively correlated with gene expression of IFN-α (P <0.0001, r = 0.84). Treatment-naïve SLE patients displayed significantly higher plasma levels of IFN-α compared to patients under treatment (P <0.001) and controls (P <0.001).

Conclusions
These results suggest an important role of vitamin D in regulating disease activity in SLE patients and the need to supplement vitamin D in their treatment.
Randomized Phase III Trial Exploring the Use of Long-Acting Release Octreotide in the Prevention of Chemotherapy-Induced Diarrhea in Patients With Colorectal Cancer: The LARCID Trial
Authors: Hoff Paulo M. , Saragiotto Daniel F. , Barrios Carlos H. , del Giglio Auro , Coutinho Anelisa K. , Andrade Aline C. , Dutra Carolina , Forones Nora M. , Correa Mariangela , Portella Maria do Socorro O. , Passos Vanessa Q. , Chinen Renata N. , van Eyll Brigitte 
Published: February 2014

Purpose Chemotherapy-induced diarrhea (CID) is a relatively common adverse event in the treatment of patients with colorectal cancer. The LAR for Chemotherapy-Induced Diarrhea (LARCID) trial evaluated the efficacy and safety of long-acting release octreotide (octreotide LAR) for the prevention of CID in this population. Patients and Methods Patients with colorectal cancer starting adjuvant or first-line treatment with a chemotherapy combination containing fluorouracil, capecitabine, and/or irinotecan were randomly assigned to receive octreotide LAR 30 mg intramuscularly every 4 weeks (experimental arm) or the physician's treatment of choice in case of diarrhea (control arm). Results A total of 139 patients were randomly assigned, most of whom received fluorouracil- and oxaliplatin-containing chemotherapy regimens. The rate of diarrhea was 76.1% in the experimental group (n = 68) and 78.9% in the control group (n = 71). Treatment with octreotide LAR did not prevent or reduce the severity of CID. Treatment choices for diarrhea management included loperamide in the majority of patients. No benefit from octreotide LAR was identified in terms of need for diarrhea treatment, opioids, or intravenous hydration or in the rate of hospitalization or quality of life. Conclusion This study could not prove the efficacy of octreotide LAR in the prevention of CID.
Impact of Craniospinal Dose, Boost Volume, and Neurologic Complications on Intellectual Outcome in Patients With Medulloblastoma
Authors: Moxon-Emre Iska , Bouffet Eric , Taylor Michael D. , Laperriere Normand , Scantlebury Nadia , Law Nicole , Spiegler Brenda J. , Malkin David , Janzen Laura , Mabbott Donald 
Published: February 2014

Purpose To examine the impact of radiation (ie, craniospinal irradiation [CSR] dose and boost volume) and complications (ie, hydrocephalus and other neurologic complications, including mutism) on patterns of change in intellectual functioning in medulloblastoma survivors. Patients and Methods We conducted a retrospective review of 113 patients treated for medulloblastoma between 1983 and 2011 who were seen for neuropsychological assessment, including longitudinal follow-up of intellectual function. Patients were treated with either standard-dose CSR with a posterior fossa (PF) boost (n = 51), standard-dose CSR plus tumor bed (TB) boost (n = 9), reduced-dose CSR plus PF boost (n = 28), or reduced-dose CSR plus TB boost (n = 23), with or without chemotherapy. A subset of patients developed hydrocephalus that required cerebrospinal fluid (CSF) diversion (n = 54) and/or other neurologic complications (n = 40), more than half of which were postoperative mutism (n = 25). Growth curve analysis was used to determine stability or change in intelligence scores over time. Results Patients treated with reduced-dose CSR plus TB boost showed stable intellectual trajectories, whereas patients treated with higher doses and larger boost volumes experienced intellectual declines. Presence of complications was associated with worse intellectual outcome; however, hydrocephalus requiring CSF diversion and mutism differed in their pattern of decline. Conclusion These results improve our understanding of factors that impair intellectual outcome in patients treated for medulloblastoma. Lower doses of CSR and smaller boost volumes seem to mitigate intellectual decline. Our findings validate the use of TB boost and suggest PF boost should be reconsidered.
From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development.
Authors: Khodiyar Varsha K , Howe Doug , Talmud Philippa J , Breckenridge Ross , Lovering Ruth C 
Published: February 2014

For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer’s vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer’s vesicle determine asymmetry in the developing heart, the direction of ‘heart jogging’ and the direction of ‘heart looping’. ‘Heart jogging’ is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward ‘jog’. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development. We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging. We found that the human, mouse and zebrafish ‘heart jogging orthologs’ are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging. This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach.
Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes
Authors: Kalbfleisch Ted , Heaton Michael P. 
Published: February 2014

Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease. High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals. Comparisons between these species have provided unique insights into mammalian gene function. However, the number of species with reference genomes is small compared to those needed for studying molecular evolutionary relationships in the tree of life. For example, among the even-toed ungulates there are approximately 300 species whose phylogenetic relationships have been calculated in the 10k trees project. Only six of these have reference genomes: cattle, swine, sheep, goat, water buffalo, and bison. Although reference sequences will eventually be developed for additional hoof stock, the resources in terms of time, money, infrastructure and expertise required to develop a quality reference genome may be unattainable for most species for at least another decade. In this work we mapped 35 Gb of next generation sequence data of a Katahdin sheep to its own species’ reference genome (Ovis aries Oar3.1) and to that of a species that diverged 15 to 30 million years ago (Bos taurus UMD3.1). In total, 56% of reads covered 76% of UMD3.1 to an average depth of 6.8 reads per site, 83 million variants were identified, of which 78 million were homozygous and likely represent interspecies nucleotide differences. Excluding repeat regions and sex chromosomes, nearly 3.7 million heterozygous sites were identified in this animal vs. bovine UMD3.1, representing polymorphisms occurring in sheep. Of these, 41% could be readily mapped to orthologous positions in ovine Oar3.1 with 80% corroborated as heterozygous. These variant sites, identified via interspecies mapping could be used for comparative genomics, disease association studies, and ultimately to understand mammalian gene function.
A Comparison of Deep Sequencing of TCRG Rearrangements vs Traditional Capillary Electrophoresis for Assessment of Clonality in T-Cell Lymphoproliferative Disorders
Authors: Schumacher Jonathan A. , Duncavage Eric J. , Mosbruger Timothy L. , Szankasi Philippe M. , Kelley Todd W. 
Published: February 2014

Abstract

Objectives:
To design and evaluate a next-generation sequencing (NGS)–based method for T-cell receptor γ (TCRG) gene-based T-cell clonality testing on the Ion Torrent Personal Genome Machine (Life Technologies, Carlsbad, CA) platform.

Methods:
We analyzed a series of peripheral blood, bone marrow, and formalin-fixed paraffin-embedded tissue specimens with NGS vs traditional capillary electrophoresis methods.

Results:
Using a custom analysis algorithm that we developed, our NGS assay identified between 2,215 and 48,222 unique TCRG rearrangements in a series of 48 samples. We established criteria for assigning clonality based on parameters derived from both the relative and absolute frequencies of reads. In a comparison with standard capillary electrophoresis, 19 of 19 polyclonal samples and 24 of 27 samples that appeared clonal were in agreement. The three discrepant samples demonstrated some of the pitfalls of amplicon length–based testing. Dilution studies with T-lymphoid cell lines demonstrated that a known clonal sequence could be routinely identified when present in as few as 0.1% of total cells demonstrating suitability in residual disease testing. A series of samples was also analyzed on a second NGS platform and yielded very similar results with respect to the frequency and sequence of the clonal rearrangement.

Conclusions:
In this proof-of-concept study, we describe an NGS-based T-cell clonality assay that is suitable for routine clinical testing either alone or as an adjunct to traditional methods.
MDM2 Copy Numbers in Well-Differentiated and Dedifferentiated Liposarcoma
Authors: Ware Patrick L. , Snow Anthony N. , Gvalani Maya , Pettenati Mark J. , Qasem Shadi A. 
Published: February 2014

Abstract

Objectives:
MDM2 gene amplification is associated with well-differentiated (WDL) and dedifferentiated liposarcomas (DDL). Using fluorescent in situ hybridization (FISH), we sought to characterize various patterns of MDM2 amplification among the morphologic spectrum of liposarcoma.

Methods:
Forty-six cases of liposarcoma in various sites were examined and included 22 WDLs, 14 DLLs, and 10 negative control subjects.

Results:
The MDM2 amplification ratio (MDM2/CEP12) was lower in WDL (10.2) compared with DDL (18.3) cases (P = .0000002). An amplification ratio of 16 showed optimal sensitivity (0.86) and specificity (0.96) as a cutoff point for progression to DDL. Borderline areas, defined as tumors with increased cellularity and atypia but with preserved lipomatous differentiation, showed a significantly higher MDM2 ratio (17.5; P = .0007) compared with WDL. Central (retroperitoneal and intra-abdominal) tumors also showed a significantly higher MDM2 ratio than peripheral ones (P = .02).

Conclusions:
Differences in MDM2 amplification profiles among liposarcomas could help further define and predict progression to high-grade neoplasia.