bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization
Authors: Abernathy J. , Li X. , Jia X. , Chou W. , Lamont S. J. , Crooijmans R. , Zhou H. 
Published: March 2014

SummaryCopy number variation refers to regions along chromosomes that harbor a type of structural variation, such as duplications or deletions. Copy number variants (CNVs) play a role in many important traits as well as in genetic diversity. Previous analyses of chickens using array comparative genomic hybridizations or single‐nucleotide polymorphism chip assays have been performed on various breeds and genetic lines to discover CNVs. In this study, we assessed individuals from two highly inbred (inbreeding coefficiency > 99.99%) lines, Leghorn G‐B2 and Fayoumi M15.2, to discover novel CNVs in chickens. These lines have been previously studied for disease resistance, and to our knowledge, this represents the first global assessment of CNVs in the Fayoumi breed. Genomic DNA from individuals was examined using the Agilent chicken 244 K comparative genomic hybridization array and quantitative PCR. We identified a total of 273 CNVs overall, with 112 CNVs being novel and not previously reported. Quantitative PCR using the standard curve method validated a subset of our array data. Through enrichment analysis of genes within CNV regions, we observed multiple chromosomes, terms and pathways that were significantly enriched, largely dealing with the major histocompatibility complex and immune responsiveness. Using an additional round of computational and statistical analysis with a different bioinformatic pipeline, we identified 43 CNVs among these as high‐confidence regions, 14 of which were found to be novel. We further compared and contrasted individuals of the two inbred lines to discover regions that have a significant difference in copy number between lines. A total of 40 regions had significant deletions or duplications between the lines. Gene Ontology analysis of genomic regions containing CNVs between lines also was performed. This between‐line candidate CNV list will be useful in studies with these two unique genetic lines, which may harbor variations that underlie quantitative trait loci for disease resistance and other important traits. Through the global discovery of novel CNVs in chicken, these data also provide resources for further genetic and functional genomics studies.
Recommendations for the allergy management in the primary care
Authors: Jutel M. , Papadopoulos N. G. , Gronlund H. , Hoffman H.‐J. , Bohle B. , Hellings P. , Braunsthal G.‐J. , Muraro A. , Schmid‐Grendelmeier P. , Zuberbier T. , Agache I. 
Published: March 2014

AbstractThe majority of patients seeking medical advice for allergic diseases are first seen in a primary care setting. Correct diagnosis with identification of all offending allergens is an absolute prerequisite for appropriate management of allergic disease by the general practitioner. Allergy diagnostic tests recommended for use in primary care are critically reviewed in accordance with the significant workload in a primary care setting. Simplified pathways for recognition and diagnosis of allergic diseases are proposed, that should be further adapted to local (national) conditions.
Initial results from mechanical compression of the cornea during crosslinking for keratoconus
Authors: Beckman Rehnman Jeannette , Behndig Anders , Hallberg Per , Lindén Christina 
Published: March 2014

AbstractPurposeTo compare refractive changes after corneal crosslinking with and without mechanical compression of the cornea.MethodsIn a prospective, open, randomized case‐control study conducted at the Department of Ophthalmology, Umeå University Hospital, Sweden, sixty eyes of 43 patients with progressive keratoconus aged 18–28 years planned for corneal crosslinking and corresponding age‐ and sex‐matched control subjects were included. The patients were randomized to conventional corneal crosslinking (CXL; n = 30) or corneal crosslinking with mechanical compression using a flat rigid contact lens sutured to the cornea during treatment (CRXL; n = 30). Subjective refraction and ETDRS best spectacle‐corrected visual acuity (BSCVA), axial length measurement, keratometry and pachymetry were performed before and 1 and 6 months after treatment.ResultsThe keratoconus patients had poorer BSCVA, higher refractive astigmatism and higher keratometry readings than the control subjects at baseline (p < 0.01). In the CXL group, BSCVA increased from 0.19 ± 0.26 to 0.14 ± 0.18 logMar (p = 0.03), and the spherical equivalent improved from −1.9 ± 2.8 D to −1.4 ± 2.4 D (p = 0.03). Maximum keratometry readings decreased after CXL from 53.1 ± 4.9 D to 52.6 ± 5.2 D (p = 0.02), and the axial length decreased in the CXL group, likely due to post‐treatment corneal thinning (p = 0.03). In the CRXL group, all the above variables were unaltered (p > 0.05).ConclusionAt 6 months, the refractive results from CRXL did not surpass those of conventional CXL treatment. Rather, some variables indicated a slightly inferior effect. Possibly, stronger crosslinking would be necessary to stabilize the cornea in the flattened configuration achieved by the rigid contact lens.
Minimally invasive surfactant therapy with a gastric tube is as effective as the intubation, surfactant, and extubation technique in preterm babies
Authors: Aguar Marta , Cernada María , Brugada María , Gimeno Ana , Gutierrez Antonio , Vento Máximo 
Published: March 2014

AbstractAimPreterm infants requiring surfactant replacement have been treated using the INSURE technique, which requires sedation and comprises tracheal intubation, surfactant instillation and extubation. However, minimally invasive surfactant therapy (MIST) does not require sedation, minimises airway injury and avoids placing positive pressure ventilation on an immature lung. This study compared the feasibility of the two techniques and the outcomes in preterm babies with respiratory distress syndrome (RDS).MethodsPreterm infants with RDS prospectively received surfactant via a gastric tube placed in the trachea by direct laryngoscopy with no sedation. Technique‐related complications and respiratory outcomes were analysed.ResultsWe compared 44 patients who received MIST with a historic cohort of 31 patients who received INSURE. This showed no differences in the rate of intubation and mechanical ventilation in the first 72 h, or secondary respiratory outcomes and relevant morbidities, between the babies who received INSURE and those who received MIST. More babies in the MIST group (35%) needed a second dose of surfactant than the INSURE group (6.5%) (p < 0.0001).ConclusionSurfactant administration using MIST, with no sedation, is feasible in preterm infants with RDS. No significant differences in secondary respiratory outcomes were found between the MIST and INSURE techniques.
Expression of MexAB‐OprM efflux pump system and susceptibility to antibiotics of different Pseudomonas aeruginosa clones isolated from patients hospitalized in two intensive care units at University Hospital in Bialystok (northeastern Poland) between January 2002 and December 2009
Authors: Sacha Paweł , Wieczorek Piotr , Ojdana Dominika , Hauschild Tomasz , Milewski Robert , Czaban Sławomir , Poniatowski Bogusław , Tryniszewska Elżbieta 
Published: March 2014

We investigated the genetic similarities and expression of the MexAB‐OprM efflux pump system in different clones of multiresistant Pseudomonas aeruginosa strains collected from 2002 to 2009 at two intensive care units (ICU). Regulatory and structural genes mexB, mexR, and mexA were found in 99%, 98%, and 94% of tested strains, respectively. The presence of class 1 integron was found in 90% of the strains, while class 2 integron in only one strain (Psa506). Class 3 integron was not found in any of the tested strains. Among the eleven clones identified, only two clones, I and D, exhibited higher levels of mexB gene expression than the other clones. Clone I had the highest expression (FC = 10.36, p < 0.05). The results of our study indicated a high level of MexAB‐OprM pump expression in groups of strains isolated in the years 2008–2009 (FC = 12.92, p < 0.03) and 2002–2006 (FC = 5.14, p < 0.03). There were no statistically significant differences in resistance to all tested antibiotics among the various clones. The high level of antimicrobial resistance may have been due to the coexistence of different resistance mechanisms among the studied P. aeruginosa strains. However, this does not exclude the contribution of the MexAB‐OprM pump, particularly in resistance to meropenem and ciprofloxacin.
Saccharomyces boulardii expresses neuraminidase activity selective for α2,3‐linked sialic acid that decreases Helicobacter pylori adhesion to host cells
Authors: Sakarya Serhan , Gunay Necati 
Published: March 2014

Helicobacter pylori is a major causative agent of gastritis and peptic ulcer disease and is an established risk factor for gastric malignancy. Antibiotic combination therapy can eradicate H. pylori. As these same regimens can evoke adverse effects and resistance, new alternative therapies or adjunctive treatments are needed. A probiotic approach may provide a novel strategy for H. pylori treatment. In the current study, two probiotic bacteria, Lactobacillus acidophilus and Lactobacillus reuteri, and a probiotic yeast, Saccharomyces boulardii, were evaluated for their ability to influence H. pylori viability, adherence to gastric and duodenal cells, as well as the effect of S. boulardii on cell surface expression of sialic acid. Our results indicate that S. boulardii contains neuraminidase activity selective for α(2‐3)‐linked sialic acid. This neuraminidase activity removes surface α(2‐3)‐linked sialic acid, the ligand for the sialic acid‐binding H. pylori adhesin, which in turn, inhibits H. pylori adherence to duodenal epithelial cells.
Decreased susceptibility to chlorhexidine and prevalence of disinfectant resistance genes among clinical isolates of Staphylococcus epidermidis
Authors: Prag Gustaf , Falk‐Brynhildsen Karin , Jacobsson Susanne , Hellmark Bengt , Unemo Magnus , Söderquist Bo 
Published: March 2014

Staphylococcus epidermidis is a versatile agent, being both a commensal and a nosocomial pathogen usually with an opportunistic role in association with implanted foreign body materials. Pre‐operative antiseptic preparation is an important strategy for reducing the risk of complications such as surgical site infection (SSI). Currently, the most widely used antiseptics are alcohols, quaternary ammonium compounds (QACs), and the bisbiguanide chlorhexidine. Occurrence of resistance to the latter agent has drawn increasing attention. The aim of this study was to investigate if decreased susceptibility to chlorhexidine among S. epidermidis was present in our setting, a Swedish university hospital. Staphylococcus epidermidis (n = 143), retrospectively collected, were obtained from prosthetic joint infections (PJI) (n = 61), post‐operative infections after cardiac surgery (n = 31), and the skin of the chest after routine disinfection prior to cardiac surgery (n = 27). In addition, 24 commensal isolates were included. Minimum inhibitory concentration (MIC) of chlorhexidine was determined on Mueller Hinton agar plates supplemented with serial dilutions of chlorhexidine. Five QAC resistance genes, qacA/B, smr, qacH, qacJ, and qacG, were detected using PCR. Decreased susceptibility to chlorhexidine was found in 54% of PJI isolates, 68% of cardiac isolates, 21% of commensal isolates, and 7% of skin isolates from cardiac patients, respectively. The qacA/B gene was present in 62/143 isolates (43%), smr in 8/143 (6%), and qacH in one isolate (0.7%). The qacA/B gene was found in 52% of PJI isolates, 61% of cardiac isolates, 25% of commensal isolates, and 19% of the skin isolates. In conclusion, decreased susceptibility to chlorhexidine, as well as QAC resistance genes, were prevalent among S. epidermidis isolates associated with deep SSIs.
Nodal distribution, stage migration due to diameter measurement and the prognostic significance of metastasis volume in melanoma sentinel lymph nodes: a validation study
Authors: Riber‐Hansen Rikke , Hamilton‐Dutoit Stephen J. , Steiniche Torben 
Published: March 2014

To validate metastasis location, maximum metastasis diameter (MMD) measurement induced stage migration and the prognostic significance of total metastatic volume (TMV) in melanoma sentinel lymph nodes (SLNs). A new 227 patient SLN cohort examined by complete step sectioning (250 μm) was tested for TMV and MMD prognostic significance; metastasis location by three different three‐level protocols (Central vs Peripheral vs Global); and potential treatment changing down‐staging by two restricted five‐level protocols [Reduced Central (250 μm) vs Reduced Even (500 μm) sections]. Both TMV and MMD independently predicted recurrence (TMV, hazard ratio (HR): 1.21; 95% confidence interval (CI) 1.07–1.37; p = 0.003; and MMD, HR: 1.46; 95% CI 1.08–1.98, p = 0.02) and melanoma‐specific death (TMV, HR: 1.30; 95% CI 1.11–1.51; p = 0.001; and MMD, HR: 1.82; 95% CI 1.25–2.66, p = 0.002). The Central, Peripheral and Global protocols detected 72%, 76% and 83% of metastases found by complete step sectioning. Based on MMD, using the Reduced Central or Reduced Even protocols, potential treatment changing down‐staging occurred in 20 (20%) or 13 (13%) of SLN‐positive patients. This validation study establishes that: (i) metastases are globally located in melanoma SLNs; (ii) MMD but not TMV leads to uni‐directional stage migration; and (iii) TMV analysis is of prognostic significance.
Immunohistochemical expression ofGPR30 in breast carcinoma of Egyptian patients: an association with immunohistochemical subtypes
Authors: Aiad Hayam A , Wahed Moshera M Abd‐el , Asaad Nancy Y , El‐Tahmody Mohamed , Elhosary Enas 
Published: March 2014

Breast carcinoma in Egyptian women is a biologically more aggressive disease than those diagnosed in Western women, although a substantial number of cases are hormone responsive. G protein–coupled receptor‐30 (GPR30), a seven transmembrane domain protein, is currently recognized as an estrogen receptor. This study aimed at evaluating the expression ofGPR30 in breast carcinomas of Egyptian patients and its association with clinicopathologic parameters and immunohistochemical subtypes of breast carcinoma. Immunohistochemical staining forGPR30 was applied on 51 archival formalin‐fixed paraffin‐embedded cases of invasive ductal carcinoma. Staining was assessed using a semiquantitative scoring system taking staining intensity and extent into consideration.GPR30 was observed in 33/51 (65%) of invasive ductal carcinoma cases.GPR30 was significantly associated with larger tumor size (p = 0.009), increased number of positive lymph nodes (p = 0.04), definite lymph‐vascular invasion (LVI) (p = 0.002), peri‐nodal invasion (p = 0.02), and the presence of coagulative tumor cell necrosis (p = 0.02). Moreover, a significant association between positiveGPR30 expression andERpositivity (p = 0.02), as well asHER2/neu positivity (p = 0.03), were also observed. Most of the luminal A and B subtypes wereGPR30 positive; however, all the triple negative cases wereGPR30 negative (p = 0.010).GPR30 might contribute to the aggressive behavior of Egyptian breast carcinoma. Therefore, it could be useful in the therapeutic decision making in breast cancer patients.
Magnetic resonance imaging pattern of bone marrow involvement as a new predictive parameter of disease progression in newly diagnosed patients with multiple myeloma eligible for autologous stem cell transplantation
Authors: Song Moo‐Kon , Chung Joo‐Seop , Lee Je‐Jung , Min Chang‐Ki , Ahn Jae‐Sook , Lee Sang‐Min , Shin Dong‐Yeop , Bae Sung‐Hwa , Hong Junshik , Lee Gyeong‐won , Lee In‐Sook , Shin Ho‐Jin 
Published: March 2014

SummaryWe investigated the prognostic value of the magnetic resonance imaging (MRI) pattern of bone marrow involvement in patients with multiple myeloma (MM) eligible for autologous stem cell transplantation (ASCT). 126 patients with untreated MM indicated for ASCT underwent spine MRI and cytogenetic analysis at diagnosis. All patients received ASCT after induction therapy of VAD (vincristine, doxorubicin, dexamethasone; n = 55) or a thalidomide‐based regimen (TCD; n = 71). Thalidomide maintenance therapy was performed in 68 patients. The MRI pattern was normal in 27, focal in 47, and diffuse/variegated in 52 patients. Patients with the diffuse/variegated pattern showed significantly higher stage (P = 0·038), higher β‐2 microglobulin level (P = 0·001) and severe anaemia (P = 0·015). However, the cytogenetics were not different among the MRI patterns (P = 0·890). Progression‐free survival (PFS) was lower in the diffuse/variegated pattern (P = 0·002) than other patterns, but not overall survival (OS) (P = 0·058). Thalidomide maintenance therapy was correlated only with PFS (P = 0·001). High‐risk cytogenetics were associated with both poorer PFS (P < 0·001) and OS (P = 0·003). In a multivariate analysis, the diffuse/variegated MRI pattern was an independent predictor of disease progression (Hazard Ratio, 1·922; 95% confidence interval, 1·185–3·118; P = 0·008). The diffuse/variegated MRI pattern is a novel prognostic factor for disease progression in MM patients eligible for ASCT.
F‐18 FDG‐PET predicts outcomes for patients receiving total lymphoid irradiation and autologous blood stem‐cell transplantation for relapsed and refractory Hodgkin lymphoma
Authors: Gentzler Ryan D. , Evens Andrew M. , Rademaker Alfred W. , Weitner Bing B. , Mittal Bharat B. , Dillehay Gary L. , Petrich Adam M. , Altman Jessica K. , Frankfurt Olga , Variakojis Daina , Singhal Seema , Mehta Jayesh , Williams Stephanie , Kaminer Lynne , Gordon Leo I. , Winter Jane N. 
Published: March 2014

SummaryTotal lymphoid irradiation (TLI) followed by high‐dose chemotherapy and autologous haematopoietic stem cell transplant (aHSCT) is an effective strategy for patients with relapsed/refractory classical Hodgkin lymphoma (HL). We report outcomes for patients with relapsed/refractory HL who received TLI followed by high‐dose chemotherapy and aHSCT. Pre‐transplant fludeoxyglucose positron emission tomography (FDG‐PET) studies were scored on the 5‐point Deauville scale. Of 51 patients treated with TLI and aHSCT, 59% had primary refractory disease and 63% had active disease at aHSCT. The 10‐year progression‐free survival (PFS) and overall survival (OS) for all patients was 56% and 54%, respectively. Patients with complete response (CR) by PET prior to aHSCT had a 5‐year PFS and OS of 85% and 100% compared to 52% and 48% for those without CR (P = 0·09 and P = 0·007, respectively). TLI and aHSCT yields excellent disease control and long‐term survival rates for patients with relapsed/refractory HL, including those with high‐risk disease features. Achievement of CR with salvage therapy is a powerful predictor of outcome.
Inhibitor eradication with rituximab in haemophilia: where do we stand?
Authors: Franchini Massimo , Mannucci Pier Mannuccio 
Published: March 2014

SummaryRituximab is a humanized chimeric anti‐CD20 monoclonal antibody initially developed for the treatment of some haematological malignancies. Thanks to its ability to rapidly and specifically deplete B cells, it has also been used in a variety of autoimmune disorders, haematological or not. In this context, during the last decade several small case series have documented successful inhibitor eradication with rituximab, alone or in combination with other immunosuppressive agents, in patients with acquired haemophilia A refractory to standard therapy. In addition, a number of investigators have recently used this agent in patients with congenital haemophilia A or B and alloantibodies refractory to first‐line treatment. This article critically reviews the current knowledge on the use of rituximab in acquired haemophilia or congenital haemophilia complicated by alloantibodies, also providing treatment algorithms for the management of these conditions.
ATF7IP as a novel PDGFRB fusion partner in acute lymphoblastic leukaemia in children
Authors: Kobayashi Kenichiro , Mitsui Kazumasa , Ichikawa Hitoshi , Nakabayashi Kazuhiko , Matsuoka Masaki , Kojima Yasuko , Takahashi Hiroyuki , Iijima Kazutoshi , Ootsubo Kaori , Oboki Keisuke , Okita Hajime , Yasuda Kazuki , Sakamoto Hiromi , Hata Kenichiro , Yoshida Teruhiko , Matsumoto Kenji , Kiyokawa Nobutaka , Ohara Akira 
Published: March 2014

SummaryWe identified ATF7IP as a novel PDGFRB fusion partner in B‐progenitor acute lymphoblastic leukaemia (B‐ALL) and showed that B‐ALL with ATF7IP/PDGFRB translocation is included within the genomic lesions of a Philadelphia chromosome (Ph)‐like ALL subgroup. Comprehensive analyses of previous repositories of gene expression data sets disclosed that B‐ALL cases with high PDGFRB expression level in the context of the Ph‐like ALL gene are likely to have a PDGFRB translocation. Thus, it is possible that measurement of the PDGFRB expression level can be utilized as a screening test for the detection of the cryptic PDGFRB translocation, especially within the Ph‐like ALL subgroup.
Discriminant content validity: A quantitative methodology for assessing content of theory‐based measures, with illustrative applications
Authors: Johnston Marie , Dixon Diane , Hart Jo , Glidewell Liz , Schröder Carin , Pollard Beth 
Published: March 2014

ObjectivesIn studies involving theoretical constructs, it is important that measures have good content validity and that there is not contamination of measures by content from other constructs. While reliability and construct validity are routinely reported, to date, there has not been a satisfactory, transparent, and systematic method of assessing and reporting content validity. In this paper, we describe a methodology of discriminant content validity (DCV) and illustrate its application in three studies.MethodsDiscriminant content validity involves six steps: construct definition, item selection, judge identification, judgement format, single‐sample test of content validity, and assessment of discriminant items. In three studies, these steps were applied to a measure of illness perceptions (IPQ‐R) and control cognitions.ResultsThe IPQ‐R performed well with most items being purely related to their target construct, although timeline and consequences had small problems. By contrast, the study of control cognitions identified problems in measuring constructs independently. In the final study, direct estimation response formats for theory of planned behaviour constructs were found to have as good DCV as Likert format.ConclusionsThe DCV method allowed quantitative assessment of each item and can therefore inform the content validity of the measures assessed. The methods can be applied to assess content validity before or after collecting data to select the appropriate items to measure theoretical constructs. Further, the data reported for each item in Appendix S1 can be used in item or measure selection.
Statement of contribution

What is already known on this subject?

There are agreed methods of assessing and reporting construct validity of measures of theoretical constructs, but not their content validity. Content validity is rarely reported in a systematic and transparent manner.

What does this study add?

The paper proposes discriminant content validity (DCV), a systematic and transparent method of assessing and reporting whether items assess the intended theoretical construct and only that construct.

In three studies, DCV was applied to measures of illness perceptions, control cognitions, and theory of planned behaviour response formats.

Appendix S1 gives content validity indices for each item of each questionnaire investigated.

Discriminant content validity is ideally applied while the measure is being developed, before using to measure the construct(s), but can also be applied after using a measure.