bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-speed digital imaging laryngoscopy of the neoglottis following supracricoid laryngectomy with cricohyoidoepiglottopexy
Authors: Hayashi S , Hirose H , Tayama N , Imagawa H , Nakayama M , Seino Y , Okamoto M , Kimura M , Nito T 
Published: May 2010

AbstractObjectives:This study aimed to analyse vocal performance and to investigate the nature of the neoglottal sound source in patients who had undergone supracricoid laryngectomy with cricohyoidoepiglottopexy, using a high-speed digital imaging system.Methods:High-speed digital imaging analysis of neoglottal kinetics was performed in two patients who had undergone supracricoid laryngectomy with cricohyoidoepiglottopexy; laryngotopography, inverse filtering analysis and multiline kymography were also undertaken.Results:In case one, laryngotopography demonstrated two vibrating areas: one matched with the primary (i.e. fundamental) frequency (75 Hz) and the other with the secondary frequency (150 Hz) at the neoglottis. In case two, laryngotopography showed two vibrating areas matched with the fundamental frequency (172 Hz) at the neoglottis. The interaction between the two areas was considered to be the sound source in both patients. The waveform of the estimated volume flow at the neoglottis, obtained by inverse filtering analysis, corresponded well to the neoglottal vibration patterns derived by multiline kymography. These findings indicated that the specific sites identified at the neoglottis by the present method were likely to be the sound source in each patient.Conclusions:High-speed digital imaging analysis is effective in locating the sites responsible for voice production in patients who have undergone supracricoid laryngectomy with cricohyoidoepiglottopexy. This is the first study to clearly identify the neoglottal sound source in such patients, using a high-speed digital imaging system.
Faeces, FACS, and functional assays – preparation of Isospora suis oocyst antigen and representative controls for immunoassays
Authors: WORLICZEK H. L. , RUTTKOWSKI B. , JOACHIM A. , SAALMÜLLER A. , GERNER W. 
Published: May 2010

SUMMARYHighly purified antigen and appropriate controls are essential for antigen-specific immunoassays. In the case of Isospora suis, the causative agent of neonatal porcine coccidiosis, the only current source of antigen is oocysts isolated from faeces. The aim of this study was to develop a procedure for high-grade purification of I. suis oocysts from piglet faeces to obtain both antigen and representative controls suitable for in vitro re-stimulation of lymphocytes. This was achieved by use of filtration, density-gradient centrifugation and fluorescence-activated cell sorting (FACS). The feasibility for immunological studies was demonstrated with IFN-γ ELISPOT assays after in vitro re-stimulation of lymphocytes from previously infected swine using the obtained antigen. The developed method allowed the production of highly purified antigen and representative controls from faeces with an oocyst recovery rate of 14%. Regarding the application of the obtained material it could be shown that lymphocytes from I. suis-infected pigs react in an antigen-specific manner in terms of an in vitro recall response by the production of IFN-γ. This demonstrates the suitability of the developed method for the production of antigen and controls for sensitive immunological readout systems. Moreover, the detected specific IFN-γ response encourages further functional studies on the cellular immune response to I. suis.
Human meningitis from Streptococcus equi subsp. zooepidemicus acquired as zoonoses
Authors: MINCES L. R. , BROWN P. J. , VELDKAMP P. J. 
Published: May 2010

SUMMARYStreptococcus equi subsp. zooepidemicus rarely causes meningitis in humans by contact with domestic animals or their unpasteurized products. In this paper we reviewed the literature pertaining to the epidemiological and clinical aspects relating to this infection on previously reported cases of human disease. Additionally, the case of a 51-year-old female who acquired meningitis with this organism after contact with a horse is described. This patient was successfully treated with ceftriaxone, yet penicillin remains the treatment of choice. This aetiological agent should be considered in the proper epidemiological context.
The role of pulmonary intravascular macrophages in porcine reproductive and respiratory syndrome virus infection
Authors: Thanawongnuwech Roongroje , Halbur Patrick G. , Thacker Eileen L. 
Published: May 2010

AbstractThe objective of this article is to summarize the current state of knowledge of the complex interaction of porcine reproductive and respiratory syndrome virus (PRRSV) and porcine pulmonary intravascular macrophages (PIMs). PIMs play an important role in pulmonary surveillance, and in the past few years we have investigated their role in PRRSV infection. PRRSV antigens and nucleic acids have been demonstrated in PIMs bothin vitroandin vivo. Examination of cultured PIMs infected with PRRSV revealed the accumulation of viral particles in the smooth-walled vesicles. PRRSV-infected PIMsin vitroyielded a virus titer similar to pulmonary alveolar macrophages. PRRSV infection induces either apoptosis or cell lysis of PIMs. Thein vitrobactericidal activity of PRRSV-infected PIMs is significantly decreased. Phagocytic activity of PIMs, as measured by pulmonary copper clearance, is significantly decreased in PRRSV-infected pigs. This evidence supports the hypothesis that PRRSV-induced damage to PIMs results in increased susceptibility to bacteremic diseases. Recent studies with PRRSV andStreptococcus suiscoinfection confirmed that PRRSV predisposes pigs toS. suisinfection and bacteremia. These results could explain the increase in bacterial respiratory diseases and septicemias observed in PRRSV-infected pigs.
A comprehensive review of goat pox and sheep pox and their diagnosis
Authors: Rao T. V. S. , Bandyopadhyay S. K. 
Published: May 2010

AbstractSheep and goats occupy a premier place in the livestock industry and contribute significantly to the world economy. Their populations are threatened by a number of health hazards, among the most notable of which are goat pox and sheep pox. These diseases inflict substantial losses in terms of reduced productivity and lower quality of wool and leather. They pose a major obstacle to the intensive rearing of sheep and goats and considerably hamper international trade. A comprehensive knowledge of goat pox and sheep pox would help in the diagnosis, prevention and control as well as the management of these diseases in a proper and effective manner. Although the two diseases are easily identified from the clinical signs and host species affected, laboratory tests are needed for confirmation. A battery of simple but highly efficient diagnostic methods and reagents is available for goat pox and sheep pox. However, the best way to control these diseases is the prophylactic immunization of all susceptible animals with a potent and efficacious vaccine, especially in areas where these diseases are endemic.
Identification of a novel UDP-sugar pyrophosphorylase with a broad substrate specificity in Trypanosoma cruzi
Authors: Yang Ting , Bar-Peled Maor 
Published: May 2010

The diverse types of glycoconjugates synthesized by trypanosomatid parasites are unique compared with the host cells. These glycans are required for the parasite survival, invasion or evasion of the host immune system. Synthesis of those glycoconjugates requires a constant supply of nucleotide-sugars (NDP-sugars), yet little is known about how these NDP-sugars are made and supplied. In the present paper, we report a functional gene from Trypanosoma cruzi that encodes a nucleotidyltransferase, which is capable of transforming different types of sugar 1-phosphates and NTP into NDP-sugars. In the forward reaction, the enzyme catalyses the formation of UDP-glucose, UDP-galactose, UDP-xylose and UDP-glucuronic acid, from their respective monosaccharide 1-phosphates in the presence of UTP. The enzyme could also convert glucose 1-phosphate and TTP into TDP-glucose, albeit at lower efficiency. The enzyme requires bivalent ions (Mg2+ or Mn2+) for its activity and is highly active between pH 6.5 and pH 8.0, and at 30–42 °C. The apparent Km values for the forward reaction were 177 μM (glucose 1-phosphate) and 28.4 μM (UTP) respectively. The identification of this unusual parasite enzyme with such broad substrate specificities suggests an alternative pathway that might play an essential role for nucleotide-sugar biosynthesis and for the regulation of the NDP-sugar pool in the parasite.
COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for mining complex motifs in whole genomes
Authors: Maccari Giuseppe , Gemignani Federica , Landi Stefano 
Published: May 2010

Abstract
Motivation: The complete sequencing of the human genome shows that only 1% of the entire genome encodes for proteins. The major part of the genome is made up of non-coding DNA, regulatory elements and junk DNA. Transcriptional regulation plays a central role in a multitude of critical cellular processes and responses, and it is a central force in the development and differentiation of multicellular organisms. Identifying regulatory elements is one of the major tasks in this challenge. To accomplish this task, we developed a solid and simple suite that allows direct access to genomic database and immediate result check. We introduce COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for motif search in entire genomes. Motifs can be partially degenerated and interrupted by spacers of variable length.
Results: We demonstrate through real biological data mining the simplicity and robustness of this tool. The test was performed on two well-known protein domains and a highly variable cis-acting element. COMPASSS successfully identifies both protein domains and cis-acting semi-conserved elements.
Availability: The COMPASSS suite is available for Windows free of charge from our web sites: compasss.sourceforge.net/; www.stefanolandi.eu/
Contact: gpmaccari@gmail.com; slandi@biologia.unipi.it
Supplementary information: Supplementary data are available at Bioinformatics online.
A quality control algorithm for filtering SNPs in genome-wide association studies
Authors: Pongpanich Monnat , Sullivan Patrick F. , Tzeng Jung-Ying 
Published: May 2010

Abstract
Motivation: The quality control (QC) filtering of single nucleotide polymorphisms (SNPs) is an important step in genome-wide association studies to minimize potential false findings. SNP QC commonly uses expert-guided filters based on QC variables [e.g. Hardy–Weinberg equilibrium, missing proportion (MSP) and minor allele frequency (MAF)] to remove SNPs with insufficient genotyping quality. The rationale of the expert filters is sensible and concrete, but its implementation requires arbitrary thresholds and does not jointly consider all QC features.
Results: We propose an algorithm that is based on principal component analysis and clustering analysis to identify low-quality SNPs. The method minimizes the use of arbitrary cutoff values, allows a collective consideration of the QC features and provides conditional thresholds contingent on other QC variables (e.g. different MSP thresholds for different MAFs). We apply our method to the seven studies from the Wellcome Trust Case Control Consortium and the major depressive disorder study from the Genetic Association Information Network. We measured the performance of our method compared to the expert filters based on the following criteria: (i) percentage of SNPs excluded due to low quality; (ii) inflation factor of the test statistics (λ); (iii) number of false associations found in the filtered dataset; and (iv) number of true associations missed in the filtered dataset. The results suggest that with the same or fewer SNPs excluded, the proposed algorithm tends to give a similar or lower value of λ, a reduced number of false associations, and retains all true associations.
Availability: The algorithm is available at http://www4.stat.ncsu.edu/˜jytzeng/software.php
Contact: jytzeng@stat.ncsu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Mind the gaps: a state-space model for analysing the dynamics of North Sea herring spawning components
Authors: Payne Mark R. 
Published: May 2010

Abstract
Payne, M. R. 2010. Mind the gaps: a state-space model for analysing the dynamics of North Sea herring spawning components. – ICES Journal of Marine Science, 67: 1939–1947. The North Sea autumn-spawning herring (Clupea harengus) stock consists of a set of different spawning components. The dynamics of the entire stock have been well characterized, but although time-series of larval abundance indices are available for the individual components, study of the dynamics at the component level has historically been hampered by missing observations and high sampling noise. A simple state-space statistical model is developed that is robust to these problems, gives a good fit to the data, and proves capable of both handling and predicting missing observations well. Furthermore, the sum of the fitted abundance indices across all components proves an excellent proxy for the biomass of the total stock, even though the model utilizes information at the individual-component level. The Orkney–Shetland component appears to have recovered faster from historic depletion events than the other components, whereas the Downs component has been the slowest. These differences give rise to changes in stock composition, which are shown to vary widely within a relatively short time. The modelling framework provides a valuable tool for studying and monitoring the dynamics of the individual components of the North Sea herring stock.
Cutaneous endometriosis in the umbilical region: The usefulness of CD10 in identifying the interstitium of ectopic endometriosis
Authors: FUKUDA Hidetsugu , MUKAI Hideki 
Published: May 2010

AbstractEndometriosis is a condition in which endometrium or endometrium‐like tissue grows in areas other than the endometrium and is often found within the pelvis such as in the uterus or ovary, but occasionally develops ectopically in the skin. In this paper, we report a case of cutaneous endometriosis in the umbilical region found in a 37‐year‐old woman with no history of pregnancy. The lesion was a brown, firm and elastic nodule, 9 mm × 7 mm in size, and caused bleeding as well as pain which increased during menstruation. Histopathological findings revealed that there were small and large glandular cavity structures in the dermis and the edematous interstitium around it. On immunohistochemical staining for estrogen and progesterone receptors, the cellular nuclei of glandular cavity walls were mainly found to be positive for both, and cells in the edematous interstitium around the glandular cavity were positive for CD10. Consequently, we diagnosed this case as cutaneous endometriosis in the umbilical region. CD10 was initially described as a tumor‐specific antigen found in acute lymphoblastic leukemia. Recently, the usefulness of CD10 in diagnosing endometriosis in addition to various types of lymphoma or blood cancer has been confirmed, and in our case it also proved to be as useful as estrogen receptor or progesterone receptor in the definitive diagnosis of endometriosis.
Amelanotic vulvar melanoma with intratumor histological heterogeneity
Authors: OISO Naoki , YOSHIDA Masuki , KAWARA Shigeru , KAWADA Akira 
Published: May 2010

AbstractAmelanotic vulvar melanoma is a rare type of malignant melanoma. This paper describes a case of an asymptomatic ulcerated nodule 20 mm in size. The tumor cells from the nodular lesion showed positive staining immunohistochemically for Melan‐A, but negative staining with HMB‐45. The cells showed negative reactivity to S‐100 except in one region. The melanoma cells in the epidermis were detected in one of the specimens from the excised tumor nodule. The cells in the epidermis showed positive staining for Melan‐A and S‐100 and partial staining with HMB‐45. The tumor was diagnosed as malignant melanoma of the vulva and immunohistochemically shown to have intratumor histological heterogeneity. This case suggests the importance of viewing non‐pigmented nodules on the vulva of elderly females as potentially malignant melanoma, and that a combination of immunohistochemical stains may be useful for recognizing the stage of the melanosomes in the melanoma cells.
Whitening efficacy of plant extracts including orchid extracts on Japanese female skin with melasma and lentigo senilis
Authors: TADOKORO Taketsugu , BONTÉ Frédéric , ARCHAMBAULT Jean C. , CAUCHARD Jean H. , NEVEU Michèle , OZAWA Kentaro , NOGUCHI Fumihito , IKEDA Aya , NAGAMATSU Maki , SHINN Sachiko 
Published: May 2010

AbstractThe purpose of this study was to assess thein vivoefficacy of a cosmetic formulation containing plant extracts including orchid extracts, compared to 3% vitamin C derivative formulated with the same excipient, in Japanese female adult volunteers with melasma and/or lentigo senilis. The ethics committee of Osaka National Hospital approved the protocol of the study. Before recruitment, selection and inclusion of a volunteer in this study, signed informed consent was obtained from each volunteer after she was given clear and precise information on the study, enabling her to appreciate the aim of the study and the consequences of her consent. Forty‐eight female volunteers aged 30–60 years applied the plant extracts and vitamin C derivative to one side of the face. After repeated application for 8 weeks, efficacy was evaluated clinically by colorimetric measurements and subjectively using a questionnaire. After 8 weeks of treatment, both the clinical evaluations by a dermatologist and the questionnaire surveys by volunteers indicated that the cosmetic formulation containing plant extracts was significantly effective in improving the size, brightness, color intensity, clarity, visibility and global appearance of the pigmented spots, and also the luminosity complexion and skin clarity of the face. The good agreement between the results of clinical evaluations and those of questionnaire surveys showed that the orchid‐rich plant extracts possess efficacy similar to vitamin C derivative in whitening the skin as well as melasma and lentigo senilis on the face of Japanese women.
Review article: the role of rapid virological response in determining treatment duration for chronic hepatitis C
Authors: POORDAD F. F. 
Published: May 2010

Aliment Pharmacol Ther 31, 1251–1267SummaryBackground  For patients with chronic hepatitis C, attaining rapid virological response (RVR) is highly predictive of attaining SVR.Aim  To consider the predictive value of RVR in terms of SVR and relapse.Methods  Data were collected from published clinical trials to define the predictive value of RVR for SVR and evaluate the proposed continuum linking RVR to relapse.Results  These data support a 24‐week regimen among genotype (G)1 patients who attain RVR with positive predictive values (PPVs) of 77.8% and 85.7% in patients with G1 infection treated for 24 and 48 weeks. Conversely, failure to attain RVR among G1 patients should not be viewed as a criterion for extending treatment duration beyond 48 weeks: negative predictive values (NPVs) were 60.9% and 52.7% in G1 patients without RVR treated for 48 and 72 weeks. Among G2/3 patients, RVR has a high PPV; however, the NPV varied with treatment duration indicating that a 24‐week treatment regimen is warranted in G2/3 patients who fail to attain RVR.Conclusions  The present analysis confirms RVR as a strong predictor of SVR that can be used to tailor treatment duration, but which also should be appreciated in the context of treatment duration and regimen.
A model of healing of Los Angeles grades C and D reflux oesophagitis: is there an optimal time of acid suppression for maximal healing?
Authors: Katz P. O. , Johnson D. A. , Levine D. , Röhss K. , Junghard O. , Åstrand M. , Nagy P. 
Published: May 2010

Aliment Pharmacol Ther 2010; 32: 443–447SummaryBackground  In patients with Los Angeles (LA) grade C or D oesophagitis, a positive relationship has been established between the duration of intragastric acid suppression and healing.Aim  To determine whether there is an apparent optimal time of intragastric acid suppression for maximal healing of reflux oesophagitis.Methods  Post hoc analysis of data from a proof‐of‐concept, double‐blind, randomized study of 134 adult patients treated with esomeprazole (10 or 40 mg od for 4 weeks) for LA grade C or D oesophagitis. A curve was fitted to pooled 24‐h intragastric pH (day 5) and endoscopically assessed healing (4 weeks) data using piecewise quadratic logistic regression.Results  Maximal reflux oesophagitis healing rates were achieved when intragastric pH >4 was achieved for approximately 50–70% (12–17 h) of the 24‐h period. Acid suppression above this threshold did not yield further increases in healing rates.Conclusion  After 4 weeks’ acid‐suppressive therapy for LA grade C or D oesophagitis, successful healing appears to reach a threshold above which improvements are unlikely to be achieved despite an increase in number of hours with intragastric pH >4.
Coronary artery calcification and cardiovascular risk: the role of RANKL/OPG signalling
Authors: Quercioli Alessandra , Montecucco Fabrizio , Bertolotto Maria , Ottonello Luciano , Pende Aldo , Mach François , Dallegri Franco 
Published: May 2010

Eur J Clin Invest 2010; 40 (7): 645–654AbstractBackground  Coronary artery disease (CAD) represents the most relevant cause of death and morbidity in the adult population of developed and developing countries. During the last decades, a strong research effort has been performed to identify more selective markers and better assess the cardiovascular risk in both primary and secondary prevention.Materials and methods  This review updates current knowledge regarding the pathophysiological relevance as possible markers of coronary calcification of the receptor activator of nuclear factor‐kappa ligand (RANKL)/osteoprotegerin (OPG) system. Furthermore, the potential clinical use of both RANKL/OPG and coronary calcium score (CAC) to assess cardiovascular vulnerability has been discussed.Results  Emerging evidence indicates that atherosclerotic plaque calcification is positively correlated with vulnerability. Several inflammatory mediators have been shown to modulate arterial calcification, thus increasing the risk of plaque rupture. Among these factors, RANKL/OPG axis might be of particular interest as a promising biomarker of plaque vulnerability in subjects with diffuse coronary calcification.Conclusion  Together with clinical parameters of coronary calcification (such as CAC), circulating RANKL/OPG levels could contribute to better assess and predict cardiac events.