bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of age and stage of endometriosis on ovarian follicular loss during laparoscopic cystectomy for endometrioma
Authors: Oh Hoon‐Kyu , Sin Jeong‐Im , Kim Ju‐Hyun , Hong Seong‐Yeon , Lee Tae‐Sung , Choi Youn‐Seok 
Published: June 2011

AbstractObjectiveTo identify the risk factors associated with inadvertent follicular loss during laparoscopic cystectomy for endometrioma.MethodsBetween April 2008 and April 2010, 114 patients who underwent laparoscopic cystectomy for endometrioma were enrolled in the study. Clinical data were collected, together with a retrospective review of medical records. Ovarian follicular loss and the thickness of the cystic wall removed were evaluated by pathologic slide review.ResultsOvarian follicular loss was more frequently observed among younger patients (P < 0.001) and those with stage 3 endometriosis than among those with stage 4 (P = 0.027), in addition to having an inverse correlation with age (P < 0.001). The thickness of the removed ovarian tissue correlated with inadvertent follicular loss (P < 0.001); however, there was no correlation between any clinical parameter tested and the thickness of the removed ovarian tissue. There was a correlation between ovarian follicular loss and the thickness of the removed ovarian tissue among patients younger than 40 years (P < 0.001), but not among patients aged 40 years or older (P = 0.123).ConclusionOvarian follicular loss was more common among younger patients and patients with lower‐stage endometriosis. The thickness of the removed ovarian tissue did not differ among patients, despite varying clinical factors.
Obstetrician–gynecologists’ beliefs about safe‐sex and abstinence counseling
Authors: Lawrence Ryan E. , Rasinski Kenneth A. , Yoon John D. , Curlin Farr A. 
Published: June 2011

AbstractObjectiveTo examine obstetrician–gynecologists’ beliefs about safe‐sex and abstinence counseling.MethodsBetween October 2008 and January 2009, a survey was mailed to a national randomized sample of 1800 practicing US obstetrician–gynecologists. Study variables were agreement with 2 statements. (1) “If physicians counsel patients about safe‐sex practices, the patients will be less likely to engage in risky sexual behaviors”. (2) “If physicians counsel patients about abstinence, the patients will be much less likely to engage in sexual activity”. Covariates included demographic, clinical, and religious characteristics of the physician.ResultsThe response rate was 66% (1154/1760 eligible physicians). Most respondents somewhat (62%) or strongly (25%) agreed that counseling patients about safe‐sex practices makes patients less likely to engage in risky sexual behaviors. Fewer agreed strongly (3%) or somewhat (28%) that counseling patients about abstinence makes patients less likely to engage in sexual activity. The belief that safe‐sex counseling reduces risky behaviors was less common among males (odds ratio [OR] 0.6) and more common among immigrants (OR 2.0). Religious physicians were more likely to believe that abstinence counseling reduces sexual activity (OR 2.2–5.3).ConclusionsMost obstetrician–gynecologists believed that counseling about safe sex is effective, and a significant minority endorsed abstinence counseling.
Retrospective analysis of follicle loss after laparoscopic excision of endometrioma compared with benign nonendometriotic ovarian cysts
Authors: Dogan Erbil , Ulukus Emine Cagnur , Okyay Emre , Ertugrul Caglan , Saygili Ugur , Koyuncuoglu Meral 
Published: June 2011

AbstractObjectiveTo evaluate follicle loss in ovarian tissue after laparoscopic excision by the stripping technique in endometriomas versus benign nonendometriotic ovarian cysts.MethodsCystectomy samples obtained from 127 ovaries from 104 patients (mean age, 29.05 ± 05 years; range, 19–40 years) by laparoscopic excision (61 endometriomas and 66 benign nonendometriotic cysts) were evaluated for follicle loss. The samples including normal ovarian tissue were graded on a semiquantitative scale from 0 to 4, where 0 was complete absence of follicles and 4 was the pattern of primary and secondary follicles seen in a normal ovary. The results from endometriomas were compared with those from nonendometriotic cysts.ResultsThere were no differences in mean tissue thickness, or number of primordial, primary, or secondary follicles between the endometriomas and the nonendometriotic cysts (P > 0.05). Ovarian cortex was detected in 92% and 82% of the endometriomas and nonendometriotic samples, respectively, (P = 0.081). Semiquantitative scoring of ovarian tissue was significantly higher in endometriomas (1.64 ± 1.35 versus 1.11 ± 1.22, P = 0.022).ConclusionIn up to 92% of the cystectomy samples, normal ovarian tissue was found adjacent to the benign cyst; however, functional follicle loss was slightly, but significantly, higher in the endometriomas.
Is scent‐enhanced memory immune to retroactive interference?
Authors: Morrin Maureen , Krishna Aradhna , Lwin May O. 
Published: June 2011

AbstractResearch shows that scent enhances memory for associated information. Current debate centers around scent's immunity to “retroactive interference,” i.e., reduced memory for earlier‐learned information after exposure to additional, subsequently‐learned information. This paper demonstrates that scent‐enhanced memory is indeed prone to retroactive interference, but that some of the information lost is restored using a scent‐based retrieval cue. Two process explanations for interference effects are proposed, with the evidence providing more support for an inhibition rather than a response competition explanation. The results enhance our understanding of the encoding and retrieval of olfactory information from long‐term memory, and reasons why interference occurs.
New data on the composition of metacinnabar and Hg-sphalerite with an isomorphous Cd admixture
Authors: Vasil’ev V.I. 
Published: June 2011

Abstract
The data on the composition of metacinnabar and Hg-sphalerite with an isomorphous Cd admixture from some mercury and complex ore objects are summarized. There are two varieties of metacinnabar: (1) cadmium-rich (9.25–15.80 wt.%), with the minimum quantity of Zn admixture (0.67–3.94 wt.%), which has the idealized formula (Hg,Cd,Zn)S (Ulandu) and (2) with increased amounts of Zn (2.21–10.83 wt.%) and Cd (6.00–14.10 wt.%), having the formula (Hg,Zn,Cd)S (Arzak, Kadyrel’, Murzinskoe, Ravnou-1, Ravnou-2). The maximum content of isomorphous Cd (15.80 wt.%) was determined in the metacinnabar from the Ulandu ore occurrence. The Hg-sphalerites are compositionally divided into two groups: (1) with an increased Cd concentration (up to 7.96 wt.%) and (2) mainly with a low content of Cd admixture (0.0n–1.63 wt.%). The sphalerites of the first group are typical of mineral assemblages including Cd-Zn-enriched metacinnabar (Arzak, Kadyrel’, Murzinskoe, Sarasa). The sphalerite of the Sarasa deposit is included into this group arbitrarily, because it contains more cadmium than the sphalerites of the second group, which are constituents of parageneses only with Zn-metacinnabar or lacking it (Nikitovka, Khaidarkan, Dzhizhikrut, Bayan-Khan, Aktash). There are some Hg-bearing varieties of sphalerite with the idealized formulas (Zn,Hg,Fe)S, (Zn,Hg,Cd)S, (Zn,Cd,Hg,Fe)S, (Zn,Fe,Cd,Hg)S, (Zn,Hg,Cd,Fe)S, (Zn,Fe,Hg,Cd)S, and (Zn,Hg,Cu)S, which transforms into (Zn,Cu,Hg)S. The maximum Cd admixture (7.96 wt.%) was established in Hg-sphalerite from the Kadyrel’ ore occurrence. It is the highest content observed in natural Hg-bearing β-ZnS. The studied metacinnabar and sphalerite varieties are the only cubic phases of the natural system Zn–Hg–Cd–S, which is sometimes expanded because of minor admixtures of other metals. These varieties have a structure identical to the cubic phases of the synthetic systems Me–S and Me–Me–S, where Me = Zn, Cd, and Hg. None of Hg-bearing hexagonal solid solutions were found in the natural system Zn–Hg–Cd–S. The continuity of the natural isomorphous series ZnScub–HgScub has not been confirmed by finding of natural intermediate solid solutions at the series fragment between (Zn0.752Hg0.248)S and (Hg0.539Zn0.461)S. The metacinnabar varieties enriched in both Zn and Cd show no correlation between these elements. It is assumed that the host rocks with an increased content of cadmium compounds were the source of Cd for the formation of specific varieties β-HgS and β-ZnS.
3D simulation of transient electromagnetic field for geosteering horizontal wells
Authors: Onegova E.V. , Epov M.I. 
Published: June 2011

Abstract
The article discusses numerical simulation of the transient electromagnetic field. The field source is an induction coil. We consider the situation when a logging tool is in a horizontal well in a medium with horizontal and vertical boundaries. The specific features of this problem are the metallic mandrel of the tool, 3D geometry, and distant boundaries. The method of separate computation of normal and anomalous fields is proposed. The finite element method is used for spatial approximation of the field, and the implicit finite-difference scheme is used for approximation of the field in time. Correctness and advantages of the method are shown. Some numerical results are demonstrated. The method proposed can be used when designing tools for geosteering.
Catalogs of historical earthquakes in East Siberia: the need for revision
Authors: Radziminovich Ya.B. , Shchetnikov A.A. 
Published: June 2011

Abstract
The paper is devoted to mistakes and omissions in earthquake catalogs for East Siberia during the historical observation period. The earthquakes of 8 March 1866 and 18 May 1904 are used as examples of misinterpretations or underuse of historical evidence. The main parameters of these events have been redetermined from primary data. The paper also analyzes the “forgotten” earthquake of 1 August 1910 and the previously unknown event of 6 August 1910, which are missing from the regional parametric catalogs. It is concluded that the existing macroseismic and parametric earthquake catalogs of the study area need a thorough revision, correction, and supplementation.
Computational Analysis of Drought Stress-Associated miRNAs and miRNA Co-Regulation Network in Physcomitrella Patens
Authors: Wan Ping , Wu Jun , Zhou Yuan , Xiao Junshu , Feng Jie , Zhao Weizhong , Xiang Shen , Jiang Guanglong , Chen Jake Y. 
Published: June 2011

Abstract
miRNAs are non-coding small RNAs that involve diverse biological processes. Until now, little is known about their roles in plant drought resistance. Physcomitrella patens is highly tolerant to drought; however, it is not clear about the basic biology of the traits that contribute P. patens this important character. In this work, we discovered 16 drought stress-associated miRNA (DsAmR) families in P. patens through computational analysis. Due to the possible discrepancy of expression periods and tissue distributions between potential DsAmRs and their targeting genes, and the existence of false positive results in computational identification, the prediction results should be examined with further experimental validation. We also constructed an miRNA co-regulation network, and identified two network hubs, miR902a-5p and miR414, which may play important roles in regulating drought-resistance traits. We distributed our results through an online database named ppt-miRBase, which can be accessed at http://bioinfor.cnu.edu.cn/ppt_miRBase/index.php. Our methods in finding DsAmR and miRNA co-regulation network showed a new direction for identifying miRNA functions.
Dietary free glutamate prevents diarrhoea during intra-gastric tube feeding in a rat model
Authors: Somekawa Shinji , Hayashi Naoki , Niijima Akira , Uneyama Hisayuki , Torii Kunio 
Published: June 2011

Recent studies indicate that l-glutamate (l-Glu), abundant in many foods, is a stimulator of gastric vagal afferent nerves. The aim of the present study was to examine the possibility that l-Glu supplementation of a protein-rich liquid diet may prevent the incidence of diarrhoea during repetitive intra-gastric tube feeding. The gastric vagal afferent nerve recording of rats indicated that intra-gastric administration of a protein-rich liquid diet supplemented with 0·5 % monosodium glutamate enhanced the basal afferent activities seen with the protein-rich diet alone. The examination of the faeces showed that the addition of monosodium glutamate to the liquid diet significantly prevented the incidence of diarrhoea induced by repetitive gastric feeding. In conclusion, supplementation of an enteral liquid diet with free l-Glu may ameliorate diarrhoea during intra-gastric tube feeding by sending visceral glutamate information from the stomach to the brain.
Fuzzy logic as a decision-making support system for the indication of bariatric surgery based on an index (MAFOI) generated by the association between body fat and body mass index.
Authors: Miyahira Susana , Azevedo Joao , Araujo Filho José 
Published: June 2011

Abstract
Background:
A fuzzy obesity index (MAFOI) for use as an alternative to bariatric surgery indication (BSI) is presented. The search for a more accurate method to evaluate obesity and to indicate a better treatment is important in the world health context. BMI (body mass index) is considered the main criteria for obesity treatment and BSI. Nevertheless, the fat excess related to the percentage of Body Fat (%BF) is actually the principal harmful factor in obesity disease that is usually neglected. This paper presents a new fuzzy mechanism for evaluating obesity by associating BMI with %BF that yields a fuzzy obesity index for obesity evaluation and treatment and allows building up a Fuzzy Decision Support System (FDSS) for BSI. Methods: Seventy-two patients were evaluated for both BMI and %BF. These data are modified and treated as fuzzy sets. Afterwards, the BMI and %BF classes are aggregated yielding a new index (MAFOI) for input linguistic variable are considered the BMI and %BF, and as output linguistic variable is employed the MAFOI, an obesity classification with entirely new classes of obesity in the fuzzy context as well as is used for BSI.

Results:
There is gradual, smooth obesity classification and BSI when using the proposed fuzzy obesity index when compared with other traditional methods for dealing with obesity.

Conclusion:
The BMI is not adequate for surgical indication in all the conditions and fuzzy logic becomes an alternative for decision making in bariatric surgery indication based on the MAFOI.
UCHIME improves sensitivity and speed of chimera detection
Authors: Edgar Robert C. , Haas Brian J. , Clemente Jose C. , Quince Christopher , Knight Rob 
Published: June 2011

Abstract
Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments.
Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is &gt;100× faster than Perseus and &gt;1000× faster than ChimeraSlayer.
Contact: robert@drive5.com
Availability: Source, binaries and data: http://drive5.com/uchime.
Supplementary information: Supplementary data are available at Bioinformatics online.
A rank-based statistical test for measuring synergistic effects between two gene sets
Authors: Shiraishi Yuichi , Okada-Hatakeyama Mariko , Miyano Satoru 
Published: June 2011

Abstract
Motivation: Due to recent advances in high-throughput technologies, data on various types of genomic annotation have accumulated. These data will be crucially helpful for elucidating the combinatorial logic of transcription. Although several approaches have been proposed for inferring cooperativity among multiple factors, most approaches are haunted by the issues of normalization and threshold values.
Results: In this article, we propose a rank-based non-parametric statistical test for measuring the effects between two gene sets. This method is free from the issues of normalization and threshold value determination for gene expression values. Furthermore, we have proposed an efficient Markov chain Monte Carlo method for calculating an approximate significance value of synergy. We have applied this approach for detecting synergistic combinations of transcription factor binding motifs and histone modifications.
Availability: C implementation of the method is available from http://www.hgc.jp/~yshira/software/rankSynergy.zip.
Contact: yshira@hgc.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
ODORactor: a web server for deciphering olfactory coding
Authors: Liu Xinyi , Su Xubo , Wang Fei , Huang Zhimin , Wang Qi , Li Zhen , Zhang Ruina , Wu Lifang , Pan Yi , Chen Yingyi , Zhuang Hanyi , Chen Guoqiang , Shi Ting , Zhang Jian 
Published: June 2011

Abstract
Summary: ODORactor is an open access web server aimed at providing a platform for identifying odorant receptors (ORs) for small molecules and for browsing existing OR-ligand pairs. It enables the prediction of ORs from the molecular structures of arbitrary chemicals by integrating two individual functionalities: odorant verification and OR recognition. The prediction of the ORs for several odorants was experimentally validated in the study. In addition, ODORactor features a comprehensive repertoire of olfactory information that has been manually curated from literature. Therefore, ODORactor may provide an effective way to decipher olfactory coding and could be a useful server tool for both basic olfaction research in academia and for odorant discovery in industry.
Availability: Freely available at http://mdl.shsmu.edu.cn/ODORactor
Contact: jian.zhang@sjtu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Do photobionts influence the ecology of lichens? A case study of environmental preferences in symbiotic green alga Asterochloris (Trebouxiophyceae)
Authors: PEKSA ONDŘEJ , ŠKALOUD PAVEL 
Published: June 2011

AbstractThe distribution patterns of symbiotic algae are thought to be conferred mainly by their hosts, however, they may originate in algal environmental requirements as well. In lichens, predominantly terrestrial associations of fungi with algae or cyanobacteria, the ecological preferences of photobionts have not been directly studied so far. Here, we examine the putative environmental requirements in lichenized alga Asterochloris, and search for the existence of ecological guilds in Asterochloris‐associating lichens. Therefore, the presence of phylogenetic signal in several environmental traits was tested. Phylogenetic analysis based on the concatenated set of internal transcribed spacer rDNA and actin type I intron sequences from photobionts associated with lichens of the genera Lepraria and Stereocaulon (Stereocaulaceae, Ascomycota) revealed 13 moderately to well‐resolved clades. Photobionts from particular algal clades were found to be associated with taxonomically different, but ecologically similar lichens. The rain and sun exposure were the most significant environmental factor, clearly distinguishing the Asterochloris lineages. The photobionts from ombrophobic and ombrophilic lichens were clustered in completely distinct clades. Moreover, two photobiont taxa were obviously differentiated based on their substrate and climatic preferences. Our study, thus reveals that the photobiont, generally the subsidiary member of the symbiotic lichen association, could exhibit clear preferences for environmental factors. These algal preferences may limit the ecological niches available to lichens and lead to the existence of specific lichen guilds.
Effect of supplementation of multi‐microbe probiotic product on growth performance, apparent digestibility, cecal microbiota and small intestinal morphology of broilers
Authors: Kim J. S. , Ingale S. L. , Kim Y. W. , Kim K. H. , Sen S. , Ryu M. H. , Lohakare J. D. , Kwon I. K. , Chae B. J. 
Published: June 2011

SummaryThe present study investigated the effect of inclusion of multi‐microbe probiotic product on growth performance, apparent digestibility of nutrients, cecal microbiota and small intestinal morphology in broilers. Four hundred days‐old Ross chicks were randomly allotted to five treatments on the basis of body weight (BW). Each treatment had four replicates of 20 chicks in each. Experimental diets were fed in two phases, starter (day 0–21) and finisher (day 22–35). Dietary treatments were; basal diet without any antimicrobial (NC), basal diet added with 20 mg Avilamycin/kg of diet (PC), 107 cfu multi‐microbe probiotic/kg of diet (P1), 108 cfu multi‐microbe probiotic/kg of diet (P2), and 109 cfu multi‐microbe probiotic/kg of diet (P3). Overall BW gain and feed conversion ratio were better (p < 0.05) for treatments PC, P2 and P3 compared with NC and P1, with P1 being better (p < 0.05) than NC. Overall feed intake in treatments PC, P1, P2 and P3 were greater (p < 0.05) than NC. Apparent digestibility of dry matter and crude protein were greater (p < 0.05) in treatments PC, P2 and P3 compared with NC, with P1 being intermediate and not different form NC, PC, P2 and P3. At d 21 and 35, treatments PC, P1, P2 and P3 showed lower (p < 0.05) cecal Clostridium and Coliforms count in relation to NC. Moreover, cecal Clostridium (d 21) and Coliforms (d 21 and 35) count were lower (p < 0.05) in treatment PC in relation to P1; with P2 and P3 being intermediate and not different from PC. However, there was no effect of dietary treatments on cecal total anaerobic bacteria and Bifidobacterium spp. count. The villus height of duodenum in treatment PC was greater (p < 0.05) than NC, with P1, P2 and P3 being intermediate. Villus height of ileum in treatment PC was greater (p < 0.05) than in treatments P1 and NC, whereas it remained comparable among treatments PC, P2 and P3. Villus height to crypt depth ratio of ileum was greater (p < 0.05) for treatment PC, P2 and P3 compared with that in P1 and NC. It is concluded that multi‐microbe probiotic inclusion at 108 and 109 cfu/kg diet had beneficial effects on broilers growth performance, apparent digestibility of nutrients and intestinal morphology and can be used as replacement to antibiotics growth promoter in broiler nutrition.