bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistical Modeling of Epistasis and Linkage Decay using Logic Regression
Authors: Parker Thomas , Szucs Peter , Mahaffee Walt , Jannink Jean-Luc , Henning John 
Published: November 2008

AbstractLogic regression has been recognized as a tool that can identify and model non-additive genetic interactions using Boolean logic groups. Logic regression, TASSEL-GLM and SAS-GLM were compared for analytical precision using a previously characterized model system to identify the best genetic model explaining epistatic interaction of vernalization-sensitivity in barley. A genetic model containing two molecular markers identified in vernalization response in barley was selected using logic regression while both TASSEL-GLM and SAS-GLM included spurious associations in their models. The results also suggest the logic regression can be used to identify dominant/recessive relationships between epistatic alleles through its use of conjugateoperators.
The mini‐resectoscope: A new instrument for office hysteroscopic surgery
Authors: PAPALAMPROS PANOS , GAMBADAURO PIETRO , PAPADOPOULOS NIKOLAOS , POLYZOS DIMITRIS , CHAPMAN LYNNE , MAGOS ADAM 
Published: November 2008

AbstractBackground. Outpatient hysteroscopy has become well‐established for the investigation abnormal uterine bleeding. Although “See and Treat” clinics have been widely introduced, the types of procedures offered are limited, and many patients with intrauterine pathology continue to be admitted as in‐patients for hysteroscopic surgery. We wanted to investigate the feasibility and acceptability of surgery for small intrauterine lesions without the need for general anesthesia by using a miniature resectoscope. Methods. This was a prospective observational study on 30 women with abnormal uterine bleeding associated with endometrial polyps or small (<3 cm) type 0 or 1 submucous fibroids. Hysteroscopic polypectomy (n = 26) or myomectomy (n = 4) was carried out using a 16 Fr gauge mini‐resectoscope. Results. Ten procedures were carried out in the outpatient clinic and 20 in the operating theatre. Sixteen procedures were done without any anaesthesia and 14 after intra‐cervical local anesthetic injections. The polyps and fibroids ranged in size from 1 to 5 cm, and all procedures took less than 15 minutes from the time the vagina was instrumented to the end of surgery. All procedures were completed successfully and were well tolerated with little discomfort. There were no complications. Conclusions. The mini‐resectoscope appears to be an efficient and acceptable instrument for hysteroscopic surgery and can be used without general anesthesia for minor procedure such as polypectomy and the resection of small submucous fibroids.
Maternal–neonatal amino acid blood levels in relation to the mode of delivery
Authors: SCHULPIS KLEOPATRA H. , VLACHOS GEORGE D. , PAPAKONSTANTINOU EVANGELOS D. , KARIKAS GEORGE A. , VLACHOS DIMITRIOS G. , ROMA ELEFTHERIA , ANTSAKLIS ARIS , PAPASSOTIRIOU IOANNIS , TSAKIRIS STYLIANOS 
Published: November 2008

AbstractObjective. To investigate the effect of the mode of delivery on maternal–neonatal amino acid levels as high blood levels of some amino acids are implicated with endurance exercise. Design. Comparative study. Sample. Thirty women in normal pregnancy divided into two groups: Group A (n = 15) with normal labor and vaginal delivery and group B (n = 15) with scheduled cesarean section. Material and methods. Blood was obtained from the mothers pre‐ versus post‐delivery as well as from the umbilical cord. Routine laboratory tests (liver enzymes, muscle enzyme, etc.) and the amino acid blood levels were measured with a clinical chemistry analyzer and tandem mass spectrometry methods, respectively. Results. Routine laboratory tests and the amino acid blood levels were similar in the two groups of mothers pre‐delivery. Total antioxidant status levels were reduced, whereas the branched‐chain amino acids (BCAAs) and alanine levels were remarkably elevated in the sera of group A post – delivery, whereas they remained unaltered in group B at the same time of study. The mentioned BCAAs and alanine levels were higher in the umbilical cord blood of group A than those in group B. The rest of the amino acids were similar. Conclusions. The increased BCAAs and alanine blood levels in mothers of group A may be related to uterine and skeletal muscle contractions during the vaginal delivery process and the high levels in the umbilical cord blood of their neonates may mirror those of the mothers. The elevation of BCAAs both in mothers of group A and their neonates may exclude or minimize tyrosine and tryptophane levels from entry in the brain resulting in decreased biogenic amine and increased prolactin production in the central nervous system of these mothers and their infants.
Are Retinal Microvascular Caliber Changes Associated with Severity of Coronary Artery Disease in Symptomatic Cardiac Patients?
Authors: KREIS ANDREAS JOSEF , NGUYEN THANH TAN , WANG JIE JIN , ROGERS SOPHIE , AL‐FIADH ALI , FREEMAN MELANIE , WONG TIEN YIN , FAROUQUE H.M. OMAR 
Published: November 2008

ABSTRACTObjectives: Recent population‐based studies have shown that retinal vascular caliber may predict the risk of clinical coronary artery disease (CAD) events. Whether this association is related to macro‐ or microvascular mechanisms remains unknown. We investigated the relationship of retinal vascular caliber with severity and extent of CAD in symptomatic cardiac patients.Materials and Methods: Overall, 98 patients attending diagnostic coronary angiography were recruited. Coronary angiography was used to assess for the severity and extent of CAD. Digital retinal photography was performed immediately prior to cardiac catheterization, and retinal vascular caliber was measured from these photographs by using a computer program and summarized as central retinal arteriolar (CRAE) and venular (CRVE) equivalents.Results: Retinal arteriolar and venular calibers were not associated with increasing severity of CAD, as assessed by Leaman scores (CRAE/CRVE: P for trend=0.17/0.57), presence of clinically significant CAD (CRAE/CRVE: P=0.35/0.32), or number of diseased vessels (CRAE/CRVE: P for trend=0.18/0.69).Conclusions: Retinal vascular caliber changes are not associated with the severity of obstructive CAD in symptomatic patients. These data suggest that the association of retinal vascular caliber with clinical CAD seen in epidemiological studies may not be applicable to clinical symptomatic patients and may be related to microvascular, rather than macrovascular, mechanisms.
A practical method for exact computation of subtree prune and regraft distance
Authors: Wu Yufeng 
Published: November 2008

AbstractMotivation: Subtree prune and regraft (SPR) is one kind of tree rearrangements that has seen applications in solving several computational biology problems. The minimum number of rooted SPR (rSPR) operations needed to transform one rooted binary tree to another is called the rSPR distance between the two trees. Computing the rSPR distance has been actively studied in recent years. Currently, there is a lack of practical software tools for computing the rSPR distance for relatively large trees with large rSPR distance.Results: In this article, we present a simple and practical method that computes the exact rSPR distance with integer linear programming. By applying this new method on several simulated and real biological datasets, we show that our new method outperforms existing software tools in term of accuracy and ef.ciency. Our experimental results indicate that our method can compute the exact rSPR distance for many large trees with large rSPR distance.Availability: A software tool, SPRDist, is available for download from the web page: http://www.engr.uconn.edu/~ywu.Contact: ywu@engr.uconn.edu
Rheological and Pasting Properties of Buckwheat (Fagopyrum esculentum Möench) Flours With and Without Jet‐Cooking
Authors: Inglett George E. , Xu Jingyuan , Stevenson David G. , Chen Diejun 
Published: November 2008

ABSTRACTPasting, rheological, and water‐holding properties of buckwheat (Fagopyrum esculentum) flour obtained from whole achenes separated into three particle sizes, and three commercial flours (Fancy, Supreme, and Farinetta) were measured with or without jet‐cooking. Fancy had instantaneous paste viscosity (measured using RVA) after jet‐cooking that was not observed for Supreme or Farinetta, and paste viscosity was lower for the latter two flours. Supreme jet‐cooked flour exhibited higher peak viscosity than flour without jet‐cooking, and paste exhibited high shear‐thinning. Fancy exhibited strongest viscoelastic properties (measured using a rheometer). Jet‐cooking damaged buckwheat flour structure, thereby reducing viscoelasticity. Buckwheat flour pastes experienced shear‐thinning over a wide range of shear rates. Jet‐cooking greatly enhanced water‐holding capacity. Buckwheat flour particle size did not greatly influence paste viscosity. Study showed buckwheat flours have unique pasting and rheological characteristics that have different food applications, which could especially be useful for people with celiac disease as buckwheat is gluten‐free.
Nixtamalized Instant Flour from Corn (Zea mays L.) Meal: Optimization of Nixtamalization Conditions
Authors: Cuevas‐Rodríguez E. O. , Reyes‐Moreno C. , Eckhoff S. R. , Milán‐Carrillo J. 
Published: November 2008

ABSTRACTThe present investigation provides a new method for the nixtamalization process wherein corn endosperm fractions (corn meal) are treated in an alkaline solution that yields quality masa or instant masa flour like traditional nixtamalization process (alkaline cooking of corn with lime). The objective of this work was to determine the best combination of nixtamalization process variables for producing nixtamalized instant flour (NIF) from corn meal. Nixtamalization conditions were selected from factorial combinations of process variables including nixtamalization time (NT 8–22 min) and cooking temperature (CT 78–88°C). A central composite rotable experimental design was chosen. Lime concentration was 1% (10 g of Ca(OH)2/L of water) and ratio of corn meal to cooking medium was 1:4. At the end of each cooking, each treatment was steeped for 5 hr at room temperature (25°C). Nixtamalized corn meal was dried (55°C/12 hr) and milled to pass through 80 U.S. mesh to obtain NIF. Response surface methodology (RSM) was applied as an optimization technique over four response variables: masa firmness (MF), masa adhesiveness (MA), tortilla cutting force (CF), and tortilla tensile strength (TS). Predictive models for response variables were developed as a function of process variables. Conventional graphic methods were applied to obtain response variable values similar to the control (MASECA). Contour plots of each response variable applied superposition surface methodology to obtain a contour plot for observation and for selecting the best combination of nixtamalization time (NT 15 min) and cooking temperature (CT 83°C) for producing an optimized NIF from corn meal. Values of MF, MA, CF, and TS obtained from the predictive models were compared with those derived from experimental tests; a close agreement (coefficient of variance < 10%) between both values was observed.
Non‐solid oncogenes in solid tumors: EML4–ALK fusion genes in lung cancer
Authors: Mano Hiroyuki 
Published: November 2008

It is generally accepted that recurrent chromosome translocations play a major role in the molecular pathogenesis of hematological malignancies but not of solid tumors. However, chromosome translocations involving the e26 transformation‐specific sequence transcription factor loci have been demonstrated recently in many prostate cancer cases. Furthermore, through a functional screening with retroviral cDNA expression libraries, we have discovered the fusion‐type protein tyrosine kinase echinoderm microtubule‐associated protein like‐4 (EML4)–anaplastic lymphoma kinase (ALK) in non‐small cell lung cancer (NSCLC) specimens. A recurrent chromosome translocation, inv(2)(p21p23), in NSCLC generates fused mRNA encoding the amino‐terminal half of EML4 ligated to the intracellular region of the receptor‐type protein tyrosine kinase ALK. EML4–ALK oligomerizes constitutively in cells through the coiled coil domain within the EML4 region, and becomes activated to exert a marked oncogenicity both in vitro and in vivo. Break and fusion points within the EML4 locus may diverge in NSCLC cells to generate various isoforms of EML4–ALK, which may constitute ~5% of NSCLC cases, at least in the Asian ethnic group. In the present review I summarize how detection of EML4–ALK cDNA may become a sensitive diagnostic means for NSCLC cases that are positive for the fusion gene, and discuss whether suppression of ALK enzymatic activity could be an effective treatment strategy against this intractable disorder. (Cancer Sci 2008; 99: 2349–2355)
Prognostic factors for patients with hepatocellular carcinoma with macroscopic portal vein or inferior vena cava tumor thrombi receiving external‐beam radiation therapy
Authors: Zeng Zhao‐Chong , Fan Jia , Tang Zhao‐You , Zhou Jian , Wang Jian‐Hua , Wang Bin‐Liang , Guo Wei 
Published: November 2008

Prognostic factors in patients with hepatocellular carcinoma (HCC) with tumor thrombosis are not well established, especially for those given external‐beam radiation therapy (EBRT). Patients (n = 136) with HCC who had portal vein (PV) or inferior vena cava (IVC) tumor thrombus received EBRT between January 1998 and October 2007. Demographic variables, laboratory values, tumor characteristics, and treatment modalities were determined at diagnosis and before EBRT. The total radiation dose ranged from 30 to 60 Gy (median, 50 Gy) and was focused on the tumor thrombi. Predictors of survival were identified using the univariate and multivariate analysis. Of the 136 patients, the tumor thrombus completely disappeared in 41 patients (30.1%), 36 patients (26.5%) had a partial response, 49 patients (36%) had stable disease, and 10 patients (7.4%) had progressive disease. On multivariate analysis, pretreatment unfavorable predictors were associated with lower albumin, higher γ‐glutamyltransferase and α‐fetoprotein levels, poorer Child–Pugh classification, intrahepatic multifocality, lymph node metastases, poorer response to EBRT, and 2‐dimension EBRT technique. Survival rates at 1, 2, and 3 years were 31.8%, 17.5%, and 8.8% for patients with PV tumor thrombi; 66.3%, 21.1%, and 15.8% for IVC tumor thrombi; and 25%, 8.3%, and 0% for PV plus IVC tumor thrombi, respectively. Overall median survival was 9.7 months. This study provides detailed information about the survival outcomes and prognostic factors of HCC with tumor thrombi in a relatively large cohort of patients treated with radiation, and the results will help in understanding the potential factors that influence survival for patients with HCC after EBRT. (Cancer Sci 2008; 99: 2510–2517)
Roles of cyclooxygenase‐2 and microsomal prostaglandin E synthase‐1 expression and β‐catenin activation in gastric carcinogenesis inN‐methyl‐N‐nitrosourea‐treated K19‐C2mE transgenic mice
Authors: Takasu Shinji , Tsukamoto Tetsuya , Cao Xue‐Yuan , Toyoda Takeshi , Hirata Akihiro , Ban Hisayo , Yamamoto Masami , Sakai Hiroki , Yanai Tokuma , Masegi Toshiaki , Oshima Masanobu , Tatematsu Masae 
Published: November 2008

K19‐C2mE transgenic (Tg) mice, simultaneously expressing cyclooxygenase‐2 (COX‐2) and microsomal prostaglandin E synthase‐1 (mPGES‐1) in the gastric mucosa under the cytokeratin 19 gene promoter, were here treated withN‐methyl‐N‐nitrosourea (MNU) and inoculated withHelicobacter pylori(H. pylori) to investigate gastric carcinogenesis. Wild‐type (WT) and Tg mice undergoing MNU treatment frequently developed tumors in the pyloric region (100% and 94.7%, respectively); multiplicity in Tg was higher than that in WT (P < 0.05) withH. pyloriinfection. Larger pyloric tumors were more frequently observed in Tg than in WT (P < 0.05). In addition, Tg developed fundic tumors, where WT did not. No gastric tumors were observed without MNU treatment. Transcripts of TNF‐α, iNOS, IL‐1β, and CXCL14 were up‐regulated withH. pyloriinfection in both genotypes and were also increased more in Tg than in WT withinH. pylori‐inoculated animals. Immunohistochemical analysis demonstrated significantly greater β‐catenin accumulation in pyloric tumors, compared with those in the fundus (P < 0.01) with mutations of exon 3; 18.2% and 31.6% in MNU‐alone and MNU + H. pylori‐treated WT, whereas 21.4% and 62.5% was observed in the Tg, respectively; the latter significantly higher (P < 0.05), suggesting the role ofH. pyloriin Wnt activation. In conclusion, K19‐C2mE mice promoted gastric cancer in both fundic and pyloric regions. Furthermore β‐catenin activation may play the important role of pyloric carcinogenesis especially inH. pylori‐infected Tg. Induction of various inflammatory cytokines in addition to overexpression of COX‐2/mPGES‐1 could be risk factors of gastric carcinogenesis and may serve as a better gastric carcinogenesis model. (Cancer Sci2008; 99: 2356–2364)
Low‐intensity ultrasound and microbubbles enhance the antitumor effect of cisplatin
Authors: Watanabe Yukiko , Aoi Atsuko , Horie Sachiko , Tomita Noriko , Mori Shiro , Morikawa Hidehiro , Matsumura Yasuhiro , Vassaux Georges , Kodama Tetsuya 
Published: November 2008

Cell permeabilization using microbubbles (MB) and low‐intensity ultrasound (US) have the potential for delivering molecules into the cytoplasm. The collapsing MB and cavitation bubbles created by this collapse generate impulsive pressures that cause transient membrane permeability, allowing exogenous molecules to enter the cells. To evaluate this methodology in vitro and in vivo, we investigated the effects of low‐intensity 1‐MHz pulsed US and MB combined with cis‐diamminedichloroplatinum (II) (CDDP) on two cell lines (Colon 26 murine colon carcinoma and EMT6 murine mammary carcinoma) in vitro and in vivo on severe combined immunodeficient mice inoculated with HT29‐luc human colon carcinoma. To investigate in vitro the efficiency of molecular delivery by the US and MB method, calcein molecules with a molecular weight in the same range as that of CDDP were used as fluorescent markers. Fluorescence measurement revealed that approximately 106–107 calcein molecules per cell were internalized. US–MB‐mediated delivery of CDDP in Colon 26 and EMT6 cells increased cytotoxicity in a dose‐dependent manner and induced apoptosis (nuclear condensation and fragmentation, and increase in caspase‐3 activity). In vivo experiments with xenografts (HT29‐luc) revealed a very significant reduction in tumor volume in mice treated with CDDP + US + MB compared with those in the US + CDDP groups for two different concentrations of CDDP. This finding suggests that the US–MB method combined with chemotherapy has clinical potential in cancer therapy. (Cancer Sci 2008; 99: 2525–2531)
The social context of parenting 3‐year‐old children with developmental delay in the UK
Authors: Emerson E. , Graham H. , McCulloch A. , Blacher J. , Hatton C. , Llewellyn G. 
Published: November 2008

AbstractBackground  Children with intellectual or developmental disability have significantly poorer health and mental health than their non‐disabled peers and are at high risk of social exclusion. The aim of the present paper is to provide information on the circumstances in which 3‐year‐old children at risk of intellectual or developmental disability are growing up in the UK.Methods  Secondary analysis of data on 12 689 families in English‐speaking monolingual households from the first two waves of the UK's Millennium Cohort Study. A total of 440 children (3% of the weighted sample) were identified as being developmentally delayed.Results  When compared with other children, children with developmental delays were more disadvantaged on every indicator of social and economic disadvantage examined. Two out of three children with developmental delays had been exposed to repeated disadvantage as measured by income poverty, material hardship, social housing and receipt of means‐tested benefits. The effect of repeated disadvantage on the risk of developmental delay remained after account was taken of parental education and occupational status.Conclusions  Young children with delayed development in the UK are likely to be exposed to repeated socio‐economic disadvantage. Implications for policy and understanding the nature of the link between poverty and child disability are discussed.
Is aggression in children with behavioural and emotional difficulties associated with television viewing and video game playing? A systematic review
Authors: Mitrofan O. , Paul M. , Spencer N. 
Published: November 2008

AbstractBackground  Possible associations between television viewing and video game playing and children's aggression have become public health concerns. We did a systematic review of studies that examined such associations, focussing on children and young people with behavioural and emotional difficulties, who are thought to be more susceptible.Methods  We did computer‐assisted searches of health and social science databases, gateways, publications from relevant organizations and for grey literature; scanned bibliographies; hand‐searched key journals; and corresponded with authors. We critically appraised all studies.Results  A total of 12 studies: three experiments with children with behavioural and emotional difficulties found increased aggression after watching aggressive as opposed to low‐aggressive content television programmes, one found the opposite and two no clear effect, one found such children no more likely than controls to imitate aggressive television characters. One case–control study and one survey found that children and young people with behavioural and emotional difficulties watched more television than controls; another did not. Two studies found that children and young people with behavioural and emotional difficulties viewed more hours of aggressive television programmes than controls. One study on video game use found that young people with behavioural and emotional difficulties viewed more minutes of violence and played longer than controls. In a qualitative study children with behavioural and emotional difficulties, but not their parents, did not associate watching television with aggression. All studies had significant methodological flaws. None was based on power calculations.Conclusion  This systematic review found insufficient, contradictory and methodologically flawed evidence on the association between television viewing and video game playing and aggression in children and young people with behavioural and emotional difficulties. If public health advice is to be evidence‐based, good quality research is needed.