bluuebunny/crossref_metadata_2025_split huggingface dataset:
Considering Dependencies Amongst Genes Helps to Adjust the Significance Rank of DEGs
Authors: Liu Qi , Ding Guohui , Huang Tao , Tan Yejun , Dai Hongyue , Xie Lu , Li Yixue 
Published: August 2010

AbstractLists of differentially expressed genes (DEGs) detected often show low reproducibility even in technique replicate experiments. The reproducibility is even lower for those real cancer data with large biological variations and limited number of samples. Since existing methods for identifying differentially expressed genes treat each gene separately, they cannot circumvent the problem of low reproducibility. Considering correlation structures of genes may help to mitigate the effect of errors on individual gene estimates and thus get more reliable lists of DEGs. We borrowed information from large amount of existing microarray data to define the expression dependencies amongst genes. We use this prior knowledge of dependencies amongst genes to adjust the significance rank of DEGs. We applied our method and four popular ranking algorithms including mean fold change (FC), SAM, t‐statistic and Wilcoxon rank sum‐test on two cancer microarray datasets. Our method achieved higher reproducibility than other methods across a range of sample sizes. Furthermore, our method obtained higher accuracy than other methods, especially when the sample size is small. The results demonstrate that considering the dependencies amongst genes helps to adjust the significance rank of genes and find those truly differentially expressed genes.
Serial histologic investigation of squamous epithelial dysplasia associated with carcinoma of the esophagus
Authors: Nagamatsu Masaaki , Mori Masaki , Kuwano Hiroyuki , Sugimachi Keizo , Akiyoshi Tsuyoshi 
Published: August 2010

AbstractEsophageal dysplasia and carcinoma were reviewed in the surgical specimens obtained from 37 patients with squamous cell carcinoma and 4 with adenocarcinoma; special attention was paid to the continuity of both lesions. Two hundred forty dysplasias and 113 carcinomas in situ (CIS) were recognized in the squamous cell carcinoma cases and 2 dysplasias and no CIS in the adenocarcinoma cases. The CIS often was accompanied continuously by severe dysplasia rather than mild or moderate dysplasia, suggesting some relationship between the CIS and the severity of dysplasia. However, many dysplastic lesions were located separately from the carcinoma. The frequency of appearance of the dysplasia near the CIS was low (11%), demonstrating a negative dysplasia‐CIS sequence in many of the esophageal cancers. Lymphocytic infiltration was investigated further beneath the dysplasia or CIS. The degree of lymphocytic infiltration with lymphoid follicles correlated with the severity of dysplasia and was the highest in CIS.
Low‐dose rate telecobalt therapy as a boost against esophageal carcinomas
Authors: Yamada Shogo , Takai Yoshihiro , Nemoto Kenji , Ogawa Yoshihiro , Kakuto Yoshihisa , Hoshi Akihiko , Sakamoto Kiyohiko 
Published: August 2010

AbstractThe results of treating 54 esophageal carcinomas with low‐dose rate telecobalt therapy (LDRT) as a boost were compared with those of treating 97 esophageal carcinomas with conventionally fractionated irradiation alone (CFI). The LDRT (100 cGy/hr, 500 to 700 cGy/day, a total dose of 1400 to 2000 cGy) was boosted at 10 days after 6000 cGy of the CFI dose. Although the LDRT group included more advanced cases than the CFI group, local effects and survival rates in the former group were slightly better than in the latter group. Late complications were more severe in the LDRT group. However, they were acceptable when the total dose administered to this group was less than 8000 cGy. Using LDRT as a boost against esophageal carcinomas was found to be satisfactory therapeutically.
T‐cell chronic lymphocytic leukemia: T‐cell function and lymphokine secretion
Authors: Raziuddin Syed , Sheikha Anwar , Latif Abdulbasit A. 
Published: August 2010

AbstractThe leukemic T‐celis of the six patients with T‐cell chronic lymphocytic leukemia (T‐CLL), four with CD4 and CD45R‐positive (CD4+ CD45R*) T‐CLL and two with CD8 and CD45R‐positive (CD8+ CD45R+) T‐CLL pheno‐type were studied for detailed immunologic phenotypic and functional characteristics. The levels of soluble in‐terleukin‐2 receptors were elevated significantly in the serum of all four patients with CD4+ CD45R+ T‐CLL. Moreover, the CD4+ CD45R+ T‐CLL patients' T‐cells, after in vitro stimulation with phytohemagglutinin and concanavalin A, expressed elevated percentages of interieukin‐2 receptors on cells and secreted high interleukin‐2 activity. The B‐cell growth factor (BCGF) activity from three patients with CD4+ CD45R+ T‐CLL was enhanced, but B‐cell differentiation factor (BCDF) activity of the all T‐CLL patients was decreased. Reduced BCGF and BCDF activity of the leukemic T‐cells was one possible mechanism of hypogammaglobulinemia detected in two patients with T‐CLL. All T‐CLL patients' leukemic T‐cells had diminished immunoregulatory functional activity in allogeneic mixed lymphocyte reactions. These observations suggest that leukemic T‐cells from T‐CLL patients have many immunologic functional defects that may be important in their proliferative potential.
Low incidence of human papillomavirus type 16 DNA in bladder tumor detected by the polymerase chain reaction
Authors: Chetsanga C. , Malmström P.‐U. , Gyllensten U. , Moreno‐Lopez J. , Dinter Z. , Pettersson U. 
Published: August 2010

AbstractHuman papillomavirus (HPV) detection was done using the polymerase chain reaction technique on tumor tissue from 44 patients with transitional cell carcinoma of the urinary bladder. Only one of the 44 was associated with HPV infection. The HPV‐positive patient was not known to have immunodeficiency or genital warts, and the tumor was not morphologically different from the other tumors. Control experiments excluded the possibility that this finding was caused by contamination of the sample. This study confirms that HPV infection is a. rare condition in bladder carcinoma.
Fachbereichstag Chemieingenieurwesen
Authors: Janßen Anton , Gombler Willy 
Published: August 2010

AbstractDer bisherige “Arbeitskreis der Chemie‐Fachbereiche an Fachhochschulen in der Bundesrepublik Deutschland (ACFH)” heißt nun “Fachbereichstag Chemieingenieurwesen an Fachhochschulen (FCFH)”. Mit dieser Umbenennung soll zu einer Vereinheitlichung beigetragen werden.
Descriptions of personal experiences: Effects on students' learning and behavioral intentions toward peers with Attention‐Deficit/Hyperactivity Disorder
Authors: Saecker Lee B. , Skinner Amy L. , Skinner Christopher H. , Rowland Emily , Kirk Emily 
Published: August 2010

AbstractHigh‐school students were shown an educational video designed to dispel 12 common myths regarding Attention‐Deficit/Hyperactivity Disorder (ADHD) by describing each myth and then presenting accurate information. The experimental group viewed a video that was supplemented by the speaker acknowledging that he had ADHD and providing descriptions of personal experiences (DPE) designed to highlight the injury caused by 6 of the 12 common myths. Findings suggest that including the DPE may have enhanced learning of the information that was highlighted by these descriptions, but interfered with learning the other six facts. Providing DPE did not alter behavioral intentions, and this analysis did not appear to be confounded by differential learning. Our discussion focuses on personalizing disability information, seductive details effects, and the role that correcting myths with accurate information may have on students with respect to their interactions with classmates with disabilities. © 2010 Wiley Periodicals, Inc.
Effectiveness of Aquatic Exercise for Obese Patients with Knee Osteoarthritis: A Randomized Controlled Trial
Authors: Lim Jae‐Young , Tchai Esther , Jang Soong‐Nang 
Published: August 2010

ObjectiveTo design an aquatic exercise (AQE) and land‐based exercise (LBE) program to enhance knee function and reduce body fat in patients with obesity and knee osteoarthritis and to investigate the effectiveness of AQE and LBE on body fat, functional fitness, and functional status.SettingOutpatient clinic at a Seoul National University Bundang Hospital.ParticipantsObese patients with knee osteoarthritis were recruited from patients who visited the rehabilitation, orthopedic surgery, and geriatric outpatient clinics at the hospital. Study participants were limited to those who met the following criteria: body mass index more than 25 kg/m2, abdominal circumference more than 90 cm (men) or 85 cm (women), clinically diagnosed osteoarthritis with Kellgren–Lawrence scale 2 or higher on radiographic studies, and independent ambulation state.MethodsParticipants were randomly allocated into 3 groups: AQE (n = 26), LBE (n = 25), and the control group (n = 24). Exercise interventions were conducted 3 times a week for 8 weeks.Outcome MeasuresBody fat analysis, brief pain inventory, Western Ontario and McMaster Universities' osteoarthritis index, Short Form‐36 questionnaire, and knee isokinetic tests were evaluated to assess changes in body fat composition, pain, physical function, and quality of life before and after the exercise program.ResultsAlthough no significant difference was found in general characteristics among the 3 groups before exercise, body fat proportion in the AQE group decreased significantly (mean ± SD, from 34.4 ± 4.7 to 33.3 ± 4.7; P = .031) after intervention. The body mass index was slightly reduced after intervention, but it was not statistically significant. The AQE group showed significant improvements in pain, disability, and quality of life. Notably, the change in pain interference in the AQE group (mean ± SD, from 25.8 ± 15.1 to 18.8 ± 13.1; P = .009) was greater than that of the LBE group. Both exercise groups showed significant improvements in Western Ontario and McMaster Universities' osteoarthritis index disability compared with the control group.ConclusionsAQE had an advantage in controlling the interference with activity because of pain. AQE may be an effective tool for patients with obesity who have difficulties with active exercise due to knee osteoarthritis.
Rehabilitation Outcomes of Stroke Patients Treated With Tissue Plasminogen Activator
Authors: Meiner Zeev , Sajin Anna , Schwartz Isabella , Tsenter Jeanna , Yovchev Ivelin , Eichel Roni , Ben‐Hur Tamir , Leker Ronen R. 
Published: August 2010

ObjectiveTo investigate the influence of thrombolysis on functional outcomes after rehabilitation.BackgroundSystemic thrombolysis with tissue plasminogen activator (tPA) is considered the mainstay of acute stroke therapy and was found to improve short‐term outcome.DesignMatched case‐controlled design.SettingInpatient neurology and rehabilitation departments.ParticipantsThirty‐seven patients given tPA and 37 control patients not treated with lytics because of protocol limits.MethodsWe retrospectively analyzed data from a cohort of stroke patients who were treated with systemic tPA. The rehabilitation outcome of thrombolysis‐treated patients was compared with that observed for tPA‐ineligible and age‐ and stroke severity‐matched patients treated at the same neurology and rehabilitation departments.Main Outcome MeasureNeurological evaluation was assessed with the National Institutes of Health stroke scale (NIHSS). Activity of daily living was measured using the Functional Independence Measure (FIM) instrument. Functional outcome was measured using the modified Rankin scale (mRS).ResultsThe treatment group included 37 patients given tPA; 37 tPA‐ineligible patients served as controls. On admission to rehabilitation, there were no significant differences in functional, neurological, and rehabilitation parameters between the groups. At the end of the rehabilitation period, NIHSS scores were significantly lower in the thrombolysis group (P = .036). More patients in the thrombolysis group reached functional independence defined as mRS ≤2 (20/37 versus 10/37; P = .03). At the end of rehabilitation, total FIM score (mean 102.8 versus 93.9; P = .039), total FIM gain (mean 27.8 versus 21.4; P = .09), and total FIM efficiency scores (0.8 versus 0.43; P = .013) were higher in the thrombolysis group and more patients in this group were discharged home.ConclusionsAlthough the bulk of neurological improvement occurred before the inpatient rehabilitation, thrombolysis‐treated patients continue to improve faster and to a larger extent during the rehabilitation period suggesting that the beneficial effects of thrombolysis continue beyond the acute phase.
QuantProReloaded: quantitative analysis of microspot immunoassays
Authors: Jöcker Anika , Sonntag Johanna , Henjes Frauke , Götschel Frank , Tresch Achim , Beißbarth Tim , Wiemann Stefan , Korf Ulrike 
Published: August 2010

Abstract
Summary: Protein microarrays are well-established as sensitive tools for proteomics. Particularly, the microspot immunoassay (MIA) platform enables a quantitative analysis of (phospho-) proteins in complex solutions (e.g. cell lysates or blood plasma) and with low consumption of samples and reagents. Despite numerous biological and clinical applications of MIAs there is currently no user-friendly open source data analysis software available with versatile options for data analysis and data visualization. Here, we introduce the open source software QuantProReloaded that is specifically designed for the analysis of data from MIA experiments.
Availability and implementation: QuantProReloaded is written in R and Java and is open for download under the BSB license at http://code.google.com/p/quantproreloaded/
Contact: a.joecker@dkfz.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Toward in Vivo Chemical Imaging of Epicuticular Waxes
Authors: Weissflog Ina , Vogler Nadine , Akimov Denis , Dellith Andrea , Schachtschabel Doreen , Svatos Ales , Boland Wilhelm , Dietzek Benjamin , Popp Jürgen 
Published: August 2010

Abstract
Epicuticular waxes, which are found on the outer surface of plant cuticles, are difficult to study in vivo. To monitor the growth, development, and structural alterations of epicuticular wax layers, coherent anti-Stokes Raman scattering (CARS) might be used. CARS, as a Raman-based technique, not only provides structural insight but also chemical information by imaging the spatial distribution of Raman-active vibrations. Here, we present a comparative study using CARS and scanning electron microscopy to characterize the structure of epicuticular waxes. The ability of CARS to provide detailed structural information on the biologically important wax layer was detailed on the examples of cherry laurel (Prunus laurocerasus), hoya (Hoya carnosa), and ceriman/Swiss cheese plant (Monstera sp. aff. deliciosa). We anticipate that the work presented will open a doorway for online monitoring of formation and alterations of epicuticular wax layers.
Do lender‐imposed sweeps affect ethanol technology investment?
Authors: Fewell Jason , Gustafson Cole 
Published: August 2010

PurposeNew federal legislation proposes to reduce greenhouse gas (GHG) emissions associated with biofuel production. To comply, existing corn ethanol plants will have to invest in new more carbon efficient production technology such as dry fractionation. However, this will be challenging for the industry given the present financial environment of surplus production, recent profit declines, numerous bankruptcies, and lender‐imposed covenants. The purpose of this paper is to examine a dry mill ethanol firm's ability to invest in dry fractionation technology in the face of declining profitability and stringent lender cash flow repayment constraints. Firm level risk aversion also is considered when determining a firm's willingness to invest in dry fractionation technology.Design /methodology/approachA Monte Carlo simulation model is constructed to estimate firm profits, cash flows, and changes in equity following new investment in fractionation to determine an optimal investment strategy.FindingsThe addition of a lender‐imposed sweep, whereby a percentage of free cash flow is used to pay off extra debt in high profit years, reduces the firm's ability to build equity and increases bankruptcy risk under investment. However, the sweep increases long‐run equity because total financing costs are reduced with accelerated debt repayment.Practical implicationsResults show that while ethanol firm profits are uncertain, imposition of a lender sweep combined with increased profit from dry fractionation technology helps the firm increase long‐run financial resiliency.Originality/valueExamination of ethanol plant financial structures and investment capabilities has received scant research attention to date.
Tax‐deferred exchanges of farmland: theory and evidence from federal tax data
Authors: Williamson James M. , Brady Michael P. , Durst Ron 
Published: August 2010

PurposeThe purpose of this paper is to examine the use of Section 1031 of the Internal Revenue Code (IRC), a piece of US tax law that allows for tax‐deferred exchanges of like‐kind property.Design/methodology/approachThe paper derives a theoretical premium value for exchanges and presents the first national level analysis of Federal tax data on the use of like‐kind exchanges involving farmland between 1999 and 2005.FindingsThere is significant interest in Section 1031 from stakeholders in rural communities because there is widespread belief that the recent growth in farmland values may have, in part, been stimulated by Section 1031 exchanges of farmland. Despite these concerns, little is known about the extent of such exchanges.Originality/valueThis paper provides insight into the value and use of the IRC's Section 1031 provision. Based on simulations of a theoretical model using plausible assumptions about asset growth, the paper shows how proposed tax changes will affect the tax value of the deferral.
The relationship between organizational socialization and commitment in the workplace among employees in long‐term nursing care facilities
Authors: Cohen Aaron , Veled‐Hecht Aya 
Published: August 2010

PurposeThis paper seeks to examine the relationship between organizational socialization and commitment in the workplace (affective organizational commitment, occupational commitment, workgroup commitment, work involvement and job involvement). It also examines whether this relationship holds when organizational justice is included in the equation.Design/methodology/approachA total of 109 employees employed no longer than 3.5 years in long‐term nursing care facilities in Israel completed the questionnaire (a 70 per cent response rate).FindingsThe results showed that organizational socialization was related to all forms of commitment, particularly to organizational commitment, workgroup commitment and job involvement. The relationship held when organizational justice was added to the equations, particularly for the previously mentioned three commitment forms. The models explained a relatively large amount of the variance in commitment forms. The implications of the findings for future research on commitment and organizational socialization are discussed.Originality/valueWhile a number of studies have explored the relationship between socialization and commitment, very few studies have examined how socialization is related to more than one focus of commitment simultaneously. This paper aims to fill this gap.
Explaining engagement in personal activities on company time
Authors: Eddy Erik R. , D'Abate Caroline P. , Thurston Paul W. 
Published: August 2010

PurposeThe purpose of this paper is to explore rationalizations individuals provide for engaging in personal activities on company time.Design/methodology/approachData were collected from 121 survey respondents working in a variety of organizations and backgrounds. Respondents provided information on the number of times they engage in various personal activities while at work, the amount of time engaged in these activities, and their rationalizations for performing personal activities during work hours.FindingsResults suggest that employees spend nearly five hours in a typical workweek engaged in personal activities. More than 90 per cent of this time is spent using the internet, email, phone, or conversing with co‐workers. Employees use a variety of rationalizations for such behavior, but only two rationalizations (i.e. boredom and convenience) were statistically reliable predictors of the extent to which they engaged in personal activities on company time.Practical implicationsThe current research finds that boredom and convenience are related to the extent that employees engage in personal activities on company time. Improvements in the work environment to reduce boredom might show a marked decrease in these behaviors, thereby mitigating the need for organizations to develop formal policies against these behaviors.Originality/valueThis is only the second quantitative study to examine the amount of time individuals spend engaged in specific personal activities on the job. It is the first quantitative exploration of the rationalizations employees use to justify these behaviors.
Reviewing sexual harassment in the workplace – an intervention model
Authors: Hunt C.M. , Davidson M.J. , Fielden S.L. , Hoel H. 
Published: August 2010

PurposeThe purpose of this literature review is to provide an intervention model, which can be used by organisations to combat sexual harassment in the workplace. Sexual harassment has been somewhat ignored over recent years, with much of the academic literature focusing on harassment specifically on workplace bullying, or psychological harassment of a generic nature. For the purpose of this review, the authors have specifically reviewed individual and organisational antecedents, particularly focusing on the organisation's culture and training programmes.Design/methodology/approachA review of the sexual harassment literature has been conducted to examine primary, secondary and tertiary interventions to combat sexual harassment in the workplace.FindingsThere are a variety of antecedents of sexual harassment which can be examined; these cover three main categories: groups and individuals; organisational and situational; and societal. Sexual harassment should be seen as an issue which needs to be addressed by the organisation, rather than simply increasing and improving an individual's skills in order to deal with harassment (Fitzgerald and Shullman).Originality/valueThis paper provides an up‐to‐date review of the sexual harassment literature and from this provides a model, which organisations can utilise when attempting to tackle the problem of sexual harassment.
Complex adaptive leading‐ship and open‐processional change processes
Authors: Ford Randal 
Published: August 2010

PurposeThis paper aims to determine what leader‐leading competencies enable management of turbulent, uncertain change and what principles from a complex adaptive systems perspective constitute it.Design/methodology/approachThe paper is a qualitative research case study.FindingsIt is found that there are three leading‐ship competencies: administrative, adaptive and enabling.Originality/valueThe paper illustrates that complex adaptive organizations oblige leaders to view differently organizational networks and their role within such networks.