bluuebunny/crossref_metadata_2025_split huggingface dataset:
Score Tests for Exploring Complex Models: Application to HIV Dynamics Models
Authors: Drylewicz Julia , Commenges Daniel , Thiébaut Rodolphe 
Published: November 2009

AbstractIn biostatistics, more and more complex models are being developed. This is particularly the case in system biology. Fitting complex models can be very time‐consuming, since many models often have to be explored. Among the possibilities are the introduction of explanatory variables and the determination of random effects. The particularity of this use of the score test is that the null hypothesis is not itself very simple; typically, some random effects may be present under the null hypothesis. Moreover, the information matrix cannot be computed, but only an approximation based on the score. This article examines this situation with the specific example of HIV dynamics models. We examine the score test statistics for testing the effect of explanatory variables and the variance of random effect in this complex situation. We study type I errors and the statistical powers of this score test statistics and we apply the score test approach to a real data set of HIV‐infected patients.
PNA zipper as a dimerization tool: Development of a bZip mimic
Authors: Pensato Soccorsa , Renda Mario , Leccia Felicia , Saviano Michele , D'Andrea Luca D. , Pedone Carlo , Pedone Paolo V. , Romanelli Alessandra 
Published: November 2009

AbstractThe article describes the use of a PNA duplex (PNA zipper) as a tool to dimerize or bring in close proximity two polypeptides or protein domains. The amino acid sequence to be dimerized is covalently bound to complementary PNA sequences. Annealing of the PNA strands results in dimer formation. To test the ability of the “PNA‐zipper” as a dimerization tool, we designed a GCN4 mimetic, where the leucine‐zipper dimerization domain was replaced by the PNA zipper, whereas the basic DNA‐binding domain was covalently attached to the PNA. The molecule was assembled by chemical ligation of the peptide corresponding to the DNA‐binding domain of GCN4 modified with a succinyl thioester with two complementary PNAs harboring a cysteine residue. Electromobility‐shift experiments show the ability of the PNA zipper‐GCN4 to bind selected DNA duplexes. The PNA zipper‐GCN4 binds both the TRE and CRE DNA sites, but it does not bind TRE and CRE mutants containing even a single base mutation, as the native GCN4. The ability to fold upon complexation with DNA was investigated by CD. A good correlation between the ability of the PNA zipper‐GCN4 to fold into α helices and the ability to bind DNA was found. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 434–441, 2010.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Australasian Laparoscopic Colon Cancer Study shows that elderly patients may benefit from lower postoperative complication rates following laparoscopic versus open resection
Authors: Allardyce R A , Bagshaw P F , Frampton C M , Frizelle F A , Hewett P J , Rieger N A , Smith J S , Solomon M J , Stevenson A R L 
Published: November 2009

Abstract

Background
A retrospective analysis of age-related postoperative morbidity in the Australia and New Zealand prospective randomized controlled trial comparing laparoscopic and open resection for right- and left-sided colonic cancer is presented.

Methods
A total of 592 eligible patients were entered and studied from 1998 to 2005.

Results
Data from 294 patients who underwent laparoscopic and 298 who had open colonic resection were analysed; 266 patients were aged less than 70 years and 326 were 70 years or older (mean(s.d.) 70·3(11·0) years). Forty-three laparoscopic operations (14·6 per cent) were converted to an open procedure. Fewer complications were reported for intention-to-treat laparoscopic resections compared with open procedures (P = 0·002), owing primarily to a lower rate in patients aged 70 years or more (P = 0·002). Fewer patients in the laparoscopic group experienced any complication (P = 0·035), especially patients aged 70 years or above (P = 0·019).

Conclusion
Treatment choices for colonic cancer depend principally upon disease-free survival; however, patients aged 70 years or over should have rigorous preoperative investigation to avoid conversion and should be considered for laparoscopic colonic resection. Registration number: NCT00202111 (http://www.clinicaltrials.gov).
Disease recurrence patterns after R0 resection of hilar cholangiocarcinoma
Authors: Kobayashi A , Miwa S , Nakata T , Miyagawa S 
Published: November 2009

Abstract

Background
There is little information regarding the clinical behaviour of hilar cholangiocarcinoma after curative resection.

Methods
A retrospective study was undertaken of 79 consecutive patients with hilar cholangiocarcinoma who had undergone major hepatectomy (three or more Couinaud segments) concomitant with caudate lobectomy, and had negative resection margins. Sites of initial disease recurrence were classified as locoregional (porta hepatis) or distant (intrahepatic, peritoneal, para-aortic lymph nodal or extra-abdominal). Univariable and multivariable analyses were performed to determine the factors potentially related to recurrence.

Results
Disease recurrence was observed in 42 (53 per cent) of the 79 patients. Cumulative recurrence rates at 3 and 4 years after surgery were 52 and 56 per cent respectively. Locoregional recurrence alone was observed in eight (10 per cent) and distant metastasis in 34 (43 per cent) of the 79 patients after R0 resection. Positive nodal involvement and high International Union Against Cancer tumour (T) stage were independent prognostic factors associated with distant metastasis.

Conclusion
Distant metastases are more common than locoregional recurrence after R0 resection for hilar cholangiocarcinoma, and associated with nodal involvement and high T stage.
Randomized clinical trial of perianal surgery performed under spinal saddle block versus total intravenous anaesthesia
Authors: Schmittner M D , Schreiber H , Janke A , Weiss C , Blunk J , Bussen D G , Luecke T 
Published: November 2009

Abstract

Background
The aim of this randomized clinical trial was to determine whether spinal saddle block (SSB) is superior to total intravenous anaesthesia (TIVA) in perianal surgery.

Methods
Suitable patients aged 18–75 years (American Society of Anesthesiologists grade I or II) scheduled to undergo perianal surgery were randomized to SSB (1·0 ml 0·5 per cent hyperbaric bupivacaine) or TIVA with propofol and fentanyl by means of a laryngeal mask. Cumulative consumption of analgesics within 24 h after surgery was recorded, and postoperative recovery and patient satisfaction were evaluated.

Results
A total of 201 patients were randomized. Supplemental analgesia within 24 h after surgery was required by 31 of 101 patients having SSB and 58 of 100 who had TIVA (P &lt; 0·001). Median monitoring time in the recovery room was 5 (range 1–45) min for SSB versus 44 (4–148) min for TIVA (P &lt; 0·001). Patients in the SSB group were able to eat and drink more quickly, although times to mobilization and micturition were not significantly different. Patients having SSB were more likely to describe the anaesthesia as ‘better than expected’.

Conclusion
SSB is superior to TIVA in patients undergoing perianal surgery in terms of analgesic consumption within 24 h after surgery and aspects of postoperative recovery. Registration number: ISRCTN41981381 (http://www.controlled-trials.com).
Randomized clinical trial of laparoscopic versus open donor nephrectomy
Authors: Nicholson M L , Kaushik M , Lewis G R R , Brook N R , Bagul A , Kay M D , Harper S J , Elwell R , Veitch P S 
Published: November 2009

Abstract

Background
This randomized controlled trial was designed to determine the safety and efficacy of laparoscopic donor nephrectomy (LDN) in comparison with short-incision open donor nephrectomy (ODN).

Methods
Eighty-four live kidney donors were randomized in a 2 : 1 ratio to LDN (56 patients) or short-incision ODN without rib resection (28). Primary endpoints were pain relief and duration of inpatient stay.

Results
There was no donor death or allograft thrombosis in either group. The first warm ischaemic time median (range) 4 (2–7) versus 2 (1–5) min; P = 0·001) and the duration of operation (160 (110–250) versus 150 (90–200); P = 0·004) were longer for LDN. LDN led to a reduction in parenteral morphine requirement 59 (6–136) versus 90 (35–312) mg; P = 0·001) and hospital stay (4 (2–6) versus 6 (2–9) days; P = 0·001), and earlier return to employment (42 (14–84) versus 66·5 (14–112) days; P = 0·004). Postoperative respiratory function was improved after LDN. There were more postoperative complications per donor in the ODN group (0·6(0·7) versus 0·3(0·5); P = 0·033). At a median follow-up of 74 months, there were no differences in renal function or allograft survival between the groups.

Conclusion
LDN removes some of the disincentives to live donation without compromising the outcome of the recipient transplant.
PCR cloning of partial nbs sequences from grape (Vitis aestivalis Michx)
Authors: Chang Ming‐Mei , DiGennaro Peter , Macula Anthony 
Published: November 2009

AbstractPlants defend themselves against pathogens via the expressions of disease resistance (R) genes. Many plant R gene products contain the characteristic nucleotide‐binding site (NBS) and leucine‐rich repeat (LRR) domains. There are highly conserved motifs within the NBS domain which could be targeted for polymerase chain reaction (PCR) cloning of R genes. Here, we report a 4‐week undergraduate laboratory exercise that mimics the research environment to PCR‐clone partial nbs sequences using degenerate primers corresponding to the phosphate‐binding loop (P‐loop) and GLPL motifs within the NBS domain of potential R gene products from the North American grape, Vitis aestivalis Michx. Students were able to complete the laboratory procedures successfully and obtained four different clones, among which three are new. Through the laboratory exercise, students learned a variety of important molecular techniques including genomic DNA isolation, DNA quantification, PCR, agarose gel electrophoresis, DNA extraction from agarose gel, ligation, bacterial transformation, and plasmid DNA isolation and purification. They also used currently available web‐based bioinformatic programs for sequence analysis. The laboratory exercise provides students the hands‐on experience on PCR cloning and shows them how it is done in a research environment. The clones obtained may be further tested for their potential use as markers to differentiate resistant cultivars from the susceptible ones, a useful tool in breeding programs.
Using Pseudomonas putida xylE gene to teach molecular cloning techniques for undergraduates
Authors: Dong Xu , Xin Yi , Ye Li , Ma Yufang 
Published: November 2009

AbstractWe have developed and implemented a serial experiment in molecular cloning laboratory course for undergraduate students majored in biotechnology. Pseudomonas putida xylE gene, encoding catechol 2, 3‐dioxygenase, was manipulated to learn molecular biology techniques. The integration of cloning, expression, and enzyme assay gave students a chance to mimic real research and product development by connecting separated techniques. This serial experiment helped students set up intact idea of molecular biology and to understand the relation of each individual operation.
Algorithm for writing a scientific manuscript
Authors: O'Connor Timothy R. , Holmquist Gerald P. 
Published: November 2009

AbstractWe present an algorithm for the construction of a strong initial draft. It is designed to overcome writer's block and to assist scientists who are not native English speakers. The writing starts with making figures and tables. These suggest several terse summary statements, the few major conclusions or observations the author will present to the scientific community. After identification of the audience, the specific community addressed, materials and methods are written to explain how the tables and figures were generated. Results are initially restricted to describing the logical data relations in each table and figure. The discussion then converts each data relationship into mechanistic cause‐and‐effect interpretations suitable for the abstract. A brief epilogue deals with the submission and the fate of the final manuscript once submitted. Although other models for the initial draft exist, this model has worked for us and new researchers in our laboratories and addresses problems we encountered while editing manuscripts.
Detergent‐based isolation of yeast membrane rafts
Authors: Willhite D. Grant , Wright Stephen E. 
Published: November 2009

AbstractLipid rafts have been implicated in numerous cellular processes including cell signaling, endocytosis, and even viral infection. Isolation of these lipid rafts often involves detergent treatment of the membrane to dissolve nonraft components followed by separation of raft regions in a density gradient. We present here an inquiry‐based lab series using these techniques to isolate membrane rafts from yeast cells designed for the upper division biochemistry or cell biology course laboratory. The co‐localization of a common raft‐associated protein with lipid rafts is then followed. This lab series involves undergraduate cell biology or biochemistry students in each step of the scientific process from experimental design to dissemination of their results. Additionally, this lab series reinforces concepts in membrane structure while exposing undergraduates to common techniques in cell biology and biochemistry.
Problem‐solving test: The effect of synonymous codons on gene expression
Authors: Szeberényi József 
Published: November 2009

AbstractTerms to be familiar with before you start to solve the test: the genetic code, codon, degenerate codons, protein synthesis, aminoacyl‐tRNA, anticodon, antiparallel orientation, wobble, unambiguous codons, ribosomes, initiation, elongation and termination of translation, peptidyl transferase, translocation, degenerate oligonucleotides, green fluorescent protein, expression plasmid, cDNA, electron microscopy, fluorescence microscopy, phase contrast microscopy, bacteriophage, promoter, gene library, Northern blotting, Western blotting, in silico analysis, and hairpin structures.
Sustainable development and intangibles: building sustainable intellectual capital
Authors: López‐Gamero María D. , Zaragoza‐Sáez Patrocinio , Claver‐Cortés Enrique , Molina‐Azorín José F. 
Published: November 2009

AbstractSustainable intellectual capital is a promising starting‐point for the incorporation of environmental aspects into the general management system of a firm. This paper examines how sustainable intellectual capital helps to overcome the shortcomings of conventional approaches to environmental management systems. It does this by extending the concept of sustainability from relational capital to the three pillars of intellectual capital: human, structural and relational intellectual capital. A multiple case study was carried out with Spanish firms characterized by their high level of environmental leadership. The findings indicated that sustainable human intellectual capital, environmental training, information and awareness sessions help in the accumulation and utilization of knowledge. As for sustainable structural intellectual capital, the environmental technology portfolio is improved and new environmental departments are created. Regarding sustainable relational intellectual capital, the firm–environment link is very important. In the primary and secondary sectors suppliers become involved to a greater extent in the environmental management process, whereas in the service sector it is the customer who becomes more involved. Copyright © 2009 John Wiley & Sons, Ltd and ERP Environment.
Effects of defendant and victim race on perceptions of juvenile sex offenders
Authors: Stevenson Margaret C. , Sorenson Katlyn M. , Smith Amy C. , Sekely Ady , Dzwairo Rukudzo A. 
Published: November 2009

AbstractWe investigated effects of defendant race, victim race, and juror gender on public perceptions of a juvenile sex offense. We predicted that participants, particularly men, would support registering a juvenile defendant as a sex offender more when he was Black than White and that participants, particularly women, would support registering the defendant more when the female crime victim was portrayed as White than as Black. We also expected that support for registration would be higher when the defendant and victim were different races than when they were the same race. As expected, women (but not men) recommended registration more when the victim was White than Black. Further, participants supported registration more when the defendant and the victim were different races than when they were the same race. These effects were mediated by retributive goals to punish the offender—not by utilitarian goals to protect society. Explanations and implications are discussed. Copyright © 2009 John Wiley & Sons, Ltd.
Differential correlates to self‐report and parent‐report of callous–unemotional traits in a sample of juvenile sexual offenders
Authors: White Stuart F. , Cruise Keith R. , Frick Paul J. 
Published: November 2009

AbstractThe association of callous–unemotional (CU) traits with violence and severe antisocial behavior has led to a recent focus on the association between CU traits and sexual offending behavior. When assessing juveniles with sexual offenses, practice standards recommend that multiple sources of data are considered. However, the differential correlates of parent‐report versus self‐report of CU traits in juvenile sex offenders have not been investigated. A sample of 94 detained male youth (mean age = 15.22, SD = 1.48) was administered both youth and parent versions of the Inventory of Callous–Unemotional Traits (ICU), a general delinquency risk assessment tool (YLS), and a sexual offending risk assessment tool (J‐SOAP‐II) to investigate concordance between self‐report and parent‐report of CU traits as well as association with general and sex‐specific risk factors. Both parent‐report and self‐report of CU traits were significantly related to higher general delinquency risk scores, with parent‐report showing stronger correlations than self‐report. Both parent‐report and self‐report were related to sex‐specific risk factors. However, only parent‐report significantly predicted static sexual risk, while self‐report significantly predicted dynamic sexual risk scores. Evidence supports the importance of including both parent‐ and self‐report of CU traits in the comprehensive assessment of sexually offending youth. Copyright © 2009 John Wiley & Sons, Ltd.
Assessment of embryonic growth in chicken eggs by means of visible transmission spectroscopy
Authors: Kemps Bart J. , Bamelis Flip R. , Mertens Kristof , Decuypere Eddy M. , De Baerdemaeker Josse G. , De Ketelaere Bart 
Published: November 2009

AbstractDuring this work, it was investigated whether spectral measurements can be used to monitor embryonic growth. An experiment was conducted in which both the transmission spectra and embryonic weight were determined on 240 eggs (Cobb, 37 weeks) between Day 5 and Day 10 of incubation. The spectral data were linked to embryonic weight by means of a partial least squares analysis. Different preprocessing procedures were compared during this work, that is, smoothing, multiplicative scatter correction (MSC), and first‐ and second‐order derivative. Compared to the remainder of the preprocessing procedures, MSC leads to a considerable improvement of the prediction capability of the embryonic weight. The ratio of performance to deviation obtained for the MSC spectra equaled 4.5 indicating that a very accurate prediction of embryonic weight is feasible based on the VIS/NIR transmission measurements. Important regions for the prediction are situated around 685–740 nm. It is suggested that the spectral changes in these spectral regions result from the displacement of carotenoids from the yolk into the blood circuitry. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010
Understanding the key factors for enzymatic conversion of pretreated lignocellulose by partial least square analysis
Authors: Huang Renliang , Su Rongxin , Qi Wei , He Zhimin 
Published: November 2009

AbstractThe relationship between the physicochemical properties of lignocellulosic substrates and enzyme digestion is still not well known. After different pretreatments, cellulase hydrolysis and measurements of physicochemical characteristics by column solute exclusion, particle size analysis, X‐ray diffraction, Fourier transform infrared spectroscopy and solid state 13C nuclear magnetic resonance were performed in this study. Partial least squares was then applied to seek the key factors limiting the rate and extent of cellulose digestion. According to the PLS results, the most important factor for cellulose digestion was accessible interior surface area, followed by delignification and the destruction of the hydrogen bonds. The cellulose digestion at 2 and 24 hr were improved with the increased accessibility of interior surface area to the reporter molecules of 5.1‐nm diameter. Removal of lignin and breaking of hydrogen bonds were also found to significantly promote cellulose conversion. Other properties, including the breakdown of intramolecular hydrogen bonds, cellulose crystallinity, and hemicellulose content, had less effect on the efficiency of enzymatic hydrolysis. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010
Mimic of a large‐scale diafiltration process by using ultra scale‐down rotating disc filter
Authors: Ma Guijun , Aucamp Jean , Gerontas Spyridon , Eardley‐Patel Ranna , Craig Alan , Hoare Mike , Zhou Yuhong 
Published: November 2009

AbstractUltra scale‐down (USD) approach is a powerful tool to predict large‐scale process performance by using very small amounts of material. In this article, we present a method to mimic flux and transmission performance in a labscale crossflow operation by an USD rotating disc filter (RDF). The Pellicon 2 labscale system used for evaluation of the mimic can readily be related to small pilot and industrial scale. Adopted from the pulsed sample injection technique by Ghosh and Cui (J Membr Sci. 2000;175:5‐84), the RDF has been modified by building in inserts to allow the flexibility of the chamber volume, so that only 1.5 mL of processing material is required for each diafiltration experiment. The reported method enjoys the simplicity of dead‐end mode operation with accurate control of operation conditions that can mimic well the crossflow operation in large scale. Wall shear rate correlations have been established for both the labscale cassette and the USD device, and a mimic has been developed by operating both scales under conditions with equivalent averaged shear rates. The studies using E. coli lysate show that the flux vs. transmembrane pressure profile follows a first‐order model, and the transmission of antibody fragment (Fab′) is independent of transmembrane pressure. Predicted flux and transmission data agreed well with the experimental results of a labscale diafiltration where the cassette resistance was considered. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010