bluuebunny/crossref_metadata_2025_split huggingface dataset:
SiteFind: A software tool for introducing a restriction site as a marker for successful site-directed mutagenesis
Authors: Evans Paul M , Liu Chunming 
Published: December 2005

Abstract

Background
Site-directed mutagenesis is a widely-used technique for introducing mutations into a particular DNA sequence, often with the goal of creating a point mutation in the corresponding amino acid sequence but otherwise leaving the overall sequence undisturbed. However, this method provides no means for verifying its success other than sequencing the putative mutant construct: This can quickly become an expensive method for screening for successful mutations. An alternative to sequencing is to simultaneously introduce a restriction site near the point mutation in manner such that the restriction site has no effect on the translated amino acid sequence. Thus, the novel restriction site can be used as a marker for successful mutation which can be quickly and easily assessed. However, finding a restriction site that does not disturb the corresponding amino acid sequence is a time-consuming task even for experienced researchers. A fast and easy to use computer program is needed for this task.

Results
We wrote a computer program, called SiteFind, to help us design a restriction site within the mutation primers without changing the peptide sequence. Because of the redundancy of genetic code, a given peptide can be encoded by many different DNA sequences. Since the list of possible restriction sites for a given DNA sequence is not always obvious, SiteFind automates this task. The number of possible sequences a computer program must search through increases exponentially as the sequence length increases. SiteFind uses a novel "moving window" algorithm to reduce the number of possible sequences to be searched to a manageable level. The user enters a nucleotide sequence, specifies what amino acid residues should be changed in the mutation, and SiteFind generates a list of possible restriction sites and what nucleotides must be changed to introduce that site. As a demonstration of its use, we successfully generated a single point mutation and a double point mutation in the wild-type sequence for Krüppel-like factor 4, an epithelium-specific transcription factor.

Conclusion
SiteFind is an intuitive, web-based program that enables the user to introduce a novel restriction site into the mutated nucleotide sequence for use as a marker of successful mutation. It is freely available from http://www.utmb.edu/scccb/software/sitefind.html
Stability of response characteristics of a Delphi panel: application of bootstrap data expansion
Authors: Akins Ralitsa B , Tolson Homer , Cole Bryan R 
Published: December 2005

Abstract

Background
Delphi surveys with panels of experts in a particular area of interest have been widely utilized in the fields of clinical medicine, nursing practice, medical education and healthcare services. Despite this wide applicability of the Delphi methodology, there is no clear identification of what constitutes a sufficient number of Delphi survey participants to ensure stability of results.

Methods
The study analyzed the response characteristics from the first round of a Delphi survey conducted with 23 experts in healthcare quality and patient safety. The panel members had similar training and subject matter understanding of the Malcolm Baldrige Criteria for Performance Excellence in Healthcare. The raw data from the first round sampling, which usually contains the largest diversity of responses, were augmented via bootstrap sampling to obtain computer-generated results for two larger samples obtained by sampling with replacement. Response characteristics (mean, trimmed mean, standard deviation and 95% confidence intervals) for 54 survey items were compared for the responses of the 23 actual study participants and two computer-generated samples of 1000 and 2000 resampling iterations.

Results
The results from this study indicate that the response characteristics of a small expert panel in a well-defined knowledge area are stable in light of augmented sampling.

Conclusion
Panels of similarly trained experts (who possess a general understanding in the field of interest) provide effective and reliable utilization of a small sample from a limited number of experts in a field of study to develop reliable criteria that inform judgment and support effective decision-making.
Etoricoxib in the treatment of osteoarthritis over 52-weeks: a double-blind, active-comparator controlled trial [NCT00242489]
Authors: Curtis Sean P , Bockow Barry , Fisher Chester , Olaleye Joseph , Compton Amy , Ko Amy T , Reicin Alise S 
Published: December 2005

Abstract
Background
The aim of this study was to evaluate the long-term efficacy and tolerability of etoricoxib, a COX-2 selective inhibitor, in osteoarthritis (OA) patients.

Methods
A double-blind, randomized, multicenter study was conducted in 617 patients with OA of the knee. The base study was 14 weeks in duration and consisted of 2 parts; in Part I (6 weeks), patients were allocated to once daily oral etoricoxib 5, 10, 30, 60, 90 mg or placebo. In Part II (8 weeks); the placebo, etoricoxib 5 and 10 mg groups were reallocated to etoricoxib 30, 60, or 90 mg qd or diclofenac 50 mg t.i.d. Treatment was continued for consecutive 12 and 26 week extensions. Primary efficacy endpoints were the WOMAC VA 3.0 pain subscale and investigator global assessment of disease status. Safety and tolerability were assessed by collecting adverse events throughout the study.

Results
Compared with placebo, the etoricoxib groups displayed significant (p < 0.05), dose-dependent efficacy for all primary endpoints in Part I; efficacy was maintained throughout the 52 weeks of the study. During the 46-week active-comparator controlled period, the etoricoxib groups demonstrated clinical efficacy that was similar to that of diclofenac 150 mg and was generally well tolerated, with a lower incidence of gastrointestinal (GI) nuisance symptoms compared with diclofenac (13.1, 14.7, and 13.5% for etoricoxib 30, 60, and 90 mg, respectively compared with 22.5% for diclofenac).

Conclusion
In this extension study, etoricoxib, at doses ranging from 30 to 90 mg, demonstrated a maintenance of significant clinical efficacy in patients with OA through 52 weeks of treatment. Etoricoxib displayed clinical efficacy similar to diclofenac 150 mg and was generally well tolerated.
Acquired factor XII deficiency in a woman with recurrent pregnancy loss: working on a differential diagnosis in a single case
Authors: D'Uva Maristella , Strina Ida , Mollo Antonio , Ranieri Antonio , De Placido Giuseppe , Di Micco Pierpaolo 
Published: December 2005

Abstract

Background
Antiphospholipid syndrome (APS) has been often associated to RPL since 1980 and some reports in the Literature rarely described antibodies to factor XII in patients with APS.

Case history
We report the case history of 34-year-old caucasian women with recurrent fetal loss and persistent prolonged activated partial thromboplastin time. Haemostatic tests revealed persistent light decrease of clotting factor XII with normal values of IgG and IgM anticardiolipin antibodies and transient positivity for lupus anticoagulant (LA). Few reports in the Literature described antibodies to factor XII in patient with antiphospholipid syndrome (APS) and transient LA. So, once other causes of RPL were excluded, the patient was diagnosed an unusual form of APS associated to antibodies to factor XII, reduced factor XII plasma levels, transient LA and prolonged activated partial thromboplastin time.

Discussion
We suggest to consider also antibodies directed to clotting factors (e.g. factor XII in our case) as second step of thrombophilia screening in RPL, in particular if a persistent prolonged aPTT is present without an apparent cause.
A general method for nested RT-PCR amplification and sequencing the complete HCV genotype 1 open reading frame
Authors: Yao Ermei , Tavis John E ,   the Virahep-C Study Group
Published: December 2005

Abstract

Background
Hepatitis C virus (HCV) is a pathogenic hepatic flavivirus with a single stranded RNA genome. It has a high genetic variability and is classified into six major genotypes. Genotype 1a and 1b cause the majority of infections in the USA. Viral genomic sequence information is needed to correlate viral variation with pathology or response to therapy. However, reverse transcription-polymerase chain reaction (RT-PCR) of the HCV genome must overcome low template concentration and high target sequence diversity. Amplification conditions must hence have both high sensitivity and specificity yet recognize a heterogeneous target population to permit general amplification with minimal bias. This places divergent demands of the amplification conditions that can be very difficult to reconcile.

Results
RT and nested PCR conditions were optimized independently and systematically for amplifying the complete open reading frame (ORF) from HCV genotype 1a and 1b using several overlapping amplicons. For each amplicon, multiple pairs of nested PCR primers were optimized. Using these primers, the success rate (defined as the rate of production of sufficient DNA for sequencing with any one of the primer pairs for a given amplicon) for amplification of 72 genotype 1a and 1b patient plasma samples averaged over 95% for all amplicons. In addition, two sets of sequencing primers were optimized for each genotype 1a and 1b. Viral consensus sequences were determined by directly sequencing the amplicons. HCV ORFs from 72 patients have been sequenced using these primers. Sequencing errors were negligible because sequencing depth was over 4-fold and both strands were sequenced. Primer bias was controlled and monitored through careful primer design and control experiments.

Conclusion
Optimized RT-PCR and sequencing conditions are useful for rapid and reliable amplification and sequencing of HCV genotype 1a and 1b ORFs.
Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert
Authors: Brosché Mikael , Vinocur Basia , Alatalo Edward R , Lamminmäki Airi , Teichmann Thomas , Ottow Eric A , Djilianov Dimitar , Afif Dany , Bogeat-Triboulot Marie-Béatrice , Altman Arie , Polle Andrea , Dreyer Erwin , Rudd Stephen , Paulin Lars , Auvinen Petri , Kangasjärvi Jaakko 
Published: December 2005

Abstract
Background
Plants growing in their natural habitat represent a valuable resource for elucidating mechanisms of acclimation to environmental constraints. Populus euphratica is a salt-tolerant tree species growing in saline semi-arid areas. To identify genes involved in abiotic stress responses under natural conditions we constructed several normalized and subtracted cDNA libraries from control, stress-exposed and desert-grown P. euphratica trees. In addition, we identified several metabolites in desert-grown P. euphratica trees.

Results
About 14,000 expressed sequence tag (EST) sequences were obtained with a good representation of genes putatively involved in resistance and tolerance to salt and other abiotic stresses. A P. euphratica DNA microarray with a uni-gene set of ESTs representing approximately 6,340 different genes was constructed. The microarray was used to study gene expression in adult P. euphratica trees growing in the desert canyon of Ein Avdat in Israel. In parallel, 22 selected metabolites were profiled in the same trees.

Conclusion
Of the obtained ESTs, 98% were found in the sequenced P. trichocarpa genome and 74% in other Populus EST collections. This implies that the P. euphratica genome does not contain different genes per se, but that regulation of gene expression might be different and that P. euphratica expresses a different set of genes that contribute to adaptation to saline growth conditions. Also, all of the five measured amino acids show increased levels in trees growing in the more saline soil.
The start of phonotactic walking in the flyOrmia ochracea: a kinematic study
Authors: Mason Andrew C. , Lee Norman , Oshinsky Michael L. 
Published: December 2005

SUMMARYOrmia ochracea (Diptera, Tachinidae) are acoustic parasitoids of crickets that have one of the most directionally sensitive auditory systems known. We studied dynamic characteristics of walking phonotaxis in these flies in response to variations in sound source azimuth, and compared phonotaxis of flies in freely walking conditions to tethered flies walking on a treadmill. Motor patterns at the initiation of phonotaxis are not stereotyped even for similar stimulus conditions. Flies respond to directional sound sources by walking in a tight curve that combines rotation and forward translation until they are oriented towards the source direction, then continue on a straight path. Translational velocity accelerates throughout the duration of the stimulus then decelerates following stimulus offset. In contrast, rotational velocity accelerates and then decelerates within the duration of the stimulus such that flies have completed the rotational component of the response and reached their final heading before the end of the stimulus. Rotational velocity is the only response parameter that varies systematically with sound source direction (azimuth). Differences in the amplitude of rotational velocity as a function of source azimuth determine the directional orientation of phonotactic responses. The relationship between rotational velocity and source azimuth is similar to a neural measure of auditory directionality(interaural latency). There were some differences between freely walking and tethered conditions, although both showed qualitatively similar responses. Flies accelerated more slowly and attained lower maximum velocities on the treadmill, consistent with the greater inertia of the treadmill sphere relative to the flies. Also, flies tended to continue walking longer on the treadmill following cessation of the stimulus.
The adaptive function of tiger moth clicks against echolocating bats: an experimental and synthetic approach
Authors: Ratcliffe John M. , Fullard James H. 
Published: December 2005

SUMMARYWe studied the efficiency and effects of the multiple sensory cues of tiger moths on echolocating bats. We used the northern long-eared bat, Myotis septentrionalis, a purported moth specialist that takes surface-bound prey (gleaning) and airborne prey (aerial hawking), and the dogbane tiger moth, Cycnia tenera, an eared species unpalatable to bats that possesses conspicuous colouration and sound-producing organs (tymbals). This is the first study to investigate the interaction of tiger moths and wild-caught bats under conditions mimicking those found in nature and to demand the use of both aerial hawking and gleaning strategies by bats. Further, it is the first to report spectrograms of the sounds produced by tiger moths while under aerial attack by echolocating bats. During both aerial hawking and gleaning trials, all muted C. tenera and perched intact C. tenera were attacked by M. septentrionalis, indicating that M. septentrionalis did not discriminate C. tenera from palatable moths based on potential echoic and/or non-auditory cues. Intact C. tenera were attacked significantly less often than muted C. tenera during aerial hawking attacks: tymbal clicks were therefore an effective deterrent in an aerial hawking context. During gleaning attacks,intact and muted C. tenera were always attacked and suffered similar mortality rates, suggesting that while handling prey this bat uses primarily chemical signals. Our results also show that C. tenera temporally matches the onset of click production to the `approach phase' echolocation calls produced by aerial hawking attacking bats and that clicks themselves influence the echolocation behaviour of attacking bats. In the context of past research, these findings support the hypotheses that the clicks of arctiid moths are both an active defence (through echolocation disruption) and a reliable indicator of chemical defence against aerial-hawking bats. We suggest these signals are specialized for an aerial context.
Analysis of the effects of turning bias on chemotaxis in C. elegans
Authors: Pierce-Shimomura Jonathan T. , Dores Michael , Lockery Shawn R. 
Published: December 2005

SUMMARY
C. elegans advances up a chemical gradient by modulating the probability of occasional large, course-correcting turns called pirouettes. However, it remains uncertain whether C. elegans also uses other behavioral strategies for chemotaxis. Previous observations of the unusual,spiral-shaped chemotaxis tracks made by the bent-head mutant unc-23point to a different strategy in which the animal continuously makes more subtle course corrections. In the present study we have combined automated tracking of individual animals with computer modeling to test the hypothesis that the pirouette strategy is sufficient on its own to account for the spiral tracks. Tracking experiments showed that the bent-head phenotype causes a strong turning bias and disrupts pirouette execution but does not disrupt pirouette initiation. A computer simulation of disrupted pirouette behavior and turning bias reproduced the spiral tracks of unc-23 chemotaxis behavior, showing that the pirouette strategy is sufficient to account for the mutant phenotype. In addition, the simulation reproduced higher order features of the behavior such as the relationship between the handedness of the spiral and the side to which the head was bent. Our results suggest that the pirouette mechanism is sufficient to account for a diverse range of chemotaxis trajectories.
To DGC or not to DGC: oxygen guarding in the termite Zootermopsis nevadensis (Isoptera: Termopsidae)
Authors: Lighton John R. B. , Ottesen Elizabeth A. 
Published: December 2005

SUMMARY
The ability of some insects to engage in complex orchestrations of tracheal gas exchange has been well demonstrated, but its evolutionary origin remains obscure. According to a recently proposed hypothesis, insects may employ spiracular control of gas exchange to guard tissues against long-term oxidative damage by using the discontinuous gas-exchange cycle (DGC) to limit internal oxygen partial pressure (PO2). This manuscript describes a different approach to oxygen guarding in the lower termite Zootermopsis nevadensis. These insects do not display a DGC but respond to elevated oxygen concentrations by restricting spiracular area,resulting in a transient decline in CO2 emission. High internal CO2 concentrations are then maintained; restoring normoxia results in a transient reciprocal increase in CO2 emission caused by release of excess endotracheal CO2. These changes in spiracular area reflect active guarding of low internal O2 concentrations and demonstrate that regulation of endotracheal hypoxia takes physiological priority over prevention of CO2 build-up. This adaptation may reflect the need to protect oxygen-sensitive symbionts (or, gut bug guarding). Termites may eschew the DGC because periodic flushing of the tracheal system with air may harm the obligate anaerobes upon which the lower termites depend for survival on their native diet of chewed wood.
Functional morphology of feeding in the scale-eating specialistCatoprion mento
Authors: Janovetz Jeff 
Published: December 2005

SUMMARYThe wimple piranha, Catoprion mento, has a narrow-range natural diet with fish scales comprising an important proportion of its total food intake. Scales are eaten throughout most of ontogeny and adults feed almost exclusively on this food source. Catoprion exhibits a novel prey capture behavior when removing scales for ingestion. Scale feeding strikes involve a high-speed, open-mouth, ramming attack where the prey is bitten to remove scales and the force of the collision knocks scales free. Unique kinematic parameters of scale-feeding strikes include a mean gape angle of nearly 120° and a `plateau' stage of prolonged maximum displacement for cranial elevation and opercular expansion. When feeding on live fish or loose scales, Catoprion performs a typical ram/suction attack that is modulated according to the elusiveness of the prey. Captures of elusive fish elicit faster strikes with greater displacement of cranial elements than do attacks on loose scales sinking in the water column. Despite its specialized diet and suite of anatomical characters, functional versatility in feeding behavior has not been reduced in Catoprion, as predicted by many analogous studies in functional morphology. On the contrary, the behavioral repertoire of Catoprion has been broadened by the addition of a novel behavior for scale feeding.
Biophysical properties of voltage-gated Na+ channels in frog parathyroid cells and their modulation by cannabinoids
Authors: Okada Yukio , Imendra Kotapola G. , Miyazaki Toshihiro , Hotokezaka Hitoshi , Fujiyama Rie , Zeredo Jorge L. , Miyamoto Takenori , Toda Kazuo 
Published: December 2005

SUMMARY
The membrane properties of isolated frog parathyroid cells were studied using perforated and conventional whole-cell patch-clamp techniques. Frog parathyroid cells displayed transient inward currents in response to depolarizing pulses from a holding potential of –84 mV. We analyzed the biophysical properties of the inward currents. The inward currents disappeared by the replacement of external Na+ with NMDG+ and were reversibly inhibited by 3 μmol l–1 TTX, indicating that the currents occur through the TTX-sensitive voltage-gated Na+channels. Current density elicited by a voltage step from –84 mV to–24 mV was –80 pA pF–1 in perforated mode and–55 pA pF–1 in conventional mode. Current density was decreased to –12 pA pF–1 by internal GTPγS (0.5 mmol l–1), but not affected by internal GDPβS (1 mmol l-1). The voltage of half-maximum (V1/2)activation was –46 mV in both perforated and conventional modes. V1/2 of inactivation was –80 mV in perforated mode and –86 mV in conventional mode. Internal GTPγS (0.5 mmol l–1) shifted the V1/2 for activation to–36 mV and for inactivation to –98 mV. A putative endocannabinoid,2-arachidonoylglycerol ether (2-AG ether, 50 μmol l–1) and a cannabinomimetic aminoalkylindole, WIN 55,212-2 (10 μmol l–1) also greatly reduced the Na+ current and shifted the V1/2 for activation and inactivation. The results suggest that the Na+ currents in frog parathyroid cells can be modulated by cannabinoids via a G protein-dependent mechanism.
Radial nerve palsy associated with fractures of the shaft of the humerus
Authors: Shao Y. C. , Harwood P. , Grotz M. R. W. , Limb D. , Giannoudis P. V. 
Published: December 2005

The management of radial nerve palsy associated with fractures of the shaft of the humerus has been disputed for several decades. This study has systematically reviewed the published evidence and developed an algorithm to guide management. We searched web-based databases for studies published in the past 40 years and identified further pages through manual searches of the bibliography in papers identified electronically. Of 391 papers identified initially, encompassing a total of 1045 patients with radial nerve palsy, 35 papers met all our criteria for eligibility. Meticulous extraction of the data was carried out according to a preset protocol. The overall prevalence of radial nerve palsy after fracture of the shaft of the humerus in 21 papers was 11.8% (532 palsies in 4517 fractures). Fractures of the middle and middle-distal parts of the shaft had a significantly higher association with radial nerve palsy than those in other parts. Transverse and spiral fractures were more likely to be associated with radial nerve palsy than oblique and comminuted patterns of fracture (p < 0.001). The overall rate of recovery was 88.1% (921 of 1045), with spontaneous recovery reaching 70.7% (411 of 581) in patients treated conservatively. There was no significant difference in the final results when comparing groups which were initially managed expectantly with those explored early, suggesting that the initial expectant treatment did not affect the extent of nerve recovery adversely and would avoid many unnecessary operations. A treatment algorithm for the management of radial nerve palsy associated with fracture of the shaft of the humerus is recommended by the authors.