bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting population responses to environmental change: the importance of considering informed dispersal strategies in spatially structured population models
Authors: Ponchon Aurore , Garnier Romain , Grémillet David , Boulinier Thierry
Published: October 2014

Aim

Because of its complexity, dispersal has often been simplified when implemented in models aiming at understanding and predicting population dynamics and persistence in a context of environmental change. In particular, informed dispersal, that is the use of personal and social information to decide whether to leave a natal or current breeding site and where to settle, has seldom been considered. Informed dispersal could nevertheless be critical for predicting population dynamics, structure and persistence, as it could help populations track environmental change. Here, we develop a simulation model to examine the consequences of four dispersal strategies (informed, semi‐informed, fixed random dispersal and philopatry) on the dynamics, structure and persistence of a spatially structured population under different environmental scenarios.

Methods

We built and parameterized a metapopulation dynamic model using a long‐lived colonial seabird species as an example, the black‐legged kittiwake Rissa tridactyla, breeding on a set of distinct patches. Various scenarios of environmental variability and multiple factors potentially driving natal and breeding dispersal decisions (local habitat quality, individual and conspecific breeding success, personal and social information use) were considered to explore their respective effects.

Results

Environmental change and dispersal strategies strongly influenced metapopulation dynamics and structure. In spatially variable environments, informed and semi‐informed dispersal maintained populations in the long term, whereas philopatry and random dispersal led to extinction. Contrasted dynamics also arose: philopatry led to ecological traps, random and semi‐informed dispersal led to source‐sink dynamics and informed dispersal drove extinction–recolonization dynamics.

Main conclusions

This study demonstrates the importance of including informed dispersal in models aiming at predicting the dynamics of spatially structured populations. It also serves to highlight the urgent need to collect more empirical data on dispersal processes to properly parameterize such models.
Role of inflammation and oxidative stress in post‐menopausal oestrogen‐dependent breast cancer
Authors: Madeddu Clelia , Gramignano Giulia , Floris Carlo , Murenu Giuseppe , Sollai Giuseppe , Macciò Antonio
Published: October 2014

Weight gain and obesity are among the most important risk factors for post‐menopausal oestrogen‐dependent breast cancer (EDBC). Weight gain is associated with oxidative stress, which in turn promotes breast cancer progression. We carried out a prospective study in 216 consecutive post‐menopausal breast cancer patients aiming to examine the correlations between traditional prognostic factors (tumour size, T, nodal, N, grading, G, and metastasis status, M), and body mass index (BMI), leptin, pro‐inflammatory cytokines (Interleukin, IL,‐6 and tumour necrosis factor‐alpha, TNF‐α), and oxidative stress (reactive oxygen species, ROS, glutathione peroxidase, GPx, superoxide dismutase, SOD) among patients with oestrogen receptor (ER)+ and ER− breast cancers. Distribution of T, N and M categories did not differ between ER+ and ER− breast cancer patients. ER− patients showed a higher incidence of G3 tumours. Weight, BMI, leptin, IL‐6 and ROS were higher in ER+ compared with ER− patients. Among ER+ patients, BMI, leptin, IL‐6 and ROS correlated with T and M. Leptin, IL‐6 and ROS were positively correlated also with N. Among ER− patients, BMI and leptin did not correlate with any of prognostic parameters, whereas a positive correlation between IL‐6, ROS and M was found. Multivariate regression analysis showed that BMI, leptin, IL‐6 and ROS were predictive for T, N and M in ER+ patients. Weight gain, inflammation and oxidative stress are involved in EDBC prognosis. Their modulation through antidiabetic, anti‐inflammatory and antioxidants drugs combined with endocrine therapy may constitute a targeted approach in post‐menopausal EDBC.
Flood seasonality in Greece and its comparison to seasonal distribution of flooding in selected areas across southern Europe
Authors: Diakakis M.
Published: October 2014

This paper examines flood seasonality in Greece and its 13 regions by studying a catalogue of 553 events between 1880 and 2010. Findings are compared with the conclusions of similar analyses in selected areas across southern Europe. Results show that flooding in Greece presents strong seasonality as 46.6% of the total events occur during autumn and mostly during November (20.6%). Examination of smaller geographical entities shows different seasonality patterns between eastern, western, southern, and northern parts of Greece. Comparison with findings in Spain, Italy, and Cyprus show that summer floods are far more frequent in the northern parts of these countries. On the contrary, winter floods present higher percentages in the south. A significant shift in seasonality was identified between the western and southeastern Mediterranean Region. Results provide new knowledge for flood prevention planning by improving the current understanding of flood seasonality across the region.
Effects of domestication on genetic diversity in Chimonanthus praecox: Evidence from chloroplast DNA and amplified fragment length polymorphism data
Authors: Lu Yi‐Jun , Chen Chuan , Wang Rui‐Hong , Egan Ashley N. , Fu Cheng‐Xin
Published: October 2014

Chimonanthus praecox (L.) Link is a widely cultivated endemic winter‐flowering plant in China that has a long cultivation history. Genetic diversity and genetic structure were compared between wild and cultivated groups to reveal the geographic origin of the cultivated genotypes using chloroplast DNA (cpDNA) sequences and amplified fragment length polymorphism (AFLP) markers. Nine haplotypes were identified using three combined chloroplast fragments. Based on chloroplast data, the wild group showed greater genetic variation and genetic differentiation and a lower measure of gene flow compared to the cultivated group. The AFLP markers also supported this trend. More than 40% of the cpDNA haplotypes were shared between wild and cultivated groups, with shared haplotypes originating from multiple wild populations, suggesting multiple origins of cultivated plants. Moreover, principal coordinate analysis, UPGMA, and structure analysis of AFLP markers revealed that two wild populations clustered with most of the cultivated populations of Ch. praecox, suggesting that most of the cultivated populations mainly originated from these two populations. The combined cpDNA and AFLP results indicated that modern cultivated Ch. praecox experienced multiple events of origin involving two geographic origins, eastern China (Tianmu Mountain) and southwestern China (the border of Hunan–Guangxi–Sichuan–Guizhou).
Wavelet‐Based Tests for Comparing Two Time Series with Unequal Lengths
Authors: Decowski Jonathan , Li Linyuan
Published: October 2014

Test procedures for assessing whether two stationary and independent time series with unequal lengths have the same spectral density (or same auto‐covariance function) are investigated. A new test statistic is proposed based on the wavelet transform. It relies on empirical wavelet coefficients of the logarithm of two spectral densities' ratio. Under the null hypothesis that two spectral densities are the same, the asymptotic normal distribution of the empirical wavelet coeffcients is derived. Furthermore, these empirical wavelet coefficients are asymptotically uncorrelated. A test statistic is proposed based on these results. The performance of the new test statistic is compared to several recent test statistics, with respect to their exact levels and powers. Simulation studies show that our proposed test is very comparable to the current test statistics in most cases. The main advantage of our proposed test statistic is that it is constructed very simply and is easy to implement.
(De)Unionization, Trade Liberalization and Selection
Authors: Montagna Catia , Nocco Antonella
Published: October 2014

The effects of union bargaining power and trade liberalization on industry selection are analysed within a two‐country heterogeneous‐firm model with firm‐specific unions and inter‐country asymmetries in size and union power. Union bargaining power is shown to have more nuanced effects on efficiency and welfare than what typically suggested by conventional wisdom. While the higher wages resulting from an unfavourable union power differential harm firms' competitiveness, by reinforcing standard market access mechanisms, they give rise to aggregate demand effects that can act as a catalyst for industry and result in a pro‐variety effect.
Reliability of serum 1,3‐beta‐d‐glucan assay in patients undergoing renal replacement therapy: a review of the literature
Authors: Prattes Juergen , Schilcher Gernot , Krause Robert
Published: October 2014

The serum 1,3‐beta‐d‐glucan (BDG) test is a pan‐fungal serum marker considered to detect the majority of pathogenic fungi, including Aspergillus spp. and Candida spp. For this review we searched for publications dealing with serum BDG levels in patients undergoing renal replacement therapy (RRT). The influence of various different membrane materials used for RRTs in these publications on serum BDG has been reviewed. We found that unmodified cellulose containing membranes increased the serum BDG levels highly, whereas conflicting results have been observed for modified cellulose containing materials. Synthetic materials (e.g. polysuflone) had no influence on serum BDG levels in the majority of the reviewed publications.
Parotid lymphangioma associated with facial nerve paralysis
Authors: Imaizumi Mitsuyoshi , Tani Akiko , Ogawa Hiroshi , Omori Koichi
Published: October 2014

Parotid lymphangioma is a relatively rare disease that is usually detected in infancy or early childhood, and which has typical features. Clinical reports of facial nerve paralysis caused by lymphangioma, however, are very rare. Usually, facial nerve paralysis in a child suggests malignancy. Here we report a very rare case of parotid lymphangioma associated with facial nerve paralysis. A 7‐year‐old boy was admitted to hospital with a rapidly enlarging mass in the left parotid region. Left peripheral‐type facial nerve paralysis was also noted. Computed tomography and magnetic resonance imaging also revealed multiple cystic lesions. Open biopsy was undertaken in order to investigate the cause of the facial nerve paralysis. The histopathological findings of the excised tumor were consistent with lymphangioma. Prednisone (40 mg/day) was given in a tapering dose schedule. Facial nerve paralysis was completely cured 1 month after treatment. There has been no recurrent facial nerve paralysis for eight years.
Case of early childhood‐onset narcolepsy with cataplexy: Comparison with a monozygotic co‐twin
Authors: Ito Hiromichi , Mori Kenji , Mori Tatsuo , Goji Aya , Kagami Shoji
Published: October 2014

We describe here a rare case of early childhood‐onset (5 years of age) narcolepsy. This case was interesting because of the ability to compare the patient's symptoms to the condition of her healthy monozygotic co‐twin sister. The only environmental difference between the co‐twins was head injury, which may be associated with the presence of narcolepsy. The co‐twin was extroverted, sociable, reliable, and dexterous. In contrast, the patient could be described as introverted, gentle, honest and persevering, but was weak at conversation, assessment of a situation, memory, planning, activity (she was inactive), a sense of time, understanding of an analog clock, operating efficiency, and physical education (due to obesity). The sisters showed the same degree of appetite and dexterity with their fingers. Narcolepsy is often under‐recognized or underdiagnosed, especially when the onset occurs in childhood. When we observe preschoolers with excessive daytime sleepiness, we should consider the possibility of narcolepsy with cataplexy.
Anticipatory cognitive stress appraisal modulates suppression of wound‐induced macrophage activation by acute psychosocial stress
Authors: Kuebler Ulrike , Wirtz Petra H. , Sakai Miho , Stemmer Andreas , Meister Rebecca E. , Ehlert Ulrike
Published: October 2014

Anticipatory cognitive stress appraisal (ACSA) can affect the stress‐induced release of stress hormones, which, in turn, can modulate microbicidal potential of macrophages. This study examines whether ACSA modulates wound‐induced activation of macrophage microbicidal potential in 22 acutely stressed compared to 17 nonstressed healthy men. After catheter‐induced wound infliction and completing the ACSA questionnaire, the stress group underwent an acute mental stress task, while the nonstressed group did not. Macrophage microbicidal potential and stress hormones were repeatedly measured. In acutely stressed men, but not in nonstressed men, higher scores in ACSA related to lower macrophage microbicidal potential. This association was statistically mediated by the norepinephrine (NE) stress response. Our data suggest that ACSA modulates stress‐induced suppression of wound‐induced macrophage activation and that the NE stress response underlies this effect.
High‐Temperature Split‐Hopkinson Pressure Bar with a Momentum Trap for Obtaining Flow Stress Behaviour and Dynamic Recrystallisation
Authors: Kajberg J. , Sundin K.G.
Published: October 2014

In hot forming processes at elevated temperatures like wire rolling, microstructural changes such as repeated dynamic recrystallisation and grain growth occur. An experimental method to obtain the flow stress behaviour and to capture the recrystallised microstructure for materials subjected to large deformations, high temperatures between 900 and 1200 °C and high strain rates around 5000 s− 1 is presented. The method is based on the split‐Hopkinson pressure bar arrangement complemented with an inductive heat source. Furthermore, a momentum trap is added to ensure that the specimen is loaded only once. By quenching the specimen directly after the single loading, the dynamically recrystallised microstructure is preserved. The quenching is performed within 0.1 s of loading by dropping the specimen into a water bath. By applying the momentum trap technique, the compressive loading of the specimen could be interrupted at a strain level slightly above the strain level corresponding to the peak stress, which is a good estimation for the onset of dynamic recrystallisation.
Hepatitis C virus acquisition among Egyptians: analysis of a 10‐year surveillance of acute hepatitis C
Authors: Mohsen Amira , Bernier Adeline , LeFouler Lenaig , Delarocque‐Astagneau Elisabeth , El‐Daly Mai , El‐Kafrawy Sherif , El‐Mango Salwa , Abdel‐Hamid Mohamed , Gadallah Mohsen , Esmat Gamal , Mohamed Mostafa K. , Fontanet Arnaud
Published: October 2014

Objective

To identify current risk factors for hepatitis C virus (HCV) acquisition among Egyptians.

Methods

Patients with acute HCV were identified through a surveillance system of acute hepatitis in four fever hospitals in Egypt between 2002 and 2012. Case–control analysis was conducted, cases being incident acute symptomatic HCV and controls being acute hepatitis A identified at the same hospitals. The questionnaire covered iatrogenic, community and household exposures to HCV in the 1–6 months prior to onset of symptoms. Multivariate models were built to identify risk factors associated with HCV acquisition among non‐drug users and drug users separately.

Results

Among non‐drug users, hospital admission was independently associated with acute HCV infection (OR = 4.2, 95% CI = 1.7–10.5). Several iatrogenic procedures, for example admission in a surgery unit, sutures, IV injections and IV infusions, highly correlated with hospital admission, were also associated with acute HCV infection and could have been used in the final model instead of hospital admission. Among drug users, identified risk factors were multiple sexual relations (OR = 4.0, 95% CI = 1.1–14.7), intravenous drug use (OR = 3.9, 95% CI = 1.2–13.0) and shaving at the barbershops (OR = 8.7, 95% CI = 2.4–31.4). Illiteracy and marriage were significant risk factors in both groups.

Conclusion

Invasive medical procedures are still a major risk for acquiring new HCV infections in Egypt, as is illicit drug use in spreading HCV infection.
Genetic variation of the invasive Campuloclinium macrocephalum, Asteraceae in South Africa, inferred from molecular markers
Authors: Gitonga L , Cron G V , McConnachie A , Byrne M J
Published: October 2014

Campuloclinium macrocephalum is native to Central and South America, but is a highly invasive weed in South Africa, where it is commonly known as the ‘pompom weed’. It is targeted for biological control, the success of which will depend on host specificity and biotype compatibility to its full genetic diversity in South Africa. We investigated the genetic diversity and phylogeography of 52 specimens from across South Africa, 14 from Argentina and three from Brazil using nuclear ribosomal ITS regions. We further explored the AFLP marker diversity in 54 South African, 25 Argentine and three Brazilian specimens. Maximum parsimony analysis of the ITS sequence data produced an unresolved phylogeny. However, three haplotypes were recognised via network analysis. All South African, one Brazilian and all bar one of the Argentine individuals shared a single haplotype. AFLP analyses generated two genetic clusters with a low net nucleotide distance of 0.115 and further revealed that most plants were a mixture of alleles from these two genetic clusters. Although there was a significant genetic variation among the populations, genetic differentiation and mean heterozygosity were low, suggesting that clonal reproduction may be occurring. The current South African populations may therefore be clonal products with different proportions of genetic admixture introduced more than once. The original point of entry appears to be Gauteng, South Africa. Long‐distance dispersal appears to have played a major role in its spread across South Africa. Candidate Argentine biological control agents should therefore be effective on C. macrocephalum in South Africa.
On Centrioles, Microtubules, and Cellular Electromagnetism
Authors: Huston Ronald L.
Published: October 2014

This paper describes the inner workings of centrioles (a pair of small organelles adjacent to the nucleus) as they create cell electropolarity, engage in cell division (mitosis), but in going awry, also promote the development of cancers. The electropolarity arises from vibrations of microtubules composing the centrioles. Mitosis begins as each centrioles duplicates itself by growing a daughter centriole on its side. If during duplication more than one daughter is grown, cancer can occur and the cells divide uncontrollably. Cancer cells with supernumerary centrioles have high electropolarity which can serve as an attractor for charged therapeutic nanoparticles.
Gettering of hydrogen and methane from a helium gas mixture
Authors: Cárdenas Rosa Elia , Stewart Kenneth D. , Cowgill Donald F.
Published: October 2014

In this study, the authors developed an approach for accurately quantifying the helium content in a gas mixture also containing hydrogen and methane using commercially available getters. The authors performed a systematic study to examine how both H2 and CH4 can be removed simultaneously from the mixture using two SAES St 172® getters operating at different temperatures. The remaining He within the gas mixture can then be measured directly using a capacitance manometer. The optimum combination involved operating one getter at 650 °C to decompose the methane, and the second at 110 °C to remove the hydrogen. This approach eliminated the need to reactivate the getters between measurements, thereby enabling multiple measurements to be made within a short time interval, with accuracy better than 1%. The authors anticipate that such an approach will be particularly useful for quantifying the He-3 in mixtures that include tritium, tritiated methane, and helium-3. The presence of tritiated methane, generated by tritium activity, often complicates such measurements.
Spatial variation of dosimetric leaf gap and its impact on dose delivery
Authors: Kumaraswamy Lalith K. , Schmitt Jonathan D. , Bailey Daniel W. , Xu Zheng Zheng , Podgorsak Matthew B.
Published: October 2014

Purpose:

During dose calculation, the Eclipse treatment planning system (TPS) retracts the multileaf collimator (MLC) leaf positions by half of the dosimetric leaf gap (DLG) value (measured at central axis) for all leaf positions in a dynamic MLC plan to accurately model the rounded leaf ends. The aim of this study is to map the variation of DLG along the travel path of each MLC leaf pair and quantify how this variation impacts delivered dose.

Methods:

6 MV DLG values were measured for all MLC leaf pairs in increments of 1.0 cm (from the line intersecting the CAX and perpendicular to MLC motion) to 13.0 cm off axis distance at dmax. The measurements were performed on two Varian linear accelerators, both employing the Millennium 120‐leaf MLCs. The measurements were performed at several locations in the beam with both a Sun Nuclear MapCHECK device and a PTW pinpoint ion chamber.

Results:

The measured DLGs for the middle 40 MLC leaf pairs (each 0.5 cm width) at positions along a line through the CAX and perpendicular to MLC leaf travel direction were very similar, varying maximally by only 0.2 mm. The outer 20 MLC leaf pairs (each 1.0 cm width) have much lower DLG values, about 0.3–0.5 mm lower than the central MLC leaf pair, at their respective central line position. Overall, the mean and the maximum variation between the 0.5 cm width leaves and the 1.0 cm width leaf pairs are 0.32 and 0.65 mm, respectively.

Conclusions:

The spatial variation in DLG is caused by the variation of intraleaf transmission through MLC leaves. Fluences centered on the CAX would not be affected since DLG does not vary; but any fluences residing significantly off axis with narrow sweeping leaves may exhibit significant dose differences. This is due to the fact that there are differences in DLG between the true DLG exhibited by the 1.0 cm width outer leaves and the constant DLG value utilized by the TPS for dose calculation. Since there are large differences in DLG between the 0.5 cm width leaf pairs and 1.0 cm width leaf pairs, there is a need to correct the TPS plans, especially those with high modulation (narrow dynamic MLC gap), with 2D variation of DLG.
Quality assurance for the clinical implementation of kilovoltage intrafraction monitoring for prostate cancer VMAT
Authors: Ng J. A. , Booth J. T. , O'Brien R. T. , Colvill E. , Huang C.‐Y. , Poulsen P. R. , Keall P. J.
Published: October 2014

Purpose:

Kilovoltage intrafraction monitoring (KIM) is a real‐time 3D tumor monitoring system for cancer radiotherapy. KIM uses the commonly available gantry‐mounted x‐ray imager as input, making this method potentially more widely available than dedicated real‐time 3D tumor monitoring systems. KIM is being piloted in a clinical trial for prostate cancer patients treated with VMAT (NCT01742403). The purpose of this work was to develop clinical process and quality assurance (QA) practices for the clinical implementation of KIM.

Methods:

Informed by and adapting existing guideline documents from other real‐time monitoring systems, KIM‐specific QA practices were developed. The following five KIM‐specific QA tests were included: (1) static localization accuracy, (2) dynamic localization accuracy, (3) treatment interruption accuracy, (4) latency measurement, and (5) clinical conditions accuracy. Tests (1)–(4) were performed using KIM to measure static and representative patient‐derived prostate motion trajectories using a 3D programmable motion stage supporting an anthropomorphic phantom with implanted gold markers to represent the clinical treatment scenario. The threshold for system tolerable latency is <1 s. The tolerances for all other tests are that both the mean and standard deviation of the difference between the programmed trajectory and the measured data are <1 mm. The (5) clinical conditions accuracy test compared the KIM measured positions with those measured by kV/megavoltage (MV) triangulation from five treatment fractions acquired in a previous pilot study.

Results:

For the (1) static localization, (2) dynamic localization, and (3) treatment interruption accuracy tests, the mean and standard deviation of the difference are <1.0 mm. (4) The measured latency is 350 ms. (5) For the tests with previously acquired patient data, the mean and standard deviation of the difference between KIM and kV/MV triangulation are <1.0 mm.

Conclusions:

Clinical process and QA practices for the safe clinical implementation of KIM, a novel real‐time monitoring system using commonly available equipment, have been developed and implemented for prostate cancer VMAT.
Radiation dose calculations for CT scans with tube current modulation using the approach to equilibrium function
Authors: Li Xinhua , Zhang Da , Liu Bob
Published: October 2014

Purpose:

The approach to equilibrium function has been used previously to calculate the radiation dose to a shift‐invariant medium undergoing CT scans with constant tube current [Li, Zhang, and Liu, Med. Phys. 39, 5347–5352 (2012)]. The authors have adapted this method to CT scans with tube current modulation (TCM).

Methods:

For a scan with variable tube current, the scan range was divided into multiple subscan ranges, each with a nearly constant tube current. Then the dose calculation algorithm presented previously was applied. For a clinical CT scan series that presented tube current per slice, the authors adopted an efficient approach that computed the longitudinal dose distribution for one scan length equal to the slice thickness, which center was at z = 0. The cumulative dose at a specific point was a summation of the contributions from all slices and the overscan.

Results:

The dose calculations performed for a total of four constant and variable tube current distributions agreed with the published results of Dixon and Boone [Med. Phys. 40, 111920 (14pp.) (2013)]. For an abdomen/pelvis scan of an anthropomorphic phantom (model ATOM 701‐B, CIRS, Inc., VA) on a GE Lightspeed Pro 16 scanner with 120 kV, N × T = 20 mm, pitch = 1.375, z axis current modulation (auto mA), and angular current modulation (smart mA), dose measurements were performed using two lines of optically stimulated luminescence dosimeters, one of which was placed near the phantom center and the other on the surface. Dose calculations were performed on the central and peripheral axes of a cylinder containing water, whose cross‐sectional mass was about equal to that of the ATOM phantom in its abdominal region, and the results agreed with the measurements within 28.4%.

Conclusions:

The described method provides an effective approach that takes into account subject size, scan length, and constant or variable tube current to evaluate CT dose to a shift‐invariant medium. For a clinical CT scan, dose calculations may be performed with a water‐containing cylinder whose cross‐sectional mass is equal to that of the subject. This method has the potential to substantially improve evaluations of patient dose from clinical CT scans, compared to CTDIvol, size‐specific dose estimate (SSDE), or the dose evaluated for a TCM scan with a constant tube current equal to the average tube current of the TCM scan.
Debunking Coriolis Force Myths
Authors: Shakur Asif
Published: October 2014

Much has been written and debated about the Coriolis force.1–8 Unfortunately, this has done little to demystify the paradoxes surrounding this fictitious force invoked by an observer in a rotating frame of reference. It is the purpose of this article to make another valiant attempt to slay the dragon of the Coriolis force! This will be done without unleashing the usual mathematical apparatus, which we believe is more of a hindrance than a help.
Helium and Sulfur Hexafluoride in Musical Instruments
Authors: Forinash Kyle , Dixon Cory L.
Published: October 2014

The effects of inhaled helium on the human voice were investigated in a recent article in The Physics Teacher.1 As mentioned in that article, demonstrations of the effect are a popular classroom activity. If the number of YouTube videos is any indication, the effects of sulfur hexafluoride on the human voice are equally popular. However, there appears to be little information available on the effects of either of these gases on musical instruments.2 We describe here the results of a student project that involved measuring the frequency shifts in an organ pipe, a trumpet, and a trombone as the result of filling the instruments with these two gases. The project was one of several possible end-of-semester projects required in an elective science of sound course for non-science majors.
Towards Explaining the Water Siphon
Authors: Jumper William D. , Stanchev Boris
Published: October 2014

Many high school and introductory college physics courses cover topics in fluidics through the Bernoulli and Poiseuille equations, and consequently one might think that siphons should present an excellent opportunity to engage students in various laboratory measurement exercises incorporating these fascinating devices. However, the flow rates (or average exit velocities) of simple water siphons have not been sufficiently explained,1 nor has an associated analytical model been developed demonstrating sufficient experimental correspondence to allow physics instructors to bring closure between theoretical concepts and laboratory experiences. We present such an explanation and analytical model for the flow rates of simple water tube siphons. Further, we report measurements that show the model gives good correspondence to flow rates of siphons over a wide range of tube lengths, inner diameters, and water heights (hydrostatic head), and for which the Reynolds numbers range from 102 to 105.
Backpack Weight and the Scaling of the Human Frame
Authors: O'Shea Michael
Published: October 2014

Modeling real-life situations is an important part of introductory physics. Here we consider the question “What is the largest weight of backpack a hiker can manage?” A quick perusal of the Internet suggests that as the weight of a healthy adult increases, the largest backpack weight Wbp also increases and should be about 25–30% of a person's body weight for a reasonably fit adult.1 We show here that a careful modeling of the hiker and backpack leads to a somewhat different result, with hikers of sufficiently large (but otherwise healthy) weight not being able to carry as much backpack weight as hikers of smaller weight.
Simple Ways to Make Real Capacitors
Authors: Herman Rhett
Published: October 2014

Many of us have grabbed two pieces of aluminum foil and a paper towel, quickly sandwiched them together, and exclaimed in lecture, “Look! It's easy to make a capacitor!” Then we move on from there, calculating things such as capacitances with various dielectrics or plate sizes, the capacitance of capacitor networks, RC circuits, etc. We typically do these calculations with capacitance values that are far removed from what we just created in our quick demonstration of a capacitor. Students might justifiably question whether the capacitor that we blithely made has any relation to the values that we are using in our calculations. It may be useful to investigate the quality of such handmade capacitors so that our students get a more intuitive feel for these ubiquitous electrical components.
Origin in Acinetobacter guillouiae and Dissemination of the Aminoglycoside-Modifying Enzyme Aph(3′)-VI
Authors: Yoon Eun-Jeong , Goussard Sylvie , Touchon Marie , Krizova Lenka , Cerqueira Gustavo , Murphy Cheryl , Lambert Thierry , Grillot-Courvalin Catherine , Nemec Alexandr , Courvalin Patrice
Published: October 2014

The amikacin resistance gene
aphA6
was first detected in the nosocomial pathogen
Acinetobacter baumannii
and subsequently in other genera. Analysis of 133 whole-genome sequences covering the taxonomic diversity of
Acinetobacter
spp. detected
aphA6
in the chromosome of 2 isolates of
A. guillouiae
, which is an environmental species, 1 of 8
A. parvus
isolates, and 5 of 34
A. baumannii
isolates. The gene was also present in 29 out of 36
A. guillouiae
isolates screened by PCR, indicating that it is ancestral to this species. The
P
native
promoter for
aphA6
in
A. guillouiae
and
A. parvus
was replaced in
A. baumannii
by
P

aphA6

, which was generated by use of the insertion sequence IS
Aba125
, which brought a −35 sequence. Study of promoter strength in
Escherichia coli
and
A. baumannii
indicated that
P

aphA6

was four times more potent than
P
native
. There was a good correlation between aminoglycoside MICs and
aphA6
transcription in
A. guillouiae
isolates that remained susceptible to amikacin. The marked topology differences of the phylogenetic trees of
aphA6
and of the hosts strongly support its recent direct transfer within
Acinetobacter
spp. and also to evolutionarily remote bacterial genera. Concomitant expression of
aphA6
must have occurred because, contrary to the donors, it can confer resistance to the new hosts. Mobilization and expression of
aphA6
via composite transposons and the upstream IS-generating hybrid
P

aphA6

, followed by conjugation, seems the most plausible mechanism. This is in agreement with the observation that, in the recipients,
aphA6
is carried by conjugative plasmids and flanked by IS that are common in
Acinetobacter
spp. Our data indicate that resistance genes can also be found in susceptible environmental bacteria.

IMPORTANCE
We speculated that the
aphA6
gene for an enzyme that confers resistance to amikacin, the most active aminoglycoside for the treatment of nosocomial infections due to
Acinetobacter
spp., originated in this genus before disseminating to phylogenetically distant genera pathogenic for humans. Using a combination of whole-genome sequencing of a collection of
Acinetobacter
spp. covering the breadth of the known taxonomic diversity of the genus, gene cloning, detailed promoter analysis, study of heterologous gene expression, and comparative analysis of the phylogenetic trees of
aphA6
and of the bacterial hosts, we found that
aphA6
originated in
Acinetobacter guillouiae
, an amikacin-susceptible environmental species. The gene conferred, upon mobilization, high-level resistance to the new hosts. This work stresses that nonpathogenic bacteria can act as reservoirs of resistance determinants, and it provides an example of the use of a genomic library to study the origin and dissemination of an antibiotic resistance gene to human pathogens.
Emergence of a New Epidemic Neisseria meningitidis Serogroup A Clone in the African Meningitis Belt: High-Resolution Picture of Genomic Changes That Mediate Immune Evasion
Authors: Lamelas Araceli , Harris Simon R. , Röltgen Katharina , Dangy Jean-Pierre , Hauser Julia , Kingsley Robert A. , Connor Thomas R. , Sie Ali , Hodgson Abraham , Dougan Gordon , Parkhill Julian , Bentley Stephen D. , Pluschke Gerd
Published: October 2014

In the African “meningitis belt,” outbreaks of meningococcal meningitis occur in cycles, representing a model for the role of host-pathogen interactions in epidemic processes. The periodicity of the epidemics is not well understood, nor is it currently possible to predict them. In our longitudinal colonization and disease surveys, we have observed waves of clonal replacement with the same serogroup, suggesting that immunity to noncapsular antigens plays a significant role in natural herd immunity. Here, through comparative genomic analysis of 100 meningococcal isolates, we provide a high-resolution view of the evolutionary changes that occurred during clonal replacement of a hypervirulent meningococcal clone (ST-7) by a descendant clone (ST-2859). We show that the majority of genetic changes are due to homologous recombination of laterally acquired DNA, with more than 20% of these events involving acquisition of DNA from other species. Signals of adaptation to evade herd immunity were indicated by genomic hot spots of recombination. Most striking is the high frequency of changes involving the
pgl
locus, which determines the glycosylation patterns of major protein antigens. High-frequency changes were also observed for genes involved in the regulation of pilus expression and the synthesis of Maf3 adhesins, highlighting the importance of these surface features in host-pathogen interaction and immune evasion.

IMPORTANCE
While established meningococcal capsule polysaccharide vaccines are protective through the induction of anticapsular antibodies, findings of our longitudinal studies in the African meningitis belt have indicated that immunity to noncapsular antigens plays a significant role in natural herd immunity. Our results show that meningococci evade herd immunity through the rapid homologous replacement of just a few key genomic loci that affect noncapsular cell surface components. Identification of recombination hot spots thus represents an eminent approach to gain insight into targets of protective natural immune responses. Moreover, our results highlight the role of the dynamics of the protein glycosylation repertoire in immune evasion by
Neisseria meningitidis
. These results have major implications for the design of next-generation protein-based subunit vaccines.
Proteolytic Processing and Activation of Clostridium perfringens Epsilon Toxin by Caprine Small Intestinal Contents
Authors: Freedman John C. , Li Jihong , Uzal Francisco A. , McClane Bruce A.
Published: October 2014

Epsilon toxin (ETX), a pore-forming toxin produced by type B and D strains of
Clostridium perfringens
, mediates severe enterotoxemia in livestock and possibly plays a role in human disease. During enterotoxemia, the nearly inactive ETX prototoxin is produced in the intestines but then must be activated by proteolytic processing. The current study sought to examine ETX prototoxin processing and activation
ex vivo
using the intestinal contents of a goat, a natural host species for ETX-mediated disease. First, this study showed that the prototoxin has a KEIS N-terminal sequence with a molecular mass of 33,054 Da. When the activation of ETX prototoxin
ex vivo
by goat small intestinal contents was assessed by SDS-PAGE, the prototoxin was processed in a stepwise fashion into an ~27-kDa band or higher-molecular-mass material that could be toxin oligomers. Purified ETX corresponding to the ~27-kDa band was cytotoxic. When it was biochemically characterized by mass spectrometry, the copresence of three ETX species, each with different C-terminal residues, was identified in the purified ~27-kDa ETX preparation. Cytotoxicity of each of the three ETX species was then demonstrated using recombinant DNA approaches. Serine protease inhibitors blocked the initial proteotoxin processing, while carboxypeptidase inhibitors blocked further processing events. Taken together, this study provides important new insights indicating that, in the intestinal lumen, serine protease (including trypsin and possibly chymotrypsin) initiates the processing of the prototoxin but other proteases, including carboxypeptidases, then process the prototoxin into multiple active and stable species.

IMPORTANCE
Processing and activation by intestinal proteases is a prerequisite for ETX-induced toxicity. Previous studies had characterized the activation of ETX using only arbitrarily chosen amounts of purified trypsin and/or chymotrypsin. Therefore, the current study examined ETX activation
ex vivo
by natural host intestinal contents. These analyses demonstrated that (i) ETX processing in host intestinal contents occurs in an ordered, stepwise fashion, (ii) processing of prototoxin by host intestinal contents results in higher-molecular-mass material and 3 distinct ~27-kDa ETX species, and (iii) serine proteases, such as trypsin, chymotrypsin, and other proteases, including carboxypeptidases, play a role in the activation of ETX by intestinal contents. These studies provide new insights into the activation and processing of ETX and demonstrate that this process is more complicated than previously appreciated.
The Effect of Electroacupuncture on Tendon Repair in a Rat Achilles Tendon Rupture Model
Authors: Inoue Motohiro , Nakajima Miwa , Oi Yuki , Hojo Tatsuya , Itoi Megumi , Kitakoji Hiroshi
Published: October 2014

Objective

To examine the effect of electroacupuncture (EA) on early post-rupture tendon repair in a rat model of Achilles tendon rupture using histological and mechanical evaluation.

Methods

An Achilles tendon rupture model was prepared in 90 Wistar rats, which were randomly assigned to EA, manual acupuncture or control groups. Rats in the EA group received EA (pulse width 5 ms; stimulation frequency 50 Hz; stimulation strength 20 μA; stimulation time 20 min) daily from 1 day following model preparation until the day of assessment (either 7 or 10 days after model preparation), when the region of interest was sampled to assess tendon repair using in vitro methods. Total cell count and the number of cells staining positive for transforming growth factor-β1 (TGF-β1) and basic fibroblast growth factor (b-FGF) were measured. Tension tests were performed 10 days after model preparation to measure the maximum breaking strength of the repaired tendon.

Results

Both the total cell count and the number of cells positive for b-FGF were significantly higher in the EA group (p<0.05). In the EA group only, immunostaining showed strong expression of TGF-β1 7 days after model preparation (p<0.05). Maximum breaking strength of the repaired tendon 10 days after model preparation was significantly higher in the EA group (p<0.01).

Conclusions

The marked increase in cell count and growth factor expression as well as increased tendon strength in the EA group suggest that EA may be a useful method for promoting tendon repair.
Effects of electronic health record use on the exam room communication skills of resident physicians: a randomized within-subjects study
Authors: Taft Teresa , Lenert Leslie , Sakaguchi Farrant , Stoddard Gregory , Milne Caroline
Published: October 2014

Background The effects of electronic health records (EHRs) on doctor–patient communication are unclear.

Objective To evaluate the effects of EHR use compared with paper chart use, on novice physicians’ communication skills.

Design Within-subjects randomized controlled trial using observed structured clinical examination methods to assess the impact of use of an EHR on communication.

Setting A large academic internal medicine training program.

Population First-year internal medicine residents.

Intervention Residents interviewed, diagnosed, and initiated treatment of simulated patients using a paper chart or an EHR on a laptop computer. Video recordings of interviews were rated by three trained observers using the Four Habits scale.

Results Thirty-two residents completed the study and had data available for review (61.5% of those enrolled in the residency program). In most skill areas in the Four Habits model, residents performed at least as well using the EHR and were statistically better in six of 23 skills areas (p<0.05). The overall average communication score was better when using an EHR: mean difference 0.254 (95% CI 0.05 to 0.45), p = 0.012, Cohen's d of 0.47 (a moderate effect). Residents scoring poorly (>3 average score) with paper methods (n = 8) had clinically important improvement when using the EHR.

Limitations This study was conducted in first-year residents in a training environment using simulated patients at a single institution.

Conclusions Use of an EHR on a laptop computer appears to improve the ability of first-year residents to communicate with patients relative to using a paper chart.
Functional evaluation of out-of-the-box text-mining tools for data-mining tasks
Authors: Jung Kenneth , LePendu Paea , Iyer Srinivasan , Bauer-Mehren Anna , Percha Bethany , Shah Nigam H
Published: October 2014

Objective The trade-off between the speed and simplicity of dictionary-based term recognition and the richer linguistic information provided by more advanced natural language processing (NLP) is an area of active discussion in clinical informatics. In this paper, we quantify this trade-off among text processing systems that make different trade-offs between speed and linguistic understanding. We tested both types of systems in three clinical research tasks: phase IV safety profiling of a drug, learning adverse drug–drug interactions, and learning used-to-treat relationships between drugs and indications.

Materials We first benchmarked the accuracy of the NCBO Annotator and REVEAL in a manually annotated, publically available dataset from the 2008 i2b2 Obesity Challenge. We then applied the NCBO Annotator and REVEAL to 9 million clinical notes from the Stanford Translational Research Integrated Database Environment (STRIDE) and used the resulting data for three research tasks.

Results There is no significant difference between using the NCBO Annotator and REVEAL in the results of the three research tasks when using large datasets. In one subtask, REVEAL achieved higher sensitivity with smaller datasets.

Conclusions For a variety of tasks, employing simple term recognition methods instead of advanced NLP methods results in little or no impact on accuracy when using large datasets. Simpler dictionary-based methods have the advantage of scaling well to very large datasets. Promoting the use of simple, dictionary-based methods for population level analyses can advance adoption of NLP in practice.
Innovative information visualization of electronic health record data: a systematic review
Authors: West Vivian L , Borland David , Hammond W Ed
Published: October 2014

Objective This study investigates the use of visualization techniques reported between 1996 and 2013 and evaluates innovative approaches to information visualization of electronic health record (EHR) data for knowledge discovery.

Methods An electronic literature search was conducted May–July 2013 using MEDLINE and Web of Knowledge, supplemented by citation searching, gray literature searching, and reference list reviews. General search terms were used to assure a comprehensive document search.

Results Beginning with 891 articles, the number of articles was reduced by eliminating 191 duplicates. A matrix was developed for categorizing all abstracts and to assist with determining those to be excluded for review. Eighteen articles were included in the final analysis.

Discussion Several visualization techniques have been extensively researched. The most mature system is LifeLines and its applications as LifeLines2, EventFlow, and LifeFlow. Initially, research focused on records from a single patient and visualization of the complex data related to one patient. Since 2010, the techniques under investigation are for use with large numbers of patient records and events. Most are linear and allow interaction through scaling and zooming to resize. Color, density, and filter techniques are commonly used for visualization.

Conclusions With the burgeoning increase in the amount of electronic healthcare data, the potential for knowledge discovery is significant if data are managed in innovative and effective ways. We identify challenges discovered by previous EHR visualization research, which will help researchers who seek to design and improve visualization techniques.