bluuebunny/crossref_metadata_2025 huggingface dataset:
Integral projections models, their construction and use in posing hypotheses in ecology
Authors: Coulson Tim
Published: August 2012

Replicated experiments at the level of the population are often not feasible for field systems. Despite this, population‐level observational studies play a critical role in biology. For example, they have revealed how environmental change generates ecological and evolutionary change in free‐living populations. When replicated experiments are impossible, constructing models and using these to conduct in silico experiments is the next best thing. Recent advances in the construction and analysis of integral projection models (IPMs) mean they offer a remarkably powerful tool to study ecological and evolutionary dynamics. IPMs can be parameterised using data frequently collected by ecologists, but the ease with which they can be constructed and analysed is perhaps not as widely appreciated as it could be. In this paper, which is loosely related to the talk I gave when receiving the Per Brinck Oikos Award in 2012, I show how easily IPMs can be constructed and analysed, and I argue they play an important role in posing and testing hypotheses in population biology.
Patterns and processes of population dynamics with fluctuating habitat size: a case study of a marine copepod inhabiting tide pools
Authors: Fukaya Keiichi , Shirotori Wakako , Kawai Momoka , Noda Takashi
Published: August 2012

The logistic model is a fundamental population model often used as the basis for analyzing wildlife population dynamics. In the classic logistic model, however, population dynamics may be difficult to characterize if habitat size is temporally variable because population density can vary at a constant abundance, which results in variable strength of density‐dependent feedback for a given population size. To incorporate habitat size variability, we developed a general population model in which changes in population abundance, density, and habitat size are taken into account. From this model, we deduced several predictions for patterns and processes of population dynamics: 1) patterns of fluctuation in population abundance and density can diverge, with respect of their correlation and relative variability; and 2) along with density dependence, habitat size fluctuation can affect population growth with a time lag because changes in habitat size result in changes in population density. In order to test these predictions, we applied our model to population dynamics data of 36 populations of Tigriopus japonicus, a marine copepod inhabiting tide pools of variable sizes caused by weather processes. As expected, we found a significant difference in the fluctuation patterns of population abundance and density of T. japonicus populations with respect to the correlation between abundance and density and their relative variability, which correlates positively with the variability of habitat size. In addition, we found direct and lagged‐indirect effects of weather processes on population growth, which were associated with density dependence and impose regulatory forces on local and regional population dynamics. These results illustrate how changes in habitat size can have an impact on patterns and processes of wildlife population dynamics. We suggest that without knowledge of habitat size fluctuation, measures of population size and its variability as well as inferences about the processes of population dynamics may be misleading.
Lys66 residue as a determinant of high mismatch extension and misinsertion rates of HIV‐1 reverse transcriptase
Authors: Lwatula Chisanga , Garforth Scott J. , Prasad Vinayaka R.
Published: August 2012

A major factor contributing to the high mutation rate of HIV‐1 reverse transcriptase (RT) is its high propensity for misincorporation. Misincorporation requires both deoxyribonucleotide triphosphate (dNTP) misinsertion and the subsequent extension of the mismatched terminus thus formed. We hypothesized that Lys66 is a determinant of mismatch extension based on its position near the primer terminus. This hypothesis was tested by steady‐state kinetic studies using wild‐type HIV‐1 RT and four Lys66 substitution mutants: Lys66Arg, Lys66Ala, Lys66Asn and Lys66Thr. The mismatch extension efficiency was reduced for all mutants, with Lys66Ala, Lys66Asn and Lys66Thr showing a four‐ to six‐fold reduction compared with wild‐type HIV‐1 RT. Surprisingly, the nonconservative substitutions also led to large decreases in misinsertion efficiency, ranging from as low as three‐fold to values much higher than 23‐fold. Thus, the Lys66Arg mutant was akin to wild‐type HIV‐1 RT, whereas all nonconservative mutants displayed significantly decreased efficiency for both events. Our results suggest that Lys66, much like Lys65, is a determinant of both dNTP misinsertion and mismatch extension efficiency. While Lys65 is known to contact the γ‐phosphate of incoming dNTP, the Lys66 side chain is in the vicinity of the primer terminus. However, our results suggest that both residues have a similar influence on dNTP misinsertion and mispair extension efficiencies of HIV‐1 RT. When we tested the mutants for susceptibility to selected nucleoside analog and non‐nucleoside analog drugs, similarly to Lys65Arg, the Lys66Ala and Lys66Asn mutants displayed mild resistance to the nucleoside analog drug 3′‐azido‐3′‐deoxythymidine‐5′‐triphosphate (AZTTP).

Database

EC 2.7.7.49, EC 2.7.7.7
Rope trauma, sedation, disentanglement, and monitoring‐tag associated lesions in a terminally entangled North Atlantic right whale (Eubalaena glacialis)
Authors: Moore Michael , Andrews Russel , Austin Trevor , Bailey James , Costidis Alex , George Clay , Jackson Katie , Pitchford Tom , Landry Scott , Ligon Allan , McLellan William , Morin David , Smith Jamison , Rotstein David , Rowles Teresa , Slay Chris , Walsh Michael
Published: August 2012

A chronically entangled North Atlantic right whale, with consequent emaciation was sedated, disentangled to the extent possible, administered antibiotics, and satellite tag tracked for six subsequent days. It was found dead 11 d after the tag ceased transmission. Chronic constrictive deep rope lacerations and emaciation were found to be the proximate cause of death, which may have ultimately involved shark predation. A broadhead cutter and a spring‐loaded knife used for disentanglement were found to induce moderate wounds to the skin and blubber. The telemetry tag, with two barbed shafts partially penetrating the blubber was shed, leaving barbs embedded with localized histological reaction. One of four darts administered shed the barrel, but the needle was found postmortem in the whale with an 80º bend at the blubber‐muscle interface. This bend occurred due to epaxial muscle movement relative to the overlying blubber, with resultant necrosis and cavitation of underlying muscle. This suggests that rigid, implanted devices that span the cetacean blubber muscle interface, where the muscle moves relative to the blubber, could have secondary health impacts. Thus we encourage efforts to develop new tag telemetry systems that do not penetrate the subdermal sheath, but still remain attached for many months.
Geographic, seasonal, and diurnal surface behavior of harbor porpoises
Authors: Teilmann Jonas , Christiansen Casper T. , Kjellerup Sanne , Dietz Rune , Nachman Gösta
Published: August 2012

During ship surveys harbor porpoises are only visible when breaking the sea surface to breathe, while during aerial surveys they may be seen down to 2 m below the surface. The fractions of time spent at these two depths can be used for correcting visual surveys to actual population estimates, which are essential information on the status and management of the species. Thirty‐five free‐ranging harbor porpoises (Phocoena phocoena) were tracked in the region between the Baltic and the North Sea for 25–349 d using Argos satellite transmitters. No differences were found in surface behavior between geographical areas or the size of the animals. Slight differences were found between the two sexes and time of day. Surface time peaked in April, where 6% was spent with the transmitter above surface and 61.5% between 0 and 2 m depth, while the minimum values occurred in February (3.4% and 42.5%, respectively). The analyses reveal that individual variation among porpoises is the most important factor in explaining variation in surface rates. However, the large number of animals documented in the present study covering a wide range of age and sex groups justifies the use of the seasonal average surface times for correcting abundance surveys.
Railroads and Immigration in the Northeast United States 1850–1900
Authors: Healey Richard G.
Published: August 2012

Both large‐scale immigration and rapid expansion of the railroad network played major roles in the economic development of the United States during the second half of the 19th century. Although the romance of the settlement of the West has received much attention in the literature, the northeast remained the industrial powerhouse of the continent, attracting large numbers of immigrants to work in its mines, factories and mills, despite the growing ascendancy of Chicago. However, new research using the complete count US 1880 census dataset demonstrates that until the latter part of the period, the US railroad industry and its associated employment opportunities were also heavily concentrated in the northeast region. This paper examines the interrelationships between processes of immigration and railroad development, in terms of the movement of people and the availability of employment opportunities, and presents evidence that different ethnic groups participated in the railroad industry to markedly varying degrees.
Gender, Militarization and Sovereignty
Authors: Dowler Lorraine
Published: August 2012

Militarization is a process that we often consider restricted to the boundaries of the state. However this essay offers a feminist reformulation of militarization as a banal process that is furtively present in our everyday spaces. This essay focuses on some of the arguments put forth by both scholars of geopolitics and feminist political geography in order to understand how the process of militarization traverses not only at the scales of global politics but also with the intimates scales of the home and the body. Most importantly, the arguments presented in this essay are in agreement that militarization is a hegemonic process, which reinforces sovereignty, resulting in the creation of gendered political identities.
Detection of the ampulla of Vater in small bowel capsule endoscopy: Experience with two different systems
Authors: Koulaouzidis Anastasios , Plevris John N
Published: August 2012

Objective

The aim of this study was to determine the detection rate of the ampulla of Vater (AoV) during small bowel capsule endoscopy (SBCE) examinations and compare the two SBCE systems used in our center.

Methods

SBCE procedures performed in our center from March 2005 to June 2011 were reviewed retrospectively. A single reviewer, following a detailed protocol, analyzed 30 min of each recording to identify the AoV.

Results

A total of 619 SBCE procedures were enrolled in the study, including 262 with a PillCam SB1, 148 with a PillCam SB2 and 209 with a MiroCam. AoV was identified in 59 SBCE examinations (9.5%), consisting of 28 with a PillCam SB1 (28/262, 10.7%), 13 with a PillCam SB2 (13/148, 8.8%) and 18 with a MiroCam (18/209, 8.6%) (P = 0.665). The AoV was visualized in 53.2 frames (median 12 frames, range 1–1056 frames); and the detection rate was low regardless of indication, patients' characteristics, SBCE system used or capsule transit parameters. Bile spout was associated with a higher AoV detection (P = 0.003).

Conclusions

The persistently low AoV detection rate using two different SBCE systems underlines the weakness of non‐steerable capsule endoscopy. Furthermore, if AoV detection is taken as a surrogate marker of small polyp detection, it becomes obvious both that non‐steerable SBCE cannot replace a side‐viewing endoscope in the evaluation of periampullary polyps in familial adenomatous polyposis and that it is an infallible method in other small bowel polyposis states.
Prevalence and Genotypic Characterization of Clostridium difficile From Ruminants in Switzerland
Authors: Romano V. , Albanese F. , Dumontet S. , Krovacek K. , Petrini O. , Pasquale V.
Published: August 2012

Clostridium difficile is an emerging enteric pathogen of humans and animals with a known main reservoir in the intestinal tract of various warm‐blooded animals. This study was carried out to evaluate the prevalence of C. difficile in 150 rectal swab samples collected from cattle and goats in Switzerland. The overall prevalence of C. difficile was 6.6%. The isolates belonged to the PCR ribotypes 033, 066, 070, 003, 001 and 137. In addition, the occurrence of C. difficile in faecal samples collected from farm ground was also evaluated and C. difficile was detected in 21% (7/30) of these samples. These isolates belonged to ribotypes 033, 066, 014 and 137. Several isolates pertained to ribotypes known to cause Clostridium difficile infections in humans.
Learner Acquisition of Dialect Variation in a Study Abroad Context: The Case of the Spanish [θ]
Authors: Ringer‐Hilfinger Kathryn
Published: August 2012

The present study aims at analyzing the acquisition of dialect variation by native English–speaking university students who study Spanish for a semester in Spain. The selected variable is the phoneme /q/ (theta). The goal is to assess learner awareness, opinion, and use of [θ]. Data were elicited through a set of oral and written tasks conducted with 15 university students prior to, during, and after attending their study abroad program in Madrid. Although post–study abroad learners demonstrated high awareness of native speaker use of this dialect feature compared to pre–study abroad learners, this did not seem to determine their use of [θ]. Data suggested that (non) acquisition varies according to the dialect employed by the native speaker(s) with whom students are in contact before and after living abroad.
Impact of professionalism in nursing on in‐hospital bedside monitoring practice
Authors: Bunkenborg Gitte , Samuelson Karin , Åkeson Jonas , Poulsen Ingrid
Published: August 2012

Aim

This article reports a study exploring nursing practice of monitoring in‐hospital patients including intra‐ and interprofessional communication and collaboration.

Background

Sub‐optimal care in general in‐hospital wards may lead to admission for intensive care, cardiac arrest, or sudden death. Reasons may include infrequent measurements of vital parameters, insufficient knowledge of their predictive values, and/or sub‐optimal use of Medical Emergency Teams. This study was designed to improve understanding of nursing practice and to identify changes required to support nursing staff in improving standards of clinical monitoring practice and patient safety in general in‐hospital wards.

Design

The study was designed as a qualitative descriptive clinical study, based on method triangulation including structured individual observations and semi‐structured individual interviews.

Methods

In the spring of 2009, structured observations and semi‐structured interviews of 13 nurses were carried out at a university hospital in Copenhagen, Denmark. The observational notes and interview transcriptions were analysed using content analysis.

Results

One theme (Professionalism influences nursing monitoring practice) and two sub‐themes (Knowledge and skills and Involvement in clinical practice through reflections) were identified. Three categories (Decision‐making, Sharing of knowledge, and Intra‐ and interprofessional interaction) were found to be associated with the theme, the sub‐themes, and with each other.

Conclusion

Clinical monitoring practice varies considerably between nurses with different individual levels of professionalism. Future initiatives to improve patient safety by further developing professionalism among nurses need to embrace individual and organizational attributes to strengthen their practice of in‐hospital patient monitoring and management.
Emergency Department Patients Self‐Report Higher Patient Inertia, Hopelessness, and Harmful Lifestyle Choices Than Community Counterparts
Authors: Joyner JaNae , Moore Ashley R. , Mount David L. , Simmons Debra R. , Ferrario Carlos M. , Cline David M.
Published: August 2012

J Clin Hypertens (Greenwich). 2012;14:828–835. ©2012 Wiley Periodicals, Inc.

Patient inertia is defined as an individual’s failure to take responsibility for proactive lifestyle change and health conditions including hypertension. Generalized and hypertension‐specific patient inertia factors were compared in 110 patients (48% women; 52% African American) from a Forsyth County, NC, emergency department (ED) and 104 community members (79% women; 70% African American) using the patient inertia–facilitated survey Patient Inertia‐36. Statistically, more ED than community participants added salt to food at the table and consumed fast foods 5 to 7 days a week. ED patients agreed less often with health literacy questions about salt and BP. Hypertension associated Patient inertia questions asked of 45 ED and 40 community participants with a personal history of hypertension revealed a statistically higher sense of hopelessness surrounding blood pressure management in ED participants. Past BP control experiences of family members had statistically greater impact on community participants regarding their own BP control. Using a logistic regression model, advancing age and being surveyed in the ED were correlated with hopelessness towards BP control. ED patients make unhealthier diet choices and possess heightened generalized and hypertension‐specific patient inertia including hopelessness towards controlling their BP that increases with age. These factors may contribute to this population’s poor BP control, particularly self‐efficacy barriers.
Clinical Application of the Five‐Factor Model
Authors: Widiger Thomas A. , Presnall Jennifer Ruth
Published: August 2012

The Five‐Factor Model (FFM) has become the predominant dimensional model of general personality structure. The purpose of this paper is to suggest a clinical application. A substantial body of research indicates that the personality disorders included within the American Psychiatric Association's (APA) Diagnostic and Statistical Manual of Mental Disorders (DSM) can be understood as extreme and/or maladaptive variants of the FFM (the acronym “DSM” refers to any particular edition of the APA DSM). In addition, the current proposal for the forthcoming fifth edition of the DSM (i.e., DSM‐5) is shifting closely toward an FFM dimensional trait model of personality disorder. Advantages of this shifting conceptualization are discussed, including treatment planning.
It Takes Two: A Longitudinal Dyadic Study on Predictors of Fertility Outcomes
Authors: Hutteman Roos , Bleidorn Wiebke , Penke Lars , Denissen Jaap J. A.
Published: August 2012

Objective

Although previous studies have found personality traits to be associated with reproductive behavior, it remains unclear whether there are dyadic associations between partners' personality and couples' decisional process to have children. The aim of the present study was to investigate the associations between partners' personality, parenthood expectations and intentions, and the couple's fertility outcomes one year later.

Method

We used dyadic longitudinal data from 2,482 couples with a mean age of 32.7 years (SD = 5.9) participating in the Panel Analysis of Intimate Relationships and Family Dynamics (PAIRFAM).

Results

Self‐esteem, shyness, and aggressiveness of both partners were related to one's own and one's partner's expectations about parenthood. These expectations were associated with one's own and one's partner's intentions to become a parent, which in turn predicted the couple's actual fertility outcomes. Personality traits of both partners were directly associated with the fertility outcome, with self‐esteem of both partners and male aggressiveness predicting the couple's decision to have their first child. The effect of self‐esteem on the decision to become a parent was mediated by the partner's intention.

Conclusions

In sum, our findings stress the importance of psychological factors in fertility outcomes and emphasize the role of dyadic processes.
Rapid immunoassay alone is insufficient for the detection of hepatitis C virus infection among high‐risk population
Authors: Firdaus R. , Saha K. , Sadhukhan P. C.
Published: August 2012

Rapid testing for HCV has become a routine practice in resource‐limited settings for initial screening. The objective of this study was to evaluate the performance of rapid immunoassay diagnostic test kits for specific and accurate diagnosis of HCV infection among different patient groups in clinical settings of Kolkata, India. Two hundred and fifty‐four randomly selected serum samples of 612 samples reported as HCV nonreactive by rapid immunodiagnostic tests were evaluated for HCV antibody, ELISA and HCV RNA testing for confirmatory diagnosis. 15.74% were HCV seropositive by ELISA, and 11.02% were RNA positive by nested RT‐PCR. Additionally, 15 HCV‐seronegative chronic liver disease patients with high ALT and AST values were screened for HCV RNA, of which five were positive whose viral load ranged from 1.2 × 102 to 4.4 × 106 IU/mL, and the samples belonged to IVDUs and HIV‐co‐infected individuals. The results showed that HCV rapid immunoassay test cannot be solely relied on as an absolute and accurate diagnostic tool for screening infection of HCV particularly in high‐risk group patients such as IVDUs, haemodialysis, thalassaemic and HIV‐co‐infected patients who need HCV screening frequently.
Is the Real In Vivo Nitric Oxide Concentration Pico or Nano Molar? Influence of Electrode Size on Unstirred Layers and NO Consumption
Authors: Bohlen H. Glenn
Published: August 2012

Objective

There is a debate if the [NO] required to influence vascular smooth muscle is below 50 nM or much higher. Electrodes with 30 μm and larger diameter report [NO] below 50 nM, whereas those with diameters of <10–12 μm report hundreds of nM. This study examined how size of electrodes influenced [NO] measurement due to NO consumption and unstirred layer issues.

Methods

Electrodes were 2 mm disk, 30 μm × 2 mm carbon fiber, and single 7 μm diameter carbon fiber within open tip microelectrode, and exposed 7 μm carbon fiber of ~15 μm to 2 mm length.

Results

All electrodes demonstrated linear calibrations with sufficient stirring. As stirring slowed, 30 μm and 2 mm electrodes reported much lower [NO] due to unstirred layers and high NO consumption. The three 7 μm microelectrodes had minor stirring issues. With limited stirring with NO present, 7 μm open tip microelectrodes advanced toward 30 μm and 2 mm electrodes experienced dramatically decreased current within 10–50 μm of the larger electrodes due to high NO consumption. None of the 7 μm microelectrodes interacted.

Conclusions

The data indicate large electrodes underestimate [NO] due to excessive NO consumption under conditions where unstirred layers are unavoidable and true microelectrodes are required for valid measurements.
Methicillin‐Resistant Staphylococcus aureus (MRSA) ST398 in Pig Farms and Multispecies Farms
Authors: Verhegghe M. , Pletinckx L. J. , Crombé F. , Vandersmissen T. , Haesebrouck F. , Butaye P. , Heyndrickx M. , Rasschaert G.
Published: August 2012

During the last few years, methicillin‐resistant Staphylococcus aureus (MRSA) ST398 has been isolated frequently from livestock, especially from pigs and to a lesser extent from cattle and poultry. To gain insight into the distribution of this bacterium in pig farms versus multispecies farms, 30 Belgian farms (10 pig, 10 pig/poultry and 10 pig/cattle farms) were screened for the presence of MRSA. On each farm, 10 nasal swabs were taken from pigs. When present, cattle (n = 10) were sampled in the nares and poultry (n = 10) in the nares, earlobes and cloaca. A selection of the obtained isolates were further characterized using multilocus sequence typing (MLST), spa typing, SCCmec typing, pulsed field gel electrophoresis (PFGE), multiple‐locus variable‐number tandem repeat analysis (MLVA) and antimicrobial susceptibility testing. On 26 of 30 farms, MRSA was isolated from pigs. Furthermore, MRSA was also isolated from poultry and cattle on one pig/poultry and five pig/cattle farms, respectively. All tested MRSA isolates belonged to ST398. Eight spa types (t011, t034, t567, t571, t1451, t2974, t3423 and t5943) were detected, among which t011 predominated. SCCmec cassettes type IVa and V were present in 20% and 72% of the isolates, respectively. When combining the results of the two remaining typing methods, PFGE and MLVA, eighteen genotypes were obtained of which one genotype predominated (56% of the positive farms). All MRSA isolates were resistant to tetracycline. Resistance to trimethoprim, aminoglycosides, macrolides, lincosamides, fluoroquinolones and chloramphenicol was also observed. In conclusion, there was no effect of the farm type on the MRSA status of the pigs. A statistically significant difference was observed when comparing the pig/poultry or the pig/cattle MRSA status on the multispecies farms. Additionally, a wide variety of MRSA ST398 strains was found within certain farms when combining different typing methods.
On the Volumetric Assessment of Tool Wear in Machining Inserts With Complex Geometries—Part 1: Need, Methodology, and Standardization
Authors: Kuttolamadom Mathew A. , Laine Mears M. , Kurfess Thomas R.
Published: August 2012

The objectives of this paper are to qualitatively assess the inadequacies of the current manner of tool wear quantification and consequently to suggest/develop a more comprehensive approach for machining tool wear characterization. Traditional parameters used for tool wear representation such as flank and crater wear are no longer self-sufficient to satisfactorily represent the advanced wear status of more recent cutting tools with complex geometric profiles. These complexities in tool geometries are all the more pronounced when catered to difficult-to-machine materials such as titanium and its alloys. Hence, alternatives to traditional tool wear assessment parameters are briefly explored and a suitable one is selected, that will help understand the very nature of the evolving wear profile itself from a three dimensional standpoint. The assessment methodology is further developed and standardized and suggestions for future use and deployment are provided. The measurement system is evaluated using an analysis of variance (ANOVA) gauge repeatability and reproducibility (R&R) study as well. In Part 2 of this paper, this method is deployed for assessing tool wear in machining Ti-6Al-4 V and concepts such as the M-ratio and its derivatives are developed to quantify the efficiency of the cutting tool during each pass.
Optimizing the Anode Structure of a Passive Tubular-Shaped Direct Methanol Fuel Cell to Operate With High Concentration Methanol
Authors: Huang Jing , Ward Travis , Faghri Amir
Published: August 2012

In order to take full advantage of the high energy density available in methanol fuel, one must use high concentration methanol in direct methanol fuel cells (DMFCs). However, this causes severe methanol crossover and leads to low power density and fuel efficiency. In this work, a tubular shape is adopted to generate higher volumetric power density; porous polytetrafluoroethylen (PTFE) membranes at the anode are used to control methanol transport with a high concentration fuel. A novel passive tubular-shaped DMFC is improved to achieve stable operation with methanol concentrations up to 20 M. It is observed that a balance between fuel transport resistance, power density, energy density, and fuel efficiency exists. Increased resistance enhances fuel efficiency, hence, energy density, but limits the fuel supply and causes low power density. With the improved anode structure and higher concentration fuel (1 M to 15 M), the energy output of the tubular DMFC increases 591%, from 0.094 Wh to 0.65 Wh with 2 ml fuel. The power densitymaintains the same level as 16 mW/cm2. For different fuel concentrations, there exists an optimum structure to generate the highest power density, which is a result of minimizing the methanol crossover while also providing sufficient fuel. The discharge characteristic at constant voltage and its effect on fuel efficiency are also discussed.
On the Volumetric Assessment of Tool Wear in Machining Inserts With Complex Geometries—Part II: Experimental Investigation and Validation on Ti-6Al-4V
Authors: Kuttolamadom Mathew A. , Laine Mears M. , Kurfess Thomas R. , Burger Uli , Bryan April
Published: August 2012

In part 1, traditional methods of tool wear characterization were qualitatively assessed, and consequently a volumetric approach of wear quantification was developed, standardized, and evaluated using a gauge R&R study. The objective of this paper is to experimentally investigate and validate this assessment methodology using the wear results from a series of controlled machining experiments on grade-5 titanium alloy. The traditionally difficult-to-machine alloy, Ti-6Al-4V, was specifically chosen as the work material in order to highlight how the use of this assessment methodology is necessitated especially because of (i) the pronounced complexities in the geometric profiles of typical cutting tools employed for machining Ti-6Al-4V and (ii) its nonconformity in behavior with standard tool wear models, such as the Taylor’s tool life model and its extensions. This assessment methodology is then validated through the simultaneous analysis and comparison of traditional flank wear and associated photomicrographs with volumetric wear and its evolution. Furthermore, the concept of the M-ratio and its derivatives are developed to quantify the efficiency of the cutting tool during each pass at a constant material removal rate (MRR).
A VASP-Rac–Soluble Guanylyl Cyclase Pathway Controls cGMP Production in Adipocytes
Authors: Jennissen Katja , Siegel Franziska , Liebig-Gonglach Michaela , Hermann Michaela-Rosemarie , Kipschull Stefanie , van Dooren Sander , Kunz Wolfram S. , Fässler Reinhard , Pfeifer Alexander
Published: August 2012

Targeting the cGMP effector VASP may enhance metabolism by stimulating the activity and abundance of brown adipocytes.
The Complex of G Protein Regulator RGS9-2 and Gβ
5
Controls Sensitization and Signaling Kinetics of Type 5 Adenylyl Cyclase in the Striatum
Authors: Xie Keqiang , Masuho Ikuo , Brand Cameron , Dessauer Carmen W. , Martemyanov Kirill A.
Published: August 2012

By suppressing cAMP production in the striatum, the RGS9-2/Gβ
5
complex could affect the development of opioid addiction.
Do Pancreatic β Cells “Taste” Nutrients to Secrete Insulin?
Authors: Henquin Jean-Claude
Published: August 2012

The role of β cell taste receptors in the control of insulin secretion is unclear.
Metabolic Sensor
Authors: Ray L. Bryan
Published: August 2012

Inhibition of a key metabolic enzyme reprograms metabolic flux toward pathways critical for cancer cell proliferation.
Repurposing Antiepileptic Drugs for Multiple Sclerosis
Authors: Gough Nancy R.
Published: August 2012

The antiepileptic drug valproic acid reduces symptoms of a mouse model of multiple sclerosis by inhibiting T cell function.
Experience with Fosfomycin for Treatment of Urinary Tract Infections Due to Multidrug-Resistant Organisms
Authors: Neuner Elizabeth A. , Sekeres Jennifer , Hall Gerri S. , van Duin David
Published: August 2012

Fosfomycin has shown promising
in vitro
activity against multidrug-resistant (MDR) urinary pathogens; however, clinical data are lacking. We conducted a retrospective chart review to describe the microbiological and clinical outcomes of urinary tract infections (UTIs) with MDR pathogens treated with fosfomycin tromethamine. Charts for 41 hospitalized patients with a urine culture for an MDR pathogen who received fosfomycin tromethamine from 2006 to 2010 were reviewed. Forty-one patients had 44 urinary pathogens, including 13 carbapenem-resistant
Klebsiella pneumoniae
(CR-Kp), 8
Pseudomonas aeruginosa
, and 7 vancomycin-resistant
Enterococcus faecium
(VRE) isolates, 7 extended-spectrum beta-lactamase (ESBL) producers, and 9 others.
In vitro
fosfomycin susceptibility was 86% (median MIC, 16 μg/ml; range, 0.25 to 1,024 μg/ml). Patients received an average of 2.9 fosfomycin doses per treatment course. The overall microbiological cure was 59%; failure was due to either relapse (24%) or reinfection UTI (17%). Microbiological cure rates by pathogen were 46% for CR-Kp, 38% for
P. aeruginosa
, 71% for VRE, 57% for ESBL producers, and 100% for others. Microbiological cure (
n
= 24) was compared to microbiological failure (
n
= 17). There were significantly more solid organ transplant recipients in the microbiological failure group (59% versus 21%;
P
= 0.02). None of the patients in the microbiological cure group had a ureteral stent, compared to 24% of patients within the microbiological failure group (
P
= 0.02). Fosfomycin demonstrated
in vitro
activity against UTIs due to MDR pathogens. For CR-KP, there was a divergence between
in vitro
susceptibility (92%) and microbiological cure (46%). Multiple confounding factors may have contributed to microbiological failures, and further data regarding the use of fosfomycin for UTIs due to MDR pathogens are needed.
Streptomycin-Starved Mycobacterium tuberculosis 18b, a Drug Discovery Tool for Latent Tuberculosis
Authors: Zhang Ming , Sala Claudia , Hartkoorn Ruben C. , Dhar Neeraj , Mendoza-Losana Alfonso , Cole Stewart T.
Published: August 2012

Mycobacterium tuberculosis
18b, a streptomycin (STR)-dependent mutant that enters a viable but nonreplicating state in the absence of STR, has been developed as a simple model for drug testing against dormant bacilli. Here, we further evaluated the STR-starved 18b (SS18b) model both
in vitro
and
in vivo
by comparing the behavior of 22 approved and experimental tuberculosis drugs. Using the resazurin reduction microplate assay (REMA), rifampin (RIF), rifapentine (RPT), TMC207, clofazimine (CFM), and linezolid (LIN) were found to be active against SS18b
in vitro
, and their bactericidal activity was confirmed by determining the number of CFU. A latent 18b infection was established in mice, and some of the above-mentioned drugs were used for treatment, either alone or in combination with RIF. RIF, RPT, TMC207, CFM, and pyrazinamide (PZA) were all active
in vivo
, while cell wall inhibitors were not. A comparative kinetic study of rifamycin efficacy was then undertaken, and the results indicated that RPT clears latent 18b infection in mice faster than RIF. Intrigued by the opposing responses of live and dormant 18b cells to cell wall inhibitors, we conducted a systematic analysis of 14 such inhibitors using REMA. This uncovered an SS18b signature (CWPRED) that accurately predicted the activities of cell wall inhibitors and performed well in a blind study. CWPRED will be useful for establishing the mode of action of compounds with unknown targets, while the SS18b system should facilitate the discovery of drugs for treating latent tuberculosis.
pEl1573 Carrying
bla
IMP-4
, from Sydney, Australia, Is Closely Related to Other IncL/M Plasmids
Authors: Partridge Sally R. , Ginn Andrew N. , Paulsen Ian T. , Iredell Jonathan R.
Published: August 2012

Complete sequencing of pEl1573, a representative IncL/M plasmid carrying
bla
IMP-4
from Sydney, Australia, revealed an ∼60-kb backbone almost identical to those of IncL/M plasmids pCTX-M3, from Poland, and pCTX-M360, from China, and less closely related to pNDM-HK, pOXA-48a, and pEL60, suggesting different lineages. The ∼28-kb Tn
2
-derived multiresistance region in pEl1573 is inserted in the same location as those in pCTX-M3 and pNDM-HK and shares some of the same components but has undergone rearrangements.
Activity of Gallidermin on Staphylococcus aureus and Staphylococcus epidermidis Biofilms
Authors: Saising Jongkon , Dube Linda , Ziebandt Anne-Kathrin , Voravuthikunchai Supayang Piyawan , Nega Mulugeta , Götz Friedrich
Published: August 2012

Due to their abilities to form strong biofilms,
Staphylococcus aureus
and
Staphylococcus epidermidis
are the most frequently isolated pathogens in persistent and chronic implant-associated infections. As biofilm-embedded bacteria are more resistant to antibiotics and the immune system, they are extremely difficult to treat. Therefore, biofilm-active antibiotics are a major challenge. Here we investigated the effect of the lantibiotic gallidermin on two representative biofilm-forming staphylococcal species. Gallidermin inhibits not only the growth of staphylococci in a dose-dependent manner but also efficiently prevents biofilm formation by both species. The effect on biofilm might be due to repression of biofilm-related targets, such as
ica
(intercellular adhesin) and
atl
(major autolysin). However, gallidermin's killing activity on 24-h and 5-day-old biofilms was significantly decreased. A subpopulation of 0.1 to 1.0% of cells survived, comprising “persister” cells of an unknown genetic and physiological state. Like many other antibiotics, gallidermin showed only limited activity on cells within mature biofilms.
In Vitro
Combination Studies of Benzothiazinone Lead Compound BTZ043 against Mycobacterium tuberculosis
Authors: Lechartier Benoit , Hartkoorn Ruben C. , Cole Stewart T.
Published: August 2012

Benzothiazinones (BTZ) are a new class of drug candidates to combat tuberculosis that inhibit decaprenyl-phosphoribose epimerase (DprE1), an essential enzyme involved in arabinan biosynthesis. Using the checkerboard method and cell viability assays, we have studied the interaction profiles of BTZ043, the current lead compound, with several antituberculosis drugs or drug candidates against
Mycobacterium tuberculosis
strain H37Rv, namely, rifampin, isoniazid, ethambutol, TMC207, PA-824, moxifloxacin, meropenem with or without clavulanate, and SQ-109. No antagonism was found between BTZ043 and the tested compounds, and most of the interactions were purely additive. Data from two different approaches clearly indicate that BTZ043 acts synergistically with TMC207, with a fractional inhibitory concentration index of 0.5. TMC207 at a quarter of the MIC (20 ng/ml) used in combination with BTZ043 (1/4 MIC, 0.375 ng/ml) had a stronger bactericidal effect on
M. tuberculosis
than TMC207 alone at a concentration of 80 ng/ml. This synergy was not observed when the combination was tested on a BTZ-resistant
M. tuberculosis
mutant, suggesting that DprE1 inhibition is the basis for the interaction. This finding excludes the possibility of synergy occurring through an off-target mechanism. We therefore hypothesize that sub-MICs of BTZ043 weaken the bacterial cell wall and allow improved penetration of TMC207 to its target. Synergy between two new antimycobacterial compounds, such as TMC207 and BTZ043, with novel targets, offers an attractive foundation for a new tuberculosis regimen.
The Urinary Antibiotic 5-Nitro-8-Hydroxyquinoline (Nitroxoline) Reduces the Formation and Induces the Dispersal of Pseudomonas aeruginosa Biofilms by Chelation of Iron and Zinc
Authors: Sobke A. , Klinger M. , Hermann B. , Sachse S. , Nietzsche S. , Makarewicz O. , Keller P. M. , Pfister W. , Straube E.
Published: August 2012

Since cations have been reported as essential regulators of biofilm, we investigated the potential of the broad-spectrum antimicrobial and cation-chelator nitroxoline as an antibiofilm agent. Biofilm mass synthesis was reduced by up to 80% at sub-MIC nitroxoline concentrations in
Pseudomonas aeruginosa
, and structures formed were reticulate rather than compact. In preformed biofilms, viable cell counts were reduced by 4 logs at therapeutic concentrations. Complexation of iron and zinc was demonstrated to underlie nitroxoline's potent antibiofilm activity.
Comparative Transcriptomic and Proteomic Analyses of Trichomonas vaginalis following Adherence to Fibronectin
Authors: Huang Kuo-Yang , Huang Po-Jung , Ku Fu-Man , Lin Rose , Alderete John F. , Tang Petrus
Published: August 2012

The morphological transformation of
Trichomonas vaginalis
from an ellipsoid form in batch culture to an adherent amoeboid form results from the contact of parasites with vaginal epithelial cells and with immobilized fibronectin (FN), a basement membrane component. This suggests host signaling of the parasite. We applied integrated transcriptomic and proteomic approaches to investigate the molecular responses of
T. vaginalis
upon binding to FN. A transcriptome analysis was performed by using large-scale expressed-sequence-tag (EST) sequencing. A total of 20,704 ESTs generated from batch culture (trophozoite-EST) versus FN-amoeboid trichomonad (FN-EST) cDNA libraries were analyzed. The FN-EST library revealed decreased amounts of transcripts that were of lower abundance in the trophozoite-EST library. There was a shift by FN-bound organisms to the expression of transcripts encoding essential proteins, possibly indicating the expression of genes for adaptation to the morphological changes needed for the FN-adhesive processes. In addition, we identified 43 differentially expressed proteins in the proteomes of FN-bound and unbound trichomonads. Among these proteins, cysteine peptidase, glyceraldehyde-3-phosphate dehydrogenase (an FN-binding protein), and stress-related proteins were upregulated in the FN-adherent cells. Stress-related genes and proteins were highly expressed in both the transcriptome and proteome of FN-bound organisms, implying that these genes and proteins may play critical roles in the response to adherence. This is the first report of a comparative proteomic and transcriptomic analysis after the binding of
T. vaginalis
to FN. This approach may lead to the discovery of novel virulence genes and affirm the role of genes involved in disease pathogenesis. This knowledge will permit a greater understanding of the complex host-parasite interplay.
Neutrophil Extracellular Traps Exhibit Antibacterial Activity against Burkholderia pseudomallei and Are Influenced by Bacterial and Host Factors
Authors: Riyapa Donporn , Buddhisa Surachat , Korbsrisate Sunee , Cuccui Jon , Wren Brendan W. , Stevens Mark P. , Ato Manabu , Lertmemongkolchai Ganjana
Published: August 2012

Burkholderia pseudomallei
is the causative pathogen of melioidosis, of which a major predisposing factor is diabetes mellitus. Polymorphonuclear neutrophils (PMNs) kill microbes extracellularly by the release of neutrophil extracellular traps (NETs). PMNs play a key role in the control of melioidosis, but the involvement of NETs in killing of
B. pseudomallei
remains obscure. Here, we showed that bactericidal NETs were released from human PMNs in response to
B. pseudomallei
in a dose- and time-dependent manner.
B. pseudomallei
-induced NET formation required NADPH oxidase activation but not phosphatidylinositol-3 kinase, mitogen-activated protein kinases, or Src family kinase signaling pathways.
B. pseudomallei
mutants defective in the virulence-associated Bsa type III protein secretion system (T3SS) or capsular polysaccharide I (CPS-I) induced elevated levels of NETs. NET induction by such mutants was associated with increased bacterial killing, phagocytosis, and oxidative burst by PMNs. Taken together the data imply that T3SS and the capsule may play a role in evading the induction of NETs. Importantly, PMNs from diabetic subjects released NETs at a lower level than PMNs from healthy subjects. Modulation of NET formation may therefore be associated with the pathogenesis and control of melioidosis.
Genome Sequence of Staphylococcus equorum subsp. equorum Mu2, Isolated from a French Smear-Ripened Cheese
Authors: Irlinger Françoise , Loux Valentin , Bento Pascal , Gibrat Jean-François , Straub Cécile , Bonnarme Pascal , Landaud Sophie , Monnet Christophe
Published: August 2012

Staphylococcus equorumsubsp.equorumis a member of the coagulase-negative staphylococcus group and is frequently isolated from fermented food products and from food-processing environments. It contributes to the formation of aroma compounds during the ripening of fermented foods, especially cheeses and sausages. Here, we report the draft genome sequence ofStaphylococcus equorumsubsp.equorumMu2 to provide insights into its physiology and compare it with otherStaphylococcusspecies.
Draft Genome Sequence of Actinomyces massiliensis Strain 4401292T
Authors: Roux Véronique , Robert Catherine , Gimenez Grégory , Gharbi Reem , Raoult Didier
Published: August 2012

A draft genome sequence ofActinomyces massiliensis, an anaerobic bacterium isolated from a patient's blood culture, is described here. CRISPR-associated proteins, insertion sequences, and toxin-antitoxin loci were found on the genome.
Whole-Genome Sequences and Comparative Genomics of Salmonella enterica Serovar Typhi Isolates from Patients with Fatal and Nonfatal Typhoid Fever in Papua New Guinea
Authors: Baddam Ramani , Thong Kwai-Lin , Avasthi Tiruvayipati Suma , Shaik Sabiha , Yap Kien-Pong , Teh Cindy Shuan Ju , Chai Lay-Ching , Kumar Narender , Ahmed Niyaz
Published: August 2012

Many of the developing countries of the Southeast Asian region are significantly affected by endemic typhoid fever, possibly as a result of marginal living standards. It is an important public health problem in countries such as Papua New Guinea, which is geographically close to some of the foci of endemicity in Asia. The severity of the disease varies in different regions, and this may be attributable to genetic diversity among the native strains. Genome sequence data on strains from different countries are needed to clearly understand their genetic makeup and virulence potential. We describe the genomes of twoSalmonellaTyphi isolates from patients with fatal and nonfatal cases of typhoid fever in Papua New Guinea. We discuss in brief the underlying sequencing methodology, assembly, genome statistics, and important features of the two draft genomes, which form an essential step in our functional molecular infection epidemiology program centering on typhoid fever. The comparative genomics of these and other isolates would enable us to identify genetic rearrangements and mechanisms responsible for endemicity and the differential severity of pathogenic salmonellae in Papua New Guinea and elsewhere.
Insights from the Genome Sequence of a Salmonella enterica Serovar Typhi Strain Associated with a Sporadic Case of Typhoid Fever in Malaysia
Authors: Yap Kien-Pong , Teh Cindy Shuan Ju , Baddam Ramani , Chai Lay-Ching , Kumar Narender , Avasthi Tiruvayipati Suma , Ahmed Niyaz , Thong Kwai-Lin
Published: August 2012

Salmonella entericaserovar Typhi is the causative agent of typhoid fever, which causes nearly 21.7 million illnesses and 217,000 deaths globally. Herein, we describe the whole-genome sequence of theSalmonellaTyphi strain ST0208, isolated from a sporadic case of typhoid fever in Kuala Lumpur, Malaysia. The whole-genome sequence and comparative genomics allow an in-depth understanding of the genetic diversity, and its link to pathogenicity and evolutionary dynamics, of this highly clonal pathogen that is endemic to Malaysia.
Genome Analysis of Mycobacterium massiliense Strain M172, Which Contains a Putative Mycobacteriophage
Authors: Choo Siew Woh , Yusoff Aini Mohamed , Wong Yan Ling , Wee Wei Yee , Ong Chia Sui , Ng Kee Peng , Ngeow Yun Fong
Published: August 2012

The genome ofMycobacterium massilienseM172, isolated from a human sputum sample, was sequenced using Illumina GA IIX technology and found to contain 5,204,460 bp, including putative genes for virulence and antibiotic resistance as well as a 92-kb genomic region most likely to correspond to a mycobacteriophage.