bluuebunny/crossref_metadata_2025 huggingface dataset:
Stable isotopes of oxygen reveal dispersal patterns of the South American sea lion in the southwestern Atlantic Ocean
Authors: Zenteno L. , Crespo E. , Goodall N. , Aguilar A. , de Oliveira L. , Drago M. , Secchi E. R. , Garcia N. , Cardona L.
Published: July 2013

Stable isotopes of oxygen have been widely used to reconstruct paleotemperatures and to investigate the thermal environment of fishes and mollusks, but they have only occasionally been used as geographical markers in marine systems. As bone apatite grows at a constant temperature in marine mammals and food is the major source of water for these animals, particularly for pinnipeds, variations in the ratio of stable isotopes of oxygen (δ18O) of bone apatite will likely reflect changes in the δ18O values of diet, and thus of the surrounding water mass, despite the potential confounding role of factors as the proximate composition of diet, sex and body size. Here, we used the δ18O values in bone apatite to investigate whether adult males of South American sea lion (Otaria byronia), from three regions in southwestern Atlantic Ocean (Brazil, Patagonia and Tierra del Fuego in Argentina), used the same water masses to forage and whether differences exist in the water masses used by sea lions differing according to sex and developmental stage. Statistically significant differences were observed among the δ18O bone values of adult males from the three regions, with those from Patagonia more enriched in 18O, as expected from the δ18Oseawater values. These results revealed restricted dispersal movements of adult males between the three areas. On the other hand, adult males and females from Patagonia did not differ in average δ18Obone values, thus indicating the use of foraging grounds within the same water mass. Finally, the variability in the δ18Obone values of young of both sexes was much wider than the adults of the same sex from the same region, which suggests the existence of a juvenile dispersal phase in both sexes, although much shorter in females than in males. These results confirm the usefulness of stable isotopes of oxygen as habitats tracers in marine mammals.
Statin‐Associated Underactive Bladder
Authors: YOKOYAMA Teruhiko , CHANCELLOR Michael B.
Published: July 2013

Case

Statins are widely used to treat hypercholesterolemia but can lead to side‐effects. We present a case of statin‐associated permanent urinary retention in a 69‐year‐old woman.

Outcome

Oral Cerivastatin was prescribed 2 months prior to the onset of retention. With the discontinuation of Cerivastatin, the patient reported modest improvement in symptoms.

Conclusion

The findings of this case support the potential risk of permanent bladder smooth muscle damage due to statin that may lead to underactive bladder and urinary retention.
Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis
Authors: Carstens Bryan C. , Brennan Reid S. , Chua Vivien , Duffie Caroline V. , Harvey Michael G. , Koch Rachel A. , McMahan Caleb D. , Nelson Bradley J. , Newman Catherine E. , Satler Jordan D. , Seeholzer Glenn , Posbic Karine , Tank David C. , Sullivan Jack
Published: July 2013

Phylogeographic inference has typically relied on analyses of data from one or a few genes to provide estimates of demography and population histories. While much has been learned from these studies, all phylogeographic analysis is conditioned on the data, and thus, inferences derived from data that represent a small sample of the genome are unavoidably tenuous. Here, we demonstrate one approach for moving beyond classic phylogeographic research. We use sequence capture probes and Illumina sequencing to generate data from >400 loci in order to infer the phylogeographic history of Salix melanopsis, a riparian willow with a disjunct distribution in coastal and the inland Pacific Northwest. We evaluate a priori phylogeographic hypotheses using coalescent models for parameter estimation, and the results support earlier findings that identified post‐Pleistocene dispersal as the cause of the disjunction in S. melanopsis. We also conduct a series of model selection exercises using IMa2, Migrate‐n and ∂a∂i. The resulting ranking of models indicates that refugial dynamics were complex, with multiple regions in the inland regions serving as the source for postglacial colonization. Our results demonstrate that new sources of data and new approaches to data analysis can rejuvenate phylogeographic research by allowing for the identification of complex models that enable researchers to both identify and estimate the most relevant parameters for a given system.
Partitioning of genetic variation across the genome using multimarker methods in a wild bird population
Authors: Robinson Matthew R. , Santure Anna W. , DeCauwer Isabelle , Sheldon Ben C. , Slate Jon
Published: July 2013

The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high‐density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex‐, age‐ and environment‐specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems.
How to fail at species delimitation
Authors: Carstens Bryan C. , Pelletier Tara A. , Reid Noah M. , Satler Jordan D.
Published: July 2013

Species delimitation is the act of identifying species‐level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting species. However, most recent investigations only utilize a handful (i.e. 2–3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.
Divergence of host range and biological properties between natural isolate and full‐length infectious cDNA clone of the Beet mild yellowing virus 2ITB
Authors: Klein Elodie , Brault Véronique , Klein Delphine , Weyens Guy , Lefèbvre Marc , Ziegler‐Graff Véronique , Gilmer David
Published: July 2013

Plant infection by poleroviruses is restricted to phloem tissues, preventing any classical leaf rub inoculation with viral RNA or virions. Efficient virus inoculation to plants is achieved by viruliferous aphids that acquire the virus by feeding on infected plants. The use of promoter‐driven infectious cDNA is an alternative means to infect plants and allows reverse genetic studies to be performed. Using Beet mild yellowing virus isolate 2ITB (BMYV‐2ITB), we produced a full‐length infectious cDNA clone of the virus (named BMYV‐EK) placed under the control of the T7 RNA polymerase and the Cauliflower mosaic virus 35S promoters. Infectivity of the engineered BMYV‐EK virus was assayed in different plant species and compared with that of the original virus. We showed that in vitro‐ or in planta‐derived transcripts were infectious in protoplasts and in whole plants. Importantly, the natural aphid vector Myzus persicae efficiently transmitted the viral progeny produced in infected plants. By comparing agroinoculation and aphid infection in a host range assay, we showed that the engineered BMYV‐EK virus displayed a similar host range to BMYV‐2ITB, except for Nicotiana benthamiana, which proved to be resistant to systemic infection with BMYV‐EK. Finally, both the BMYV‐EK P0 and the full‐length clone were able to strongly interfere with post‐transcriptional gene silencing.
Confidence‐weighted testing: A descriptive study of Japanese nursing students
Authors: Aoyama Michiyo , Tamura Yumi , Ishikawa Yuichi , Yada Mamiko , Miyawaki Ikuko
Published: July 2013

Nurses' lack of self‐confidence in their own nursing skills is one of the main reasons that novice nurses leave the profession in Japan. Nursing education must help students gain self‐confidence in their nursing skills in order to allow more novice nurses to stay in their profession. In this study, we evaluated whether confidence‐weighted testing feedback actually improves students' self‐confidence in their basic nursing skills. Confidence‐weighted testing, which provides quantifiable results, might allow students to objectively assess their skill‐related self‐confidence. Sixty‐seven first‐year nursing students took two confidence‐rating examinations on the knowledge and practical skills related to pulse and blood pressure measurement of immobile patients. Feedback was given to each participant after the first examination. After the first examination with confidence‐weighted testing feedback, students showed higher levels of self‐confidence in their practical skills, but not in knowledge. The improvement of self‐confidence in practical skills suggests that there is still room for improvement in confidence‐weighted testing feedback in knowledge. Further research is required to identify more effective feedback methods to improve students' self‐confidence levels in knowledge using the results of confidence‐weighted testing.
Development of lacosamide for the treatment of partial‐onset seizures
Authors: Doty Pamela , Hebert David , Mathy Francois‐Xavier , Byrnes William , Zackheim James , Simontacchi Kelly
Published: July 2013

Lacosamide is an antiepileptic drug (AED) available in multiple formulations that was first approved in 2008 as adjunctive therapy for partial‐onset seizures (POS) in adults. Unlike traditional sodium channel blockers affecting fast inactivation, lacosamide selectively enhances sodium channel slow inactivation. This mechanism of action results in stabilization of hyperexcitable neuronal membranes, inhibition of neuronal firing, and reduction in long‐term channel availability without affecting physiological function. Lacosamide has a well‐characterized and favorable pharmacokinetic profile, including a fast absorption rate, minimal or no interaction with cytochrome P‐450 izoenzymes, and a low potential for drug–drug interactions. Lacosamide clinical development included three placebo‐controlled, double‐blind, randomized trials conducted in more than 1300 patients, each demonstrating safety and efficacy of lacosamide compared to placebo as adjunctive therapy for adults with POS. The clinical use of lacosamide may broaden, pending results of trials evaluating its use as monotherapy for POS in adults, as treatment for epilepsy in pediatric subjects, and as adjunctive treatment for uncontrolled primary generalized tonic–clonic seizures in those with idiopathic generalized epilepsy.
Ambulatory arterial stiffness index in children after kidney transplantation
Authors: Dégi Arianna , Kerti Andrea , Cseprekál Orsolya , Kis Éva , Sallay Péter , Szabó Attila J. , Reusz George S.
Published: July 2013

Given the increase in CV morbidity after RTx and the scarcity of CV events in pediatrics, surrogate markers should be assessed to characterize CV damage in this population. AASI is a marker of arterial stiffness in adults, predicting cardio‐ and cerebrovascular morbidity. Our aim was to assess the determinants of AASI in RTx children (n = 54, 15.5 ± 3.5 yr) and to examine its relationship to central PWV. AASI was calculated from 24 h ABPM. PWV was determined by applanation tonometry, body composition by multifrequency bioimpedance measurement. The dipping state, volume overload, and time on dialysis were the main predictors of AASI (p < 0.05). Children with established HT (n = 34) had increased AASI, extracellular body water, and BNP (p < 0.05). In contrast to AASI, PWV did not differ between HT and normotensive RTx patient groups. There was no correlation between AASI and PWV. PWV was increased in children who spent more than one yr on dialysis prior to RTx. In conclusion, increased AASI in HT RTx children better characterizes the actual volume‐ and pressure‐dependent arterial rigidity rather than long‐term morphological changes in large arteries as reflected by PWV.
Oral findings and dental treatment in a patient with Dandy–Walker syndrome: a case report
Authors: Kusumoto Yasuka , Shinozuka Osamu
Published: July 2013

Dandy–Walker syndrome (DWS) is congenital disease characterized by hypoplasia of the cerebellum, the formation of cysts that communicate with the fourth ventricle of the posterior cranial fossa, and hydrocephalus. In addition to various other complications, cleft lip/palate, facial retrognathia, a high‐arched palate, and maldentition occur at an increased frequency in patients with DWS. However, few studies have reported the dental manifestations of DWS. Herein, we report the clinical manifestations, oral findings, and dental management of a DWS patient who was treated under general anesthesia. Poor oral hygiene, gingivitis, and several congenital dental abnormalities (e.g., generalized microdontia, conical tooth, transposition, and congenitally missing teeth) were observed. This report is the first to describe the oral findings and dental treatment of DWS. Our findings emphasize the importance of a multidisciplinary approach in the diagnosis and treatment of DWS.
Serum thymidine kinase 1 and C‐reactive protein as biomarkers for screening clinically healthy dogs for occult disease
Authors: Selting K. A. , Sharp C. R. , Ringold R. , Knouse J.
Published: July 2013

Thymidine kinase (TK1) is a biomarker that correlates well with diagnosis and prognosis in certain canine cancers. Canine C‐reactive protein (cCRP) is a widely accepted marker of inflammation correlated with increased risk and severity of various diseases. We evaluated serum TK1 and cCRP concentrations in apparently healthy dogs (n = 360). All dogs were followed up for a minimum of 6 months by health questionnaire. All dogs with cancer were identified using a proprietary dual‐biomarker algorithm [termed Neoplasia Index (NI)]. Specificity of positive NI is 0.91 and high positive is 0.98. All‐cause mortality was 20% in dogs with elevated cCRP and 3% in dogs with low cCRP. The performance of serum TK1 and cCRP as tools for screening for occult cancer is improved when evaluated together. Serum TK1 and cCRP (unified in the NI) are useful in the screening of occult canine cancer. cCRP is useful in screening for other serious diseases.
Hyperthermia does not alter the increase in cerebral perfusion during cognitive activation
Authors: Schlader Zachary J. , Lucas Rebekah A. I. , Pearson James , Crandall Craig G.
Published: July 2013

New Findings

What is the central question of this study?

Decreases in baseline cerebral perfusion impair the capacity to increase cerebral perfusion during cognitive activation. Hyperthermia reduces baseline cerebral perfusion, but it remains unknown whether hyperthermia also impairs the increase in cerebral perfusion during the execution of a cognitive task.

What is the main finding and its importance?

This study shows that hyperthermia does not alter the increase in cerebral perfusion during a cognitive task. These findings have implications for individuals who are frequently exposed to heat stress in concert with a cognitive challenge.

This study tested the hypothesis that hyperthermia attenuates the increase in cerebral perfusion during cognitive activation. Mean middle cerebral artery blood velocity (MCAVmean) served as an index of cerebral perfusion, while the nBack test (a test of working memory) was the cognitive task. Hyperthermia was characterized by elevations (P < 0.001) in skin (by 5.0 ± 0.8°C) and intestinal temperatures (by 1.3 ± 0.1°C) and reductions (P < 0.020) in mean arterial pressure (by 11 ± 10 mmHg), end‐tidal CO2 tension (by 3 ± 6 mmHg) and MCAVmean (by 10 ± 9 cm s−1). Hyperthermia had no influence on nBack test performance (mean difference from normothermia to hyperthermia, −1 ± 11%; P= 0.276) or, counter to the hypothesis, the increase in MCAVmean during nBack testing (mean difference from normothermia to hyperthermia: 0 ± 16 cm s−1; P= 0.608). These findings indicate that the capacity to increase cerebral perfusion during cognitive activation is unaffected by hyperthermia.
Acute inhibition of diacylglycerol lipase blocks endocannabinoid‐mediated retrograde signalling: evidence for on‐demand biosynthesis of 2‐arachidonoylglycerol
Authors: Hashimotodani Yuki , Ohno‐Shosaku Takako , Tanimura Asami , Kita Yoshihiro , Sano Yoshikazu , Shimizu Takao , Di Marzo Vincenzo , Kano Masanobu
Published: July 2013

Key points

2‐Arachidonoylglycerol (2‐AG), one of the best‐characterized retrograde messengers at central synapses, has been thought to be produced ‘on demand’ through a diacylglycerol lipase α (DGLα)‐dependent pathway upon activation of postsynaptic neurons (on‐demand synthesis hypothesis).

However, recent studies propose an alternative hypothesis that 2‐AG is pre‐synthesized by DGLα, stored in neurons, and released from such ‘pre‐formed pools’ without the participation of DGLα (pre‐formed pool hypothesis).

To test these hypotheses, we examined the effects of acute pharmacological inhibition of DGL by a novel potent DGL inhibitor, OMDM‐188, on retrograde 2‐AG signalling.

We found that 2‐AG‐mediated retrograde signalling was blocked after 1 h treatment with OMDM‐188 in acute slices from the hippocampus, striatum and cerebellum, and was blocked several minutes after OMDM‐188 application in cultured hippocampal neurons.

These results fit well with the on‐demand synthesis hypothesis, rather than the pre‐formed pool hypothesis.

Abstract  The endocannabinoid (eCB) 2‐arachidonoylglycerol (2‐AG) produced by diacylglycerol lipase α (DGLα) is one of the best‐characterized retrograde messengers at central synapses. It has been thought that 2‐AG is produced ‘on demand’ upon activation of postsynaptic neurons. However, recent studies propose that 2‐AG is pre‐synthesized by DGLα and stored in neurons, and that 2‐AG is released from such ‘pre‐formed pools’ without the participation of DGLα. To address whether the 2‐AG source for retrograde signalling is the on‐demand biosynthesis by DGLα or the mobilization from pre‐formed pools, we examined the effects of acute pharmacological inhibition of DGL by a novel potent DGL inhibitor, OMDM‐188, on retrograde eCB signalling triggered by Ca2+ elevation, Gq/11 protein‐coupled receptor activation or synergy of these two stimuli in postsynaptic neurons. We found that pretreatment for 1 h with OMDM‐188 effectively blocked depolarization‐induced suppression of inhibition (DSI), a purely Ca2+‐dependent form of eCB signalling, in slices from the hippocampus, striatum and cerebellum. We also found that at parallel fibre–Purkinje cell synapses in the cerebellum OMDM‐188 abolished synaptically induced retrograde eCB signalling, which is known to be caused by the synergy of postsynaptic Ca2+ elevation and group I metabotropic glutamate receptor (I‐mGluR) activation. Moreover, brief OMDM‐188 treatments for several minutes were sufficient to suppress both DSI and the I‐mGluR‐induced retrograde eCB signalling in cultured hippocampal neurons. These results are consistent with the hypothesis that 2‐AG for synaptic retrograde signalling is supplied as a result of on‐demand biosynthesis by DGLα rather than mobilization from presumptive pre‐formed pools.
Ca2+ and cAMP cross‐talk in mitochondria
Authors: Di Benedetto Giulietta , Pendin Diana , Greotti Elisa , Pizzo Paola , Pozzan Tullio
Published: July 2013

While mitochondrial Ca2+ homeostasis has been studied for several decades and many of the functional roles of Ca2+ accumulation within the matrix have been at least partially clarified, the possibility of modulation of the organelle functions by cAMP remains largely unknown. In this contribution we briefly summarize the key aspects of Ca2+ and cAMP signalling pathways in mitochondria. In particular, we focus on recent findings concerning the discovery of an autonomous cAMP toolkit within the mitochondrial matrix, its crossroad with mitochondrial Ca2+ signalling and its role in controlling ATP synthesis. The discovery of a cAMP signalling, and the demonstration of a cross‐talk between cAMP and Ca2+ inside mitochondria, open the way to a re‐evaluation of these organelles as integrators of multiple second messengers. A description of the main methods presently available to measure Ca2+ and cAMP in mitochondria of living cells with genetically encoded probes is also presented.
Reconfiguration Analysis of a Fully Reconfigurable Parallel Robot
Authors: Daniel Finistauri Allan , (Jeff) Xi Fengfeng
Published: July 2013

This paper presents a new method for the combined topological and geometric reconfiguration of a parallel robot to achieve task-based reconfiguration. Using the existing structure of a six degree-of-freedom (DOF) parallel robot, reconfiguration to limited mobility modes, a configuration with less than six degrees-of-freedom, can be achieved easily without the need to remove branches from the robot structure. Branch modules are instead, reconfigured from an unconstrained-active to a constrained-passive state by means of hybrid active/passive motors and reconfigurable universal-to-revolute joints. In doing so, the robot is capable of assuming a configuration in which the number of task-based degrees-of-freedom match the number of controllable actuators within the robot structure. The selection of branch modules for reconfiguration is independent of the limited mobility mode required and leads to multiple isomorphic configurations. A comparative study is thus needed to understand not only the implication of morphing, but also the capabilities of the reconfigured robot. For this purpose, a branch-based mobility analysis is performed and isomorphic configurations are identified. These isomorphic configurations are then compared based on their workspace and kinematic capabilities for which a parametric kinematic constraint formulation is developed. The comparative study evaluates the abilities of each configuration and is used for guidance in selecting an appropriate configuration for a particular task. The developed tools can also be used for design evaluation purposes.
Finite Element Analysis of Pedestrian-Bridge Dynamic Interaction
Authors: Qin J. W. , Law S. S. , Yang Q. S. , Yang N.
Published: July 2013

The pedestrian-bridge dynamic interaction problem in the vertical direction based on a bipedal walking model and damped compliant legs is presented in this work. The classical finite element method, combined with a moving finite element, represents the motion of the pedestrian in the dynamic analysis of a footbridge. A control force is provided by the pedestrian to compensate for the energy loss due to the system damping in walking and to regulate the walking performance of the pedestrian. The effects of leg stiffness, the landing angle of attack, the damping ratio of the leg and the mass ratio of the human and structure are investigated in the numerical studies. Simulation results show that the dynamic interaction will increase with a larger vibration level of the structure. More external energy must be input to maintain steady walking and uniform dynamic behavior of the pedestrian in the process. The simple bipedal walking model could well describe the human-structure dynamic interaction.
Optimal Material Properties for Mitigating Brain Injury During Head Impact
Authors: Begley Matthew R. , Zok Frank W.
Published: July 2013

We present a methodology for identifying constitutive responses of crushable, linear-softening materials that would reduce the severity of brain injury caused by head impact in a typical automobile or sports collision. It is based on analysis of accelerations imparted to a spherical mass (representative of the human head) upon impact at prescribed velocity onto a flat padded structure. The resulting acceleration–time histories are used to calculate the corresponding Head Injury Criterion (HIC): a weighted product of acceleration and impact duration that has been found to correlate with the severity of brain injury. In the best-case scenario, the HIC is reduced by a factor of 1.84 relative to that obtained for a system optimized with a perfectly plastic foam. The optimal combinations of yield stress and crushing strain are not unique; that is, the optimum can be achieved with a range of strengths and crushing strains. The present solutions are expected to find utility in guiding the design of new polymer lattice materials for use in impact protection systems.
Health Check Performed by DFA of Heartbeat
Authors: Yazawa Toru , Shimoda Yukio
Published: July 2013

If a small, simple heartbeat recorder, (i.e., a wearable monitoring device that is not as sophisticated or as expensive as a Holter heart monitor) could be attached to an individual, and the heartbeat timing information sent to a health center via the Internet, a significant public health benefit could be achieved. At the health center, sophisticated nonlinear computation could be performed for all the data derived from people connected to the center by such a device. This idea is important because more than 4 in 10 heart attacks (43%) go undiagnosed at the time they occur [1]. Such incidents often take people by surprise. Hence, continuous heartbeat monitoring would be an important technology.
Quantification of Gait Characteristics Through a Functional iPhone Wireless Accelerometer Application Mounted to the Spine
Authors: LeMoyne Robert , Mastroianni Timothy , Cozza Michael , Coroian Cristian
Published: July 2013

The capacity to quantify gait in autonomous scenarios may substantially alleviate the rampant strain on limited, scarce, and highly specialized medical resources. A strategy for enabling application autonomy, for which the subject may reside at a remote distant from the clinical resources, has been demonstrated through the research, development, test, and evaluation of wireless accelerometers for gait analysis. An approach for maximizing accuracy and reliability has been demonstrated through the selection of a predetermined anatomical mounting position relative to the human anatomy. Wireless accelerometer systems have presented quantified disparity for the gait of hemiparetic subjects. For the quantification of hemiparetic gait, the selected mounting positions were the lateral epicondyle of the femur and also the lateral malleolus [1].
Improving Cell Loading Efficiency Into Microfluidic Devices Using LCATs
Authors: Lin Robert , Patel Maulik , Lee Abraham
Published: July 2013

Due to the nature of the interfaces used by microfluidic devices — syringes, syringe pumps, and tubing, delivering cells into microfluidic devices faces some practical challenges. Specifically, the unwanted settling and adhesion of cells onto various surfaces can significantly impact the effective transport of cells into the device.[1] One particular challenge is the cell settling that occurs inside devices and especially at the inlet connection port. As most tubing connections are vertical, the cell suspension moves downwards into the device before making a 90° turn into the fluidic channels. This orientation causes cells to settle, clump and adhere to surfaces around the inlet port and eventually causes clogging that prevent more cells from entering the microfluidic channels.
A review of impact noise
Authors: Akay Adnan
Published: July 2013

In this paper, available literature concerned with impact noise generation and control is reviewed with emphasis on generation mechanisms. Basic research studies are considered under five different classes according to the mechanism of sound generation. These are air ejection, rigid body radiation, radiation due to rapid surface deformations, pseudo-steady-state radiation, and sound radiation due to material fracture. A brief characterization of impact sounds in addition to a description of efforts to standardize impact noise exposure criteria is given in the Introduction. A bibliography on impact noise control is included in order to permit assessment of the state of the art.
Receptor Tyrosine Kinases Fall into Distinct Classes Based on Their Inferred Signaling Networks
Authors: Wagner Joel P. , Wolf-Yadlin Alejandro , Sevecka Mark , Grenier Jennifer K. , Root David E. , Lauffenburger Douglas A. , MacBeath Gavin
Published: July 2013

Clustering receptor tyrosine kinase networks reveals potentially useful combination cancer therapies to overcome resistance.
Keeping the Inflammasome in Check
Authors: Mueller Kristen L.
Published: July 2013

Adenosine diphosphate binding to the NOD-like receptor keeps it inactive in the absence of ligands.
Chimeric Cyanovirin-MPER Recombinantly Engineered Proteins Cause Cell-Free Virolysis of HIV-1
Authors: Contarino Mark , Bastian Arangassery R. , Kalyana Sundaram Ramalingam Venkat , McFadden Karyn , Duffy Caitlin , Gangupomu Vamshi , Baker Michelle , Abrams Cameron , Chaiken Irwin
Published: July 2013

Human immunodeficiency virus (HIV) is the primary etiologic agent responsible for the AIDS pandemic. In this work, we used a chimeric recombinant protein strategy to test the possibility of irreversibly destroying the HIV-1 virion using an agent that simultaneously binds the Env protein and viral membrane. We constructed a fusion of the lectin cyanovirin-N (CVN) and the gp41 membrane-proximal external region (MPER) peptide with a variable-length (Gly
4
Ser)

x

linker (where
x
is 4 or 8) between the C terminus of the former and N terminus of the latter. The His-tagged recombinant proteins, expressed in BL21(DE3)pLysS cells and purified by immobilized metal affinity chromatography followed by gel filtration, were found to display a nanomolar efficacy in blocking BaL-pseudotyped HIV-1 infection of HOS.T4.R5 cells. This antiviral activity was HIV-1 specific, since it did not inhibit cell infection by vesicular stomatitis virus (VSV) or amphotropic-murine leukemia virus. Importantly, the chimeric proteins were found to release intraviral p24 protein from both BaL-pseudotyped HIV-1 and fully infectious BaL HIV-1 in a dose-dependent manner in the absence of host cells. The addition of either MPER or CVN was found to outcompete this virolytic effect, indicating that both components of the chimera are required for virolysis. The finding that engaging the Env protein spike and membrane using a chimeric ligand can destabilize the virus and lead to inactivation opens up a means to investigate virus particle metastability and to evaluate this approach for inactivation at the earliest stages of exposure to virus and before host cell encounter.
The
R
Enantiomer of the Antitubercular Drug PA-824 as a Potential Oral Treatment for Visceral Leishmaniasis
Authors: Patterson Stephen , Wyllie Susan , Stojanovski Laste , Perry Meghan R. , Simeons Frederick R. C. , Norval Suzanne , Osuna-Cabello Maria , De Rycker Manu , Read Kevin D. , Fairlamb Alan H.
Published: July 2013

The novel nitroimidazopyran agent (
S
)-PA-824 has potent antibacterial activity against
Mycobacterium tuberculosis
in vitro
and
in vivo
and is currently in phase II clinical trials for tuberculosis (TB). In contrast to
M. tuberculosis
, where (
R
)-PA-824 is inactive, we report here that both enantiomers of PA-824 show potent parasiticidal activity against
Leishmania donovani
, the causative agent of visceral leishmaniasis (VL). In leishmania-infected macrophages, (
R
)-PA-824 is 6-fold more active than (
S
)-PA-824. Both des-nitro analogues are inactive, underlining the importance of the nitro group in the mechanism of action. Although the
in vitro
and
in vivo
pharmacological profiles of the two enantiomers are similar, (
R
)-PA-824 is more efficacious in the murine model of VL, with >99% suppression of parasite burden when administered orally at 100 mg kg of body weight
−1
, twice daily for 5 days. In
M. tuberculosis
, (
S
)-PA-824 is a prodrug that is activated by a deazaflavin-dependent nitroreductase (Ddn), an enzyme which is absent in
Leishmania
spp. Unlike the case with nifurtimox and fexinidazole, transgenic parasites overexpressing the leishmania nitroreductase are not hypersensitive to either (
R
)-PA-824 or (
S
)-PA-824, indicating that this enzyme is not the primary target of these compounds. Drug combination studies
in vitro
indicate that fexinidazole and (
R
)-PA-824 are additive whereas (
S
)-PA-824 and (
R
)-PA-824 show mild antagonistic behavior. Thus, (
R
)-PA-824 is a promising candidate for late lead optimization for VL and may have potential for future use in combination therapy with fexinidazole, currently in phase II clinical trials against VL.
DNA Microarray for Genotyping Antibiotic Resistance Determinants in Acinetobacter baumannii Clinical Isolates
Authors: Dally Simon , Lemuth Karin , Kaase Martin , Rupp Steffen , Knabbe Cornelius , Weile Jan
Published: July 2013

In recent decades,
Acinetobacter baumannii
has emerged as an organism of great concern due to its ability to accumulate antibiotic resistance. In order to improve the diagnosis of resistance determinants in
A. baumannii
in terms of lead time and accuracy, we developed a microarray that can be used to detect 91 target sequences associated with antibiotic resistance within 4 h from bacterial culture to result. The array was validated with 60 multidrug-resistant strains of
A. baumannii
in a blinded, prospective study. The results were compared to phenotype results determined by the automated susceptibility testing system VITEK2. Antibiotics considered were piperacillin-tazobactam, ceftazidime, imipenem, meropenem, trimethoprim-sulfamethoxazole, amikacin, gentamicin, tobramycin, ciprofloxacin, and tigecycline. The average positive predictive value, negative predictive value, sensitivity, and specificity were 98, 98, 99, and 94%, respectively. For carbapenemase genes, the array results were compared to singleplex PCR results provided by the German National Reference Center for Gram-Negative Pathogens, and results were in complete concordance. The presented array is able to detect all relevant resistance determinants of
A. baumannii
in parallel. The short handling time of 4 h from culture to result helps to provide fast results in order to initiate adequate anti-infective therapy for critically ill patients. Another application would be data acquisition for epidemiologic surveillance.
Basis for Early and Preferential Selection of the E138K Mutation in HIV-1 Reverse Transcriptase
Authors: McCallum Matthew , Oliveira Maureen , Ibanescu Ruxandra-Ilinca , Kramer Victor G. , Moisi Daniela , Asahchop Eugene L. , Brenner Bluma G. , Harrigan P. Richard , Xu Hongtao , Wainberg Mark A.
Published: July 2013

E138K, a G→A mutation in HIV-1 reverse transcriptase (RT), is preferentially selected by etravirine (ETR) and rilpivirine over other substitutions at position E138 that offer greater drug resistance. We hypothesized that there was a mutational bias for the E138K substitution and designed an allele-specific PCR to monitor the emergence of E138A/G/K/Q/R/V during ETR selection experiments. We also performed competition experiments using mutated viruses and quantified the prevalence of E138 minority species in drug-naive patients. E138K, as well as E138G, consistently emerged first during ETR selection experiments, followed by E138A and E138Q; E138R was never selected. Surprisingly, E138K was identified as a tiny minority in 23% of drug-naive subtype B patients, a result confirmed by ultradeep sequencing (UDS). This result could reflect a low fitness cost of E138K; however, E138K was one of the least fit substitutions at codon E138, even after taking into account the deoxynucleoside triphosphate pools of the cells used in competition experiments. Further UDS analysis revealed other minority species in a pattern consistent with the mutational bias of HIV RT. There was no evidence of APOBEC3-hypermutation in these selection experiments or in patients. Our results confirm the mutational bias of HIV-1 in patients and highlight the importance of G→A mutations in HIV-1 drug resistance evolution.
Abiotic and Microbiotic Factors Controlling Biofilm Formation by Thermophilic Sporeformers
Authors: Zhao Yu , Caspers Martien P. M. , Metselaar Karin I. , de Boer Paulo , Roeselers Guus , Moezelaar Roy , Nierop Groot Masja , Montijn Roy C. , Abee Tjakko , Kort Remco
Published: July 2013

One of the major concerns in the production of dairy concentrates is the risk of contamination by heat-resistant spores from thermophilic bacteria. In order to acquire more insight in the composition of microbial communities occurring in the dairy concentrate industry, a bar-coded 16S amplicon sequencing analysis was carried out on milk, final products, and fouling samples taken from dairy concentrate production lines. The analysis of these samples revealed the presence of DNA from a broad range of bacterial taxa, including a majority of mesophiles and a minority of (thermophilic) spore-forming bacteria. Enrichments of fouling samples at 55°C showed the accumulation of predominantly
Brevibacillus
and
Bacillus
, whereas enrichments at 65°C led to the accumulation of
Anoxybacillus
and
Geobacillus
species. Bacterial population analysis of biofilms grown using fouling samples as an inoculum indicated that both
Anoxybacillus
and
Geobacillus
preferentially form biofilms on surfaces at air-liquid interfaces rather than on submerged surfaces. Three of the most potent biofilm-forming strains isolated from the dairy factory industrial samples, including
Geobacillus thermoglucosidans
,
Geobacillus stearothermophilus
, and
Anoxybacillus flavithermus
, have been characterized in detail with respect to their growth conditions and spore resistance. Strikingly,
Geobacillus thermoglucosidans
, which forms the most thermostable spores of these three species, is not able to grow in dairy intermediates as a pure culture but appears to be dependent for growth on other spoilage organisms present, probably as a result of their proteolytic activity. These results underscore the importance of abiotic and microbiotic factors in niche colonization in dairy factories, where the presence of thermophilic sporeformers can affect the quality of end products.
The Evolutionary Divergence of Shiga Toxin-Producing Escherichia coli Is Reflected in Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Spacer Composition
Authors: Yin Shuang , Jensen Mark A. , Bai Jiawei , DebRoy Chitrita , Barrangou Rodolphe , Dudley Edward G.
Published: July 2013

The Shiga toxin-producing
Escherichia coli
(STEC) strains, including those of O157:H7 and the “big six” serogroups (i.e., serogroups O26, O45, O103, O111, O121, and O145), are a group of pathogens designated food adulterants in the United States. The relatively conserved nature of
c
lustered
r
egularly
i
nterspaced
s
hort
p
alindromic
r
epeats (CRISPRs) in phylogenetically related
E. coli
strains makes them potential subtyping markers for STEC detection, and a quantitative PCR (qPCR)-based assay was previously developed for O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 isolates. To better evaluate the sensitivity and specificity of this qPCR method, the CRISPR loci of 252 O157 and big-six STEC isolates were sequenced and analyzed along with 563 CRISPR1 and 624 CRISPR2 sequences available in GenBank. General conservation of spacer content and order was observed within each O157 and big-six serogroup, validating the qPCR method. Meanwhile, it was found that spacer deletion, the presence of an insertion sequence, and distinct alleles within a serogroup are sources of false-negative reactions. Conservation of CRISPR arrays among isolates expressing the same flagellar antigen, specifically, H7, H2, and H11, suggested that these isolates share an ancestor and provided an explanation for the false positives previously observed in the qPCR results. An analysis of spacer distribution across
E. coli
strains provided limited evidence for temporal spacer acquisition. Conversely, comparison of CRISPR sequences between strains along the stepwise evolution of O157:H7 from its O55:H7 ancestor revealed that, over this ∼7,000-year span, spacer deletion was the primary force generating CRISPR diversity.
Generation of Affinity-Tagged Fluoromycobacteriophages by Mixed Assembly of Phage Capsids
Authors: Piuri Mariana , Rondón Liliana , Urdániz Estefanía , Hatfull Graham F.
Published: July 2013

Addition of affinity tags to bacteriophage particles facilitates a variety of applications, including vaccine construction and diagnosis of bacterial infections. Addition of tags to phage capsids is desirable, as modification of the tails can lead to poor adsorption and loss of infectivity. Although tags can readily be included as fusions to head decoration proteins, many phages do not have decoration proteins as virion components. The addition of a small (10-amino-acid) Strep-tag II (STAG II) to the mycobacteriophage TM4 capsid subunit, gp9, was not tolerated as a genetically homogenous recombinant phage but could be incorporated into the head by growth of wild-type phage on a host expressing the capsid-STAG fusion. Particles with capsids composed of wild-type and STAG-tagged subunit mixtures could be grown to high titers, showed good infectivities, and could be used to isolate phage-bacterium complexes. Preparation of a STAG-labeled fluoromycobacteriophage enabled capture of bacterial complexes and identification of infected bacteria by fluorescence.
Transfer Efficiency of Bacteria and Viruses from Porous and Nonporous Fomites to Fingers under Different Relative Humidity Conditions
Authors: Lopez Gerardo U. , Gerba Charles P. , Tamimi Akrum H. , Kitajima Masaaki , Maxwell Sheri L. , Rose Joan B.
Published: July 2013

Fomites can serve as routes of transmission for both enteric and respiratory pathogens. The present study examined the effect of low and high relative humidity on fomite-to-finger transfer efficiency of five model organisms from several common inanimate surfaces (fomites). Nine fomites representing porous and nonporous surfaces of different compositions were studied.Escherichia coli,Staphylococcus aureus,Bacillus thuringiensis, MS2 coliphage, and poliovirus 1 were placed on fomites in 10-μl drops and allowed to dry for 30 min under low (15% to 32%) or high (40% to 65%) relative humidity. Fomite-to-finger transfers were performed using 1.0 kg/cm2of pressure for 10 s. Transfer efficiencies were greater under high relative humidity for both porous and nonporous surfaces. Most organisms on average had greater transfer efficiencies under high relative humidity than under low relative humidity. Nonporous surfaces had a greater transfer efficiency (up to 57%) than porous surfaces (<6.8%) under low relative humidity, as well as under high relative humidity (nonporous, up to 79.5%; porous, <13.4%). Transfer efficiency also varied with fomite material and organism type. The data generated can be used in quantitative microbial risk assessment models to assess the risk of infection from fomite-transmitted human pathogens and the relative levels of exposure to different types of fomites and microorganisms.
Identification and Characterization of a NaCl-Responsive Genetic Locus Involved in Survival during Desiccation in Sinorhizobium meliloti
Authors: Vriezen Jan A. C. , de Bruijn Frans J. , Nüsslein Klaus
Published: July 2013

The
Rhizobiaceae
are a bacterial family of enormous agricultural importance due to the ability of its members to fix atmospheric nitrogen in an intimate relationship with plants. Their survival as naturally occurring soil bacteria in agricultural soils as well as popular seed inocula is affected directly by drought and salinity. Survival after desiccation in the presence of NaCl is enabled by underlying genetic mechanisms in the model organism
Sinorhizobium meliloti
1021. Since salt stress parallels a loss in water activity, the identification of NaCl-responsive loci may identify loci involved in survival during desiccation. This approach enabled identification of the loci
asnO
and
ngg
by their reduced ability to grow on increased NaCl concentrations, likely due to their inability to produce the osmoprotectant N-acetylglutaminylglutamine (NAGGN). In addition, the mutant harboring
ngg
::Tn
5luxAB
was affected in its ability to survive desiccation and responded to osmotic stress. The desiccation sensitivity may have been due to secondary functions of Ngg (N-acetylglutaminylglutamine synthetase)-like cell wall metabolism as suggested by the presence of a
d
-alanine-
d
-alanine ligase (dAla-dAla) domain and by sensitivity of the mutant to β-lactam antibiotics.
asnO
::Tn
5luxAB
is expressed during the stationary phase under normal growth conditions. Amino acid sequence similarity to enzymes producing β-lactam inhibitors and increased resistance to β-lactam antibiotics may indicate that
asnO
is involved in the production of a β-lactam inhibitor.
New Type of Antimicrobial Protein Produced by the Plant Pathogen Clavibacter michiganensis subsp. michiganensis
Authors: Liu Zhanliang , Ma Ping , Holtsmark Ingrid , Skaugen Morten , Eijsink Vincent G. H. , Brurberg May B.
Published: July 2013

It has previously been shown that the tomato pathogen
Clavibacter michiganensis
subsp.
michiganensis
secretes a 14-kDa protein,
C. michiganensis
subsp.
michiganensis
AMP-I (
Cmm
AMP-I), that inhibits growth of
Clavibacter michiganensis
subsp.
sepedonicus
, the causal agent of bacterial ring rot of potato. Using sequences obtained from tryptic fragments, we have identified the gene encoding
Cmm
AMP-I and we have recombinantly produced the protein with an N-terminal intein tag. The gene sequence showed that
Cmm
AMP-I contains a typical N-terminal signal peptide for Sec-dependent secretion. The recombinant protein was highly active, with 50% growth inhibition (IC
50
) of approximately 10 pmol, but was not toxic to potato leaves or tubers.
Cmm
AMP-I does not resemble any known protein and thus represents a completely new type of bacteriocin. Due to its high antimicrobial activity and its very narrow inhibitory spectrum,
Cmm
AMP-1 may be of interest in combating potato ring rot disease.