bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in interspecies association patterns of Atlantic bottlenose dolphins, Tursiops truncatus, and Atlantic spotted dolphins, Stenella frontalis, after demographic changes related to environmental disturbance
Authors: Elliser Cindy R. , Herzing Denise L.
Published: January 2016

Animal populations can be affected by environmental disturbances in many ways including demographic and behavioral changes. This can affect interspecies associations for regularly interacting sympatric species, like bottlenose and spotted dolphins in the Bahamas (observed since 1985 and interspecies associations analyzed since 1993). After two hurricanes in 2004 each species lost roughly 30% of their respective communities resulting in differing social structure and behavioral changes. During mixed species encounters (MSE) group sizes for spotted dolphins ( = 14.1 ± 9.2) were significantly larger than bottlenose dolphins ( = 6.0 ± 7.3; F = 11.74, df = 1, P < 0.001), however, t‐tests revealed no differences between aggressive vs. affiliative encounters. Sexual/aggressive behavior regularly seen previously was not observed posthurricanes and aggressive encounters were greatly reduced. Generally results were similar to prehurricane data including high resightings of spotted dolphins with male alliances prevalent (including new juvenile alliances seen only posthurricane), and individualized bottlenose participation with few male alliances. However temporal associations varied compared to prehurricane. Interspecies association and behavior patterns were altered and likely affected by the changes in intraspecies association patterns following the hurricanes. However both species still participated in MSE, suggesting this is an important component of their ability to coexist as sympatric species.
Elevational gradient and vegetation‐environmental relationships in the central Hyrcanian forests of northern Iran
Authors: Moradi Halime , Naqinezhad Alireza , Siadati Soudeh , Yousefi Yadollah , Attar Farideh , Etemad Vahid , Reif Albert
Published: January 2016

Tertiary‐relict Hyrcanian (Caspian) forest along the shores of the southern Caspian Sea is a center of biodiversity. Still, there is little information on plant diversity patterns in this area. This study evaluated plant diversity, variation in life forms, and geographical distribution of the zonal vegetation types and their relationships with environmental variables, in the educational and experimental forest of Kheyrudkenar, an important protected area in the central Hyrcanian forest of northern Iran. For this purpose, 226 vegetation plots of 400 m2 were laid out along two altitudinal transects from the lowlands (100 m a.s.l.) to the timberline (2000 m a.s.l.). Four vegetation types were identified using modified TWINSPAN, indirect and direct gradient analyses. Species‐related (species diversity indices, life form and phytogeographical elements) and environmental variables (climate, topographic and soil variables) were calculated and subjected to one‐way ANOVA among the vegetation types. Both constrained (CCA) and unconstrained (DCA) ordination analyses showed an almost identical variation of the floristic composition along their axes and demonstrated that there are two main gradients in the Hyrcanian forest. Elevation together with annual precipitation and mean annual temperature were the most important factors controlling the floristic composition in the area. Topographic features such as slope inclination and heat index were found to be important within an elevation zone/vegetation type. Soil physical and chemical properties were of secondary importance for the separation of the vegetation types. This knowledge will be useful for forest management and conservation practices in the Hyrcanian area with its distinct and unique flora and vegetation.
Lectotypification of Acrostichum spicatum (Lepisorus spicatus, Polypodiaceae)
Authors: Mazumdar Jaideep
Published: January 2016

The original material of the fern species name Acrostichum spicatum (Polypodiaceae) was detected in the Linnaean Herbarium in London. It is selected as the lectotype in consultation with the protologue of the name, thus superseding the neotypes in the collections of Commerson and Sonnerat.
Fruit and seed morphology of the tribe Orobancheae (Orobanchaceae) genera in Turkey and its taxonomic significance
Authors: Zare Golshan , Dönmez Ali A.
Published: January 2016

Seed and fruit morphology of four genera of Orobanchaceae: Cistanche, Diphelypaea, Orobanche and Phelipanche, native to Turkey, were studied using light and scanning electron microscopy. In this study, 100 accessions belonging to 39 species were investigated. The examined fruits had loculicidal capsules, generally dehiscing with 2 slits, and the seeds were small and with reticulate ornamentation. The basic shape of the seeds in most of the studied taxa was oblong, ellipsoid to ovoid, globose or subglobose. The results indicate that characters such as seed size, shape and color are useless for identification of the taxa at the species level. However, the anticlinal wall pattern and periclinal wall ornamentation proved useful for identifying the different genera. Four morphological types could be distinguished: smooth, perforate, microfibrillar and granulate. Type I corresponds to the genus Cistanche and Orobanche anatolica, whereas types II, III and IV were found in Diphelypaea, Orobanche and Phelipanche, respectively. The utility of seed characteristics is discussed in terms of inter‐ and intra‐generic taxonomy.
Dendromyza hiepkoana sp. nov. from Irian Jaya and D. staufferi sp. nov. from Papua New Guinea (Amphorogynaceae)
Authors: Macklin Jill , Parnell John
Published: January 2016

The genus Dendromyza (Amphorogynaceae) comprises approximately 21 species with a distribution from the Malay Archipelago to southern Australia. Two new hemiparasitic species in this genus: D. hiepkoana from Irian Jaya and D. staufferi from Papua New Guinea are here described, illustrated and compared. Dendromyza hiepkoiana is similar to members of the genus Phacellaria (Benth.) where the leaves are very small and bract‐like, but differs in its separate stigmas and chambered fruits that possess a crown of fibers on the endocarp. Dendromyza staufferi is allied to D. reinwardtiana (Bl. ex Korth.) Danser but differs from this species by broader, ovate rather than narrower, spathulate leaves and sessile inflorescences. Dendromyza staufferi also has an ovoid rather than elliptical endocarp and the crown of fibres at the apex of the endocarp are pilose. Due to their hemiparasitic nature and aerial habitat, species of Dendromyza are generally considered to be vulnerable in terms of conservation status. Based on the information available to us, however, the species described here are categorised as locally common or near threatened.
Interaction between hormonal and mitochondrial signalling during growth, development and in plant defence responses
Authors: Berkowitz Oliver , De Clercq Inge , Van Breusegem Frank , Whelan James
Published: January 2016

Mitochondria play a central role in plant metabolism as they are a major source of ATP through synthesis by the oxidative phosphorylation pathway and harbour key metabolic reactions such as the TCA cycle. The energy and building blocks produced by mitochondria are essential to drive plant growth and development as well as to provide fuel for responses to abiotic and biotic stresses. The majority of mitochondrial proteins are encoded in the nuclear genome and have to be imported into the organelle. For the regulation of the corresponding genes intricate signalling pathways exist to adjust their expression. Signals directly regulate nuclear gene expression (anterograde signalling) to adjust the protein composition of the mitochondria to the needs of the cell. In parallel, mitochondria communicate back their functional status to the nucleus (retrograde signalling) to prompt transcriptional regulation of responsive genes via largely unknown signalling mechanisms. Plant hormones are the major signalling components regulating all layers of plant development and cellular functions. Increasing evidence is now becoming available that plant hormones are also part of signalling networks controlling mitochondrial function and their biogenesis. This review summarizes recent advances in understanding the interaction of mitochondrial and hormonal signalling pathways.
Eruptive Penile Syringomas in an Adolescent: Novel Approach with Serial Microexcisions and Suture–Adhesive Repair
Authors: Todd Patricia S. , Gordon Samantha C. , Rovner Rebecca L. , Tung Rebecca
Published: January 2016

Penile syringomas are benign adnexal tumors that are usually asymptomatic but can be cosmetically distressing. Because of the delicate nature of skin in this region, treatment is difficult, and there are few case reports of procedural destruction of these tumors. We report a case of successful surgical excision using Castroviejo ophthalmic scissors followed by primary closure with fast‐absorbing plain gut suture and a cyanoacrylate adhesive application. This procedure was well tolerated and had an impressive cosmetic outcome.
Periungual Bowen's Disease in a 12‐Year‐Old Boy Treated with Photodynamic Therapy
Authors: Hyun Dong J. , Seo Seong R. , Kim Dong H. , Yoon Moon S. , Lee Hee J.
Published: January 2016

Bowen's disease (BD) usually occurs on sun‐exposed areas in elderly patients. BD rarely occurs in childhood and lesions of the nail unit and periungual area are likely associated with human papillomavirus infection. Herein, we report a case of BD presenting on the periungual area in a 12‐year‐old boy which was successfully treated with two sessions of photodynamic therapy.
Does Helicobacter pylori play a role in the pathogenesis of non‐cystic fibrosis bronchiectasis?
Authors: Aydın Teke Turkan , Akyön Yakut , Yalcin Ebru , Ozen Hasan , Doğru Deniz , Kiper Nural , Ozcelik Ugur
Published: January 2016

Background

The aim of this study was to investigate whether Helicobacter pylori plays a role in the pathogenesis and severity of non‐cystic fibrosis bronchiectasis, and its relationship with gastroesophageal reflux (GER).

Methods

Forty‐one patients and 16 controls between 5 and 18 years of age were enrolled. H. pylori was investigated on polymerase chain reaction and culture in gastric juice (GJ) and bronchoalveolar lavage fluid (BALF). Urea breath test (UBT) was also used for defining H. pylori infection. GER was detected on 24 h pH monitoring or scintigraphy. Computed tomography (CT) scoring was used to quantify the severity and extent of bronchiectasis.

Results

Nine patients (22%) in the bronchiectasis group (BG) and three patients (18.8%) in the control group (CG) had H. pylori‐positive BALF. Sixteen BG patients (39%) and seven CG patients (43.8%) had H. pylori‐positive GJ. UBT was positive in 11 BG patients (26.8%) and in three CG patients (18.8%). H. pylori positivity in BALF, GJ and UBT was not significantly different between the two groups (P > 0.05). Six patients with GER and five patients without GER in BG had H. pylori‐positive BALF and GJ (P = 0.827). No association was found between BALF H. pylori positivity and forced expiratory volume in 1 s (FEV1) in BG. CT score was significantly higher in BG patients with H. pylori‐positive compared with H. pylori‐negative BALF (P < 0.05).

Conclusions

Helicobacter pylori is not associated with the pathogenesis of bronchiectasis but it may be responsible for the severity of the disease.
Musculoskeletal abnormalities in congenital diaphragmatic hernia survivors: Patterns and risk factors: Report of a Japanese multicenter follow‐up survey
Authors: Takayasu Hajime , Masumoto Kouji , Goishi Keiji , Hayakawa Masahiro , Tazuke Yuko , Yokoi Akiko , Terui Keita , Okuyama Hiroomi , Usui Noriaki , Nagata Kouji , Taguchi Tomoaki ,   Japanese Congenital Diaphragmatic Hernia Study Group
Published: January 2016

Background

The aim of this study was to investigate the natural history and associated predictors of musculoskeletal deformities in congenital diaphragmatic hernia (CDH) survivors.

Methods

A multicenter retrospective survey was conducted among CDH patients between January 2006 and December 2010 in Japan, and a follow‐up survey was performed between September 2013 and October 2013. One hundred and eighty‐two (79.8%) of the 228 patients were alive. An orthopedic survey of 159 survivors without severe coexisting congenital anomalies was subsequently carried out, and the rates of pectus excavatum (PE), scoliosis and chest asymmetry were evaluated.

Results

Scoliosis, PE and chest asymmetry were found in 20 (12.6%), 19 (11.9%) and 12 (7.5%) patients, respectively. In total, 44 patients (27.7%) developed orthopedic abnormalities. Reduction in the oxygenation index within 24 h after birth (P = 0.044), large diaphragmatic defects (P = 0.047) and patch repair (P = 0.014) were predictive for scoliosis. In addition, Apgar score at 5 min was significantly lower in the patients who developed PE (P = 0.034); and stomach herniation (P = 0.004) and liver herniation (P = 0.013) at prenatal diagnosis and large diaphragmatic defects (P = 0.036) were predictive of chest asymmetry.

Conclusions

Approximately one‐quarter of the survivors developed musculoskeletal abnormalities in the present survey of CDH patients. These data suggest that each musculoskeletal abnormality has its own specific predictors.
Love styles, coping, and relationship satisfaction: A dyadic approach
Authors: VEDES ANA , HILPERT PETER , NUSSBECK FRIDTJOF W. , RANDALL ASHLEY K. , BODENMANN GUY , LIND WOLFGANG R.
Published: January 2016

Romantic partners have different attitudes on what love is and what it means to be in a romantic relationship. These attitudes are conceptualized as love styles that relate to relationship‐maintenance behaviors and relationship satisfaction. Specifically, love styles could be associated with how partners cope with stress (dyadic coping), which in turn may be associated with relationship satisfaction. Using self‐report data from 92 heterosexual couples, findings showed that: (a) eros and agape love styles have positive direct effects on dyadic coping and relationship satisfaction, whereas ludus has a negative direct effect on dyadic coping and relationship satisfaction and (b) dyadic coping partially mediated the association between love styles and relationship satisfaction. Overall, associations were stronger for women than for men.
Discussion of care, contribution, and perceived (in)gratitude in the family caregiver and sibling relationship
Authors: AMARO L. M. , MILLER K. I.
Published: January 2016

This qualitative analysis focuses on the discussion of care, division of labor, and perceptions of gratitude and ingratitude between an adult primary caregiver of an elderly parent and his or her sibling(s). Interviews with 20 caregivers addressed the following questions: When do caregivers feel appreciated or unappreciated by siblings? How do siblings communicate that appreciation? How does gratitude influence the experience of caregiving and family relationships during caregiving? Findings revealed that gratitude was manifested through verbal and behavioral expressions, with antithetical communication that left the caregiver feeling unappreciated. Verbal expressions of gratitude included a simple “thank you,” thanks for what the caregiver does, and for who the caregiver is. The inverse of these expressions included neglecting to say “thank you,” failing to identify the extent of the caregiver's work, and communicating criticism. Behavioral expressions took the form of following through on promises, and failing to do so presented as ingratitude.
A Simplified Approach to Risk Assessment Based on System Dynamics: An Industrial Case Study
Authors: Garbolino Emmanuel , Chery Jean‐Pierre , Guarnieri Franck
Published: January 2016

Seveso plants are complex sociotechnical systems, which makes it appropriate to support any risk assessment with a model of the system. However, more often than not, this step is only partially addressed, simplified, or avoided in safety reports. At the same time, investigations have shown that the complexity of industrial systems is frequently a factor in accidents, due to interactions between their technical, human, and organizational dimensions. In order to handle both this complexity and changes in the system over time, this article proposes an original and simplified qualitative risk evaluation method based on the system dynamics theory developed by Forrester in the early 1960s. The methodology supports the development of a dynamic risk assessment framework dedicated to industrial activities. It consists of 10 complementary steps grouped into two main activities: system dynamics modeling of the sociotechnical system and risk analysis. This system dynamics risk analysis is applied to a case study of a chemical plant and provides a way to assess the technological and organizational components of safety.
Factors associated with mouth breathing in children with ­developmental ­disabilities
Authors: de Castilho Lia Silva , Abreu Mauro Henrique Nogueira Guimarães , de Oliveira Renata Batista , Souza e Silva Maria Elisa , Resende Vera Lúcia Silva
Published: January 2016

Objective

To investigate the prevalence and factors associated with mouth breathing among patients with developmental disabilities of a dental service.

Methods

We analyzed 408 dental records. Mouth breathing was reported by the patients’ parents and from direct observation. Other variables were as ­follows: history of asthma, bronchitis, palate shape, pacifier use, thumb ­sucking, nail biting, use of medications, gastroesophageal reflux, bruxism, gender, age, and diagnosis of the patient. Statistical analysis included descriptive analysis with ratio calculation and multiple logistic regression. Variables with p < 0.25 were included in the model to estimate the adjusted OR (95% CI), calculated by the forward stepwise method. Variables with p ​​< 0.05 were kept in the model.

Results

Being male (p = 0.016) and use of centrally acting drugs (p = 0.001) were the variables that remained in the model.

Conclusion

Among patients with ­developmental disabilities, boys and psychotropic drug users had a greater chance of being mouth breathers.
Oral Health‐related quality of life in pediatric patients with cystic fibrosis
Authors: Patrick Jonathan R. D. , da Fonseca Marcio A. , Kaste Linda M. , Fadavi Shahrbanoo , Shah Neal , Sroussi Hervé
Published: January 2016

Purpose

To compare the oral health‐related quality of life (OHRQoL) of 8‐ to 12‐year‐old children and 13‐ to 17‐year‐old adolescents diagnosed with cystic fibrosis (CF).

Materials and methods

Participants were recruited from a Midwest CF center. Parents provided demographic information and their assessment of the child's health. Patients completed the Child Oral Health Impact Profile (COHIP).

Results

Thirty‐nine child‐parent pairs participated. Fifty four percent of the patients were male, 87% Caucasian, and 56% adolescent, with 66% of families reporting an annual income of over $100,000. Excellent or very good health, including oral health, was reported by 67% of the patients. Individuals taking 10 or more medications reported better OHRQoL while Caucasians reported better oral health and total scores than other races. Adolescents had poorer total COHIP, social‐emotional well‐being, and self‐image scores.

Conclusion

Although most patients reported good or excellent oral health, adolescents reported a poorer OHRQoL than younger patients.
Navigating in an unpredictable daily life: a metasynthesis on children's experiences living with a parent with severe mental illness
Authors: Dam Kristianna , Hall Elisabeth O. C.
Published: January 2016

A large group of individuals suffering from mental illness are parents living with their children. These children are invisible in the health care even though at risk for illhealth. The aim of this metasynthesis was to advance knowledge of how children of parents with mental illness experience their lives, thus contributing to the evidence of this phenomenon. The metasynthesis is following Sandelowski and Barroso's guidelines. Literature searches covering the years 2000 to 2013 resulted in 22 reports which were synthesised into the theme ‘navigating in an unpredictable everyday life’ and the metaphor compass. Children of parents with mental illness irrespective of age are responsible, loving and worrying children who want to do everything to help and support. Children feel shame when the parent behaves differently, and they conceal their family life being afraid of stigmatisation and bullying. When their parent becomes ill, they distance to protect themselves. The children cope through information, knowledge, frankness and trustful relationships. These children need support from healthcare services because they subjugate own needs in favour of the parental needs, they should be encouraged to talk about their family situation, and especially, young children should to be child‐like, playing and seeing friends.
The tyrosine kinase inhibitor toceranib in feline injection site sarcoma: efficacy and side effects
Authors: Holtermann N. , Kiupel M. , Hirschberger J.
Published: January 2016

Because of their locally invasive growth and high recurrence rate despite of aggressive local therapy, treatment of feline sarcomas is challenging. The tyrosine kinase inhibitor (TKI) toceranib is currently licensed for the treatment of canine mast cell tumours. There are only few reports aboutTKIusage in cats. Previous studies indicated promising potential ofTKIfor the treatment of feline injection site sarcoma (FISS). In this prospective clinical trial, 18 cats with unresectableFISSwere treated at a target dosage of 3.25 mg kg−1every other day to evaluate the clinical efficacy and toxicity of toceranib. There was no clinical response measurable. Adverse events were generally mild and temporary. Grade 3 or 4 adverse events developed infrequently and all resolved with drug holidays and dose reductions.
FEASIBILITY FOR ULTRASOUND‐GUIDED INJECTION OF THE COLLATERAL LIGAMENTS OF THE DISTAL INTERPHALANGEAL JOINT IN HORSES
Authors: Lewis Danyse , Scott Mike , Fischer Carrie D. , Bond Stephanie L. , Léguillette Renaud
Published: January 2016

Desmitis of the collateral ligament of the distal interphalangeal joint is a cause of lameness in performance horses. The objective of this prospective, experimental, ex vivo feasibility study was to evaluate the success of ultrasound‐guided injection of the collateral ligaments of the distal interphalangeal joint in the equine forelimb. Seventy‐six ultrasound‐guided dye injections of the collateral ligament of the distal interphalangeal joint were performed on horses’ cadaver limbs. The hooves were sectioned transversely to verify the location of the dye relative to the collateral ligaments and surrounding structures. Evaluations of transverse sections were performed independently by two experienced observers. A scoring system was used to assess injection of the collateral ligament of the distal interphalangeal joint at the proximal, middle, and distal aspect over the length of the ligament. The collateral ligament was injected at any point in 97.4% of cases. The ligament was injected over the entire scored length in 43.2% of cases (32/74), over two scored length areas in 45.9% of cases (34/74), and in one area in 10.8% of cases (8/74). The distal interphalangeal joint and the common digital extensor tendon were also injected in 81.6% (62/76) and 43.4% (33/76) of the cases, respectively. Use of the ultrasound had a positive and negative predictive value of 98% and 9%, respectively. In this study, ultrasound guidance was useful for confirming injection of the collateral ligament of the distal interphalangeal joint but did not prevent injecting the distal interphalangeal joint and the common digital extensor tendon.
Stability and Performance Analysis of Time-Delayed Actuator Control Systems
Authors: Ai Bing , Sentis Luis , Paine Nicholas , Han Song , Mok Aloysius , Fok Chien-Liang
Published: January 2016

Time delay is a common phenomenon in robotic systems due to computational requirements and communication properties between or within high-level and low-level controllers as well as the physical constraints of the actuator and sensor. It is widely believed that delays are harmful for robotic systems in terms of stability and performance; however, we propose a different view that the time delay of the system may in some cases benefit system stability and performance. Therefore, in this paper, we discuss the influences of the displacement-feedback delay (single delay) and both displacement and velocity feedback delays (double delays) on robotic actuator systems by using the cluster treatment of characteristic roots (CTCR) methodology. Hence, we can ascertain the exact stability interval for single-delay systems and the rigorous stability region for double-delay systems. The influences of controller gains and the filtering frequency on the stability of the system are discussed. Based on the stability information coupled with the dominant root distribution, we propose one nonconventional rule which suggests increasing time delay to certain time windows to obtain the optimal system performance. The computation results are also verified on an actuator testbed.
Localization-in-noise and binaural medial olivocochlear functioning in children and young adults
Authors: Boothalingam Sriram , Macpherson Ewan , Allan Chris , Allen Prudence , Purcell David
Published: January 2016

Children as young as 5 yr old localize sounds as accurately as adults in quiet in the frontal hemifield. However, children's ability to localize in noise and in the front/back (F/B) dimension are scantily studied. To address this, the first part of this study investigated localization-in-noise ability of children vs young adults in two maskers: broadband noise (BBN) and speech-babble (SB) at three signal-to-noise ratios: −12, −6, and 0 dB. In the second part, relationship between binaural medial olivocochlear system (MOC) function and localization-in-noise was investigated. In both studies, 21 children and 21 young adults participated. Results indicate, while children are able to differentiate sounds arriving in the F/B dimension on par with adults in quiet and in BBN, larger differences were found for SB. Accuracy of children's localization in noise (for both maskers) in the lateral plane was also poorer than adults'. Significant differences in binaural MOC interaction (mBIC; the difference between the sum of two monaural- and binaural-MOC strength) between adults and children were also found. For reasons which are not clear, adult F/B localization in BBN correlates better with mBIC while children's F/B localization in SB correlated better with binaural MOC strength.
Enhancing Adoption of a Home-Based Exercise Program for Mild Balance Dysfunction: A Qualitative Study
Authors: Meyer Claudia , Williams Susan , Batchelor Frances , Hill Keith
Published: January 2016

Introduction:

The aim was to identify barriers and opportunities facing community health physiotherapists in delivering a home-based balance exercise program to address mild balance dysfunction and, secondly, to understand the perspectives of older people in adopting this program.

Method:

Focus groups, written surveys, and data recording sheets were used with nine older people and five physiotherapists. Focus groups were audio taped, transcribed, and coded independently by two researchers.

Results:

Thematic content analysis was undertaken. Emerging themes were: engaging in preventive health (various benefits, enhancing independence); adoption of strategies (acceptable design and implementation feasibility); exercising in context (convenience, practicality, and safety); and broader implementation issues (program design, proactive health messages, and a solid evidence base).

Conclusion:

The views of older people and physiotherapists were sought to understand the adoption of a previously successful home-based program for mild balance dysfunction. Understanding the unique context and circumstances for individuals and organizations will enhance adoption.
Exercise Impacts Age-Related Changes in Cognitive Function and Neural Complexity
Authors: Heisz Jennifer J. , Kovacevic Ana
Published: January 2016

Age-related changes in the brain can compromise cognitive function. However, in some cases, the brain is able to functionally reorganize to compensate for some of this loss. The present paper reviews the benefits of exercise on executive functions in older adults and discusses a potential mechanism through which exercise may change the way the brain processes information for better cognitive outcomes. Specifically, older adults who are more physically active demonstrate a shift toward local neural processing that is associated with better executive functions. We discuss the use of neural complexity as a sensitive measure of the neural network plasticity that is enhanced through exercise. We conclude by highlighting the future work needed to improve exercise prescriptions that help older adults maintain their cognitive and physical functions for longer into their lifespan.
Personalized medical education: Reappraising clinician-scientist training
Authors: DeLuca Gabriele C. , Ovseiko Pavel V. , Buchan Alastair M.
Published: January 2016

Revitalizing the Oslerian ideal of the clinician-scientist-teacher may help in the training of the next generation of translational researchers.
Correlates of Protection against Influenza in the Elderly: Results from an Influenza Vaccine Efficacy Trial
Authors: Dunning Andrew J. , DiazGranados Carlos A. , Voloshen Timothy , Hu Branda , Landolfi Victoria A. , Talbot H. Keipp
Published: January 2016

Although a number of studies have investigated and quantified immune correlates of protection against influenza in adults and children, data on immune protection in the elderly are sparse. A recent vaccine efficacy trial comparing standard-dose with high-dose inactivated influenza vaccine in persons 65 years of age and older provided the opportunity to examine the relationship between values of three immunologic assays and protection against community-acquired A/H3N2 influenza illness. The high-dose vaccine induced significantly higher antibody titers than the standard-dose vaccine for all assays. For the hemagglutination inhibition assay, a titer of 40 was found to correspond with 50% protection when the assay virus was antigenically well matched to the circulating virus—the same titer as is generally recognized for 50% protection in younger adults. A dramatically higher titer was required for 50% protection when the assay virus was a poor match to the circulating virus. With the well-matched virus, some protection was seen at the lowest titers; with the poorly matched virus, high levels of protection were not achieved even at the highest titers. Strong associations were also seen between virus neutralization test titers and protection, but reliable estimates for 50% protection were not obtained. An association was seen between titers of an enzyme-linked lectin assay for antineuraminidase N2 antibodies and protection; in particular, the proportion of treatment effect explained by assay titer in models that included both this assay and one of the other assays was consistently higher than in models that included either assay alone. (This study has been registered at ClinicalTrials.gov under registration no. NCT01427309.)
Rapid Detection of Vancomycin-Intermediate Staphylococcus aureus by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Mather Cheryl A. , Werth Brian J. , Sivagnanam Shobini , SenGupta Dhruba J. , Butler-Wu Susan M.
Published: January 2016

Vancomycin is the standard of care for the treatment of invasive methicillin-resistant
Staphylococcus aureus
(MRSA) infections. Infections with vancomycin-nonsusceptible MRSA, including vancomycin-intermediate
S. aureus
(VISA) and heterogeneous VISA (hVISA), are clinically challenging and are associated with poor patient outcomes. The identification of VISA in the clinical laboratory depends on standard susceptibility testing, which takes at least 24 h to complete after isolate subculture, whereas hVISA is not routinely detected in clinical labs. We therefore sought to determine whether VISA and hVISA can be differentiated from vancomycin-susceptible
S. aureus
(VSSA) using the spectra produced by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). Strains of MRSA were characterized for vancomycin susceptibility phenotype by broth microdilution and modified population analysis. We tested 21 VISA, 21 hVISA, and 38 VSSA isolates by MALDI-TOF MS. Susceptibility phenotypes were separated by using a support vector machine (SVM) machine learning algorithm. The resulting model was validated by leave-one-out cross validation. Models were developed and validated by using spectral profiles generated under various subculture conditions, as well as with and without hVISA strains. Using SVM, we correctly identified 100% of the VISA and 97% of the VSSA isolates with an overall classification accuracy of 98%. Addition of hVISA to the model resulted in 76% hVISA identification, 100% VISA identification, and 89% VSSA identification, for an overall classification accuracy of 89%. We conclude that VISA/hVISA and VSSA isolates are separable by MALDI-TOF MS with SVM analysis.
Gyrase Mutations Are Associated with Variable Levels of Fluoroquinolone Resistance in Mycobacterium tuberculosis
Authors: Farhat Maha R. , Jacobson Karen R. , Franke Molly F. , Kaur Devinder , Sloutsky Alex , Mitnick Carole D. , Murray Megan
Published: January 2016

Molecular diagnostics that rapidly and accurately predict resistance to fluoroquinolone drugs and especially later-generation agents promise to improve treatment outcomes for patients with multidrug-resistant tuberculosis and prevent the spread of disease. Mutations in the
gyr
genes are known to confer most fluoroquinolone resistance, but knowledge about the effects of
gyr
mutations on susceptibility to early- versus later-generation fluoroquinolones and about the role of mutation-mutation interactions is limited. Here, we sequenced the full
gyrA
and
gyrB
open reading frames in 240 multidrug-resistant and extensively drug-resistant tuberculosis strains and quantified their ofloxacin and moxifloxacin MIC by testing growth at six concentrations for each drug. We constructed a multivariate regression model to assess both the individual mutation effects and interactions on the drug MICs. We found that
gyrB
mutations contribute to fluoroquinolone resistance both individually and through interactions with
gyrA
mutations. These effects were statistically significant. In these clinical isolates, several
gyrA
and
gyrB
mutations conferred different levels of resistance to ofloxacin and moxifloxacin. Consideration of
gyr
mutation combinations during the interpretation of molecular test results may improve the accuracy of predicting the fluoroquinolone resistance phenotype. Further, the differential effects of
gyr
mutations on the activity of early- and later-generation fluoroquinolones requires further investigation and could inform the selection of a fluoroquinolone for treatment.
Evaluation of a New Device for Simplifying and Standardizing Stool Sample Preparation for Viral Molecular Testing with Limited Hands-On Time
Authors: Feghoul Linda , Salmona Maud , Cherot Janine , Fahd Mony , Dalle Jean-Hugues , Vachon Carole , Perrod Aurélie , Bourgeois Philippe , Scieux Catherine , Baruchel André , Simon François , LeGoff Jérôme
Published: January 2016

Sensitive molecular assays have greatly improved the diagnosis of viral gastroenteritis. However, the proper preparation of stool samples for clinical testing remains an issue. bioMérieux has developed a stool preprocessing device (SPD) that includes a spoon for calibrated sampling and a vial containing buffer, glass beads, and two filters. The resulting stool filtrate is used for nucleic acid extraction. The purpose of this study was to evaluate the performance of the SPD for the quantification of human adenovirus (HAdV) DNA in stool samples collected from hematopoietic stem cell transplant (HSCT) recipients. HAdV DNA was quantified with the Adenovirus R-gene kit. The suitability of the device to reproducibly quantify HAdV DNA in stools using different extraction platforms (easyMAG and QIAsymphony) was determined using archived HAdV-positive stool samples. Coefficients of variation of HAdV DNA quantifications ranged from 1.79% to 1.83%, and no difference in quantification was observed between the two extraction systems. The HAdV DNA limit of quantification using the SPD was 3.75 log
10
copies/g of stool. HAdV DNA quantification using the SPD was then compared to that of the routine preprocessing technique on 75 fresh stool samples collected prospectively from pediatric HSCT recipients at risk for HAdV infections. Thirty-eight samples were HAdV DNA positive with both the SPD and routine preprocessing methods. HAdV DNA loads were on average 1.14-log
10
copies/g of stool higher with the SPD (
P
< 0.0001) than with routine methods. This new device enabled a standardized preparation of stool samples in <5 min and a reproducible and sensitive quantification of HAdV DNA. The use of the SPD for the detection of other gastrointestinal infections warrants further evaluation.
Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples
Authors: Budding Andries E. , Hoogewerf Martine , Vandenbroucke-Grauls Christina M. J. E. , Savelkoul Paul H. M.
Published: January 2016

Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice.
Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing
Authors: Hasan Mohammad R. , Rawat Arun , Tang Patrick , Jithesh Puthen V. , Thomas Eva , Tan Rusung , Tilley Peter
Published: January 2016

Next-generation sequencing (NGS) technology has shown promise for the detection of human pathogens from clinical samples. However, one of the major obstacles to the use of NGS in diagnostic microbiology is the low ratio of pathogen DNA to human DNA in most clinical specimens. In this study, we aimed to develop a specimen-processing protocol to remove human DNA and enrich specimens for bacterial and viral DNA for shotgun metagenomic sequencing. Cerebrospinal fluid (CSF) and nasopharyngeal aspirate (NPA) specimens, spiked with control bacterial and viral pathogens, were processed using either a commercially available kit (MolYsis) or various detergents followed by DNase prior to the extraction of DNA. Relative quantities of human DNA and pathogen DNA were determined by real-time PCR. The MolYsis kit did not improve the pathogen-to-human DNA ratio, but significant reductions (>95%;
P
< 0.001) in human DNA with minimal effect on pathogen DNA were achieved in samples that were treated with 0.025% saponin, a nonionic surfactant. Specimen preprocessing significantly decreased NGS reads mapped to the human genome (
P
< 0.05) and improved the sensitivity of pathogen detection (
P
< 0.01), with a 20- to 650-fold increase in the ratio of microbial reads to human reads. Preprocessing also permitted the detection of pathogens that were undetectable in the unprocessed samples. Our results demonstrate a simple method for the reduction of background human DNA for metagenomic detection for a broad range of pathogens in clinical samples.
Detection and Prevalence of Penicillin-Susceptible Staphylococcus aureus in the United States in 2013
Authors: Richter S. S. , Doern G. V. , Heilmann K. P. , Miner S. , Tendolkar S. , Riahi F. , Diekema D. J.
Published: January 2016

Using
blaZ
PCR as the “gold standard,” the sensitivities of CLSI penicillin zone edge and nitrocefin-based tests for β-lactamase production in
Staphylococcus aureus
were 64.5% and 35.5%, respectively, with specificity of 99.8% for both methods. In 2013, 13.5% of 3,083
S. aureus
isolates from 31 U.S. centers were penicillin susceptible.
Morphological, Biochemical, and Functional Study of Viral Replication Compartments Isolated from Adenovirus-Infected Cells
Authors: Hidalgo Paloma , Anzures Lourdes , Hernández-Mendoza Armando , Guerrero Adán , Wood Christopher D. , Valdés Margarita , Dobner Thomas , Gonzalez Ramón A.
Published: January 2016

Adenovirus (Ad) replication compartments (RC) are nuclear microenvironments where the viral genome is replicated and a coordinated program of late gene expression is established. These virus-induced nuclear sites seem to behave as central hubs for the regulation of virus-host cell interactions, since proteins that promote efficient viral replication as well as factors that participate in the antiviral response are coopted and concentrated there. To gain further insight into the activities of viral RC, here we report, for the first time, the morphology, composition, and activities of RC isolated from Ad-infected cells. Morphological analyses of isolated RC particles by superresolution microscopy showed that they were indistinguishable from RC within infected cells and that they displayed a dynamic compartmentalization. Furthermore, the RC-containing fractions (RCf) proved to be functional, as they directed
de novo
synthesis of viral DNA and RNA as well as RNA splicing, activities that are associated with RC
in vivo
. A detailed analysis of the production of viral late mRNA from RCf at different times postinfection revealed that viral mRNA splicing occurs in RC and that the synthesis, posttranscriptional processing, and release from RC to the nucleoplasm of individual viral late transcripts are spatiotemporally separate events. The results presented here demonstrate that RCf are a powerful system for detailed study into RC structure, composition, and activities and, as a result, the determination of the molecular mechanisms that induce the formation of these viral sites of adenoviruses and other nuclear-replicating viruses.

IMPORTANCE
RC may represent molecular hubs where many aspects of virus-host cell interaction are controlled. Here, we show by superresolution microscopy that RCf have morphologies similar to those of RC within Ad-infected cells and that they appear to be compartmentalized, as nucleolin and DBP display different localization in the periphery of these viral sites. RCf proved to be functional, as they direct
de novo
synthesis of viral DNA and mRNA, allowing the detailed study of the regulation of viral genome replication and expression. Furthermore, we show that the synthesis and splicing of individual viral late mRNA occurs in RC and that they are subject to different temporal patterns of regulation, from their synthesis to their splicing and release from RC to the nucleoplasm. Hence, RCf represent a novel system to study molecular mechanisms that are orchestrated in viral RC to take control of the infected cell and promote an efficient viral replication cycle.
Equine Arteritis Virus Uses Equine CXCL16 as an Entry Receptor
Authors: Sarkar Sanjay , Chelvarajan Lakshman , Go Yun Young , Cook Frank , Artiushin Sergey , Mondal Shankar , Anderson Kelsi , Eberth John , Timoney Peter J. , Kalbfleisch Theodore S. , Bailey Ernest , Balasuriya Udeni B. R.
Published: January 2016

Previous studies in our laboratory have identified equine CXCL16 (EqCXCL16) to be a candidate molecule and possible cell entry receptor for equine arteritis virus (EAV). In horses, the CXCL16 gene is located on equine chromosome 11 (ECA11) and encodes a glycosylated, type I transmembrane protein with 247 amino acids. Stable transfection of HEK-293T cells with plasmid DNA carrying EqCXCL16 (HEK-EqCXCL16 cells) increased the proportion of the cell population permissive to EAV infection from <3% to almost 100%. The increase in permissiveness was blocked either by transfection of HEK-EqCXCL16 cells with small interfering RNAs (siRNAs) directed against EqCXCL16 or by pretreatment with guinea pig polyclonal antibody against EqCXCL16 protein (Gp anti-EqCXCL16 pAb). Furthermore, using a virus overlay protein-binding assay (VOPBA) in combination with far-Western blotting, gradient-purified EAV particles were shown to bind directly to the EqCXCL16 proteinin vitro. The binding of biotinylated virulent EAV strain Bucyrus at 4°C was significantly higher in HEK-EqCXCL16 cells than nontransfected HEK-293T cells. Finally, the results demonstrated that EAV preferentially infects subpopulations of horse CD14+monocytes expressing EqCXCL16 and that infection of these cells is significantly reduced by pretreatment with Gp anti-EqCXCL16 pAb. The collective data from this study provide confirmatory evidence that the transmembrane form of EqCXCL16 likely plays a major role in EAV host cell entry processes, possibly acting as a primary receptor molecule for this virus.

IMPORTANCEOutbreaks of EVA can be a source of significant economic loss for the equine industry from high rates of abortion in pregnant mares, death in young foals, establishment of the carrier state in stallions, and trade restrictions imposed by various countries. Similar to other arteriviruses, EAV primarily targets cells of the monocyte/macrophage lineage, which, when infected, are believed to play a critical role in EVA pathogenesis. To this point, however, the host-specified molecules involved in EAV binding and entry into monocytes/macrophages have not been identified. Identification of the cellular receptors for EAV may provide insights to design antivirals and better prophylactic reagents. In this study, we have demonstrated that EqCXCL16 acts as an EAV entry receptor in EAV-susceptible cells, equine monocytes. These findings represent a significant advance in our understanding of the fundamental mechanisms associated with the entry of EAV into susceptible cells.