bluuebunny/crossref_metadata_2025 huggingface dataset:
Introductions and Evolution of Human-Origin Seasonal Influenza A Viruses in Multinational Swine Populations
Authors: Nelson Martha I. , Wentworth David E. , Culhane Marie R. , Vincent Amy L. , Viboud Cecile , LaPointe Matthew P. , Lin Xudong , Holmes Edward C. , Detmer Susan E.
Published: June 2014

The capacity of influenza A viruses to cross species barriers presents a continual threat to human and animal health. Knowledge of the human-swine interface is particularly important for understanding how viruses with pandemic potential evolve in swine hosts. We sequenced the genomes of 141 influenza viruses collected from North American swine during 2002 to 2011 and identified a swine virus that possessed all eight genome segments of human seasonal A/H3N2 virus origin. A molecular clock analysis indicates that this virus—A/sw/Saskatchewan/02903/2009(H3N2)—has likely circulated undetected in swine for at least 7 years. For historical context, we performed a comprehensive phylogenetic analysis of an additional 1,404 whole-genome sequences from swine influenza A viruses collected globally during 1931 to 2013. Human-to-swine transmission occurred frequently over this time period, with 20 discrete introductions of human seasonal influenza A viruses showing sustained onward transmission in swine for at least 1 year since 1965. Notably, human-origin hemagglutinin (H1 and H3) and neuraminidase (particularly N2) segments were detected in swine at a much higher rate than the six internal gene segments, suggesting an association between the acquisition of swine-origin internal genes via reassortment and the adaptation of human influenza viruses to new swine hosts. Further understanding of the fitness constraints on the adaptation of human viruses to swine, and vice versa, at a genomic level is central to understanding the complex multihost ecology of influenza and the disease threats that swine and humans pose to each other.

IMPORTANCE
The swine origin of the 2009 A/H1N1 pandemic virus underscored the importance of understanding how influenza A virus evolves in these animals hosts. While the importance of reassortment in generating genetically diverse influenza viruses in swine is well documented, the role of human-to-swine transmission has not been as intensively studied. Through a large-scale sequencing effort, we identified a novel influenza virus of wholly human origin that has been circulating undetected in swine for at least 7 years. In addition, we demonstrate that human-to-swine transmission has occurred frequently on a global scale over the past decades but that there is little persistence of human virus internal gene segments in swine.
Modulation of CD163 Expression by Metalloprotease ADAM17 Regulates Porcine Reproductive and Respiratory Syndrome Virus Entry
Authors: Guo Longjun , Niu Junwei , Yu Haidong , Gu Weihong , Li Ren , Luo Xiaolei , Huang Mingming , Tian Zhijun , Feng Li , Wang Yue
Published: June 2014

As a consequence of their effects on ectodomain shedding, members of the A disintegrin and metalloprotease (ADAM) family have been implicated in the control of various cellular processes. Although ADAM family members are also involved in cancer, inflammation, and other pathologies, it is unclear whether they affect porcine reproductive and respiratory syndrome virus (PRRSV) infection. Here, we demonstrate for the first time that inhibition of ADAM17 enhances PRRSV entry in Marc-145 and porcine alveolar macrophages (PAMs). We also demonstrate that the inhibition of ADAM17 upregulates membrane CD163 expression, a putative PRRSV receptor that is exogenously expressed in BHK-21 and endogenously expressed in Marc-145 and PAMs. Furthermore, overexpression of ADAM17 induced downregulation of CD163 expression and a reduction in PRRSV infection, whereas ablation of ADAM17 expression using specific small interfering RNA resulted in upregulation of CD163 expression with a corresponding increase in PRRSV infection. These ADAM17-mediated effects were confirmed with PRRSV nonpermissive BHK-21 cells transfected with CD163 cDNA. Overall, these findings indicate that ADAM17 downregulates CD163 expression and hinders PRRSV entry. Hence, downregulation of ADAM17 particular substrates may be an additional component of the anti-infection defenses.

IMPORTANCEADAM17 is one of the important membrane-associated metalloproteases that mediate various cellular events, as well as inflammation, cancer, and other pathologies. Here, we investigate for the first time the role of the metalloprotease ADAM17 in PRRSV infection. By using inhibitor and genetic modification methods, we demonstrate that ADAM17 negatively regulate PRRSV entry by regulating its substrate(s). More specifically, ADAM 17 mediates the downregulation of the PRRSV cellular receptor CD163. The reduction in CD163 expression represents another component of the anti-infection response initiated by ADAM17.
Impact of Distinct Poxvirus Infections on the Specificities and Functionalities of CD4+T Cell Responses
Authors: Siciliano Nicholas A. , Hersperger Adam R. , Lacuanan Aimee M. , Xu Ren-Huan , Sidney John , Sette Alessandro , Sigal Luis J. , Eisenlohr Laurence C.
Published: June 2014

The factors that determine CD4+T cell (TCD4+) specificities, functional capacity, and memory persistence in response to complex pathogens remain unclear. We explored these parameters in the C57BL/6 mouse through comparison of two highly related (>92% homology) poxviruses: ectromelia virus (ECTV), a natural mouse pathogen, and vaccinia virus (VACV), a heterologous virus that nevertheless elicits potent immune responses. In addition to elucidating several previously unidentified major histocompatibility complex class II (MHC-II)-restricted epitopes, we observed many qualitative and quantitative differences between the TCD4+repertoires, including responses not elicited by VACV despite complete sequence conservation. In addition, we observed functional heterogeneity between ECTV- and VACV-specific TCD4+at both a global and individual epitope level, particularly greater expression of the cytolytic marker CD107a from TCD4+following ECTV infection. Most striking were differences during the late memory phase where, in contrast to ECTV, VACV infection failed to elicit measurable epitope-specific TCD4+as determined by intracellular cytokine staining. These findings illustrate the strong influence of epitope-extrinsic factors on TCD4+responses and memory.

IMPORTANCEMuch of our understanding concerning host-pathogen relationships in the context of poxvirus infections stems from studies of VACV in mice. However, VACV is not a natural mouse pathogen, and therefore, the relevance of results obtained using this model may be limited. Here, we explored the MHC class II-restricted TCD4+repertoire induced by mousepox (ECTV) infection and the functional profile of the responding epitope-specific TCD4+, comparing these results to those induced by VACV infection under matched conditions. Despite a high degree of homology between the two viruses, we observed distinct specificity and functional profiles of TCD4+responses at both acute and memory time points, with VACV-specific TCD4+memory being notably compromised. These data offer insight into the impact of epitope-extrinsic factors on the resulting TCD4+responses.
Structure of 2G12 Fab
2
in Complex with Soluble and Fully Glycosylated HIV-1 Env by Negative-Stain Single-Particle Electron Microscopy
Authors: Murin Charles D. , Julien Jean-Philippe , Sok Devin , Stanfield Robyn L. , Khayat Reza , Cupo Albert , Moore John P. , Burton Dennis R. , Wilson Ian A. , Ward Andrew B.
Published: June 2014

The neutralizing anti-HIV-1 antibody 2G12 is of particular interest due to the sterilizing protection it provides from viral challenge in animal models. 2G12 is a unique, domain-exchanged antibody that binds exclusively to conserved N-linked glycans that form the high-mannose patch on the gp120 outer domain centered on a glycan at position N332. Several glycans in and around the 2G12 epitope have been shown to interact with other potent, broadly neutralizing antibodies; therefore, this region constitutes a supersite of vulnerability on gp120. While crystal structures of 2G12 and 2G12 bound to high-mannose glycans have been solved, no structural information that describes the interaction of 2G12 with gp120 or the Env trimer is available. Here, we present a negative-stain single-particle electron microscopy reconstruction of 2G12 Fab
2
in complex with a soluble, trimeric Env at ∼17-Å resolution that reveals the antibody's interaction with its native and fully glycosylated epitope. We also mapped relevant glycans in this epitope by fitting high-resolution crystal structures and by performing neutralization assays of glycan knockouts. In addition, a reconstruction at ∼26 Å of the ternary complex formed by 2G12 Fab
2
, soluble CD4, and Env indicates that 2G12 may block membrane fusion by induced steric hindrance upon primary receptor binding, thereby abrogating Env's interaction with coreceptor(s). These structures provide a basis for understanding 2G12 binding and neutralization, and our low-resolution model and glycan assignments provide a basis for higher-resolution studies to determine the molecular nature of the 2G12 epitope.

IMPORTANCE
HIV-1 is a human virus that results in the deaths of millions of people around the world each year. While there are several effective therapeutics available to prolong life, a vaccine is the best long-term solution for curbing this global epidemic. Here, we present structural data that reveal the viral binding site of one of the first HIV-1-neutralizing antibodies isolated, 2G12, and provide a rationale for its effectiveness. These structures provide a basis for higher-resolution studies to determine the molecular nature of the 2G12 epitope, which will aid in vaccine design and antibody-based therapies.
Development of Giant Bacteriophage ϕKZ Is Independent of the Host Transcription Apparatus
Authors: Ceyssens Pieter-Jan , Minakhin Leonid , Van den Bossche An , Yakunina Maria , Klimuk Evgeny , Blasdel Bob , De Smet Jeroen , Noben Jean-Paul , Bläsi Udo , Severinov Konstantin , Lavigne Rob
Published: June 2014

Pseudomonas aeruginosa
bacteriophage ϕKZ is the type representative of the giant phage genus, which is characterized by unusually large virions and genomes. By unraveling the transcriptional map of the ∼280-kb ϕKZ genome to single-nucleotide resolution, we combine 369 ϕKZ genes into 134 operons. Early transcription is initiated from highly conserved AT-rich promoters distributed across the ϕKZ genome and located on the same strand of the genome. Early transcription does not require phage or host protein synthesis. Transcription of middle and late genes is dependent on protein synthesis and mediated by poorly conserved middle and late promoters. Unique to ϕKZ is its ability to complete its infection in the absence of bacterial RNA polymerase (RNAP) enzyme activity. We propose that transcription of the ϕKZ genome is performed by the consecutive action of two ϕKZ-encoded, noncanonical multisubunit RNAPs, one of which is packed within the virion, another being the product of early genes. This unique, rifampin-resistant transcriptional machinery is conserved within the diverse giant phage genus.

IMPORTANCE
The data presented in this paper offer, for the first time, insight into the complex transcriptional scheme of giant bacteriophages. We show that
Pseudomonas aeruginosa
giant phage ϕKZ is able to infect and lyse its host cell and produce phage progeny in the absence of functional bacterial transcriptional machinery. This unique property can be attributed to two phage-encoded putative RNAP enzymes, which contain very distant homologues of bacterial β and β′-like RNAP subunits.
Comparison of Effects of Inhibitors of Viral and Cellular Protein Kinases on Human Cytomegalovirus Disruption of Nuclear Lamina and Nuclear Egress
Authors: Sharma Mayuri , Coen Donald M.
Published: June 2014

Human cytomegalovirus (HCMV) kinase UL97 is required for efficient nuclear lamina disruption during nuclear egress. However, cellular protein kinase C (PKC) has been implicated in this process in other systems. Comparing the effects of UL97 and cellular kinase inhibitors on HCMV nuclear egress confirms a role for UL97 in lamina disruption and nuclear egress. A pan-PKC inhibitor did not affect lamina disruption but did reduce the number of cytoplasmic capsids more than the number of nuclear capsids.
Structure of the Herpes Simplex Virus 1 Genome: Manipulation of Nicks and Gaps Can Abrogate Infectivity and Alter the Cellular DNA Damage Response
Authors: Smith Samantha , Reuven Nina , Mohni Kareem N. , Schumacher April J. , Weller Sandra K.
Published: June 2014

The herpes simplex virus 1 (HSV-1) virion DNA contains nicks and gaps, and in this study a novel assay for estimating the size and number of gaps in virion DNA was developed. Consistent with previous reports, we estimate that there are approximately 15 gaps per genome, and we calculate the average gap length to be approximately 30 bases. Virion DNA was isolated and treated with DNA-modifying enzymes in order to fill in the gaps and modify the ends. Interestingly, filling in gaps, blunting the ends, or adding random sequences to the 3′ ends of DNA, producing 3′ flaps, did not impair the infectivity of treated DNA following transfection of Vero cells. On the other hand, the formation of 5′ flaps in the DNA following treatment resulted in a dramatic reduction (95 to 100%) in infectivity. Virion DNA stimulated DNA-PKcs activity in transfected cells, and DNA with 5′ flaps stimulated a higher level of DNA-PKcs activity than that observed in cells transfected with untreated virion DNA. The infectivity of 5′-flapped DNA was restored in cells that do not express DNA-PKcs and in cells cotransfected with the immediate early protein ICP0, which degrades DNA-PKcs. These results are consistent with previous reports that DNA-dependent protein kinase (DNA-PK) and the nonhomologous end joining (NHEJ) repair pathway are intrinsically antiviral and that ICP0 can counteract this effect. We suggest that HSV-1 DNA with 5′ flaps may induce an antiviral state due to the induction of a DNA damage response, primarily mediated by NHEJ, that renders the HSV-1 genome less efficient for lytic infection.

IMPORTANCE
For productive lytic infection to occur, HSV-1 must counteract a variety of cellular intrinsic antiviral mechanisms, including the DNA damage response (DDR). DDR pathways have been associated with silencing of gene expression, cell cycle arrest, and induction of apoptosis. In addition, the fate of viral genomes is likely to play a role in whether viral genomes adopt a configuration suitable for lytic DNA replication. This study demonstrates that virion DNA activates the cellular DDR kinase, DNA-PK, and that this response is inhibitory to viral infection. Furthermore, we show that HSV-1 ubiquitin ligase, ICP0, plays an important role in counteracting the negative effects of DNA-PK activation. These findings support the notion that DNA-PK is antiviral and suggest that the fate of incoming viral DNA has important consequences for the progression of lytic infection. This study underscores the complex evolutionary relationships between HSV and its host.
Laparoscopic management of midgut malrotation and tuberculous peritonitis in an adolescent boy
Authors: Patel Ramnik V , Jackson Paul , Zani Augusto , De Coppi Paolo
Published: June 2014

An unusual case of miliary plastic peritonitis associated with midgut malrotation in an adolescent in whom various diagnostic investigations, medical management and staged initial laparoscopic diagnostic followed by therapeutic procedure was curative have been presented. Tuberculous miliary plastic peritonitis causes dense adhesions between bowel loops and prevents midgut volvulus in a pre-existing malrotation. Diagnosis can be a challenge and threshold for diagnostic laparoscopy should be low. Interval correction of malrotation by laparoscopy after complete resolution of tuberculosis is easy, safe and effective, and cosmetically more pleasing. Midgut malrotation is a congenital anomaly referring to either lack of or incomplete rotation of fetal axis around the axis of superior mesenteric artery during fetal development. Most patients present with bilious vomiting in the first month of life because of duodenal obstruction or a volvulus. This is an unusual case of midgut malrotation in association with tuberculous peritonitis in an adolescent boy.
Oral neurovascular hamartoma: an extraordinary verdict in the oral cavity
Authors: Junaid Montasir , Ahmed Sadaf Qadeer , Kazi Maliha , Haroon Saroona
Published: June 2014

The presence of a neurovascular hamartoma within the oral cavity is truly a rare entity. Scarcely reported in the literature, these hamartomas are smooth, pinkish masses and are painless, and therefore difficult to diagnose. They are benign in nature and apply pressure to their surroundings. The histological diagnosis remains the gold standard as it comprises of neural tissue and vascular components. Treatment is surgical excision with adequate margins. Recurrence is reported in cases of incomplete resection.
Isolated unilateral idiopathic transient hypoglossal nerve palsy
Authors: Ahmed Syed Viqar , Akram Muhammad Saqub
Published: June 2014

A 52-year-old Caucasian man presented with sudden onset of difficulty in moving his tongue to the left with preceding left-sided headache with no neck pain. Earlier, he had self-limiting chest infection without rashes or tonsillar enlargement. His medical and surgical history was unremarkable with no recent trauma. Oral examination revealed difficulty in protruding his tongue to the left with muscle bulk loss and fasciculation on the same side, suggesting left hypoglossal nerve palsy. Examination of the rest of the cranial nerves and nervous system was normal. The patient's oropharyngeal and laryngeal examination was unremarkable with no cervical lymphadenopathy. He had normal laboratory investigations and cerebrospinal fluid examination. Extensive imaging of the head, neck and chest failed to reveal any pathology. Further review by an otorhinologist and rheumatologist ruled out any other underlying pathology. He made a good recovery without treatment. English literature search revealed very few cases of idiopathic, transient, unilateral hypoglossal nerve palsy.
Leadership and management in the undergraduate medical curriculum: a qualitative study of students’ attitudes and opinions at one UK medical school
Authors: Quince Thelma , Abbas Mark , Murugesu Sughashini , Crawley Francesca , Hyde Sarah , Wood Diana , Benson John
Published: June 2014

Objective

To explore undergraduate medical students’ attitudes towards and opinions about leadership and management education.

Design

Between 2009 and 2012 we conducted a qualitative study comprising five focus group discussions, each devoted to one of the five domains in the Medical Leadership Competency Framework, (Personal Qualities, Working with Others, Managing Services, Improving Services and Setting Direction). Each discussion examined what should be learnt, when should learning occur, what methods should be used, how should learning be assessed, what are the barriers to such education.

Participants

28 students from all three clinical years (4–6) of whom 10 were women.

Results

2 inter-related themes emerged: understanding the broad perspective of patients and other stakeholders involved in healthcare provision and the need to make leadership and management education relevant in the clinical context. Topics suggested by students included structure of the National Health Service (NHS), team working skills, decision-making and negotiating skills. Patient safety was seen as particularly important. Students preferred experiential learning, with placements seen as providing teaching opportunities. Structured observation, reflection, critical appraisal and analysis of mistakes at all levels were mentioned as existing opportunities for integrating leadership and management education. Students’ views about assessment and timing of such education were mixed. Student feedback figured prominently as a method of delivery and a means of assessment, while attitudes of medical professionals, students and of society in general were seen as barriers.

Conclusions

Medical students may be more open to leadership and management education than thought hitherto. These findings offer insights into how students view possible developments in leadership and management education and stress the importance of developing broad perspectives and clinical relevance in this context.
A health economic model for the development and evaluation of innovations in aged care: an application to consumer-directed care—study protocol
Authors: Ratcliffe Julie , Lancsar Emily , Luszcz Mary , Crotty Maria , Gray Len , Paterson Jan , Cameron Ian D
Published: June 2014

Introduction

Consumer-directed care is currently being embraced within Australia and internationally as a means of promoting autonomy and choice in the delivery of health and aged care services. Despite its wide proliferation little research has been conducted to date to assess the views and preferences of older people for consumer-directed care or to assess the costs and benefits of such an approach relative to existing models of service delivery.

Methods and analysis

A comprehensive health economic model will be developed and applied to the evolution, implementation and evaluation of consumer-directed care in an Australian community aged care setting. A mixed methods approach comprising qualitative interviews and a discrete choice experiment will determine the attitudes and preferences of older people and their informal carers for consumer-directed care. The results of the qualitative interviews and the discrete choice experiment will inform the introduction of a new consumer-directed care innovation in service delivery. The cost-effectiveness of consumer-directed care will be evaluated by comparing incremental changes in resource use, costs and health and quality of life outcomes relative to traditional services. The discrete choice experiment will be repeated at the end of the implementation period to determine the extent to which attitudes and preferences change as a consequence of experience of consumer-directed care. The proposed framework will have wide applicability in the future development and economic evaluation of new innovations across the health and aged care sectors.

Ethics and dissemination

The study is approved by Flinders University Social and Behavioural Research Ethics Committee (Project No. 6114/SBREC). Findings from the qualitative interviews, discrete choice experiments and the economic evaluation will be reported at a workshop of stakeholders to be held in 2015 and will be documented in reports and in peer reviewed journal articles.
Customising turnaround time indicators to requesting clinician: a 10-year study through balanced scorecard indicators
Authors: Salinas Maria , López-Garrigós Maite , Santo-Quiles Ana , Gutierrez Mercedes , Lugo Javier , Lillo Rosa , Leiva-Salinas Carlos
Published: June 2014

Aim

The purpose of this study is, first to present a 10-year monitoring of postanalytical turnaround time (TAT) adapted to different clinicians and patient situations, second to evaluate and analyse the indicators results during that period of time, and finally to show a synthetic appropriate indicator to be included in the balanced scorecard management system.

Methods

TAT indicator for routine samples was devised as the percentage of certain key tests that were verified before a specific time on the phlebotomy day. A weighted mean synthetic indicator was also designed. They were calculated for inpatients at 15:00 and 12:00 and for primary care patients only at 15:00. The troponin TAT of emergency department patients, calculated as the difference between the troponin verification and registration time, was selected as the stat laboratory TAT indicator.

Results

The routine and stat TAT improved along the 10-year study period. The synthetic indicator showed the same trend.

Conclusions

The implementation of systematic and continuous monitoring over years, promoted a continuous improvement in TAT which will probably benefit patient outcome and safety.
Imaging of degenerative lumbar intervertebral discs; linking anatomy, pathology and imaging
Authors: Adams Ashok , Roche Oran , Mazumder Asif , Davagnanam Indran , Mankad Kshitij
Published: June 2014

Low back pain is a common medical condition that has significant implications for healthcare providers and the UK economy. Low back pain can be classified as ‘specific’ in which an underlying pathophysiological mechanism is identified (eg, herniated intervertebral disc). Advanced imaging should be performed in this situation and in those patients in whom systemic disease is strongly suspected. In the majority (approximately 90%), low back pain in ‘non specific’ and there is a weak correlation with imaging abnormalities. This is an area of ongoing research and remains controversial in terms of imaging approach and treatment (eg, theory of discogenic pain, interpretation and treatment of endplate changes). With regards Modic endplate changes, current research suggests that an infective component may be involved that may identify novel potential treatments in patients with chronic low back pain refractory to other treatment modalities. MRI is the imaging modality of choice for the assessment of degenerative changes in intervertebral discs. MRI has superior soft tissue contrast resolution when compared to other imaging modalities (eg, plain radiography, CT). An understanding of normal anatomy and MR appearances of intervertebral discs, particularly with regards to how these appearances change with advancing age, is required to aid image interpretation. Knowledge of the spectrum of degenerative processes that may occur in the intervertebral discs is required in order to identify and explain abnormal MRI appearances. As the communication of MRI findings may guide therapeutic decision making and surgical intervention, the terminology used by radiologists must be accurate and consistent. Therefore, description of degenerative disc changes in the current paper is based on the most up-to-date recommendations, the aim being to aid reporting by radiologists and interpretation of reports by referring clinicians.
Synthesis and characterization of several series of 4-acyl-1-[2-aryl-1-diazenyl]piperazines
Authors: Little Vanessa Renee , Vaughan Keith
Published: June 2014

Five series of a novel class of 4-acyl-1-[2-aryl-1-diazenyl]piperazines have been synthesized and characterized: the 4-acetyl-1-[2-aryl-1-diazenyl]piperazines [series 1]; the 4-cyclohexylcarbonyl-1-[2-aryl-1-diazenyl]piperazines [series 2]; the 4-benzoyl-1-[2-aryl-1-diazenyl]piperazines [series 3]; the benzyl 4-[2-aryl-1-diazenyl]-1-piperazinecarboxylates [series 4]; and the t-butyl 4-[2-aryl-1-diazenyl]-1-piperazinecarboxylates [series 5]. The compounds were synthesized by diazotization of a primary aromatic amine and subsequent coupling to an appropriate secondary amine: 1-acetylpiperazine [series 1]; 1-(cyclohexylcarbonyl)-piperaizine [series 2]; 1-benzoylpiperazine [series 3]; benzyl 1-piperazinecarboxylate [series 4]; and t-butyl piperazine-1-carboxylate (1-BOC-piperazine) [series 5]. The compounds of series 1–5 were characterized by 1H NMR, 13C NMR, high-resolution MS and IR spectroscopy. The model compounds 1,4-di[2-aryl-1-diazenyl]piperazines, and ethyl 4-[2-aryl-1-diazenyl]-1-piperazinecarboxylates were used to facilitate the assignment of the chemical shifts specific to the piperazine ring carbons. HSQC spectra of select compounds established the correlation between proton and carbon resonance signals.
Modeling turbidity type and intensity effects on the growth and starvation mortality of age-0 yellow perch
Authors: Manning Nathan F. , Bossenbroek Jonathan M. , Mayer Christine M. , Bunnell David B. , Tyson Jeff T. , Rudstam Lars G. , Jackson James R.
Published: June 2014

We sought to quantify the possible population-level influence of sediment plumes and algal blooms on yellow perch (Perca flavescens), a visual predator found in systems with dynamic water clarity. We used an individual-based model (IBM), which allowed us to include variance in water clarity and the distribution of individual sizes. Our IBM was built with laboratory data showing that larval yellow perch feeding rates increased slightly as sediment turbidity level increased, but that both larval and juvenile yellow perch feeding rates decreased as phytoplankton level increased. Our IBM explained a majority of the variance in yellow perch length in data from the western and central basins of Lake Erie and Oneida Lake, with R2values ranging from 0.611 to 0.742. Starvation mortality was size dependent, as the greatest daily mortality rates in each simulation occurred within days of each other. Our model showed that turbidity-dependent consumption rates and temperature are key components in determining growth and starvation mortality of age-0 yellow perch, linking fish production to land-based processes that influence water clarity. These results suggest the timing and persistence of sediment plumes and algal blooms can drastically alter the growth potential and starvation mortality of a yellow perch cohort.
Effects of benthic macrofauna bioturbation on the bacterial community composition in lake sediments
Authors: Zeng Jin , Zhao Da-Yong , Liu Peng , Yu Zhong-Bo , Huang Rui , Wu Qinglong L.
Published: June 2014

Benthic macrofauna are considered to be an important part of the lacustrine ecosystem, and bioturbation may greatly affect the biogeochemical processes and microbial activities in sediments. In the present study, the bacterial community composition in sediments inhabited by 3 different types of benthic macrofauna (Corbicula fluminea, Chironomidae larvae, and tubificid worms) in the shallow and eutrophic Lake Taihu was studied to investigate the different effects of bioturbation on the composition of these communities. Microcosms were constructed, and culture-independent methods, including terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis, were performed to evaluate the bacterial communities. Analysis of similarities (ANOSIM) and multidimensional scaling (MDS) analysis of T-RFLP patterns demonstrated that differences in the bacterial community composition between the control and the macrofauna-inhabited sediments were not as great as expected, although the chemical properties of the sediments changed remarkably. Nevertheless, the dominant bacterial group in each type of macrofauna-inhabited sediment was different. Acidobacteria, Betaproteobacteria, and Deltaproteobacteria were the dominant bacterial groups in sediments inhabited by C. fluminea, tubificid worms, and Chironomidae larvae, respectively. The data obtained in this study are helpful for understanding the effects of bioturbation in a shallow, eutrophic lake.
The role of the chi1 gene from the endophytic bacteria Serratia proteamaculans 336x in the biological control of wheat take-all
Authors: Wang Miao , Xing Yuwan , Wang Junfang , Xu Yubin , Wang Gang
Published: June 2014

Take-all, a disease caused by the fungus Gaeumannomyces graminis var. tritici, is the most important root disease of wheat and causes severe yield losses worldwide. Using microorganisms as biological agents to control the disease is important because no resistant cultivars or effective chemical fungicides are available. In this study, we tested the biological control capability of a chitinase produced by the endophytic bacterium Serratia proteamaculans 336x against wheat take-all. The chitinase gene chi1 of S. proteamaculans 336x was cloned and heterologously expressed in Escherichia coli. The recombinant protein exhibited chitinase activity and in vitro antifungal activity against G. graminis var. tritici. With in-frame deletion of the chi1 gene by homologous recombination, the chi1-deleted mutant was devoid of chitinase activity and the biocontrol efficacy was reduced by 42.5%. The complementation of the Δchi1 mutant strain by the chi1 gene resulted in the partial restoration of the chitinase activity and biocontrol efficacy. These results support a role for the Chi1 protein in the biocontrol process of S. proteamaculans 336x against wheat take-all.
Monte Carlo Localization for Humanoid Robot Navigation in Complex Indoor Environments
Authors: Hornung Armin , Oßwald Stefan , Maier Daniel , Bennewitz Maren
Published: June 2014

Accurate and reliable localization is a prerequisite for autonomously performing high-level tasks with humanoid robots. In this paper, we present a probabilistic localization method for humanoid robots navigating in arbitrary complex indoor environments using only onboard sensing, which is a challenging task. Inaccurate motion execution of biped robots leads to an uncertain estimate of odometry, and their limited payload constrains perception to observations from lightweight and typically noisy sensors. Additionally, humanoids do not walk on flat ground only and perform a swaying motion while walking, which requires estimating a full 6D torso pose. We apply Monte Carlo localization to globally determine and track a humanoid's 6D pose in a given 3D world model, which may contain multiple levels and staircases. We present an observation model to integrate range measurements from a laser scanner or a depth camera as well as attitude data and information from the joint encoders. To increase the localization accuracy, e.g., while climbing stairs, we propose a further observation model and additionally use monocular vision data in an improved proposal distribution. We demonstrate the effectiveness of our methods in extensive real-world experiments with a Nao humanoid. As the experiments illustrate, the robot is able to globally localize itself and accurately track its 6D pose while walking and climbing stairs.
STUDIES ON THE DYNAMIC FRACTURE PROPERTIES AND FAILURE MODES OF A PBX
Authors: CHEN R. , CHENG L. , LIN Y. , LU F.
Published: June 2014

Polymer-bonded explosives (PBXs) are particulate composite materials composed of crystalline explosive grains bound in a relatively soft polymeric binder. It is important to optimize the fracture properties, while still maintaining the low sensitiveness and high explosiveness of PBX. This paper describes a study on the fracture properties and failure modes of a PBX by adopting a newly proposed dynamic fracture experimentation method — notched semi-circular bend (NSCB) specimen loaded with split Hopkinson pressure bar (SHPB) which was used in this study. This method offers the advantage of simultaneously determining the fracture initiation toughness, fracture energy, fracture propagation toughness and fracture velocity. The crack propagation is monitored by using a synchronous high-speed camera, which allows the observation of strain field history via digital image correlation process. The experimental results indicate that both the initiation toughness and the propagation toughness linearly increase with loading rate. The propagation fracture toughness is found to increase with fracture velocity, and a limiting fracture velocity is obtained. The failure modes are interpreted by using various theoretical models. Results suggest that the debonding strength of the binder is much smaller than the crystal fracture strength. The tensile strength is similar to the debonding strength, while the compression strength is somewhere intermediate between them.
AN EXPERIMENTAL STUDY ON PERFORMANCE IMPROVEMENT FOR AN AIR SOURCE HEAT PUMP BY ALTERNATE DEFROSTING OF OUTDOOR HEAT EXCHANGER
Authors: JUNG HOON , HWANG JUNGHO , JEON CHANGDUK
Published: June 2014

For a space heating air source heat pump (ASHP) in the condition of low temperature and high humidity, frost on the surface of heat exchanger becomes the major cause decreasing heating surface area and thus the performance of heat pump. In this study, we showed a method of delaying the implantation of frost using alternate defrost control. First, we acquired the performance data for conventional periodic reversed-cycle defrosting with a 5RT heat pump. After the experiment, the heat pump was modified to verify the effects of newly introduced alternate defrosting and compared with the conventional periodic reverse cycled method. It was found that heating coefficient of performance (COP) of heat pump using newly proposed alternate defrost method was about 17% higher than conventional heat pump using periodic reverse cycled defrosting.
Coastal structure, sea-level changes and vertical motion of the land in the Mediterranean
Authors: Anzidei Marco , Lambeck Kurt , Antonioli Fabrizio , Furlani Stefano , Mastronuzzi Giuseppe , Serpelloni Enrico , Vannucci Gianfranco
Published: June 2014

The Mediterranean basin is an important area of the Earth for studying the interplay between geodynamic processes and landscape evolution affected by tectonic, glacio-hydro-isostatic and eustatic factors. We focus on determining vertical deformations and relative sea-level change of the coastal zone utilizing geological, archaeological, historical and instrumental data, and modelling. For deformation determinations on recent decadal to centennial time scales, seismic strain analysis based on about 6000 focal mechanisms, surface deformation analysis based on some 850 continuous GPS stations, and 57 tide gauge records were used. Utilizing data from tectonically stable areas, reference surfaces were established to separate tectonic and climate (eustatic) signals throughout the basin for the last 20 000 years. Predominant Holocene subsidence (west coast of Italy, northern Adriatic sea, most of Greece and Turkey are areas at risk of flooding owing to relative sea-level rise), uplift (local areas in southwestern Italy and southern Greece) or stability (northwestern and central western Mediterranean and Levant area) were determined. Superimposed on the long trends, the coasts are also impacted by sudden extreme events such as recurring large storms and numerous, but unpredictable tsunamis caused by the high seismicity of parts of the basins.

Supplementary material:

A table of locations and timings of the largest tsunamis in the Mediterranean during the last 5660 years BP is available at
http://www.geolsoc.org.uk/SUP18757
.
Evidence from simultaneous intracellular- and surface-pH transients that carbonic anhydrase IV enhances CO2 fluxes across Xenopus oocyte plasma membranes
Authors: Musa-Aziz Raif , Occhipinti Rossana , Boron Walter F.
Published: June 2014

Human carbonic anhydrase IV (CA IV) is GPI-anchored to the outer membrane surface, catalyzing CO2/HCO3− hydration-dehydration. We examined effects of heterologously expressed CA IV on intracellular-pH (pHi) and surface-pH (pHS) transients caused by exposing oocytes to CO2/HCO3−/pH 7.50. CO2 influx causes a sustained pHi fall and a transient pHS rise; CO2 efflux does the opposite. Both during CO2 addition and removal, CA IV increases magnitudes of maximal rate of pHi change (dpHi/d t)max, and maximal pHS change (ΔpHS) and decreases time constants for pHi changes (τpHi) and pHS relaxations (τpHS). Decreases in time constants indicate that CA IV enhances CO2 fluxes. Extracellular acetazolamide blocks all CA IV effects, but not those of injected CA II. Injected acetazolamide partially reduces CA IV effects. Thus, extracellular CA is required for, and the equivalent of cytosol-accessible CA augments, the effects of CA IV. Increasing the concentration of the extracellular non-CO2/HCO3− buffer (i.e., HEPES), in the presence of extracellular CA or at high [CO2], accelerates CO2 influx. Simultaneous measurements with two pHS electrodes, one on the oocyte meridian perpendicular to the axis of flow and one downstream from the direction of extracellular-solution flow, reveal that the downstream electrode has a larger (i.e., slower) τpHS, indicating [CO2] asymmetry over the oocyte surface. A reaction-diffusion mathematical model (third paper in series) accounts for the above general features, and supports the conclusion that extracellular CA, which replenishes entering CO2 or consumes exiting CO2 at the extracellular surface, enhances the gradient driving CO2 influx across the cell membrane.
Evidence from simultaneous intracellular- and surface-pH transients that carbonic anhydrase II enhances CO2 fluxes across Xenopus oocyte plasma membranes
Authors: Musa-Aziz Raif , Occhipinti Rossana , Boron Walter F.
Published: June 2014

The α-carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the interconversion of CO2 and HCO3−. Here, we focus on human CA II (CA II), a ubiquitous cytoplasmic enzyme. In the second paper in this series, we examine CA IV at the extracellular surface. After microinjecting recombinant CA II in a Tris solution (or just Tris) into oocytes, we expose oocytes to 1.5% CO2/10 mM HCO3−/pH 7.50 while using microelectrodes to monitor intracellular pH (pHi) and surface pH (pHS). CO2 influx causes the familiar sustained pHi fall as well as a transient pHS rise; CO2 efflux does the opposite. Both during CO2 addition and removal, CA II increases the magnitudes of the maximal rate of pHi change, (dpHi/d t)max, and the maximal change in pHS, ΔpHS. Preincubating oocytes with the inhibitor ethoxzolamide eliminates the effects of CA II. Compared with pHS, pHi begins to change only after a delay of ∼9 s and its relaxation has a larger (i.e., slower) time constant (τpHi > τpHS). Simultaneous measurements with two pHi electrodes, one superficial and one deep, suggest that impalement depth contributes to pHi delay and higher τpHi. Using higher CO2/HCO3− levels, i.e., 5%/33 mM HCO3− or 10%/66 mM HCO3−, increases (dpHi/d t)max and ΔpHS, though not in proportion to the increase in [CO2]. A reaction-diffusion mathematical model (described in the third paper in this series) accounts for the above general features and supports the conclusion that cytosolic CA—consuming entering CO2 or replenishing exiting CO2—increases CO2 fluxes across the cell membrane.
Diverse mechanisms for body fluid regulation in teleost fishes
Authors: Takei Yoshio , Hiroi Junya , Takahashi Hideya , Sakamoto Tatsuya
Published: June 2014

Teleost fishes are the major group of ray-finned fishes and represent more than one-half of the total number of vertebrate species. They have experienced in their evolution an additional third-round whole genome duplication just after the divergence of their lineage, which endowed them with an extra adaptability to invade various aquatic habitats. Thus their physiology is also extremely diverse compared with other vertebrate groups as exemplified by the many patterns of body fluid regulation or osmoregulation. The key osmoregulatory organ for teleosts, whose body fluid composition is similar to mammals, is the gill, where ions are absorbed from or excreted into surrounding waters of various salinities against concentration gradients. It has been shown that the underlying molecular physiology of gill ionocytes responsible for ion regulation is highly variable among species. This variability is also seen in the endocrine control of osmoregulation where some hormones have distinct effects on body fluid regulation in different teleost species. A typical example is atrial natriuretic peptide (ANP); ANP is secreted in response to increased blood volume and acts on various osmoregulatory organs to restore volume in rainbow trout as it does in mammals, but it is secreted in response to increased plasma osmolality, and specifically decreases NaCl, and not water, in the body of eels. The distinct actions of other osmoregulatory hormones such as growth hormone, prolactin, angiotensin II, and vasotocin among teleost species are also evident. We hypothesized that such diversity of ionocytes and hormone actions among species stems from their intrinsic differences in body fluid regulation that originated from their native habitats, either fresh water or seawater. In this review, we summarized remarkable differences in body fluid regulation and its endocrine control among teleost species, although the number of species is still limited to substantiate the hypothesis.
Chronic rapamycin treatment causes diabetes in male mice
Authors: Schindler Christine E. , Partap Uttara , Patchen Bonnie K. , Swoap Steven J.
Published: June 2014

Current evidence indicates that the mammalian target of rapamycin inhibitor rapamycin both increases longevity and, seemingly contradictorily, impairs glucose homeostasis. Most studies exploring the dimensions of this paradox have been based on rapamycin treatment in mice for up to 20 wk. We sought to better understand the metabolic effects of oral rapamycin over a substantially longer period of time in HET3 mice. We observed that treatment with rapamycin for 52 wk induced diabetes in male mice, characterized by hyperglycemia, significant urine glucose levels, and severe glucose and pyruvate intolerance. Glucose intolerance occurred in male mice by 4 wk on rapamycin and could be only partially reversed with cessation of rapamycin treatment. Female mice developed moderate glucose intolerance over 1 yr of rapamycin treatment, but not diabetes. The role of sex hormones in the differential development of diabetic symptoms in male and female mice was further explored. HET3 mice treated with rapamycin for 52 wk were gonadectomized and monitored over 10 wk. Castrated male mice remained glucose intolerant, while ovariectomized females developed significant glucose intolerance over the same time period. Subsequent replacement of 17β-estradiol (E2) in ovariectomized females promoted a recovery of glucose tolerance over a 4-wk period, suggesting the protective role of E2against rapamycin-induced diabetes. These results indicate that 1) oral rapamycin treatment causes diabetes in male mice, 2) the diabetes is partially reversible with cessation of treatment, and 3) E2plays a protective role against the development of rapamycin-induced diabetes.
Activation of the renin-angiotensin system, specifically in the subfornical organ is sufficient to induce fluid intake
Authors: Coble Jeffrey P. , Cassell Martin D. , Davis Deborah R. , Grobe Justin L. , Sigmund Curt D.
Published: June 2014

Increased activity of the renin-angiotensin system within the brain elevates fluid intake, blood pressure, and resting metabolic rate. Renin and angiotensinogen are coexpressed within the same cells of the subfornical organ, and the production and action of ANG II through the ANG II type 1 receptor in the subfornical organ (SFO) are necessary for fluid intake due to increased activity of the brain renin-angiotensin system. We generated an inducible model of ANG II production by breeding transgenic mice expressing human renin in neurons controlled by the synapsin promoter with transgenic mice containing a Cre-recombinase-inducible human angiotensinogen construct. Adenoviral delivery of Cre-recombinase causes SFO-selective induction of human angiotensinogen expression. Selective production of ANG II in the SFO results in increased water intake but did not change blood pressure or resting metabolic rate. The increase in water intake was ANG II type 1 receptor-dependent. When given a choice between water and 0.15 M NaCl, these mice increased total fluid and sodium, but not water, because of an increased preference for NaCl. When provided a choice between water and 0.3 M NaCl, the mice exhibited increased fluid, water, and sodium intake, but no change in preference for NaCl. The increase in fluid intake was blocked by an inhibitor of PKC, but not ERK, and was correlated with increased phosphorylated cyclic AMP response element binding protein in the subfornical organ. Thus, increased production and action of ANG II specifically in the subfornical organ are sufficient on their own to mediate an increase in drinking through PKC.