bluuebunny/crossref_metadata_2025 huggingface dataset:
In‐situ incubation of iron‐sulfur mineral reveals a diverse chemolithoautotrophic community and a new biogeochemical role for Thiomicrospira
Authors: Barco Roman A. , Hoffman Colleen L. , Ramírez Gustavo A. , Toner Brandy M. , Edwards Katrina J. , Sylvan Jason B.
Published: January 2017

Sulfide mineral precipitation occurs at mid‐ocean ridge (MOR) spreading centers, both in the form of plume particles and seafloor massive sulfide structures. A common constituent of MOR is the iron‐bearing sulfide mineral pyrrhotite, which was chosen as a substrate for in‐situ incubation studies in shallow waters of Catalina Island, CA to investigate the colonization of iron‐oxidizing bacteria. Microbial community datasets were obtained from in‐situ incubated pyrrhotite, allowing for direct comparison to microbial communities of iron‐sulfides from active and inactive chimneys in deep‐sea environments. Unclassified Gammaproteobacteria and Alphaproteobacteria (Magnetovibrio) largely dominated the bacterial community on pyrrhotite samples incubated in the water column while samples incubated at the surface sediment showed more even dominance by Deltaproteobacteria (Desulfobulbus), Gammaproteobacteria (Piscirickettsiaceae), Alphaproteobacteria (Rhodobacteraceae), and Bacteroidetes (Flavobacteriia). Cultivations that originated from pyrrhotite samples resulted in the enrichment of both, sheath‐forming and stalk‐forming Zetaproteobacteria. Additionally, a putative novel species of Thiomicrospira was isolated and shown to grow autotrophically with iron, indicating a new biogeochemical role for this ubiquitous microorganism.
Competence in the use of supraglottic airways by Australian surf lifesavers for cardiac arrest ventilation in a manikin
Authors: Holbery‐Morgan Lachlan , Angel Cara , Murphy Michelle , Carew James , Douglas Finn , Murphy Robert , Hood Natalie , Rechtman Andrew , Scarff Christopher , Simpson Nicholas , Stewardson Andrew , Steinfort Daniel , Radford Sam , Douglas Ned , Johnson Douglas
Published: January 2017

Objectives

Lifesavers in Australia are taught to use pocket mask (PM) rescue breathing and bag valve mask (BVM) ventilation, despite evidence that first responders might struggle with these devices. Novices have successfully used the Laryngeal Mask Airway (LMA) Supreme and iGel devices previously, but there has been no previous comparison of the ability to train lifesavers to use the supraglottic airways compared to standard techniques for cardiac arrest ventilation.

Methods

The study is a prospective educational intervention whereby 113 lifesavers were trained to use the LMA and iGel supraglottic airways. Comparisons were made to standard devices on plastic manikins. Successful ventilation was defined as achieving visible chest rise.

Results

The median time to first effective ventilation was similar between the PM (16 s, 95% confidence interval 16–17 s), BVM (17 s, 16–17 s) and iGel devices (18 s, 16–20 s), but longer for the LMA (36 s, 33–38 s). The iGel frequently failed to achieve ventilation (10%) compared with the PM (1%, P < 0.01) and LMA (3%, P < 0.01) but was not worse than the BVM (3%, P < 0.57). Hands‐off time was similar between the BVM, LMA and iGel (10 s for each device), but worse for the PM (13 s, P = 0.001).

Conclusion

Lifesavers using the PM and BVM perform ventilation for cardiopulmonary resuscitation well. There appears to be a limited role for supraglottic airway devices because of limitations in terms of time to first effective ventilation and reliability. Clinical validation of manikin data with live resuscitation performance is required.
Therapeutic Apheresis in Immunologic Renal and Neurological Diseases
Authors: Bambauer Rolf , Latza Reinhard , Burgard Daniel , Schiel Ralf
Published: January 2017

Since the mid 1970s, when membrane modules became available, plasma separation techniques have gained in importance especially in the past few years. The advantages of this method are a complete separation of the corpuscular components from the plasma and due to increased blood flow rate and higher efficacy. Systemic autoimmune diseases based on an immune pathogenesis produce autoantibodies and circulating immune complexes, which cause inflammation in the tissues of various organs. In most cases, these diseases have a poor prognosis without treatment. Therapeutic apheresis (TA) in combination with immunosuppressive therapies has led to a steady increase in survival rates over the last 40 years. The updated information on immunology and molecular biology of different immunologic diseases are discussed in relation to the rationale for apheresis therapy and its place in combination with other modern treatments. The different diseases can be treated by various apheresis methods such as therapeutic plasma exchange (TPE) with substitution solution, or with online plasma or blood purification using adsorption columns, which contain biological or non‐biological agents. Here, the authors provide an overview of the most important pathogenic aspects indicating that TA can be a supportive therapy in systemic autoimmune diseases such as renal and neurological disorders. For the immunological diseases that can be treated with TA, the guidelines of the German Working Group of Clinical Nephrology and of the Apheresis Committee of the American Society for Apheresis are cited.
Lamellar events related to insulin‐like growth factor‐1 receptor signalling in two models relevant to endocrinopathic laminitis
Authors: Lane H. E. , Burns T. A. , Hegedus O. C. , Watts M. R. , Weber P. S. , Woltman K. A. , Geor R. J. , McCutcheon L. J. , Eades S. C. , Mathes L. E. , Belknap J. K.
Published: January 2017

Background

Insulin dysregulation, obesity, and exposure to high‐nonstructural carbohydrate (NSC) forage are risk factors for equine metabolic syndrome‐associated laminitis (EMSAL); high systemic insulin concentrations in EMSAL are proposed to induce cellular dysregulation in the digital lamellae through activation of the insulin‐like growth factor‐1 receptor.

Objectives

To use a dietary challenge model (DCM) and a euglycaemic–hyperinsulinaemic clamp (EHC) model to assess lamellar growth factor‐related signalling.

Study design

Lamellar phospho (P)‐protein concentrations of signalling proteins important in growth factor‐related signalling were assessed in 2 models: 1) lean and obese ponies on a low‐ or high‐NSC diet; and 2) EHC model using Standardbred horses.

Methods

Ponies stratified for body condition (lean [LN, n = 11] and obese [OB, n = 11]) were exposed to a low‐NSC diet (LO, n = 5 per group for LN LO and OB LO) or a high NSC diet (HI, n = 6 per group for LN HI and OB HI groups) for 7 days. For the EHC model, horses were administered insulin (constant rate infusion [6 mIU/kg bwt/min] combined with 50% dextrose, EHC group, n = 8)] or saline (0.57 mL/kg bwt/h, CON group, n = 8) for 48 h. Immunoblotting was employed to assess concentrations of activated/phosphorylated and total protein for members of the PI3K/Akt/mTORC1 and Ras/ERK pathways in lamellar samples from both models.

Results

In the DCM, lamellar P‐(Ser 240/244) RPS6 was increased in OB HI ponies (vs. OB LO, P<0.05); positive correlations existed (P<0.05; r>0.5) between Day 7 basal serum insulin concentrations and lamellar concentrations of P‐p70S6K and P‐(Ser 240/244) RPS6. In the EHC model, lamellar concentrations of P‐Akt, P‐p70S6K, P‐ERK 1/2, P‐p90RSK, and both P‐(Ser 235/236) and P‐(Ser 240/244) RPS6 were increased in the EHC group (vs. CON, P<0.05).

Main limitations

The primary limitations of this study are the small number of animals per group in the DCM study, and the fact that many animals did not develop laminitis as that was not the endpoint of either study.

Conclusions

These results support further investigation of mTORC1/RPS6 signalling as a potential therapeutic target(s) in EMSAL.

The Summary is available in Chinese – see Supporting Information.
The effect of additives on the quality of white lupin–wheat silage assessed by fermentation pattern and qPCR quantification of clostridia
Authors: König W. , Lamminen M. , Weiss K. , Tuomivirta T. T. , Sanz Muñoz S. , Fritze H. , Elo K. , Puhakka L. , Vanhatalo A. , Jaakkola S.
Published: January 2017

The efficacy of different silage additives on different mixtures of white lupin and spring wheat was investigated in four separate trials. The bicrop was harvested 96 days (trials 1 and 2) and 110 days (trials 3 and 4) after sowing. For each maturity stage, two mixtures of white lupin and spring wheat were reformed in the ratios of 1:2 and 2:1 on fresh matter (FM) basis respectively. The crops were treated with formic acid (FA), sodium nitrite–hexamine mixture (NaHe) or homofermentative lactic acid bacteria (LAB). The control silage was made without additive. Additives were not able to improve the quality of white lupin–wheat silage in all trials, compared with untreated silage. The treatment with LAB showed good results only at the first stage of crop maturity with sufficient amounts of water‐soluble carbohydrate in the pre‐ensiling crops. The FA treatment showed elevated butyric acid levels in all trials, which suggests that the FA application level used (4 L t−1 FM, 100% FA) was insufficient to decrease pH enough for preventing the growth of clostridia and butyric acid fermentation. NaHe was the only additive that was able to inhibit the activity of clostridia in all trials.
Development and feasibility testing of the Pediatric Emergency Discharge Interaction Coding Scheme
Authors: Curran Janet A. , Taylor Alexandra , Chorney Jill , Porter Stephen , Murphy Andrea , MacPhee Shannon , Bishop Andrea , Haworth Rebecca
Published: January 2017

Background

Discharge communication is an important aspect of high‐quality emergency care. This study addresses the gap in knowledge on how to describe discharge communication in a paediatric emergency department (ED).

Objective

The objective of this feasibility study was to develop and test a coding scheme to characterize discharge communication between health‐care providers (HCPs) and caregivers who visit the ED with their children.

Design

The Pediatric Emergency Discharge Interaction Coding Scheme (PEDICS) and coding manual were developed following a review of the literature and an iterative refinement process involving HCP observations, inter‐rater assessments and team consensus.

Setting and participants

The coding scheme was pilot‐tested through observations of HCPs across a range of shifts in one urban paediatric ED.

Main variables studied

Overall, 329 patient observations were carried out across 50 observational shifts. Inter‐rater reliability was evaluated in 16% of the observations. The final version of the PEDICS contained 41 communication elements.

Results

Kappa scores were greater than .60 for the majority of communication elements. The most frequently observed communication elements were under the Introduction node and the least frequently observed were under the Social Concerns node. HCPs initiated the majority of the communication.

Conclusion

Pediatric Emergency Discharge Interaction Coding Scheme addresses an important gap in the discharge communication literature. The tool is useful for mapping patterns of discharge communication between HCPs and caregivers. Results from our pilot test identified deficits in specific areas of discharge communication that could impact adherence to discharge instructions. The PEDICS would benefit from further testing with a different sample of HCPs.
Recycling zinc oxide varistor blocks for electro‐active silicone composites
Authors: Metz Renaud , Boudehen Loic , Tahir Said , Phou Ty , Prevost Guillaume , Jelinek Remi , Dieudonné Philippe , Hassanzadeh Merdad
Published: January 2017

The recycling process toward the elimination of varistor wastes into new electro‐active silicon composites has been investigated. We studied the dependence of the E‐J characteristics on the aggregate content in the polymer matrix. Formulations with 40 vol.% metal oxide varistor aggregates in the 100‐200 μm range exhibit reliable nonlinear behavior with a switching voltage of 280±30 V/mm. The breakdown voltage of the composite decreases as both filler's diameter and filler's volume fraction increases in the 550‐220 V/mm and 440‐280 V/mm range, respectively. This paves the way for the valorization of varistors based zinc oxide (ZnO) ceramics.
Rapid automated landmarking for morphometric analysis of three‐dimensional facial scans
Authors: Li Mao , Cole Joanne B. , Manyama Mange , Larson Jacinda R. , Liberton Denise K. , Riccardi Sheri L. , Ferrara Tracey M. , Santorico Stephanie A. , Bannister Jordan J. , Forkert Nils D. , Spritz Richard A. , Mio Washington , Hallgrimsson Benedikt
Published: January 2017

Automated phenotyping is essential for the creation of large, highly standardized datasets from anatomical imaging data. Such datasets can support large‐scale studies of complex traits or clinical studies related to precision medicine or clinical trials. We have developed a method that generates three‐dimensional landmark data that meet the requirements of standard geometric morphometric analyses. The method is robust and can be implemented without high‐performance computing resources. We validated the method using both direct comparison to manual landmarking on the same individuals and also analyses of the variation patterns and outlier patterns in a large dataset of automated and manual landmark data. Direct comparison of manual and automated landmarks reveals that automated landmark data are less variable, but more highly integrated and reproducible. Automated data produce covariation structure that closely resembles that of manual landmarks. We further find that while our method does produce some landmarking errors, they tend to be readily detectable and can be fixed by adjusting parameters used in the registration and control‐point steps. Data generated using the method described here have been successfully used to study the genomic architecture of facial shape in two different genome‐wide association studies of facial shape.
Adolescent Athletic Participation Patterns and Self‐Perceived Competence: Associations With Later Participation, Depressive Symptoms, and Health
Authors: Agans Jennifer P. , Johnson Sara K. , Lerner Richard M.
Published: January 2017

Physical activity is important for well‐being across the life span. However, links between patterns of adolescent activity, competence perceptions, and young adult outcomes are underexplored. We used data from seven waves of the 4‐H Study of Positive Youth Development (N = 5,961) to assess patterns of adolescent athletic participation, whether these patterns were associated with self‐perceived athletic competence and young adult physical activity, depressive symptoms, and health, and associations between changes in participation across adolescence and young adult outcomes. Competence perceptions were associated with increased participation, and more active adolescents had higher rates of adult athletic activity, with links to better health and fewer depressive symptoms. We discuss results in light of the importance of using person‐centered analyses to understand active lifestyles.
The effect of aging on mastication and swallowing parameters according to the hardness change of solid food
Authors: Park Hyoung Su , Kim Don‐Kyu , Lee Sang Yi , Park Ki‐Hwan
Published: January 2017

As part of the aging process, multiple oral physiologic changes occur and these changes may cause individuals to reduce food intake or switch the types of food texture. Thus, the need to develop food products for the elderly has increased. To evaluate the suitability of the food products for the elderly, the evaluation method should be verified and it is important to identify the parameters of mastication and swallowing. Therefore, the purpose of this study was to compare the differences of mastication and swallowing parameters between the young adults and the elderly depending on the varying hardness of rice food product. Subjects included 20 young adults and 40 elderly and bolus transit times of video‐fluoroscopic swallowing study (VFSS) were used. Four types of rice products with different hardness were provided including cooked rice, soft‐boiled rice, rice gruel and thin rice gruel. In the elderly group, the chewing number, oral processing time, post‐faucial aggregation time, valleculae aggregation time (VAT), first subsequence duration and total duration were significantly different according to the changes in food hardness. Of the bolus transit times, the VAT and the second subsequence duration (S‐S2) were significantly different between the two groups. These results suggest that VAT and S‐S2, key VFSS parameters, as well as the chewing number and total duration are useful tools for evaluating the effect of aging on mastication and swallowing of solid foods.

Practical applications

In Korea, the aging population is rapidly increasing. According to recent surveys, a large number of elderly Koreans have reported chewing difficulties and many of them are in the state of under‐nutrition. As aging progresses, multiple physiologic changes occur in mastication and swallowing functions. These changes may cause individuals to reduce their food intake or switch to soft food products. Therefore, the development of texture‐modified food products for the elderly is needed and they should be developed based on the understandings of the physiology of mastication and swallowing according to different rheological properties of food products consumed in Korea, which are quite different from those of the western countries. In this study, we compared the differences of mastication and swallowing parameters between the young adults and the elderly depending on the varying hardness of rice food product.
Lost in transformation? Reviving ethics of care in hospital cultures of evidence‐based healthcare
Authors: Norlyk Annelise , Haahr Anita , Dreyer Pia , Martinsen Bente
Published: January 2017

Drawing on previous empirical research, we provide an exemplary narrative to illustrate how patients have experienced hospital care organized according to evidence‐based fast‐track programmes. The aim of this paper was to analyse and discuss if and how it is possible to include patients’ individual perspectives in an evidence‐based practice as seen from the point of view of nursing theory. The paper highlights two conflicting courses of development. One is a course of standardization founded on evidence‐based recommendations, which specify a set of rules that the patient must follow rigorously. The other is a course of democratization based on patients’ involvement in care. Referring to the analysis of the narrative, we argue that, in the current implementation of evidence‐based practice, the proposed involvement of patients resembles empty rhetoric. We argue that the principles and values from evidence‐based medicine are being lost in the transformation into the current evidence‐based hospital culture which potentially leads to a McDonaldization of nursing practice reflected as ‘one best way’. We argue for reviving ethics of care perspectives in today's evidence practice as the fundamental values of nursing may potentially bridge conflicts between evidence‐based practice and the ideals of patient participation thus preventing a practice of ‘McNursing’.
Objectively diagnosing rumination syndrome in children using esophageal pH‐impedance and manometry
Authors: Singendonk M. M. J. , Oors J. M. , Bredenoord A. J. , Omari T. I. , van der Pol R. J. , Smits M. J. , Benninga M. A. , van Wijk M. P.
Published: January 2017

Background

Rumination syndrome is characterized by recurrent regurgitation of recently ingested food into the mouth. Differentiation with other diagnoses and gastroesophageal reflux disease (GERD) in particular, is difficult. Recently, objective pH‐impedance (pH‐MII) and manometry criteria were proposed for adults. The aim of this study was to determine diagnostic ambulatory pH‐MII and manometry criteria for rumination syndrome in children.

Methods

Clinical data and 24‐hour pH‐MII and manometry recordings of children with a clinical suspicion of rumination syndrome were reviewed. Recordings were analyzed for retrograde bolus flow extending into the proximal esophagus. Peak gastric and intraesophageal pressures closely related to these events were recorded and checked for a pattern compatible with rumination. Events were classified into primary, secondary, and supragastric belch–associated rumination.

Key Results

Twenty‐five consecutive patients (11 males, median age 13.3 years [IQR 5.9‐15.8]) were included; recordings of 18 patients were suitable for analysis. Rumination events were identified in 16/18 patients, with 50% of events occurring <30 minutes postprandially. Fifteen of 16 patients showed ≥1 gastric pressure peak >30 mmHg, while only 50% of all events was characterized by peaks >30 mmHg and an additional 20% by peaks >25 mmHg. Four patients had evidence of acid GERD, all showing secondary rumination.

Conclusions and Inferences

Combined 24‐hour pH‐MII and manometry can be used to diagnose rumination syndrome in children and to distinguish it from GERD. Rumination patterns in children are similar compared with adults, albeit with lower gastric pressure increase. We propose a diagnostic cutoff for gastric pressure increase >25 mmHg associated with retrograde bolus flow into the proximal esophagus.
A fern AINTEGUMENTA gene mirrors BABY BOOM in promoting apogamy in Ceratopteris richardii
Authors: Bui Linh T. , Pandzic Dzevida , Youngstrom Christopher E. , Wallace Simon , Irish Erin E. , Szövényi Péter , Cheng Chi‐Lien
Published: January 2017

Asexual reproduction is widespread in land plants, including ferns where 10% of all species are obligate asexuals. In these ferns, apogamous sporophytes are generated directly from gametophytes, bypassing fertilization. In the model fern Ceratopteris richardii, a sexual species, apogamy can be induced by culture on high sugar media. BABY BOOM (BBM) genes in angiosperms are known to promote somatic embryogenesis, which like apogamy produce sporophytes without fertilization. Here, a Brassica napus BBM (BnBBM) was used to investigate genetic similarity between apogamy in ferns and somatic embryogenesis in angiosperms. A C. richardii transcriptome was constructed from which one AINTEGUMENTA‐LIKE unigene, CrANT, was identified. Whole mount in situ hybridization showed that CrANT is expressed in sperm and fertilized eggs. Phylogenetic analysis grouped CrANT with other non‐seed‐plant ANT genes to the euANT clade but in a branch separate from BBM genes. Overexpression of CrANT or BnBBM promotes apogamy in C. richardii without sugar supplement. CrANT knockdown gametophytes responded weakly to sugar for apogamy promotion. Theses results suggest some genetic conservation between apogamy and somatic embryogenesis and that such asexual reproduction may be ancient.
Purging the nation: race, conviviality and embodied encounters in the lives of British Bangladeshi Muslim young women
Authors: Nayak Anoop
Published: January 2017

This paper critically engages with debates on race, conviviality and the geography of encounters. Where much of this work is undertaken in multicultural places, far less is known about the doing and undoing of conviviality in mainly white localities. The study further contributes to this work by offering a richly embodied account of racism and belonging based on the biographical testimonies of British Bangladeshi Muslim young women. Through these accounts, I identify topographies of power, social inequality and forms of exclusion that disrupt the melody of multicultural conviviality. I demonstrate the visceral aspects of race as it is summoned to life in live encounters, where it is lived on the body, bleeds into the locality and congeals around imaginary ideas of the nation state. I argue that antagonistic encounters that serve to mark out British Bangladeshi Muslims as ‘Other’ perform a bigger role: purging the nation, detoxifying it from encroaching multicultural intimacies and stabilising it as white. Despite this ritual cleansing I demonstrate how respondents are implicated in new forms of civic belonging, laying claim to nationhood, locality and rights to the city that subvert and hollow out the fantasy of a white nation.
In vitro anti‐tubulin effects of mebendazole and fenbendazole on canine glioma cells
Authors: Lai S. R. , Castello S. A. , Robinson A. C. , Koehler J. W.
Published: January 2017

Benzimidazole anthelmintics have reported anti‐neoplastic effects both in vitro and in vivo. The purpose of this study was to evaluate the in vitro chemosensitivity of three canine glioma cell lines to mebendazole and fenbendazole. The mean inhibitory concentration (IC50) (±SD) obtained from performing the MTT [3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide] assay after treating J3T, G06‐A, and SDT‐3G cells for 72 h with mebendazole were 0.030 ± 0.003, 0.080 ± 0.015 and 0.030 ± 0.006 μM respectively, while those for fenbendazole were 0.550  ± 0.015, 1.530 ± 0.159 and 0.690 ± 0.095 μM; treatment of primary canine fibroblasts for 72 h at IC50 showed no significant effect. Immunofluorescence studies showed disruption of tubulin after treatment. Mebendazole and fenbendazole are cytotoxic in canine glioma cell lines in vitro and may be good candidates for treatment of canine gliomas. Further in vivo studies are required.
A Platform for Mechanical Assembly Education Using the Microsoft Kinect
Authors: Chang Yizhe , Aziz El-Sayed , Zhang Zhou , Zhang Mingshao , Esche Sven , Chassapis Constantin
Published: January 2017

Mechanical assembly activities involve multiple factors including humans, mechanical parts, tools and assembly environments. In order to simulate assembly processes by computers for educational purposes, all these factors should be considered. Virtual reality (VR) technology, which aims to integrate natural human motion into real-world scenarios, provides an ideal simulation medium. Novel VR devices such as 3D glasses, motion-tracking gloves, haptic sensors, etc. are able to fulfill fundamental assembly simulation needs. However, most of these implementations focus on assembly simulations for computer-aided design, which are geared toward professionals rather than students, thus leading to complicated assembly procedures not suitable for students. Furthermore, the costs of these novel VR devices and specifically designed VR platforms represent an untenable financial burden for most educational institutions.

In this paper, a virtual platform for mechanical assembly education based on the Microsoft Kinect sensor and Garry’s Mod (GMod) is presented. With the help of the Kinect’s body tracking function and voice recognition technology in conjunction with the graphics and physics simulation capabilities of GMod, a low-cost VR platform that enables educators to author their own assembly simulations was implemented. This platform utilizes the Kinect as the sole input device. Students can use voice commands to navigate their avatars inside of a GMod powered virtual laboratory as well as use their body’s motions to integrate pre-defined mechanical parts into assemblies. Under this platform, assembly procedures involving the picking, placing and attaching of parts can be performed collaboratively by multiple users. In addition, the platform allows collaborative learning without the need for the learners to be co-located. A pilot study for this platform showed that, with the instructor’s assistance, mechanical engineering undergraduate students are able to complete basic assembly operations.
Design and Analysis of an Example Lathe Spindle
Authors: Vyasa Rupal , Echempati Raghu
Published: January 2017

This paper discusses the modeling and analysis of an example medium speed medium precision lathe spindle. This and few other similar topics have been assigned as term projects in an introductory senior undergraduate/graduate level finite element analysis course taught at Kettering University. The experiences and the general feedback from the students of the class show satisfactory organization of the course material that includes modeling and analysis of real life examples.

With reference to the specific topic on design of machine tool spindles, it is not a new area, however, it is generally taught at the graduate and research levels. Use of modern computational tools to perform iterative design and analysis calculations of such spindles make the senior undergraduate and/or graduate master students aware of the implications of modeling a real life system using the 1D and 3D finite beam elements and to validate those results by a CAE tool. Final course projects such as this serve as a good learning tool to the graduating engineers. Sample results obtained from various CAE tools such as UG-NX 7.5 are presented in the paper and discussed.
Synthesis and characterization of Ga2O3 nanosheets on 3C-SiC-on-Si by low pressure chemical vapor deposition
Authors: Rafique Subrina , Han Lu , Lee Jaesung , Zheng Xu-Qian , Zorman Christian A. , Feng Philip X.-L. , Zhao Hongping
Published: January 2017

This study presents the synthesis of single crystalline β-Ga2O3 nanosheets on SiC by low pressure chemical vapor deposition. High purity gallium (Ga) metal and oxygen as source materials and argon as carrier gas were utilized for the synthesis of the nanosheets on a 3C-SiC-on-Si substrate. These single-crystal Ga2O3 nanosheets are free-standing 2D extrusions from their 1D rods, typically 1.5–7 μm in lateral size and 20–140 nm in thickness, featuring aspect ratios ranging from ∼10 to 350. Structural studies based on transmission electron microscopy and Raman spectroscopy revealed the monoclinic phase of Ga2O3 with a single crystalline nature. High resolution transmission electron microscopy with a selected area electron diffraction pattern recorded on a single β-Ga2O3 nanosheet further confirmed their single crystalline nature, with a growth direction perpendicular to (111) crystallographic plane. The growth process governing the formation of these nanosheets is a vapor-solid growth mechanism since no metal catalyst was used. These β-Ga2O3 nanosheets exhibit new possibilities and potential for future functional nanodevices that would benefit from their extremely large surface area to volume ratios.
An analysis of pilot whale vocalization activity using hidden Markov models
Authors: Popov Valentin , Langrock Roland , DeRuiter Stacy L. , Visser Fleur
Published: January 2017

Vocalizations of cetaceans form a key component of their social interactions. Such vocalization activity is driven by the behavioral states of the whales, which are not directly observable, so that latent-state models are natural candidates for modeling empirical data on vocalizations. In this paper, hidden Markov models are used to analyze calling activity of long-finned pilot whales (Globicephala melas) recorded over three years in the Vestfjord basin off Lofoten, Norway. Baseline models are used to motivate the use of three states, while more complex models are fit to study the influence of covariates on the state-switching dynamics. The analysis demonstrates the potential usefulness of hidden Markov models to concisely yet accurately describe the stochastic patterns found in animal communication data, thereby providing a framework for drawing meaningful biological inference.
Strong peak in
T
c
of Sr
2
RuO
4
under uniaxial pressure
Authors: Steppke Alexander , Zhao Lishan , Barber Mark E. , Scaffidi Thomas , Jerzembeck Fabian , Rosner Helge , Gibbs Alexandra S. , Maeno Yoshiteru , Simon Steven H. , Mackenzie Andrew P. , Hicks Clifford W.
Published: January 2017

Squeezing out the oddness

The material Sr
2
RuO
4
has long been thought to exhibit an exotic, odd-parity kind of superconductivity, not unlike the superfluidity in
3
He. How would perturbing this material's electronic structure affect its superconductivity? Steppke
et al.
put the material under large uniaxial pressure and found that the critical temperature more than doubled and then fell as a function of strain (see the Perspective by Shen). The maximum critical temperature roughly coincided with the point at which the material's Fermi surface underwent a topological change. One intriguing possibility is that squeezing changed the parity of the superconducting gap from odd to even.

Science
, this issue p.
10.1126/science.aaf9398
; see also p.
133
Braiding a molecular knot with eight crossings
Authors: Danon Jonathan J. , Krüger Anneke , Leigh David A. , Lemonnier Jean-François , Stephens Alexander J. , Vitorica-Yrezabal Iñigo J. , Woltering Steffen L.
Published: January 2017

Three strands ironed closely together

It is not uncommon when braiding hair or bread to intertwine three different strands. At the molecular level, however, synthetic knots have thus far been restricted to architectures accessible from two-strand braids. Danon
et al.
used iron ion coordination to guide three organic ligand strands to form a knot geometry with eight separate crossings.

Science
, this issue p.
159
Macrocyclic bis-thioureas catalyze stereospecific glycosylation reactions
Authors: Park Yongho , Harper Kaid C. , Kuhl Nadine , Kwan Eugene E. , Liu Richard Y. , Jacobsen Eric N.
Published: January 2017

A cyclic catalyst to pair up sugars

Linking sugar molecules together to make complex carbohydrates is a geometrical challenge. For a six-carbon sugar such as glucose, there are six different possible linkage sites and also two possible configurations in which to anchor the incipient bond. Park
et al.
developed a ring-shaped, dimeric catalyst that pairs sugars after one of them has been modified with a chloride. The thiourea-based catalyst appears to pull away the chloride while simultaneously activating the incoming second sugar. The resultant bond-forming process reliably inverts the initial C–Cl configuration.

Science
, this issue p.
162
Monophosphoryl Lipid A Enhances Efficacy of a Francisella tularensis LVS-Catanionic Nanoparticle Subunit Vaccine against F. tularensis Schu S4 Challenge by Augmenting both Humoral and Cellular Immunity
Authors: Richard Katharina , Mann Barbara J. , Qin Aiping , Barry Eileen M. , Ernst Robert K. , Vogel Stefanie N.
Published: January 2017

Francisella tularensis
, a bacterial biothreat agent, has no approved vaccine in the United States. Previously, we showed that incorporating lysates from partially attenuated
F. tularensis
LVS or fully virulent
F. tularensis
Schu S4 strains into catanionic surfactant vesicle (V) nanoparticles (LVS-V and Schu S4-V, respectively) protected fully against
F. tularensis
LVS intraperitoneal (i.p.) challenge in mice. However, we achieved only partial protection against
F. tularensis
Schu S4 intranasal (i.n.) challenge, even when employing heterologous prime-boost immunization strategies. We now extend these findings to show that both LVS-V and Schu S4-V immunization (i.p./i.p.) elicited similarly high titers of anti-
F. tularensis
IgG and that the titers could be further increased by adding monophosphoryl lipid A (MPL), a nontoxic Toll-like receptor 4 (TLR4) adjuvant that is included in several U.S. FDA-approved vaccines. LVS-V+MPL immune sera also detected more
F. tularensis
antigens than LVS-V immune sera and, after passive transfer to naive mice, significantly delayed the time to death against
F. tularensis
Schu S4 subcutaneous (s.c.) but not i.n. challenge. Active immunization with LVS-V+MPL (i.p./i.p.) also increased the frequency of gamma interferon (IFN-γ)-secreting activated helper T cells, IFN-γ production, and the ability of splenocytes to control intramacrophage
F. tularensis
LVS replication
ex vivo
. Active LVS-V+MPL immunization via heterologous routes (i.p./i.n.) significantly elevated IgA and IgG levels in bronchoalveolar lavage fluid and significantly enhanced protection against i.n.
F. tularensis
Schu S4 challenge (to ∼60%). These data represent a significant step in the development of a subunit vaccine against the highly virulent type A strains.
Evaluation of Alere i RSV for Rapid Detection of Respiratory Syncytial Virus in Children Hospitalized with Acute Respiratory Tract Infection
Authors: Peters Rebecca Marie , Schnee Sarah Valerie , Tabatabai Julia , Schnitzler Paul , Pfeil Johannes
Published: January 2017

Alere i RSV is a novel rapid test which applies a nicking enzyme amplification reaction to detect respiratory syncytial virus in point-of-care settings. In this study, we evaluated the Alere i RSV assay by using frozen nasopharyngeal swab samples that were collected in viral transport medium from children hospitalized with acute respiratory tract infection during the 2015-2016 winter season. Alere i RSV assay results were compared to those for Altona RealStar RSV real-time reverse transcription-PCR (RT-PCR). We found that the overall sensitivity and specificity of the Alere i RSV test was 100% (95% confidence intervals [CI], 93% to 100%) and 97% (95% CI, 89% to 100%), respectively. Positive samples were identified within 5 to 7 min from sample collection. Overall, the Alere i RSV test performed well compared to the RT-PCR assay and has the potential to facilitate the detection of RSV in point-of-care settings.
Melanin or a Melanin-Like Substance Interacts with the N-Terminal Portion of Prion Protein and Inhibits Abnormal Prion Protein Formation in Prion-Infected Cells
Authors: Hamanaka Taichi , Nishizawa Keiko , Sakasegawa Yuji , Oguma Ayumi , Teruya Kenta , Kurahashi Hiroshi , Hara Hideyuki , Sakaguchi Suehiro , Doh-ura Katsumi
Published: January 2017

Prion diseases are progressive fatal neurodegenerative illnesses caused by the accumulation of transmissible abnormal prion protein (PrP). To find treatments for prion diseases, we searched for substances from natural resources that inhibit abnormal PrP formation in prion-infected cells. We found that high-molecular-weight components from insect cuticle extracts reduced abnormal PrP levels. The chemical nature of these components was consistent with that of melanin. In fact, synthetic melanin produced from tyrosine or 3-hydroxy-l-tyrosine inhibited abnormal PrP formation. Melanin did not modify cellular or cell surface PrP levels, nor did it modify lipid raft or cellular cholesterol levels. Neither did it enhance autophagy or lysosomal function. Melanin was capable of interacting with PrP at two N-terminal domains. Specifically, it strongly interacted with the PrP region of amino acids 23 to 50 including a positively charged amino acid cluster and weakly interacted with the PrP octarepeat peptide region of residues 51 to 90. However, thein vitroandin vivodata were inconsistent with those of prion-infected cells. Abnormal PrP formation in protein misfolding cyclic amplification was not inhibited by melanin. Survival after prion infection was not significantly altered in albino mice or exogenously melanin-injected mice compared with that of control mice. These data suggest that melanin, a main determinant of skin color, is not likely to modify prion disease pathogenesis, even though racial differences in the incidence of human prion diseases have been reported. Thus, the findings identify an interaction between melanin and the N terminus of PrP, but the pathophysiological roles of the PrP-melanin interaction remain unclear.

IMPORTANCEThe N-terminal region of PrP is reportedly important for neuroprotection, neurotoxicity, and abnormal PrP formation, as this region is bound by many factors, such as metal ions, lipids, nucleic acids, antiprion compounds, and several proteins, including abnormal PrP in prion disease and the Aβ oligomer in Alzheimer's disease. In the present study, melanin, a main determinant of skin color, was newly found to interact with this N-terminal region and inhibits abnormal PrP formation in prion-infected cells. However, the data for prion infection in mice lacking melanin production suggest that melanin is not associated with the prion disease mechanism, although the incidence of prion disease is reportedly much higher in white people than in black people. Thus, the roles of the PrP-melanin interaction remain to be further elucidated, but melanin might be a useful competitive tool for evaluating the functions of other ligands at the N-terminal region.
Expression of
Ifnlr1
on Intestinal Epithelial Cells Is Critical to the Antiviral Effects of Interferon Lambda against Norovirus and Reovirus
Authors: Baldridge Megan T. , Lee Sanghyun , Brown Judy J. , McAllister Nicole , Urbanek Kelly , Dermody Terence S. , Nice Timothy J. , Virgin Herbert W.
Published: January 2017

Lambda interferon (IFN-λ) has potent antiviral effects against multiple enteric viral pathogens, including norovirus and rotavirus, in both preventing and curing infection. Because the intestine includes a diverse array of cell types, however, the cell(s) upon which IFN-λ acts to exert its antiviral effects is unclear. Here, we sought to identify IFN-λ-responsive cells by generation of mice with lineage-specific deletion of the receptor for IFN-λ,
Ifnlr1
. We found that expression of IFNLR1 on intestinal epithelial cells (IECs) in the small intestine and colon is required for enteric IFN-λ antiviral activity. IEC
Ifnlr1
expression also determines the efficacy of IFN-λ in resolving persistent murine norovirus (MNoV) infection and regulates fecal shedding and viral titers in tissue. Thus, the expression of
Ifnlr1
by IECs is necessary for the response to both endogenous and exogenous IFN-λ. We further demonstrate that IEC
Ifnlr1
expression is required for the sterilizing innate immune effects of IFN-λ by extending these findings in
Rag1
-deficient mice. Finally, we assessed whether our findings pertained to multiple viral pathogens by infecting mice specifically lacking IEC
Ifnlr1
expression with reovirus. These mice phenocopied
Ifnlr1
-null animals, exhibiting increased intestinal tissue titers and enhanced reovirus fecal shedding. Thus, IECs are the critical cell type responding to IFN-λ to control multiple enteric viruses. This is the first genetic evidence that supports an essential role for IECs in IFN-λ-mediated control of enteric viral infection, and these findings provide insight into the mechanism of IFN-λ-mediated antiviral activity.

IMPORTANCE
Human noroviruses (HNoVs) are the leading cause of epidemic gastroenteritis worldwide. Type III interferons (IFN-λ) control enteric viral infections in the gut and have been shown to cure mouse norovirus, a small-animal model for HNoVs. Using a genetic approach with conditional knockout mice, we identified IECs as the dominant IFN-λ-responsive cells in control of enteric virus infection
in vivo
. Upon murine norovirus or reovirus infection,
Ifnlr1
depletion in IECs largely recapitulated the phenotype seen in
Ifnlr1
−/−
mice of higher intestinal tissue viral titers and increased viral shedding in the stool. Moreover, IFN-λ-mediated sterilizing immunity against murine norovirus requires the capacity of IECs to respond to IFN-λ. These findings clarify the mechanism of action of this cytokine and emphasize the therapeutic potential of IFN-λ for treating mucosal viral infections.
Exosome-Mediated Intercellular Communication between Hepatitis C Virus-Infected Hepatocytes and Hepatic Stellate Cells
Authors: Devhare Pradip B. , Sasaki Reina , Shrivastava Shubham , Di Bisceglie Adrian M. , Ray Ranjit , Ray Ratna B.
Published: January 2017

Fibrogenic pathways in the liver are principally regulated by activation of hepatic stellate cells (HSC). Fibrosis is associated with chronic hepatitis C virus (HCV) infection, although the mechanism is poorly understood. HSC comprise the major population of nonparenchymal cells in the liver. Since HCV does not replicate in HSC, we hypothesized that exosomes secreted from HCV-infected hepatocytes activate HSC. Primary or immortalized human hepatic stellate (LX2) cells were exposed to exosomes derived from HCV-infected hepatocytes (HCV-exo), and the expression of fibrosis-related genes was examined. Our results demonstrated that HCV-exo internalized to HSC and increased the expression of profibrotic markers. Further analysis suggested that HCV-exo carry miR-19a and target SOCS3 in HSC, which in turn activates the STAT3-mediated transforming growth factor β (TGF-β) signaling pathway and enhances fibrosis marker genes. The higher expression of miR-19a in exosomes was also observed from HCV-infected hepatocytes and in sera of chronic HCV patients with fibrosis compared to healthy volunteers and non-HCV-related liver disease patients with fibrosis. Together, our results demonstrated that miR-19a carried through the exosomes from HCV-infected hepatocytes activates HSC by modulating the SOCS-STAT3 axis. Our results implicated a novel mechanism of exosome-mediated intercellular communication in the activation of HSC for liver fibrosis in HCV infection.

IMPORTANCE
HCV-associated liver fibrosis is a critical step for end-stage liver disease progression. However, the molecular mechanisms for hepatic stellate-cell activation by HCV-infected hepatocytes are underexplored. Here, we provide a role for miR-19a carried through the exosomes in intercellular communication between HCV-infected hepatocytes and HSC in fibrogenic activation. Furthermore, we demonstrate the role of exosomal miR-19a in activation of the STAT3–TGF-β pathway in HSC. This study contributes to the understanding of intercellular communication in the pathogenesis of liver disease during HCV infection.
Role of Litopenaeus vannamei Yin Yang 1 in the Regulation of the White Spot Syndrome Virus Immediate Early Gene
ie1
Authors: Huang Ping-Han , Huang Ting-Yi , Cai Pei-Si , Chang Li-Kwan
Published: January 2017

Yin Yang 1 (YY1) is a multifunctional zinc finger transcription factor that regulates many key cellular processes. In this study, we report the cloning of YY1 from
Litopenaeus vannamei
shrimp (LvYY1). This study shows that LvYY1 is ubiquitously expressed in shrimp tissues, and knockdown of LvYY1 expression by double-stranded RNA (dsRNA) injection in white spot syndrome virus (WSSV)-infected shrimp reduced both mRNA levels of the WSSV immediate early gene
ie1
as well as overall copy numbers of the WSSV genome. The cumulative mortality rate of infected shrimp also declined with LvYY1 dsRNA injection. Using an insect cell model, we observed that LvYY1 activates
ie1
expression, and a mutation introduced into the
ie1
promoter subsequently repressed this capability. Moreover, reporter assay results suggested that LvYY1 is involved in basal transcriptional regulation via an interaction with
L. vannamei
TATA-binding protein (LvTBP). Electrophoretic mobility shift assay (EMSA) results further indicated that LvYY1 binds to a YY1-binding site in the region between positions −119 and −126 in the
ie1
promoter. Chromatin immunoprecipitation analysis also confirmed that LvYY1 binds to the
ie1
promoter in WSSV-infected shrimp. Taken together, these results indicate that WSSV uses host LvYY1 to enhance
ie1
expression via a YY1-binding site and the TATA box in the
ie1
promoter, thereby facilitating lytic activation and viral replication.

IMPORTANCE
WSSV has long been a scourge of the shrimp industry and remains a serious global threat. Thus, there is a pressing need to understand how the interactions between WSSV and its host drive infection, lytic development, pathogenesis, and mortality. Our successful cloning of
L. vannamei
YY1 (LvYY1) led to the elucidation of a critical virus-host interaction between LvYY1 and the WSSV immediate early gene
ie1
. We observed that LvYY1 regulates
ie1
expression via a consensus YY1-binding site and TATA box. LvYY1 was also found to interact with
L. vannamei
TATA-binding protein (LvTBP), which may have an effect on basal transcription. Knockdown of LvYY1 expression inhibited
ie1
transcription and subsequently reduced viral DNA replication and decreased cumulative mortality rates of WSSV-infected shrimp. These findings are expected to contribute to future studies involving WSSV-host interactions.