bluuebunny/crossref_metadata_2025 huggingface dataset:
The Sociocognitive Imperative of L2 Pedagogy
Authors: Toth Paul D. , Davin Kristin J.
Published: February 2016

As a new century begins for The Modern Language Journal, we argue that highly effective pedagogy requires viewing language and language learning as both cognitive and social phenomena, and that teachers who seek to truly understand the nature of their responsibilities do not have the luxury of choosing one perspective over the other. We first identify what we consider to be theory‐neutral nonnegotiable boundaries within which pedagogical decision making takes place, including (a) participants’ background knowledge, (b) the nature of the object of instruction, (c) the nature of human cognition and social interaction, and (d) available time. Then we discuss learning goals, learning means, and instructional support as the negotiable elements that teachers may manipulate through their instructional decisions. At the heart of the article, we describe in greater detail cognitive versus social perspectives on the dynamic relationship between teaching and learning, and we identify ways in which they diverge and converge in characterizing linguistic development. We then synthesize these perspectives in a holistic, sociocognitive view of pedagogy, which we define as ‘a meeting of minds within social worlds.’ We conclude by outlining current pedagogical proposals that exemplify sociocognitive pedagogy by engaging learners in iterative cycles of modeling, guidance, and handover to independent language use.
Improvement of meal‐related symptoms and epigastric pain in patients with functional dyspepsia treated with acotiamide was associated with acylated ghrelin levels in Japan
Authors: Yamawaki H. , Futagami S. , Kawagoe T. , Maruki Y. , Hashimoto S. , Nagoya H. , Sato H. , Kodaka Y. , Gudis K. , Akamizu T. , Sakamoto C. , Iwakiri K.
Published: February 2016

Background

The aim of this study is to clarify whether acotiamide and rabeprazole combination therapy can improve clinical symptoms, gastric emptying, and satisfaction with treatment in functional dyspepsia (FD) patients more effectively than acotiamide or rabeprazole monotherapy alone. We also aimed to determine whether acotiamide affects these changes via its effect on gastric emptying and appetite‐related hormones such as ghrelin.

Methods

We used Rome III criteria to evaluate upper abdominal symptoms and anxiety by the State‐Trait Anxiety Inventory (STAI). Gastric motility was evaluated by the 13C‐acetate breath test. Eighty‐one FD patients were treated with acotiamide (300 mg/day) (n = 35), acotiamide (300 mg/day) and rabeprazole (10 mg/day) (n = 28), or rabeprazole (10 mg/day) (n = 18) for a period of 4 weeks and followed after 4 weeks of no treatment. Adenocorticotropic hormone (ACTH), cortisol, leptin and ghrelin levels were measured in all FD patients.

Key Results

Acotiamide and rabeprazole combination therapy significantly improved postprandial distress syndrome (PDS)‐like symptoms (p = 0.018, p = 0.04 and p = 0.041, respectively) and epigastric pain (p = 0.024) as wells as STAI‐state scores (p = 0.04) compared to rabeprazole monotherapy. Both acotiamide monotherapy, and acotiamide taken in combination with rabeprazole, significantly (p = 0.001 and p = 0.02, respectively) improved satisfaction with treatment, compared to rabeprazole monotherapy. Acotiamide and rabeprazole combination therapy had no significant effect on ACTH and cortisol levels in FD patients. Of interest, acotiamide monotherapy, and acotiamide and rabeprazole combination therapy, significantly (p < 0.0001 and p = 0.018, respectively) increased acylated ghrelin/total ghrelin ratios and significantly (p = 0.04) improved impaired gastric emptying compared to rabeprazole monotherapy.

Conclusions & Inferences

Further studies are warranted to clarify how acotiamide treatment improves clinical symptoms in FD patients.
Induced plant volatiles: plant body odours structuring ecological networks
Authors: Dicke Marcel
Published: February 2016

This article is a Commentary on Rowen & Kaplan, 210: 284‐294.
The dope on l‐DOPA formation for betalain pigments
Authors: Schwinn Kathy E.
Published: February 2016

This article is a Commentary on Polturak et al., 210: 269‐283.
European Integration and the Feldstein–Horioka Puzzle
Authors: Katsimi Margarita , Zoega Gylfi
Published: February 2016

We apply the differences‐in‐differences method to study the effect of the European single market in 1993 and the euro in 1999 on the Feldstein–Horioka equation where countries outside the single market serve as a control group and those within as a treatment group. We find structural breaks that coincide with both events, in addition to the financial crisis in 2008. The results suggest that the correlation between investment and savings depends on institutions, exchange rate risk and credit risk. Furthermore, the pattern of capital flows within the single market leaves a significant part of the flows unexplained by fundamentals.
Bipolar Versus Unipolar Temporary Epicardial Ventricular Pacing Leads Use in Congenital Heart Disease: A Prospective Randomized Controlled Study
Authors: MOHARI NIVEDITA , STARR JOANNE P. , GATES RICHARD N. , DOMICO MICHELE B. , BATRA ANJAN S.
Published: February 2016

Background

To compare the pacing parameters of unipolar versus bipolar temporary ventricular epicardial pacing leads.

Design

Prospective Randomized Unblinded Controlled Study.

Patients and Methods

Fifty patients undergoing surgery for congenital heart disease who were anticipated to require temporary ventricular pacing leads were recruited preoperatively: 25 patients were randomized to receive unipolar temporary ventricular epicardial pacing leads; the remaining 25 were randomized to receive bipolar temporary ventricular epicardial leads. The baseline characteristics of the groups were similar. The pacing parameters were measured daily for up to first seven postoperative days (PODs) with the day of surgery recorded as POD 0.

Results

On the day of insertion, the mean pacing and sensing thresholds were similar for both unipolar and bipolar leads. Thresholds progressively deteriorated with each subsequent POD. By POD 4, the mean ± standard deviation pacing threshold of ventricular bipolar lead was 2.87 ± 0.37 mA compared with 5.6 ± 0.85 mA for the unipolar leads (P = 0.005). The decrease in sensing threshold of the unipolar ventricular pacing leads was significantly more than that of bipolar leads (by POD 5, 5.7 ± 2.64 vs 10.33 ± 2.8, P = 0.01).

Conclusions

Our study shows that the bipolar leads (Medtronic 6495, Medtronic Inc., Minneapolis, MN, USA) have superior sensing and pacing thresholds in the ventricular position in patients undergoing surgery for congenital heart disease when compared to the unipolar leads (Medical Concepts Europe VF608ABB, Medical Concepts Europe Inc., Buffalo, NY, USA).
Precocious flowering of juvenile citrus induced by a viral vector based on Citrus leaf blotch virus: a new tool for genetics and breeding
Authors: Velázquez Karelia , Agüero Jesús , Vives María C. , Aleza Pablo , Pina José A. , Moreno Pedro , Navarro Luis , Guerri José
Published: February 2016

The long juvenile period of citrus trees (often more than 6 years) has hindered genetic improvement by traditional breeding methods and genetic studies. In this work, we have developed a biotechnology tool to promote transition from the vegetative to the reproductive phase in juvenile citrus plants by expression of the Arabidopsis thaliana or citrus FLOWERING LOCUS T (FT) genes using a Citrus leaf blotch virus‐based vector (clbvINpr‐AtFT and clbvINpr‐CiFT, respectively). Citrus plants of different genotypes graft inoculated with either of these vectors started flowering within 4–6 months, with no alteration of the plant architecture, leaf, flower or fruit morphology in comparison with noninoculated adult plants. The vector did not integrate in or recombine with the plant genome nor was it pollen or vector transmissible, albeit seed transmission at low rate was detected. The clbvINpr‐AtFT is very stable, and flowering was observed over a period of at least 5 years. Precocious flowering of juvenile citrus plants after vector infection provides a helpful and safe tool to dramatically speed up genetic studies and breeding programmes.
Roles of reactive oxygen species in UVA‐induced oxidation of 5,6‐dihydroxyindole‐2‐carboxylic acid‐melanin as studied by differential spectrophotometric method
Authors: Ito Shosuke , Kikuta Marina , Koike Shota , Szewczyk Grzegorz , Sarna Michal , Zadlo Andrzej , Sarna Tadeusz , Wakamatsu Kazumasa
Published: February 2016

Eumelanin photoprotects pigmented tissues from ultraviolet (UV) damage. However, UVA‐induced tanning seems to result from the photooxidation of preexisting melanin and does not contribute to photoprotection. We investigated the mechanism of UVA‐induced degradation of 5,6‐dihydroxyindole‐2‐carboxylic acid (DHICA)‐melanin taking advantage of its solubility in a neutral buffer and using a differential spectrophotometric method to detect subtle changes in its structure. Our methodology is suitable for examining the effects of various agents that interact with reactive oxygen species (ROS) to determine how ROS is involved in the UVA‐induced oxidative modifications. The results show that UVA radiation induces the oxidation of DHICA to indole‐5,6‐quinone‐2‐carboxylic acid in eumelanin, which is then cleaved to form a photodegraded, pyrrolic moiety and finally to form free pyrrole‐2,3,5‐tricarboxylic acid. The possible involvement of superoxide radical and singlet oxygen in the oxidation was suggested. The generation and quenching of singlet oxygen by DHICA‐melanin was confirmed by direct measurements of singlet oxygen phosphorescence.
Developmental characteristics of urinary coproporphyrin I/(I + III) ratio
Authors: Kunikata Jun , Okada Hitoshi , Itoh Susumu , Kusaka Takashi
Published: February 2016

Background

The ratio of urinary coproporphyrin (UCP) I to total urinary coproporphyrin I and III [UCP {I/(I + III)]] serves as a biomarker of the ATP‐binding cassette, sub‐family C, member 2 (ABCC2) function. The aim of this study was to clarify the characteristics of the developmental pattern of UCP [I/(I + III)] in order to estimate ABCC2 function in children, especially in the neonatal period, by measuring it throughout the entirety of childhood.

Method

Measurement of UCP [I/(I + III)] was done high‐performance liquid chromatography, using urine samples collected from children from 1 day to 15 years old, involving one sample per child. Urine samples from children with liver and kidney disease and urinary tract infection were excluded.

Results

UCP [I/(I + III)] varied widely in infants younger than 6 months old, and was ≥0.3 in 80% of the infants. In contrast, it decreased to <0.30, the lowest, at 1–2 years old. In the 0–6‐month‐old group, no significant correlation was noted between postnatal age and UCP [I/(I + III)], but a moderate inverse correlation was noted between corrected gestational age and UCP [I/(I + III)].

Conclusion

UCP [I/(I + III)] is inversely correlated with corrected gestational age and is lowest at 1–2 years old. This suggests that ABCC2 activity is correlated with corrected gestational age and is highest at 1–2 years old.
Infections and neutrophils in the pathogenesis of bronchiolitis obliterans syndrome in children after allogeneic stem cell transplantation
Authors: Gassas Adam , Krueger Joerg , Zaidman Irina , Schechter Tal , Craig‐Barnes Hayley , Ali Muhammad , Palaniyar Nades
Published: February 2016

It is plausible that infections post‐hematopoietic SCT play a role in the pathogenesis of BOS. A prospective study for children with history, questionnaire, examination, PFTs, and blood counts at one, three, six, nine, 12, 18, and 24 months post‐SCT was conducted. Between September 2009 and September 2011 (n = 39), six developed BOS at 200 days (range 94–282), three patients had probable clinical respiratory infection, and all six had higher neutrophil count compared to non‐BOS patients (4.7 vs. 2.4 at three months and 6.3 vs. 2.9 at six months ×109/L, p = 0.03). Contribution of clinical and subclinical infection needs to be considered in the pathogenesis of BOS.
The Narrative Rationality of Violent Extremism
Authors: Corman Steven R.
Published: February 2016

Objective

This essay explores the narratives that are used to justify terrorist attacks by perpetrators and their supporters.

Method

The author examines the ways in which narratives rationalizing violence have been constructed and repeated by Islamist extremists and, in the case of Oklahoma City bombing, by McVeigh and other members of the Patriot movement.

Results

The analysis of these two case studies demonstrates the power of narrative rationality to motivate terrorist acts and suggests narrative counterstrategies are key to undermining that power.
Operational Dynamics of Boko Haram's Terrorist Campaign Following Leadership Succession
Authors: Regens James L. , Mould Nick , Vernon Elizabeth , Montgomery Amanda
Published: February 2016

Objective

This article analyzes the operational dynamics of Boko Haram, the largest radical Islamist organization engaged in acts of terrorism in Nigeria.

Method

We analyze Boko Haram's terrorist campaign using information gathered from 1,086 successful attacks that occurred between July 2009 and December 2014. We examine the operational tempo of attacks on a monthly basis, identify the primary tactics employed in and targets of those attacks, and assess the outcome of each successful attack in terms of severity metrics.

Results

We find that despite leadership changes, Boko Haram has increased the frequency of attacks, gained international media attention, and continues to pose a serious threat to security in West Africa.

Conclusions

The analysis provides a series of insights into why Boko Haram was able to complete a leadership succession and achieve this success after its initial defeat despite internal and external factors that have undermined prior terrorist campaigns. Consequently, unless the internal and/or external dynamics are altered, Boko Haram is likely to continue to conduct attacks and remain a serious threat to Nigeria and to the security of adjoining countries in West Africa.
Media in the Wake of the Alfred P. Murrah Federal Building Bombing: A 20‐Year Retrospective*
Authors: Fenwick Ben
Published: February 2016

Objective

This essay examines how communications breakdowns in the aftermath of the 1995 bombing of the Alfred P. Murrah Federal Building in Oklahoma City led to errors in media reports.

Method

Drawing on my personal experience as a journalist who covered the event, combined with a comprehensive review of accounts and reports published since 1995, this essay examines how the errors originated and were disseminated. Furthermore, it reviews the communications systems in place then and now in order to consider how media and government might best confront communications challenges in postdisaster situations.

Results

The analysis of communications problems and errors in reporting offers lessons as to how government officials and media might better coordinate efforts to avoid such errors in the case of terrorist events.
The Social Impact of Terrorism on Civilian Populations: Lessons Learned from Decades of Terrorism in Israel and Abroad
Authors: Siman‐Tov Maya , Bodas Moran , Peleg Kobi
Published: February 2016

Objective

This article considers the sociopsychological implications of terrorism, which are sometimes neglected in preparedness plans.

Methods

Using Israeli experiences as a case study, this article briefly reviews four points of connection between terrorism and its psychological and social legacies: the sociopolitical aspects of terrorism, the unexpected nature of terrorism, normalization of terrorism and public resilience, and social aspects of medical care for terror‐related injuries.

Results

The Israeli experience suggests preparedness plans should include planning for the sociopsychological effects of terrorism on targeted populations and may, in certain contexts, use Israeli approaches as a model.

Conclusions

Experience gained in Israel and elsewhere can set the stage for an appropriate response plan striving not only for preparedness but also resilience. Efforts should be made to advance local capabilities, response plans, and resilience by drawing on the experience of others in coping with the terror threat.
Interview with Hans Butzer and Torrey Butzer, Designers of the Oklahoma City National Memorial*
Authors: Person Angela , Butzer Hans E. , Butzer Torrey
Published: February 2016

Objective

This interview with Hans Butzer and Torrey Butzer, designers of the Oklahoma City National Memorial, documents their experience learning about the bombing while living in Germany, as well as specific challenges they encountered during the design and construction process.

Method

The Butzers describe their memories of the event and traveling to Oklahoma City for the jury after being named finalists, where the project became “a very personal matter where our work would potentially impact how others would understand life, death and fate.” After learning they won the design competition, the Butzers worked with the community to finalize their design for the site, and recall memorable exchanges with community members during this process.

Results

The Butzers recount how they feel the community has responded to their lasting presence in the city ever since the completion of the memorial.

Conclusion

The Butzers' participatory design of the Oklahoma City National Memorial continues to offer “comfort, strength, peace, hope, and serenity” and to serve as a symbol of resilience in its community.
A Survivor's Perspective on Memory and Memorial Culture: Recollections on the 20th Anniversary of the Oklahoma City Bombing*
Authors: Williamson Jason
Published: February 2016

Objective

In this essay, Jason Williamson, a survivor of the Murrah building bombing, recounts how his memories of the event have evolved since 1995.

Method

This first‐person narrative reflection offers insight into how individual memories intersect with public memorial culture.

Results

The essay details the dynamic and at times perplexing relationship between Williamson's memories and the public memorials and events.
Differential ecological traits of two Phlebotomus sergenti mitochondrial lineages in southwestern Europe and their epidemiological implications
Authors: Merino‐Espinosa G. , Corpas‐López V. , Callejón‐Fernández R. , Porcel‐Rodríguez L. , Díaz‐Sáez V. , Gállego M. , Ballart C. , Molina R. , Jiménez M. , Morillas‐Márquez F. , Martín‐Sánchez J.
Published: February 2016

Objectives

The introduction of leishmaniasis in a new area requires a well‐established population of the sandfly vector species of the parasite. No autochthonous cases of anthroponotic cutaneous leishmaniasis have been detected in southwestern Europe, and Leishmania infantum is the only causative agent of leishmaniasis in this area. Phlebotomus sergenti, the main vector of Leishmania tropica, is commonly found in the Iberian Peninsula at sufficient densities to be able to act as a vector. It is characterised by high genetic diversity and classified in four mitochondrial lineages. Our aim was to analyse the composition and distribution of P. sergenti mitochondrial lineages in southwestern Europe given the possibility of phenotypic differences of biomedical importance between them.

Methods

Sandflies were captured in the Iberian Peninsula and on the Canary and Balearic Islands. Mitochondrial lineage identification of 137 P. sergenti was performed using a novel PCR‐RFLP that avoids the necessity of gene sequencing.

Results

Two lineages were evidenced, the typical Iberian one (lineage I) and another, held in common with North Africa (lineage III), that show a distinctive distribution. P. sergenti lineage I shows a better correlation to the bioclimatic diversity in southwestern Europe. Conversely, P. sergenti lineage III prefers warmer temperatures and less precipitation, which are typical of the Mediterranean.

Conclusion

Lineage I seems to have adaptive advantages given its wider tolerance to temperature and altitude than lineage III, and it would seem more suitable to lead a potential geographical expansion towards the rest of Europe.
Characterization of type 2 diacylglycerol acyltransferases in Chlamydomonas reinhardtii reveals their distinct substrate specificities and functions in triacylglycerol biosynthesis
Authors: Liu Jin , Han Danxiang , Yoon Kangsup , Hu Qiang , Li Yantao
Published: February 2016

Diacylglycerol acyltransferases (DGATs) catalyze a rate‐limiting step of triacylglycerol (TAG) biosynthesis in higher plants and yeast. The genome of the green alga Chlamydomonas reinhardtii has multiple genes encoding type 2 DGATs (DGTTs). Here we present detailed functional and biochemical analyses of Chlamydomonas DGTTs. In vitro enzyme analysis using a radiolabel‐free assay revealed distinct substrate specificities of three DGTTs: CrDGTT1 preferred polyunsaturated acyl CoAs, CrDGTT2 preferred monounsaturated acyl CoAs, and CrDGTT3 preferred C16 CoAs. When diacylglycerol was used as the substrate, CrDGTT1 preferred C16 over C18 in the sn‐2 position of the glycerol backbone, but CrDGTT2 and CrDGTT3 preferred C18 over C16. In vivo knockdown of CrDGTT1, CrDGTT2 or CrDGTT3 resulted in 20–35% decreases in TAG content and a reduction of specific TAG fatty acids, in agreement with the findings of the in vitro assay and fatty acid feeding test. These results demonstrate that CrDGTT1, CrDGTT2 and CrDGTT3 possess distinct specificities toward acyl CoAs and diacylglycerols, and may work in concert spatially and temporally to synthesize diverse TAG species in C. reinhardtii. CrDGTT1 was shown to prefer prokaryotic lipid substrates and probably resides in both the endoplasmic reticulum and chloroplast envelope, indicating its role in prokaryotic and eukaryotic TAG biosynthesis. Based on these findings, we propose a working model for the role of CrDGTT1 in TAG biosynthesis. This work provides insight into TAG biosynthesis in C. reinhardtii, and paves the way for engineering microalgae for production of biofuels and high‐value bioproducts.
Nitrogen starvation‐induced accumulation of triacylglycerol in the green algae: evidence for a role forROC40, a transcription factor involved in circadian rhythm
Authors: Goncalves Elton C. , Koh Jin , Zhu Ning , Yoo Mi‐Jeong , Chen Sixue , Matsuo Takuya , Johnson Jodie V. , Rathinasabapathi Bala
Published: February 2016

Microalgal triacylglycerol (TAG), a promising source of biofuel, is induced upon nitrogen starvation (−N), but the proteins and genes involved in this process are poorly known. We performed isobaric tagging for relative and absolute quantification (iTRAQ)‐based quantitative proteomics to identifyChlorellaproteins with modulated expression under short‐term −N. Out of 1736 soluble proteins and 2187 membrane‐associated proteins identified, 288 and 56, respectively, were differentially expressed under −N. Gene expression analysis on select genes confirmed the same direction ofmRNAmodulation for most proteins. TheMYB‐related transcription factorROC40 was the most induced protein, with a 9.6‐fold increase upon −N. In a previously generatedChlamydomonasmutant, gravimetric measurements of crude total lipids revealed thatroc40was impaired in its ability to increase the accumulation ofTAGupon −N, and this phenotype was complemented when wild‐type Roc40 was expressed. Results from radiotracer experiments were consistent with theroc40mutant being comparable to the wild type in recycling membrane lipids toTAGbut being impaired in additionalde novosynthesis ofTAGduring −N stress. In this study we provide evidence to support the hypothesis that transcription factorROC40 has a role in −N‐induced lipid accumulation, and uncover multiple previously unknown proteins modulated by short‐term −N in green algae.
Renal biomarkers in domestic species
Authors: Hokamp Jessica A. , Nabity Mary B.
Published: February 2016

Current conventional tests of kidney damage and function in blood (serum creatinine and urea nitrogen) and urine (urine protein creatinine ratio and urine specific gravity) are widely used for diagnosis and monitoring of kidney disease. However, they all have important limitations, and additional markers of glomerular filtration rate and glomerular and tubular damage are desirable, particularly for earlier detection of renal disease when therapy is most effective. Additionally, urinary markers of kidney damage and function may help localize damage to the affected portion of the kidney. In general, the presence of high‐ and intermediate‐molecular weight proteins in the urine are indicative of glomerular damage, while low‐molecular weight proteins and enzymes in the urine suggest tubular damage due to decreased reabsorption of proteins, direct tubular damage, or both. This review aims to discuss many of these new blood and urinary biomarkers in domestic veterinary species, focusing primarily on dogs and cats, how they may be used for diagnosis of renal disease, and their limitations. Additionally, a brief discussion of serum creatinine is presented, highlighting its limitations and important considerations for its improved interpretation in domestic species based on past literature and recent studies.
Sysmex XT‐2000iV scattergram analysis in a cat with basophilia
Authors: Stranieri Angelica , Ferrari Roberta , Zanzani Sergio , Rossi Gabriele
Published: February 2016

A 13‐year‐old female Domestic Shorthair cat was presented to the Veterinary Teaching Hospital of the University of Milan for an interscapular mass suspected to be a mesenchymal malignant tumor. A preoperative CBC performed with Sysmex XT‐2000iV showed leukocytosis with neutrophilia and eosinophilia. The Sysmex WBC/DIFF scattergram showed an additional, well‐separated cluster of events between the neutrophil, eosinophil, and lymphocyte clusters. Blood smear evaluation revealed the presence of a significant number of basophils; thus, it was hypothesized that the additional cluster could represent the basophilic population. A second CBC, 24 days later, showed the same pattern on the WBC/DIFF scattergram in the absence of leukocytosis and neutrophilia. After surgical excision of the mass, a definitive diagnosis of feline injection site sarcoma was made. To the author's knowledge, there are no previous reports about the identification of feline basophils in the WBC/DIFF scattergram of Sysmex XT‐2000iV.
The ageing neuromuscular system and sarcopenia: a mitochondrial perspective
Authors: Rygiel Karolina A. , Picard Martin , Turnbull Doug M.
Published: February 2016

Skeletal muscles undergo structural and functional decline with ageing, culminating in sarcopenia. The underlying neuromuscular mechanisms have been the subject of intense investigation, revealing mitochondrial abnormalities as potential culprits within both nerve and muscle cells. Implicated mechanisms involve impaired mitochondrial dynamics, reduced organelle biogenesis and quality control via mitophagy, accumulation of mitochondrial DNA (mtDNA) damage and respiratory chain defect, metabolic disturbance, pro‐apoptotic signalling, and oxidative stress. This article provides an overview of the cellular mechanisms whereby mitochondria may promote maladaptive changes within motor neurons, the neuromuscular junction (NMJ) and muscle fibres. Lifelong physical activity, which promotes mitochondrial health across tissues, is emerging as an effective countermeasure for sarcopenia.

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Application of systems and control theory‐based hazard analysis to radiation oncology
Authors: Pawlicki Todd , Samost Aubrey , Brown Derek W. , Manger Ryan P. , Kim Gwe‐Ya , Leveson Nancy G.
Published: February 2016

Purpose:

Both humans and software are notoriously challenging to account for in traditional hazard analysis models. The purpose of this work is to investigate and demonstrate the application of a new, extended accident causality model, called systems theoretic accident model and processes (STAMP), to radiation oncology. Specifically, a hazard analysis technique based on STAMP, system‐theoretic process analysis (STPA), is used to perform a hazard analysis.

Methods:

The STPA procedure starts with the definition of high‐level accidents for radiation oncology at the medical center and the hazards leading to those accidents. From there, the hierarchical safety control structure of the radiation oncology clinic is modeled, i.e., the controls that are used to prevent accidents and provide effective treatment. Using STPA, unsafe control actions (behaviors) are identified that can lead to the hazards as well as causal scenarios that can lead to the identified unsafe control. This information can be used to eliminate or mitigate potential hazards. The STPA procedure is demonstrated on a new online adaptive cranial radiosurgery procedure that omits the CT simulation step and uses CBCT for localization, planning, and surface imaging system during treatment.

Results:

The STPA procedure generated a comprehensive set of causal scenarios that are traced back to system hazards and accidents. Ten control loops were created for the new SRS procedure, which covered the areas of hospital and department management, treatment design and delivery, and vendor service. Eighty three unsafe control actions were identified as well as 472 causal scenarios that could lead to those unsafe control actions.

Conclusions:

STPA provides a method for understanding the role of management decisions and hospital operations on system safety and generating process design requirements to prevent hazards and accidents. The interaction of people, hardware, and software is highlighted. The method of STPA produces results that can be used to improve safety and prevent accidents and warrants further investigation.
3.5-Ga hydrothermal fields and diamictites in the Barberton Greenstone Belt—Paleoarchean crust in cold environments
Authors: de Wit Maarten J. , Furnes Harald
Published: February 2016

Data on 3.5-Ga volcanic and sedimentary rocks of the Barberton Greenstone Belt suggest formation in cold environments.
Constraints on Earth’s inner core composition inferred from measurements of the sound velocity of hcp-iron in extreme conditions
Authors: Sakamaki Tatsuya , Ohtani Eiji , Fukui Hiroshi , Kamada Seiji , Takahashi Suguru , Sakairi Takanori , Takahata Akihiro , Sakai Takeshi , Tsutsui Satoshi , Ishikawa Daisuke , Shiraishi Rei , Seto Yusuke , Tsuchiya Taku , Baron Alfred Q. R.
Published: February 2016

Experimental determination of
V
P
of hcp-Fe can show potential candidates for major light elements in Earth’s inner core.
Engineering two-photon high-dimensional states through quantum interference
Authors: Zhang Yingwen , Roux Filippus S. , Konrad Thomas , Agnew Megan , Leach Jonathan , Forbes Andrew
Published: February 2016

A simple approach to preparing high-dimensional entangled states by quantum interference.
Resolving thermoelectric “paradox” in superconductors
Authors: Shelly Connor D. , Matrozova Ekaterina A. , Petrashov Victor T.
Published: February 2016

Researchers bring the theory of thermoelectricity in superconductors and experiment into agreement.
Acoustic metamaterials: From local resonances to broad horizons
Authors: Ma Guancong , Sheng Ping
Published: February 2016

A review of the development of acoustic metamaterials, guided by their physical characteristics and novel functionalities.
Bidirectional radial Ca
2+
activity regulates neurogenesis and migration during early cortical column formation
Authors: Rash Brian G. , Ackman James B. , Rakic Pasko
Published: February 2016

Calcium activity along radial glial cell fibers influences neurogenesis during early cortical column development.
Functional Analysis of an S-Layer-Associated Fibronectin-Binding Protein in Lactobacillus acidophilus NCFM
Authors: Hymes Jeffrey P. , Johnson Brant R. , Barrangou Rodolphe , Klaenhammer Todd R.
Published: February 2016

Bacterial surface layers (S-layers) are crystalline arrays of self-assembling proteinaceous subunits called S-layer proteins (Slps) that comprise the outermost layer of the cell envelope. Many additional proteins that are associated with or embedded within the S-layer have been identified in
Lactobacillus acidophilus
NCFM, an S-layer-forming bacterium that is widely used in fermented dairy products and probiotic supplements. One putative S-layer-associated protein (SLAP), LBA0191, was predicted to mediate adhesion to fibronectin based on the
in silico
detection of a fibronectin-binding domain. Fibronectin is a major component of the extracellular matrix (ECM) of intestinal epithelial cells. Adhesion to intestinal epithelial cells is considered an important trait for probiotic microorganisms during transit and potential association with the intestinal mucosa. To investigate the functional role of LBA0191 (designated FbpB) in
L. acidophilus
NCFM, an
fbpB
-deficient strain was constructed. The
L. acidophilus
mutant with a deletion of
fbpB
lost the ability to adhere to mucin and fibronectin
in vitro
. Homologues of
fbpB
were identified in five additional putative S-layer-forming species, but no homologues were detected in species outside the
L. acidophilus
homology group.
Mutations in Novel Lipopolysaccharide Biogenesis Genes Confer Resistance to Amoebal Grazing in Synechococcus elongatus
Authors: Simkovsky Ryan , Effner Emily E. , Iglesias-Sánchez Maria José , Golden Susan S.
Published: February 2016

In natural and artificial aquatic environments, population structures and dynamics of photosynthetic microbes are heavily influenced by the grazing activity of protistan predators. Understanding the molecular factors that affect predation is critical for controlling toxic cyanobacterial blooms and maintaining cyanobacterial biomass production ponds for generating biofuels and other bioproducts. We previously demonstrated that impairment of the synthesis or transport of the O-antigen component of lipopolysaccharide (LPS) enables resistance to amoebal grazing in the model predator-prey system consisting of the heterolobosean amoeba HGG1 and the cyanobacterium
Synechococcus elongatus
PCC 7942 (R. S. Simkovsky et al., Proc Natl Acad Sci U S A 109:16678–16683, 2012,
http://dx.doi.org/10.1073/pnas.1214904109
). In this study, we used this model system to identify additional gene products involved in the synthesis of O antigen, the ligation of O antigen to the lipid A-core conjugated molecule (including a novel ligase gene), the generation of GDP-fucose, and the incorporation of sugars into the lipid A core oligosaccharide of
S. elongatus
. Knockout of any of these genes enables resistance to HGG1, and of these, only disruption of the genes involved in synthesis or incorporation of GDP-fucose into the lipid A-core molecule impairs growth. Because these LPS synthesis genes are well conserved across the diverse range of cyanobacteria, they enable a broader understanding of the structure and synthesis of cyanobacterial LPS and represent mutational targets for generating resistance to amoebal grazers in novel biomass production strains.
A New Strategy for Production of 5-Aminolevulinic Acid in Recombinant Corynebacterium glutamicum with High Yield
Authors: Yang Peng , Liu Wenjing , Cheng Xuelian , Wang Jing , Wang Qian , Qi Qingsheng
Published: February 2016

5-Aminolevulinic acid (ALA), a nonprotein amino acid involved in tetrapyrrole synthesis, has been widely applied in agriculture, medicine, and food production. Many engineered metabolic pathways have been constructed; however, the production yields are still low. In this study, several 5-aminolevulinic acid synthases (ALASs) from different sources were evaluated and compared with respect to their ALA production capacities in an engineered
Corynebacterium glutamicum
CgS1 strain that can accumulate succinyl-coenzyme A (CoA). A codon-optimized ALAS from
Rhodobacter capsulatus
SB1003 displayed the best potential. Recombinant strain CgS1/pEC-SB produced 7.6 g/liter ALA using a mineral salt medium in a fed-batch fermentation mode. Employing two-stage fermentation, 12.46 g/liter ALA was produced within 17 h, with a productivity of 0.73 g/liter/h, in recombinant
C. glutamicum
. Through overexpression of the heterologous nonspecific ALA exporter RhtA from
Escherichia coli
, the titer was further increased to 14.7 g/liter. This indicated that strain CgS1/pEC-SB-rhtA holds attractive industrial application potential for the future.

IMPORTANCE
In this study, a two-stage fermentation strategy was used for production of the value-added nonprotein amino acid 5-aminolevulinic acid from glucose and glycine in a generally recognized as safe (GRAS) host,
Corynebacterium glutamicum
. The ALA titer represented the highest in the literature, to our knowledge. This high production capacity, combined with the potential easy downstream processes, made the recombinant strain an attractive candidate for industrial use in the future.
Relationship of Enhanced Butyrate Production by Colonic Butyrate-Producing Bacteria to Immunomodulatory Effects in Normal Mice Fed an Insoluble Fraction of Brassica rapa L
Authors: Tanaka Sachi , Yamamoto Kana , Yamada Kazuki , Furuya Kanon , Uyeno Yutaka
Published: February 2016

This study was performed to determine the effects of feeding a fiber-rich fraction ofBrassicavegetables on the immune response through changes in enteric bacteria and short-chain fatty acid (SCFA) production in normal mice. The boiled-water-insoluble fraction ofBrassica rapaL. (nozawana), which consists mainly of dietary fiber, was chosen as a test material. A total of 31 male C57BL/6J mice were divided into two groups and housed in a specific-pathogen-free facility. The animals were fed either a control diet or the control diet plus the insolubleB. rapaL. fraction for 2 weeks and sacrificed to determine microbiological and SCFA profiles in lower-gut samples and immunological molecules. rRNA-based quantification indicated that the relative population ofBacteroideteswas markedly lower in the colon samples of the insolubleB. rapaL. fraction-fed group than that in the controls. Populations of theEubacterium rectalegroup andFaecalibacterium prausnitzii, both of which are representative butyrate-producing bacteria, doubled after 2 weeks of fraction intake, accompanying a marginal increase in the proportion of colonic butyrate. In addition, feeding with the fraction significantly increased levels of the anti-inflammatory cytokine interleukin-10 (IL-10) and tended to increase splenic regulatory T cell numbers but significantly reduced the population of cells expressing activation markers. We demonstrated that inclusion of the boiled-water-insoluble fraction ofB. rapaL. can alter the composition of the gut microbiota to decrease the numbers ofBacteroidetesand to increase the numbers of butyrate-producing bacteria, either of which may be involved in the observed shift in the production of splenic IL-10.
Visualizing the Translocation and Localization of Bacterial Type III Effector Proteins by Using a Genetically Encoded Reporter System
Authors: Gawthorne Jayde A. , Audry Laurent , McQuitty Claire , Dean Paul , Christie John M. , Enninga Jost , Roe Andrew J.
Published: February 2016

Bacterial type III secretion system (T3SS) effector proteins are critical determinants of infection for many animal and plant pathogens. However, monitoring of the translocation and delivery of these important virulence determinants has proved to be technically challenging. Here, we used a genetically engineered LOV (light-oxygen-voltage) sensing domain derivative to monitor the expression, translocation, and localization of bacterial T3SS effectors. We found the
Escherichia coli
O157:H7 bacterial effector fusion Tir-LOV was functional following its translocation and localized to the host cell membrane in discrete foci, demonstrating that LOV-based reporters can be used to visualize the effector translocation with minimal manipulation and interference. Further evidence for the versatility of the reporter was demonstrated by fusing LOV to the C terminus of the
Shigella flexneri
effector IpaB. IpaB-LOV localized preferentially at bacterial poles before translocation. We observed the rapid translocation of IpaB-LOV in a T3SS-dependent manner into host cells, where it localized at the bacterial entry site within membrane ruffles.
Packaging of Campylobacter jejuni into Multilamellar Bodies by the Ciliate Tetrahymena pyriformis
Authors: Trigui Hana , Paquet Valérie E. , Charette Steve J. , Faucher Sébastien P.
Published: February 2016

Campylobacter jejuni
is the leading cause of bacterial gastroenteritis worldwide. Transmission to humans occurs through consumption of contaminated food or water. The conditions affecting the persistence of
C. jejuni
in the environment are poorly understood. Some protozoa package and excrete bacteria into multilamellar bodies (MLBs). Packaged bacteria are protected from deleterious conditions, which increases their survival. We hypothesized that
C. jejuni
could be packaged under aerobic conditions by the amoeba
Acanthamoeba castellanii
or the ciliate
Tetrahymena pyriformis
, both of which are able to package other pathogenic bacteria.
A. castellanii
did not produce MLBs containing
C. jejuni
. In contrast, when incubated with
T. pyriformis
,
C. jejuni
was ingested, packaged in MLBs, and then expelled into the milieu. The viability of the bacteria inside MLBs was confirmed by microscopic analyses. The kinetics of
C. jejuni
culturability showed that packaging increased the survival of
C. jejuni
up to 60 h, in contrast to the strong survival defect seen in ciliate-free culture. This study suggests that
T. pyriformis
may increase the risk of persistence of
C. jejuni
in the environment and its possible transmission between different reservoirs in food and potable water through packaging.
Versatile Vectors for Efficient Mutagenesis of Bradyrhizobium diazoefficiens and Other Alphaproteobacteria
Authors: Ledermann Raphael , Strebel Silvan , Kampik Clara , Fischer Hans-Martin
Published: February 2016

Analysis of bacterial gene function commonly relies on gene disruption or replacement followed by phenotypic characterization of the resulting mutant strains. Deletion or replacement of targeted regions is commonly achieved via two homologous recombination (HR) events between the bacterial genome and a nonreplicating plasmid carrying DNA fragments flanking the region to be deleted. The counterselection of clones that have integrated the entire plasmid in their genome via a single HR event is crucial in this procedure. Various genetic tools and well-established protocols are available for this type of mutagenesis in model bacteria; however, these methods are not always efficiently applicable in less established systems. Here we describe the construction and application of versatile plasmid vectors pREDSIX and pTETSIX for marker replacement and markerless mutagenesis, respectively. Apart from an array of restriction sites optimized for cloning of GC-rich DNA fragments, the vector backbone contains a constitutively expressed gene for mCherry, enabling the rapid identification of clones originating from single or double HR events by fluorescence-assisted cell sorting (FACS). In parallel, we constructed a series of plasmids from which gene cassettes providing resistance against gentamicin, kanamycin, hygromycin B, streptomycin and spectinomycin, or tetracycline were excised for use with pREDSIX-based marker replacement mutagenesis. In proof-of-concept mutagenesis experiments, we demonstrated the potential for the use of the developed tools for gene deletion mutagenesis in the nitrogen-fixing soybean symbiont
Bradyrhizobium diazoefficiens
(formerly
Bradyrhizobium japonicum
) and three additional members of the alphaproteobacteria.

IMPORTANCE
Mutation and phenotypic analysis are essential to the study of gene function. Efficient mutagenesis protocols and tools are available for many bacterial species, including various model organisms; however, genetic analysis of less-well-characterized organisms is often impaired by the lack of efficient methods. Here we describe a set of novel genetic tools for facilitated mutagenesis of the nitrogen-fixing soybean symbiont
Bradyrhizobium diazoefficiens
and related alphaproteobacteria. We demonstrated their usefulness by generating several mutant strains lacking defined genes. Isolation of both antibiotic resistance gene-containing and markerless deletion mutants is greatly facilitated because undesired clones which contain the entire mutagenic plasmid integrated in the genome can be identified on the basis of their fluorescent phenotype derived from the
mCherry
gene carried by the vector backbone. The possibility to generate markerless mutants assists with the isolation of strains carrying multiple deletions, which can be crucial while studying functionally redundant genes.
Just-in-time delivery of sterilised surgical instruments
Authors: Guédon A CP , Rakers T J , Wauben L S G L , Meeuwsen F C , Hoeijmans V , van der Elst M , Dankelman J , van den Dobbelsteen J J
Published: February 2016

The unavailability of the required surgical instruments at the start of a procedure is undesirable. It causes delays and stress in the operating room (OR), which can lead to additional risks for the patients. Issues with availability of surgical instruments may become visible just before the start of the procedure but are induced earlier in the delivery process. Therefore, efficient and safe supply chain management is essential. Just in time (JIT) is a concept widely applied in industrial sectors to improve efficiency and quality. The aim of this study is to design a JIT process for the delivery of surgical instruments and to assess the potential risks. The JIT delivery process of surgical instruments was designed for a Dutch hospital working with an external Central Sterile Supply Department (CSSD). Hazards (ie, sources of potential adverse events) were identified according to the Healthcare Failure Mode and Effects Analysis (HFMEA) methodology. The risks of applying JIT principles to the delivery of surgical instruments were compared to the risks involved with the current situation of the hospital at the time of this study (supply-driven delivery). The results showed that the total (high-)risk score of the JIT situation was similar to that of the current situation, although the number of (high-risk) hazards was slightly higher. However, almost half of the hazards were ‘controlled’ (when actions to remove the hazard were taken later in the process), in contrast to the current situation in which only about 10% of the (high-risk) hazards were ‘controlled’. The JIT delivery of surgical instruments is expected to present less risks compared to the current situation. The multiple requirements for information technology support and a higher level of trust between the CSSD and OR department should be taken into account in order to improve the supply chain management of surgical instruments.