bluuebunny/crossref_metadata_2025 huggingface dataset:
Key biocultural values to guide restoration action and planning in New Zealand
Authors: Lyver Phil O'B. , Akins Ashli , Phipps Hilary , Kahui Viktoria , Towns David R. , Moller Henrik
Published: December 2015

A pluralist and cross‐cultural approach that accommodates differing values while encouraging the collaboration and social cohesion necessary for the complex task of ecological restoration is needed. We used qualitative and quantitative analyses to investigate value assigned to biocultural restoration of coastal forests in northern New Zealand by 26 interviewees from three groups (environmental managers, Māori community members, and community project leaders). Māori community members primarily emphasized the importance ofCultural StewardshipandUsein the restoration process, while placing less emphasis onEcological Integrity. Otherwise, all participants shared common trends, culminating in three interrelated value sets: (1)Personal Engagement, (2)Connection, and (3) the generation and transfer ofKnowledge & Wisdom. These values demonstrate that restoration's benefits to people and community are as significant as its reparations of ecological components. Despite differences, all stakeholders were united in a broadly common goal to restore socio‐ecological systems. Their knowledge and shared passion for conservation signal enormous promise for accelerated and effective restoration of coastal forests, if it is conducted using a pluralistic approach. Because some values expressed were intangible and complex, with cross‐cultural dimensions, current valuation tools used by ecological economists to guide management investment fail to adequately account for, in particular, Māori values of ecological restoration.
Invasive diagnostic techniques in idiopathic interstitial pneumonias
Authors: Poletti Venerino , Ravaglia Claudia , Gurioli Carlo , Piciucchi Sara , Dubini Alessandra , Cavazza Alberto , Chilosi Marco , Rossi Andrea , Tomassetti Sara
Published: December 2015

Fibrosing interstitial lung diseases (f‐ILDs) represent a heterogeneous group of disorders in which the aetiology may be identified or, not infrequently, remain unknown. Establishing a correct diagnosis of a distinct f‐ILD requires a multidisciplinary approach, integrating clinical profile, physiological and laboratory data, radiological appearance and, when appropriate, histological findings. Surgical lung biopsy is still considered the most important diagnostic tool as it is able to provide lung samples large enough for identification of complex patterns such as usual interstitial pneumonitis (UIP) and nonspecific interstitial pneumonitis. However, this procedure is accompanied by significant morbidity and mortality. Bronchoalveolar lavage is still a popular diagnostic tool allowing identification of alternative diagnoses in patients with suspected idiopathic pulmonary fibrosis (IPF) when an increase in lymphocytes is detected. Conventional transbronchial lung biopsy has a very low sensitivity in detecting the UIP pattern and its role in this clinical‐radiological context is marginal. The introduction of less invasive methods such as transbronchial cryobiopsy show great promise to clinical practice as they can be used to obtain samples large enough to morphologically support a diagnosis of IPF or other idiopathic interstitial pneumonias, along with fewer complications. Recent advances in the field suggest that less invasive methods of lung sampling, without significant side effects, in combination with other diagnostic methods could replace the need for surgical lung biopsy in the future. Indeed, these new multidisciplinary procedures may become the main diagnostic work‐up method for patients with suspected idiopathic interstitial pneumonia.
J-Divergence Measurements of Economic Inequality
Authors: Rohde Nicholas
Published: December 2015

The paper uses a symmetric entropy statistic to study income inequality. The index quantifies the information content of a two-way message that transforms the empirical income distribution into an egalitarian reference distribution, and then back to the original. This allows the measure to be interpreted as an average of n income-to-mean divergences such that the inequality estimate can be broken down into contributions across population subgroups. Various properties of the index are analysed and an application comparing the USA, Germany and Britain is provided. We focus on the sensitivity of inequality to the tails of the income distribution and show that the extreme right-hand tail accounts for a large and generally increasing proportion of total inequality. This result holds even if incomes are measured at the household level, averaged over a 5-year period and taken after government taxes and transfers.
The use of portable ultrasound devices in low‐ and middle‐income countries: a systematic review of the literature
Authors: Becker Dawn M. , Tafoya Chelsea A. , Becker Sören L. , Kruger Grant H. , Tafoya Matthew J. , Becker Torben K.
Published: December 2015

Objectives

To review the scientific literature pertaining to the use of hand‐carried and hand‐held ultrasound devices in low‐ and middle‐income countries (LMIC), with a focus on clinical applications, geographical areas of use, the impact on patient management and technical features of the devices used.

Methods

The electronic databases PubMed and Google Scholar were searched. No language or date restrictions were applied. Case reports and original research describing the use of hand‐carried ultrasound devices in LMIC were included if agreed upon as relevant by two‐reviewer consensus based on our predefined research questions.

Results

A total of 644 articles were found and screened, and 36 manuscripts were included for final review. Twenty‐seven studies were original research articles, and nine were case reports. Several reports describe the successful diagnosis and management of difficult, often life‐threatening conditions, using hand‐carried and hand‐held ultrasound. These portable ultrasound devices have also been studied for cardiac screening exams, as well as a rapid triage tool in rural areas and after natural disaster. Most applications focus on obstetrical and abdominal complaints. Portable ultrasound may have an impact on clinical management in up to 70% of all cases. However, no randomised controlled trials have evaluated the impact of ultrasound‐guided diagnosis and treatment in resource‐constrained settings. The exclusion of articles published in journals not listed in the large databases may have biased our results. Our findings are limited by the lack of higher quality evidence (e.g. controlled trials).

Conclusions

Hand‐carried and hand‐held ultrasound is successfully being used to triage, diagnose and treat patients with a variety of complaints in LMIC. However, the quality of the current evidence is low. There is an urgent need to perform larger clinical trials assessing the impact of hand‐carried ultrasound in LMIC.
Outcome of phacoemulsification following corneal and lens laceration in cats and dogs (2000–2010)
Authors: Braus Barbara K. , Tichy Alexander , Featherstone Heidi J. , Renwick Peter W. , Rhodes Michael , Heinrich Christine L.
Published: December 2015

Objective

To investigate the success rate of phacoemulsification following corneal and lens laceration in dogs and cats.

Procedure

Retrospective review of cats and dogs presenting with corneal and lens laceration and treated with phacoemulsification.

Results

The records of 33 patients (33 eyes: six feline, 27 canine) presenting to a private referral center were reviewed. Affected dogs were younger (median 18 months) than affected cats (median 30 months). The lacerations were caused by cat scratch trauma (9/33), thorn injury (6/33), and glass shards (1/33); the cause was unknown in 17/33 cases. All cats and 85.2% of all dogs were visual at the last examination. The median follow‐up was 4 and 8 months for cats and dogs, respectively. In all canine cases that developed vision loss, this occurred within the first 14 weeks postoperatively. The ultimate cause for vision loss in dogs was secondary glaucoma (4/4) and retinal detachment (1/4).

Conclusion

Cats have an excellent outcome and dogs a very good outcome following surgery for corneal and lens laceration. The cause of the trauma, the size of the lesion, the time interval between the ocular trauma and surgery, and the type of surgery were not found to have an influence on the outcome of patients in this study. We postulate that vision loss might develop more often in cases with complications associated with the initial corneal laceration wound.
Keloid‐derived, plasma/fibrin‐based skin equivalents generate de novo dermal and epidermal pathology of keloid fibrosis in a mouse model
Authors: Lee Yun‐Shain , Hsu Tim , Chiu Wei‐Chih , Sarkozy Heidi , Kulber David A. , Choi Aaron , Kim Elliot W. , Benya Paul D. , Tuan Tai‐Lan
Published: December 2015

Keloids are wounding‐induced tumor‐like human scars. Unclear etiology and lack of animal models to reveal disease mechanisms and invent therapies deepen the grievous health and psychosocial state of vulnerable individuals. Epitomizing the injury–repair environment which triggers and fosters keloid formation and essential dermal/epidermal interactions in disease development, the novel animal model was established by implanting porous polyethylene ring‐supported plasma/fibrin‐based epidermal–dermal skin constructs on the dorsum of athymic NU/J mice. The implants were stable to 18 weeks, contained abundant human cells, and remodeled to yield scar architecture characteristic of keloid fibrosis compared with normal implants and clinical specimens: (1) macroscopic convex or nodular scar morphology; (2) morphogenesis and accumulation of large collagen bundles from collagen‐null initial constructs; (3) epidermal hyperplasia, aberrant epidermal–dermal patency, and features of EMT; (4) increased vasculature, macrophage influx, and aggregation; and (5) temporal‐spatial increased collagen‐inducing PAI‐1 and its interactive partner uPAR expression. Development of such pathology in the NU/J host suggests that T‐cell participation is less important at this stage than at keloid initiation. These accessible implants also healed secondary excisional wounds, enabling clinically relevant contemporaneous wounding and treatment strategies, and evaluation. The model provides a robust platform for studying keloid formation and testing knowledge‐based therapies.
One Health in Practice: A Pilot Project for Integrated Care of Zoonotic Infections in Immunocompromised Children and Their Pets in Chile
Authors: Peña A. , Abarca K. , Weitzel T. , Gallegos J. , Cerda J. , García P. , López J.
Published: December 2015

Although pets provide physiological and psychological benefits to their owners, they are a potential source of zoonotic infections, especially for vulnerable individuals such as immunocompromised patients. During 1 year, we therefore performed a pilot project, which included 32 immunocompromised Chilean children and their family pets (35 dogs and 9 cats) with the aim of detecting, treating and preventing zoonotic infections. Children were examined by Infectious Diseases paediatricians and demographical and clinical information related to zoonotic infections were recorded. Pets were examined and sampled by veterinarians, who also administered missing routine vaccines and anti‐parasitics. During family visits, all members were informed and educated about zoonoses and a satisfaction survey was performed. Visits also included vector control and indoor residual spraying with pyrethroids. Children were re‐examined and re‐tested according to the findings of their pets, and all detected zoonotic infections were treated both in children and pets. Physical examination revealed abnormalities in 18 dogs (51.4%) and three cats (33.3%). Twenty‐eight (63.6%) of the pets were diagnosed with a zoonotic pathogen, and seven (15.9%) with a facultative pathogen. Most zoonotic agents were isolated from the pet's external ear and intestine. Bacteria with the highest pathogenic potential were Campylobacter jejuni and Brucella canis. In two children and their respective pets, the same zoonotic diseases were diagnosed (toxocariasis and giardiasis). Arthropods serving as potential vectors of zoonotic infections were found in 49% of dogs and 44% of cats. The pilot project was positively evaluated by the participating families. Our pilot project confirmed that pets are reservoir for various zoonotic agents in Chile and that the implementation of an integrated multidisciplinary programme was a valuable tool to prevent, diagnose and treat such zoonotic infections in vulnerable patients such as immunocompromised children.
Molecular Epidemiology of Mycobacterium bovis in Humans and Cattle
Authors: El‐Sayed A. , El‐Shannat S. , Kamel M. , Castañeda‐Vazquez M. A. , Castañeda‐Vazquez H.
Published: December 2015

Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), is a serious re‐emerging disease in both animals and humans. The evolution of the Multi‐ and Extensively drug‐resistant M. bovis strains (MDR‐TB and XDR‐TB) represents a global threat to public health. Worldwide, the disease is responsible for great economic losses in the veterinary field, serious threat to the ecosystem, and about 3.1% of human TB cases, up to 16% in Tanzania. Only thorough investigation to understand the pathogen's epidemiology can help in controlling the disease and minimizing its threat. For this purpose, various tools have been developed for use in advanced molecular epidemiological studies of bTB, either alone or in combination with standard conventional epidemiological approaches. These techniques enable the analysis of the intra‐ and inter‐species transmission dynamics of bTB. The delivered data can reveal detailed insights into the source of infection, correlations among human and bovine isolates, strain diversity and evolution, spread, geographical localization, host preference, tracing of certain virulence factors such as antibiotic resistance genes, and finally the risk factors for the maintenance and spread of M. bovis. They also allow for the determination of epidemic and endemic strains. This, in turn, has a significant diagnostic impact and helps in vaccine development for bTB eradication programs. The present review discusses many topics including the aetiology, epidemiology and importance of M. bovis, the prevalence of bTB in humans and animals in various countries, the molecular epidemiology of M. bovis, and finally applied molecular epidemiological techniques.
Polarizing PVC — A Discrepant Event
Authors: Headly David , Karabatek Mohamed
Published: December 2015

Each year when teaching polarization phenomena and the Triboelectric Series in a unit on electrostatics, I would balance some rods (2–3 ft in length) made from wood, aluminum, PVC, and Plexiglas on an inverted watch glass and demonstrate to the class how a party balloon rubbed with fake rabbit fur (charging the balloon negative) would always attract the uncharged rods, causing them to rotate towards the balloon (see Fig. 1). The fact that a charged object always attracts a neutral object due to the induced dipole in the latter is a great way to test if something is in fact charged. Surprisingly, the PVC pipe would usually, but not always, repel the charged balloon and rotate away! Repulsion means that neither of the objects are electrically neutral. In a separate test, after rubbing together a Plexiglas rod with a polyethylene grocery bag (making the rod positively charged and the bag negatively charged), the PVC usually attracts the rod. With the help of a student as part of his senior project, I finally decided to investigate further the source of the negative charge that exists on PVC. Specifically, is it nothing more than static charge that builds up on the pipe from unavoidable contact with its surroundings, or is it somehow intrinsic to the manufacturing process?
Exploding Water Drops
Authors: Reich Gary
Published: December 2015

Water has the unusual property that it expands on freezing, so that ice has a specific gravity of 0.92 compared to 1.0 for liquid water. The most familiar demonstration of this property is ice cubes floating in a glass of water. A more dramatic demonstration is the ice bomb shown in Fig. 1. Here a cast iron flask is filled with water and tightly stoppered. The flask is then cooled, either by leaving it outdoors in winter or by immersing it in a cryogenic fluid, until the water freezes. As the water freezes and expands, the pressure inside the flask increases dramatically, eventually becoming sufficient to fracture the metal walls of the enclosure. A related, but much less familiar, phenomenon is the explosive fracturing of small water drops upon freezing. That water drops can fracture in this way has been known for many years, and the phenomenon has been described in detail in the atmospheric sciences literature, where it is seen as relevant to the freezing of raindrops as they fall through cold air. Carefully controlled experiments have been done documenting how the character and frequency of fracture is affected by such variables as drop size, rate of cooling, chemistry of dissolved gases, etc. Here I describe instead a simple demonstration of fracture suitable for video analysis and appropriate for study at the introductory physics level. Readers may also be interested in other characteristics of freezing and fragmenting water drops, for example, charge separation upon fracture and the appearance of spikes and bulges on the surface.
High school physics enrollments by socioeconomic status and type of class
Authors: White Susan C.
Published: December 2015

Since September, we have been examining the relationship between high school physics enrollments by race/ethnicity and socioeconomic status. We have seen that the number of seniors and the number of physics teachers is roughly evenly divided into each type of school: those where students are typically better off economically than their peers at other schools in the area, those where students' economic status is typical for the area, and those where students are worse off. We have seen that even though the number of seniors and the number of physics teachers is roughly equal, the number of students taking physics is not. As we see in the figure, the enrollments in various types of physics classes are not equivalent either. While the total number of students taking Physics First or conceptual physics is about the same, the number of students in advanced classes—honors, AP, or second-year physics—is heavily skewed toward the better off schools. It is hard to know the direction of any cause and effect, but it is clear the students attending better off schools are more likely to take physics and are more likely to take more advanced physics classes in high school.
Active Learning Strategies for Introductory Light and Optics
Authors: Sokoloff David R.
Published: December 2015

There is considerable evidence that traditional approaches are ineffective in teaching physics concepts, including light and optics concepts. A major focus of the work of the Activity Based Physics Group has been on the development of active learning curricula like RealTime Physics (RTP) labs and Interactive Lecture Demonstrations (ILDs). Among the characteristics of these curricula are: (1) use of a learning cycle in which students are challenged to compare predictions—discussed with their peers in small groups—to observations of the physical world, (2) use of guided hands-on work to construct basic concepts from observations, and (3) use of computer-based tools. It has been possible to change the lecture and laboratory learning environments at a large number of universities, colleges, and high schools without changing the structure of the introductory course. For example, in the United States, nearly 200 physics departments have adopted RTP, and many others use pre-publication, open-source versions or have adopted the RTP approach to develop their own labs. Examples from RTP and ILDs (including optics magic tricks) are described in this paper.
Surprising Behavior of Spinning Tops and Eggs on an Inclined Plane
Authors: Cross Rod
Published: December 2015

A spinning top or a spinning hard-boiled egg is fascinating to observe since both objects can remain upright for a relatively long time without falling over. If spun at sufficient speed on a horizontal surface, the spin axis rises to a vertical position and the bottom end tends to remain fixed in position on the surface. If the initial spin is insufficient, then the spin axis will not rise all the way to the vertical, in which case a spinning top or a spinning egg will precess slowly around a vertical axis. If the bottom end is rounded, as it is with an egg or with a top having a round rather than a pointed peg, then the vertical precession axis does not necessarily pass through the center of mass. Instead, the precession axis may be located several centimeters away from the center of mass, depending on the radius of the bottom end. As a result, the whole egg or the whole top then rolls along the surface in an approximately circular path, several centimeters in diameter. The essential physics is described in Ref. 1 and the references therein, and in the many more books and papers since the early 1900s quoted in each of the references therein.
FormScanner: Open-Source Solution for Grading Multiple-Choice Exams
Authors: Young Chadwick , Lo Glenn , Young Kaisa , Borsetta Alberto
Published: December 2015

The multiple-choice exam remains a staple for many introductory physics courses. In the past, people have graded these by hand or even flaming needles. Today, one usually grades the exams with a form scanner that utilizes optical mark recognition (OMR). Several companies provide these scanners and particular forms, such as the eponymous “Scantron.” OMR scanners combine hardware and software—a scanner and OMR program—to read and grade student-filled forms.
Some Daytime Activities in Solar Astronomy
Authors: Burin Michael J.
Published: December 2015

This century's transits of Venus (2004, 2012) captured significant public attention, reminding us that the wonders of astronomy need not be confined to the night. And while nighttime telescope viewing gatherings (a.k.a. “star parties”) are perennially popular, astronomy classes are typically held in the daytime. The logistics of coordinating students outside of class can often be problematic, leading to dark-sky activities that are relegated to extra credit for only those who can attend.
A New Lecture-Tutorial for Teaching about Molecular Excitations and Synchrotron Radiation
Authors: Wallace Colin S. , Prather Edward E. , Hornstein Seth D. , Burns Jack O. , Schlingman Wayne M. , Chambers Timothy G.
Published: December 2015

Light and spectroscopy are among the most important and frequently taught topics in introductory college-level general education astronomy courses (hereafter Astro 101). This is due to the fact that the vast majority of observational data studied by astronomers arrives at Earth in the form of light. While there are many processes by which matter can emit and absorb light, Astro 101 courses typically limit their instruction to the Bohr model of the atom and electron energy level transitions. In this paper, we report on the development of a new Lecture-Tutorial to help students learn about other processes that are responsible for the emission and absorption of light, namely molecular rotations, molecular vibrations, and the acceleration of charged particles by magnetic fields. Note that this paper primarily focuses on describing the variety of representations and reasoning tasks designed for this Lecture-Tutorial; while the end of this paper highlights some data that are suggestive of the Lecture-Tutorial's effectiveness, our more comprehensive analysis of its efficacy will be presented in a future publication.
Operation of AC Adapters Visualized Using Light-Emitting Diodes
Authors: Regester Jeffrey
Published: December 2015

A bridge rectifier is a diamond-shaped configuration of diodes that serves to convert alternating current (AC) into direct current (DC). In our world of AC outlets and DC electronics, they are ubiquitous. Of course, most bridge rectifiers are built with regular diodes, not the light-emitting variety, because LEDs have a number of disadvantages. For educational purposes, however, an LED-based rectifier is ideal because it allows students to literally see the rectifier operating. Here I'll discuss the practical aspects of building a full AC adapter incorporating an LED-based rectifier and ideas on how to use it in class.
More sound of church bells: Authors' correction
Authors: Vogt Patrik , Kasper Lutz , Burde Jan-Philipp
Published: December 2015

In the recently published article “The Sound of Church Bells: Tracking Down the Secret of a Traditional Arts and Crafts Trade,” the bell frequencies have been erroneously oversimplified. The problem affects Eqs. (2) and (3), which were derived from the elementary “coffee mug model” and in which we used the speed of sound in air. However, this does not make sense from a physical point of view, since air only acts as a sound carrier, not as a sound source in the case of bells. Due to the excellent fit of the theoretical model with the empirical data, we unfortunately failed to notice this error before publication. However, all other equations, e.g., the introduction of the correction factor in Eq. (4) and the estimation of the mass in Eqs. (5) and (6) are not affected by this error, since they represent empirical models. However, it is unfortunate to introduce the speed of sound in air as a constant in Eqs. (4) and (6). Instead, we suggest the following simple rule of thumb for relating the radius of a church bell R to its humming frequency fhum: R≈100 ms−1fhum.(1)
Period and pulse duration with “strobe” lights
Authors: Birriel Jennifer
Published: December 2015

Strobe lights have traditionally been discussed in The Physics Teacher in the context of stop action strobe photography. During the Halloween season most department and hardware stores sell inexpensive, compact “strobe” lights (although these can be found online year round). These lights generally sell for under $10 and usually employ LED lights. Most such devices have a rotary switch to adjust the rate at which the LED bulbs flash. This rotary switch is not calibrated—i.e., it has no markings to indicate the rate, but in general the greater the rotation of the switch from the off position, the faster the rate of flashing. We show how these simple devices can be used with a light sensor to study both the frequency of flashing and the duration of the light pulse. We briefly discuss if these devices are truly strobe lights.
Increasing your body of physics knowledge
Authors: Donaldson Nancy
Published: December 2015

Our body is a wonderful machine! A great way to bring physics to life for students is to incorporate physics principles necessary to the functioning of our human body. This article will focus on three areas in which physics principles guide an understanding and appreciation of the wonders of human mechanical design.
Is there life after teaching physics?
Authors: Martin David S.
Published: December 2015

Why an article about retirement in the primary journal for the teachers of introductory physics courses? There is the all-too-common reason that little or no thought may have been given to an impending near certainty. But just as physics teachers have a unique place in their schools, they have equally unique perspectives and talents that can be put to fruitful application in retirement.
Numerical analysis of the transportation characteristics of a self-running sliding stage based on near-field acoustic levitation
Authors: Feng Kai , Liu Yuanyuan , Cheng Miaomiao
Published: December 2015

Owing to its distinct non-contact and oil-free characteristics, a self-running sliding stage based on near-field acoustic levitation can be used in an environment, which demands clean rooms and zero noise. This paper presents a numerical analysis on the lifting and transportation capacity of a non-contact transportation system. Two simplified structure models, namely, free vibration and force vibration models, are proposed for the study of the displacement amplitude distribution of two cases using the finite element method. After coupling the stage displacement into the film thickness, the Reynolds equation is solved by the finite difference method to obtain the lifting and thrusting forces. Parametric analyses of the effects of amplitude, frequency, and standing wave ratio (SWR) on the sliding stage dynamic performance are investigated. Numerical results show good agreement with published experimental values. The predictions also reveal that greater transportation capacity of the self-running sliding stage is generally achieved at less SWR and at higher amplitude.
A single-ligand ultra-microporous MOF for precombustion CO
2
capture and hydrogen purification
Authors: Nandi Shyamapada , De Luna Phil , Daff Thomas D. , Rother Jens , Liu Ming , Buchanan William , Hawari Ayman I. , Woo Tom K. , Vaidhyanathan Ramanathan
Published: December 2015

A single small-ligand–based ultra-microporous MOF showing high CO
2
selectivity and PSA working capacity for H
2
purification.
Regulated lysosomal exocytosis mediates cancer progression
Authors: Machado Eda , White-Gilbertson Shai , van de Vlekkert Diantha , Janke Laura , Moshiach Simon , Campos Yvan , Finkelstein David , Gomero Elida , Mosca Rosario , Qiu Xiaohui , Morton Christopher L. , Annunziata Ida , d’Azzo Alessandra
Published: December 2015

LAMP1 oversialylation results in excessive lysosomal exocytosis, promoting tumor invasion and drug resistance.
Mechanisms of murine cerebral malaria: Multimodal imaging of altered cerebral metabolism and protein oxidation at hemorrhage sites
Authors: Hackett Mark J. , Aitken Jade B. , El-Assaad Fatima , McQuillan James A. , Carter Elizabeth A. , Ball Helen J. , Tobin Mark J. , Paterson David , de Jonge Martin D. , Siegele Rainer , Cohen David D. , Vogt Stefan , Grau Georges E. , Hunt Nicholas H. , Lay Peter A.
Published: December 2015

Multimodal spectroscopic imaging resolved controversies on biochemical changes associated with cerebral malaria pathology.
Active quantum plasmonics
Authors: Marinica Dana Codruta , Zapata Mario , Nordlander Peter , Kazansky Andrey K. , M. Echenique Pedro , Aizpurua Javier , Borisov Andrei G.
Published: December 2015

The optical response of a metallic cavity is electrically controlled by changing the tunneling barrier with an external dc bias.
Defaunation affects carbon storage in tropical forests
Authors: Bello Carolina , Galetti Mauro , Pizo Marco A. , Magnago Luiz Fernando S. , Rocha Mariana F. , Lima Renato A. F. , Peres Carlos A. , Ovaskainen Otso , Jordano Pedro
Published: December 2015

Populations of large frugivores are declining in tropical rainforests with potential consequences for carbon storage and climate.
All-polymeric control of nanoferronics
Authors: Xu Beibei , Li Huashan , Hall Asha , Gao Wenxiu , Gong Maogang , Yuan Guoliang , Grossman Jeffrey , Ren Shenqiang
Published: December 2015

The centimeter-sized polymeric crystalline superstructures reveal charge transfer–controlled nanoferronic properties.
Connecting multiple spatial scales to decode the population activity of grid cells
Authors: Stemmler Martin , Mathis Alexander , Herz Andreas V. M.
Published: December 2015

Reading the neural code for space: discrete scales of grid-cell activity enable goal-directed navigation and localization.
Intracellular and Extracellular Expression of Bacillus thuringiensis Crystal Protein Cry5B in Lactococcus lactis for Use as an Anthelminthic
Authors: Durmaz Evelyn , Hu Yan , Aroian Raffi V. , Klaenhammer Todd R.
Published: December 2015

The
Bacillus thuringiensis
crystal (Cry) protein Cry5B (140 kDa) and a truncated version of the protein, tCry5B (79 kDa), are lethal to nematodes. Genes encoding the two proteins were separately cloned into a high-copy-number vector with a strong constitutive promoter (pTRK593) in
Lactococcus lactis
for potential oral delivery against parasitic nematode infections. Western blots using a Cry5B-specific antibody revealed that constitutively expressed Cry5B and tCry5B were present in both cells and supernatants. To increase production,
cry5B
was cloned into the high-copy-number plasmid pMSP3535H3, carrying a nisin-inducible promoter. Immunoblotting revealed that 3 h after nisin induction, intracellular Cry5B was strongly induced at 200 ng/ml nisin, without adversely affecting cell viability or cell membrane integrity. Both Cry5B genes were also cloned into plasmid pTRK1061, carrying a promoter and encoding a transcriptional activator that invoke low-level expression of prophage holin and lysin genes in
Lactococcus
lysogens, resulting in a leaky phenotype. Cry5B and tCry5B were actively expressed in the lysogenic strain
L. lactis
KP1 and released into cell supernatants without affecting culture growth. Lactate dehydrogenase (LDH) assays indicated that Cry5B, but not LDH, leaked from the bacteria. Lastly, using intracellular lysates from
L. lactis
cultures expressing both Cry5B and tCry5B,
in vivo
challenges of
Caenorhabditis elegans
worms demonstrated that the Cry proteins were biologically active. Taken together, these results indicate that active Cry5B proteins can be expressed intracellularly in and released extracellularly from
L. lactis
, showing potential for future use as an anthelminthic that could be delivered orally in a food-grade microbe.
Comparison of Four Comamonas Catabolic Plasmids Reveals the Evolution of pBHB To Catabolize Haloaromatics
Authors: Chen Kai , Xu Xihui , Zhang Long , Gou Zhenjiu , Li Shunpeng , Freilich Shiri , Jiang Jiandong
Published: December 2015

Comamonasplasmids play important roles in shaping the phenotypes of their hosts and the adaptation of these hosts to changing environments, and understanding the evolutionary strategy of these plasmids is thus of great concern. In this study, the sequence of the 119-kb 3,5-dibromo-4-hydroxybenzonitrile-catabolizing plasmid pBHB fromComamonassp. strain 7D-2 was studied and compared with those of three otherComamonashaloaromatic catabolic plasmids. Incompatibility group determination based on a phylogenetic analysis of 24 backbone gene proteins, as well as TrfA, revealed that these four plasmids all belong to the IncP-1β subgroup. Comparison of the four plasmids revealed a conserved backbone region and diverse genetic-load regions. The four plasmids share a core genome consisting of 40 genes (>50% similarities) and contain 12 to 50 unique genes each, most of which are xenobiotic-catabolic genes. Two functional reductive dehalogenase gene clusters are specifically located on pBHB, showing distinctive evolution of pBHB for haloaromatics. The higher catabolic ability of thebhbA2B2cluster than thebhbABcluster may be due to the transcription levels and the character of the dehalogenase gene itself rather than that of its extracytoplasmic binding receptor gene. The plasmid pBHB is riddled with transposons and insertion sequence (IS) elements, and ISs play important roles in the evolution of pBHB. The analysis of the origin of thebhbgenes on pBHB suggested that these accessory genes evolved independently. Our work provides insights into the evolutionary strategies ofComamonasplasmids, especially into the adaptation mechanism employed by pBHB for haloaromatics.
Levan-Producing Leuconostoc citreum Strain BD1707 and Its Growth in Tomato Juice Supplemented with Sucrose
Authors: Han Jin , Xu Xiaofen , Gao Caixia , Liu Zhenmin , Wu Zhengjun
Published: December 2015

A levan-producing strain, BD1707, was isolated from Tibetan kefir and identified as
Leuconostoc citreum
. The effects of carbon sources on the growth of
L. citreum
BD1707 and levan production in tomato juice were measured. The changes in pH, viable cell count, sugar content, and levan yield in the cultured tomato juice supplemented with 15% (wt/vol) sucrose were also assayed.
L. citreum
BD1707 could synthesize more than 28 g/liter of levan in the tomato juice-sucrose medium when cultured at 30°C for 96 h. Based on the monosaccharide composition, molecular mass distribution, Fourier transform infrared (FTIR) spectra, and nuclear magnetic resonance (NMR) spectra, the levan synthesized by
L. citreum
BD1707 was composed of a linear backbone consisting of consecutive β-(2→6) linked
d
-fructofuranosyl units, with an estimated average molecular mass of 4.3 × 10
6
Da.
Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C
1
Compound Oxidation
Authors: Denef Vincent J. , Mueller Ryan S. , Chiang Edna , Liebig James R. , Vanderploeg Henry A.
Published: December 2015

The
Chloroflexi
CL500-11 clade contributes a large proportion of the bacterial biomass in the oxygenated hypolimnia of deep lakes worldwide, including the world's largest freshwater system, the Laurentian Great Lakes. Traits that allow CL500-11 to thrive and its biogeochemical role in these environments are currently unknown. Here, we found that a CL500-11 population was present mostly in offshore waters along a transect in ultraoligotrophic Lake Michigan (a Laurentian Great Lake). It occurred throughout the water column in spring and only in the hypolimnion during summer stratification, contributing up to 18.1% of all cells. Genome reconstruction from metagenomic data suggested an aerobic, motile, heterotrophic lifestyle, with additional energy being gained through carboxidovory and methylovory. Comparisons to other available streamlined freshwater genomes revealed that the CL500-11 genome contained a disproportionate number of cell wall/capsule biosynthesis genes and the most diverse spectrum of genes involved in the uptake of dissolved organic matter (DOM) substrates, particularly peptides.
In situ
expression patterns indicated the importance of DOM uptake and protein/peptide turnover, as well as type I and type II carbon monoxide dehydrogenase and flagellar motility. Its location in the water column influenced its gene expression patterns the most. We observed increased bacteriorhodopsin gene expression and a response to oxidative stress in surface waters compared to its response in deep waters. While CL500-11 carries multiple adaptations to an oligotrophic lifestyle, its investment in motility, its large cell size, and its distribution in both oligotrophic and mesotrophic lakes indicate its ability to thrive under conditions where resources are more plentiful. Our data indicate that CL500-11 plays an important role in nitrogen-rich DOM mineralization in the extensive deep-lake hypolimnion habitat.
Ectomycorrhizal Fungal Protein Degradation Ability Predicted by Soil Organic Nitrogen Availability
Authors: Rineau Francois , Stas Jelle , Nguyen Nhu H. , Kuyper Thomas W. , Carleer Robert , Vangronsveld Jaco , Colpaert Jan V. , Kennedy Peter G.
Published: December 2015

In temperate and boreal forest ecosystems, nitrogen (N) limitation of tree metabolism is alleviated by ectomycorrhizal (ECM) fungi. As forest soils age, the primary source of N in soil switches from inorganic (NH
4
+
and NO
3
−
) to organic (mostly proteins). It has been hypothesized that ECM fungi adapt to the most common N source in their environment, which implies that fungi growing in older forests would have greater protein degradation abilities. Moreover, recent results for a model ECM fungal species suggest that organic N uptake requires a glucose supply. To test the generality of these hypotheses, we screened 55 strains of 13
Suillus
species with different ecological preferences for their
in vitro
protein degradation abilities.
Suillus
species preferentially occurring in mature forests, where soil contains more organic matter, had significantly higher protease activity than those from young forests with low-organic-matter soils or species indifferent to forest age. Within species, the protease activities of ecotypes from soils with high or low soil organic N content did not differ significantly, suggesting resource partitioning between mineral and organic soil layers. The secreted protease mixtures were strongly dominated by aspartic peptidases. Glucose addition had variable effects on secreted protease activity; in some species, it triggered activity, but in others, activity was repressed at high concentrations. Collectively, our results indicate that protease activity, a key ectomycorrhizal functional trait, is positively related to environmental N source availability but is also influenced by additional factors, such as carbon availability.
Contribution of the Salmonella enterica KdgR Regulon to Persistence of the Pathogen in Vegetable Soft Rots
Authors: George Andrée S. , Salas González Isai , Lorca Graciela L. , Teplitski Max
Published: December 2015

During their colonization of plants, human enteric pathogens, such as
Salmonella enterica
, are known to benefit from interactions with phytopathogens. At least in part, benefits derived by
Salmonella
from the association with a soft rot caused by
Pectobacterium carotovorum
were shown to be dependent on
Salmonella
KdgR, a regulator of genes involved in the uptake and utilization of carbon sources derived from the degradation of plant polymers. A
Salmonella
kdgR
mutant was more fit in soft rots but not in the lesions caused by
Xanthomonas
spp. and
Pseudomonas
spp. Bioinformatic, phenotypic, and gene expression analyses demonstrated that the KdgR regulon included genes involved in uptake and metabolism of molecules resulting from pectin degradation as well as those central to the utilization of a number of other carbon sources. Mutant analyses indicated that the Entner-Doudoroff pathway, in part controlled by KdgR, was critical for the persistence within soft rots and likely was responsible for the
kdgR
phenotype.
Chirality Matters: Synthesis and Consumption of the
d
-Enantiomer of Lactic Acid by Synechocystis sp. Strain PCC6803
Authors: Angermayr S. Andreas , van der Woude Aniek D. , Correddu Danilo , Kern Ramona , Hagemann Martin , Hellingwerf Klaas J.
Published: December 2015

Both enantiomers of lactic acid,
l
-lactic acid and
d
-lactic acid, can be produced in a sustainable way by a photosynthetic microbial cell factory and thus from CO
2
, sunlight, and water. Several properties of polylactic acid (a polyester of polymerized lactic acid) depend on the controlled blend of these two enantiomers. Recently, cyanobacterium
Synechocystis
sp. strain PCC6803 was genetically modified to allow formation of either of these two enantiomers. This report elaborates on the
d
-lactic acid production achieved by the introduction of a
d
-specific lactate dehydrogenase from the lactic acid bacterium
Leuconostoc mesenteroides
into
Synechocystis
. A typical batch culture of this recombinant strain initially shows lactic acid production, followed by a phase of lactic acid consumption, until production “outcompetes” consumption at later growth stages. We show that
Synechocystis
is able to use
d
-lactic acid, but not
l
-lactic acid, as a carbon source for growth. Deletion of the organism's putative
d
-lactate dehydrogenase (encoded by
slr1556
), however, does not eliminate this ability with respect to
d
-lactic acid consumption. In contrast,
d
-lactic acid consumption does depend on the presence of glycolate dehydrogenase GlcD1 (encoded by
sll0404
). Accordingly, this report highlights the need to match a product of interest of a cyanobacterial cell factory with the metabolic network present in the host used for its synthesis and emphasizes the need to understand the physiology of the production host in detail.
Activating and Elucidating Metabolism of Complex Sugars in Yarrowia lipolytica
Authors: Ryu Seunghyun , Hipp Julie , Trinh Cong T.
Published: December 2015

The oleaginous yeast
Yarrowia lipolytica
is an industrially important host for production of organic acids, oleochemicals, lipids, and proteins with broad biotechnological applications. Albeit known for decades, the unique native metabolism of
Y. lipolytica
for using complex fermentable sugars, which are abundant in lignocellulosic biomass, is poorly understood. In this study, we activated and elucidated the native sugar metabolism in
Y. lipolytica
for cell growth on xylose and cellobiose as well as their mixtures with glucose through comprehensive metabolic and transcriptomic analyses. We identified 7 putative glucose-specific transporters, 16 putative xylose-specific transporters, and 4 putative cellobiose-specific transporters that are transcriptionally upregulated for growth on respective single sugars.
Y. lipolytica
is capable of using xylose as a carbon source, but xylose dehydrogenase is the key bottleneck of xylose assimilation and is transcriptionally repressed by glucose.
Y. lipolytica
has a set of 5 extracellular and 6 intracellular β-glucosidases and is capable of assimilating cellobiose via extra- and intracellular mechanisms, the latter being dominant for growth on cellobiose as a sole carbon source. Strikingly,
Y. lipolytica
exhibited enhanced sugar utilization for growth in mixed sugars, with strong carbon catabolite activation for growth on the mixture of xylose and cellobiose and with mild carbon catabolite repression of glucose on xylose and cellobiose. The results of this study shed light on fundamental understanding of the complex native sugar metabolism of
Y. lipolytica
and will help guide inverse metabolic engineering of
Y. lipolytica
for enhanced conversion of biomass-derived fermentable sugars to chemicals and fuels.
Identification of Unknown Carboxydovore Bacteria Dominant in Deciduous Forest Soil via Succession of Bacterial Communities,
coxL
Genotypes, and Carbon Monoxide Oxidation Activity in Soil Microcosms
Authors: Lalonde Isabelle , Constant Philippe
Published: December 2015

Surveys of the
coxL
gene, encoding the large subunit of the CO dehydrogenase, are used as a standard approach in ecological studies of carboxydovore bacteria scavenging atmospheric CO. Recent soil surveys unveiled that the distribution of
coxL
sequences encompassing the atypical genotype
coxL
type I group x was correlated to the CO oxidation activity. Based on phylogenetic analysis including the available
coxL
reference genome sequences, this unusual genotype was assigned to an unknown member of the
Deltaproteobacteria
, with the
coxL
sequence from
Haliangium ochraceum
being the sole and closest reference sequence. Here we seek to challenge the proposed taxonomic assignation of the
coxL
group x genotype through the monitoring of CO consumption activity and microbial community successions during the colonization of sterile soil microcosms inoculated with indigenous microorganisms. In our study, we established that the estimated population density of
Deltaproteobacteria
was too small to account for the abundance of the
coxL
group x genotype detected in soil. Furthermore, we computed a correlation network to relate 16S rRNA gene profiles with the succession of
coxL
genotypes and CO uptake activity in soil. We found that most of the
coxL
genotypes for which the colonization profile displayed covariance with CO uptake activity were related to potential carboxydovore bacteria belonging to
Actinobacteria
and
Alphaproteobacteria
. Our analysis did not provide any evidence that
coxL
group x genotypes belonged to
Deltaproteobacteria
. Considering the colonization profile of CO-oxidizing bacteria and the theoretical energy yield of measured CO oxidation rates in soil microcosms, we propose that unknown carboxydovore bacteria harboring the atypical
coxL
group x genotype are mixotrophic
K
-strategists.