bluuebunny/crossref_metadata_2025 huggingface dataset:
Geobacillus thermoglucosidasius Endospores Function as Nuclei for the Formation of Single Calcite Crystals
Authors: Murai Rie , Yoshida Naoto
Published: March 2013

Geobacillus thermoglucosidasius
colonies were placed on an agar hydrogel containing acetate, calcium ions, and magnesium ions, resulting in the formation of single calcite crystals (calcites) within and peripheral to the plating area or parent colony. Microscopic observation of purified calcites placed on the surface of soybean casein digest (SCD) nutrient medium revealed interior crevices from which bacterial colonies originated. Calcites formed on the gel contained [1-
13
C]- and [2-
13
C]acetate, demonstrating that
G. thermoglucosidasius
utilizes carbon derived from acetate for calcite formation. During calcite formation, vegetative cells swam away from the parent colony in the hydrogel. Hard-agar hydrogel inhibited the formation of calcites peripheral to the parent colony. The calcite dissolved completely in 1 M HCl, with production of bubbles, and the remaining endospore-like particles were easily stained with Brilliant green dye. The presence of DNA and protein in calcites was demonstrated by electrophoresis. We propose that endospores initiate the nucleation of calcites. Endospores of
G. thermoglucosidasius
remain alive and encapsulated in calcites.
Lsr2 of Mycobacterium leprae and Its Synthetic Peptides Elicit Restitution of T Cell Responses in Erythema Nodosum Leprosum and Reversal Reactions in Patients with Lepromatous Leprosy
Authors: Saini Chaman , Prasad H. K. , Rani Rajni , Murtaza A. , Misra Namita , Shanker Narayan N. P. , Nath Indira
Published: February 2013

The Lsr2 protein ofMycobacterium lepraeand its synthetic peptides have been shown to elicit lymphoproliferation and gamma interferon (IFN-γ) release by peripheral blood mononuclear cells (PBMCs) of patients with lepromatous leprosy (M. Chaduvula, A. Murtaza, N. Misra, N. P. Narayan, V. Ramesh, H. K. Prasad, R. Rani, R. K. Chinnadurai, I. Nath, Infect. Immun. 80:742–752, 2012). PBMCs from 16 patients with lepromatous leprosy who were undergoing erythema nodosum leprosum (ENL) (type 2) and 5 patients with reversal reactions (RR) (type 1) were stimulated withM. leprae, recombinant Lsr2, and six end-to-end synthetic peptides (A through F) spanning the Lsr2 sequence. During the reaction all patients with ENL showed lymphoproliferation (stimulation index, >2) in response to peptides A and F, with other peptides eliciting responses in 75 to 88% of the subjects. In PBMC cultures, both lymphoproliferation and IFN-γ release for peptide E were significantly higher than for peptides B and C and recombinant Lsr2 (P< 0.05, Wilcoxon signed-rank test). Five patients with RR also showed enhanced lymphoproliferative responses and IFN-γ release in response to Lsr2,M. leprae, and peptide E. Six months postreaction, 14 patients with ENL continued to exhibit responses to Lsr2 and its peptides, with the highest responses being elicited by peptide E. However, 5 subjects showed no lymphoproliferation and had reduced IFN-γ release in response to Lsr2 peptides (P< 0.001, Kruskal-Wallis test) but responded to recombinant Lsr2. Six patients with ENL had HLA-A*68.01, which the STFPEITHI program showed to have high peptide-binding scores of 20 to 21 for peptides E, B, and C. Eleven patients had HLA-DRB1*1501 and HLA-DRB1*1502, which had high binding scores for peptides C and E. Thus, Lsr2 and its peptides are recognized in leprosy reactions during and well after the subsidence of clinical signs.
Detection of Fungal DNA in Human Body Fluids and Tissues during a Multistate Outbreak of Fungal Meningitis and Other Infections
Authors: Gade Lalitha , Scheel Christina M. , Pham Cau D. , Lindsley Mark D. , Iqbal Naureen , Cleveland Angela Ahlquist , Whitney Anne M. , Lockhart Shawn R. , Brandt Mary E. , Litvintseva Anastasia P.
Published: March 2013

Exserohilum rostratum
was the major cause of an outbreak of fungal infections linked to injections of contaminated methylprednisolone acetate. Because almost 14,000 persons were exposed to product that was possibly contaminated with multiple fungal pathogens, there was unprecedented need for a rapid throughput diagnostic test that could detect both
E. rostratum
and other unusual agents of fungal infection. Here we report development of a novel PCR test that allowed for rapid and specific detection of fungal DNA in cerebrospinal fluid (CSF), other body fluids and tissues of infected individuals. The test relied on direct purification of free-circulating fungal DNA from fluids and subsequent PCR amplification and sequencing. Using this method, we detected
Exserohilum rostratum
DNA in 123 samples from 114 case-patients (28% of 413 case-patients for whom 627 samples were available), and
Cladosporium
DNA in one sample from one case-patient. PCR with novel
Exserohilum
-specific ITS-2 region primers detected 25 case-patients with samples that were negative using broad-range ITS primers. Compared to fungal culture, this molecular test was more sensitive: of 139 case-patients with an identical specimen tested by culture and PCR,
E. rostratum
was recovered in culture from 19 (14%), but detected by PCR in 41 (29%), showing a diagnostic sensitivity of 29% for PCR compared to 14% for culture in this patient group. The ability to rapidly confirm the etiologic role of
E. rostratum
in these infections provided an important contribution in the public health response to this outbreak.
Secretion of Quinolinic Acid, an Intermediate in the Kynurenine Pathway, for Utilization in NAD
+
Biosynthesis in the Yeast Saccharomyces cerevisiae
Authors: Ohashi Kazuto , Kawai Shigeyuki , Murata Kousaku
Published: March 2013

NAD
+
is synthesized from tryptophan either via the kynurenine (
de novo
) pathway or via the salvage pathway by reutilizing intermediates such as nicotinic acid or nicotinamide ribose. Quinolinic acid is an intermediate in the kynurenine pathway. We have discovered that the budding yeast
Saccharomyces cerevisiae
secretes quinolinic acid into the medium and also utilizes extracellular quinolinic acid as a novel NAD
+
precursor. We provide evidence that extracellular quinolinic acid enters the cell via Tna1, a high-affinity nicotinic acid permease, and thereby helps to increase the intracellular concentration of NAD
+
. Transcription of genes involved in the kynurenine pathway and Tna1 was increased, responding to a low intracellular NAD
+
concentration, in cells bearing mutations of these genes; this transcriptional induction was suppressed by supplementation with quinolinic acid or nicotinic acid. Our data thus shed new light on the significance of quinolinic acid, which had previously been recognized only as an intermediate in the kynurenine pathway.
The Response of Nannochloropsis gaditana to Nitrogen Starvation Includes
De Novo
Biosynthesis of Triacylglycerols, a Decrease of Chloroplast Galactolipids, and Reorganization of the Photosynthetic Apparatus
Authors: Simionato Diana , Block Maryse A. , La Rocca Nicoletta , Jouhet Juliette , Maréchal Eric , Finazzi Giovanni , Morosinotto Tomas
Published: March 2013

Microalgae of the genus
Nannochloropsis
are capable of accumulating triacylglycerols (TAGs) when exposed to nutrient limitation (in particular, nitrogen [N]) and are therefore considered promising organisms for biodiesel production. Here, after nitrogen removal from the medium,
Nannochloropsis gaditana
cells showed extensive triacylglycerol accumulation (38% TAG on a dry weight basis). Triacylglycerols accumulated during N deprivation harbored signatures, indicating that they mainly stemmed from freshly synthesized fatty acids, with a small proportion originating from a recycling of membrane glycerolipids. The amount of chloroplast galactoglycerolipids, which are essential for the integrity of thylakoids, decreased, while their fatty acid composition appeared to be unaltered. In starved cells, galactolipids were kept at a level sufficient to maintain chloroplast integrity, as confirmed by electron microscopy. Consistently, N-starved
Nannochloropsis
cells contained less photosynthetic membranes but were still efficiently performing photosynthesis. N starvation led to a modification of the photosynthetic apparatus with a change in pigment composition and a decrease in the content of all the major electron flow complexes, including photosystem II, photosystem I, and the cytochrome
b
6
f
complex. The photosystem II content was particularly affected, leading to the inhibition of linear electron flow from water to CO
2
. Such a reduction, however, was partially compensated for by activation of alternative electron pathways, such as cyclic electron transport. Overall, these changes allowed cells to modify their energetic metabolism in order to maintain photosynthetic growth.
Epidemiology of Clostridium difficile Infection and Risk Factors for Unfavorable Clinical Outcomes: Results of a Hospital-Based Study in Barcelona, Spain
Authors: Rodríguez-Pardo Dolors , Almirante Benito , Bartolomé Rosa M. , Pomar Virginia , Mirelis Beatriz , Navarro Ferran , Soriano Alex , Sorlí Luisa , Martínez-Montauti Joaquín , Molins Maria Teresa , Lung Maily , Vila Jordi , Pahissa Albert
Published: February 2013

Prospective hospital-based surveillance for
Clostridium difficile
-associated disease (CDAD) was conducted in Barcelona (Spain) to describe the epidemiology of this condition and investigate the risk factors for an unfavorable outcome. All patients diagnosed with CDAD during 2009 were included. Using logistic regression modeling, we analyzed the potential risk factors associated with recurrent and complicated CDAD, defined as a need for colectomy or death within 30 days. There were 365 episodes of CDAD, yielding an incidence of 22.5 cases/10
5
person-years, 1.22 cases/10
3
hospital discharges, and 1.93 cases/10
4
patient-days. The main PCR ribotypes identified were 241 (26%), 126 (18%), 078 (7%), and 020 (5%). PCR ribotype 027 was not detected. Among the 348 cases analyzed, 232 (67%) patients were cured, 63 (18%) had a recurrence of CDAD, and 53 (15%) developed complicated CDAD. Predictors of complicated CDAD were continued use of antibiotics following CDAD diagnosis (odds ratio [OR], 2.009; 95% confidence interval [CI], 1.012 to 3.988;
P
= 0.046), Charlson comorbidity index score (OR, 1.265; 95% CI, 1.105 to 1.449;
P
= 0.001), and age (OR, 1.028; 95% CI, 1.005 to 1.053;
P
= 0.019). A leukocyte count of >15 × 10
3
cells/ml (OR, 2.277; 95% CI, 1.189 to 4.362;
P
= 0.013), continuation of proton pump inhibitor (PPI) use after CDAD diagnosis (OR, 2.168; 95% CI, 1.081 to 4.347;
P
= 0.029), and age (OR, 1.021; 95% CI, 1.001 to 1.041;
P
= 0.036) were independently associated with higher odds of recurrence. The incidence of CDAD in Barcelona during 2009 was on the lower end of the previously described range for all of Europe. Our analysis suggests that the continuation of non-
C. difficile
antibiotics and use of PPIs in patients diagnosed with CDAD are associated with unfavorable clinical outcomes.
Bilateral Tension Pneumothorax Related to Acupuncture
Authors: Tagami Rumi , Moriya Takashi , Kinoshita Kosaku , Tanjoh Katsuhisa
Published: March 2013

We report on a patient with a rare case of bilateral tension pneumothorax that occurred after acupuncture. A 69-year-old large-bodied man, who otherwise had no risk factors for spontaneous pneumothorax, presented with chest pressure, cold sweats and shortness of breath. Immediately after bilateral pneumothorax had been identified on a chest radiograph in the emergency room, his blood pressure and percutaneous oxygen saturation suddenly decreased to 78 mm Hg and 86%, respectively. We confirmed deterioration in his cardiopulmonary status and diagnosed bilateral tension pneumothorax. We punctured his chest bilaterally and inserted chest tubes for drainage. His vital signs promptly recovered. After the bilateral puncture and drainage, we learnt that he had been treated with acupuncture on his upper back. We finally diagnosed a bilateral tension pneumothorax based on the symptoms that appeared 8 h after the acupuncture. Because the patient had no risk factors for spontaneous pneumothorax, no alternative diagnosis was proposed. We recommend that patients receiving acupuncture around the chest wall must be adequately informed of the possibility of complications and expected symptoms, as a definitive diagnosis can be difficult without complete information.
How far you can trust c-ANCA?
Authors: Akturk Halis Kaan , Vashisht Priyanka
Published: March 2013

The suspicion of a serious condition arises if a smoker is coughing and losing weight constantly. Serology and imaging are great options for diagnosis, but what is their specificity? A 62-year-old man presented with persistent cough, weight loss and hypoxia. A chest x-ray revealed bilateral interstitial infiltrates. Treatment with several antibiotics failed. Serological results showed antineutrophil cytoplasmic antibodies (c-ANCA) positivity. However, biopsy result indicated cryptogenic organising pneumonia. This case report discloses the differential diagnosis of c-ANCA positive interstitial lung disease in detail.
‘Nevi of Ota: the unusual birthmarks’: a case review
Authors: Mohan Ravi Prakash Sasankoti , Verma Sankalp , Singh Amit Kumar , Singh Udita
Published: March 2013

Nevi of Ota are usually characterised by unilateral, mottled, slate blue or dark brown macules on the forehead and face around the eye area. These are unusual skin discolorations in which melanocytes are found deeper than normal. Ota's nevus is usually congenital but may appear in early childhood or in puberty. We summarise a case report along with histological and management aspects of this cosmetically unappealing condition.
Sympathetic skin response and heart rate variability as diagnostic tools for the differential diagnosis of Lewy body dementia and Alzheimer's disease: a diagnostic test study
Authors: Negami Masako , Maruta Takahiro , Takeda Chie , Adachi Yumi , Yoshikawa Hiroaki
Published: March 2013

Objective

The purpose of this study is to investigate the usefulness of sympathetic skin response (SSR) and heart rate variability (HRV) for the differential diagnosis of patients with dementia with Lewy bodies (DLB).

Design

A diagnostic test study.

Setting

Single centre in Japan.

Participants

We examined 20 patients with probable Alzheimer's disease (AD) diagnosed with NINCDS-ADRDA criteria and 20 with probable DLB diagnosed with the criteria of the third international DLB workshop.

Methods

For the SSR measurement, surface electrodes were used: the active recording electrode was placed on the palm of the hand and the reference electrode was placed on the dorsum of the same hand. SSR was induced by a median nerve electrical stimulation at an amplitude of 20 mA. For the HRV measurement, the A–A intervals were measured twice for 2 min with an interval of 5 min in a sitting position after a rest of 5 min. From the low-frequency power (LF; 0.02–0.15 Hz) and high-frequency power (HF; 0.15–0.50 Hz), the ratio of LF to HF power (LF/HF) was calculated using the maximal entropy method.

Results

SSR and HRV could detect the abnormality of autonomic function in patients with DLB at sensitivities of 85% and 90%, respectively. On the other hand, SSR and HRV detected an abnormality of autonomic function in patients with AD at sensitivities of 15% and 25% (p<0.05). The combination of the SSR and the HRV (double-positive) indicated abnormal autonomic function was recorded in only 1 of 20 patients (5%) with AD. In contrast, this combination indicated autonomic abnormality in 15 of 20 patients with DLB by our criteria (75%).

Conclusions

SSR and HRV can be applied to differentiate DLB from AD.
Peer-to-peer mentoring for individuals with early inflammatory arthritis: feasibility pilot
Authors: Sandhu Sharron , Veinot Paula , Embuldeniya Gayathri , Brooks Sydney , Sale Joanna , Huang Sicong , Zhao Alex , Richards Dawn , Bell Mary J
Published: March 2013

Objectives

To examine the feasibility and potential benefits of early peer support to improve the health and quality of life of individuals with early inflammatory arthritis (EIA).

Design

Feasibility study using the 2008 Medical Research Council framework as a theoretical basis. A literature review, environmental scan, and interviews with patients, families and healthcare providers guided the development of peer mentor training sessions and a peer-to-peer mentoring programme. Peer mentors were trained and paired with a mentee to receive (face-to-face or telephone) support over 12 weeks.

Setting

Two academic teaching hospitals in Toronto, Ontario, Canada.

Participants

Nine pairs consisting of one peer mentor and one mentee were matched based on factors such as age and work status.

Primary outcome measure

Mentee outcomes ofdisease modifying antirheumatic drugs (DMARDs)/biological treatment use, self-efficacy, self-management, health-related quality of life, anxiety, coping efficacy, social supportanddisease activitywere measured using validated tools. Descriptive statistics and effect sizes were calculated to determine clinically important (>0.3) changes. Peer mentorself-efficacywas assessed using a self-efficacy scale. Interviews conducted with participants examined acceptability and feasibility of procedures and outcome measures, as well as perspectives on the value of peer support for individuals with EIA. Themes were identified through constant comparison.

Results

Mentees experienced improvements in the overall arthritis impact on life, coping efficacy and social support (effect size >0.3). Mentees also perceived emotional, informational, appraisal and instrumental support. Mentors also reported benefits and learnt from mentees’ fortitude and self-management skills. The training was well received by mentors. Their self-efficacy increased significantly after training completion. Participants’ experience of peer support was informed by the unique relationship with their peer. All participants were unequivocal about the need for peer support for individuals with EIA.

Conclusions

The intervention was well received. Training, peer support programme and outcome measures were demonstrated to be feasible with modifications. Early peer support may augment current rheumatological care.

Trial registration number

NCT01054963,NCT01054131.
Hospitalisation rates for children with intellectual disability or autism born in Western Australia 1983–1999: a population-based cohort study
Authors: Bebbington Ami , Glasson Emma , Bourke Jenny , de Klerk Nicholas , Leonard Helen
Published: March 2013

Objectives

To describe the hospitalisation patterns in children with intellectual disability (ID) and/or autism spectrum disorder (ASD) after the first year of life and compare with those unaffected.

Design

Prospective cohort study using data linkage between health, ID and hospitalisation population-based datasets.

Setting

Western Australia.

Participants

416 611 individuals born between 1983 and 1999 involving 1 027 962 hospital admission records. Five case categories were defined (mild/moderate ID, severe ID, biomedically caused ID, ASD with ID and ASD without ID) and compared with the remainder of children and young people.

Primary and secondary outcome measures

Time to event analysis was used to compare time hospitalisation and rate of hospitalisation between the different case-groups by estimating HR, accounting for birth year and preterm birth status.

Results

ID and/or ASD were found to be associated with an increased risk of hospitalisation compared with the remainder of the population. The increase in risk was highest in those with severe ID and no ASD (HR=10.33, 95% CI 8.66 to 12.31). For those with ID of known biomedical cause or mild ID of unknown cause, the risk of hospitalisation was lower (HR=7.36, 95% CI 6.73 to 8.07 and HR=3.08, 95% CI 2.78 to 3.40, respectively). Those with ASDs had slightly increased risk (HR=2.82, 95% CI 2.26 to 3.50 for those with ID and HR=2.09, 95% CI 1.85 to 2.36 for those without ID).

Conclusions

Children with an ID or ASD experience an increased risk of hospitalisation after the first year of life which varied from 2 to 10 times that of the rest of the population. Findings can inform service planning or resource allocation for these children with special needs.
The association of patient characteristics and surgical variables on symptoms of pain and function over 5 years following primary hip-replacement surgery: a prospective cohort study
Authors: Judge Andy , Arden Nigel K , Batra Rajbir N , Thomas Geraint , Beard David , Javaid M Kassim , Cooper Cyrus , Murray David ,   Exeter Primary Outcomes Study (EPOS) group
Published: March 2013

Objectives

To identify patient characteristics and surgical factors associated with patient-reported outcomes over 5 years following primary total hip replacement (THR).

Design

Prospective cohort study.

Setting

Seven hospitals across England and Scotland.

Participants

1431 primary hip replacements for osteoarthritis.

Main outcome measures

The Oxford Hip Score (OHS) was collected preoperatively and each year up to 5 years postoperatively. Repeated measures such as linear regression modelling are used to identify patient and surgical predictors of outcome and describe trends over time.

Results

The majority of patients demonstrated substantial improvement in pain/function in the first year after surgery—between 1 and 5 years follow-up, there was neither further improvement nor decline. The strongest determinant of attained postoperative OHS was the preoperative OHS—those with worse preoperative pain/function had worse postoperative pain/function. Other predictors with small but significant effects included: femoral component offset—women with an offset of 44 or more had better outcomes; age—compared to those aged 50–60, younger (age <50) and older patients (age >60) had worse outcome, increasing body mass index (BMI), more coexisting diseases and worse Short Form 36 mental health (MH) was related to worse postoperative pain/function. Assessment of change in OHS between preoperative  and postoperative assessments revealed that patients achieved substantial and clinically relevant symptomatic improvement (change), regardless of variation in these patient and surgical factors.

Conclusions

Patients received substantial benefit from surgery, regardless of their preoperative assessments and surgical characteristics (baseline pain/function, age, BMI, comorbidities, MH and femoral component offset). Further research is needed to identify other factors that can improve our ability to identify patients at risk of poor outcomes from THR surgery.
Developing a service for patients with very severe chronic obstructive pulmonary disease (COPD) within resources
Authors: Boland Jason , Owen Janet , Ainscough Rachel , Mahdi Hazim
Published: March 2013

Chronic obstructive pulmonary disease (COPD) is a common life-limiting illness with significant burden for patient and carer. Despite this, access to supportive and specialist palliative care is inconsistent and implementation of published good practice recommendations may be challenging within current resources. The aim of this service development was to improve local service provision in Barnsley, within the currently available resources, for patients with very severe COPD, to improve patient identification and symptom management, increase advance care planning and the numbers of patients dying in their preferred place, and increase patient and carer support and satisfaction. To do this a working group was formed, the service problems identified and baseline data collected to identify the needs of people with very severe COPD. A multidisciplinary team meeting was piloted and assessed by community matron feedback, patient case studies and an after death analysis. These indicated a high level of satisfaction, with improvements in advance care planning, co-ordination of management and support for patients’ preferred place of care at the end of life. In conclusion this is the first reported very severe COPD service development established in this way and within current resources. Preliminary data indicates the development of the multidisciplinary team meeting has been positive. The appointment of a coordinator will aid this development. Further evaluations particularly seeking patient views and estimations of cost savings will be performed.
Pension Contributions and Earnings Quality
Authors: Kim John , Li John , Sun Fang
Published: March 2013

We investigate whether defined benefit (DB) pension contributions convey information about earnings quality proxied by different measurements of discretionary accruals (DA). We find that greater DA are negatively is associated with discretionary pension contributions. Since greater DA is associated with lower earnings quality, the result implies a positive relationship between earnings quality and voluntary pension contributions. In contrast, our evidence does not suggest a similar relationship holds for earnings quality and mandatory pension contributions. In addition, while our analysis identifies a negative relation between DA and total pension contributions, the relation is statistically weaker than that between DA and voluntary pension contribution. Robustness tests are conducted and results are found to continue to hold. Our results are consistent with the theoretical argument that voluntary pension contributions are indicative of firms' earnings quality since both the voluntary pension contributions and earnings quality result from the same set of incentives behind managerial discretions. Our study sheds light on the management's motivation for making voluntary pension contributions and improves our understanding of firms' consideration in funding strategies for DB pension plans.
DISCORD-ENTANGLEMENT INTERPLAY IN THE THERMODYNAMIC LIMIT: THE XY-MODEL
Authors: BATLE J. , PLASTINO A. , PLASTINO A. R. , CASAS M.
Published: March 2013

We investigate thermal properties of quantum correlations in the thermodynamic limit with reference to the XY-model and the finite two-qubit Heisenberg model. Although this model has been the subject of active entanglement-research, the bulk of the pertinent work refers to finite instantiations. As a consequence, the temperature cannot be properly defined in such circumstances, a problem that is overcome here. Our effort should be of interest because quantum discord notion.
RECAPITULATING THE VASCULAR MICROENVIRONMENT IN MICROFLUIDIC PLATFORMS
Authors: ABACI HASAN E. , DRAZER GERMAN , GERECHT SHARON
Published: March 2013

The vasculature is regulated by various chemical and mechanical factors. Reproducing these factors in vitro is crucial for the understanding of the mechanisms underlying vascular diseases and the development of new therapeutics and delivery techniques. Microfluidic technology offers opportunities to precisely control the level, duration and extent of various cues, providing unprecedented capabilities to recapitulate the vascular microenvironment. In the first part of this article, we review existing microfluidic technology that is capable of controlling both chemical and mechanical factors regulating the vascular microenvironment. In particular, we focus on micro-systems developed for controlling key parameters such as oxygen tension, co-culture, shear stress, cyclic stretch and flow patterns. In the second part of this article, we highlight recent advances that resulted from the use of these microfluidic devices for vascular research.
SOFT GRAVITONS SCREEN COUPLING IN DE SITTER SPACE
Authors: KITAMOTO HIROYUKI , KITAZAWA YOSHIHISA
Published: March 2013

On the de Sitter background, the gravitational propagator contains an infra-red logarithm term which breaks the de Sitter symmetry. We investigate how such soft gravitons affect the local dynamics of matter fields. We show that the infra-red logarithms do not spoil Lorentz invariance in scalar, Dirac and gauge field theories. In the interacting field theory with quartic, Yukawa and gauge interactions, we find that the effective couplings are time dependent and the evolutions are physical as their relative scaling exponents are gauge invariant.
THE CLASSICAL EQUIVALENCE OF MONODROMY MATRICES IN SQUASHED SIGMA MODEL
Authors: KAWAGUCHI IO , MATSUMOTO TAKUYA , YOSHIDA KENTAROH
Published: March 2013

We show Yangian and quantum affine symmetries are realized in two-dimensional non-linear sigma models with squashed spheres target spaces. According to these symmetries, there are two descriptions for the classical dynamics. In each description, a Lax pair and the corresponding monodromy matrix are constructed. Both Lax pairs reproduce the same equations of motion and hence they are equivalent. We show the gauge-equivalence by constructing a map between monodromy matrices with the relation of spectral parameters.
Synthetic Nanoelectronic Probes for Biological Cells and Tissues
Authors: Tian Bozhi , Lieber Charles M.
Published: March 2013

Research at the interface between nanoscience and biology could yield breakthroughs in fundamental science and lead to revolutionary technologies. In this review, we focus on the interfaces between nanoelectronics and biology. First, we discuss nanoscale field effect transistors (nanoFETs) as probes to study cellular systems; specifically, we describe the development of nanoFETs that are comparable in size to biological nanostructures involved in communication through synthesized nanowires. Second, we review current progress in multiplexed extracellular sensing using planar nanoFET arrays. Third, we describe the designs and implementation of three distinct nanoFETs used to perform the first intracellular electrical recording from single cells. Fourth, we present recent progress in merging electronic and biological systems at the three-dimensional tissue level by use of macro-porous nanoelectronic scaffolds. Finally, we discuss future developments in this research area, unique challenges and opportunities, and the tremendous impact these nanoFET-based technologies might have on biological and medical sciences.
A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes
Authors: Olsen Kenneth M. , Wendel Jonathan F.
Published: March 2013

Human selection during crop domestication has resulted in remarkable transformations of plant phenotypes, providing a window into the genetic basis of morphological evolution. Recent progress in our understanding of the genetic architecture of novel plant traits has emerged from combining advanced molecular technologies with improved experimental designs, including nested association mapping, genome-wide association studies, population genetic screens for signatures of selection, and candidate gene approaches. These studies reveal a diversity of underlying causative mutations affecting phenotypes important in plant domestication and crop improvement, including coding sequence substitutions, presence/absence and copy number variation, transposon activation leading to novel gene structures and expression patterns, diversification following gene duplication, and polyploidy leading to altered combinatorial capabilities. The genomic regions unknowingly targeted by human selection include both structural and regulatory genes, often with results that propagate through the transcriptome as well as to other levels in the biosynthetic and morphogenetic networks.
The Endodermis
Authors: Geldner Niko
Published: March 2013

A Casparian strip–bearing endodermis is a feature that has been invariably present in the roots of ferns and angiosperms for approximately 400 million years. As the innermost cortical layer that surrounds the central vasculature of roots, the endodermis acts as a barrier to the free diffusion of solutes from the soil into the stele. Based on an enormous body of anatomical and physiological work, the protective endodermal diffusion barrier is thought to be of major importance for many aspects of root biology, reaching from efficient water and nutrient transport to defense against soil-borne pathogens. Until recently, however, we were ignorant about the genes and mechanisms that drive the differentiation of this intricately structured barrier. Recent work in Arabidopsis has now identified the first major players in Casparian strip formation. A mechanistic understanding of endodermal differentiation will finally allow us to specifically interfere with endodermal barrier function and study the effects on plant growth and survival under various stress conditions. Here, I critically review the major findings and models related to endodermal structure and function from other plant species and assess them in light of recent molecular data from Arabidopsis, pointing out where the older, descriptive work can provide a framework and inspiration for further molecular dissection.
Future Scenarios for Plant Phenotyping
Authors: Fiorani Fabio , Schurr Ulrich
Published: March 2013

With increasing demand to support and accelerate progress in breeding for novel traits, the plant research community faces the need to accurately measure increasingly large numbers of plants and plant parameters. The goal is to provide quantitative analyses of plant structure and function relevant for traits that help plants better adapt to low-input agriculture and resource-limited environments. We provide an overview of the inherently multidisciplinary research in plant phenotyping, focusing on traits that will assist in selecting genotypes with increased resource use efficiency. We highlight opportunities and challenges for integrating noninvasive or minimally invasive technologies into screening protocols to characterize plant responses to environmental challenges for both controlled and field experimentation. Although technology evolves rapidly, parallel efforts are still required because large-scale phenotyping demands accurate reporting of at least a minimum set of information concerning experimental protocols, data management schemas, and integration with modeling. The journey toward systematic plant phenotyping has only just begun.
Tapping the Promise of Genomics in Species with Complex, Nonmodel Genomes
Authors: Hirsch Candice N. , Robin Buell C.
Published: March 2013

Genomics is enabling a renaissance in all disciplines of plant biology. However, many plant genomes are complex and remain recalcitrant to current genomic technologies. The complexities of these nonmodel plant genomes are attributable to gene and genome duplication, heterozygosity, ploidy, and/or repetitive sequences. Methods are available to simplify the genome and reduce these barriers, including inbreeding and genome reduction, making these species amenable to current sequencing and assembly methods. Some, but not all, of the complexities in nonmodel genomes can be bypassed by sequencing the transcriptome rather than the genome. Additionally, comparative genomics approaches, which leverage phylogenetic relatedness, can aid in the interpretation of complex genomes. Although there are limitations in accessing complex nonmodel plant genomes using current sequencing technologies, genome manipulation and resourceful analyses can allow access to even the most recalcitrant plant genomes.
Electrophysiological Characterization of Membrane Transport Proteins
Authors: Grewer Christof , Gameiro Armanda , Mager Thomas , Fendler Klaus
Published: March 2013

Active transport in biological membranes has been traditionally studied using a variety of biochemical and biophysical techniques, including electrophysiology. This review focuses on aspects of electrophysiological methods that make them particularly suited for the investigation of transporter function. Two major approaches to electrical recording of transporter activity are discussed: (a) artificial planar lipid membranes, such as the black lipid membrane and solid supported membrane, which are useful for studies on bacterial transporters and transporters of intracellular compartments, and (b) patch clamp and voltage clamp techniques, which investigate transporters in native cellular membranes. The analytical power of these methods is highlighted by several examples of mechanistic studies of specific membrane proteins, including cytochrome c oxidase, NhaA Na+/H+ exchanger, ClC-7 H+/Cl− exchanger, glutamate transporters, and neutral amino acid transporters. These examples reveal the wealth of mechanistic information that can be obtained when electrophysiological methods are used in combination with rapid perturbation approaches.
Quantitative Modeling of Bacterial Chemotaxis: Signal Amplification and Accurate Adaptation
Authors: Tu Yuhai
Published: March 2013

We review the recent developments in understanding the bacterial chemotaxis signaling pathway by using quantitative modeling methods. The models developed are based on structural information of the signaling complex and the dynamics of the underlying biochemical network. We focus on two important functions of the bacterial chemotaxis signaling pathway: signal amplification and adaptation. We describe in detail the structure and the dynamics of the mathematical models and how they compare with existing experiments, emphasizing the predictability of the models. Finally, we outline future directions for developing the modeling approach to better understand the bacterial chemosensory system.
Equilibrium Theory–Based Analysis of Nonlinear Waves in Separation Processes
Authors: Mazzotti Marco , Rajendran Arvind
Published: March 2013

Different areas of engineering, particularly separation process technology, deal with one-dimensional, nonstationary processes that under reasonable assumptions, namely negligible dispersion effects and transport resistances, are described by mathematical models consisting of systems of first-order partial differential equations. Their behavior is characterized by continuous or discontinuous composition (or thermal) fronts that propagate along the separation unit. The equilibrium theory (i.e., the approach discussed here to determine the solution to these model equations) predicts this with remarkable accuracy, despite the simplifications and assumptions. Interesting applications are in adsorption, chromatography and ion-exchange, distillation, gas injection, heat storage, sedimentation, precipitation, and dissolution waves. We show how mathematics can enlighten the engineering aspects, and we guide the researcher not only to reach a synthetic understanding of properties of fundamental and applicative interest but also to discover new, unexpected, and fascinating phenomena. The tools presented here are useful to teachers, researchers, and practitioners alike.
CO2 Mineralization—Bridge Between Storage and Utilization of CO2
Authors: Geerlings Hans , Zevenhoven Ron
Published: March 2013

CO2 mineralization comprises a chemical reaction between suitable minerals and the greenhouse gas carbon dioxide. The CO2 is effectively sequestered as a carbonate, which is stable on geological timescales. In addition, the variety of materials that can be produced through mineralization could find applications in the marketplace, which makes implementation of the technology more attractive. In this article, we review recent developments and assess the current status of the CO2 mineralization field. In an outlook, we briefly describe a few mineralization routes, which upon further development have the potential to be implemented on a large scale.
Experimental Dynamos and the Dynamics of Planetary Cores
Authors: Olson Peter
Published: March 2013

Laboratory experiments using liquid metals and nonmetallic liquids reveal a rich set of dynamical processes active in Earth's core and in the cores of other terrestrial planets. These processes include thermochemical convection and a variety of instabilities driven by irregularities in rotation, such as precession, libration, and tides. The spectrum of fluid motions in these experiments ranges from turbulence and inertial wave motions at high frequencies to global-scale zonal flows at low frequencies, and they result from the interplay between buoyant forces, rotational effects, melting and solidification, magnetic fields, and the spherical geometry of the core. This review summarizes strengths and limitations of laboratory fluid experiments for modeling core dynamics, identifies the key physical parameters, and highlights recent advances in understanding the complex flows that control the evolution of the core. Special emphasis is given to ongoing efforts to develop self-sustaining fluid dynamos.
Nanoscale Hard X-Ray Microscopy Methods for Materials Studies
Authors: Holt Martin , Harder Ross , Winarski Robert , Rose Volker
Published: March 2013

This review discusses recent progress in the development of hard X-ray microscopy techniques for materials characterization at the nanoscale. Although the utility of traditionally ensemble-based X-ray techniques in materials research has been widely recognized, the utility of X-ray techniques as a tool for local characterization of nanoscale materials properties has undergone rapid development in recent years. Owing to a confluence of improvements in synchrotron source brightness, focusing optics fabrication, detection, and data analysis, nanoscale X-ray imaging techniques have moved beyond proof-of-principle experiments to play a central role in synchrotron user programs worldwide with high-impact applications made to materials science questions. Here, we review the current state of synchrotron-based, hard X-ray nanoscale microscopy techniques—including 3D tomographic visualization, spectroscopic elemental and chemical mapping, microdiffraction-based structural analysis, and coherent methods for nanomaterials imaging—with particular emphasis on applications to materials research.
Why Social Relations Matter for Politics and Successful Societies
Authors: Hall Peter A. , Lamont Michèle
Published: March 2013

Political science can gain from incorporating richer conceptions of social relations into its analyses. In place of atomistic entities endowed with assets but few social relationships, social actors should be seen as relational entities embedded in social and cultural structures that connect them to others in multifaceted ways. Understanding those relationships requires a deeper understanding of how institutional and cultural frameworks interact to condition the terrain for social action. More intensive dialogue with sociology can inform such an understanding. We review the analytical tools cultural sociology now offers those interested in such a perspective and illustrate it in operation in studies of inequalities in population health and the effects of neoliberalism. We close by outlining several issues to which this perspective can usefully be applied, including the problems of understanding social resilience, how societies build collective capacities, and why some institutions remain robust while others deteriorate.
The Analytical Foundations of Collective Action Theory: A Survey of Some Recent Developments
Authors: Medina Luis Fernando
Published: March 2013

The theory of collective action has long since moved beyond the “free-rider problem” as originally stated by Olson (1965) . It is now recognized that large-scale participation is possible even without selective incentives, but this has raised new questions. I discuss two types of contributions from the past few years. Some of the recent literature has remained close to the canonical game-theoretic framework, clarifying many analytical issues and proving important results in participation games that had remained elusive. We now know that the “turnout paradox” had been grossly overstated. Another set of contributions has expanded the original framework, incorporating results from psychology and social sciences with the aim of obtaining more realistic models with better empirical performance.
The Use and Misuse of the “Minorities at Risk” Project
Authors: Hug Simon
Published: March 2013

The “Minorities at Risk” (MAR) project and data have offered an innovative, systematic view of communal and ethnic groups. By collecting detailed information on groups that are mobilized and/or discriminated against, and thus “at risk,” MAR has allowed researchers to offer new insights in many areas dealing with relationships among groups. However, scholars have also used this dataset in ways for which it was not designed or is hardly appropriate. This article offers an overview of the main contributions of MAR and identifies research questions for which the MAR data have to be used with care.
Influenza matrix protein 2 alters CFTR expression and function through its ion channel activity
Authors: Londino James D. , Lazrak Ahmed , Jurkuvenaite Asta , Collawn James F. , Noah James W. , Matalon Sadis
Published: March 2013

The human cystic fibrosis transmembrane conductance regulator (CFTR) is a cyclic AMP-activated chloride (Cl−) channel in the lung epithelium that helps regulate the thickness and composition of the lung epithelial lining fluid. We investigated whether influenza M2 protein, a pH-activated proton (H+) channel that traffics to the plasma membrane of infected cells, altered CFTR expression and function. M2 decreased CFTR activity in 1) Xenopus oocytes injected with human CFTR, 2) epithelial cells (HEK-293) stably transfected with CFTR, and 3) human bronchial epithelial cells (16HBE14o−) expressing native CFTR. This inhibition was partially reversed by an inhibitor of the ubiquitin-activating enzyme E1. Next we investigated whether the M2 inhibition of CFTR activity was due to an increase of secretory organelle pH by M2. Incubation of Xenopus oocytes expressing CFTR with ammonium chloride or concanamycin A, two agents that alkalinize the secretory pathway, inhibited CFTR activity in a dose-dependent manner. Treatment of M2- and CFTR-expressing oocytes with the M2 ion channel inhibitor amantadine prevented the loss in CFTR expression and activity; in addition, M2 mutants, lacking the ability to transport H+, did not alter CFTR activity in Xenopus oocytes and HEK cells. Expression of an M2 mutant retained in the endoplasmic reticulum also failed to alter CFTR activity. In summary, our data show that M2 decreases CFTR activity by increasing secretory organelle pH, which targets CFTR for destruction by the ubiquitin system. Alteration of CFTR activity has important consequences for fluid regulation and may potentially modify the immune response to viral infection.
Limits in motor control bandwidth during stick balancing
Authors: Reeves N. Peter , Pathak Pramod , Popovich John M. , Vijayanagar Vilok
Published: February 2013

Why can we balance a yardstick but not a pencil on the tip of our finger? As with other physical systems, human motor control has constraints, referred to as bandwidth, which restricts the range of frequency over which the system can operate within some tolerated level of error. To investigate control bandwidth, the natural frequency of a stick used during a stick-balancing task was modified by adjusting the height of a mass attached to the stick. The ability to successfully balance the stick with the mass positioned at four different heights was determined. In addition, electromyographic signals from forearm and trunk muscles were recorded during the trials. We hypothesized that 1) the probability of successfully balancing would decrease as mass height decreased; and 2) the level of muscle activation in both agonist and antagonist would increase as the natural frequency of the stick increased. Results showed that as the mass height decreased the probability of successfully balancing the stick decreased. Changes in the probability of success with respect to mass height showed a threshold effect, suggesting that limits in human control bandwidth were approached at the lowest mass height. Also, the level of muscle activation in both the agonist and antagonist of the forearm and trunk increased linearly as the natural frequency of the stick increased. These changes in muscle activation suggest that the central nervous system adapts muscle activation to task dynamics, possibly to improve control bandwidth.