bluuebunny/crossref_metadata_2025 huggingface dataset:
Kingella kingae as the Main Cause of Septic Arthritis
Authors: Hernández-Rupérez María Belén , Suárez-Arrabal María del Carmen , Villa-García Ángel , Zarzoso-Fernández Sara , Navarro-Gómez Marisa , Santos-Sebastián María del Mar , García-Martín Azucena , Marín Mercedes , González-Martínez Felipe , Narbona-Cárceles Javier , Cervera-Bravo Paloma , González-López José Luis , Hernández-Sampelayo Teresa , Saavedra-Lozano Jesús
Published: April 2018

Background:

Kingella kingae is an emergent pathogen causing septic arthritis (SA) in children.

The objective of this study was to analyze the etiology of SA in children before and after the implementation of universal 16S rRNA gene polymerase chain reaction and sequencing (16SPCR) in synovial fluid.

Methods:

Children ≤14 years with acute SA from a Madrid cohort (2002–2013) were reviewed. Differences in etiology were analyzed before (period 1) and after (period 2) the implementation of bacterial 16SPCR in 2009. A comparison in epidemiology, clinical syndromes, therapy and outcome between infections caused by K. kingae and other bacteria was performed.

Results:

Bacteria were detected from 40/81 (49.4%) children, with a higher proportion of diagnosis after 16SPCR establishment (period 2, 63% vs. period 1, 31.4%; P = 0.005). The main etiologies were Staphylococcus aureus (37.5%) and K. kingae (35%), although K. kingae was the most common microorganism in P2 (48.3%). Children with K. kingae SA were less likely to be younger than 3 months (0 vs. 42.3%; P < 0.001), had less anemia (21.4 vs. 50%; P = 0.010), lower C-reactive protein (3.8 vs. 8.9 mg/dL; P = 0.039), less associated osteomyelitis (0 vs. 26.9%; P = 0.033), shorter intravenous therapy (6 vs. 15 days; P < 0.001), and had a nonsignificant lower rate of sequelae (0 vs. 30%; P = 0.15) than children with SA caused by other bacteria. However, they tended to have higher rate of fever (86 vs. 57%; P = 0.083).

Conclusions:

K. kingae was frequently recovered in children with SA after the implementation of bacterial 16SPCR, producing a milder clinical syndrome and better outcome. Therefore, the use of molecular techniques may be important for the management of these children.
Pediatric Coccidioidomycosis
Authors: Lee Lauren A. , Sondermeyer Cooksey Gail L. , Kim Janice J. , Kahal Amandeep , Gilliss Debra , Naeem Fouzia , McCarty James M. , Vugia Duc J.
Published: April 2018

Background:

Coccidioidomycosis is not as well described in the pediatric population as it is in the adult population. We describe clinical findings, diagnosis and management of coccidioidomycosis in 108 pediatric patients seen in an outpatient clinic in the California Central Valley, an area endemic for coccidioidomycosis.

Methods:

We reviewed medical records of a convenience sample of pediatric patients (≤17 years of age) diagnosed with coccidioidomycosis who visited an infectious diseases clinic in Madera, CA, during January 1 to October 1, 2012. We described demographic characteristics, symptoms, diagnostic testing, extent of infection (acute/pulmonary or disseminated), treatment and management.

Results:

Of 108 patients, 90 (83%) had acute/pulmonary coccidioidomycosis and 18 (17%) had disseminated disease. The median age at diagnosis was 9 years (range, 5 months to 17 years). Only 3 (3%) patients were immunocompromised. Before coccidioidomycosis diagnosis, 72 (82%) patients received antibiotics, and 31 (29%) had at least 1 negative coccidioidomycosis serology at the time of or before diagnosis. Coccidioidomycosis was diagnosed significantly later after symptom onset among patients with disseminated (median, 57 days) than with acute/pulmonary (median, 16 days) disease (p < 0.01). A total of 104 (96%) patients received antifungal therapy, 51 (47%) visited an emergency room and 59 (55%) were hospitalized with a median stay of 44 days (range, 1–272 days).

Conclusions:

Substantial acute/pulmonary and disseminated coccidioidomycosis was seen among pediatric patients at this infectious disease clinic in California. In endemic areas, increased coccidioidomycosis awareness and vigilance among families and providers is necessary to facilitate early diagnosis and appropriate management.
Misuse of Trihexyphenidyl (Artane) on Réunion Island
Authors: Torrents Romain , Ferré Jean Francois , Konareff Annie , Hemery Patrice , Sherwin Kenneth , Lassalle Christian , Simon Nicolas , Scerra Sami
Published: April 2018

Background

Trihexyphenidyl (THP) is an anticholinergic drug misused to procure hallucination, sedation, and anxiolysis. The aim of this cohort was to show and describe, within a public health risk management policy, the risks of a long-standing but relatively unknown addiction: THP addiction.

Methods

On Réunion island, a cohort with systematic data collection has been set up by addictologists working in the Centres for Addiction Prevention and Treatment, in the university hospital, and in general practices who have active lists of patients misusing THP. Data collection included socioeconomic data and clinical data concerning addiction.

Results

This cohort included 69 patients during November 2016. The average age of the patients was 36 years; 97% were men; 93% had living accommodation but only 32 % were employed. In this cohort drug administration was exclusively oral. The most common reasons for use were anxiolytic (46%), stimulation (26%), and sedation (10%), the main effects described were dyskinesia and behavioral disorders. Over half (61%) of the patients reported a coaddiction, mainly to benzodiazepines, cannabis, tobacco, alcohol, and buprenorphine.

Conclusions

This cohort describing the clinical characteristics of 69 patients is the largest cohort studied for THP addiction. Patients from the Centres for Addiction Prevention and Treatment were the youngest and most recently addicted, whereas general practice patients had been addicted for longer and were more socially integrated. This clinical description of THP addiction therefore enables us to identify the patients who are the most at risk, to set up an adapted care protocol.
Radiation-induced Cataracts in Children With Brain Tumors Receiving Craniospinal Irradiation
Authors: Whelan Ros J. , Saccomano Benjamin , King Robert , Dorris Kathleen , Hemenway Molly , Hankinson Todd C. , Liu Arthur K.
Published: April 2018

Radiation is a well-known cause of the development of cataracts. For children with brain tumors, craniospinal irradiation (CSI) would be expected to result in a significant risk of cataract development. We reviewed the incidence of cataracts in children with brain tumors who received CSI at our institution. Of 45 children who received CSI and had ophthalmologic examinations, 13 developed cataracts. The median time to develop cataracts was 27.6 months. Seven children underwent surgery for cataract. Given this high incidence of cataracts, we suggest routine eye examinations for all children receiving CSI.
Quantitative Ultrasound of Proximal Phalanxes in Childhood Acute Lymphoblastic Leukemia Survivors
Authors: De Matteo Antonia , Petruzziello Fara , Parasole Rosanna , Esposito Antonella , Mangione Argia , Giagnuolo Giovanna , Menna Giuseppe , Del Puente Antonio
Published: April 2018

Reduced bone mineral density (BMD) is a well-known complication in childhood acute lymphoblastic leukemia (ALL) survivors; the optimal method to assess BMD is still debated. We studied BMD by quantitative ultrasound (QUS) in 72 ALL survivors, and evaluated any correlation with cumulative doses of steroids and cytotoxic agents. Mean age at diagnosis was 61±45 months, while mean age at QUS was 318.3±129.6 months; mean period of follow-up was 41.2±37.8 months. Mean amplitude-dependent speed of sound z-score was −1.22±1.19. Ten survivors (13.8%) presented a z-score below −2 SD. A negative correlation was found between amplitude-dependent speed of sound z-score and age at diagnosis (P=0.01). A positive correlation was observed with length of follow-up (P=0.01). No correlation was found with cytotoxic drugs. This study represents the largest cohort of childhood ALL survivors studied by QUS. Our results suggest that QUS for its characteristics of being radiation free may be an effective option to assess BMD in pediatric age. In addition, our data outline the importance to improve the awareness about the specific expression of this complication in the pediatric age, concerning the major determinants of bone impairment, which are the disease itself and the phase of bone growth when the disease occurs.
Coexistence of BRAF V600E and TERT Promoter Mutations in Low-grade Serous Carcinoma of Ovary Recurring as Carcinosarcoma in a Lymph Node: Report of a Case
Authors: Tavallaee Mahkam , Steiner David F. , Zehnder James L. , Folkins Ann K. , Karam Amer K.
Published: April 2018

Low-grade serous carcinomas only rarely coexist with or progress to high-grade tumors. We present a case of low-grade serous carcinoma with transformation to carcinosarcoma on recurrence in the lymph node. Identical BRAF V600E and telomerase reverse transcriptase promoter mutations were identified in both the original and recurrent tumor. Given that telomerase reverse transcriptase promotor mutations are thought to play a role in progression of other tumor types, the function of telomerase reverse transcriptase mutations in BRAF mutated low-grade serous carcinoma deserves investigation.
The Influence of Pain-Related Expectations on Intensity Perception of Nonpainful Somatosensory Stimuli
Authors: Zaman Jonas , Wiech Katja , Claes Nathalie , Van Oudenhove Lukas , Van Diest Ilse , Vlaeyen Johan W.S.
Published: April 2018

Objective

The extent to which pain-related expectations, known to affect pain perception, also affect perception of nonpainful sensations remains unclear, as well as the potential role of unpredictability in this context.

Methods

In a proprioceptive fear conditioning paradigm, various arm extension movements were associated with predictable and unpredictable electrocutaneous pain or its absence. During a subsequent test phase, nonpainful electrocutaneous stimuli with a high or low intensity were presented during movement execution. We used hierarchical drift diffusion modeling to examine the influence of expecting pain on the perceptual decision-making process underlying intensity perception of nonpainful sensations. In the first experiment (n = 36), the pain stimulus was never presented during the test phase after conditioning. In the second experiment (n = 39), partial reinforcement was adopted to prevent extinction of pain expectations.

Results

In both experiments, movements that were associated with (un)predictable pain led to higher pain expectancy, self-reported fear, unpleasantness, and arousal as compared with movements that were never paired with pain (effect sizes η2
p ranging from 0.119 to 0.557; all p values < .05). Only in the second experiment—when the threat of pain remained present—we found that the expectation of pain affected decision making. Compared with the no pain condition, an a priori decision-making bias toward the high-intensity decision threshold was found with the strongest bias during unpredictable pain (effect sizes η2
p ranging from 0.469 to 0.504; all p-values < .001).

Conclusions

Thus, the expectation of pain affects inferential processes not only for subsequent painful but also for nonpainful bodily stimuli, with unpredictability moderating these effects, and only when the threat of pain remains present due to partial reinforcement.
Diffusion-Weighted Imaging With Apparent Diffusion Coefficient Mapping for Breast Cancer Detection as a Stand-Alone Parameter
Authors: Pinker Katja , Moy Linda , Sutton Elizabeth J. , Mann Ritse M. , Weber Michael , Thakur Sunitha B. , Jochelson Maxine S. , Bago-Horvath Zsuzsanna , Morris Elizabeth A. , Baltzer Pascal AT , Helbich Thomas H.
Published: April 2018

Purpose

The aims of this study were to compare dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) with diffusion-weighted imaging (DWI) with apparent diffusion coefficient mapping as a stand-alone parameter without any other supportive sequence for breast cancer detection and to assess its combination as multiparametric MRI (mpMRI) of the breast.

Materials and Methods

In this institutional review board–approved single-center study, prospectively acquired data of 106 patients who underwent breast MRI from 12/2010 to 09/2014 for an imaging abnormality (Breast Imaging Reporting and Data System 0, 4/5) were retrospectively analyzed. Four readers independently assessed DWI and DCE as well as combined as mpMRI. Breast Imaging Reporting and Data System categories, lesion size, and mean apparent diffusion coefficient values were recorded. Histopathology was used as the gold standard. Appropriate statistical tests were used to compare diagnostic values.

Results

There were 69 malignant and 41 benign tumors in 106 patients. Four patients presented with bilateral lesions. Dynamic contrast-enhanced MRI was the most sensitive test for breast cancer detection, with an average sensitivity of 100%. Diffusion-weighted imaging alone was less sensitive (82%; P < 0.001) but more specific than DCE-MRI (86.8% vs 76.6%; P = 0.002). Diagnostic accuracy was 83.7% for DWI and 90.6% for DCE-MRI. Multiparametric MRI achieved a sensitivity of 96.8%, not statistically different from DCE-MRI (P = 0.12) and with a similar specificity as DWI (83.8%; P = 0.195), maximizing diagnostic accuracy to 91.9%. There was almost perfect interreader agreement for DWI (κ = 0.864) and DCE-MRI (κ = 0.875) for differentiation of benign and malignant lesions.

Conclusion

Dynamic contrast-enhanced MRI is most sensitive for breast cancer detection and thus still indispensable. Multiparametric MRI using DCE-MRI and DWI maintains a high sensitivity, increases specificity, and maximizes diagnostic accuracy, often preventing unnecessary breast biopsies. Diffusion-weighted imaging should not be used as a stand-alone parameter because it detects significantly fewer cancers in comparison with DCE-MRI and mpMRI.
Building Ultrasound Phantoms With Modified Polyvinyl Chloride
Authors: Pepley David Frederick , Sonntag Cheyenne Cassel , Prabhu Rohan Sunil , Yovanoff Mary Alice , Han David C. , Miller Scarlett Rae , Moore Jason Zachary
Published: April 2018

Introduction

Training using ultrasound phantoms allows for safe introduction to clinical skills and is associated with improved in-hospital performance. Many materials have been used to simulate human tissue in phantoms including commercial manikins, agar, gelatin, and Ballistics Gel; however, phantom tissues could be improved to provide higher-fidelity ultrasound images or tactile sensation. This article describes a novel phantom tissue mixture of a modified polyvinyl chloride (PVC) polymer, mineral oil, and chalk powder and evaluates needle cutting and ultrasonic properties of the modified PVC polymer mixture compared with a variety of phantom tissues.

Methods

The first experiment measured axial needle forces of a needle insertion into nine phantom materials, including three formulations of modified PVC. The second experiment used a pairwise comparison survey of ultrasound images to determine the perceived realism of phantom ultrasound images.

Results

It was found that the materials of Ballistics Gel and one of the PVC mixtures provide stiff force feedback similar to cadaver tissue. Other phantom materials including agar and gelatin provide very weak unrealistic force feedback. The survey results showed the PVC mixtures being viewed as the most realistic by the survey participants, whereas agar and Ballistics Gel were seen as the least realistic.

Conclusions

The realism in cutting force and ultrasound visualization was determined for a variety of phantom materials. Novel modified PVC polymer has great potential for use in ultrasound phantoms because of its realistic ultrasound imaging and modifiable stiffness. This customizability allows for easy creation of multilayer tissue phantoms.
Long-term Outcomes of ABO-incompatible Pediatric Living Donor Liver Transplantation
Authors: Honda Masaki , Sugawara Yasuhiko , Kadohisa Masashi , Shimata Keita , Sakisaka Masataka , Yoshii Daiki , Uto Keiichi , Hayashida Shintaro , Ohya Yuki , Yamamoto Hidekazu , Yamamoto Hirotoshi , Inomata Yukihiro , Hibi Taizo
Published: April 2018

Background

ABO-incompatible (ABOi) living donor liver transplantation (LDLT) has been performed to compensate for donor shortage. To date, few studies have reported detailed B-cell desensitization protocols and long-term outcomes of ABOi pediatric LDLT.

Methods

Twenty-nine pediatric ABOi LDLT recipients were retrospectively analyzed. We compared the clinical outcomes between ABOi (n = 29) and non-ABOi (n = 131) pediatric LDLT recipients. Furthermore, we evaluated the safety and efficacy of our rituximab-based regimen for ABOi pediatric LDLT (2 ≤ age < 18; n = 10).

Results

There were no significant differences in the incidence of infection, vascular complications, biliary complications, and acute cellular rejection between ABOi and non-ABOi groups. The cumulative graft survival rate at 1, 3, and 5 years for non-ABOi group were 92.1%, 87.0%, and 86.1%, and those for ABOi group were 82.8%, 82.8%, and 78.2%, respectively. Rituximab-based desensitization protocol could be performed safely, and reduced CD19+ lymphocyte counts effectively. Although rituximab-treated ABOi group showed comparable clinical outcomes and graft survival rate, 2 patients developed antibody-mediated rejection.

Conclusions

ABOi LDLT is a feasible option for pediatric end-stage liver disease patients. However, it should be noted that current desensitization protocol does not completely prevent the onset of antibody-mediated rejection in several cases.
C-terminal domain small phosphatase-like 2 promotes epithelial-to-mesenchymal transition via Snail dephosphorylation and stabilization
Authors: Zhao Yulan , Liu Jinquan , Chen Fenfang , Feng Xin-Hua
Published: April 2018

The epithelial-to-mesenchymal transition (EMT) is a cellular reprogramming process converting epithelial cells into mesenchymal cell morphology. Snail is a critical regulator of EMT by both suppressing epithelial gene expression and promoting mesenchymal gene expression. Expression and activity of Snail are tightly controlled at transcriptional and post-translational levels. It has previously been reported that Snail undergoes phosphorylation and ubiquitin-dependent proteasome degradation. Here, we report nuclear phosphatase SCP4/CTDSPL2 acts as a novel Snail phosphatase. SCP4 physically interacts with and directly dephosphorylates Snail. SCP4-mediated dephosphorylation of Snail suppresses the ubiquitin-dependent proteasome degradation of Snail and consequently enhances TGFβ-induced EMT. The knockdown of SCP4 in MCF10A mammary epithelial cells leads to attenuated cell migration. Collectively, our finding demonstrates that SCP4 plays a critical role in EMT through Snail dephosphorylation and stabilization.
In situ
epoxide generation by dimethyldioxirane oxidation and the use of epichlorohydrin in the flow synthesis of a library of β-amino alcohols
Authors: Cossar Peter J. , Baker Jennifer R. , Cain Nicholas , McCluskey Adam
Published: April 2018

The flow coupling of epichlorohydrin with substituted phenols, while efficient, limits the nature of the epoxide available for the development of focused libraries of β-amino alcohols. This limitation was encountered in the production of analogues of 1-(4-nitrophenoxy)-3-((2-((4-(trifluoromethyl)pyrimidin-2-yl)amino)ethyl)amino)propan-2-ol
1
, a potential antibiotic lead. The
in situ
(flow) generation of dimethyldoxirane (DMDO) and subsequent flow olefin epoxidation abrogates this limitation and afforded facile access to structurally diverse β-amino alcohols. Analogues of
1
were readily accessed either via (i) a flow/microwave hybrid approach, or (ii) a sequential flow approach. Key steps were the
in situ
generation of DMDO, with olefin epoxidation in typically good yields and a flow-mediated ring opening aminolysis to form an expanded library of β-amino alcohols
1
and
10a
–
18g
, resulting in modest (
11a
, 21%) to excellent (
12g
, 80%) yields. Alternatively flow coupling of epichlorohydrin with phenols
4a
–
4m
(22%–89%) and a Bi(OTf)
3
catalysed microwave ring opening with amines afforded a select range of β-amino alcohols, but with lower levels of aminolysis regiocontrol than the sequential flow approach.
Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes
Authors: Heiss Aaron A. , Kolisko Martin , Ekelund Fleming , Brown Matthew W. , Roger Andrew J. , Simpson Alastair G. B.
Published: April 2018

Modern syntheses of eukaryote diversity assign almost all taxa to one of three groups: Amorphea, Diaphoretickes and Excavata (comprising Discoba and Metamonada). The most glaring exception is Malawimonadidae, a group of small heterotrophic flagellates that resemble Excavata by morphology, but branch with Amorphea in most phylogenomic analyses. However, just one malawimonad,
Malawimonas jakobiformis
, has been studied with both morphological and molecular-phylogenetic approaches, raising the spectre of interpretation errors and phylogenetic artefacts from low taxon sampling. We report a morphological and phylogenomic study of a new deep-branching malawimonad,
Gefionella okellyi
n. gen. n. sp. Electron microscopy revealed all canonical features of ‘typical excavates’, including flagellar vanes (as an opposed pair, unlike
M. jakobiformis
but like many metamonads) and a composite fibre. Initial phylogenomic analyses grouped malawimonads with the Amorphea-related orphan lineage
Collodictyon
, separate from a Metamonada+Discoba clade. However, support for this topology weakened when more sophisticated evolutionary models were used, and/or fast-evolving sites and long-branching taxa (FS/LB) were excluded. Analyses of ‘–FS/LB’ datasets instead suggested a relationship between malawimonads and metamonads. The ‘malawimonad+metamonad signal’ in morphological and molecular data argues against a strict Metamonada+Discoba clade (i.e. the predominant concept of Excavata). A Metamonad+Discoba clade should therefore not be assumed when inferring deep-level evolutionary history in eukaryotes.
Environment-friendly wood fibre composite with high bonding strength and water resistance
Authors: Ji Xiaodi , Dong Yue , Nguyen Tat Thang , Chen Xueqi , Guo Minghui
Published: April 2018

With the growing depletion of wood-based materials and concerns over emissions of formaldehyde from traditional wood fibre composites, there is a desire for environment-friendly binders. Herein, we report a green wood fibre composite with specific bonding strength and water resistance that is superior to a commercial system by using wood fibres and chitosan-based adhesives. When the mass ratio of solid content in the adhesive and absolute dry wood fibres was 3%, the bonding strength and water resistance of the wood fibre composite reached the optimal level, which was significantly improved over that of wood fibre composites without adhesive and completely met the requirements of the Chinese national standard GB/T 11718-2009. Fourier transform infrared (FTIR), X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD) characterizations revealed that the excellent performance of the binder might partly be due to the amide linkages and hydrogen bonding between wood fibres and the chitosan-based adhesive. We believe that this strategy could open new insights into the design of environment-friendly wood fibre composites with high bonding strength and water resistance for multifunctional applications.
WASABI: a dynamic iterative framework for gene regulatory network inference
Authors: Bonnaffoux Arnaud , Herbach Ulysse , Richard Angélique , Guillemin Anissa , Giraud Sandrine , Gros Pierre-Alexis , Gandrillon Olivier
Published: April 2018

Inference of gene regulatory networks from gene expression data has been a long-standing and notoriously difficult task in systems biology. Recently, single-cell transcriptomic data have been massively used for gene regulatory network inference, with both successes and limitations. In the present work we propose an iterative algorithm called WASABI, dedicated to inferring a causal dynamical network from time-stamped single-cell data, which tackles some of the limitations associated with current approaches. We first introduce the concept of waves, which posits that the information provided by an external stimulus will affect genes one-by-one through a cascade, like waves spreading through a network. This concept allows us to infer the network one gene at a time, after genes have been ordered regarding their time of regulation. We then demonstrate the ability of WASABI to correctly infer small networks, which have been simulatedin silicousing a mechanistic model consisting of coupled piecewise-deterministic Markov processes for the proper description of gene expression at the single-cell level. We finally apply WASABI onin vitrogenerated data on an avian model of erythroid differentiation. The structure of the resulting gene regulatory network sheds a fascinating new light on the molecular mechanisms controlling this process. In particular, we find no evidence for hub genes and a much more distributed network structure than expected. Interestingly, we find that a majority of genes are under the direct control of the differentiation-inducing stimulus. In conclusion, WASABI is a versatile algorithm which should help biologists to fully exploit the power of time-stamped single-cell data.
Universal kinetics for engagement of mechanosensing pathways in cell adhesion
Authors: Terentjev Eugene , Bell Samuel , Redmann Anna-Lena
Published: April 2018

When plated onto substrates, cell morphology and even stem cell differentiation are influenced by the stiffness of their environment. Stiffer substrates give strongly spread (eventually polarized) cells with strong focal adhesions, and stress fibers; very soft substrates give a less developed cytoskeleton, and much lower cell spreading. The kinetics of this process of cell spreading is studied extensively, and important universal relationships are established on how the cell area grows with time. Here we study the population dynamics of spreading cells, investigating the characteristic processes involved in cell response to the substrate. We show that unlike the individual cell morphology, this population dynamics does not depend on the substrate stiffness. Instead, a strong activation temperature dependence is observed. Different cell lines on different substrates all have long-time statistics controlled by the thermal activation over a single energy barrier ∆G≈ 19 kcal/mol, while the early-time kinetics follows a power law ~t5. This implies that the rate of spreading depends on an internal process of adhesion-mechanosensing complex assembly and activation: the operational complex must have 5 component proteins, and the last process in the sequence (which we believe is the activation of focal adhesion kinase) is controlled by the binding energy ∆G.
Uniform distribution of 35S promoter-driven mDII auxin control sensor in leaf primordia
Authors: Guan Chunmei , Du Fei , Jiao Yuling
Published: April 2018

The DII sensor has been an invaluable tool to map spatiotemporal auxin response and distribution in the model plant Arabidopsis thaliana. The DII sensor and mDII control sensor are driven by the widely used constitutive 35S promoter. However, the reliability of DII sensor has recently been questioned (Bhatia and Heisler, 2018). Here we provide additional evidence to show that the mDII control sensor is indeed uniformly distributed in early leaf primordia, which echoes the original reports (Vernoux et al., 2011; Brunoud et al., 2012). We also use DII/mDII and the PRS5A promoter-driven R2D2 sensors to confirm asymmetric auxin signaling in early leaf primordia. On the other hand, we provide evidence that light penetration may lead to artifacts during whole-mount imaging.
Microbial diversity and metabolic potential in cyanotoxin producing cyanobacterial mats throughout a river network
Authors: Bouma-Gregson Keith , Olm Matthew R. , Probst Alexander J. , Anantharaman Karthik , Power Mary E. , Banfield Jillian F.
Published: April 2018

Microbial mats formed by Cyanobacteria of the genusPhormidiumproduce the neurotoxin anatoxin-a that has been linked to animal deaths. Blooms of planktonic Cyanobacteria have long been of concern in lakes, but recognition of potential harmful impacts of riverine benthic cyanobacterial mats is more recent. Consequently little is known about the diversity of the biosynthetic capacities of cyanobacterial species and associated microbes in mats throughout river networks. Here we performed metagenomic sequencing for 22Phormidium-dominated microbial mats collected across the Eel River network in Northern California to investigate cyanobacterial and co-occurring microbial assemblage diversity, probe their metabolic potential and evaluate their capacities for toxin production. We genomically defined four Cyanobacterial species clusters that occur throughout the river network, three of which have not been described previously. From the genomes of seven strains from one species group we describe the first anatoxin-a operon from the genusPhormidium. Community composition within the mat appears to be associated with the presence of Cyanobacteria capable of producing anatoxin-a. Bacteroidetes, Proteobacteria, and novel Verrucomicrobia dominated the microbial assemblages. Interestingly, some mats also contained organisms from candidate phyla such asCanditatusKapabacteria, as well as Absconditabacteria (SR1), Parcubacteria (OD1) and Peregrinibacteria (PER) within the Candidate Phyla Radiation. Oxygenic photosynthesis and carbon respiration were the most common metabolisms detected in mats but other metabolic capacities include aerobic anoxygenic photosynthesis, sulfur compound oxidation and breakdown of urea. The results reveal the diversity of metabolisms fueling the growth of mats, and a relationship between microbial assemblage composition and the distribution of anatoxin-a producing cyanobacteria within freshwaterPhormidiummats in river networks.
High-throughput mapping of long-range neuronal projection using in situ sequencing
Authors: Chen Xiaoyin , Sun Yu-Chi , Zhan Huiqing , Kebschull Justus M , Fischer Stephan , Matho Katherine , Josh Huang Z. , Gillis Jesse , Zador Anthony M
Published: April 2018

Understanding neural circuits requires deciphering interactions among myriad cell types defined by spatial organization, connectivity, gene expression, and other properties. Resolving these cell types requires both single neuron resolution and high throughput, a challenging combination with conventional methods. Here we introduce BARseq, a multiplexed method based on RNA barcoding for mapping projections of thousands of spatially resolved neurons in a single brain, and relating those projections to other properties such as gene or Cre expression. Mapping the projections to 11 areas of 3579 neurons in mouse auditory cortex using BARseq confirmed the laminar organization of the three top classes (IT, PT-like and CT) of projection neurons. In depth analysis uncovered a novel projection type restricted almost exclusively to transcriptionally-defined subtypes of IT neurons. By bridging anatomical and transcriptomic approaches at cellular resolution with high throughput, BARseq can potentially uncover the organizing principles underlying the structure and formation of neural circuits.
Analysis of the Resuscitation-Availability of Viable-But-Nonculturable Cells ofVibrio parahaemolyticusupon Exposure to the Refrigerator Temperature
Authors: Yoon Jae-Hyun , Bae Young-Min , Rye Buom-Young , Choi Chang-Sun , Moon Sung-Gwon , Lee Sun-Young
Published: April 2018

Major pathogenic strains ofVibrio parahaemolyticuscan enter into the viable-but-nonculturable (VBNC) state when subjected to environmental conditions commonly encountered during food processing. Especially, VBNC cells can be recovered to the culturable state reversibly by removing the causative stress, expressing higher levels of virulence factors. Therefore, the aim of this study was to determine if VBNCV. parahaemolyticusstrains retain the resuscitation-availability upon eliminating the adverse condition, followed by the enrichment in developed resuscitation-facilitating buffers. Bacterial cells were shown to enter into the VBNC state in artificial sea water (ASW, pH 6) microcosms at 4°C within 70 days. VBNC cells were harvested, inoculated in formulated resuscitation-buffers, and then incubated at 25°C for several days. TSB (pH 8) supplemented with 3% NaCl (TSBA) exhibited the higher resuscitation-availability of VBNC cells. It was also shown that TSBAcontaining 10,000 U/mg/protein catalase, 2% sodium pyruvate, 20 mM MgSO4, 5 mM ethylenediaminetetraacetic acid (EDTA), and cell free supernatants extracted from the pure cultures ofV. parahaemolyticuswas more effective in resuscitating VBNC cells ofV. parahaemolyticus, showing by 7.69-8.91 log10CFU/ml.

IMPORTANCE

Generally, higher concentrations (≤40%) of NaCl are used for preserving different sorts of food products from bacterial contaminations. However, it was shown from the present study that strains ofV. parahaemolyticuswere able to persist in maintaining the cellular viability, thereby entering into the VBNC state upon exposure to the refrigerator temperature for 80 days. Hence, the ability of VBNCV. parahaemolyticusto re-enter into the culturable state was examined, using various resuscitation buffers that were formulated in this study. VBNC cells re-gained the culturability successfully when transferred onto the resuscitation-buffer D, and then incubated at 25°C for several days. Resuscitation-facilitating agent D is consisting of antioxidizing agents, mineral, an emulsifier, and cell free supernatants from the actively growing cells ofV. parahaemolyticus. It appeared that such a reversible conversion of VBNC cells to the culturable state would depend on multiple resuscitation-related channels.
Mechanical unfold and transport of Green Florescent Protein through a nanopore
Authors: Shahzad Muhammad Adnan
Published: April 2018

We report the unfold and trans-location of Green Fluorescent protein (GFP) mechanically by a constant force acting parallel along the axis of nanopore. A coarse-grained numerical model (Go-model) were implemented both for the protein and the nanopore. Detail description of each peptide unfold by the constant force is presented. Depending on the GFP topological structure, β-sheet barrel, the protein unfold and transport as a double loop conformation in the confinement geometry. The result is compared with maltose binding protein (MBP), having majority of alpha helix, which unfold and trans-locate as single profile conformation through nanopore. The result emphasis that protein with different topological structure unfold and trans-locate in different fashion depending on their native fold structure.
The practical value of an explicit response model in quantitative uses Biacore™ biosensors
Authors: Whyte Jason M.
Published: April 2018

Suppose we aim to use data obtained by studying a biomolecular interaction system with a surface plasmon resonance (SPR) biosensor in quantifying some system feature. We assume a parametric mathematical model for biosensor response due to sources of mass such as analyte-ligand complexes. Some parameters represent interaction features, such as rate constants. Whenever we attempt to estimate parameters from data, we may obtain multiple estimates, regardless of the amount and quality of data. Inconveniently, we may be unable to distinguish between alternatives. This is problematic when alternative parameter values lead to very different predictions of system behaviour for a situation where we lack data. Anticipating this issue prior to data collection allows us to redesign the combination of planned experiments and model, replacing a certain failure to achieve our study’s aim with the possibility of success. The literature on SPR biosensors (and computational biology more generally) has paid little attention to this matter. In order to remedy this, it is appropriate to begin with a consideration of the assumed models. These are rarely specified completely, causing ambiguity that impedes scrutiny of their properties and comparison with other models. We demonstrate this by reviewing some model types seen in the Biacore™ biosensor literature. We propose to eliminate model ambiguity by providing a suitable framework for specifing models for biosensor data. This framework will aid future efforts to compose models for data arising from particular interaction mechanisms in a form that is amenable to scrutiny. We expect that the issues raised here will have relevance to the modelling of data obtained from other apparatus employed in quantifying binding behaviour.
Smart metering projects: an interpretive framework for successful implementation
Authors: Cagno Enrico , Micheli Guido J.L. , Di Foggia Giacomo
Published: April 2018

Purpose

The purpose of this paper is to analyze a set of smart meters implementation projects and provide insights and recommendations to facilitate smart metering deployment strategies.

Design/methodology/approach

Several significant projects are analyzed on different fronts: scale, technology, economics and regulation, using a common methodology to unfold patterns that constitute key components of successful smart meters diffusion.

Findings

Key elements and controllable enabling patterns from Europe-wide SM implementation projects are identified together with drivers and barriers for patterns replication.

Research limitations/implications

The authors provide a framework considering different stakeholders that will help distribution system operators to accelerate and extend smart meters’ penetration.

Originality/value

Based on the Meter-ON project (supported by the 7th Framework Program of the European Commission), we provide valuable information aimed at facilitating the large-scale deployment of smart meters.
Electrochemical DNA biosensors: a review
Authors: Rafique Bushra , Iqbal Mudassir , Mehmood Tahir , Shaheen Muhammad Ashraf
Published: April 2018

Purpose

This review aims to focus on recent reported research work on the construction and function of different electrochemical DNA biosensors. It also describes different sensing materials, chemistries of immobilization probes, conditions of hybridization and principles of transducing and amplification strategies.

Design/methodology/approach

The human disease-related mutated genes or DNA sequence detection at low cost can be verified by the electrochemical-based biosensor. A range of different chemistries is used by the DNA-based electrochemical biosensors, out of which the interactions of nanoscale material with recognition layer and a solid electrode surface are most interesting. A diversity of advancements has been made in the field of electrochemical detection.

Findings

Some important aspects are also highlighted in this review, which can contribute in the creation of successful biosensing devices in the future.

Originality/value

This paper provides an updated review of construction and sensing technologies in the field of biosensing.
Aldo‐keto reductases‐mediated cytotoxicity of 2‐deoxyglucose: A novel anticancer mechanism
Authors: Zhang Shi‐Qing , Yung Kin‐Lam Ken , Chung Sookja Kim , Chung Sum‐Man Stephen
Published: April 2018

2‐Deoxyglucose (2DG) is a non‐metabolizable glucose analog currently in clinical trials to determine its efficacy in enhancing the therapeutic effects of radiotherapy and chemotherapy of several types of cancers. It is thought to preferentially kill cancer cells by inhibiting glycolysis because cancer cells are more dependent on glycolysis for their energy needs than normal cells. However, we found that the toxicity of 2DG in cancer cells is mediated by the enzymatic activities of AKR1B1 and/or AKR1B10 (AKR1Bs), which are often overexpressed in cancer cells. Our results show that 2DG kills cancer cells because, in the process of being reduced by AKR1Bs, depletion of their cofactor NADPH leads to the depletion of glutathione (GSH) and cell death. Furthermore, we showed that compounds that are better substrates for AKR1Bs than 2DG are more effective than 2DG in killing cancer cells that overexpressed these 2 enzymes. As cancer cells can be induced to overexpress AKR1Bs, the anticancer mechanism we identified can be applied to treat a large variety of cancers. This should greatly facilitate the development of novel anticancer drugs.
Management of adrenal emergencies in educated patients with adrenal insufficiency—A prospective study
Authors: Burger‐Stritt Stephanie , Kardonski Pavel , Pulzer Alina , Meyer Gesine , Quinkler Marcus , Hahner Stefanie
Published: April 2018

Objective

To evaluate the management of adrenal emergencies (AE) requiring parenteral glucocorticoid (GC) treatment in patients with chronic adrenal insufficiency (AI).

Design

Prospective, multicentre, questionnaire‐based study.

Patients and measurements

Participating patients (n = 150) with chronic AI were provided with a questionnaire on the management of emergency situations, which had to be completed and sent back in case of an AE. In addition, patients were contacted by phone on a regular basis.

Results

Fifty‐nine AE in 39 patients were documented. The time interval from contact to arrival of a medical professional was 20 minutes (1‐240). In total, in 43 AE, patients received parenteral GC by a medical professional. The time interval between showing the emergency card and GC injection by a medical professional was 60 minutes (5‐360). A total of 26 patients administered GC by self‐injection. The time from the beginning of symptoms to GC injection was significantly shorter in case of self‐injection (self‐injection vs injection by medical professional; 85 minutes [20‐280] vs 232.5 minutes [1‐3135]; P < .001). After self‐injection, 62% of the patients were treated outpatient, compared to 27% of the patients after exclusive injection by a medical professional (P = .008). To improve the emergency management, most of the patients (84%) indicated a need for an easier way of self‐injection.

Conclusion

While management of AE by both patients and medical professionals still shows high variability, patients profit from the option of self‐injection. Patient care, including education of patients and health‐professionals, as well as the way of GC administration, needs further optimization.
Small arteries stay stiff for a longer period following vibration exercises in combination with blood flow restriction
Authors: Karabulut Ulku , Karabulut Murat , James Eric G.
Published: April 2018

Purpose

The aim of this study was to assess the effect of isometric exercises performed during whole‐body vibration (WBV) with and without blood flow restriction (BFR) on arterial elasticity and hemodynamic variables.

Methods

Eight male subjects performed static upper body (UB) and lower body (LB) exercises on a vibration platform with and without BFR. During BFR sessions, BFR cuffs were placed on the arms or legs and inflated to a target pressure. Exercises consisted of eight 45‐s sets for UB, and ten 1‐min sets for LB. Arterial elasticity and hemodynamic variables were assessed before, at 10 min and 40 min postexercise. Repeated measures ANOVA was used to test the mean differences in related variables.

Results

A significant condition (BFR versus no‐BFR) main effect was detected for small arterial elasticity (P<0·05). For heart rate (HR), there were significant time (P<0·01), condition (P = 0·02) and body (P = 0·04) main effects during exercise and condition (P<0·04) and time (P<0·01) main effects following exercise. Significantly lower values in systemic vascular resistance were detected at 10 min post compared to 40 min post (P<0·02) and UB compared to LB (P = 0·02).

Conclusions

Results showed that small arteries stayed stiffer for a longer period of time after vibration exercises with BFR and BFR placed a greater demand on cardiovascular system. Findings also indicated that the type of exercises performed and/or the measurement location are very important and should be taken into account when examining arterial response.
Differential diagnosis between a granuloma and radicular cyst: effectiveness of magnetic resonance imaging
Authors: Lizio G. , Salizzoni E. , Coe M. , Gatto M. R. , Asioli S. , Balbi T. , Pelliccioni G. A.
Published: April 2018

Aim

To investigate the diagnostic reliability and accuracy of magnetic resonance imaging (MRI) to differentiate periapical lesions of endodontic origin and to compare the results with histopathological information.

Methodology

The radiolucent periapical jaw lesions of 34 patients, which were surgically enucleated, were investigated by two radiologists using MRI, based on the same six criteria, to categorize the lesions as granulomas, radicular cysts or others. After apicoectomies, two oral pathologists (blinded to the radiologist's diagnoses) analysed all specimens by referring to seven specific parameters and diagnosed the specimens as granulomas, radicular cysts or other conditions. The inter‐rater agreements between the radiologists and pathologists in terms of MRI and histological diagnoses, respectively, along with the discriminant power of the adopted criteria and the accuracy of the MRI assessments compared with the histopathological results, were calculated. Cohen's kappa test was adopted to examine inter‐rater agreement between the two radiologists and two pathologists. Guttman's lambda coefficient (λ6) was used to evaluate the internal consistency of the items used for the differential diagnosis by radiologists. The accuracy resulted from a receiver operator characteristic (ROC) analysis.

Results

A strong inter‐rater reliability was observed between the two radiologists (k‐statistic = 0.86, P = 0.0001) and the two pathologists (k‐statistic = 0.88, P = 0.0001). The internal consistency of the diagnostic items was 0.605 for cysts and 0.771 for granulomas. The accuracy (true positives plus true negatives) of the radiologists was greater than that of the pathologists based on analysis (area under the curve = 0.87 and 0.91, respectively).

Conclusions

The reliability and accuracy of MRI were high and comparable to histopathological reliability, highlighting the usefulness of this noninvasive technique as a pre‐treatment diagnostic method for periapical endodontic lesions.