bluuebunny/crossref_metadata_2025 huggingface dataset:
Recent developments in the surgical management of complex intra-abdominal infection
Authors: Soop M , Carlson G L
Published: January 2017

Background

Current guidance on the management of sepsis often applies to infection originating from abdominal or pelvic sources, which presents specific challenges and opportunities for efficient and rapid source control. Advances made in the past decade are presented in this article.

Methods

A qualitative systematic review was undertaken by searching standard literature databases for English-language studies presenting original data on the clinical management of abdominal and pelvic complex infection in adults over the past 10 years. High-quality studies relevant to five topical themes that emerged during review were included.

Results

Important developments and promising preliminary work are presented, relating to: imaging and other diagnostic modalities; antimicrobial therapy and the importance of antimicrobial stewardship; the particular challenges posed by fungal sepsis; novel techniques in percutaneous and endoscopic source control; and current issues relating to surgical source control and managing the abdominal wound. Logistical challenges relating to rapid access to cross-sectional imaging, interventional radiology and operating theatres need to be addressed so that international benchmarks can be met.

Conclusion

Important advances have been made in the diagnosis, non-operative and surgical control of abdominal or pelvic sources, which may improve outcomes in the future. Important areas for continued research include the diagnosis and therapy of fungal infection and the challenges of managing the open abdomen.
Update on surgical sepsis syndrome
Authors: Vincent J-L
Published: January 2017

Background

Sepsis is a serious complication in surgical patients, and is associated with prolonged hospital stay and high mortality rates. The definitions of sepsis have been revisited recently. This article reviews how definitions have changed over the years, and provides an update on basic pathobiology and essential aspects of treatment.

Methods

PubMed was searched for reports published in English before October 2016, using the search terms ‘surgical sepsis’ AND ‘surgical ICU’. The reference lists of articles identified in the search were also checked. Other relevant literature was selected based on personal knowledge of developments in the field of sepsis.

Results

Sepsis is defined as the presence of infection plus associated organ dysfunction. It occurs as the result of a dysregulated host response to the infection. Prevention of infection is an important means of limiting the development of sepsis. Treatment relies on source control, appropriate antibiotics and organ support. Research continues in an attempt to identify effective immunomodulatory therapies.

Conclusion

Sepsis is an important and serious complication of surgery, and precautions must be taken to try to prevent infection in surgical patients. If sepsis develops, rapid diagnosis is crucial so that appropriate source control, antimicrobial therapy and organ support can be started early in the course of disease. New techniques enabling a better classification of a patient's particular sepsis profile will enable more personalized therapy.
Surgical infection
Authors: Hinchliffe R J , Earnshaw J J
Published: January 2017

Real and present danger
Study on the Sorption of Eu(III) onto Natural Red Earth and its Solid Components by Linear and Non‐Linear Methods
Authors: Yu Tao , Liang Shimin , Li Hong
Published: January 2017

The sorption of Eu(III) on natural red earth (NRE), iron oxides removed red earth (IORRE), and organic matter removed red earth (OMRRE) were studied under ambient conditions. The kinetic and thermodynamic studies of Eu(III) sorption were discussed by linear and non‐linear approaches. The results showed that sorption of Eu(III) on the three red earth was strongly dependent on ionic strength below pH~7.0 and independent of ionic strength above pH~7.0. Ion exchange, outer‐sphere surface complexes, and inner‐sphere surface complexes were controlling Eu(III) sorption in the whole observed pH range. Furthermore, the presence of iron oxides can inhibit Eu(III) sorption to some extent; however, organic matters enhance Eu(III) sorption in a certain range of pH and temperature. Sorption of Eu(III) on red earth samples can be represented by a pseudo‐second‐order rate equation, and the non‐linear pseudo‐second‐order kinetic expression could fit the kinetics better compared with the linear forms. Freundlich non‐linear isotherm model is the best‐fit model to Eu(III) sorption on the samples. Meanwhile, non‐linear method is found to be a better way to describe the sorption kinetics and thermodynamics than the linear method.
Tumor necrosis factor suppresses interleukin 10 in peripheral B cells via upregulating Bcl2‐like protein 12 in patients with inflammatory bowel disease
Authors: Guo Xiutian , Li Mao‐Gang , Li Shan‐Shan , Liu Feng‐Hua , Liu Zhan‐Ju , Yang Ping‐Chang
Published: January 2017

The pathogenesis of the immune regulation dysfunction is unclear. Bcl2‐like protein 12 (Bcl2L12) has immune suppression function. This study tests a hypothesis that tumor necrosis factor (TNF) increases Bcl2L12 to suppress the expression of interleukin (IL) 10 in peripheral B cells of patients with inflammatory bowel disease (IBD). In this study, peripheral blood samples were collected from IBD patients and healthy controls. B cells were isolated from the blood samples. The expression of IL‐10 and Bcl2L12 in B cells was analyzed by quantitative reverse transcription polymerase chain reaction and Western blotting. We observed that the expression of Bcl2L12 in the peripheral B cells was higher in IBD patients than that in healthy controls. The IL‐10 levels in B cells were negatively correlated with the expression of Bcl2L12. Exposure of B cells to TNF in the culture enhanced the expression of Bcl2L12. The Bcl2L12 mediated the effects of TNF on suppression of IL‐10 in B cells. In conclusion, Bcl2L12 mediates the effects of TNF to suppress the expression of IL‐10 in B cells. The data suggest that Bcl2L12 may be a therapeutic target for the treatment of IBD.
Molecular Cross‐Talk between Nonribosomal Peptide Synthetase Carrier Proteins and Unstructured Linker Regions
Authors: Harden Bradley J. , Frueh Dominique P.
Published: January 2017

Nonribosomal peptide synthetases (NRPSs) employ multiple domains separated by linker regions to incorporate substrates into natural products. During synthesis, substrates are covalently tethered to carrier proteins that translocate between catalytic partner domains. The molecular parameters that govern translocation and associated linker remodeling remain unknown. Here, we used NMR to characterize the structure, dynamics, and invisible states of a peptidyl carrier protein flanked by its linkers. We showed that the N‐terminal linker stabilizes and interacts with the protein core while modulating dynamics at specific sites involved in post‐translational modifications and/or domain interactions. The results detail the molecular communication between peptidyl carrier proteins and their linkers and could guide efforts in engineering NRPSs to obtain new pharmaceuticals.
Thermally Converted CoO Nanoparticles Embedded into N‐Doped Carbon Layers as Highly Efficient Bifunctional Electrocatalysts for Oxygen Reduction and Oxygen Evolution Reactions
Authors: Kim Hyeonghun , Kim Youngmin , Noh Yuseong , Lee Seonhwa , Sung Jaekyung , Kim Won Bae
Published: January 2017

Hybrid materials that consist of transition‐metal oxides and heteroatom‐doped carbon materials have been researched recently as promising bifunctional electrocatalysts for both oxygen‐reduction reaction (ORR) and oxygen‐evolution reaction (OER) in alkaline media. Herein, CoO nanoparticles embedded into N‐doped carbon layers were synthesized by a thermal conversion process of polypyrrole‐coated Co3O4 nanoparticles supported on a carbon layer in Ar atmosphere at 900 °C. During the process, the initial Co3O4 phase was transformed to the CoO phase along with the thermal carbonization of the polypyrrole layer to the N‐doped carbon layer. Owing to the oxidative combustion induced by the O species released from the Co3O4 nanoparticles, the N‐doped carbon layer could contain pores around the CoO nanoparticles. Alkaline electrolytes could penetrate the N‐doped carbon layer toward the CoO nanoparticles through the pores. The nanocomposites with the well‐assembled CoO nanoparticles and porous N‐doped carbon layer could exhibit superior catalytic activity for ORR and OER. In addition, the N‐doped carbon layers effectively prevent the degradation of the catalyst by protecting the CoO nanoparticles from aggregation during the electrocatalytic processes. The hybrid material of CoO and N‐doped carbon showing highly active and durable catalytic characteristics for ORR and OER is a promising electrocatalyst in fuel cells, metal–air batteries, and water‐splitting systems and could be used instead of precious metals such as Pt, Ru, and Ir.
System level design and analysis of a fourth‐order continuous‐time delta‐sigma modulator using relaxed gain‐band‐width amplifiers
Authors: Hasanzadeh Mohammad Reza , Abrishamifar Adib
Published: January 2017

In this paper, based on mathematical approaches and behavioral modeling of internal blocks, an algorithm of designing a continuous‐time delta‐sigma modulator (CT ΔΣM) with aggressive noise shaping is discussed. Using proposed methods, the coefficients of modulator can be calculated directly while the finite gain‐band‐width of amplifiers and rise/fall time of digital‐to‐analog convertors (DACs) in feedback path are included in the transfer function of CT loop filter. To decrease the number of amplifiers, a unique resonator is proposed. Also, an extra feedback DAC is introduced to further reduction of gain‐band‐width requirement of last amplifier. To verify the effectiveness of proposed methods, a fourth‐order, single loop, CT ΔΣM that benefits proportional‐integrator element for compensation of excess‐loop‐delay is realized in system and behavioral circuit levels. It has a 4‐bit quantizer, over‐sampling‐ratio of 10, and out‐of‐band‐gain of 12 dB. The peaking in signal‐transfer‐function is alleviated using a feed‐forward capacitor along with proper choosing of rest coefficients. The designed modulator has 78‐dB signal‐to‐noise‐ratio; even the non‐ideal behaviors of amplifiers and DACs are involved in simulations. Independent to sampling frequency, the proposed methods can be applied to other topologies of CT ΔΣMs. Copyright © 2017 John Wiley & Sons, Ltd.
Heterogenic response of prokaryotes toward silver nanoparticles and ions is facilitated by phenotypes and attachment of silver aggregates to cell surfaces
Authors: Guo Yuting , Stärk Hans J. , Hause Gerd , Schmidt Matthias , Harms Hauke , Wick Lukas Y. , Müller Susann
Published: January 2017

Tons of anthropogenic silver nanoparticles (AgNPs) are assumed to be released into the environment due to their use in many consumer products. AgNPs are known to be toxic toward microorganisms and thus may harm their specific functions in ecosystems. Here we explore the impact of AgNPs on functioning of single cells in microbial populations at doses typically found in anthropogenic environments. The response of single cells to AgNPs was analyzed by flow cytometry and using the fluorescent dyes propidium iodide and DiBAC4(3) as markers for cell membrane disintegration and depolarization, respectively. The effects of 10‐nm and 30‐nm AgNPs on three bacterial species (Mycobacterium frederiksbergense, Pseudomonas putida, and Escherichia coli) showed that the populations split into affected cells and others not showing any malfunction, with varying abundances depending on strains and cell growth states. Further, the dissolution of AgNPs measured with 3 KDa ultrafiltration and inductively coupled plasma‐mass‐spectrometry to distinguish particle‐related effects from toxicity of dissolved Ag revealed that Ag ions were the principal toxicant. AgNP aggregate formation was followed by dynamic light scattering and the aggregates’ attachment to cell surfaces was visualized by transmission electron microscopy and scanning electron microscopy‐energy dispersive X‐ray spectroscopy. An increased AgNP‐affected cell fraction relative to the Ag ion impact was identified. The study shows that individual cells in a population cope differently with AgNP induced stress by evolving heterogeneous phenotypes. The response is linked to cell death and cell energy depletion depending on cell type and cell growth states. The attachment of AgNP aggregates to cell surfaces seems to amplify the heterogeneous response. © 2017 International Society for Advancement of Cytometry
Urine cytology findings of primary paraganglioma of the urinary bladder: Case report
Authors: Lee Junghye , Park Sanghui , Cho Min‐Sun , Sung Sun Hee , Kim Kwang Hyun
Published: January 2017

Paraganglioma (PG) of the urinary bladder was detected in a 64‐year‐old male who was admitted to the hospital with gross hematuria. In voided urine, atypical cells were scattered as nests and single cells on low‐power view. On higher‐power view, tumor nests were composed of epithelioid cells with fine chromatin and moderate cytoplasm admixed with occasional spindle sustentacular cells. Single cells were discohesive and large with moderate cytoplasm and inconspicuous nucleoli. Subsequent cystoscopy revealed a solid oval mass. Histologically, tumor from the resected bladder showed infiltrating nested tumor cells with abundant cytoplasm. Immunohistochemically, the tumor cells were positive for synaptophysin, chromogranin, and CD56. The patient underwent partial cystectomy and was discharged without complications. Diagn. Cytopathol. 2017;45:350–353. © 2016 Wiley Periodicals, Inc.
Abundance distributions for tree species in Great Britain: A two‐stage approach to modeling abundance using species distribution modeling and random forest
Authors: Hill Louise , Hector Andy , Hemery Gabriel , Smart Simon , Tanadini Matteo , Brown Nick
Published: January 2017

High‐quality abundance data are expensive and time‐consuming to collect and often highly limited in availability. Nonetheless, accurate, high‐resolution abundance distributions are essential for many ecological applications ranging from species conservation to epidemiology. Producing models that can predict abundance well, with good resolution over large areas, has therefore been an important aim in ecology, but poses considerable challenges. We present a two‐stage approach to modeling abundance, combining two established techniques. First, we produce ensemble species distribution models (SDMs) of trees in Great Britain at a fine resolution, using much more common presence–absence data and key environmental variables. We then use random forest regression to predict abundance by linking the results of the SDMs to a much smaller amount of abundance data. We show that this method performs well in predicting the abundance of 20 of 25 tested British tree species, a group that is generally considered challenging for modeling distributions due to the strong influence of human activities. Maps of predicted tree abundance for the whole of Great Britain are provided at 1 km2 resolution. Abundance maps have a far wider variety of applications than presence‐only maps, and these maps should allow improvements to aspects of woodland management and conservation including analysis of habitats and ecosystem functioning, epidemiology, and disease management, providing a useful contribution to the protection of British trees. We also provide complete R scripts to facilitate application of the approach to other scenarios.
Long‐term acclimation to reciprocal light conditions suggests depth‐related selection in the marine foundation speciesPosidonia oceanica
Authors: Dattolo Emanuela , Marín‐Guirao Lazaro , Ruiz Juan M. , Procaccini Gabriele
Published: January 2017

Phenotypic differences among populations of the same species reflect selective responses to ecological gradients produced by variations in abiotic and biotic factors. Moreover, they can also originate from genetic differences among populations, due to a reduced gene flow. In this study, we examined the extent of differences in photo‐acclimative traits ofPosidonia oceanica(L.)Delileclones collected above and below the summer thermocline (i.e., −5 and −25 m) in a continuous population extending along the water depth gradient. During a reciprocal light exposure and subsequent recovery in mesocosms, we assessed degree of phenotypic plasticity and local adaptation of plants collected at different depths, by measuring changes in several traits, such as gene expression of target genes, photo‐physiological features, and other fitness‐related traits (i.e., plant morphology, growth, and mortality rates). Samples were also genotyped, using microsatellite markers, in order to evaluate the genetic divergence among plants of the two depths. Measures collected during the study have shown a various degree of phenotypic changes among traits and experimental groups, the amount of phenotypic changes observed was also dependent on the type of light environments considered. Overall plants collected at different depths seem to be able to acclimate to reciprocal light conditions in the experimental time frame, through morphological changes and phenotypic buffering, supported by the plastic regulation of a reduced number of genes. Multivariate analyses indicated that plants cluster better on the base of their depth origin rather than the experimental light conditions applied. The two groups were genetically distinct, but the patterns of phenotypic divergence observed during the experiment support the hypothesis that ecological selection can play a role in the adaptive divergence ofP. oceanicaclones along the depth gradient.
Differential butterfly performance on host plant variants from populations under intense vs. low mammalian herbivory
Authors: Kohyama Tetsuo , Horikawa Chika , Kawai Shizuka , Shikata Megumi , Kato Teiko , Sato Hiroaki
Published: January 2017

Evolutionary interactions between a pair of species can be modified by the presence of another species that interacts with either or both species. However, only a few studies have demonstrated such complex interactions. Here, we report a case where a population of the red admiral butterfly (Vanessa indica) is assumed to change fitness traits in response to an evolutionary change in its major host plant, the Japanese stinging nettle (Urtica thunbergiana), caused by intense browsing pressure from sika deer (Cervus nippon). Nara Park (NP) in Japan has been home to several hundred protected sika deer for approximately 1200 yr, and their intense browsing pressure is assumed to have selected for heavily haired nettles that are more resistant to deer browsing compared to normal lightly haired nettles occurring in areas with low densities of sika deer. We found that the water and nitrogen contents of leaves are lower and the specific leaf mass is higher in heavily haired nettles at NP compared to the lightly haired nettles at the Takatori Castle Site (TCS) 30 km south of NP. Feeding experiments showed that V. indica larvae from NP reared on heavily haired nettles reach a greater adult body mass and relative abdomen mass than those from TCS, suggesting the possibility that the NP V. indica population has adapted to the heavily haired, nutritionally poorer variant. Analysis of the nucleotide sequence of the mitochondrial cytochrome c oxidase subunit I gene of V. indica from NP and nearby locations including TCS found one haplotype exclusive to NP, suggesting that movement of this butterfly is somewhat restricted. However, analysis using amplified fragment length polymorphism markers showed no genetic differentiation between the seven V. indica populations including the NP and TCS populations. These results suggest that adaptation of the NP population to the heavily haired nettle occurred in a relatively short period. Our study demonstrates a rare example of an indirect evolutionary impact of one herbivore (sika deer) on another herbivore (red admiral butterfly) through an evolutionary change in their shared food plant (Japanese nettle).
Social buffering in a eusocial invertebrate: termite soldiers reduce the lethal impact of competitor cues on workers
Authors: Tian Li , Preisser Evan L. , Haynes Kenneth F. , Zhou Xuguo
Published: January 2017

While the impact of predator‐induced stress on prey has received considerable attention, there has been far less research into the effect of competitors. Cues from aggressive competitors should be particularly likely to evoke behavioral and/or physiological responses, since they may be indicative of both direct (interference) and indirect (exploitative) threats. The danger posed by such competitors, and the “fear” they evoke, should be reduced at lower competitor densities and by the presence of individual conspecifics specialized for defense. We assessed how Reticulitermes flavipes termite workers and soldiers were affected by cues from conspecific nestmates, conspecific non‐nestmates, and the heterospecific competitor R. virginicus. Competitor cues altered flavipes worker and soldier behavior, decreasing worker growth and increasing their mortality. The presence of flavipes soldiers largely ameliorated these negative impacts: adding even a single soldier (5% of flavipes individuals) decreased worker mortality by 50–80%. Although worker mortality increased with competitor density, increased soldier densities did not increase the benefit to workers. The small number of soldiers required to substantially alter cue‐mediated interactions suggests that this caste, in addition to providing direct defense, also occupies a “keystone role” by providing homeostatic feedback to workers functioning in stressful environments.
Distinctive expression pattern of cystathionine‐β‐synthase and cystathionine‐γ‐lyase identifies mesenchymal stromal cells transition to mineralizing osteoblasts
Authors: Gambari Laura , Lisignoli Gina , Gabusi Elena , Manferdini Cristina , Paolella Francesca , Piacentini Anna , Grassi Francesco
Published: January 2017

Mesenchymal stromal cells (MSCs) are key players in the repair or regeneration of the damaged bone tissue. However, heterogeneity exists between MSCs derived from different donors in their bone formation ability both in vitro and in vivo. The identification of markers defining MSCs with different functional phenotypes is fundamental to maximize their clinical potential. In our previous in vivo study, impaired expression in MSCs of cystathionine‐β‐synthase (CBS) and cystathionine‐γ‐lyase (CSE), the two key enzymes in the catabolic pathway of homocysteine, was associated to decreased bone formation and to the onset of osteoporosis in mice. Here, we investigated whether osteogenic differentiation of human MSCs (hMSCs) modulates the expression of CBS and CSE. The expression of CBS and CSE was also assessed during chondrogenesis to confirm the specificity of their expression during osteogenesis. hMSCs displayed a heterogeneous mineralizing capacity between donors (70% of the samples mineralized, while 30% did not mineralize). Inducible expression of CBS and CSE was found to be associated with a mineralizing phenotype in hMSCs. In particular, up‐regulation of CSE was restricted to hMSCs undergoing mineralization. During chondrogenesis, CBS was significantly up‐regulated while CSE expression was not affected.Ex‐vivofindings confirmed that mature h‐osteoblasts (hOBs) show consistently higher expression of CBS and CSE than hMSCs. Our data provide the first evidence that the expression of CBS and CSE in hMSCs closely correlates with the transition of hMSCs toward the osteoblastic phenotype and that CSE may constitute a novel marker of osteogenic differentiation.
Evaluation of carotid plaque vulnerability in vivo: Correlation between dynamic contrast‐enhanced MRI and MRI‐modified AHA classification
Authors: Ge Xiaoqian , Zhou Zien , Zhao Huilin , Li Xiao , Sun Beibei , Suo Shiteng , Hackett Maree L. , Wan Jieqing , Xu Jianrong , Liu Xiaosheng
Published: January 2017

Purpose

To noninvasively monitor carotid plaque vulnerability by exploring the relationship between pharmacokinetic parameters (PPs) of dynamic contrast‐enhanced magnetic resonance imaging (DCE‐MRI) and plaque types based on MRI‐modified American Heart Association (AHA) classification, as well as to assess the ability of PPs in discrimination between stable and vulnerable plaques suspected on MRI.

Materials and Methods

Of 70 consecutive patients with carotid plaques who volunteered for 3.0T MRI (3D time‐of‐flight [TOF], T1‐weighted, T2‐weighted, 3D magnetization‐prepared rapid acquisition gradient‐echo [MP‐RAGE] and DCE‐MRI), 66 participants were available for analysis. After plaque classification according to MRI‐modified AHA Lesion‐Type (LT), PPs (Ktrans, kep, ve, and vp) of DCE‐MRI were measured. The Extended Tofts model was used for calculation of PPs. For participants with multiple carotid plaques, the plaque with the worst MRI‐modified AHA LT was chosen for analysis. Correlations between PPs and plaque types and the ability of these parameters to distinguish stable and vulnerable plaques suspected on MRI were assessed.

Results

Significant positive correlation between Ktrans and LT III to VI was found (ρ = 0.532, P < 0.001), as was the correlation between kep and LT III to VI (ρ = 0.409, P < 0.001). Stable and vulnerable plaques suspected on MRI could potentially be distinguished by Ktrans (sensitivity 83%, specificity 100%) and kep (sensitivity 77%, specificity 91%).

Conclusion

Ktrans and kep from DCE‐MRI can provide quantitative information to monitor plaque vulnerability in vivo and differentiate vulnerable plaques suspected on MRI from stable ones. These two parameters could be adopted as imaging biomarkers for plaque characterization and risk stratification.

Level of Evidence: 1

Technical Efficacy: Stage 2

J. MAGN. RESON. IMAGING 2017;46:870–876
Seroepidemiology of hepatitis B and C virus infections among blood donors in Ethiopia
Authors: Hundie Gadissa Bedada , Raj Victor Stalin , GebreMichael Daniel , Haagmans Bart L.
Published: January 2017

This study was conducted to investigate the prevalence of hepatitis B virus (HBV) and hepatitis C virus (HCV) infections among blood donors in different regions in Ethiopia. A total of 56 885 sera were tested for HBsAg and anti‐HCV antibodies. Of these, 3.9% were found HBsAg‐positive, 0.52% anti‐HCV‐positive, and 0.054% dual positive. HBV prevalence was relatively higher in Adama (5.91%) than Gondar (4.05%), Jimma (3.87%), Addis Ababa (3.75%), and Tigray (3.7%); and in males (4.64%) than females (2.1%). Overall, HBV and HCV prevalence increased with age. In conclusion, HBV and HCV seroprevalence among blood donors in Ethiopia is intermediate and low, respectively.
Edaphic Conditions, Aboveground Carbon Stocks and Plant Diversity on Nickel Mine Tailings Dump Vegetated with Senegalia polyacantha (Willd.) Seigler & Ebinger
Authors: Mukaro Edeth , Nyakudya Innocent Wadzanayi , Jimu Luke
Published: January 2017

Revegetation accelerates soil fertility improvement and enhances biodiversity on mine dumps. The objective of the study was to determine the status of edaphic conditions; aboveground carbon stocks; and plant diversity. The study was conducted on nickel tailings dump revegetated with Senegalia polyacantha aged 8, 9, 10 and 11 years in Zimbabwe. Results showed high bulk densities and pH values; low organic carbon; deficiency in K; and toxic levels for Ni and As implying that the tailings materials are still marginal for vegetation establishment. Limited presence of woody species suggests that the substrate is not yet suitable for colonization by such species. Copyright © 2017 John Wiley & Sons, Ltd.
Antibiotic discovery throughout the Small World Initiative: A molecular strategy to identify biosynthetic gene clusters involved in antagonistic activity
Authors: Davis Elizabeth , Sloan Tyler , Aurelius Krista , Barbour Angela , Bodey Elijah , Clark Brigette , Dennis Celeste , Drown Rachel , Fleming Megan , Humbert Allison , Glasgo Elizabeth , Kerns Trent , Lingro Kelly , McMillin MacKenzie , Meyer Aaron , Pope Breanna , Stalevicz April , Steffen Brittney , Steindl Austin , Williams Carolyn , Wimberley Carmen , Zenas Robert , Butela Kristen , Wildschutte Hans
Published: January 2017

The emergence of bacterial pathogens resistant to all known antibiotics is a global health crisis. Adding to this problem is that major pharmaceutical companies have shifted away from antibiotic discovery due to low profitability. As a result, the pipeline of new antibiotics is essentially dry and many bacteria now resist the effects of most commonly used drugs. To address this global health concern, citizen science through the Small World Initiative (SWI) was formed in 2012. As part of SWI, students isolate bacteria from their local environments, characterize the strains, and assay for antibiotic production. During the 2015 fall semester at Bowling Green State University, students isolated 77 soil‐derived bacteria and genetically characterized strains using the 16S rRNA gene, identified strains exhibiting antagonistic activity, and performed an expanded SWI workflow using transposon mutagenesis to identify a biosynthetic gene cluster involved in toxigenic compound production. We identified one mutant with loss of antagonistic activity and through subsequent whole‐genome sequencing and linker‐mediated PCR identified a 24.9 kb biosynthetic gene locus likely involved in inhibitory activity in that mutant. Further assessment against human pathogens demonstrated the inhibition of Bacillus cereus, Listeria monocytogenes, and methicillin‐resistant Staphylococcus aureus in the presence of this compound, thus supporting our molecular strategy as an effective research pipeline for SWI antibiotic discovery and genetic characterization.
Independent variant analysis of TEAD1 and OCEL1 in 38 Aicardi syndrome patients
Authors: Wong Bibiana K. Y. , Sutton Vernon R. , Lewis Richard A. , Van den Veyver Ignatia B.
Published: January 2017

Background

Aicardi syndrome is a severe neurodevelopmental disorder characterized by infantile spasms, typical chorioretinal lacunae, agenesis of the corpus callosum, and other neuronal migration defects. It has been reported recently that de novo variants in TEAD1 and OCEL1 each may cause Aicardi syndrome in a single individual of a small cohort of females with this clinical diagnosis. These data were interpreted to suggest that the clinical diagnosis of Aicardi syndrome may be genetically heterogeneous.

Methods

To investigate this further, we sequenced TEAD1 and OCEL1 coding regions using DNA from 38 clinically well‐characterized girls with Aicardi syndrome.

Results

We did not detect the previously reported or any other deleterious variants in any of the analyzed samples.

Conclusions

This suggests that the published variants represent either an extremely rare cause of Aicardi syndrome or an incidental finding.
The use of vascularised bone capping to prevent and treat amputation stump spiking in the paediatric population
Authors: Murphy Adrian D , Atkins Sara E , Thomas Damon J , McCombe David , Coombs Chris J
Published: January 2017

Background

Overgrowth of the stump skeleton is a major complication seen in children after an amputation. In advanced cases, perforation of the bone spike through the skin can occur. Many surgical treatments have been employed to treat and prevent this, with best results seen when non‐vascularised osteo‐chondral bone grafts are placed to try to mimic a trans‐articular amputation. We reviewed our outcomes using vascularized bone flaps to prevent and treat spiking.

Patients and Methods

Between 2000 and 2016 we carried out six vascularised osteo‐cartilaginous bone capping procedures. Five patients underwent the procedure as an adjunct to primary amputation and in a single patient it was used to treat established bone spiking. Trauma accounted for three cases, with the other three being tumour, vascular malformation and ischemia. Three patients had pedicled bone flaps placed on the amputation stump and three underwent free tissue transfer (free calcaneus, free scapular angle, and free proximal tibia). Five cases involved lower limb amputations, with one in the upper limb.

Results

One patient had an early post‐operative complication in the form of partial skin flap necrosis that required debridement and skin grafting. All bone flaps survived. Mean follow‐up was 6.5 years. All patients had bony union with no development of stump spiking. Two patients required further procedures unrelated to the bone flaps.

Conclusion

Vascularised bone flaps to cap amputation stumps may be a safe and effective method of preventing and treating long‐bone stump spiking following amputation in children
Novel variant in the PYGM gene causing late‐onset limb‐girdle myopathy, ptosis, and camptocormia
Authors: Chéraud Chrystel , Froissart Roseline , Lannes Béatrice , Echaniz‐Laguna Andoni
Published: January 2017

Introduction

McArdle disease is a glycogen storage disease caused by mutations in the PYGM gene encoding myophosphorylase. It manifests classically with childhood‐onset exercise‐induced pain.

Methods

We report the characteristics of 2 unrelated patients with a new homozygous mutation of the PYGM gene.

Results

Two patients, aged 76 and 79 years, presented with severe upper and lower limb atrophy and weakness. Additionally, 1 patient presented with bilateral ptosis, and the other with camptocormia. In both patients, symptoms had developed progressively in the 2 preceding years, and there was no history of exercise intolerance. Both patients demonstrated myogenic abnormalities on electromyography, multiple glycogen‐containing vacuoles and undetectable muscle myophosphorylase activity on muscle biopsy, and a novel homozygous frameshift p.Lys42Profs*48 PYGM mutation.

Conclusions

This report expands the phenotype and genotype of McArdle disease and suggests that PYGM mutations should be looked for in patients with very late‐onset myopathy with no previous history of exercise intolerance. Muscle Nerve 57: 157–160, 2018
A combinatorial scoring function for protein–RNA docking
Authors: Zhang Zhao , Lu Lin , Zhang Yue , Hua Li Chun , Wang Cun Xin , Zhang Xiao Yi , Tan Jian Jun
Published: January 2017

Protein–RNA docking is still an open question. One of the main challenges is to develop an effective scoring function that can discriminate near‐native structures from the incorrect ones. To solve the problem, we have constructed a knowledge‐based residue‐nucleotide pairwise potential with secondary structure information considered for nonribosomal protein–RNA docking. Here we developed a weighted combined scoring function RpveScore that consists of the pairwise potential and six physics‐based energy terms. The weights were optimized using the multiple linear regression method by fitting the scoring function to L_rmsd for the bound docking decoys from Benchmark II. The scoring functions were tested on 35 unbound docking cases. The results show that the scoring function RpveScore including all terms performs best. Also RpveScore was compared with the statistical mechanics‐based method derived potential ITScore‐PR, and the united atom‐based statistical potentials QUASI‐RNP and DARS‐RNP. The success rate of RpveScore is 71.6% for the top 1000 structures and the number of cases where a near‐native structure is ranked in top 30 is 25 out of 35 cases. For 32 systems (91.4%), RpveScore can find the binding mode in top 5 that has no lower than 50% native interface residues on protein and nucleotides on RNA. Additionally, it was found that the long‐range electrostatic attractive energy plays an important role in distinguishing near‐native structures from the incorrect ones. This work can be helpful for the development of protein–RNA docking methods and for the understanding of protein–RNA interactions. RpveScore program is available to the public at http://life.bjut.edu.cn/kxyj/kycg/2017116/14845362285362368_1.html Proteins 2017; 85:741–752. © 2016 Wiley Periodicals, Inc.
Chinese process safety management core elements and control measures
Authors: Zhou Aitao , Fan Lingpeng , Ma Mingfei , Tao Bo
Published: January 2017

With the popularization and application of chemical process safety management (PSM) systems in the chemical industry, the use of such systems in China has become the focus of a large volume of research. In this article, 12 elements included in the current Chinese PSM system are divided into four stages from a structural point of view. This division will be helpful in the follow‐up analysis. After a careful analysis of the evaluation results for one PSM pilot study in Nanjing, some correlations have been found between the results of the elemental evaluation. Small‐ and medium‐sized chemical plants make up a large proportion of Chinese chemical plants and many chemical accidents take place in these plants, so a simplified PSM system in practical operation need to be found. Based on a previous PSM structural analysis, the secondary elements of the PSM system can be removed. This allows researchers to avoid the traditional method of analyzing PSM elements individually. In the concrete analysis process, a theoretical analysis of the correlation degree between elements can be combined with the results of accident investigations. The simplified Chinese PSM system consists of four core elements: Process safety information, process hazard analysis, training, and emergency management. Based on the current applications of these four core elements in China, a consideration of correlations between these elements is used to make several suggestions for improving China's PSM systems. © 2017 American Institute of Chemical Engineers Process Saf Prog 36: 378–381, 2017
Dynamic predictions using flexible joint models of longitudinal and time‐to‐event data
Authors: Barrett Jessica , Su Li
Published: January 2017

Joint models for longitudinal and time‐to‐event data are particularly relevant to many clinical studies where longitudinal biomarkers could be highly associated with a time‐to‐event outcome. A cutting‐edge research direction in this area is dynamic predictions of patient prognosis (e.g., survival probabilities) given all available biomarker information, recently boosted by the stratified/personalized medicine initiative. As these dynamic predictions are individualized, flexible models are desirable in order to appropriately characterize each individual longitudinal trajectory. In this paper, we propose a new joint model using individual‐level penalized splines (P‐splines) to flexibly characterize the coevolution of the longitudinal and time‐to‐event processes. An important feature of our approach is that dynamic predictions of the survival probabilities are straightforward as the posterior distribution of the random P‐spline coefficients given the observed data is a multivariate skew‐normal distribution. The proposed methods are illustrated with data from the HIV Epidemiology Research Study. Our simulation results demonstrate that our model has better dynamic prediction performance than other existing approaches. © 2017 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.
On an enhanced rank‐preserving structural failure time model to handle treatment switch, crossover, and dropout
Authors: Li Lingling , Tang Shijie , Jiang Liewen
Published: January 2017

It is very challenging to estimate the comparative treatment effect between a treatment therapy and a control therapy on overall survival in the presence of treatment crossover, switch to an alternative non‐study therapy, and non‐random patient dropout. Existing methods (e.g., intent‐to‐treat and per‐protocol) are known to be biased. We proposed two new estimators to address these analytical challenges and evaluated their performance via a comprehensive simulation study. The new estimators were constructed by combining an enhanced rank‐preserving structural failure time model and the inverse probability censoring weighting approach. In the simulation study, we assessed and compared the performance of the two new estimators with four estimators from existing methods. The simulation results show that the new estimators have much better performance in almost all considered settings compared with the existing estimators. Copyright © 2017 John Wiley & Sons, Ltd.
Poly(amidoamine) Dendrimer Functionalized Carbon Nanotube for Efficient Sorption of Trivalent f‐Elements: A Comparison Between 1st And 2nd Generation
Authors: Kumar Parveen , Sengupta Arijit , Deb Ashish Kumar Singha , Ali Sk. Musharaf
Published: January 2017

Poly(amidoamine) dendrimer functionalized carbon nano tubes were synthesized, characterized and used for the sorption of americium from aqueous acidic waste solution. The sorption of Am3+ has been found to take place through pseudo second order kinetics with the rate constants of 8.61E‐05 and 5.38E‐05 mg g−1 min−1for 1st and 2nd generation, respectively, followingLangmuir isotherm. The MWCNT‐PAMAMG1 and MWCNT‐PAMAMG2 have high radiolytic stability. The stripping study revealed that EDTA can be effectively used for almost quantitative back extraction of metal ion from both generation of dendrimer. Luminescence investigation revealed the presence of single species with no inner sphere water molecule. The 1st generation dendrimer complex was found to be more asymmetric compared to the 2nd generation. The analysis of Judd Offelt parameters and evaluation of photo‐physical properties were carried out to understand the complexation of Am3+ with these sorbents.
Retinal thickness in Alzheimer's disease: A systematic review and meta‐analysis
Authors: den Haan Jurre , Verbraak Frank D. , Visser Pieter Jelle , Bouwman Femke H.
Published: January 2017

Introduction

Retinal characteristics are increasingly recognized as biomarkers for neurodegenerative diseases. Retinal thickness measured by optical coherence tomography may reflect the presence of Alzheimer's disease (AD). We performed a meta‐analysis on retinal thickness in AD and mild cognitive impairment (MCI) patients and healthy controls (HCs).

Methods

We selected 25 studies with measurements of retinal thickness including 887 AD patients, 216 MCI patients, and 864 HCs that measured retinal thickness. Outcomes were peripapillary retinal nerve fiber layer (RNFL) and macular thickness. The main outcome was the standardized mean differences (SMDs). We used STATA to perform the meta‐analysis (StataCorp, Texas; version 14.0).

Results

Relative to HCs, AD and MCI patients had lower peripapillary RNFL (SMD 0.98 [CI −1.30, −0.66, P < .0001] and SMD 0.71 [CI −1.24, −0.19, P = .008]). Total macular thickness was decreased in AD patients (SMD 0.88 [CI −1.12, −0.65, P = .000]).

Discussion

Retinal thickness is decreased in AD and MCI patients compared to HC. This confirms that neurodegenerative diseases may be reflected by retinal changes.
Effects of early or late prenatal immune activation in mice on behavioral and neuroanatomical abnormalities relevant to schizophrenia in the adulthood
Authors: da Silveira Vivian T. , de Castro Medeiros Daniel , Ropke Jivago , Guidine Patricia A. , Rezende Gustavo H. , Moraes Marcio Flavio D. , Mendes Eduardo Mazoni A.M. , Macedo Danielle , Moreira Fabricio A. , de Oliveira Antonio Carlos P.
Published: January 2017

Maternal immune activation (MIA) during pregnancy in rodents increases the risk of the offspring to develop schizophrenia‐related behaviors, suggesting a relationship between the immune system and the brain development. Here we tested the hypothesis that MIA induced by the viral mimetic polyinosinic‐polycytidylic acid (poly I:C) in early or late gestation of mice leads to behavioral and neuroanatomical disorders in the adulthood. On gestational days (GDs) 9 or 17 pregnant dams were treated with poly I:C or saline via intravenous route and the offspring behaviors were measured during adulthood. Considering the progressive structural neuroanatomical alterations in the brain of individuals with schizophrenia, we used magnetic resonance imaging (MRI) to perform brain morphometric analysis of the offspring aged one year. MIA on GD9 or GD17 led to increased basal locomotor activity, enhanced motor responses to ketamine, a psychotomimetic drug, and reduced time spent in the center of the arena, suggesting an increased anxiety‐like behavior. In addition, MIA on GD17 reduced glucose preference in the offspring. None of the treatments altered the relative volume of the lateral ventricles. However, a decrease in brain volume, especially for posterior structures, was observed for one‐year‐old animals treated with poly I:C compared with control groups. Thus, activation of the maternal immune system at different GDs lead to neuroanatomical and behavioral alterations possibly related to the positive and negative symptoms of schizophrenia. These results provide insights on neuroimmunonological and neurodevelopmental aspects of certain psychopathologies, such as schizophrenia.
Measuring neuroplasticity associated with cerebral palsy rehabilitation: An MRI based power analysis
Authors: Reid Lee B. , Pagnozzi Alex M. , Fiori Simona , Boyd Roslyn N. , Dowson Nicholas , Rose Stephen E.
Published: January 2017

Researchers in the field of child neurology are increasingly looking to supplement clinical trials of motor rehabilitation with neuroimaging in order to better understand the relationship between behavioural training, brain changes, and clinical improvements. Randomised controlled trials are typically accompanied by sample size calculations to detect clinical improvements but, despite the large cost of neuroimaging, not equivalent calculations for concurrently acquired imaging neuroimaging measures of changes in response to intervention. To aid in this regard, a power analysis was conducted for two measures of brain changes that may be indexed in a trial of rehabilitative therapy for cerebral palsy: cortical thickness of the impaired primary sensorimotor cortex, and fractional anisotropy of the impaired, delineated corticospinal tract. Power for measuring fractional anisotropy was assessed for both region‐of‐interest‐seeded and fMRI‐seeded diffusion tractography. Taking into account practical limitations, as well as data loss due to behavioural and image‐processing issues, estimated required participant numbers were 101, 128 and 59 for cortical thickness, region‐of‐interest‐based tractography, and fMRI‐seeded tractography, respectively. These numbers are not adjusted for study attrition. Although these participant numbers may be out of reach of many trials, several options are available to improve statistical power, including careful preparation of participants for scanning using mock simulators, careful consideration of image processing options, and enrolment of as homogeneous a cohort as possible. This work suggests that smaller and moderate sized studies give genuine consideration to harmonising scanning protocols between groups to allow the pooling of data.