bluuebunny/crossref_metadata_2025 huggingface dataset:
On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes
Authors: Bernatchez L.
Published: September 2016

The first goal of this paper was to overview modern approaches to local adaptation, with a focus on the use of population genomics data to detect signals of natural selection in fishes. Several mechanisms are discussed that may enhance the maintenance of genetic variation and evolutionary potential, which have been overlooked and should be considered in future theoretical development and predictive models: the prevalence of soft sweeps, polygenic basis of adaptation, balancing selection and transient polymorphisms, parallel evolution, as well as epigenetic variation. Research on fish population genomics has provided ample evidence for local adaptation at the genome level. Pervasive adaptive evolution, however, seems to almost never involve the fixation of beneficial alleles. Instead, adaptation apparently proceeds most commonly by soft sweeps entailing shifts in frequencies of alleles being shared between differentially adapted populations. One obvious factor contributing to the maintenance of standing genetic variation in the face of selective pressures is that adaptive phenotypic traits are most often highly polygenic, and consequently the response to selection should derive mostly from allelic co‐variances among causative loci rather than pronounced allele frequency changes. Balancing selection in its various forms may also play an important role in maintaining adaptive genetic variation and the evolutionary potential of species to cope with environmental change. A large body of literature on fishes also shows that repeated evolution of adaptive phenotypes is a ubiquitous evolutionary phenomenon that seems to occur most oftenviadifferent genetic solutions, further adding to the potential options of species to cope with a changing environment. Moreover, a paradox is emerging from recent fish studies whereby populations of highly reduced effective population sizes and impoverished genetic diversity can apparently retain their adaptive potential in some circumstances. Although more empirical support is needed, several recent studies suggest that epigenetic variation could account for this apparent paradox. Therefore, epigenetic variation should be fully integrated with considerations pertaining to role of soft sweeps, polygenic and balancing selection, as well as repeated adaptation involving different genetic basis towards improving models predicting the evolutionary potential of species to cope with a changing world.
Radicalize Multiculturalism? Garifuna Activism and the Double‐Bind of Participation in Postcoup Honduras
Authors: Loperena Christopher
Published: September 2016

En este artículo analizo la resistencia Garífuna ante el golpe de estado contra Manuel Rosales Zelaya. Me baso en entrevistas y conversaciones con activistas y observación participante en las protestas contra el golpe de estado en Tegucigalpa con el fin de explorar el significado y los objetivos de la resistencia cultural Garífuna en el periodo post‐golpe. Argumento que la etnopolítica sirve para reforzar y desafiar las representaciones dominantes de la subjetividad folklórica Garífuna, las cuales son ampliamente diseminadas por la propaganda turística y la construcción de la identidad nacional por políticas multiculturales. También subrayo la forma en que los activistas Garífunas articularon sus demandas para la autonomía y los derechos territoriales con los objetivos del movimiento de resistencia nacional. Participación Garífuna en la Resistencia brindó la oportunidad de ser reconocidos como sujetos políticos—no como objetos—y para aspirar a otra Honduras dentro de este movimiento multiétnico emergente.
Vascular patterns in the heads of crocodilians: blood vessels and sites of thermal exchange
Authors: Porter William Ruger , Sedlmayr Jayc C. , Witmer Lawrence M.
Published: September 2016

Extant crocodilians are a highly apomorphic archosaur clade that is ectothermic, yet often achieve large body sizes that can be subject to higher heat loads. Therefore, the anatomical and physiological roles that blood vessels play in crocodilian thermoregulation need further investigation to better understand how crocodilians establish and maintain cephalic temperatures and regulate neurosensory tissue temperatures during basking and normal activities. The cephalic vascular anatomy of extant crocodilians, particularly American alligator (Alligator mississippiensis) was investigated using a differential‐contrast, dual‐vascular injection technique and high resolution X‐ray micro‐computed tomography (μCT). Blood vessels were digitally isolated to create representations of vascular pathways. The specimens were then dissected to confirmCTresults. Sites of thermal exchange, consisting of the oral, nasal, and orbital regions, were given special attention due to their role in evaporative cooling and cephalic thermoregulation in other diapsids. Blood vessels to and from sites of thermal exchange were studied to detect conserved vascular patterns and to assess their ability to deliver cooled blood to neurosensory tissues. Within the orbital region, both the arteries and veins demonstrated consistent branching patterns, with the supraorbital, infraorbital, and ophthalmotemporal vessels supplying and draining the orbit. The venous drainage of the orbital region showed connections to the dural sinuses via the orbital veins and cavernous sinus. The palatal region demonstrated a vast plexus that comprised both arteries and veins. The most direct route of venous drainage of the palatal plexus was through the palatomaxillary veins, essentially bypassing neurosensory tissues. Anastomotic connections with the nasal region, however, may provide an alternative route for palatal venous blood to reach neurosensory tissues. The nasal region in crocodilians is probably the most prominent site of thermal exchange, as it offers a substantial surface area and is completely surrounded by blood vessels. The venous drainage routes from the nasal region offer routes directly to the dural venous sinuses and the orbit, offering evidence of the potential to directly affect neurosensory tissue temperatures. The evolutionary history of crocodilians is complex, with large‐bodied, terrestrial, and possibly endothermic taxa that may have had to deal with thermal loads that likely provided the anatomical building‐blocks for such an extensive vascularization of sites of thermal exchange. A clear understanding of the physiological abilities and the role of blood vessels in the thermoregulation of crocodilians neurosensory tissues is not available but vascular anatomical patterns of crocodilian sites of thermal exchange indicate possible physiological abilities that may be more sophisticated than in other extant diapsids.
Mesenchymal stem cells and vascular regeneration
Authors: Gu Wenduo , Hong Xuechong , Potter Claire , Qu Aijuan , Xu Qingbo
Published: September 2016

In recent years, MSCs have emerged as a promising therapeutic cell type in regenerative medicine. They hold great promise for treating cardiovascular diseases, such as myocardial infarction and limb ischemia. MSCs may be utilized in both cell‐based therapy and vascular graft engineering to restore vascular function, thereby providing therapeutic benefits to patients. The efficacy of MSCs lies in their multipotent differentiation ability toward vascular smooth muscle cells, endothelial cells and other cell types, as well as their capacity to secrete various trophic factors, which are potent in promoting angiogenesis, inhibiting apoptosis and modulating immunoreaction. Increasing our understanding of the mechanisms of MSC involvement in vascular regeneration will be beneficial in boosting present therapeutic approaches and developing novel ones to treat cardiovascular diseases. In this review, we aim to summarize current progress in characterizing the in vivo identity of MSCs, to discuss mechanisms involved in cell‐based therapy utilizing MSCs, and to explore current and future strategies for vascular regeneration.
Amiloride modifies the progression of lithium‐induced renal interstitial fibrosis
Authors: Kalita‐De Croft Priyakshi , Bedford Jennifer J , Leader John P , Walker Robert J
Published: September 2016

Aim

Long‐term administration of lithium has been associated with the development of a chronic interstitial fibrosis in addition to nephrogenic diabetes insipidus (NDI). Earlier studies have demonstrated that amiloride, by blocking the epithelial sodium channel ENaC and thus preventing lithium uptake into the principal cells of the collecting ducts, can partially reverse lithium‐induced NDI. However, there are no long‐term studies examining whether or not amiloride also modifies the progressive chronic interstitial fibrosis and tubular atrophy often evident with long‐term lithium exposure.

Methods

Using an established animal model of lithium‐induced chronic interstitial fibrosis, rats were treated with amiloride and lithium for 5 months following 1 month of exposure to lithium alone and compared with control animals and those given only lithium.

Results and Conclusions

In this study, the 5 months of amiloride therapy partially mitigated the lithium‐induced NDI and limited the further progression of lithium‐induced kidney fibrosis. This improvement was associated with decreased expression of the pro‐fibrotic connective tissue growth factor (CTGF), along with reduced myofibroblast infiltration and decreased collagen deposition around the distended cortical collecting ducts. This may, in part, be mediated by modifying lithium‐induced alterations in β‐catenin activity through its effects on GSK‐3β.
Biparental chloroplast inheritance leads to rescue from cytonuclear incompatibility
Authors: Barnard‐Kubow Karen B. , McCoy Morgan A. , Galloway Laura F.
Published: September 2016

Although organelle inheritance is predominantly maternal across animals and plants, biparental chloroplast inheritance has arisen multiple times in the angiosperms. Biparental inheritance has the potential to impact the evolutionary dynamics of cytonuclear incompatibility, interactions between nuclear and organelle genomes that are proposed to be among the earliest types of genetic incompatibility to arise in speciation.

We examine the interplay between biparental inheritance and cytonuclear incompatibility in Campanulastrum americanum, a plant species exhibiting both traits. We first determine patterns of chloroplast inheritance in genetically similar and divergent crosses, and then associate inheritance with hybrid survival across multiple generations.

There is substantial biparental inheritance in C. americanum. The frequency of biparental inheritance is greater in divergent crosses and in the presence of cytonuclear incompatibility. Biparental inheritance helps to mitigate cytonuclear incompatibility, leading to increased fitness of F1 hybrids and recovery in the F2 generation.

This study demonstrates the potential for biparental chloroplast inheritance to rescue cytonuclear compatibility, reducing cytonuclear incompatibility's contribution to reproductive isolation and potentially slowing speciation. The efficacy of rescue depended upon the strength of incompatibility, with a greater persistence of weak incompatibilities in later generations. These findings suggest that incompatible plastids may lead to selection for biparental inheritance.
Quantitative PCR for HTLV‐1 provirus in adult T‐cell leukemia/lymphoma using paraffin tumor sections
Authors: Kato Junki , Masaki Ayako , Fujii Keiichiro , Takino Hisashi , Murase Takayuki , Yonekura Kentaro , Utsunomiya Atae , Ishida Takashi , Iida Shinsuke , Inagaki Hiroshi
Published: September 2016

Detection of HTLV‐1 provirus using paraffin tumor sections may assist the diagnosis of adult T‐cell leukemia/lymphoma (ATLL). For the detection, non‐quantitative PCR assay has been reported, but its usefulness and limitations remain unclear. To our knowledge, quantitative PCR assay using paraffin tumor sections has not been reported. Using paraffin sections from ATLLs and non‐ATLL T‐cell lymphomas, we first performed non‐quantitative PCR for HTLV‐1 provirus. Next, we determined tumor ratios and carried out quantitative PCR to obtain provirus copy numbers. The results were analyzed with a simple regression model and a novel criterion, cut‐off using 95 % rejection limits. Our quantitative PCR assay showed an excellent association between tumor ratios and the copy numbers (r = 0.89, P < 0.0001). The 95 % rejection limits provided a statistical basis for the range for the determination of HTLV‐1 involvement. Its application suggested that results of non‐quantitative PCR assay should be interpreted very carefully and that our quantitative PCR assay is useful to estimate the status of HTLV‐1 involvement in the tumor cases. In conclusion, our quantitative PCR assay using paraffin tumor sections may be useful for the screening of ATLL cases, especially in HTLV‐1 non‐endemic areas where easy access to serological testing for HTLV‐1 infection is limited.
Assemble‐to‐Order Inventory Management via Stochastic Programming: Chained BOMs and the M‐System
Authors: Doğru Mustafa K. , Reiman Martin I. , Wang Qiong
Published: September 2016

We study an inventory management mechanism that uses two stochastic programs (SPs), the customary one‐period assemble‐to‐order (ATO) model and its relaxation, to conceive control policies for dynamic ATO systems. We introduce a class of ATO systems, those that possess what we call a “chained BOM.” We prove that having a chained BOM is a sufficient condition for both SPs to be [Formula: see text] convex in the first‐stage decision variables. We show by examples the necessity of the condition. For ATO systems with a chained BOM, our result implies that the optimal integer solutions of the SPs can be found efficiently, and thus expedites the calculation of control parameters. The M system is a representative chained BOM system with two components and three products. We show that in this special case, the SPs can be solved as a one‐stage optimization problem. The allocation policy can also be reduced to simple, intuitive instructions, of which there are four distinct sets, one for each of four different parameter regions. We highlight the need for component reservation in one of these four regions. Our numerical studies demonstrate that achieving asymptotic optimality represents a significant advantage of the SP‐based approach over alternative approaches. Our numerical comparisons also show that outside of the asymptotic regime, the SP‐based approach has a commanding lead over the alternative policies. Our findings indicate that the SP‐based approach is a promising inventory management strategy that warrants further development for more general systems and practical implementations.
Commentary: Goals and Collaborative Advantage: What's the Relationship?
Authors: Potapchuk William
Published: September 2016

Related Content: Bryson, Ackermann, and Eden (PAR November/December 2016)
A three‐dimensional alginate system for in vitro culture of cumulus‐denuded feline oocytes
Authors: Morselli MG , Canziani S , Vigo D , Luvoni GC
Published: September 2016

Contents

In the case of high valuable individuals with very precious genetic material, widening the genetic pool including gametes with poor morphological characteristics, as cumulus‐denuded oocytes (CDOs), could be an option. To improve the in vitro culture of low‐competence feline CDOs, an enriched three‐dimensional (3D) system in association with competent cumulus–oocyte complexes (COCs) was developed. For this purpose, domestic cat CDOs were cultured with or without companion COCs in the 3D barium alginate microcapsules. The overall viability and the meiotic progression of feline CDOs cocultured with COCs or cultured separately in 3D or in 2D (traditional microdrops) system were compared. The 3D system was able to support viability and meiotic resumption of the feline oocytes, as well as the 2D microdrops. In 3D microcapsules, the presence of COCs resulted in a higher viability of CDOs (91.1%, p < .05), than that obtained without COCs or in 2D microdrops (71.2% and 67.3%, respectively), but the percentages of meiotic resumption were similar of those of CDOs cultured separately (55.4% vs. 40.4%, p > .05). It is notable that the presence of CDOs seemed to enhance the meiotic progression of the associated COCs. In conclusion, the 3D barium alginate microcapsules are a suitable system for feline oocytes in vitro culture, but more specific enriched conditions should be developed to improve the CDOs full competence in vitro.
Increased neutrophil expression of pattern recognition receptors during COPD exacerbations
Authors: Pouwels Simon D. , van Geffen Wouter H. , Jonker Marnix R. , Kerstjens Huib A. M. , Nawijn Martijn C. , Heijink Irene H.
Published: September 2016

Previously, we observed increased serum levels of damage‐associated molecular patterns (DAMPs) during COPD exacerbations. Here, gene expression of DAMP receptors was measured in peripheral blood neutrophils of COPD patients during stable disease and severe acute exacerbation. The expression of toll‐like receptor (TLR)2, TLR4 and NLR family, pyrin domain‐containing 3 (NLRP3) was significantly increased, while serum levels of the soluble form of the decoy receptor for advanced glycation end‐product (sRAGE) were decreased during exacerbation. Together, these data indicate that increased DAMP signalling contributes to activation of neutrophils during COPD exacerbations.
Cytomegalovirus sinusitis complicated by orbital apex syndrome in an immunocompromised host
Authors: Nomura Jim H. , Eichhorn Knut , Cao Thai M. , Sahebi Firoozeh
Published: September 2016

Sinusitis in immunocompromised patients can be caused by a wide variety of pathogens, primarily bacterial and fungal in nature. Tissue invasion can extend into the orbital apex and result in ophthalmoplegia and blindness. We report the first histologically proven case, to our knowledge, caused by cytomegalovirus infection.
Induction, management, and complications of streptozotocin‐induced diabetes mellitus in rhesus monkeys
Authors: Kim Jong‐Min , Shin Jun‐Seop , Min Byoung‐Hoon , Kim Hyun‐Je , Kim Jung‐Sik , Yoon Il‐Hee , Jeong Won‐Young , Lee Ga‐Eul , Kim Min‐Sun , Kim Ju‐Eun , Jin Sang‐Man , Park Chung‐Gyu
Published: September 2016

Background

Diabetes mellitus (DM) model using streptozotocin (STZ) which induces chemical ablation of β cell in the pancreas has been widely used for various research purposes in non‐human primates. However, STZ has been known to have a variety of adverse effects such as nephrotoxicity, hepatotoxicity, and even mortality. The purpose of this study is to report DM induction by STZ, toxicity associated with STZ and procedure and complication of exogenous insulin treatment for DM management in rhesus monkeys (Macaca mulatta) that are expected to be transplanted with porcine islets within 2 months.

Methods

Streptozotocin (immediately dissolved in normal saline, 110 mg/kg) was slowly infused via central catheter for 10 minutes in 22 rhesus monkeys. Clinical signs, complete blood count and blood chemistry were monitored to evaluate toxicity for 1 week after STZ injection. Monkey basal C‐peptides were measured and intravenous glucose tolerance test was performed to confirm complete induction of DM. Exogenous insulin was subcutaneously injected to maintain blood glucose in diabetic rhesus monkeys and the complications were recorded while in insulin treatment.

Results

Severe salivation and vomiting were observed within 1 hour after STZ injection in 22 rhesus monkeys. One monkey died at 6 hours after STZ injection and the reason for the death was unknown. Pancreatitis was noticed in one monkey after STZ injection, but the monkey recovered after 5 days by medical treatment. Serum total protein and albumin decreased whereas the parameters for the liver function such as aspartate aminotransferase, alanine aminotransferase, and lactate dehydrogenase significantly increased (P<.05) after STZ injection, but they were resolved within 1 week. Azotemia was not observed. Monkey fasting C‐peptide levels after STZ injection were <0.1 ng/mL in 18 rhesus monkeys, but 0.34, 0.22, 0.16 ng/mL in three monkeys, respectively. The value of daily insulin requirement was 0.92±0.26IU/kg/d (range=0.45–1.29) in the monkeys. Diabetic ketoacidosis was observed in one rhesus monkeys, but the monkey recovered after 24 hours by fluid and insulin treatment.

Conclusions

Streptozotocin was effective for inducing DM in rhesus monkeys, but various adverse effects such as pancreatitis, liver toxicity or death were observed. Therefore, careful and suitable medical managements should be implemented to eliminate the risks of mortality and severe adverse effects.
Molecular mechanisms of Slo2 K+ channel closure
Authors: Giese M. Hunter , Gardner Alison , Hansen Angela , Sanguinetti Michael C.
Published: September 2016

Key points

Intracellular Na+‐activated Slo2 potassium channels are in a closed state under normal physiological conditions, although their mechanisms of ion permeation gating are not well understood.

A cryo‐electron microscopy structure of Slo2.2 suggests that the ion permeation pathway of these channels is closed by a single constriction of the inner pore formed by the criss‐crossing of the cytoplasmic ends of the S6 segments (the S6 bundle crossing) at a conserved Met residue.

Functional characterization of mutant Slo2 channels suggests that hydrophobic interactions between Leu residues in the upper region of the S6 segments contribute to stabilizing the inner pore in a non‐conducting state.

Mutation of the conserved Met residues in the S6 segments to the negatively‐charged Glu did not induce constitutive opening of Slo2.1 or Slo2.2, suggesting that ion permeation of Slo2 channels is not predominantly gated by the S6 bundle crossing.

Large conductance K+‐selective Slo2 channels are in a closed state unless activated by elevated [Na+]i. Our previous studies suggested that the pore helix/selectivity filter serves as the activation gate in Slo2 channels. In the present study, we evaluated two other potential mechanisms for stabilization of Slo2 channels in a closed state: (1) dewetting and collapse of the inner pore (hydrophobic gating) and (2) constriction of the inner pore by tight criss‐crossing of the cytoplasmic ends of the S6 α‐helical segments. Slo2 channels contain two conserved Leu residues in each of the four S6 segments that line the inner pore region nearest the bottom of the selectivity filter. To evaluate the potential role of these residues in hydrophobic gating, Leu267 and Leu270 in human Slo2.1 were each replaced by 15 different residues. The relative conductance of mutant channels was highly dependent on hydrophilicity and volume of the amino acid substituted for Leu267 and was maximal with L267H. Consistent with their combined role in hydrophobic gating, replacement of both Leu residues with the isosteric but polar residue Asn (L267N/L270N) stabilized channels in a fully open state. In a recent cryo‐electron microscopy structure of chicken Slo2.2, the ion permeation pathway of the channel is closed by a constriction of the inner pore formed by criss‐crossing of the S6 segments at a conserved Met. Inconsistent with the S6 segment crossing forming the activation gate, replacement of the homologous Met residues in human Slo2.1 or Slo2.2 with the negatively‐charged Glu did not induce constitutive channel opening.
Deterministic and Stochastic Approaches for Day-Ahead Solar Power Forecasting
Authors: Pierro Marco , Bucci Francesco , De Felice Matteo , Maggioni Enrico , Perotto Alessandro , Spada Francesco , Moser David , Cornaro Cristina
Published: September 2016

Photovoltaic (PV) power forecasting has the potential to mitigate some of effects of resource variability caused by high solar power penetration into the electricity grid. Two main methods are currently used for PV power generation forecast: (i) a deterministic approach that uses physics-based models requiring detailed PV plant information and (ii) a data-driven approach based on statistical or stochastic machine learning techniques needing historical power measurements. The main goal of this work is to analyze the accuracy of these different approaches. Deterministic and stochastic models for day-ahead PV generation forecast were developed, and a detailed error analysis was performed. Four years of site measurements were used to train and test the models. Numerical weather prediction (NWP) data generated by the weather research and forecasting (WRF) model were used as input. Additionally, a new parameter, the clear sky performance index, is defined. This index is equivalent to the clear sky index for PV power generation forecast, and it is here used in conjunction to the stochastic and persistence models. The stochastic model not only was able to correct NWP bias errors but it also provided a better irradiance transposition on the PV plane. The deterministic and stochastic models yield day-ahead forecast skills with respect to persistence of 35% and 39%, respectively.
Tungsten Nanowire Metamaterials as Selective Solar Thermal Absorbers by Excitation of Magnetic Polaritons
Authors: Chang Jui-Yung , Wang Hao , Wang Liping
Published: September 2016

The present study focuses on nanowire-based metamaterials selective solar absorbers. Finite-difference time-domain (FDTD) simulation is employed for numerically designing a broadband solar absorber made of lossy tungsten nanowires which exhibit spectral selectivity due to the excitation of magnetic polariton (MP). An inductor–capacitor circuit model of the nanowire array is developed in order to predict the resonance wavelengths of the MP harmonic modes. The effects of geometric parameters such as nanowire diameter, height, and array period are investigated and understood by the sweep of geometric parameters, which tunes the MP resonance and the resulting optical and radiative properties. In addition, the optical properties and conversion efficiency of this nanowire-based absorber are both demonstrated to be insensitive on incidence angles, which illustrates the potential applicability of the proposed nanowire-based metamaterial as a high-efficiency wide-angle selective solar absorber. The results show that the nanowire-based selective solar absorber with base geometric parameters can reach 83.6% of conversion efficiency with low independence of incident angle. The results will facilitate the design of novel low-cost and high-efficiency materials for enhancing solar thermal energy harvesting and conversion.
Online 4D ultrasound guidance for real‐time motion compensation by MLC tracking
Authors: Ipsen Svenja , Bruder Ralf , O’Brien Rick , Keall Paul J. , Schweikard Achim , Poulsen Per R.
Published: September 2016

Purpose

With the trend in radiotherapy moving toward dose escalation and hypofractionation, the need for highly accurate targeting increases. While MLC tracking is already being successfully used for motion compensation of moving targets in the prostate, current real‐time target localization methods rely on repeated x‐ray imaging and implanted fiducial markers or electromagnetic transponders rather than direct target visualization. In contrast, ultrasound imaging can yield volumetric data in real‐time (3D + time = 4D) without ionizing radiation. The authors report the first results of combining these promising techniques—online 4D ultrasound guidance and MLC tracking—in a phantom.

Methods

A software framework for real‐time target localization was installed directly on a 4D ultrasound station and used to detect a 2 mm spherical lead marker inside a water tank. The lead marker was rigidly attached to a motion stage programmed to reproduce nine characteristic tumor trajectories chosen from large databases (five prostate, four lung). The 3D marker position detected by ultrasound was transferred to a computer program for MLC tracking at a rate of 21.3 Hz and used for real‐time MLC aperture adaption on a conventional linear accelerator. The tracking system latency was measured using sinusoidal trajectories and compensated for by applying a kernel density prediction algorithm for the lung traces. To measure geometric accuracy, static anterior and lateral conformal fields as well as a 358° arc with a 10 cm circular aperture were delivered for each trajectory. The two‐dimensional (2D) geometric tracking error was measured as the difference between marker position and MLC aperture center in continuously acquired portal images. For dosimetric evaluation, VMAT treatment plans with high and low modulation were delivered to a biplanar diode array dosimeter using the same trajectories. Dose measurements with and without MLC tracking were compared to a static reference dose using 3%/3 mm and 2%/2 mm γ‐tests.

Results

The overall tracking system latency was 172 ms. The mean 2D root‐mean‐square tracking error was 1.03 mm (0.80 mm prostate, 1.31 mm lung). MLC tracking improved the dose delivery in all cases with an overall reduction in the γ‐failure rate of 91.2% (3%/3 mm) and 89.9% (2%/2 mm) compared to no motion compensation. Low modulation VMAT plans had no (3%/3 mm) or minimal (2%/2 mm) residual γ‐failures while tracking reduced the γ‐failure rate from 17.4% to 2.8% (3%/3 mm) and from 33.9% to 6.5% (2%/2 mm) for plans with high modulation.

Conclusions

Real‐time 4D ultrasound tracking was successfully integrated with online MLC tracking for the first time. The developed framework showed an accuracy and latency comparable with other MLC tracking methods while holding the potential to measure and adapt to target motion, including rotation and deformation, noninvasively.
An iterative projection‐based motion estimation and compensation scheme for head x‐ray CT
Authors: Sun Tao , Kim Jung‐Ha , Fulton Roger , Nuyts Johan
Published: September 2016

Purpose

Although current computed tomography (CT) systems can scan the head in a very short time, patient motion sometimes still induces artifacts. If motion occurs, one has to repeat the scan; to avoid motion, sedation or anesthesia is sometimes applied.

Methods

The authors propose a method to iteratively estimate and compensate this motion during the reconstruction. In every iteration, the rigid motion was estimated view‐by‐view and then used to update the system matrix. A multiresolution scheme was used to speed up the convergence of this joint estimation of the image and the motion of the subject. A final iterative reconstruction was performed with the last motion estimate.

Results

The method was evaluated on simulations, patient scans, and a phantom study. The quality of the reconstructed images was improved substantially after the compensation. In simulation and phantom studies, root‐mean‐square error was reduced and mean structural similarity was increased. In the patient studies, most of the motion blurring in the reconstructed images disappeared after the compensation.

Conclusions

The proposed method effectively eliminated motion‐induced artifacts in head CT scans. Since only measured raw data are needed for the motion estimation and compensation, the proposed method can be applied retrospectively to clinical helical CT scans affected by motion.
Technical assessment of a prototype cone‐beam CT system for imaging of acute intracranial hemorrhage
Authors: Xu Jennifer , Sisniega Alejandro , Zbijewski Wojciech , Dang Hao , Stayman J. Webster , Mow Michael , Wang Xiaohui , Foos David H. , Koliatsos Vassillis E. , Aygun Nafi , Siewerdsen Jeffrey H.
Published: September 2016

Purpose

A cone‐beam CT scanner has been developed for detection and monitoring of traumatic brain injury and acute intracranial hemorrhage (ICH) at the point of care. This work presents a technical assessment of imaging performance and dose for the scanner in phantom and cadaver studies as a prerequisite to clinical translation.

Methods

The scanner incorporates a compact, rotating‐anode x‐ray source and a flat‐panel detector (43 × 43 cm2) on a mobile U‐arm gantry with source‐axis distance = 550 mm and source‐detector distance = 1000 mm. Central and peripheral doses were measured in 16 cm diameter CTDI phantoms using a 0.6 cm3 Farmer ionization chamber for various scan techniques and as a function of longitudinal position, including out of field. Spatial resolution, contrast, noise, and image uniformity were assessed in quantitative and anthropomorphic head phantoms. Two reconstruction protocols were evaluated, including filtered backprojection (FBP) for high‐resolution bone imaging and penalized weighted least squares (PWLS) reconstruction for low‐contrast soft tissue (ICH) visualization. A fresh cadaver was imaged with and without simulated ICH using the scanner as well as a diagnostic multidetector CT (MDCT) scanner using a standard head protocol. Images were interpreted by a fellowship‐trained neuroradiologist for imaging tasks of ICH detection, gray‐white‐CSF differentiation, detection of midline shift, and fracture detection.

Results

The nominal scan protocol involved 720 projections acquired over a 360° orbit at 100 kV and 216 mAs, giving a dose (weighted CTDI) of 22.8 mGy (∼1.2 mSv effective dose). Out‐of‐field dose decreased to <10% within 6 cm of the field edge (approximate to the thyroid position). Image uniformity demonstrated <1% variation between the edge of the field (near the cranium) and center of the image. The high‐resolution FBP reconstruction protocol showed ∼0.9 mm point spread function (PSF) full‐width at half‐maximum (FWHM). The smooth PWLS reconstruction protocol yielded ∼1.2 mm PSF FWHM and contrast‐to‐noise ratio exceeding 5.7 in ∼50 HU spherical ICH, resulting in conspicuous depiction of ICH down to ∼2 mm (the smallest diameter investigated). Cadaver images demonstrated good differentiation of brain and CSF (sufficient, but inferior to MDCT, recognizing that the CBCT dose was one‐third that of MDCT), excellent visualization of cranial sutures and fracture (potentially superior to MDCT), clear detection of midline shift, and conspicuous detection of ICH.

Conclusions

Technical assessment of the prototype demonstrates dose characteristics and imaging performance consistent with point‐of‐care detection and monitoring of head injury—most notably, conspicuous detection of ICH—and supports translation of the system to clinical studies.
The acoustic environment of inpatient hospital wards in the United Kingdom
Authors: Shield Bridget , Shiers Nicola , Glanville Rosemary
Published: September 2016

Many hospital noise surveys have shown that patients are subject to high levels of noise, in excess of current World Health Organization guidelines. Much of the previous research has focused on areas perceived to be noisy, such as intensive care units and operating theatres. This paper presents the results of a comprehensive noise survey of five general inpatient hospital wards in the UK. The survey involved continuous noise monitoring over several days, including identification of noise sources, in 31 locations representing a range of typical patient accommodations including single rooms and multi-bed bays, and nurse stations. The results were consistent with those of previous studies with daytime levels ranging from 50 to 61 dB LAeq and nighttime levels from 41 to 51 dB LAeq. Noise levels were not correlated with room/bay size, with single rooms having some of the highest levels. Overall levels were related to reverberation times and to the numbers of high level noise events. Analysis of noise sources showed that much of the noise could be eliminated or reduced through improved design of equipment and ward layouts. In general, noise levels in wards built since the year 2000 were lower than those in the older buildings.
Genome Sequences of 11 Human Vaginal
Actinobacteria
Strains
Authors: Lewis Amanda L. , Deitzler Grace E. , Ruiz Maria J. , Weimer Cory , Park SoEun , Robinson Lloyd S. , Hallsworth-Pepin Kymberlie , Wollam Aye , Mitreva Makedonka , Lewis Warren G.
Published: September 2016

The composition of the vaginal microbiota is an important health determinant. Several members of the phylum
Actinobacteria
have been implicated in bacterial vaginosis, a condition associated with many negative health outcomes. Here, we present 11 strains of vaginal
Actinobacteria
(now available through BEI Resources) along with draft genome sequences.
Complete Genome Sequence of a
Myoviridae
Bacteriophage Infecting Salmonella enterica Serovar Typhimurium
Authors: Paradiso Rubina , Orsini Massimiliano , Bolletti Censi Sergio , Borriello Giorgia , Galiero Giorgio
Published: September 2016

The bacteriophage 118970_sal3 was isolated from water buffalo feces in southern Italy, exhibiting lytic activity against
Salmonella enterica
serovar Typhimurium. This bacteriophage belongs to the
Myoviridae
family and has a 39,464-bp double-stranded DNA (ds-DNA) genome containing 53 coding sequences (CDSs).
Complete Genome Sequence of a Lytic
Siphoviridae
Bacteriophage Infecting Several Serovars of Salmonella enterica
Authors: Paradiso Rubina , Lombardi Serena , Iodice Maria Grazia , Riccardi Marita Georgia , Orsini Massimiliano , Bolletti Censi Sergio , Galiero Giorgio , Borriello Giorgia
Published: September 2016

The bacteriophage 100268_sal2 was isolated from water buffalo feces in southern Italy, exhibiting lytic activity against several subspecies of
Salmonella enterica
. This bacteriophage belongs to the
Siphoviridae
family and has a 125,114-bp double-stranded DNA (ds-DNA) genome containing 188 coding sequences (CDSs).
Complete Genome Sequence of Gordonia terrae 3612
Authors: Russell Daniel A. , Guerrero Bustamante Carlos A. , Garlena Rebecca A. , Hatfull Graham F.
Published: September 2016

Here, we report the complete genome sequence of
Gordonia terrae
3612, also known by the strain designations ATCC 25594, NRRL B-16283, and NBRC 100016. The genome sequence reveals it to be free of prophage and clustered regularly interspaced short palindromic repeats (CRISPRs), and it is an effective host for the isolation and characterization of
Gordonia
bacteriophages.
Draft Genome Sequence of Bacillus litoralis C44, Isolated from Chinese Scholar Tree (
Sophora japonica
) Forest Soil
Authors: Lyu Weili , Wu Yunlong , Liu Ya , Lyu Zhitang
Published: September 2016

Bacillus litoralis
C44 can hydrolyze rutin to produce isoquercetin by the enzyme α-
l
-rhamnosidase. We report here the genome sequence and annotation result of strain C44. The genomic information will serve as references to the physiology, genetics, and evolution of this species and further genetic engineering research in this species.
Draft Genome Sequence of Salmonella enterica subsp.
enterica
Serovar Orion Strain CRJJGF_00093 (Phylum
Gammaproteobacteria
)
Authors: Gupta Sushim K. , McMillan Elizabeth A. , Jackson Charlene R. , Desai Prerak T. , Porwollik Steffen , McClelland Michael , Hiott Lari M. , Humayoun Shaheen B. , Frye Jonathan G.
Published: September 2016

Here, we report a 4.70-Mbp draft genome sequence of
Salmonella enterica
subsp.
enterica
serovar Orion strain CRJJGF_00093, isolated from a dog in 2005.
Peripheral nerve involvement in classic homocystinuria: an unusual association
Authors: Oliveira Santos Miguel , Geraldes Ruth , Conceição Isabel
Published: September 2016

Classic homocystinuria is one of the most common causes of hereditary hyperhomocysteinemia. It is an autosomal recessive and multisystemic disorder due to cystathionine β-synthase deficiency. We described a case of an 18-year-old Portuguese man with an ischaemic stroke, who was subsequently diagnosed with classic homocystinuria [Thr191Met (c.572C>T)CBSmutation] associated with a sensorimotor neuropathy. The patient had a good clinical and metabolic response to pyridoxine plus methionine-restricted diet after 12 months of treatment. Neurophysiological re-evaluation with nerve conduction studies disclosed an improvement on the peripheral nerve lesion. Central nervous system manifestations in classic homocystinuria have been well documented, but this is to the best of our knowledge the first report of an association with peripheral neuropathy, which improved after hyperhomocysteinemia treatment.
Structural equation model for estimating risk factors in type 2 diabetes mellitus in a Middle Eastern setting: evidence from the STEPS Qatar
Authors: Roman-Urrestarazu Andres , Ali Faleh Mohamed Hussain , Reka Husein , Renwick Matthew J , Roman Gabriela D , Mossialos Elias
Published: September 2016

Aims

Understanding type 2 diabetes mellitus is critical for designing effective diabetes prevention policies in Qatar and the Middle East.

Methods

Using the Qatar 2012 WHO STEPwise approach to surveillance survey, a subsample of 1224 Qatari participants aged 18–64 years was selected. Subjects had their fasting blood glucose levels tested, had not been diagnosed with or treated for diabetes, had a fasting time >12 hours and were not pregnant. We applied a hypothesized structural equation model (SEM) to assess sociodemographic, behavioral, anthropometric and metabolic variables affecting persons with type 2 diabetes mellitus.

Results

There is a direct effect of triglyceride levels (0.336) and body mass index (BMI) (0.164) on diabetes status. We also found that physical activity levels negatively affect BMI (−0.148) and positively affect high-density lipoprotein (HDL) (0.106); sociodemographic background negatively affects diet (−0.522) and BMI (−0.352); HDL positively affects total cholesterol (0.230) and has a negative effect on BMI (−0.108), triglycerides (−0.128) and waist circumference (−0.104). Diet has a positive effect on triglycerides (0.281) while family history of diabetes negatively affects total cholesterol (−0.104). BMI has a positive effect on waist circumference (0.788) and mediates the effects of physical activity over diabetes status (−0.028). BMI also mediates the effects that sociodemographic factors (−0.058) and physical activity (−0.024) have on diabetes status. BMI and HDL (−0.002) together mediate the effect of physical activity on diabetes status and similarly HDL and tryglycerides (−0.005) also mediate the effect of physical activity on diabetes status. Finally diet and tryglycerides mediate the effects that sociodemographic factors have on diabetes status (−0.049).

Conclusions

This study's main finding is that triglyceride levels and BMI are the main variables directly affecting diabetes status in the Qatari population.
Guidelines of the International Federation of Red Cross and Red Crescent Societies: an overview and quality appraisal using AGREE II
Authors: Vande veegaete Axel , Borra Vere , De Buck Emmy , Vandekerckhove Philippe
Published: September 2016

Objectives

To appraise the quality of guidelines developed by the International Federation of Red Cross and Red Crescent Societies (IFRC) between 2001 and 2015.

Study design

Cross-sectional.

Methods

2 authors independently assessed the quality of IFRC guidelines using the Appraisal of Guidelines for Research and Evaluation (AGREE II) instrument. Average domain scores were calculated and overall quality scores and recommendation for use were determined.

Results

Out of 77 identified guidelines, 27 met the inclusion criteria and were assessed. The domains with the highest average scores across guidelines were ‘scope and purpose’, ‘clarity of presentation’ and ‘applicability’. The lowest scoring domains were ‘rigour of development’ and ‘editorial independence’. No guideline can be ‘recommended for immediate use’, 23 guidelines are ‘recommended with modifications’ and 4 guidelines are ‘not recommended’.

Conclusions

The IFRC produces guidelines that should be adhered to by millions of staff and volunteers in 190 countries. These guidelines should therefore be of high quality. Up until now, the IFRC had no uniform guideline development process. The results of the AGREE II appraisal indicate that the quality of the guidelines needs to be improved.
Evidence-based interventions to reduce adverse events in hospitals: a systematic review of systematic reviews
Authors: Zegers Marieke , Hesselink Gijs , Geense Wytske , Vincent Charles , Wollersheim Hub
Published: September 2016

Objective

To provide an overview of effective interventions aimed at reducing rates of adverse events in hospitals.

Design

Systematic review of systematic reviews.

Data sources

PubMed, CINAHL, PsycINFO, the Cochrane Library and EMBASE were searched for systematic reviews published until October 2015.

Study selection

English-language systematic reviews of interventions aimed at reducing adverse events in hospitals, including studies with an experimental design and reporting adverse event rates, were included. Two reviewers independently assessed each study's quality and extracted data on the study population, study design, intervention characteristics and adverse patient outcomes.

Results

Sixty systematic reviews with moderate to high quality were included. Statistically significant pooled effect sizes were found for 14 types of interventions, including: (1) multicomponent interventions to prevent delirium; (2) rapid response teams to reduce cardiopulmonary arrest and mortality rates; (3) pharmacist interventions to reduce adverse drug events; (4) exercises and multicomponent interventions to prevent falls; and (5) care bundle interventions, checklists and reminders to reduce infections. Most (82%) of the significant effect sizes were based on 5 or fewer primary studies with an experimental study design.

Conclusions

The evidence for patient-safety interventions implemented in hospitals worldwide is weak. The findings address the need to invest in high-quality research standards in order to identify interventions that have a real impact on patient safety. Interventions to prevent delirium, cardiopulmonary arrest and mortality, adverse drug events, infections and falls are most effective and should therefore be prioritised by clinicians.
Elevated levels of autophagy-related marker ULK1 and mitochondrion-associated autophagy inhibitor LRPPRC are associated with biochemical progression and overall survival after androgen deprivation therapy in patients with metastatic prostate cancer
Authors: Zhang Hong-Yi , Ma Ya-Dong , Zhang Ye , Cui Jie , Wang Zi-Ming
Published: September 2016

Aim

To evaluate the expression levels and prognostic significance of autophagy-related markers, UNC-51-like kinase1 (ULK1), Beclin1, microtubule-associated protein light chain 3 (LC3), autophagy-related gene 5 (ATG5) and mitochondrion-associated autophagy inhibitor, LRPPRC, in patients with metastatic prostate cancer (PCa) after androgen deprivation therapy (ADT).

Methods

Expressions of ULK1, Beclin1, LC3, ATG5 and LRPPRC were assessed by immunohistochemical examination in 198 patients with metastatic PCa who were receiving ADT (goserelin and bicalutamide).

Results

High expression levels of LRPPRC and ULK1were significantly associated with Gleason score, serum prostate-specific antigen (PSA) levels, PSA levels after ADT and number of metastatic sites. High expression of ULK1 in patients with concomitant high expression of LRPPRC was significantly associated with multiple metastases, shorter biochemical progression (BCP)-free survival and shorter overall survival (OS). ULK1 expression, LRPPRC expression, Gleason score, PSA levels after ADT and number of metastatic sites were independently associated with shorter BCP-free survival and OS on multivariate analysis. Furthermore, two-year BCP rate of patients with ≥3 risk factors was found to be significantly higher as compared with that of patients with ≤1 and 2 risk factors. Three-year OS rate in patients with ≥3 risk factors was significantly lower than that of those with ≤1 and 2 risk factors.

Conclusions

High expression of ULK1 concomitant with high expression of LRPPRC may serve as useful markers for shorter BCP-free survival and OS in patients with metastatic PCa after ADT.