bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated image segmentation of haematoxylin and eosin stained skeletal muscle cross‐sections
Authors: LIU F. , MACKEY A.L. , SRIKUEA R. , ESSER K.A. , YANG L.
Published: October 2013

The ability to accurately and efficiently quantify muscle morphology is essential to determine the physiological relevance of a variety of muscle conditions including growth, atrophy and repair. There is agreement across the muscle biology community that important morphological characteristics of muscle fibres, such as cross‐sectional area, are critical factors that determine the health and function (e.g. quality) of the muscle. However, at this time, quantification of muscle characteristics, especially from haematoxylin and eosin stained slides, is still a manual or semi‐automatic process. This procedure is labour‐intensive and time‐consuming. In this paper, we have developed and validated an automatic image segmentation algorithm that is not only efficient but also accurate. Our proposed automatic segmentation algorithm for haematoxylin and eosin stained skeletal muscle cross‐sections consists of two major steps: (1) A learning‐based seed detection method to find the geometric centres of the muscle fibres, and (2) a colour gradient repulsive balloon snake deformable model that adopts colour gradient in colour space. Automatic quantification of muscle fibre cross‐sectional areas using the proposed method is accurate and efficient, providing a powerful automatic quantification tool that can increase sensitivity, objectivity and efficiency in measuring the morphometric features of the haematoxylin and eosin stained muscle cross‐sections.
Efficacy of narrowband ultraviolet phototherapy on renal pruritus
Authors: Wang Tsae‐Jyy , Lan Li‐Ching , Lu Chia‐Sheng , Lin Kuan‐Chia , Tung Heng‐Hsing , Wu Shu‐Fang Vivienne , Liang Shu‐Yuan
Published: October 2013

Aims and objectives

To test the efficacy of narrowband ultraviolet B phototherapy in reducing renal pruritus.

Background

Renal pruritus is a disabling symptom affecting approximately 50% of patients undergoing maintenance haemodialysis. Managing refractory pruritus can be a great challenge for healthcare providers and patients as well. For patients who do not respond to conventional treatments, ultraviolet B phototherapy is considered the treatment of choice. Few investigators, however, have studied the efficacy of narrowband ultraviolet B phototherapy in this condition.

Design

The study was based on a quasi‐experimental design with repeated measures.

Methods

A convenience sample of 42 haemodialysis patients with pruritus was recruited from haemodialysis units of a general hospital in Taipei, Taiwan. Two groups were created according to the dates of haemodialysis. The intervention participants received narrowband ultraviolet B phototherapy three times a week for two weeks. The control participants were maintained on their prior pruritus treatment. The pruritus intensity was measured with a numerical rating scale at baseline and on alternating days for seven times. Data were collected during the year 2008.

Results

The generalised estimating equation showed statistically significant group‐by‐time interactions in pruritus intensity. Using the control group as the reference group and baseline as the reference time, the intervention group had significantly lower pruritus intensity than the control group: 3·14 (p < 0·001) at time seven, 1·71 (p < 0·001) at time six and 1·24 at time five (p < 0·001). The group‐by‐time interactions were statistically significant after four sessions of narrowband‐UVB irradiation.

Conclusion

The study findings support the efficacy of narrowband ultraviolet B phototherapy in alleviating renal pruritus.

Relevance to clinical practice

Clinicians may consider prescribing phototherapy for haemodialysis patients who have intractable renal pruritus and do not respond to conventional treatments.
Spinal muscular atrophy type I: Do the benefits of ventilation compensate for its burdens?
Authors: Gray Kelly , Isaacs David , Kilham Henry A , Tobin Bernadette
Published: October 2013

We report the progress of an 8‐year‐old child with spinal muscular atrophy (SMA) type 1. The parents elected in infancy that the child should be on long‐term ventilation, but all attempts to establish this care at home have failed, so the child remains ventilated in the hospital. The leader of the long‐term ventilation team reports on the child's progress and describes a week in the child's life. Two paediatricians argue that the benefits of long‐term ventilation have not and do not compensate the child for the burdens imposed on her by this treatment and explain why they would not support the withdrawal of long‐term ventilation now. They argue that long‐term ventilation might have been avoided by applying to a court of law when the child was an infant. An ethicist discusses ethical aspects of decision‐making in SMA type 1.
Using Syndromic Surveillance to Estimate Baseline Rates for Healthcare‐Associated Infections in Critical Care Units of Small Animal Referral Hospitals
Authors: Ruple‐Czerniak A. , Aceto H.W. , Bender J.B. , Paradis M.R. , Shaw S.P. , Van Metre D.C. , Weese J.S. , Wilson D.A. , Wilson J.H. , Morley P.S.
Published: October 2013

Background

Expected rates of healthcare‐associated infections (HCAI) have not been established in veterinary hospitals. Baseline rates are critically needed as benchmarks for quality animal care.

Objective

To estimate the occurrence of events related to HCAI identified using a standardized syndromic surveillance system in small animals in critical care cases at referral hospitals.

Animals

Weaned dogs and cats (n = 1,951) that were hospitalized in the critical care unit of referral teaching hospitals during a 12‐week period.

Methods

Multicenter, prospective longitudinal study. A survey was completed for all enrolled animals to record basic demographics, information about procedures and treatments that animals received, and to document the occurrence of defined nosocomial syndromes. Data were analyzed to identify risk factors associated with the occurrence of these nosocomial syndromes.

Results

Controlling for hospital of admission, 16.3% of dogs (95% confidence intervals [CI], 14.3–18.5) and 12% of cats (95% CI, 9.3–15.5) were reported to have had ≥1 nosocomial syndrome occur during hospitalization. Risk factors found to have a positive association with the development of a nosocomial syndrome were longer hospital stays, placement of a urinary catheter, surgical procedures being performed, and the administration of antiulcer medications and antimicrobial drugs excluding those given perioperatively.

Conclusions and Clinical Importance

Syndromic surveillance systems can be successfully standardized for use across multiple hospitals to effectively collect data pertinent to HCAI rates and risk factors for occurrence.
Creating Room for Manoeuvre: a Strategy to Generate Political Budget Cycles under Fiscal Rules
Authors: Benito Bernardino , Bastida Francisco , Vicente Cristina
Published: October 2013

We examine the effect of a balanced budget rule on the local political budget cycle. Specifically, we pay attention to the evolution of budget deficit, taxes and capital spending around elections. Using a sample of the Spanish largest municipalities in 1994–2009, we find that the balanced budget rule has not dampened the political budget cycle in budget deficit. Therefore, our results indicate that although governments are constrained by such rule they engage in electoral‐induced fiscal manipulation. In non‐electoral years, they create room for manoeuvre to implement expansionary fiscal policies in electoral years. Specifically, there is saving in the pre‐electoral year and deficit increase in the electoral year. This has been achieved largely through tax and fee increases during the pre‐electoral year and by shifting the bulk of the capital spending increased from the pre‐electoral year to the election year. Furthermore, our findings indicate that the balanced budget rule has succeeded in limiting the budget deficit.
Right‐Wing Extremism and the Well‐Being of Immigrants
Authors: Knabe Andreas , Rätzel Steffen , Thomsen Stephan L.
Published: October 2013

This study analyzes the effects of right‐wing extremism on the well‐being of immigrants based on data from the German Socio‐Economic Panel (SOEP) for the years 1984 to 2006 merged with state‐level information on election outcomes. The results show that the life satisfaction of immigrants is significantly reduced if right‐wing extremism in the native‐born population increases. Moreover, the life satisfaction of highly educated immigrants is affected more strongly than that of low‐skilled immigrants. This supports the view that policies aimed at making immigration more attractive to the high‐skilled have to include measures that reduce xenophobic attitudes in the native‐born population.
Violence and Insecurity in Mexico: Guidelines for a New Strategy on Public Safety
Authors: Herrera‐Lasso Luis
Published: October 2013

Mexico's public safety strategies have had serious flaws that may explain their limited success and that have led to an increase in violence and insecurity. The flaws in the Calderón administration resided in building a strategy with certain characteristics. It was based on the war against drug trafficking and not on building an integral plan for public safety. It had serious interinstitutional coordination problems. It was based on police action rather than on a plan where the politicians engaged in dialogue with the proponents of security policies. It was built from the top down, from the federal to the city level, where communities had little or no participation and where there was no coordination between city and state efforts and those at the federal level. It integrated the military into the public safety realm without taking into account the effects and consequences. It was unable to articulate efficiently efforts with foreign powers. Instead of noting ways to fight insecurity, this article concentrates on the conditions needed to create safety systems. We have created a model that considers 11 variables that lead to a propensity for violence and insecurity. Based on these variables, we arrive at some important conclusions for reformulating the national strategy for public safety.
Hyperammonaemia induces hepatic injury with alteration of gene expression profiles
Authors: Jia Bin , Yu Zu‐Jiang , Duan Zhen‐Feng , Lü Xin‐Quan , Li Jing‐Jing , Liu Xiao‐Rui , Sun Ran , Gao Xiao‐Juan , Wang Yan‐Fang , Yan Jing‐Ya , Kan Quan‐Cheng
Published: October 2013

Background

Hyperammonaemia is a serious metabolic disorder commonly observed in patients with hepatic failure. However, it is unknown whether hyperammonaemia has a direct adverse effect on the hepatocytes and thereby serves as both a cause and effect of hepatic failure.

Aims

The purposes were to determine whether hepatic injury can be caused by hyperammonaemia, and if so, screen the key genes involved in hyperammonaemia.

Methods

Hyperammonaemic rats were established via intragastric administration of the ammonium chloride solution. The liver tissues were assessed via biochemistry, histology, immunohistochemistry and microarray analysis. Selected genes were confirmed by quantitative RT‐PCR.

Results

Administration of the ammonium chloride caused the hyperammonaemia, accompanied with the changes of plasma markers indicating hepatic injury. A pathological assessment demonstrated increased apoptosis and higher level of cyclin D1 and cyclin A in hyperammonaemic rat liver. Microarray was performed on the liver samples and 198 differentially expressed genes were identified in hyperammonaemic rats and validated by quantitative RT‐PCR. These genes were associated with many vital functional classes and belonged to different signal transduction pathways.

Conclusions

This study demonstrates that hyperammonaemia can directly induce hepatic injury via the hepatocyte apoptosis. Gene expression profile may provide the possible explanations and mechanisms for the hepatic injury induced by hyperammonaemia.
Review: Neuropathological features of unexplained sudden unexpected death in infancy: current evidence and controversies
Authors: Paine Simon ML , Jacques Thomas S , Sebire Neil J
Published: October 2013

Sudden infant death syndrome (SIDS) is a leading cause of postneonatal infant death in the developed world. The cause of SIDS is unknown but several hypotheses have been proposed, including the ‘triple risk hypothesis’, which predicts that foetal development of infants who subsequently succumb to SIDS is abnormal, leaving them unable to respond appropriately to stressors. Consistent with this hypothesis, a large number of studies have reported changes in the brain in SIDS. However, on nearly every subject, the reported findings vary widely between studies. Inconsistencies in the definitions of SIDS used and in control group selection are likely to underlie much of this variability. Therefore, in our analysis, we have included only those studies that met simple criteria for both the definition of SIDS and the control group. Of the 153 studies retrieved by our review of the literature, 42 (27%) met these criteria. Foremost among the findings reported by these studies are abnormalities of the brain stem, in particular brain stem gliosis and defects of neurotransmission in the medulla. However, these studies have not identified what could be considered in diagnostic terms a causative structural or biochemical abnormality for use in routine clinical practice. An assessment of changes in the architecture and composition of brain regions and changes in neurotransmission in multiple systems in a single, large cohort of well‐ and consistently characterized infants dying suddenly of a range of causes is needed before the inter‐relation of these different features can be appreciated.
Anti‐coagulation, anti‐platelets or no therapy in haemodialysis patients with atrial fibrillation: A decision analysis
Authors: Wyld Melanie LR , Clayton Philip A , Morton Rachael L , Chadban Steven J
Published: October 2013

Background

Optimal treatment of atrial fibrillation (AF) in the haemodialysis population is uncertain due to the exclusion of this group from randomized trials. The risk‐benefit profile for anticoagulation and anti‐platelet therapy in haemodialysis differs from the general population due to platelet dysfunction from uraemia, altered pharmacokinetics and increased falls risk.

Methods

This decision analysis used aMarkov‐state transition model that took a patient perspective over a 5 year timeframe. TheMarkov model compared life‐years gained and quality‐adjusted life‐years gained (QALY) for threeAFtreatment strategies: warfarin, aspirin and no treatment. The base case was a 70‐year‐old man on haemodialysis with non‐valvularAF.

Results

In the base case, the total health outcomes in life‐years andQALYwere 2.37 and 1.47 respectively for warfarin, 2.38 and 1.61 respectively for aspirin, and 2.39 and 1.61 respectively for no treatment. Thus, warfarin led to 0.14 fewerQALYor 1.7 fewer months of life lived in full health, compared with either aspirin or no therapy. The finding that warfarin generated the lowest expectedQALYwas robust to one‐way, two‐way and probabilistic sensitivity analyses.

Conclusions

Our results suggest that warfarin should not be the default choice for older haemodialysis patients with non‐valvularAFas it provides the fewestQALYcompared with aspirin or no therapy.
Challenges in interpreting allergen microarrays in relation to clinical symptoms: A machine learning approach
Authors: Prosperi Mattia C. F. , Belgrave Danielle , Buchan Iain , Simpson Angela , Custovic Adnan
Published: October 2013

Background

Identifying different patterns of allergens and understanding their predictive ability in relation to asthma and other allergic diseases is crucial for the design of personalized diagnostic tools.

Methods

Allergen‐IgE screening using ImmunoCAP ISAC® assay was performed at age 11 yrs in children participating a population‐based birth cohort. Logistic regression (LR) and nonlinear statistical learning models, including random forests (RF) and Bayesian networks (BN), coupled with feature selection approaches, were used to identify patterns of allergen responses associated with asthma, rhino‐conjunctivitis, wheeze, eczema and airway hyper‐reactivity (AHR, positive methacholine challenge). Sensitivity/specificity and area under the receiver operating characteristic (AUROC) were used to assess model performance via repeated validation.

Results

Serum sample for IgE measurement was obtained from 461 of 822 (56.1%) participants. Two hundred and thirty‐eight of 461 (51.6%) children had at least one of 112 allergen components IgE > 0 ISU. The binary threshold >0.3 ISU performed less well than using continuous IgE values, discretizing data or using other data transformations, but not significantly (p = 0.1). With the exception of eczema (AUROC~0.5), LR, RF and BN achieved comparable AUROC, ranging from 0.76 to 0.82. Dust mite, pollens and pet allergens were highly associated with asthma, whilst pollens and dust mite with rhino‐conjunctivitis. Egg/bovine allergens were associated with eczema.

Conclusions

After validation, LR, RF and BN demonstrated reasonable discrimination ability for asthma, rhino‐conjunctivitis, wheeze and AHR, but not for eczema. However, further improvements in threshold ascertainment and/or value transformation for different components, and better interpretation algorithms are needed to fully capitalize on the potential of the technology.
Current Evidence of Percutaneous Nucleoplasty for the Cervical Herniated Disk: A Systematic Review
Authors: Wullems Jorgen A. , Halim Willy , van der Weegen Walter
Published: October 2013

Background

Although percutaneous cervical nucleoplasty (PCN) has been shown to be both safe and effective, its application is still debated. PCN applied in disk herniation has not been systematically reviewed before, resulting in a limited insight into its effectiveness and safety, and the quality of available evidence. Therefore, we systematically reviewed the evidence on the efficacy and safety of PCN in patients with a (contained) herniated disk.

Methods

MEDLINE, EMBASE, and the Cochrane Library (Central Register of Controlled Trials) were searched for randomized controlled trials (RCTs) and nonrandomized studies using the following keywords: “Nucleoplasty,” “Cervical,” “Hernia,” “Herniation,” “Prolapse,” “Protrusion,” “Intervertebral disk,” and “Percutaneous disk decompression.” First, all articles were appraised for methodological quality, and then, RCTs were graded for the level of evidence according a best‐evidence synthesis, because a meta‐analysis was not possible. Finally, the RCTs' applicability and clinical relevance also was assessed.

Results

Of 75 identified abstracts, 10 full‐text articles were included (3 RCTs and 7 nonrandomized studies). These studies represented a total of 1021 patients: 823 patients (≥ 892 disks) were treated by PCN. All studies showed low methodological quality, except for two. The level of evidence of the RCTs was graded as moderate, with low to moderate applicability and clinical relevance.

Conclusion

All included studies showed PCN to be an effective and safe procedure in the treatment of (contained) herniated disks at short‐, mid‐, and long‐term follow‐up. However, the level of evidence is moderate and shows only low to moderate applicability and clinical relevance.
Estimates of variance components and repeatability for total forage yield in rye: implications for breeding
Authors: Webb Stephen L. , Mosali Jagadeesh , Baker Jerry L. , Newell Mark A.
Published: October 2013

Cereal rye (Secale cereale L.) is an important forage crop in the USA for stocker cattle (Bos sp.) production, thus making forage yield an important breeding objective for the crop. However, little information is known about the repeatability for forage yield in this crop. The objectives of this research were to: (i) estimate variance components for forage yield from long‐term variety trials, (ii) estimate the repeatability for forage yield and (iii) relate this to breeding strategies for increased forage yield in rye. Trials were conducted over 14 years where 97 USA open‐pollinated varieties (OPVs) were evaluated. Repeatability ranged from 0.57 to 0.86 when the data were analysed by year for the 3 years with significant genotype main effects. Possible explanations for the lack of significant genotype main effects are discussed. Practical implications of these findings indicate that the development of improved cultivars with greater forage yield will require improved methods of selection based on family performance rather than the current methods based primarily on single plant visual selection.
Immunology of lymphatic filariasis
Authors: Babu S. , Nutman T. B.
Published: October 2013

The immune responses to filarial parasites encompass a complex network of innate and adaptive cells whose interaction with the parasite underlies a spectrum of clinical manifestations. The predominant immunological feature of lymphatic filariasis is an antigen‐specific Th2 response and an expansion of IL‐10 producing CD4+ T cells that is accompanied by a muted Th1 response. This antigen‐specific T‐cell hyporesponsiveness appears to be crucial for the maintenance of the sustained, long‐standing infection often with high parasite densities. While the correlates of protective immunity to lymphatic filariasis are still incompletely understood, primarily due to the lack of suitable animal models to study susceptibility, it is clear that T cells and to a certain extent B cells are required for protective immunity. Host immune responses, especially CD4+ T‐cell responses clearly play a role in mediating pathological manifestations of LF, including lymphedema, hydrocele and elephantiasis. The main underlying defect in the development of clinical pathology appears to be a failure to induce T‐cell hyporesponsiveness in the face of antigenic stimulation. Finally, another intriguing feature of filarial infections is their propensity to induce bystander effects on a variety of immune responses, including responses to vaccinations, allergens and to other infectious agents. The complexity of the immune response to filarial infection therefore provides an important gateway to understanding the regulation of immune responses to chronic infections, in general.
U–Pb and Re–Os Geochronology of Karamay Porphyry Mo–Cu Deposit in Western Junggar, NW China
Authors: Wang Ran , Li Yong‐Jun , Han Xin , Wang Jun‐Nian , Yan Jing , Zhao Yu‐Mei
Published: October 2013

The Karamay porphyry Mo–Cu deposit, discovered in 2010, is located in the West Junggar region of Xinjiang of northwest China. The deposit is hosted within the Karamay granodiorite porphyry that intruded into Early Carboniferous sedimentary strata and its exo‐contact zone. The LA‐ICPMS U–Pb method was used to date the zircons from the granodiorite samples of the porphyry. Analyses of 12 spots of zircons from the granodiorite samples yield a U–Pb weighted mean age of 300.8 ± 2.1 Ma (2σ). Re–Os dating for five molybdenite samples obtained from two prospecting trenches and three outcrops in the deposit yield a Re–Os isochron age of 294.6 ± 4.6 Ma (2σ), with an initial 187Os/188Os of 0.0 ± 1.1. The isochron age is within the error of the Re–Os model ages, demonstrating that the age result is reliable. The Re–Os isochron age of the molybdenite is consistent with the U–Pb age of the granodiorite porphyry, which indicates that the deposit is genetically related with an Early Permian porphyry system. The ages of the Karamay Mo–Cu deposit and the ore‐bearing porphyry are similar to the ages of intermediate‐acid intrusions and Cu–Mo–Au polymetallic deposits in the West Junggar region. This consistency suggests the same geodynamic process to the magmatism and related mineralization.
Women, Children and Patience: Experimental Evidence from Indian Villages
Authors: Bauer Michal , Chytilová Julie
Published: October 2013

Researchers have observed that women in developing countries often make more development friendly choices than men. We implemented experimental tasks among a large and diverse sample of married individuals in rural India and found women to make on average more patient and more risk‐averse choices than men. We find important heterogeneity in gender differences in patience: there is no difference for spouses with no children but patience levels diverge if there are small children in a family. The findings imply that conflicting spousal preferences are most likely in poor families with children.
Regulatory Barriers and Entry into a New Competitive Industry
Authors: Bennett John , Estrin Saul
Published: October 2013

We model the effects of license fees and bureaucratic delay on firm entry into a new competitive industry, whose profitability is initially unknown. A license fee alone reduces the number of first movers and the steady‐state number of firms. The combination of license fee and delay may cause some entrepreneurs to purchase licenses speculatively, only using them to enter production later if profitability is revealed to be sufficiently favourable. Alternatively, some entrepreneurs may wait, possibly buying a license only after profitability is revealed; but it is never found that some entrepreneurs adopt one of these strategies and some the other.
Agricultural Productivity and Poverty Reduction in Nepal
Authors: Devkota Satis , Upadhyay Mukti
Published: October 2013

This paper provides for the first time a clear quantitative link between agricultural productivity and poverty among rural households in Nepal. Using data from a nationwide Nepal Living Standard Survey 2004, we first estimate household‐specific productivity per worker under both Cobb–Douglas and translog production functions. Second, the paper identifies the determinants of productivity. Third, we explore a theoretical link between productivity and poverty using Sen's poverty index and find empirically that productivity growth substantially helps poverty reduction. Finally, the integrated effects of changes in productivity determinants are found to be stronger than the outcomes of sectoral policies taken in isolation.
Effects of rocuronium bromide on globe position and respiratory function in isoflurane‐anesthetized dogs: a comparison between three different dosages
Authors: Briganti Angela , Barsotti Giovanni , Portela Diego A. , Di Nieri Camilla , Breghi Gloria
Published: October 2013

Objective

To evaluate the effect on globe position and respiration of three dosages of intravenous rocuronium in isoflurane‐anesthetized dogs.

Animal studied

Thirty‐two dogs anesthetized for ophthalmic procedures.

Procedures

The dogs were divided into four groups, each of eight animals (G1‐G4). G1, G2, G3 received 0.075, 0.05, 0.03 mg/kg of IV rocuronium, respectively; G4 received 0.9% NaCl IV; all the treatments were administered when an end‐tidal isoflurane of 1.1–1.2% was reached. Anesthesia was obtained with dexmedetomidine (2.5 mcg/kg IV), methadone (0.1 mg/kg IV), propofol (2 mg/kg IV), and isoflurane in oxygen. Neuromuscular function was assessed with acceleromyography by stimulation of the peroneal nerve using the train‐of‐four (ToF) and the ToF ratio (ToFR). Monitoring of cardiovascular and respiratory functions was performed. Changes in globe position were recorded.

Results

All three dosages of rocuronium produced centralization of the globe. Duration was 24.3 ± 4.2, 23.4 ± 3.6, and 8.7 ± 2.8 min, for G1, G2, and G3, respectively. The control group did not show globe centralization. No significant differences were found among the four groups in cardiovascular and respiratory parameters. Minute volume and ToFR were significantly lower in G1 compared with baseline values.

Conclusions

All doses of rocuronium resulted in globe centralization. The higher dose provoked a transient respiratory depression and some degree of skeletal muscular blockade detectable with ToFR. No alterations in respiratory activity were present when 0.05 mg/kg was used. The 0.03 mg/kg dosage could be useful for very short ophthalmic procedures.
An investigation to enhance understanding of the stimulation of weed seedling emergence by soil disturbance
Authors: Schutte B J , Tomasek B J , Davis A S , Andersson L , Benoit D L , Cirujeda A , Dekker J , Forcella F , Gonzalez‐Andujar J L , Graziani F , Murdoch A J , Neve P , Rasmussen I A , Sera B , Salonen J , Tei F , Tørresen K S , Urbano J M
Published: October 2013

Enhanced understanding of soil disturbance effects on weed seedling recruitment will help guide improved management approaches. Field experiments were conducted at 16 site‐years at 10 research farms across Europe and North America to (i) quantify superficial soil disturbance (SSD) effects on Chenopodium album emergence and (ii) clarify adaptive emergence behaviour in frequently disturbed environments. Each site‐year contained factorial combinations of two seed populations (local and common, with the common population studied at all site‐years) and six SSD timings [0, 50, 100, 150, 200 day‐degrees (d°C, base temperature 3°C) after first emergence from undisturbed soil]. Analytical units in this study were emergence flushes. Flush magnitudes (maximum weekly emergence per count flush) and flush frequencies (flushes year−1) were compared between disturbed and undisturbed seedbanks. One year after burial, SSD promoted seedling emergence relative to undisturbed seedbanks by increasing flush magnitude rather than increasing flush frequency. Two years after burial, SSD promoted emergence through increased flush magnitude and flush frequency. The promotional effects of SSD on emergence were strongest within 500 d°C following SSD; however, low levels of SSD‐induced emergence were detected as late as 3000 d°C following SSD. Accordingly, stale seedbed practices that eliminate weed seedlings should occur within 500 d°C of disturbance, because few seedlings emerge after this time. However, implementation of stale seedbed practices will probably cause slight increases in weed population densities throughout the year. Compared with the common population, local populations exhibited reduced variance in total emergence measured within sites and across SSD treatments, suggesting that C. album adaptation to local pedo‐climatic conditions involves increased consistency in SSD‐induced emergence.
Single‐stage application of a novel decellularized dermis for treatment‐resistant lower limb ulcers: Positive outcomes assessed by SIAscopy, laser perfusion, and 3D imaging, with sequential timed histological analysis
Authors: Greaves Nicholas S. , Benatar Brian , Baguneid Mohamed , Bayat Ardeshir
Published: October 2013

We present results of an original clinical study investigating efficacy of a decellularized dermal skin substitute (DCD) as part of a one‐stage therapeutic strategy for recalcitrant leg ulcers. Twenty patients with treatment‐resistant ulcers underwent hydrosurgical debridement, after which DCD was applied and covered with negative pressure dressings for 1 week. Participants were reviewed on seven occasions over 6 months. 3D photography, full‐field laser perfusion imaging, spectrophotometric intracutaneous analysis, and sequential biopsies were used to monitor healing. Mean ulcer duration and surface area prior to DCD placement were 4.76 years (range 0.25–40 years) and 13.11 cm2 (range 1.06–40.75 cm2), respectively. Seventy percent of ulcers were venous. Surface area decreased in all patients after treatment (range 23–100%). Mean reduction was 87% after 6 months, and 60% of patients healed completely. Wound bed hemoglobin flux increased significantly 6 weeks after treatment (p = 0.005). Histological and immunohistochemical analysis confirmed progressive DCD integration with colonization by host fibroblasts, lymphocytes, and neutrophils, resulting in fibroplasia, reepithelialisation, and angiogenesis, with correlating raised CD31, collagen I, and collagen III levels. Subgroup analysis showed differing cellular behavior depending on wound duration, with delayed angiogenesis, reduced collagen deposition, and smaller reductions in surface area in ulcers present for over 1 year. The stain intensities of immunohistochemical markers including fibronectin, collagen, and CD31 differed depending on depth from the wound surface and presence of intact epithelium. DCD safely produced significant improvement in treatment‐resistant leg ulcers. With no requirement for hospital admission, anesthetic, or autogenic skin grafting, this treatment could be administered in hospital and community settings.
Combined Kinetic Monte Carlo—Molecular Dynamics Approach for Modeling Phonon Transport in Quantum Dot Superlattices
Authors: Zuckerman Neil , Lukes Jennifer R.
Published: October 2013

A new kinetic Monte Carlo method for modeling phonon transport in quantum dot superlattices is presented. The method uses phonon scattering phase functions and cross sections to describe collisions between phonons and quantum dots. The phase functions and cross sections are generated using molecular dynamics simulation, which is capable of including atomistic effects otherwise unavailable in Monte Carlo approaches. The method is demonstrated for a test case featuring a Si-Ge quantum dot superlattice, and the model is compared against published experiments. It is found that molecular dynamics-derived cross sections must be weighted by diffuse mismatch model-type weighting factors in order to satisfy detailed balance considerations. Additionally, it is found that thin alloy “base layer” films strongly reduce thermal conductivity in these systems and must be included in the modeling to obtain agreement with published experimental data.
EWPL CP System: A Case Study
Authors: Vyas Sandeep H.
Published: October 2013

Reliance Gas Transportation Infrastructure Limited (RGTIL) is operating its prestigious East-West Gas pipeline (EWPL), since 2008–2009; project comprising of 48” dia. 1375 km long trunk pipeline, with 11 nos of compressor stations and several spur lines of different diameters varying from 10” to 30”.

Cathodic Protection (CP) system for buried pipeline, piping and structures is critical for ensuring protection against external corrosion due to environmental interaction. For successful implementation of CP system from day one of pipeline laying; planning and considerations starts at conceptual stage of project itself, then proper planning, design and implementation to follow.

Other than considerable length and diameter of pipeline; uniqueness for EWPL CP requirements are in form of 3 nos. Micro-tunnel crossings, 11 nos of Compressor stations (CS) with underground piping, more than 100 cased crossings, several HDD, third-party pipelines, AC & DC Railway traction crossings and pipeline passing through different geography from East to West.

Paper discusses the implementation of CP system for EWPL; highlighting critical points for execution of the job in each phase from Engineering till commissioning and O&M, CS CP system, CP for pipe within Micro-tunnelling, several interference and mitigation actions, post-commissioning surveys etc.
Design Challenges and Technological Advancement: A Case Study of Pipeline Through Sand Dunes (in Thar Desert)
Authors: Kumar Raj , Gunjiyal M. S. , Sinha Nitesh
Published: October 2013

This paper highlights the design challenges encountered during the project execution phase of HMPL’s Mundra - Bathinda Pipeline (MBPL), a crude import pipeline for feeding Guru Gobind Singh Refinery of HMEL at Bathinda in Punjab State. For the first time in India, a cross-country pipeline was planned through a terrain wherein section of more than 270 km length runs through the eastern fringe of Thar desert in the state of Rajasthan. MBPL routed in newer and exotic expanse of Great Indian Thar desert posed greater challenges in respect of pipeline routing, design and construction.

The pipeline route across the bygone desert is characterized by severe climate and remote locations. The summer daytime temperature reaches upto 50 deg C while in winter it drops to near freezing temperature. Sand dunes at some places along the route were more than 40 m high and were of different kinds and separated by inter-dunal sandy plains of varying stretches.
Evaluation of an aSi‐EPID with flattening filter free beams: Applicability to the GLAaS algorithm for portal dosimetry and first experience for pretreatment QA of RapidArc
Authors: Nicolini G. , Clivio A. , Vanetti E. , Krauss H. , Fenoglietto P. , Cozzi L. , Fogliata A.
Published: October 2013

Purpose:

To demonstrate the feasibility of portal dosimetry with an amorphous silicon mega voltage imager for flattening filter free (FFF) photon beams by means of the GLAaS methodology and to validate it for pretreatment quality assurance of volumetric modulated arc therapy (RapidArc).

Methods:

The GLAaS algorithm, developed for flattened beams, was applied to FFF beams of nominal energy of 6 and 10 MV generated by a Varian TrueBeam (TB). The amorphous silicon electronic portal imager [named mega voltage imager (MVI) on TB] was used to generate integrated images that were converted into matrices of absorbed dose to water. To enable GLAaS use under the increased dose‐per‐pulse and dose‐rate conditions of the FFF beams, new operational source‐detector‐distance (SDD) was identified to solve detector saturation issues. Empirical corrections were defined to account for the shape of the profiles of the FFF beams to expand the original methodology of beam profile and arm backscattering correction. GLAaS for FFF beams was validated on pretreatment verification of RapidArc plans for three different TB linacs. In addition, the first pretreatment results from clinical experience on 74 arcs were reported in terms of γ analysis.

Results:

MVI saturates at 100 cm SDD for FFF beams but this can be avoided if images are acquired at 150 cm for all nominal dose rates of FFF beams. Rotational stability of the gantry‐imager system was tested and resulted in a minimal apparent imager displacement during rotation of 0.2 ± 0.2 mm at SDD = 150 cm. The accuracy of this approach was tested with three different Varian TrueBeam linacs from different institutes. Data were stratified per energy and machine and showed no dependence with beam quality and MLC model. The results from clinical pretreatment quality assurance, provided a gamma agreement index (GAI) in the field area for six and ten FFF beams of (99.8 ± 0.3)% and (99.5 ± 0.6)% with distance to agreement and dose difference criteria set to 3 mm/3% with 2 mm/2% thresholds, GAI resulted (95.7.0 ± 2.3)% and (97.2 ± 2.1)%.

Conclusions:

The GLAaS methodology, introduced in clinical practice for conventional flattened photon beams for machine, IMRT, and RapidArc quality assurance, was successfully adapted for FFF beams of Varian TrueBeam Linac. The detector saturation effects could be eliminated if the portal images acquired at 150 cm for all nominal dose rates of FFF beams.
A Complete Skull from Dmanisi, Georgia, and the Evolutionary Biology of Early
Homo
Authors: Lordkipanidze David , Ponce de León Marcia S. , Margvelashvili Ann , Rak Yoel , Rightmire G. Philip , Vekua Abesalom , Zollikofer Christoph P. E.
Published: October 2013

A Heady Find

In the past two decades, excavations at the archaeological site at Dmanisi, Georgia, have revealed hominin fossils from the earliest Pleistocene, soon after the genus
Homo first
dispersed beyond Africa.

Lordkipanidze
et al.

(p.
326
; see the cover) now describe a fossil cranium from the site. Combined with mandibular remains that had been found earlier, this find completes the first entire hominin skull from this period.
Sleep Drives Metabolite Clearance from the Adult Brain
Authors: Xie Lulu , Kang Hongyi , Xu Qiwu , Chen Michael J. , Liao Yonghong , Thiyagarajan Meenakshisundaram , O’Donnell John , Christensen Daniel J. , Nicholson Charles , Iliff Jeffrey J. , Takano Takahiro , Deane Rashid , Nedergaard Maiken
Published: October 2013

Taking Out the Trash

The purpose of sleep remains mysterious. Using state-of-the-art in vivo two-photon imaging to directly compare two arousal states in the same mouse,

Xie
et al.

(p.
373
; see the Perspective by

Herculano-Houzel

) found that metabolic waste products of neural activity were cleared out of the sleeping brain at a faster rate than during the awake state. This finding suggests a mechanistic explanation for how sleep serves a restorative function, in addition to its well-described effects on memory consolidation.
Genomically Recoded Organisms Expand Biological Functions
Authors: Lajoie Marc J. , Rovner Alexis J. , Goodman Daniel B. , Aerni Hans-Rudolf , Haimovich Adrian D. , Kuznetsov Gleb , Mercer Jaron A. , Wang Harris H. , Carr Peter A. , Mosberg Joshua A. , Rohland Nadin , Schultz Peter G. , Jacobson Joseph M. , Rinehart Jesse , Church George M. , Isaacs Farren J.
Published: October 2013

Changing the Code

Easily and efficiently expanding the genetic code could provide tools to genome engineers with broad applications in medicine, energy, agriculture, and environmental safety.

Lajoie
et al.

(p.
357
) replaced all known UAG stop codons with synonymous UAA stop codons in
Escherichia coli
MG1655, as well as release factor 1 (RF1; terminates translation at UAG), thereby eliminating natural UAG translation function without impairing fitness. This made it possible to reassign UAG as a dedicated codon to genetically encode nonstandard amino acids while avoiding deleterious incorporation at native UAG positions. The engineered
E. coli
incorporated nonstandard amino acids into its proteins and showed enhanced resistance to bacteriophage T7. In a second paper,

Lajoie
et al.

(p.
361
) demonstrated the recoding of 13 codons in 42 highly expressed essential genes in
E. coli.
Codon usage was malleable, but synonymous codons occasionally were nonequivalent in unpredictable ways.
Electron-Hole Diffusion Lengths Exceeding 1 Micrometer in an Organometal Trihalide Perovskite Absorber
Authors: Stranks Samuel D. , Eperon Giles E. , Grancini Giulia , Menelaou Christopher , Alcocer Marcelo J. P. , Leijtens Tomas , Herz Laura M. , Petrozza Annamaria , Snaith Henry J.
Published: October 2013

Unrestricted Travel in Solar Cells

In the past 2 years, organolead halide perovskites have emerged as a promising class of light-harvesting media in experimental solar cells, but the physical basis for their efficiency has been unclear (see the Perspective by

Hodes

). Two studies now show, using a variety of time-resolved absorption and emission spectroscopic techniques, that these materials manifest relatively long diffusion paths for charge carriers energized by light absorption.

Xing
et al.

(p.
344
) independently assessed (negative) electron and (positive) hole diffusion lengths and found them well-matched to one another to the ~100-nanometer optical absorption depth.

Stranks
et al.

(p.
341
) uncovered a 10-fold greater diffusion length in a chloride-doped material, which correlates with the material's particularly efficient overall performance. Both studies highlight effective carrier diffusion as a fruitful parameter for further optimization.
Did the Denisovans Cross Wallace's Line?
Authors: Cooper A. , Stringer C. B.
Published: October 2013

The distribution of Denisovan DNA in modern human populations raises questions about where these ancient humans lived and where they interbred with modern humans.
Sleep It Out
Authors: Herculano-Houzel Suzana
Published: October 2013

Change in the brain's extracellular space between sleep and waking states may drive the clearance of metabolites and toxins.

[Also see Report by

Xie
et al.

]
Clinical and Diagnostic Developments of a Gamma Interferon Release Assay for Use in Bovine Tuberculosis Control Programs
Authors: Bass K. E. , Nonnecke B. J. , Palmer M. V. , Thacker T. C. , Hardegger R. , Schroeder B. , Raeber A. J. , Waters W. R.
Published: October 2013

Currently, the Bovigam assay is used as an official supplemental test within bovine tuberculosis control programs. The objectives of the present study were to evaluate twoMycobacterium bovis-specific peptide cocktails and purified protein derivatives (PPDs) from two sources, liquid and lyophilized antigen preparations. PPDs and peptide cocktails were also used for comparison of a second-generation gamma interferon (IFN-γ) release assay kit with the currently licensed first-generation kit (Bovigam; Prionics AG). Three strains ofM. boviswere used for experimental challenge:M. bovis95-1315,M. bovisRavenel, andM. bovis10-7428. Additionally, samples from a tuberculosis-affected herd (i.e., naturally infected) were evaluated. Robust responses to both peptide cocktails, HP (PC-HP) and ESAT-6/CFP10 (PC-EC), and the PPDs were elicited as early as 3 weeks after challenge. Only minor differences in responses to Commonwealth Serum Laboratories (CSL) and Lelystad PPDs were detected with samples from experimentally infected animals. For instance, responses to LelystadM. avium-derived PPD (PPDa) exceeded the respective responses to the CSL PPDa inM. bovisRavenel-infected and control animals. However, a 1:4 dilution of stimulated plasma demonstrated greater separation of PPDb from PPDa responses (i.e., PPDb minus PPDa) with the use of Lelystad PPDs, suggesting that Lelystad PPDs provide greater diagnostic sensitivity than CSL PPDs. The responses to lyophilized and liquid antigen preparations did not differ. Responses detected with first- and second-generation IFN-γ release assay kits (Bovigam) did not differ throughout the study. In conclusion, antigens may be stored in a lyophilized state without loss in potency, PC-HP and PC-EC are dependable biomarkers for aiding in the detection of bovine tuberculosis, and second-generation Bovigam kits are comparable to currently used kits.
Evaluation of a Commercial Enzyme-Linked Immunosorbent Assay for the Diagnosis of Bovine Tuberculosis from Milk Samples from Dairy Cows
Authors: Buddle Bryce M. , Wilson Tania , Luo Dongwen , Voges Hinrich , Linscott Richard , Martel Edmond , Lawrence John C. , Neill Mark A.
Published: October 2013

Milk samples from dairy cows provide a ready source of material for measuring antibody responses to
Mycobacterium bovis
antigens. In this study, we evaluated the IDEXX enzyme-linked immunosorbent assay (ELISA) for the measurement of antibody responses to
M. bovis
antigens MPB70 and MPB83 in milk samples from New Zealand cattle. Test sensitivities for individual milk and serum samples were assessed in samples collected from 44
M. bovis
-infected cows, and test specificities were assessed in milk samples collected from 356 cows from tuberculosis (TB)-free herds. Milk vat samples were collected from 505 herds from regions with relatively high or low prevalences of infection. The ELISA had a sensitivity of 50% and a specificity of 97.5% for milk samples, and the test sensitivities for milk and serum samples were the same. Dilution of the positive test milk samples in milk from noninfected cows at 1/10, 1/20, and 1/50 dilutions reduced the proportions of positive responses to 13/21, 9/21, and 4/21, respectively. Small differences were observed in the ELISA responses of milk samples from individual TB-free cows collected at different times during lactation. No significant differences were detected in the ELISA responses of milk vat samples collected from infected and noninfected herds. This study shows that milk samples can be substituted for serum samples for screening individual cows for
M. bovis
infection, and pooling of milk samples from 10 to 20 animals can result in a reduction in the sensitivity by approximately 50%. However, screening of milk vat samples is unlikely to be useful in countries with low prevalences of
M. bovis
in cattle and large herd sizes.