bluuebunny/crossref_metadata_2025 huggingface dataset:
Factors associated with successful tobacco use cessation among teachers in Bihar state, India: a mixed-method study
Authors: Nagler E M , Aghi M , Rathore A , Lando H , Pednekar M S , Gupta P C , Stoddard A M , Kenwood C , Penningroth B , Sinha D N , Sorensen G
Published: January 2020

Although tobacco use is declining in several countries including India (dropping from 35% in 2009–10 to 29% 2016–17 among adults)—it still poses a huge burden on India, as the world’s second largest consumer of tobacco products. In Bihar state, with a prevalence of 25%, the Bihar School Teachers Study (BSTS) successfully enlisted teachers as role models for encouraging quitting and changing social norms pertaining to tobacco. The study used a mixed-methods approach to identify factors associated with teachers’ quitting. Qualitative data were collected through focus groups with teachers and school principals. Quantitative data were collected through a written survey administered to school personnel post-intervention. Key findings from focus groups were that teachers and principals quit using tobacco and promoted cessation because they wanted to model positive behaviors; specific information about tobacco’s harms aided cessation; and the BSTS intervention facilitated a school environment that supported quitting. Survey results indicated teachers who reported knowing people who quit using tobacco in the prior year were far more likely to quit as were teachers who reported that their school’s tobacco policy was completely enforced. The combination of qualitative and quantitative data yielded important insights with strong implications for future interventions.
Constitution-making and liberal democracy: The role of citizens and representative elites
Authors: Negretto Gabriel
Published: January 2020

This article discusses the impact of citizen participation and elite cooperation in constitution-making on the deepening of an already existing electoral democracy. It argues that while direct citizen involvement in the drafting of constitutions may be desirable on normative grounds or necessary for pragmatic reasons, only cooperation among a plurality of elected political representatives at the constitution-making stage is likely to improve the liberal dimension of democracy after the enactment of the new constitution. Inclusive constitutional agreements at the level of representative elites not only establish legal limits on state action but may also provide opposition parties and citizens alike with the means to make institutional constraints on executive power and civil liberties effective. This effect is usually observed during the early years of life of the new constitution, when the balance of power among the political forces that created the constitution tends to remain stable. I find preliminary support for this argument analyzing aggregate data and selected case studies from all episodes of democratic constitution-making in the world between 1900 and 2015.
Qualification, knowledge, tasks and responsibilities of the clinical perfusionist in Germany
Authors: Bauer Adrian , Benk Christoph , Thiele Holger , Bauersachs Johann , Dittrich Sven , Dähnert Ingo , Schirmer Uwe , Zwißler Bernhard , Jannsens Uwe , Karagiannidis Christian , Kluge Stefan , Markewitz Andreas , Beckmann Andreas
Published: January 2020

Consensus paper of the German Society of Cardiovascular Engineering, the German Society for Thoracic and Cardiovascular Surgery, the German Society of Cardiology, the German Society of Pediatric Cardiology, the German Society of Anesthesiology and Intensive Care Medicine, the German Interdisciplinary Association of Intensive Care Medicine and Emergency Medicine and the German Society of Medical Intensive Care and Emergency Medicine.
Evolution and Ecology of Silent Flight in Owls and Other Flying Vertebrates
Authors: Clark Christopher J ,  LePiane Krista , Liu Lori
Published: January 2020

Synopsis

We raise and explore possible answers to three questions about the evolution and ecology of silent flight of owls: (1) do owls fly silently for stealth, or is it to reduce self-masking? Current evidence slightly favors the self-masking hypothesis, but this question remains unsettled. (2) Two of the derived wing features that apparently evolved to suppress flight sound are the vane fringes and dorsal velvet of owl wing feathers. Do these two features suppress aerodynamic noise (sounds generated by airflow), or do they instead reduce structural noise, such as frictional sounds of feathers rubbing during flight? The aerodynamic noise hypothesis lacks empirical support. Several lines of evidence instead support the hypothesis that the velvet and fringe reduce frictional sound, including: the anatomical location of the fringe and velvet, which is best developed in wing and tail regions prone to rubbing, rather than in areas exposed to airflow; the acoustic signature of rubbing, which is broadband and includes ultrasound, is present in the flight of other birds but not owls; and the apparent relationship between the velvet and friction barbules found on the remiges of other birds. (3) Have other animals also evolved silent flight? Wing features in nightbirds (nocturnal members of Caprimulgiformes) suggest that they may have independently evolved to fly in relative silence, as have more than one diurnal hawk (Accipitriformes). We hypothesize that bird flight is noisy because wing feathers are intrinsically predisposed to rub and make frictional noise. This hypothesis suggests a new perspective: rather than regarding owls as silent, perhaps it is bird flight that is loud. This implies that bats may be an overlooked model for silent flight. Owl flight may not be the best (and certainly, not the only) model for “bio-inspiration” of silent flight.
Oxidative and nitrosative stresses in cerebral malaria: can we target them to avoid a bad prognosis?
Authors: Pereira Domingos Magno Santos , Carvalho Júnior Alexsander Rodrigues , Lacerda Eliza Maria da Costa Brito , da Silva Luis Cláudio Nascimento , Marinho Cláudio Romero Farias , André Eunice , Fernandes Elizabeth Soares
Published: January 2020

There is currently a global effort to reduce malaria morbidity and mortality. However, malaria still results in the deaths of thousands of people every year. Malaria is caused by Plasmodium spp., parasites transmitted through the bite of an infected female Anopheles mosquito. Treatment timing plays a decisive role in reducing mortality and sequelae associated with the severe forms of the disease such as cerebral malaria (CM). The available antimalarial therapy is considered effective but parasite resistance to these drugs has been observed in some countries. Antimalarial drugs act by increasing parasite lysis, especially through targeting oxidative stress pathways. Here we discuss the roles of reactive oxygen species and reactive nitrogen intermediates in CM as a result of host–parasite interactions. We also present evidence of the potential contribution of oxidative and nitrosative stress-based antimalarial drugs to disease treatment and control.
Simultaneous multi-component seismic denoising and reconstruction via K-SVD
Authors: Hou Sian , Zhang Feng , Li Xiangyang , Zhao Qiang , Dai Hengchang
Published: January 2020

Data denoising and reconstruction play an increasingly significant role in seismic prospecting for their value in enhancing effective signals, dealing with surface obstacles and reducing acquisition costs. In this paper, we propose a novel method to denoise and reconstruct multicomponent seismic data simultaneously. This method lies within the framework of machine learning and the key points are defining a suitable weight function and a modified inner product operator. The purpose of these two processes are to perform missing data machine learning when the random noise deviation is unknown, and building a mathematical relationship for each component to incorporate all the information of multi-component data. Two examples, using synthetic and real multicomponent data, demonstrate that the new method is a feasible alternative for multi-component seismic data processing.
Molecular and genetic bases of heat stress responses in crop plants and breeding for increased resilience and productivity
Authors: Janni Michela , Gullì Mariolina , Maestri Elena , Marmiroli Marta , Valliyodan Babu , Nguyen Henry T , Marmiroli Nelson
Published: January 2020

To ensure the food security of future generations and to address the challenge of the ‘no hunger zone’ proposed by the FAO (Food and Agriculture Organization), crop production must be doubled by 2050, but environmental stresses are counteracting this goal. Heat stress in particular is affecting agricultural crops more frequently and more severely. Since the discovery of the physiological, molecular, and genetic bases of heat stress responses, cultivated plants have become the subject of intense research on how they may avoid or tolerate heat stress by either using natural genetic variation or creating new variation with DNA technologies, mutational breeding, or genome editing. This review reports current understanding of the genetic and molecular bases of heat stress in crops together with recent approaches to creating heat-tolerant varieties. Research is close to a breakthrough of global relevance, breeding plants fitter to face the biggest challenge of our time.
Floral organ development goes live
Authors: Rambaud-Lavigne Léa , Hay Angela
Published: January 2020

The chance to watch floral organs develop live is not to be missed! Here, we outline reasons why quantitative, live-cell imaging is an important approach to study floral morphogenesis, and provide a basic workflow of how to get started. We highlight key advances in morphodynamics of lateral organ development, and discuss recent work that uses live confocal imaging to address the regulation of floral organ number, its robustness, and patterning mechanisms that exploit stochasticity.
T-Cell Molecular Modulation Responses in Atherosclerosis Anergy
Authors: Pakzad Bahram , Rajae Elham , Shahrabi Saeid , Mansournezhad Somayeh , Davari Nader , Azizidoost Shirin , Saki Najmaldin
Published: January 2020

Atherosclerosis continues to be a major cause of death in patients with cardiovascular diseases. The cooperative role of immunity has been recently considered in atherosclerotic plaque inflammation, especially adaptive immune response by T cells. In this review, we examine the possible role of T cells in atherosclerosis-mediated inflammation and conceivable therapeutic strategies that can ameliorate complications of atherosclerosis. The cytokines secreted by T-lymphocyte subsets, different pathophysiological profiles of microRNAs (miRs), and the growth factor/receptor axis have diverse effects on the inflammatory cycle of atherosclerosis. Manipulation of miRNA expression and prominent growth factor receptors involved in inflammatory cytokine secretion in atherosclerosis can be considered diagnostic biomarkers in the induction of anergy and blockade of atherosclerotic development. This manuscript reviews immunomodulation of T cells responses in atherosclerosis anergy.
Weighing the stellar constituents of the galactic halo with APOGEE red giant stars
Authors: Mackereth J Ted , Bovy Jo
Published: January 2020

The stellar mass in the halo of the Milky Way is notoriously difficult to determine, owing to the paucity of its stars in the solar neighbourhood. With tentative evidence from Gaia that the nearby stellar halo is dominated by a massive accretion event – referred to as Gaia-Enceladus or Sausage – these constraints are now increasingly urgent. We measure the mass in kinematically selected mono-abundance populations (MAPs) of the stellar halo between −3 < [Fe/H] < −1 and 0.0 < [Mg/Fe] < 0.4 using red giant star counts from APOGEE DR14. We find that MAPs are well fit by single power laws on triaxial ellipsoidal surfaces, and we show that that the power-law slope α changes such that high [Mg/Fe] populations have α ∼ 4, whereas low [Mg/Fe] MAPs are more extended with shallow slopes, α ∼ 2. We estimate the total stellar mass to be $M_{*,\mathrm{tot}} = 1.3^{+0.3}_{-0.2}\times 10^{9}\ \mathrm{M_{\odot}}$, of which we estimate ${\sim}0.9^{+0.2}_{-0.1} \times 10^{9}\ \mathrm{M_{\odot}}$ to be accreted. We estimate that the mass of accreted stars with e > 0.7 is M*,accreted, e > 0.7 = 3 ± 1 (stat.) ± 1 (syst.) × 108 M⊙, or ${\sim}30{-}50{{\ \rm per\ cent}}$ of the accreted halo mass. If the majority of these stars are the progeny of a massive accreted dwarf, this places an upper limit on its stellar mass, and implies a halo mass for the progenitor of ∼1010.2 ± 0.2 M⊙. This constraint not only shows that the Gaia-Enceladus/Sausage progenitor may not be as massive as originally suggested, but that the majority of the Milky Way stellar halo was accreted. These measurements are an important step towards fully reconstructing the assembly history of the Milky Way.
A radio parallax to the black hole X-ray binary MAXI J1820+070
Authors: Atri P , Miller-Jones J C A , Bahramian A , Plotkin R M , Deller A T , Jonker P G , Maccarone T J , Sivakoff G R , Soria R , Altamirano D , Belloni T , Fender R , Koerding E , Maitra D , Markoff S , Migliari S , Russell D , Russell T , Sarazin C L , Tetarenko A J , Tudose V
Published: January 2020

Using the Very Long Baseline Array and the European Very Long Baseline Interferometry Network, we have made a precise measurement of the radio parallax of the black hole X-ray binary MAXI J1820+070, providing a model-independent distance to the source. Our parallax measurement of (0.348 ± 0.033) mas for MAXI J1820+070 translates to a distance of (2.96 ± 0.33) kpc. This distance implies that the source reached (15 ± 3) per cent of the Eddington luminosity at the peak of its outburst. Further, we use this distance to refine previous estimates of the jet inclination angle, jet velocity, and the mass of the black hole in MAXI J1820+070 to be (63 ± 3)°, (0.89 ± 0.09) c, and (9.2 ± 1.3) M⊙, respectively.
The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases
Authors: Schiltz Carl J , Adams Myfanwy C , Chappie Joshua S
Published: January 2020

OLD family nucleases contain an N-terminal ATPase domain and a C-terminal Toprim domain. Homologs segregate into two classes based on primary sequence length and the presence/absence of a unique UvrD/PcrA/Rep-like helicase gene immediately downstream in the genome. Although we previously defined the catalytic machinery controlling Class 2 nuclease cleavage, degenerate conservation of the C-termini between classes precludes pinpointing the analogous residues in Class 1 enzymes by sequence alignment alone. Our Class 2 structures also provide no information on ATPase domain architecture and ATP hydrolysis. Here we present the full-length structure of the Class 1 OLD nuclease from Thermus scotoductus (Ts) at 2.20 Å resolution, which reveals a dimerization domain inserted into an N-terminal ABC ATPase fold and a C-terminal Toprim domain. Structural homology with genome maintenance proteins identifies conserved residues responsible for Ts OLD ATPase activity. Ts OLD lacks the C-terminal helical domain present in Class 2 OLD homologs yet preserves the spatial organization of the nuclease active site, arguing that OLD proteins use a conserved catalytic mechanism for DNA cleavage. We also demonstrate that mutants perturbing ATP hydrolysis or DNA cleavage in vitro impair P2 OLD-mediated killing of recBC−Escherichia coli hosts, indicating that both the ATPase and nuclease activities are required for OLD function in vivo.
Bevacizumab for pediatric radiation necrosis
Authors: Baroni Lorena V , Alderete Daniel , Solano-Paez Palma , Rugilo Carlos , Freytes Candela , Laughlin Suzanne , Fonseca Adriana , Bartels Ute , Tabori Uri , Bouffet Eric , Huang Annie , Laperriere Normand , Tsang Derek S , Sumerauer David , Kyncl Martin , Ondrová Barbora , Malalasekera Vajiranee S , Hansford Jordan R , Zápotocký Michal , Ramaswamy Vijay
Published: January 2020

Background

Radiation necrosis is a frequent complication occurring after the treatment of pediatric brain tumors; however, treatment options remain a challenge. Bevacizumab is an anti-VEGF monoclonal antibody that has been shown in small adult cohorts to confer a benefit, specifically a reduction in steroid usage, but its use in children has not been well described.

Methods

We describe our experience with bevacizumab use for symptomatic radiation necrosis at 5 institutions including patients treated after both initial irradiation and reirradiation.

Results

We identified 26 patients treated with bevacizumab for symptomatic radiation necrosis, with a wide range of underlying diagnoses. The average age at diagnosis of radiation necrosis was 10.7 years, with a median time between the last dose of radiation and the presentation of radiation necrosis of 3.8 months (range, 0.6-110 months). Overall, we observed that 13 of 26 patients (50%) had an objective clinical improvement, with only 1 patient suffering from significant hypertension. Radiological improvement, defined as reduced T2/fluid-attenuated inversion recovery signal and mass effect, was observed in 50% of patients; however, this did not completely overlap with clinical response. Both early and late radiation necrosis responded equally well to bevacizumab therapy. Overall, bevacizumab was very well tolerated, permitting a reduction of corticosteroid dose and/or duration in the majority of patients.

Conclusions

Bevacizumab appears to be effective and well-tolerated in children as treatment for symptomatic radiation necrosis and warrants more robust study in the context of controlled clinical trials.
Atomic origin of spin-valve magnetoresistance at the SrRuO3 grain boundary
Authors: Li Xujing , Yin Li , Lai Zhengxun , Wu Mei , Sheng Yu , Zhang Lei , Sun Yuanwei , Chen Shulin , Li Xiaomei , Zhang Jingmin , Li Yuehui , Liu Kaihui , Wang Kaiyou , Yu Dapeng , Bai Xuedong , Mi Wenbo , Gao Peng
Published: January 2020

Defects exist ubiquitously in crystal materials, and usually exhibit a very different nature from the bulk matrix. Hence, their presence can have significant impacts on the properties of devices. Although it is well accepted that the properties of defects are determined by their unique atomic environments, the precise knowledge of such relationships is far from clear for most oxides because of the complexity of defects and difficulties in characterization. Here, we fabricate a 36.8° SrRuO3 grain boundary of which the transport measurements show a spin-valve magnetoresistance. We identify its atomic arrangement, including oxygen, using scanning transmission electron microscopy and spectroscopy. Based on the as-obtained atomic structure, the density functional theory calculations suggest that the spin-valve magnetoresistance occurs because of dramatically reduced magnetic moments at the boundary. The ability to manipulate magnetic properties at the nanometer scale via defect control allows new strategies to design magnetic/electronic devices with low-dimensional magnetic order.
Fulminant Acanthamoeba castellanii Encephalitis in an Ibrutinib-Treated Patient
Authors: Crothers Jessica W , Hsu Liangge , Marty Francisco M
Published: January 2020

We report a case of fulminant Acanthamoeba castellanii encephalitis in a patient with chronic lymphocytic leukemia treated with ibrutinib. The unusually rapid neurologic decline and fatal outcome observed are probably related to alterations in immunologic function associated with inhibition of Bruton tyrosine kinase.
Mathematical processing is affected by daily but not cumulative glucocorticoid dose in patients with systemic lupus erythematosus
Authors: Teo Rachel , Dhanasekaran Preeti , Tay Sen Hee , Mak Anselm
Published: January 2020

Objectives

The impact of glucocorticoids on neurocognitive performance in patients with SLE is not fully addressed. We aimed to study the effect of daily and cumulative glucocorticoid dose on neurocognitive performance in SLE patients.

Methods

Consecutive SLE patients and gender- and age-matched healthy controls (HCs) underwent the computer-based Automated Neuropsychological Assessment Matric (ANAM), which evaluates eight neurocognitive domains including learning, recall, visual perception, mental rotation, short-term memory, attention, sustained attention and working memory. The total and individual-domain throughput scores (TPSs) and the presence of cognitive dysfunction (total TPS <1.5 s.d. below the mean TPS of HCs) were compared between SLE patients and HCs. Within the SLE group, univariate and independent associations between prednisolone dose (daily and cumulative) and individual-domain TPS were studied by univariate and multivariable linear regression, respectively.

Results

A total of 96 SLE patients and 96 HCs were studied. SLE patients scored significantly worse across all the neurocognitive domains and had a significantly lower mean total TPS (P < 0.001) and a higher prevalence of cognitive dysfunction compared with HCs (25.0 vs 7.3%, P = 0.001). In SLE patients, daily prednisolone dose was significantly and negatively correlated with mathematical-processing TPS, which probes working memory (P = 0.018). No significant correlation between cumulative prednisolone dose and any of the individual-domain TPSs was found. In multivariable regression, higher daily prednisolone dose and doses >9 mg daily remained independently associated with lower mathematical-processing TPSs (P = 0.031).

Conclusion

Daily prednisolone dose ≥9 mg, but not cumulative glucocorticoid dose, had an independent negative impact on mathematical processing in SLE patients.
Attainment of treat-to-target endpoints in SLE patients with high disease activity in the atacicept phase 2b ADDRESS II study
Authors: Morand Eric F , Isenberg David A , Wallace Daniel J , Kao Amy H , Vazquez-Mateo Cristina , Chang Peter , Pudota Kishore , Aranow Cynthia , Merrill Joan T
Published: January 2020

Objective

Low disease activity (LDA) and remission are emerging treat-to-target (T2T) endpoints in SLE. However, the rates at which these endpoints are met in patients with high disease activity (HDA) are unknown. Atacicept, which targets B lymphocyte stimulator and a proliferation-inducing ligand, improved disease outcomes in SLE patients with HDA (SLEDAI-2K ≥10) at baseline in the phase 2b ADDRESS II study. This is a post hoc analysis of T2T endpoints in these patients.

Methods

Patients received weekly atacicept (75 or 150 mg s.c.) or placebo for 24 weeks (1:1:1 randomization). Attainment of three T2T endpoints, LDA (SLEDAI-2K ≤ 2), Lupus Low Disease Activity State (LLDAS) and remission (clinical SLEDAI-2K = 0, prednisone-equivalent ≤5mg/day and Physician’s Global Assessment <0.5), was assessed and compared with SLE Responder Index (SRI)-4 and SRI-6 response.

Results

Of 306 randomized patients, 158 (51.6%) had baseline HDA. At week 24, 37 (23.4%) HDA patients attained LDA, 25 (15.8%) LLDAS and 17 (10.8%) remission. Each of these endpoints was more stringent than SRI-4 (n = 87; 55.1%) and SRI-6 (n = 67; 42.4%). Compared with placebo (n = 52), at week 24, patients treated with atacicept 150 mg (n = 51) were more likely to attain LDA [odds ratio (OR) 3.82 (95% CI: 1.44, 10.15), P = 0.007], LLDAS [OR 5.03 (95% CI: 1.32, 19.06), P = 0.018] or remission [OR 3.98 (95% CI: 0.78, 20.15), P = 0.095].

Conclusion

At week 24, LDA, LLDAS and remission were more stringent than SRI-4 and SRI-6 response, were attainable in the HDA population and discriminated between treatment with atacicept 150 mg and placebo. These results suggest that T2T endpoints are robust outcome measures in SLE clinical trials and support further evaluation of atacicept in SLE.

Trail registration

ClinicalTrials.gov, http://clinicaltrials.gov, NCT01972568.
A comparative capitalism perspective on the privatization of governance: Business power, nonbusiness resistance and state enforcement in Germany, 2000–2010
Authors: Kaplan Rami , Lohmeyer Nora
Published: January 2020

The privatization of governance including the institution of nonbinding corporate social responsibility (CSR) frameworks to govern the social and economic conduct of large corporations is a controversial global process, which unfolds between and within nations. Studies of transnational private governance suggest that CSR frameworks reflect bargains between business and nonbusiness actors, reached on the background of the unfeasibility of intergovernmental binding regulation. But what explains the rise of such multi-stakeholder initiatives on the national level—and particularly in European coordinated market economies—where public forms of governance are historically well-institutionalized and more feasible? Based on our power resource theory (PRT)-informed study of Germany’s adoption of a national CSR framework, we argue that such settings motivate nonbusiness actors to resist, rather than engage in, business-driven processes of the privatization of governance. The struggle is decided by the state, which in Germany used its public power to enforce multi-stakeholder consensus around privatized forms. Our findings thus extend scholarly recognition of the role played by public authority in the privatization of governance. More generally, we promote a comparative capitalism perspective for the study of the politics of private governance.
A novel NAC transcription factor, MdNAC42, regulates anthocyanin accumulation in red-fleshed apple by interacting with MdMYB10
Authors: Zhang Shuangyi , Chen Yixi , Zhao Lingling , Li Chenqi , Yu Jingyun , Li Tongtong , Yang Weiyao , Zhang Shengnan , Su Hongyan , Wang Lei
Published: January 2020

Anthocyanin pigmentation is an important consumption trait of apple (Malus domestica Borkh.). In this study, we focused on the identification of NAC (NAM, ATAF1/2 and CUC2) proteins involved in the regulation of anthocyanin accumulation in apple flesh. A group of MdNACs was selected for comparison of expression patterns between the white-fleshed cultivar ‘Granny Smith’ and red-fleshed ‘Redlove’. Among them, MdNAC42 was screened, which exhibited a higher expression level in red-fleshed than in white-fleshed fruit, and has a positive correlation with anthocyanin content as fruits ripened. Moreover, overexpression of MdNAC42 in apple calli resulted in the up-regulation of flavonoid pathway genes, including MdCHS, MdCHI, MdF3H, MdDFR, MdANS and MdUFGT, thereby increasing the accumulation of anthocyanins, which confirmed the roles of MdNAC42 in anthocyanin biosynthesis. Notably, MdNAC42 was demonstrated to have an obvious interaction with MdMYB10 either in vitro or in vivo by yeast two-hybrid combined with bimolecular fluorescence complementation, further suggesting that MdNAC42 is an important part of the regulatory network controlling the anthocyanin pigmentation of red-fleshed apples. To the best of our knowledge, this is the first report identifying the MdNAC gene as related to anthocyanin accumulation in red-fleshed apples. This study provides valuable information for improving the regulatory model of anthocyanin biosynthesis in apple fruit.
Combining QTL Mapping with Genome Resequencing Identifies an Indel in an R Gene that is Associated with Variation in Leaf Rust Disease Resistance in Poplar
Authors: Nvsvrot Tashbek , Xia Wenxiu , Xiao Zheng’ang , Zhan Chang , Liu Meifeng , Yang Xiaoqing , Zhang Yan , Wang Nian
Published: January 2020

Poplar trees (Populus spp.) are important and are widely grown worldwide. However, the extensive occurrence of leaf rust disease caused by Melampsora spp. seriously inhibits their growth and reduces their biomass. In our previous study, a high-quality genetic map was constructed for the poplar F1 population I-69 × XYY by using next-generation sequencing-based genotyping-by-sequencing. Here, we collected phenotypic data on leaf rust disease resistance on three different dates for all 300 progenies of the F1 population. Combining a high-quality genetic map and phenotypic data, we were able to detect 11 major quantitative trait loci (QTLs) for leaf rust disease resistance. Among these 11 QTLs, two pairs were detected on at least two dates. In the corresponding genomic sequence, we found that resistance (R) gene clusters were located in these two QTL regions. By using genome resequencing, PCR confirmation and statistical analysis, a 611-bp deletion within an R gene in one QTL region was found to be associated with variation in leaf rust disease resistance. A PCR-based examination of this 611-bp deletion was performed. This 611-bp deletion was also found to affect mRNA splicing and form a new protein with the loss of some key protein domains. Based on this study, we were able to determine the genetic architecture of variation in poplar leaf rust disease resistance, and the 611-bp deletion in the R gene could be used as a diagnostic marker for future poplar molecular breeding.
Initiation of Therapeutic Hypothermia in the Emergency Department
Authors: Yochum Cody , Utley Rose
Published: January 2020

Therapeutic hypothermia (TH) postresuscitation has been recommended by the American Heart Association (AHA) since 2005. Early initiation of TH and fast achievement of goal temperatures have been associated with better neurological outcomes. The objective of this study was to evaluate the effectiveness of a specific TH protocol for the emergency department (ED) in increasing ED use of TH and decreasing the time from return of spontaneous circulation (ROSC) to initiation of cooling measures. An ED protocol for TH as recommended by the AHA was implemented. A random sample of 10 patients who received TH prior to the implementation of an ED protocol were analyzed and compared with the first 10 patients who received TH after the ED protocol was implemented. The time from ROSC to initiation of cooling measures and survival to discharge rates were analyzed. After implementation of the ED protocol, 7 of the 10 patients were treated with the ED protocol. The mean time to initiation of TH for the preimplementation group was 127.8 min (SD = 52.9) compared with 15.71 min (SD = 9.552) for the postimplementation group. The difference in initiation time between the pre- and postimplementation study groups was statistically significant, t(9.826) = 6.55, p < 0.05. Survival to discharge rates were 30% for the preimplementation group and 20% for the postimplementation group. The difference was not statistically significant, χ2 (1, N = 20) = 0.73, p = 0.78. Implementation of an ED protocol for TH reduced mean time to initiation of therapy. Additional study is warranted to determine whether differences in survival and functional recovery for ED patients receiving TH were influenced by age, comorbidities, and total resuscitation time.
An Unusual Case of Chest Pain in an Adolescent Male
Authors: Jordan Kathleen S. , Mannle Sarah E.
Published: January 2020

Chest pain is a common presenting symptom in the pediatric population, and in contrast to adults, the etiology is rarely cardiac or life-threatening. The majority of chest pain complaints in children and adolescents are benign and can be managed with reassurance and follow-up. The emergency care provider must obtain a comprehensive history and physical examination, as the differential diagnosis of pediatric chest pain is extensive and serious underlying organic pathology may be present. This article describes the case of an adolescent male with an unusual case of chest pain with a serious underlying medical condition. A systematic approach to the clinical decision-making process is discussed to identify those patients who may have a serious underlying organic cause. Information is also included to guide the provider in the identification of red flags for cardiac etiologies of chest pain and indications for a pediatric cardiology consultation.
On the cost of iterative computations
Authors: Carson Erin , Strakoš Zdeněk
Published: January 2020

With exascale-level computation on the horizon, the art of predicting the cost of computations has acquired a renewed focus. This task is especially challenging in the case of iterative methods, for which convergence behaviour often cannot be determined with certainty
a priori
(unless we are satisfied with potentially outrageous overestimates) and which typically suffer from performance bottlenecks at scale due to synchronization cost. Moreover, the amplification of rounding errors can substantially affect the practical performance, in particular for methods with short recurrences. In this article, we focus on what we consider to be key points which are crucial to understanding the cost of iteratively solving linear algebraic systems. This naturally leads us to questions on the place of numerical analysis in relation to mathematics, computer science and sciences, in general.

This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.
Rethinking arithmetic for deep neural networks
Authors: Constantinides G. A.
Published: January 2020

We consider efficiency in the implementation of deep neural networks. Hardware accelerators are gaining interest as machine learning becomes one of the drivers of high-performance computing. In these accelerators, the directed graph describing a neural network can be implemented as a directed graph describing a Boolean circuit. We make this observation precise, leading naturally to an understanding of practical neural networks as discrete functions, and show that the so-called
binarized neural networks
are functionally complete. In general, our results suggest that it is valuable to consider
Boolean circuits as neural networks
, leading to the question of which circuit topologies are promising. We argue that continuity is central to generalization in learning, explore the interaction between data coding, network topology, and node functionality for continuity and pose some open questions for future research. As a first step to bridging the gap between continuous and Boolean views of neural network accelerators, we present some recent results from our work on LUTNet, a novel Field-Programmable Gate Array inference approach. Finally, we conclude with additional possible fruitful avenues for research bridging the continuous and discrete views of neural networks.

This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.
Stochastic rounding and reduced-precision fixed-point arithmetic for solving neural ordinary differential equations
Authors: Hopkins Michael , Mikaitis Mantas , Lester Dave R. , Furber Steve
Published: January 2020

Although double-precision floating-point arithmetic currently dominates high-performance computing, there is increasing interest in smaller and simpler arithmetic types. The main reasons are potential improvements in energy efficiency and memory footprint and bandwidth. However, simply switching to lower-precision types typically results in increased numerical errors. We investigate approaches to improving the accuracy of reduced-precision fixed-point arithmetic types, using examples in an important domain for numerical computation in neuroscience: the solution of ordinary differential equations (ODEs). The Izhikevich neuron model is used to demonstrate that rounding has an important role in producing accurate spike timings from explicit ODE solution algorithms. In particular, fixed-point arithmetic with stochastic rounding consistently results in smaller errors compared to single-precision floating-point and fixed-point arithmetic with round-to-nearest across a range of neuron behaviours and ODE solvers. A computationally much cheaper alternative is also investigated, inspired by the concept of
dither
that is a widely understood mechanism for providing resolution below the least significant bit in digital signal processing. These results will have implications for the solution of ODEs in other subject areas, and should also be directly relevant to the huge range of practical problems that are represented by partial differential equations.

This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.
Ornithinicoccus soli sp. nov., isolated from farmland soil
Authors: Jiang Wan-Kui , Gao Qin-Qin , Zhang Lu , Sun Gao-Jie , Zhang Ming-Liang , Liu Xiao-An , Wang Hui , Zhou Yi-Dong , Ke Zhi-Jian , Hong Qing
Published: January 2020

A Gram-stain-positive, aerobic, non-motile and coccoid-shaped bacterium, designated XNB-1T, was isolated from farmland soil in Taian, Shandong province, China. Strain XNB-1T contained iso-C15 : 0 and iso-C16 : 0 as the predominant fatty acids. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn←Gly(1, 2)←d-Glu. The polar lipid profile of strain XNB-1T consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid and three unidentified phospholipids. The predominant menaquinone of strain XNB-1T was MK-8(H4) and the DNA G+C content was 70.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XNB-1T belonged to the genus

Ornithinicoccus

, and shared the highest similarity with

Ornithinicoccus hortensis

HKI 0125T (96.0 %), followed by

Ornithinicoccus halotolerans

EGI 80423T (95.5 %). Genome-based analysis of average nucleotide identity of strain XNB-1T with

O. hortensis

HKI 0125T and

O. halotolerans

EGI 80423T yielded values of 73.1 and 73.3 %, respectively, while the digital DNA–DNA hybridization values were 19.5 and 19.9 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain XNB-1T is considered to represent a novel species of the genus

Ornithinicoccus

, for which the name Ornithinicoccus soli sp. nov. is proposed. The type strain is XNB-1T (=CCTCC AB 2019099T=KCTC 49259T).
Encapsulated cyclosporine does not change the composition of the human microbiota when assessed ex vivo and in vivo
Authors: O'Reilly Catherine , O’Sullivan Órla , Cotter Paul D. , O’Connor Paula M. , Shanahan Fergus , Cullen Alan , Rea Mary C. , Hill Colin , Coulter Ivan , Ross R. Paul
Published: January 2020

Introduction.Management of steroid-refractory ulcerative colitis has predominantly involved treatment with systemic cyclosporine A (CyA) and infliximab.

Aim.The purpose of this study was to assess the effect of using a colon-targeted delivery system CyA formulation on the composition and functionality of the gut microbiota.

Methodology.Ex vivofaecal fermentations from six healthy control subjects were treated with coated minispheres (SmPill) with (+) or without (−) CyA and compared with a non-treated control in a model colon system. In addition, thein vivoeffect of the SmPill+CyA formulation was investigated by analysing the gut microbiota in faecal samples collected before the administration of SmPill+CyA and after 7 consecutive days of administration from eight healthy subjects who participated in a pilot study.

Results.Analysis of faecal samples by 16S rRNA gene sequencing indicated little variation in the diversity or relative abundance of the microbiota composition before or after treatment with SmPill minispheres with or without CyAex vivoor with CyAin vivo. Short-chain fatty acid profiles were evaluated using gas chromatography, showing an increase in the concentration of n-butyrate (P=0.02) and acetate (P=0.32) in the faecal fermented samples incubated in the presence of SmPill minispheres with or without CyA. This indicated that increased acetate and butyrate production was attributed to a component of the coated minispheres rather than an effect of CyA on the microbiota. Butyrate and acetate levels also increased significantly (P=0.05 for both) in the faecal samples of healthy individuals following 7 days’ treatment with SmPill+CyA in the pilot study.

Conclusion.SmPill minispheres with or without CyA at the clinically relevant doses tested here have negligible direct effects on the gut microbiota composition. Butyrate and acetate production increased, however, in the presence of the beads in anex vivomodel system as well asin vivoin healthy subjects. Importantly, this study also demonstrates the relevance and value of usingex vivocolon models to predict thein vivoimpact of colon-targeted drugs directly on the gut microbiota.
‘Community evolution’ – laboratory strains and pedigrees in the age of genomics
Authors: Dorman Matthew J. , Thomson Nicholas R.
Published: January 2020

Molecular microbiologists depend heavily on laboratory strains of bacteria, which are ubiquitous across the community of research groups working on a common organism. However, this presumes that strains present in different laboratories are in fact identical. Work on a culture of

Vibrio cholerae

preserved from 1916 provoked us to consider recent studies, which have used both classical genetics and next-generation sequencing to study the heterogeneity of laboratory strains. Here, we review and discuss mutations and phenotypic variation in supposedlyisogenic reference strains of

V. cholerae

and

Escherichia coli

, and we propose that by virtue of the dissemination of laboratory strains across the world, a large ‘community evolution’ experiment is currently ongoing.
Paracingulate sulcus length is shorter in voice-hearers regardless of need for care
Authors: Powers Albert R. , van Dyck Laura I. , Garrison Jane R. , Corlett Philip R.
Published: January 2020

While hallucinations are often considered to be the sine qua non of serious mental illness, they are commonly experienced by those without a need for care. Such non-clinical, hallucinating individuals offer a window into the etiology of hallucinations. Garrison et al. (2015) recently assessed structural variability in paracingulate sulcus (PCS) of medial prefrontal cortex. They found a reduction of 10mm in left hemisphere PCS length increased the likelihood of hallucinations by 19.9%. However, these findings were in clinical hallucinators, and reduced leftward asymmetry in PCS has been repeatedly demonstrated in schizophrenia and associated with reduced reality monitoring. Similar analyses have been conducted in non-clinical voice hearers and in those particpants, no reduction in PCS length was reported. However, there is considerable variability in the voice experiences of non-clinical voice hearers. Put simply, some may be more clinical than others. We recently identified a relatively homogenous group of non-clinical voice hearers who identify as clairaudient psychics. Their voice experiences are extremely redolent of those reported by a matched patient voice hearing group and their brain and behavioral responses to a perceptual inference task were, at least at the level of prior beliefs, similarly perturbed to patients who hear voices. These observations are consistent with a continuum model of voice hearing, along which clairaudient voice hearers are nearer to patients with schizophrenia in some respects. The PCS data reported by Garrison et al would militate against such a continuum. Before rejecting the continuum model, we sought to determine if the differences in PCS length also applied to the clairaudient non-clinical voice hearers. If PCS length is to be developed as a biomarker for clinical hallucination risk, then it is important to demonstrate that it is not similarly reduced in non-clinical voice hearers. We find that it is reduced, both in clinical and non-clinical voice-hearers.
Intratumor Heterogeneity and Evolution of Colorectal Cancer
Authors: Banerjee Santasree , Zhang Xianxiang , Kuang Shan , Wang Jigang , Li Lei , Fan Guangyi , Luo Yonglun , Sun Shuai , Han Peng , Wu Qingyao , Yang Shujian , Ji Xiaobin , Li Yong , Deng Li , Tian Xiaofen , Wang Zhiwei , Zhang Yue , Wu Kui , Zhu Shida , Bolund Lars , Yang Huanming , Xu Xun , Liu Junnian , Lu Yun , Liu Xin
Published: January 2020

Intratumor heterogeneity (ITH) enable us to understand the evolution of cancer. ITH and evolution of colorectal cancer (CRC) has not been well studied. In this prospective study, we recruited different stages of 68 CRC patients with primary tumor at right-sided colon, left-sided colon and rectum. We performed high-depth whole exome sequencing of 206 multi-region tumor samples including primary tumors, lymph node metastasis (LN) and extranodal tumor deposits (ENTD). Our result showed extreme ITH with Darwinian pattern of CRC evolution, evolution pattern of left-sided CRC was more complex and divergent than right-sided CRC and both LN and ENTD were of polyclonal in origin. Extensive ITH was found in driver mutations inKRASandPIK3CAgenes, suggesting major limitations of single biopsies in clinical diagnosis for the CRC patients. In conclusion, our study showed the Darwinian pattern of CRC evolution with differences in evolution pattern between right-sided and left-sided CRC patients.
Silicone Induced Granuloma of Breast Implant Capsule (SIGBIC) diagnosis: Breast Magnetic Resonance (BMR) ability to detect silicone bleeding
Authors: de Faria Castro Fleury Eduardo
Published: January 2020

Objective

To evaluate the ability of BMRI to detect silicone gel bleeding in a prospective observational study including consecutive patients referred for BMRI scan. Methods: From January 2017 to March 2018, patients referred for BMRI were evaluated in a prospective observational study. Patients who had breast implants were included. BMRI recorded 9 findings according to BI-RADS lexicon and SIGBIC findings, considered equivocal features to detect gel bleeding (GB). Three new original imaging features were added for SIGBIC diagnosis: black drop signal; T2* hypersignal mass; and delayed contrast enhancement, considered as irrevocable signs. The presence of silicone corpuscle was confirmed by percutaneous biopsy or surgical capsulectomy. Accuracy of BMRI SIGBIC findings to predict GB was determined. We also used univariate analysis for the equivocal features for GB diagnosis. The Backward method was applied for a multivariate Logistic Regression model for the equivocal features. Results: SIGBIC was diagnosed in 208 patients and GB was histologically confirmed in all cases. No false positive results were observed. The most important imaging equivocal feature associated with GB was capsular contracture. In order of prevalence, the main equivocal BMRI features associated to GB with statistically significance (P < =0.001) were as follows: 1.water droplets (OR=2.8; 95%CI 1.8-4.4); 2.enlarged intramammary lymph node (OR=3.1; 95%CI 1.5-6.1); 3.pericapsular edema (OR=5.0; 95%CI 2.3-11.1); and 4.intracapsular seroma (OR=2.4; 95%CI 1.4-4.1).

Conclusion

SIGBIC diagnosis has high sensitivity to predict GB by the 3 irrevocable BMRI features described by the authors. We suppose GB is underdiagnosed in clinical practice by BI-RADS features.
Behavioral and structural barriers to human post-exposure prophylaxis and other preventive practices during a canine rabies epidemic
Authors: Castillo-Neyra Ricardo , Buttenheim Alison M. , Brown Joanna , Ferrara James F. , Arevalo-Nieto Claudia , Borrini-Mayorí Katty , Levy Michael Z. , Becerra Victor , Paz-Soldan Valerie A.
Published: January 2020

A canine rabies epidemic started in early 2015 in Arequipa, Peru; the rabies virus continues to circulate in the dog population. Some city residents who suffer dog bites do not seek care or do not complete indicated post-exposure prophylaxis (PEP) regimens, increasing the risk of human rabies. The objectives of our study were to qualitatively assess knowledge about rabies, and preventive practices, such as PEP vaccination, following a dog bite. We conducted eight focus group discussions in peri-urban and urban communities with 70 total participants. We observed low awareness of rabies severity and fatality. Participants, especially those in per-urban communities, recounted applying herbs or the hair of the dog that bit them to wounds rather than seeking appropriate care. Misconceptions about rabies vaccines and mistreatment at health centers also commonly prevents initiating or completing PEP vaccination. We identify important behavioral and structural barriers and knowledge gaps that limit evidence-based preventive strategies against rabies and may threaten successful prevention of dog-mediated human rabies in this setting.