bluuebunny/crossref_metadata_2025 huggingface dataset:
Heterogeneous genetic invasions of three insecticide resistance mutations in Indo‐Pacific populations of Aedes aegypti (L.)
Authors: Endersby‐Harshman Nancy M. , Schmidt Thomas L. , Chung Jessica , van Rooyen Anthony , Weeks Andrew R. , Hoffmann Ary A.
Published: April 2020

Nations throughout the Indo‐Pacific region use pyrethroid insecticides to control Aedes aegypti, the mosquito vector of dengue, often without knowledge of pyrethroid resistance status of the pest or origin of resistance. Two mutations (V1016G + F1534C) in the sodium channel gene (Vssc) of Ae. aegypti modify ion channel function and cause target‐site resistance to pyrethroid insecticides, with a third mutation (S989P) having a potential additive effect. Of 27 possible genotypes involving these mutations, some allelic combinations are never seen whereas others predominate. Here, five allelic combinations common in Ae. aegypti from the Indo‐Pacific region are described and their geographical distributions investigated using genome‐wide SNP markers. We tested the hypothesis that resistance allele combinations evolved de novo in populations versus the alternative that dispersal of Ae. aegypti between populations facilitated genetic invasions of allele combinations. We used latent factor mixed‐models to detect SNPs throughout the genome that showed structuring in line with resistance allele combinations and compared variation at SNPs within the Vssc gene with genome‐wide variation. Mixed‐models detected an array of SNPs linked to resistance allele combinations, all located within or in close proximity to the Vssc gene. Variation at SNPs within the Vssc gene was structured by resistance profile, whereas genome‐wide SNPs were structured by population. These results demonstrate that alleles near to resistance mutations have been transferred between populations via linked selection. This indicates that genetic invasions have contributed to the widespread occurrence of Vssc allele combinations in Ae. aegypti in the Indo‐Pacific region, pointing to undocumented mosquito invasions between countries.
Strategies in herbivory by mammals revisited: The role of liver metabolism in a juniper specialist (Neotoma stephensi) and a generalist (Neotoma albigula)
Authors: Orr Teri J. , Kitanovic Smiljka , Schramm Katharina M. , Skopec Michele M. , Wilderman P. Ross , Halpert James R. , Dearing M. Denise
Published: April 2020

Although herbivory is widespread among mammals, few species have adopted a strategy of dietary specialization. Feeding on a single plant species often exposes herbivores to high doses of plant secondary metabolites (PSMs), which may exceed the animal's detoxification capacities. Theory predicts that specialists will have unique detoxification mechanisms to process high levels of dietary toxins. To evaluate this hypothesis, we compared liver microsomal metabolism of a juniper specialist, Neotoma stephensi (diet >85% juniper), to a generalist, N. albigula (diet ≤30% juniper). Specifically, we quantified the concentration of a key detoxification enzyme, cytochrome P450 2B (CYP2B) in liver microsomes, and the metabolism of α‐pinene, the most abundant terpene in the juniper species consumed by the specialist woodrat. In both species, a 30% juniper diet increased the total CYP2B concentration (2–3×) in microsomes and microsomal α‐pinene metabolism rates (4‐fold). In N. stephensi, higher levels of dietary juniper (60% and 100%) further induced CYP2B and increased metabolism rates of α‐pinene. Although no species‐specific differences in metabolism rates were observed at 30% dietary juniper, total microsomal CYP2B concentration was 1.7× higher in N. stephensi than in N. albigula (p < .01), suggesting N. stephensi produces one or more variant of CYP2B that is less efficient at processing α‐pinene. In N. stephensi, the rates of α‐pinene metabolism increased with dietary juniper and were positively correlated with CYP2B concentration. The ability of N. stephensi to elevate CYP2B concentration and rate of α‐pinene metabolism with increasing levels of juniper in the diet may facilitate juniper specialization in this species.
Posaconazole delayed‐release tablets in paediatric haematology–oncology patients
Authors: Mauro Margherita , Colombini Antonella , Perruccio Katia , Zama Daniele , D'Amico Maria Rosaria , Calore Elisabetta , Carraro Francesca , Muggeo Paola , Tridello Gloria , Baretta Valentina , Cesaro Simone
Published: April 2020

Background

To date, there are few studies that describe pharmacokinetics, safety and efficacy of posaconazole delayed‐release tablet (DRT) formulation in the paediatric population.

Objectives

We evaluated retrospectively posaconazole plasma concentrations and safety of posaconazole DRT in paediatric haematology–oncology patients.

Patients and methods

Posaconazole DRT was assessed in 28 haematological paediatric patients with a median age 15 of years (range 5‐18) and a median body weight of 50 kg (range 22‐83 kg). Twenty‐one patients received posaconazole DRT as prophylaxis and 7 patients as therapy.

Results

As prophylaxis, the median daily dose was 5.5 mg/kg/day (range 2.2‐22.2) with posaconazole trough level ≥ 0.7 μg/mL in 80% by first week, 62.5% by second week and 87.5% by fourth week. As therapy, the median daily dose was 4 mg/kg/day (range 3.3‐4.5) with trough level ≥ 1 μg/mL 100% by first week, 80% by second week and 33.4% by fourth week.

Conclusions

Posaconazole DRT is feasible in paediatric patients capable to swallow tablets. Specific pharmacokinetic studies are needed.
Advances in understanding large‐scale responses of the water cycle to climate change
Authors: Allan Richard P. , Barlow Mathew , Byrne Michael P. , Cherchi Annalisa , Douville Hervé , Fowler Hayley J. , Gan Thian Y. , Pendergrass Angeline G. , Rosenfeld Daniel , Swann Abigail L. S. , Wilcox Laura J. , Zolina Olga
Published: April 2020

Globally, thermodynamics explains an increase in atmospheric water vapor with warming of around 7%/°C near to the surface. In contrast, global precipitation and evaporation are constrained by the Earth's energy balance to increase at ∼2–3%/°C. However, this rate of increase is suppressed by rapid atmospheric adjustments in response to greenhouse gases and absorbing aerosols that directly alter the atmospheric energy budget. Rapid adjustments to forcings, cooling effects from scattering aerosol, and observational uncertainty can explain why observed global precipitation responses are currently difficult to detect but are expected to emerge and accelerate as warming increases and aerosol forcing diminishes. Precipitation increases with warming are expected to be smaller over land than ocean due to limitations on moisture convergence, exacerbated by feedbacks and affected by rapid adjustments. Thermodynamic increases in atmospheric moisture fluxes amplify wet and dry events, driving an intensification of precipitation extremes. The rate of intensification can deviate from a simple thermodynamic response due to in‐storm and larger‐scale feedback processes, while changes in large‐scale dynamics and catchment characteristics further modulate the frequency of flooding in response to precipitation increases. Changes in atmospheric circulation in response to radiative forcing and evolving surface temperature patterns are capable of dominating water cycle changes in some regions. Moreover, the direct impact of human activities on the water cycle through water abstraction, irrigation, and land use change is already a significant component of regional water cycle change and is expected to further increase in importance as water demand grows with global population.
Forecasting GDP Growth from Outer Space
Authors: Galimberti Jaqueson K.
Published: April 2020

We evaluate the usefulness of satellite‐based data on night‐time lights for forecasting GDP growth across a global sample of countries, proposing innovative location‐based indicators to extract new predictive information from the lights data. Our findings are generally favourable to the use of night lights data to improve the accuracy of model‐based forecasts. We also find a substantial degree of heterogeneity across countries in the relationship between lights and economic activity: individually estimated models tend to outperform panel specifications. Key factors underlying the night lights performance include the country's size and income level, logistics infrastructure, and the quality of national statistics.
Does autoimmune thyroid disorder act as a predisposing factor in the development of oral lichen planus?
Authors: Hirota Silvio , Marui Suemi , Migliari Dante
Published: April 2020

Considering previous data from our clinic, as had consistently demonstrated a significant number of OLP patients also reporting thyroid disease (Hashimoto's thyroiditis, in particular), the present study investigated the prevalence of OLP in patients with autoimmune thyroid disease, including Hashimoto's thyroiditis and Graves’ disease.
The challenge of long‐term follow‐up of survivors of childhood acute leukemia after hematopoietic stem cell transplantation in resource‐limited countries: A single‐center report from Brazil
Authors: Marinho Daniela Hespanha , Ribeiro Lisandro Lima , Nichele Samantha , Loth Gisele , Koliski Adriana , Mousquer Rebeca Toassa Gomes , Funke Vaneuza Araujo Moreira , Page Kristin , Fasth Anders , Pasquini Ricardo , Boguszewski Margaret Cristina da Silva , Bonfim Carmem
Published: April 2020

With the number of long‐term HSCT survivors steadily increasing, attention needs to be focused on the late complications and quality of life. We therefore analyzed the outcome of 101 pediatric patients (<18 years old at the time of HSCT) transplanted for acute leukemia between 1981 and 2015 at Complexo Hospital de Clínicas, Federal University of Paraná, Brazil, and who survived at least two years after HSCT. The median follow‐up was 5.9 years (2.0‐29.0); median age at follow‐up was 17.5 years (2.98‐39.0). The 5‐year cumulative incidence of relapse was 27.5% (95% CI 18.6%‐36.4%). Two‐year cumulative incidence of chronic GVHD was 21.8% (95% CI 13.7%‐29.8%). Of the 101 patients, 72 patients (71.3%) presented with late effects. Those surviving longer after HSCT experienced more complications. Patients who received TBI‐based regimen developed more late effects (P = .013) and more endocrinological complications (P = .024). Endocrinological complications were the most common late sequelae found in this study. For childhood survivors, quality of life was not influenced by age (at HSCT or at last visit), time from HSCT, gender, donor, or GVHD. For survivors that no longer were children, only age at last visit impacted financial domain measures, irrespective of gender, donor, or GVHD. The current study confirms the high burden late complications after pediatric HSCT have on the survivors and underlines the importance of extended follow‐up.
Photochemical Behavior of Some Estrone Aryl and Methyl Sulfonates in Solution: Preparative and Mechanistic Studies
Authors: Quindt Matías I. , Gola Gabriel F. , Ramirez Javier A. , Bonesi Sergio M.
Published: April 2020

Direct irradiation of estrone aryl and methyl sulfonates in different organic solvents under nitrogen atmosphere was investigated under steady‐state conditions. The estrone derivatives reacted efficiently through the photo‐Fries rearrangement reaction involving [1;3]‐sulfonyl migration providing the ortho‐sulfonyl estrone derivatives and estrone as the photoproducts. In addition, estrone and 2‐arylsulfonyl estrone derivatives were epimerized involving a Norrish Type‐I reaction. Chemical quenching and photosensitization experiments on the photoreaction have been also carried out to establish the photoreactive excited state. Likewise, the solvent effect and the nature of the sulfonyl group on the photoreactions have been also studied.
Strong differentiation within Diplocarpon rosae strains based on microsatellite markers and greenhouse‐based inoculation protocol on Rosa
Authors: Marolleau Brice , Petiteau Aurélien , Bellanger Marie‐Noëlle , Sannier Mélanie , Le Pocreau Nadège , Porcher Laetitia , Paillard Sophie , Foucher Fabrice , Thouroude Tatiana , Serres‐Giardi Laurana , Aguileta Gabriela , Chastellier Annie , Bonneau Caroline , Le Cam Bruno , Soufflet‐Freslon Vanessa , Hibrand‐Saint Oyant Laurence
Published: April 2020

The haploid ascomycete Diplocarpon rosae is the causal agent of black spot disease on roses, a widespread and devastating disease in the outdoor landscape. In this study, we established a Eurasian collection of 77 monoconidial strains of D. rosae: 50 strains collected on cultivated roses in Europe and Asia, and 27 strains on wild roses in Kazakhstan. To provide tools to describe its biology and to study its genetic diversity, we sequenced two strains of D. rosae using Illumina paired‐end technology. The genome sizes of these two strains were estimated at 31.1 and 35.2 Mb, which are two times smaller than the genome size of the unique strain previously published. A BUSCO analysis confirmed a genome duplication of the strain previously sequenced and partial gene duplication of strains analysed in this study. Using the two genome sequences, 27 polymorphic microsatellite markers were identified. Polymorphism analysis of the 77 strains revealed a strong genetic differentiation between strains from cultivated and wild roses, and a lower diversity within the fungal population from cultivated roses compared to the population from wild roses. Pathogenicity of 10 strains was evaluated on 9 rose cultivars inoculated in the greenhouse. Disease scoring allowed the classification of strains into three groups and the characterization of resistance of rose cultivars. Good correlation observed between resistance scoring in greenhouse conditions and in the field indicates that pathogenicity assays in controlled conditions could be very useful in the near future to rapidly characterize the resistance of new rose varieties to black spot disease.
Genetic diversity of Grapevine rupestris stem pitting‐associated virus isolates from Tunisian grapevine germplasm
Authors: Selmi Ilhem , Pacifico Davide , Lehad Arezki , Stigliano Egidio , Crucitti Dalila , Carimi Francesco , Mahfoudhi Naima
Published: April 2020

Grapevine rupestris stem pitting‐associated virus (GRSPaV) is one of the most widespread grapevine viruses and is transmitted mainly by grafting. GRSPaV presence was tested in 487 samples representative of the Tunisian grapevine germplasm (including autochthonous, table, wine, wild grape, and rootstock varieties) from different Tunisian regions. GRSPaV infection was detected in 51.3% of samples from different Tunisian regions, among which the table grapevine cultivars were the most commonly infected (68.7%). Genetic variability of GRSPaV isolates from wild and cultivated grapevines was assessed by sequencing the partial capsid protein (CP) gene of 19 Tunisian isolates and 1 Italian GRSPaV isolate from Sicily, and the partial RNA‐dependent RNA polymerase (RdRp) gene of 13 Tunisian GRSPaV isolates. According to phylogenetic analysis of CP nucleotide sequences obtained in this study and sequences retrieved from GenBank, Tunisian isolates fell into four phylogenetic groups already described (I, II, III, and IV) and two new phylogenetic groups (VI and VIII). Phylogenetic analysis of the partial RdRp gene revealed that Tunisian isolates of GRSPaV are distributed into four phylogroups. This study highlights the importance of regular monitoring of GRSPaV infections in Tunisia, with special regard to those grapevine accessions employed in conservation and selection programmes. In particular, the presence of new GRSPaV genetic variants and infection of wild grapevines must be taken into account in order to choose a correct control strategy.
Measurement of large, discontinuous displacement from digital images
Authors: Luo Zhilei , Hu Xu , Wang Linlin , Lu Yangxiao
Published: April 2020

One main limitation of conventional digital image correlation (DIC) methods is their incapacity to treat with large, discontinuous displacements. This paper seeks to resolve this issue using a variational method. Specifically, the objective function is written in a form of L1‐norm instead of L2‐norm for discontinuity preservation. This convex, non‐differentiable objective function is resolved by a proximal gradient method. Then, the entire correlation process is embedded into a multi‐level image pyramid, enabling large displacements to be measured accurately. The proposed method is first validated on images with prescribed small displacements; its performance to treat with discontinuous, large displacements is then examined. The results show that the proposed method exhibits an acceptable performance when measuring some extreme displacements up to 16.5 pixels in a 500 × 500 pixels resolution image. Concerning subpixel accuracy, the errors can be lessened to a very low level with optimised parameters even for a dense correlation at each pixel. Good performance is also demonstrated in forms of noise proof and illumination fluctuation tolerance. Finally, an application is conducted on an experiment concerned with cracking in desiccated soils, in which the proposed method succeeds in tracking the nucleation and propagation processes of multiple cracks.
The discovery of a HLA‐C*17:51 variant, C*17:51:02, found in a Brazilian individual
Authors: Vianna Romulo , Secco Danielle , Santos Angela , Porto Luís Cristóvão
Published: April 2020

Identification of the HLA‐C*17:51:02 that differs from HLA‐C*17:51:01:01 by a synonymous substitution in exon 5.
Size‐dependent secretory protein reflux into the cytosol in association with acute endoplasmic reticulum stress
Authors: Lajoie Patrick , Snapp Erik L.
Published: April 2020

Once secretory proteins have been targeted to the endoplasmic reticulum (ER) lumen, the proteins typically remain partitioned from the cytosol. If the secretory proteins misfold, they can be unfolded and retrotranslocated into the cytosol for destruction by the proteasome by ER‐Associated protein Degradation (ERAD). Here, we report that correctly folded and targeted luminal ER fluorescent protein reporters accumulate in the cytosol during acute misfolded secretory protein stress in yeast. Photoactivation fluorescence microscopy experiments reveal that luminal reporters already localized to the ER relocalize to the cytosol, even in the absence of essential ERAD machinery. We named this process “ER reflux.” Reflux appears to be regulated in a size‐dependent manner for reporters. Interestingly, prior heat shock stress also prevents ER stress‐induced reflux. Together, our findings establish a new ER stress‐regulated pathway for relocalization of small luminal secretory proteins into the cytosol, distinct from the ERAD and preemptive quality control pathways. Importantly, our results highlight the value of fully characterizing the cell biology of reporters and describe a simple modification to maintain luminal ER reporters in the ER during acute ER stress.
Low prevalence red blood cell antigens: transfusions, babies, and changing demographics
Authors: Hamilton Janis R.
Published: April 2020

See article on page 870–874, in this issue
Prognostic factors for short‐term survival of dogs that experience postattenuation seizures after surgical correction of single congenital extrahepatic portosystemic shunts: 93 cases (2005‐2018)
Authors: Mullins Ronan A. , Sanchez Villamil Carlos , Selmic Laura E. , Tivers Michael S. , Case J. Brad , Singh Ameet , Thieman Mankin Kelley M. , Anderson Davina M. , White Robert N. , Pratschke Kathryn M. , de Rooster Hilde , Kummeling Anne , Yool Donald A. , Olive Melanie , Dr vét Jean‐Philippe Billet , Gordo Ines , Brissot Herve , Broome Cameron , Kirby Barbara M.
Published: April 2020

Objective

To identify prognostic factors for short‐term survival of dogs that experience seizures within 7 days after surgical correction of single congenital extrahepatic portosystemic shunts (cEHPSS).

Study design

Multi‐institutional retrospective study.

Sample population

Ninety‐three client‐owned dogs.

Methods

Medical records at 14 veterinary institutions were reviewed to identify dogs that underwent surgical attenuation of a single cEHPSS from January 1, 2005 through February 28, 2018 and experienced postattenuation seizures (PAS) within 7 days postoperatively. Logistic regression analysis was performed to identify factors associated with 1‐month survival. Factors investigated included participating institution, signalment, shunt morphology, concurrent/historical conditions, presence of preoperative neurologic signs, presence of preoperative seizures, aspects of preoperative medical management, surgical details including method and degree of shunt attenuation, type of PAS (focal only or generalized ± focal), drugs administered as part of the treatment of PAS, and development of complications during treatment of PAS.

Results

Thirty (32.3%) dogs survived to 30 days. Seventy‐six (81.7%) dogs experienced generalized PAS. Factors positively associated with short‐term survival included having a history of preoperative seizures (P= .004) and development of focal PAS only (P= .0003). Most nonsurvivors were humanely euthanized because of uncontrolled or recurrent seizures.

Conclusion

Dogs that experienced PAS that had a history of preoperative seizures and those that experienced focal PAS only had significantly improved short‐term survival.

Clinical significance

The results of this study provide information that will help in the counseling of owners who seek treatment for PAS after surgical correction of cEHPSS.

© 2020 The American College of Veterinary Surgeons.
The hypertrophic cardiomyopathy mutations R403Q and R663H increase the number of myosin heads available to interact with actin
Authors: Sarkar Saswata S. , Trivedi Darshan V. , Morck Makenna M. , Adhikari Arjun S. , Pasha Shaik N. , Ruppel Kathleen M. , Spudich James A.
Published: April 2020

Hypertrophic cardiomyopathy–causing mutations disrupt a key regulatory off state of myosin in thick filaments.
Scattering of adiabatically aligned molecules by nonresonant optical standing waves
Authors: Kim Lee Yeong , Jin Byung Gwun , Kim Tae Woo , Lee Ju Hyeon , Zhao Bum Suk
Published: April 2020

The state-dependent alignment of molecules affects their scattering from nonresonant standing waves.
Lubricated friction around nanodefects
Authors: Cafolla Clodomiro , Foster William , Voïtchovsky Kislon
Published: April 2020

Nanoscale lubrication measurements around nanodefects point to local molecular ordering as the main cause for friction.
Evaluating management strategies for marine mammal populations: an example for multiple species and multiple fishing sectors in Iceland
Authors: Punt André E. , Siple Margaret , Sigurðsson Guðjón Már , Víkingsson Gísli , Francis Tessa B. , Granquist Sandra M. , Hammond Philip S. , Heinemann Dennis , Long Kristy J. , Moore Jeffrey E. , Sepúlveda Maritza , Reeves Randall R. , Wade Paul R. , Williams Rob , Zerbini Alexandre N.
Published: April 2020

A management strategy evaluation (MSE) is used to estimate success at achieving conservation goals for marine mammals while also aiming to minimize impacts on commercial fisheries. It is intended to improve understanding of US import rules that require countries exporting fish and fish products to the USA to adhere to marine mammal bycatch standards “comparable” to those used by the USA. The MSE framework is applied, for illustrative purposes, to export fisheries in Iceland that impact harbor porpoises (Phocoena phocoena), harbor seals (Phoca vitulina), and grey seals (Halichoerus grypus). Several management strategies are evaluated. The harbor porpoise population is estimated to be close to or above its maximum net productivity level (MNPL) and, according to the model, will continue to increase even if current levels of human-caused mortality are unchanged. In contrast, the grey seal and harbor seal populations are below MNPL, and bycatch mortality in the lumpfish (Cyclopterus lumpus) fishery will need to be reduced to allow them to recover to MNPL.
The liquid-argon scintillation pulseshape in DEAP-3600
Authors:   DEAP Collaboration, Adhikari P. , Ajaj R. , Araujo G. R. , Batygov M. , Beltran B. , Bina C. E. , Boulay M. G. , Broerman B. , Bueno J. F. , Butcher A. , Cai B. , Cárdenas-Montes M. , Cavuoti S. , Chen Y. , Cleveland B. T. , Corning J. M. , Daugherty S. J. , Di Stefano P. , Dering K. , Doria L. , Duncan F. A. , Dunford M. , Erlandson A. , Fatemighomi N. , Fiorillo G. , Flower A. , Ford R. J. , Gagnon R. , Gallacher D. , Garcés E. A. , Abia P. García , Garg S. , Giampa P. , Goeldi D. , Golovko V. V. , Gorel P. , Graham K. , Grant D. R. , Grobov A. , Hallin A. L. , Hamstra M. , Harvey P. J. , Hearns C. , Ilyasov A. , Joy A. , Jillings C. J. , Kamaev O. , Kaur G. , Kemp A. , Kochanek I. , Kuźniak M. , Langrock S. , La Zia F. , Lehnert B. , Levashko N. , Li X. , Litvinov O. , Lock J. , Longo G. , Machulin I. , Majewski P. , McDonald A. B. , McElroy T. , McGinn T. , McLaughlin J. B. , Mehdiyev R. , Mielnichuk C. , Monroe J. , Nadeau P. , Nantais C. , Ng C. , Noble A. J. , Oliviéro G. , Ouellet C. , Pal S. , Pasuthip P. , Peeters S. J. M. , Pesudo V. , Piro M.-C. , Pollmann T. R. , Rand E. T. , Rethmeier C. , Retière F. , García E. Sanchez , Sánchez-Pastor T. , Santorelli R. , Seeburn N. , Skensved P. , Smith B. , Smith N. J. T. , Sonley T. , Stainforth R. , Stone C. , Strickland V. , Stringer M. , Sur B. , Vázquez-Jáuregui E. , Veloce L. , Viel S. , Walding J. , Waqar M. , Ward M. , Westerdale S. , Willis J. , Zuñiga-Reyes A.
Published: April 2020

DEAP-3600 is a liquid-argon scintillation detector looking for dark matter. Scintillation events in the liquid argon (LAr) are registered by 255 photomultiplier tubes (PMTs), and pulseshape discrimination (PSD) is used to suppress electromagnetic background events. The excellent PSD performance of LAr makes it a viable target for dark matter searches, and the LAr scintillation pulseshape discussed here is the basis of PSD. The observed pulseshape is a combination of LAr scintillation physics with detector effects. We present a model for the pulseshape of electromagnetic background events in the energy region of interest for dark matter searches. The model is composed of (a) LAr scintillation physics, including the so-called intermediate component, (b) the time response of the TPB wavelength shifter, including delayed TPB emission at $${\mathcal {O}}$$O(ms) time-scales, and c) PMT response. TPB is the wavelength shifter of choice in most LAr detectors. We find that approximately 10% of the intensity of the wavelength-shifted light is in a long-lived state of TPB. This causes light from an event to spill into subsequent events to an extent not usually accounted for in the design and data analysis of LAr-based detectors.
Architectural knowledge discovery
Authors: de Boer Remco C.
Published: April 2020

The need for a method for architectural knowledge discovery stems from the difficulty to find relevant architectural knowledge in the documentation that accompanies a software product. This difficulty arises in particular when the document set is very large, and has been expressed by auditors as a need for a "reading guide" during a case study we conducted at a company that performs software product audits. Based on the needs of these auditors, we identify the main characteristics an architectural knowledge discovery method should exhibit. This paper argues that Latent Semantic Analysis (LSA) is a promising technique for architectural knowledge discovery.
A web-based tool for managing architectural design decisions
Authors: Capilla Rafael , Nava Francisco , Pérez Sandra , Dueñas Juan C.
Published: April 2020

Software architectures represent the design for describing the main parts of a software system. In software projects, different stakeholders with different roles may need to share the documentation generated during the project. Also, during the architecture construction phase we need to communicate the architecture to the stakeholders involved in the process, but the lack of tools for documenting, managing and sharing this architectural knowledge constitutes a big barrier. In other cases it can be useful to recreate the design decisions taken because such decisions are frequently lost during the development process. To cover these issues, we outline in this paper a web-based tool able to record and manage architecture design decisions.
Using variability modeling principles to capture architectural knowledge
Authors: Sinnema Marco , van der Ven Jan Salvador , Deelstra Sybren
Published: April 2020

In the field of software architectures, there is an emerging awareness of the importance of architectural decisions. In this view, the architecting process is explained as a decision process, while the design and eventually the software system are seen as the result of this decision process. However, the effects of different alternatives on the quality of the system often remain implicit. In the field of software product families, the same issues arise when configuring products. We propose to use the proven expertise from COVAMOF, a framework for managing variability, to solve the issues that arise when relating quality attributes to architectural decisions.
CETS
Authors: Nagarakatte Santosh , Zhao Jianzhou , Martin Milo M.K. , Zdancewic Steve
Published: April 2020

Temporal memory safety errors, such as dangling pointer dereferences and double frees, are a prevalent source of software bugs in unmanaged languages such as C. Existing schemes that attempt to retrofit temporal safety for such languages have high runtime overheads and/or are incomplete, thereby limiting their effectiveness as debugging aids. This paper presents CETS, a compile-time transformation for detecting all violations of temporal safety in C programs. Inspired by existing approaches, CETS maintains a unique identifier with each object, associates this metadata with the pointers in a disjoint metadata space to retain memory layout compatibility, and checks that the object is still allocated on pointer dereferences. A formal proof shows that this is sufficient to provide temporal safety even in the presence of arbitrary casts if the program contains no spatial safety violations. Our CETS prototype employs both temporal check removal optimizations and traditional compiler optimizations to achieve a runtime overhead of just 48% on average. When combined with a spatial-checking system, the average overall overhead is 116% for complete memory safety
Collecting hollywood's garbage
Authors: Petricek Tomas , Syme Don
Published: April 2020

The reactive programming model is largely different to what we're used to as we don't have full control over the application's control flow. If we mix the declarative and imperative programming style, which is usual in the ML family of languages, the situation is even more complex. It becomes easy to introduce patterns where the usual garbage collector for objects cannot automatically dispose all components that we intuitively consider garbage.

In this paper we discuss a duality between the definitions of garbage for
objects
and
events
. We combine them into a single one, to specify the notion of garbage for reactive programming model in a mixed functional/imperative language and we present a formal algorithm for collecting garbage in this environment.

Building on top of the theoretical model, we implement a library for reactive programming that does not cause leaks when used in the mixed declarative/imperative model. The library allows us to safely combine both of the reactive programming patterns. As a result, we can take advantage of the clarity and simplicity of the declarative approach as well as the expressivity of the imperative model.
The locality of concurrent write barriers
Authors: Hellyer Laurence , Jones Richard , Hosking Antony L.
Published: April 2020

Concurrent and incremental collectors require barriers to ensure correct synchronisation between mutator and collector. The overheads imposed by particular barriers on particular systems have been widely studied. Somewhat fewer studies have also compared barriers in terms of their termination properties or the volume of floating garbage they generate. Until now, the consequences for locality of different barrier choices has not been studied, although locality will be of increasing importance for emerging architectures. This paper provides a study of the locality of concurrent write barriers, independent of the processor architecture, virtual machine, compiler or garbage collection algorithm.
Efficient memory shadowing for 64-bit architectures
Authors: Zhao Qin , Bruening Derek , Amarasinghe Saman
Published: April 2020

Shadow memory is used by dynamic program analysis tools to store metadata for tracking properties of application memory. The efficiency of mapping between application memory and shadow memory has substantial impact on the overall performance of such analysis tools. However, traditional memory mapping schemes that work well on 32-bit architectures cannot easily port to 64-bit architectures due to the much larger 64-bit address space.

This paper presents EMS64, an efficient memory shadowing scheme for 64-bit architectures. By taking advantage of application reference locality and unused regions in the 64-bit address space, EMS64 provides a fast and flexible memory mapping scheme without relying on any underlying platform features or requiring any specific shadow memory size. Our experiments show that EMS64 is able to reduce the runtime shadow memory translation overhead to 81% on average, which almost halves the overhead of the fastest 64-bit shadow memory system we are aware of.
The economics of garbage collection
Authors: Singer Jeremy , Jones Richard E. , Brown Gavin , Luján Mikel
Published: April 2020

This paper argues that economic theory can improve our understanding of memory management. We introduce the
allocation curve
, as an analogue of the demand curve from microeconomics. An allocation curve for a program characterises how the amount of garbage collection activity required during its execution varies in relation to the heap size associated with that program. The standard treatment of microeconomic demand curves (shifts and elasticity) can be applied directly and intuitively to our new allocation curves. As an application of this new theory, we show how
allocation elasticity
can be used to control the heap growth rate for variable sized heaps in Jikes RVM.
Parametric inference of memory requirements for garbage collected languages
Authors: Albert Elvira , Genaim Samir , Gómez-Zamalloa Miguel
Published: April 2020

The accurate prediction of program's memory requirements is a critical component in software development. Existing heap space analyses either do not take deallocation into account or adopt specific models of garbage collectors which do not necessarily correspond to the actual memory usage. We present a novel approach to inferring upper bounds on memory requirements of Java-like programs which is
parametric
on the notion of
object lifetime
, i.e., on when objects become collectible. If objects lifetimes are inferred by a reachability analysis, then our analysis infers accurate upper bounds on the memory consumption for a
reachability
-based garbage collector. Interestingly, if objects lifetimes are inferred by a
heap liveness
analysis, then we approximate the program minimal memory requirement, i.e., the peak memory usage when using an optimal garbage collector which frees objects as soon as they become dead. The key idea is to integrate information on objects lifetimes into the process of generating the
recurrence equations
which capture the memory usage at the different program states. If the heap size limit is set to the memory requirement inferred by our analysis, it is ensured that execution will not exceed the memory limit with the only assumption that garbage collection works when the limit is reached. Experiments on Java bytecode programs provide evidence of the feasibility and accuracy of our analysis.
What Icons Communicate
Authors: Mitsock Mark
Published: April 2020

Communicating complex ideas within the limited space of an icon is one of the most challenging tasks for user interface designers. Horton's book provides a variety of tools to make this task easier and as a result, is likely to achieve the same status as a standard reference for technical communicators as his
Designing and Writing Online Documentation
.
A tested semantics for getters, setters, and eval in JavaScript
Authors: Politz Joe Gibbs , Carroll Matthew J. , Lerner Benjamin S. , Pombrio Justin , Krishnamurthi Shriram
Published: April 2020

We present S5, a semantics for the strict mode of the ECMAScript 5.1 (JavaScript) programming language. S5 shrinks the large source language into a manageable core through an implemented transformation. The resulting specification has been tested against real-world conformance suites for the language. This paper focuses on two aspects of S5: accessors (getters and setters) and eval. Since these features are complex and subtle in JavaScript, they warrant special study. Variations on both features are found in several other programming languages, so their study is likely to have broad applicability.
Patterns as objects in grace
Authors: Homer Michael , Noble James , Bruce Kim B. , Black Andrew P. , Pearce David J.
Published: April 2020

Object orientation and pattern matching are often seen as conflicting approaches to program design. Object-oriented programs place type-dependent behavior inside objects and invoke it via dynamic dispatch, while pattern-matching programs place type-dependent behavior outside data structures and invoke it via multiway conditionals (case statements).

Grace is a new, dynamic, object-oriented language designed to support teaching: to this end, Grace needs to support both styles. We explain how this conflict can be resolved gracefully: by modelling patterns and cases as partial functions, reifying those functions as objects, and then building up complex patterns from simpler ones using pattern combinators. We describe the implementation of this design as an object-oriented framework, and a case study of its effectiveness.
Adaptive data parallelism for internet clients on heterogeneous platforms
Authors: Pignotti Alessandro , Welc Adam , Mathiske Bernd
Published: April 2020

Today's Internet is long past static web pages filled with HTML-formatted text sprinkled with an occasional image or animation. We have entered an era of Rich Internet Applications executed locally on Internet clients such as web browsers: games, physics engines, image rendering, photo editing, etc. Yet today's languages used to program Internet clients have limited ability to tap to the computational capabilities of the underlying, often heterogeneous, platforms. In this paper we present how a Domain Specific Language(DSL) can be integrated into ActionScript, one of the most popular scripting languages used to program Internet clients and a close cousin of JavaScript. We demonstrate how our DSL, called ASDP (ActionScript Data Parallel), can be used to enable data parallelism for existing sequential programs. We also present a prototype of a system where data parallel workloads can be executed on either CPU or a GPU, with the runtime system transparently selecting the best processing unit, depending on the type of workload as well as the architecture and current load of the execution platform. We evaluate performance of our system on a variety of benchmarks, representing different types of workloads: physics, image processing, scientific computing and cryptography.
Ownership, filters and crossing handlers
Authors: Wernli Erwann , Maerki Pascal , Nierstrasz Oscar
Published: April 2020

Sharing mutable objects can result in broken invariants, exposure of internal details, and other subtle bugs. To prevent such issues, it is important to control accessibility and aliasing of objects. Dynamic Ownership is an effective way to do so, but its owner-as-dominator discipline is too restrictive: objects are either accessible or not. We propose in this paper to control accessibility and aliasing with more flexibility using two mechanisms, filters and crossing handlers. We demonstrate the benefits of the flexibility offered by these mechanisms, and report on the adaptation of a Smalltalk web server with our approach. We conclude that our variant of dynamic ownership is flexible enough to accommodate an existing design, while at the same time constraining it enough to highlight design anomalies.
Detecting conflicts among declarative UI extensions
Authors: Lerner Benjamin S. , Grossman Dan
Published: April 2020

We examine overlays, a flexible aspect-like mechanism for third-party declarative extensions of declarative UIs. Overlays can be defined for any markup language and permit extensions to define new content that is dynamically woven into a base UI document. While powerful, overlays are inherently non-modular and may conflict with each other, by defining duplicate or contradictory UI components. We construct an abstract language to capture core overlay semantics, and design an automatic analysis to detect inter-extension conflicts. We apply the analysis to a case study of Firefox extensions, finding several real-world bugs. Our analysis provides low-level feedback to extension developers and high-level reports to end users. Finally, we show how variants of overlays more expressive than those of Firefox complicate conflict detection.
Paragon
Authors: Delimitrou Christina , Kozyrakis Christos
Published: April 2020

Large-scale datacenters (DCs) host tens of thousands of diverse applications each day. However, interference between colocated workloads and the difficulty to match applications to one of the many hardware platforms available can degrade performance, violating the quality of service (QoS) guarantees that many cloud workloads require. While previous work has identified the impact of heterogeneity and interference, existing solutions are computationally intensive, cannot be applied online and do not scale beyond few applications.

We present Paragon, an online and scalable DC scheduler that is heterogeneity and interference-aware. Paragon is derived from robust analytical methods and instead of profiling each application in detail, it leverages information the system already has about applications it has previously seen. It uses collaborative filtering techniques to quickly and accurately classify an unknown, incoming workload with respect to heterogeneity and interference in multiple shared resources, by identifying similarities to previously scheduled applications. The classification allows Paragon to greedily schedule applications in a manner that minimizes interference and maximizes server utilization. Paragon scales to tens of thousands of servers with marginal scheduling overheads in terms of time or state.

We evaluate Paragon with a wide range of workload scenarios, on both small and large-scale systems, including 1,000 servers on EC2. For a 2,500-workload scenario, Paragon enforces performance guarantees for 91% of applications, while significantly improving utilization. In comparison, heterogeneity-oblivious, interference-oblivious and least-loaded schedulers only provide similar guarantees for 14%, 11% and 3% of workloads. The differences are more striking in oversubscribed scenarios where resource efficiency is more critical.
ConAir
Authors: Zhang Wei , de Kruijf Marc , Li Ang , Lu Shan , Sankaralingam Karthikeyan
Published: April 2020

Many concurrency bugs are hidden in deployed software and cause severe failures for
end-users
. When they finally manifest and become known by
developers
, they are difficult to fix correctly. To support end-users, we need techniques that help software survive hidden concurrency bugs during production runs. To help developers, we need techniques that fix exposed concurrency bugs.

The state-of-the-art techniques on concurrency-bug fixing and survival only satisfy a subset of four important properties: compatibility, correctness, generality, and performance.We aim to develop a system that satisfies all of these four properties. To achieve this goal, we leverage two observations: (1) rolling back a
single
thread is sufficient to recover from most concurrency-bug failures; (2) reexecuting an
idempotent
region, which requires no memory-state checkpoint, is sufficient to recover from many concurrency-bug failures. Our system ConAir includes a static analysis component that automatically identifies potential failure sites, a static analysis component that automatically identifies the idempotent code regions around every failure site, and a code-transformation component that inserts rollback-recovery code around the identified idempotent regions.

We evaluated ConAir on 10 real-world concurrency bugs in widely used C/C++ open-source applications. These bugs cover different types of failure symptoms and root causes. Quantitatively, ConAir helps software survive failures caused by all of these bugs with negligible run-time overhead (<1%) and short recovery time. Qualitatively, ConAir can help recover from failures caused by unknown bugs. It guarantees that program semantics remain unchanged and requires no change to operating systems or hardware.
DeAliaser
Authors: Ahn Wonsun , Duan Yuelu , Torrellas Josep
Published: April 2020

Alias analysis is a critical component in many compiler optimizations. A promising approach to reduce the complexity of alias analysis is to use speculation. The approach consists of performing optimizations assuming the alias relationships that are true most of the time, and repairing the code when such relationships are found not to hold through runtime checks.

This paper proposes a general alias speculation scheme that leverages upcoming hardware support for transactions with the help of some ISA extensions. The ability of transactions to checkpoint and roll back frees the compiler to pursue aggressive optimizations without having to worry about recovery code. Also, exposing the memory conflict detection hardware in transactions to software allows runtime checking of aliases with little or no overhead. We test the potential of the novel alias speculation approach with Loop Invariant Code Motion (LICM), Global Value Numbering (GVN), and Partial Redundancy Elimination (PRE) optimization passes. On average, they are shown to reduce program execution time by 9% in SPEC FP2006 applications and 3% in SPEC INT2006 applications over the alias analysis of a state-of-the-art compiler.