bluuebunny/crossref_metadata_2025 huggingface dataset:
Strategy to identify resistance to white mould associated with high yield for irrigated common bean in Brazil
Authors: Lima Renan C. , Teixeira Pablo H. , Souza Ari F. F. , Paula Júnior Trazilbo J. , Teixeira Hudson , Lehner Miller S. , Carneiro José E. S. , Marçal Tiago S. , Vieira Rogerio F.
Published: April 2020

Development of common bean cultivars with partial white mould resistance through breeding techniques has been a challenge in Brazil. As yet, lines/cultivars from breeding programmes have not been investigated for resistance; therefore, this study screened 107 lines/cultivars for their reactions to white mould in 14 preliminary trials conducted under irrigation. Thirteen resistant lines/cultivars (three of Andean origin) and six Mesoamerican cultivars (three intermediately resistant and three susceptible) were selected for further investigation. These lines/cultivars and the resistant control A195 were evaluated in six advanced trials and two straw tests to assess the effectiveness of the screening procedure. In 11 preliminary trials, screenings were performed under moderate/high or higher disease pressure. These pressures occurred in two advanced trials in which, when yields were averaged across moderate/high and high pressures, 10 Mesoamerican lines/cultivars selected for resistance yielded 14%, 23%, and 38% more than intermediately resistant cultivars, A195, and susceptible cultivars, with median disease ratings (1–9 scale) of 4.5, 5.7, 5.7, and 6.7, respectively. In the straw test, three Andean lines/cultivars (A195 included) and two susceptible cultivars in the field were among those with the highest levels of physiological resistance. Thus, field rating under high disease pressure and greenhouse rating did not correlate significantly, suggesting that field trials are critical to evaluating resistance and to identifying high‐yielding beans. Therefore, lines/cultivars from breeding programmes assessed in field trials may provide a low cost and fast way to identify high‐yielding bean cultivars with partial resistance to white mould in the subtropical southern hemisphere.
Plausible association between drought stress tolerance of barley (Hordeum vulgare L.) and programmed cell death via MC1 and TSN1 genes
Authors: Shamloo‐Dashtpagerdi Roohollah , Lindlöf Angelica , Aliakbari Massume , Pirasteh‐Anosheh Hadi
Published: April 2020

Studying the drought‐responsive transcriptome is of high interest as it can serve as a blueprint for stress adaptation strategies. Despite extensive studies in this area, there are still many details to be uncovered, such as the importance of each gene involved in the stress response as well as the relationship between these genes and the physiochemical processes governing stress tolerance. This study was designed to address such important details and to gain insights into molecular responses of barley (Hordeum vulgare L.) to drought stress. To that, we combined RNA‐seq data analysis with field and greenhouse drought experiments in a systems biology approach. RNA‐sequence analysis identified a total of 665 differentially expressed genes (DEGs) belonging to diverse functional categories. A gene network was derived from the DEGs, which comprised of a total of 131 nodes and 257 edges. Gene network topology analysis highlighted two programmed cell death (PCD) modulating genes, MC1 (metacaspase 1) and TSN1 (Tudor‐SN 1), as important (hub) genes in the predicted network. Based on the field trial, a drought‐tolerant and a drought‐susceptible barley genotype was identified from eight tested cultivars. Identified genotypes exhibited different physiochemical characteristics, including proline content, chlorophyll concentration, percentage of electrolyte leakage and malondialdehyde content as well as expression profiles of MC1 and TSN1 genes. Machine learning and correspondence analysis revealed a significant relationship between drought tolerance and measured characteristics in the context of PCD. Our study provides new insights which bridge barley drought tolerance to PCD through MC1 and TSN1 pathway.
Early elbow osteoarthritis in competitive enduro motorcyclist
Authors: Guglielmino Claudia , Musumeci Giuseppe
Published: April 2020

This case report speculates that prolonged vibration from enduro off‐road sport is deleterious for the elbow joint. This contribution could also aid sports physicians in better understanding this complex unknown phenomenon. No published data are present in the current literature that demonstrates the correlation between early elbow osteoarthritis in enduro motorcyclist overuse.
Early time course of change in angiogenic proteins in human skeletal muscle and vascular cells with endurance training
Authors: Hoier Birgitte , Olsen Karina , Hanskov Dorte J. A. , Jorgensen Maria , Norup Liselotte R. , Hellsten Ylva
Published: April 2020

Angiogenic, mitochondrial, and related transcriptional proteins were assessed in human skeletal muscle and isolated vascular cells during the early phase of endurance training. Thigh muscle biopsies were obtained in healthy young subjects, after one acute bout (n = 9) and after 3, 5, 7, and 14 days (n = 9) of cycle ergometer training. Whole muscle homogenates were analyzed for angiogenic, mitochondrial, and regulatory mRNA and protein levels. Angiogenic proteins were determined in muscle‐derived endothelial cells and pericytes sorted by fluorescence‐activated cell sorting. Acute exercise induced an increase in whole muscle mRNA of peroxisome proliferator‐activated receptor gamma coactivator 1α (4.5‐fold; P = .002) and vascular endothelial growth factor (VEGF) (2.4‐fold; P = .001) at 2 hours post. After 14 days of training, there was an increase in CD31 protein (63%; P = .010) in whole muscle indicating capillary growth. There was also an increase in muscle VEGF receptor 2 (VEGFR2) (1.5‐fold; P = .013), in OXPHOS proteins (complex I, II, IV, V; 1.4‐ to 1.9‐fold; P < .05) after 14 days of training and an increase in estrogen‐related receptorα protein (1.5‐fold; P = .039) at 14 days compared to 5 days of training. Both endothelial cells and pericytes expressed VEGF and other angiogenic factors at the protein level but with a distinctively lower expression of VEGFR2 and thrombospondin‐1 (TSP‐1) in pericytes. The findings illustrate that initiation of capillary and mitochondrial adaptations occurs within 14 days of training and suggest that sustained changes in angiogenic proteins including VEGF and TSP‐1 are moderate in whole muscle and vascular cells.
Effects of active commuting on health‐related quality of life and sickness‐related absence
Authors: Neumeier Luis M. , Loidl Martin , Reich Bernhard , Fernandez La Puente de Battre Maria Dolores , Kissel Christine K. , Templin Christian , Schmied Christian , Niebauer Josef , Niederseer David
Published: April 2020

Increased physical activity is associated with numerous health benefits. This study investigated the effect of active commuting (walking and cycling to work) on health‐related quality of life (HRQoL) and absence days from work due to sickness in healthy working adults. In total, 73 participants (age: 46 ± 9 years), all working at a tertiary university hospital in Salzburg, Austria, were randomized into an intervention group (IG, n = 51) and a control group (CG, n = 22). The IG was asked to commute actively for twelve months, whereas the CG did not have to change their usual commuting behavior. IG was divided into two subgroups: IG‐C (cycling, n = 26) was asked to commute by bicycle and IG‐PT (public transport, n = 25) partially using public transportation and walked the remaining distance to work. Significant positive changes in IG were observed in four subcomponents of the SF‐36 (physical functioning (95 [10] to 100 [8.8], P = .023), mental health (82 [15] to 86 [15], P = .036), vitality (65 [20] to 70 [14], P = .005), and general health (70 [19] to 80 [24], P = .004)) as well as the physical component summary score (56.5 [9] to 59.2 [6.3], P = .002). IG‐C showed greater and more statistically significant changes regarding HRQoL compared to IG‐PT. Associations between active commuting and sick‐leave days were only observed in IG‐PT (7.5 [14.8] to 4.0 [11.3] days, P = .038). In conclusion, active commuting improves various components of HRQoL and might therefore be a possible strategy to increase quality of life in the workforce.
Sentential Names in Tiv1
Authors: Mensah Eyo , Ishima Jighjigh
Published: April 2020

This article explores and analyses Tiv personal names which are composed of sentences. The structural, semantic and pragmatic characteristics of these sentence names are described, and simplex sentence names with their unique grammatical peculiarities and propositional contents are identified. Ethnographic data for this research was obtained through interviews, metalinguistic conversations and participant observations in two Tiv speaking communities: Gboko and Makurdi in Benue State, North‐central Nigeria. In this article, Tiv sentential names are presented and it is argued that they are not mere referential expressions but also provide a reflection of the grammatical structure of the Tiv language. We conclude that the structure of Tiv sentential names is not constrained to any particular set of expressions; as they have semantic and pragmatic attributes which denote some extralinguistic realities that also contribute to the organization of Tiv grammar and the mental representation of the native speakers’ linguistic competence.
HLA‐B*51:315, identified using next‐generation sequencing‐based typing in a Korean individual
Authors: Ham Ji Yeon , Choi So‐Jung , Ryu Jimin , Lee Nan Young , Song Kyung Eun
Published: April 2020

HLA‐B*51:315 differs from B*51:01:01:01 by a single nucleotide polymorphism in codon 87 (CAG → CGG).
HLA‐DQB1*05:66:01, a novel variant of HLA‐DQB1*05, identified in a Singaporean Malay bone marrow donor
Authors: Cho Louise , Kaur Ashminder , Cereb Nezih , Lin Py‐Yu , Yang Kuo‐Liang
Published: April 2020

Nucleotide substitutions in codon 38 of HLA‐DQB1*05:03:01:01 result in a novel allele, HLA‐DQB1*05:66:01
Biological behaviour and ezrin expression in canine rhabdomyosarcomas: 25 cases (1990‐2012)
Authors: Connell Dana R. , Rodriguez Carlos O. , Sternberg Rachel A. , Singh Kuldeep , Barger Anne , Garrett Laura D.
Published: April 2020

There are few published reports of canine rhabdomyosarcomas. In human paediatrics, rhabdomyosarcomas account for 5%‐10% of all tumours and >50% of soft tissue sarcomas. They have an aggressive biologic behaviour; most patients develop diffuse metastatic disease. Ezrin, a cytoskeleton linker protein, has been correlated with metastasis in a number of tumours, including rhabdomyosarcomas. The goal of this study was to describe dogs with non‐urinary rhabdomyosarcomas including clinical findings, ezrin expression and outcome. Twenty‐five dogs with rhabdomyosarcomas were identified from two institutions' databases. Signalment, primary tumour location, cytologic and histologic findings, metastatic sites, treatments, survival time and necropsy results were recorded. Immunohistochemical staining for ezrin expression was performed on archived samples; cellular localization of ezrin was characterized. The mean and median age of all patients was 4.3 and 2 years, respectively. Subcutaneous and retrobulbar/orbital were the most common primary tumour locations. Sixteen dogs had metastatic disease at diagnosis. Three dogs presented with diffuse disease where a primary tumour could not be identified. A round cell tumour was the initial diagnosis in 32% of cases, and 76% of cases required immunohistochemistry to establish the diagnosis. The median survival was 10 days. Twenty‐one cases had archived samples available for ezrin staining; all but one was positive and exhibited both membranous and cytoplasmic localization. Rhabdomyosarcomas occur in young dogs, may have a round cell appearance, and exhibit aggressive biologic behaviour. Given ezrin's defined role in metastasis, its observed expression in the tumours in this study suggest its possible role in canine rhabdomyosarcoma's aggressive biologic behaviour.
Multicenter flow cytometry proficiency testing of canine blood and lymph node samples
Authors: Meichner Kristina , Stokol Tracy , Tarigo Jaime , Avery Anne , Burkhard Mary J. , Comazzi Stefano , Fogle Jonathan , Stowe Devorah Marks , Rütgen Barbara , Seelig Davis , Wasserkrug‐Naor Adi , Vernau William , Bienzle Dorothee
Published: April 2020

Background

Flow cytometry (FC) is used increasingly in veterinary medicine for further characterization of hematolymphoid cells. Guidelines for optimizing assay performance and interpretation of results are limited, and concordance of results across laboratories is unknown.

Objectives

This study aimed to determine inter‐investigator agreement on the interpretation of FC results from split samples analyzed in different laboratories using various protocols, cytometers, and software; and on the interpretation of archived FC standard (FCS) data files contributed by the different investigators.

Methods

This was a multicenter observational cross‐sectional study. Anticoagulated blood or lymph node aspirate samples from nine client‐owned dogs were aliquoted and shipped to participating laboratories. Samples were analyzed with individual laboratory‐developed protocols. In addition, FCS files from a set of separate samples from 11 client‐owned dogs were analyzed by participating investigators. A person not associated with the study tabulated the results and interpretations. Agreement of interpretations was assessed with Fleiss’ kappa statistic.

Results

Prolonged transit times affected sample quality for some laboratories. Overall agreement among investigators regarding the FC sample interpretation was strong (κ = 0.86 ± 0.19, P < .001), and for specific categories, ranged from moderate to perfect. Agreement of the lymphoproliferation or other leukocyte sample category from the analysis of the FCS files was weak (κ = 0.58 ± 0.05, P < .001).

Conclusions

Lymphoproliferations were readily identified by FC, but identification of the categories of hematolymphoid neoplasia in fresh samples or archived files was variable. There is a need for a more standardized approach to maximize the enormous potential of FC in veterinary medicine.
Finite and non‐finite complement clauses in postcolonial Englishes
Authors: García‐Castro Laura
Published: April 2020

This paper explores the variability between finite and non‐finite complement clauses (CCs) afterremembermeaning ‘recall,’ looking at three postcolonial Englishes (PCEs), Indian, English and Sri Lankan Englishes, and British English as represented in the Corpus of Global Web‐based English (GloWbE). Taking a holistic approach, it examines the distribution and the potential language‐external and internal factors which may cause divergence between L1 and L2 varieties. Language‐external factors, such as innovation, language contact and second‐language (SLA) acquisition processes (Schneider, 2007: 88), appear to prompt the greater proportion of finite complement clauses found in the postcolonial Englishes, as expected based on the alleged tendency towards simplification of these varieties (Williams, 1987). However, the binary logistic regression analyses of language‐internal variables, largely related to the complexity principle (Rohdenburg, 1996, 2006), reveal that common language‐internal factors, apart from variety of English, also condition the choice of complement clause in the four varieties.
Use of Evidence‐based Practice Models and Research Findings in Magnet‐Designated Hospitals Across the United States: National Survey Results
Authors: Speroni Karen Gabel , McLaughlin Maureen Kirkpatrick , Friesen Mary Ann
Published: April 2020

Background

All nurses have responsibilities to enculturate evidence‐based practice (EBP) and translate and implement research findings into nursing care, practices, and procedures.

Aims

To report EBP‐related findings from the national Hospital‐Based Nursing Research Characteristics, Care Delivery Outcomes, and Economic Impact Survey questionnaire.

Methods

In this cross‐sectional survey research study of 181 nursing research leaders, 127 responded to these questions: “Has your hospital adopted or does it use a model of evidence‐based practice?” “If yes, what is the name of the model and how is it used?” “Does your hospital implement (translate) findings from nursing research into clinical practice?” “Describe how your hospital implements these findings and whose responsibility it is.” “What factors do you believe facilitate the implementation of findings from nursing research into clinical practice at your hospital?” Qualitative content analyses were used.

Results

Over 90% of nursing research leaders specified that their hospital used an EBP model and implements findings into practice. The most frequently reported models were the Iowa Model of Evidence‐Based Practice, Johns Hopkins Nursing Evidence‐Based Practice Model, and Advancing Research and Clinical Practice Through Close Collaboration Model. EBP models were used most frequently for education and training, nurse residency programs, and EBP and research fellowships. Findings were implemented through policy and procedure committee processes, shared governance structures, and EBP processes. Those responsible for implementing findings were project leads, nursing professional practice councils, and clinical nurse specialists and advanced practice nurses. Implementation facilitators were nursing leadership, dissemination of findings, and engaged and educated nurses.

Linking Evidence to Action

These new findings report >90% EBP model use and implementation. All nurses, especially our leaders, have responsibilities to evaluate EBP and how nursing research findings are implemented (translated) into practice. Ideally, engaged and educated nurses who enculturate, support, and sustain EBP will facilitate advancing nursing practice to improve patient and work environment–related outcomes.
Evaluating the fake news problem at the scale of the information ecosystem
Authors: Allen Jennifer , Howland Baird , Mobius Markus , Rothschild David , Watts Duncan J.
Published: April 2020

Mainstream news, mainly on television, vastly outweighs fake news, and news itself is a small fraction of U.S. media consumption.
Quantum computation solves a half-century-old enigma: Elusive vibrational states of magnesium dimer found
Authors: Yuwono Stephen H. , Magoulas Ilias , Piecuch Piotr
Published: April 2020

Quantum computations unravel the mystery of spectral lines that have escaped experimental detection for decades.
Direct observation of minibands in a twisted graphene/WS
2
bilayer
Authors: Ulstrup Søren , Koch Roland J. , Singh Simranjeet , McCreary Kathleen M. , Jonker Berend T. , Robinson Jeremy T. , Jozwiak Chris , Rotenberg Eli , Bostwick Aaron , Katoch Jyoti , Miwa Jill A.
Published: April 2020

We show the first direct observation of minibands in the electronic structure of a twisted heterobilayer using microfocused ARPES.
Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation
Authors: Sharma Nandini , Ahalawat Navjeet , Sandhu Padmani , Strauss Erick , Mondal Jagannath , Anand Ruchi
Published: April 2020

Transfer of labile intermediate in bifunctional enzymes occurs via transient molecular tunnels controlled by allosteric signals.
Methanotrophic bacterial symbionts fuel dense populations of deep-sea feather duster worms (Sabellida, Annelida) and extend the spatial influence of methane seepage
Authors: Goffredi Shana K. , Tilic Ekin , Mullin Sean W. , Dawson Katherine S. , Keller Abigail , Lee Raymond W. , Wu Fabai , Levin Lisa A. , Rouse Greg W. , Cordes Erik E. , Orphan Victoria J.
Published: April 2020

Hidden in plain sight: Methanotrophic feather duster worms redefine the methane seep sphere of influence.
Metal-free activation of molecular oxygen by covalent triazine frameworks for selective aerobic oxidation
Authors: Abednatanzi Sara , Gohari Derakhshandeh Parviz , Leus Karen , Vrielinck Henk , Callens Freddy , Schmidt Johannes , Savateev Aleksandr , Van Der Voort Pascal
Published: April 2020

Low-cost metal-free catalysts enable O
2
activation as a key step in many important sustainable processes.
Quantum biology revisited
Authors: Cao Jianshu , Cogdell Richard J. , Coker David F. , Duan Hong-Guang , Hauer Jürgen , Kleinekathöfer Ulrich , Jansen Thomas L. C. , Mančal Tomáš , Miller R. J. Dwayne , Ogilvie Jennifer P. , Prokhorenko Valentyn I. , Renger Thomas , Tan Howe-Siang , Tempelaar Roel , Thorwart Michael , Thyrhaug Erling , Westenhoff Sebastian , Zigmantas Donatas
Published: April 2020

We revise the interpretation of coherence signals in photosynthetic systems and clarify what they tell us about light harvesting.
Symmetry breaking in hydrodynamic forces drives meiotic spindle rotation in mammalian oocytes
Authors: Wang HaiYang , Li Yizeng , Yang Jing , Duan Xing , Kalab Petr , Sun Sean X. , Li Rong
Published: April 2020

Actin cytoskeletal asymmetry produces unbalanced hydrodynamic forces to drive spindle rotation during mouse meiotic division.
Goldilocks conditions required for earthquakes to trigger basaltic eruptions: Evidence from the 2015 Ambrym eruption
Authors: Hamling I. J. , Kilgour G.
Published: April 2020

Modeling suggests that partially cooled and crystallized basaltic magmas are more susceptible to triggering from earthquakes.
Vaporizable endoskeletal droplets via tunable interfacial melting transitions
Authors: Shakya Gazendra , Hoff Samuel E. , Wang Shiyi , Heinz Hendrik , Ding Xiaoyun , Borden Mark A.
Published: April 2020

Interfacial melting of an internal solid hydrocarbon “skeletal” phase initiates vaporization of liquid fluorocarbon droplets.
Genome elimination mediated by gene expression from a selfish chromosome
Authors: Dalla Benetta Elena , Antoshechkin Igor , Yang Ting , Nguyen Hoa Quang My , Ferree Patrick M. , Akbari Omar S.
Published: April 2020

A selfish B chromosome in the jewel wasp actively mediates its own drive by expression of the
haploidizer
gene.
Fluctuation-induced force in homogeneous isotropic turbulence
Authors: Spandan Vamsi , Putt Daniel , Ostilla-Mónico Rodolfo , Lee Alpha A.
Published: April 2020

We find an analog to the quantum Casimir effect in a turbulent fluid.
Design decision rationale
Authors: Falessi Davide , Becker Martin , Cantone Giovanni
Published: April 2020

Design decisions crucially influence the success of every software project. While the resulting design is typically documented quite well, the situation is usually different for the underlying rationale and decision-making process. Despite being recognized as a helpful approach in general, the explicit documentation of Design Decision Rationale (DDR) is not yet largely utilized due to some inhibitors (e.g., additional documentation effort). Experience with other qualities, e.g. software reusability, evidently shows that an improvement of these qualities only pays off on a large scale and therefore has to be pursued in a strategic, pre-planned, and carefully focused way. In this paper we argue that this also has to be considered for documenting DDR. To this end the paper presents: (i) the Decision, Goal, and Alternatives (DGA) DDR framework, (ii) experience in dealing with DGA, (iii) motivators and inhibitors of using DDR, and (iv) an approach for systematic DDR use that follows value-based software engineering principles.
Tailoring knowledge sharing to the architecting process
Authors: Farenhorst Rik
Published: April 2020

Sharing knowledge pertaining to software architectures becomes increasingly important. If this knowledge is not explicitly stored or communicated, valuable knowledge dissipates. However, knowledge sharing is challenged by the fact that stakeholders are often located at large distances from each other, now that offshoring and virtual organizations become the trend. We conjecture that successful architectural knowledge sharing is only possible when the sharing mechanisms are tailored to the architecting process. We base this claim on observations made during a case study in a large software organization, and some important lessons learned from these observations.
Declarative programming for artificial intelligence applications
Authors: Lloyd John W.
Published: April 2020

In this talk, I will consider some possible extensions to existing functional programming languages that would make them more suitable for the important and growing class of artificial intelligence applications. First, I will motivate the need for these language extensions. Then I will give some technical detail about these extensions that provide the logic programming idioms, probabilistic computation, and modal computation. Some examples will be given to illustrate these ideas which have been implemented in the Bach programming language that is an extension of Haskell.
A Commentary on Horton's Designing and Writing Online Documentation
Authors: Simpson Mark
Published: April 2020

The technical writing community is fortunate to have William Horton's book because it is among the first to provide comprehensive, well thought-out advice about the issues writers and online designers face almost daily. But as one reviewer has already pointed out, "gaps exist, and we should be willing to review" Horton's book (Johnson, 1990, p. 181).
Online Documentation and Social Construction
Authors: Barrett Edward
Published: April 2020

Designing and Writing Online Documentation: Help Files to Hypertextby William Horton is a valuable reference guide. This guide addresses designers and writers of various kinds of text that will appear in some fashion and for a variety of reasons on the display monitor of a computer. (The computer might also have a connection to a network.) This books presents the best of current research and commentary by experts from various fields about the subject of online documentation. I assume this is the opinion of all reviewers of this text. What I want to say in this commentary rests upon the assumption that this text belongs on your shelf.
PHALANX
Authors: Vechev Martin , Yahav Eran , Yorsh Greta
Published: April 2020

Unrestricted use of heap pointers makes software systems difficult to understand and to debug. To address this challenge, we developed PHALANX -- a practical framework for dynamically checking expressive heap properties such as ownership, sharing and reachability. PHALANX uses novel parallel algorithms to efficiently check a wide range of heap properties utilizing the available cores.

PHALANX runtime is implemented on top of IBM's Java production virtual machine. This has enabled us to apply our new techniques to real world software. We checked expressive heap properties in various scenarios and found the runtime support to be valuable for debugging and program understanding. Further, our experimental results on DaCapo and other benchmarks indicate that evaluating heap queries using parallel algorithms can lead to significant performance improvements, often resulting in linear speedups as the number of cores increases.

To encourage adoption by programmers, we extended an existing JML compiler to translate expressive JML assertions about the heap into their efficient implementation provided by PHALANX. To debug her program, a programmer can annotate it with expressive heap assertions in JML, that are efficiently checked by PHALANX.
Speculative parallelization using state separation and multiple value prediction
Authors: Tian Chen , Feng Min , Gupta Rajiv
Published: April 2020

With the availability of chip multiprocessor (CMP) and simultaneous multithreading (SMT) machines, extracting thread level parallelism from a sequential program has become crucial for improving performance. However, many sequential programs cannot be easily parallelized due to the presence of dependences. To solve this problem, different solutions have been proposed. Some of them make the optimistic assumption that such dependences rarely manifest themselves at runtime. However, when this assumption is violated, the recovery causes very large overhead. Other approaches incur large synchronization or computation overhead when resolving the dependences. Consequently, for a loop with frequently arising cross-iteration dependences, previous techniques are not able to speed up the execution. In this paper we propose a compiler technique which uses state separation and multiple value prediction to speculatively parallelize loops in sequential programs that contain frequently arising cross-iteration dependences. The key idea is to generate multiple versions of a loop iteration based on multiple predictions of values of variables involved in cross-iteration dependences (i.e., live-in variables). These speculative versions and the preceding loop iteration are executed in separate memory states simultaneously. After the execution, if one of these versions is correct (i.e., its predicted values are found to be correct), then we merge its state and the state of the preceding iteration because the dependence between the two iterations is correctly resolved. The memory states of other incorrect versions are completely discarded. Based on this idea, we further propose a runtime adaptive scheme that not only gives a good performance but also achieves better CPU utilization. We conducted experiments on 10 benchmark programs on a real machine. The results show that our technique can achieve 1.7x speedup on average across all used benchmarks.
Improved replication-based incremental garbage collection for embedded systems
Authors: Ugawa Tomoharu , Iwasaki Hideya , Yuasa Taiichi
Published: April 2020

We have developed an incremental compacting garbage collector for embedded Java systems. The collector divides the heap into equal sized pages and uses the segregated free lists for fast allocation. Collectors that have such a heap layout have a problem of fragmentation in allocating objects larger than the page size. We solve this problem by using the replication-based incremental compaction. The compactor evacuates all objects in one area, the evacuation area, of the heap, thereby creating a large chunk of free space. We developed an algorithm for choosing the evacuation area that effectively cures fragmentation. The compactor does not use any read-barriers. Instead, it uses a technique similar to the replication-based incremental copying collection. This needs forwarding pointers for all evacuated objects. Rather than introducing an extra field for each object, we use a hash table to store forwarding pointers.

Evaluation of this garbage collector implemented in Sun's J2ME Java Virtual Machine showed that all the benchmarks used were able to run without memory starvation using the heap sizes of only 151%-286% of the maximum amount of live data plus 8 KB of the hash table. Experiments on a desktop computer, though it is not a platform for embedded systems, showed that the maximum pause time was shorter than 200 μs, which was comparable to that of our implementation of the snapshot-at-the-beginning collector without compaction. On an ARM processor, the runtime overhead was 1%-16% with 8.0% on average compared to the mark-sweep collector.
Book review: Chemical Searching on an Array Processor by Terence Wilson, John Wiley & Sons, New York (ISBN 0-471-93436-4) Research Studies Press, Somerset, England (ISBN 9-86380-125-5) Hard cover, 197 pages, $115
Authors: Sherwood Peter
Published: April 2020

This book is apparently the author's 1991 Ph.D. thesis, completed at the University of Sheffield under the supervision of Peter Willett. The goal of the work was to explore the use of parallel processing to search a database of molecular structures for partial matches. The structure of a molecule may be expressed as a graph, so the partial matching is a search for subgraph isomorphisms. Since in general this is an NP- complete problem, a set of heuristics was used.
Book review: Research Directions in Concurrent Object-Oriented Programming (Gul Agha, Peter Wegner, and Akinorl Yonezawa, eds; MIT Press, 1993; 532pp.
Authors: Hooper John
Published: April 2020

From the preface: "Because parallelism is a natural consequence of the use of objects, the development of systems for concurrent object-oriented programming is providing important software support for a new generation of concurrent computers."
Robust scripting via patterns
Authors: Bloom Bard , Hirzel Martin J.
Published: April 2020

Dynamic typing in scripting languages is a two-edged sword. On the one hand, it can be more flexible and more concise than static typing. On the other hand, it can lead to less robust code. We argue that patterns can give scripts much of the robustness of static typing, without losing the flexibility and concision of dynamic typing. To make this case, we describe a rich pattern system in the dynamic language Thorn. Thorn patterns interact with its control constructs and scoping rules to support concise and robust test-and-extract idioms. Thorn patterns encompass an extensive set of features from ML-style patterns to regular expressions and beyond. And Thorn patterns can be first-class and support pattern-punning (mirror constructor syntax). Overall, this paper describes a powerful pattern system that makes scripting more robust.
CoExist
Authors: Steinert Bastian , Cassou Damien , Hirschfeld Robert
Published: April 2020

Programmers make many changes to the program to eventually find a good solution for a given task. In this course of change, every intermediate development state can of value, when, for example, a promising ideas suddenly turn out inappropriate or the interplay of objects turns out more complex than initially expected before making changes. Programmers would benefit from tool support that provides immediate access to source code and run-time of previous development states of interest. We present IDE extensions, implemented for Squeak/Smalltalk, to preserve, retrieve, and work with this information. With such tool support, programmers can work without worries because they can rely on tools that help them with whatever their explorations will reveal. They no longer have to follow certain best practices only to avoid undesired consequences of hanging code.
Incremental graph pattern matching
Authors: Fan Wenfei , Wang Xin , Wu Yinghui
Published: April 2020

Graph pattern matching is commonly used in a variety of emerging applications such as social network analysis. These applications highlight the need for studying the following two issues. First, graph pattern matching is traditionally defined in terms of subgraph isomorphism or graph simulation. These notions, however, often impose too strong a topological constraint on graphs to identify meaningful matches. Second, in practice a graph is typically large, and is frequently updated with small changes. It is often prohibitively expensive to recompute matches starting from scratch via batch algorithms when the graph is updated.

This article studies these two issues. (1) We propose to define graph pattern matching based on a notion of
bounded simulation
, which extends graph simulation by specifying the connectivity of nodes in a graph within a predefined number of hops. We show that bounded simulation is able to find sensible matches that the traditional matching notions fail to catch. We also show that matching via bounded simulation is in cubic time, by giving such an algorithm. (2) We provide an account of results on incremental graph pattern matching, for matching defined with graph simulation, bounded simulation, and subgraph isomorphism. We show that the incremental matching problem is
unbounded
, that is, its cost is not determined alone by the size of
the changes
in the input and output, for all these matching notions. Nonetheless, when matching is defined in terms of simulation or bounded simulation, incremental matching is
semibounded
, that is, its worst-time complexity is bounded by a polynomial in the size of the changes in the input, output, and auxiliary information that is necessarily maintained to reuse previous computation, and the size of graph patterns. We also develop incremental matching algorithms for graph simulation and bounded simulation, by minimizing unnecessary recomputation. In contrast, matching based on subgraph isomorphism is neither bounded nor semibounded. (3) We experimentally verify the effectiveness and efficiency of these algorithms, and show that: (a) the revised notion of graph pattern matching allows us to identify communities commonly found in real-life networks, and (b) the incremental algorithms substantially outperform their batch counterparts in response to small changes. These suggest a promising framework for real-life graph pattern matching.
GPUDet
Authors: Jooybar Hadi , Fung Wilson W.L. , O'Connor Mike , Devietti Joseph , Aamodt Tor M.
Published: April 2020

Nondeterminism is a key challenge in developing multithreaded applications. Even with the same input, each execution of a multithreaded program may produce a different output. This behavior complicates debugging and limits one's ability to test for correctness. This non-reproducibility situation is aggravated on massively parallel architectures like graphics processing units (GPUs) with thousands of concurrent threads. We believe providing a deterministic environment to ease debugging and testing of GPU applications is essential to enable a broader class of software to use GPUs.

Many hardware and software techniques have been proposed for providing determinism on general-purpose multi-core processors. However, these techniques are designed for small numbers of threads. Scaling them to thousands of threads on a GPU is a major challenge. This paper proposes a scalable hardware mechanism, GPUDet, to provide determinism in GPU architectures. In this paper we characterize the existing deterministic and nondeterministic aspects of current GPU execution models, and we use these observations to inform GPUDet's design. For example, GPUDet leverages the inherent determinism of the SIMD hardware in GPUs to provide determinism within a wavefront at no cost. GPUDet also exploits the Z-Buffer Unit, an existing GPU hardware unit for graphics rendering, to allow parallel out-of-order memory writes to produce a deterministic output. Other optimizations in GPUDet include deterministic parallel execution of atomic operations and a workgroup-aware algorithm that eliminates unnecessary global synchronizations.

Our simulation results indicate that GPUDet incurs only 2X slowdown on average over a baseline nondeterministic architecture, with runtime overheads as low as 4% for compute-bound applications, despite running GPU kernels with thousands of threads. We also characterize the sources of overhead for deterministic execution on GPUs to provide insights for further optimizations.
Parallelizing data race detection
Authors: Wester Benjamin , Devecsery David , Chen Peter M. , Flinn Jason , Narayanasamy Satish
Published: April 2020

Detecting data races in multithreaded programs is a crucial part of debugging such programs, but traditional data race detectors are too slow to use routinely. This paper shows how to speed up race detection by spreading the work across multiple cores. Our strategy relies on
uniparallelism
, which executes time intervals of a program (called
epochs
) in parallel to provide scalability, but executes all threads from a single epoch on a single core to eliminate locking overhead. We use several techniques to make parallelization effective: dividing race detection into three phases, predicting a subset of the analysis state, eliminating sequential work via transitive reduction, and reducing the work needed to maintain multiple versions of analysis via factorization. We demonstrate our strategy by parallelizing a happens-before detector and a lockset-based detector. We find that uniparallelism can significantly speed up data race detection. With 4x the number of cores as the original application, our strategy speeds up the median execution time by 4.4x for a happens-before detector and 3.3x for a lockset race detector. Even on the same number of cores as the conventional detectors, the ability for uniparallelism to elide analysis locks allows it to reduce the median overhead by 13% for a happens-before detector and 8% for a lockset detector.
Cooperative empirical failure avoidance for multithreaded programs
Authors: Lucia Brandon , Ceze Luis
Published: April 2020

Concurrency errors in multithreaded programs are difficult to find and fix. We propose Aviso, a system for avoiding schedule-dependent failures. Aviso monitors events during a program's execution and, when a failure occurs, records a history of events from the failing execution. It uses this history to generate schedule constraints that perturb the order of events in the execution and thereby avoids schedules that lead to failures in future program executions. Aviso leverages scenarios where many instances of the same software run, using a statistical model of program behavior and experimentation to determine which constraints most effectively avoid failures. After implementing Aviso, we showed that it decreased failure rates for a variety of important desktop, server, and cloud applications by orders of magnitude, with an average overhead of less than 20% and, in some cases, as low as 5%.
ReQoS
Authors: Tang Lingjia , Mars Jason , Wang Wei , Dey Tanima , Soffa Mary Lou
Published: April 2020

As multicore processors with expanding core counts continue to dominate the server market, the overall utilization of the class of datacenters known as
warehouse scale computers
(WSCs) depends heavily on colocation of multiple workloads on each server to take advantage of the computational power provided by modern processors. However, many of the applications running in WSCs, such as websearch, are user-facing and have quality of service (QoS) requirements. When multiple applications are co-located on a multicore machine, contention for shared memory resources threatens application QoS as severe cross-core performance interference may occur. WSC operators are left with two options: either disregard QoS to maximize WSC utilization, or disallow the co-location of high-priority user-facing applications with other applications, resulting in low machine utilization and millions of dollars wasted.

This paper presents ReQoS, a static/dynamic compilation approach that enables low-priority applications to adaptively manipulate their own contentiousness to ensure the QoS of high-priority co-runners. ReQoS is composed of a profile guided compilation technique that identifies and inserts markers in contentious code regions in low-priority applications, and a lightweight runtime that monitors the QoS of high-priority applications and reactively reduces the pressure low-priority applications generate to the memory subsystem when cross-core interference is detected. In this work, we show that ReQoS can accurately diagnose contention and significantly reduce performance interference to ensure application QoS. Applying ReQoS to SPEC2006 and SmashBench workloads on real multicore machines, we are able to improve machine utilization by more than 70% in many cases, and more than 50% on average, while enforcing a 90% QoS threshold. We are also able to improve the energy efficiency of modern multicore machines by 47% on average over a policy of disallowing co-locations.
Production-run software failure diagnosis via hardware performance counters
Authors: Arulraj Joy , Chang Po-Chun , Jin Guoliang , Lu Shan
Published: April 2020

Sequential and concurrency bugs are widespread in deployed software. They cause severe failures and huge financial loss during production runs. Tools that diagnose production-run failures with low overhead are needed. The state-of-the-art diagnosis techniques use software instrumentation to sample program properties at run time and use off-line statistical analysis to identify properties most correlated with failures. Although promising, these techniques suffer from high run-time overhead, which is sometimes over 100%, for concurrency-bug failure diagnosis and hence are not suitable for production-run usage.

We present PBI, a system that uses existing hardware performance counters to diagnose production-run failures caused by sequential and concurrency bugs with low overhead. PBI is designed based on several key observations. First, a few widely supported performance counter events can reflect a wide variety of common software bugs and can be monitored by hardware with almost no overhead. Second, the counter overflow interrupt supported by existing hardware and operating systems provides a natural and effective mechanism to conduct event sampling at user level. Third, the noise and non-determinism in interrupt delivery complements well with statistical processing.

We evaluate PBI using 13 real-world concurrency and sequential bugs from representative open-source server, client, and utility programs, and 10 bugs from a widely used software-testing benchmark. Quantitatively, PBI can effectively diagnose failures caused by these bugs with a small overhead that is never higher than 10%. Qualitatively, PBI does not require any change to software and presents a novel use of existing hardware performance counters.
Transparent mutable replay for multicore debugging and patch validation
Authors: Viennot Nicolas , Nair Siddharth , Nieh Jason
Published: April 2020

We present Dora, a mutable record-replay system which allows a recorded execution of an application to be replayed with a modified version of the application. This feature, not available in previous record-replay systems, enables powerful new functionality. In particular, Dora can help reproduce, diagnose, and fix software bugs by replaying a version of a recorded application that is recompiled with debugging information, reconfigured to produce verbose log output, modified to include additional print statements, or patched to fix a bug.

Dora uses lightweight operating system mechanisms to record an application execution by capturing nondeterministic events to a log without imposing unnecessary timing and ordering constraints. It replays the log using a modified version of the application even in the presence of added, deleted, or modified operations that do not match events in the log. Dora searches for a replay that minimizes differences between the log and the replayed execution of the modified program. If there are no modifications, Dora provides deterministic replay of the unmodified program.

We have implemented a Linux prototype which provides transparent mutable replay without recompiling or relinking applications. We show that Dora is useful for reproducing, diagnosing, and fixing software bugs in real-world applications, including Apache and MySQL. Our results show that Dora (1) captures bugs and replays them with applications modified or reconfigured to produce additional debugging output for root cause diagnosis, (2) captures exploits and replays them with patched applications to validate that the patches successfully eliminate vulnerabilities, (3) records production workloads and replays them with patched applications to validate patches with realistic workloads, and (4) maintains low recording overhead on commodity multicore hardware, making it suitable for production systems.
Using likely invariants for automated software fault localization
Authors: Sahoo Swarup Kumar , Criswell John , Geigle Chase , Adve Vikram
Published: April 2020

We propose an automatic diagnosis technique for isolating the root cause(s) of software failures. We use likely program invariants, automatically generated using correct inputs that are close to the fault-triggering input, to select a set of candidate program locations which are possible root causes. We then trim the set of candidate root causes using software-implemented dynamic backwards slicing, plus two new filtering heuristics: dependence filtering, and filtering via multiple failing inputs that are also close to the failing input. Experimental results on reported software bugs of three large open-source servers show that we are able to narrow down the number of candidate bug locations to between 5 and 17 program expressions, even in programs that are hundreds of thousands of lines long.