bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploration of predictive biomarkers for postoperative recurrence of stage II/III colorectal cancer using genomic sequencing
Authors: Kishigami Fumishi , Tanaka Yosuke , Yamamoto Yoko , Ueno Toshihide , Kojima Shinya , Sato Kazuhito , Inoue Satoshi , Sugaya Saori , Ishihara Soichiro , Mano Hiroyuki , Kawazu Masahito 
Published: March 2022

AbstractPostoperative recurrence of colorectal cancer (CRC) eventually leads to therapeutic failure; therefore, treatment strategies based on accurate prediction of recurrence are urgently required. To identify biomarkers that can predict treatment outcomes, we compared the mutational profiles of surgically resected specimens from patients with recurrent cancer with those from patients with non‐recurrent cancer. Target sequencing, whole‐exome sequencing (WES), or whole‐genome sequencing (WGS) was performed on 89 and 58 tumors from recurrent and non‐recurrent cases, respectively. WGS revealed the driver mutations that were not detected with target sequencing or WES, including the structural variations affecting ZFP36L2. Loss of function of ZFP36L2 was frequently observed in primary tumors from recurrent cases. Furthermore, the recurrence‐free survival of patients with loss of function of ZFP36L2 was significantly shorter relative to patients with no loss of ZFP36L2 function. In summary, the study demonstrated that detailed genomic analysis could help improve precision medicine for CRC.
Does large dam removal restore downstream riparian vegetation diversity? Testing predictions on the Elwha River, Washington, USA
Authors: Brown Rebecca L. , Thomas Cody C. , Cubley Erin S. , Clausen Aaron J. , Shafroth Patrick B. 
Published: March 2022

AbstractLarge dams and their removal can profoundly affect riparian ecosystems by altering flow and sediment regimes, hydrochory, and landform dynamics, yet few studies have documented these effects on downstream plant communities. Ecological theory and empirical results suggest that by altering disturbance regimes, reducing hydrochory, and shifting communities to later successional stages, dams reduce downstream plant diversity. Dam removal could reverse these processes, but the release of large volumes of sediment could have unexpected, transient effects. Two large dams were removed on the Elwha River in Washington State, USA, from 2011 to 2014, representing an unprecedented opportunity to study large dam removal effects on riparian plant communities. Our research objectives were to determine: (1) whether the Elwha River dams were associated with lower downstream plant diversity and altered species composition across riparian landforms pre‐dam removal, and (2) whether dam removal has begun to restore downstream diversity and composition. To address these objectives, we compared plant species richness and community composition in river segments above, below, and between the two dams. Plant communities were sampled twice before (2005 and 2010) and four times after (2013, 2014, 2016, and 2017) the start of dam removal, with 2013 and 2014 sampled while the upstream dam removal was ongoing. Prior to dam removal, native species richness was 41% lower below dams compared with the upstream segment; 6 years after dam removal began, it increased ~31% between the dams, whereas nonnative species richness and cover were not apparently affected by dams or their removal. Deposition caused by large volumes of released reservoir sediment had mixed effects on native species richness (increased on floodplains, decreased elsewhere) in the lowest river segment. Plant community composition was also different downstream from dams compared with the upstream reference, and has changed in downstream floodplains and bars since dam removal. In the long term, we expect that diversity will continue to increase in downstream river segments. Our results provide evidence that (1) large dams reduce downstream native plant diversity, (2) dam removal may restore it, and (3) given the natural dynamics of riparian vegetation, long‐term, multiyear before‐and‐after monitoring is essential for understanding dam removal effects.
Do metapopulations and management matter for relict headwater bull trout populations in a warming climate?
Authors: Isaak Daniel J. , Young Michael K. , Horan Dona L. , Nagel David , Schwartz Michael K. , McKelvey Kevin S. 
Published: March 2022

AbstractMountain headwater streams have emerged as important climate refuges for native cold‐water species due to their slow climate velocities and extreme physical conditions that inhibit non‐native invasions. Species persisting in refuges often do so as fragmented, relict populations from broader historical distributions that are subject to ongoing habitat reductions and increasing isolation as climate change progresses. Key for conservation planning is determining where remaining populations will persist and how habitat restoration strategies can improve biological resilience to enhance the long‐term prospects for species of concern. Studying bull trout, a headwater species in the northwestern USA, we developed habitat occupancy models using a data set of population occurrence in 991 natal habitat patches with a suite of novel geospatial covariates derived from high‐resolution hydroclimatic scenarios and other sources representing watershed and instream habitat conditions, patch geometry, disturbance, and biological interactions. The best model correctly predicted bull trout occupancy status in 82.6% of the patches and included effects for: patch size estimated as habitat volume, extent of within‐patch reaches <9°C mean August temperature, distance to nearest occupied patch, road density, invasive brook trout prevalence, patch slope, and frequency of high winter flows. The model was used to assess 16 scenarios of bull trout occurrence within the study streams that represented a range of restoration strategies under three climatic conditions (baseline, moderate change, and extreme change). Results suggested that regional improvements in bull trout status were difficult to achieve in realistic restoration strategies due to the pervasive nature of climate change and the limited extent of restoration actions given their high costs. However, occurrence probabilities in a subset of patches were highly responsive to restoration actions, suggesting that targeted investments to improve the resilience of some populations may be contextually beneficial. A possible strategy, therefore, is focusing effort on responsive populations near more robust population strongholds, thereby contributing to local enclaves where dispersal among populations further enhances resilience. Equally important, strongholds constituted a small numerical percentage of patches (5%–21%), yet encompassed the large majority of occupied habitat by volume (72%–89%) and their protection could have significant conservation benefits for bull trout.
Self‐navigated prospective motion correction for 3D‐EPI acquisition
Authors: Bayih Samuel Getaneh , Jankiewicz Marcin , Alhamud A. , van der Kouwe André J. W. , Meintjes Ernesta M. 
Published: March 2022

PurposeAlthough 3D EPI is more susceptible to motion artifacts than 2D EPI, it presents some benefits for functional MRI, including the absence of spin‐history artifacts, greater potential for parallel imaging acceleration, and better functional sensitivity in high‐resolution imaging. Here we present a self‐navigated 3D‐EPI sequence suitable for prospective motion‐corrected functional MRI without additional hardware or pulses.MethodsFor each volume acquisition, the first 24 of the 52 partitions being acquired are accumulated to a new feedback block that was added to the image reconstruction pipeline. After zero‐filling the remaining partitions, the feedback block constructs a volumetric self‐navigator (vSNav), co‐registers it to the reference vSNav acquired during the first volume acquisition, and sends motion estimates to the sequence. The sequence then updates its FOV and acquires subsequent partitions with the adjusted FOV, until the next update is received. The sequence was validated without and with intentional motion in phantom and in vivo on a 3T Skyra.ResultsFor phantom scans, the FOV was updated 0.704 s after acquisition of the vSNav partitions, and for in vivo scans after 0.768 s. Both phantom and in vivo data demonstrated stable motion estimates in the absence of motion. For in vivo acquisitions, prospective head‐pose estimates using the vSNav's and retrospective estimates with FLIRT (FMRIB's Linear Image Registration Tool) agreed to within 0.23 mm (< 10% of the slice thickness) and 0.14° in all directions.ConclusionDepending when motion occurs during a volume acquisition, the proposed method fully corrects the FOV and recovers image quality within one volume acquisition.
Study on friction and wear of preform Z‐directional fiber
Authors: Guo Zitong , Shan Zhongde , Huang Jihua , Wang Dong , Huang Hao , Xue Debo , Hou Zhuojian 
Published: March 2022

AbstractIn order to reduce the wear and tear of Z‐yarn implantation into the preform, the frictional behavior of Z‐yarn during implantation into the preform was studied. According to the actual implantation conditions of Z‐yarns, we designed a guiding array clamping device and a tensile force sensor to study the changes of tensile strength of Z‐yarns at different implantation positions and implantation times, results show that the tensile strength of Z‐yarns decreases significantly after 25 implantations at the position of 4 N friction force, and it's necessary to replace Z‐yarns in time to avoid their fracture in the preform. The use of unadulterated solvent dimethyl silicone oil applied to the Z‐yarns, can significantly reduce their wear, the tensile strength of Z‐yarns after 60 implantations is only 5.6% lower than that of Z‐yarns after 10 implantations. Design the tension control system, and when the tension is 0.46 N, the tensile strength of Z‐yarns during implantation is 34.2% higher than without tension. Meanwhile, the relationship between the normal force applied to Z‐yarn and the implantation length and fiber bundle width are established by combining Hertzian theory and experimental data, and the friction coefficient algorithm during Z‐yarn implantation is derived by combining Howell's equation, which solves the problem that the fiber friction coefficient cannot be measured due to the complicated working condition of Z‐yarn implantation. The frictional wear mechanism of yarn during Z‐yarn implantation into the preform is revealed, and a method to reduce yarn wear and increase its continuous implantation number is proposed.
Defect Nanostructure and its Impact on Magnetism of α‐Cr2O3 Thin Films
Authors: Veremchuk Igor , Liedke Maciej Oskar , Makushko Pavlo , Kosub Tobias , Hedrich Natascha , Pylypovskyi Oleksandr V. , Ganss Fabian , Butterling Maik , Hübner René , Hirschmann Eric , Attallah Ahmed G. , Wagner Andreas , Wagner Kai , Shields Brendan , Maletinsky Patrick , Fassbender Jürgen , Makarov Denys 
Published: March 2022

AbstractThin films of the magnetoelectric insulator α‐Cr2O3 are technologically relevant for energy‐efficient magnetic memory devices controlled by electric fields. In contrast to single crystals, the quality of thin Cr2O3 films is usually compromised by the presence of point defects and their agglomerations at grain boundaries, putting into question their application potential. Here, the impact of the defect nanostructure, including sparse small‐volume defects and their complexes is studied on the magnetic properties of Cr2O3 thin films. By tuning the deposition temperature, the type, size, and relative concentration of defects is tailored, which is analyzed using the positron annihilation spectroscopy complemented with electron microscopy studies. The structural characterization is correlated with magnetotransport measurements and nitrogen‐vacancy microscopy of antiferromagnetic domain patterns. Defects pin antiferromagnetic domain walls and stabilize complex multidomain states with a domain size in the sub‐micrometer range. Despite their influence on the domain configuration, neither small open‐volume defects nor grain boundaries in Cr2O3 thin films affect the Néel temperature in a broad range of deposition parameters. The results pave the way toward the realization of spin‐orbitronic devices where magnetic domain patterns can be tailored based on defect nanostructures without affecting their operation temperature.
Rationing of Personalised Cancer Drugs: Rethinking the Co-production of Evidence and Priority Setting Practices
Authors: Tranvåg Eirik Joakim , Strand Roger 
Published: March 2022

AbstractRising health care costs is a challenge for all health care systems, and new and expensive cancer drugs is an important contributor to this. Many countries – like Norway – have therefore established priority setting institutions and systems for drug appraisals where equal treatment, neutrality and transparency are key values. Despite this, controversy surrounding drug reimbursement decisions are persistent.The development of personalised cancer medicine is seen by many as a potential solution to difficult priority setting decisions, by tailoring the right drug to the right patient at the right time. We, however, see personalised oncology and medicine in general not only as a solution, but also as a potential contributor high costs and to persisting controversy. We will argue that attempts to improve and strengthen the priority setting system – without accepting that a wider perspective on science and society is required – is likely to fuel even more controversy.In contrast, our suggestion takes a different approach building on post-normal science. From a co-production perspective, scientific, technological and societal developments are causally entangled into each other. Alongside refining priority setting principles, one can and ought to raise normative questions about the trajectory of personalised cancer medicine and of how to create a well-functioning public sphere. How can we imagine a well-functioning system of technological development and health care priority setting? Which changes in research policy and funding could support such a system? And which properties could biomarkers have in order to help society manage the health gap?
On probability-raising causality in Markov decision processes
Authors: Baier Christel , Funke Florian , Piribauer Jakob , Ziemek Robin 
Published: March 2022

AbstractThe purpose of this paper is to introduce a notion of causality in Markov decision processes based on the probability-raising principle and to analyze its algorithmic properties. The latter includes algorithms for checking cause-effect relationships and the existence of probability-raising causes for given effect scenarios. Inspired by concepts of statistical analysis, we study quality measures (recall, coverage ratio and f-score) for causes and develop algorithms for their computation. Finally, the computational complexity for finding optimal causes with respect to these measures is analyzed.
Parameterized Analysis of Reconfigurable Broadcast Networks
Authors: Balasubramanian A. R. , Guillou Lucie , Weil-Kennedy Chana 
Published: March 2022

AbstractReconfigurable broadcast networks (RBN) are a model of distributed computation in which agents can broadcast messages to other agents using some underlying communication topology which can change arbitrarily over the course of executions. In this paper, we conduct parameterized analysis of RBN. We consider cubes, (infinite) sets of configurations in the form of lower and upper bounds on the number of agents in each state, and we show that we can evaluate boolean combinations over cubes and reachability sets of cubes in . In particular, reachability from a cube to another cube is a -complete problem.To prove the upper bound for this parameterized analysis, we prove some structural properties about the reachability sets and the symbolic graph abstraction of RBN, which might be of independent interest. We justify this claim by providing two applications of these results. First, we show that the almost-sure coverability problem is -complete for RBN, thereby closing a complexity gap from a previous paper [3]. Second, we define a computation model using RBN, à la population protocols, called RBN protocols. We characterize precisely the set of predicates that can be computed by such protocols.
Separators in Continuous Petri Nets
Authors: Blondin Michael , Esparza Javier 
Published: March 2022

AbstractLeroux has proved that unreachability in Petri nets can be witnessed by a Presburger separator, i.e. if a marking $$\boldsymbol{m}_\text {src}$$

m

src

cannot reach a marking $$\boldsymbol{m}_\text {tgt}$$

m

tgt

, then there is a formula $$\varphi $$
φ
of Presburger arithmetic such that: $$\varphi (\boldsymbol{m}_\text {src})$$

φ
(

m

src

)

holds; $$\varphi $$
φ
is forward invariant, i.e., $$\varphi (\boldsymbol{m})$$

φ
(

m

)

and $$\boldsymbol{m} \rightarrow \boldsymbol{m}'$$

m

→

m

′

imply $$\varphi (\boldsymbol{m}'$$

φ
(

m

′

); and $$\lnot \varphi (\boldsymbol{m}_\text {tgt})$$

¬
φ
(

m

tgt

)

holds. While these separators could be used as explanations and as formal certificates of unreachability, this has not yet been the case due to their (super-)Ackermannian worst-case size and the (super-)exponential complexity of checking that a formula is a separator. We show that, in continuous Petri nets, these two problems can be overcome. We introduce locally closed separators, and prove that: (a) unreachability can be witnessed by a locally closed separator computable in polynomial time; (b) checking whether a formula is a locally closed separator is in NC (so, simpler than unreachablity, which is P-complete).
Compiling Universal Probabilistic Programming Languages with Efficient Parallel Sequential Monte Carlo Inference
Authors: Lundén Daniel , Öhman Joey , Kudlicka Jan , Senderov Viktor , Ronquist Fredrik , Broman David 
Published: March 2022

AbstractProbabilistic programming languages (PPLs) allow users to encode arbitrary inference problems, and PPL implementations provide general-purpose automatic inference for these problems. However, constructing inference implementations that are efficient enough is challenging for many real-world problems. Often, this is due to PPLs not fully exploiting available parallelization and optimization opportunities. For example, handling probabilistic checkpoints in PPLs through continuation-passing style transformations or non-preemptive multitasking—as is done in many popular PPLs—often disallows compilation to low-level languages required for high-performance platforms such as GPUs. To solve the checkpoint problem, we introduce the concept of PPL control-flow graphs (PCFGs)—a simple and efficient approach to checkpoints in low-level languages. We use this approach to implement RootPPL: a low-level PPL built on CUDA and C++ with OpenMP, providing highly efficient and massively parallel SMC inference. We also introduce a general method of compiling universal high-level PPLs to PCFGs and illustrate its application when compiling Miking CorePPL—a high-level universal PPL—to RootPPL. The approach is the first to compile a universal PPL to GPUs with SMC inference. We evaluate RootPPL and the CorePPL compiler through a set of real-world experiments in the domains of phylogenetics and epidemiology, demonstrating up to 6$$\times $$
×
speedups over state-of-the-art PPLs implementing SMC inference.
Concurrent NetKAT
Authors: Wagemaker Jana , Foster Nate , Kappé Tobias , Kozen Dexter , Rot Jurriaan , Silva Alexandra 
Published: March 2022

AbstractWe introduce Concurrent (), an extension of with operators for specifying and reasoning about concurrency in scenarios where multiple packets interact through state. We provide a model of the language based on partially-ordered multisets (pomsets), which are a well-established mathematical structure for defining the denotational semantics of concurrent languages. We provide a sound and complete axiomatization of this model, and we illustrate the use of through examples. More generally, can be understood as an algebraic framework for reasoning about programs with both local state (in packets) and global state (in a global store).
Verified Security for the Morello Capability-enhanced Prototype Arm Architecture
Authors: Bauereiss Thomas , Campbell Brian , Sewell Thomas , Armstrong Alasdair , Esswood Lawrence , Stark Ian , Barnes Graeme , Watson Robert N. M. , Sewell Peter 
Published: March 2022

AbstractMemory safety bugs continue to be a major source of security vulnerabilities in our critical infrastructure. The CHERI project has proposed extending conventional architectures with hardware-supported capabilities to enable fine-grained memory protection and scalable compartmentalisation, allowing historically memory-unsafe C and C++ to be adapted to deterministically mitigate large classes of vulnerabilities, while requiring only minor changes to existing system software sources. Arm is currently designing and building Morello, a CHERI-enabled prototype architecture, processor, SoC, and board, extending the high-performance Neoverse N1, to enable industrial evaluation of CHERI and pave the way for potential mass-market adoption. However, for such a major new security-oriented architecture feature, it is important to establish high confidence that it does provide the intended protections, and that cannot be done with conventional engineering techniques.In this paper we put the Morello architecture on a solid mathematical footing from the outset. We define the fundamental security property that Morello aims to provide, reachable capability monotonicity, and prove that the architecture definition satisfies it. This proof is mechanised in Isabelle/HOL, and applies to a translation of the official Arm specification of the Morello instruction-set architecture (ISA) into Isabelle. The main challenge is handling the complexity and scale of a production architecture: 62,000 lines of specification, translated to 210,000 lines of Isabelle. We do so by factoring the proof via a narrow abstraction capturing essential properties of arbitrary CHERI ISAs, expressed above a monadic intra-instruction semantics. We also develop a model-based test generator, which generates instruction-sequence tests that give good specification coverage, used in early testing of the Morello implementation and in Morello QEMU development, and we use Arm’s internal test suite to validate our model.This gives us machine-checked mathematical proofs of whole-ISA security properties of a full-scale industry architecture, at design-time. To the best of our knowledge, this is the first demonstration that that is feasible, and it significantly increases confidence in Morello.
The Trusted Computing Base of the CompCert Verified Compiler
Authors: Monniaux David , Boulmé Sylvain 
Published: March 2022

Abstract is the first realistic formally verified compiler: it provides a machine-checked mathematical proof that the code it generates matches the source code. Yet, there could be loopholes in this approach. We comprehensively analyze aspects of where errors could lead to incorrect code being generated. Possible issues range from the modeling of the source and the target languages to some techniques used to call external algorithms from within the compiler.
Advances in Automatic Software Testing: Test-Comp 2022
Authors: Beyer Dirk 
Published: March 2022

AbstractTest-Comp 2022 is the 4th edition of the Competition on Software Testing. Research competitions are a means to provide annual comparative evaluations. Test-Comp focusses on fully automatic software test generators for C programs. The results of the competition shall be reproducible and provide an overview of the current state of the art in the area of automatic test-generation. The competition was based on 4 236 test-generation tasks for C programs. Each test-generation task consisted of a program and a test specification (error coverage, branch coverage). Test-Comp 2022 had 12 participating test generators from 5 countries.