bluuebunny/crossref_metadata_2025_split huggingface dataset:
CCT3-LINC00326axis regulates hepatocarcinogenic lipid metabolism
Authors: Søndergaard Jonas Nørskov , Sommerauer Christian , Atanasoai Ionut , Hinte Laura C , Geng Keyi , Guiducci Giulia , Bräutigam Lars , Aouadi Myriam , Stojic Lovorka , Barragan Isabel , Kutter Claudia 
Published: January 2022

ObjectiveTo better comprehend transcriptional phenotypes of cancer cells, we globally characterised RNA-binding proteins (RBPs) to identify altered RNAs, including long non-coding RNAs (lncRNAs).DesignTo unravel RBP-lncRNA interactions in cancer, we curated a list of ~2300 highly expressed RBPs in human cells, tested effects of RBPs and lncRNAs on patient survival in multiple cohorts, altered expression levels, integrated various sequencing, molecular and cell-based data.ResultsHigh expression of RBPs negatively affected patient survival in 21 cancer types, especially hepatocellular carcinoma (HCC). After knockdown of the top 10 upregulated RBPs and subsequent transcriptome analysis, we identified 88 differentially expressed lncRNAs, including 34 novel transcripts. CRISPRa-mediated overexpression of four lncRNAs had major effects on the HCC cell phenotype and transcriptome. Further investigation of four RBP-lncRNA pairs revealed involvement in distinct regulatory processes. The most noticeable RBP-lncRNA connection affected lipid metabolism, whereby the non-canonical RBP CCT3 regulatedLINC00326in a chaperonin-independent manner. Perturbation of the CCT3-LINC00326regulatory network led to decreased lipid accumulation and increased lipid degradationin celluloas well as diminished tumour growthin vivo.ConclusionsWe revealed that RBP gene expression is perturbed in HCC and identified that RBPs exerted additional functions beyond their tasks under normal physiological conditions, which can be stimulated or intensified via lncRNAs and affected tumour growth.
Incidence of outbreak-associated COVID-19 cases by industry in Ontario, Canada, 1 April 2020–31 March 2021
Authors: Buchan Sarah A , Smith Peter M , Warren Christine , Murti Michelle , Mustard Cameron , Kim Jin Hee , Menon Sandya , Brown Kevin A , van Ingen Trevor , Smith Brendan T 
Published: January 2022

ObjectivesThe objective of our study was to estimate the rate of workplace outbreak-associated cases of COVID-19 by industry in labour market participants aged 15–69 years who reported working the majority of hours outside the home in Ontario, Canada.MethodsWe conducted a population-based cross-sectional study of COVID-19 workplace outbreaks and associated cases reported in Ontario between 1 April 2020 and 31 March 2021. All outbreaks were manually classified into two-digit North American Industry Classification System codes. We obtained monthly denominator estimates from the Statistics Canada Labour Force Survey to estimate the incidence of outbreak-associated cases per 100 000 000 hours among individuals who reported the majority of hours were worked outside the home. We performed this analysis across industries and in three distinct time periods.ResultsOverall, 12% of cases were attributed to workplace outbreaks among working-age adults across our study period. While incidence varied across the time periods, the five industries with the highest incidence rates across our study period were agriculture, healthcare and social assistance, food manufacturing, educational services, and transportation and warehousing.ConclusionsCertain industries have consistently increased the incidence of COVID-19 over the course of the pandemic. These results may assist in ongoing efforts to reduce transmission of COVID-19 by prioritising resources, as well as industry-specific guidance, vaccination and public health messaging.
Comparative frenectomy with conventional scalpel and dual-waved laser in labial frenulum
Authors: Xie Ling , Wang Ping , Ding Yue , Zhang Liang 
Published: January 2022

AimThe purpose of the study is to compare the labial frenectomy between the laser surgery (erbium yttrium aluminum garnet and neodymium-doped yttrium aluminum garnet (Er:YAG and Nd:YAG)) and the scalpel method.MethodsThe trial was a randomized controlled test. Thirty four patients aged from 5 to 10 years requiring the frenectomy were included in this study. Patients were randomly divided into two groups: group A: Er:YAG and Nd:YAG laser group and group B: scalpel group. In addition, this comparison considered the following factors: surgical time and Visual Analog Scale (VAS) pain score, which includes intraoperative pain, postoperative pain and complications, such as speaking and chewing, for 1 day and 7 days following labial frenectomy. After 3 months, we recorded the healing outcome by photos.ResultsThere was a statistically significant difference in mean surgical time between laser surgery (mean=224±59 s) and scalpel surgery (mean=740±168 s). According to VAS scores of the intraoperative period (3 hours after the operation and 1st postoperative day of pain), chewing and speaking were statistically higher in group B than those in group A; but in the 7th postoperative day of pain, there was no significant difference in speaking and chewing. After 1 month, all of the patient results were recorded, including the healing of wound and scar. Except for one patient in group B who had a scar, all patients achieved good results.ConclusionBased on the results of this study, it can be concluded that Nd:YAG laser is an efficient and more comfortable alternative to the scalpel for a frenectomy in upper lip frenulum.
Symmetries in reversible programming: from symmetric rig groupoids to reversible programming languages
Authors: Choudhury Vikraman , Karwowski Jacek , Sabry Amr 
Published: January 2022

The Pi family of reversible programming languages for boolean circuits is presented as a syntax of combinators witnessing type isomorphisms of algebraic data types. In this paper, we give a denotational semantics for this language, using weak groupoids à la Homotopy Type Theory, and show how to derive an equational theory for it, presented by 2-combinators witnessing equivalences of type isomorphisms.
We establish a correspondence between the syntactic groupoid of the language and a formally presented univalent subuniverse of finite types. The correspondence relates 1-combinators to 1-paths, and 2-combinators to 2-paths in the universe, which is shown to be sound and complete for both levels, forming an equivalence of groupoids. We use this to establish a Curry-Howard-Lambek correspondence between Reversible Logic, Reversible Programming Languages, and Symmetric Rig Groupoids, by showing that the syntax of Pi is presented by the free symmetric rig groupoid, given by finite sets and bijections.
Using the formalisation of our results, we perform normalisation-by-evaluation, verification and synthesis of reversible logic gates, motivated by examples from quantum computing. We also show how to reason about and transfer theorems between different representations of reversible circuits.
Property-directed reachability as abstract interpretation in the monotone theory
Authors: Feldman Yotam M. Y. , Sagiv Mooly , Shoham Sharon , Wilcox James R. 
Published: January 2022

Inferring inductive invariants is one of the main challenges of formal verification. The theory of abstract interpretation provides a rich framework to devise invariant inference algorithms. One of the latest breakthroughs in invariant inference is property-directed reachability (PDR), but the research community views PDR and abstract interpretation as mostly unrelated techniques.
This paper shows that, surprisingly, propositional PDR can be formulated as an abstract interpretation algorithm in a logical domain. More precisely, we define a version of PDR, called Λ-PDR, in which all generalizations of counterexamples are used to strengthen a frame. In this way, there is no need to refine frames after their creation, because all the possible supporting facts are included in advance. We analyze this algorithm using notions from Bshouty’s monotone theory, originally developed in the context of exact learning. We show that there is an inherent overapproximation between the algorithm’s frames that is related to the monotone theory. We then define a new abstract domain in which the best abstract transformer performs this overapproximation, and show that it captures the invariant inference process, i.e., Λ-PDR corresponds to Kleene iterations with the best transformer in this abstract domain. We provide some sufficient conditions for when this process converges in a small number of iterations, with sometimes an exponential gap from the number of iterations required for naive exact forward reachability. These results provide a firm theoretical foundation for the benefits of how PDR tackles forward reachability.
Twist: sound reasoning for purity and entanglement in Quantum programs
Authors: Yuan Charles , McNally Christopher , Carbin Michael 
Published: January 2022

Quantum programming languages
enable developers to implement algorithms for quantum computers that promise computational breakthroughs in classically intractable tasks. Programming quantum computers requires awareness of
entanglement
, the phenomenon in which measurement outcomes of qubits are correlated. Entanglement can determine the correctness of algorithms and suitability of programming patterns.

In this work, we formalize
purity
as a central tool for automating reasoning about entanglement in quantum programs. A pure expression is one whose evaluation is unaffected by the measurement outcomes of qubits that it does not own, implying freedom from entanglement with any other expression in the computation.

We present Twist, the first language that features a type system for sound reasoning about purity. The type system enables the developer to identify pure expressions using type annotations. Twist also features purity assertion operators that state the absence of entanglement in the output of quantum gates. To soundly check these assertions, Twist uses a combination of static analysis and runtime verification.
We evaluate Twist’s type system and analyses on a benchmark suite of quantum programs in simulation, demonstrating that Twist can express quantum algorithms, catch programming errors in them, and support programs that existing languages disallow, while incurring runtime verification overhead of less than 3.5%.
Mœbius: metaprogramming using contextual types: the stage where system f can pattern match on itself
Authors: Jang Junyoung , Gélineau Samuel , Monnier Stefan , Pientka Brigitte 
Published: January 2022

We describe the foundation of the metaprogramming language, Mœbius, which supports the generation of polymorphic code and, more importantly, the analysis of polymorphic code via pattern matching.
Mœbius has two main ingredients: 1) we exploit contextual modal types to describe open code together with the context in which it is meaningful. In Mœbius, open code can depend on type and term variables (level 0) whose values are supplied at a later stage, as well as code variables (level 1) that stand for code templates supplied at a later stage. This leads to a multi-level modal lambda-calculus that supports System-F style polymorphism and forms the basis for polymorphic code generation. 2) we extend the multi-level modal lambda-calculus to support pattern matching on code. As pattern matching on polymorphic code may refine polymorphic type variables, we extend our type-theoretic foundation to generate and track typing constraints that arise. We also give an operational semantics and prove type preservation.
Our multi-level modal foundation for Mœbius provides the appropriate abstractions for both generating and pattern matching on open code without committing to a concrete representation of variable binding and contexts. Hence, our work is a step towards building a general type-theoretic foundation for multi-staged metaprogramming that, on the one hand, enforces strong type guarantees and, on the other hand, makes it easy to generate and manipulate code. This will allow us to exploit the full potential of metaprogramming without sacrificing the reliability of and trust in the code we are producing and running.
Layered and object-based game semantics
Authors: Oliveira Vale Arthur , Melliès Paul-André , Shao Zhong , Koenig Jérémie , Stefanesco Léo 
Published: January 2022

Large-scale software verification relies critically on the use of compositional languages, semantic models, specifications, and verification techniques. Recent work on certified abstraction layers synthesizes game semantics, the refinement calculus, and algebraic effects to enable the composition of heterogeneous components into larger certified systems. However, in existing models of certified abstraction layers, compositionality is restricted by the lack of encapsulation of state.
In this paper, we present a novel game model for certified abstraction layers where the semantics of layer interfaces and implementations are defined solely based on their observable behaviors. Our key idea is to leverage Reddy's pioneer work on modeling the semantics of imperative languages not as functions on global states but as objects with their observable behaviors. We show that a layer interface can be modeled as an object type (i.e., a layer signature) plus an object strategy. A layer implementation is then essentially a regular map, in the sense of Reddy, from an object with the underlay signature to that with the overlay signature. A layer implementation is certified when its composition with the underlay object strategy implements the overlay object strategy. We also describe an extension that allows for non-determinism in layer interfaces.
After formulating layer implementations as regular maps between object spaces, we move to concurrency and design a notion of concurrent object space, where sequential traces may be identified modulo permutation of independent operations. We show how to express protected shared object concurrency, and a ticket lock implementation, in a simple model based on regular maps between concurrent object spaces.
The leaky semicolon: compositional semantic dependencies for relaxed-memory concurrency
Authors: Jeffrey Alan , Riely James , Batty Mark , Cooksey Simon , Kaysin Ilya , Podkopaev Anton 
Published: January 2022

Program logics and semantics tell a pleasant story about sequential composition: when executing (S1;S2), we first execute S1 then S2. To improve performance, however, processors execute instructions out of order, and compilers reorder programs even more dramatically. By design, single-threaded systems cannot observe these reorderings; however, multiple-threaded systems can, making the story considerably less pleasant. A formal attempt to understand the resulting mess is known as a “relaxed memory model.” Prior models either fail to address sequential composition directly, or overly restrict processors and compilers, or permit nonsense thin-air behaviors which are unobservable in practice.
To support sequential composition while targeting modern hardware, we enrich the standard event-based approach with preconditions and families of predicate transformers. When calculating the meaning of (S1; S2), the predicate transformer applied to the precondition of an event e from S2 is chosen based on the set of events in S1 upon which e depends. We apply this approach to two existing memory models.
Physician Approaches to Imaging and Revascularization for Acutely Symptomatic Carotid Stenosis: Insights from the Hot Carotid Qualitative Study
Authors: Ganesh Aravind , Beland Benjamin , Jewett Gordon A.E. , Campbell David J.T. , Varma Malavika , Singh Ravinder‐Jeet , Al‐Sultan Abdulaziz , Wong John H. , Menon Bijoy K. 
Published: January 2022

Background
Evidence informing the choice between carotid endarterectomy and carotid artery stenting for acutely symptomatic carotid stenosis (“hot carotid”) is dated and does not factor in contemporary therapies or techniques. The optimal imaging modality is also uncertain. We explored the attitudes of stroke physicians regarding imaging and revascularization of patients with acute symptomatic carotid stenosis.

Methods
We used a qualitative descriptive methodology to examine decision‐making approaches and opinions of physicians regarding the choice of imaging and revascularization procedures for hot carotids. We conducted semistructured interviews with purposive sampling of 22 stroke physicians from 16 centers in 6 world regions and various specialties: 11 neurologists, 3 geriatricians, 5 interventional neuroradiologists, and 3 neurovascular surgeons.

Results
Qualitative analysis revealed several themes regarding clinical decision‐making for hot carotids. Whereas CT angiography was favored by most participants, timely imaging availability, breadth of information gained, and surgeon/interventionalist preferences were important themes influencing the choice of imaging modality. Carotid endarterectomy was generally favored over carotid artery stenting, but participants’ choice of intervention was influenced by healthcare system factors such as use of multidisciplinary vascular teams and operating room or angiography suite availability, and patient factors like age and infarct size. Areas of uncertainty included choice of imaging modality for borderline stenosis, utility of carotid plaque imaging, timing of revascularization, and the role of intervention with borderline stenosis or intraluminal thrombus.

Conclusions
This qualitative study highlights practice patterns common in different centers around the world, such as the general preference for CT angiography imaging and carotid endarterectomy over carotid artery stenting but also identified important differences in availability, selection, and timing of imaging and revascularization options. To gain widespread support, future carotid trials will need to accommodate identified variations in practice patterns and address areas of uncertainty, such as optimal timing of revascularization with modern best medical management and risk‐stratification with imaging features other than just degree of stenosis.
Mechanical Thrombectomy Beyond 2b Reperfusion: Should We Pursue a Higher Reperfusion Grade after Achievement of 2b?
Authors: Koge Junpei , Tanaka Kanta , Yoshimoto Takeshi , Shiozawa Masayuki , Ohta Tsuyoshi , Satow Tetsu , Kataoka Hiroharu , Ihara Masafumi , Koga Masatoshi , Toyoda Kazunori 
Published: January 2022

Background
Extended thrombolysis in cerebral infarction (eTICI) 2c/3 reperfusion after mechanical thrombectomy (MT) is associated with better stroke outcomes than eTICI 2b. Whether additional MT attempt after achieving eTICI 2b (beyond 2b attempt) leads to better outcomes is unknown.

Methods
Consecutive patients with acute anterior circulation stroke who achieved eTICI 2b during MT were divided into 2 groups: those who further tried MT (beyond‐2b group) and those without (nonbeyond‐2b group). The patients who directly achieved eTICI 2c/3 without experiencing 2b (direct‐2c/3 group) were also studied. The outcomes included the reperfusion status, favorable outcome (3‐month modified Rankin scale score of 0–2), neurological improvement (a ≥10‐point decrease of the National Institutes of Health Stroke Scale score from baseline or the score of 0) at 24 hours and symptomatic intracranial hemorrhage.

Results

Of 308 patients, 50 were in the beyond‐2b group, 87 in the nonbeyond‐2b group, and the remaining 171 in the direct‐2c/3 group. Perfusion of middle cerebral artery branches supplying the primary motor cortex was worse in the beyond‐2b than the nonbeyond‐2b group at the time of eTICI 2b (
P
=0.007). Favorable outcome was similarly common (48% for each,
P
=0.40). Neurological improvement was more frequent (52% versus 37%;
P
=0.04) and symptomatic intracranial hemorrhage tended to be more common (6% versus 1%,
P
=0.11) in the beyond‐2b than the nonbeyond‐2b group. Eighteen patients (36%) in the beyond‐2b group finally achieved eTICI 2c/3; 10 of these (56%) and 14 of the remaining 32 (44%) had favorable outcome (
P
=0.83). The former rate was similar to that in the direct‐2c/3 group (58%;
P
=0.99).

Conclusions
Patients undergoing additional MT attempt after achieving eTICI 2b had numerically but not significantly more symptomatic intracranial hemorrhage and showed a similar level of functional outcome at 3 months than those who did not. When eTICI 2c/3 was finally achieved by additional attempts, functional outcome was similar with that of patients who directly achieved eTICI 2c/3 without experiencing 2b.

Clinical Trial Registration Information

URL:
https://www.clinicaltrials.gov
. Unique identifier: NCT02251665.
An application of neighbourhoods in digraphs to the classification of binary dynamics
Authors: Conceição Pedro , Govc Dejan , Lazovskis Jānis , Levi Ran , Riihimäki Henri , Smith Jason P. 
Published: January 2022

Abstract
A binary state on a graph means an assignment of binary values to its vertices. A time-dependent sequence of binary states is referred to as binary dynamics. We describe a method for the classification of binary dynamics of digraphs, using particular choices of closed neighbourhoods. Our motivation and application comes from neuroscience, where a directed graph is an abstraction of neurons and their connections, and where the simplification of large amounts of data is key to any computation. We present a topological/graph theoretic method for extracting information out of binary dynamics on a graph, based on a selection of a relatively small number of vertices and their neighbourhoods. We consider existing and introduce new real-valued functions on closed neighbourhoods, comparing them by their ability to accurately classify different binary dynamics. We describe a classification algorithm that uses two parameters and sets up a machine learning pipeline. We demonstrate the effectiveness of the method on simulated activity on a digital reconstruction of cortical tissue of a rat, and on a nonbiological random graph with similar density.
The prevalence and impact of university affiliation discrepancies between four bibliographic databases—Scopus, Web of Science, Dimensions, and Microsoft Academic
Authors: Purnell Philip J. 
Published: January 2022

Abstract
Research managers benchmarking universities against international peers face the problem of affiliation disambiguation. Different databases have taken separate approaches to this problem and discrepancies exist between them. Bibliometric data sources typically conduct a disambiguation process that unifies variant institutional names and those of its subunits so that researchers can then search all records from that institution using a single unified name. This study examined affiliation discrepancies between Scopus, Web of Science (WoS), Dimensions, and Microsoft Academic for 18 Arab universities over a 5-year period. We confirmed that digital object identifiers (DOIs) are suitable for extracting comparable scholarly material across databases and quantified the affiliation discrepancies between them. A substantial share of records assigned to the selected universities in any one database were not assigned to the same university in another. The share of discrepancy was higher in the larger databases (Dimensions and Microsoft Academic). The smaller, more selective databases (Scopus and especially WoS) tended to agree to a greater degree with affiliations in the other databases. Manual examination of affiliation discrepancies showed that they were caused by a mixture of missing affiliations, unification differences, and assignation of records to the wrong institution.