bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial intelligence to identify genetic alterations in conventional histopathology
Authors: Cifci Didem , Foersch Sebastian , Kather Jakob Nikolas 
Published: March 2022

AbstractPrecision oncology relies on the identification of targetable molecular alterations in tumor tissues. In many tumor types, a limited set of molecular tests is currently part of standard diagnostic workflows. However, universal testing for all targetable alterations, especially rare ones, is limited by the cost and availability of molecular assays. From 2017 to 2021, multiple studies have shown that artificial intelligence (AI) methods can predict the probability of specific genetic alterations directly from conventional hematoxylin and eosin (H&E) tissue slides. Although these methods are currently less accurate than gold standard testing (e.g. immunohistochemistry, polymerase chain reaction or next‐generation sequencing), they could be used as pre‐screening tools to reduce the workload of genetic analyses. In this systematic literature review, we summarize the state of the art in predicting molecular alterations from H&E using AI. We found that AI methods perform reasonably well across multiple tumor types, although few algorithms have been broadly validated. In addition, we found that genetic alterations inFGFR,IDH,PIK3CA,BRAF,TP53, and DNA repair pathways are predictable from H&E in multiple tumor types, while many other genetic alterations have rarely been investigated or were only poorly predictable. Finally, we discuss the next steps for the implementation of AI‐based surrogate tests in diagnostic workflows. © 2022 The Authors.The Journal of Pathologypublished by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Noninvasive prenatal testing of hereditary colorectal cancer syndromes using cell‐free DNA in maternal plasma
Authors: Wang Yao , Li Suqing , Wu Di , Yan Hongli 
Published: March 2022

AbstractObjectiveThis study aimed to establish a practical protocol for early noninvasive prenatal testing (NIPT) for fetuses at risk of Peutz‐Jeghers syndrome or familial adenomatous polyposis, two classical types of hereditary colorectal cancer syndromes, for risk evaluation and whole‐life monitoring.MethodTarget enrichment was performed using hybridization probes coordinating the serine‐threonine kinase 11 gene region and APC gene region, with 1458 highly heterozygous Single Nucleotide Polymorphisms included. Semitarget amplification random sequencing was used for large fragment deletion detection. For relative haplotype dosage (RHDO) analysis, haplotype construction was performed by segmented haplotype estimation and imputation tool software, the circular binary segmentation algorithm was used for recombination event calculation, and Bayes factor was used for the determination of whether the fetus was affected.ResultsHaplotypes were successfully constructed in the nine recruited families with different pedigree characteristics, and the results for the RHDO analysis were consistent with the amniocentesis sampling detection results. The cell‐free fetal DNA fraction can be detected as low as 2% in maternal plasma.ConclusionThis is the first NIPT assay on hereditary colorectal cancer syndromes based upon RHDO analysis.
Contribution of pharmaceutical drugs of dependence to the incidence of neonatal abstinence syndrome in Western Australia between 2003 and 2018
Authors: Kelty Erin A. , Cumming Craig N. , Preen David B. 
Published: March 2022

AbstractStudy objectiveThe aim of this study was to examine the incidence of neonatal abstinence syndrome (NAS) in Western Australia (WA) and estimate the contribution of pharmaceutical drugs of dependence (PDD) to NAS.DesignA population‐based birth cohort study.Data sourceNeonates were identified through the Midwives Notification Scheme. Linked medication dispensing and hospital records were used to identify exposure to PDD and NAS diagnosis.PatientsAll live born neonates born in WA between 2003 and 2018.MeasurementsThe incidence of NAS and percentage of NAS diagnoses associated with exposure to PDD.Main resultsDuring the study period, the incidence of NAS did not significantly change (annual percentage change (APC): 0.6, 95%CI: −1.3, 2.6), with 3.8 neonates per 1,000 live births diagnosed with NAS. PDD were dispensed to 41.4% of mothers of neonates with NAS, with PDD used to treat opioid use disorders the most commonly prescribed (35.2% of neonates with NAS), while opioid PDD used in the treatment of pain contributed to 5.2% of NAS cases. Non‐opioid PDD contributed to 1.7% of cases of NAS. The incidence of NAS associated with the use of opioids used to treat opioid use disorders (OUD) decreased over the study period (APC: −6.5, 95%CI: −9.5, −3.4), while NAS associated with opioids used to treat pain remained stable (APC: −2.7, 95%CI: −7.1, 1.9).ConclusionThe incidence of neonatal abstinence syndrome in WA remained stable from 2003 to 2018. Medications used to treat opioid use disorders were a substantial driver of NAS, although NAS associated with these medications has declined over time.
Robot joint friction compensation learning enhanced by 6D virtual sensor
Authors: Roveda Loris , Bussolan Andrea , Braghin Francesco , Piga Dario 
Published: March 2022

AbstractHigh‐performance robot control is one of the most investigated topics in both research and industry. Being able to compensate for robot dynamics is indeed one major challenge. Joint friction is commonly the main issue, especially in sensorless (i.e., no availability of torque/force sensors) compliance‐controlled robots for interaction application purposes. The presented paper aims to propose a methodology for sensorless Cartesian impedance controlled robots to learn local friction compensation controllers. Exploiting a 6D virtual sensor to quantify the joint friction effects, a Bayesian optimization (BO)‐based algorithm is proposed to minimize the estimated external interaction in free‐motion tasks (related to friction effects). The BO algorithm enhances the impedance control performance by tuning the model‐based friction compensator parameters. To validate the proposed approach, experimental tests have been executed on a Franka EMIKA panda robot, highlighting the suitability of the proposed 6D virtual sensor and BO‐based algorithm to minimize the estimated external interaction for joint friction compensation purposes.
Finite‐time tracking for state‐constrained strict‐feedback systems without feasibility conditions
Authors: Li Zeqiang , Wang Yujuan 
Published: March 2022

AbstractThis paper investigates the finite‐time tracking control problem for a class of nonlinear strict‐feedback systems subject to asymmetric and time‐varying full‐state constraints. The proposed method is able to achieve practical finite‐time tracking stability without the feasibility conditions, that is, the tracking error converges to a small region around zero in a finite time that can be explicitly expressed and adjusted, which is different from most existing results on strict‐feedback systems subject to constraints where only ultimately uniformly bounded results are obtained and the feasibility conditions are normally required. Three major design steps are utilized. Firstly, by introducing a novel barrier function, the technical obstacle associated with the feasibility conditions is removed; Secondly, to circumvent the technical difficulty in finite‐time stability analysis, a time‐varying index is introduced and incorporated into the adaptive law; And thirdly, both a linear feedback term and a fractional feedback term are included into the virtual filter of the dynamic surface control‐based method. It is the combination of these design skills that allows the practical finite‐time tracking results to be established. The effectiveness of the proposed scheme is verified by the numerical simulation.
PillarX: A Microfluidic Device to Profile Circulating Tumor Cell Clusters Based on Geometry, Deformability, and Epithelial State
Authors: Green Brenda J. , Marazzini Margherita , Hershey Ben , Fardin Amir , Li Qingsen , Wang Zongjie , Giangreco Giovanni , Pisati Federica , Marchesi Stefano , Disanza Andrea , Frittoli Emanuela , Martini Emanuele , Magni Serena , Beznoussenko Galina V. , Vernieri Claudio , Lobefaro Riccardo , Parazzoli Dario , Maiuri Paolo , Havas Kristina , Labib Mahmoud , Sigismund Sara , Fiore Pier Paolo Di , Gunby Rosalind H. , Kelley Shana O. , Scita Giorgio 
Published: March 2022

AbstractCirculating tumor cell (CTC) clusters are associated with increased metastatic potential and worse patient prognosis, but are rare, difficult to count, and poorly characterized biophysically. The PillarX device described here is a bimodular microfluidic device (Pillar‐device and an X‐magnetic device) to profile single CTCs and clusters from whole blood based on their size, deformability, and epithelial marker expression. Larger, less deformable clusters and large single cells are captured in the Pillar‐device and sorted according to pillar gap sizes. Smaller, deformable clusters and single cells are subsequently captured in the X‐device and separated based on epithelial marker expression using functionalized magnetic nanoparticles. Clusters of established and primary breast cancer cells with variable degrees of cohesion driven by different cell‐cell adhesion protein expression are profiled in the device. Cohesive clusters exhibit a lower deformability as they travel through the pillar array, relative to less cohesive clusters, and have greater collective invasive behavior. The ability of the PillarX device to capture clusters is validated in mouse models and patients of metastatic breast cancer. Thus, this device effectively enumerates and profiles CTC clusters based on their unique geometrical, physical, and biochemical properties, and could form the basis of a novel prognostic clinical tool.
Artificial Nanoplatelets Depend on Size for Precisely Inducing Thrombosis in Tumor Vessels
Authors: Zong Xiaoqing , Liu Lamei , Yang Haiyuan , Wu Jinpei , Yuan Pengfei , Chen Xinjie , Yang Caiqi , Li Xiaodi , Li Yuchao , Ji Xin , Shi Changzheng , Xue Wei , Dai Jian 
Published: March 2022

AbstractDue to the heterogeneity of a tumor, the tumor vascular interruption‐based therapy has become an ideal treatment strategy. Herein, artificial nanoplatelets are reported to induce selective thrombosis in tumor vessels, which can achieve rapid and large‐scale necrosis of tumor cells. For one, the nanoplatelets are exploited to specially release thrombin into target regions without affecting the established coagulation factors system. For another, the thrombin elicits vascular infarction to provide tumor‐ablation effects. More importantly, the size‐dependent effect of nanoplatelets (with diameters of 200, 400, and 800 nm) in vivo on blocking the tumor vessels is evaluated. The results show that the nanoplatelets from nanometer to submicron have achieved different biodistribution and therapeutic effects through the vascular transport. Notably, 400 nm scale nanoplatelets can induce thrombosis in tumor vessels and achieve 83% of the tumor elimination rate, thus manifesting the effectiveness of anti‐tumor strategy compared with the other two scales of nanoplatelets (200 and 800 nm). These findings highlight the need of concern about nanoparticle size, providing a promising strategy for the future design of advanced vascular targeting reagents and the clinical translation of tumor vascular interruption‐based therapy.
A first-order logic characterisation of safety and co-safety languages
Authors: Cimatti Alessandro , Geatti Luca , Gigante Nicola , Montanari Angelo , Tonetta Stefano 
Published: March 2022

AbstractLinear Temporal Logic ($$\mathsf {LTL}$$
LTL
) is one of the most popular temporal logics, that comes into play in a variety of branches of computer science. Its widespread use is also due to its strong foundational properties. One of them is Kamp’s theorem, showing that $$\mathsf {LTL}$$
LTL
and the first-order theory of one successor ($$\mathsf {S1S}[\mathsf {FO}]$$

S
1
S

[
FO
]

) are expressively equivalent. Safety and co-safety languages, where a finite prefix suffices to establish whether a word does not or does belong to the language, respectively, play a crucial role in lowering the complexity of problems like model checking and reactive synthesis for $$\mathsf {LTL}$$
LTL
. $$\mathsf {Safety\text {-} \mathsf {LTL}}$$

Safety
-
LTL

(resp., $$\mathsf {coSafety\text {-} \mathsf {LTL}}$$

coSafety
-
LTL

) is a fragment of $$\mathsf {LTL}$$
LTL
where only universal (resp., existential) temporal modalities are allowed, that recognises safety (resp., co-safety) languages only. In this paper, we introduce a fragment of $$\mathsf {S1S}[\mathsf {FO}]$$

S
1
S

[
FO
]

, called $$\mathsf {Safety\text {-} FO}$$

Safety
-
FO

, and its dual $$\mathsf {coSafety\text {-} FO}$$

coSafety
-
FO

, which are expressively complete with regards to the $$\mathsf {LTL}$$
LTL
-definable safety languages. In particular, we prove that they respectively characterise exactly $$\mathsf {Safety\text {-} \mathsf {LTL}}$$

Safety
-
LTL

and $$\mathsf {coSafety\text {-} \mathsf {LTL}}$$

coSafety
-
LTL

, a result that joins Kamp’s theorem, and provides a clearer view of the charactisations of (fragments of) $$\mathsf {LTL}$$
LTL
in terms of first-order languages. In addition, it gives a direct, compact, and self-contained proof that any safety language definable in $$\mathsf {LTL}$$
LTL
is definable in $$\mathsf {Safety\text {-} \mathsf {LTL}}$$

Safety
-
LTL

as well. As a by-product, we obtain some interesting results on the expressive power of the weak tomorrow operator of $$\mathsf {Safety\text {-} \mathsf {LTL}}$$

Safety
-
LTL

interpreted over finite and infinite traces.
Modal Logics and Local Quantifiers: A Zoo in the Elementary Hierarchy
Authors: Fervari Raul , Mansutti Alessio 
Published: March 2022

AbstractWe study a family of modal logics interpreted on tree-like structures, and featuring local quantifiers $$\exists ^{k}p$$

∃
k

p

that bind the proposition p to worlds that are accessible from the current one in at most k steps. We consider a first-order and a second-order semantics for the quantifiers, which enables us to relate several well-known formalisms, such as hybrid logics, $$\textsf {S5Q}$$

S
5
Q

and graded modal logic. To better stress these connections, we explore fragments of our logics, called herein round-bounded fragments. Depending on whether first or second-order semantics is considered, these fragments populate the hierarchy $${2\textsc {NExp} \subset 3\textsc {NExp} \subset \cdots }$$

2
NE

X
P

⊂
3
NE

X
P

⊂
⋯

or the hierarchy $${2\textsc {AExp}_{pol} \subset 3\textsc {AExp}_{pol} \subset \cdots }$$

2
AE

X
P

pol

⊂
3
AE

X
P

pol

⊂
⋯

, respectively. For formulae up-to modal depth k, the complexity improves by one exponential.
The Different Shades of Infinite Session Types
Authors: Gay Simon J. , Poças Diogo , Vasconcelos Vasco T. 
Published: March 2022

AbstractMany type systems include infinite types. In session type systems, infinite types are important because they specify communication protocols that are unbounded in time. Usually infinite session types are introduced as simple finite-state expressions "Equation missing" or by non-parametric equational definitions "Equation missing". Alternatively, some systems of label- or value-dependent session types go beyond simple recursive types. However, leaving dependent types aside, there is a much richer world of infinite session types, ranging through various forms of parametric equational definitions, to arbitrary infinite types in a coinductively defined space. We study infinite session types across a spectrum of shades of grey on the way to the bright light of general infinite types. We identify four points on the spectrum, characterised by different styles of equational definitions, and show that they form a strict hierarchy by establishing bidirectional correspondences with classes of automata: finite-state, 1-counter, pushdown and 2-counter. This allows us to establish decidability and undecidability results for type formation, type equivalence and duality in each class of types. We also consider previous work on context-free session types (and extend it to higher-order) and nested session types, and locate them on our spectrum of infinite types.
Complete and tractable machine-independent characterizations of second-order polytime
Authors: Hainry Emmanuel , Kapron Bruce M. , Marion Jean-Yves , Péchoux Romain 
Published: March 2022

AbstractThe class of Basic Feasible Functionals $$\mathtt{BFF}$$
BFF
is the second-order counterpart of the class of first-order functions computable in polynomial time. We present several implicit characterizations of $$\mathtt{BFF}$$
BFF
based on a typed programming language of terms. These terms may perform calls to imperative procedures, which are not recursive. The type discipline has two layers: the terms follow a standard simply-typed discipline and the procedures follow a standard tier-based type discipline. $$\mathtt{BFF}$$
BFF
consists exactly of the second-order functionals that are computed by typable and terminating programs. The completeness of this characterization surprisingly still holds in the absence of lambda-abstraction. Moreover, the termination requirement can be specified as a completeness-preserving instance, which can be decided in time quadratic in the size of the program. As typing is decidable in polynomial time, we obtain the first tractable (i.e., decidable in polynomial time), sound, complete, and implicit characterization of $$\mathtt{BFF}$$
BFF
, thus solving a problem opened for more than 20 years.
Variable binding and substitution for (nameless) dummies
Authors: Hirschowitz André , Hirschowitz Tom , Lafont Ambroise , Maggesi Marco 
Published: March 2022

AbstractBy abstracting over well-known properties of De Bruijn’s representation with nameless dummies, we design a new theory of syntax with variable binding and capture-avoiding substitution. We propose it as a simpler alternative to Fiore, Plotkin, and Turi’s approach, with which we establish a strong formal link. We also show that our theory easily incorporates simple types and equations between terms.
On the Translation of Automata to Linear Temporal Logic
Authors: Boker Udi , Lehtinen Karoliina , Sickert Salomon 
Published: March 2022

AbstractWhile the complexity of translating future linear temporal logic (LTL) into automata on infinite words is well-understood, the size increase involved in turning automata back to LTL is not. In particular, there is no known elementary bound on the complexity of translating deterministic$$\omega $$ω-regular automata to LTL.Our first contribution consists of tight bounds for LTL over a unary alphabet: alternating, nondeterministic and deterministic automata can be exactly exponentially, quadratically and linearly more succinct, respectively, than any equivalent LTL formula. Our main contribution consists of a translation of general counter-free deterministic$$\omega $$ω-regular automata into LTL formulas of double exponential temporal-nesting depth and triple exponential length, using an intermediate Krohn-Rhodes cascade decomposition of the automaton. To our knowledge, this is the first elementary bound on this translation. Furthermore, our translation preserves the acceptance condition of the automaton in the sense that it turns a looping, weak, Büchi, coBüchi or Muller automaton into a formula that belongs to the matching class of the syntactic future hierarchy. In particular, it can be used to translate an LTL formula recognising a safety language to a formula belonging to the safety fragment of LTL (over both finite and infinite words).
Categorical composable cryptography
Authors: Broadbent Anne , Karvonen Martti 
Published: March 2022

AbstractWe formalize the simulation paradigm of cryptography in terms of category theory and show that protocols secure against abstract attacks form a symmetric monoidal category, thus giving an abstract model of composable security definitions in cryptography. Our model is able to incorporate computational security, set-up assumptions and various attack models such as colluding or independently acting subsets of adversaries in a modular, flexible fashion. We conclude by using string diagrams to rederive the security of the one-time pad and no-go results concerning the limits of bipartite and tripartite cryptography, ruling out e.g., composable commitments and broadcasting.
Comparing the expressiveness of the $$\pi $$-calculus and CCS
Authors: van Glabbeek Rob 
Published: March 2022

AbstractThis paper shows that the $$\pi $$
π
-calculus with implicit matching is no more expressive than $$\mathrm {CCS}_{\gamma }$$

CCS
γ

, a variant of CCS in which the result of a synchronisation of two actions is itself an action subject to relabelling or restriction, rather than the silent action $$\tau $$
τ
. This is done by exhibiting a compositional translation from the $$\pi $$
π
-calculus with implicit matching to $$\mathrm {CCS}_{\gamma }$$

CCS
γ

that is valid up to strong barbed bisimilarity.The full $$\pi $$
π
-calculus can be similarly expressed in $$\mathrm {CCS}_{\gamma }$$

CCS
γ

enriched with the triggering operation of Meije.I also show that these results cannot be recreated with CCS in the rôle of $$\mathrm {CCS}_{\gamma }$$

CCS
γ

, not even up to reduction equivalence, and not even for the asynchronous $$\pi $$
π
-calculus without restriction or replication.Finally I observe that CCS cannot be encoded in the $$\pi $$
π
-calculus.
View-Based Owicki–Gries Reasoning for Persistent x86-TSO
Authors: Bila Eleni Vafeiadi , Dongol Brijesh , Lahav Ori , Raad Azalea , Wickerson John 
Published: March 2022

AbstractThe rise of persistent memory is disrupting computing to its core. Our work aims to help programmers navigate this brave new world by providing a program logic for reasoning about x86 code that uses low-level operations such as memory accesses and fences, as well as persistency primitives such as flushes. Our logic, Pierogi, benefits from a simple underlying operational semantics based on views, is able to handle optimised flush operations, and is mechanised in the Isabelle/HOL proof assistant. We detail the proof rules of Pierogi and prove them sound. We also show how Pierogi can be used to reason about a range of challenging single- and multi-threaded persistent programs.
An Institutional Approach to Communicating UML State Machines
Authors: Rosenberger Tobias , Knapp Alexander , Roggenbach Markus 
Published: March 2022

AbstractWe present a new approach on how to provide institution-based semantics for communicating UML state machines in form of a hybrid modal logic $$\mathcal {M}^{\downarrow }_{\mathcal {D}}$$

M

D
↓

. A theoroidal comorphism maps $$\mathcal {M}^{\downarrow }_{\mathcal {D}}$$

M

D
↓

into the $$\textsc {Casl}$$

C

A
S
L

institution. This allows for symbolic reasoning on communicating UML state machines.