bluuebunny/crossref_metadata_2025 huggingface dataset:
Soundly Handling Linearity
Authors: Tang Wenhao , Hillerström Daniel , Lindley Sam , Morris J. Garrett
Published: January 2024

We propose a novel approach to soundly combining linear types with multi-shot effect handlers. circear type systems statically ensure that resources such as file handles and communication channels are used exactly once. Effect handlers provide a rich modular programming abstraction for implementing features ranging from exceptions to concurrency to backtracking. Whereas conventional linear type systems bake in the assumption that continuations are invoked exactly once, effect handlers allow continuations to be discarded (e.g. for exceptions) or invoked more than once (e.g. for backtracking). This mismatch leads to soundness bugs in existing systems such as the programming language Links, which combines linearity (for session types) with effect handlers. We introduce control-flow linearity as a means to ensure that continuations are used in accordance with the linearity of any resources they capture, ruling out such soundness bugs.

We formalise the notion of control-flow linearity in a System F-style core calculusFeff∘equipped with linear types, an effect type system, and effect handlers. We define a linearity-aware semantics in order to formally prove thatFeff∘preserves the integrity of linear values in the sense that no linear value is discarded or duplicated. In order to show that control-flow linearity can be made practical, we adapt circks based on the design ofFeff∘, in doing so fixing a long-standing soundness bug.

Finally, to better expose the potential of control-flow linearity, we define an ML-style core calculusQeff∘, based on qualified types, which requires no programmer provided annotations, and instead relies entirely on type inference to infer control-flow linearity. Both linearity and effects are captured by qualified types.Qeff∘overcomes a number of practical limitations ofFeff∘, supporting abstraction over linearity, linearity dependencies between type variables, and a much more fine-grained notion of control-flow linearity.
A Case for Synthesis of Recursive Quantum Unitary Programs
Authors: Deng Haowei , Tao Runzhou , Peng Yuxiang , Wu Xiaodi
Published: January 2024

Quantum programs are notoriously difficult to code and verify due to unintuitive quantum knowledge associated with quantum programming. Automated tools relieving the tedium and errors associated with low-level quantum details would hence be highly desirable. In this paper, we initiate the study of program synthesis for quantum unitary programs that recursively define a family of unitary circuits for different input sizes, which are widely used in existing quantum programming languages. Specifically, we present QSynth, the first quantum program synthesis framework, including a new inductive quantum programming language, its specification, a sound logic for reasoning, and an encoding of the reasoning procedure into SMT instances. By leveraging existing SMT solvers, QSynth successfully synthesizes ten quantum unitary programs including quantum adder circuits, quantum eigenvalue inversion circuits and Quantum Fourier Transformation, which can be readily transpiled to executable programs on major quantum platforms, e.g., Q#, IBM Qiskit, and AWS Braket.
Parikh’s Theorem Made Symbolic
Authors: Hague Matthew , Jeż Artur , Lin Anthony W.
Published: January 2024

Parikh’s Theorem is a fundamental result in automata theory with numerous applications in computer science. These include software verification (e.g. infinite-state verification, string constraints, and theory of arrays), verification of cryptographic protocols (e.g. using Horn clauses modulo equational theories) and database querying (e.g. evaluating path-queries in graph databases), among others. Parikh’s Theorem states that the letter-counting abstraction of a language recognized by finite automata or context-free grammars is definable in Linear Integer Arithmetic (a.k.a. Presburger Arithmetic). In fact, there is a linear-time algorithm computing existential Presburger formulas capturing such abstractions, which enables an efficient analysis via SMT-solvers. Unfortunately, real-world applications typically require large alphabets (e.g. Unicode, containing a ‍million of characters) — which are well-known to be not amenable to explicit treatment of the alphabets — or even worse infinite alphabets.

Symbolic automata have proven in the last decade to be an effective algorithmic framework for handling large finite or even infinite alphabets. A symbolic automaton employs an effective boolean algebra, which offers a symbolic representation of character sets (i.e. in terms of predicates) and often lends itself to an exponentially more succinct representation of a language. Instead of letter-counting, Parikh’s Theorem for symbolic automata amounts to counting the number of times different predicates are satisfied by an input sequence. Unfortunately, naively applying Parikh’s Theorem from classical automata theory to symbolic automata yields existential Presburger formulas of exponential size. In this paper, we provide a new construction for Parikh’s Theorem for symbolic automata and grammars, which avoids this exponential blowup: our algorithm computes an existential formula in polynomial-time over (quantifier-free) Presburger and the base theory. In fact, our algorithm extends to the model of parametric symbolic grammars, which are one of the most expressive models of languages over infinite alphabets. We have implemented our algorithm and show it can be used to solve string constraints that are difficult to solve by existing solvers.
Predictive Monitoring against Pattern Regular Languages
Authors: Ang Zhendong , Mathur Umang
Published: January 2024

While current bug detection techniques for concurrent software focus on unearthing low-level issues such as data races or deadlocks, they often fall short of discovering more intricate temporal behaviours that can arise even in the absence of such low-level issues. In this paper, we focus on the problem of dynamically analysing concurrent software against high-level temporal specifications such as LTL. Existing techniques for runtime monitoring against such specifications are primarily designed for sequential software and remain inadequate in the presence of concurrency — violations may be observed only in intricate thread interleavings, requiring many re-runs of the underlying software in conjunction with the analysis. Towards this, we study the problem of
predictive runtime monitoring
, inspired by the analogous problem of
predictive data race detection
studied extensively recently. The predictive runtime monitoring question asks, given an execution σ, if it can be soundly
reordered
to expose violations of a specification. In general, this problem may become easily intractable when either the specifications or the notion of reorderings used is complex.

In this paper, we focus on specifications that are given in regular languages. Our notion of reorderings is
trace equivalence
, where an execution is considered a reordering of another if it can be obtained from the latter by successively commuting adjacent independent actions. We first show that, even in this simplistic setting, the problem of predictive monitoring admits a super-linear lower bound of
O
(
n
α
), where
n
is the number of events in the execution, and α is a parameter describing the degree of commutativity, and typically corresponds to the number of threads in the execution. As a result, predictive runtime monitoring even in this setting is unlikely to be efficiently solvable, unlike in the non-predictive setting where the problem can be checked using a deterministic finite automaton (and thus, a constant-space streaming linear-time algorithm).

Towards this, we identify a sub-class of regular languages, called
pattern languages
(and their extension
generalized pattern languages
). Pattern languages can naturally express specific ordering of some number of (labelled) events, and have been inspired by popular empirical hypotheses underlying many concurrency bug detection approaches such as the “small bug depth” hypothesis. More importantly, we show that for pattern (and generalized pattern) languages, the predictive monitoring problem can be solved using a constant-space streaming linear-time algorithm. We implement and evaluate our algorithm PatternTrack on benchmarks from the literature and show that it is effective in monitoring large-scale applications.
ReLU Hull Approximation
Authors: Ma Zhongkui , Li Jiaying , Bai Guangdong
Published: January 2024

Convex hulls are commonly used to tackle the non-linearity of activation functions in the verification of neural networks. Computing the exact convex hull is a costly task though. In this work, we propose a fast and precise approach to over-approximating the convex hull of the ReLU function (referred to as the ReLU hull), one of the most used activation functions. Our key insight is to formulate a convex polytope that ”wraps” the ReLU hull, by reusing the linear pieces of the ReLU function as the lower faces and constructing upper faces that are adjacent to the lower faces. The upper faces can be efficiently constructed based on the edges and vertices of the lower faces, given that an
n
-dimensional (or simply
n
d hereafter) hyperplane can be determined by an (
n
−1)d hyperplane and a point outside of it. We implement our approach as WraLU, and evaluate its performance in terms of precision, efficiency, constraint complexity, and scalability. WraLU outperforms existing advanced methods by generating fewer constraints to achieve tighter approximation in less time. It exhibits versatility by effectively addressing arbitrary input polytopes and higher-dimensional cases, which are beyond the capabilities of existing methods. We integrate WraLU into PRIMA, a state-of-the-art neural network verifier, and apply it to verify large-scale ReLU-based neural networks. Our experimental results demonstrate that WraLU achieves a high efficiency without compromising precision. It reduces the number of constraints that need to be solved by the linear programming solver by up to half, while delivering comparable or even superior results compared to the state-of-the-art verifiers.
Commutativity Simplifies Proofs of Parameterized Programs
Authors: Farzan Azadeh , Klumpp Dominik , Podelski Andreas
Published: January 2024

Commutativity
has proven to be a powerful tool in reasoning about concurrent programs. Recent work has shown that a commutativity-based
reduction
of a program may admit simpler proofs than the program itself. The framework of lexicographical program reductions was introduced to formalize a broad class of reductions which accommodate sequential (thread-local) reasoning as well as synchronous programs. Approaches based on this framework, however, were fundamentally limited to program models with a
fixed/bounded
number of threads. In this paper, we show that it is possible to define an effective parametric family of program reductions that can be used to find simple proofs for
parameterized programs
, i.e., for programs with an unbounded number of threads. We show that reductions are indeed useful for the simplification of proofs for parameterized programs, in a sense that can be made precise: A reduction of a parameterized program may admit a proof which uses
fewer
or
less sophisticated ghost variables
. The reduction may therefore be within reach of an automated verification technique, even when the original parameterized program is not. As our first technical contribution, we introduce a notion of reductions for parameterized programs such that the reduction
R
of a parameterized program
P
is again a parameterized program (the thread template of
R
is obtained by source-to-source transformation of the thread template of
P
). Consequently, existing techniques for the verification of parameterized programs can be directly applied to
R
instead of
P
. Our second technical contribution is that we define an appropriate family of
pairwise preference orders
which can be effectively used as a parameter to produce different lexicographical reductions. To determine whether this theoretical foundation amounts to a usable solution in practice, we have implemented the approach, based on a recently proposed framework for parameterized program verification. The results of our preliminary experiments on a representative set of examples are encouraging.
Sound Gradual Verification with Symbolic Execution
Authors: Zimmerman Conrad , DiVincenzo Jenna , Aldrich Jonathan
Published: January 2024

Gradual verification, which supports explicitly partial specifications
and verifies them with a combination of static and dynamic checks, makes
verification more incremental and provides earlier feedback to developers.
While an abstract, weakest precondition-based approach to gradual verification
was previously proven sound, the approach did not provide sufficient guidance
for implementation and optimization of the required run-time checks. More
recently, gradual verification was implemented using symbolic execution
techniques, but the soundness of the approach (as with related static
checkers based on implicit dynamic frames) was an open question. This paper
puts practical gradual verification on a sound footing with a formalization
of symbolic execution, optimized run-time check generation, and run time
execution. We prove our approach is sound; our proof also covers a core
subset of the Viper tool, for which we are aware of no previous soundness result.
Our formalization enabled us to find a soundness bug in an implemented gradual
verification tool and describe the fix necessary to make it sound.
Effectful Software Contracts
Authors: Moy Cameron , Dimoulas Christos , Felleisen Matthias
Published: January 2024

Software contracts empower programmers to describe functional properties of components. When it comes to constraining effects, though, the literature offers only one-off solutions for various effects. It lacks a universal principle. This paper presents the design of an effectful contract system in the context of effect handlers. A key metatheorem shows that contracts cannot unduly interfere with a program's execution. An implementation of this design, along with an evaluation of its generality, demonstrates that the theory can guide practice.
Answer Refinement Modification: Refinement Type System for Algebraic Effects and Handlers
Authors: Kawamata Fuga , Unno Hiroshi , Sekiyama Taro , Terauchi Tachio
Published: January 2024

Algebraic effects and handlers are a mechanism to structure programs with computational effects in a modular way. They are recently gaining popularity and being adopted in practical languages, such as OCaml. Meanwhile, there has been substantial progress in program verification via
refinement type systems
. While a variety of refinement type systems have been proposed, thus far there has not been a satisfactory refinement type system for algebraic effects and handlers. In this paper, we fill the void by proposing a novel refinement type system for languages with algebraic effects and handlers. The expressivity and usefulness of algebraic effects and handlers come from their ability to manipulate
delimited continuations
, but delimited continuations also complicate programs’ control flow and make their verification harder. To address the complexity, we introduce a novel concept that we call
answer refinement modification
(ARM for short), which allows the refinement type system to precisely track what effects occur and in what order when a program is executed, and reflect such information as modifications to the refinements in the types of delimited continuations. We formalize our type system that supports ARM (as well as answer
type
modification, or ATM) and prove its soundness. Additionally, as a proof of concept, we have extended the refinement type system to a subset of OCaml 5 which comes with a built-in support for effect handlers, implemented a type checking and inference algorithm for the extension, and evaluated it on a number of benchmark programs that use algebraic effects and handlers. The evaluation demonstrates that ARM is conceptually simple and practically useful. Finally, a natural alternative to directly reasoning about a program with delimited continuations is to apply a
continuation passing style
(CPS) transformation that transforms the program to a pure program without delimited continuations. We investigate this alternative in the paper, and show that the approach is indeed possible by proposing a novel CPS transformation for algebraic effects and handlers that enjoys bidirectional (refinement-)type-preservation. We show that there are pros and cons with this approach, namely, while one can use an existing refinement type checking and inference algorithm that can only (directly) handle pure programs, there are issues such as needing type annotations in source programs and making the inferred types less informative to a user.
Graph Learning based Performance Analysis for Queueing Networks
Authors: Niu Zifeng
Published: January 2024

Queueing networks serve as a popular performance model in the analysis of business processes and computer systems [4]. Solving queueing network models helps the decision making of system designers. System response time and throughput are two key performance measures in queueing networks. The most widely used algorithms for solving these measures are mean value analysis (MVA) and its approximate extensions [3, §8-9]. However, conventional analytic methods are inaccurate at solving non-product form queueing networks that are frequently encountered in modeling most real systems. Approximation formulas typically rely on assumptions that may lead, on particular regions of the parameters, to inaccurate and misleading results. Simulation modeling is an accurate way, but it requires to be designed for each specific problem, and usually takes longer time to converge.
Enhancing Security and Privacy in Head-Mounted Augmented Reality Systems Using Eye Gaze
Authors: Corbett Matthew
Published: January 2024

Augmented Reality (AR) devices offer a rich, immersive experience that provides the user with a blend of the physical and the synthetic, digitally augmented world. This augmentation is made possible by the AR device's sensors, which are constantly absorbing information about both the user's physical environment (using sensors such as depth and photographic cameras) and about the users themselves (using eye gaze sensors, for example). This information presents both problems and unique solutions. For example, user eye gaze has been shown to be effective in creating efficient and usable local pairing methods between two or more devices and to provide salience in determining what visual data should not be included in raw sensor outputs.
Theory of Timely Remote Estimation and Application toSituational Awareness
Authors: Zaman Ornee Tasmeen
Published: January 2024

Brief Biography: Tasmeen Zaman Ornee is a PhD candidate at the Electrical and Computer Engineering Department of Auburn University. She joined the Real-time Networking lab in Fall 2018. Her PhD supervisor is Prof. Yin Sun. She completed her M.Sc. in Electrical Engineering from Auburn University in 2022. She received her B.Sc. degree in Electrical & Electronic Engineering from Bangladesh University of Engineering and Technology in 2017. Her research interests include information freshness, remote estimation, robotic control, and wireless communication networks. She has worked on designing novel sampling and scheduling policies for the remote estimation of diffusion processes involving single and multiple sources. In addition, she has worked on designing low-complexity scheduling algorithms for improving situational awareness in safety-critical systems. She received the IEEE/IFIP WiOpt Best Paper Award in 2019, one of her IEEE/ACM ToN journals was recommended for fast-tracked review, and she had an invited paper at IEEE SPAWC 2021. She is also one of the authors of a book chapter published by CUP. She is a graduate student member of IEEE and ACM.
NADPH oxidase overexpression and mitochondrial OxPhos impairment are more profound in human hearts donated after circulatory death than brain death
Authors: Mondal Nandan K. , Li Shiyi , Elsenousi Abdussalam E. , Mattar Aladdein , Nordick Katherine V. , Lamba Harveen K. , Hochman-Mendez Camila , Rosengart Todd K. , Liao Kenneth K.
Published: January 2024

First human DCD heart research studied cardiac stress and mitochondrial dysfunction concerning WIT and the efficacy of del Nido cardioplegia as an organ procurement solution and subsequent cold storage. Mild to moderate cardiac stress and mitochondrial dysfunction were noticed in DCD hearts with WIT 20 and 40 min and cold storage for 4 and 2 h, respectively. These changes can serve as biomarkers, allowing interventions to preserve mitochondria and extend WIT in DCD hearts.
A novel method for the percutaneous induction of myocardial infarction by occlusion of small coronary arteries in the rabbit
Authors: Freeman Michael , Huethorst Eline , Boland Erin , Dunne Michael , Burton Francis , Denning Chris , Myles Rachel , Smith Godfrey
Published: January 2024

Surgical coronary ligation is the standard technique to induce myocardial infarction (MI) in rabbits but is associated with procedural trauma and the generation of thoracic adhesions. Percutaneous coronary occlusion avoids these shortcomings and is established in pigs but has only been applicable to large rabbits because of a mismatch between the equipment used and target vessel size. Here, we describe a new scalable approach to percutaneous MI induction that is safe and effective in 2.5–3.5-kg rabbits.
Design, Fabrication, and Characterization of 3D-Printed Multiphase Scaffolds Based on Triply Periodic Minimal Surfaces
Authors: Vigil Josette , Lewis Kailey , Norris Nicholas , Karakoç Alp , Becker Timothy A.
Published: January 2024

The present work investigates the influence of material phases and their volume fractions on the elastic behavior of triply periodic minimal surface (TPMS) scaffolds for the potential modeling of bone scaffolds. A graphical tool using TPMS functions, namely Schwarz-D (diamond), gyroid, and modified gyroid, was developed and used to design and additively manufacture 3D multiphase scaffold models. A PolyJet, UV-cured 3D-printer system was used to fabricate the various TPMS scaffold models using three polymer materials with high, medium, and low stiffness properties. All TPMS models had the same volume fractions of the three polymer materials. Final models were printed into cylinders with a diameter of 20 mm and a height of 8 mm for mechanical testing. The models were subjected to compressive and shear testing using a dynamic mechanical analysis rheometer. All samples were tested at physiologically relevant temperature (37°C) to provide detailed structural characterizations. Microscopic imaging of 3D-printed scaffold longitudinal and cross sections revealed that additive manufacturing adequately recreated the TPMS functions, which created anisotropic materials with variable structures in the longitudinal and transverse directions. Mechanical testing showed that all three TPMS 3D-printed scaffold types exhibited significantly different shear and compressive properties (verifying anisotropic properties) despite being constructed of the same volume fractions of the three UV-printed polymer materials. The gyroid and diamond scaffolds demonstrated complex moduli values that ranged from 1.2 to 1.8 times greater than the modified gyroid scaffolds in both shear and compression. Control scaffolds printed from 100% of each of the three polymers had statistically similar mechanical properties, verifying isotropic properties.
Synthesis and Morphology of Flexible Polyurethane Foams Containing Neem Oil and Clove Powder
Authors: Kuranchie Charles , Yaya Abu , Aboagye-Antwi Fred , Bensah Yaw Delali
Published: January 2024

Polyurethane foams are a versatile class of polymeric materials whose physico‐chemical structure and properties can be modified by incorporating additives. This study examined the effect of naturally occurring insect‐repelling additives such as neem oil (NO) and clove powder (CP) on the formulation and morphology of flexible polyurethane foam (FPUF) composites. The foams were prepared by the prepolymer method using a box test as applied in the foam industry. The composite material was formulated by varying the isocyanate index (103 and 108) as an excess amount of isocyanate was required to react with the additives. The formulation at 103 was unsuccessful as the foams collapsed immediately after rising. However, at 108, two main categories of foams were successfully prepared: foams containing either NO or CP and the other containing both additives. The effect of these additives on the formulation was examined by monitoring the foam reaction using the cream, tack‐free, and rising times. It was observed that the cream, tack‐free, and rising times increased with increasing NO/CP content. Conversely, the morphology was studied using scanning electron microscopy (SEM) and optical microscope (OP). The SEM images revealed disruption of the foam network with 1 wt% NO, likewise those containing 1 wt% CP. The cellular network of the foams with simultaneous addition of NO and CP was similar to that of the neat foams and had no broken cell joints and struts due to better dispersion of the additives in the polyurethane matrix. The study indicates that the combined addition of NO and CP modifies the morphology of FPUF, which can influence their physico‐mechanical properties.
Supplementary Figure S5 from Inhibition of PORCN Blocks Wnt Signaling to Attenuate Progression of Oral Carcinogenesis
Authors: Peña-Oyarzún Daniel , Flores Tania , Torres Vicente A. , Quest Andrew F.G. , Lobos-González Lorena , Kretschmar Catalina , Contreras Pamela , Maturana-Ramírez Andrea , Criollo Alfredo , Reyes Montserrat
Published: January 2024

Clinical presentation of human oral lesions used as oral carcinogenesis ex vivo modeL
Supplementary Figure S4 from Inhibition of PORCN Blocks Wnt Signaling to Attenuate Progression of Oral Carcinogenesis
Authors: Peña-Oyarzún Daniel , Flores Tania , Torres Vicente A. , Quest Andrew F.G. , Lobos-González Lorena , Kretschmar Catalina , Contreras Pamela , Maturana-Ramírez Andrea , Criollo Alfredo , Reyes Montserrat
Published: January 2024

Effect of C59 on cell invasion in CAL-27 cells
Supp Figure 2 from FAK Drives Resistance to Therapy in HPV-Negative Head and Neck Cancer in a p53-Dependent Manner
Authors: Pifer Phillip M. , Yang Liangpeng , Kumar Manish , Xie Tongxin , Frederick Mitchell , Hefner Andrew , Beadle Beth , Molkentine David , Molkentine Jessica , Dhawan Annika , Abdelhakiem Mohamed , Osman Abdullah A. , Leibowitz Brian J. , Myers Jeffrey N. , Pickering Curtis R. , Sandulache Vlad C. , Heymach John , Skinner Heath D.
Published: January 2024

Supp Figure 2
Supp Figure 1 from FAK Drives Resistance to Therapy in HPV-Negative Head and Neck Cancer in a p53-Dependent Manner
Authors: Pifer Phillip M. , Yang Liangpeng , Kumar Manish , Xie Tongxin , Frederick Mitchell , Hefner Andrew , Beadle Beth , Molkentine David , Molkentine Jessica , Dhawan Annika , Abdelhakiem Mohamed , Osman Abdullah A. , Leibowitz Brian J. , Myers Jeffrey N. , Pickering Curtis R. , Sandulache Vlad C. , Heymach John , Skinner Heath D.
Published: January 2024

Supp Figure 1
Full Western Blot Images 1 from FAK Drives Resistance to Therapy in HPV-Negative Head and Neck Cancer in a p53-Dependent Manner
Authors: Pifer Phillip M. , Yang Liangpeng , Kumar Manish , Xie Tongxin , Frederick Mitchell , Hefner Andrew , Beadle Beth , Molkentine David , Molkentine Jessica , Dhawan Annika , Abdelhakiem Mohamed , Osman Abdullah A. , Leibowitz Brian J. , Myers Jeffrey N. , Pickering Curtis R. , Sandulache Vlad C. , Heymach John , Skinner Heath D.
Published: January 2024

Full Western Blot Images
Supplementary Table S2 from A Fully Automated Deep-Learning Model for Predicting the Molecular Subtypes of Posterior Fossa Ependymomas Using T2-Weighted Images
Authors: Cheng Dan , Zhuo Zhizheng , Du Jiang , Weng Jinyuan , Zhang Chengzhou , Duan Yunyun , Sun Ting , Wu Minghao , Guo Min , Hua Tiantian , Jin Ying , Peng Boyang , Li Zhaohui , Zhu Mingwang , Imami Maliha , Bettegowda Chetan , Sair Haris , Bai Harrison X. , Barkhof Frederik , Liu Xing , Liu Yaou
Published: January 2024

Prediction performance of T2-nnU-net and age using optimal threshold for high specificity of PFB
Table S1 from Analysis of Tumor Microenvironment Changes after Neoadjuvant Chemotherapy with or without Bevacizumab in Advanced Ovarian Cancer (GEICO-89T/MINOVA Study)
Authors: Tavira Beatriz , Iscar Teresa , Manso Luis , Santaballa Ana , Gil-Martin Marta , García García Yolanda , Romeo Margarita , Iglesias Maria , de Juan Ferré Ana , Barretina-Ginesta María Pilar , Manzano Aranzazu , Gaba Lydia , Rubio María Jesús , de Andrea Carlos E. , González-Martín Antonio
Published: January 2024

Supplementary Table 1. Clinical characteristics of the patients included in the study diagnosed with epithelial ovarian cancer.
Supplementary Table S1 from A Fully Automated Deep-Learning Model for Predicting the Molecular Subtypes of Posterior Fossa Ependymomas Using T2-Weighted Images
Authors: Cheng Dan , Zhuo Zhizheng , Du Jiang , Weng Jinyuan , Zhang Chengzhou , Duan Yunyun , Sun Ting , Wu Minghao , Guo Min , Hua Tiantian , Jin Ying , Peng Boyang , Li Zhaohui , Zhu Mingwang , Imami Maliha , Bettegowda Chetan , Sair Haris , Bai Harrison X. , Barkhof Frederik , Liu Xing , Liu Yaou
Published: January 2024

Details of the MR acquisition protocols
Supplementary Methods 1 from Analysis of Tumor Microenvironment Changes after Neoadjuvant Chemotherapy with or without Bevacizumab in Advanced Ovarian Cancer (GEICO-89T/MINOVA Study)
Authors: Tavira Beatriz , Iscar Teresa , Manso Luis , Santaballa Ana , Gil-Martin Marta , García García Yolanda , Romeo Margarita , Iglesias Maria , de Juan Ferré Ana , Barretina-Ginesta María Pilar , Manzano Aranzazu , Gaba Lydia , Rubio María Jesús , de Andrea Carlos E. , González-Martín Antonio
Published: January 2024

Supplementary Methods. Detailed description of methodology.
Supplementary Document S1 from A Fully Automated Deep-Learning Model for Predicting the Molecular Subtypes of Posterior Fossa Ependymomas Using T2-Weighted Images
Authors: Cheng Dan , Zhuo Zhizheng , Du Jiang , Weng Jinyuan , Zhang Chengzhou , Duan Yunyun , Sun Ting , Wu Minghao , Guo Min , Hua Tiantian , Jin Ying , Peng Boyang , Li Zhaohui , Zhu Mingwang , Imami Maliha , Bettegowda Chetan , Sair Haris , Bai Harrison X. , Barkhof Frederik , Liu Xing , Liu Yaou
Published: January 2024

DNA methylation profiling
Supplementary Table S4 from Overall Survival and Exploratory Biomarker Analyses of Abemaciclib plus Trastuzumab with or without Fulvestrant versus Trastuzumab plus Chemotherapy in HR+, HER2+ Metastatic Breast Cancer Patients
Authors: Tolaney Sara M. , Goel Shom , Nadal Jorge , Denys Hannelore , Borrego Manuel R. , Litchfield Lacey M. , Liu Jiangang , Appiah Adams K. , Chen Yanyun , André Fabrice
Published: January 2024

ORA for 216 differentially expressed genes.
Supplementary Table S3 from Tumor Volume Growth Rates and Doubling Times during Active Surveillance of IDH-mutant Low-Grade Glioma
Authors: Bhatia Ankush , Moreno Raquel , Reiner Anne S. , Nandakumar Subhiksha , Walch Henry S. , Thomas Teena M. , Nicklin Philip J. , Choi Ye , Skakodub Anna , Malani Rachna , Prabhakaran Vivek , Tiwari Pallavi , Diaz Maria , Panageas Katherine S. , Mellinghoff Ingo K. , Bale Tejus A. , Young Robert J.
Published: January 2024

Supplementary Table S3. Baseline Radiological Characteristics Stratified by Molecular Grade.
Supplementary Table S1 from Overall Survival and Exploratory Biomarker Analyses of Abemaciclib plus Trastuzumab with or without Fulvestrant versus Trastuzumab plus Chemotherapy in HR+, HER2+ Metastatic Breast Cancer Patients
Authors: Tolaney Sara M. , Goel Shom , Nadal Jorge , Denys Hannelore , Borrego Manuel R. , Litchfield Lacey M. , Liu Jiangang , Appiah Adams K. , Chen Yanyun , André Fabrice
Published: January 2024

Updated objective response rate for the ITT population.
Supplementary Table S2 from Tumor Volume Growth Rates and Doubling Times during Active Surveillance of IDH-mutant Low-Grade Glioma
Authors: Bhatia Ankush , Moreno Raquel , Reiner Anne S. , Nandakumar Subhiksha , Walch Henry S. , Thomas Teena M. , Nicklin Philip J. , Choi Ye , Skakodub Anna , Malani Rachna , Prabhakaran Vivek , Tiwari Pallavi , Diaz Maria , Panageas Katherine S. , Mellinghoff Ingo K. , Bale Tejus A. , Young Robert J.
Published: January 2024

Supplementary Table S2. Baseline Radiological Characteristics Overall and Stratified by 1p19q Status.
Supplementary Table S5 from Intraoperative Integrated Diagnostic System for Malignant Central Nervous System Tumors
Authors: Hayashi Takahiro , Tateishi Kensuke , Matsuyama Shinichiro , Iwashita Hiromichi , Miyake Yohei , Oshima Akito , Honma Hirokuni , Sasame Jo , Takabayashi Katsuhiro , Sugino Kyoka , Hirata Emi , Udaka Naoko , Matsushita Yuko , Kato Ikuma , Hayashi Hiroaki , Nakamura Taishi , Ikegaya Naoki , Takayama Yutaro , Sonoda Masaki , Oka Chihiro , Sato Mitsuru , Isoda Masataka , Kato Miyui , Uchiyama Kaho , Tanaka Tamon , Muramatsu Toshiki , Miyake Shigeta , Suzuki Ryosuke , Takadera Mutsumi , Tatezuki Junya , Ayabe Junichi , Suenaga Jun , Matsunaga Shigeo , Miyahara Kosuke , Manaka Hiroshi , Murata Hidetoshi , Yokoyama Takaakira , Tanaka Yoshihide , Shuto Takashi , Ichimura Koichi , Kato Shingo , Yamanaka Shoji , Cahill Daniel P. , Fujii Satoshi , Shankar Ganesh M. , Yamamoto Tetsuya
Published: January 2024

Mismatch ratio of genomic alterations in the prospective cohort
Supplementary Table S3 from Intraoperative Integrated Diagnostic System for Malignant Central Nervous System Tumors
Authors: Hayashi Takahiro , Tateishi Kensuke , Matsuyama Shinichiro , Iwashita Hiromichi , Miyake Yohei , Oshima Akito , Honma Hirokuni , Sasame Jo , Takabayashi Katsuhiro , Sugino Kyoka , Hirata Emi , Udaka Naoko , Matsushita Yuko , Kato Ikuma , Hayashi Hiroaki , Nakamura Taishi , Ikegaya Naoki , Takayama Yutaro , Sonoda Masaki , Oka Chihiro , Sato Mitsuru , Isoda Masataka , Kato Miyui , Uchiyama Kaho , Tanaka Tamon , Muramatsu Toshiki , Miyake Shigeta , Suzuki Ryosuke , Takadera Mutsumi , Tatezuki Junya , Ayabe Junichi , Suenaga Jun , Matsunaga Shigeo , Miyahara Kosuke , Manaka Hiroshi , Murata Hidetoshi , Yokoyama Takaakira , Tanaka Yoshihide , Shuto Takashi , Ichimura Koichi , Kato Shingo , Yamanaka Shoji , Cahill Daniel P. , Fujii Satoshi , Shankar Ganesh M. , Yamamoto Tetsuya
Published: January 2024

IDH- and pTERT-wildtype gliomas at intraoperative integrated diagnosis in the retrospective cohort
Supplementary Table S1 from Intraoperative Integrated Diagnostic System for Malignant Central Nervous System Tumors
Authors: Hayashi Takahiro , Tateishi Kensuke , Matsuyama Shinichiro , Iwashita Hiromichi , Miyake Yohei , Oshima Akito , Honma Hirokuni , Sasame Jo , Takabayashi Katsuhiro , Sugino Kyoka , Hirata Emi , Udaka Naoko , Matsushita Yuko , Kato Ikuma , Hayashi Hiroaki , Nakamura Taishi , Ikegaya Naoki , Takayama Yutaro , Sonoda Masaki , Oka Chihiro , Sato Mitsuru , Isoda Masataka , Kato Miyui , Uchiyama Kaho , Tanaka Tamon , Muramatsu Toshiki , Miyake Shigeta , Suzuki Ryosuke , Takadera Mutsumi , Tatezuki Junya , Ayabe Junichi , Suenaga Jun , Matsunaga Shigeo , Miyahara Kosuke , Manaka Hiroshi , Murata Hidetoshi , Yokoyama Takaakira , Tanaka Yoshihide , Shuto Takashi , Ichimura Koichi , Kato Shingo , Yamanaka Shoji , Cahill Daniel P. , Fujii Satoshi , Shankar Ganesh M. , Yamamoto Tetsuya
Published: January 2024

Summary of intraoperative integrated diagnosis (i-ID) and permanent integrated diagnosis (p-ID) for retrospective cohort (153 cases)
Supplementary Fig. S7 from Intraoperative Integrated Diagnostic System for Malignant Central Nervous System Tumors
Authors: Hayashi Takahiro , Tateishi Kensuke , Matsuyama Shinichiro , Iwashita Hiromichi , Miyake Yohei , Oshima Akito , Honma Hirokuni , Sasame Jo , Takabayashi Katsuhiro , Sugino Kyoka , Hirata Emi , Udaka Naoko , Matsushita Yuko , Kato Ikuma , Hayashi Hiroaki , Nakamura Taishi , Ikegaya Naoki , Takayama Yutaro , Sonoda Masaki , Oka Chihiro , Sato Mitsuru , Isoda Masataka , Kato Miyui , Uchiyama Kaho , Tanaka Tamon , Muramatsu Toshiki , Miyake Shigeta , Suzuki Ryosuke , Takadera Mutsumi , Tatezuki Junya , Ayabe Junichi , Suenaga Jun , Matsunaga Shigeo , Miyahara Kosuke , Manaka Hiroshi , Murata Hidetoshi , Yokoyama Takaakira , Tanaka Yoshihide , Shuto Takashi , Ichimura Koichi , Kato Shingo , Yamanaka Shoji , Cahill Daniel P. , Fujii Satoshi , Shankar Ganesh M. , Yamamoto Tetsuya
Published: January 2024

Genomic profiling of EGFR, PTEN, and TERT in IDH-wildtype lower-grade astrocytomas
Supplementary Table S3 from PET/CT Biomarkers Enable Risk Stratification of Patients with Relapsed/Refractory Diffuse Large B-cell Lymphoma Enrolled in the LOTIS-2 Clinical Trial
Authors: Alderuccio Juan Pablo , Reis Isildinha M. , Hamadani Mehdi , Nachiappan Muthiah , Leslom Salman , Kahl Brad S. , Ai Weiyun Z. , Radford John , Solh Melhem , Ardeshna Kirit M. , Hess Brian T. , Lunning Matthew A. , Zinzani Pier Luigi , Stathis Anastasios , Carlo-Stella Carmelo , Lossos Izidore S. , Caimi Paolo F. , Han Sunwoo , Yang Fei , Kuker Russ A. , Moskowitz Craig H.
Published: January 2024

Baseline PET/CT metrics (N=138).
Supplementary Fig. S5 from Intraoperative Integrated Diagnostic System for Malignant Central Nervous System Tumors
Authors: Hayashi Takahiro , Tateishi Kensuke , Matsuyama Shinichiro , Iwashita Hiromichi , Miyake Yohei , Oshima Akito , Honma Hirokuni , Sasame Jo , Takabayashi Katsuhiro , Sugino Kyoka , Hirata Emi , Udaka Naoko , Matsushita Yuko , Kato Ikuma , Hayashi Hiroaki , Nakamura Taishi , Ikegaya Naoki , Takayama Yutaro , Sonoda Masaki , Oka Chihiro , Sato Mitsuru , Isoda Masataka , Kato Miyui , Uchiyama Kaho , Tanaka Tamon , Muramatsu Toshiki , Miyake Shigeta , Suzuki Ryosuke , Takadera Mutsumi , Tatezuki Junya , Ayabe Junichi , Suenaga Jun , Matsunaga Shigeo , Miyahara Kosuke , Manaka Hiroshi , Murata Hidetoshi , Yokoyama Takaakira , Tanaka Yoshihide , Shuto Takashi , Ichimura Koichi , Kato Shingo , Yamanaka Shoji , Cahill Daniel P. , Fujii Satoshi , Shankar Ganesh M. , Yamamoto Tetsuya
Published: January 2024

Illustrative mismatch cases in the prospective cohort
Supplementary Fig. S4 from Intraoperative Integrated Diagnostic System for Malignant Central Nervous System Tumors
Authors: Hayashi Takahiro , Tateishi Kensuke , Matsuyama Shinichiro , Iwashita Hiromichi , Miyake Yohei , Oshima Akito , Honma Hirokuni , Sasame Jo , Takabayashi Katsuhiro , Sugino Kyoka , Hirata Emi , Udaka Naoko , Matsushita Yuko , Kato Ikuma , Hayashi Hiroaki , Nakamura Taishi , Ikegaya Naoki , Takayama Yutaro , Sonoda Masaki , Oka Chihiro , Sato Mitsuru , Isoda Masataka , Kato Miyui , Uchiyama Kaho , Tanaka Tamon , Muramatsu Toshiki , Miyake Shigeta , Suzuki Ryosuke , Takadera Mutsumi , Tatezuki Junya , Ayabe Junichi , Suenaga Jun , Matsunaga Shigeo , Miyahara Kosuke , Manaka Hiroshi , Murata Hidetoshi , Yokoyama Takaakira , Tanaka Yoshihide , Shuto Takashi , Ichimura Koichi , Kato Shingo , Yamanaka Shoji , Cahill Daniel P. , Fujii Satoshi , Shankar Ganesh M. , Yamamoto Tetsuya
Published: January 2024

Summary of the retrospective cohort
Supplementary Fig. S2 from Intraoperative Integrated Diagnostic System for Malignant Central Nervous System Tumors
Authors: Hayashi Takahiro , Tateishi Kensuke , Matsuyama Shinichiro , Iwashita Hiromichi , Miyake Yohei , Oshima Akito , Honma Hirokuni , Sasame Jo , Takabayashi Katsuhiro , Sugino Kyoka , Hirata Emi , Udaka Naoko , Matsushita Yuko , Kato Ikuma , Hayashi Hiroaki , Nakamura Taishi , Ikegaya Naoki , Takayama Yutaro , Sonoda Masaki , Oka Chihiro , Sato Mitsuru , Isoda Masataka , Kato Miyui , Uchiyama Kaho , Tanaka Tamon , Muramatsu Toshiki , Miyake Shigeta , Suzuki Ryosuke , Takadera Mutsumi , Tatezuki Junya , Ayabe Junichi , Suenaga Jun , Matsunaga Shigeo , Miyahara Kosuke , Manaka Hiroshi , Murata Hidetoshi , Yokoyama Takaakira , Tanaka Yoshihide , Shuto Takashi , Ichimura Koichi , Kato Shingo , Yamanaka Shoji , Cahill Daniel P. , Fujii Satoshi , Shankar Ganesh M. , Yamamoto Tetsuya
Published: January 2024

qPCR-based CDKN2A genotyping
Supplementary Figure S1 from PET/CT Biomarkers Enable Risk Stratification of Patients with Relapsed/Refractory Diffuse Large B-cell Lymphoma Enrolled in the LOTIS-2 Clinical Trial
Authors: Alderuccio Juan Pablo , Reis Isildinha M. , Hamadani Mehdi , Nachiappan Muthiah , Leslom Salman , Kahl Brad S. , Ai Weiyun Z. , Radford John , Solh Melhem , Ardeshna Kirit M. , Hess Brian T. , Lunning Matthew A. , Zinzani Pier Luigi , Stathis Anastasios , Carlo-Stella Carmelo , Lossos Izidore S. , Caimi Paolo F. , Han Sunwoo , Yang Fei , Kuker Russ A. , Moskowitz Craig H.
Published: January 2024

CONSORT diagram.
Figure S1 from Tumor-Infiltrating CD103+ Tissue-Resident Memory T Cells and CD103−CD8+ T Cells in HNSCC Are Linked to Outcome in Primary but not Metastatic Disease
Authors: von Witzleben Adrian , Ellis Matthew , Thomas Gareth J. , Hoffmann Thomas K. , Jackson Richard , Laban Simon , Ottensmeier Christian H.
Published: January 2024

suppl. Figure 1
Supplementary Table S4 from Phase I Dose-Escalation Study of the Safety and Pharmacokinetics of AGS15E Monotherapy in Patients with Metastatic Urothelial Carcinoma
Authors: Petrylak Daniel P. , Eigl Bernhard J. , George Saby , Heath Elisabeth I. , Hotte Sebastien J. , Chism David D. , Nabell Lisle M. , Picus Joel , Cheng Susanna Y. , Appleman Leonard J. , Sonpavde Guru P. , Morgans Alicia K. , Pourhosseini Pourya , Wu Ruishan , Standley Laura , Croitoru Ruslan , Yu Evan Y.
Published: January 2024

Supplementary Table S4. TEAEs (≥10% Patients) by SOC and PT: Part A, Escalation Phase
Supplementary Methods 1 from Comprehensive DNA Methylation Profiling of Medullary Thyroid Carcinoma: Molecular Classification, Potential Therapeutic Target, and Classifier System
Authors: Shen Cenkai , Shi Xiao , Wen Duo , Zhang Yuqing , Du Yuxin , Zhang Yu , Ma Ben , Tang Haitao , Yin Min , Huang Naisi , Liao Tian , Zhang Ting-Ting , Kong Chang’e , Wei Wenjun , Ji Qinghai , Wang Yu
Published: January 2024

Supplementary Methods
Figure S3 from Comprehensive DNA Methylation Profiling of Medullary Thyroid Carcinoma: Molecular Classification, Potential Therapeutic Target, and Classifier System
Authors: Shen Cenkai , Shi Xiao , Wen Duo , Zhang Yuqing , Du Yuxin , Zhang Yu , Ma Ben , Tang Haitao , Yin Min , Huang Naisi , Liao Tian , Zhang Ting-Ting , Kong Chang’e , Wei Wenjun , Ji Qinghai , Wang Yu
Published: January 2024

Hyperparameter optimization of elastic net mixing parameter (alpha) in the machine learning model
Supplementary Table S15 from Phase I Dose-Escalation Study of the Safety and Pharmacokinetics of AGS15E Monotherapy in Patients with Metastatic Urothelial Carcinoma
Authors: Petrylak Daniel P. , Eigl Bernhard J. , George Saby , Heath Elisabeth I. , Hotte Sebastien J. , Chism David D. , Nabell Lisle M. , Picus Joel , Cheng Susanna Y. , Appleman Leonard J. , Sonpavde Guru P. , Morgans Alicia K. , Pourhosseini Pourya , Wu Ruishan , Standley Laura , Croitoru Ruslan , Yu Evan Y.
Published: January 2024

Supplementary Table S15. DCR With Confirmation; Parts A, B, and C, Expansion Phase
Supplementary Table S11 from Phase I Dose-Escalation Study of the Safety and Pharmacokinetics of AGS15E Monotherapy in Patients with Metastatic Urothelial Carcinoma
Authors: Petrylak Daniel P. , Eigl Bernhard J. , George Saby , Heath Elisabeth I. , Hotte Sebastien J. , Chism David D. , Nabell Lisle M. , Picus Joel , Cheng Susanna Y. , Appleman Leonard J. , Sonpavde Guru P. , Morgans Alicia K. , Pourhosseini Pourya , Wu Ruishan , Standley Laura , Croitoru Ruslan , Yu Evan Y.
Published: January 2024

Supplementary Table S11. Statistical Assessment of Dose Proportionality for ADC, Power Model, PK Analysis Set
Supplementary Table S6 from Olaparib plus Durvalumab, with or without Bevacizumab, as Treatment in PARP Inhibitor-Naïve Platinum-Sensitive Relapsed Ovarian Cancer: A Phase II Multi-Cohort Study
Authors: Drew Yvette , Kim Jae-Weon , Penson Richard T. , O'Malley David M. , Parkinson Christine , Roxburgh Patricia , Plummer Ruth , Im Seock-Ah , Imbimbo Martina , Ferguson Michelle , Rosengarten Ora , Steeghs Neeltje , Kim Min Hwan , Gal-Yam Einav , Tsoref Daliah , Kim Jae-Hoon , You Benoit , De Jonge Maja , Lalisang Roy , Gort Eelke , Bastian Sara , Meyer Kassondra , Feeney Laura , Baker Nigel , Ah-See Mei-Lin , Domchek Susan M. , Banerjee Susana
Published: January 2024

AEs leading to study treatment discontinuation
Supplementary Table S1 from Phase I Dose-Escalation Study of the Safety and Pharmacokinetics of AGS15E Monotherapy in Patients with Metastatic Urothelial Carcinoma
Authors: Petrylak Daniel P. , Eigl Bernhard J. , George Saby , Heath Elisabeth I. , Hotte Sebastien J. , Chism David D. , Nabell Lisle M. , Picus Joel , Cheng Susanna Y. , Appleman Leonard J. , Sonpavde Guru P. , Morgans Alicia K. , Pourhosseini Pourya , Wu Ruishan , Standley Laura , Croitoru Ruslan , Yu Evan Y.
Published: January 2024

Supplementary Table S1. Inclusion Criteria Details for Parts A, B, and C
Supplementary Figure S3 from Phase I Dose-Escalation Study of the Safety and Pharmacokinetics of AGS15E Monotherapy in Patients with Metastatic Urothelial Carcinoma
Authors: Petrylak Daniel P. , Eigl Bernhard J. , George Saby , Heath Elisabeth I. , Hotte Sebastien J. , Chism David D. , Nabell Lisle M. , Picus Joel , Cheng Susanna Y. , Appleman Leonard J. , Sonpavde Guru P. , Morgans Alicia K. , Pourhosseini Pourya , Wu Ruishan , Standley Laura , Croitoru Ruslan , Yu Evan Y.
Published: January 2024

Supplementary Figure S3. Box Plot of H-Score for SLITRK6 Expression in Tissue by Confirmed BOR (Full Analysis Set)
Supplementary Figure S2 from Phase I Dose-Escalation Study of the Safety and Pharmacokinetics of AGS15E Monotherapy in Patients with Metastatic Urothelial Carcinoma
Authors: Petrylak Daniel P. , Eigl Bernhard J. , George Saby , Heath Elisabeth I. , Hotte Sebastien J. , Chism David D. , Nabell Lisle M. , Picus Joel , Cheng Susanna Y. , Appleman Leonard J. , Sonpavde Guru P. , Morgans Alicia K. , Pourhosseini Pourya , Wu Ruishan , Standley Laura , Croitoru Ruslan , Yu Evan Y.
Published: January 2024

Supplementary Figure S2. PFS, 1.00 mg/kg vs Total Study Population and CPIExposed Population (Parts A, B, and C, FAS)
Supplementary Table S2 from Olaparib plus Durvalumab, with or without Bevacizumab, as Treatment in PARP Inhibitor-Naïve Platinum-Sensitive Relapsed Ovarian Cancer: A Phase II Multi-Cohort Study
Authors: Drew Yvette , Kim Jae-Weon , Penson Richard T. , O'Malley David M. , Parkinson Christine , Roxburgh Patricia , Plummer Ruth , Im Seock-Ah , Imbimbo Martina , Ferguson Michelle , Rosengarten Ora , Steeghs Neeltje , Kim Min Hwan , Gal-Yam Einav , Tsoref Daliah , Kim Jae-Hoon , You Benoit , De Jonge Maja , Lalisang Roy , Gort Eelke , Bastian Sara , Meyer Kassondra , Feeney Laura , Baker Nigel , Ah-See Mei-Lin , Domchek Susan M. , Banerjee Susana
Published: January 2024

Relative dose intensity of study treatments
Supplementary Table S1 from Olaparib plus Durvalumab, with or without Bevacizumab, as Treatment in PARP Inhibitor-Naïve Platinum-Sensitive Relapsed Ovarian Cancer: A Phase II Multi-Cohort Study
Authors: Drew Yvette , Kim Jae-Weon , Penson Richard T. , O'Malley David M. , Parkinson Christine , Roxburgh Patricia , Plummer Ruth , Im Seock-Ah , Imbimbo Martina , Ferguson Michelle , Rosengarten Ora , Steeghs Neeltje , Kim Min Hwan , Gal-Yam Einav , Tsoref Daliah , Kim Jae-Hoon , You Benoit , De Jonge Maja , Lalisang Roy , Gort Eelke , Bastian Sara , Meyer Kassondra , Feeney Laura , Baker Nigel , Ah-See Mei-Lin , Domchek Susan M. , Banerjee Susana
Published: January 2024

Representativeness of study participants