Miracle-dz/UniFAR-FTUs huggingface dataset:
Is there value in measuring near visual acuity during occlusion therapy for amblyopia?

ABSTRACT Introduction: The purpose of this study was to investigate near and distance visual acuity (VA) prior to, during and on completion of occlusion therapy for amblyopia. Method: Fifty-four patients aged 4–7 years (mean 4.9; ±0.44) with untreated strabismic, anisometropic or mixed amblyopia were recruited to the study following refractive adaptation where applicable. All patients underwent conventional occlusion (patching). Uniocular near and distance VA was tested using age and ability appropriate Crowded LogMAR VA tests prior to, during and upon conclusion of occlusion therapy. Results: In amblyopic eyes, there was no significant difference between near and distance VA prior to occlusion therapy with LogMAR Crowded (p = .66; mean distance VA at 3 m = 0.6 LogMAR; mean near VA at 40 cm = 0.58 LogMAR), or with LogMAR Crowded Kay Picture test (p = .78, mean distance VA at 3 m = 0.44 LogMAR; mean near VA at 33 cm = 0.46 LogMAR;). No significant difference was found between near and distance VA at any visit during occlusion therapy, or on completion of occlusion therapy with LogMAR Crowded (p = .86, mean final distance VA at 3 m = 0.266 LogMAR; mean final near VA at 40 cm = 0.25 LogMAR) or LogMAR Crowded Kay Pictures (p = .74, mean final distance VA at 3 m = 0.16 LogMAR; mean final near VA at 33 cm = 0.16 LogMAR). There was no significant difference in the VA of the fellow (non-amblyopic) eyes prior to and on completion of occlusion therapy with LogMAR Crowded at distance (3 m) or near (40 cm) (p = .05, p = .40 respectively); or with LogMAR Crowded Kay Pictures at distance (3 m) or near (33 cm) (p = .89, p = .35 respectively). Discussion: Improvement in VA of amblyopic eyes did not significantly differ between near and distance testing proximites at any point during the course of occlusion therapy for amblyopia in our study. These findings may aid clinicians with appropriate test selection and help with clinical time pressures. Where patient concentration does not allow for uniocular distance vision, uniocular near vision may be used to diagnose amblyopia, and vice versa. This could prevent delay in the treatment of amblyopia.
FAOT-Net: A 1.5-Stage Framework for 3D Pelvic Lymph Node Detection With Online Candidate Tuning

Accurate and automatic detection of pelvic lymph nodes in computed tomography (CT) scans is critical for diagnosing lymph node metastasis in colorectal cancer, which in turn plays a crucial role in its staging, treatment planning, surgical guidance, and postoperative follow-up of colorectal cancer. However, achieving high detection sensitivity and specificity poses a challenge due to the small and variable sizes of these nodes, as well as the presence of numerous similar signals within the complex pelvic CT image. To tackle these issues, we propose a 3D feature-aware online-tuning network (FAOT-Net) that introduces a novel 1.5-stage structure to seamlessly integrate detection and refinement via our online candidate tuning process and takes advantage of multi-level information through the tailored feature flow. Furthermore, we redesign the anchor fitting and anchor matching strategies to further improve detection performance in a nearly hyperparameter-free manner. Our framework achieves the FROC score of 52.8 and the sensitivity of 91.7% with 16 false positives per scan on the PLNDataset. Code will be available at: github.com/SCUsomebody/FAOT-Net/.
Sexual dimorphism of osteoclast reliance on mitochondrial oxidation of energy substrates in the mouse

Osteoclasts specialize in bone resorption and are critical for bone remodeling. Previous studies have shown that osteoclasts possess abundant mitochondria and derive most energy through oxidative phosphorylation (OXPHOS). However, the energy substrates fueling OXPHOS in osteoclasts remain to be fully defined. Here, we showed that osteoclast differentiation was coupled with increased oxidation of glucose, glutamine, and oleate. Transcriptomic analyses with RNA sequencing revealed marked upregulation of genes participating in OXPHOS and mitochondrial fatty acid oxidation, during osteoclast differentiation. Increased mitochondrial oxidation of long-chain fatty acids was required for osteoclast differentiation in vitro. However, blocking fatty acid oxidation in vivo, by deletion of carnitine palmitoyltransferase 1a (Cpt1a) in osteoclast progenitors, impaired osteoclast formation only in the female mice. The Cpt1a-deficient females were further protected from osteoclast activation by a high-fat diet. The males, on the contrary, exhibited normal bone resorption despite Cpt1a deletion, regardless of the dietary fat content. Moreover, concurrent deletion of mitochondrial pyruvate carrier 1 and Cpt1a, blocking mitochondrial oxidation of both glucose and fatty acids in the osteoclast lineage, failed to impede bone resorption in the males. The study therefore uncovers a female-specific dependence on mitochondrial oxidation of fatty acids and glucose in osteoclasts in vivo.
Development and Validation of a Prostate Biopsy Risk Calculator in Black Men

Purpose: We sought to develop and validate a prostate biopsy risk calculator for Black men and compare it with the Prostate Cancer Prevention Trial version 2.0, Prostate Biopsy Collaborative Group, and Kaiser Permanente Prostate Cancer Risk Calculators for the detection of Gleason Grade Group (GG) ≥ 2 prostate cancer (PCa). Materials and Methods: We prospectively recruited 2 cohorts of men undergoing prostate biopsy from 5 facilities in Chicago. The first cohort was split into development (70%) and internal validation (30%) groups. The second was used for external validation. Iterative logistic regression was used to develop 3 models for predicting GG ≥ 2 PCa. Models were compared for discrimination using the C statistics, calibration curves, and net benefit curves. The frequency of unnecessary biopsies and missed PCas was compared at 10% and 30% risk thresholds. Results: The 2 cohorts included 393 and 292 Black men, respectively. Our first model, Mistry-Sun 1, used serum PSA and prior negative biopsy. Mistry-Sun 2 added abnormal digital rectal exam (DRE) and an interaction term with abnormal DRE and PSA to Mistry-Sun 1. Mistry-Sun 3 added prostate volume, abnormal DRE, and age to Mistry-Sun 1. The C statistics were 0.74, 0.74, and 0.78, respectively, and were similar to or higher than established calculators. At the 10% and 30% risk thresholds our models had the fewest unnecessary biopsies and an appropriate proportion of missed GG ≥ 2 PCas. Conclusions: Tailoring a risk calculator to detect clinically significant PCa in Black men may improve biopsy decision-making and outcomes compared to tools developed in non-Black populations.
Brain edema growth after thrombectomy is associated with comprehensive collateral blood flow

Background We determined whether a comprehensive assessment of cerebral collateral blood flow is associated with ischemic lesion edema growth in patients successfully treated by thrombectomy. Methods This was a multicenter retrospective study of ischemic stroke patients who underwent thrombectomy treatment of large vessel occlusions. Collateral status was determined using the cerebral collateral cascade (CCC) model, which comprises three components: arterial collaterals (Tan Scale) and venous outflow profiles (Cortical Vein Opacification Score) on CT angiography, and tissue-level collaterals (hypoperfusion intensity ratio) on CT perfusion. Quantitative ischemic lesion net water uptake (NWU) was used to determine edema growth between admission and follow-up non-contrast head CT (ΔNWU). Three groups were defined: CCC+ (good pial collaterals, tissue-level collaterals, and venous outflow), CCC− (poor pial collaterals, tissue-level collaterals, and venous outflow), and CCCmixed (remainder of patients). Primary outcome was ischemic lesion edema growth (ΔNWU). Multivariable regression models were used to assess the primary and secondary outcomes. Results 538 patients were included. 157 patients had CCC+, 274 patients CCCmixed, and 107 patients CCC− profiles. Multivariable regression analysis showed that compared with patients with CCC+ profiles, CCC− (β 1.99, 95% CI 0.68 to 3.30, P=0.003) and CCC mixed (β 1.65, 95% CI 0.75 to 2.56, P<0.001) profiles were associated with greater ischemic lesion edema growth (ΔNWU) after successful thrombectomy treatment. ΔNWU (OR 0.74, 95% CI 0.68 to 0.8, P<0.001) and CCC+ (OR 13.39, 95% CI 4.88 to 36.76, P<0.001) were independently associated with functional independence. Conclusion A comprehensive assessment of cerebral collaterals using the CCC model is strongly associated with edema growth and functional independence in acute stroke patients successfully treated by endovascular thrombectomy.
Multi-purpose neural network for French categorial grammars

Categorial grammar (CG) is a lexicalized grammar formalism that can be used to identify and extract the semantics of natural language sentences. However, despite being used actively to solve natural language understanding tasks such as natural language inference or recognizing textual entailment, most of the tools exploiting the capacities of CG are available in a limited set of languages. This paper proposes a first step toward developing a set of tools enabling the use of CG for the French language by proposing a neural network tailored for part-of-speech and type-logical-grammar supertagging, located at the frontier between computational linguistics and artificial intelligence. Experiments show that our model can compete with state-of-the art models while retaining a simple architecture.
The Sequence Notation: Catching Complex Meanings in Simple Graphs

Current symbolic semantic representations proposed to capture the semantics of human language have served well to give us insight in how meaning is expressed. But they are either too complicated for large-scale annotation tasks or lack expressive power to play a role in inference tasks. What we propose is a meaning representation system that it is interlingual, model-theoretic, and variable-free. It divides the labour involved in representing meaning along three levels: concept, roles, and contexts. As natural languages are expressed as sequences of phonemes or words, the meaning representations that we propose are likewise sequential. However, the resulting meaning representations can also be visualised as directed acyclic graphs.
Triadic temporal representations and deformations

Triadic representations that temporally order events and states are described, consisting of strings and sets of strings of bounded but refinable granularities. The strings are compressed according to J.A. Wheeler’s dictum it-from-bit, with bits given by statives and non-statives alike. A choice of vocabulary and constraints expressed in that vocabulary shape representations of cause-and-effect with deformations characteristic, Mumford posits, of patterns at various levels of cognitive processing. These deformations point to an ongoing process of learning, formulated as grammatical inference of finite automata, structured around Goguen and Burstall’s institutions.
The DARPA Wikidata Overlay: Wikidata as an ontology for natural language processing

With 102,530,067 items currently in its crowd-sourced knowledge base, Wikidata provides NLP practitioners a unique and powerful resource for inference and reasoning over real-world entities. However, because Wikidata is very entity focused, events and actions are often labeled with eventive nouns (e.g., the process of diagnosing a person’s illness is labeled “diagnosis”), and the typical participants in an event are not described or linked to that event concept (e.g., the medical professional or patient). Motivated by a need for an adaptable, comprehensive, domain-flexible ontology for information extraction, including identifying the roles entities are playing in an event, we present a curated subset of Wikidata in which events have been enriched with PropBank roles. To enable richer narrative understanding between events from Wikidata concepts, we have also provided a comprehensive mapping from temporal Qnodes and Pnodes to the Allen Interval Temporal Logic relations.
Evaluation of Universal Semantic Representation (USR)

Universal Semantic Representation (USR) is designed as a language-independent information packaging system that captures information at three levels: (a) Lexico-conceptual, (b) Syntactico-Semantic, and (c) Discourse. Unlike other representations that mainly encode predicates and their argument structures, our proposed representation captures the speaker’s vivakṣā- how the speaker views the activity. The idea of “speaker’s vivakṣā is inspired by Indian Grammatical Tradition. There can be some amount of idiosyncrasy of the speaker in the annotation since it is the speaker’s view- point that has been captured in the annotation. Hence the evaluation metrics of such resources need to be also thought through from scratch. This paper presents an extensive evaluation procedure of this semantic representation from two perspectives (a) Inter- Annotator Agreement and (b) one downstream task, namely multilingual Natural Language Generation. We also qualitatively evaluate the experience of natural language generation by manual parsing of USR, so as to understand the readability of USR. We have achieved above 80% Inter-Annotator Agreement for USR annotations and above 80% semantic closeness in multi-lingual generation tasks suggesting the reliability of USR annotations and utility for multi-lingual generations. The qualitative evaluation also suggests high readability and hence the utility of USR as a semantic representation.
metAMoRphosED, a graphical editor for Abstract Meaning Representation

This paper presents a graphical editor for directed graphs, serialised in the PENMAN format, as used for annotations in Abstract Meaning Representation (AMR). The tool supports creating and modifying of AMR graphs and other directed graphs, adding and deletion of instances, edges and literals, renaming of concepts, relations and literals, setting a “top node” and validating the edited graph.
The Universal Anaphora Scorer 2.0

The aim of the Universal Anaphora initiative is to push forward the state of the art both in anaphora (coreference) annotation and in the evaluation of models for anaphora resolution. The first release of the Universal Anaphora Scorer (Yu et al., 2022b) supported the scoring not only of identity anaphora as in the Reference Coreference Scorer (Pradhan et al., 2014) but also of split antecedent anaphoric reference, bridging references, and discourse deixis. That scorer was used in the CODI-CRAC 2021/2022 Shared Tasks on Anaphora Resolution in Dialogues (Khosla et al., 2021; Yu et al., 2022a). A modified version of the scorer supporting discontinuous markables and the COREFUD markup format was also used in the CRAC 2022 Shared Task on Multilingual Coreference Resolution (Zabokrtsky et al., 2022). In this paper, we introduce the second release of the scorer, merging the two previous versions, which can score reference with discontinuous markables and zero anaphora resolution.
Estimation of Ground Reaction Force for Coupled Dynamic Modelling and Control of the Lower Limb Exoskeleton

In order to achieve the desired control of a lower limb exoskeleton, an understanding of the dynamics of the coupled human-exoskeleton system is required. A major input towards modelling the dynamics of the coupled system is the ground reaction force (GRF) generated by the human wearing the exoskeleton. Therefore, the GRF from the coupled system needs to be either computed, measured or estimated. This paper presents work on the estimation of GRF and subsequently on the control of a lower-limb exoskeleton. The approach to estimating GRF is based on the multiple variable regression technique, which considers the body weight, height and walking speed of the exoskeleton user. A mathematical model based on the Euler-Lagrange formulation was used to model the complete system. Once the dynamic model is ready, strength augmentation for the purpose of load-carrying exoskeletons is set as a desired control objective, and further computed torque control is tested on the coupled system. In summary, this paper tries to achieve three goals: estimation of GRF, dynamic modelling of the coupled human-exoskeleton system and formulation of a control framework from the modelled dynamics for testing computed-torque control.
Dynamic Modeling and Locomotion Control of Reconfigurable Robot Smorphi

Smorphi is a shape-changing robot that can take seven different shapes. This feature makes it capable of performing tasks in narrow spaces. The paper presents a modeling and locomotion control method for Smorphi. The dynamics of Smorphi for a particular configuration are obtained using the Euler-Lagrange method. A direct synthesis controller is used to track the angular velocity of the wheels of each block of the shape-changing robot. Simulation results for the control of the proposed configuration are presented, compared, and discussed.
Integrating IT Security Aspects into Business Process Models: A Taxonomy of BPMN Extensions

Protecting themselves from IT security breaches is a crucial and cost-intensive task for the organizations of today. To achieve this, organizations implement bundles of IT security measures to secure their assets, which substantially influences their business processes. Therefore, aspects from the IT security domain must be integrated into business process models to adequately represent reality. There are various papers introducing extensions that integrate these aspects into the Business Process Model and Notation (BPMN) language. However, existing literature reviews are outdated and do not identify common characteristics among BPMN extensions that integrate IT security aspects. Based on the analysis of 18 papers that were identified during a structured literature review, this article develops a multi-dimensional taxonomy of BPMN extensions. This taxonomy identifies common characteristics and dimensions of the extensions and therefore gives a structured overview of the field and provides profound insights into the existing work.
Non-deterministic multi-valued logics and their applications

Non-deterministic multi-valued matrices (Nmatrices) are a new, fruitful and quickly expanding field of research first introduced a few years ago by Avron and Lev. Since then it has been rapidly developing towards a foundational logical theory and has found numerous applications in different research areas, such as reasoning under uncertainty, automated reasoning, and proof theory. The novelty of Nmatrices is in extending the usual algebraic deterministic semantics of logical systems by importing the idea of nondeterministic computations from Computer Science, and allowing the truth-value of a formula to be chosen non-deterministically out of a given set of options. Nmatrices have proved to be a powerful tool, the use of which preserves all the advantages of ordinary many-valued matrices, but is applicable to a much wider range of logics. Indeed, there are many useful (propositional) non-classical logics, which have no finite many-valued characteristic matrices, but do have finite Nmatrices, and thus are decidable. Another important advantage of the framework of Nmatrices is its modularity. Each syntactic rule in a proof system corresponds to a certain semantic condition, leading to a refinement of some basic Nmatrix. In many cases the semantics of a complex system can be obtained by straightforwardly combining the semantic effects of each of the added rules. As a result, the semantic effect of a syntactic rule can be analyzed separately. This is impossible in standard multi-valued matrices, where the semantics of a system can only be presented as a whole. Nmatrices have also found important applications in proof theory. In particular, for a natural class of Gentzen-type propositional systems called canonical systems, there is a strong connection between the existence of a characteristic 2-valued Nmatrix for a given proof system and the ability to eliminate cuts in it. So far most of the work on the framework of Nmatrices has been done on the purely propositional level. However, no semantic framework can be considered really useful unless it can be naturally extended to the first-order level and beyond. Accordingly, the main goal of this thesis is to extend the framework of Nmatrices to languages with quantifiers and to explore its applications in different areas. We consider several generalizations of first-order quantifiers: unary, multi-ary and (n, k)-ary ones. We provide interpretations of such quantifiers in the framework of Nmatrices, and resolve various problems related to the principles of α-equivalence, identity and void quantification, using special congruence relations between formulas. Some important properties of the extended framework, such as analycity, are investigated. Then we turn to several appli-
Efficient cryptographic protocols: secure two-party computation and refereed delegation of computation

This thesis is about efficient cryptographic protocols for two fundamental problems: Secure Two-Party Computation and Verifiable Delegation of Computation. Even though solutions to both problems exist, their concrete efficiency is not satisfactory and other, more efficient solutions are needed for solving these problems for real-world applications. Secure Two-Party Computation. We present two contributions in this topic. First, we consider a variant of secure two-party computation called Non-Interactive Secure Computation (NISC), in which the players are allowed to have only one-round of interaction (i.e. two messages). We present several protocols that work in the NISC setting, and the first prototype implementation of a NISC protocol. Second, we show how to significantly reduce the overheads of previous secure two-party computation protocols based on the cut-and-choose method of Lindell and Pinkas (Eurocrypt, 2007). Verifiable Delegation of Computation. We suggest a new model called Refereed Delegation of Computation (RDoC), in which a client delegates its computation to several servers and is able to learn the correct output of its computation if there is (at least) one honest server. We present two efficient protocols that are secure in the RDoC model. The first does not require any computational assumptions and allows the client to delegate any L-uniform circuit, requiring the client to work in time n ·poly(d, log(S)), where d and S are the depth and size (respectively) of the circuit that computes the language, and n is the input length. This protocol requires only a single round of interaction between the client and each server. The second protocol is more practical and generic, works with any reasonable computational model, and specifically does not require an expensive translation of a computation to a boolean circuit. We prove its flexibility by adapting it to work directly with the X86 architecture, provide a prototype implementation of the protocol and evaluate its practicality on “live” clouds.