bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gradual Tensor Shape Checking
Authors: Hattori Momoko , Kobayashi Naoki , Sato Ryosuke 
Published: April 2023

AbstractTensor shape mismatch is a common source of bugs in deep learning programs. We propose a new type-based approach to detect tensor shape mismatches. One of the main features of our approach is the best-effort shape inference. As the tensor shape inference problem is undecidable in general, we allow static type/shape inference to be performed only in a best-effort manner. If the static inference cannot guarantee the absence of the shape inconsistencies, dynamic checks are inserted into the program. Another main feature is gradual typing, where users can improve the precision of the inference by adding appropriate type annotations to the program. We formalize our approach and prove that it satisfies the criteria of gradual typing proposed by Siek et al. in 2015. We have implemented a prototype shape checking tool based on our approach and evaluated its effectiveness by applying it to some deep neural network programs.
A Type System for Effect Handlers and Dynamic Labels
Authors: de Vilhena Paulo Emílio , Pottier François 
Published: April 2023

AbstractWe consider a simple yet expressive $$\lambda $$
λ
-calculus equipped with references, effect handlers, and dynamic allocation of effect labels, and whose operational semantics does not involve coercions or rely on type information. We equip this language with a type system that supports type and effect polymorphism, allows reordering row entries and extending a row with new entries, and supports (but is not restricted to) lexically scoped handlers. This requires addressing the issue of potential aliasing between effect names. Our original solution is to interpret a row not only as a permission to perform certain effects but also as a disjointness requirement bearing on effect names. The type system guarantees strong type soundness: a well-typed program cannot crash or perform an unhandled effect. We prove this fact by encoding the type system into a novel Separation Logic for effect handlers, which we build on top of Iris. Our results are formalized in Coq.
Coverability in 2-VASS with One Unary Counter is in NP
Authors: Mazowiecki Filip , Sinclair-Banks Henry , Węgrzycki Karol 
Published: April 2023

AbstractCoverability in Petri nets finds applications in verification of safety properties of reactive systems. We study coverability in the equivalent model: Vector Addition Systems with States (VASS).A k-VASS can be seen as k counters and a finite automaton whose transitions are labelled with k integers. Counter values are updated by adding the respective transition labels. A configuration in this system consists of a state and k counter values. Importantly, the counters are never allowed to take negative values. The coverability problem asks whether one can traverse the k-VASS from the initial configuration to a configuration with at least the counter values of the target.In a well-established line of work on k-VASS, coverability in 2-VASS is already -hard when the integer updates are encoded in binary. This lower bound limits the practicality of applications, so it is natural to focus on restrictions. In this paper we initiate the study of 2-VASS with one unary counter. Here, one counter receives binary encoded updates and the other receives unary encoded updates. Our main result is that coverability in 2-VASS with one unary counter is in . This improves upon the inherited state-of-the-art upper bound. Our main technical contribution is that one only needs to consider runs in a certain compressed linear form.
Fixed Points and Noetherian Topologies
Authors: Lopez Aliaume 
Published: April 2023

AbstractNoetherian spaces are a generalisation of well-quasi-orderings to topologies, that can be used to prove termination of programs. They find applications in the verification of transition systems, some of which are better described using topology. The goal of this paper is to allow the systematic description of computations using inductively defined datatypes via Noetherian spaces. This is achieved through a fixed point theorem based on a topological minimal bad sequence argument.
A Formal Logic for Formal Category Theory
Authors: New Max S. , Licata Daniel R. 
Published: April 2023

AbstractWe present a domain-specific type theory for constructions and proofs in category theory. The type theory axiomatizes notions of category, functor, profunctor and a generalized form of natural transformations. The type theory imposes an ordered linear restriction on standard predicate logic, which guarantees that all functions between categories are functorial, all relations are profunctorial, and all transformations are natural by construction, with no separate proofs necessary. Important category-theoretic proofs such as the Yoneda lemma and Co-yoneda lemma become simple type-theoretic proofs about the relationship between unit, tensor and (ordered) function types, and can be seen to be ordered refinements of theorems in predicate logic. The type theory is sound and complete for a categorical model in virtual equipments, which model both internal and enriched category theory. While the proofs in our type theory look like standard set-based arguments, the syntactic discipline ensure that all proofs and constructions carry over to enriched and internal settings as well.
Non-operative management for osteochondral lesions of the talus: a systematic review of treatment modalities, clinical- and radiological outcomes
Authors: Buck Tristan M. F. , Lauf Kenny , Dahmen Jari , Altink J. Nienke , Stufkens Sjoerd A. S. , Kerkhoffs Gino M. M. J. 
Published: April 2023

Abstract
Purpose
The purpose of the present study was to assess the overall clinical success rate of non-operative management for osteochondral lesions of the talus (OLT).

Methods
A literature search was conducted in the PubMed (MEDLINE), COCHRANE and EMBASE (Ovid) databases. Clinical success rates per separate study were calculated at the latest moment of follow-up and were defined as successful when a good or excellent clinical result at follow-up was reported in a qualitative manner or when a post-operative American Orthopaedic Foot and Ankle Society (AOFAS) score at or above 80 was reached. When clinical outcomes were based on other clinical scoring systems, outcomes reported as good or excellent were considered as clinical success. Studies methodologically eligible for a simplified pooling method were combined to calculate an overall pooled clinical success rate. Radiological changes over the course of conservative treatment were assessed either considering local OLT changes and/or overall ankle joint changes.

Results
Thirty articles were included, including an overall of 868 patients. The median follow-up of the included studies was 37 months (range: 3–288 months). A simplified pooling method was possible among 16 studies and yielded an overall pooled clinical success rate of 45% (95% CI 40–50%). As assessed with plain radiographs, progression of ankle joint osteoarthritis was observed in of 9% (95% CI 6–14%) of the patients. As assessed through a Computed Tomography (CT) scan, focal OLT deterioration was observed in 11% (95% CI 7–18%) of the patients. As assessed with a Magnetic Resonance Imaging (MRI) scan, focal OLT deterioration was observed in 12% (95% CI 6–24%) of the patients. An unchanged lesion was detected on plain radiographs in 53% (48/91; CI 43–63%), 76% (99/131; 95% CI 68–82%) on a CT scan and on MRI in 84% (42/50; 95% CI 71–92%) of the patients.

Conclusion
The current literature on non-operative management of OLTs is scarce and heterogeneous on indication and type of treatment. Promising clinical results are presented but need to interpreted with caution due to the heterogeneity in indication, duration and type of treatment. Further studies need to focus on specific types on conservative management, indications and its results.

Level of evidence
Systematic review, Level IV.
Switchable CAR T cell strategy against osteosarcoma
Authors: Hidalgo Laura , Somovilla-Crespo Beatriz , Garcia-Rodriguez Patricia , Morales-Molina Alvaro , Rodriguez-Milla Miguel Angel , Garcia-Castro Javier 
Published: April 2023

AbstractImmunotherapy with chimeric antigen receptor T (CAR T) cells has changed the treatment of hematological malignances, but they are still a challenge for solid tumors, including pediatric sarcomas. Here, we report a switchable CAR T cell strategy based on anti-FITC CAR T cells and a switch molecule conjugated with FITC for targeting osteosarcoma (OS) tumors. As a potential target, we analyzed the expression of B7-H3, an immune checkpoint inhibitor, in OS cell lines. In addition, we evaluate the capacity of an anti-B7-H3 monoclonal antibody conjugated with FITC (anti-B7-H3-FITC mAb) to control the antitumor activity of anti-FITC CAR T cells. The effector functions of anti-FITC CAR T cells against OS, measured in vitro by tumor cell killing activity and cytokine production, are dependent on the presence of the anti-B7-H3-FITC mAb switch. Moreover, OS cells stimulate anti-FITC CAR T cells migration. In vivo, anti-B7-H3 mAb penetrates in the tumor and binds 143B OS tumor cells. Furthermore, anti-FITC CAR T cells reach tumor region and exert antitumor effect in an OS NSG mouse model only in the presence of the switch molecule. We demonstrate that anti-B7-H3-FITC mAb redirects the cytotoxic activity of anti-FITC CAR T cells against OS tumors suggesting that switchable CAR T cell platforms might be a plausible strategy against OS.
ACL reconstruction provides superior stability than ACL repair in patients with Schenck III and IV knee joint dislocations: first results of a 12 month follow-up study
Authors: Fahlbusch H. , Behrendt P. , Akoto R. , Frosch K. H. , Krause M. 
Published: April 2023

Abstract
Purpose
Acute knee dislocation is a rare but devastating multi-ligamentous knee injury with only limited evidence-based surgical technique recommendations. The aim of this study was a comparison of two different anterior cruciate ligament (ACL) restoration techniques as part of an early total surgical care concept: (1) repair of ACL with additional internal bracing (ACLIB) compared to; (2) ACL reconstruction with autograft (ACLR).

Methods
Retrospective, clinical-study of patients with an acute type III or IV knee dislocation (according to Schenck classification), in which the ACL was treated with ACLIB or ACLR within 12 days. The PCL was sutured and internally braced in all cases. Medial and lateral complex injuries were repaired and additionally laterally augmented by an Arciero reconstruction. After a minimum 12 months follow-up different patient-reported outcome measurements (IKDC, Lysholm, VAS, Tegner Score) and instrumental stability assessment by Rolimeter -test and stress radiographs (Telos™) were analyzed. Groups were compared by t test with p < 0.05 considered significant.

Results
In total, 20 patients (5 IIIM, 5 IIIL and 10 IV) were included in this study with an average follow-up of 13.7 ± 2.6 months. There were significant differences in instrumental stability testing (side-to-side difference (SSD) of anterior tibial translation: ACLIB 2.7 ± 1.5 mm vs. ACLR 1.3 ± 1.3; p = 0.0339) and stress radiography (SSD ACL: ACLIB 3.4 ± 2.2 mm vs. ACLR 0.4 ± 2.7; p = 0.0249) between groups. ACLIB group showed greater ROM in terms of flexion (SSD Flexion: ACLIB 7.8 ± 9.9° vs. ACLR 16 ± 7.0°; p = 0.0466; Total Flexion overall 125.5 ± 11.8°). No clinically relevant differences in patient-reported outcome scores (Lysholm Score: ACLIB 82 ± 16.4 vs. ACLR 85 ± 10.4; IKDC subjective score: ACLIB 70.4 ± 17 vs. ACLR 76.6 ± 8.3) were determined.

Conclusion
ACLR provides superior translational stability than ACLIB in terms of instrumental testing and stress radiography. Both techniques were equivalent with respect to PROMS and led to good and excellent clinical results.

Level of evidence
Retrospective cohort study, III.
Patient- and cycle-specific factors affecting the outcome of frozen–thawed embryo transfers
Authors: Holschbach Verena , Kordes Hannah , Dietrich Jens Erik , Bruckner Thomas , Strowitzki Thomas , Germeyer Ariane 
Published: April 2023

Abstract
Purpose
This study attempted at identifying the main parameters influencing the outcome of frozen embryo transfers.

Methods
This is a single-center retrospective cohort study of 830 frozen-embryo-transfer cycles performed at a German university hospital from January 2012 to December 2016. Main outcome parameters were the clinical pregnancy and live birth rate. Twelve patient- and cycle-dependent factors were analyzed in terms of their influence on the outcome of frozen embryo transfers. Multivariate logistic regression analysis was used for the modelling of the dependency of the different parameters on outcomes.

Results
The clinical pregnancy rate in our study was 25.5%, the live birth rate was 16.1% with an average maternal age of 34.2 years at the time of the oocyte retrieval. In the univariate analysis age, number of transferred embryos, blastocyst versus cleavage stage transfer, embryo quality and mode of endometrial preparation affected the birth rate significantly. The birth rate after artificial endometrial preparation was significantly lower than the birth rate after transfers in modified natural cycles (12.8 versus 20.6% with p = 0.031). The multivariate logistic regression analysis showed a significant independent influence of age, number of transferred embryos, culture duration and mode of endometrial preparation on the frozen embryo transfer success rates. Body mass index, nicotine abuse, a history of PCO syndrome or endometriosis and the co-transfer of a second poor-quality embryo to a good-quality embryo appeared to be irrelevant for the outcome in our collective.

Conclusion
Age, number of transferred embryos, embryo culture duration and the mode of endometrial preparation are independent predictive factors of frozen embryo transfer outcomes.
Space radiation quality factor for Galactic Cosmic Rays and typical space mission scenarios using a microdosimetric approach
Authors: Papadopoulos Alexis , Kyriakou Ioanna , Incerti Sébastien , Santin Giovanni , Nieminen Petteri , Daglis Ioannis A. , Li Weibo , Emfietzoglou Dimitris 
Published: April 2023

AbstractSpace radiation exposure from omnipresent Galactic Cosmic Rays (GCRs) in interplanetary space poses a serious carcinogenic risk to astronauts due to the—limited or absent—protective effect of the Earth’s magnetosphere and, in particular, the terrestrial atmosphere. The radiation risk is directly influenced by the quality of the radiation, i.e., its pattern of energy deposition at the micron/DNA scale. For stochastic biological effects, radiation quality is described by the quality factor, $$Q$$
Q
, which can be defined as a function of Linear Energy Transfer (LET) or the microdosimetric lineal energy ($$y$$
y
). In the present work, the average $$Q$$
Q
of GCR for different mission scenarios was calculated using a modified version of the microdosimetric Theory of Dual Radiation Action (TDRA). NASA’s OLTARIS platform was utilized to generate the radiation environment behind different aluminum shielding (0–30 g/cm2) for a typical mission scenario in low-earth orbit (LEO) and in deep space. The microdosimetric lineal energy spectra of ions ($$Z\ge 1$$

Z
≥
1

) in 1 μm liquid water spheres were calculated by a generalized analytical model which considers energy-loss fluctuations and δ-ray transport inside the irradiated medium. The present TDRA-based $$Q$$
Q
-values for the LEO and deep space missions were found to differ by up to 10% and 14% from the corresponding ICRP-based $$Q$$
Q
-values and up to 3% and 6% from NASA’s $$Q$$
Q
-model. In addition, they were found to be in good agreement with the $$Q$$
Q
-values measured in the International Space Station (ISS) and by the Mars Science Laboratory (MSL) Radiation Assessment Detector (RAD) which represent, respectively, a LEO and deep space orbit.
An observational cohort study on pulmonary function in adult patients with 5q-spinal muscular atrophy under nusinersen therapy
Authors: Bjelica Bogdan , Wohnrade Camilla , Osmanovic Alma , Schreiber-Katz Olivia , Petri Susanne 
Published: April 2023

Abstract
Background
Few studies assessed the effect of nusinersen on respiratory function in adult patients with spinal muscular atrophy (SMA). The aim of this single-center study was to analyze pulmonary function and its association with muscle function and quality of life (QoL) in adult patients with 5q-SMA under nusinersen.

Methods
We recorded forced vital capacity (FVC), forced expiratory volume in the first second (FEV1) and peak expiratory flow (PEF) during nusinersen treatment in 38 adult SMA patients. Revised Upper Limb Module (RULM), Hammersmith Functional Motor Scale Expanded (HFMSE), 36-Item Short Form Health Survey (SF-36) questionnaire and Fatigue Severity Scale (FSS) were recorded and correlations between muscle function, QoL, fatigue and respiratory parameters were analyzed.

Results
No differences were detected between mean FVC, FEV1, PEF at different timepoints versus baseline. Ambulatory patients showed significant improvement in mean PEF at month 30, compared to non-ambulatory patients (+ 0.8 ± 0.5 vs. − 0.0 ± 0.5, p < 0.05). Patients with fatigue at baseline showed significant improvement in mean PEF at month 10, compared to patients without fatigue at baseline (+ 0.6 ± 0.9 vs. − 0.4 ± 0.5, p < 0.05). Physical domains of SF-36 positively correlated with the change in FVC and FEV1. FSS negatively correlated with the change in mean PEF.

Conclusion
Mean pulmonary function remained stable during nusinersen treatment over a period of up to 30 months. Improvement in pulmonary function was associated with improvement in motor function, fatigue and QoL, early after nusinersen initiation.
Cancer of unknown primary (CUP) through the lens of precision oncology: a single institution perspective
Authors: Weiss L. , Heinrich K. , Zhang D. , Dorman K. , Rühlmann K. , Hasselmann K. , Klauschen F. , Kumbrink J. , Jung A. , Rudelius M. , Mock A. , Ormanns Steffen , Kunz W. G. , Roessler D. , Beyer G. , Corradini S. , Heinzerling L. , Haas M. , von Bergwelt-Baildon M. , Boeck S. , Heinemann V. , Westphalen C. B. 
Published: April 2023

Abstract
Purpose
For patients with cancer of unknown primary (CUP), treatment options are limited. Precision oncology, the interplay of comprehensive genomic profiling (CGP) and targeted therapies, aims to offer additional treatment options to patients with advanced and hard-to-treat cancers. We aimed to highlight the use of a molecular tumor board (MTB) in the therapeutic management of CUP patients.

Methods
In this single-center observational study, CUP patients, presented to the MTB of the Comprehensive Cancer Center Munich LMU, a tertiary care center, were analyzed retrospectively. Descriptive statistics were applied to describe relevant findings.

Results
Between June 2016 and February 2022, 61 patients with unfavorable CUP were presented to the MTB, detected clinically relevant variants in 74% (45/61) of patients, of which 64% (29/45) led to therapeutic recommendation. In four out of 29 patients (14%), the treatment recommendations were implemented, unfortunately without resulting in clinical benefit. Reasons for not following the therapeutic recommendation were mainly caused by the physicians’ choice of another therapy (9/25, 36%), especially in the context of worsening of general condition, lost to follow-up (7/25, 28%) and death (6/25, 24%).

Conclusion
CGP and subsequent presentation to a molecular tumor board led to a high rate of therapeutic recommendations in patients with CUP. Recommendations were only implemented at a low rate; however, late GCP diagnostic and, respectively, MTB referral were found more frequent for the patients with implemented treatment. This contrast underscores the need for early implementation of CGP into the management of CUP patients.
Clinical and genome-wide association analysis of chemoradiation-induced hearing loss in nasopharyngeal carcinoma
Authors: He Yong-Qiao , Luo Lu-Ting , Wang Tong-Min , Xue Wen-Qiong , Yang Da-Wei , Li Dan-Hua , Diao Hua , Xiao Ruo-Wen , Deng Chang-Mi , Zhang Wen-Li , Liao Ying , Wu Yan-Xia , Wang Qiao-Ling , Zhou Ting , Li Xi-Zhao , Zheng Xiao-Hui , Zhang Pei-Fen , Zhang Shao-Dan , Hu Ye-Zhu , Sun Ying , Jia Wei-Hua 
Published: April 2023

AbstractChemoradiation-induced hearing loss (CRIHL) is one of the most devasting side effects for nasopharyngeal carcinoma (NPC) patients, which seriously affects survivors’ long-term quality of life. However, few studies have comprehensively characterized the risk factors for CRIHL. In this study, we found that age at diagnosis, tumor stage, and concurrent cisplatin dose were positively associated with chemoradiation-induced hearing loss. We performed a genome-wide association study (GWAS) in 777 NPC patients and identified rs1050851 (within the exon 2 of NFKBIA), a variant with a high deleteriousness score, to be significantly associated with hearing loss risk (HR = 5.46, 95% CI 2.93–10.18, P = 9.51 × 10–08). The risk genotype of rs1050851 was associated with higher NFKBIA expression, which was correlated with lower cellular tolerance to cisplatin. According to permutation-based enrichment analysis, the variants mapping to 149 hereditary deafness genes were significantly enriched among GWAS top signals, which indicated the genetic similarity between hereditary deafness and CRIHL. Pathway analysis suggested that synaptic signaling was involved in the development of CRIHL. Additionally, the risk score integrating genetic and clinical factors can predict the risk of hearing loss with a relatively good performance in the test set. Collectively, this study shed new light on the etiology of chemoradiation-induced hearing loss, which facilitates high-risk individuals’ identification for personalized prevention and treatment.
A maintenance planning framework using online and offline deep reinforcement learning
Authors: Bukhsh Zaharah A. , Molegraaf Hajo , Jansen Nils 
Published: April 2023

AbstractCost-effective asset management is an area of interest across several industries. Specifically, this paper develops a deep reinforcement learning (DRL) solution to automatically determine an optimal rehabilitation policy for continuously deteriorating water pipes. We approach the problem of rehabilitation planning in an online and offline DRL setting. In online DRL, the agent interacts with a simulated environment of multiple pipes with distinct lengths, materials, and failure rate characteristics. We train the agent using deep Q-learning (DQN) to learn an optimal policy with minimal average costs and reduced failure probability. In offline learning, the agent uses static data, e.g., DQN replay data, to learn an optimal policy via a conservative Q-learning algorithm without further interactions with the environment. We demonstrate that DRL-based policies improve over standard preventive, corrective, and greedy planning alternatives. Additionally, learning from the fixed DQN replay dataset in an offline setting further improves the performance. The results warrant that the existing deterioration profiles of water pipes consisting of large and diverse states and action trajectories provide a valuable avenue to learn rehabilitation policies in the offline setting, which can be further fine-tuned using the simulator.