Miracle-dz/UniFAR-FTUs huggingface dataset:
Reset Controller Synthesis by Reach-avoid Analysis for Delay Hybrid Systems

A reset controller plays a crucial role in designing hybrid systems. It restricts the initial set and redefines the reset map associated with discrete transitions, in order to guarantee the system to achieve its objective. Reset controller synthesis, together with feedback controller synthesis and switching logic controller synthesis, provides a correct-by-construction approach to designing hybrid systems. However, time-delay is an inevitable factor in hybrid systems, which can degrade control performance and render verification certificates obtained by abstracting away time-delay invalid in practice. In this paper, we investigate this issue in a practical manner by taking time-delay into account. We propose an approach that reduces the synthesis of reset controllers to the generation of reach-avoid sets for the hybrid system under consideration, which can be efficiently solved using off-the-shell convex optimization solvers.
Fast Sparse PCA via Positive Semidefinite Projection for Unsupervised Feature Selection

In the field of unsupervised feature selection, sparse principal component analysis (SPCA) methods have attracted more and more attention recently. Compared to spectral-based methods, SPCA methods don't rely on the construction of a similarity matrix and show better feature selection ability on real-world data. The original SPCA formulates a nonconvex optimization problem. Existing convex SPCA methods reformulate SPCA as a convex model by regarding the reconstruction matrix as an optimization variable. However, they are lack of constraints equivalent to the orthogonality restriction in SPCA, leading to larger solution space. In this paper, it's proved that the optimal solution to a convex SPCA model falls onto the Positive Semidefinite (PSD) cone. A standard convex SPCA-based model with PSD constraint for unsupervised feature selection is proposed. Further, a two-step fast optimization algorithm via PSD projection is presented to solve the proposed model. Two other existing convex SPCA-based models are also proven to have their solutions optimized on the PSD cone in this paper. Therefore, the PSD versions of these two models are proposed to accelerate their convergence as well. We also provide a regularization parameter setting strategy for our proposed method. Experiments on synthetic and real-world datasets demonstrate the effectiveness and efficiency of the proposed methods.
RAP-Gen: Retrieval-Augmented Patch Generation with CodeT5 for Automatic Program Repair

Automatic program repair (APR) is crucial to reduce manual debugging efforts for developers and improve software reliability. While conventional search-based techniques typically rely on heuristic rules or a redundancy assumption to mine fix patterns, recent years have witnessed the surge of deep learning (DL) based approaches to automate the program repair process in a data-driven manner. However, their performance is often limited by a fixed set of parameters to model the highly complex search space of APR. To ease such burden on the parametric models, in this work, we propose a novel Retrieval-Augmented Patch Generation framework (RAP-Gen) by explicitly leveraging relevant fix patterns retrieved from a codebase of previous bug-fix pairs. Specifically, we build a hybrid patch retriever to account for both lexical and semantic matching based on the raw source code in a language-agnostic manner, which does not rely on any code-specific features. In addition, we adapt a code-aware language model CodeT5 as our foundation model to facilitate both patch retrieval and generation tasks in a unified manner. We adopt a stage-wise approach where the patch retriever first retrieves a relevant external bug-fix pair to augment the buggy input for the CodeT5 patch generator, which synthesizes a ranked list of repair patch candidates. Notably, RAP-Gen is a generic APR framework that can flexibly integrate different patch retrievers and generators to repair various types of bugs. We thoroughly evaluate RAP-Gen on three benchmarks in two programming languages, including the TFix benchmark in JavaScript, and Code Refinement and Defects4J benchmarks in Java, where the bug localization information may or may not be provided. Experimental results show that RAP-Gen significantly outperforms previous state-of-the-art (SoTA) approaches on all benchmarks, e.g., boosting the accuracy of T5-large on TFix from 49.70% to 54.15% (repairing 478 more bugs) and repairing 15 more bugs on 818 Defects4J bugs. Further analysis reveals that our patch retriever can search for relevant fix patterns to guide the APR systems.
DESI luminous red galaxy samples for cross-correlations

We present two galaxy samples, selected from DESI Legacy Imaging Surveys (LS) DR9, with approximately 20,000 square degrees of coverage and spectroscopic redshift distributions designed for cross-correlations such as with CMB lensing, galaxy lensing, and the Sunyaev-Zel'dovich effect. The first sample is identical to the DESI Luminous Red Galaxy (LRG) sample, and the second sample is an extended LRG sample with 2–3 times the DESI LRG density. We present the improved photometric redshifts, tomographic binning and their spectroscopic redshift distributions and imaging systematics weights, and magnification bias coefficients. The catalogs and related data products will be made publicly available. The cosmological constraints using this sample and Planck lensing maps are presented in a companion paper. We also make public the new set of general-purpose photometric redshifts trained using DESI spectroscopic redshifts, which are used in this work, for all galaxies in LS DR9.
Introduction to Cosmology

These notes form an introduction to cosmology with special emphasis on large scale structure, the cmb anisotropy and inflation. In some places a basic familiarity with particle physics is assumed, but otherwise no special knowledge is needed. Most of the material in the first two sections can be found in several texts, except that the discussion of dark matter and the cosmological constant is more up to date. Most of that in the remaining sections can be found in a review of structure formation and inflation done with Andrew Liddle, which describes original work by various authors including ourselves and Ewan Stewart. The reader is referred to these works for more detail, and a very complete list of references.
Quantification of the Field of View for Standard Lateral Arthroscopy of the Canine Shoulder

Abstract Objective The aim of this study was to define the extent of the biceps tendon, subscapularis tendon, and cranial border of the medial glenohumeral ligament within the field of view during standard lateral shoulder arthroscopy in the dog. We also examine the effect of joint flexion on the field of view of the biceps tendon. Study Design This was a cadaveric study using 21 shoulders of large breed dogs. Each shoulder was explored with a 30-degree arthroscope using standard lateral ports. For each supporting structure, the margins within the arthroscopic field of view were marked with ink. In 11 shoulders, the distal margin of the biceps tendon was identified and marked first with the limb at a standing angle and then in flexion. The margins of the cranial border of the medial glenohumeral ligament were marked at the standing angle. In 10 additional shoulders, the margins of the subscapularis tendon were evaluated. Each joint was fully dissected and the portion of each stabilizing structure within the field of view was quantified. Results Fifty-eight percent of the cranial border of the medial glenohumeral ligament was within the arthroscopic view. At a standing angle, 48% of the intra-articular length of the biceps tendon was within the arthroscopic view, compared to 63% with the limb flexed. Twenty percent of the subscapularis tendon was within the arthroscopic view. Conclusion A significant portion of the biceps tendon and medial stabilizing structures of the canine shoulder are outside the field of view of arthroscopy through a standard lateral approach. The limitations of the arthroscopic field of view should be appreciated when evaluating the shoulder.
New Systemic Therapy Strategies for HER2-Positive Metastatic Breast Carcinoma

Abstract HER2 positivity is predictive of the response to anti-HER2 therapies. The treatment of HER2-positive tumors is continuously improving through the development of new anti-HER2-directed agents. Many different anti-HER2 therapies are now available which belong to the classes of anti-HER2 antibodies, tyrosine kinase inhibitors (TKI) and antibody-drug conjugates (ADC). A combination of trastuzumab, pertuzumab and a taxane (THP) remains the preferred first-line (1L) therapy, whereas T‑DXd is the new standard for 2L metastatic breast cancer based on a highly significant improvement in progression-free survival compared to T-DM1 as shown in the DESTINY-Breast03 study. A tucatinib-based regimen (dual anti-HER2 therapy with trastuzumab and tucatinib plus capecitabine) is the preferred 3L option, which may already be used for 2L treatment in patients with active brain metastases. Different anti-HER2 therapies are available in the 3L setting and beyond. Molecular biomarkers in addition to the quantification of HER2 expression, such as the PD‑L1 status and PIK3CA mutations, can further guide the decision-making process in the future. Zusammenfassung Die HER2-Positivität ist prädiktiv für das Ansprechen auf Anti-HER2-gerichtete Therapien. Durch die Entwicklung neuer Anti-HER2-Strategien verbessert sich die Behandlung von HER2-positiven Tumoren stetig, sodass mittlerweile eine Vielzahl verschiedener Anti-HER2-Therapien verfügbar ist, welche die Substanzklassen der Anti-HER2-Antikörper, Tyrosinkinase-Inhibitoren (TKI) und Antikörper-Wirkstoff-Konjugate (ADC) umfassen. Die bevorzugte Erstlinien-Therapie bleibt die Kombination aus Trastuzumab, Pertuzumab und einem Taxan (THP). In der 2. Therapielinie (2L) löst T‑DXd, basierend auf einem hochsignifikanten Vorteil des progressionsfreien Überlebens in der DESTINY-Breast03-Studie T-DM1 ab. Bei aktiven Hirnmetastasen kann ein Tucatinib-basiertes Regime (duale Anti-HER2-Therapie aus Trastuzumab und Tucatinib plus Capecitabin) bereits in der 2L Anwendung finden, andernfalls priorisiert in der 3L. Ab der 3L stehen verschiedene Anti-HER2-Therapien zur Verfügung. Molekulare Charakteristika, die neben der Quantifizierung der HER2-Expression auch die Bestimmung weiterer Biomarker wie PD‑L1-Status und PIK3CA-Mutationen umfasst, können in Zukunft differenziertere Therapieentscheidungen ermöglichen.
Understanding Human Dynamic Sampling Objectives to Enable Robot-assisted Scientific Decision Making

Truly collaborative scientific field data collection between human scientists and autonomous robot systems requires a shared understanding of the search objectives and tradeoffs faced when making decisions. Therefore, critical to developing intelligent robots to aid human experts, is an understanding of how scientists make such decisions and how they adapt their data collection strategies when presented with new information in situ. In this study we examined the dynamic data collection decisions of 108 expert geoscience researchers using a simulated field scenario. Human data collection behaviors suggested two distinct objectives: an information-based objective to maximize information coverage, and a discrepancy-based objective to maximize hypothesis verification. We developed a highly-simplified quantitative decision model that allows the robot to predict potential human data collection locations based on the two observed human data collection objectives. Predictions from the simple model revealed a transition from information-based to discrepancy-based objective as the level of information increased. The findings will allow robotic teammates to connect experts’ dynamic science objectives with the adaptation of their sampling behaviors, and in the long term, enable the development of more cognitively-compatible robotic field assistants.
Avoiding the 1 TB Storage Wall: Leveraging Ethereum’s DHT to Reduce Peer Storage Needs

Blockchains face many challenges in time, among which the ever-growing storage needs for blockchains’ data. In particular, Ethereum is quickly approaching the 1 TB storage limit for a node, what may significantly reduce the candidates able to run an Ethereum fullnode. In this paper, we propose a new synchronization and storage strategy for Ethereum that takes full advantage of the Distributed Hash Table implemented in all clients but left unused. By digging into the history of Ethereum’s synchronization and storage strategies, we justify why such distribution of storage duties among peers makes much sense today. We implemented our solution in the official Ethereum client Geth and validated its smooth operation on a private Ethereum instance. Our solution can save around 60% of the storage of a node (360 GB) which represents a total of 12 PB of data at the network scale, while being fully backward compatible with current clients.
Harmful Workplace Experiences and Women’s Occupational Well-Being

We report a meta-analytic review of studies examining the relations among harmful workplace experiences and women’s occupational well-being. Based on previous research, a classification of harmful workplace experiences affecting women is proposed and then used in the analysis of 88 studies with 93 independent samples, containing 73,877 working women. We compare the associations of different harmful workplace experiences and job stressors with women’s work attitudes and health. Random-effects meta-analysis and path analysis showed that more intense yet less frequent harmful experiences (e.g., sexual coercion and unwanted sexual attention) and less intense but more frequent harmful experiences (e.g., sexist organizational climate and gender harassment) had similar negative effects on women’s well-being. Harmful workplace experiences were independent from and as negative as job stressors in their impact on women’s occupational well-being. The power imbalance between the target and the perpetrator appeared as a potential factor to explain the type and impact of harmful workplace experiences affecting women’s occupational well-being. In the discussion, we identify several gaps in the literature, suggest directions for future research, and suggest organizational policy changes and interventions that could be effective at reducing the incidence of harmful workplace experiences. Additional online materials for this article are available to PWQ subscribers on PWQ's website at http://pwq.sagepub. com/supplemental.
Study of How Adiposity in Pregnancy has an Effect on outcomeS (SHAPES): protocol for a prospective cohort study

Introduction Maternal obesity increases the risk of multiple maternal and infant pregnancy complications, such as gestational diabetes and pre-eclampsia. Current UK guidelines use body mass index (BMI) to identify which women require additional care due to increased risk of complications. However, BMI may not accurately predict which women will develop complications during pregnancy as it does not determine amount and distribution of adipose tissue. Some adiposity measures (eg, waist circumference, ultrasound measures of abdominal visceral fat) can better identify where body fat is stored, which may be useful in predicting those women who need additional care. Methods and analysis This prospective cohort study (SHAPES, Study of How Adiposity in Pregnancy has an Effect on outcomeS) aims to evaluate the prognostic performance of adiposity measures (either alone or in combination with other adiposity, sociodemographic or clinical measures) to estimate risk of adverse pregnancy outcomes. Pregnant women (n=1400) will be recruited at their first trimester ultrasound scan (11+2–14+1 weeks’) at Newcastle upon Tyne National Health Service Foundation Trust, UK. Early pregnancy adiposity measures and clinical and sociodemographic data will be collected. Routine data on maternal and infant pregnancy outcomes will be collected from routine hospital records. Regression methods will be used to compare the different adiposity measures with BMI in terms of their ability to predict pregnancy complications. If no individual measure performs better than BMI, multivariable models will be developed and evaluated to identify the most parsimonious model. The apparent performance of the developed model will be summarised using calibration, discrimination and internal validation analyses. Ethics and dissemination Ethical favourable opinion has been obtained from the North East: Newcastle & North Tyneside 1 Research Ethics Committee (REC reference: 22/NE/0035). All participants provide informed consent to take part in SHAPES. Planned dissemination includes peer-reviewed publications and additional dissemination appropriate to target audiences, including policy briefs for policymakers, media/social-media coverage for public and conferences for research Trial registration number ISRCTN82185177.
Multivariate comparison of taxonomic, chemical and technical data from 80 full-scale an-aerobic digester-related systems

This study represents one of the most comprehensive characterisations of the anaerobic digestion (AD) microbiome with 80 samples from 45 different large-scale reactors in three coun-tries. Technical, chemical and taxonomic data was thoroughly collected, analyzed and correlated to identify the main drivers of AD processes. Our results showed that MBA03, Proteiniphilum, a member of Dethiobacteraceae, and Caldicoprobacter were present in all the samples, while Meth-anosarcina was the most abundant and prevalent archaea. Two distinct bacterial clusters were iden-tified by correlating microbial abundances. One was correlated with hydrogenotrophic and the other with acetoclastic methanogenesis. Organic acids, ammonia, nitrogen, COD and the trace el-ements Fe, Mo, and the macro nutrient P had the greatest impact on AD microbiomes. Temperature, reactor type and substrate also influenced the formation of a specialized microbial community. Overall, this work sheds light on the microbial key players involved in AD and evaluates how they are affected by technical and chemical parameters. Highlights Generation of a holistic dataset of chemical, taxonomic and technical parameters of 80 large-scale anaerobic digestion systems. Identification of a core microbiome comprising MBA03, Proteiniphilum, an uncultured or-ganism from the Dethiobacteraceae family, and the Caldicoprobacter family. Identification of the main influencing parameters that determine the occurrence and non-occurrence of specific genera. Correlation of bacterial taxa with hydrogenotrophic and/or acetoclastic archaea.
SARS-CoV-2 ORF7a Mutation Found in BF.5 and BF.7 Sublineages Impacts Its Functions

A feature of the SARS-CoV-2 Omicron subvariants BF.5 and BF.7 that recently circulated mainly in China and Japan was the high prevalence of ORF7a: H47Y mutation. Here we evaluated the effect of this mutation on the three main functions ascribed to SARS-CoV-2 ORF7a protein. Our findings show that H47Y mutation impairs the ability of SARS-CoV-2 ORF7a to antagonize type-I interferon (IFN-I) response and to downregulate Major Histocompatibility Complex-I (MHC-I) cell surface levels, but had no effect in its anti-SERINC5 function. Overall, our results suggest that the H47Y mutation of ORF7a affects important functions of this protein resulting in changes in virus pathogenesis. Importance In late 2021, the Omicron (B.1.1.529) VOC emerged and outcompeted the circulating VOC Delta (B.1.617.2). Soon afterwards, Omicron VOC has expanded and diversified in the world. Among the emerged subvariants of Omicron are BF.5 and BF.7 that are characterized by the presence of a number of mutations across their genome and spread quite effectively across China and other countries later on. One such mutation that was found in the vast majority of isolates of the BF.5 and BF.7 subvariants was ORF7a: H47Y, whose effect on ORF7a is unknown. In this report, we show that H47Y inhibits a number of ORF7a functions, which can potentially affect virus pathogenesis.
Unveiling the Intercompartmental Signaling Axis: Mitochondrial to ER Stress Response (MERSR) and its Impact on Proteostasis

Maintaining protein homeostasis is essential for cellular health. During times of proteotoxic stress, cells deploy unique defense mechanisms to achieve resolution. Our previous research uncovered a cross-compartmental Mitochondrial to Cytosolic Stress Response (MCSR), a unique stress response activated by the perturbation of mitochondrial proteostasis, which ultimately results in the improvement of proteostasis in the cytosol. Here, we found that this signaling axis also influences the unfolded protein response of the endoplasmic reticulum (UPRER), suggesting the presence of a Mitochondria to ER Stress Response (MERSR). During MERSR, the IRE1 branch of UPRER is inhibited, introducing a previously unknown regulatory component of MCSR. Moreover, proteostasis is enhanced through the upregulation of the PERK-eIF2a signaling pathway, increasing phosphorylation of eIF2a and improving the ER’s capacity to manage greater proteostasis load. MERSR activation in both poly-glutamine (poly-Q) and amyloid-beta (Aβ) C. elegans disease models also led to improvement in both aggregate burden and overall disease outcome. These findings shed light on the coordination between the mitochondria and the ER in maintaining cellular proteostasis and provides further evidence for the importance of intercompartmental signaling.
A dynamic bias in chromatin protein deposition at G-quadruplex sites

Previous studies indicate that genomic loci harboring G-quadruplexes (G4s)—stacked structures that can form in single-stranded DNA—can be linked to epigenetic instability. However, the role of chromatin redistribution and the genome-wide nature of this process need further investigation. Here, we provide experimental evidence that connects G4s to alterations in the deposition of chromatin proteins. We have used metabolic labelling and immunoprecipitation of new and parental proteins in hRPE-1 cells to investigate global chromatin deposition dynamics. We identify a reciprocal, local bias in chromatin protein deposition at G4 sites favoring the association of parental proteins with the G4 and new proteins with the C4 DNA strand. The deposition bias at G4 sites does not depend on replication directionality and is strengthened by G4 stabilization. Slowing down replication forks upon hydroxyurea treatment reverses the bias, supposedly affected by decoupling between helicase and polymerase. Interestingly, upon combined G4 stabilization and slowing of the replication forks, new proteins exhibit a redistribution pattern similar to G4 stabilization alone, while parental protein redistribution more resembles one after hydroxyurea treatment, hinting at mechanistic differences between parental and new histone distribution. We also report that the genomic distribution of putative quadruplexes is not random and depends on loop size, where G4s with shorter loops have a preference for the DNA strand replicated by leading and G4s with longer loops by lagging strand replication. These findings provide insight into the mechanisms behind G4 occurrence and its role in epigenetic instability and help to improve our understanding of the factors influencing biases in global chromatin protein redeposition.