Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast and Low Overhead Metadata Operations for NVM-Based File System Using Slotted Paging

Existing nonvolatile memory (NVM)-based file systems can fully leverage the characteristics of NVM to obtain better performance than traditional disk-based file systems. It has the potential capacity to efficiently manage metadata and perform fast metadata operations. However, most NVM-based file systems mainly focus on managing file metadata (inode), while pay little attention to directory metadata (dentry), which also has a noticeable impact on the file system performance. Besides, the traditional journaling technique that guarantees metadata consistency may not yield satisfactory performance on NVM-based file systems. To solve these problems, in this article we propose a fast and low overhead metadata operation mechanism, called FLOMO. It first adopts a novel slotted-paging structure in NVM to reorganize dentry for efficiently performing dentry operations, and utilizes the red–black tree in DRAM to accelerate dentry lookup and the search process of dentry deletion. Moreover, FLOMO presents a selective journaling scheme for metadata updates, which partially logs the changes related to dentry in the proposed slotted page, thereby, mitigating the redundant journaling overhead. To verify FLOMO, we implement it in a typical NVM-based file system, the persistent memory file system (PMFS). Experimental results show that FLOMO accelerates the metadata operations in PMFS by 34.4%<inline-formula> <tex-math notation="LaTeX">$\sim 59$ </tex-math></inline-formula>%, and notably reduces the journaling overhead for metadata, shortening the latency by 59% on average. For real-world applications, FLOMO has higher throughput compared with PMFS, PMFS without journal, and NOVA, achieving up to <inline-formula> <tex-math notation="LaTeX">$2.1\times $ </tex-math></inline-formula>, <inline-formula> <tex-math notation="LaTeX">$1.1\times $ </tex-math></inline-formula>, and <inline-formula> <tex-math notation="LaTeX">$1.3\times $ </tex-math></inline-formula> performance improvement, respectively.
Coupling and Decoupling in IEC 61499 and IEC 61131-3 Applications

The history of the software industry has shown and proved that coupling and cohesion are a never-ending story in this industry. Quantifying the quality of software systems by measuring the strength of coupling and cohesion and considering it a rule that good software has low coupling between its parts and high cohesion within each part, is currently widely accepted. Every paradigm shift, new technology, language, etc. that didn`t consider this fact had to sooner or later leave this industry. It is, therefore, crucial to study and consider this fact in every new topic in the software industry. Surprisingly neither the IEC 61499 nor IEC 61131 communities have yet conducted a deep study to evaluate what coupling and cohesion really mean for Industrial Control and Automation Applications. We hope this paper will manage to fulfill this considerable gap, if not fully at least partially.
Time to start using checklists for reporting artificial intelligence in health care and biomedical research: a rapid review of available tools

While the volume of using artificial intelligence (AI) and machine learning (ML) in medical research has grown considerable over the past years, the reporting quality for the majority of such studies has been poor, raising concerns about the replicability, biasedness, validity and overall value for a vast amount of research. This rapid review aims to summarize reporting guidelines for medical AI studies. Following a systematic search in the PubMed database up to May 2022 and the reference lists of previously published reviews in the field, we identified 22 reporting checklists published or under development for a variety of study designs and clinical fields or general use. The main aims, the target audience and specific focus of the identified checklists has been summarized. Given the documented positive impact of checklists on the reporting quality of medical research, we encourage researchers using AI or ML in medicine to start using them.
Perpendicular lensed optical fibers for biomedical & defense applications: (Exploring the workability of lensed fibers in practical domains)

The diversity of modern biomedical, industrial, and military requirements is increasing the level of innovation and workability required to deploy modern solutions. A key aspect of this technological innovation has been required in the photonics industry to explore potential applications and workability avenues. Across leading industrial areas, lensing technology is emerging as the primary method to bridge existing gaps and paving forward solutions that provide viable solutions to the existing gaps in technology and application.The aspects of the innovative lensed fibers are emerging as the cornerstone to fulfill existing gaps and pave forward new applications across security, biomedical and industrial performance utilizing the core aspects of laser technology through lensed fibers. The technological application using particularly perpendicular lensed fibers is a key aspect of the innovation explored through directed research and coordinated solution management in biomedical and defense areas.
Purchase Obligations and Hedging*

Commodity price shocks have negative consequences for developed economies that rely heavily on imported materials. Consequently, firms employ risk-management instruments to reduce their exposure. In this paper we study how the use of supply contracts by firms can shape the transmission of commodity price shocks to aggregate variables. We focus on purchase obligations, which are supply contracts with fixed prices for the delivery of goods in future periods. We rely on a novel dataset to document two empirical findings. First, we find a large exposure reduction to commodity price risk for firms using these contracts; our estimates suggest a reduction of about 10.2% to 45.2% compared with non-users. Second, sector output and labor compensation have a smaller negative correlation with commodity prices when firms trade larger contracts. We assess the aggregate quantitative role of these contracts by introducing and calibrating a tractable general equilibrium model. We measure the contribution of purchase obligations to dampening the aggregate transmission of commodity price shocks by constructing a counterfactual in which firms are not allowed to trade these contracts. Our results show that when firms engage in purchase obligations, real consumption has a relative response of 4.32% less to a 10% commodity price shock. We are grateful to Ariel Burstein, Saki Bigio, and Oleg Itskhoki for invaluable guidance and support. We would also like to thank Francisco Arroyo Marioli, Andy Atkeson, Victoria Barone, Pablo Fajgelbaum, Gaston Lopez, David Kohn, Tyler Muir, Augusto Ospital, Bruno Pellegrino, Jonathan Vogel, and Pierre-Olivier Weill. The paper also benefited form fruitful conversations with Julien Acalin and Ritt Keerati (discussants). We finally thank numerous participants in the UCLA International Seminar, UCLA Macroeconomics Seminar, Trans-Atlantic Doctoral Conference, Young Economist Symposium, Economics Graduate Student Conference, and 94th IAES Conference. This work was supported by the Lewis L. Clarke Fellowship Fund and Institute for Humane Studies. alvaro.boitier@gmail.com bgpustilnik@gmail.com
ABECTO: Assessing Accuracy and Completeness of RDF Knowledge Graphs

Accuracy and completeness of RDF knowledge graphs are crucial quality criteria for their fitness for use. However, assessing accuracy and completeness of knowledge graphs requires a basis for comparison. Unfortunately, in most cases, there is no gold standard to compare against. As an alternative, we propose the comparison with other, overlapping RDF knowledge graphs of arbitrary quality. We present ABECTO, a command line tool that implements a pipeline based framework for the comparison of multiple RDF knowledge graphs. For these knowledge graphs, ABECTO provides quality annotations like value deviations and quality measurements like completeness. This enables knowledge graph curators to monitor the quality and can help potential users to select an appropriated knowledge graph for their purpose. We demonstrate the usefulness of ABECTO for the improvement of knowledge graphs with two example use case applications.
The Jump Point Search Pathfinding System in 3D

The ability to quickly compute shortest paths in 3D grids is a technological enabler for several applications such as pipe routing and computer video games. The main challenge is how to deal with the many symmetric permutations of each shortest path. We tackle this problem by adapting Jump Point Search (JPS), a well-known symmetry breaking technique developed for fast pathfinding in 2D grids. We give a rigorous reformulation of the JPS pathfinding system into 3D and we prove that our new algorithm, JPS-3D, is optimality preserving. We also develop a novel method for limiting scan depth during jump operations, which can further reduce search time. Experimental results show significant improvements versus on-line A* search and previous attempts at generalising JPS. We demonstrate that searching with adaptive scan limits can yield additional speedups of over an order of magnitude.
PyHopper - A Plug-and-Play Hyperparameter Optimization Engine

Hyperparameter tuning is a fundamental aspect of machine learning research. Setting up the infrastructure for systematic optimization of hyperparameters can take a significant amount of time. Here, we present PyHopper, an open-source black-box optimization platform designed to streamline the hyperparameter tuning work-flow of machine learning research. PyHopper’s goal is to integrate with existing code with minimal effort and run the optimization process with minimal necessary manual oversight. With simplicity as the primary theme, PyHopper is powered by a single robust Markov-chain Monte-Carlo optimization algorithm that scales to millions of dimensions. Compared to existing tuning packages, focusing on a single algorithm frees the user from having to decide between several algorithms and makes PyHopper easily customizable. PyHopper is publicly available under the Apache-2.0 license at https://github.com/PyHopper/PyHopper .
Hierarchical Agents by Combining Language Generation and Semantic Goal Directed RL

Learning to solve long horizon temporally extended tasks with reinforcement learn-1 ing has been a challenge for several years now. We believe that it is important to 2 leverage both the hierarchical structure of complex tasks and to use expert supervi-3 sion whenever possible to solve such tasks. This work introduces an interpretable 4 hierarchical agent framework by combining sub-goal generation using language 5 and semantic goal directed reinforcement learning. We assume access to certain 6 spatial and haptic predicates and construct a simple and powerful semantic goal 7 space. These semantic goal representations act as an intermediate representation 8 between language and raw states. We evaluate our framework on a robotic block 9 manipulation task and show that it performs better than other methods, including 10 both sparse and dense reward functions. We also suggest some next steps and 11 discuss how this framework makes interaction and collaboration with humans 12 easier. 13
A comparative analysis of sustainability of the usual food intakes of the Iranian population, Iranian food-based dietary guidelines, and optimized dietary models

Promoting sustainable diets might contribute toward achieving sustainable development goals. Considering the importance of national food-based dietary guidelines (FBDGs), this study aimed to assess and compare the sustainability dimensions of the usual Iranian dietary intakes with sustainable optimal diets based on Iranian (2006 and 2015 versions), Mediterranean, and vegetarian FBDGs. The usual dietary intakes of Iranian households were estimated using household expenditure survey data. Diet sustainability, including environmental (water, carbon, and land) footprints, cost, and nutrient-rich food (NRF) index, was calculated for the usual diet and compared with those of different FBDGs. Using linear and goal programming, optimal food models were calculated by minimizing environmental footprints and cost and maximizing NRF simultaneously for each FBDG, while maintaining nutritional considerations recommended by the FBDGs. Replacing the usual dietary intake of Iranians with the optimal diet based on the 2016 Iranian FBDG was associated with reductions equal to 20.9% for water footprint, 22.48% for carbon footprint, 20.39% for land footprint, 31.83% for cost, and 7.64% increase in NRF index. The optimal model based on the 2016 Iran FBDG was 10% more sustainable compared with the 2005 version. Changing the usual consumption of Iranians to the optimal model based on the Mediterranean pyramid was accompanied by the highest NRF index, lower environmental footprints, and cost compared to other models. The recent Iranian FBDG, compared with the older one, was more sustainable. Considering the dimensions of a sustainable diet for future FBDG revisions is recommended.
Enzymatic fingerprinting reveals specific xyloglucan and pectin signatures in the cell wall purified with primary plasmodesmata

Plasmodesmata (PD) pores connect neighbouring plant cells and enable direct transport across the cell wall. Understanding the molecular composition of these structures is essential to address their formation and later dynamic regulation. Here we provide a biochemical characterisation of the cell wall co-purified with primary PD of Arabidopsis thaliana cell cultures. To achieve this result we combined subcellular fractionation, polysaccharide analyses and enzymatic fingerprinting approaches. Relative to the rest of the cell wall, specific patterns were observed in the PD fraction. Most xyloglucans, although possibly not abundant as a group, were fucosylated. Homogalacturonans displayed short methylated stretches while rhamnogalacturonan I species were remarkably abundant. Full rhamnogalacturonan II forms, highly methyl-acetylated, were also present. We additionally showed that these domains, compared to the broad wall, are less affected by wall modifying activities during a time interval of days. Overall, the protocol and the data presented here open new opportunities for the study of wall polysaccharides associated with PD.
Fabry disease: Mechanism and therapeutics strategies

Fabry disease is a monogenic disease characterized by a deficiency or loss of the α-galactosidase A (GLA). The resulting impairment in lysosomal GLA enzymatic activity leads to the pathogenic accumulation of enzymatic substrate and, consequently, the progressive appearance of clinical symptoms in target organs, including the heart, kidney, and brain. However, the mechanisms involved in Fabry disease-mediated organ damage are largely ambiguous and poorly understood, which hinders the development of therapeutic strategies for the treatment of this disorder. Although currently available clinical approaches have shown some efficiency in the treatment of Fabry disease, they all exhibit limitations that need to be overcome. In this review, we first introduce current mechanistic knowledge of Fabry disease and discuss potential therapeutic strategies for its treatment. We then systemically summarize and discuss advances in research on therapeutic approaches, including enzyme replacement therapy (ERT), gene therapy, and chaperone therapy, as well as strategies targeting subcellular compartments, such as lysosomes, the endoplasmic reticulum, and the nucleus. Finally, the future development of potential therapeutic strategies is discussed based on the results of mechanistic studies and the limitations associated with these therapeutic approaches.
Contrasting particle fluxes and composition in a submarine canyon affected by natural sediment transport events and bottom trawling

Submarine canyons are important conduits of sediment and organic matter to deep-sea environments, mainly during high-energy natural events such as storms, river floods, or dense shelf water cascading, but also due to human activities such as bottom trawling. The contributions of natural and trawling-induced sediment and organic matter inputs into Palamós Canyon (NW Mediterranean) were assessed from three instrumented moorings deployed in the axis and northern flank of the canyon covering the trawling closure (February) and the trawling season (March-December) of 2017. During the trawling closure, large sediment fluxes with high contents of labile marine organic matter content were registered in the canyon axis, associated to storm resuspension on the shelf that coincided with dense shelf water cascading and high surface water productivity. Although no major natural sediment transport events occurred during the following spring and summer months, near-daily trawling-induced sediment gravity flows were recorded in the northern flank mooring, placed directly below a fishing ground, which sometimes reached the canyon axis. Compositionally, the organic matter transferred by trawling resuspension was impoverished in the most labile biomarkers (fatty acids, amino acids, and dicarboxylic acids) and had a high degree of degradation, which was similar to surficial sediment from the adjacent fishing ground. Trawling resuspended particles masked the transfer of organic matter enriched in labile biomarkers that naturally occur during the quiescent summer months. Overall, bottom trawling enhances the magnitude of particle fluxes while modifying its organic carbon composition, increasing the re-exposure and transfer of degraded organic carbon and potentially affecting benthic communities that rely on the arrival of fresh organic matter.
A feasibility study of noninvasive prenatal diagnosis in facioscapulohumeral muscular dystrophy type 1 in a Chinese family

Objective: To demonstrate the feasibility of haplotype-based noninvasive prenatal diagnosis of Facioscapulohumeral Muscular Dystrophy type 1 (FSHD1). Methods: Bionano optical mapping was used to identify the D4Z4 structural variation of the genomic DNA sample from the proband affected with FSHD1. In addition, based on the technique of next generation sequencing, the pathogenic haplotype was determined by using trio strategy through genotyping his parents, and also fetal inheritance of paternal haplotypes was then deduced using the Hidden Markov Model. Results: Bionano optical mapping analysis revealed that the proband has only three D4Z4 repeats left in the 4q35 chromosomal region and a disease-permitting 4qA haplotype. The other normal allele of the proband contains 29 D4Z4 repeats and also a 4qA haplotype. The noninvasive cell-free fetal DNA (cffDNA)-based haplotype analysis suggested that the fetus inherited the pathogenic allele from his father and thus was predicted to be affected by FSHD1. In addition, Bionano optical mapping also demonstrated the presence of the pathogenic allele in the fetus by interrogating the genomic DNA from the amniotic fluid cells. Conclusion: Our study showed the cffDNA-based haplotyping was feasible for the noninvasive prenatal diagnosis of FSHD1, which is able to provide earlier testing results with a lower risk of miscarriage and infection than invasive techniques.
A systematic review and network meta-analysis of first-line immune checkpoint inhibitor combination therapies in patients with advanced non-squamous non-small cell lung cancer

Introduction Clinical evidence suggests that first-line immune checkpoint inhibitor (ICI) combination therapies can improve survival in patients with advanced non-squamous non-small cell lung cancer (nsq-NSCLC). However, the optimal strategy remains unknown without a systematic comparison of their long-term effects. Methods We performed a systematic review and network meta-analysis by retrieving up-to-date literature from PubMed® (National Library of Medicine, Bethesda, MD, USA), Embase® (Elsevier, Amsterdam, Netherlands), MEDLINE® (National Library of Medicine), ClinicalTrials.gov (National Library of Medicine), and major international conference publications. Published studies and abstracts comparing first-line ICI combination therapies with other treatments for patients with advanced nsq-NSCLC were included. Restricted mean survival time (RMST) was measured over 12 months for progression-free survival (PFS) and 18 months for overall survival (OS), and the Royston–Parmar model was used to extrapolate and compare data for the long-term outcomes. Results We included a total of 11 trials involving 12 therapies and 6,130 patients. Pembrolizumab plus chemotherapy exhibited the best overall survival (OS) benefit at both 18 and 60 months [RMST = 2.95, 95% confidence interval (CI) 1.96 to 3.97; life-years gained over a 5-year period = 2.18 years]. Nivolumab plus bevacizumab plus chemotherapy was found to present the best progression-free survival (PFS) benefit at 12 months (RMST 3.02, 95% CI 2.11 to 3.91), whereas atezolizumab plus bevacizumab plus chemotherapy showed the best PFS benefit at 36 months (life-years gained over 3 years = 1.22 years). Subgroup analyses showed that among patients with programmed death-ligand 1 (PD-L1) expression ≥ 50%, atezolizumab plus chemotherapy and nivolumab plus ipilimumab resulted in superior OS benefits at 18 and 60 months, respectively. Among patients with PD-L1 expression< 1%, pembrolizumab plus chemotherapy was associated with OS benefits at both 18 and 60 months. Sintilimab plus chemotherapy was associated with relatively fewer grade ≥ 3 adverse events than other ICI combination therapies. Conclusion Our results show that ICI combination therapies showed better survival benefits than chemotherapy. Pembrolizumab plus chemotherapy could provide the best OS benefits to patients with advanced nsq-NSCLC, whereas atezolizumab plus bevacizumab plus chemotherapy could bring the best PFS benefits. The optimal ICI combination therapy varies depending on PD-L1 expression level. Systematic Review Registration https://www.crd. york.ac. uk/PROSPERO/display_record. php? RecordID=325005, identifier CRD42022325005.
Editorial: Campylobacter-associated food safety

COPYRIGHT © 2022 Zhang, Konkel, Gölz and Lu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: Campylobacter-associated food safety
The evolving role of multi-modality imaging in transcatheter tricuspid valve interventions

Tricuspid valve pathophysiology is not well-understood. Emergence of novel transcatheter tricuspid therapies has fueled the requirements for improved imaging visualization techniques and interventional imaging physician skillsets in guiding these complex transcatheter procedures. There is growing understanding on the clinical significance of tricuspid regurgitation which expanded the interest for percutaneous tricuspid valve interventions. The present review concentrates on three essential aspects of tricuspid valve pathophysiology: anatomical considerations for tricuspid interventions, optimal timing of tricuspid interventions by imaging guidance, and the role of interventional imaging physicians’ skillset and knowledge in this field.