Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial communities in the rhizosphere, phyllosphere and endosphere of tomato plants

Plants harbor diverse bacterial communities, which play crucial roles in plant health and growth, in their rhizosphere, phyllosphere and endosphere. Tomato is an important model for studying plant-microbe interactions, but comparison of its associated bacterial community is still lacking. In this study, using Illumina sequencing of 16S rRNA amplicons, we characterized and compared the bacterial size and community from rootzone soil as well as the rhizosphere, phyllosphere and endosphere of roots, stems, leaves, fruits and seeds of tomato plants that were grown in greenhouse conditions. Habitat (soil, phyllospheric, and endophytic) structured the community. The bacterial communities from the soil-type samples (rootzone soil and rhizosphere) showed the highest richness and diversity. The lowest bacterial diversity occurred in the phyllospheric samples, while the lowest richness occurred in the endosphere. Among the endophytic samples, both bacterial diversity and richness varied in different tissues, with the highest values in roots. The most abundant phyla in the tomato-associated community was Proteobacteria, with the exception of the seeds and jelly, where both Proteobacteria and Firmicutes were dominant. At the genus level, the sequences of Pseudomonas and Acinetobacter were prevalent in the rhizosphere, and in the phyllosphere, more than 97% of the sequences were assigned to Acinetobacter. For the endophytes, Acinetobacter, Enterobacter, and Pseudomonas were the abundant genera in the roots, stems and leaves. In the fruits, the bacterial endophytes varied in different compartments, with Enterobacter being enriched in the pericarp and seeds, Acinetobacter in the placenta, and Weissella in the jelly. The present data provide a comprehensive description of the tomato-associated bacterial community and will be useful for better understanding plant-microbe interactions and selecting suitable bacterial taxa for tomato production.
Stable and Practical AS Relationship Inference with ProbLink

Knowledge of the business relationships between Autonomous Systems (ASes) is essential to understanding the behavior of the Internet routing system. Despite significant progress in the development of sophisticated relationship inference algorithms, the resulting datasets are impractical for many critical real-world applications, cannot offer adequate predictability in the configuration of routing policies, and suffer from inference oscillations. To achieve more practical and stable relationship inferences we first illuminate the root causes of the contradictions between these shortcomings and the near-perfect validation results of AS-Rank, the state-of-the-art relationship inference algorithm. Using a "naive" inference approach as a benchmark, we find that the available validation datasets over-represent AS links with easier inference requirements. We identify which types of links are harder to infer, and we develop appropriate validation subsets to enable more representative evaluation. We then develop a probabilistic algorithm, ProbLink, to overcome the inference barriers for hard links, such as non-valley-free routing, limited visibility, and non-conventional peering practices. To this end, we identify key interconnection features that provide stochastically informative and highly predictive relationship inference signals. Compared to AS-Rank, our approach reduces the error rate for all links by 1.6\times×, and importantly, by up to 6.1 times for different types of hard links. We demonstrate the practical significance of our improvements by evaluating their impact on three applications. Compared to the current state-of-the-art, ProbLink increases the precision and recall of route leak detection by 4.1 times and 3.4 times respectively, reveals 27% more complex relationships, and increases the precision of predicting the impact of selective advertisements by 34%.
Monoxide: Scale out Blockchains with Asynchronous Consensus Zones

Cryptocurrencies have provided a promising infrastructure for pseudonymous online payments. However, low throughput has significantly hindered the scalability and usability of cryptocurrency systems for increasing numbers of users and transactions. Another obstacle to achieving scalability is the requirement for every node to duplicate the communication, storage, and state representation of the entire network. In this paper, we introduce the Asynchronous Consensus Zones, which scales blockchain system linearly without compromising decentralization or security. We achieve this by running multiple independent and parallel instances of single-chain consensus systems termed as zones. The consensus happens independently within each zone with minimized communication, which partitions the workload of the entire network and ensures a moderate burden for each individual node as the network grows. We propose eventual atomicity to ensure transaction atomicity across zones, which achieves the efficient completion of transactions without the overhead of a two-phase commit protocol. Additionally, we propose Chu-ko-nu mining to ensure the effective mining power in each zone to be at the same level of the entire network, making an attack on any individual zone as hard as that on the full network. Our experimental results show the effectiveness of our work: on a testbed including 1,200 virtual machines worldwide to support 48,000 nodes, our system delivers 1,000× throughput and 2,000× capacity over the Bitcoin and Ethereum networks.
End-to-end I/O Monitoring on Leading Supercomputers

This paper offers a solution to overcome the complexities of production system I/O performance monitoring. We present Beacon, an end-to-end I/O resource monitoring and diagnosis system for the 40960-node Sunway TaihuLight supercomputer, currently the fourth-ranked supercomputer in the world. Beacon simultaneously collects and correlates I/O tracing/profiling data from all the compute nodes, forwarding nodes, storage nodes, and metadata servers. With mechanisms such as aggressive online and offline trace compression and distributed caching/storage, it delivers scalable, low-overhead, and sustainable I/O diagnosis under production use. With Beacon’s deployment on TaihuLight for more than three years, we demonstrate Beacon’s effectiveness with real-world use cases for I/O performance issue identification and diagnosis. It has already successfully helped center administrators identify obscure design or configuration flaws, system anomaly occurrences, I/O performance interference, and resource under- or over-provisioning problems. Several of the exposed problems have already been fixed, with others being currently addressed. Encouraged by Beacon’s success in I/O monitoring, we extend it to monitor interconnection networks, which is another contention point on supercomputers. In addition, we demonstrate Beacon’s generality by extending it to other supercomputers. Both Beacon codes and part of collected monitoring data are released.1
Software Wear Management for Persistent Memories

The commercial release of byte-addressable persistent memories (PMs) is imminent. Unfortunately, these devices suffer from limited write endurance—without any wear management, PM lifetime might be as low as 1.1 months. Existing wear-management techniques introduce an additional indirection layer to remap memory across physical frames and require hardware support to track ﬁne-grain wear. These mechanisms incur storage overhead and increase access latency and energy consumption. We present Kevlar , an OS-based wear-management technique for PM that requires no new hardware. Kevlar uses existing virtual memory mechanisms to remap pages, enabling it to perform both wear leveling —shufﬂing pages in PM to even wear; and wear reduction —transparently migrating heavily written pages to DRAM. Crucially, Kevlar avoids the need for hardware support to track wear at ﬁne grain. Instead, it relies on a novel wear-estimation technique that builds upon Intel’s Precise Event Based Sampling to approximately track processor cache contents via a software-maintained Bloom ﬁl-ter and estimate write-back rates at ﬁne grain. We implement Kevlar in Linux and demonstrate that it achieves lifetime improvement of 18.4 × (avg.) over no wear management while incurring 1.2% performance overhead.
Validation of two frailty questionnaires in older patients with rheumatoid arthritis; a cross-sectional study.

OBJECTIVES Several questionnaires exist to assess frailty, a geriatric syndrome. None of these has been validated in older patients with rheumatoid arthritis (RA). Our objective was to assess aspects of validity of two frailty questionnaires: Groningen Frailty Indicator (GFI) and Geriatric 8 (G8) among RA patients. METHODS In a cross-sectional study among patients ≥65 years information was collected on socio-demographics, disease characteristics including comorbidities and physical function and on frailty using the GFI and G8. Content validity was assessed by linking items of the GFI and G8 to the International Classification of Functioning, Disability and Health (ICF). Classic psychometric methods were used to test hypotheses on construct validity and interpretability. RESULTS Eighty patients (74.6 years (SD 5.9); 66% female) participated. The GFI has more items on social and mental functions; the G8 more on functions of the digestive system (e.g. nutritional status). As hypothesised, correlations (r) with physical function (RGFI=0.54; RG8=0.56) and disease activity (RGFI=0.24; RG8=0.36) were moderate to weak. However, correlations with age (RGFI=0.20; RG8=0.11) or comorbidities (RGFI=0.30; RG8=0.16) were lower than expected. Instrument-specific thresholds classified 43 (54%) of participants as frail on the GFI and 44 (55%) on the G8; 33 (41%) were frail on both instruments. CONCLUSIONS The GFI and G8 differ in content with more emphasis on nutritional status for the G8. Both instruments are insensitive to age and comorbidities. Before deciding on their usefulness in RA, their predictive validity for mortality and resource utilisation independent of disease activity and physical function should be further evaluated.
Reliability and validity of the Arabic translation of the palliative performance scale

Abstract Objective The aim of this study was to translate the Palliative Performance Scale (PPSv2) into Arabic and to test the reliability and validity of the PPS Arabic translation (PPS-Arabic). Method The PPSv2 was translated into Modern Standard Arabic using a forward–backward method. Inter-rater and intra-rater reliabilities were tested in a pilot study that included 20 patients. The validation study included 150 cancer patients. Patients were divided according to their treatment plan into three groups (in-remission, palliative chemotherapy, and best supportive care) to perform hypothesis-testing construct validity. Validity was further evaluated by correlating PPS-Arabic with the Karnofsky Performance Scale (KPS), the Eastern Cooperative Oncology Group (ECOG) scale, and Physical Functioning (PF2) and Role Functioning (RF2) scales of the European Organization for Research and Treatment of Cancer quality of life questionnaire (EORTC QLQ-C30). Results The intraclass correlation coefficients for the intra-rater and inter-rater reliability were 0.935 (95% CI: 0.88–0.965; p < 0.001) and 0.965 (95% CI: 0.934–0.981; p < 0.001), respectively. The PPS-Arabic internal consistency Cronbach's alpha was 0.986. The average PPS-Arabic score differed significantly (p < 0.001) between the three groups of patients being 89 for in-remission, 58 for palliative chemotherapy, and 38 for best supportive care. The PPS-Arabic score correlated significantly (p < 0.001) with the KPS, ECOG performance scale, and the EORTC QLQ-C30 PF2 and RF2 scales. Conclusion The PPS-Arabic is a reliable and valid tool for the assessment of performance status of cancer patients.
Concerning gamer identity: An examination of individual factors associated with accepting the label of gamer

This study examined characteristics of players that self-identified as gamers. Participants (N=476) were asked to complete an online survey and provide information about their video game play. Analyses of the survey responses found support for gamers being younger, men, and playing more. We also found that some of the genres of play and technology used diverged from previous research. The two most surprising findings were that gamers preferred to play on consoles more than on computers, and massive-multiplayer online games were not the most played genre. This paper contributed to research in three ways: previous assumptions surrounding gamer identity and demographics were tested, the genre of games and method of play were examined to refine the definition of a gamer, and the implications of gamer identity were discussed.
Epitranscriptomic marks: Emerging modulators of RNA virus gene expression

Epitranscriptomics, the study of posttranscriptional chemical moieties placed on RNA, has blossomed in recent years. This is due in part to the emergence of high‐throughput detection methods as well as the burst of discoveries showing biological function of select chemical marks. RNA modifications have been shown to affect RNA structure, localization, and functions such as alternative splicing, stabilizing transcripts, nuclear export, cap‐dependent and cap‐independent translation, microRNA biogenesis and binding, RNA degradation, and immune regulation. As such, the deposition of chemical marks on RNA has the unique capability to spatially and temporally regulate gene expression. The goal of this article is to present the exciting convergence of the epitranscriptomic and virology fields, specifically the deposition and biological impact of N7‐methylguanosine, ribose 2′‐O‐methylation, pseudouridine, inosine, N6‐methyladenosine, and 5‐methylcytosine epitranscriptomic marks on gene expression of RNA viruses.
Association of homocysteine with carotid-femoral pulse wave velocity in a southern Chinese population

This study aimed to investigate whether plasma homocysteine levels were associated with carotid-femoral pulse wave velocity (cfPWV), a golden standard of arterial stiffness, in a population from southern China. A cross-sectional study was conducted on 713 patients admitted to the First Affiliated Hospital of Fujian Medical University from February 2016 to August 2017. They were divided into four groups based on gender-specific quartile of homocysteine levels. Age, cfPWV, uric acid levels, and percentage of hypertension increased with ascending quartiles. The duration of hypertension and systolic blood pressure were higher in the highest quartile than in the lowest quartile. Pearson’s correlation analysis and multivariate regression showed a correlation of homocysteine levels with cfPWV. A nearly twofold increased risk of cfPWV ≥10 m/s was observed in the highest quartile compared with the lowest quartile (in the highest quartile: odds ratio = 2.917, 95% confidence interval: 1.635–5.202, P < 0.001). After stratification, this correlation was present in both sexes, in patients aged over 65 years, and those with hypertension. The plasma homocysteine levels were independently associated with cfPWV in the population from southern China, especially in the elderly and those with hypertension.
Absorbing Knowledge from and with External Partners: The Role of Social Integration Mechanisms

Dynamic capabilities that enable innovation are crucial to survival and success in today's highly competitive business environment, because they enable organizational adaptation, transformation, and seizing of opportunities. Absorptive capacity is an important dynamic capability that enables organizations to leverage external knowledge for innovation purposes. In this theory-building article, we address the fundamental research question of how organizations can leverage external partners as external sources of knowledge. We offer three primary contributions to the literature on managerial decision-making. First, by conceptualizing knowledge absorption as a collaborative, interorganizational endeavor, we extend the literature on absorptive capacity, thereby enabling its application to innovation-related contexts aside from R&D, to which it has traditionally been applied. Second, by focusing on social integration mechanisms as links between the capabilities, expertise, and knowledge of individuals, groups, and the organization as a whole, we heed calls to clarify the microfoundations of organizational capabilities. Third, although social integration is a multidimensional construct, few studies have addressed the influence of its individual dimensions. We outline how individual social integration dimensions exert differing influences on the individual knowledge absorption stages, thereby taking a first step toward unraveling the multidimensional nature of social integration and laying the foundation for future social integration research both in and beyond the absorptive capacity context.
A tailored cognitive behavioral program for juvenile justice-referred females at risk of substance use and delinquency: A pilot quasi-experimental trial

This pilot quasi-experimental trial tested a gender-responsive cognitive behavioral group intervention with 87 court-involved female adolescents (5 juvenile courts) who were at indicated risk for substance use disorder. Participants in the intervention (n = 57) received twice weekly group sessions for 10 weeks (20 sessions) focused on building emotional, thought and behavior regulation skills and generalizing these skills to relationally-based scenarios (GOAL: Girls Only Active Learning). Youth in the control condition (n = 30) received services as usual, which included non-gender-specific aggression management training, individual counseling and no services. The GOAL program was found to be acceptable to youth and parents and feasible to implement within a juvenile court setting using skilled facilitators. Compared to services as usual, the program significantly and meaningfully reduced self-reported delinquent behavior (β = 0.84, p < 0.05) over 6 months, and exhibited trend level effects for reduced substance use (β = 0.40, p = 0.07). The program had mixed or no effects on family conflict and emotion regulation skills. These findings are discussed in light of treatment mechanisms and gender-responsive services.
Tinnitus Correlates with Downregulation of Cortical Glutamate Decarboxylase 65 Expression But Not Auditory Cortical Map Reorganization

Hearing loss is the biggest risk factor for tinnitus, and hearing-loss-related pathological changes in the auditory pathway have been hypothesized as the mechanism underlying tinnitus. However, due to the comorbidity of tinnitus and hearing loss, it has been difficult to differentiate between neural correlates of tinnitus and consequences of hearing loss. In this study, we dissociated tinnitus and hearing loss in FVB mice, which exhibit robust resistance to tinnitus following monaural noise-induced hearing loss. Furthermore, knock-down of glutamate decarboxylase 65 (GAD65) expression in auditory cortex (AI) by RNA interference gave rise to tinnitus in normal-hearing FVB mice. We found that tinnitus was significantly correlated with downregulation of GAD65 in the AI. By contrast, cortical map distortions, which have been hypothesized as a mechanism underlying tinnitus, were correlated with hearing loss but not tinnitus. Our findings suggest new strategies for the rehabilitation of tinnitus and other phantom sensation, such as phantom pain. SIGNIFICANCE STATEMENT Hearing loss is the biggest risk factor for tinnitus in humans. Most animal models of tinnitus also exhibit comorbid hearing loss, making it difficult to dissociate the mechanisms underlying tinnitus from mere consequences of hearing loss. Here we show that, although both C57BL/6 and FVB mice exhibited similar noise-induced hearing threshold increase, only C57BL/6, but not FVB, mice developed tinnitus following noise exposure. Although both strains showed frequency map reorganization following noise-induced hearing loss, only C57BL/6 mice had reduced glutamate decarboxylase 65 (GAD65) expression in the auditory cortex (AI). Knocking down GAD65 expression in the AI resulted in tinnitus in normal-hearing FVB mice. Our results suggest that reduced inhibitory neuronal function, but not sensory map reorganization, underlies noise-induced tinnitus.
CAUDIT: Continuous Auditing of SSH Servers To Mitigate Brute-Force Attacks

This paper describes CAUDIT 1 , an operational system deployed at the National Center for Supercomputing Applications (NCSA) at the University of Illinois. CAUDIT is a fully automated system that enables the identiﬁcation and exclusion of hosts that are vulnerable to SSH brute-force attacks. Its key features include: 1) a honeypot for attracting SSH-based attacks over a /16 IP address range and extracting key meta-data (e.g., source IP, password, SSH-client version, or key ﬁngerprint) from these attacks; 2) executing audits on the live production network by replaying of attack attempts recorded by the honeypot; 3) using the IP addresses recorded by the honeypot to block SSH attack attempts at the network border by using a Black Hole Router (BHR) while signiﬁcantly reducing the load on NCSA’s security monitoring system; and 4) the ability to inform peer sites of attack attempts in real-time to ensure containment of coordinated attacks. The system is composed of existing techniques with custom-built components, and its novelty is its ability to execute at a scale that has not been validated earlier (with thousands of nodes and tens of millions of attack attempts per day). Experience over 463 days shows that CAUDIT successfully blocks an average of 57 million attack attempts on a daily basis using the proposed BHR. This represents a 66 × reduction in the number of SSH attempts compared to the daily average and has reduced the trafﬁc to the NCSA’s internal network-security-monitoring infrastructure by 78%.
Understanding Lifecycle Management Complexity of Datacenter Topologies

Most recent datacenter topology designs have focused on performance properties such as latency and throughput. In this paper, we explore a new dimension, life cycle management complexity, which attempts to understand the complexity of deploying a topology and expanding it. By analyzing current practice in lifecycle management, we devise complexity metrics for lifecycle management, and show that existing topology classes have low lifecycle management complexity by some measures, but not by others. Motivated by this, we design a new class of topologies, FatClique, that, while being performance-equivalent to existing topologies, is comparable to, or better than them by all our lifecycle management complexity metrics.
Efficient frequent subgraph mining on large streaming graphs

We propose an efﬁcient, approximate algorithm to solve the problem of ﬁnding frequent subgraphs in large streaming graphs. The graph stream is treated as batches of labeled nodes and edges. Our proposed algorithm ﬁnds the set of frequent subgraphs as the graph evolves after each batch. The computational complexity is bounded to linear limits by looking only at the changes made by the most recent batch, and the historical set of frequent subgraphs. As a part of our approach, we also propose a novel sampling algorithm that samples regions of the graph that have been changed by the most recent update to the graph. The performance of the proposed approach is evaluated using ﬁve large graph datasets, and our approach is shown to be faster than the state of the art large graph miners while maintaining their accuracy. We also compare our sampling algorithm against a well known sampling algorithm for network motif mining, and show that our sampling algorithm is faster, and capable of discovering more types of patterns. We provide theoretical guarantees of our algorithm’s accuracy using the well known Chernoff bounds, as well as an analysis of the computational complexity of our approach.