Miracle-dz/UniFAR-FTUs huggingface dataset:
OS scheduling with nest: keeping tasks close together on warm cores

To best support highly parallel applications, Linux's CFS scheduler tends to spread tasks across the machine on task creation and wakeup. It has been observed, however, that in a server environment, such a strategy leads to tasks being unnecessarily placed on long-idle cores that are running at lower frequencies, reducing performance, and to tasks being unnecessarily distributed across sockets, consuming more energy. In this paper, we propose to exploit the principle of core reuse, by constructing a nest of cores to be used in priority for task scheduling, thus obtaining higher frequencies and using fewer sockets. We implement the Nest scheduler in the Linux kernel. While performance and energy usage are comparable to CFS for highly parallel applications, for a range of applications using fewer tasks than cores, Nest improves performance 10%--2× and can reduce energy usage.
DAMYSUS: streamlined BFT consensus leveraging trusted components

Recently, streamlined Byzantine Fault Tolerant (BFT) consensus protocols, such as HotStuff, have been proposed as a means to circumvent the inefficient view-changes of traditional BFT protocols, such as PBFT. Several works have detailed trusted components, and BFT protocols that leverage them to tolerate a minority of faulty nodes and use a reduced number of communication rounds. Inspired by these works we identify two basic trusted services, respectively called the Checker and Accumulator services, which can be leveraged by streamlined protocols. Based on these services, we design Damysus, a streamlined protocol that improves upon HotStuff's resilience and uses less communication rounds. In addition, we show how the Checker and Accumulator services can be adapted to develop Chained-Damysus, a chained version of Damysus where operations are pipelined for efficiency. We prove the correctness of Damysus and Chained-Damysus, and evaluate their performance showcasing their superiority compared to previous protocols.
SafePM: a sanitizer for persistent memory

Memory safety violation is a major root cause of reliability and security issues in software systems. Byte-addressable persistent memory (PM), just like its volatile counterpart, is also susceptible to memory safety violations. While there is a couple of decades of work in ensuring memory safety for programs based on volatile memory, the existing approaches are incompatible for PM since the PM programming model introduces a persistent pointer representation for persistent memory objects and allocators, where it is imperative to design a crash consistent safety mechanism. We introduce SafePM, a memory safety mechanism that transparently and comprehensively detects both spatial and temporal memory safety violations for PM-based applications. SafePM's design builds on a shadow memory approach, and augments it with crash consistent data structures and system operations to ensure memory safety even across system reboots and crashes. We implement SafePM based on the AddressSanitizer compiler pass, and integrate it with the PM development kit (PMDK) runtime library. We evaluate SafePM across three dimensions: overheads, effectiveness, and crash consistency. SafePM overall incurs reasonable overheads while providing comprehensive memory safety, and has uncovered real-world bugs in the widely-used PMDK library.
High performance GPU concurrent B+tree

Concurrent B+trees have been widely used in many systems from file systems to databases. With the volume of data requests expanding exponentially, the systems are facing tremendous performance pressure. GPUs have shown their potential to accelerate the concurrent B+trees operations with their high volume of parallel computing resources and large memory bandwidth. In concurrent B+tree, the conflicts should be detected and resolved when multiple concurrent requests are traversing and operating on the tree. However, conflict detection and handling in concurrent B+tree complicates the request processing logic, increases the number of memory accesses and leads to execution path divergence. That leads to performance degradation and increased response time variance. We present a high performance GPU concurrent B+tree. To reduce the performance impact introduced by conflict detection, an optimization is proposed to detect and resolve key conflicts before concurrent requests are issued to the execution phase. Then another optimization is used to reduce structure conflicts and concurrent control overheads. Finally, an optimization is used to reduce structure conflicts and improve memory performance by exploiting the locality among requests. Evaluations on a TITAN V GPU show that our GPU concurrent B+tree is efficient with a throughput of 1.23 billion per second. Compared to a state-of-the-art GPU B+tree system, it can achieve 5.1X speedup and reduce the response time variance from 38% to 4%.
Hybrid anomaly detection and prioritization for network logs at cloud scale

Monitoring the health of large-scale systems requires significant manual effort, usually through the continuous curation of alerting rules based on keywords, thresholds and regular expressions, which might generate a flood of mostly irrelevant alerts and obscure the actual information operators would like to see. Existing approaches try to improve the observability of systems by intelligently detecting anomalous situations. Such solutions surface anomalies that are statistically significant, but may not represent events that reliability engineers consider relevant. We propose ADEPTUS, a practical approach for detection of relevant health issues in an established system. ADEPTUS combines statistics and unsupervised learning to detect anomalies with supervised learning and heuristics to determine which of the detected anomalies are likely to be relevant to the Site Reliability Engineers (SREs). ADEPTUS overcomes the labor-intensive prerequisite of obtaining anomaly labels for supervised learning by automatically extracting information from historic alerts and incident tickets. We leverage ADEPTUS for observability in the network infrastructure of IBM Cloud. We perform an extensive real-world evaluation on 10 months of logs generated by tens of thousands of network devices across 11 data centers and demonstrate that ADEPTUS achieves higher alerting accuracy than the rule-based log alerting solution, curated by domain experts, used by SREs daily.
On-farm Implementation of Midseason Drainage to Decrease Greenhouse Gas Emissions and Grain Arsenic Concentration in Rice Systems

Rice (Oryza sativa L.) is an important staple crop throughout much of the world, however, it is also a significant source of agricultural methane (CH4) emissions and exposure to arsenic (As). Introduction of soil aerobic events through practices such as alternate wetting and drying or midseason drainage, in flooded rice systems can significantly decrease grain As concentration and seasonal CH4 emissions. Previous on small research plots research has shown that a single midseason drain accomplishes these goals without yield reduction, but the degree of benefit depends on soil-drying severity. A midseason drain also has the potential to fit in well within current management practices of California rice systems, however, it has not been tested across a wide range of soil types or at a scale that farmers typically manage in this region. Therefore, in this three-year study, we aimed to determine if the results from previous small plot research are similar to what can be expected on-farm. At seven on-farm trials we implemented a single midseason drain and compared the grain yields, GHG emissions, and As concentration to the traditional farmer practice (FP) practiced in an adjacent part of the field. Soil moisture parameters [perched water table, volumetric water content, gravimetric water content (GWC), and soil water potential], CH4 and nitrous oxide (N2O) emissions, grain As and cadmium concentration, and grain yield were quantified. Across site-years, midseason drainage reduced seasonal CH4 emissions by 20-77%, compared to the FP control with the magnitude of reduction related to the soil-drying severity. For every 1% reduction in soil GWC during the drainage period, CH4 emissions were reduced by approximately 3.2%, compared to 2.5% in previous on-station research using small plots. Midseason drainage increased N2O emissions (average = 0.248 kg N2O-N ha-1) compared to the control but this accounted for only 3% of the seasonal global warming potential across all drainage treatments. Drainage also decreased grain As concentration by approximately 20%, on average, but was not related to the degree of soil-drying. Importantly, midseason drainage had no significant impact on grain yields. Overall, these results confirm findings from previous on-station research, indicating that midseason drainage may be a viable on-farm management practice for GHG mitigation and for reducing grain As concentration in flooded rice fields with limited risk of yield reduction.
Candida albicans Filamentation Does Not Require the cAMP-PKA Pathway In Vivo

The fungus Candida albicans causes a wide range of disease in humans from common diaper rash to life-threatening infections in patients with compromised immune systems. As such, the mechanisms for its ability to cause disease are of wide interest. ABSTRACT Candida albicans is one of the most prevalent human fungal pathogens. Its ability to transition between budding yeast and filamentous morphological forms (pseudohyphae and hyphae) is tightly associated with its pathogenesis. Based on in vitro studies, the cAMP-protein kinase A (PKA) pathway is a key regulator of C. albicans morphogenesis. Using an intravital imaging approach, we investigated the role of the cAMP-PKA pathway during infection. Consistent with their roles in vitro, the downstream effectors of the cAMP-PKA pathway Efg1 and Nrg1 function, respectively, as an activator and a repressor of in vivo filamentation. Surprisingly, strains lacking the adenylyl cyclase, CYR1, showed only slightly reduced filamentation in vivo despite being completely unable to filament in RPMI + 10% serum at 37°C. Consistent with these findings, deletion of the catalytic subunits of PKA (Tpk1 and Tpk2), either singly or in combination, generated strains that also filamented in vivo but not in vitro. In vivo transcription profiling of C. albicans isolated from both ear and kidney tissue showed that the expression of a set of 184 environmentally responsive genes correlated well with in vitro filamentation (R2, 0.62 to 0.68) genes. This concordance suggests that the in vivo and in vitro transcriptional responses are similar but that the upstream regulatory mechanisms are distinct. As such, these data emphatically emphasize that C. albicans filamentation is a complex phenotype that occurs in different environments through an intricate network of distinct regulatory mechanisms. IMPORTANCE The fungus Candida albicans causes a wide range of disease in humans from common diaper rash to life-threatening infections in patients with compromised immune systems. As such, the mechanisms for its ability to cause disease are of wide interest. An intensely studied virulence property of C. albicans is its ability to switch from a round yeast form to filament-like forms (hyphae and pseudohyphae). Surprisingly, we have found that a key signaling pathway that regulates this transition in vitro, the protein kinase A pathway, is not required for filamentation during infection of the host. Our work not only demonstrates that the regulation of filamentation depends upon the specific environment C. albicans inhabits but also underscores the importance of studying these mechanisms during infection.
Classifying gene coexpression networks using discriminative pattern mining

Several algorithms for graph classification have been proposed. Algorithms that map graphs into feature vectors encoding the presence/absence of specific subgraphs, have shown excellent performance. Most of the existing algorithms mine for subgraphs that appear frequently in graphs belonging to one class label and not so frequently in the other graphs. Gene coexpression networks classification attracted a lot of attention in the recent years from researchers in both biology and data mining because of its numerous useful applications. The advances in high-throughput technologies that provide an easy access to large microarray datasets necessitated the development of new techniques that can scale well with large datasets and produce a very accurate results. In this thesis, we propose a novel approach for mining discriminative patterns. We propose two algorithms for mining discriminative patterns and then we use these patterns for graph classification. Experiments on large coexpression graphs show that the proposed approach has excellent performance and scales to graphs with millions of edges. We compare our proposed algorithm to two baseline algorithms and we show that our algorithm outperforms the baseline techniques with a very high accurate graph classification. Moreover, we perform topological and biological enrichment analysis on the discriminative patterns reported by our mining algorithm and we show that the reported patterns are significantly enriched.
Isolation of Biofilm-Forming Bacteria from the Secondary Effluent of the Wastewater Treatment Plant and its Ability to Produce N-Acylhomoserine Lactone as Quorum Sensing Signal

Bacterial quorum sensing (QS) is one of the cell-to-cell communication systems. N-Acyl-homoserine lactones (AHLs) are the most common QS signals and responsible for biofilm formation in gram-negative bacteria. Inactivation of QS, also referred to as quorum quenching, has been regarded as a popular strategy to control membrane bioreactor (MBR) operations because biofouling in MBR wastewater treatment systems is often caused by biofilm formation. In the present study, 24 bacterial strains were isolated from the secondary effluent of a wastewater treatment plant and AHL productivity and biofilm formation were evaluated on 8 out of 24 isolates. The isolated 8 strains can produce AHLs that only possess a long (C8-C14) acyl side chain. The representative 3 strains were selected from these isolates based on the higher activity of biofilm formation. The AHL separation analysis with a thin layer chromatography clearly showed that N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexanoyl-L-homoserine lactone (C6-HSL) existed in the secondary effluent sample, while no C6-HSL producing strain was isolated. C8-HSL was identified as the product of isolate No. 6. These results suggest that the secondary effluent probably contains various cell-to-cell signaling molecules derived not only from the inhabitants but also from the other microorganisms involved in the activated sludge for the biological pre-treatment. In this secondary effluent, AHL trapping techniques can be proposed as one of the acceptable strategies for the control of the QS systems because the remaining AHLs have relatively long acyl side chain and low concentrations.
The role of the university in accelerated learning and innovation as a regional ecosystem integrator

Purpose The purpose of this paper is to present an adaptation of a program that is at the intersection of two dynamic force fields. The first relates to imperatives impinging upon and inherent in higher education. The second ties to the concept of ecosystems as spaces for aligning actors and resources to create value. Design/methodology/approach Tables I-III present pre-test and post-test means and p-values for the paired sample t-tests for the measures. Findings As expected, post-test means are consistently significantly higher (or lower depending on item wording) for a shift in beliefs away from self-censoring and prejudging ideas during ideation and more toward greater openness in the ideation process. Originality/value The paper examines the outcome of an educational program.
Six-Month Impairment in Cognition, Mental Health, and Physical Function Following COVID-19–Associated Respiratory Failure

OBJECTIVES: To determine the prevalence and extent of impairments impacting health-related quality of life among survivors of COVID-19 who required mechanical ventilation, 6 months after hospital discharge. DESIGN: Multicenter, prospective cohort study, enrolling adults 18 years old or older with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 infection who received mechanical ventilation for 48 hours or more and survived to hospital discharge. Eligible patients were contacted 6 months after discharge for telephone-based interviews from March 2020 to December 2020. Assessments included: Montreal Cognitive Assessment-Blind, Hospital Anxiety and Depression Scale, Impact of Event Scale-6, EuroQOL 5 domain quality-of-life questionnaire, and components of the Multidimensional Dyspnea Profile. SETTING: Two tertiary academic health systems. PATIENTS: Of 173 eligible survivors, a random sample of 63 were contacted and 60 consented and completed interviews. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Mean age was 57 + 13 years and mean duration of invasive mechanical ventilation was 14 + 8.2 days. Six months post-discharge, 48 patients (80%; 95% CI, 68–88%) met criteria for post-intensive care syndrome (PICS), with one or more domains impaired. Among patients with PICS, 28 (47%; 95% CI, 35–59%) were impaired in at least 2 domains, and 12 (20%; 95% CI, 12–32%) impaired in all three domains. Significant symptoms of post-traumatic stress were present in 20 patients (33%; 95% CI, 23–46%), anxiety in 23 (38%; 95% CI, 27–51%), and depression in 25 (42%; 95% CI, 30–54%). Thirty-three patients (55%; 95% CI, 42–67%) had impairments in physical activity; 25 patients (42%; 95% CI, 30–54%) demonstrated cognitive impairment. CONCLUSIONS: Eighty percent of COVID-19 survivors who required mechanical ventilation demonstrated PICS 6 months after hospital discharge. Patients were commonly impaired in multiple PICS domains as well as coexisting mental health domains.
Regarding Care Giving Family Members Stray Radiation Exposures from Discharged Patients after Administration of Large Dose Therapeutic Radioactive Iodine in Differentiated Carcinoma Thyroid

An interesting article is published[1] on the measured radiation exposures by the care givers to discharged cancer thyroid‐treated patients after administration of high doses of Iodine‐131. In the Paper introduction, 5 mSv (500 mRem) is wrongly printed as 5 mSv/h (500 mRem/h), 0.05 mSv/h (50 mR/h) misleading the readers. The authors estimated whole body doses to care givers of 22 discharged cancer thyroid patients who received radioactive I‐131 3.79 ± 1.07GBq (range 1.85–5.55 [50–150 mCi]).
Central Heating System Optimization

Optimization of a building, the only requirement is to promote the welfare and quality of life without increasing costs. Among the components of energy consumption in buildings, heating systems that use more fossil fuels. Are major consumers of energy, because 70% of Iran's natural gas consumption is allocated to heating buildings. Due to various factors that contribute to the building heating energy consumption, the guidelines provide savings in buildings and reducing energy consumption in the domestic sector, will affect the frequency. Climate and weather, architecture, building, building materials, efficient heating systems, using equipment with the capacity required, the amount of time in building thermal control systems are effective and also efficient heating of the heating energy consumption are considered. In this paper a complete analysis system, central heating we are.
Gate automation system evaluation

Purpose This study has two purposes. The first is to identify the determinants influencing the selection of a container number recognition system via a quantitative method to thereby establish an evaluation structure. The second purpose is to conduct an empirical study to determine the weights of the criteria and alternatives. Design/methodology/approach The exploratory factor analysis (EFA) and fuzzy analytic hierarchy process (AHP) were applied to determine the evaluation structure and weights of the criteria and alternatives, respectively. Findings An empirical study based on a dedicated terminal at Keelung Port is conducted. The result demonstrates that the radio-frequency identification (RFID) system is a suitable system for the terminal under consideration in this study. Originality/value The value of this study is twofold. First, EFA was applied to extract common factors from a wide questionnaire survey, thereby establishing a hierarchical analysis structure. This method and comprehensive evaluation structure are useful references for both practitioners and researchers to deal with problems of gate automation. Second, fuzzy AHP was used to decide the weights of the hierarchical structure. The weights obtained by this method are more objective and rational as the imprecision expressions in returned samples have been considered and dealt with.
Leading and managing change

As the new year begins many of us would have reflected on the year that was and considered how we could improve processes and procedures in our schools. This can be an exciting and stimulating process if managed correctly. Even more exciting still, some of us will be moving into new schools and systems, however, managing the change process in a new work place is a very daunting prospect. I am finding myself in the latter situation where I will be taking up a position in a school that has experienced rapid growth and with that comes significant change.
Economic analysis of oil production by applying steam-assisted gravity drainage (SAGD) to reservoirs from the Potiguar basin

ABSTRACT The steam-assisted gravity drainage (SAGD) is an enhanced oil recovery process, used successfully by many countries, such as Canada, United States, and Venezuela, where there are many bitumen and heavy oil reservoirs. The SAGD is a process that uses two parallel horizontal wells, one of them for injecting steam and the other to produce oil. This process has not been applied in Brazil yet, where there are many heavy oil reservoirs, especially in Brazilian Northeast. Motivated by this context, this research aimed at studying the application of the SAGD process in a semisynthetic reservoir, with characteristics similar to those found in the Brazilian Northeast. The steam injection rates and their net present value were analyzed, indicating that there is a limit for steam injection rate to reach a good efficiency and that limit presents economic viability, evidencing that it can be applied in Brazilian Northeast.
Research on Corrosion Protection of Buried Steel Pipeline

The corrosion types of buried steel pipelines were summarized from two aspects of internal corrosion and external corrosion; the main detection technology for internal and external corrosion was introduced; and the protective measures for corrosion and corrosion of buried steel pipelines were presented. The study of corrosion protection for buried steel pipeline provided the basis for the corrosion protection of buried steel pipeline.