Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of mitigating interventions and temperature on the instantaneous reproduction number in the COVID-19 epidemic among 30 US metropolitan areas

Background: After more than three months into the coronavirus disease (COVID-19) epidemic, over 170,000 people had died worldwide. The current study aims to evaluate how mitigating interventions affected the epidemic process in the 30 largest metropolitan areas in the US and whether temperature played a role in the epidemic process. Methods: Publicly available COVID-19 cases and deaths data and weather data were analyzed at the metropolitan level. The time-varying reproductive numbers were used to explore the trends. Results: We found that virus transmissibility, measured by instantaneous reproduction number (Rt), had declined significantly since the end of March for all areas and almost all of them reached a Rt of 1 or below by April 15, 2020. Cities with warm temperature tended to have a lower peak Rt than that of cities with cold temperature. However, large geographic variations exist. Conclusions: Though the end of epidemic of COVID-19 is near, temperature may have some weak effects on the virus transmission, and the return of the coronavirus outbreak is still possible.
Nefele: Process Orchestration for the Cloud

Virtualization, either at OS- or hardware level, plays an important role in cloud computing. It enables easier automation and faster deployment in distributed environments. While virtualized infrastructures provide a level of management flexibility, they lack practical abstraction of the distributed resources. A developer in such an environment still needs to deal with all the complications of building a distributed software system. Different orchestration systems are built to provide that abstraction; however, they do not solve the inherent challenges of distributed systems, such as synchronization issues or resilience to failures. This paper introduces Nefele, a decentralized process orchestration system that automatically deploys and manages individual processes, rather than containers/VMs, within a cluster. Nefele is inspired by the Single System Image (SSI) vision of mitigating the intricacies of remote execution, yet it maintains the flexibility and performance of virtualized infrastructures. Nefele offers a set of APIs for building cloud-native applications that lets the developer easily build, deploy, and scale applications in a cloud environment. We have implemented and deployed Nefele on a cluster in our datacenter and evaluated its performance. Our evaluations show that Nefele can effectively deploy, scale, and monitor processes across a distributed environment, while it incorporates essential primitives to build a distributed software system.
Contribution to the study of Agrocybe pediades complex (Agaricales) in Russia based on nrITS sequences

Agrocybe pediades is a rather widespread species mentioned in many Russian regional check-lists. However, there is no agreement among diff erent authors concerning the volume of this species. Some of them recognize single polymorphic species A. pediades with several intraspecies groups. In this case Agrocybe arenicola, A. semiorbicularis and A. subpediades are accepted as synonyms of A. pediades. Under another above-listed species are considered as a group of close but separate taxa. In this research the representatives of A. pediades species complex collected in diff erent parts of Russia have been studied using both molecular and morphological techniques. Th e analysis of nrITS1-5.8-ITS2 regions has revealed one large well supported clade consisting of specimens labeled before this study as Agrocybe arenicola, A. pediades, A. semiorbicularis and A. subpediades. Th is clade was characterized by the absence of the reliable morphological diff erences between included collections. Th e obtained results correspond to the wide species concept of A. pediades. Several small subclades have been also revealed inside the main clade. Most of them were inconstant with low bootstrap support in NJ, MP and ML analyses. Th ey were shown to belong presumably to A. pediades var. pediades. One subclade recovered in all analyses with high bootstrap support was characterized by some distinct morphological features and was considered afterwards as a new variety of A. pediades – var. bispora. Th erefore, all known so far Russian collections belong to A. pediades var. pediades and A. pediades var. bispora.
A Revision of the Leafhopper Genus Xyphon (Hemiptera: Cicadellidae)

The leafhopper genus Xyphon, included in the sharpshooters, is a widely distributed group of insects whose species are vectors for various plant diseases. Xyphon has historically contained up to 9 species. These species have been poorly delimited in the past and their identification has been difficult using published keys. The genus is revised here based on a new species level phylogenetic assessment that incorporates both morphological and molecular data. The genus Xyphon was erected to contain leafhoppers that possessed a reticulated forewing apex but lacked both a median sulcus on the crown and a carinate anterolateral crown-face margin both of which are present in the closely related genus Draeculacephala. Young (1977) revised most of the genera included in Xyphon's containing subfamily. He did not attempt a revision of Carneocephala (the genus that formerly contained most Xyphon species), but noted the need for a revision of its species. This revision of the genus Xyphon is based on the examination of approximately 8,000 specimens and includes a phylogenetic analysis of the genus that includes data from one gene (NDI) and 47 morphological characters. A generalized model of each preliminary taxonomic unit was used to test the monophyly of each species. These tests resulted in the synonomization of 4 former species: Xyphon gillettei to include X. balli; and X. reticulatum to include X. diductum, X. dyeri, and X. sagittiferum. Parsimony and Bayesian techniques were used to infer relationships among species. These analyses resulted in almost identical tree topologies. In all analyses Xyphon was monophyletic and Draeculacephala was its sister genus although clade support for the genus was generally low. The analyses found that X. flaviceps and X. fulgidum form a basal clade within Xyphon, above which X. gillettei and X. n. sp. 1 (new species 1) form a clade that is sister to a third clade containing X. triguttatum, X. nudum, and X. reticulatum.
Modeling Task Effects on Meaning Representation in the Brain via Zero-Shot MEG Prediction

How meaning is represented in the brain is still one of the big open questions in neuroscience. Does a word (e.g., bird) always have the same representation, or does the task under which the word is processed alter its representation (answering "can you eat it? " versus "can it fly? ")? The brain activity of subjects who read the same word while performing different semantic tasks has been shown to differ across tasks. However, it is still not understood how the task itself contributes to this difference. In the current work, we study Magnetoencephalography (MEG) brain recordings of participants tasked with answering questions about concrete nouns. We investigate the effect of the task (i.e. the question being asked) on the processing of the concrete noun by predicting the millisecond-resolution MEG recordings as a function of both the semantics of the noun and the task. Using this approach, we test several hypotheses about the task-stimulus interactions by comparing the zero-shot predictions made by these hypotheses for novel tasks and nouns not seen during training. We find that incorporating the task semantics significantly improves the prediction of MEG recordings, across participants. The improvement occurs 475-550ms after the participants first see the word, which corresponds to what is considered to be the ending time of semantic processing for a word. These results suggest that only the end of semantic processing of a word is task-dependent, and pose a challenge for future research to formulate new hypotheses for earlier task effects as a function of the task and stimuli.
Reliability-aware Garbage Collection for Hybrid HBM-DRAM Memories

Emerging workloads in cloud and data center infrastructures demand high main memory bandwidth and capacity. Unfortunately, DRAM alone is unable to satisfy contemporary main memory demands. High-bandwidth memory (HBM) uses 3D die-stacking to deliver 4–8× higher bandwidth. HBM has two drawbacks: (1) capacity is low, and (2) soft error rate is high. Hybrid memory combines DRAM and HBM to promise low fault rates, high bandwidth, and high capacity. Prior OS approaches manage HBM by mapping pages to HBM versus DRAM based on hotness (access frequency) and risk (susceptibility to soft errors). Unfortunately, these approaches operate at a coarse-grained page granularity, and frequent page migrations hurt performance. This article proposes a new class of reliability-aware garbage collectors for hybrid HBM-DRAM systems that place hot and low-risk objects in HBM and the rest in DRAM. Our analysis of nine real-world Java workloads shows that: (1) newly allocated objects in the nursery are frequently written, making them both hot and low-risk, (2) a small fraction of the mature objects are hot and low-risk, and (3) allocation site is a good predictor for hotness and risk. We propose RiskRelief, a novel reliability-aware garbage collector that uses allocation site prediction to place hot and low-risk objects in HBM. Allocation sites are profiled offline and RiskRelief uses heuristics to classify allocation sites as DRAM and HBM. The proposed heuristics expose Pareto-optimal trade-offs between soft error rate (SER) and execution time. RiskRelief improves SER by 9× compared to an HBM-Only system while at the same time improving performance by 29% compared to a DRAM-Only system. Compared to a state-of-the-art OS approach for reliability-aware data placement, RiskRelief eliminates all page migration overheads, which substantially improves performance while delivering similar SER. Reliability-aware garbage collection opens up a new opportunity to manage emerging HBM-DRAM memories at fine granularity while requiring no extra hardware support and leaving the programming model unchanged.
Effectiveness and safety of proton pump inhibitors for treating acute pancreatitis

Abstract Background: Previous studies have showed that anti-acid therapy with proton pump inhibitors (PPIs) can inhibit pancreatic secretion and it may be used in treating acute pancreatitis (AP). But at present, there is no systematic reviews for the evidence and the therapeutic effectiveness and safety of anti-acid therapy with PPIs in AP were not unclear. Therefore, we will undertake a systematic review of the literature to summarize previous evidence regarding this topic, in order to clarify the effectiveness and safety of anti-acid therapy with PPIs in AP. Methods: We will search the EMBASE, WANFANG DATA, Web of Knowledge, China National Knowledge Infrastructure, PubMed, ClinicalTrials.gov and Cochrane Library from inception to June 30,2021 to retrieve relevant studies using the search strategy: (“Proton pump inhibitors” OR “PPI” OR “PPIs” OR “Omeprazole” OR “Tenatoprazole” OR “Pantoprazole” OR “acid suppression therapy” OR “acid suppression drugs”) AND (“pancreatitis” OR “pancreatitides”). Two authors independently judged study eligibility and extracted data. Heterogeneity will be examined by computing the Q statistic and I2 statistic. Results: This study assessed the efficiency and safety of proton pump inhibitors for treating acute pancreatitis. Conclusions: This study will provide reliable evidence-based evidence for the clinical application of PPIs for treating AP. Ethics and dissemination: Ethical approval is unnecessary as this protocol is only for systematic review and does not involve privacy data. The findings of this study will be disseminated electronically through a peer-review publication or presented at a relevant conference.
An application of the SERVQUAL model to study the quality perceived by customers in a pizzeria

1. lucasoliveira2516@gmail.com, https://orcid.org/0000-0002-4862-9612; 2. Avenida Quirino, 1020. Cond. Recanto dos Guaras, Bloco 02, Apt. 102, Inácio Barbosa, Aracaju SE, CEP: 49040-700, Brasil, eng.prod. emerson@gmail.com; https://orcid.org/0000-0002-9233-0618; 3. emily.nadine. ufs@gmail.com, https://orcid.org/0000-0002-3663-5468; 4. gertrudes.dandolini@ufsc.br, https://orcid.org/0000-0003-0867-9495; 5. jartur@gmail.com, https://orcid.org0000-0002-7133-8944 SANTOS, L.O. ; MUNIZ, E.C. L. ; PEREIRA, E.N. ; DANDOLINI, G.A. ; SOUZA, J.A. An application of the SERVQUAL model to study the quality perceived by customers in a pizzeria GEPROS. Gestão da Produção, Operações e Sistemas, v.16, no 1, p. 01 22, 2021. DOI: http://dx.doi. org/10.15675/gepros.v16i1. 2339 Editor Responsável: Prof. Dr. Hermes Moretti Ribeiro da Silva
YjbH Requires Its Thioredoxin Active Motif for the Nitrosative Stress Response, Cell-to-Cell Spread, and Protein-Protein Interactions in <named-content content-type='genus-species'>Listeria monocytogenes</named-content>

Listeria monocytogenes is a model facultative intracellular pathogen. Tight regulation of virulence proteins is essential for a successful infection, and the gene encoding the annotated thioredoxin YjbH was identified in two forward genetic screens as required for virulence factor production. Accordingly, an L. monocytogenes strain lacking yjbH is attenuated in a murine model of infection. However, the function of YjbH in L. monocytogenes has not been investigated. Here, we provide evidence that L. monocytogenes YjbH is involved in the nitrosative stress response, likely through its interaction with the redox-responsive transcriptional regulator SpxA1. YjbH physically interacted with SpxA1, and our data support a model in which YjbH is a protease adaptor that regulates SpxA1 protein abundance. Wholecell proteomics identified eight additional proteins whose abundance was altered by YjbH, and we demonstrated that YjbH physically interacted with each in bacterial two-hybrid assays. Thioredoxin proteins canonically require active motif cysteines for function, but thioredoxin activity has not been tested for L. monocytogenes YjbH. We demonstrated that cysteine residues of the YjbH thioredoxin domain active motif are essential for L. monocytogenes sensitivity to nitrosative stress, cell-to-cell spread in a tissue culture model of infection, and several protein-protein interactions. Together, these results demonstrated that the function of YjbH in L. monocytogenes requires its thioredoxin active motif and that YjbH has a role in the posttranslational regulation of several proteins, including SpxA1. IMPORTANCE The annotated thioredoxin YjbH in Listeria monocytogenes has been implicated in virulence, but its function in the cell is unknown. In other bacterial species, YjbH is a protease adaptor that mediates degradation of the transcriptional regulator Spx. Here, we investigated the function of L. monocytogenes YjbH and demonstrated its role in the nitrosative stress response and posttranslational regulation of several proteins with which YjbH physically interacts, including SpxA1. Furthermore, we demonstrated that the cysteine residues of the YjbH thioredoxin active motif are required for the nitrosative stress response, cell-to-cell spread, and some protein-protein interactions. YjbH is widely conserved among Firmicutes, and this work reveals its unique requirement of the thioredoxin-active motif in L. monocy-
Phonetics of White Hmong vowel and tonal contrasts

Hmong languages, particularly White Hmong, are well studied for their complex tone systems that incorporate pitch, phonation, and duration differences. Still, prior work has made use mostly of tones elicited in their citation forms in carrier phrases. In this paper, we provide a detailed description of both the vowel and tone systems of White Hmong from recordings of read speech. We confirm several features of the language, including the presence of nasal vowels (rather than derived nasalized vowels through coarticulation with a coda [ŋ]), the description of certain tone contours, and the systematic presence of breathy and creaky voice on two of the tones. We also find little evidence of additional intonational f0 targets. However, we show that some tones vary greatly by their position in utterance, and propose novel descriptions for several of them. Finally, we show that $\textrm{H}1^{\! *}$ –H2*, a widely used measure of voice quality and phonation in Hmong and across languages, does not adequately distinguish modal from non-modal phonation in this data set, and argue that noise measures like Cepstral Peak Prominence (CPP) are more robust to phonation differences in corpora with more variability.
Mass Spectrometry based Approaches for Analysing Proteins in Processed Food and Feed

Food and feed traceability and authentication have become major societal issues, requiring adequate analytical approaches. Proteins in food and feed are of paramount importance for providing amino acids to humans and animals. Processing (in particular cooking at high temperature) and rendering, drastically affect proteins [1], leading to denaturation, amino acid modifications, cleavage and aggregation, hampering their extraction. That is why for characterizing food and feed, for their authentication in particular regarding the species origin, DNA-based methods were first developed, as well as alternative methods such as microscopy at least for Processed Animal Proteins (PAPs). Regarding the proteins, ELISAs have been proposed and even commercialised. However these approaches have shown their limitations: PCR-based approaches are highly discriminative for species, but can be problematic in complex matrices, frequent in food and feed and do not provide information about cell/tissue origin, which is a major issue in feed, given the mad cow disease epidemics. In food, in particular for allergenic proteins, which we will focus on, proteins are the target to monitor, and not DNA, and ELISAs at least for some proteins face the problem of cross-reactivity and low sensitivity. The developments in mass-spectrometry, but also in proteomics bioinformatics, computation and data mining over the last years (see for instance [2-4]), have paved the way for expanding peptidomic/proteomic approaches in food and feed characterization and authentication (for a recent review in food, [5]). Table 1 summarizes the possible MS based strategies in proteomics, with their characteristics, pros and cons, when searching for biomarkers. We will illustrate some of these approaches in food and feed proteomics. For the processed food, we will limit ourselves to allergenic proteins, which are a major health issue all over the word, while for feed we will focus on PAPs, in particular as by-products of pig and poultry breeding, since they are a convenient sustainable source of proteins for non-ruminants including farmed fish.
A rare case of postpartum ovarian vein thrombosis

Ovarian vein thrombosis is a rare but potentially fatal condition. The prevalence of postpartum ovarian vein thrombosis (POVT) is 0.05–0.18% in natural birth and 2% in birth by caesarean section. Other causes of ovarian vein thrombosis are abdominal surgeries and pelvic inflammatory disease. Rarely, it may have an idiopathic cause. Up to 90% of POVT occurs in the right ovarian vein. Complications include the extension of thrombus into the renal vein, inferior vene cava (IVC) and consequently, the pulmonary artery resulting in pulmonary embolism (PE). Clinically, POVT patients present with acute abdominal pain and fever, typically within 4–10 days post-partum. Due to the demographic of patients with POVT – young women of reproductive age and its non-specific clinical presentation, ultrasound is often the initial imaging study of choice. Moreover, POVT often causes right iliac fossa pain, which mimics more common pathologies such as appendicitis, ectopic pregnancy, pelvic infections and ovarian pathologies. However, previous studies have found ultrasound to have low accuracy and subsequent cross-sectional imaging such as computed tomography (CT) and magnetic resonance imaging (MRI) are commonly needed to diagnose this condition. This case study aims to increase sonographer awareness of POVT and its ultrasound appearance to avoid prolonged investigation and unnecessary intervention.
Mapping Soil Cation Exchange Capacity in a Semiarid Region through Predictive Models and Covariates from Remote Sensing Data

ABSTRACT: Planning sustainable use of land resources requires reliable information about spatial distribution of soil physical and chemical properties related to environmental processes and ecosystemic functions. In this context, cation exchange capacity (CEC) is a fundamental soil quality indicator; however, it takes money and time to obtain this data. Although many studies have been conducted to spatially quantify soil properties on various scales and in different environments, not much is known about interactions between soil properties and environmental covariates in [. ]
Horizontal Steering Control in Docking the ARIES AUV

Abstract : To keep the operational cost down and increase the mission time with minimum human intervention, autonomous recovery or docking operation of an Autonomous Underwater Vehicle (AUV) is required. Central to the successful autonomous docking process of the AUV is the capability of the AUV being able to track and steer itself accurately towards the dock which is constantly perturbed by wave motion effects. In addition, for accurate acoustic homing during the final stages of the docking, the AUV requires acoustic systems with high update rates. Equipped with acoustic modem, ARIES had experimentally been tested to have an update rate of only about 0.3 Hz. These delayed data can potentially cause a false commanded reference input to the tracking system in between the updates and cause ARIES to miss the moving cage's entrance. This thesis attempts to investigate the effectiveness on the use of cross track error and line of sight error sliding mode controller coupled with dynamic waypoints allocation in horizontal steering of ARIES in docking operations. In the absence of cage heading updates, a predictive method based on angular rate and direction of motion was used to estimate the dynamics of the moving cage. Further analysis was performed in order to understand the limitations of such an implementation.