Miracle-dz/UniFAR-FTUs huggingface dataset:
Working Set Size Estimation Techniques in Virtualized Environments

Energy consumption is a primary concern for datacenters? management. Numerous datacenters are relying on virtualization, as it provides flexible resource management means such as virtual machine (VM) checkpoint/restart, migration and consolidation. However, one of the main hindrances to server consolidation is physical memory. In nowadays cloud, memory is generally statically allocated to VMs and wasted if not used. Techniques (such as ballooning) were introduced for dynamically reclaiming memory from VMs, such that only the needed memory is provisioned to each VM. However, the challenge is to precisely monitor the needed memory, i.e., the working set of each VM. In this paper, we thoroughly review the main techniques that were proposed for monitoring the working set of VMs. Additionally, we have implemented the main techniques in the Xen hypervisor and we have defined different metrics in order to evaluate their efficiency. Based on the evaluation results, we propose Badis, a system which combines several of the existing solutions, using the right solution at the right time. We also propose a consolidation extension which leverages Badis in order to pack the VMs based on the working set size and not the booked memory. The implementation of all techniques, our proposed system, and the benchmarks we have used are publicly available in order to support further research in this domain.
Integrative Transcriptomic Analysis Uncovers Novel Gene Modules That Underlie the Sulfate Response in Arabidopsis thaliana

Sulfur is an essential nutrient for plant growth and development. Sulfur is a constituent of proteins, the plasma membrane and cell walls, among other important cellular components. To obtain new insights into the gene regulatory networks underlying the sulfate response, we performed an integrative meta-analysis of transcriptomic data from five different sulfate experiments available in public databases. This bioinformatic approach allowed us to identify a robust set of genes whose expression depends only on sulfate availability, indicating that those genes play an important role in the sulfate response. In relation to sulfate metabolism, the biological function of approximately 45% of these genes is currently unknown. Moreover, we found several consistent Gene Ontology terms related to biological processes that have not been extensively studied in the context of the sulfate response; these processes include cell wall organization, carbohydrate metabolism, nitrogen compound transport, and the regulation of proteolysis. Gene co-expression network analyses revealed relationships between the sulfate-responsive genes that were distributed among seven function-specific co-expression modules. The most connected genes in the sulfate co-expression network belong to a module related to the carbon response, suggesting that this biological function plays an important role in the control of the sulfate response. Temporal analyses of the network suggest that sulfate starvation generates a biphasic response, which involves that major changes in gene expression occur during both the early and late responses. Network analyses predicted that the sulfate response is regulated by a limited number of transcription factors, including MYBs, bZIPs, and NF-YAs. In conclusion, our analysis identified new candidate genes and provided new hypotheses to advance our understanding of the transcriptional regulation of sulfate metabolism in plants.
IL-33 induced inflammation exacerbated the development of chronic obstructive pulmonary disease through oxidative stress.

OBJECTIVE We aimed at exploring the role of IL-33 in mouse chronic obstructive pulmonary disease and its potential molecular mechanism. MATERIALS AND METHODS The chronic obstructive pulmonary disease (COPD) mice model was established by cigarette smoking (CS). COPD mice were randomly assigned into PBS group and IL-33 antibody group. The peripheral blood and lung tissues of mice from two groups were collected for the following experiments. Pathological changes of the lung tissues in both groups were analyzed by hematoxylin and eosin (HE) staining. IL-33 positive cells in lung tissues were detected by immunohistochemistry. Then, the mRNA and protein levels of IL-33, sST2, ERK and TNF-α in the mice peripheral blood of the two groups were accessed by Real-time polymerase chain reaction (RT-PCR) and Western blot. Finally, the indicators related to oxidative stress, including superoxide dismutase (SOD), malondialdehyde (MDA) and reactive oxygen species (ROS) in the mice serum of two groups were measured. RESULTS After successful construction of COPD mouse model by CS, HE staining illustrated that the structure of airway wall of lung tissue in mice from PBS group was irregular. The ciliated columnar epithelium presented significant degeneration, necrosis and shedding. A large amount of inflammation cell infiltration was observed in vascular tissues. The alveolar epithelial structure was severely damaged and alveolar septum was narrowed and ruptured. Adjacent alveoli were found to be fused into larger cysts. The above pathological changes were relatively better in mice from IL-33 antibody group. Immunohistochemical results demonstrated that IL-33 was remarkably deposited in the lung tissue of PBS group. The mRNA and protein levels of IL-33, sST2, ERK and TNF-α in peripheral blood of PBS group were much higher than those of IL-33 antibody group. At the same time, SOD level in PBS group decreased, while MDA level and ROS production increased. CONCLUSIONS IL-33 aggravates lung injury in COPD mice by increasing inflammation response and oxidative stress, which may serve as a target for predicting and treating COPD.
Diversity and Serendipity in Recommender Systems

The present age of digital information has presented a heterogeneous online environment which makes it a formidable mission for a noble user to search and locate the required online resources timely. Recommender systems were implemented to rescue this information overload issue. However, majority of recommendation algorithms focused on the accuracy of the recommendations, leaving out other important aspects in the definition of good recommendation such as diversity and serendipity. This results in low coverage, long-tail items often are left out in the recommendations as well. In this paper, we present and explore a recommendation technique that ensures that diversity, accuracy and serendipity are all factored in the recommendations. The proposed algorithm performed comparatively well as compared to other algorithms in literature.
Not quite unreasonable effectiveness of machine learning algorithms

State-of-the-art machine learning algorithms demonstrate close to absolute performance in selected challenges. We provide arguments that the reason can be in low variability of the samples and high effectiveness in learning typical patterns. Due to this fact, standard performance metrics do not reveal model capacity and new metrics are required for the better understanding of state-of-the-art.
Ribosome Shunting, Polycistronic Translation, and Evasion of Antiviral Defenses in Plant Pararetroviruses and Beyond

Viruses have compact genomes and usually translate more than one protein from polycistronic RNAs using leaky scanning, frameshifting, stop codon suppression or reinitiation mechanisms. Viral (pre-)genomic RNAs often contain long 5′-leader sequences with short upstream open reading frames (uORFs) and secondary structure elements, which control both translation initiation and replication. In plants, viral RNA and DNA are targeted by RNA interference (RNAi) generating small RNAs that silence viral gene expression, while viral proteins are recognized by innate immunity and autophagy that restrict viral infection. In this review we focus on plant pararetroviruses of the family Caulimoviridae and describe the mechanisms of uORF- and secondary structure-driven ribosome shunting, leaky scanning and reinitiation after translation of short and long uORFs. We discuss conservation of these mechanisms in different genera of Caulimoviridae, including host genome-integrated endogenous viral elements, as well as in other viral families, and highlight a multipurpose use of the highly-structured leader sequence of plant pararetroviruses in regulation of translation, splicing, packaging, and reverse transcription of pregenomic RNA (pgRNA), and in evasion of RNAi. Furthermore, we illustrate how targeting of several host factors by a pararetroviral effector protein can lead to transactivation of viral polycistronic translation and concomitant suppression of antiviral defenses. Thus, activation of the plant protein kinase target of rapamycin (TOR) by the Cauliflower mosaic virus transactivator/viroplasmin (TAV) promotes reinitiation of translation after long ORFs on viral pgRNA and blocks antiviral autophagy and innate immunity responses, while interaction of TAV with the plant RNAi machinery interferes with antiviral silencing.
An investigation of barriers to the use of the World Health Organization Surgical Safety Checklist in theatres.

BACKGROUND The World Health Organization (WHO) has implemented the Surgical Safety Checklist (SSCL) as part of the Safe Surgery Saves Lives campaign. This is aimed at improving surgical safety worldwide. Despite many perceived benefits of the SSCL, compliance and acceptance in many areas remain poor. OBJECTIVES To investigate perceptions of theatre staff regarding the checklist and to identify reasons and barriers for poor compliance and implementation. METHODS Questionnaires were handed out to theatre teams across all surgical disciplines at two large hospitals in Durban, South Africa, over a 2-week period. Data collected included role in theatre, intention of the SSCL, training received, as well as questions regarding previously identified barriers and staff perceptions. RESULTS Questionnaires were distributed to 225 practitioners, with a response rate of 81.7% from 51 nurses, 54 anaesthetists and 79 surgeons. Rank of medical staff included 52 seniors (consultants) and 81 juniors (registrars and medical officers). The majority (95%) of respondents perceived the SSCL as intended to improve safety, prevent errors or reduce morbidity and mortality. A total of 146 respondents (79.3%) received no SSCL training. No new barriers were identified, but previously identified barriers were confirmed. Our key factors were time-related issues and lack of buy-in from team members. Surgeons were perceived as being supportive by 45.1% of respondents, in contrast to nurses (62.5%), anaesthetists (70.1%) and management (68.5%). When compared with junior staff, senior staff were 5-fold more likely to feel that staff did not need to be trained and 8-fold more likely to indicate that the checklist did not improve patient safety. CONCLUSIONS The WHO SSCL is an important tool in the operating room environment. The barriers in our setting are similar to those identified in other settings. There needs to be widespread training in the use of the SSCL, including adaptation of the checklist to make it fit for purpose in our setting. Improving use of the checklist will allow theatre staff to work together towards ensuring a safer theatre environment for both patients and staff.
Discrepancies between subjective perception and waist-to-height ratio measurement of obesity, and their policy implications

In social sciences, researchers rely on subjective perceptions of obesity measures to examine the determinants of obesity and the likely effects of obesity on health outcomes. However, subjective perception tends to produce estimation biases. In this study, we investigated the misreporting behavior of individuals regarding obesity using waist-to-height ratio as an objective measurement of obesity. Using the Korean National Health and Nutrition Examination Survey for 2008–2011, we showed that false-reporting behavior was significantly associated with socio-economic status. Furthermore, we presented that subjective perception of obesity yielded misleading estimates in both the determinants and the consequences of obesity.
Split Tolerance in a Murine Model of Heterotopic En Bloc Chest Wall Transplantation

Background: Congenital and acquired chest wall deformities represent a significant challenge to functional reconstruction and may impact feasibility of heart transplantation for patients with end-stage organ failure. In the recent past, the concept of replacing like-with-like tissue by using vascularized composite allografts (VCA) has been enthusiastically employed for reconstruction of complex tissue defects. Methods: In this study, we introduce a novel murine model for en bloc chest wall, heart, and thymus transplantation and thereby the use of complex tissue allografts for reconstruction of both chest wall defects and also end-stage organ failure. Additionally, this model allows us to study the features of combined vascularized bone marrow (VBM), thymus, and heart transplantation on allograft survival and function. Heterotopic chest wall, thymus, and heart transplants were performed in untreated syngeneic and allogeneic combinations and in allogeneic combinations treated with costimulation blockade (CTLA4-Ig and MR-1). Results: Indefinite (ie, 150 d, N = 3) graft survival was observed in syngeneic controls. In untreated recipients of allogeneic grafts, the skin component was rejected after 10 (±1) days, whereas rejection of the heart occurred after 13 (± 1) days (N = 3). Costimulation blockade treatment prolonged survival of the heart and chest wall component (130 d, N = 3) as well as the VBM niche as evidenced by donor-specific chimerism (average: 2.35 ± 1.44%), whereas interestingly, the skin component was rejected after 13 (±1) days. Conclusion: Thus, this novel microsurgical model of VCA combined with solid organ transplantation is technically feasible and results in split tolerance when treated with costimulatory blockade.
The Inner and Outer Qualities of Extracellular Vesicles for Translational Purposes in Breast Cancer

Breast cancer (BC) is the second most common cause of cancer mortality of women worldwide. BC is a systemic disease with a highly heterogeneous course of disease. Therefore, prognostic and diagnostic biomarkers are required to improve the clinical risk management. Cancer-derived or cancer-associated extracellular vesicles (EVs) procured from the bloodstream of BC patients offer a novel platform for the qualitative and quantitative screening and establishment of biomarkers. Here, we focus on common aspects of EVs, on the function of BC-derived EVs and their translational potential considering the EV abundancy, intravesicular as well as outer membrane-anchored composition and current challenges of implementation in clinical practice.
Zebrafish cdc6 hypomorphic mutation causes Meier-Gorlin syndrome-like phenotype

Abstract Cell Division Cycle 6 (Cdc6) is a component of pre-replicative complex (preRC) forming on DNA replication origins in eukaryotes. Recessive mutations in ORC1, ORC4, ORC6, CDT1 or CDC6 of the preRC in human cause Meier-Gorlin syndrome (MGS) that is characterized by impaired post-natal growth, short stature and microcephaly. However, vertebrate models of MGS have not been reported. Through N-ethyl-N-nitrosourea mutagenesis and Cas9 knockout, we generate several cdc6 mutant lines in zebrafish. Loss-of-function mutations of cdc6, as manifested by cdc6tsu4305 and cdc6tsu7cd mutants, lead to embryonic lethality due to cell cycle arrest at the S phase and extensive apoptosis. Embryos homozygous for a cdc6 hypomorphic mutation, cdc6tsu21cd, develop normally during embryogenesis. Later on, compared with their wild-type (WT) siblings, cdc6tsu21cd mutant fish show growth retardation, and their body weight and length in adulthood are greatly reduced, which resemble human MGS. Surprisingly, cdc6tsu21cd mutant fish become males with a short life and fail to mate with WT females, suggesting defective reproduction. Overexpression of Cdc6 mutant forms, which mimic human CDC6(T323R) mutation found in a MGS patient, in zebrafish cdc6tsu4305 mutant embryos partially represses cell death phenotype, suggesting that the human CDC6(T323R) mutation is a hypomorph. cdc6tsu21cd mutant fish will be useful to detect more tissue defects and develop medical treatment strategies for MGS patients.
Uncertainty Modeling in Wireless Sensor Networks

In wireless sensor networks, the certainty of the data created by a node can change due to many reasons such as drained energy, outer factors. In addition dynamic physical environment and hardware failures (broken sensor etc.) might cause sensors to produce erred or incomplete data. Therefore raw wireless sensor network data reflects an approximate observation of the monitored environment and it can be faulty or partially wrong. Wireless sensor network applications that are used in military and health systems are used in critical decision-making. To make a healthy decision and to analyze the data correctly, the end users have to know the uncertainty level of the collected data. As a result, a model that can represent the uncertainty associated with different types of sensor data in varying models is needed. There has been some efforts of modeling uncertainty in database community. We aim to develop an uncertaintymodeling framework to aid decision-making. The methodology that we will use in this work is as follows (1) developing an uncertainty model by referring to database literature (2) designing the algorithms and equations (3) modeling finite state machines to characterize the behavior of the nodes and the transitions between different uncertainty states (4) improving a distributed architecture that defines the actions taken by the network based on the uncertainty levels (such as omitting a node with a low uncertainty level and replacing it) (5) calculating the energy and memory requirements of our architecture by carrying simulations. We have done previous work on trust computation of wireless sensor networks. In this position paper, we give a general overview of the planned research.
ASK family kinases mediate cellular stress and redox signaling to circadian clock

Significance The cellular stress response and circadian clock system are fundamental functions in homeostatic regulation in almost all organisms. However, whether these two mechanisms are interlocked with each other, and the key molecule that links cellular stress and the circadian clock, remain unclear. Here we identify ASK family kinases that are essential for the circadian clock to respond to cellular stress, and report that Ask1 transcription is rhythmically controlled by the circadian clock. Moreover, LC-MS/MS–based proteomic analysis provides insight into a molecular mechanism in which dephosphorylation-triggered changes to the ASK complex mediate cellular stress to the circadian clock. From the perspective of cell signaling, our present findings expand previously reported roles of stress signaling toward regulation of the circadian clock. Daily rhythms of behaviors and physiologies are generated by the circadian clock, which is composed of clock genes and the encoded proteins forming transcriptional/translational feedback loops (TTFLs). The circadian clock is a self-sustained oscillator and flexibly responds to various time cues to synchronize with environmental 24-h cycles. However, the key molecule that transmits cellular stress to the circadian clockwork is unknown. Here we identified apoptosis signal-regulating kinase (ASK), a member of the MAPKKK family, as an essential mediator determining the circadian period and phase of cultured cells in response to osmotic changes of the medium. The physiological impact of ASK signaling was demonstrated by a response of the clock to changes in intracellular redox states. Intriguingly, the TTFLs drive rhythmic expression of Ask genes, indicating ASK-mediated association of the TTFLs with intracellular redox. In behavioral analysis, Ask1, Ask2, and Ask3 triple-KO mice exhibited compromised light responses of the circadian period and phase in their activity rhythms. LC-MS/MS–based proteomic analysis identified a series of ASK-dependent and osmotic stress-responsive phosphorylations of proteins, among which CLOCK, a key component of the molecular clockwork, was phosphorylated at Thr843 or Ser845 in the carboxyl-terminal region. These findings reveal the ASK-dependent stress response as an underlying mechanism of circadian clock flexibility.
Effects of training pre-movement sensorimotor rhythms on behavioral performance

Objective. Brain–computer interface (BCI) technology might contribute to rehabilitation of motor function. This speculation is based on the premise that modifying the electroencephalographic (EEG) activity will modify behavior, a proposition for which there is limited empirical data. The present study asked whether learned modulation of pre-movement sensorimotor rhythm (SMR) activity can affect motor performance in normal human subjects. Approach. Eight individuals first performed a joystick-based cursor-movement task with variable warning periods. Targets appeared randomly on a video monitor and subjects moved the cursor to the target and pressed a select button within 2 s. SMR features in the pre-movement EEG that correlated with performance speed and accuracy were identified. The subjects then learned to increase or decrease these features to control a two-target BCI task. Following successful BCI training, they were asked to increase or decrease SMR amplitude in order to initiate the joystick task. Main results. After BCI training, pre-movement SMR amplitude was correlated with performance in subjects with initial poor performance: lower amplitude was associated with faster and more accurate movement. The beneficial effect on performance of lower SMR amplitude was greater in subjects with lower initial performance levels. Significance. These results indicate that BCI-based SMR training can affect a standard motor behavior. They provide a rationale for studies that integrate such training into rehabilitation protocols and examine its capacity to enhance restoration of useful motor function.
The Relationship Between Dopamine Neurotransmitter Dynamics and the Blood-Oxygen-Level-Dependent (BOLD) Signal: A Review of Pharmacological Functional Magnetic Resonance Imaging

Functional magnetic resonance imaging (fMRI) is widely used in investigations of normal cognition and brain disease and in various clinical applications. Pharmacological fMRI (pharma-fMRI) is a relatively new application, which is being used to elucidate the effects and mechanisms of pharmacological modulation of brain activity. Characterizing the effects of neuropharmacological agents on regional brain activity using fMRI is challenging because drugs modulate neuronal function in a wide variety of ways, including through receptor agonist, antagonist, and neurotransmitter reuptake blocker events. Here we review current knowledge on neurotransmitter-mediated blood-oxygen-level dependent (BOLD) fMRI mechanisms as well as recently updated methodologies aimed at more fully describing the effects of neuropharmacologic agents on the BOLD signal. We limit our discussion to dopaminergic signaling as a useful lens through which to analyze and interpret neurochemical-mediated changes in the hemodynamic BOLD response. We also discuss the need for future studies that use multi-modal approaches to expand the understanding and application of pharma-fMRI.