Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Putative Mek1 Substrates during Meiosis in Saccharomyces cerevisiae Using Quantitative Phosphoproteomics

Meiotic recombination plays a key role in sexual reproduction as it generates crossovers that, in combination with sister chromatid cohesion, physically connect homologous chromosomes, thereby promoting their proper segregation at the first meiotic division. Meiotic recombination is initiated by programmed double strand breaks (DSBs) catalyzed by the evolutionarily conserved, topoisomerase-like protein Spo11. Repair of these DSBs is highly regulated to create crossovers between homologs that are distributed throughout the genome. This repair requires the presence of the mitotic recombinase, Rad51, as well as the strand exchange activity of the meiosis-specific recombinase, Dmc1. A key regulator of meiotic DSB repair in Saccharomyces cerevisiae is the meiosis-specific kinase Mek1, which promotes interhomolog strand invasion and is required for the meiotic recombination checkpoint and the crossover/noncrossover decision. Understanding how Mek1 regulates meiotic recombination requires the identification of its substrates. Towards that end, an unbiased phosphoproteomic approach utilizing Stable Isotope Labeling by Amino Acids in Cells (SILAC) was utilized to generate a list of potential Mek1 substrates, as well as proteins containing consensus phosphorylation sites for cyclin-dependent kinase, the checkpoint kinases, Mec1/Tel1, and the polo-like kinase, Cdc5. These experiments represent the first global phosphoproteomic dataset for proteins in meiotic budding yeast.
Retrospective Lightweight Distributed Snapshots Using Loosely Synchronized Clocks

In order to take a consistent snapshot of a distributed system, it is necessary to collate and align local logs from each node to construct a pairwise concurrent cut. By leveraging NTP synchronized clocks, and augmenting them with logical clock causality information, Retroscope provides a lightweight solution for taking unplanned retrospective snapshots of past distributed system states. Instead of storing a multiversion copy of the entire system data, this is achieved efficiently by maintaining a configurable-size sliding window-log at each node to capture recent operations. In addition to retrospective snapshots, Retroscope also provides incremental and rolling snapshots that utilize an existing snapshot to reduce the cost of constructing a new snapshot in proximity. This capability is useful for performing stepwise debugging and root-cause analysis, and supporting data integrity monitoring and checkpoint-recovery. We implement Retroscope for the Voldemort distributed datastore and evaluate its performance under varying workloads.
The Nanostructuring of the Functional Surface of the Oil Pipelines

The current state of oil pipelines is characterized by decrease of operational reliability and efficiency which are caused by intensive corrosion processes and accumulation of asphaltens-resinous-wax formations on internal surfaces. Formation of accumulations is the reason of essential increase in hydraulic resistance of pipeline. The most suitable way for decrease of hydraulic resistance of oil pipelines is the modifying of internal surfaces at the expense of formation of molecular fluorine SAS layers. Nano-structural modification of internal surfaces is carried out at the expense of the focused adsorption of fluorine SAS molecules from the transported environment and formation so-called «a paling of Lengmjura». It is established that updating of internal surfaces of the pipeline at the expense of formation on them of molecular fluorine SAS layers leads to reduction of their hydraulic resistance on 30 ÷ 23 %. Molecular fluorine SAS layers, generated on a metal surface, considerably improves its hydraulic characteristics without dependence from roughness size. This peculiarity of molecular fluorine SAS layers allows not only to restore hydraulic resistance of the oil pipelines which have grown during of operating process, but also to improve their initial hydraulic characteristics. Characteristics of interaction of a stream of oil and an internal surface are optimized by nano-structural processing. The given technology allows to lower hydraulic resistance by changing the roughness of the internal surface of the pipeline, to lower power expenses for transportation of hydrocarbons raw materials, to raise operational reliability and to extend the between-repairs period.
Micromechanics of Failure Mode in Fiber Reinforced Plastics

Discontinuous fiber reinforced plastics have superior productivity and formability in comparison with continuous fiber reinforced plastics. However, their strengths are remarkably low. Thus there is an urgent need to establish a fundamental model in order to improve the strength of discontinuous fiber reinforced plastics. In the present work, we utilized numerical simulations that consider the microscopic damage in the composite and incorporate an individual constitutive law of thermosetting resin or thermoplastic resin. The fundamental mechanism that affected the strength and failure of the composite was investigated when the fiber length and/or matrix properties were varied from continuous glass fiber reinforced plastics to discontinuous glass fiber reinforced plastics. Our results clarified two factors that cause the strength degradation of discontinuous fiber reinforced plastics. One is the low yield stress of thermoplastic resin, which is frequently used for the matrix of discontinuous fiber reinforced plastics. As the other factor, the final failure mode is changed from fiber breaking mode to matrix cracking mode in the case of the low fiber volume fraction of discontinuous glass fiber reinforced plastics. Moreover, we investigated the relationship between fiber length and strength of carbon fiber reinforced polypropylene and the effect of thermoplastic matrix properties depending on the loading rate as well.
On Software Productivity Analysis with Propensity Score Matching

[Context:] Software productivity analysis is an essential activity for software process improvement. It specifies critical factors to be resolved or accepted from project data. As the nature of project data is observational, not experimental, the project data involves bias that can cause spurious relationships among analyzed factors. Analysis methods based on linear regression suffer from the spurious relationships and sometimes lead an inappropriate causal relation. The propensity score is a solution for this problem but has rarely been used. [Objective:] To investigate what differences the use of propensity score brings to software productivity analysis in comparison to a conventional method. [Method:] We revisited classical software productivity analyses on ISBSG and Finnish datasets. The differences of critical factors between the propensity score and the linear regression were investigated. [Results:] Both analysis methods specified different critical factors on the two datasets. The specified factors were both reasonable to some extent, and further considerations are needed for the propensity score results. [Conclusions:] The use of propensity score can lead new possible factors to be tackled. Although the contradiction does not necessarily indicate a flaw of the linear regression, the results by the propensity score should also be noticed for better actions.
Role of Wax Ester Synthase/Acyl Coenzyme A:Diacylglycerol Acyltransferase in Oleaginous Streptomyces sp. Strain G25

ABSTRACT Recently, we isolated a novel Streptomyces strain which can accumulate extraordinarily large amounts of triacylglycerol (TAG) and consists of 64% fatty acids (dry weight) when cultivated with glucose and 50% fatty acids (dry weight) when cultivated with cellobiose. To identify putative gene products responsible for lipid storage and cellobiose utilization, we analyzed its draft genome sequence. A single gene encoding a wax ester synthase/acyl coenzyme A (CoA):diacylglycerol acyltransferase (WS/DGAT) was identified and heterologously expressed in Escherichia coli. The purified enzyme AtfG25 showed acyltransferase activity with C12- or C16-acyl-CoA, C12 to C18 alcohols, or dipalmitoyl glycerol. This acyltransferase exhibits 24% amino acid identity to the model enzyme AtfA from Acinetobacter baylyi but has high sequence similarities to WS/DGATs from other Streptomyces species. To investigate the impact of AtfG25 on lipid accumulation, the respective gene, atf G25, was inactivated in Streptomyces sp. strain G25. However, cells of the insertion mutant still exhibited DGAT activity and were able to store TAG, albeit in lower quantities and at lower rates than the wild-type strain. These findings clearly indicate that AtfG25 has an important, but not exclusive, role in TAG biosynthesis in the novel Streptomyces isolate and suggest the presence of alternative metabolic pathways for lipid accumulation which are discussed in the present study. IMPORTANCE A novel Streptomyces strain was isolated from desert soil, which represents an extreme environment with high temperatures, frequent drought, and nutrient scarcity. We believe that these harsh conditions promoted the development of the capacity for this strain to accumulate extraordinarily large amounts of lipids. In this study, we present the analysis of its draft genome sequence with a special focus on enzymes potentially involved in its lipid storage. Furthermore, the activity and importance of the detected acyltransferase were studied. As discussed in this paper, and in contrast to many other bacteria, streptomycetes seem to possess a complex metabolic network to synthesize lipids, whereof crucial steps are still largely unknown. This paper therefore provides insights into a range of topics, including extremophile bacteria, the physiology of lipid accumulation, and the biotechnological production of bacterial lipids.
A Compact Nanostructure Integrated Pool Boiler for Microscale Cooling Applications

An efficient cooling system consisting of a plate, on which copper nanorods (nanorods of size ∼100nm) are integrated to copper thin film (which is deposited on Silicon substrate), a heater, an Aluminum base, and a pool was developed. Heat is transferred with high efficiency to the liquid within the pool above the base through the plate by boiling heat transfer. Near the boiling temperature of the fluid, vapor bubbles started to form with the existence of wall superheat. Phase change took place near the nanostructured plate, where the bubbles emerged from. Bubble formation and bubble motion inside the pool created an effective heat transfer from the plate surface to the pool. Nucleate boiling took place on the surface of the nanostructured plate helping the heat removal from the system to the liquid above. The heat transfer from nanostructured plate was studied using the experimental setup. The temperatures were recorded from the readings of thermocouples, which were successfully integrated to the system. The surface temperature at boiling inception was 102.1°C without the nanostructured plate while the surface temperature was successfully decreased to near 100°C with the existence of the nanostructured plate. In this study, it was proved that this device could have the potential to be an extremely useful device for small and excessive heat generating devices such as MEMS or Micro-processors. This device does not require any external energy to assist heat removal which is a great advantage compared to its counterparts. © 2009 ASME
Virtual Machine Scaling Method Considering Performance Fluctuation of Public Cloud

Cloud computing has been adapted for various application areas because it can reduce the time required for system development and the cost of hardware. One of the factors that degrades performance stability of applications running in the cloud is “unexpected loads”, caused by interference between Virtual Machines (VMs) coexisting on the same physical machine. In this paper, we propose a VM scaling method that forecasts performance fluctuation caused by unexpected loads to adjust the number of VMs appropriately. We evaluate the proposed method with simulation to verify that the proposed method can improve performance stability of MQTT brokers.
DuoFS: An Attempt at Energy-Saving and Retaining Reliability of Storage Systems

As issues of the Energy Wall and the Reliability Wall become unavoidable, it is a demanding and challenging task to reduce energy consumption in large-scale storage systems in modern data centres while retaining acceptable systems reliability. Most energy conservation techniques inevitably have adverse impacts on the parallel disk systems. To address the reliability issues of energy-efficient parallel storage systems, we propose a reliable energy-efficient storage system called DuoFS, which aims at improving both energy efficiency and reliability of parallel storage systems by seamlessly integrating HDDs and SSDs. With the help of the middleware layer, DuoFS can distribute popular data to SSD-based nodes and put HDD-based nodes into the low-power mode under light workload conditions without modification of the parallel systems.
MICROSTRUCTURAL ANALYSIS OF CONCRETE FRACTURE USING INTERFACE ELEMENTS

A microstructural model for the mechanical behavior of concrete is developed and verified for concrete specimens subject to several load scenarios. The model is based on interface elements equipped with a constitutive law representing non-linear fracture, which may be considered a mixed-mode generalization of Hillerborg's "Fictitious Crack Model" 1 . Specimens with 4x4 and 6x6 arrays of aggregates are discretized into finite elements. Interface elements are inserted along the main lines in the mesh, representing potential crack lines. The continuum elements themselves are assumed to remain linear elastic. In this paper, some numerical results obtained in meshes under various loading cases, such as pure tension and compression, as well as Brazilian test are presented. The results show a good qualitative agreement with experimental observations and illustrate the capabilities of the model.
[POSTER] A Predictive Approach to On-line Time Warping of Motion

The paper presents a novel approach to real-time temporal alignment of motion sequences, called On-line Predictive Warping (OPW) and considers potential uses in interactive applications. The approach develops on the methods of aligning motions based on least cost, used in dynamic time warping (DTW), with the short term predictions of smoothing algorithms, in an iterative step through approach. The approach allows a recorded motion sequence to be warped to align it with a users motion as it is being captured. The paper demonstrates the potential feasibility of the approach to support applications in MR and VR, allowing virtual characters to perform and interact with users and live actors in a variety of rehearsal, training, visualisation and performance scenarios.
Methylated free‐circulating HPP1 DNA is an early response marker in patients with metastatic colorectal cancer

Detection of methylated free‐circulating DNA (mfcDNA) for hyperplastic polyposis 1 (HPP1) in blood is correlated with a poor prognosis for patients with metastatic colorectal cancers (mCRC). Here, we analyzed the plasma levels of HPP1 mfcDNA in mCRC patients treated with a combination therapy containing a fluoropyrimidine, oxaliplatin and bevacizumab to test whether HPP1 mfcDNA is a suitable prognostic and response biomarker. From 467 patients of the prospective clinical study AIO‐KRK‐0207, mfcDNA was isolated from plasma samples at different time points and bisulfite‐treated mfcDNA was quantified using methylation specific PCR. About 337 of 467 patients had detectable levels for HPP1 mfcDNA before start of treatment. The detection was significantly correlated with poorer overall survival (OS) (HR = 1.86; 95%CI 1.37–2.53). About 2–3 weeks after the first administration of combination chemotherapy, HPP1 mfcDNA was reduced to non‐detectable levels in 167 of 337 patients. These patients showed a better OS compared with patients with continued detection of HPP1 mfcDNA (HR HPP1(sample 1: pos/ sample 2: neg) vs. HPP1(neg/neg) = 1.41; 95%CI 1.00–2.01, HPP1(neg,pos/pos) vs. HPP1(neg/neg) = 2.60; 95%CI 1.86–3.64). Receiver operating characteristic analysis demonstrated that HPP1 mfcDNA discriminates well between patients who do (not) respond to therapy according to the radiological staging after 12 or 24 weeks (AUC = 0.77 or 0.71, respectively). Detection of HPP1 mfcDNA can be used as a prognostic marker and an early marker for response (as early as 3–4 weeks after start of treatment compared with radiological staging after 12 or 24 weeks) to identify patients who will likely benefit from a combination chemotherapy with bevacizumab.
Bayesian molecular dating: opening up the black box

Molecular dating analyses allow evolutionary timescales to be estimated from genetic data, offering an unprecedented capacity for investigating the evolutionary past of all species. These methods require us to make assumptions about the relationship between genetic change and evolutionary time, often referred to as a ‘molecular clock’. Although initially regarded with scepticism, molecular dating has now been adopted in many areas of biology. This broad uptake has been due partly to the development of Bayesian methods that allow complex aspects of molecular evolution, such as variation in rates of change across lineages, to be taken into account. But in order to do this, Bayesian dating methods rely on a range of assumptions about the evolutionary process, which vary in their degree of biological realism and empirical support. These assumptions can have substantial impacts on the estimates produced by molecular dating analyses. The aim of this review is to open the ‘black box’ of Bayesian molecular dating and have a look at the machinery inside. We explain the components of these dating methods, the important decisions that researchers must make in their analyses, and the factors that need to be considered when interpreting results. We illustrate the effects that the choices of different models and priors can have on the outcome of the analysis, and suggest ways to explore these impacts. We describe some major research directions that may improve the reliability of Bayesian dating. The goal of our review is to help researchers to make informed choices when using Bayesian phylogenetic methods to estimate evolutionary rates and timescales.
University of Southern Denmark Relatives' level of satisfaction with advanced cancer care in Greenland

Palliative cancer care in Greenland is provided by health professionals at local level, the national Queen Ingrid’s Hospital and at Rigshospitalet in Denmark. To improve and develop care for relatives of patients with advanced cancer, we conducted a mixed method study examining relatives’ level of satisfaction with care and treatment and their current main concerns. The aim was to investigate relatives’ level of satisfaction with advanced cancer care and bring to light their current main concerns. The FAMCARE-20 questionnaire was translated to Greenlandic and pilot tested. The questionnaire was supplemented by open-ended questions about relative’s current main concerns and analyzed with a phenomenological hermeneutical approach. Greenlandic patients with advanced cancer who were previously participating in a prospective study were asked if their closest adult relative would participate in the study. Telephone interviews were conducted and relatives responded to the questionnaire. A total of thirty-two relatives were contacted by telephone and 30 (94%) completed the FAMCARE-20 questionnaire and answered open-ended questions. The highest rate of satisfaction was with the availability of a hospital bed (66%) and relatives were the most dissatisfied with the lack of inclusion in decision making related to treatment and care (71%) and the length of time required to diagnose cancer (70%). Responses to the open-ended questions revealed that relatives faced challenges in gaining access to information from health professionals. They experienced a lack of security, worries about the future and a lack of support at home. The study showed a substantial level of dissatisfaction among relatives of patients with advanced cancer. We strongly recommend a focus on psychosocial care, more access to information and to include relatives in decision making and in the future planning of palliative care services. An assessment of relatives’ needs is essential to develop an adequate palliative care in a range of settings. ARTICLE HISTORY Received 19 February 2017 Accepted 19 May 2017
Polysialic acid blocks mononuclear phagocyte reactivity, inhibits complement activation, and protects from vascular damage in the retina

Age‐related macular degeneration (AMD) is a major cause of blindness in the elderly population. Its pathophysiology is linked to reactive oxygen species (ROS) and activation of the complement system. Sialic acid polymers prevent ROS production of human mononuclear phagocytes via the inhibitory sialic acid‐binding immunoglobulin‐like lectin‐11 (SIGLEC11) receptor. Here, we show that low‐dose intravitreal injection of low molecular weight polysialic acid with average degree of polymerization 20 (polySia avDP20) in humanized transgenic mice expressing SIGLEC11 on mononuclear phagocytes reduced their reactivity and vascular leakage induced by laser coagulation. Furthermore, polySia avDP20 prevented deposition of the membrane attack complex in both SIGLEC11 transgenic and wild‐type animals. In vitro, polySia avDP20 showed two independent, but synergistic effects on the innate immune system. First, polySia avDP20 prevented tumor necrosis factor‐α, vascular endothelial growth factor A, and superoxide production by SIGLEC11‐positive phagocytes. Second, polySia avDP20 directly interfered with complement activation. Our data provide evidence that polySia avDP20 ameliorates laser‐induced damage in the retina and thus is a promising candidate to prevent AMD‐related inflammation and angiogenesis.
Exploring how a traditional diluted yoghurt drink may mitigate heat strain during medium-intensity intermittent work: a multidisciplinary study of occupational heat strain

It is common practice in India to consume the dairy drink buttermilk as a way of mitigating occupational heat strain. This paper explores the thermoregulatory and hydration benefits of drinking buttermilk but also the impacts of work in a hot environment on the gut microbiota, renal and cognitive function. Twelve healthy participants were subjected to a 3-h period of medium load physical intermittent work in a climatic chamber (34°C, 60% RH). The subjects were given water, buttermilk (700 ml) or no rehydration at random. Mean body temperatures when no rehydration was given were significantly higher (p≤0.001). When subjects drank water or buttermilk they had a lower sweat rate than with no rehydration (p≤0.05) and the perception of feeling hot, uncomfortable, thirsty and physically exerted was significantly reduced (p≤0.05). A hormonal stress response at the end of the exposure was seen when not drinking (p≤0.05). No differences in cognitive abilities and gut microbiota were found. The exposure lowered the renal blood flow suggesting an acute impact of short term heat exposure. It was also found that buttermilk has a protective effect on this impact. Our results demonstrated that keeping hydrated by water/buttermilk consumption mitigates heat strain in well-nourished subjects.