Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic and Metabolomic Profiling of Deinococcus radiodurans Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions

The polyextremophile, gram-positive bacterium Deinococcus radiodurans can withstand harsh conditions of real and simulated outer space environment, e.g., UV and ionizing radiation. A long-term space exposure of D. radiodurans has been performed in Low Earth Orbit (LEO) in frames of the Tanpopo orbital mission aiming to investigate the possibility of interplanetary life transfer. Space vacuum (10-4–10-7 Pa) is a harmful factor, which induces dehydration and affects microbial integrity, severely damaging cellular components: lipids, carbohydrates, proteins, and nucleic acids. However, the molecular strategies by which microorganisms protect their integrity on molecular and cellular levels against vacuum damage are not yet understood. In a simulation experiment, we exposed dried D. radiodurans cells to vacuum (10-4–10-7 Pa), which resembles vacuum pressure present outside the International Space Station in LEO. After 90 days of high vacuum exposure, survival of D. radiodurans cells was 2.5-fold lower compared to control cells. To trigger molecular repair mechanisms, vacuum exposed cells of D. radiodurans were recovered in complex medium for 3 and 6 h. The combined approach of analyzing primary metabolites and proteins revealed important molecular activities during early recovery after vacuum exposure. In total, 1939 proteins covering 63% of D. radiodurans annotated protein sequences were detected. Proteases, tRNA ligases, reactive oxygen species (ROS) scavenging proteins, nucleic acid repair proteins, TCA cycle proteins, and S-layer proteins are highly abundant after vacuum exposure. The overall abundance of amino acids and TCA cycle intermediates is reduced during the recovery phase of D. radiodurans as they are needed as carbon source. Furthermore, vacuum exposure induces an upregulation of Type III histidine kinases, which trigger the expression of S-layer related proteins. Along with the highly abundant transcriptional regulator of FNR/CRP family, specific histidine kinases might be involved in the regulation of vacuum stress response. After repair processes are finished, D. radiodurans switches off the connected repair machinery and focuses on proliferation. Combined comparative analysis of alterations in the proteome and metabolome helps to identify molecular key players in the stress response of D. radiodurans, thus elucidating the mechanisms behind its extraordinary regenerative abilities and enabling this microorganism to withstand vacuum stress.
Squibs: Nouveau-ROUGE: A Novelty Metric for Update Summarization

An update summary should provide a fluent summarization of new information on a time-evolving topic, assuming that the reader has already reviewed older documents or summaries. In 2007 and 2008, an annual summarization evaluation included an update summarization task. Several participating systems produced update summaries indistinguishable from human-generated summaries when measured using ROUGE. However, no machine system performed near human-level performance in manual evaluations such as pyramid and overall responsiveness scoring. We present a metric called Nouveau-ROUGE that improves correlation with manual evaluation metrics and can be used to predict both the pyramid score and overall responsiveness for update summaries. Nouveau-ROUGE can serve as a less expensive surrogate for manual evaluations when comparing existing systems and when developing new ones.
Convergence-speed enhancement of two classes of (Ω,α)-fair rate allocation algorithms

In the current paper, a fast second-order rate allocation algorithm is proposed that can improve the convergence speed of conventional methods. Under certain (and almost) practical premises about the network topology, an end-to-end implementation of well-known proportional and minimum potential delay fair rate allocation algorithms is introduced. The proposed algorithm has been compared with the conventional method and TCP using simulation. The simulation results show that the proposed method outperforms the conventional ones in convergence rate.
Compact Value-Function Representations for Qualitative Preferences

We consider the challenge of preference elicitation in systems that help users discover the most desirable item(s) within a given database. Past work on preference elicitation focused on structured models that provide a factored representation of users' preferences. Such models require less information to construct and support efficient reasoning algorithms. This paper makes two substantial contributions to this area: (1) Strong representation theorems for factored value functions. (2) A methodology that utilizes our representation results to address the problem of optimal item selection.
Statin‐induced muscle damage and atrogin‐1 induction is the result of a geranylgeranylation defect

Statins are widely used to treat hypercholesterolemia but can lead to a number of side effects in muscle, including rhabdomyolysis. Our recent findings implicated the induction of atrogin‐1, a gene required for the development of muscle atrophy, in statin‐induced muscle damage. Since statins inhibit many biochemical reactions besides cholesterol synthesis, we sought to define the statin‐inhibited pathways responsible for atrogin‐1 expression and muscle damage. We report here that lovastatin‐induced atrogin‐1 expression and muscle damage in cultured mouse myotubes and zebrafish can be prevented in the presence of geranylgeranol but not farnesol. Further, inhibitors of the transfer of geranylgeranyl isoprene units to protein targets cause statin muscle damage and atrogin‐1 induction in cultured cells and in fish. These findings support the concept that dysfunction of small GTP‐binding proteins lead to statin‐induced muscle damage since these molecules require modification by geranylgeranyl moieties for their cellular localization and activity. Collectively, our animal and in vitro findings shed light on the molecular mechanism of statin‐induced myopathy and suggest that atrogin‐1 may be regulated by novel signaling pathways. —Cao, P., Hanai, J., Tanksale, P., Imamura, S. , Sukhatme, V. P., Lecker, S. H. Statin‐induced muscle damage and atrogin‐1 induction is the result of a geranylgeranylation defect. FASEB J. 23, 2844–2854 (2009). www.fasebj. org
Conceptual Model Construction of Accounting Practitioners' Employability in Business English Major Graduates

This paper first reviews the development and definition of employability and then analyzed one influential employability model, the Key to Employability Model. To investigate the employability of accounting practitioners among Business English (BE) graduates, the authors suggest to specify the professional knowledge and skills in traditional employability model as English ability plus occupational ability of accounting. The authors construct the Four-Dimension Employability Model of Accounting Practitioners among Business English Graduates based on the Key to Employability Model and the Occupational Ability of Accounting. This model divides the employability of accounting practitioners among BE graduates into English ability & occupational ability of accounting, generic skills, emotional intelligence and career development learning.
SynMapN : Interactive Visual Comparison for Multiple Genomes

Interactive visualization has become a powerful means to explore syntenic relationships among two genomes, with a variety of available tools for domain scientists to employ. However, these tools do not tend to scale well in the case where many genomes are compared against one another. This poster describes ongoing efforts to build techniques and tools to help geneticists understand sets of genomes and their syntenic relationships. Our main contribution is a mechanism that defines set distances: this can be used to compare entire genomes to one another, as well as sets of genomes to each other. Currently, we use this mechanism to generate dimensionality reduction visualizations. We discuss limitations of this approach, as well as future directions.
Follow‐up by cytogenetic and fluorescence in situ hybridization analysis of allogeneic bone marrow transplantation in two children with Fanconi's anaemia in transformation

Results of bone marrow transplantation (BMT) in patients with Fanconi's anaemia (FA) in transformation are very poor and only a few cases with favourable outcome have been reported. We present the follow‐up of two FA‐myelodysplastic syndrome (MDS) patients with monosomy 7 and complex karyotype implicating chromosome 1. Both relapsed with acute myeloid leukaemia (AML) following an allogeneic BMT from an HLA‐identical brother. The patients showed clonal cytogenetic evolution coinciding with the leukaemic transformation. In one patient, fluorescence in situ hybridization using X and Y chromosome probes detected an increase of host cells before clinical relapse. Both patients received a successful second allogeneic BMT from the same donor using a more intensive treatment regimen and remain in clinical and cytogenetic remission more than 3 years later.
Aminopyridines Potentiate Synaptic and Neuromuscular Transmission by Targeting the Voltage-activated Calcium Channel β Subunit*♦

Aminopyridines such as 4-aminopyridine (4-AP) are widely used as voltage-activated K+ (Kv) channel blockers and can improve neuromuscular function in patients with spinal cord injury, myasthenia gravis, or multiple sclerosis. Here, we present novel evidence that 4-AP and several of its analogs directly stimulate high voltage-activated Ca2+ channels (HVACCs) in acutely dissociated neurons. 4-AP, 4-(aminomethyl)pyridine, 4-(methylamino)pyridine, and 4-di(methylamino)pyridine profoundly increased HVACC, but not T-type, currents in dissociated neurons from the rat dorsal root ganglion, superior cervical ganglion, and hippocampus. The widely used Kv channel blockers, including tetraethylammonium, α-dendrotoxin, phrixotoxin-2, and BDS-I, did not mimic or alter the effect of 4-AP on HVACCs. In HEK293 cells expressing various combinations of N-type (Cav2.2) channel subunits, 4-AP potentiated Ca2+ currents primarily through the intracellular β3 subunit. In contrast, 4-AP had no effect on Cav3.2 channels expressed in HEK293 cells. Furthermore, blocking Kv channels did not mimic or change the potentiating effects of 4-AP on neurotransmitter release from sensory and motor nerve terminals. Thus, our findings challenge the conventional view that 4-AP facilitates synaptic and neuromuscular transmission by blocking Kv channels. Aminopyridines can directly target presynaptic HVACCs to potentiate neurotransmitter release independent of Kv channels.
Dendritic cell vaccine therapy for acute myeloid leukemia: Questions and answers

The knowledge that our immune system can be exploited for control or even eradication of acute myeloid leukemia (AML) has sparked a strong interest in therapeutic vaccine strategies to mount effective anti-leukemic immunity in AML patients. One of the most tantalizing approaches in this regard involves the use of dendritic cell-based vaccines. Dendritic cells (DCs) are antigen-presenting cells, capable of inducing anti-leukemic immune responses directed against leukemia-associated antigens. They can be obtained in high numbers following in vitro differentiation of peripheral blood monocytes. Research efforts are now focused on optimizing in vitro culture conditions and antigen loading strategies of DCs in order to maximize their potential to induce anti-leukemic immunity. Here, we will highlight some important aspects in the design of a potent DC vaccine for AML. We also discuss the importance of natural killer cells and combination strategies to further improve the outcome of DC-based vaccination in AML patients.
Effects of dietary mannanoligosaccharide on performance of Japanese quail affected by aflatoxicosis

The potential of the yeast component, mannanoligosaccharide (MOS) to ameliorate the effects of aflatoxicosis was examined in growing Japanese quail. The product was incorporated in the diet at 1 g/kg and was evaluated for its ability to reduce the deleterious effects of 2 mg total aflatoxin (AF; 82.30% AFB 1 , 2.06% AFB 2 , 7.68% AFG 1 and 7.96% AFG 2 )/kg diet on Japanese quail chicks from 10 to 45 days of age. Forty 10-d old Japanese quail chicks were assigned in a 2x2 factorial arrangement of treatments to four groups (Control, AF, MOS, AF plus MOS), each consisting of 10 quails. The addition of AF alone significantly decreased feed consumption and body weight gain from the first week onwards. A significant adverse effect of AF on the feed conversion ratio was also observed from week 4 onwards. The addition of MOS to the AF-containing diet significantly reduced these adverse effects of AF on feed consumption, body weight gain and feed conversion ratio. The cumulative body weight gain was 22.0% lower in the quails consuming a diet containing AF without MOS as compared to the control group. However, it was only 2.3% lower that the control in the birds fed the diet containing the AF plus MOS. Key Words: Aflatoxin, Mannanoligosaccharide, Quail, Preventive effect South African Journal of Animal Science Vol.34(3) 2004: 144-148
Inferring Accurate Histories of Malware Evolution from Structural Evidence

An important problem in malware forensics is generating a partial ordering of a collection of variants of a malware program, reflecting a history of the malware’s evolution as it is adapted by the original or new authors. Frequently the only temporal clue to which variants were developed earlier is the date on which they were first observed in the wild. In the absence of reliable temporal clues, our approach leverages heuristic evidence based on common trends in the evolution of software structure over time. We extract structural features from each variant binary executable and generate from them three different forms of evidence that one variant is a likely ancestor of another. We then combine this evidence using a truth maintenance system to create a family tree of malware variants.
The Value of Green IT: a Theoretical Framework and Exploratory Assessment of Cloud Computing

The phenomenon of climate change and the resulting focus on energy consumption has created a consensus among businesses about the need for a collective reduction in carbon emissions. A range of new Green technologies, such as Cloud computing, provide unprecedented opportunities to improve the efficiency of business operations and represent a realistic opportunity to reduce energy costs and combat global warming. Enterprises are equally concerned with optimising the business value derived from investments in Green IT. However, evidence from the literature shows that the measurement of IT value is a complex, challenge involving multiple stakeholders. Green IT, such as Cloud computing, adds further complexity to the understanding of IT value as the expected operational and business benefits should also be complemented by environmental and societal concerns. This paper contributes to the area of Cloud computing and Green IT research through the development of a framework that measures the value of Green IT. The framework expands on the work of Corbett (2010) and is developed as a result of a comprehensive literature review of both seminal works in the IT value field and also the most recent studies in Green IT. This paper demonstrates the efficacy of the value framework by reporting from a series of case studies involving Cloud computing. Using exploratory case studies, this study highlights the utility of the model and its applicability to multiple contexts. Although the framework can be applied in multiple settings, the findings highlight a number of areas that are prominent in SMEs and those in need of further attention.
Applicability of Waterside Corrosion Models in Range of IFPE Database

: Fuel rod cladding waterside corrosion is one of the phenomena that limit the life time of nuclear fuel. Corrosion performance depends on the cladding material properties as well as operating conditions during the irradiation of the fuel. As a function of temperature, power history, water chemistry, time, etc., waterside corrosion is of great concern in fuel performance evaluation, especially for high burnup fuels. This paper is dedicated to the study of the waterside corrosion phenomenon using the IFPE database by COPERNIC, which is developed for the analysis of fuel rod behaviors in normal operation and transient conditions. Different models, MATPRO, FRAMATOME and EPRI models, for example, are adopted in the simulations. The results derived from the models are compared and the unconformities are analyzed. Based on the comparative analysis, reasonable models are chosen to simulate certain irradiated fuel rods. Our analyses indicate that potential affecting factors which are not considered in COPERNIC code, such as water chemistry and alloy composition, should be responsible for discrepancies of certain rod predictions.
Assessment of surgeon's stress level and alertness using EEG during laparoscopic simple nephrectomy

Laparoscopic simple nephrectomy (LSN) is an accepted treatment modality for nonfunctioning kidneys. Besides decreased postoperative morbidity, LSN is an advantage with decreased analgesic requirements and convalescence. LSN is a highly stressful operation, and the procedure requires high concentration level and experience. Emotions recognized from Electroencephalogram (EEG) may lead to detect the real emotions of the human. In this study, we proposed a subject-dependent stress level detection from EEG using the (Fpz beta/alpha) ratio to recognize high and low dominance levels of feelings based on the 2D Valence-Arousal model. The stress level of the surgeon is monitored via EEG during the operation. The most stressful phase of LSN and its change over time are determined using wireless EEG headset with real-time measurements. The aim here is to monitor and utilize objective information on the mental effort and stress demanded.
Reducing maternal deaths through state maternal mortality review.

BACKGROUND Illinois has one of the highest rates of maternal death in the United States, and in 2000, the Illinois Maternal Mortality Review Committee (MMRC) was created to address this high rate of maternal death. METHODS This is a detailed description of the development of the MMRC, its process of review, its impact on the state's attention to maternal mortality and its obstetric hospitals, and a summary of its initial findings. RESULTS The Illinois MMRC, specifically designed to be multidisciplinary, was created to provide secondary review of select maternal deaths. Between 2000 and 2010, 45 of the 93 deaths reviewed had complete analysis. Hemorrhage was the leading cause of death, and 69% of all cases were deemed potentially avoidable. Compared to the primary required review conducted by the State Perinatal Center, the secondary review by the MMRC changed the cause of death in 20% of cases and changed the determination of avoidability in 36% of cases. Based on these findings and advocacy by the MMRC, in 2008, Illinois mandated that every M.D. and R.N. provider working in the obstetric unit of every obstetric hospital must complete the maternal hemorrhage education program. CONCLUSIONS The MMRC has had a positive impact on Illinois' approach to reducing maternal deaths by being instrumental in getting the state to mandate that every obstetric hospital must comply with the Obstetric Hemorrhage Education Project to maintain its credentials. Further, the high rates at which cause of death and potential avoidability of death were changed by the MMRC underscore the need for multidisciplinary independent review of maternal deaths to achieve more accurate data and, hence, ultimately institute focused interventions to decrease preventable deaths.
A High Speed CMOS Transmitter and Rail-to-Rail Receiver

This paper presents a high speed low voltage differential signal (LVDS) interface circuit for CPU, LCD, FPGA and other fast links. In the proposed transmitter a stable reference and a common mode feedback circuit are applied into the LVDS drivers, which enable the transmitter to tolerate the variations of process, temperature and supply voltage. The proposed receiver implements a rail-to-rail amplifier architecture which allows a 1.6 Gb/s transmission. The transmitter and receiver are implemented in HJ TC 3.3 v, 0.18 plusmn CMOS technology. Transmission operations up to 1.6 Gb/s with random data patterns were demonstrated. The transmitter and receiver pad cells exhibit a power consumption of 35 mW and 6 mW respectively.
Surgical technique: coupling of intrastromal corneal ring segments for ectatic corneal disorders in eye bank corneas

The management of corneal ectasia is evolving, with intrastromal corneal ring segments playing an important role in delaying or eliminating the need for penetrating keratoplasty. This paper describes a modification in the implantation technique of intrastromal corneal ring segments that allows for coupling of the two segments with suture, affording more structural support.
Interactions between algal‐bacterial populations and trace metals in fjord surface waters during a nutrient‐stimulated summer bloom

We examined how variations in algal‐bacterial community structure relate to Cu, Zn, and Mn speciation during a diatom‐rich bloom that was induced by daily additions of inorganic macronutrients to fjord waters in August 2002. The experiments were carried out in 11‐m3 floating mesocosm bags deployed in the Raunefjord, near Bergen, Norway, and operated in a chemostat (flow‐through) mode. Copper speciation was controlled by the formation of very strong organic complexes (log K1' = 15.2–15.8; log 1' = 13.0–13.4) whose likely source was the cyanobacterium Synechococcus sp. Strong ligand concentrations were comparable to dissolved Cu levels. This covariation kept the free Cu2+ concentration within the range of 10-12.4 to 10-11.2 mol L-1, i.e., below the toxicity threshold for Synechococcus. Weaker ligands (log 1' = 8.2–9.4) were released during—and up to 4 d following—the exponential 93 growth of algae. During this period, the weaker Cu‐binding ligands appeared to have the same source or production process as the proteinlike fluorophores detected in these coastal waters. Zinc speciation was controlled by complexation with a single class of organic ligands that appeared to be released inadvertently upon the death and/or grazing of phytoplankton. Labile manganese fluctuations were inversely synchronized with the abundance of heterotrophic bacteria until the coastal waters experienced a massive rain event on day 17 of the experiment. The rainfall, which was a source of nitrogen and micronutrients, appeared to stimulate the growth of larger cells (diatoms) but to inhibit that of the smaller cells (heterotrophic bacteria and cyanobacteria).
Stern-Judging: A Simple, Successful Norm Which Promotes Cooperation under Indirect Reciprocity

We study the evolution of cooperation under indirect reciprocity, believed to constitute the biological basis of morality. We employ an evolutionary game theoretical model of multilevel selection, and show that natural selection and mutation lead to the emergence of a robust and simple social norm, which we call stern-judging. Under stern-judging, helping a good individual or refusing help to a bad individual leads to a good reputation, whereas refusing help to a good individual or helping a bad one leads to a bad reputation. Similarly for tit-for-tat and win-stay-lose-shift, the simplest ubiquitous strategies in direct reciprocity, the lack of ambiguity of stern-judging, where implacable punishment is compensated by prompt forgiving, supports the idea that simplicity is often associated with evolutionary success.