nils-herrmann/clean_scirepeval huggingface dataset:
Specific Enrichment and Proteomics Analysis of Escherichia coli Persisters from Rifampin Pretreatment.
Venue: Journal of proteome research
Year: 2018

Bacterial persisters, a dormant and multidrug tolerant subpopulation that are able to resuscitate after antibiotic treatment, have recently received considerable attention as a major cause of relapse of various infectious diseases in the clinic. However, because of their low abundance and inherent transience, it is extremely difficult to study them by proteomics. Here we developed a magnetic beads based separation approach to enrich Escherichia coli persisters and then subjected them to shotgun proteomics. Rifampin pretreatment was employed to increase persister formation, and the resulting cells were exposed to a high concentration of ampicillin (10x MIC) to remove nonpersisters. The survivors were analyzed by spectral counting based quantitative proteomics. On average, 710 proteins were identified at a false discovery rate of 0.01 for enriched E. coli persisters. By spectral counting based quantification, 105 proteins (70 down regulated, 35 up regulated) were shown to be differentially expressed compared with normal cells. A comparison of the differentially expressed proteins between the magnetic beads enriched persisters and nonenriched persisters (a mixture of persisters and intact dead cells) shows only around half ~58% overlap and different protein protein interaction networks. This suggest that persister enrichment is important to eliminate the cumulative effect of dead cells that will obscure the proteome of persisters. As expected, proteins involved in carbohydrate metabolism, fatty acid and amino acid biosynthesis, and bacterial chemotaxis were found to be down regulated in the persisters. Interestingly, membrane proteins including some transport proteins were up regulated, indicating that they might be important for the drug tolerance of persisters. Knockout of the pal gene expressing peptidoglycan associated lipoprotein, one of the most up regulated proteins detected in persisters, led to 10 fold reduced persister formation under ampicillin treatment.
The AEC Challenges and The Curriculum Change in Indonesia Guidance and Counseling Perspective
Year: 2015

Education especialy in terms of the educational system affect the efforts to overcome the problem of unemployment. The Indonesian unemployment rate based on Human development Index reached its highest number which is up 7.24 million people. Research showed that the higher the education quality is, the better the quality of human resources will be. The problems of education in Indonesia lie on the educational system, curriculum, and not targeted graduates. Those become the main problems in resulting the increasing unemployment rate in Indonesia. Meanwhile, the AEC (ASEAN Economic Community) soon will be implemented in Indonesia. Increasing the quality of the human resopurces becomes the main objective of government to deal with the ASEAN free trade. Curriculum is the document or the blue print of the education quality which must be possessed by the student and also becomes the reference is not an exuse for the less optimal implementation of the Indonesia education. The 2013 Curriculum in Indonesia is based on the IQF (KKNI) in which it become the basis of the educational rules that will be the ideal way to confront with the 2015 AEC. On the other side, the guidance and counseling field which based on the IQF (KKNI) has the major influence to increase and succeed the human resources that will be able to compete in the global market and to be front pillar of understanding and application in preparing the most qualified human resources.
Cutaneous Immune Related Adverse Events (irAEs) to Immune Checkpoint Inhibitors: A Dermatology Perspective on Management
Venue: Journal of cutaneous medicine and surgery
Year: 2020

Immune checkpoint inhibitors have proven to be efficacious for a broad spectrum of solid organ malignancies. These monoclonal antibodies lead to cytotoxic T cell activation and subsequent elimination of cancer cells. However, they can also lead to immune intolerance and immune related adverse event (irAEs) that are new and specific to these therapies. Cutaneous irAEs are the most common, arising in up to 34% of patients on PD 1 inhibitors and 43% to 45% on CTLA 4 inhibitors. The most common skin manifestations include maculopapular eruption, pruritus, and vitiligo like lesions. A grading system has been proposed, which guides management of cutaneous manifestations based on the percent body surface area (BSA) involved. Cutaneous irAEs may prompt clinicians to reduce drug doses, add systemic steroids to the regiment, and/or discontinue lifesaving immunotherapy. Thus, the goal is for early identification and concurrent management to minimize treatment interruptions. We emphasize here that the severity of the reaction should not be graded based on BSA involvement alone, but rather on the nature of the primary cutaneous pathology. For instance, maculopapular eruptions rarely affect <30% BSA and can often be managed conservatively with skin directed therapies, while Stevens Johnson syndrome (SJS) affecting even 5% BSA should be managed aggressively and the immunotherapy should be discontinued at once. There is limited literature available on the management of the cutaneous irAEs and most studies present anecdotal evidence. We review the management strategies and provide recommendations for psoriatic, immunobullous, maculopapular, lichenoid, acantholytic eruptions, vitiligo, alopecias, vasculitides, SJS/toxic epidermal necrolysis, and other related skin toxicities.
A multi ATL method for transfer learning across multiple domains with arbitrarily different distribution
Venue: Knowl. Based Syst.
Year: 2016

This paper addresses a novel learning problem where data from multiple domains are generated from distributions that are allowed to be arbitrarily different. Domain adaptation and transfer learning have been addressed previously for two domains with different distributions, but based on the assumption that the distributions are sufficiently related to each other. However, in many real world applications, multiple domains may have arbitrarily different distributions. In this paper, a general framework is proposed, called Multi ATL, for bridging knowledge from multiple domains with arbitrarily different distributions. The proposed framework consists of three key components: latent feature space extraction, co training with multiple views, and active sample selection. The basic concept is to explore each domain and characterize it with an extracted latent feature space, and then apply a co training algorithm to the latent spaces to use multiple views simultaneously for training. In the co training process, active sample selection is used to determine how much knowledge should be transferred from a source domain to the target domain. Experimental results on one synthetic and two real world datasets show that the proposed framework significantly improves classification accuracy (13.5% on the synthetic and +17.79% +23.87% on the real datasets) with only a few (2 5) active selections.
Atomic force microscopy of a ctpA mutant in Rhizobium leguminosarum reveals surface defects linking CtpA function to biofilm formation.
Venue: Microbiology
Year: 2011

Atomic force microscopy was used to investigate the surface ultrastructure, adhesive properties and biofilm formation of Rhizobium leguminosarum and a ctpA mutant strain. The surface ultrastructure of wild type R. leguminosarum consists of tightly packed surface subunits, whereas the ctpA mutant has much larger subunits with loose lateral packing. The ctpA mutant strain is not capable of developing fully mature biofilms, consistent with its altered surface ultrastructure, greater roughness and stronger adhesion to hydrophilic surfaces. For both strains, surface roughness and adhesive forces increased as a function of calcium ion concentration, and for each, biofilms were thicker at higher calcium concentrations.
Heat and mass transfer comparisons of desiccant coated microchannel and fin and tube heat exchangers
Venue: Applied Thermal Engineering
Year: 2019

Two types of DCHEs, desiccant coated microchannel heat exchanger (DMHE) and desiccant coated fin and tube heat exchanger (DFHE) are manufactured and tested. The heat transfer, mass transfer and pressure drop performances of two DCHEs are analyzed and compared by experimental results. In the same conditions, the heat transfer coefficients of DMHE are almost twice as large as those of DFHE, no matter for sensible heat or latent heat. In dehumidification, the ratios of latent heat to total heat for DFHE and DMHE are 90% and 83% separately. In regeneration, the ratios of latent heat to total heat for two DCHEs are both approximately 60% The mass transfer coefficient of DMHE is 15% larger than that of DFHE. The pressure drops per unit transfer area of DMHE is almost 125% larger than that of DFHE. In a conclusion, DMHE shows lower heat capacity, higher heat and mass transfer capacity compared with DFHE.
Using Kotter's Eight Stage Process to Manage an Organisational Change Program: Presentation and Practice
Year: 2015

Kotter's eight stage process for creating a major change is one of the most widely recognised models for change management, and yet there are few case studies in the academic literature that enquire into how this process has been used in practice. This paper describes a change manager's action research enquiring into the use of this Process to manage a major organisational change. The change was initiated in response to the organisation's ageing workforce, introducing a knowledge management program focusing on the interpersonal aspects of knowledge retention. Although Kotter's process emphasises a top led model for change, the change team found it was necessary to engage at many levels of the organisation to implement the organisational change. The process is typically depicted as a linear sequence of steps. However, this image of the change process was found to not represent the complexity of the required action. Managing the change required the change team to facilitate multiple concurrent instances of Kotter's process throughout the organisation, to re create change that was locally relevant to participants in the change process.
Survey and Planning of High Payload Human Robot Collaboration: Multi modal Communication Based on Sensor Fusion
Year: 2019

Human Robot Collaboration (HRC) has gained increased attention with the widespread commissioning and usage of collaborative robots. However, recent studies show that the fenceless collaborative robots are not as harmless as they look like. In addition, collaborative robots usually have a very limited payload (up to 12 kg) which is not satisfactory for most of the industrial applications. To use high payload industrial robots in HRC, today's safety systems has only one option, limiting speeds of robot motion execution and redundant systems for supervision of forces. The reduction of execution speed, reduces efficiency, which limits more widespread of automation. To overcome this limitation, in this paper, we propose novel sensor fusion of different safety related sensors and combine these in a way that they ensure safety, while the human operator can focus on task execution and communicate with the system in a natural way. Different communication channels are explored (multi modal) and demonstration scenarios are presented.
Gel combustion synthesis and magnetic properties of CoFe2O4, ZnFe2O4, and MgFe2O4 using 6 aminohexanoic acid as a new fuel
Year: 2020

For the first time, 6 aminohexanoic acid is used as an alternative fuel in the synthesis of the spinel ferrites with compositions CoFe2O4, ZnFe2O4 and MgFe2O4 using gel combustion synthesis with different oxidizer to fuel (O/F) ratios. The gel precursors were studied by differential thermal analysis and thermogravimetry (DTA/TG) which showed that the ignition temperature depends on the gel precursor, being around 230 degC, 130 degC and 275 degC for CoFe2O4, ZnFe2O4, and MgFe2O4, respectively. These results showed than the 6 aminohexanoic acid has an ignition temperature lower than the urea and the citric acid when were used in the synthesis of the spinel ferrites by gel combustion. Moreover, the adiabatic flame temperature (Tad) of the reactions of combustion were calculated using thermodynamic analysis, which showed that Tad increases when the mass of the 6 aminohexanoic acid increases. X ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) techniques confirmed the formation of the spinel structures for all the O/F ratios, but there is a minor impurity phase for some experiments. The particle morphology was evaluated using scanning electron microscopy (SEM) showing aggregated particles with a sponge like structure due to the released gases during the combustion. A vibrating sample magnetometer (VSM) was used for measuring the magnetic properties of the as prepared powders. The values of saturation magnetization, Ms, and coercitivity, Hc, were Ms 66.9 emu/g and Hc 1505 Oe for CoFe2O4, Ms 44.6 emu/g and Hc 75.2 Oe for ZnFe2O4 and Ms 28.66 emu/g and Hc 111.4 Oe for MgFe2O4. The optical band gap for CoFe2O4, ZnFe2O4, and MgFe2O4 were 1.11 eV, 1.37 eV and 1.64 eV, respectively. These results show that 6 aminohexanoic acid can be used as an alternative fuel in the synthesis of spinel ferrites using gel combustion synthesis.
Performance Investigation of High Temperature Application of Molten Solar Salt Nanofluid in a Direct Absorption Solar Collector
Venue: Molecules
Year: 2019

Nanofluids have great potential in a wide range of fields including solar thermal applications, where molten salt nanofluids have shown great potential as a heat transfer fluid (HTF) for use in high temperature solar applications. However, no study has investigated the use of molten salt nanofluids as the HTF in direct absorption solar collector systems (DAC) In this study, a two dimensional CFD model of a direct absorption high temperature molten salt nanofluid concentrating solar receiver has been developed to investigate the effects design and operating variables on receiver performance. It has been found that the Carnot efficiency increases with increasing receiver length, solar concentration, increasing height and decreasing inlet velocity. When coupled to a power generation cycle, it is predicted that total system efficiency can exceed 40% when solar concentrations are greater than 100x. To impart more emphasis on the temperature rise of the receiver, an adjusted Carnot efficiency has been used in conjunction with the upper temperature limit of the nanofluid. The adjusted total efficiency also resulted in a peak efficiency for solar concentration, which decreased with decreasing volume fraction, implying that each receiver configuration has an optimal solar concentration.
Learning in Multi agent Systems with Sparse Interactions by Knowledge Transfer and Game Abstraction
Venue: AAMAS
Year: 2015

In many multi agent systems, the interactions between agents are sparse and exploiting interaction sparseness in multi agent reinforcement learning (MARL) can improve the learning performance. Also, agents may have already learnt some single agent knowledge (e.g. local value function) before the multi agent learning process. In this work, we investigate how such knowledge can be utilized to learn better policies in multi agent systems with sparse interactions. We adopt game theory based MARL as the basic learning approach since it can coordinate agents better. We contribute three knowledge transfer mechanisms. The first one is value function transfer, which directly transfers agents' local value functions to the learning algorithm. The second one is selective value function transfer, which only transfers the value functions in states where the environmental dynamics change slightly. The last mechanism is model transfer based game abstraction, which further improves the former two mechanisms by abstracting the one shot game in each state and reducing equilibrium computation. Experimental results in benchmarks show that with the three knowledge transfer mechanisms, all of the tested game theory based MARL algorithms are drastically improved and also achieve better asymptotic performance than the state of the art algorithm CQ learning.
The costimulatory molecule CD226 signals through VAV1 to amplify TCR signals and promote IL 17 production by CD4+ T cells
Venue: Science Signaling
Year: 2018

VAV1 mediates cross talk between the CD226 and TCR signaling pathways to enhance production of the proinflammatory cytokine IL 17. VAV1, a T cell hub The guanine nucleotide exchange factor VAV1 is required for T cell receptor (TCR) signaling and activation of T cells. By analyzing the VAV1 interactome, Gaud et al. found that VAV1 also interacted with the costimulatory molecule CD226. Engagement of CD226 activated VAV1, which in turn enhanced the TCR dependent production of the proinflammatory cytokine IL 17 by human T cells. A variant of CD226 that is associated with autoimmune diseases stimulated more VAV1 activity and IL 17 production than did wild type CD226, demonstrating that VAV1 mediated cross talk between the CD226 and TCR signaling pathways affects both normal and pathological T cell activation. The activation of T cells requires the guanine nucleotide exchange factor VAV1. Using mice in which a tag for affinity purification was attached to endogenous VAV1 molecules, we analyzed by quantitative mass spectrometry the signaling complex that assembles around activated VAV1. Fifty VAV1 binding partners were identified, most of which had not been previously reported to participate in VAV1 signaling. Among these was CD226, a costimulatory molecule of immune cells. Engagement of CD226 induced the tyrosine phosphorylation of VAV1 and synergized with T cell receptor (TCR) signals to specifically enhance the production of interleukin 17 (IL 17) by primary human CD4+ T cells. Moreover, co engagement of the TCR and a risk variant of CD226 that is associated with autoimmunity (rs763361) further enhanced VAV1 activation and IL 17 production. Thus, our study reveals that a VAV1 based, synergistic cross talk exists between the TCR and CD226 during both physiological and pathological T cell responses and provides a rational basis for targeting CD226 for the management of autoimmune diseases.
Emotion recognition using facial feature extraction
Year: 2019

.ii List of Figures .vii  Hypothesis..1 Significance of Research..2 Research Approach .3 Literature Survey .3 Applied Software .4 Feature Extraction .5 Classification..6 Accuracy Assessment .6 Thesis Structure .7 Chapter 2: Literature Survey .8  What is it? .8 Universality of vs. Cultural Influence on Facial Expressions .9 Varied Approaches to Emotion Recognition .13 Principle Component Analysis .14 Discrete Cosine Transform .21 Fast Walsh Hadamard Transform .24 Facial Action Coding System .26
Response of pearl millet and mungbean intercropping under custard apple orchard of Vindhyan region.
Year: 2015

A field experiment was conducted during 2010 and 2011 to know the response of pearl millet and mungbean intercropping under custard apple orchard of vindhyan region. The highest grain, straw, biological and mean pearl millet grain equivalent yield were recorded under pearl millet sole and mungbean sole as compared to other treatments. Whereas grain wt. (g)/ear head, test weight (g) ear diameter (cm) ear length (cm) and ear wt (g) of pearl millet and pod length, number of pod/plant and number of grain/pod, test weight (g) of mungbean were maximum recorded under pearl millet+mungbean (2:2) in intercropping row ratio. The highest harvest index of mungbean and aggresivity were recorded in treatment pearl millet+mungbean (2:1) in intercropping row ratio as compared to other treatments. Nitrogen in grain and phosphorus in grain, straw and total nitrogen and phosphorus uptake were maximum recorded in pearl millet sole and mungbean sole as compared to other treatments. The maximum nitrogen in straw protein content in pearl millet and mungbean grain land equivalent ratio and relative crowding coefficient were observed in pearl millet+mungbean (2:2) in intercropping row ratio.
Evaluation of Dose Rate and Photon Energy Dependence of Gafchromic EBT3 Film Irradiating with 6 MV and Co 60 Photon Beams
Venue: Journal of medical signals and sensors
Year: 2019

Gafchromic films are utilized for two dimensional dose distribution measurements, especially in radiotherapy. In this study, we investigated a close connection between energy and dose rate of Gafchromic EBT3 films irradiating with 6 MV and Co 60 photon beams over a broad dose range. EBT3 films were exposed to 6 MV and Co 60 photon beams using 4 and 2 Gy/min dose rates over a 10 400 cGy dose range. The films were scanned in red, green, and blue channels to obtain the optical density (OD) dose curves. The OD dose curves resulted from three color scans for different photon energies and dose rates were compared by statistical independent t test. For the radiations of Co 60 and 6 MV photon beams, the highest correlation was obtained between the 2 and 4 Gy/min dose rates with red and green channels, respectively. Moreover, the red channel had a greater OD response per dose value, following the green and blue channels. There was no significant difference between different photon energies' (Co 60 and 6 MV) and dose rates' (2 and 4 Gy/min) dependence on OD dose response of EBT3 films over a broad domain of radiation dose, except for different photon energies in the blue channel. Our results revealed that the OD dose response of EBT3 films is independent on photon energies (Co 60 and 6 MV) and dose rate (2 and 4 Gy/min) in the evaluated dose range (10 400 cGy) Therefore, the EBT3 films are suitable, consistent, and reliable instruments for dose measurements in radiotherapy.
Assessment of the efficacy of acupuncture and chiropractic on treating Cervical spondylosis radiculopathy
Venue: Medicine
Year: 2019

Cervical spondylosis radiculopathy (CSR) is often described as neck pain accompanied with radiating pain and neurologic symptoms, such as numbness, muscle weakness, and diminished reflexes, in 1 or both upper extremities. As people's lifestyle changes and the population ages, the incidence of CSR continues to increase. Many clinical trials have proven that acupuncture and chiropractic has a significant effect in the treatment of CSR. In this systematic review, we aim to evaluate the effectiveness and safety of acupuncture and chiropractic for CSR.  We will search PubMed, Cochrane Library, AMED, EMbase, WorldSciNet;  Science online and China Journal  The time is limited from the construction of the library to February, 2019. We will use the criteria provided by Cochrane 5.1.0 for quality assessment and risk assessment of the included studies, and use the Revman 5.3 and Stata13.0 software for meta analysis of the effectiveness, recurrence rate, and symptom scores of CSR.