nils-herrmann/clean_scirepeval huggingface dataset:
Diversity and functional prediction of microbial communities involved in the first aerobic bioreactor of coking wastewater treatment system
Venue: PloS one
Year: 2020

The pre aerobic process of coking wastewater treatment has strong capacity of decarbonization and detoxification, which contribute to the subsequent dinitrogen of non carbon source/heterotrophic denitrification. The COD removal rate can reach 90% in the first aerobic bioreactor of the novel O/H/O coking wastewater treatment system during long term operation. The physico chemical characteristics of influent and effluent coking wastewater in the first aerobic bioreactor were analyzed to examine how they correlated with bacterial communities. The diversity of the activated sludge microbial community was investigated using a culture independent molecular approach. The microbial community functional profiling and detailed pathways were predicted from the 16S rRNA gene sequencing data by the PICRUSt software and the KEGG database. High throughput MiSeq sequencing results revealed a distinct microbial composition in the activated sludge of the first aerobic bioreactor of the O/H/O system. Proteobacteria, Bacteroidetes, and Chlorobi were the decarbonization and detoxification dominant phyla with the relative abundance of 84.07 5.45, 10.89 6.31, and 2.96 1.12% respectively. Thiobacillus, Rhodoplanes, Lysobacter, and Leucobacter were the potential major genera involved in the crucial functional pathways related to the degradation of phenols, cyanide, benzoate, and naphthalene. These results indicated that the comprehensive understanding of the structure and function diversity of the microbial community in the bioreactor will be conducive to the optimal coking wastewater treatment.
The welfare of dairy cattle: perspectives of industry stakeholders
Year: 2013

The aim of the current study was to describe the perspectives of stakeholders within the dairy industry on key issues affecting the welfare of dairy cattle. A secondary aim was to examine if these stakeholders believed that people outside of the industry should also have a voice in formulating solutions to these issues. Five heterogeneous focus groups were conducted during a dairy cattle industry meeting in Guelph, Canada in October 2012. Each group contained between 7 10 participants and consisted of a mix of dairy producers, veterinarians, researchers, students, and industry specialists. The 1 h facilitatorled discussions focused on participants' perceptions of the key welfare issues and the role of different stakeholder groups in addressing these concerns. Discussions were audio recorded and transcribed verbatim, and the resulting transcripts coded and the themes identified. Lameness was uniformly recognized as the most important welfare issue facing dairy cattle; cow comfort, painful procedures (like dehorning) and production diseases (like mastitis) were also commonly discussed. Participants had mixed views on the roles of different stakeholders in formulating solutions. Most felt that producers and others working within the dairy industry (particularly veterinarians) should be primarily responsible, but many participants acknowledged that the general public, as consumers and as citizens, also play an important role. Participants seemed to focus on a two fold knowledge deficit first between researchers and producers, and second between dairy industry groups and the public and agreed that improved knowledge translation was required to develop solutions to welfare concerns. These results indicate that many people within the dairy industry see value in more inclusive engagement with non industry stakeholders about dairy cattle welfare. Future work will assess perspectives of people outside of the dairy industry to identify areas of shared concern and provide a basis for policy solutions that better incorporate societal values.
EVERWORSE: WHAT'S WRONG WITH SELECTING FOR DISABILITY?
Year: 2011

the fortunes and characteristics of their future children; all they need do is time conception in the hope that birth will occur with the sun in a suitably propitious constellation. But the astrologers are not to be believed. Instead, prospective parents are turning to new reproductive technologies, including pre implantation genetic screening and embryo selection, as a means to exert some influence over the characteristics of future offspring. Although the significance of genetics is often exaggerated our genes are not our destiny genetic selection has a far better claim to efficacy than astrological selection. We distinguish three applications of genetic selection: selection on non disease characteristics; selection against disease or disability; and selection for disease or disability. Selection on non disease characteristics (whether aimed at enhance ment, such as selection for high IQ, or simply at satisfying parental preferences for a baby of a particular sex or with a particular eye color) is the most controversial application of genetic selection, evoking fears of eugenics, designer babies, and toxic parental expectations.1 Although selection against genetic disease or dis ability has its critics,2 it is already widely accepted in actual medical practice. But it is the third application, selection for disability, that comes closest to being uncontroversial, striking many people as just obviously wrong. In this paper we challenge the moral consensus against selection for disability. Our discussion will concern only those disabilities that are compatible with a life worth living from the point of view of the disabled individual. We will argue that an influential, impersonal argument against selection for disability falls to a counterexample. We will then show how the reach of the counterexample can be broadened to make trouble for anyone who objects to selection for disability. If we are right about the problems for objections to selection for disability, the question arises as to why such objections are so widespread. We suggest that intuitions are being skewed against selection for disability by certain quirks in
Comparison of 3 anesthetic protocols for the elective cesarean section in the dog: Effects on the bitch and the newborn puppies.
Venue: Animal reproduction science
Year: 2018

This study assessed the influence of 3 different anesthetic protocols based on the quality of anesthesia induction and maintenance in four dog breeds (French Bulldog, n 13; Yorkshire terrier, n 12; Chihuahua, n 10; Bull Terrier, n 10) subjected to cesarean section. Neonatal mortality, birth defects and newborn viability were assessed. All females were pre medicated with morphine (IM) and then were assigned to three different anesthetic protocols: group P (n 17) anesthesia was induced with propofol (IV) and then also maintained with propofol until the complete delivery of puppies and then anesthesia was maintained afterwards with sevoflurane; group PS (n 14) anesthesia was induced with IV propofol, and maintenance of the anesthesic plan was performed with sevoflurane; group PES (n 14) the females were induced by propofol and an epidural anesthesia was then performed, anesthesia was then maintained with propofol until the complete extraction of all puppies and then anesthesia was maintained afterwards with sevoflurane. Throughout the surgery, group PES required a lower concentration of sevoflurane (p 0.05) and extra doses of propofol or fentanyl during inhalatory anesthesia were not required. Mean values of heart rate (p 0.01) were higher in females from groups P and PS. Mean values of blood pressure values were lower (p 0.01) in group PES as compared with the other two groups. Birth defects were detected in 3.1% (5/162) of the neonates, with a significantly higher incidence (p 0.05) in French bulldog puppies. Neonatal viability was assessed using a modified Apgar score model; Apgar score was defined immediately after delivery (Apgar0) and a second score was assessed 60 min after delivery (Apgar60) Apgar0 scores were significantly different between the groups, showing neonates of group PES the highest values (p 0.05) In Apgar60, more than 94% of puppies were already classified as normal viability neonates (7 10 score) and no differences were observed between groups. This study confirmed that females of group PES showed a higher quality of anesthesia during surgery and a vitality of puppies immediately after delivery. Regardless of the anesthetic protocol used, French bulldog females and puppies required more clinical care than other breeds.
Computing for Medicine: Can We Prepare Medical Students for the Future?
Venue: Academic medicine journal of the Association of American Medical Colleges
Year: 2019

Technology can transform health care; future physicians need to keep pace to ensure optimal patient care. Because future doctors are poorly prepared in computer literacy, the authors designed a computer programming certificate course. This Innovation Report describes the course and findings from a qualitative study to understand the ways it prepares medical students to use computing science and technology in medicine.  The 14 month Computing for Medicine certificate course (C4M, offered beginning in February 2016) University of Toronto, is comprised of hands on workshops to introduce programming accompanied by homework exercises, seminars by computer science experts on the application of programming to medicine, and coding projects. Using purposive and maximal variation sampling, 17 students who completed the course were interviewed from April May 2017. Thematic analysis was performed using an iterative constant comparison approach.  Participants praised the C4M as an opportunity to achieve computer literacy including language, syntax, and fundamental computational ideas (and their application to medicine) and acquire or strengthen algorithmic and logical thinking skills for approaching problems. They highlighted that the course illustrated linkages between computer science and medicine. Participants acknowledged a sometimes existent chasm between producers and users of technology in medicine, recommending two way communication between the disciplines when developing technology for use in medicine. Next Steps We recommend that medical schools consider computer literacy an essential skill to foster future collaborative computing partnerships for improved technology use by physicians and optimal patient care. We encourage further evaluation of future iterations of the C4M and similar courses.
Plasma assisted catalytic dry reforming of methane (DRM) over metal organic frameworks (MOFs) based catalysts
Year: 2020

Plasma assisted dry reforming of methane (DRM) was performed in a dielectric barrier discharge (DBD) reactor. The effect of different packing materials including ZrO2, UiO 67 MOF and PtNP@UiO 67 on plasma discharge was investigated, showing that ZrO2 suppressed the plasma generation while UiO 67 improves it due to its porous nature which favours the formation of filamentary microdischarges and surface discharges. The improved plasma discharge increased the conversion of CH4 and CO2 by about 18% and 10% respectively, compared to the plasma alone mode. In addition, the distribution of hydrocarbon products changed from dominant C2H6 in the plasma alone mode to C2H2 and C2H4 in the UiO 67 promoted plasma assisted DRM. The UiO 67 MOF was stable in plasma, showing no significant changes in its properties under different treatment times, discharge powers and gases. Pt nanoparticles (NPs) on UiO 67 improved plasma assisted DRM, especially the selectivity due to the presence of surface reactions. Due to the dehydrogenation of hydrocarbons over Pt NPs, the selectivity to hydrocarbons decreased by 30% compared to the UiO 67 packing. In situ diffuse reflectance infrared Fourier transformed spectroscopy (DRIFTS) was carried out to probe the surface reactions on PtNP@UiO 67 catalyst, showing the decomposition of surface formats to CO and C2H4 dehydrogenation over the metallic Pt. The PtNP@UiO 67 catalyst showed good reusability in the plasma assisted DRM, and H2 production was improved by high CH4/CO2 molar ratio and low feed flow rate.
Personal Digital Assistant (PDA) woher und wohin?
Year: 2008

This paper describes the development of modern PDAs and traces some historical roots because personal information management is an idea Helmut Dollfuss with a long tradition. It was put into practice early in human history 1 Medizinische Universitat Wien, Universitatsbibliothek, Wien, Osterreich based on different materials as data carrier. Fromwax plates and paper the idea was grafted onto microprocessor powered calculators. Further on the concept was transferred to coat pocket sized handheld computers. These were called PDAs forming a device class on their own though functions of a PDA are ingreasingly integrated into other mobile devices. Finally the paper discusses the future of PDAs as spearhead of the mobile library. The PDA can be seen as a prophet in this movement followed by a range of new to be mobile devices. Out of this we can expect to meet an even greater variety of operating systems, display sizes and communication channels in the future. PDA projects are an ideal way to gain expert knowledge now for a mobile future in library information technology.
Coffee, Caffeine, and Health Outcomes: An Umbrella Review.
Venue: Annual review of nutrition
Year: 2017

To evaluate the associations between coffee and caffeine consumption and various health outcomes, we performed an umbrella review of the evidence from meta analyses of observational studies and randomized controlled trials (RCTs) Of the 59 unique outcomes examined in the selected 112 meta analyses of observational studies, coffee was associated with a probable decreased risk of breast, colorectal, colon, endometrial, and prostate cancers; cardiovascular disease and mortality; Parkinson's disease; and type 2 diabetes. Of the 14 unique outcomes examined in the 20 selected meta analyses of observational studies, caffeine was associated with a probable decreased risk of Parkinson's disease and type 2 diabetes and an increased risk of pregnancy loss. Of the 12 unique acute outcomes examined in the selected 9 meta analyses of RCTs, coffee was associated with a rise in serum lipids, but this result was affected by significant heterogeneity, and caffeine was associated with a rise in blood pressure. Given the spectrum of conditions studied and the robustness of many of the results, these findings indicate that coffee can be part of a healthful diet.
Important classes of reactions for the proactive and reactive resource constrained project scheduling problem
Venue: Ann. Oper. Res.
Year: 2019

The proactive and reactive resource constrained project scheduling problem (PR RCPSP) that has been introduced recently (Davari and Demeulemeester, 2017) deals with activity duration uncertainty in a very unique way. The optimal solution to an instance of the PR RCPSP is a proactive and reactive policy (PR policy) that is a combination of a baseline schedule and a set of required transitions (reactions) In this research, we introduce two interesting classes of reactions, namely the class of selection based reactions and the class of buffer based reactions, the latter in fact being a subset of the class of selection based reactions. We also discuss the theoretical relevance of these two classes of reactions. We run some computational results and report the contributions of the selection based reactions and the buffer based reactions in the optimal solution. The results suggest that although both selection based reactions and buffer based reactions contribute largely in the construction of the optimal PR policy, the contribution of the buffer based reactions is of much greater importance. These results also indicate that the contributions of non selection based reactions (reactions that are not selection based) and selection but not buffer based reactions (selection based reactions that are not buffer based) are very limited.
Cross biome metagenomic analyses of soil microbial communities and their functional attributes
Venue: Proceedings of the National Academy of Sciences
Year: 2012

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant free cold desert soils typically had the lowest levels of functional diversity (diversity of protein coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.
The Smac Mimetic BV6 Improves NK Cell Mediated Killing of Rhabdomyosarcoma Cells by Simultaneously Targeting Tumor and Effector Cells
Venue: Front. Immunol.
Year: 2017

Rhabdomyosarcoma (RMS) the most common cancer of connective tissues in pediatrics, is often resistant to conventional therapies. One underlying mechanism of this resistance is the overexpression of Inhibitor of Apoptosis (IAP) proteins, leading to a dysfunctional cell death program within tumor cells. Smac mimetics (SM) are small molecules that can reactivate the cell death program by antagonizing IAP proteins and thereby compensating their overexpression. Here, we report that SM sensitize two RMS cell lines (RD and RH30) toward natural killer (NK) cell mediated killing on the one hand, and increase the cytotoxic potential of NK cells on the other. The SM induced sensitization of RH30 cells toward NK cell mediated killing is significantly reduced through blocking tumor necrosis factor related apoptosis inducing ligand (TRAIL) on NK cells prior to coculture. In addition, the presence of zVAD.fmk, a pancaspase inhibitor, rescues tumor cells from the increase in killing, indicating an apoptosis dependent cell death. On the NK cell side, the presence of SM in addition to IL 2 during the ex vivo expansion leads to an increase in their cytotoxic activity against RH30 cells. This effect is mainly TNFa dependent and partially mediated by NK cell activation, which is associated with transcriptional upregulation of NF kB target genes such as IkBa and RelB. Taken together, our findings implicate that SM represent a novel double hit strategy, sensitizing tumor and activating NK cells with one single drug.
Assessing attention and cognitive function in completely locked in state with event related brain potentials and epidural electrocorticography.
Venue: Journal of neural engineering
Year: 2014

Patients in the completely locked in state (CLIS) due to, for example, amyotrophic lateral sclerosis (ALS) no longer possess voluntary muscle control. Assessing attention and cognitive function in these patients during the course of the disease is a challenging but essential task for both nursing staff and physicians.  An electrophysiological cognition test battery, including auditory and semantic stimuli, was applied in a late stage ALS patient at four different time points during a six month epidural electrocorticography (ECoG) recording period. Event related cortical potentials (ERP) together with changes in the ECoG signal spectrum, were recorded via 128 channels that partially covered the left frontal, temporal and parietal cortex.  Auditory but not semantic stimuli induced significant and reproducible ERP projecting to specific temporal and parietal cortical areas. N1/P2 responses could be detected throughout the whole study period. The highest P3 ERP was measured immediately after the patient's last communication through voluntary muscle control, which was paralleled by low theta and high gamma spectral power. Three months after the patient's last communication, i.e. in the CLIS, P3 responses could no longer be detected. At the same time, increased activity in low frequency bands and a sharp drop of gamma spectral power were recorded.  Cortical electrophysiological measures indicate at least partially intact attention and cognitive function during sparse volitional motor control for communication. Although the P3 ERP and frequency specific changes in the ECoG spectrum may serve as indicators for CLIS, a close meshed monitoring will be required to define the exact time point of the transition.
Public Opinions on Using Social Media Content to Identify Users With Depression and Target Mental Health Care Advertising: Mixed Methods Survey
Venue: JMIR mental health
Year: 2019

Depression is a common disorder that still remains underdiagnosed and undertreated in the UK National Health Service. Charities and voluntary organizations offer mental health services, but they are still struggling to promote these services to the individuals who need them. By analyzing social media (SM) content using machine learning techniques, it may be possible to identify which SM users are currently experiencing low mood, thus enabling the targeted advertising of mental health services to the individuals who would benefit from them.  This study aimed to understand SM users' opinions of analysis of SM content for depression and targeted advertising on SM for mental health services.  A Web based, mixed methods, cross sectional survey was administered to SM users aged 16 years or older within the United Kingdom. It asked participants about their demographics, their usage of SM, and their history of depression and presented structured and open ended questions on views of SM content being analyzed for depression and views on receiving targeted advertising for mental health services.  A total of 183 participants completed the survey, and 114 (62.3% of them had previously experienced depression. Participants indicated that they posted less during low moods, and they believed that their SM content would not reflect their depression. They could see the possible benefits of identifying depression from SM content but did not believe that the risks to privacy outweighed these benefits. A majority of the participants would not provide consent for such analysis to be conducted on their data and considered it to be intrusive and exposing.  In a climate of distrust of SM platforms' usage of personal data, participants in this survey did not perceive that the benefits of targeting advertisements for mental health services to individuals analyzed as having depression would outweigh the risks to privacy. Future work in this area should proceed with caution and should engage stakeholders at all stages to maximize the transparency and trustworthiness of such research endeavors.