nils-herrmann/clean_scirepeval huggingface dataset:
Soil microbial carbon use efficiency and biomass turnover in a long term fertilization experiment in a temperate grassland.

Soil microbial carbon use efficiency (CUE) defined as the ratio of organic C allocated to growth over organic C taken up, strongly affects soil carbon (C) cycling. Despite the importance of the microbial CUE for the terrestrial C cycle, very little is known about how it is affected by nutrient availability. Therefore, we studied microbial CUE and microbial biomass turnover time in soils of a long term fertilization experiment in a temperate grassland comprising five treatments (control, PK, NK, NP, NPK) Microbial CUE and the turnover of microbial biomass were determined using a novel substrate independent method based on incorporation of 18 O from labeled water into microbial DNA. Microbial respiration was 28 37% smaller in all three N treatments (NK, NP, and NPK) compared to the control, whereas the PK treatment did not affect microbial respiration. N fertilization decreased microbial C uptake, while the microbial growth rate was not affected. Microbial CUE ranged between 0.31 and 0.45, and was 1.3 to 1.4 fold higher in the N fertilized soils than in the control. The turnover time ranged between 80 and 113 days and was not significantly affected by fertilization. Net primary production (NPP) and the abundance of legumes differed strongly across the treatments, and the fungal:bacterial ratio was very low in all treatments. Structural equation modeling revealed that microbial CUE was exclusively controlled by N fertilization and that neither the abundance of legumes (as a proxy for the quality of the organic matter inputs) nor NPP (as a proxy for C inputs) had an effect on microbial CUE. Our results show that N fertilization did not only decrease microbial respiration, but also microbial C uptake, indicating that less C was intracellularly processed in the N fertilized soils. The reason for reduced C uptake and increased CUE in the N fertilization treatments is likely an inhibition of oxidative enzymes involved in the degradation of aromatic compounds by N in combination with a reduced energy requirement for microbial N acquisition in the fertilized soils. In conclusion, the study shows that N availability can control soil C cycling by affecting microbial CUE, while plant community mediated changes in organic matter inputs and P and K availability played no important role for C partitioning of the microbial community in this temperate grassland.
Microbial carbon use efficiency and biomass turnover times depending on soil depth Implications for carbon cycling

Processing of organic carbon (C) by soil microorganisms is a key process of terrestrial C cycling. For this reason we studied (i) microbial carbon use efficiency (CUE) defined as C allocated to growth over organic C taken up by the microbial community, and (ii) the turnover time of microbial biomass in a pasture and in two forest soils. We hypothesized that microbial CUE decreases in mineral soils with depth from the topsoil to the subsoil, while the turnover time of the microbial biomass increases due to energetic constrains. We determined microbial CUE and turnover of microbial biomass C using a novel substrate independent method based on incorporation of 18O from labeled water into microbial DNA with concurrent measurements of basal respiration. Microorganisms showed decreasing C uptake rates with decreasing C contents in the deeper soil layers. In the forest soils, no adaptation of microbial CUE with soil depth took place, i.e. microbes in the forest topsoil used C at the same efficiency as microbes in the subsoil. However, in the pasture soil, microbial CUE decreased in the lower soil layers compared to the topsoil, indicating that microorganisms in the deeper soil layers allocated relatively more C to respiration. In the organic soil layer, microorganisms respired more per unit microbial biomass C than in the subsoil, but had a similar CUE despite the high C to nitrogen and C to phosphorus ratios of the litter layers. The turnover time of microbial biomass increased with soil depth in the two forest soils. Thus, in the forest soils, a lower microbial C uptake rate in the deeper soil layers was partially compensated by a longer turnover time of microbial biomass C. In conclusion, our findings emphasize that in addition to microbial CUE, the turnover time of the microbial biomass strongly affects soil C cycling.
Towards automatically generating descriptive names for unit tests
Venue: 2016 31st IEEE/ACM International Conference on Automated Software Engineering (ASE)

During maintenance, developers often need to understand the purpose of a test. One of the most potentially useful sources of information for understanding a test is its name. Ideally, test names are descriptive in that they accurately summarize both the scenario and the expected outcome of the test. Despite the benefits of being descriptive, test names often fall short of this goal. In this paper we present a new approach for automatically generating descriptive names for existing test bodies. Using a combination of natural language program analysis and text generation, the technique creates names that summarize the test's scenario and the expected outcome. The results of our evaluation show that, (1) compared to alternative approaches, the names generated by our technique are significantly more similar to human generated names and are nearly always preferred by developers, (2) the names generated by our technique are preferred over or are equivalent to the original test names in 83% of cases, and (3) our technique is several orders of magnitude faster than manually writing test names.
Combining Fully Convolutional and Recurrent Neural Networks for 3D Biomedical Image Segmentation
Venue: NIPS

Segmentation of 3D images is a fundamental problem in biomedical image analysis. Deep learning (DL) approaches have achieved state of the art segmentation perfor mance. To exploit the 3D contexts using neural networks, known DL segmentation methods, including 3D convolution, 2D convolution on planes orthogonal to 2D image slices, and LSTM in multiple directions, all suffer incompatibility with the highly anisotropic dimensions in common 3D biomedical images. In this paper, we propose a new DL framework for 3D image segmentation, based on a com bination of a fully convolutional network (FCN) and a recurrent neural network (RNN) which are responsible for exploiting the intra slice and inter slice contexts, respectively. To our best knowledge, this is the first DL framework for 3D image segmentation that explicitly leverages 3D image anisotropism. Evaluating using a dataset from the ISBI Neuronal Structure Segmentation Challenge and in house image stacks for 3D fungus segmentation, our approach achieves promising results comparing to the known DL based 3D segmentation approaches.
Fully convolutional networks for multi modality isointense infant brain image segmentation
Venue: 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI)

The segmentation of infant brain tissue images into white matter (WM) gray matter (GM) and cerebrospinal fluid (CSF) plays an important role in studying early brain development. In the isointense phase (approximately 6 8 months of age) WM and GM exhibit similar levels of intensity in both T1 and T2 MR images, resulting in extremely low tissue contrast and thus making the tissue segmentation very challenging. The existing methods for tissue segmentation in this isointense phase usually employ patch based sparse labeling on single T1, T2 or fractional anisotropy (FA) modality or their simply stacked combinations without fully exploring the multi modality information. To address the challenge, in this paper, we propose to use fully convolutional networks (FCNs) for the segmentation of isointense phase brain MR images. Instead of simply stacking the three modalities, we train one network for each modality image, and then fuse their high layer features together for final segmentation. Specifically, we conduct a convolution pooling stream for multimodality information from T1, T2, and FA images separately, and then combine them in high layer for finally generating the segmentation maps as the outputs. We compared the performance of our approach with that of the commonly used segmentation methods on a set of manually segmented isointense phase brain images. Results showed that our proposed model significantly outperformed previous methods in terms of accuracy. In addition, our results also indicated a better way of integrating multi modality images, which leads to performance improvement.
Researching and Working for Transgender Youth: Contexts, Problems and Solutions

In May 2016, two events epitomized the complexities of working for global transgender youth rights. First, United Nations Educational Scientific and Cultural Organisation (UNESCO) hosted a ministerial event in which education ministers from around the world released a call to action for protection of students on the basis of their gender identity and expression in schools. Second, the United Nations (UN) hosted an event celebrating the family, attended by conservative ministers and activists who mobilized family protectionist discourse against transgender students. This article contemplates, in light of transgender activist Raewyn Connell's Southern Theory contributions, the complexity of global research and work for transgender youth. It considers key informant interviews with 50 stakeholders in the global push for transgender student rights in education, including members of government and non government organisations, and academics from Northern and Southern countries. Problems in aiding transgender youth at the global level included safety concerns, the impacts of conservative advocates and media backlash (within family and national protectionist discourses) cultural complexities hampering engagement and translation, dissemination hindrances pertaining to established publishing biases, and financial and collaboration barriers. Solutions including virtual work; multi level leadership; alliance building; representation; visibility of transgender youth citizenship and family membership; and legal, financial and capacity building aid are considered.
Lesbian, Gay, Bisexual, and Transgender Inclusion in Physical Therapy: Advocating for Cultural Competency in Physical Therapist Education Across the United States

People who are lesbian, gay, bisexual, transgender, or queer (LGBTQ) should be considered in the discussion of improving cultural competency within physical therapy education to improve both culturally competent health care and the classroom learning environment. It is important to recognize the health care disparities affecting the LGBTQ community because people who are LGBTQ have higher risks of certain types of cancer, substance and tobacco use, sexually transmitted infections (such as human immunodeficiency virus and hepatitis B) and mental health issues (such as depression, anxiety, eating disorders, and suicidal ideation) Along with these health risks, patients who are LGBTQ typically face discrimination and bias, insensitivity of providers, a lack of knowledge about LGBTQ health care issues among providers, and decreased access to care; these problems may lead to substandard care. Position and Rationale. Current events in the news about the rights of lesbian, gay, bisexual, and transgender people bring to light the discrimination faced by this community. The topic of LGBTQ health care disparities has not been well researched or discussed in the profession of physical therapy. We assert that the inclusion of LGBTQ content in health care professional education programs will lead to better care for people who are LGBTQ. Although patient care is a primary concern, it is also crucial to create safe learning environments for students who are LGBTQ and enrolled in health care professional education programs because this population has higher rates of mental health disorders, weight related issues, and suicide as well as higher self reported levels of perceived emotional stress. Discrimination and disparaging comments directed at students who are LGBTQ are common in health care professional education programs and need to be addressed to provide these students with the same opportunities as their counterparts who are heterosexual and/or cisgender.  This position paper provides recommendations to health care educators for improving cultural competency and outcomes for patients who are LGBTQ as well as suggestions for creating an inclusive learning environment and climate for students who are LGBTQ. Specifically, curriculum content should highlight the appropriate usage of language and terminology for people who are LGBTQ, evidence of health care disparities and challenges faced by people who are LGBTQ, and active training in understanding the unconscious (implicit) bias of health care providers and how bias can affect both the treatment of patients and students. Furthermore, we recommend adding "sexual orientation" and "gender identity" to the nondiscrimination policies of physical therapist education programs, LGBTQ training for faculty and staff, concerted efforts to hire faculty members who are LGBTQ, orientation events for students who are LGBTQ, and targeted programs for students and staff members who are LGBTQ.
Olive Stone Ash as Secondary Raw Material for Fired Clay Bricks

This work evaluates the effect of incorporation of olive stone ash, as secondary raw material, on the properties of fired clay bricks. To this end, three compositions containing 10, 20, and 30 wt% olive stone ash in a mixture of clays (30 wt% red, 30 wt% yellow, and 40 wt% black clay) from Spain were prepared. The raw materials, clay and olive stone ash, were characterized by means of XRD, XRF, SEM EDS, and TG TDA analysis. The engineering properties of the press molded specimens fired at 900degC (4 h) such as linear shrinkage, bulk density, apparent porosity, water absorption, and compressive strength were evaluated. The results indicated that the incorporation of 10 wt% of olive stone ash produced bricks with suitable technological properties, with values of compressive strength of 41.9 MPa but with a reduced bulk density, by almost 4% By contrast, the incorporation of 20 wt% and 30 wt% sharply increased the water absorption as a consequence of the large amount of open porosity and low mechanical strength presented by these formulations, which do not meet the standards for their use as face bricks. The bricks do not present environmental problems according to the leaching test.
Refractoriness to pharmacological treatment for tics: A multicentre European audit
Venue: Journal of the Neurological Sciences

Recently, a consensus definition of treatment responsiveness for obsessive compulsive disorder has been reached through Delphi survey methodology, showing great potential for practical application in clinical care  A standardized definition of refractoriness to pharmacological treatment of tics in TD (chronic tic disorders including Tourette Syndrome) would aid decisions on drug switch, psychological treatment or access to invasive treatments like functional surgery [2,3] We conducted a European audit survey in order to: i) explore the main features that would define refractoriness of tics to pharmacological treatment, and ii) assess how consistently these features are taken into account in routine clinical practice. Itemsdefining treatment refractoriness in TDwas discussedwithin a panel of seven expert clinicians (panel clinicians) across different European countries. All panel members were invited to rate each item according to whether the domain measured was 'essential' or not for the definition of refractoriness. Only those items for which a unanimous judgement of 'essential'was reachedwere then considered for the audit survey. This procedure yielded the following list of 'essential' items: duration of treatment (weeks) dichotomous judgement of improvement of tic severity (improved/not improved) documented change of the Yale Global Tic Severity Scale (YGTSS) 0 50 severity score; reason for themaximum dose reached; number of single doses missed on average over a 10 day period. A clinical questionnaire (Appendix file) was used to collect information related to the selected items from other seven European expert clinicians (survey clinicians) The questionnaire was completed by survey clinicians related to outpatients with a diagnosis of TD (according to DSM\\V) who had been previously judged by the clinician as refractory to an anti tic monotherapy. A judgement of refractoriness implied that the clinician had already decided either to discontinue that particular anti tic monotherapy, or to change the regime by adding on another treatment. With respect to the main reason for the refractoriness judgement, refractoriness was categorised either as due to lack of efficacy at the highest tolerated dose or as due to lack of tolerability at initial or effective dosage. This studywas selectively based on the clinical information carried out as part of the routine clinical care of the patients. Sixty eight TD patients (56male, median age: 14 years; range 8 44) were enrolled consecutively across 7 European tertiary centres for TD; at each participating centre, all patients were identified by the same clinician throughout a period of 18 months. The median age at tic onset
Learning Deep Representations of Fine Grained Visual Descriptions
Venue: 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)

State of the art methods for zero shot visual recognition formulate learning as a joint embedding problem of images and side information. In these formulations the current best complement to visual features are attributes: manually encoded vectors describing shared characteristics among categories. Despite good performance, attributes have limitations: (1) finer grained recognition requires commensurately more attributes, and (2) attributes do not provide a natural language interface. We propose to overcome these limitations by training neural language models from scratch, i.e. without pre training and only consuming words and characters. Our proposed models train end to end to align with the fine grained and category specific content of images. Natural language provides a flexible and compact way of encoding only the salient visual aspects for distinguishing categories. By training on raw text, our model can do inference on raw text as well, providing humans a familiar mode both for annotation and retrieval. Our model achieves strong performance on zero shot text based image retrieval and significantly outperforms the attribute based state of the art for zero shot classification on the Caltech UCSD Birds 200 2011 dataset.
Preferences for Truth Telling

Private information is at the heart of many economic activities. For decades, economists have assumed that individuals are willing to misreport private information if this maximizes their material payoff. We combine data from 72 experimental studies in economics, psychology and sociology, and show that, in fact, people lie surprisingly little. We then formalize a wide range of potential explanations for the observed behavior, identify testable predictions that can distinguish between the models and conduct new experiments to do so. None of the most popular explanations suggested in the literature can explain the data. We show that only combining a preference for being honest with a preference for being seen as honest can organize the empirical evidence.
A manifesto for the valorization of wild edible plants.
Venue: Journal of ethnopharmacology

ETHNOPHARMACOLOGICAL RELEVANCE Wild foods constitute an essential component of people's diets around the world, but despite their widespread use and their cultural importance, wild edible plants (WEPs) lack recognition as significant contributors to the human diet in developed countries.  We stimulate national and international bodies dealing with food and agriculture, to increase their attention and investments on WEPs, leveraging the results of scientific investigation, enhancing the link between in situ conservation strategies and sustainable use of plant genetic diversity.  WEPs should be reconsidered throughout their value chain, capturing their important socio cultural, health, and economic benefits to indigenous and local communities and family farmers who are engaged in their production and wild harvesting.
Protect Syria's doctors: an open letter to world leaders
Venue: The Lancet

www.thelancet.com Vol 388 September 10, 2016 1055 advocated by the USA. The fi rst line of the report stated: "the threatened war on Iraq could have disastrous short, medium and long term consequences not only for the Iraqi population and its neighbours, but also further afi eld" The report proved tragically accurate in anticipating the ensuing death and destruction of what is now widely regarded as an illegal, pernicious, and unjustifi ed war. As noted by Richard Horton (July 9, p 114) one lesson from this terrible episode in history is that international health organisations can do better at anticipating and responding to the consequences of war. But another is that the health community must be more actively engaged in peace building. Although mainstream reporting on the Chilcot Inquiry has focused on the particular role of Tony Blair in pursuing the case for war, the Chilcot report also described a wider militaristic culture across the establishment that did not see the folly of using war to combat terrorism or promote human rights in the Middle East. Medact is one of a few health organisations with an explicit remit to use public health principles and arguments to promote peace and oppose violence. With the UK Parliament having recently approved the renewal of the Trident Nuclear Weapons system (risking more militaristic folly in pursuit of humanitarian catastrophe) we urge all health professionals to seek better and more eff ective ways to secure security and good health for all.