nils-herrmann/clean_scirepeval huggingface dataset:
Evolution and ecology of antibiotic resistance genes.

A new perspective on the topic of antibiotic resistance is beginning to emerge based on a broader evolutionary and ecological understanding rather than from the traditional boundaries of clinical research of antibiotic-resistant bacterial pathogens. Phylogenetic insights into the evolution and diversity of several antibiotic resistance genes suggest that at least some of these genes have a long evolutionary history of diversification that began well before the 'antibiotic era'. Besides, there is no indication that lateral gene transfer from antibiotic-producing bacteria has played any significant role in shaping the pool of antibiotic resistance genes in clinically relevant and commensal bacteria. Most likely, the primary antibiotic resistance gene pool originated and diversified within the environmental bacterial communities, from which the genes were mobilized and penetrated into taxonomically and ecologically distant bacterial populations, including pathogens. Dissemination and penetration of antibiotic resistance genes from antibiotic producers were less significant and essentially limited to other high G+C bacteria. Besides direct selection by antibiotics, there is a number of other factors that may contribute to dissemination and maintenance of antibiotic resistance genes in bacterial populations.
GROMACS 3 . 0 : a package for molecular simulation and trajectory analysis

is the latest release of a versatile and very well optimized package for molecular simulation. Much effort has been devoted to achieving extremely high performance on both workstations and parallel computers. The design includes an extraction of vi-rial and periodic boundary conditions from the loops over pairwise interactions, and special software routines to enable rapid calculation of x –1/2. Inner loops are generated automatically in C or Fortran at compile time, with optimizations adapted to each architecture. Assembly loops using SSE and 3DNow! Multimedia instructions are provided for x86 processors, resulting in exceptional performance on inexpensive PC workstations. The interface is simple and easy to use (no scripting language), based on standard command line arguments with self-explanatory functionality and integrated documentation. All binary files are independent of hardware endian and can be read by versions of GROMACS compiled using different floating-point precision. A large collection of flexible tools for trajectory analysis is included, with output in the form of finished Xmgr/Grace graphs. A basic trajectory viewer is included, and several external visualization tools can read the GROMACS trajectory format. Starting with version 3.0, GROMACS is available under the GNU General Public License from
The Neurobehavioral Nature of Fishes and the Question of Awareness and Pain

This review examines the neurobehavioral nature of fishes and addresses the question of whether fishes are capable of experiencing pain and suffering. The detrimental effects of anthropomorphic thinking and the importance of an evolutionary perspective for understanding the neurobehavioral differences between fishes and humans are discussed. The differences in central nervous system structure that underlie basic neurobehavioral differences between fishes and humans are described. The literature on the neural basis of consciousness and of pain is reviewed, showing that: (1) behavioral responses to noxious stimuli are separate from the psychological experience of pain, (2) awareness of pain in humans depends on functions of specific regions of cerebral cortex, and (3) fishes lack these essential brain regions or any functional equivalent, making it untenable that they can experience pain. Because the experience of fear, similar to pain, depends on cerebral cortical structures that are absent from fish brains, it is concluded that awareness of fear is impossible for fishes. Although it is implausible that fishes can experience pain or emotions, they display robust, nonconscious, neuroendocrine, and physiological stress responses to noxious stimuli. Thus, avoidance of potentially injurious stress responses is an important issue in considerations about the welfare
Privacy Leakage through Innocent Content Sharing in Online Social Networks

The increased popularity and ubiquitous availability of online social networks and globalised Internet access have affected the way in which people share content. The information that users willingly disclose on these platforms can be used for various purposes, from building consumer models for advertising, to inferring personal, potentially invasive, information. In this work, we use Twitter, Instagram and Foursquare data to convey the idea that the content shared by users, especially when aggregated across platforms, can potentially disclose more information than was originally intended. We perform two case studies: First, we perform user deanonymization by mimicking the scenario of finding the identity of a user making anonymous posts within a group of users. Empirical evaluation on a sample of real-world social network profiles suggests that cross-platform aggregation introduces significant performance gains in user identification. In the second task, we show that it is possible to infer physical location visits of a user on the basis of shared Twitter and Instagram content. We present an informativeness scoring function which estimates the relevance and novelty of a shared piece of information with respect to an inference task. This measure is validated using an active learning framework which chooses the most informative content at each given point in time. Based on a large-scale data sample, we show that by doing this, we can attain an improved inference performance. In some cases this performance exceeds even the use of the user’s full timeline.
A critical assessment of algorithms and challenges in the development of a closed-loop artificial pancreas.

The development of an artificial pancreas is placed in the context of the history of the field of feedback control systems, beginning with the water clock of ancient Greece, and including a discussion of current efforts in the control of complex systems. The first generation of artificial pancreas devices included two manipulated variables (insulin and glucose infusion) and nonlinear functions of the error (difference between desired and measured glucose concentration) to minimize hyperglycemia while avoiding hypoglycemia. Dynamic lags between insulin infusion and glucose measurement were relatively small for these intravenous-based systems. Advances in continuous glucose sensing, fast-acting insulin analogs, and a mature insulin pump market bring us close to commercial realization of a closed-loop artificial pancreas. Model predictive control is discussed in-depth as an approach that is well suited for a closed-loop artificial pancreas. A major challenge that remains is handling an unknown glucose disturbance (meal), and an approach is proposed to base a current insulin infusion action on the predicted effect of a meal on future glucose values. Better "meal models" are needed, as a limited knowledge of the effect of a meal on the future glucose values limits the performance of any control algorithm.
A Compact Virtual-Source Model for Carbon Nanotube FETs in the Sub-10-nm Regime—Part I: Intrinsic Elements

We present a data-calibrated compact model of carbon nanotube (CNT) FETs (CNTFETs) based on the virtual-source (VS) approach, describing the intrinsic current-voltage and charge-voltage characteristics. The features of the model include: 1) carrier VS velocity extracted from experimental devices with gate lengths down to 15 nm; 2) carrier effective mobility and velocity depending on the CNT diameter; 3) short channel effect such as inverse subthreshold slope degradation and drain-induced barrier lowering depending on the device dimensions; and 4) small-signal capacitances including the CNT quantum capacitance effect to account for the decreasing gate capacitance at high gate bias. The CNTFET model captures the dimensional scaling effects and is suitable for technology benchmarking and performance projection at the sub-10-nm technology nodes.
Source-side Prediction for Neural Headline Generation

The encoder-decoder model is widely used in natural language generation tasks. However, the model sometimes suffers from repeated redundant generation, misses important phrases, and includes irrelevant entities. Toward solving these problems we propose a novel source-side token prediction module. Our method jointly estimates the probability distributions over source and target vocabularies to capture a correspondence between source and target tokens. The experiments show that the proposed model outperforms the current state-of-the-art method in the headline generation task. Additionally, we show that our method has an ability to learn a reasonable token-wise correspondence without knowing any true alignments.
Impaired TNFα-induced A20 expression in E1A/Ras-transformed cells

Tumour necrosis factor (TNF) is capable of activating the cell death pathway, and has been implicated in killing transformed cells. However, TNF also activates survival signals, including NF-κB activation and the subsequent expression of anti-apoptotic genes, leading to protection against TNF toxicity.In this study, we show that, although untransformed mouse embryonic fibroblasts (MEFs) were resistant to TNF killing, E1A/Ras-transformed MEFs were susceptible to extensive apoptosis induced by TNF. The key factors for determining TNF sensitivity were explored by comparing wild-type and E1A/Ras-transformed MEFs.TNF signalling to NF-κB and to its target genes such as IκBα seemed to be mostly intact in E1A/Ras-transformed cells. Instead, the induction of A20 was completely abolished in E1A/Ras-transformed MEFs, although A20 is known to be NF-κB dependent. Reintroduction of A20 into E1A/Ras-transformed MEFs rescued these cells from TNF-induced death and reduced the formation of the FADD/caspase-8 complex. This impaired A20 induction in E1A/Ras MEFs was not because of the stabilisation of p53 or a defective TNF-induced p38 and Jun N-terminal kinase (JNK) signalling. Consistently, we found a reduced A20 promoter activity but normal NF-κB activity in TNF-treated E1A/Ras MEFs. However, Bcl-3 seemed to have a role in the transactivation of the A20 promoter in E1A/Ras cells.Our results suggest that specific inhibition of certain survival factors, such as A20, may determine the sensitivity to TNF-induced apoptosis in transformed cells such as E1A/Ras MEFs.
Population pharmacokinetic modeling of the Qishe pill in three major traditional Chinese medicine-defined constitutional types of healthy Chinese subjects: study protocol for a randomized controlled trial

High incidences of neck pain morbidity are challenging in various situations for populations based on their demographic, physiological and pathological characteristics. Chinese proprietary herbal medicines, as Complementary and Alternative Medicine (CAM) products, are usually developed from well-established and long-standing recipes formulated as tablets or capsules. However, good quantification and strict standardization are still needed for implementation of individualized therapies. The Qishe pill was developed and has been used clinically since 2009. The Qishe pill's personalized medicine should be documented and administered to various patients according to the ancient TCM system, a classification of personalized constitution types, established to determine predisposition and prognosis to diseases as well as therapy and life-style administration. Therefore, we describe the population pharmacokinetic profile of the Qishe pill and compare its metabolic rate in the three major constitution types (Qi-Deficiency, Yin-Deficiency and Blood-Stasis) to address major challenges to individualized standardized TCM.



Healthy subjects (N = 108) selected based on constitutional types will be assessed, and standardized pharmacokinetic protocol will be used for assessing demographic, physiological, and pathological data. Laboratory biomarkers will be evaluated and blood samples collected for pharmacokinetics(PK) analysis and second-generation gene sequencing. In single-dose administrations, subjects in each constitutional type cohort (N = 36) will be randomly divided into three groups to receive different Qishe pill doses (3.75, 7.5 and 15 grams). Multiomics, including next generation sequencing, metabolomics, and proteomics, will complement the Qishe pill's multilevel assessment, with cytochrome P450 genes as targets. In a comparison with the general population, a systematic population pharmacokinetic (PopPK) model for the Qishe pill will be established and verified.
Expression of human cell cycle regulators in the primary cell line of the African savannah elephant (loxodonta africana) increases proliferation until senescence, but does not induce immortalization

The African savannah elephant (Loxodonta africana) is one of the critically endangered animals. Conservation of genetic and cellular resources is important for the promotion of wild life-related research. Although primary cultured cells are a useful model for the physiology and genomics of the wild-type animals, their distribution is restricted due to the limited number of cell divisions allowed in them. Here, we tried to immortalize a primary cell line of L. africana with by overexpressing human mutant form of cyclin-dependent kinase 4 (CDK4R24C), cyclin D, and telomerase (TERT). It has been shown before that the combination of human CDK4R24C, cyclin D, and TERT induces the efficient cellular immortalization of cells derived from humans, bovine, swine, and monkeys. Interestingly, although the combination of these three genes extended the cellular proliferation of the L. africana-derived cells, they did not induce cellular immortalization. This study suggest that control of cellular senescence in L. africana-derived cells would be different molecular mechanisms compared to those governing human, bovine, swine, and monkey cells.
Real Virtuality: A Code of Ethical Conduct. Recommendations for Good Scientific Practice and the Consumers of VR-Technology

The goal of this article is to present a first list of ethical concerns that may arise from research and personal use of virtual reality (VR) and related technology, and to offer concrete recommendations for minimizing those risks. Many of the recommendations call for focused research initiatives. In the first part of the article, we discuss the relevant evidence from psychology that motivates our concerns. In Section “Plasticity in the Human Mind,” we cover some of the main results suggesting that one’s environment can influence one’s psychological states, as well as recent work on inducing illusions of embodiment. Then, in Section “Illusions of Embodiment and Their Lasting Effect,” we go on to discuss recent evidence indicating that immersion in VR can have psychological effects that last after leaving the virtual environment. In the second part of the article, we turn to the risks and recommendations. We begin, in Section “The Research Ethics of VR,” with the research ethics of VR, covering six main topics: the limits of experimental environments, informed consent, clinical risks, dual-use, online research, and a general point about the limitations of a code of conduct for research. Then, in Section “Risks for Individuals and Society,” we turn to the risks of VR for the general public, covering four main topics: long-term immersion, neglect of the social and physical environment, risky content, and privacy. We offer concrete recommendations for each of these 10 topics, summarized in Table 1.
Haru: Hardware Design of an Experimental Tabletop Robot Assistant

This paper discusses the design and development of an experimental tabletop robot called "Haru" based on design thinking methodology. Right from the very beginning of the design process, we have brought an interdisciplinary team that includes animators, performers and sketch artists to help create the first iteration of a distinctive anthropomorphic robot design based on a concept that leverages form factor with functionality. Its unassuming physical affordance is intended to keep human expectation grounded while its actual interactive potential stokes human interest. The meticulous combination of both subtle and pronounced mechanical movements together with its stunning visual displays, highlight its affective affordance. As a result, we have developed the first iteration of our tabletop robot rich in affective potential for use in different research fields involving long-term human-robot interaction.
SafeRNet: Safe transportation routing in the era of Internet of vehicles and mobile crowd sensing

World wide road traffic fatality and accident rates are high, and this is true even in technologically advanced countries like the USA. Despite the advances in Intelligent Transportation Systems, safe transportation routing i.e., finding safest routes is largely an overlooked paradigm. In recent years, large amount of traffic data has been produced by people, Internet of Vehicles and Internet of Things (IoT). Also, thanks to advances in cloud computing and proliferation of mobile communication technologies, it is now possible to perform analysis on vast amount of generated data (crowd sourced) and deliver the result back to users in real time. This paper proposes SafeRNet, a safe route computation framework which takes advantage of these technologies to analyze streaming traffic data and historical data to effectively infer safe routes and deliver them back to users in real time. SafeRNet utilizes Bayesian network to formulate safe route model. Furthermore, a case study is presented to demonstrate the effectiveness of our approach using real traffic data. SafeRNet intends to improve drivers' safety in a modern technology rich transportation system.
Facial Feature Extraction Techniques for Face Recognition

Face recognition is one of the biometric techniques sed for identification of humans. The design of the face recognition system includes two basic step s. The first step is the extraction of the image’s features and the second one is the classification o f patterns. Feature extracting is a very important step in face recognition. The recognition rate of the sy stem depends on the meaningful data extracted from the face image. If the features belong to the diffe rent classes and the distance between these classes re bigger then these features are important for recogn ition of the images. In this study, the design of f ace recognition system using three different feature ex traction techniquesPrincipal Component Analysis (PCA), Fisher Linear Discriminant Analysis (FLD) an d Fast Pixel Based Matching (FPBM) is presented. The comparative analysis of the simulati on results of these methods is presented.
Comparing inverted files and signature files for searching a large lexicon

Signature files and inverted files are well-known index structures. In this paper we undertake a direct comparison of the two for searching for partially-specified queries in a large lexicon stored in main memory. Using n-grams to index lexicon terms, a bit-sliced signature file can be compressed to a smaller size than an inverted file if each n-gram sets only one bit in the term signature. With a signature width less than half the number of unique n-grams in the lexicon, the signature file method is about as fast as the inverted file method, and significantly smaller. Greater flexibility in memory usage and faster index generation time make signature files appropriate for searching large lexicons or other collections in an environment where memory is at a premium.
An Unusual Finding of Proliferative Periostitis in a Child : a Case Report

Proliferative periostitis is a pathologic lesion that displays an osteo-productive and proliferative inflammatory response of the periosteum to infection or other irritation. This lesion is a form of chronic osteomyelitis that is often asymptomatic, occurring primarily in children, and found only in the mandible. The lesion can be odontogenic or non-odontogenic in nature. A 12 year-old boy presented with an unusual odontogenic proliferative periostitis that originated from the lower left first molar, however, the radiographic radiolucent area and proliferative response were discovered at the apices of the lower left second molar. The periostitis was treated by single-visit non-surgical endodontic treatment of lower left first molar without antibiotic therapy. The patient has been recalled regularly; the lesion had significantly reduced in size 3-months postoperatively. Extraoral symmetry occurred at approximately one year recall. At the last visit, 2 years after initial treatment, no problems or signs of complications have occurred; the radiographic examination revealed complete resolution of the apical lesion and apical closure of the lower left second molar. Odontogenic proliferative periostitis can be observed at the adjacent normal tooth. Besides, this case demonstrates that non-surgical endodontics is a viable treatment option for management of odontogenic proliferative periostitis.
Control system design and small signal analysis of APWM resonant inverter for induction heating

This paper proposes an asymmetrical pulse width modulation (APWM) with frequency tracking control of full bridge series resonant inverter for induction heating application. In this method, APWM is used as power regulation, and phased locked loop (PLL) is used to attain zero-voltage-switching (ZVS) over a wide load range. The complete closed loop control model is obtained using small signal analysis. The validity of the proposed control is verified by simulation results.
Reproducibility in critical care: a mortality prediction case study

Mortality prediction of intensive care unit (ICU) patients facilitates hospital benchmarking and has the opportunity to provide caregivers with useful summaries of patient health at the bedside. The development of novel models for mortality prediction is a popular task in machine learning, with researchers typically seeking to maximize measures such as the area under the receiver operator characteristic curve (AUROC). The number of ’researcher degrees of freedom’ that contribute to the performance of a model, however, presents a challenge when seeking to compare reported performance of such models. In this study, we review publications that have reported performance of mortality prediction models based on the Medical Information Mart for Intensive Care (MIMIC) database and attempt to reproduce the cohorts used in their studies. We then compare the performance reported in the studies against gradient boosting and logistic regression models using a simple set of features extracted from MIMIC. We demonstrate the large heterogeneity in studies that purport to conduct the single task of ’mortality prediction’, highlighting the need for improvements in the way that prediction tasks are reported to enable fairer comparison between models. We reproduced datasets for 38 experiments corresponding to 28 published studies using MIMIC. In half of the experiments, the sample size we acquired was 25% greater or smaller than the sample size reported. The highest discrepancy was 11,767 patients. While accurate reproduction of each study cannot be guaranteed, we believe that these results highlight the need for more consistent reporting of model design and methodology to allow performance improvements to be compared. We discuss the challenges in reproducing the cohorts used in the studies, highlighting the importance of clearly reported methods (e.g. data cleansing, variable selection, cohort selection) and the need for open code and publicly available benchmarks.