nils-herrmann/clean_scirepeval huggingface dataset:
Speciation and intrasubspecific variation of Bornean orangutans, Pongo pygmaeus pygmaeus.

Mitochondrial DNA control region sequences of orangutans (Pongo pygmaeus) from six different populations on the island of Borneo were determined and analyzed for evidence of regional diversity and were compared separately with orangutans from the island of Sumatra. Within the Bornean population, four distinct subpopulations were identified. Furthermore, the results of this study revealed marked divergence, supportive evidence of speciation between Sumatran and Bornean orangutans. This study demonstrates that, as an entire population, Bornean orangutans have not experienced a serious genetic bottleneck, which has been suggested as the cause of low diversity in humans and east African chimpanzees. Based on these new data, it is estimated that Bornean and Sumatran orangutans diverged approximately 1.1 MYA and that the four distinct Bornean populations diverged 860,000 years ago. These findings have important implications for management, breeding, and reintroduction practices in orangutan conservation efforts.
Causes and effects of teacher conflict-inducing attitudes towards pupils : a path analysis model

A model explaining several causes and consequences of negative teacher–pupil relationships was developed. Data from 109 teachers and 946 high school pupils was analyzed using path analysis. The results suggest that teachers who prefer a custodial approach of controlling pupils, who have lower morale due to school climate conditions and who are less likely to burn out, tend to adopt conflict-inducing attitudes towards pupils. The results also demonstrate a high incidence of educational, psychological and somatic complaints in students whose characterized teachers are perceived as more hostile in their attitude towards pupils. Implications of these findings are discussed. r 2002 Elsevier
Presence : Experiments in the Psychology of Virtual Environments

Previous research has suggested that presence in a virtual environment (VE) is important for several reasons (Sheridan, 1992; Barfield et al., 1995; Slater et al., 1996). A highly present individual is more likely to behave in the VE in a manner similar to their behaviour n similar circumstances in everyday reality. Therefore, an immersive virtual environment (IVE) may b e a useful system for training and skill acquisition, where to train or gain the skill in the real world may be too expensive or dangerous. This formulation of the effect of presence may be used to cons truct a measure of the degree of presence. Suppose that individuals are placed in an environment which is f amiliar relative to everyday reality. Those individuals who have a high degree of presence would be l ikely to exhibit similar behaviours to that in the real world for example, obeying social conventions, pe rceived psycho-physical limitations, and egocentric interactions. Those individuals who are less present may be mor likely to break these conventions (for example, walking through virtual walls and off virtual clif fs). This paper discusses research in presence within IVEs and presents an experiment using a measure of p resence based on observable behaviours of people placed in a VE that is a representation of a famili r environment.
Cross-lingual Transfer of Named Entity Recognizers without Parallel Corpora

We propose an approach to cross-lingual named entity recognition model transfer without the use of parallel corpora. In addition to global de-lexicalized features, we introduce multilingual gazetteers that are generated using graph propagation, and cross-lingual word representation mappings without the use of parallel data. We target the e-commerce domain, which is challenging due to its unstructured and noisy nature. The experiments have shown that our approaches beat the strong MT baseline, where the English model is transferred to two languages: Spanish and Chinese.
LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression

Long non-coding RNAs (lncRNAs) have emerged as critical regulators of genes at epigenetic, transcriptional and post-transcriptional levels, yet what genes are regulated by a specific lncRNA remains to be characterized. To assess the effects of the lncRNA on gene expression, an increasing number of researchers profiled the genome-wide or individual gene expression level change after knocking down or overexpressing the lncRNA. Herein, we describe a curated database named LncRNA2Target, which stores lncRNA-to-target genes and is publicly accessible at http://www.lncrna2target.org. A gene was considered as a target of a lncRNA if it is differentially expressed after the lncRNA knockdown or overexpression. LncRNA2Target provides a web interface through which its users can search for the targets of a particular lncRNA or for the lncRNAs that target a particular gene. Both search types are performed either by browsing a provided catalog of lncRNA names or by inserting lncRNA/target gene IDs/names in a search box.
Maximal exercise testing variables and 10-year survival: fitness risk score derivation from the FIT Project.

To determine which routinely collected exercise test variables most strongly correlate with survival and to derive a fitness risk score that can be used to predict 10-year survival.



This was a retrospective cohort study of 58,020 adults aged 18 to 96 years who were free of established heart disease and were referred for an exercise stress test from January 1, 1991, through May 31, 2009. Demographic, clinical, exercise, and mortality data were collected on all patients as part of the Henry Ford ExercIse Testing (FIT) Project. Cox proportional hazards models were used to identify exercise test variables most predictive of survival. A "FIT Treadmill Score" was then derived from the β coefficients of the model with the highest survival discrimination.



The median age of the 58,020 participants was 53 years (interquartile range, 45-62 years), and 28,201 (49%) were female. Over a median of 10 years (interquartile range, 8-14 years), 6456 patients (11%) died. After age and sex, peak metabolic equivalents of task and percentage of maximum predicted heart rate achieved were most highly predictive of survival (P<.001). Subsequent addition of baseline blood pressure and heart rate, change in vital signs, double product, and risk factor data did not further improve survival discrimination. The FIT Treadmill Score, calculated as [percentage of maximum predicted heart rate + 12(metabolic equivalents of task) - 4(age) + 43 if female], ranged from -200 to 200 across the cohort, was near normally distributed, and was found to be highly predictive of 10-year survival (Harrell C statistic, 0.811).



The FIT Treadmill Score is easily attainable from any standard exercise test and translates basic treadmill performance measures into a fitness-related mortality risk score. The FIT Treadmill Score should be validated in external populations.
Law and the Rise of the Firm Henry Hansmann

Organizational law empowers firms to hold assets and enter contracts as entities that are legally distinct from their owners and managers. Legal scholars and economists have commented extensively on one form of this partitioning between firms and owners: namely, the rule of limited liability that insulates firm owners from business debts. But a less-noticed form of legal partitioning, which we call "entity shielding," is both economically and historically more significant than limited liability. While limited liability shields owners' personal assets from a firm's creditors, entity shielding protects firm assets from the owners' personal creditors (and from creditors of other business ventures), thus reserving those assets for the firm's creditors. Entity shielding creates important economic benefits, including a lower cost of credit for firm owners, reduced bankruptcy administration costs, enhanced stability, and the possibility of a market in shares. But entity shielding also imposes costs by requiring specialized legal and business institutions and inviting opportunism vis-d-vis both personal and business creditors. The changing balance of these benefits and costs illuminates the evolution of legal entities across time and societies. To both illustrate and test this proposition, we describe the development of entity shielding in four historical epochs: ancient Rome, the Italian Middle Ages, England of the seventeenth to nineteenth centuries, and the United States from the nineteenth century to the present.
Event-Based Visual Flow

This paper introduces a new methodology to compute dense visual flow using the precise timings of spikes from an asynchronous event-based retina. Biological retinas, and their artificial counterparts, are totally asynchronous and data-driven and rely on a paradigm of light acquisition radically different from most of the currently used frame-grabber technologies. This paper introduces a framework to estimate visual flow from the local properties of events' spatiotemporal space. We will show that precise visual flow orientation and amplitude can be estimated using a local differential approach on the surface defined by coactive events. Experimental results are presented; they show the method adequacy with high data sparseness and temporal resolution of event-based acquisition that allows the computation of motion flow with microsecond accuracy and at very low computational cost.
Toxicology of silica nanoparticles: an update

Large-scale production and use of amorphous silica nanoparticles (SiNPs) have increased the risk of human exposure to SiNPs, while their health effects remain unclear. In this review, scientific papers from 2010 to 2016 were systematically selected and sorted based on in vitro and in vivo studies: to provide an update on SiNPs toxicity and to address the knowledge gaps indicated in the review of Napierska (Part Fibre Toxicol 7:39, 2010). Toxicity of SiNPs in vitro is size, dose, and cell type dependent. SiNPs synthesized by wet route exhibited noticeably different biological effects compared to thermal route-based SiNPs. Amorphous SiNPs (particularly colloidal and stöber) induced toxicity via mechanisms similar to crystalline silica. In vivo, route of administration and physico-chemical properties of SiNPs influences the toxicokinetics. Adverse effects were mainly observed in acutely exposed animals, while no significant signs of toxicity were noted in chronically dosed animals. The correlation between in vitro and in vivo toxicity remains less well established mainly due to improper—unrealistic—dosing both in vitro and in vivo. In conclusion, notwithstanding the multiple studies published in recent years, unambiguous linking of physico-chemical properties of SiNPs types to toxicity, bioavailability, or human health effects is not yet possible.
Mirtazapine for anorexia nervosa with depression.

To report the use of Mirtazapine in the treatment of anorexia nervosa with depression primarily regarding its propensity for weight gain.



We present an outpatient case report of anorexia nervosa with depression. The patient's subsequent progress was recorded.



The patient gained 2.5 kg within 3 months to eventually attain a body mass index of 15 after 5 months. Her depression achieved full remission at 6 weeks of treatment.



Mirtazapine is the choice medication in this case. However, treating depression requires caution, given these patients' physical vulnerability. Controlled trials of Mirtazapine for anorexia nervosa are needed.
Does real-time objective feedback and competition improve performance and quality in manikin CPR training – a prospective observational study from several European EMS

Previous studies have reported that the quality of cardiopulmonary resuscitation (CPR) is important for patient survival. Real time objective feedback during manikin training has been shown to improve CPR performance. Objective measurement could facilitate competition and help motivate participants to improve their CPR performance. The aims of this study were to investigate whether real time objective feedback on manikins helps improve CPR performance and whether competition between separate European Emergency Medical Services (EMS) and between participants at each EMS helps motivation to train.



Ten European EMS took part in the study and was carried out in two stages. At Stage 1, each EMS provided 20 pre-hospital professionals. A questionnaire was completed and standardised assessment scenarios were performed for adult and infant out of hospital cardiac arrest (OHCA). CPR performance was objectively measured and recorded but no feedback given. Between Stage 1 and 2, each EMS was given access to manikins for 6 months and instructed on how to use with objective real-time CPR feedback available. Stage 2 was undertaken and was a repeat of Stage 1 with a questionnaire with additional questions relating to usefulness of feedback and the competition nature of the study (using a 10 point Likert score). The EMS that improved the most from Stage 1 to Stage 2 was declared the winner. An independent samples Student t-test was used to analyse the objective CPR metrics with the significance level taken as p < 0.05.



Overall mean Improvement of CPR performance from Stage 1 to Stage 2 was significant. The improvement was greater for the infant assessment. The participants thought the real-time feedback very useful (mean score of 8.5) and very easy to use (mean score of 8.2). Competition between EMS organisations recorded a mean score of 5.8 and competition between participants recorded a mean score of 6.0.



The results suggest that the use of real time objective feedback can significantly help improve CPR performance. Competition, especially between participants, appeared to encourage staff to practice and this study suggests that competition might have a useful role to help motivate staff to perform CPR training.
Recommendations for the Evaluation of Left Ventricular Diastolic Function by Echocardiography: An Update from the American Society of Echocardiography and the European Association of Cardiovascular Imaging.

Sherif F. Nagueh, Chair, MD, FASEa1, Otto A. Smiseth, Co-Chair, MD, PhDb2, Christopher P. Appleton, MDc1, Benjamin F. Byrd III, MD, FASEd1, Hisham Dokainish, MD, FASEe1, Thor Edvardsen, MD, PhDb2, Frank A. Flachskampf, MD, PhD, FESCf2, Thierry C. Gillebert, MD, PhD, FESCg2, Allan L. Klein, MD, FASEh1, Patrizio Lancellotti, MD, PhD, FESCi2, Paolo Marino, MD, FESCj2, Jae K. Oh, MDk1, Bogdan Alexandru Popescu, MD, PhD, FESC, FASEl2, and Alan D. Waggoner, MHS, RDCSm1, Houston, Texas; Oslo, Norway; Phoenix, Arizona; Nashville, Tennessee; Hamilton, Ontario, Canada; Uppsala, Sweden; Ghent and Liège, Belgium; Cleveland, Ohio; Novara, Italy; Rochester, Minnesota; Bucharest, Romania; and St. Louis, Missouri
The many faces of histone H3K79 methylation.

Dot1/DOT1L (disruptor of telomeric silencing-1) is an evolutionarily conserved histone methyltransferase that methylates lysine 79 located within the globular domain of histone H3. Dot1 was initially identified by a genetic screen as a disruptor of telomeric silencing in Saccharomyces cerevisiae; further, it is the only known non-SET domain containing histone methyltransferase. Methylation of H3K79 is involved in the regulation of telomeric silencing, cellular development, cell-cycle checkpoint, DNA repair, and regulation of transcription. hDot1L-mediated H3K79 methylation appears to have a crucial role in transformation as well as disease progression in leukemias involving several oncogenic fusion proteins. This review summarizes the multiple functions of Dot1/hDOT1L in a range of cellular processes.
Chromosome inversions, local adaptation and speciation.

We study the evolution of inversions that capture locally adapted alleles when two populations are exchanging migrants or hybridizing. By suppressing recombination between the loci, a new inversion can spread. Neither drift nor coadaptation between the alleles (epistasis) is needed, so this local adaptation mechanism may apply to a broader range of genetic and demographic situations than alternative hypotheses that have been widely discussed. The mechanism can explain many features observed in inversion systems. It will drive an inversion to high frequency if there is no countervailing force, which could explain fixed differences observed between populations and species. An inversion can be stabilized at an intermediate frequency if it also happens to capture one or more deleterious recessive mutations, which could explain polymorphisms that are common in some species. This polymorphism can cycle in frequency with the changing selective advantage of the locally favored alleles. The mechanism can establish underdominant inversions that decrease heterokaryotype fitness by several percent if the cause of fitness loss is structural, while if the cause is genic there is no limit to the strength of underdominance that can result. The mechanism is expected to cause loci responsible for adaptive species-specific differences to map to inversions, as seen in recent QTL studies. We discuss data that support the hypothesis, review other mechanisms for inversion evolution, and suggest possible tests.
STAMP: components of observable behaviour that indicate potential for patient violence in emergency departments.

This paper is the report of a study to explicate the components of observable behaviour that indicate a potential for violence in patients, their family and friends when presenting at an emergency department.



Violence towards nurses is a contemporary, multifaceted problem for the healthcare workforce globally. International literature identifies emergency departments as having high levels of violence.



A mixed method case study design was adopted, and data were collected by means of 290 hours of participant observation, 16 semi-structured interviews and 13 informal field interviews over a 5-month period in 2005. Thematic analysis of textual data was undertaken using NVivo2. Frequency counts were developed from the numerical data.



Five distinctive elements of observable behaviour indicating potential for violence in patients, their families and friends were identified. These elements can be conceptualized as a potential nursing violence assessment framework and described through the acronym STAMP: Staring and eye contact, Tone and volume of voice, Anxiety, Mumbling and Pacing.



Staring and eye contact, Tone and volume of voice, Anxiety, Mumbling and Pacing provides a useful, practical nursing violence assessment framework to assist nurses to quickly identify patients, families and friends who have a potential for violence.
Art therapy improved depression and influenced fatigue levels in cancer patients on chemotherapy.

Cancer patients are particularly vulnerable to depression and anxiety, with fatigue as the most prevalent symptom of those undergoing treatment. The purpose of this study was to determine whether improvement in depression, anxiety or fatigue during chemotherapy following anthroposophy art therapy intervention is substantial enough to warrant a controlled trial.



Sixty cancer patients on chemotherapy and willing to participate in once-weekly art therapy sessions (painting with water-based paints) were accrued for the study. Nineteen patients who participated in > or =4 sessions were evaluated as the intervention group, and 41 patients who participated in < or =2 sessions comprised the participant group. Hospital Anxiety and Depression Scale (HADS) and the Brief Fatigue Inventory (BFI) were completed before every session, relating to the previous week.



BFI scores were higher in the participant group (p=0.06). In the intervention group, the median HADS score for depression was 9 at the beginning and 7 after the fourth appointment (p=0.021). The median BFI score changed from 5.7 to 4.1 (p=0.24). The anxiety score was in the normal range from the beginning.



Anthroposophical art therapy is worthy of further study in the treatment of cancer patients with depression or fatigue during chemotherapy treatment.
The Diagnosis Of Some Tweens Childhood Diseases In A Prolog Expert System

An expert system to diagnose the main childhood diseases among the tweens is proposed. The diagnosis is made taking into account the symptoms that can be seen or felt. The childhood diseases have many common symptoms and some of them are very much alike. This creates many difficulties for the doctor to reach at a right decision or diagnosis. The proposed system can remove these difficulties and it is having knowledge of many childhood diseases. The proposed expert system is implemented using SWI-Prolog.
On Fairness, Diversity and Randomness in Algorithmic Decision Making

Consider a binary decision making process where a single machine learning classifier replaces a multitude of humans. We raise questions about the resulting loss of diversity in the decision making process. We study the potential benefits of using random classifier ensembles instead of a single classifier in the context of fairness-aware learning and demonstrate various attractive properties: (i) an ensemble of fair classifiers is guaranteed to be fair, for several different measures of fairness, (ii) an ensemble of unfair classifiers can still achieve fair outcomes, and (iii) an ensemble of classifiers can achieve better accuracy-fairness trade-offs than a single classifier. Finally, we introduce notions of distributional fairness to characterize further potential benefits of random classifier ensembles.
Zero-Shot Dialog Generation with Cross-Domain Latent Actions

This paper introduces zero-shot dialog generation (ZSDG), as a step towards neural dialog systems that can instantly generalize to new situations with minimal data. ZSDG enables an end-to-end generative dialog system to generalize to a new domain for which only a domain description is provided and no training dialogs are available. Then a novel learning framework, Action Matching, is proposed. This algorithm can learn a cross-domain embedding space that models the semantics of dialog responses which, in turn, lets a neural dialog generation model generalize to new domains. We evaluate our methods on a new synthetic dialog dataset, and an existing human-human dialog dataset. Results show that our method has superior performance in learning dialog models that rapidly adapt their behavior to new domains and suggests promising future
LDA Revisited: Entropy, Prior and Convergence

Inference algorithms of latent Dirichlet allocation (LDA), either for small or big data, can be broadly categorized into expectation-maximization (EM), variational Bayes (VB) and collapsed Gibbs sampling (GS). Looking for a unified understanding of these different inference algorithms is currently an important open problem. In this paper, we revisit these three algorithms from the entropy perspective, and show that EM can achieve the best predictive perplexity (a standard performance metric for LDA accuracy) by minimizing directly the cross entropy between the observed word distribution and LDA's predictive distribution. Moreover, EM can change the entropy of LDA's predictive distribution through tuning priors of LDA, such as the Dirichlet hyperparameters and the number of topics, to minimize the cross entropy with the observed word distribution. Finally, we propose the adaptive EM (AEM) algorithm that converges faster and more accurate than the current state-of-the-art SparseLDA [20] and AliasLDA  from small to big data and LDA models. The core idea is that the number of active topics, measured by the residuals between E-steps at successive iterations, decreases significantly, leading to the amortized σ(1) time complexity in terms of the number of topics. The open source code of AEM is available at GitHub.