jimnoneill/paper-to-field-training huggingface dataset:
Automatic Artifact Removal from Electroencephalogram Data Based on A Priori Artifact Information

Field: Neuroscience (Life Sciences)

Electroencephalogram (EEG) is susceptible to various nonneural physiological artifacts. Automatic artifact removal from EEG data remains a key challenge for extracting relevant information from brain activities. To adapt to variable subjects and EEG acquisition environments, this paper presents an automatic online artifact removal method based on a priori artifact information. The combination of discrete wavelet transform and independent component analysis (ICA), wavelet-ICA, was utilized to separate artifact components. The artifact components were then automatically identified using a priori artifact information, which was acquired in advance. Subsequently, signal reconstruction without artifact components was performed to obtain artifact-free signals. The results showed that, using this automatic online artifact removal method, there were statistical significant improvements of the classification accuracies in both two experiments, namely, motor imagery and emotion recognition.
Identifying Adverse Drug Events by Relational Learning

Field: Computer Science (Physical Sciences)

The pharmaceutical industry, consumer protection groups, users of medications and government oversight agencies are all strongly interested in identifying adverse reactions to drugs. While a clinical trial of a drug may use only a thousand patients, once a drug is released on the market it may be taken by millions of patients. As a result, in many cases adverse drug events (ADEs) are observed in the broader population that were not identiﬁed during clinical trials. Therefore, there is a need for continued, postmarketing surveillance of drugs to identify previously-unanticipated ADEs. This paper casts this problem as a reverse machine learning task, related to relational subgroup discovery and provides an initial evaluation of this approach based on experiments with an actual EMR/EHR and known adverse drug events.
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis.
The Mystery of Iniquity: Kuzmin's “Temnye ulitsy rozhdaiut temnye mysli”

Field: Arts and Humanities (Social Sciences)

There can be little doubt that the name Mikhail Alekseevich Kuzmin (1872–1936) would be near the top of any list of important twentieth-century Russian writers neglected both in and outside their homeland. Even though he was regarded as an original and major poet by writers as diverse as Briusov, Blok, Gumilev, Khlebnikov, Mayakovsky, Tsvetaeva, and Pasternak, Kuzmin still awaits rehabilitation in the Soviet Union and rediscovery in the West. There are some signs of a partial rehabilitation in Soviet Russia today, but the chances for a full rehabilitation—a major publication of his works—are slight. Obstacles to a Western rediscovery exist as well. Clichés die hard and perhaps no harder than in literary history. Kuzmin himself must share part of the blame for the major one. By writing the article “On Beautiful Clarity” he unwittingly gave critics and literary historians the tag for comments on his verse. That the article is about prose and that Kuzmin chose not to republish it in his one volume of collected essays is ignored.
Molar Functional Analyses Associated to Acceptance and Commitment Therapy in a Case of Obsessive-Compulsive Disorder

Field: Psychology (Social Sciences)

Obsessive-Compulsive Disorder (OCD) is a psychiatric disorder characterized by obsessions and compulsions, with losses in social, family and labor contexts. This study aimed to show the relevance of molar functional analyses associated to ACT interventions, illustrating it with a case of OCD. Along 68 sessions, it has been possible to identify ample behavior patterns of aggressive communication, search for control and verbal argumentation skills, functionally related to OCD symptoms, as well as ample sensitivity to social/verbal contexts of literality and reason giving, leading to a strong pattern of experiential avoidance. Understanding of current and historical contingencies led to the acceptance of aversive private states and commitment to the exposure to therapeutic contexts, in order to weaken behaviors that were functionally related to the obsessive-compulsive ones, but less emotionally relevant, which led to weakening of OCD symptoms and improvements in relationships with relatives and coworkers.
Genetic Divergence among Populations of the Yellow-Bellied Slider Turtle (Pseudemys scripta) Separated by Aquatic and Terrestrial Habitats

Field: Agricultural and Biological Sciences (Life Sciences)

Allelic variation at 18 loci is described for Pseudemys scripta (N = 367) livetrapped from 12 populations, representing three habitat types separated by different types of intervening habitat (terrestrial vs aquatic). Of the 18 loci examined 13 were polymorphic. Mean heterozygosity was 0.131. Significant allele frequency differences were observed among the 12 populations. Patterns of allelic differentiation and overall genetic divergence among populations were not consistent across habitat types. Populations from aquatically separated habitats had significantly higher heterozygosities than did populations from terrestrially separated habitat and showed less interpopulation genetic distance/unit distance. However, genetic similarities among populations appear to be a function of geographic proximity, regardless of the intervening habitat and potential for dispersal and interpopulation gene flow.
SH3243648.08FU

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
Site of action and biphasic effect of neutral salts in the phosphorylase kinase reaction

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

The inhibition of phosphorylase kinase catalytic activity by 0.1 M neutral salts was predicted by the Hofmeister series of anions. The site of action of the salts was determined by the following evidence to be on the phosphorylase kinase molecule directly, rather than on its protein substrate. (1) Nonactivated kinase was more sensitive to salt inhibition than the activated form. (2) Ca2+ partially overcame the inhibition of nonactivated kinase. (3) Inhibition by Cl- occurred with either phosphorylase or a tetradecapeptide containing the convertible seryl residue as substrate. (4) Phosphorylation of nonactivated phosphorylase kinase by protein kinase was markedly inhibited by NaNO3, but this salt had little effect on the phosphorylation of histone by protein kinase. The influence of neutral salts on phosphorylase kinase activity was biphasic. Although activity was inhibited at low salt concentrations, it actually was stimulated as the salt concentration was increased. A similar biphasic response to various salt concentrations was observed in the velocities of autophosphorylation of phosphorylase kinase. The lag in the rate of product formation seen during the activity assay was less pronounced at inhibitory salt concentrations and was abolished at stimulatory salt concentrations. How the influence of salts relates to autophosphorylation and the lag is considered.
In vitro tolerance of rice pathogen Rhizoctonia solaniby orchid mycorrhizal fungi isolated fromorchids in BRIS, Setiu Wetlands

Field: Agricultural and Biological Sciences (Life Sciences)

Rice (Oryza sativa) is a major staple food that feeds more than half of the human population in the world. However, rice
production faces major loss in yield due to rice diseases including Rice Sheath Blight (RSB), which is caused by a soil-borne
fungal pathogen, Rhizoctonia solani. Interestingly, the same pathogenic R. solani in rice has also been isolated from orchids
and is known to form a vital symbiotic relationship, called orchid mycorrhiza. Thus, this study aims at isolating and identifying
the orchid mycorrhizal fungi (OMF) present in roots of orchids at beach ridges interspersed with swales (BRIS), Setiu
Wetlands and to determine their antagonistic activity towards pathogenic R. solani through dual culture bioassay. Mycorrhizal
fungi were isolated from the roots of Phalaenopsis pulcherrima, Bromheadia finlaysoniana and Dendrobium crumenatum.
Three isolates were identified through morphological identification to be Rhizoctonia species namely A, B and C along with
one fungal isolate as Daldinia species. In vitro antagonistic test against pathogenic R. solani showed Rhizoctonia species (B)
displayed the strongest anti-fungal activity with 60.46% of Percentage Inhibition of Radial Growth (PIRG) value followed
by Rhizoctonia species (C) with 59.9%, Rhizoctonia species (A) with 51.02% and Daldinia species with 39.80%. This
preliminary investigation shows the potential of orchid mycorrhizal fungi to be developed as a biocontrol agent.
Microbiome and women's health (literature review)

Field: Medicine (Health Sciences)

In recent decades increased interest in natural microbiome - microbial communities colonizing the mucous membranes and skin of human. Microbiome is involved in metabolic and genetic regulatory mechanisms of human life, and also creates a powerful defense of microorganism from colonizing alien microorganisms. Mouth, upper respiratory tract, gastrointestinal and urogenital tract, skin are populated by different types of microorganisms.It was found that the breach of the vaginal microbiome associated with the development of bacterial vaginosis, nonspecific (aerobic), vaginitis and mycotic vaginitis. Numerous studies have confirmed the effectiveness of probiotic therapy in the treatment of patients with various forms of urological and obstetrical and gynecological pathology, aimed at restoring the natural microbiome.
An Examination of the Role of Local and Distant Knowledge Spillovers on the US Regional Knowledge Creation

Field: Economics, Econometrics and Finance (Social Sciences)

This article examines the role of academic and private R&D spending in the frame of a knowledge production function estimated across 3,109 US counties. We distinguish the role of local, face-to-face, knowledge spillovers that are determined by geographical proximity from distant spillovers captured by a matrix of patent creation–citation flows. The advantage of the latter matrix is its capacity to capture the direction of the spillovers. We control for the spatial heterogeneity between metropolitan and nonmetropolitan counties as well as between states. Our empirical results show that spillovers due to private knowledge contribute to higher returns in metropolitan counties than in nonmetropolitan regions. On the other hand, knowledge created in the academia leads to spillovers displaying spatially homogeneous returns. Our results imply that future innovation policies need to grasp more fully the role of distant knowledge spillovers, especially those generated in the academia, and recognize better the presence of heterogeneity in the sources and location of knowledge creation.
Virtual Teacher and Classroom for Assessment of Neurodevelopmental Disorders

Field: Computer Science (Physical Sciences)

En nuestros días gran cantidad de información es generada, esto es causado por los significativos avances de la computación que han permitido utilizar la tecnología en cada una de las actividades desarrolladas por el hombre, en este caso se puede notar en el campo de la medicina, precisamente en la parte sicológica. La combinación entre la tecnología y los tratamientos aplicados en los pacientes que sufren trastornos cognitivos leves, esto a través de juegos desarrollados especialmente para la estimulación de la atención, donde jugar creará gran cantidad de información que será almacenada. \n \n \n \nPara este estudio se seleccionó una muestra de datos, a los cuales se le aplico la metodología de minería de datos CRISP-DM, donde se hizo uso de las teorías y técnicas de aprendizaje automatizado, como son los algoritmos de aprendizaje no supervisado y supervisado. Las etapas utilizadas fueron el procesamiento de los datos, la adecuación para el análisis, creación de unas variables y aplicación de los algoritmos de agrupamiento, clasificación y regresión para poder identificar en los datos los patrones, tendencia y características de los juego y jugadores. A partir de lo anterior se generaron gráficas que permiten entender de una forma más fácil la información y los resultados obtenidos. \n \n \n \nCon la información que está contenida en los datos, se pudo establecer que, al realizar la aplicación de los modelos de aprendizaje automático, se encontraron patrones que permitieron demostrar que el aprendizaje se realizó de forma intuitiva y que cada vez que se jugaba, las posibilidades de hacer más aciertos aumentaban. Adicionalmente se pudo establecer que los juegos que fueron diseñados para cada uno de los tratamientos tienen características en común las cuales permitieron realizar agrupaciones con los datos existentes. \n \n \n \nPalabras Clave: inteligencia artificial, aprendizaje automático, aprendizaje profundo, analítica de datos, algoritmos, identificación de patrones y tendencias, técnicas de análisis de datos, visualización de datos, bases de datos, metodologías, estadística, probabilidades, juegos serios, tratamientos pacientes.
Bioacoustics as Forms of Resistance: Growing Mycelium Instruments and Mushroom Communication in a High-Tech City-State

Field: Arts and Humanities (Social Sciences)

AbstractSingapore-based experimental band The Observatory (天文台樂團) recently showcased their bio-sonification exhibition at Singapore Art Museum: REFUSE (14 January–17 April 2022). Set against imagery of manicured gardens in a celebration of organic growth and decomposition, REFUSE is a critical pun. First, REFUSE means to reject the current anthropocentric worldview in a time of ecological crises, and secondly it embraces inter-media arts that fuse recycled instruments with bio-sounds. Instruments were either the platform to grow mushrooms onto, or even themselves fully bio-fabricated by mushrooms – including a fully playable lap steel mycelium guitar that is simultaneously played by a mushroom. To amaze the audience further, these instruments were all wired to vibrate, their rhythms controlled by a growing mycelium whose organic growth is visually mapped and translated into signals that trigger the vibration. As the humidity and density of the mushroom jar changes, the sounds also vary, each sound unique even during the same day. As Obervatory band-member Yuen Chee Wai (袁志偉) told En-Chieh Chiao of our cover-image curating team when describing the mycelium's sounds, “They play like a decomposing composition.” The cover team chose this exhibition because it speaks to a research note and to an article in this issue that respectively address the issue of noise control and aging in Singapore. While the city–state endeavors to contain both noise and health in old age as parts of governance, here the artists renounce control over sound and let biological non-human actors set the course of subtle sensory experiences. Disclosure StatementNo potential conflict of interest was reported by the author(s).
INDUCED MIGRATION

Field: Social Sciences (Social Sciences)

Forced migration due to climate change will present one of the most severe challenges to the resilience of communities forced to migrate as well as to local and national governments. The Intergovernmental Panel on Climate Change (IPCC) has identified the regions of the world most vulnerable to climate change and predicts that 150 million people will be displaced by 2050. Alaska is projected to experience increased climatic change more rapidly. Temperature increases since 1974 confirm this projection. Several communities in Alaska are faced with permanent relocation due to climate change. Erosion, flooding, and sea level rise are the primary causes of displacement. This paper describes the experience of Alaskan indigenous communities and outlines a legal and institutional framework, based in human rights doctrine, to respond to climate-induced human migration.
Molecular mechanisms behind acetic acid resistance: Insights from Zygosaccharomyces bailii

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Biomass derived products will play a significant role in the development towards a sustainable society. The feasibility of the production of bio-based chemicals relies on robust industrial microorganisms. One major issue reducing process productivity is the high concentration of acetic acid, released during pretreatment of lignocellulose raw material. Acetic acid effect on yeast has been widely investigated: reduced intracellular pH [1], accumulation of the acetate anion [2], and signaling effects triggering cell death [3] are some of the mechanisms indicated as responsible for its toxicity. Zygosaccharomyces bailii is a yeast species that tolerates low pH and high concentrations of weak organic acids [4]. It is a common food spoilage yeast, typically isolated from acetic acid rich environments such as vinegar or pickles. Z. bailii is extensively investigated from a food science perspective, for the development of food preservatives. Its potential for industrial applications as a model organism for acetic acid resistance has been less investigated. Its tolerance has been explained to some extent by retained intracellular pH and plasma membrane integrity [5,6], specific acetate transporter supporting growth on acetate even in the presence of glucose [7], and higher metabolic flux through the unique ZbACS2 acetyl-CoA syntethase [8]. In the present study, the metabolic response of Z.bailii (CBS 7555) to acetic acid was characterized in a comparative investigation together with Saccharomyces cerevisiae (CEN.PK.0113_7D). Fermentation results indicate that S. cerevisiae tolerates significantly lower acetic acid concentrations compared to Z. bailii. Acetic acid affected S. cerevisiae mainly by decreasing maximum specific growth rate and specific substrate consumption rate. Z. bailii on the other hand was mainly affected by an increased lag phase. Z. bailii displayed sustained growth at acetic acid concentrations as high as 36 g/L, while concentrations above 9 g/L severely decreased the maximum specific growth rate of S. cerevisiae. The molecular mechanisms behind acetic acid resistance in Z. bailii are currently being investigated in order to formulate strategies to improve acetic acid tolerance in S. cerevisiae.References[1] Casal et al. FEMS Microbiol Rev (2008) 32(6): 974[2] Russel. J. Appl Bacteriol (1992) 73: 363[3] Ludovico et al. Microbiology (2001) 147:2409[4] Fleet G. Crit. Rev. Biotechnol (1992) 12: 1[5] Arneborg et al. Arch Microbiol (2000) 174:125[6] Prudenico et al. Cytometry (1998) 31:307[7] Sousa et al. Appl. Environ. Microbiol. (1996) 62:3152[8] Rodrigues et al. PLOSone (2012) 7(12): e52402
Genetic Gain in Fiber Properties of Upland Cotton under Varying Plant Densities

Field: Agricultural and Biological Sciences (Life Sciences)

Competition from foreign grown cotton ( Gossypium hirsutum L.) and artificial fibers have increased the demand for improved fiber quality. The genetic potential for effecting change in many traits can be judged by previous gains from selection. Nine upland cotton cultivars developed over the past century were grown during 2004 and 2005 in five plant densities to evaluate varying levels of interplant competition on genetic gain estimates for high volume instrument fiber properties. The rates of genetic gain since 1905 among this set of genotypes for fiber length and strength were significantly higher under the greatest planting densities, implying that genetic gains for these characteristics have been made for tolerance to interplant competition as well as for the fiber trait per se. Both fiber elongation and uniformity index appear to be largely unaffected by the stresses of increased interplant competition. Plant density impacted genetic gain in micronaire but cultivars were essentially unchanged over the century, reflecting that the market demands fiber micronaire to be within a range that neither maximizes nor minimizes this trait. Caution should be practiced in the interpretation of these data since the capability to objectively measure these traits has been widely available to breeders only since the 1980s and because selection pressure for these traits has been sporadic with little concentrated effort to maximize or minimize each characteristic.