jimnoneill/paper-to-field-training huggingface dataset:
Interplay of YEATS2 and GCDH mediates histone crotonylation and drives EMT in head and neck cancer

Abstract The regulation of gene expression is an integral cellular process orchestrated by epigenetic marks like histone modifications. Perturbations in the activity or abundance of epigenetic factors can lead to tumorigenesis. Remarkably, several metabolites influence the epigenetic landscape in cells. Here, we investigated the interplay between a highly expressed epigenetic factor, YEATS2, and a metabolic enzyme, GCDH, in regulating epithelial-to-mesenchymal transition in head and neck cancer. We report that the histone reader YEATS2 is responsible for increased invasive potential in head and neck cancer in an SP1-dependent manner. YEATS2 functions by maintaining histone crotonylation, and its abrogation leads to a global decrease in the H3K27Cr mark. Mechanistically, we report that YEATS2 maintains high H3K27Cr levels at the promoter of the EMT-promoting gene SPARC. Further, we found that the addition of the H3K27Cr mark is also dependent on the crotonyl-CoA-producing enzyme GCDH. Overall, we describe a novel mechanism of interplay between epigenetics and metabolism in head and neck tumorigenesis, which results in the enhanced expression of EMT-related genes in a histone crotonylation-dependent manner.

Topic: RNA modifications and cancer
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
SCHIZOPHRENIC REACTION TIME RESPONSES TO VARIABLE PREPARATORY INTERVALS

1. No difference was observed in speed of reaction when a group of patients with schizophrenic illnesses was compared to a control group. 2. Previously reported differential responsiveness of patients and controls to variation in length of preparatory interval and regularity of stimulus presentation was not observed. The usefulness of such a technique for differentiating schizophrenics from normals is questioned. 3. Variability of speed of reaction tends to be significantly greater in the patient group. This result is consistent with previous findings. It is suggested that this represents an increase in the amplitude of fluctuations in readiness which are oscillatory in character.

Topic: Mental Health Research Topics
Subfield: Experimental and Cognitive Psychology
Field: Psychology
Domain: Social Sciences
Identification of Morphologic and Chemical Markers of Aestivation Conditions in Female Anopheles gambiae Mosquitoes

Increased understanding of the dry season survival mechanisms of Anopheles gambiae (An. gambiae) in semi-arid regions could benefit vector control efforts by identifying weak links in the transmission cycle of malaria. In this study we examine effect of seasonal indicators on morphologic and chemical characteristics known to contribute to suppression of water loss in mosquitoes. An. gambiae body size (indexed by wing length), mesothoracic spiracular index ((spiracle-length/wing-length)*100), and cuticular hydrocarbon (CHC) profiles were examined for their ability to differentiate mosquitoes exposed to aestivating and non-aestivating conditions in a laboratory setting. Mosquitoes exposed to aestivating conditions exhibited larger wing lengths, larger mesothoracic spiracular indices, and greater total CHC amount (standardized) than mosquitoes exposed to non-aestivating conditions. Total CHC amount increased with both mating and age. Mean n-alkane retention time (a measure of mean n-alkane chain-length) was lower in mosquitoes exposed to aestivating conditions, and increased with age. Individual CHC peaks were examined, and several CHCs were identified as potential biomarkers of aestivation, age, and insemination status. This study indicates that aestivation status of nulliparous female An. gambiae can be determined using both morphologic and chemical biomarkers.

Topic: Malaria Research and Control
Subfield: Public Health, Environmental and Occupational Health
Field: Medicine
Domain: Health Sciences
Progressive hydrocephalus in two members of a family with autosomal dominant Noonan phenotype

We present a family with an autosomal dominant phenotype characterized by pulmonary valve stenosis, craniofacial dysplasia with marked hypertelorism and, as a variable feature, progressive hydrocephalus. This phenotype is manifested in four patients from three subsequent generations of a family, with expression ranging from mild pulmonary stenosis combined with slight but characteristic facial dysmorphism to severe cyanotic pulmonary valve stenosis with multiple malformations lethal in early childhood. We consider this to be an unusual variant of Noonan syndrome.

Topic: Protein Tyrosine Phosphatases
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Integrating oncology and palliative home care in Italy: the experience of the "L'Aquila per la Vita" Home Care Unit.

A multidisciplinary and expert team, closely integrated with the hospital, can guarantee a long length of home care, avoiding hospitalization and closing the gap between the patients' preferences and the services offered regarding the place of death.

Topic: Palliative Care and End-of-Life Issues
Subfield: Public Health, Environmental and Occupational Health
Field: Medicine
Domain: Health Sciences
Supplementary Figures 1-4 from Mitochondrial Cytochrome B Gene Mutation Promotes Tumor Growth in Bladder Cancer

Supplementary Figures 1-4 from Mitochondrial Cytochrome B Gene Mutation Promotes Tumor Growth in Bladder Cancer

Topic: Cancer, Lipids, and Metabolism
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
CCDC 720862: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Topic: Crystallization and Solubility Studies
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Vision and Virtue in Psychoanalysis and Buddhism:<i>Anatta</i>and Its Implications for Social Responsibility

Buddhism and psychoanalysis have long been accused of privileging internal transformation over active social and political engagement. Yet, as representatives of non-theistic and secular paths toward the realization of human potential, both traditions embody an important aspect of the Romantic quest for progress, that is, the transcendence of internal and external division. Insight into the Buddhist notion of self as ontologically interdependent and non-dualistic optimally yields not only personal transformation but also an expanded circle of identification, with important implications for social responsibility. Erich Fromm, in interpreting the influential work of D. T. Suzuki, represents a historical and philosophical link between the psychoanalytic legacy of social responsibility and the Buddhist concept of Enlightenment. With dewdrops dripping, I wish somehow I could wash this perishing world. —Basho (1643–1694)

Topic: Theology and Philosophy of Evil
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
Iatrogenic Prion Infection

To the Editor: Prusiner1 and Roos2 (May 17 issue) do not mention the spread of prions by contaminated surgical instruments. Since prions are not inactivated by the usual methods of sterilization, surgical procedures may account for some cases of sporadic Creutzfeldt–Jakob disease.3 Responding to this concern, the United Kingdom Department of Health has mandated that all tonsillectomy procedures be carried out with single-use instruments and has identified other procedures in which single-use instruments must be used. Instruments should not be reused after use in a patient with known or suspected Creutzfeldt–Jakob disease. Since it is unrealistic to expect that all . . .

Topic: Prion Diseases and Protein Misfolding
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Care needed with i.v. acetaminophen

On November 2, 2010, the Food and Drug Administration (FDA) approved the first i.v. formulation of acetaminophen,1 which is labeled in the United States for use in patients two years of age or older. I.V. acetaminophen has been available in Europe since 2002, and oral acetaminophen has been available in the United States since the mid-1950s.2 Although the new formulation is intriguing, there are safety and logistic challenges associated with its administration that warrant consideration. In January 2011, in response to numerous reports of liver damage attributable to high doses of acetaminophen, FDA announced that manufacturers will be required to limit acetaminophen content in prescription products to 325 mg per single dosage unit and add a boxed warning to the label of acetaminophen-containing products by 2014.3 These requirements were intended to reduce the occurrence of liver failure, the need for liver transplantation, and death due to acetaminophen toxicity from unintentional overdose.4 Unintentional acetaminophen overdose has been defined as “a multiple-timepoint ingestion to relieve pain or other somatic symptoms.”5 In a population-based surveillance study of acute liver failure (ALF), the most common cause of ALF in adult patients (41%) was acetaminophen related; among these patients, unintentional acetaminophen overdose was the most common cause of ALF (61% of patients).6

Topic: Drug-Induced Hepatotoxicity and Protection
Subfield: Pharmacology
Field: Pharmacology, Toxicology and Pharmaceutics
Domain: Life Sciences
Instrument for Stability - IFS/2008/157866 - Expert Support Facility - Lot 5: CBRN training Centre on Safety and Security - FINAL REPORT

Twelve field missions have been carried out. Three of them have addressed the South East Asia region (Singapore, Indonesia and the Philippines), two the Middle East region (Jordan and UAE) and seven the African region (Morocco, Egypt, South Africa, Nigeria, Ghana, Kenya, Cameroon). Evaluations were based on a SWOT (Strength, Weaknesses, Opportunities and Threats) analysis and on the criteria identified at the Lot 5 kick-off meeting in May 20, 2008 (Willingness; Infrastructure; Sustainability; International Cooperation; Stability; and Regional Influence). Furthemore, two regional workshops have been held: the first in Singapore on 23rd November 2009, and the second in Amman, Jordan, on 26th-27th May 2010. I Detailed reports on the outcomes of the missions and of the regional workshops are attached.

Topic: Hermeneutics and Narrative Identity
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
Novel Cytotoxic Copper(<scp>II</scp>) Complexes of 8‐Aminoquinoline Derivatives: Crystal Structure and Different Reactivity towards Glutathione

Abstract Two novel Cu II complexes [Cu(CMQA)(H 2 O)] ( 1 ) (CMQA = N ‐carboxymethyl‐ L ‐methionine‐ N ′‐8‐quinolylamide) and [Cu(MQA)(OAc)] ( 2 ) (MQA = L ‐methionine‐ N ′‐8‐quinolylamide, OAc = CH 3 COO − ) have been synthesized and structurally characterized. Complex 1 crystallizes in the orthorhombic system with space group P 2 1 2 1 2 1 [ a = 5.556(1) Å, b = 15.002(3) Å, c = 20.886(4) Å] while complex 2 crystallizes in the monoclinic system with space group C 2 [ a = 28.463(6) Å, b = 5.264(1) Å, c = 13.345(3) Å, β = 109.142(3)°]. In both complexes the Cu II center is coordinated by three N atoms of the ligand and one O atom of H 2 O ( 1 ) or OAc ( 2 ). The in vitro cytotoxicity of both complexes and their corresponding ligands have been tested against the murine leukemia P‐388 and lung adenocarcinoma A‐549 cell lines. Complex 2 shows a potent activity against both cell lines with an inhibitory rate of 100% for the murine leukemia P‐388 cell line and 93.4% for the lung adenocarcinoma A‐549 cell line at a concentration of 10 −6 mol·L −1 , while complex 1 shows only a marginal activity against the same cell lines. The reactivity of the two complexes towards γ‐glutathione (GSH) has been investigated and is discussed in association with their different cytotoxicity. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2004)

Topic: Metal complexes synthesis and properties
Subfield: Oncology
Field: Medicine
Domain: Health Sciences
Alchemy Methodology ‑ Applying the Arts to Research

With the growing interest in arts-based approaches to research, I believe it has become necessary to make this distinction: the difference between art and research is that, whereas art can speak for itself, research must be explained. Unlike research, art invites open interpretation from the viewers, without any need to justify or explicate its existence or the artist’s intentions. Research however, by its very nature, is a cognitive and rational product – at least in its final stages. The appreciation of postmodern perspectives in academia has given rise to methodologies for first-person inquiries and arts-based methods. Arts methods may provide the researcher with great insights into a research question, however I believe the inquiry needs to be situated in a rational and philosophically aligned research framework. In this paper I present Alchemy Methodology as a theoretical framework for such research. It has been developed as an application of the pure phenomenology of Edmund Husserl, and it uses arts practice and subjective insights to inform and transform this data into universal, phenomenological insights.

Topic: Empathy and Medical Education
Subfield: Psychiatry and Mental health
Field: Medicine
Domain: Health Sciences
Discovering Agent Models using Process Mining: Initial Approach and a Case Study

Agent-based modeling is widely used for modeling and simulation of self-organizing sociotechnical systems that are composed of distributed autonomous agents. In these systems, macro level behaviors emerge from local micro level behaviors of agents that follow rules and interact with each other and the environment. Although the individual agents' behaviors are typically described by sets of simple rules, the many interactions, heterogeneous populations, and complex topologies can make it challenging, or even impossible, to predict or steer the emergent behaviors beyond micro levels. Hence, the actual behaviors of such systems are generally hard to know beforehand, and they need to be observed to extract realistic models. In this paper, we propose a proof-of-concept approach to discover agents' underlying models from log data generated from their behaviors, utilizing process mining. To conceptualize and demonstrate our initial approach, we use an illustrative example of the popular Schelling's model of segregation. Our findings provide encouraging initial evidence on how agent models can be extracted utilizing process mining techniques.

Topic: Business Process Modeling and Analysis
Subfield: Management Information Systems
Field: Business, Management and Accounting
Domain: Social Sciences
A Millimeter-Wave CMOS Transceiver With Digitally Pre-Distorted PAM-4 Modulation for Contactless Communications

This paper presents a millimeter-wave (127 GHz) CMOS transceiver with a digital pre-distortion capable PAM-4 modulator for contactless communications. The transmitter upconverts PAM-4 modulated baseband signals through a free-running 127-GHz oscillator and single-balanced mixer, and it delivers PAM-4 modulated carrier signals to a folded-dipole antenna, which is designed on a FR408HR substrate. The receiver's low-noise amplifier provides a 10-dB gain, and the self-mixer downconverts carrier-modulated PAM-4 signals to baseband signals without the necessity of carrier synchronization. The PAM-4 modulator pre-distorts the baseband signals and corrects the non-linear characteristics of the transmitter's upconversion mixer and the receiver's downconversion self-mixer. Designed and fabricated in a 65-nm CMOS process, the demonstrated system transfers 20 Gb/s of PAM-4 modulated data through a 1-mm air gap and consumes 79.5 mW (transmitter: 50.8 mW and receiver: 28.7 mW) of power under a 1.2-V supply, achieving a 3.98-pJ/bit energy efficiency. The communication distance is extended to 3 cm by inserting a dielectric waveguide between the same transceiver.

Topic: Radio Frequency Integrated Circuit Design
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
Self-assembly of the first heterodinuclear d–f triple helix in solution

The segmental bidentate–tridentate ligand L2 reacts with LnIII and ZnII in acetonitrile to give the first self-assembled heterodinuclear d–f triple-helical complexes [LnZn(L2)3]5+(Ln = La, Eu), as determined from solution-phase studies.

Topic: Magnetism in coordination complexes
Subfield: Electronic, Optical and Magnetic Materials
Field: Materials Science
Domain: Physical Sciences
Nonparametric identification in panels using quantiles

This paper considers identification and estimation of ceteris paribus effects of con- tinuous regressors in nonseparable panel models with time homogeneity. The effects of interest are derivatives of the average and quantile structural functions of the model. We find that these derivatives are identified with two time periods for 'stayers', i.e. for individuals with the same regressor values in two time periods. We show that the identifi- cation results carry over to models that allow location and scale time effects. We propose nonparametric series methods and a weighted bootstrap scheme to estimate and make inference on the identified effects. The bootstrap proposed allows uniform inference for function-valued parameters such as quantile effects over a region of quantiles or regressor values. An empirical application to Engel curve estimation with panel data illustrates the results.

Topic: Spatial and Panel Data Analysis
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
Aggregating algorithms in high dimensional data classification

With the improvements in computer performance and innovations in biological technology, a huge amount of genetic and protein information relevant to diseases can be obtained and recorded rather easily. Analyzing this data however is difficult due to its high dimensionality and the existence of many redundant or noisy features. Many methods have been used, aggregating algorithms have been among the most promising for tackling high dimensional data classification. The most widely used is the Random Forests algorithm. This method is especially attractive because of its prediction accuracy and computational efficiency compared to other tree based methods. Interestingly, despite its wide use, few theoretical studies investigating the factors that may impact the performance of Random Forests, including the number of informative and noisy features, the sample size, and the number of randomly selected features at each node split, have been reported. In this dissertation I take an initial step to analyze the Random Forests algorithm by considering a two-class classification problem where all the features are normally distributed within a class and a stump-tree classifier is used as the base learner. My analysis shows that the random feature selection improves the overall classification accuracy by adaptively assigning voting weights to the weak classifiers according to their performances on the training set. But the adjustment of the weights induced by changing the random selected subset size is very limited. I also claim that bootstrapping original training set enables a larger variety of possible weak classifiers being generated. But the perturbation introduced by bootstrap may deviate from the underlying true distribution of the samples and result in deteriorated weak classifiers. My motivation is to find alternative ways to generate a rich ensemble of weak classifiers that can keep original information and generalize well, and to find a better way to assign weights to the weak classifiers according to their performances and correlations. I proposed the weighted random subspace method. In this method, I addressed the optimal weight assignment problem and proposed solutions under both the independence and dependence assumptions among weak classifiers. Finally, I compared various algorithms on gene expression and protein expression data and confirmed that the weight assignment procedure improves prediction accuracy.

Topic: Neural Networks and Applications
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Aeromicrobium halocynthiae sp. nov., a taurocholic acid-producing bacterium isolated from the marine ascidian Halocynthia roretzi

A marine bacterium, strain KME 001 T , was isolated from the siphon tissue of a marine ascidian, Halocynthia roretzi , collected off the coast of Gangneung, Korea. Strain KME 001 T was a Gram-positive, aerobic, non-spore-forming, rod-shaped and non-motile bacterium. Phylogenetic analysis using 16S rRNA gene sequences revealed that strain KME 001 T clustered with the genus Aeromicrobium and was closely related to Aeromicrobium ginsengisoli , Aeromicrobium erythreum and Aeromicrobium ponti with 97.7, 97.6 and 97.5 % sequence similarities, respectively. The strain was capable of growth at a variety of temperatures (10–42 °C) and over a broad pH range (5.0–10.0). NaCl was required for robust growth of the strain. The diagnostic diamino acid of the cell-wall peptidoglycan was ll -diaminopimelic acid. The predominant menaquinone was MK-9(H 4 ). The predominant fatty acids were C 18 : 1 ω 9 c , C 16 : 0 and 10-methyl C 18 : 0 . The DNA–DNA hybridization analyses showed that DNA–DNA relatedness values between strain KME 001 T and its nearest neighbours, A. ginsengisoli KCTC 19207 T , A. erythreum KCCM 41104 T and A. ponti KACC 20565 T , were 49.6, 57.1 and 63.5 %, respectively. The DNA G+C content of strain KME 001 T was 75.9 mol%. Chemical investigation of the liquid culture medium of strain KME 001 T led to the isolation of taurocholic acid as a major secondary metabolite. On the basis of phylogenetic and phenotypic data, strain KME 001 T is classified as representing a novel species of the genus Aeromicrobium , for which the name Aeromicrobium halocynthiae sp. nov. is proposed. The type strain is KME 001 T (=JCM 15749 T =KCCM 90079 T ).

Topic: Genomics and Phylogenetic Studies
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences